Frontiers in Drug Design and Discovery

Volume 3

by

Atta-ur-Rahman, Gary W. Caldwell, Mohammad Iqbal Choudhary, Mark R. Player

DOI: 10.2174/97816080520111070301
eISBN: 978-1-60805-201-1, 2007
ISBN: 978-1-60805-671-2
ISSN: 1574-0889

  
  




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Table of Contents

Editorial: Structure-Based Drug Design in the 21st Century , Pp. i-iii (3)

Atta-ur-Rahman, M. Iqbal Choudhary, Gary W. Caldwell and Mark R. Player
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Alpha-Helix Mimetics: Progress Toward Effective Modulation of Protein-Protein Complexes , Pp. 5-44 (40)

Daniel J. Parks and Mark R. Player
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Structures of HIV Protease Guide Inhibitor Design to Overcome Drug Resistance , Pp. 45-62 (18)

Irene T. Weber, Andrey Y. Kovalevsky and Robert W. Harrison
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Structure and Function of G Protein-Coupled Receptors Studied Using Sequence Analysis, Molecular Modeling and Receptor Engineeri , Pp. 63-79 (17)

Stefano Costanzi, Andrei A. Ivanov, Irina G. Tikhonova and Kenneth A. Jacobson
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Virtual Docking: How Are We Doing And How Can We Improve? , Pp. 81-103 (23)

Renee L. DesJarlais, Maxwell D. Cummings and Alan C. Gibbs
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Fragment-Based Lead Discovery by NMR , Pp. 105-119 (15)

Markus Schade
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Targeting Drug Resistant Mutations Using Novel Binding Interactions - Lessons Learned from Abl-T315I and their Implications in D , Pp. 121-144 (24)

Glen Noronha, Jianguo Cao, Chun Chow, Elena Dneprovskaia, Linda Hwang, Dan Lohse, Chi Ching Mak, Andrew McPherson, Richard M. Fine, Xinshan Kang, Boris Klebansky, Moorthy S.S. Palanki, Ved P. Pathak, Joel Renick, Richard Soll and Binqi Zeng
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Recent Advances in the Structure-Guided Design of Protein Kinase Inhibitors , Pp. 145-170 (26)

Campbell McInnes
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Fragment-Based Approaches to Lead Discovery , Pp. 171-202 (32)

Daniel F. Wyss and Hugh L. Eaton
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Recent Advances in Structure-Based Design of Nuclear Hormone Receptors , Pp. 203-224 (22)

Ronald L. Magolda, William S. Somers and Rayomand J. Unwalla
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Structure-Based Drug Development Against Malaria , Pp. 225-255 (31)

Kathrin Buchholz, Boniface Mwongela Mailu, R. Heiner Schirmer and Katja Becker
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Virtual Screening of Compound Libraries Using In silico Three Dimensional Pharmacophores to Aid the Discovery and Design of Anti , Pp. 257-292 (36)

Apurba K. Bhattacharjee
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DNA Helicases Implicated in Chromosomal Instability Disorders as Targets for the Discovery of Novel Anti-Cancer Agents , Pp. 293-316 (24)

Rigu Gupta and Robert M. Brosh
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Scoring Functions for Virtual Screening , Pp. 317-379 (63)

Francesca Spyrakis, Glen E. Kellogg, Alessio Amadasi and Pietro Cozzini
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Reactivators of Tabun-Inhibited Acetylcholinesterase: Structure-Biological Activity Relationship , Pp. 381-394 (14)

Kamil Kuca, Daniel Jun, Kamil Musilek and Jiri Bajgar
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Peptide Diversity in Drug Discovery , Pp. 395-432 (38)

Marian P. Brennan, Dermot Cox and Anthony J. Chubb
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Protection of Neurovascular Injury by Vasoprotective Agents: A Novel Therapeutic Strategy for Ischemic Brain Edema , Pp. 433-454 (22)

Feng Han, Norifumi Shioda, Yasufumi Shirasaki and Kohji Fukunaga
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Protein Flexibility and Mobility in Structure-Based Drug Design , Pp. 455-476 (22)

Aqeel Ahmed, Sina Kazemi and Holger Gohlke
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Structure-Based Virtual Screening , Pp. 477-502 (26)

György M. Keseru
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Computer-Aided Engineering of GPCRS and Its Application to Drug Discovery , Pp. 503-523 (21)

Antonio Lavecchia
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Antibody-Drug Conjugates in Targeted Therapy for Cancer , Pp. 525-537 (13)

Ruoping Tang, Simy Cohen, Ollivier Legrand and Jean-Pierre Marie
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Structure-Activity Relationships in Peptides: from Modelling to Rational Drug Design , Pp. 539-558 (20)

Ettore Benedetti, Carlo Pedone and Michele Saviano
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Rational Design Strategies for the Development of Synthetic Quinoline and Acridine Based Antimalarials , Pp. 559-609 (51)

Michael J. Dascombe, Michael G.B. Drew, Philip G. Evans and Fyaz M.D. Ismail
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Contributors , Pp. 611-617 (7)

Atta-ur-Rahman, Gary W. Caldwell, M. Iqbal Choudhary and Mark R. Player
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Subject Index to Volume 3 , Pp. 619-634 (16)

Atta-ur-Rahman, Gary W. Caldwell, M. Iqbal Choudhary and Mark R. Player
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List of Contributors

Co-Editor(s):
Prof. Atta-ur-Rahman FRS
Federal Minister & Advisor to the Prime Minister on Science and Technology
H.E.J Research Institute of Chemistry, International Center for Chemical Sciences
Ebook XML verification This Week Yes
Karachi, 75270
Pakistan


Gary W. Caldwell
Senior Research Fellow, Drug Discovery, Johnson & Johnson Pharmaceutical Research & Development LLC
Welsh & McKean Roads, PO Box 776
Spring House
PA , 19477
USA


Mohammad Iqbal Choudhary
Director (Acting), H.E.J. Research Institute of Chemistry, International Center for Chemical Sciences
University of Karachi
Karachi , 75270
Pakistan


Mark R. Player
Team Leader, Lead Generation Chemistry, Research & Early Development, Johnson & Johnson Pharmaceutical Research & Development L.L.C.
665 Stockton Dr. Exton
PA , 19341
USA




Contributor(s):
Daniel J. Parks
Johnson & Johnson Pharmaceutical Research and Development
665 Stockton Drive
Exton
PA, 19341
USA


Mark R. Player
Johnson & Johnson Pharmaceutical Research and Development
665 Stockton Drive
Exton
PA, 19341
USA


Irene T. Weber
Department of Biology
Georgia State University
402 Kell Hall, 24 Peachtree Center Avenue
Atlanta
GA, 30303
USA


Andrey Y. Kovalevsky
Department of Biology
Georgia State University
402 Kell Hall, 24 Peachtree Center Avenue
Atlanta
GA, 30303
USA


Robert W. Harrison
Department of Computer Science
Georgia State University
Suite 1440, 34 Peachtree Street
Atlanta
GA, 30303
USA


Stefano Costanzi
Laboratory of Biological Modeling
National Institute of Diabetes & Digestive & Kidney Diseases
National Institutes of Health, 12A Center Drive, Rm 4051
Bethesda
MD, 20892-5621
USA


Andrei A. Ivanov
Molecular Recognition Section, LBC
National Institute of Diabetes & Digestive & Kidney Diseases
National Institutes of Health, 12A Center Drive, Rm 4051
Bethesda
MD, 20892-0810
USA


Irina G. Tikhonova
Laboratory of Biological Modeling
National Institute of Diabetes & Digestive & Kidney Diseases
National Institutes of Health, 12A Center Drive, Rm 4051
Bethesda
MD, 20892-5621
USA


Kenneth A. Jacobson
Chief Molecular Recognition Section, LBC
National Institute of Diabetes & Digestive & Kidney Diseases
National Institutes of Health, Bldg. 8A, Rm. B1A-19
Bethesda
MD, 20892-0810
USA


Renee L. DesJarlais
Johnson & Johnson Pharmaceutical Research and Development, LLC
665 Stockton Drive
Exton
PA, 19341
USA


Maxwell D. Cummings
Johnson & Johnson Pharmaceutical Research and Development, LLC
665 Stockton Drive
Exton
PA, 19341
USA


Alan C. Gibbs
Johnson & Johnson Pharmaceutical Research and Development, LLC
8 Clarke Drive
Cranbury
NJ, 08512
USA


Markus Schade
Combinature Biopharm AG
Robert-Roessle-Str. 10
Berlin, 13125
Germany


Glenn Noronha
TargeGen, Inc
9380 Judicial Drive
San Diego
CA, 92121
USA


Jianguo Cao
TargeGen, Inc
9380 Judicial Drive
San Diego
CA, 92121
USA


Chun Chow
TargeGen, Inc
9380 Judicial Drive
San Diego
CA, 92121
USA


Elena Dneprovskaia
TargeGen, Inc
9380 Judicial Drive
San Diego
CA, 92121
USA


Linda Hwang
TargeGen, Inc
9380 Judicial Drive
San Diego
CA, 92121
USA


Dan Lohse
TargeGen, Inc
9380 Judicial Drive
San Diego
CA, 92121
USA


Chi Ching Mak
TargeGen, Inc
9380 Judicial Drive
San Diego
CA, 92121
USA


Andrew McPherson
TargeGen, Inc
9380 Judicial Drive
San Diego
CA, 92121
USA


Richard M. Fine
BioPredict, Inc
Suite 201, 660 Kinderkamack Road
Oradell
NJ, 07649 -1525
USA


Xinshan Kang
BioPredict, Inc
Suite 201, 660 Kinderkamack Road
Oradell
NJ, 07649 -1525
USA


Boris Klebansky
BioPredict, Inc
Suite 201, 660 Kinderkamack Road
Oradell
NJ, 07649 -1525
USA


Moorthy S.S. Palanki
TargeGen, Inc
9380 Judicial Drive
San Diego
CA, 92121
USA


Ved P. Pathak
TargeGen, Inc
9380 Judicial Drive
San Diego
CA, 92121
USA


Joel Renick
TargeGen, Inc
9380 Judicial Drive
San Diego
CA, 92121
USA


Richard Soll
TargeGen, Inc
9380 Judicial Drive
San Diego
CA, 92121
USA


Binqi Zeng
TargeGen, Inc
9380 Judicial Drive
San Diego
CA, 92121
USA


Campbell McInnes
Pharmaceutical and Biomedical Sciences
South Carolina College of Pharmacy, University of South Carolina
Columbia
SC, 29063
USA


Daniel Wyss
Fellow - Chemical Research, Schering-Plough Research Institute
2015 Galloping Hill Road
Kenilworth
NJ, 07033
USA


Dawn A. Scott
New Lead Discovery, Schering Plough Research Institute
K-15-4 4920, 2015 Galloping Hill Road
Kenilworth
NJ, 07033
USA


Hugh L. Eaton
Schering-Plough Research Institute
2015 Galloping Hill Road
Kenilworth
NJ, 07033
USA


Ronald L. Magolda
Wyeth Research, PTN 1114
865 Ridge Road
Monmouth Junction
NJ, 08852-9514
USA


William S. Somers
Wyeth Research
200 CambridgePark Drive
Cambridge
MA, 02140
USA


Rayomand J. Unwalla
S-2421, Wyeth Research
500 Arcola Road
Collegeville
PA, 19426
USA


Boniface Mailu
Nutritional Biochemistry, Interdisciplinary Research Center
Justus-Liebig University Giessen
Heinrich-Buff-Ring 26- 32
Giessen, D-35392
Germany


Katja Becker
Nutritional Biochemistry, Interdisciplinary Research Center
Justus-Liebig University Giessen
Heinrich-Buff-Ring 26- 32
Giessen, D-35392
Germany


Kathrin Buchholz
Biochemistry Centre Heidelberg
Ruprecht-Karls University Heidelberg
Im Neuenheimer Feld 504
Heinrich-Buff-Ring 26-32
Heidelberg, D-69120
Germany


Heiner Schirmer
Biochemistry Centre Heidelberg
Ruprecht-Karls University Heidelberg
Im Neuenheimer Feld 504
Heidelberg, D-69120
Germany


Apurba K. Bhattacharjee
Department of Medicinal Chemistry, Division of Experimental Therapeutics
Walter Reed Army Institute of Research
503 Robert Grant Avenue
Silver Spring
MD, 20910
USA


Rigu Gupta
Laboratory of Molecular Gerontology
National Institute on Aging, NIH
5600 Nathan Shock Drive
Baltimore
MD, 21224
USA


Robert M. Brosh Jr
Laboratory of Molecular Gerontology
National Institute on Aging, NIH
5600 Nathan Shock Drive
Baltimore
MD, 21224
USA


Francesca Spyrakis
Department of Biochemistry and Molecular Biology
University of Parma
via G.P.Usberti, 23/A
Parma, 43100
Italy


Glen E. Kellogg
Department of Medicinal Chemistry & Institute for Structural Biology and Drug Discovery
Virginia Commonwealth University
800 East Leigh St., Suite 212, P.O. Box 980133
Richmond
VA, 23298-0540
US


Alessio Amadasi
Department of Biochemistry and Molecular Biology
University of Parma
via G.P.Usberti, 23/A
Parma, 43100
Italy


Pietro Cozzini
Molecular Modeling Laboratory, Department of General and Inorganic Chemistry
University of Parma
via G.P.Usberti, 17/A
Parma, 43100
Italy


Kamil Kuca
Center of Advanced Studies, Faculty of Military Health Sciences
University of Defence
Trebesska 1575
Trebesska 1575
Horeni 13, 400 96
Hradec Kralove, 500 01
Czech Republic


Daniel Jun
Center of Advanced Studies, Faculty of Military Health Sciences
University of Defence
Trebesska 1575
Trebesska 1575
Heyrovskeho 1203
Hradec Kralove
500 05, 500 01
Czech Republic


Kamil Musilek
Department of Toxicology
Faculty of Military Health Sciences, University of Defence
Trebesska 1575
Heyrovskeho 1203
Hradec Kralove, 500 01
Czech Republic


Jiri Bajgar
Department of Toxicology, Faculty of Military Health Sciences
University of Defence
Trebesska 1575
Hradec Kralove, 500 01
Czech Republic


Anthony J. Chubb
Centre for Synthesis and Chemical Biology, Department of Pharmaceutical and Medicinal Chemistry
Royal College of Surgeons inIreland
123 St Stephen’s Green, Dublin 2
Ireland


Marian P. Brennan
Molecular and Cellular Therapeutics
Royal College of Surgeons inIreland
123 St Stephen’s Green, Dublin 2
Ireland


Dermot Cox
Molecular and Cellular Therapeutics
Royal College of Surgeons inIreland
123 St Stephen’s Green, Dublin 2
Ireland


Feng Han
Department of Pharmacology
Tohoku University Graduate School of Pharmaceutical Sciences Aramaki-Aoba, Aoba-Ku
Sendai
Japan


Kohji Fukunaga
Department of Pharmacology
Tohoku University Graduate School of Pharmaceutical Sciences Aramaki-Aoba, Aoba-Ku
Sendai
Japan


Holger Gohlke
Department of Biological Sciences
Molecular Bioinformatics Group, J.W. Goethe-University
Max-von-Laue-Str. 9, 60438
Frankfurt
Germany


Aqeel Ahmed
Department of Biological Sciences, Molecular Bioinformatics Group
J.W. Goethe-University, Max-von-Laue-Str. 9
Frankfurt, 60438
Germany


Sina Kazemi
Department of Biological Sciences, Molecular Bioinformatics Group
J.W. Goethe-University, Max-von-Laue-Str. 9
Frankfurt, 60438
Germany


György M. Keser
Manager, Discovery Chemistry, API Research & Development
Gedeon Richter Plc., Gyömri út 19-21, H- 1103
Budapest
Hungary


Timea Polgar
Lead Discovery Unit, API Research & Development
Gedeon Richter Plc., Gyömri út 19-21, H- 1103
Budapest
Hungary


Antonio Lavecchia
Dipartimento Chimica Farmaceutica e Tossicologica
Università di Napoli "Federico II", via D. Montesano 49
Napoli, I-80131
Italy


Ruoping Tang
INSERM
Université Pierre et Marie Curie
U872 Equipe 18
Paris6, UMR S U872
1 place du Parvis de Notre-Dame, Paris6, UMR S U872
Paris, F-75006
France


Simy Cohen
INSERM
Université Pierre et Marie Curie
U872 Equipe 18
Paris6, UMR S U872
1 place du Parvis de Notre-Dame, Paris6, UMR S U872
Paris, F-75006
France


Ollivier Legrand
INSERM
Université Pierre et Marie Curie
U872 Equipe 18
Paris6, UMR S U872
1 place du Parvis de Notre-Dame, Paris6, UMR S U872
Paris, F-75006
France


Jean-Pierre Marie
INSERM
Université Pierre et Marie Curie
U872 Equipe 18
Paris6, UMR S U872
1 place du Parvis de Notre-Dame, Paris6, UMR S U872
Paris, F-75006
France


Michele Saviano
CNR- Istituto di Biostrutture e Bioimmagini
Via Mezzocannone, 16
Napoli, 80134
Italy


Ettore Benedetti
Department of Biological Sciences University of Napoli "Federico II"
Via Mezzocannone, 16
Napoli, 80134
Italy


Carlo Pedone
Department of Biological Sciences University of Napoli "Federico II"
Via Mezzocannone, 16
Napoli, 80134
Italy


Michael J. Dascombe
Faculty of Life Sciences
The University of Manchester
Stopford Building 1.124, Oxford Road, Manchester M13 9PT
Manchester , 80134
UK


Michael G.B. Drew
Department of Chemistry
University of Reading
Reading RG6 6AD
UK


Philip G. Evans
Department of Chemistry
University of Reading
Reading RG6 6AD
UK


Fyaz M.D. Ismail
The Medicinal Chemistry Research Group
The School of Pharmacy and Chemistry, Liverpool John Moores University
Reading RG6 6AD
Liverpool L3 3AF
UK




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