Pharmaceutical Biotechnology [1 ed.] 1441911316, 9781441911315

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Pharmaceutical Biotechnology

ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY Editorial Board: NATHAN BACK,State University ofNew York at Buffalo IRUNR. COHEN, The Weizmann Institute ofScience ABELLAJTHA, N.S. KlineInstitutefor Psychiatric Research JOHND. LAMBRIS, University ofPennsylvania RODOLFO PAOLETII, University ofMilan

RecentVolumes in this Series Volume 648 ARTERIAL ANDALLIED CHEMORECEPTORS Editedby Constancio Gonzalez, ColinA. Nurse,and ChrisPeers Volume 649 MOLECULAR MECHANISMS OF SPONDYLOARATHROPATHIES Editedby CarlosLopez-Larrea, and Roberto Diaz-Peila Volume 650 V(D)JRECOMBINATION Editedby PierreFerrier Volume 651 DEVEOPLMENT ANDENGINEERING OF DOPAMINE NEURONS Editedby R. JeroenPasterkamp, MartenP. Smidt,andJ. PeterH. Burbach Volume 652 INHERITED NEUROMUSCULAR DISEASES: TRANSLATION FROM PATHOMECHANISMS TOTHERAPIES Editedby Carmen Espin6s, Vicente Felipo, and Francese Palau Volume 653 TARGET PATTERN RECOGNITION IN INNATE IMMUNITY Editedby UdayKishore Volume 654 THE ISLETS OF LANGERHANS Editedby Md. Shahidullslam Volume 655 PHARMACEUTICAL BIOTECHNOLOGY Editedby CarlosA. Guzman and GioraZ. Feuerstein

AContinuation Order Plan isavailable forthis series. Acontinuation order will bring delivery ofeachnew volume immediately upon publication. Volumes arebilled onlyupon actual shipment. Forfurther information please contact thepublisher.

Pharmaceutical Biotechnology Editedby Carlos A. Guzman, MD, PhD Department of Vaccinology andAppliedMicrobiology, HZI-Helmholtz Centre for Infection Research. Braunschweig. Germany Giora Z. Feuerstein, MD, MSc, FAHA

Wyeth Research, Collegeville, Pennsylvania, USA

Springer Science+Business Media, LLC Landes Bioscience

SpringerScience-Business Media,LLC LandesBioscience Copyright ©2oo9 Landes Bioscience and Springer Science+Business Media, LLC All rightsreserved. Nopartof thisbookmaybe reproduced ortransmitted inanyformorbyanymeans, electronic or mechanical, including photocopy, recording, or anyinformation storageandretrieval system, without permission in writingfromthe publisher, withthe exception of any material supplied specifically forthe purpose of beingenteredand executed on a computer system; for exclusive use by the Purchaser of the work. Printedin the USA. SpringerScience+Business Media, LLC,233 Spring Street,NewYork, NewYork 10013, USA http://www.springer.com Pleaseaddress all inquiries to the publishers: LandesBioscience, 1002West Avenue, Austin, Texas 78701, USA Phone: 512/6376050; FAX: 512/6376079 http://www.landesbioscience.com The chaptersin this book are availablein the Madame Curie Bioscience Database. http://www.landesbioscience.com/curie Pharmaceutical Biotechnology, editedbyCarlos A.Guzman andGioraZ. Feuerstein. Landes Bioscience I Springer Science+Business Media, LLC dual imprint I Springer series: Advances in Experimental Medicine and Biology ISBN: 978-1-4419-1131-5 Whiletheauthors, editors andpublisher believe thatdrugselection anddosage andthespecifications and usage of equipment and devices, as set forth in this book,are in accordwith currentrecommendations and practiceat the time of publication, they make no warranty, expressed or implied, with respectto material described in this book. In view of the ongoing research, equipment development, changes in governmental regulations andtherapidaccumulationof information relating to thebiomedical sciences, the readeris urgedto carefully reviewand evaluate the information provided herein.

Library of Congress Cataloging-in-Publication Data Pharmaceutical biotechnology I editedby CarlosAlberto Guzman, GioraZeevFeuerstein. p. ; ern, -- (Advances in experimental medicine and biology ; v. 655) Includes bibliographical references and index. ISBN978-1-4419-1131-5 1. Pharmaceutical biotechnology. 1. Guzman, CarlosAlberto, 1959- II. Feuerstein, GioraZ., 1946-III. Series: Advances in experimental medicine and biology, v. 655. 0065-2598 ; [DNLM: 1. Technology, Pharmaceutical. 2. Biotechnology. 3. Drug Discovery. WI AD559 v.655 2009I QV 778 P53522 2009] RS380.P4755 2009 615'.I9--dc22 2009024877

DEDICATION

To Michela Morgana and Alessia Federica

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PREFACE

Pharmaceutical Biotechnology is a unique compilation of reviews addressing frontiers in biologicals as a rich source for innovative medicines. This book fulfills the needs of a broad community of scientists interested in biologicals from diverse perspectives-basic research, biotechnology, protein engineering, protein delivery, medicines, pharmaceuticals andvaccinology. The diverse topicsrangefromadvanced biotechnologies aimedtointroduce novel, potentengineered vaccines ofunprecedented efficacy and safety for a wide scope of human diseases to natural products, small peptides andpolypeptides engineered fordiscrete prophylaxis andtherapeutic purposes. Modembiologicals promise to dramatically expandthe scopeof preventive medicine beyond the infectious disease arena into broad applications in immune and cancer treatment, as exemplified by anti-EGFRreceptors antibodies forthetreatment ofbreast cancer. Theexponential growthinbiologicals suchasengineered proteins andvaccines hasbeenboostedby unprecedented scientific breakthroughs madein thepastdecades culminating in an in-depth fundamental understanding of the scientific underpinnings of immune mechanisms together withknowledge of proteinandpeptidescaffolds that can be deliberately manipulated. This has in turn led to new strategies and processes. Deciphering the human, mammalian and numerous pathogens' genomes provides opportunities thatneverbeforehavebeenavailable-identification of discrete antigens (genomes and antigenomes) that lend themselves to considerably improved antigens and monoclonal antibodies, which with more sophisticated engineered adjuvants and agonists of patternrecognition receptors present in immune cells, deliverunprecedented safetyand efficacy. Technological development sucha nanobiotechnologies (dendrimers, nanobodies and fullerenes), biological particles (viral-like particles and bacterial ghosts) andinnovative vectors (replication-competent attenuated, replicationincompetent recombinant and defective helper-dependent vectors) fulfill a broad rangeof cutting-edge research, drugdiscovery and delivery applications. Mostrecent examples ofbreakthrough biologicals include thehuman papilloma virus vaccine (HPY, prevention ofwomen genital cancer) andthemultivalent Pneumoccocal vaccines, which hasvirtually eradicated insomepopulations a mostprevalent bacterial earinfection (i.e., otitis media). It is expected that in the yearsto come similarsuccess will be obtained in the development of vaccines for diseases which still represent major threats for vii

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human health, suchasAIDS, aswellasforthegeneration ofimproved vaccines against diseases like pandemic flu for which vaccines are currently available. Furthermore, advances in comparative immunology andinnate immunity revealed opportunities for innovative strategies for ever smaller biologicals and vaccines derived from species suchas llamaandsharks, whichcarrytremendous potential forinnovative biologicals already in development stages in manypharmaceutical companies. Suchrecentdiscoveries and knowledge exploitations holdthepromise forbreakthrough biologicals, withthecoming decade. Finally, thisbookcaters to individuals notdirectly engaged in thepharmaceutical drugdiscovery process viaa chapter outlining discovery, preclinical development, clinical development and translational medicine issues that are critical the drugdevelopment process. The authors and editors hope that this compilation of reviews will help readers rapidly and completely update knowledge and understanding of the frontiers in pharmaceutical biotechnologies. Car/os A. Guzman, MD, PhD Giora Z. Feuerstein, MD, MSC, FAHA

ABOUT THE EDITORS...

CARLOS A. GUZMAN, MD, PhD is Head of the Department ofVaccinology and Applied Microbiology at the Helmholtz Centre for Infection Research (Braunschweig, Germany) andAPL-Professor at the Medical School of Hannover. He is also German Coordinator for the International Doctorate in "Experimental Oncology" and Chair for "Vaccines & Antiinfectives " from the Indo-German Science Centre for Infectious Diseases. He graduated in Medicine at the National University ofRosario and obtained his Board Certification in Medical Bacteriology in Argentina. Then he moved to the Institute of Microbiology at the University of Genoa (Italy), as Research Fellow of the Italian Foreign Office Ministry. In Italy he also graduated as Doctor of Medicine and Surgery and obtained his Doctorate of Research in Microbiological Sciences. In 1994 he moved to Germany, where he became Head of the Vaccine Research Group at the German Research Centre for Biotechnology. He has been working in the field of vaccinology since 1989. His work has been instrumental for the development of new adjuvants , and the establishment of Salmonella spp. as a delivery system for DNA vaccines and therapeutic molecules. He has published more than 150 topic-related papers in international peer-reviewed journals and is co-inventor in several international patents. He is member ofthe Editorial Boards ofInfection andImmunity, Microbial Biotechnology, Open Immunology Journal, Current Immunology Reviews, Open Vaccine Journal and Open Microbiology Journal, and Associate Editor of Human Vaccines.

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ABOUT THE EDITORS...

GIORA Z. FEUERSTEIN, MD, MSC, FAHA is Assistant Vice President and Head of Discovery Translational Medicine, Wyeth Research. Prior to joining Wyeth, Dr. Feuerstein has maintained Executive Directorship positionin discovery of cardiovascular, stroke, thrombosis and metabolic disease programs for 16 years in SmithKline Beecham, DuPont Pharma and Merck USA. Dr. Feuerstein led the discovery program ofCarvedilol (COREG) for heart failure, eprosartan for hypertension and many development programs in stroke, anti-arrhythmics, thrombosis and metabolicdiseases. Dr. Feuerstein servesas Editor, Biochemical Pharmacology, editorial boardmemberofJournalofPharmacology and Experimental Therapeutics, Journal ofCerebral Blood Flow Metabolism, Circulation Research, and Stroke. Dr. Feuerstein is therecipient of several national andinternational awards including Award of Excellent inCardiovascular Research,AHA; PrixGalien Award forDrugDiscovery (endothelin antagonist), Conrad R. Lam Award for cardiovascular research, Henry FordFoundation andWyeth R&DPresident award. GioraFeuerstein hasauthored and coauthored over 400 peer-reviewed publications and is co-inventor on 12patents.

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PARTICIPANTS Shizuo Akira Department of Host Defense and 21st Century COE Program Research Institute for Microbial Diseases Osaka University Osaka Japan Rafaela Argnani Department of Experimental and Diagnostic Medicine Section of Microbiology University of Ferrara Ferrara Italy Caroline Barelle Wyeth Research Foresterhill, Aberdeen Scotland Aurelio Cafaro National AIDS Center Istituto Superiore di Sanita Rome Italy Keith Charlton Wyeth Research Foresterhill, Aberdeen Scotland

Cevayir Coban Department of Host Defense and 21st Century COE Program Osaka University Osaka Japan Mark Day Wyeth Research Collegeville, Pennsylvania USA Thomas Ebensen Department ofVaccinology and Applied Microbiology Helmholtz Centre for Infection Research Braunschweig Germany Barbara Ensoli National AIDS Center Istituto Superiore di Sanita Rome Italy Alberto L. Epstein Centre de Genetique Moleculaire et Cellulaire Universite Lyon Villeurbanne France

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participants

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Diana Felnerova Bema BiotechLtd. a CrucellNV Berne Switzerland Giora Z. Feuerstein Wyeth Research Collegeville, Pennsylvania USA Epifanio Fichera Etna Biotech Catania Italy CarmenGiefmg Intercell AG CampusVienna Biocenter Vienna Austria DavinderS. Gill Wyeth Research Biological Technologies Cambridge, Massachusetts USA ReinhardGlueck Etna Biotech Catania Italy CarlosA. Guzman Department of Vaccinology and AppliedMicrobiology Helmholtz Centrefor Infection Research Braunschweig Germany

Ken llshii Department of Host Defense and Exploratory Research for Advanced Technology Japan Scienceand Technology Agency and Research Institute for Microbial Diseases Osaka University Osaka Japan KewalK. Jain Jain PharmaBiotech Basel Switzerland RichardJ. Lewis XenomeLimited and Institutefor Molecular Biosciences The University of Queensland Brisbane Australia Petra Lubitz University of Vienna Department of Medicinal Chemistry Vienna and BIRD-C GmbH and CoKEG Kritzendorf Austria Werner Lubitz University of Vienna Department of Medicinal Chemistry Vienna and BIRD-C GmbHand CoKEG Kritzendorf Austria

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Participants

Iole Macchia NationalAIDS Center Istituto Superiore di Sanita Rome Italy MariaTeresaMaggiorella NationalAIDS Center IstitutoSuperiore di Sanita Rome Italy RobertoManservigi Department of Experimental and Diagnostic Medicine Sectionof Microbiology University of Ferrara Ferrara Italy PeggyMarconi Department of Experimental and Diagnostic Medicine Sectionof Microbiology University of Ferrara Ferrara Italy Vega Masignani Novartis Vaccines Siena Italy Ulrike BeateMayr University of Vienna Department of Medicinal Chemistry Vienna and BIRD-CGmbHand CoKEG Kritzendorf Austria Robert Mischler Mibiotec Limited Worblaufen Switzerland

GabriellaMolinari Environmental Microbiology Helmholtz Centrefor Infection Research Braunschweig Germany MarirosaMora NovartisVaccines Siena Italy Danilo GomesMoriel NovartisVaccines Siena Italy EszterNagy IntercellAG CampusVienna Biocenter Vienna Austria Rob Noad Department of Infectious and Tropical Diseases LondonSchool of Hygiene and Tropical Medicine London UK Rino Rappuoli Novartis Vaccines Siena Italy Polly Roy LondonSchoolof Hygiene and Tropical Medicine London UK J. LynnRutkowski

Wyeth Research Collegeville, Pennsylvania USA

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Maria Scarselli Novartis Vaccines Siena Italy Laura Serino Novartis Vaccines Siena Italy Fausto Titti NationalAIDS Center Istituto Superiore di Sanita Rome Italy

Participants

Jean-Francois Viret Berna BiotechLtd a CrucellNY Berne Switzerland Alexandervon Gabain IntercellAG CampusViennaBiocenter Vienna Austria

CONTENTS 1. TRANSLATIONAL MEDICINE-A PARADIGM SHIFT IN MODERN DRUG DISCOVERY AND DEVELOPMENT: THE ROLE OF BIOMARKERS 1 MarkDay, J. LynnRutkowski and GioraZ. Feuerstein Abstract Drug Targets-Historical Perspectives Translational Medicine: Definition Biomarkers-Utilitarian Classification Principles of Target Selection Class A-Disease Specific Class B-Target Present Physiologically but in a Non-Active Form, but Is Activated and Contributes to the Disease Class C- Target Functions Physiologically but at Augmented, Uncontrolled Fashion That Contributes to the Disease Class D-Target Maintains Physiological Functions in Normaland Disease States Conclusion

1 1 2 2 7 8 8 9 10 11

2. NATURAL PRODUCTS IN DRUG DISCOVERY: PRESENT STATUS AND PERSPECTIVES 13 Gabriella Molinari Abstract Introduction Drug Discovery Evolution Natural Products Properties The Urgent Need for New Drugs From Microbial Diversity to Drug Discovery Microbial Sources Microbial Extracts Chemical Screening Biological Screening Production, Purification and Characterization of a New Natural Product

13 13 17 17 18 19 19 21 22 22 22

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Contents

Metagenomics for Drug Discovery ••...••.•..•......•••..••.••••••••••..•.•..•....••••......•••••••••...........•••.• 23 Natural Products Under Development•.•..•.•.•..••.•••.••••••••••........•.••.•....•.•..•.•••••••......•.••.•..••23 New Strategies in Fighting Infectious Diseases 24 Conclusion 24

3. PROTEIN PHARMACEUTICALS: DISCOVERY AND PRECLINICAL DEVELOPMENT

28

DavinderS. Gill Abstract Introduction Protein Drug Discovery Novel Agents Challenges and Opportunities Next Generation Proteins Conclusion

28 28 29 32 33 34 34

4. THE ROLE OF NANOBIOTECHNOLOGY IN DRUG DISCOVERy

37

KewalK. Jain Abstract Introduction Role of Nanoparticles in Drug Discovery Role of Nanoproteomics in Drug Discovery Atomic Force Microscopy for Drug Discovery Role of Nanoscale Biosensors in Drug Discovery Nanofluidics, Nanoarrays and Nanobiochips Nanomaterials as Drug Candidates Nanobiotechnology and Drug Discovery for Personalized Medicine Conclusion

37 37 37 39 40 40 41 41 42 42

5. CONOTOXIN VENOM PEPTIDE THERAPEUTICS

44

Richard J. Lewis Abstract Introduction Calcium Channel Inhibitors Sodium Channel Inhibitors Antagonists of Nicotinic Acetylcholine Receptors Norepinephrine Transporter Inhibitors NMDA Receptor Antagonists Neurotensin Receptor Agonists

44 44 45 45 46 47 47 47

Contents

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6. SHARK NOVEL ANTIGEN RECEPTORS-THE NEXT GENERATION OF BIOLOGIC THERAPEUTICS?

49

CarolineBarelle, Davinder S. Gill and Keith Charlton Abstract Introduction The Rise and Rise of Antibodies What Are IgNARs? How Diverse Are IgNARs? What Is the Function of IgNAR? Developing IgNARs as Therapeutics Intrinsic Therapeutic Attributes of IgNARs Isolation of Antigen-Specific Clones In Vitro Maturation Formatting Conclusion

49 49 50 51 54 55 56 56 57 57 58 59

7. IMMUNE INTERVENTIONS OF HUMAN DISEASES THROUGH TOLL-LIKE RECEPTORS

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Cevayir Coban,Ken J. Ishii and ShizuoAkira Abstract Introduction Toll-Like Receptors and Their Known Ligands Toll-Like Receptor Signaling The Role of Toll-Like Receptors in the Human Immune System TLR-Based Immune Intervention in Humans: Promise and Caution TLR2 TLR4 TLR5 TLR7 and TLR8 TLR9 TLR3, TLRIO Other Signaling Molecules Conclusion

63 63 64 64 67 68 68 69 71 72 72 73 73 74

8. GENOME-BASED VACCINE DEVELOPMENT: A SHORT CUT FOR THE FUTURE

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Danilo Gomes Moriel, Maria Scarselli, Laura Serino, MarirosaMora, Rino Rappuoli and Vega Masignani Abstract Conventional Vaccinology Reverse Vaccinology The Classical Reverse VaccinologyApproach Comparative Genome Analysis: The Second Phase of Reverse Vaccinology Subtractive Genome Analysis: Third Phase of Reverse Vaccinology? Conclusion

81 81 82 83 84 85 88

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9. THE ANTIGENOME: FROM PROTEIN SUBUNIT VACCINES TO ANTIBODY TREATMENTS OF BACTERIAL INFECTIONS?...... 90 Carmen Giefing, Eszter Nagy and Alexandervon Gabain Abstract 90 Introduction 90 A New Paradigm in Bacterial Vaccine Development 92 The Advent of Monoclonal Antibodies in Disease Treatment 98 From Serum Treatment to Anti-Infective Monoclonal Antibodies 103 The Next Chapter of the Antibody Success Story: Bacterial Infections •••••••••••.•..•..••• 105

10. HSV AS A VECTOR IN VACCINE DEVELOPMENT AND GENE THERAPY

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Peggy Marconi,RafaelaArgnani, Alberto L. Epstein and Roberto Manservigi Abstract Introduction HSV-1 Genome and HSV-Derived Vectors Engineering Techniques HSV-1 Based Vectors Applications HSV-1 Based Vectors for Gene Therapy of Nervous System Conclusion

118 118 120 123 125 127 133

11. VIRUS-LIKE PARTICLES AS A VACCINE DELIVERY SYSTEM: MYTHS AND FACTS

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Polly Roy and Rob Noad Abstract Introduction Insect Cells and Baculovirus Expression System as Preferred System for VLP Production VLPs Produced for Structurally Simple Non-Enveloped Viruses

145 145 148 149

12. APPLICATIONS OF BACTERIAL GHOSTS IN BIOMEDICINE...... 159 Petra Lubitz, Ulrike Beate Mayr and WernerLubitz Abstract Introduction Basic Structure of Bacterial Ghosts Bacterial Ghosts as Vaccines Bacterial Ghosts as Carrier of Subunit Vaccine Bacterial Ghosts as Carrier of DNA Bacterial Ghosts as Carrier Vehicles for Active Substances in Tumour Therapy Other Medical Applications for Bacterial Ghost Packaged Active Substances Bacterial Ghosts as Enzyme Reactors for Novel Probiotics Conclusion

159 159 160 162 163 166 167 168 168 169

Contents

13. IMMUNE MODULATORS WITH DEFINED MOLECULAR TARGETS: CORNERSTONE TO OPTIMIZE RATIONAL VACCINE DESIGN

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171

Thomas Ebensen and Carlos A. Guzman Abstract 171 Introduction•.•..••..•.••••••••••.•••••••••.•.••..•.....•..............•.•.•.....................•......•.•.•..••••..•.••.••...... 171 Immune Modulators with Defined Molecular Targets 175 Bacterial Toxins and Their Derivatives 179 CDld Agonists .......•.•.•••••••••••••••••.•.....••••.•.......•...........•...............•.••..••.•••••••.••.•••••••••••••••.•• 179 Cytokines 180 Cell Wall Components 180 Co-Stimulatory Molecules 181 Bis-(3',5')-Cyclic Dimeric Guanosine Monophosphate (cdiGMP) 182 Conclusion ..................................................••.••....•.•..........................................................182

14. INNOVATIVE APPROACHES TO DEVELOP PROPHYLACTIC AND THERAPEUTIC VACCINES AGAINST HIV/AIDS

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AurelioCafaro, Iole Macchia, MariaTeresaMaggiorella, FaustoTitti and BarbaraEnsoli Abstract•..........................•.......................................•................•..•••••••••••••••••••.•....•............ 189 Introduction.............•....•..•..•..•••••••••••.••••.••••••.••••.••.•.....................•..•.........•.....•.•.•••••••••••.••189 191 Rationale and Roadblocks to mv Vaccine Development Correlates of Protection.•....................................•.•••.•••.•••.••••••••.•.•.••............•................... 191 General Strategies Adopted to Induce Protective Immunity 198 Key Issues Relevant to mv Vaccine Development: How to Get the Right Responses in the Right Places 205 New Particulate Delivery Systems 219 VLPs 220 Prime Boost Strategies•••••.••.•••••••••.•••••••.••••....•.................••.•.••.•••••.•.•••••••••.••.•....•.............220 International Networking to Ease and Accelerate mV/AIDS Vaccine Development...............•....................................••................................................•......221 Conclusion 222

15. NEW STRATEGIES TO OVERCOME THE DRAWBACKS OF CURRENTLY AVAILABLE FLU VACCINES

243

EpifanioFichera, Diana Felnerova, RobertMischler, Jean-Francois Viret and Reinhard Glueck Abstract Introduction Manufacturing of Influenza Vaccines Strategies to Improve the Immunogenicity and Efficacy of Current Influenza Vaccines Conclusion

243 243 244

INDEX

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246 250

ACKNOWLEDGEMENTS To my daughters Michela Morgana and Alessia Federica Guzman; thanks a lot not only for your continued support, but also for your inexhaustible patience. Only once and half-joking you mildly complain with a "Papi, du kummerst dich nicht urn uns" after a long business trip in 16 years . I cannot conceive my life without my little witches. To my family who supported me in my career development; my wife Nili, my son Ron and my daughter Sheira Feuerstein. We would also like to express our deep acknowledgement to all contributors, without your engagement this book would have never come to life. We are indebted with you for sharing your knowledge, experience and insights. Finally, we would like to thank the staff of Landes Bioscience for your outstanding support during this enterprise, in particular to Cynthia Conomos, Celeste Carlton and Erin O'Brien; any mistakes are ours-you did a terrific job .

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CHAPTER!

Translational Medicine-A Paradigm Shift in Modern Drug Discovery and Development: The Role ofBiomarkers Mark Day, J. Lynn Rutkowski and Giora Z. Feuerstein"

Abstract

T

he success rate ofnovel medical entities that are submitted for registration by the regulatory agencies and followed successful marketing hasbeen stagnating for the past decade. Failure in efficacy and safety continue to be the prime hurdles and causes offailure. Translational medicine is a new function within the pharmaceutical industry R&D organization aimed to improve the predictability and success ofdrug discovery and development. Biomarkers are the essence of the translational medicine strategy focus on disease biomarker, patient selection, pharmacodynamic responses (efficacy and safety) target validation, compound-target interaction). Successful deployment of biomarkers research, validation and implementation is adopted and embraced as key strategy to improved the drug discovery and development towards new medical entities.

Drug Targets-Historical Perspectives Drugs are natural or designed substan ces used deliberately to produce pharmacological effects in humans or animals. Drugs have been part ofhuman civilizations for millennia. However, until the very recent modern era, drugs have been introduced to humans by empiricism and largely by serendipitous events such as encounters with natural products in search of food or by avoiding hazardous plants and animal products. The emergence ofthe scientific era in drug discovery evolved along-side the emergence of physical and chemical sciences at large , first as knowledge to distill, isolate and enrich the desired substance from its natural environment, followed by deliberate attempts to modify natural substances to better serve the human needs and desires . Scientific evolution throughout the past two centuries enabled identification of biologically active substances in humans (e.g., hormones), which were manipulated chemically to improve (potency, duration of action and exposure), or to mitigate or abrogate undesirable actions. The cumulative knowledge ofhuman, animal and plant biology and chemistry provided the scientific foundation and technical capabilities to purposely alter natural substances in order to improve them. Such evolution marked the era of"forward pharmacology" The era offorward pharmacology is about drug design that emanates from primary knowledge of the action of the biological target that has clear biological action. The exponential progress in molecular biology since the mid-20th century, culminating in deciphering the complete human genome in the year 2000, brought the dawn ofpharmacogenomics ·Corresponding Author: Giora Z. Feuerste in-Wyeth Research, 500 Arcola Road, COL 5230 7, Collegeville, Pennsylvan ia 19426, USA. Email: feuersgwwy eth .corn

Pharmaceutical Biotechnology, edited by Carlos A . Guzman and Giora Z. Feuerstein. ©200 9 Landes Bioscience and Springer Sciences-Business Media.

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Pharmaceu!iCllIBiotechnology

and the "reverse pharmacology" era.The "reverse pharmacology" eraisdefinedby the need to first clarifythe biologyand medicalperspectives ofthe target soasto qualifyit asa drugableand pharmaceutically exploitablefor drug discovery and developmentscheme. The pharmacogenomic era providesvastopportunities for selectionofnew moleculartargetsfrom a gamut of approximately 30,000primarygenes, over100,000proteinsand multiplesoftheir translationaland metabolomics products. Thus, the permutations in respect to opportunities for pharmacological interventions are unprecedented,vast and most promisingfor innovativemedicines. The pharmacogenomics era as a source for drug targets also posesunprecedented hurdles in selection,validation and translation into effective and safedrugs. New technologies continue to drive efficiency and robustness of mining the genomicdrug discovery opportunities but physiologicaland integrated biologyknowledge is lagging. In this perspective, translationalmedicine and biomarkers researchhave taken center stagein validation of the moleculartarget for pharmaceuticalexploitation. In this chapterweoffera utilitarian approachto biomarkers and targetselectionand validation that isdrivenbythe translational medicineprospectof the targetto becomeasuccessful drug target. We hereby offer classification and analytical process aimed to assess risk, innovation, feasibility and predictability of success of translating novel targets into successful drugs. This manuscript provides cleardefinitions on the type ofbiomarkers that are core to translationalmedicine and biomarkersresearchin modern pharmaceutical companies.

Translational Medicine: Definition Translational medicinein the pharmaceutical industryisa research discipline aimedto improve the predictability of success of drug discovery and development. Translational medicineresearch aimsto discovery,validateand implementbiomarkers in lieueof clinicaloutcomestudies,improve the congruencyof preclinicalmodelsto clinicalrealityand establishproofof concept for efficacy and safety based on targeted mechanismof action. In particular, translationalmedicine aims to establishsurrogatebiomarkers to aid in earlyregistrationand promote personalizedmedicinefor better patients selectionfor targeted mechanismof action.

Biomarkers-Utilitarian Classification Biomarkers arethe stepping-stones for moderndrugdiscovery and development.1-4 Biomarkers are defined as biologicalsubstances or biophysical parametersthat can be monitored objectively and reproduciblyand used to predict drug effector outcome. This broad definition is however, oflittle utility to the pharmaceutical processsinceit carries no qualification for the significance and useof the biomarker. Thefollowing classes and definitionsof biomarkers arethereforeoffered (see Fig. I}: I. Disease Biomarkers: disease biomarkers are biomarkers that correlatestatistically with the disease phenotype (syndrome)for which therapeuticsare developed. Correlation of levels (in the circulation,other fluidsor tissue)or expression patterns (gene, protein) in peripheralblood cellsor tissues should signifydisease initiation, progression, regression, remission or relapse. When we applythese criteria to our empiricalapproach to current strategiesto developdrugs for certain diseases, it becomesapparent that our current approachesemployedin clinicaltestingaresub-optimal.One pertinent example isprovided by the wayindustry has approachedthe developmentoftreatments in schizophrenia. a. Disease Initiation Misconceptions: Unfortunately in the past SO years all marketed therapieshavebeendeveloped around the dopamineD2 receptor, eitherin the formof full antagonismor partial agonism. Thesetreatmentsareonlyeffective on the positive symptoms in around 70% ofpatients and are associated with treatment resistance and poor sideeffectprofiles. Current clinicalpracticeand drug discovery is basedaround the conceptthat the onsetof positivesymptomsrepresents the initiationof the disease. Arguably, however, these symptomsarrivelate in the chapter of schizophrenia. The focuson the positivesymptomshas impeded the developmentof noveltherapeutics

Translational Medicine-A Paradigm Shift in ModernDrugDiscoveryand Development

Type 1

Biomarkers that validate the importance of the target in human disease and drug development

Type 2

Biomarkers that define the chemical-physical interaction of the compound/biolog ical with Its discrete target

Type '3

Biomarkers that define consequences of compound/biolog ical Interaction with the target

Type 4

Biomarkers that correlate with disease Init iation. progression. regression . rem ission. relapse or mod ification

Type 5

Biomarkers that define likelihood of pat ients to respond or not to compound/biological

3

Figure 1. Utilitarian classification of biomarkers types 1-5

driven by an under appreciation ofthe disease processes. Translational medicine focuses on disease biomarkers and brings new focus and hypotheses to the drugdevelopment process. For example. cognitive symptoms manifest prior to positive ones. We now know that individuals who are at risk of becoming schizophrenic manifest. in early adolescence. clear cognitive deficits often associated with low I Q Some. but not all. of those individuals will go on to manifest positive symptoms (hallucinations. delusions. paranoia). b. Remission: A second issue is that the treatments that are used to control positive symptoms do not improve functional outcome. In contrast. attenuation ofthe cognitive deficits do predict functional outcome and in some cases lead to patient rehabilitation into the work place," c. Relapse: Relapse is associated with thought disorder and cognitive disorganization. As such . cognitive endpoints are seen early on in life and can be seen as an early milestone in the initiation ofthe disease. worsens when the positive symptoms appear and remission ofpositive symptoms with improved cognitive function tracks with augmented rehabilitation and functional outcome. Therefore, as cognitive endpoints track more readily with initiation, progression. remission and relapse in schizophrenia it fulfills all the criteria in the disease biomarker definition. In addition. the duration of aberrantly expressed biomarkers could also be associated with risk for disease even if the level of the biomarker does not change over time. In schizophrenia, this is typified by the fact that these at risk individuals also show sensory gating deficits (e.g., prepulse inhibition) do not "normalize" with the majority of successful treatments of positive symptoms," Since disease biomarkers are defined by their statistical correlation to features of the disease it is imperative that the clinical phenotype is clearly defined. Stratification of all possible phenotypic variables in clearly a prerequisite for accurate assessment of the discrete relationships ofthe biomarker to the disease. Gender. age. life-style, medications. physiological and biochemical similarities are often not sufficiently inclusive resulting in plethora of disease biomarkers claims that are often confusing and futile. II. Target Validation: biomarkers that assess the relevance and the potential for a given target to become the subject ofmanipulation that will modify the disease to provide clear

4

PharmaceuticalBiotuhno/Qgy

therapeuticbenefitswhilesecuringasufficient therapeuticindexofsafetyand tolerability. This biomarkeris intrinsicallylinked to our understandingof the disease. a. PostmortemStutliesasSouru ofMjskaJing TargetItlmtiJiution: Often our understandingor employmentof our strategies to a developdrugs isoften sub-optimaland maythereforeleadto targetsbeinginappropriatelyor incorrectlyidentified. However, many of our approaches to target identificationare based upon receptor expression from post mortem brain tissues. For example, post mortem brain tissues taken from schizophrenics show heterogeneous neuropathology's ranging from ventricular enlargement,disorganizedcelllayering [e.g.,Layers II and III of the cortex)and reduced dendrite spinecount and arborizationin regionsof the CNS such as the DLPC and hippocampus (e.g., ref8). b. Anima/Models as TargetValiJation Biomarkers: However, recent preclinicaldata has demonstratedthat chronicexposureto antipsychotictreatments(e.g., haloperidol and olanzapine)is alsoassociated with significant decreases in total brain weight and volume, gray matter volume, glial cell number." As such, investigation of selective targeted "risk"genedisruption in mice,not only serveasetiologically relevantanimal models,but by virtue of modelingthe geneticcomponent of the disease can serveas model systems of target validation. A pertinent casein point, several of the emerging "schizophrenia gene" disruptions are showing neuropathology that is seen in post mortem brain tissueasdescribedin sectionlla . m. Compound-Target Interaction Biomarkers: biomarkers that definethe discreteparameters of the compound (or biological) interaction with the moleculartarget.Typifiedby PET and SPECT, such parameters include binding of the compound to the target, its residencytimeon the target,the specific siteofinteractionwith the targetand the physical or chemical consequences to the targetinducedbythe compound(orbiological). Industry needsto engageearlyin the discovery process and developSARfor TCI biomarkers early on in the process. IV. Pharmacodynamic Biomarkers: biomarkers that predict the consequence(s) of compound (biological) interactionwith the target.Thepharmacodynamic biomarkers include eventsthat are therapeutically desiredor adverse eventsbasedon mechanismofaction. a. The Conupt: pharmacodynamic biomarkers can best be described by the employment of a new molecularentity [e.g., "compoundX"), that hasno PET ligand,whose therapeutic benefitis derivedfrom indirect action upon a separatetarget system (e.g., dopamine) to which there exists a TCI biomarkers (Raclopride"R"). As such we can examinethe effects of "X" (e.g., S-HT2c agonist) for the displacement of dopamine via the useof"R". b. Trackingthe Divergenu and Convergence ofSignaling Pathways: However, pharmacodynamic biomarkers can be used to report on discretemoleculareventsthat are proximal to the biochemicalpathwaythat is modified by the manipulated target or remote consequences such as in vivoor clinicaloutcomes (morbidity or mortality). Pharmacodynamic biomarkers arediverse and frequentlynonobvious. Advancedand sophisticated bioinformatics tools are required for trackingthe divergence and convergence of signalingpathways triggeredby compound interaction with the target. c. "OffTarget"Effects: A subsetof the pharmacodynamic biomarkers areconsequences inducedbythecompoundoutsideitsintendedmechanism ofaction.Suchpharmacodynamiceffects areoftentermed"offtarget"effecrs, astheyarenot the directconsequence ofthe compound interaction with the target. Usually, such pharmacodynamic events are due to unforeseen lack of selectivity or metabolic transformations that yielded metabolites not present (or detected) in the animalsused for safetyand metabolic studiesprior to launchofthe compound into humans trailsor into human use. These issues will not be dealt with in this chapter.

Translational Medicine-A Paradigm Shift in Modern DrugDiscoveryandDevelopment

5

V. Patient Selection: biomarkers that are used for selection of patients for clinical studies, specifically proof-of-concept studies or confirmation Phase 3 clinical trials that are required for drug registration. These biomarkers are important in order to help in the selection of patients likely to respond (or conversely, not respond) to a particular treatment or a drug's specific mechanism ofaction and potentially predict those patients who may experience adverse effects. Such biomarkers are frequently genetic (single nucleotide polymorphism, haplotypes) or pharmacogenomic biomarkers (gene expression), but could be any of the primary pharmacodynamic biomarkers. Biomarkers for patient selection are now mainstream ofexploratory clinical trials in oncology where genotyping of tumors in view of establishing the key oncogenic 'driver(s)' are critical for prediction potential therapeutic benefits of modern treatments with molecular targeting drugs. The success ofthe new era of molecular oncology (as compared to the cytotoxic era) will largely depend on the ability to define these oncogenic signaling pathways via biomarkers such as phosphorylated oncogenes, or functional state due to mutations that cause gain or loss offunction. a. Imaging regional cerebral activation whilst patients perform tests of cognitive performance can be used to dissect the discrete neural regions and substrates supporting cognitive performance. In contrast to oncology, it is rare that there are concrete physical matter to quantify based on the heterogeneous nature ofneuropathological abnormalities (see section I). However, imaging techniques such as functional MRI (fMRI) are bridging this gap. fMRI has the potential to be a powerful, sensitive and repeatable tool in our armamentarium. This technology affords the potential to dissect patients with cognitive deficits that are driven by, for example, either medial temporal lobe or by frontal lobe dysfunction (e.g., episodic memory vs. executive function deficits) within a clinical trial. Applied in early clinical POC studies we can, in essence, turn our current heterogeneous clinical population into discrete, focused sub groups with which to answer specific and focused hypothesis about the target, patient population and ultimately increase the probability of seeing an effect with our compound whilst improving the potential for d ifferentiation from comparators. This in turn can aid patient selection in larger Phase III confi rm studies and can be driven by adaptive trial design, VI . Adaptive Trial Design: The overall objective ofadaptive trial design is to enable real time learning. The method is based on computer modeling and simulation to guide clinical drug development. In a first step, decision criteria and assumptions are defined and analyzed str ateg y and stu dy designs are formulated to test competing hypotheses in one aligned approach. Once this framework is established, a formal scenario analy sis, comparing the fingerprints of alternative designs through simulation is conducted. Designs that appear particularly attractive to the program are further subjected to more extensive simulation. Decision criteria steer away from doses that are either unsafe or nonefficacious and aim to quickly hone in onto the most attractive dose -range. Response-adaptive dose-ranging studies deploy dynamic termination rules, i.e., as soon no effect dose scenario is established and the study is recommended for termination. Bayesian approaches are ideally suited to enable ongoing learning and dynamic decision-making.' The integrator role of "adaptive trials" is particularly strong in establishing links between regulatory accepted "confirm" type endpoints and translational medicine's efforts to develop biomarkers. Search for biomarkers that may enable early decision making need to be read out early to gain h igher confidence in basing decisions on them. A biomarker can be ofvalue , even if it only allows a pruning decision. These considerations highlight the importance of borrowing strength from indirect observations and use mathematical modeling techniques to enhance learning about the research question. For instance, in a dose -ranging study, it is assumed that there should be some relationship bet ween the response ofadjacent do ses and this assumption can be

6

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the nucleus. Following the release of the viral DNA into the nucleus, the viralgenome circularizesand a cascade is initiated with the transcriptionof five immediateearly(IE) genes (infected cellprotein ICP4. ICP27. ICPO. ICP22, ICP47) through the binding of a viralprotein present in the tegument (VP16). in combinationwith cellular factors. to the enhancerelementpresent in all IE promoters (TAATGARAT)?The products of the abovegenes are responsible of the transactivationof the earlygenes (E) which are encodingenzymes and DNA binding proteins required for the viralsynthesis; the IE and E are followed by expression oflate genes (L) which products are principally structural proteinsof the capsid. tegument and envelope (primarilyviral structural components).3.5 Following natural infection the virus is know to be axonaltransported from the peripheryto the cellbodyof the sensory ganglionwhereestablishes alyticor alatent infection.8 HSV-1persists in the latent statein the nervoussystems of the host for a lifetimewherethe viralgenomepersists in an epichromosomal state associated with histoneswithout integratinginto the host genome," During a latent infectionthe virusisin a relative quiescentstatewherethe transcriptionislimited to a singleregionofthe viralgenomeand only a groupoflatency-specific RNAsaredetectablein the nucleiofneuronalinfectedcells. Due to several stimuli. the viruscan be reactivated from the latency and usually by anterogradetransport gets back to the site of primaryinfection where it starts a newlyticcycle. Only in fewcases the viralparticleis retrogradetransported to the central nervous system (CNS) and starts a latent or a lytic infection, which evolves in encephalhis.'?" The newlyreplicatedvirustransported anterograde. usually to a siteat or near the portal of entry. maycausea localized coldsoredisease lasting2-10dayswith subsequentremission when the cold soresdisappear. Over time. periods of remission generally increase in length and the duration of cold soresdecrease. until the person rarelyhas active disease. Thisprocess is regulatedby specific immunity developed by the patient againstthe virus." The virusinfection is. however, life-long and can be retriggered in some individuals by specific events. such as sunburn. stress or other infections. 13,14

HSV-l GenomeandHSV-Derived Vectors Thecompleteknowledge of the HSVsequences andprogress ofmolecular techniques has leaded to the development ofHSV asavectorforseveral potentialapplications in humanhealth.15.19These include (i) delivery and expression of human genes to the nervoussystem cells.20,21 (ii) selective destruction of cancercells,22,23 (iii) prophylaxis and immunotherapyagainsttumors 24,25 and (iv) prophylaxis againstinfections with HSV and other infectious diseases,z6.27 In the viralgenomethere areapproximately 80 geneproductschatcanbe classified asimmediateearly(IE or a). early(E or ll) and late (Lory) dependingon their kineticsofexpression during replication. Theviralgenes can alsobe categorizedaccording to whetherthey areessential or non essential for virusreplication (Fig. 1).Essential genes are required to producenewinfectious viral particlesin permissive cellculture infections. Non essential. or accessory, genesencodeproduces that are not absolutely requiredin cellculture but are important for optimum lyticreplication or affectthe natural lifecycle ofthe virusin vivo. contributingto host range. pathogenesis. or latency. The viral DNA contains at least 37 essential genes. The USregionof the genomecontains only one essential gene encoding the glycoprotein D. which offers the opportunity to replace large segments ofviralsequenceswith foreign DNA.4.28,29 The modifiedHSV genomeshould be ableto accommodate up to 40-50 kbof exogenous sequences. However. the modification oftheseviruses to reducepathogenicityand increase safery often resultsin the lossof viral activities. which are required for efficient genedelivery and lifelong association with the host. In recentyears, newtechnologies haveallowed researchers to get deeperinto these problems." The challenge for manyresearch groupsis to developthe toolsto rendertheseorganisms harmless yet effective for targeted gene transfer and appropriategene expression. Vectors based on HSV Type 1 are currently (a) arnplicon vectors, (b) replication-defective viruses and (c) genetically engineeredreplication-competent viruses with restrictedhost range. 19.31

121

HSVas a Vector in Vaccine Development and Gmt!1ht!rapy

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Amplicon Vectors Amplicon vectors are HSV-l particles identical to wild type HSV-l from the structural, immunological and host-range points of view, but which carry a concatemeric form of a plasmid DNA. named the amplicon plasmid. instead of the viral genomeY ':l4 Amplicon vectors possess several advantages as gene delivery vehicles: (a) a large transgene capacity (150 kb), (b) the repetitive character ofthe genome carried by the amplicon particle ensures the introduction ofmultiple copies ofthe transgene per infected cell; (c) the ability to infect a wide variety ofcell types. including dendritic cells; (d) the ease ofvector construction; (e) the limited toxicity due to the lack of viral coding sequences. Amplicons are bacterial plasmids that contain one or more transgene cassettes and two non coding viral sequences, an origin ofDNA replication (ori) and a D NA cleavage/packaging signal (pac) and they require a helper system to be produced. In the presence ofHSV-l helper functions. a circular amplicon can be replicated and amplified as head-to-tail concatemers and packaged into HSV-l particles as approx 152 kb linear DNA (Fig. 2).35 Classically. amplicon vectors were prepared in cells transfected with the amplicon plasmid and superinfected with helper HSV-l. As the helper virus was generally a replication-defective mutant ofHSV-l , the amplicon stocks were produced in transcomplementing cell lines. However. the use of standard HSV-l as helper resulted in the production of helper -contaminated vector stocks. 36•37 The contaminant helper particles. even if defective. induced significant cytotoxicity and inflammatory responses. prevent ing their use in gene therapy or vaccination protocols." To overcome these obstacles. different helper systems that produce essentially helper-free vector stocks have been recently developed ." The last generation of helper system consists of the entire HSV-l genome. without pac signals. cloned as a bacterial artificial chromosome (HAC) in E. coli supplying the full set of transacting HSV-l functions.39,40 Another different helper system recently developed is based on the deletion. by Cre/loxP-based site-specific recombination. ofthe packaging signals ofthe helper virus in the cells that are producing the arnplicons."

122

PharmaceuticalBiotechnology

Replication-Defective vectors The replication-defective viruses are viral vectors where "essential" genes for in vitro viral replicationare either mutated or deleted.Therefore, these mutants cannot growexceptin transformed cell lines, where they are complemented in trans. To date, several replication-defective vectors havebeen constructed in which the IE genes, expressing infected cellproteins (ICP) 0, 4, 22, 27 and 47, havebeen deleted in various combinations. IE genes are expressed shortly a.tter viral entry into the host cell and are required for initiation of a cascade of E and L viral gene transcription. ICP4 and ICP27 are essential for replicationand the deletion of one or both of thesegenesrequiresadequatecomplementing celllinescapable of providingin trans the proteins encoded bydeletedviralgenes.42-44 ICPO, 4 and 27 areresponsible for Eand Lgeneexpression.45.46 Beside its transcriptionalfunctions,ICP27 alsoaffects the splicing, polyadenylation and stability of mRNAs. ICPOis a promiscuous transactivator actingon ICP6 gene,which encodesthe viral ribonucleotidereductase largesubunitand possesses a hybridpromoter,whichisactivated asan IE and an E fUnction.47.48 ICP22, the viralproduct that might be involved in sequestering of cellular DNA polymerase 49 is phosphorylatedby two accessory genes ULl3 and US3-encoded proteins 50-52 and isrequiredfor the optimalexpression of the ICPOprotein. Deletionof the ICP22 IE gene can be responsible for an overexpression OfICPO.53 ICP47 inhibits MHC class I antigenpresentation contributing to the virusescape from the immune surveillance.54-S6The "firstgeneration" of replication-defective HSV-l basedvectorsconsistedof mutants deletedin the single essential IE gene encoding ICP4, namelyd120.4s Although these vectors show reduced pathogenicity and can be used to efficiently transfer and transiently express reporter genes in brain, they are nonetheless cytotoxicfor neurons in culture. Cell lines that complementICP4 and ICP27 have permitted the construction of a "second generation" of highlydefective mutants.43,S7.S9 To date, several replication-defective vectorshavebeenconstructedin which ICPO, ICP4, ICP27, ICP22 and ICP47 geneshavebeendeletedinvarious cornbinations.w" Deletionof allfive IE genes(ICP 0,4,22,27 and 47) preventsvirustoxicityfor cells at high multiplicityof infection, allowing the vector geneto persistin cells for longperiods 60-62 demonstratingthat the residual cytotoxicityof the "firstgeneration" of replication-defective HSV-l basedvectorsresultsfrom the expression of the other four IE genes.28The multiplydeleted mutants showan unusually prolongedtransgene expression from the ICPOIE promoter or the HCMV IE promoter in neurons.v The advantages of these second generations of replication-defective vectorsare characterized by absence ofearly and lateviralgeneexpression and provideenoughspace to introducedistinct and independently regulatedexpression cassettes for differenttransgenes.?

AttenuatedHSVvectors Deletion of somenon essential viralgenes resultsin viruses that retain the abilityto replicate in vitro, but are compromised in vivo, in a contextdependent manner.64•6SAmongthe limitations to the useofHSV is the fact that wt virusishighlypathogenicand cerebralinjectioncauses fatal encephalitis. Toxic and/or pathogenicproperties of the virus must, therefore, be disabledprior its useas a genedelivery vector. Several genes involved in HSV replication, virulence and immuneevasion, which are non essentialforvirallifecycle in vitro,havebeenidentified. Thesegenes areusually involved in multiple interactions with cellular proteins,which optimize the ability of the virus to growwithin cells. Understandingsuch interactionshas permitted the deletion/modification of these genes, alone or in combination, to createHSV mutants with a reducedabilityto replicate in normalquiescent cells, but that can replicate in tumor or dividingcells. These attenuated viruses harbor further modificationso they alsoserveas therapeuticgenedelivery vehicles.6S.66 ManyHSV-l and HSV-2 genes that arenon essential in culturealtervirulence in animal models. Among these genes, the ones encoding thymidine kinase (TK), ribonucleotide reductase (RR), the virion-host shut off (Vhs)67and the ICP34.S proteins havebeen extensively studied.68 TK is involved in optimizingnucleic acid metabolism for virusgrowth and is necessary for efficient replicationin neurons. RRis necessary for the conversion of rNTPs to dNTPs in neurons,which

HSVas a Vector in Vaccine Development and Gene1herapy

123

are otherwise lacking but necessary for the synthesis ofnew viral DNA during virus replication/" The Vhs function of HSV causes rapid destabilization of host RNAs and translational arrest." Vhs also destabilizes viral messages, resulting in over accumulation of IE and E genes during lytic infection?Q-72The ICP34.5 neurovirulence factor has been found to be essential for HSV pathogenicity?' It appears to provide multiple functions to the virus life cycle, one ofwhich is to block the arrest in translation, which usually occurs in virus-infected cells as an anti-viral response preventingvirus replication. This effect is mediated through the cellular PKR kinase, which phosphorylares the translation initiation factor eIF2a, thereby stopping translation. ICP34.5 recruits protein phosphatase Ia, to rephosphorylare eIF2a, allowing protein translation and continued virus replication. Tumor cells often display an impaired PKR pathway and/or elevated levels of eIF2a, that allow replication ofICP34.5-deleted viruses, as the inactivation ofthe PKR response is less critical in this contest.V" Secondly, ICP34.5 seems to be involved in allowing new virions to become packaged and leave infected cells in a cell type-specific fashion . Consequently, in non permissive cells in the absence of ICP34.5 the nucleo capsids are retained in the nucleus and a productive infection cannot ensue. Use of non replicating viruses or non viral systems as vectors can limit the maximum achievable efficiency ofgene transfer. In contrast, use ofreplicating vectors to allow replication ofgenes delivered initially to a small number of cells and their subsequent transfer to neighboring cells, as infection spreads, can significantly increase the efficacy of gene delivery?6-78Attenuated HSV vectors have been tested as live viral vaccines, as oncolytic viruses and as gene therapy vectors to deliver transgenes to the nervous system.

Engineering Techniques Alterations of the HSV genome can be achieved in a number ofways. These usually require a two-step process (named: marker transfer/marker rescue) in which portions ofthe herpes genome , which have been cloned into a plasmid vector, are first modified in vitro. The plasmid DNA is then cotransfected into cultured cells with infectious viral DNA and recombinant viruses are selected . Several methods have been described to insert DNA sequences into the viral genome. Efficient recombination into specific sites within the viral genome has been achieved in vitro using a recombination system der ived from phage Pl.79 It is also possible to enhance the frequency of recombination.59 The initial requirement is the insertion ofa reporter gene such as ｾ Ｍｧ｡ｬ｣ｴｯｳｩ､･ (lacZ) cassette flanked by Pac! or Pmei restriction enzyme sites not otherwise found in the viral genome. The second phase is the substitution of the reponer gene with other foreign cDNAs by digestion ofthe vecto r DNA with Pac! or Pmei to remove the lacZ gene and subsequent repair of the vector genome by homologous recombination with a transgene expression plasmid. Potential recombinant identified by a "clear plaque " phenotype after X-gal staining arose at high frequency (80-100%) (Fig. 3).59 A different procedure involves transfection ofcells with overlapping cosmids containing appropriate insertion or deletions. Expression of genes contained in cosmids leads through recombination to the con struction of full-length viral genome. f -" To select recombinant vectors it is critical to have a system by which to identify successful recombinants. The viral TK gene is particularly useful site for insertion since its inactivation does not affect in vitro the replication ofthe virus. TK mutants can be easily selected in the presence ofbromovinyl deoxyuridine or acyclovir.82.83Another marker system involves disruption of nonessential viral envelope glycoprotein genes, such as the ones encoding gC or gE. Recombinant viruses are identified by loss ofan antigenic determinant ofthe glycoprotein using specific monoclonal antibodies (black or white plaques staining). Traditionally, recombinant HSV vectors have been generated through homologous recombi nation between the HSV genome and a recombination plasmid, which usually requires laborious screening or selection and can take several months. Recent advances in bacterial artificial chromosome (BAC) technology have enabled cloning ofthe whole HSV genome as a BAC plasmid and subsequent manipulation in E. coli. Thus, we sought a method to generate recombinant HSV vectors more easily and qu ickly using th e bacterial recombination machinery. 84.85

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'Mice efficacy is evaluated as the capability of HLA-A2 transgeni c C57BI/6 mice to elimi nate the engraftment of HIV-l /M uLV-infected syngeneic splenocyte s injected int raperltona llv.v" 2P: Preven tive ; T: Therapeutic; 3L\V 2Env: Env deleted in V2 (see text for further deta il s); 4M VA : Modified Vaccinia An kara vi rus; 5M ulti HIV, also terme d MultiHIV DNA vacci ne is a pl asmid exp ressing an antige nic fusio n protein compo sed of the regul ator y HIV-l proteins Rev, N ef and Tat, Gag p17/p24 and a stretch of 11 cytotox ic T-Iymphocyte (CTL) epitope clusters fro m Pol and Env, wh ich w as cloned into a nov el DNA vector named the Ge ne Transport Unit (GTU). Four differe nt pl asmids expressing the same im munogens but originating from subty pes A , B, C consensus, or FG H ancestral seq uences, are currently und er evaluat ion; 6M ultigene is a coc ktail of seven plasmids enc odi ng cl ade B Nef, Rev, Tat, RT, clade A and B Gag and clade A, B and C Env prot eins.

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Vaccine Product (Clade)

Vaccines Based on Combined HIV Structural and Nonstructural Gene Products

continued on next page

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ADARC: Aaron Diamond AIDS Research Center; ANRS: Agence Nationale de Recherches sur Ie SIDA (France); DAIDS: Division of AIDS; DoD: US Department of Defense; EuroVacc: European Vaccine Effort Against HIV/AIDS; Guangxi CDC: Guangxi Centre for Disease Control and Prevention; HPTN: HIV Prevention Trials Network; HVTN: HIV Vaccine Trials Network; IAVI: International AIDS Vaccine Initiative; MoPH: Ministry of Public Health; MUCHS: Muhimbill University College of Health Science; NIAID: US National Institute Allergy and Infectious Diseases; NIH: US National Institutes of Health; SGUL: St George's, University of london; SMI: Swedish Institute for Infectious Disease Control; St. Jude: St. Jude Children's Research Hospital; TAVEG: Thai AIDS Vaccine Evaluation Group; USMHRP: US Military HIV Research Program; VRC: Vaccine Research Center; WRAIR: Walter Reed Army Institute of Research; MVA: Modified Vaccinia Ankara; FPV; fowl poxvirus; vCP: viral Canarypox; LT·K63: nontoxic mutant of heat labile enterotoxin (IT); PLG: Polylactide- coglycolide; GM-CFS: Granulocyte-macrophage colony stimulating factor.

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PhaseIII trialwith a HIV-l Env-based vaccine in which a canarypox prime isfollowed byboosting with the VaxGen gpl20 protein (Table6). Similarly. despitepromisingresultsin the monkey model.l" a PhaseI therapeutic trial with a fowlpox vector expressing Gag and Pol failed to displayany immunogenicityof the transgenes, althoughit inducedanti-vector Abs.37SImmunogenicity wasdemonstratedin a morecomplex therapeutic trial in which immunizationwith fowlpox expressing several HIV antigenswascombined with HIV lipopeptides(syntheticfragments of HI V proteins associated with lipidsthat facilitate the induction of a cellularimmuneresponse) and followed byadministration ofIL- 2. confirming the intrinsicweakimmunogenicityof this vector.376Fowlpox vectoredvaccines performedpoorly alsoin heterologousDNA prime-fowlpox boost approachesboth in monkeys and PhaseI preventiveor therapeutic trials.375.377.378 Subsequentstudies in the monkey model suggest that the poor immunogenicityobservedin human as compared to monkeysmight be due to the vaccine dose used. which might be insufficient to triggeradequate responses.t" However. higher production costs,multiple inoculations and reactogenicity are seriousobstacles to scalingup vaccine dosing and might hamper further developmentof vaccines of this type.

Adeno andAdeno-Associated Vectors Adenoviralvectorshavea broad host rangeand infect both proliferatingand quiescentcells. The tropism of adenoviruses for mucosalepithelium makesthem extremely attractiveas vectors for HIV vaccinedevelopment since they can been delivered orally or intranasallyand induce mucosalimmune responses.P? Recombinantadenovirus vectorscan accommodatelargerinserts, mediate transient but high levels of protein expression and can be easily produced at high titers. Furthermore. adenoviruses targets DCs in which they up-regulatecostimulatorymolecules and MH C class II expression and induceproduction ofTh-l and pro-inflammatory cytokines.381.382 Of note. Adenovirus-based vaccine candidateshaveproduced the most impressive cellularimmune responses seenso far. 383Bothreplication-competent and-incompetent vectors arebeingdeveloped asvaccine againstHIV. However,whilereplication-competent adenovirus vectorsinducestronger and more persistenthumoral and cellularimmuneresponses comparedto the nonreplicatingvectors. there are safetyconcernsabout their use in clinicaltrials.383.38s The replication-incompetent recombinant adenovirus Type S (rAdS) is a modified form of AdS, the virus that causes some formsof the common cold. It is replication-defective to enhance safetyand represents one of the most promisingviralvectors for HIV vaccines. However. prior exposure to AdS mayboost anti Ad-Santibody response blunting the expression ofthe transgene and the percentageof volunteers respondingto the vaccine. This anti-vectorimmunity mayrepresent a major problem in the developing world, where the prevalence of prior exposure to AdS isgreatest.386Thishasprompted the developmentby Merck. Crucelland Transgene, in collaboration with IAVI. of candidatevaccines basedon less prevalenthuman Adenovirus serotypes (Ad6. Ad3S. Adl l, or Ad 24) to replace the AdS vector in fusion HIV trials.387.39o Another approach to circumventpre-existing immunity to AdS has been to modify the vector by substituting key neutralizing epitopes on the surface of viral capsidproteins with those from the less prevalent serotypeAd48. Suchchimericvector is calledAdSHVR48.391 Finally. pre-existing immunity to adenovirus maybe overcome by heterologousprime-boost strategies, including DNA priming followed by adenovirus vector boosting.96.392 or the use of different adenovirus serotypes, including the above mentioned AdSHVR48. for priming and boosting.393•394 Upon extensive testingin nonhuman primatesMerckfoundout that intramuscular vaccination with SIV Gag delivered by AdS (El- deleted) was superior to DNA or MVAat inducing CTL responses and at protecting against disease followingpathogenic intravenous challengedwith SHIV_89.6P.141.142but not against an intrarectal challenge with SIVmac239.143 Noteworthy.the limited protection upon SIVmac239 occurredin the presenceofT-cell responses that correlated with protection in the formerstudy.144 Co-immunizationwith AdScarryingGagand Envwasless effective than Gagaloneat controllinginfectionin rhesusmacaques challenged intravenously with

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SHIV-89.6p238confirmingthe detrimental roleofCTL responses to Envobservedin the natural infection.63 In order to increasethe breadth of response against HIV-l and to improve the vaccine efficacy, replicationdefective AdSvectorscarryingpol and nef wereconstructed and a Phase lIb trial started in 2004 in which 3,000 high riskindividuals wereimmunizedintramuscularly 3 timeswith replicationdefective AdSvectorsexpressinggag, pol and nef(AdSMRKAdStrivalent). This trivalentvaccinewasgenerally safeand welltolerated at all dosesstudied and immunogenic eliciting responses against the 3 antigens included in the vaccine. However, preliminary data indicate that vaccinationdid not protect from infection or loweredviral loads. Further, there wasan apparent higher susceptibility to infection in vaccinees with pre-existing immunity to the vector.146.395 Reducedexpression and immunogenicityofthe transgenes, assuggested bythe much lowerproportion of vaccinees respondingto allthe three HIV antigens(Gag,Poland Nef) in the group with pre-existing immunityto AdSascomparedto vaccinees with no pre-existingimmunity, immune activation generated by the response to the vector and/or an increaseof HIV-specific target T-cells induced by the vaccine!" are some of the hypotheses that have been proposed to explain these findings. Thus,although verypreliminary, overallpreclinicaland clinicaldata may suggestthat SIV is a more rigorouschallenge virus and a better predictor of vaccine efficacy in human and that boostingof pre-existing immunityto the vector mayactuallyenhancethe susceptibility to infection ascomparedto placeboor vaccinees with no pre-existing immunity.Another nonreplicativeadenoviral vector (deleted of the genes coding for El and E3 proteins) has been developedby NIH Vaccine Research Center (VRe), together with a DNA-basedvaccine. These are multicomponent vaccines, which express the Env glycoprotein from clades A, B and C and the Gag, Pol and Nef proteins from cladeB and aredesignedfor usein a DNA prime-AdS boost regimenstrategy.396 Despitedifferences in the vaccine design, initiation ofPhaseII trialshas been postponed to late 2008,when a better understandingofthe reasons of the Merck's vaccinefailure will clarifywhether vaccination with the VRC candidatewould posethe same risks. Replication-competent adenoviral vectorshavealsobeen developedasvehicles for AIDS vaccines.397Studiesin both chimpanzeeand rhesusmacaquemodelshavedemonstratedthat priming with replicatingAd recombinantsencoding HIV or SIV genesfollowed by boosting with viral protein subunits elicitspotent humoral,cellularand mucosalimmuneresponses.385.398-405 Ofnote, vaccinationofRhesus macaques with Advectorsexpressing HIV-l Tat and Envconferreda strong protection against a challenge with the pathogenicSHIV 89.6P, which wassuperiorto that provided by a largervaccine formulation includingSIV Gag and Nef in addition to HIV-l Tat and Env.268 This underscores the importance ofproperly selecting the antigens to combine together and providesone of the strongestevidence in favorof the Tat + Envvaccine. Other viral vectors used as AIDS vaccines in clinicaltrials includeAdeno-associated viruses (AAV) which are not adenoviruses but are often found in adenovirus infections.406•407These vectors arecurrentlyusedin PhaseI and PhaseII clinicaltrials," However, the weakimmunogenicity recorded in a multicentric Phase I studr has led to halting the initiation of Phase II trials in India and spurred a debate on the ethics of conducting the ongoing Phase II trials in Africa in the faceof such disappointingPhaseI results. Theslightlybetter immunogenicityrecordedat the highest dose tested in the PhaseI trialsmaysuggestthat a doseincreasecould solve this problem. However, recent data indicate that, in mice,vaccination with high dosesofAAV expressing Gag inducedGag-specific effector CD8+CTLs that wereweakproducers ofIFN-y,expressedexhaustion markersand failedto becomememorycells.Transitionto the memoryphenotype and restoration of full functionalitywasachievedupon adoptivetransfer, suggesting that chronicexposure to the trangene might havebeen the cause of the CTL dysfunceion.f"

Other Viral vectors Other viral vectors have been tested as vaccine vectors for HIV-l and have shown various degrees of success (for a reviewsee ref. 410). Among them, the alphaviruses include weakened formsof three viruses named Venezuelan Equine Encephalitis (VEE), Sindbis(SIN) and Semliki ForestVirus(SFV).The firstalphavirus vectorcandidate,AlphaVax's VEE,isdesignedasa replicon

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particles containing self-replicatingRNA encoding the VEE replicase proteins and expressing a gene of interest in placeof the viralstructural protein genes. An appealingfeatureof alphaviruses is their known ability to induce apoptosis of transduced cells, favouring DC cross-priming."! Thesereplicon particleshaveshown protection againstother virusesand haveelicitedsignificant cell-mediatedand antibody immune responses with SIV antigens,perhaps due to the propensity of the vector to target antigen-presentingcells.412 The VEE vector is currently being tested in clinicaltrials.4I3 Viruses belonging to the rhabdovirus family and in particular the vesicularstomatitis virus (VSV) are also being used. These vectors offer the advantage to be highly flexible, easy to manipulate and ableto express largeand multiple foreigngenes.414Intramuscularvaccinationof mice with a single-cycle vector expressing HIV Env elicited strong Env-specific humoral and cellular responses."? Furthermore, immunization of macaques with recombinant VSVs (rVSVs) expressing SIV Gagand HIV Envhas been reported to protect from pathogenic SHIV89.6P.416.417 These promising resultshaveled to the developmentofrVSVfor use in humans.t" However, sincethe prototypic rVSVvector was found to be insufficiently attenuated for clinical evaluation, novel highlyattenuated vectorshavebeendesigned, whicharelessneurovirulentand moreimmunogenic than the prototypic rVSVvector," ? Other potentially powerful vaccinedeliverysystems are represented by Polioviruses.f" Both replication-competent and replication-deficient recombinants have been shown to be immunogenic in nonhuman primates when used through various routes of immunization, including mucosaldelivery.t" However, restrictionsto the useof thesevectors include the stabilityand size of heterologous gene inserts422and the presenceof high levels of pre-existingimmunity to polio vectors in the generalpopulation. Replication-competent and replication-defective herpesviruses (HSVs), including HSV-I, represent suitable vaccinevectors against AIDS. Important advantages include broad host cell range,high infectivityand easyof production of high-titer stocksof viruses, long-termexpression of foreign antigens and stimulation of both humoral and cellular arms of the immune system. Vaccination with replication-competent or replication-defective HSVsvaccinevectors expressing SIV Env and Nef, protected macaques against a challengewith SIVmac239.423 However, the overalltoxicityand the pre-existingimmunity against the vector may represent a safetyissuefor their use in humans and current strategies focus on the development of replication-incompetent virusesused in prime-boost regimenwith DNA. 424

New Particulate Delivery Systems Microparticles havebeeneffectively usedformanyyearsasparticulatedelivery systems fordrugs, therapeuticproteins and varioustypesofvaccines includingrecombinantproteins, plasmidDNA, peptides and other vaccine components (e.g., immune potentiators).42S·426 Among antigen-loaded microspheres, injectable, biodegradable polymericparticlespreparedwith poly(d.l-lactide-co-glycolide)(PLG) or poly(d.l-lactide) (PL) polymersrepresentasuccessful method for in vivodelivery of peptide, protein or DNA antigens." ?Both particleshavebeen shown to be effective, especially for oral delivery.t" Antigen instabilityand manufacturingdifficulties havebeen overcomeby the recent findings that adsorption rather than microencapsulation of the antigen onto PLGA is easier, cheaperand ensuresbetter antigen stability.429 In comparisonto standard aluminum-based adjuvants,these microspheres have many desirable features, including the ability to enhance the bioavalaibility of the antigen,allowingpulsatingantigen release and to reducethe number of doses in the immunization schedule,mimicking the conventionalprime-boost regimen.Furthermore, for adjuvantingvaccines against intracellularpathogens and cancer, selective targeting of PLGA microparticlesto DCs has been achievedand induction of CTLs has been attained in both small animalsand nonhuman primares.v"In particular PLGs havebeen demonstrated to enhance the immunogenicityof DNA vaccines to HIV-Gagand HIV-Envin rhesusmacaques.t" PLG particles are currently beingevaluatedin a gag + env DNA/PLG prime-AV2 Envprotein boost preventive PhaseI trial.189

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Two novel classes ofbiocompatible core-shell anionic microspheres havebeen used as an efficientdelivery system for vaccinationwith the Tat protein.432Thesernicrospheres, synthesized by dispersion polymerization, arecharacterized byan increased shelf-life and the capability of reversibly adsorbingnativeproteins at their surface. In particular.thesemicroparticles consistofnegatively charged microspheres, made ofeither poly(styrene) or poly(methylmethacrylate) and in which hemisuccinatedpoly(vinylalcohol)or EudragitLl OO/S Swereused,respectively, asstericstabilizers.432Thesemicrospheres preventedTat from oxidation, maintainingthe nativeand biologically active conformation required for vaccine efficacy and efficiently delivered Tat intracellularly. In the mousemodel, delivery of Tat by these microspheres wassafeand immunogenic.433•434

VLPs Virus-like particles(VLPs) are self-assembling. nonreplicating,nonpathogenic particlesthat aresimilarin sizeand conformationto intact virions.43s.436 VLPsoffera number ofadvantages over conventional protein immunogens and havebeen therefore consideredas an ideal HIV vaccine candidare.i" In fact,theseparticlescanbe easily producedin largeamount in heterologousexpressionsystems (baculovirus, vaccinia virus)and easily purified. In addition,sinceVLPslackregulatory proteinsaswellasinfectious geneticmaterial, theyareboth replication- and infection-incompetent, makingVLPssaferthan live-attenuatedviruses. Further,VLPsexpress viralproteinsin their native conformation and generally induce more effective humoral and cellularimmune response than their solublecounterparts. in both the systemic and mucosalimmune compartments.437-439 However. due to their nonreplicatingproperties,VLPsareless effective at inducingcellularimmune responses ascomparedto live-attenuatedviruses or replicatingviralvectorvaccines. For this reason,novelapproaches arebeingdeveloped in order to increase their immunogenicity, including DC targeting.440 The mucosaladministration ofVLP vaccines has also emergedas a promising strategy to elicit mucosaland systemic anti-HIV humoral and cellularimmune responses.r" To date. numerous typesofVLPs havebeen produced utilisingthe abilityofcapsidand envelope proteins to self-assemble into highlyorganisedparticulatestructures. In particular.the Gag protein is required for their assembly. budding and release from host cell. VLPs,basedon HIV-I pSSgag, presentingthe entiregpI20 moleculefrom an UgandancladeA HIV-I isolate, havebeen shownto inducestrongsystemic and mucosal humoraland cellular immuneresponses in mice.442,443 More recently, IN administration in a mousemodelof theseVLPstogether with the EurocineL3 mucosal adjuvant (a monoglycerides/fatty acid lipid suspensionsr'" in a heterologous (DNA + VLPs)prime-booststrategyinduced higher titersof NAbs and strongeranti-EnvT-cellresponses as compared to vaccination with adjuvanted VLPs only.44s Further, a combined multiepitope VLP-based HIV vaccine (Combi HIVvac) carryingboth B- and T-cell epitopes (from HIV-I Env,Gag. Poland Nefproteins) resultedsafeand highlyimmunogenicin mice.446 Ofinterest,vaccination ofrhesusmacaques with pSSgagVLPsin the absence of adjuvantinduced broad.durable anti-GagCTLs.447However, therapeuticvaccination with HIV-I p l?Ip24:Tyvirus-like particles. which contain part of the HIV-I lIl B Gagsequenceand areproduced byexpressing a TYA 17/p24 fusion genein yeast448did not appear to slowerHIV-I disease progression.t?or to impact CD4+ T-celldecline in patients with advancedHIV infection.4so

Prime Boost Strategies Manyofthe vaccinestudiescombinevariousapproaches in a prime-boostfashion to optimize the immune responses elicited. A heterologousprime boost strategyis the administration ofone type of vaccine(the primer is usually DNA) followed by the administration of another form of the vaccine(the booster is usually recombinant proteins or attenuated viralvectors).The goal of this approach is to complement the priming by a differentstimulation of the immune systemto enhance the body's overallimmune response to HIV, a result that may not be achieved with a singletype ofvaccine. For example. whileDNA or microparticles areoptimal for inducingT-cell responses. they arepoor inducersof Ab, which.however, are readily induced upon boostingwith protein or a recombinant vector. Another advantage of this strategy is that it circumvents the

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relatively common and detrimental immunodominanceof the vector that mayresultin a reduced immunogenicityof the transgeneand the impossibility to use the samevector twice because immunity to the vectorstronglyreduces or preventsthe transgeneexpression. Toovercome thislatter problem sequential immunizationswith different viral vectors have been used as an alternative prime-boost approach,as reported in nonhuman primate modelsagainst SHIV451 and SIV143.l44 challenges. DNA prime-viral vectorboost approaches mayalsobe exploitedto target mucosalsite either because of the intrinsic tropism of the vector or because they can be applied mucosally. A varietyof protocols usingalternative viralvectorsfor both priming and boosting havealsobeen reported, both alone and in combinationwith DNA and havebeen successful at limitingdisease progression, but not at offeringprotection againstinfection. Forexample, DNA primingfollowed bya recombinantMYAexpressing multipleHIV proteinsdid not preventbut effectively controlled infection upon challenge with pathogenic SHIV89.6P in rhesus macaques.361.452 Based on the promising resultsin monkeys, GEOVAXis currentlytesting in 4 different PhaseI trials a DNA prime-MYA boost approachin which primingwith DNA encodingTat, Rev, Vpuand Gagis followedbyboostingwith MYAexpressingEnv, Gag,Protease and RT.Preliminary dataindicategood safetyand CTL responses in over 50%of the vaccineesv! and a PhaseII trial isplanned for 2008. Similarly, McMichaeland coworkers at the Oxford Universityhaveshown in PhaseI studiesthat DNA prime-MVA boost HIV vaccines are well-tolerated and immunogenic, but the percentage of volunteersrespondingto the vector and the durability of CD8· cell-mediated responses have not matchedsofar the responses observedwith the rAd5vector.132.366.4S4 However, the lackofsolid correlates of protection and the largebody of evidence showingthat natural control of infection is not necessarily associated with strong immune responses should not impede advancement of these type of vaccines to Phase II trials.

International Networking to Ease and Accelerate HIV/AIDS Vaccine Development The firstPhaseI trial of an HIV vaccine wasconducted in the USA in 1987. Sincethen, more than SO candidatevaccines havebeen tested in about 100 PhaselIII clinicaltrials,involving more than 35,000 healthyhuman volunteers. Two PhaseIII trialshavebeen completedand a third one is in progress. The vast majority of these vaccine candidates,including those tested in PhaseIII trials, werebased on structural HIV-1 proteins and primarilyaimed at inducing NAbs. Most of the effortsto developand evaluate HIV vaccines is borne by the NIH, CDC and WRAIR in the USA and by ANRS in France, with strong help from the International AIDS Vaccine Initiative (lAVI) in New York (http:/ / www.iavi.org). the European Union (EU). initiatives in WHO (http://www.who.int/en)andUNAIDS (http://www.unaids.it) and the recent commitment of the Bill and Melinda Gates Foundation for a Global Enterprise (http://www.gatesfoundation. org/GlobalHealth/Pri_Diseases/HIVAIDS). The HIVVaccineTrialNetwork (HVTN) established byNIAID in 2000,with 25 clinical sites in four continents, represents a major resource for clinicalHIV vaccine research (http://www3. niaid.nih.gov/about/organization/daids),The EU has alsoestablisheda comprehensive program aimed at strengtheningintegration of science amongcountriesof the EU and promoting, among the others, vaccine development against poverty diseases (i.e., HIV/AIDS, TB, Malaria). The AIDS Vaccine IntegratedProject(AVIP) (http:/ /www.avip-eu.org),Mucosal Vaccines for Poverty Related Diseases (MUVAPRED) (http:/ / www.mucosalimmunity.org/ muvapred/index.asp) and the European Vaccine effort against HIV/ AIDS (EUROVAC) (http:/ /www.eurovac.net). are among the most important projects recentlycofunded by the EU. In addition, the European and DevelopingCountries Clinical Trials Partnership (EDCTP) has been created with the aim of helping developing countries to build up their capacity in testing the efficacy of new drugs, microbicides and vaccines.

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Conclusion Several advancements have been made over the past few years to improvevaccine strategies aimed at inducing protection against HIV. Ideally, the aim of an effective vaccine would be to produce sterilizingimmunity in allrecipients. However, alsoa vaccine ableto control rather than prevent the infection might haveimportant benefits, reducing HIV levels in the body,delaying progression to AIDS and initiation of anti-retroviral therapy and reducing the chance of HIV transmission. The current knowledge suggests that an effective HIV candidateshould induce both humoral and cellularimmune responses, to ensuredurableimmunological memoryand to boost both the adaptative and innate immune system. The latter one is particularlyimportant at mucosalsites ofHI V transmission.v' One of the majorimpedimentsto the developmentofan HIV-I vaccine is the lack of knowledgeof the immune correlates ofprotection. Although studiesof MEV and LTNPs continue to providevaluable informationon mechanisms of naturalprotection, whichcan then be appliedto vaccine design, it shouldbe kept in mind that immuneresponses in LTNPs may representa correlateof preservationof immunecompetencein a host containinginfection rather than the actualfactorscontrollingthe virus.Natural resistance to infectionhasbeen attributed to a combinationofgenetic,innate and acquiredimmunesystem-mediated mechanisms."Therefore, a novelapproach for treatment and/or preventionof HIV infection might be representedby the manipulation of these restriction factorsin order to improveand broaden their activities.456The earlycontainment of HI V-I and SIV replicationin acutelyinfected individuals and monkeys is temporally associated with the emergence of a virus-specific CTL response and high levels of circulatingCTLs areassociated with good clinicalstatus in chronicallyinfected individuals457.458 and acutelyinfected monkeys,"? Importantly, experimentalin vivodepletion ofCD8- T-cellsin monkeys, abrogatedcontrolofSIV replication duringprimaryinfectionand the animalsdied after a rapidlyprogressive disease course.460462 While this has generally been interpreted as the definitive proofof the keyroleof CD8- T-cellsin the containment ofinfection, it should be reminded that alsoNK cellsexpress the CD8 moleculeand their experimentaldepletion maycontribute to the lossof virus control. Interestingly, lossof control of infection has been reported also upon B-celldepletion during primarySIVmac infectionof rhesusmonkeys,460·463.464 suggestingthat eitherAbsareindeed crucial for containing the virusevenat the verybeginningof the infectionor, more in general, that severe disturbance of a component of the immune system disrupts the proper function of system as a whole, underscoringthe integrated nature of the defensesystem360•463.465-469 and the contribution ofmultiple arms to an effective control of infection (for a reviewseeref 470). Because of safetyconcerns, traditional immunization approaches, including those based on liveattenuated and inactivatedviruses, havebeen almostabandoned.Vaccine candidatesbasedon purifiedor syntheticproteinsaremainlydeveloped to induceNAbs,whereas recentadvances in molecularbiologyand geneticengineeringhaveled to the development ofa newgeneration ofvaccines, whichincludes DNA- and microorganism-vectoredvaccines,whichareprimarily aimedat inducing T-cellresponses. In this regard,vaccinia viruses, canarypox constructs,replication-competent and replication-defective adenovirus vectorsare the main livevectors currentlybeing evaluated. The success of these vectors is believed to depend also on their capabilityto trigger innate immune responses, which would induce proper adaptive immunity. Although replication-competent adenoviruses have the advantage of persistentlyinfecting the host and stimulating the immune system,383 safetyissues need to be fullyaddressed beforetheir advancement to clinicaltrials. The recent failure of the Merck trial clearly indicates that even replication-defective adenoviralvectors maybe harmful in the presence of pre-existing immunity to the vector.Thus,DNA vaccines with increasedimmunogenicityand microbialvectors that circumvent pre-existing immunity to the vector are needed. In this regard,optimization and further explorationof new adjuvants for DNA and protein antigensare currentlybeingheavily pursued.f" Vl.Ps havealsobeen employed asmulti-epitopevaccine sincetheyofferthe advantages of [i) mimickingthe virionwithout having the safetyconcernsof live-attenuatedviruses, (ii) inducing both mucosaland systemic immune

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responses , (iii) activating both endogenous and exogenous antigen presentation pathways (MHC class I and II, respectively) and (iv) maintaining the antigens in their native conformation. Effective vaccination may ultimately require two or more vaccines used in conjunction (heterologous prime-boost strategies), an approach to vaccine development that differs from traditional vaccine design and is presently the preferred strategy for many vaccine candidates against HIV/ AIDS (Table 6). In this regard, there is a general agreement that when exploited combined, the vaccine components used for the prime and the boost are expected to stimulate a broader and more diversified immune response than using any ofthem repeatedly. In addition, the single use ofa viral or bacterial vector will avoid the interference, on a second administration, ofpre-existing immunity to the vector. Effective anti-HIV/AIDS vaccines may require targeting of several HIV-l antigens. Among these multi-component vaccines novel minimalistic vaccination strategies, combining structural ＨｾｖＲＭｅｮｶＩ and nonstruetural (Tat or Nef) proteins have been rationally designed to induce NAbs and T-cell responses against keyearly and late HIV antigens. In particular, preclinical testing ofthe Tat/ ｾ V2-Env combination in macaques has shown efficacy (ref. 26S and Ensoli B, in preparation) and clinical trials with this vaccine candidate will start in 200S . However, HIV vaccine development still faces significant challenges. The availability ofan effective HIV vaccine requires scientific and public-health efforts and the establishment ofConsortia such as the "European Consortia for HIV vaccine development" (includingAVIP, MUVAPRED, VIAV) , the "N eutralizing Antibody Consortium"; the "HIV Global Enterprise", an international Consortium ofnongovernamental and governamental organizarions.f? Clinical trials must also be performed with appropriate ethical rules, especially in developing countries, avoiding duplication of efforts, using standardized genetic inserts as immunogens and implementing immunological assaysfor preclinical and clinical testing to compare candidate vaccines. This is important because the laboratory assaysused to assess immune responses may not be comparable, severelyhampering decisions about which candidates to pursue for further testing. In addition, new knowledge about the immune response to HIV is raising concerns that current assays overlook important aspects of those imm une respon ses. Open questions remain to be answered, such as how to induce high titers of NAbs; whether any of the vaccines being currently developed will elicit cellular immune responses that will correlate with protection from infection or disease progression; the type (poly- or mono-functional) of CD4' and CDS' T-cell responses elicited by the vaccines currently being developed; the magnitude, breath and durability of the vaccine-induced CD4' and CDS' T-cell responses; the best combination ofvaceines that in the prime-boost immunization strategies will stimulate an immune response similar to that thought to confer protection from disease progression. The challenges the scientific community still faces are formidable. However, looking back , enormous progresses have been made in each aspect of vaccine development, from basic science to clinical testing, that let us be optimistic about the eventual generation of effective preventive and therapeutic vaccines against HIV/ AIDS. While vaccines able to slow disease progression and decrease transmission rate should be at reach in the medium term , recent advancements in the generation ofEnv-based immunogens, their association to key regulatory or accessory HIV-l proteins and present reconsideration of the several Ab effector functions, make us hoping that even a sterilizing vaccine may be not too far distant.

Acknowledgements The research activities described in this publication were funded by the EC Commission under the VI Framework Programme of Research and Technological Development (2002-2006), Project no . LSHP-CT-2004-S034S7 , AIDS Vaccine Integrated Project ("AVIP") and Project no . LSHP-CT-2003-S03240, Mucosal Vaccines for Poverty Related Diseases ("MUVAPRED"). The authors wish to thank Mrs. P. Sergiampietri for the editorial assistance and Mr. Leonardo Sernicola for preparing the tables. Please note that Aurelio Cafaro and Iole Macchia have equall y contributed to this chapter.

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411. Albert ML, Sauter B. Bhardwaj N. Dendritic cells acquire antigen from apoptoric cells and induce class l-restri cted CTLs. Nature 1998: 392:86-89. 412. MacDonald GH, Johnston RE. Role of dendritic cell targeting in Venezuelan equine encephalitis virus pathogenesis. J Virol 2000: 74:914-922. 413. Davis NL. West A, Reap E et al. Alphavirus replicon part icles as candidate HIV vaccines. IUBMB Life 2002 ; 53:209-211. 414. McKenna PM. McGettigan JP. Pomerantz RJ et al. Recombinant rhabdoviruses as potential vaccines for HIV-l and other diseases. Curr HIV Res 2003; 1:229-237. 415. Publicover J. Ramsburg E, Rose JK. A single-cycle vaccine vector based on vesicular stomatitis virus can induce immune responses comparable to those generated by a replication-competent vector. J Virol 2005; 79:13231-13238. 416. Egan MA, Chong SY. Rose NF et al. Immunogenicity of attenuated vesicular stomatitis virus vectors expressing HIV type 1 Env and SIV Gag proteins : comparison of int ranasal and intramuscular vaccination routes. AIDS Res Hum Retroviruses 2004: 20:989-1004. 417. Rose NF, Marx PA, Luckay A er al. An effective AIDS vaccine based on live attenuated vesicular stomatitis virus recombinants. Cell 2001: 106:539-549. 418. Clarke DK. Cooper D, Egan MA et al. Recombinant vesicular stomatitis virus as an HIV-l vaccine vector. Springer Semin Immunopathol 2006; 28:239-253. 419. Cooper D. Wright K], Calderon PC et al. Attenuation of recombinant vesicular stomatitis virus-human immunodeficiency virus type 1 vaccine vectors by gene translocations and g gene truncation reduces neurovirulence and enhances immunogenicity in mice. J Viro12008; 82:207-219. 420. Crotty S, Andino R. Poliovirus vaccine strains as mucosal vaccine vectors and their potential use to develop an AIDS vaccine. Adv Drug Dc:liv Rev 2004: 56:835-852. 421. Crotty S, Miller CJ, Lohman BL er al. Protection against simian immunodeficiency virus vaginal challenge by using Sabin poliovirus vectors. J Virol 2001; 75 :7435-7452. 422. Mueller S. Wimmer E. Expression of foreign proteins by poliovirus polyprotein fusion: analysis of genetic stability reveals rapid deletions and formation of cardioviruslike open reading frames. J Virol 1998; 72:20-31. 423. Murphy CG , Lucas WT, Means RE et al. Vaccine protection against simian immunodeficiency virus by recombinant strains of herpes simplex virus. J Virol 2000: 74:7745-7754. 424. Kaur A, Sanford HB, Garry D et al. Ability of herpes simplex virus vectors to boost immune responses to DNA vectors and to protect against challenge by simian immunodeficiency virus. Virology 2007: 357:199-214. 425. O'Hagan DT, Singh M. Micropart icles as vaccine adjuvants and delivery systems. Expert Rev Vaccines 2003 : 2:269-283. 426. O'Hagan DT, Singh M, Ulmer JB. Microparticles for the delivery of DNA vaccines. Immunol Rev 2004 ; 199:191-200. 427. Johansen P, Men Y. Merkle HP er al. Revisiting PLA/PLGA microspheres: an analysis of their potential in parenteral vaccination. Eur J Pharm Biopharm 2000; 50:129-146. 428. Bowersock TL . HogenEsch H. Suckow M et al. Oral vaccination of animals with ant igens encapsulated in alginate microspheres, Vaccine 1999: 17:1804-1811. 429 . O'Hagan DT, Singh M, Ulmer JB. Microparticle-based technologies for vaccines. Methods 2006: 40:10-19. 430. Johansen P. Martinez Gomez JM , Gander B. Development of synthetic biodegradable microparticulate vaccines: a roller coaster story. Expert Rev Vaccines 2007: 6:471-474. 431. Otten GR, Schaefer M, Doe B et al. Enhanced potency of plasmid DNA microparcicle human immunodeficiency virus vaccines in rhesus macaques by using a priming -boosting regimen with recombinant proteins. J Virol 2005 ; 79:8189-8200. 432. Caputo A, Brocca-Cofano E, Casraldello A et al. Novc:l blocompatible anionic polymeric microspheres for the delivery of the HIV-l Tat protein for vaccine application. Vaccine 2004; 22:2910-2924. 433. Castaldello A, Brocca-Cofano E, Voltan R et al. DNA prime and protein boost immunization with innovative polymeric cationic core-shell nanoparticles elicits broad immune responses and strongl y enhance cc:llularresponses of HIV-l tat DNA vaccination. Vaccine 2006: 24:5655-5669. 434. Voltan R, Ca staldello A, Brocca-Cofano E er al. Preparation and characterization of innovative protein-coated poly(methylmethacrylate) core-shell nanoparticles for vaccine purposes. Pharm Res 2007; 24: 1870-1882. 435. Buonaguro L. Buonaguro FM. Tornesello ML et al. High efficient produc tion of Pr55(gag) virus-like: particles expressingmultiple HIV-l epitopes, including a gp120 protein derived from an Ugandan HIV-I isolate of subtype A. Antiviral Res 200 1: 49:35-47. 436. Gheysen D. Jacobs E. de Foresta F et al. Assembly and release of HIV-I precursor Pr55gag virus-like: particles from recombinant baculovirus-infected insect cells. Cell 1989: 59:103-112.

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437 . Young KR. McBurney SP. Karkhanis LV er al. Virus-like particles : designing an effective AIDS vaccine. Methods 2006; 4O:98-117. 438. McBurney SP. Young KR, Nwaigwe CI et al. Lenrivirus-like particles without reverse transcriptase elicit efficient immune responses. Curr HIV Res 2006; 4:475-484. 439. Wagner R, Deml L, Notka F et al. Safety and immunogenicity of recombinant human immunodeficiency virus-like particles in rodents and rhesus macaques. Intervirology 1996; 39:93-103. 440. Sailaja G, Skountzou I. Quan FS et al. Human immunodeficiency virus-like particles activate multiple types of immune cells. Virology 2007 ; 362:331-341. 441. Doan LX , Li M , Chen C et al. Virus -like particles as HIV-I vaccines. Rev Med Virol 2005 ; 15:75-88. 442. Buonaguro L. Racioppi L. Torncsello ML et al. Induction of neutralizing ant ibodies and cytotoxic T-lymphocytes in Balblc mice immunized with virus-like particles presenting a gp120 molecule from a HIV-l isolate of clade A. Antiviral Res 2002; 54:189-201. 443. Buonaguro L, Visciano ML , Tornesello ML et al. Induction of systemic and mucosal cross-clade neutralizing antibodies in BALB/c mice immunized with human immunodeficiency virus type 1 clade A virus-like particles administered by different routes of inoculation. J Virol 2005 ; 79:7059-7067. 444 . Schroder V, Svenson SB. Nasal and parenteral immunizations with diphtheria toxoid using monoglyceride/facty acid lipid suspensions as adjuvants. Vaccine 1999; 17:2096-2103 . 445. Buonaguro L. Devito C, 'Iornesello ML et al. DNA-VLP prime-boost intra-nasal immunization induces cellular and humoral anti -Hl'V-I systemic and mucosal immunity with cross-clade neutralizing activity. Vaccine 2007; 25:5968-5977. 446 . Karpenko LI, Ilyichev AA, Eroshkin AM er al. Combined virus-like particle-based polyepitope DNAI protein HIV-l vaccine design, immunogenicity and toxicity studie s. Vaccine 2007 ; 25:4312-4323. 447. Paliard X. Liu Y, Wagner R et al. Priming of strong, broad and long-lived HIV type 1 p55gag-specific CD8+ cytotoxic T-cells afier admin istration of a virus-like particle vaccine in rhesus macaques. AIDS Res Hum Retroviruses 2000 ; 16:273-282. 448 . Adams SE, Dawson KM. Gull K er al. The expression of hybrid HIV:Ty virus-like particles in yeast. Nature 1987; 329:68-70. 449. Lindenberg CE, Stolte I, Langendam MW et al. Long-term follow-up: no effect of therapeutic vacvirus-like particles on HIV-l disease progression . Vaccine 2002 ; cination with HIV-I p17/p24 20:2343 -2347. 450 . Smith D, Hales G, Roth N et al. A random ized trial of nelfinavir, ritonavir, or delavirdine in combina tion with saquinavir-SGC and stavudine in treatment -experienced HIV-I -infected pat ients. HIV Clin Trials 2001; 2:97-107. 451. Nabd GJ. HIV vaccine strategies. Vaccine 2002; 20:1945 -1947. 452 . Amara RR, Villinger F. Altman JD et al. Control of a mucosal challenge and prevention of AIDS by a mult iprotein vaccine. Vaccine 2002; 20:1949 -1955. 453 . Goepfert P, Hay C, Frey S er al. HIY-I DNA prime followed by recombinant MVA boost is well tolerated and immunogenic when admini stered to healthy HIV-I seronegative adults in HVTN 065. (Poster OA02-04, oral presentation. AIDS VAccine Conference, Seattle. Washington-USA; 2007), 2007. 454 . Mwau M, Cebere I, Sutton J et al. A human immunodeficien cy virus I (HIV-l ) clade A vaccine in clinical trials: stimulation of Hlv-specific Tvcell responses by DNA and recombinant modified vaccinia virus Ankara (MVA) vaccines in human s. J Gen Virol 2004 ; 85:911-919 . 455. LevyJA . The importance of the innate immune system in controlling HIV infection and disease. Trends Immunol 2001; 22 :312-316. 456 . Goff SP. Retrovirus restriction factors. Mol Cdl 2004; 16:849-859. 457. Koup RA. Safrit JT, Cao Y cr al. Temporal association of cellular immune responses with the initial control of viremia in primary human immunodeficiency viru s type 1 syndrome. J Viral 1994 ; 68:4650-4655. 458 . Musey L, Hughes J. Schacker T et al. Cyrotoxic-Tvcell responses. viral load and disease progression in early human immunodeficien cy virus type 1 infection. N Engl J Med 1997; 337:126 7-1274. 459 . Yasutomi Y, Reimann KA, Lord CI er al. Simian immunodeficiency virus-specific CD8+ lymphoc yte response in acutely infected rhesus monkeys. J Viro11993; 67:1707-1711. 460. Jin X, Bauer DE, Tunleron SE et al. Dramat ic rise in plasma viremia alier CD8{ - ) 'f-cell depletion in simian immunodeficienc y virus-infected macaques. J Exp Med 1999; 189:991-998. 461. Schmitz JE. Kuroda MJ. Santra S et al. Control of viremia in simian immunodeficiency virus infection by CD8+ lymphocytes. Science 1999; 283:857-860. 462. Schmitz JE. Johnson RP. McClure HM et aL Effect of CD8+ lymphocyte depletion on virus containment alier simian immunodeficiency virus SIVmac251 challenge of live attenuated SIVmac239ddta3-vaccinated rhesus macaques. J Virol 2005; 79:8131-8141.

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463. Miller C], Genesca M. Abel K et al. Antiviral antibodies are necessary for control of simian immunode6ciency virus replication. J Virol 2007; 81:5024-5035. 464. Schmitz]E. Kuroda MJ. Sanna S er al. Effect of humoral immune responses on controlling viremia during primary infection of rhesus monkeys with simian immunodeficiency virus. J Virol2oo3; n:2165-2173. 465. Dittmer U. Brooks DM. Hasenkrug KJ. Requirement for multiple lymphocyte subsets in protection by a live attenuated vaccine against retroviral infection. Nat Med 1999; 5:189-193. 466. Mao H. Lafont BA. Igarashi T er al. CD8+ and CD20+ lymphocytes cooperate to control acute simian immunodeficiency virus/human immunodeficiency virus chimeric virus infections in rhesus monkeys: modulation by major histocompatibility complex genotype. J Virol2oo5; 79 :14887-14898. 467. Qin Z. Richter G. Schuler T er aL B-cells inhibit induction of T-cell-dependenr tumor immunity. Nat Med 1998; 4:627-630. 468. Recher M. Lang KS. Hunziker L er al. Deliberate removal of T-cell help improves virus-neutralizing antibody production. Nat lmmunol 2004; 5:934-942. 469. Stager S. Alexander J. Kirby AC er al. Natural antibodies and complement are endogenous adjuvants for vaccine-induced CD8+ T-cell responses. Nat Med 2003; 9:1287-1292. 470. Zinkernagel RM. Immunity. immunopathology and vaccines against HN? Vaccine 2002; 20:1913 -1917. 471. Guy B. The perfect mix: recent progress in adjuvant research. Nat Rev Microbiol2oo7; 5:505-517. 472. Klausner RD. Fauci AS. Corey L et al. Medicine. The need for a global HIV vaccine enterprise. Science 2003; 300:2036-2039. 473. loannidis JP. Rosenberg PS. Goeden JJ et al. Effects of CCRS-Delta32. CCR2-641 and SDF-l 3i\ alleles on HIV-l disease progression: An international meta-analysis of individual-patient data. Ann Intern Med 2001; 135:782-795. 474. Martin MP. Gao X. Lee JH er al. Epistatic interaction between KIR3DSI and HLA-B delays the progression to AIDS . Nat Genet 2002; 31:429-434. 475. Lopalco L. BarassiC. Pastori C et al. CCRS -reactiveantibodies in seronegativepartners ofHN-seropositive individuals down-modulate surface CCR5 in vivo and neutralize the infectivity of R5 strains of HIV-l in vitro. J lmmunol 2000; 164:3426-3433. 476. Pastori C. Weiser B. BarassiC ec al. Long-lastingCCR5 internalization by antibodies in a subset oflong-term nonprogressors: a possible protective effect against disease progression. Blood 2006; 107:4825-4833. 477. Belec L. Ghys PD. Hocini H et al. Cervicovaginal secretory antibodies to human immunode6ciency virus type 1 (HN- I) that block viral transcytosis through tight epithelial barriers in highly exposed HN-l -seronegative African women. J Infect Dis 2001; 184:1412-1422. 478. O'Connor GM. Holmes A. Mulcahy F er al. Natural Killer cells from long-term nonprogressor HN patients are characterized by altered phenotype and function . Clin Immunol2007; 124:2n-283. 479 . Broliden K. Hinkula J. Devito C et al. Functional HIV-l specific IgA antibodies in HN-l exposed, persistently IgG seronegative female sex workers. Immunol Lett 2001: 79:29-36. 480. Kannanganat S. Kapogiannis BG. Ibegbu C et al. Human immunodeficiency virus type 1 controllers but not noncontrollers maintain CD4 T-cells coexpressing three cytokines, J Virol 2007: 81:12071-12076 . 481. Rezza G. Titti F. Pezzotti P ec al. Anti-nef antibodies and other predictors of disease progression in HN-l seropositive injecting drug users.J Bioi Regul Homeost Agents 1992; 6:15-20. 482. Inwoley A. Recordon-Pinson p. Dupuis M et al. Cross-cladeconservation of HN type 1 Nef immunodominant regions recognized by CD8+ T-cells ofHN type 1 CRF02_AG-infected Ivorian (West Africa). AIDS Res Hum Retroviruses 2005; 21:620-628. 483 . Wilson CC. McKinney D. Anders M et al. Development of a DNA vaccine designed to induce cytotoxic Tdymphocyte responses to multiple conserved epiropes in HIV-1. J lmmunol2oo3; 171:5611-5623. 484. Brave A. Ljungberg K. Wahren B et al. Vaccine delivery methods using viral vectors. Mol Pharm 2007; 4:18-32.

CHAPTER

15

New Strategies to Overcome the Drawbacks ofCurrently Available Flu Vaccines Epifanio Fichera: Diana Felnerova, Robert Mischler, jean-Francois Viret and Reinhard Glueck Abstract accination represents the most efficient tool to control morbidity and mortality resulting from influenza infections in humans. The currently licensed influenza vaccines provide good protection levels in healthy adults . whereas lower protection is generally achieved in ageing individuals who are at a higher risk ofdeveloping severe clinical man ifestations. Future improvements in influenza vaccines should address the needs of high risk groups including the elderly. small children and chronic patients. Recently. due to the increased incidence of avian influenza pandemic outbreaks. the prevention of a potential human influenza pandemic turned into another crucial issue in the influenza vaccination field. The development and validation of manufacturing processes for efficient and safe pandemic vaccines became one of the top priorities of health. regulatory and funding agencies all over the world. In the pandemic cont ext. the development of novel vaccines administered via the mucosal route may playa significant role by reducing virus shedding from infected individuals. This chapter provides insights in the limitations of existing manufacturing processes. new approaches to overcome limitation in vaccine production. mechanisms ofaction ofcurrent vaccines and discuss potential strategies to improve the imm unogenicity and efficacy ofinfluenza vaccines.

V

Introduction Influenza viruses A . B and C are enveloped viruses with a segment ed . negative single-stranded RNA genome. They are members ofthe Orthomyxoviridaefamily together with the Thogotovirus and Isavirus. Within each influenzavirus genus no separate species has been recognized. but there are clusters ofstrains that can genetically reassort with each orher.P Studies on the ecology ofthe influenza viruses led the hypothesis that all mammalian influenza viruses derive from an avian influenza reservoir. Thus. after long periods ofevolution. human viruses originate from reassorted influenza viruses ofavian/mammalian origin. The level ofnonhuman virus adaptation to the human host has a considerable impact on the severity ofhuman influenza disease. Human influenza is mainly caused by Influenza virus A and . to a less extent by Influenza virus B.' Based on the antigenicity ofthe surface glycoproteins hemagglutinin (HA) and neuraminidase (N) the influenza virus A is further classified in different subtypes. Actually. 16 different HA and 9 different N have been identified. In the past . human influen za virus A infection has been caused by 3 different HA ·Corresponding Author: Epifanio Fichera -Etna Biotech Sr.l., Piazz a Stes icoro 59, 9513 1 Catania, Italy. Email: efichera @etnabiotech.it

Pharmaceutical Biotechnology. edited by Carlos A. Guzman and Giora Z. Feuerstein. ©2009 Landes Bioscience and Springer Science+Business Media.

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(H I, H2 and H3) and 2 different N (N 1 and N2) . However,new avianrestricted strains (HSN 1, H7N2, H7N3, H7N7, H9N2 and HI ON7)have recentlybeen reported to infect humans. v' Although associatedwith a significantmorbidity and mortality on groups at risk, such as the elderly, small children and patients sufferingof chronic diseases (e.g... chronic heart, lung and kidney diseases, diabetes or immunosuppressive conditions), annual epidemicsusuallyresulring from infections with circulating influenza A strains represent reduced threats, as compared to a pandemic situation. Indeed, pandemic avian/mammalian influenza viruseswhich were able to cross a speciesbarrier and infect humans as a result ofgenetic re-assortmentsare associatedwith severecomplications and high mortality rates," Human influenza epidemics are caused by circulating viru ses and usually begin in November-Decemberin the northern hemisphereand in May-June in the southern hemisphere, favoredbylowertemperatureandlowerrelative humidity? in spiteof theavailabilityofprophylacticvaccineswith provenepidemiological and clinicalbenefits. One reasonfor this isthe naturalhighgenetic instabilityofinfluenzaA viruses. Repeatedlyoccurringpoint mutations in antigenically important regionsofthe genesencodingboth the viralHA and N without affectingreplicationcapacity,leads to significantalterationsin the immunogenicityofthese surface glycoproteins (so-called antigenic drift). The new so originatingvirusstrain is able to escapepre-existing host immunity allowingthe new strain to spread.6 The frequencyofantigenicdrifts represents one of the most crucialhurdlesin the manufacturingofeffective inrerpandemicvaccines. To overcome this obstacle, accordingto the current WHO recommendations, all manufacturers worldwide produce yearly trivalent vaccines containingantigensfrom two differentsubtypesofinfluenzaA strains(currentlyH IN1and H3N2) and one strain ofinfluenzaType B. The specific strain selectionis basedon surveillance data from the worldwidenetwork of nationalinfluenzacentersand WHO collaboratingcenters.Because vaccineshaveto be manufacturedbefore the actualepidemicstrainsare known, a failure to anticipate emergenceof a strain relative to the vaccine will result in a substantialreduction or abrogation of vaccine-mediated protection Human pandemic influenza, againstwhich various vaccines are stillunder development, results ofthe combinationofseveral factorsin a stepwise manner;"Historicalinfluenzapandemicsemerged throughan adaptationprocess ofavian or mammalian influenza viruses to thehumanhost.Thecrucial stepsin such adapting processare the developmentofhybrid virus. termed reassortants, harboring geneticinformationfrom both human and animalviruses. Indeed.due to the factthat the segmented genome of influenza viruses consistsof eight individualRNA segments, human-avian virus RNA reassortants can be produced by cdIs co-infected with both viruses.t Thereby completely novel subtypesoflnfluenza A viruscan emergein a processcalledantigenicshift,which ismechanistically different from the much more frequent genetic drifi:s resultingofpoint mutations.Thus, genome segmentationis a characteristic featureof influenzaA viruses enablinga rapid and drasticevolution ofthe virusresultingin the escapeof immunosurveillance in newlyinfectedimmunologically naive humans.Currently,the establishment of efficient vaccines to preventpandemicinfluenzarepresents one ofthe most crucialglobalproblemsto be solvedby scientists and the vaccine industry.

Manufacturing ofInfluenza Vaccines The influenza virus was for the first time isolated in 1933 by Smith. Andrewes and Laidlaw," In the 1940s the virus could be propagated in embryonated hen'seggs.The first vaccinesagainst influenza were formaldehydeinactivated whole virus vaccines. They havebeen developed by the US armed services and made commercially available in 1945 in USA. However,these pioneering vaccineswere highly pyrogenic due to the suboptimal virus purification process and exhibited low efficacy. An improvement in the purification processwasachievedmer introduction ofzonal ultracentrifugation in the 1960s.9 Nowadays the purification ofvirus from infected chicken embryos usingzonal ultracentrifugation is still the manufacturing processofchoice for all marketed influenza. Currently, severalmanufacturersprovide worldwideinterpandemic influenzavaccines mainly in the form ofinactivated split or surfaceantigen (subunit) vaccines (seeTable 1).10 Split vaccinesare prepared from sucrosedensity gradient purified whole virusesby fragmenting viral

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particlesinto smallerpiecesusingdetergents. Subunit vaccines contain further purifiedantigenic proteins.Theconventionalproductscompriseboth majorsurface glycoproteins HA and N and are generally appliedintramuscularly."FluMist,a coldadaptedinfluenzavirusvaccineisadministered intranasally; it is commercially available in the USAsince2003 for activeimmunizationof people between2 and 49 years of age.11 Thisvaccine is a liveattenuated wholevirusvaccine characterized by a satisfying protective efficacy in adult. However the vaccine faces some issues related to the biosafetyprofileof liveattenuated influenzaviruses. The manufacturing of current seasonal influenzavaccines is associated with several hurdles that maylimit vaccine production capacity. Natural isolates of new epidemicinfluenzastrains to be included in the recommendedvaccine composition haveto be genetically modified to create high-yielding strainssuitablefor antigen production. This is achievedusingclassical methods of virusreassortment usingembryonatedchickeneggs asa growsubstrate.Reassortants aregenerated by co-infection of eggs with the current epidemicstrain and a high yielddonor strain. Next, the selectedstrain is used as a seedvirus stock to grow and manufacturethe desiredvirus type. Seed virus strain bearingthe recommendedHA and N are provided to vaccine manufacturers by one of the Control Agencies, such as the Center for Biologics Evaluation and Research (CBER) in the US, or the National Institute for Biological Standards and Control (NIBSC) in the UK. In order to maximize virusyieldfromeggs, reassortants of influenza A strainsareoftenutilized.These possess the surfaceproteins from the desiredwild-typeHINI and H3N2 strains, whilethe other viral proteins are from a high-yielding strain, such as A/Puerto Rico/8/34. For logistic reasons new virusproduction substratesthat would avoidthe dependenceon henns eggswould be a key improvementof the manufacturingprocessfor influenzavaccines," Indeed,the limited availability of eggsas a growingsubstratemaysometimes be critical, especially in an avianflu pandemicsituation. Further disadvantages linked to eggproduction concern the riskof the presence of residual

Table 1. Currently marketedinterpandemic influenza vaccines Subunit Vaccines

Split Vaccines

Whole Virus

Virosomes

Aggripal Chiron/Novartis, I

Afluria CSL

FluMist (live attenuated, intranasal) Medimmune,

Inflex al V Berna Biotech/CruceJl, CH

Fluad (MF-59 adjuvanted)

Begrivac Chiron/Novertis

Chiron/Novsrtis, I Fluvir in Evans/Ch iron/ No vsrtis, UK

Influvac Solvay, NL

Fluarix GSK, UK FluLaval 10 Biomedicals, Fluvax CSL,

Fluviral S/F

JD Biomedicals, Fluzone Sanofi Pasteur, F

TIV Medimmune, Vaxigrip Sanofi Pasteur, F

Invivac Solvay, NL

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allergenicegg's proteins in the finalproduct: the presenceof microbialcontaminants that might interrupt the antigen supplyconsideringthe removal ofthimerosalfrom the production process and finally the eggwastedisposal Currently, 90%of the worldwide influenza vaccine production capacityis concentratedin the USAand Europe,which in turn represents only 10%ofthe world's population.Thecurrentglobalmanufacturingcapacity(-300 milliondoses peryearof the seasonal trivalent vaccine, containing 15 ug/dose of each antigen) would be inadequate to meet global needs during a pandemic, especially as it is expected that higher antigen dosageand a two dose regimewould be required for protection against a pandemic strain.' Novel approaches, including application routes other than intramuscular, the useof noveladjuvants, alternativecell-based substrates for antigen production, new vaccine formulation (naked DNA immunization, viral vector basedvaccines) could pavethe wayto greatervaccineaccessibility with associated public health benefits. Strongeffortsto replace embryonatedhen'seggsasthe growingsubstratein the manufacturing processhave been exploredafter the introduction of reverse geneticsinto the influenzavaccine field.. The reverse geneticstechnologyisan egg independentmethod allowingto generateinfluenza vaccinestrainswith selectedgenecombinations, while avoidingthe time-consuming selectionof appropriate reassortants," Several manufacturers areactively workingtowardsthe establishment of influenzaantigen production in mammaliancellculturesor evenin plants. Firstexperiences with the cellculture system werepromising,howeverthe firstcellline (293T) used to express antigens could not be licenseddue to regulatoryrestrictions.Theimprovementwasachievedbythe implementation ofMDCK,12Vero13or PER.C6·14 cells into manufacturingprocess. Accordingto public available information,Vero (Chiron, D ; BaxterAu), MDCK (Solvay, NL) and PER.C6· (Sanofi Pasteur)cellculturebasedinfluenzavaccines arecurrently underclinical evaluation"(Sanofi Pasteur pressreleases 26 Sept2006). In 2007 EMEAhasissuedthe marketingauthorizationvalidthrought the European Union for the OptaAu (NovartisVaccine and Diagnostics GmbH & Co. KG), an influenzavaccinebasedon purified Ha and N, derivedfrom viruses propagatedin MDCK cells. Moreover, the need for faster and more flexible production systems leadsto the tentativedesign ofnovelrecombinantvaccines. NakedplasmidDNA or immunizationwith recombinantvectors encoding HA wereprovento be efficient in animalmodels," but wereless successful in humans,'? PurifiedHA and N vaccine antigensproduced with the baculovirus expression system havebeen shown to be effective in a mouse model," Recent studies haveshown that adenovirus-vectored influenzavaccines areableto elicitrobusthumanimmuneresponses ifdelivered inrranasally,'? Using an adenoviralvector system, a new HA strain can be constructedwithin one month. A featurein the development ofvectoredvaccines seems to be the establishment of molecular strategies enabling forviraltropismmodulation. However, due to selection pressure, suchkindof modifications might leadto expandedtropismor abolishmentof the adenoviral nativetropism,which can in turn lead to unintended spreadto new and undesiredcelltypes,aswellas to horizontal transmission of the vector. However, all these approaches are still far from commercialization.

Strategies to Improve the Immunogenicity and Efficacy ofCurrent Influenza Vaccines The immunogenicityof influenzavaccines is currentlymeasuredby their capacityto induce functional neutralizing HA-specific antibodies in serum," which have been proved to provide acceptable protection against disease. However, the levelof vaccine's protective capacitydiffers depending on age and health status of population groups. In case of a good antigenic match between vaccineand circulatinginfluenzastrains healthyadults, who usually undergo only mild symptoms of disease and recoverwithin time period up to two weeks, show70-90%protection againstproven influenzaillness upon conventional immunization. As stressed above, individuals at the highest risksof severe seasonal influenzainfectionsare elderly, aswellas adults or children sufferingof chronichealth conditions,suchascancer, immunosuppression or immunodeficiency, cardiac and pulmonary disorders,diabetes and other metabolic diseases, or renal disease, who require regular medical follow-up or hospital care. Only 50-70%individuals belongingto these

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populationgroupsareprotectedbyconventionalvaccines.21 Lowerefficacy ofvaccination in elderly might be relatedto decreased function of cellularcomponentsofimmune system." Also, the immune system of smallchildren differs from the one of adults who haveusually been facinga long history of contactswith flu viruses. Therefore, current influenzavaccines generate more efficient immune responses in healthyadults than in infants. Moreover, due to the fact that vaccination is recommendedin children,elderlyand immunocompromisedindividuals, the safetyprofileof the vaccine should be very carefully considered. Liveattenuated influenzavaccine FluMist exhibits high efficacy in protection againstinfluenzain healthyadults. However, due to the riskof residual replicationofvirusin the respiratorytract, it is not recommendedto be usedin high riskpopulation groups." Takenall these aspectstogether,the challenges for future interpandemicinfluenza vaccine manufacturersis clearly concernedwith the improvementof immunizationstrategies for individuals belongingto high riskpopulation groups. The most evident immunogenic effect of conventional influenza vaccines is the generation of systemic antibodies specific to the surfaceglycoproteins of influenzavirus. New vaccination strategies are focusedon the induction of more balancedand broadened immune responses. The improvementof the immunogenicityof vaccines can be achievedby: (i) immunopotentiatingthe immune responses via the addition of an adjuvant; (ii) the induction of a mucosalimmunity in addition to the systemic immunity; and (iii)broadeningthe immuneresponses byincludingmore conservedantigenicepitopes, mainlyderivedfrom internal proteins ofinfluenza viruses."

Immunopotentiating ofImmune Responses byAdjuvants Currently marketed inactivated split- or subunit-vaccines provide superior safety over traditional whole-virus vaccines. However, the immunogenicity of these vaccines leaves space for improvement. Immunogenic properties of subunit vaccines can be improvedby the addition of immunostimulating molecules that targetsignalingpathways of defense immunity. An appropriate antigen-adjuvant combination could overcome this obstacle. In caseof a pandemic flu vaccine, the requirement for a higher antigen dosageseems to be an important issue. It seems that a conventionalvaccineformulated with an adjuvantcan allowfor antigensparing. Currently,threeadjuvants areapprovedfor humanuse:Aluminiumprecipitate,25.26 liposome (virosome}" and MFS9 water/oil suspension.P'" Virosomalformulationsof influenza surfaceantigens have been shown to possess significant adjuvanteffectdue to the repetitivearrangement of presented surface antigensas wellas the maintenanceof viral HA in its nativeand biologically active conformation." In search for optimal adjuvant candidates highly attractive targetsbecomeTLR-ligands that activate appropriateSignaling pathways in a highly natural and specific way,31'33Some adjuvant candidatescurrently tested to improveefficacy of influenza vaccinesare listed in Table 2. The general safety requirements for any vaccine are extremely high, driven by the fact that vaccines are generally administrated to healthyindividuals. Particularrisk/benefit ratio consider-

Table 2. Adjuvant vaccine candidates under evaluation for influenza vaccines Proteosornes"

OMP of Neisseria meningitis (TLR-2/1 ligand)

LTK63/Biovector" CTA-l D[)36,37

Escherichia

LT mutants

CT derivative (Al subunit of CT + Ig-binding element of

Human Human Mouse model

aureus ISCOMATRIX38•40

Quil-A-based TLR "2/6 agonist

In vitro human mode l mouse model

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ationsare required ifimmunocompromisedindividuals areconcerned.Regardingthe selectionof adjuvantmolecules the following characteristics shouldbe considered: (i) preferentially, adjuvant molecules should be produced synthetically rather then biologically, (ii) the sizeand structure of moleculesshould be precisely defined, (iii) adjuvantsignalingand functional pathways must be deciphered; and (iv) a specific wayofaction will be preferred.

Improvement ofImmune Responses Using Alternative Application Routes Theintramuscularapplication route isroutinelyusedforvaccines administration. However, the implementation ofalternativeroutes, e.g., intranasally, could resultin the triggeringofadditional immune pathways to those activatedby intramuscularimmunization. Thepathogenscausingrespiratorydiseases invadetheir host viathe nasal/trachealmucosa. On the other hand, parenteralimmunizationisnot appropriateto inducea localimmuneresponse in the respiratorytract.42 Therefore, the earlyviralcolonizationof upper respiratory areaduringinfection and the postinfectionprocess ofvirussheddingcannot bepreventedbyparenteralvaccines.7.43 Conversely,pre-existingmucosalimmunityisableto reduceor preventboth colonization andvirus shedding.Thus, the intranasalroute appearsmost attractiveto prevent influenzainfection. For several years, live-attenuatedinfluenzavaccines for nasalapplicationhavebeen used successfully in the Russian Federation.ThecurrentliveRussian vaccine isbasedcold-adaptedvariants of an H2N2 strain which is reassortedwith epidemic HINI and H3N2 strains and combined with a cold-adaptedreassortantofinfluenza B virus," FluMist,is a live-attenuatedintranasalinfluenzavaccine, has been shown to be safeand effective in healthy adults, but its role in the generalprevention of influenza is yet to be defined.The vaccineinduces IgA antibodies in mucosalsecretions, IgG antibodies in serum, as well as CTL cellularresponses, leadingto an increased efficacy and crossprotective potential between several subtypesofviruses. As stressedabove, the livevirusvaccine approach ensuresan acceptable immunogenicitybut includesinherent safetyconcerns(geneticstabilityofthe vaccine strains, potential reassortments with circulatingviralstrains,sheddingin immunocompromisedvaccinees).ln addition, the intranasal applicationof vaccine is otten associated with mucosaldiscomfort,inflammatoryreactions causingsore throat, aswellas febrile reactions in vaccines.t' The efficacy of a proteosomal influenzavaccine containing outer membrane proteins from Neisseria meningitidis (Flulnsure, GSK) and a LTK63IBiovector adjuvanted influenza vaccine are currentlytested in clinical srudies.!

Inclusion ofConserved Epitopes Derivedfrom Influenza Proteins in VaccineFormulations The inclusion of new conserved immunoepitopes is expectedto strengthencellular responses againstinfluenza, facilitating the directelimination of infectedcells from organism. Moreover, due to the conserved character ofepitopes, thegenerated immunocompetent cells mightbecross-reactive and mayhavea significant impacton cross-protection betweendifferentvirussubtypes. Thiscould be of help in the control of pandemic influenza outbreaks." Someinternal componentsof influenzavirusmight haveimpacton the generation of immuneresponses againstinfluenza. The outer envelope of the virusisbuilt up bya phospholipidic membranewith intercalated, outsideprojected influenza surface proteinsHA and N. Theinnersideof the membraneislinedbythe matrixprotein (MI).The integralprotein (M2)isformingion channels within the membrane.Theinternalprotein nucleocapsid is surroundedby the viralenvelope. The nucleocapsid oflnfluenzaA virusconsistsof 8 genomesegments, packaged into the core. Eachsegmentisformedbyhelically organizednucleoprotein (NP) bindinga negative-strandssRNA molecule. Threepolymerase polypeptidic subunits (PA,PBI, PB2)areassociated with the NP-RNA structure.NonstructuralproteinsNS-I and NS-2 are located at the inner site of nucleocapsid I. The functionalcharacteristics of individual proteins aresummarized in Table3. Currentlyavailable influenzavaccines whichareparenterally administered areknownto stimulate effectively MHCl! restrictedimmune responses involving activation ofB-cells and CD4 T-cells

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specific for influenza surface glycoproteins, mainlythe genetically highlyvariable HA.Thisprocess seemsto be sufficient to achieve good levels ofprotection against the homologoussubtypeof influenzavirusin healthy adults, however, it issuboptimal in high riskpopulations, e.g.; the elderly. Sincethe surface glycoprotein NA wasshown to undergo genetic mutations to a lesser extent as comparedto HA,the molecule haveattractedattention and studies performedsofar have confirmed the potential ofN-based vaccines to induce efficient immune responses and protection against

Table 3. The protein-components of influenza virus and theirproperties Protein

Segment

Biological Properties

Anti-Viral or Immunological Properties

HA

4

- Binding to sialic acid receptors on cell surface

Induction of B-cell responses, C04 T-cell s responses, antibody production

- Fusion of viru s w ith endosomal membrane inside of endo somes NA

6

Release of new ly synthetized viruses from infected cells

Induction of B-cell responses, antibody produ ction?

NP

5

RNA binding, nuclear/c ytop lasmic transport of vi ral RNA

Induction of COB T-cell responses

Ml

7

M atrix protein forming capsid

Induction of COB T-cell responses

M2

7

Ion channel through memb rane, important in the uncoating of viruses in endosomes

Induction of B-cell responses, antibody product ion

Target molecule of anti-vi rals amantadine and rimantadine PA

3

Transcript ase

Unkn own

PBl

2

Transcriptase

Induction of COB T-cell responses

Transcriptase

Induct ion of COB T-cell responses

PB2 NSl

B

Effect s on cellular RNA transport, splicing , translation, anti- IFN protein

Induction of COB T-cell responses

NS2

B

Unknow n

Unknow n

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drifted viruseS.46.47 Enhancingthe NA in HA basedvaccines could be of help to control influenza via the induction of more balancedand broadened influenzaspecific humoral responses The stimulation of cytotoxic CDS- T-cells responses specifically targeted to the conserved antigenicdeterminantsderivedmostlyfrominternalproteinsseems to be apromisingapproachto improveefficacy of interpandemicvaccines, aswellasto developefficient pandemicinfluenzavaccines. Following MH Cl-reserictedepitopepresentation,cytotoxiclymphocytes induceapoptosis ofinfectedcells.An approachincludingconserved internalCTL epitopeswouldhavean advantage over conventional HA-based strategies by potentially conferringan heterologous cross-reactive immunity betweendifferentsubtypes.48.49 Although not sterilizing, cellularimmunitywasshown to prevent illnessand deaths in animal models. Due to HA antigenic drifi:, HA-basedstockpiledvaccines mightonlyprovidelimitedprotection againstan emergingpandemicinfluenza strain.Themonitoringofpandemicstrainsderived fromthe sameviralsubtypeallows to identifythe mostconserved humanepitopeswithinthe internalproteins ofinfluenza virus.50Newstrategies aremostlyfocused on the inclusion ofnucleoprotein (NP),or M1, M2 proteins into vaccines. The efficient induction of heterologous crossprotective responses after immunization withimmunodominantNP epitopeshavebeendemonstratedin mousemodels.51.52 A conjugatedM2 peptidebasedvaccines (M2 coupledto KLH or OMP from Neisseria meningitidis) weretestedin mouse, ferretand rhesus monkeys. Thevaccines havebeenshownto be highlyimmunogenicand to conferprotectionagainstlethalchallengewith H INI andH3N2 strainsinallspecies. Monkeyantiseratestedfor reactivity with different strainsof humaninfluenza A werecrossreactive, however, they failedto reactwith M2 peptidesderived from highlypathogenic H5Nl strain." In contrast, if the M2 peptidewascoupledto a hepatitisB coreparticlecarrier, the conjugate failedto generate protective responses evenagainstinterpandemic strains.54 Anotherapproachmadeuseofan adjuvanted plasmidvaccine encodingthe M proteinencodinggeneapplied topicallyon the skin.The vaccine inducedcytotoxicand humoralresponses and providedcross-reactive protection in mice," A new generationofliveattenuated vaccines against influenza is basedon NSI protein mutants. The nonstructuralprotein 1 has beenshownto inhibit TypeI interferons mediatedresponses. Such cytokines havea highimpacton the regulation ofpathogeniceffects inducedbyinfluenza infection. The attenuation and immunogenicity ofNSI truncated mutants wasconfirmed in vivo in mouse model, in whichwasableto conferprotection." Thus, a variety of approaches have been tested in animal, mainly mouse models so far. The proof-of-concept in humansstill has to be established. The general immunoregularory factors that need to be considered in the development of vaccines targetingcellular immuneresponses are still unclear. Up to now we havelearned, mostlyfrom mousestudies, about the immune mechanisms triggered bysuchvaccines. Antigenavailability, antigenprocessing, epitopestabilityand individual T-cell repertoires seemto be critical elements to be taken in accountduring the vaccine development process. In addition,the formulation ofindividual components needsto be optimizedand an alternative wayof administration of the vaccine shouldbe evaluated aswell.

Conclusion Influenza vaccines available todayarein usesinceover50years. During this timetheyunderwent onlysmallimprovements.Theefficacy ofvaccines isacceptable in healthyadultsbut suboptimalin at riskpopulation groups, in whichthe infectioncanprogress to verysevere, complicated disease and evento a fatalend. Furthermore, thereiscurrentlyno efficient tool to efficiently fightthe predicted next influenza pandemy. The avian H9N2, H7N2 or H5Nl influenza strainshave been already shownto cause human infections, althoughtheseavain strainsdid not acquire the capability ofhuman to human transmission yet.It isessential to improve our understanding of disease mechanisms to facilitate the development of better measures to control influenza. In order to protect humans againstpandemicinfluenza threats, aswellas to improve existing interpandemic vaccines for high risk population groups, new vaccine approaches must urgentlybe identified and developed. That will imply major scientific and industrial investments in order to convert promising improved candidatevaccines into marketable products.

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References 1. Lamb RA. Krug RM. Orthomyxoviridae: The viruses and their replication. In: Fields BN. Knipe DM . Howly PM. eds, Fields Virology. Philadelphia: Lippincott-Raven Publishers. 1996:1353-1395. 2. The Universal Virus Database ICTVdB: http ://www.ncbi.nlm.nih.gov/ICTVdb/Ictv/index.htm 3. Nicholson KG. Human influenza. In: Nicholson KG. Webster RG. Hay A], eds, Textbook of Influenza. Oxford : Blackwell Science; 1998:219-264 4. Nicholson KG, Wood JM . Zambon M. Influenza. Lancet 2003; (362):1733-44. 5. Weekly epidemiological record, 2005; Nr. 33 (80):277-288. 6. Influenza repott 2006. edited by Kamps BS. Holfman C and Preisser \v, Flying Publisher, 2006. 7. Hemmes JH. Winkler KC. Kool SM. Virus survival as a seasonal factor in influenza and polimyelitis. Nature 1960; (188):430-1. 8. 8 Smith W, Andrewes CH. Laidlaw PP. A virus obtained from influenza patients. Lancet 1933; (1):66-68. 9. WoodJM, Williams MS. Histo ry ofinactivated influenza vaccines. In: Nicholson KG. Webster RG, Hay AJ eds, Textbook of Influenza. Oxford :BlackwellScience: 1998:317-23. 10. Furminger IGS. Vaccineproduction. In: Nicholson KG. Webster RG, Hay AJ. eds, Textbook of Influenza Oxford:Blackwell Science Ltd : 1998:324-332. 11. www.medimmune.com 12. Medema J. Wijnands DT, Palache AM. The role of MDCK-based influenza vaccine Influvac TC in inter(pandemics). International Congress Series 2004; 1263:822-825. 13. Ozaki H , Govorkova EA, Li C et al. Generation of ｨｩｧ Ｍｹｩ･ｬ､ ｮｾ influenza A viruses in Mrican green monkey kidney (Vero) cells by reverse genetics. J ViroI2004; 78(4):1851 -7. 14. Pau MG , Ophorst C. Koldijk MH et aI. The human cell line PER.C6 provides a new manufacturing system for the production of influenza vaccines. Vaccine 2001; 19(17-19):2716-21. 15. www.clinicaltrials.gov 16. Wang D, Christopher ME, Nagata LP et aI. Intranasal immunization with liposome-encapsularedplasmid DNA encoding influenza virus hemagglutinin elicits mucosal. cellular and humoral immune responses. J Clin Virol 2004; 31(Suppll):S99-106. 17. Tamura S. Tanimoto T. Kurata T. Mechanisms of broad cross-protection provided by influenza virus infection and their application to vaccines. Jpn J Infect Dis 2005; 58(4) :195-207. 18. Brett IC ,Johansson BE. Immunization against influenza A virus: comparison of conventional inactivated. live-attenuated and recombinant baculovirusproduced purified hemagglutinin and neuraminidase vaccines in a murine model system. Virology 2005; 339(2) :273-80. 19. Van Kampen KR, Shi Z, Gao P et aI. Safety and immunogenicity of adenovirus-vectored nasal and epicuraneous influenza vaccines in humans. Vaccine 2005 ; 23(8):1029-36. 20. Cassetti MC , Katz JM. Wood J. Report of a consultation on role of immunological assays to evaluate efficacy of influenza vaccines. Initiative for Vaccine Research and Global Influenza Programme. World Health Organization. Geneva. Switzerland. 2005. Vaccine 2006; 24(5) :541-3. 21. Nichol KL. Efficacy/clinical effectiveness of inactivated influenza virus vaccines in adults. In: Nicholson KG. Webster RG, Hay AJ. eds, Textbook of Influenza. Oxford :BlackwellScience Ltd : 1998:358-372. 22. McElhaney JE, Xie D. Hager WD er aI. T-cell responses are better correlates of vaccine protection in the elderly.J ImmunoL 2006 ; 176(10) :6333-9. 23. Belshe RB. Couch RB, Glezen WP et al. Live attenuated intranasal influenza vaccine. Vaccine 2002; 20(29 -30):3429-30. 24. Thomas PG. Keatinll R. Hulse-Post DJ et al. Cell-mediated protect ion in influenza infection. Emerg Infect Dis 2006; 12(1):48-54. 25. BressonJL, Perronne C. Launay 0 et al. Safety and immunogenicity of an inactivated split-virion influenza ANietnam/1194/2004 (H5Nl) vaccine: phase I randomised trial. Lancet 2006; 367(9523) :1657-64. 26. Gupta RK. Relyved ER, Lindblad EB er aI. Adjuvants-a balance between toxicity and adjuvanticity. Vaccine 1993; 11(3) 293-306. 27. Gliick R, Mischler R. Finkel Bf er al. Immunogenicity of new virosome influenza vaccine in the elderly people Lancet 1994; (344):160-163. 28. Stephenson I, Bugarini R. Nicholson KG et aI. Cross-reactivity to highly pathogenic avian influenza H5Nl viruses after vaccination with nonadjuvanted and MF59-adjuvanted influenza A/Duck/ Singapore/97 (H5N3) vaccine: a potential priming strategy. J Infect Dis 2005; 191(8):1210-5. 29. Banzhoff A, Nacci P, Podda A. A new MF59-adjuvanted influenza vaccine enhances the immune response in the elderly with chronic diseases: results from an immunogenicity meta-analysis. Gerontolog y 2003; 49(3) :177-84. 30. Moser C, Metcalfe IC . Viret JF. Virosomal adjuvanted antigen delivery systems. Expert Rev Vaccines 2003; 2(2) :189-96. Review. Erratum in: Expert Rev Vaccines 2003; 2(6) :842. 31. Takeshita F, Tanaka T. Matsuda T et aI. Toll-Like Receptor Adaptor Molecules Enhance DNA-Raised Adaptive Immune Responses against Influenza and Tumors through Activation of Innate Immunity. J Viro12006; 80(13):6218-24.

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32. Guillot L, Le Goffic R, Bloch S ee at Involvement of toll-like receptor 3 in the immune response of lung epithelial cells to double-stranded RNA and influenza A virus. J BioI Chern 2005; 280(7) :5571-80. 33. Lund JM, Alexopoulou L, Saro A et aI. Recognition of single-stranded RNA viruses by Toll-like receptor 7. Proc Nad Acad Sci USA 2004; 101(15):5598-5603. 34. Treanor J. Nolan C, O'Brien D et al. Intranasal administration of a proteosome-influenza vaccine is well-tolerated and induces serum and nasal secretion influenza antibodies in healthy human subjects. Vaccine 2006: 24(3):254-62. 35. Stephenson I, Zambon MC. Rudin A er al. Phase I evaluation of intranasal trivalent inactivated influenza vaccine with nontoxigenic Escherichia coli enterotoxin and novel biovector as mucosal adjuvants. using adult volunteers. J ViroI2006; 80(10):4962-70. 36. Eriksson AM, Schon KM, Lycke NY. The cholera toxin-derived CTAI-DD vaccine adjuvant administered intranasally docs not cause inflammation or accumulate in the nervous tissues. J Immunol 2004: 173(5) :3310-9. 37. Helgeby A. Robson NC , Donachie AM et aI. The combined CTAI-DD/ISCOM adjuvant vector promotes priming of mucosal and systemic immunity to incorporated antigens by specific targeting of B-cells. J ImmunoI2006; 176(6):3697-706. 38. Rimmelzwaan GF. Boon AC, Geelhocd-Mieras MM et aI. Human airway epithelial cells present antigen to influenza virus-specific CD8· CTL inefficiendy alter incubation with viral protein together with ISCOMATRIX. Vaccine 2004; 22(21-22) :2769-75. 39. Coulter A, Harris R. Davis R et al. Intranasal vaccination with ISCOMATRIX adjuvanted influenza vaccine. Vaccine 2003; 21(9-10):946-9. 40. Ennis FA. Cruz J. Jameson J et al. Augmentation of human influenza A virus-specific cytotoxic T-Iymphoeyre memory by influenza vaccine and adjuvanted carriers (ISCOMS). Virology 1999: 259(2) :256-61. 41. Borsutzky S. Kretschmer K. Becker PD et at The mucosal adjuvant macrophage-activating Iipopeptide-2 directly stimulates B-Iymphocytes via the TLR2 without the need of accessory cells.J Immuriol 2005: 174(10):6308-13. 42. Muszkat M, Greenbaum E, Ben-Yehuda A er al. Local and systemic immune response in nursinghome elderly following intranasal or intramuscular immunization with inactivated influenza vaccine. Vaccine 2003: (21):1180-1186. 43. Gliick U. Gebbers J-O , Gliick R. Phase 1 evaluation of intranasal virosomal influenza vaccine with and without Escherichia coli heat-labile toxin in adult volunteers. J Viro11999; 73(9) :7780-7786. 44. http://www.medlctter.com/freedocs/flumist.pdf 45. Epstein SL. Control of influenza virus infection by immunity to conserved viral features. Expert Rev Anti Infect Ther 2003; 1(4):627-38. 46. Deroo T. Jou WM, Piers Recombinant neuraminidase vaccine protects against lethal influenza. Vaccine 1996; 14(6):561-9. 47. Epstein SL, Misplon JA. Lawson CM et aI. Beta 2-microglobulin-deficient mice can beprotected against influenza A infection by vaccination with vaccinia-influenza recombinants expressinghemagglutinin and neuraminidase. J Immuno11993; 150(12):5484-93. 48. Gianfrani C, Oseroff C, Sidney J et aI. Human memory CTL response specific for influenza A virus is broad and mulcispecific, Hum Immunol20oo: 61(5):438-52. 49. Cox MM . Cell-based protein vaccines for influenza. Curr Opin Mol Ther 2005; 7(1) :24-9. 50. Thomas PG, Keatinl: R. Hulse-Post DJ et al, Cell-mediated protection in influenza infection. Emerg Infect Dis 2006: 12(1):48-54. 51. Turner SJ, Kedzierska K. Komodromou H et aI. Lack of prominent peptide-major histocompatib ility complex features limits repertoire diversity in virus-specific CD8· T-cell populations. Nat Immunol 2005: 6(4) :382-9. 52. Kedz ierska K. Turner Doherty PC . Conserved T-cell receptor usage in primary and recall responses to an immunodominant influenza virus nucleoprotein epitope. Proc Nad Acad Sci USA 2004: 101(14) :4942-7. 53. Fan J, Liang X, Horton MS et al. Preclinical study of influenza virus A M2 peptide conjugate vaccines in mice, ferrets and rhesus monkeys. Vaccine 2004: 22(23-24) :2993-3003. 54. Jegerlehner A. Schmitz N, Storni T et aI. InfluenzaA vaccinebased on the extracellulardomain of M2: weak protection mediated via antibody-dependent NK cell activity.J Immunol 2004; 172(9):5598-605. 55. Ozaki T, Yauchi M. Xin KQ et aI. Cross-reactive protection against influenza A virus by a topically applied DNA vaccine encoding M gene with adjuvant. Viral Immunol 2005: 18(2):373-80. 56. Falcon AM . Fernandez-Sesma A, Nakaya Y et al. Attenuation and immunogenicity in mice of temperature-sensitive influenza viruses expressing truncated NSI proteins. J Gen Virol 2005: 86(Pt 10):2817-21.

w:

CHAPTER 4

The Role ofNanobiotechnology in Drug Discovery KewalK.Jain* Abstract

T

he potential applications ofnanotechnology in life sciences, particularly nanobiotechnology, include those for drug discovery. This chapter shows how several of the nanotechnologies including nanoparticles and various nanodevices such as nanobiosensors and nanobiochips are being used to improve drug discovery. Nanoscale assaysusing nanolirer volume s contribute to cost saving. Some nanosubstances such as fullerenes are drug candidates. There are some safety concerns about the in vivo use ofnanoparticles that are being investigated. However. future prospects for applications in healthcare ofdrugs discovered through nanotechnology and their role in the development of personalized medicine appear to be excellent .

Introduction Current drug discovery process needs improvement in several areas. Although many target s are being discovered through genomics and proteornics, the efficiency of screening and validation processes need to be improved. This chapter will show how nanotechnology will playa role in improving this process. Nanotechnology is the creation and utilization of materials . devices and systems through the control ofmatter on the nanometer scale. Given the inherent nanoscale functional compo nents of living cells. it was inevitable that nanotechnology will be applied in life sciences giving rise to the term nanobtorechnology,' Technical achievements in nanotechnology are being applied to improve drug discovery. drug delivery and pharmaceutical manufacturing. A product incorporating the NanoCrystal° technology ofElan Drug Deliver y Inc (King ofPrussia, PA). a solid-dose formulation ofthe immunosuppressant sirolimus , was approved by the FDA in 2000. Nanotechnologies are already being used in molecular diagnostics.' Analyses of Signaling pathways by nanobiotechnology techniques may provide new insight into the understanding of disease processes, developing more efficient biomarkers and understanding mechanisms ofaction ofdrugs. This will help in designing new approaches to drug discovery. Various nanotechnologies used for drug discovery are listed in Table 1 according to various stages ofdrug discovery.3 Selected technologies are described briefly in the following text .

Role ofNanoparticles in Drug Discovery Older imaging tools such as fluorescent dyes or polymer sphere s are either too unstable or too big to effectively perform single-molecule tracking. The role of nanoparticles for drug discovery has been explored but no one type of nanoparticle is suitable for universal application in drug discovery.

°Kewal K. Jain-Jain PharmaBiolech, Blaesiring 7, CH-4057 Basel, Switzerland. Email: [email protected]

PharmaceuticalBiotechnology, edited by Carlos A. Guzman and Giora Z. Feuerstein. ©2009 Landes Bioscience and Springer Science+Business Media.

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Table 1. Application of nanobiotechnology at various stages of drugdiscovery Target identification and validation Nanoproteomics Single wall carbon tube nanosensors High-field asymmetr ic waveform ion mobility mass spectrometry Investigatingbiomolecular interactions with atomic force microscopy Study of molecular interactions using cantilevers Study of molecular interactions using nanoprobes Lead identification Biosensor Nanowire devices Assays based on endocytosis at the nanoscale Surface plasma resonance Nanofluidics, nanoarrays and nanobioch ips Nanoflow liquid chromatography Lead optimizat ion Nanoparticles Quantum dots Gold nanoparticles Lipoparticles Use of small molecules attached to nanoparticles Fluorescence planar wave guide technology Nanomaterials as drug cand idates Dendrimers Fullerenes Nanobodies © Jain PharmaBiotech

Quantum DotsfOr DrugDiscovery The use ofquantwn dots (QDs) for drug discovery has been explored.' Several QDs are commercially available. Qdot" conjugates (Quantum Dot Corporation, Hayward, CA) can produce photo resolutions up to eight times more detailed than the older imaging tools. The Qdot" conjugates are almost "an order ofmagnitude" brighter than fluorescent dyes and can be observed for as long as 40 minutes compared to about five seconds for the dyes. Length ofobservation time is critical to studying cellular processes, which change rapidly over a span of several minutes. Since cellular receptors are critical targets for new drug candidates, a more detailed understanding of the behavior of these receptors can open up new treatment options. QDs are ideal for targeting cancer for both diagnosis and therapy. However, some limitations for QD use in drug discovery studies have yet to be resolved. i.e., toxicity, size variation, agglomeration, potential multiple drug attachment to a single QD and blinking.

Gold Nanoparticles Gold nanopartieles are the most commonly used nanomaterial in diagnostics and have many other uses as well such as a connecting point to build biosensors for detection of disease DNA. Instead ofa fluorescent molecule, a gold nanoparticle can beattached to the antibody and other molecules such as DNA, which can beadded to the nanoparticle to produce bar codes. Because many copies ofthe antibodies and DNA can be attached to a single nanoparticle, this approach is much

The RoleofNanobiotechnology in DrugDiscovery

39

more sensitive and accurate than the fluorescent-molecule tests used currently. Although they can be used for drug discovery, they need to be combined with another technology for visualization. Gold nanoparticles have been used to demonstrate multiphoton absorption induced luminescence (MAIL), in which specific tissues or cells are fluorescently-labeled using special stains that enable them to be stu died. Gold nanoparticles can emit light so intense that it is readily possible to observe a single nanoparticle at laser intensities lower than those commonly used for MAIL, i.e., sub-lOO-fs pulse s of790-nm lighr.' Moreover, gold nanoparticles do not blink or burn out, even after hours ofobservation suggesting that metal nanoparticles are a viable alternative to fluorophores or semiconductor nanoparticles for biological labeling and imaging. Other advantages ofthe technique are that the gold particles can be prepared easily, have very low toxicity and can readily be attached to mole cules ofbiological interest. In addition, the laser light used to visualize the particles is a wavelength that causes only minimal damage to most biological tissues. This technology could enable tracking ofa single molecule ofa drug in a cell or other biological samples.

SmallMolecules Attached to Nanoparticles Multivalent attachment of small molecules to nanoparticles can be used to increase specific binding affinity and to reveal new biological properties ofsuch nanomaterials. Gelatin nanoparticles have been used for the attachment ofbiotinylated anti-CD3 antibodies by avidin-biotin complex formation to provide a carrier system for specific drug targeting to Tdyrnphocytes," A union between small molecule chemistry and nanotechnology, has the potential ofdevelopment ofa wide range ofnanomaterials for biomedical application? One ofthe applications is in target screening in high throughput drug discover y.This technique can enable small molecule modification to impart desirable biological functions for in vivo visualization of targets and for delivery of therapeutics thus enabling combination ofdiagnostics and therapeutics, particularly in case of cancer.

Role ofNanoproteomics in Drug Discovery Proteomics is playing an important rofe in the target identification and validation phases of the drug discover y proces s. Application of nanotechnologies in proteomics has been termed nanoproteomics, which is an extens ion of the scope of proteomics on nanoscale. Most current protocols including protein purifi cation/display and automated identification scheme s yield unacceptably low recoveries, thus limiting the overall process with respect to sensitivity and speed and the requirement ofgreater amounts ofstarting material. Low abundant proteins and proteins that can only be isolated from limited source material can be subjected to nanoscale protein analysis, nano-capture of specific proteins and complexes and optimization ofall subsequent sample handling step s leading to mass analysis ofpeptide fragments. Some nanotechnologies are refining the application of proteomics for drug d iscovery and examples are described here briefly. A technology called magnetism-based interaction capture (MAGIC) identifies molecular targets on the basis ofinduced movement ofsuperparamagnetic nanoparticles inside living cells.8 These nanoprobes capture the small molecule's labeled target protein and are translocated in a direction specified by the magnetic field. Use ofMAGIC in genome-wide expression screening can identify multiple protein targets ofa drug. MAGIC can also be used to monitor signal-dependent modification and multiple interactions of proteins.

Single-Walled Carbon Nanotubes Single-walled carbon nanotubes as a platform have been used for investigating surface-protein and protein-protein binding and developing highly specific electronic biomolecule detectors. Nonspecific binding on nanotubes, a phenomenon found with a wide range of proteins, is overcome by immobilization of pol yeth ylene oxide chains. A general approach is then advanced to enable the selective recognition and binding of target proteins by conjugation of their specific receptors to pol yethylene oxide-functionallzed nanotubes. These arrays are attractive because no labeling is required and all aspects of the assay can be carried out in the solution phase. This scheme, combined with the sensitivity of nanotube electronic devices, enables higWy specific

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electronicsensors for detecting clinically important biomolecules such as antibodiesassociated with human autoimmunediseases.

Nanoflow Liquid Chromatography The use of liquid chromatography (LC) in analytical chemistryis well established but the relatively low sensitivity associated with conventional LC makes it unsuitablefor the analysis of certain biological samples. Furthermore,standard LC flow rates are frequently not compatible with the use of specific detectors,such as electrospray ionization mass spectrometers. Therefore, due to the analytical demandsofbiological samples, miniaturizedLC techniquesweredeveloped to allow for the analysis of samples with greater sensitivity than that affordedby conventional LC. In nanoflowLC (nanoLC), chromatographic separations are performedusingflowrates in the rangeoflow nanoliterper minute, which resultin high analytical sensitivity due to the large concentration efficiency affordedby this type of chromatography. NanoLC, in combination to tandem mass spectrometry, wasfirst used to analyze peptidesand as an alternative to other mass spectrometricmethodsto identifygel-separatedproteins.Gel-free analytical approaches basedon LC and nanoLC separations havebeendeveloped, whichareallowingproteornics to beperformed in faster and more comprehensive manner than by usingstrategies basedon the classical 2D gel electrophoresis approaches. Protein identification using nanoflowliquid chromatography-mass spectrometry(MS)-MS (LC-MS-MS) provides reliable sequencing information forlowfemtomole levelofprotein digests. However, this task is more challenging for subfemtomole peptide levels. An ion mobilitytechnology, high-field asymmetric waveform ion mobilitymassspectrometry (FAIMS), has been introduced as an online ion selection method compatible with electrospray ionization (ESI).FAIMSuses ion separationto improve the detectionlimitsofpeptide ionswhen usedin conjunctionwith electrospray and nanoelectrospray MS.Thisfacilitates the identification of low-abundance peptide ions often present at ppm levels in complex proteolytic digests and expandsthe sensitivity and selectivity of nanoLC-MSanalyses in globaland targetedproteomics approaches.Thisfunctionality will probablyplayan importantrolein drug discoveryandbiomarker programsfor monitoring disease progression and drug efficacy.

Atomic Force Microscopy for Drug Discovery Atomic force microscopy (AFM) has become a well-established technique for imaging single biomolecules under physiological conditions. The exceptionally high spatial resolution and signal-to-noise ratio ofthe AFM enables the substructureofindividualmolecules to be observed. Usedas a sensor, the AFM tip can alsoprobe the charges of biological surfaces immersed in a buffersolution. So far,such approaches havesuccessfully characterized protein interactions but in the future they could be appliedto imagingand detectingmultipleparameters on a Single moleculesimultaneously. If a ligand is attached to the end of an AFM probe, one can simulate variousphysiological conditions and look at the strength of the interaction between the ligand and receptor in a widerangeof circumstances. Byfunctionalizing the tip, it can be usedto probe biological systems and identifyparticular chemical entitieson the surface of a biological sample. This opens the door to more effective useof AFM in drug discovery.

Role ofNanoscale Biosensors in Drug Discovery Biosensors arecurrentlyusedin the areas oftargetidentification, validation,assay development, leadoptimization and ADMET, but arebest suited for applications relatedto solublemolecules. Biosensors can overcome manyof these limitations of currentlyused cell-based assays. Theyare particularlyusefulin the study ofreceptors, in that biosensors do not require the removal of the receptor from the lipid membraneof the cellas might be necessary with other assay methods.A primary applicationof current biosensor technologies is the optimizationof limited-scope drug librariesagainstspecific targets.

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41

OpticalBiosensors Optical biosensors capable of exploitingsurface plasmon resonance (SPR), waveguides and resonant mirrorshavebeen usedwidelyoverthe past decadeto analyze biomolecularinteractions. Thesesensors allow the determination of the affinityand kineticsof a wide varietyof molecular interactions in real time, without the need for a molecular tag or label. Conventional SPR is applied in specialized biosensing instruments. These instruments use expensive sensor chips of limited reuse capacityand require complexchemistry for ligand or protein immobilization. A sensitive techniqueisbeingdeveloped for opticaldetection ofgoldnanoparticle-labeled molecules on protein microarray by applyingthe surface plasmon resonance and specific molecularbinding usingrollingcircleamplification."

Cantilevers Cantilevers transform a chemicalreaction into a mechanicalmotion on the nanometer scale and this motion canbe measureddirectlybydeflecting a light beamfrom the cantilever surface.'? A state-of-the-art position sensitive detector isemployedasdetectiondevice. Thestaticmode isused to obtain information regardingthe presenceof certain target molecules in the samplesubstance. The surfacestress causedby the adsorption of these molecules resultsin minute deflections of the cantilever. This deflectiondirectlycorrelates with the concentration of the target substance. The dynamicmode allows quantitative analysis of massloadsin the sub-picogram area. As molecules areadsorbed,minimalshiftsin the resonance frequency of an oscillating cantilever canbe measured and associated with reference data of the target substance. Both modescan alsobe operatedsimultaneously. Thecontrolleddepositionof functional layers isthe keyto convertingnanomechanical cantilevers into chemicalor biochemical sensors. Inkjet printing is a rapid method to coat cantileverarrays efficiently with various sensorlayers. Applicationsrelevantto drug discovery include label-free biochemicalassays and investigation ofb iomolecularinteractionsaswellasmultiplexed assays. Byattachingspecific antibodiesto cantilevers the simultaneousimagingof target antigens and identificationof antigen-antibodyinteractionshavebeen demonstrated.

NanoHuidics, Nanoarrays and Nanobiochips Nanofluidics impliesextremereduction in quantity of fluidanalytein a microchip compared with standard methods. The use of the word "nano" in nanoliter (nl) is in a different dimension than in nanoparticle,which is in nanometer (nrn) scale. From one printing run that consumes < 1 nanomole of each compound, large combinatorial libraries can be subjected to numerous separation-freehomogeneousassays at volumes that are a smallfraction of those used in current high-throughput methods. Nanoarrays are the next stage in the evolution of miniaturization of microarrays. Whereas microarrays are prepared by robotic spotting or optical lithography, limiting the smallest sizeto several microns,nanoarrays requirefurther developments in lithographystrategies suchaselectron beamlithography, dip-pen nanolithography, scanningprobe lithography, finely focusedion beam lithography and nano-imprintlithography.Nanoarrays canmeasure interactions betweenindividual molecules down to resolutions of aslittle asone nanometer and can be usedin bioaffinitytestsfor proteins, nucleicacidsand receptor-ligandpairs.

N anomaterials as Drug Candidates Dendrimers Dendrimers are a novelclass of three-dimensional nanoscale, core-shellstructures that can be precisely synthesized for a wide rangeof applications. Specialized chemistry techniquesallowfor precise controloverthe physical and chemical propertiesof the dendrimers.Theyaremostusefulin drugdelivery but can also be usedfor the development of newpharmaceuticals with novelactivities. Polyvalent dendrirnersinteract simultaneously with multipledrug targets.Theycanbe developed into noveltargeted cancertherapeutics. Dendrimerscan be conjugatedto differentbiofunctional

42

PharmaceuticalBiottchno/qgy

moieties such as folic acid using complementary DNA oligonucleotides to produce clustered molecules, which target cancer cellsthat over-express the high affinityfolate receptor.11

Fullerenes A keyattribute ofthe fullerenemoleculesistheir numerous points of attachment, allowingfur precise grafting of active chemicalgroups in three-dimensional orientations. This attribute, the hallmark of rational drug design,allowsfor positional control in matching fullerenecompounds to biologicaltargets. In concert with other attributes, namely the sizeof the fullerene molecules, their redoxpotential and its relativeinertnessin biologicalsystems, it ispossibleto tailor requisite pharmacokinetic characteristics to fullerene-based compounds and optimize their therapeutic effect [25]. Fullereneantioxidants bind and inactivatemultiple circulatingintracellularfree radicals, giving them unusualpower to stop free radicalinjury and to halt the progressionofdiseases caused by excess free radicalproduction . Fullerenes provide effective defenseagainstall of the principal damaging forms ofreactiveoxygenspecies. C-60 fullerene has thirty conjugated carbon-carbon double bonds, all of which can react with a radicalspecies. In addition, the capture ofradicalsby fullerenesis too fast to measureand is referred to as «diffusion controlled", meaningthe fullerene forms a bond with a radical every time it encounters one. Numerous studies demonstrate that fullerene antioxidants work significantly better as therapeutic antioxidants than other natural and synthetic antioxidants, at least for CNS degenerative diseases. In oxidative injury or disease, Fullerene antioxidants can enter cells and modulate free radical levels, thereby substantiallyreducing or preventing permanent cellinjury and cell death. A tris-rnalonicacid derivative ofthe fullerene C-sixty molecule (C3) functionally replaces manganesesuperoxidedismuraseand acts as a biologically effective superoxidedisrnutasemirnecic."

Nanohodies Nanobodies (Ablynx , Ghent, Belgium) are the smallest available intact antigen-binding fragments harboring the full antigen-binding capacity of the naturally occurring heavy-chain antibodies. Nanobodies havethe potential of a new generation of antibody-based therapeuticsas well as diagnosticsfor diseases such as cancer," They are extremelystableand bind antigen with nanomolar affinity. They combine the advantages of conventional antibodies with important features of small molecule drugs and can address therapeutic targets not easily recognized by conventional antibodies such as activesites of enzymes.

Nanobiotechnology and Drug Discovery for Personalized Medicine Personalizedmedicine simplymeans the prescription ofspecific treatments and therapeutics best suited for an individual It is also referred to as individualizedor individual-based therapy. Personalizedmedicine isbasedon the ideaofusinga patient'sgenotype as a factor in decidingon treatment options but other factorsare alsotaken into consideration.Moleculardiagnosticsis an important component of personalizedmedicineand nanobiotechnologiesare alreadybeingused in moleculardiagnostics.Although current effortsusingpharmacogenomics and pharmacogeneticsinclude matching the existingdrugs to the right patients for optimal efficacy and safetyfuture personalized medicines could be discovered and designed for specific groups of patients using pharmacoproteomics. Nanobiotechnologyshowspromiseoffacilitatingdiscoveryofpersonalized medicinesapart from facilitatingintegration of diagnosticsand therapeurics,"

Conclusion The examples given in this chapter cover a number of different nanotechnologies, Some of these are alreadyestablishedin researchthrough other well known technologiessuch as biosensors and biochips. Nanoparticlesare still used extensively for developingdiagnosticsand someof the assays for drug discovery. With a largenumber of nanotechnologiesand nanomaterials,no generalizations can bemade about the overall safety and toxicity. In vitro diagnostic use does not carry any risks to people

The RoleofNanobiouchnologyin DrugDiscovery

43

but there is a concern for in vivouseof nanoparticles, particularlythose that areless than SO nrn, which can enter the cells. Therearestill manyunansweredquestionsabout their fate in the living body. Because of the hugediversityof materials used and the wide rangein sizeof nanoparticles, these effects will vary a lot. It is conceivable that particular sizes of some materials may turn out to have toxic effects. Further investigations will be needed. The FDA approval is essential for clinicalapplications of nanotechnologyand substantialregulatoryproblemsmaybe encountered in the approval of nanotechnology-based products. Pharmaceuticals, biologicals and devices are all regulateddifferently by the FDA and it is not yet clear how emergingnanotherapeutics will be evaluated.

Future ofNanotechnology-BasedDrug Discovery An increasing useof nanobiotechnologyby the pharmaceuticaland biotechnologyindustries isanticipated.Apart from innovationsbasedon nanoparticles, several other nanotechnologies are in developmentfor applicationin lifesciences. In the near future. it maybepossible to fullymodel an individualcell's structureand function bycomputersconnected to nanobiotechnologysystems. Such a detailed virtual representationof how a cell functions might enablescientists to develop noveldrugs with unprecedented speed and precisionwithout any experiments in livinganimals. Nanotechnology will be applied at all stages of drug development-from formulations for optimaldelivery to diagnosticapplications in clinicaltrials. Nanobiotechnologywould fit in with the conceptsfor integration of diagnostics and therapeuticsfor the developmentof personalized medicine.

References 1. Jain KK. Nanobiotechnology: applications, markets and compan ies. Jain PharmaBiotech Publications. Basel: Switzerland. 2007:1-695. 2. Jain KK. Nanobiotechnology in Molecular Diagnostics. Norw ich. UK : Hor izon Scient ific Press. 2006 :1-185. 3. Jain KK. The role of nanobiotechnology in drug discovery. Drug Discov Today 2005; 10:1435-1442. 4. Ozkan M. Quanrum dots and other nanoparticles: what can they offer to drug discovery? Drug Discov Today 2004 ; 9:1065-71. 5. Farrer RA. Butterfield FL. Chen VW et al Highly efficient mulriphoton-absorprion-lnduced luminescence from gold nanoparticles. Nano Lett 2005; 5:1139-42. 6. Balthasar S, Michaelis K. Dinauer N et aL Preparation and characterisation of antibody modified gelatin nanoparticles as drug carrier system for uptake in lymphocytes. Biomaterials 2005 ; 26:2723-32. 7. Jain KK. Nanoparticles as targeting ligands. Trends Biotechnol 2006 Apr; 24:143-5. 8. Won]. Kim M. Yi YW er aL A magnetic nanoprobe technolog y for detecting molecular interactions in live cells. Science 2005; 309:121-5. 9. Hsu HY, Huang IT. RCA combined nanoparticle-based optical detection techn ique for protein microarray: a novel approach. Biosens Bioeleccron 2004 ; 20.123-6 . 10. Ziegler C. Cantilever-based biosensors. Anal Bioanal Chern 2004 ; 379:946-59. 11. Kukowska-Latallo JF Cand ido KA. Cao Z et aI. Nanoparticle targeting of anticancer drug improves therapeutic response in animal model of human epithelial cancer. Cancer Res 2005; 65:5317-24. 12. Ali SS. Hardt Quick KL et aL A biologically effective fullerene (C60) derivative with superoxide d ismutase mimetic properties. Free Radic Bioi Med 2004 ; 37:1191-202. 13. Revers H. De Baetselier P, Muyldermans S. Nanobodies as novel agents for cancer therapy. Expert Opin Bioi Ther 2005 ; 5:111-24. 14. Jain KK. Personalized Medi cine: scienti fic and commercial aspect s. Basel: Jain Pharmalliorech, 2007:1-600.

INDEX

A Acetylcholine receptor 8, 44,46 Adaptive design 11 Adjuvant 64,68 ,69,71 ,72 ,149,150,159, 163,166,167 ,1 71-175,177-182,200, ＲＰ

ＬＲｾＰ

Ｗ ＬＲＰＹ

ＬＲＱＰ

ＬＲＱＹ ＬＲＰ

Ｌ

246-248 Affinity 17,30,31-34,39,41,42, 47,51 , 55·58,90,91,100,101,179,192 Agonist 4,45 -47,64,68,69,72-74,1 75, 178,179,181 ,182,247 Allergy 63,175 ,216 Ampliconvector 120,121, 125, 128-130, 134 Antagonist 9,10,21 , 45-47,64,69, 71-74, 181 Antibiotic 13-16,18,19,69,90,91, 93,103 , 105,110-112,125,159 ,162,167 Antibody 8,28-34,38-42,49-52,54-60,68, 72, 90-103, 105-110, 112, 123, 126, 129, 146, 149, 151-154, 163, 164, 174, 176, 181,182,191,192,19 4-196,205 ,208 , 217,219,223,246-249 Antigen 29,30 ,32,33,41 , 42,49-53,55-60, 67, 72, 73,81,82,85,87,88 ,90-98,100, 101,105-110,112,122,125-127,131 , 145,146,149,150,152 ,154,160 ,163 , 164,166-168,171- 175,1 77-182,193, 195,19 7,199 ,201 , 202,204-212,21 4, 217-219,222 ,223 ,244-247,250 Antigenometechnology 97,98 Asthma 64,68-71, 73, 175 Atherosclerosis 63,64 ,68,69,74 Autoimmunedisease 40,63 ,68,72-74,91 , 174,1 79,181

Bacterial vaccine 110 Bacteriophage 30,50,100,159 Bioinformatic 4, 83, 96-98 Biologic 28-30,32,49-51, 56, 58-60,72, 106,196,245 Biological screening 22 Biomarker 1-11,37,40 Bystander effect 130, 131, 133

c Calciumchannel 45 Calicheamicin 32 Cancer 10,13,28,30,32,33,38 ,39,41 , 42, 44-47,49,59 ,63,67,71 -73, 90, 91,101 , 103,108 ,109 ,112 ,118 ,120,129-134, 146,149 ,168 ,1 78,180,182,219 ,246 Cell wall component 64,180 Chemicalscreening 22 Chlamydia pneumoniaes 66, 84 Combinatorial chemistry 13, 17, 18,23, 175 Comparativegenomeanalysis 84, 85, 88 Complementarity 33,98,100 Conopeptide 44-47 Conotoxin 44-47 Conventionalvaccinology 81-83 Correlate 2,41,53,82,83 ,166 ,191, 193-199,201, 221-223 Cultivation 20-23 Cytokine 32, 49,63 ,65 ,67,69 ,72, 102, 125,126,130-133,172-175,178-182, 191-194,206,210,211,21 7,250 CytotoxicT lymphocyte(CTL ) 126,146, 154,1 72,174,175,178,180,181, 191,193 ,194,197.199,201 -203,205 , 207-210,213 ,21 7-222,248,250

B

D

Bacillus antbracis 66, 84-86,97 Bacterial artificial chromosome (BAC) 23, 121,123,125,128 Bacterial ghost 160, 164 Bacterial infection 63,69 ,71 ,74,90-93,96, 103,105 , 110, 112 Bacterial toxin 179

Delivery 33,37,39,41,43,59,85,118, 120-123,125 ,126,128-132,145,146, 152,154,159,167.168 ,174,182, ＲｾＰＷＬＹＭＱ

Dendrimer 38,41

ＬＲＱＹ ＬＲＰ

254

Dendritic cell 56.63.64.67.71.72. 121. 125-127.131.163,171.194.195 DISC 126 DNA-basedvaccine 218 Drift 244.250 Drug 1-8,10,11.13,17-19.22-24.28-30. 32-35.37-44.47.49,51,57-59.64.67, 92-95.101.105-111.125.129.130.133. 159.160,163.164.167-169.178.219. 221 Drugdiscovery 1,2.6.11.13.17-19.22-24. 29.30.32-35,37-43

E Earlygene 120,130,131 Env 125,126,189,191,195-199,202-205, 210,212-221,223 Enzyme reactor 160,168 Epidemic 105.189,191.244.245.248

F Fab 30.32.34.101,102.108 Flu 243. 245. 247 Fullerene 37,38.42 Fusionprotein 28-30,32.58.66,69,101. 108,126,129,130.131,164.176,203 . 204

G Gancyclovir 131-133 Genetherapy 118,121.123.125.127-130. 134 Gene transfer 24. 120.123. 128.129, 133. 159.162.166.167

H Hemagglutinin 66.174,180.243 Herpes simplex virus 118.119,206 High performance liquid chromatography (HPLC) 22 High-throughputscreening (HTS) 13, 17. 21.30 .41, 82, 83 Hit 17,29 HIV/AlDS 189,191.200,201.206,216. 221.223 Horizontal genetransfer 24. 159. 162. 167

PharmaceuticalBiotechnology

Humoral 146.149.152-154,166.167.174, 177,178,180-182.189,195.199,201. ＲｾＱＰＮＷ

ＭＲＱＹＬＰＵ

Hybridoma 29.30.33,34.50.98 .100,103. 105 Hypermutation 34,51.54-57.100 Hypervariable 199

I ICP34.5 122,123.126,131-133 Immediate earlygene 130 Immunemodulator 175 Immunity 55,63.68,72,74.82.90,91.110, 112,120.125,127,130,145,146,159. 160.163,166,171.172,175,181,182. 191.193-195.197-199,201.204-211. 217-219.221-223,244,247 .248,250 Immunization 30.34. 50. 55,81, 82. 85, 91, 92,100.103,110.125,126,149.150. 152.154,163.166,177,195,198,199, 201,202,205.206.208-211.217.219, 222,223.245 -248,250 Immunogen 34.90.126,146.152.178,196. 198.206.207.216 Immunogenicity 30.33.50.57,59.60,83. 97,98.126,145.150.152.159.167, 171.172.1 74,177.180,197.199.203, 204.206.208-211,217-222.243 .244. 246-248,250 Immunoglobulin 28.34.51,52,54.55,63. 72.95,98,100.101,181.192,202 Immunology 212 Inactivated vaccine 146, 159.163 Infectedcellprotein (ICP) 122 Infectious disease 13.17,19,63.64,67.68, 69.71,72,81.90-92,99.102,103,105. 110,118,120.133,145,171,172.178, 210 Influenza 66,72,82.107.108.146.147. 152,153,174,176.180,243-250 Innate immunity 55.68.74,193,194 Intranasal 178,180,205,245.248

L Lategene 120 Latency 120. 126,127,129. 133 Lead 3.4.13.17-19.23.29.30.38.40.44. 45,49 ,51.57-59.74.83,85.86.103,

255

Index

110,123,126,129,130,133,146.153. 160,169,172-175.181.244,246 Library 17,18,21-24.31,32,34,40,41,52, 57.96-98,100,105,194,199 Lipopeptide 14-16,66.173,176,177,217 Long-termnonprogressors (LTNPs) 191, 193,194,198.222 Lymphocyte 29,39.52,54.55,146.191, 195,202.203.205,250

M Macrophage-activating lipopeptideof2 kD (MALP-2) 173.176 .177 Metagenomes 23 MF59 171,174,212.247 Microbialdiversity 19,20.23 Microbialextract 21 Microorganism 13,19-21.23.24,64.69, 81-88,102,175.210.222 Microparticle 161.209,212 ,219.220 Monoclonalantibody 28.29 ,32-34, SO, 59, 90-92, 95, 98-103. 105, 108-110,112, 123 MonophosphorillipidA(MPL) 173.177 Mucosal 69. 126, 150, 152, 160. 163, 166, 167.171-173. 177-182. 189,205 -211. 217-223.243.247,248 Mucosal administration 167,220 Mucosal immunity 209,247,248 Multi-component 223 Muramyldipeptide 173,181

N Nanobiosensor 37 Nanobiotechnology 37,38,42,43 Nanofluidics 38, 41 Nanomaterials 38,39.41, 42 Nanoparticle 37-39.41-43,206 Nanoproteomics 38, 39 Nanotechnology 37.39 ,42.43 Nativebiologics 28-30,32 Natural product 1, 13, 17-21,23, 24 Nervoussystem 6,9 ,46. 118, 120. 123, 127, 129,132 Neuraminidase 243 Neurotensin receptor 44,45.47 Neurotrophic factor 128. 129

Neutralizing 8,29,90.102,105 ,151.152. 192-199,217.223,246 Nicotinic 44-46 NMDA receptor 44.47 Norepinephrinetransporter (NET) 44- 47 Nosocomialpathogen 105. 111

o Oncolyticvector 132 Optimization 21,30 ,31.38-40,174.222

p Pain 44-47,129.172,173,178 Painpathway 44-46 Pandemic 189,191,243-248.250 Pan-genome 85,87.88 Passive vaccination 90-92 rca 29-32.101,163 Peptide 32.34.39,40.44-47.69,96,98. 101,127 ,164.174.181.194,199.206, 207.210,215.219.250 Personalized medicine 2,37,42.43 Phagedisplay 30,32.34, SO. 57. 59, 100. 101 Porphyromonasgingivalis 57,70.84 Prime-boost 126,146,207,210,214,217. 219-221.223 Probiotic 85.159.160,168,169 Protection 71.81 -83.85.88,91, 92, 98. 103.105.107.112.126,129.145, 146.149.151-153.163.166.180 .181, 191.193-198.205-207,210,217-219, 221-223.243.244,246-250

R Receptor 2,4,8. 10. 17.28,29 .32,34, 38-42.44-47,49.51,52,55,59,60, 63-67.70,86.91,94.98,101,102, 105, 107.108,127,129-131,163.171.175, 176.179-181.192.193.195.196.199, 201, 202, 211, 249. Recombinant 29,30.33,34,49.51,57,81 , 91.92,95-98.101,105.109,118.123, 124.126-128.130,132,133.148.150 , 152.153.166,167,205.207.210,211. 217.219.220,221,246 Replication competent vector 129, 131

Pharmauuticalｂｪｯｴｾ｣ｨｮｬｧｹ

256

Replicationdefective vector 126 Reversevaccinology 81-85,87,88,96,199 Ribonucleotidereductase 122,127,129, 131,132 Ribosome display 32

s Saponin 173,174 Secondarymetabolites 13, 14,21,23 Serumtherapy 99,103,104 Shift 1,24,41,244 Signaling 4,5,10,37,63,64,65,67,69-71, 73,74,171,175,179,182,247,248 Single-chain 30, 58 Single nucleotidepolymorphism 5, 63, 64 Sodium channel 44-46 Source 2,4, 13, 19,21,23,29,30,34,39,44, 52,58,66,67,100,105,149,169,176 Specificity 8,10,17,29,44,46,50,55, 57-59,67,100-102,159,179,180,191, 192,195,197 Splitvaccine 244, 245 Stability 23, 29, 30,44, 56, 57, 59, 60, 86, 122,126,127,167,199,207,209,219, 248,250 Streptococcus agalactiae 81, 84 Streptococcus pneumoniae 19,68, 84, 86, 98 Streptococcus pyogene 84, 86, 103 Subtractive genomeanalysis 85 Subunit 13-16,32,65,81,82,90-92,95,98, 112,122,128,129,131,145,146,150, 152,154,163,167,171,172,179,180, 182,198,201,205-207,218,244,245, 247,248 Suicidegene 129-131 Synthetic 13,17,18,33,42,47,57,66,67, 72,98,100,164,175-178,181,182, 199,217,222

T Target 1-11,13-17,21, 23, 24, 29, 30, 32, 37-42,44,46,47,49-51,55-59,65,68, 74,82,90-103,105-112,128,129,131, 134,147,152,163,164,166-168,171, 174,175,177,179,181,182,193,195, 198,201,202,205-207,217-219,221, 247,249

Targeting 5,24,28,34,38,39,51,57-59,95, 103,108,130,134,149,154,159,168, 173,174,180,182,193,195,199,201, 202,206,209,219,220,223,250 Targetvalidation 1,3,4,6-8, 11 Tat 126,189,193,199-204,218,220,221, 223 Thymidinekinase 122 Toll-like receptor (TLR) 63, 64, 66, 67, 70, 163,171,176 TLRagonist 68,74,175 Translational medicine 1-3,5,7-9, 11 Trial 5,33,43,45,47,50,71-73,92,100, 127,129,131-133,149-152,174,178, 189,191,194,198-200,202-207, 210-219,221-223 Tumor 5,33,50,57,59,65,66,101-103, 105,108,120,122,123,125,126, 129-134,159,174,176,178-182,210

v Vaccine 64,68,69,71-73, 81-88,90-92, 96-98,110,112,118,123,125-127,130, 132-134,145-152,154,159,160,162, 163,166,167,169,171-175,177-182, 189,191-223,243-250 Vector 23,101,118,120-123,125-134,150, 197,198,202-211,217-223,246 Venom 44,91 Viralvector 122, 125, 128, 197,205,207, 211,217,218,220,221,246 Virion host shut-off 122, 123, 127 Virosome 174,206,245,247 Virus-like particle (Vhs) 145-154,220

y Yeast display 32,101