Keynote review: Structural biology and drug discovery

[1]  Eric F. Johnson,et al.  The Structure of Human Microsomal Cytochrome P450 3A4 Determined by X-ray Crystallography to 2.05-Å Resolution* , 2004, Journal of Biological Chemistry.

[2]  Stanislav Miertus,et al.  Combinatorial chemistry and high-throughput screening in drug discovery: Different strategies and formats , 2004, Molecular Diversity.

[3]  T. Blundell,et al.  Comparative protein modelling by satisfaction of spatial restraints. , 1993, Journal of molecular biology.

[4]  J Moult,et al.  Analysis of the steric strain in the polypeptide backbone of protein molecules , 1991, Proteins.

[5]  R Miller,et al.  Optimizing Shake-and-Bake for proteins. , 1999, Acta crystallographica. Section D, Biological crystallography.

[6]  Paul D Lyne,et al.  Structure-based virtual screening: an overview. , 2002, Drug discovery today.

[7]  B. Shoichet,et al.  Soft docking and multiple receptor conformations in virtual screening. , 2004, Journal of medicinal chemistry.

[8]  T. O'Brien,et al.  Fragment-based drug discovery. , 2004, Journal of medicinal chemistry.

[9]  William R. Taylor,et al.  A structural model for the retroviral proteases , 1987, Nature.

[10]  M. Swindells,et al.  Protein clefts in molecular recognition and function. , 1996, Protein science : a publication of the Protein Society.

[11]  Bernhard Rupp High-throughput crystallography at an affordable cost: the TB Structural Genomics Consortium Crystallization Facility. , 2003, Accounts of chemical research.

[12]  Tom L. Blundell,et al.  Insulin: The Structure in the Crystal and its Reflection in Chemistry and Biology by , 1972 .

[13]  T. Blundell Structure-based drug design. , 1996, Nature.

[14]  D. Diller,et al.  Kinases, homology models, and high throughput docking. , 2003, Journal of medicinal chemistry.

[15]  T L Blundell,et al.  FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. , 2001, Journal of molecular biology.

[16]  Christopher W Murray,et al.  Fragment-based lead discovery using X-ray crystallography. , 2005, Journal of medicinal chemistry.

[17]  Lance Stewart,et al.  High-throughput crystallization and structure determination in drug discovery. , 2002, Drug discovery today.

[18]  Peter Traxler,et al.  Phenylamino-pyrimidine (PAP) — derivatives: a new class of potent and highly selective PDGF-receptor autophosphorylation inhibitors , 1996 .

[19]  Krystal J Alligood,et al.  A Unique Structure for Epidermal Growth Factor Receptor Bound to GW572016 (Lapatinib) , 2004, Cancer Research.

[20]  D. Fabbro,et al.  Discovery of a potent and selective protein kinase CK2 inhibitor by high-throughput docking. , 2003, Journal of medicinal chemistry.

[21]  John P. Overington,et al.  X-ray analysis of HIV-1 proteinase at 2.7 Å resolution confirms structural homology among retroviral enzymes , 1989, Nature.

[22]  T. Blundell,et al.  Knowledge based modelling of homologous proteins, Part I: Three-dimensional frameworks derived from the simultaneous superposition of multiple structures. , 1987, Protein engineering.

[23]  D W Cushman,et al.  Design of potent competitive inhibitors of angiotensin-converting enzyme. Carboxyalkanoyl and mercaptoalkanoyl amino acids. , 1977, Biochemistry.

[24]  H. Jhoti,et al.  Structure-based screening of low-affinity compounds. , 2002, Drug discovery today.

[25]  A. W. Dean,et al.  Solution‐Phase Combinatorial Chemistry in Lead Discovery , 1998 .

[26]  John P. Overington,et al.  Alignment and searching for common protein folds using a data bank of structural templates. , 1993, Journal of molecular biology.

[27]  James F Blake,et al.  Structure-based generation of viable leads from small combinatorial libraries. , 2004, Current opinion in drug discovery & development.

[28]  Thomas Lengauer,et al.  Flexible docking under pharmacophore type constraints , 2002, J. Comput. Aided Mol. Des..

[29]  M. Congreve,et al.  Fragment-based lead discovery , 2004, Nature Reviews Drug Discovery.

[30]  J. Whisstock,et al.  Protein structural alignments and functional genomics , 2001, Proteins.

[31]  B. Shoichet,et al.  Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B. , 2002, Journal of medicinal chemistry.

[32]  D. Kostrewa,et al.  Novel inhibitors of DNA gyrase: 3D structure based biased needle screening, hit validation by biophysical methods, and 3D guided optimization. A promising alternative to random screening. , 2000, Journal of medicinal chemistry.

[33]  R. Spencer,et al.  High-throughput screening of historic collections: observations on file size, biological targets, and file diversity. , 1998, Biotechnology and bioengineering.

[34]  George M Sheldrick,et al.  [37] Patterson superposition and ab initio phasing. , 1997, Methods in enzymology.

[35]  Tom L Blundell,et al.  High-throughput X-ray crystallography for drug discovery. , 2004, Current opinion in pharmacology.

[36]  O. Witte,et al.  The BCR-ABL story: bench to bedside and back. , 2004, Annual review of immunology.

[37]  L. Pustilnik,et al.  Inhibition of epidermal growth factor receptor-associated tyrosine phosphorylation in human carcinomas with CP-358,774: dynamics of receptor inhibition in situ and antitumor effects in athymic mice. , 1999, The Journal of pharmacology and experimental therapeutics.

[38]  K. Parang,et al.  Design strategies for protein kinase inhibitors. , 2004, Current opinion in drug discovery & development.

[39]  J. Irwin,et al.  Lead discovery using molecular docking. , 2002, Current opinion in chemical biology.

[40]  Aled Edwards,et al.  High-throughput protein crystallization. , 2003, Journal of structural biology.

[41]  A. Hopkins,et al.  Ligand efficiency: a useful metric for lead selection. , 2004, Drug discovery today.

[42]  Philip M. Dean,et al.  A validation study on the practical use of automated de novo design , 2002, J. Comput. Aided Mol. Des..

[43]  L. Wodicka,et al.  A small molecule–kinase interaction map for clinical kinase inhibitors , 2005, Nature Biotechnology.

[44]  P J Goodford,et al.  COMPOUNDS DESIGNED TO FIT A SITE OF KNOWN STRUCTURE IN HUMAN HAEMOGLOBIN , 1976, British journal of pharmacology.

[45]  Ajay,et al.  The SHAPES strategy: an NMR-based approach for lead generation in drug discovery. , 1999, Chemistry & biology.

[46]  K. Büssow,et al.  An automated method for high-throughput protein purification applied to a comparison of His-tag and GST-tag affinity chromatography , 2003, BMC biotechnology.

[47]  Philip M Dean,et al.  De novo drug design: integration of structure-based and ligand-based methods. , 2004, Current opinion in drug discovery & development.

[48]  P. Goodford,et al.  THE INTERACTION OF HUMAN HAEMOGLOBIN WITH ALLOSTERIC EFFECTORS AS A MODEL FOR DRUG‐RECEPTOR INTERACTIONS , 1980, British journal of pharmacology.

[49]  Christopher W Murray,et al.  Identification of novel p38alpha MAP kinase inhibitors using fragment-based lead generation. , 2005, Journal of medicinal chemistry.

[50]  D. M. Ryan,et al.  Rational design of potent sialidase-based inhibitors of influenza virus replication , 1993, Nature.

[51]  A. Hopkins,et al.  The druggable genome , 2002, Nature Reviews Drug Discovery.

[52]  K Fujikawa,et al.  The coagulation cascade: initiation, maintenance, and regulation. , 1991, Biochemistry.

[53]  Robin Taylor,et al.  A new test set for validating predictions of protein–ligand interaction , 2002, Proteins.

[54]  O. Lichtarge,et al.  Evolutionary predictions of binding surfaces and interactions. , 2002, Current opinion in structural biology.

[55]  P. Argos,et al.  Strain in protein structures as viewed through nonrotameric side chains: II. effects upon ligand binding , 1999, Proteins.

[56]  B. L. Sibanda,et al.  Three-dimensional structure, specificity and catalytic mechanism of renin , 1983, Nature.

[57]  John P. Overington,et al.  Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction , 1990, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[58]  M. Sternberg,et al.  Prediction of protein secondary structure and active sites using the alignment of homologous sequences. , 1987, Journal of molecular biology.

[59]  Konrad Büssow,et al.  Facilities and methods for the high-throughput crystal structural analysis of human proteins. , 2003, Accounts of chemical research.

[60]  Jürgen Bajorath,et al.  Integration of virtual and high-throughput screening , 2002, Nature Reviews Drug Discovery.

[61]  P. Hajduk,et al.  Discovering High-Affinity Ligands for Proteins: SAR by NMR , 1996, Science.

[62]  Teruki Honma,et al.  Recent advances in de novo design strategy for practical lead identification , 2003, Medicinal research reviews.

[63]  J J Baldwin,et al.  Thienothiopyran-2-sulfonamides: novel topically active carbonic anhydrase inhibitors for the treatment of glaucoma. , 1989, Journal of medicinal chemistry.

[64]  E. Lindahl,et al.  Identification of related proteins on family, superfamily and fold level. , 2000, Journal of molecular biology.

[65]  M C Peitsch,et al.  Protein modelling for all. , 1999, Trends in biochemical sciences.

[66]  Dale J. Kempf,et al.  ABT-378, a Highly Potent Inhibitor of the Human Immunodeficiency Virus Protease , 1998, Antimicrobial Agents and Chemotherapy.

[67]  G. Klebe,et al.  DrugScore meets CoMFA: adaptation of fields for molecular comparison (AFMoC) or how to tailor knowledge-based pair-potentials to a particular protein. , 2002, Journal of medicinal chemistry.

[68]  M. DePristo,et al.  Heterogeneity and inaccuracy in protein structures solved by X-ray crystallography. , 2004, Structure.

[69]  Michal Vieth,et al.  SDOCKER: a method utilizing existing X-ray structures to improve docking accuracy. , 2004, Journal of medicinal chemistry.

[70]  J M Thornton,et al.  Three-dimensional structure analysis of PROSITE patterns. , 1999, Journal of molecular biology.

[71]  W G Laver,et al.  Structure-activity relationship studies of novel carbocyclic influenza neuraminidase inhibitors. , 1998, Journal of medicinal chemistry.

[72]  D. T. Jones,et al.  A new approach to protein fold recognition , 1992, Nature.

[73]  D E McRee,et al.  Mammalian microsomal cytochrome P450 monooxygenase: structural adaptations for membrane binding and functional diversity. , 2000, Molecular cell.

[74]  M Stahl,et al.  Structure-based library design: molecular modelling merges with combinatorial chemistry. , 2000, Current opinion in chemical biology.

[75]  Jonathan W. Essex,et al.  A review of protein-small molecule docking methods , 2002, J. Comput. Aided Mol. Des..

[76]  D Eisenberg,et al.  A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence. , 1997, Journal of molecular biology.

[77]  T. Blundell,et al.  Distinguishing structural and functional restraints in evolution in order to identify interaction sites. , 2004, Journal of molecular biology.

[78]  John A. Lowe,et al.  A guide to drug discovery: The role of the medicinal chemist in drug discovery — then and now , 2004, Nature Reviews Drug Discovery.

[79]  Amos Bairoch,et al.  The PROSITE database, its status in 1999 , 1999, Nucleic Acids Res..

[80]  J. Bajorath,et al.  Docking and scoring in virtual screening for drug discovery: methods and applications , 2004, Nature Reviews Drug Discovery.

[81]  Thomas Lengauer,et al.  FlexE: efficient molecular docking considering protein structure variations. , 2001, Journal of molecular biology.

[82]  Andrew J. Sharff HIGH THROUGHPUT CRYSTALLOGRAPHY ON AN IN-HOUSE SOURCE, USING ACTOR , 2003 .

[83]  Clive McCarthy,et al.  Mapping the kinase domain of Janus Kinase 3. , 2003, Bioorganic & medicinal chemistry letters.

[84]  Steven W Muchmore,et al.  Crystallography, NMR and virtual screening: integrated tools for drug discovery. , 2003, Current opinion in drug discovery & development.

[85]  Darren R. Flower,et al.  Drug design : cutting edge approaches , 2002 .

[86]  Bohdan Waszkowycz,et al.  PRO_SELECT: combining structure-based drug design and array-based chemistry for rapid lead discovery. 2. The development of a series of highly potent and selective factor Xa inhibitors. , 2002, Journal of medicinal chemistry.

[87]  Ajay N. Jain,et al.  Virtual screening in lead discovery and optimization. , 2004, Current opinion in drug discovery & development.

[88]  Jan Pieter Abrahams,et al.  The prospects of protein nanocrystallography. , 2002, Acta crystallographica. Section D, Biological crystallography.

[89]  A. Jeltsch,et al.  High-throughput purification of polyHis-tagged recombinant fusion proteins. , 2003, Methods in molecular biology.

[90]  A Wlodawer,et al.  Structure of complex of synthetic HIV-1 protease with a substrate-based inhibitor at 2.3 A resolution. , 1989, Science.

[91]  Anastassis Perrakis,et al.  Automated protein model building combined with iterative structure refinement , 1999, Nature Structural Biology.

[92]  N. Chayen,et al.  Protein crystallization for genomics: towards high-throughput optimization techniques. , 2002, Acta crystallographica. Section D, Biological crystallography.

[93]  R. Dolle Comprehensive survey of combinatorial library synthesis: 2000. , 2001, Journal of combinatorial chemistry.

[94]  A Abrahamsson,et al.  The direct thrombin inhibitor melagatran and its oral prodrug H 376/95: intestinal absorption properties, biochemical and pharmacodynamic effects. , 2001, Thrombosis research.

[95]  John P. Overington,et al.  Knowledge‐based protein modelling and design , 1988 .

[96]  Ceslovas Venclovas,et al.  Assessment of progress over the CASP experiments , 2003, Proteins.

[97]  N C Cohen,et al.  Generation of new-lead structures in computer-aided drug design. , 1995, Progress in drug research. Fortschritte der Arzneimittelforschung. Progres des recherches pharmaceutiques.

[98]  Adam Godzik,et al.  Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[99]  Jürg Zimmermann,et al.  Potent and Selective Inhibitors of the AbL-Kinase: Phenylaminopyrimidine (PAP) Derivatives. , 1997 .

[100]  I. Kuntz,et al.  Molecular docking to ensembles of protein structures. , 1997, Journal of molecular biology.

[101]  Martin Stahl,et al.  Novel dihydrofolate reductase inhibitors. Structure-based versus diversity-based library design and high-throughput synthesis and screening. , 2003, Journal of medicinal chemistry.

[102]  R. Abagyan,et al.  Predictions of protein flexibility: First‐order measures , 2004, Proteins.

[103]  T. Sawasaki,et al.  High-throughput, genome-scale protein production method based on the wheat germ cell-free expression system. , 2003, Biotechnology advances.

[104]  R Abagyan,et al.  High-throughput docking for lead generation. , 2001, Current opinion in chemical biology.

[105]  Anastassis Perrakis,et al.  Current state of automated crystallographic data analysis , 2000, Nature Structural Biology.

[106]  S. P. Chambers High-throughput protein expression for the post-genomic era. , 2002, Drug discovery today.

[107]  Vicki L. Nienaber,et al.  Discovering novel ligands for macromolecules using X-ray crystallographic screening , 2000, Nature Biotechnology.

[108]  J F Davies,et al.  Viracept (nelfinavir mesylate, AG1343): a potent, orally bioavailable inhibitor of HIV-1 protease. , 1997, Journal of medicinal chemistry.

[109]  David C. Jones,et al.  GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. , 1999, Journal of molecular biology.

[110]  M. Murcko,et al.  Crystal Structure of HIV-1 Protease in Complex with Vx-478, a Potent and Orally Bioavailable Inhibitor of the Enzyme , 1995 .

[111]  J. Greer,et al.  Automated crystal mounting and data collection for protein crystallography. , 2000, Structure.

[112]  Jose Cosme,et al.  Crystal Structures of Human Cytochrome P450 3A4 Bound to Metyrapone and Progesterone , 2004, Science.

[113]  A. Gill,et al.  New lead generation strategies for protein kinase inhibitors - fragment based screening approaches. , 2004, Mini reviews in medicinal chemistry.

[114]  S F Campbell,et al.  Science, art and drug discovery: a personal perspective. , 2000, Clinical science.

[115]  Jean-Pierre Marquette,et al.  SAR and X-ray. A new approach combining fragment-based screening and rational drug design: application to the discovery of nanomolar inhibitors of Src SH2. , 2002, Journal of medicinal chemistry.

[116]  T Lengauer,et al.  The particle concept: placing discrete water molecules during protein‐ligand docking predictions , 1999, Proteins.

[117]  J. Varghese,et al.  Development of neuraminidase inhibitors as anti‐influenza virus drugs , 1999 .

[118]  Roland E Dolle,et al.  Comprehensive survey of combinatorial library synthesis: 2003. , 2004, Journal of combinatorial chemistry.

[119]  D. Fabbro,et al.  Structural insights into the conformational selectivity of STI-571 and related kinase inhibitors. , 2004, Current opinion in drug discovery & development.

[120]  Zhan Deng,et al.  Interaction profiles of protein kinase-inhibitor complexes and their application to virtual screening. , 2005, Journal of medicinal chemistry.

[121]  Jeffrey W. Peng,et al.  Leveraging structural approaches: applications of NMR-based screening and X-ray crystallography for inhibitor design. , 2004, Journal of synchrotron radiation.

[122]  Matthew P. Repasky,et al.  Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. , 2004, Journal of medicinal chemistry.

[123]  Todd J. A. Ewing,et al.  DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases , 2001, J. Comput. Aided Mol. Des..

[124]  A M Lesk,et al.  Domain closure in mitochondrial aspartate aminotransferase. , 1992, Journal of molecular biology.

[125]  Jürg Zimmermann,et al.  Potent and selective inhibitors of the Abl-kinase: phenylamino-pyrimidine (PAP) derivatives , 1997 .