Use of Pharmacophores in Structure-Based Drug Design

[1]  R. Cramer,et al.  Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. , 1988, Journal of the American Chemical Society.

[2]  P. Willett,et al.  Effectiveness of retrieval in similarity searches of chemical databases: a review of performance measures. , 2000, Journal of molecular graphics & modelling.

[3]  A. Chamberlin,et al.  Blockers of human T cell Kv1.3 potassium channels using de novo ligand design and solid-phase parallel combinatorial chemistry. , 1999, Bioorganic & medicinal chemistry letters.

[4]  Weida Tong,et al.  QSAR Models Using a Large Diverse Set of Estrogens , 2001, J. Chem. Inf. Comput. Sci..

[5]  M C Nicklaus,et al.  HIV-1 integrase pharmacophore: discovery of inhibitors through three-dimensional database searching. , 1997, Journal of medicinal chemistry.

[6]  Mary E. McGrath,et al.  A structural role for hormone in the thyroid hormone receptor , 1995, Nature.

[7]  P. Goodford A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. , 1985, Journal of medicinal chemistry.

[8]  P. Chambon,et al.  Conformational adaptation of agonists to the human nuclear receptor RARγ , 1998, Nature Structural Biology.

[9]  A Palomer,et al.  Derivation of pharmacophore and CoMFA models for leukotriene D(4) receptor antagonists of the quinolinyl(bridged)aryl series. , 2000, Journal of medicinal chemistry.

[10]  D. Rognan,et al.  Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations. , 2000, Journal of medicinal chemistry.

[11]  Y. Pommier,et al.  Design and discovery of HIV-1 integrase inhibitors , 1997 .

[12]  Marvin Waldman,et al.  Application of structure‐based focusing to the estrogen receptor , 2001, J. Comput. Chem..

[13]  Zbigniew Dauter,et al.  Molecular basis of agonism and antagonism in the oestrogen receptor , 1997, Nature.

[14]  Osman F. Güner,et al.  Pharmacophore perception, development, and use in drug design , 2000 .

[15]  Carl R. Woese,et al.  Progress in Molecular and Subcellular Biology , 1969, Progress in Molecular and Subcellular Biology.

[16]  C. A. Stone,et al.  A new class of angiotensin-converting enzyme inhibitors , 1980, Nature.

[17]  Gerhard Klebe,et al.  What Can We Learn from Molecular Recognition in Protein–Ligand Complexes for the Design of New Drugs? , 1996 .

[18]  F. Bushman,et al.  Developing a dynamic pharmacophore model for HIV-1 integrase. , 2000, Journal of medicinal chemistry.

[19]  Kirsch,et al.  Virtual Screening for Bioactive Molecules by Evolutionary De Novo Design Special thanks to Neil R. Taylor for his help in preparation of the manuscript. , 2000, Angewandte Chemie.

[20]  F. Bushman,et al.  Human Immunodeficiency Virus Type 1 cDNA Integration: New Aromatic Hydroxylated Inhibitors and Studies of the Inhibition Mechanism , 1998, Antimicrobial Agents and Chemotherapy.

[21]  Robert Powers,et al.  Structure-based design of a novel, potent, and selective inhibitor for MMP-13 utilizing NMR spectroscopy and computer-aided molecular design , 2000 .

[22]  D. Goodsell,et al.  Automated docking of substrates to proteins by simulated annealing , 1990, Proteins.

[23]  L. Bladh,et al.  Pharmacophores incorporating numerous excluded volumes defined by X-ray crystallographic structure in three-dimensional database searching: application to the thyroid hormone receptor. , 1998, Journal of medicinal chemistry.

[24]  M. Gelb,et al.  Adenosine analogues as inhibitors of Trypanosoma brucei phosphoglycerate kinase: elucidation of a novel binding mode for a 2-amino-N(6)-substituted adenosine. , 2000, Journal of medicinal chemistry.

[25]  Ronan Bureau,et al.  Definition of a Pharmacophore for Partial Agonists of Serotonin 5-HT3 Receptors , 1999, J. Chem. Inf. Comput. Sci..

[26]  J M Blaney,et al.  A geometric approach to macromolecule-ligand interactions. , 1982, Journal of molecular biology.

[27]  J. Baldwin,et al.  An alpha-carbon template for the transmembrane helices in the rhodopsin family of G-protein-coupled receptors. , 1997, Journal of molecular biology.

[28]  Steven L. Teig,et al.  Chemical Function Queries for 3D Database Search , 1994, J. Chem. Inf. Comput. Sci..

[29]  C. Fraser,et al.  In vitro mutagenesis and the search for structure-function relationships among G protein-coupled receptors. , 1992, The Biochemical journal.

[30]  P Willett,et al.  Development and validation of a genetic algorithm for flexible docking. , 1997, Journal of molecular biology.

[31]  M. Karplus,et al.  Functionality maps of binding sites: A multiple copy simultaneous search method , 1991, Proteins.

[32]  Hans-Joachim Böhm,et al.  The computer program LUDI: A new method for the de novo design of enzyme inhibitors , 1992, J. Comput. Aided Mol. Des..

[33]  F. Bushman,et al.  Differential inhibition of HIV-1 preintegration complexes and purified integrase protein by small molecules. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

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

[35]  Thomas Lengauer,et al.  A fast flexible docking method using an incremental construction algorithm. , 1996, Journal of molecular biology.

[36]  Aalt Bast,et al.  Comprehensive medicinal chemistry , 1991 .

[37]  D. Davies,et al.  Three new structures of the core domain of HIV-1 integrase: an active site that binds magnesium. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[38]  M C Nicklaus,et al.  Discovery of HIV-1 integrase inhibitors by pharmacophore searching. , 1997, Journal of medicinal chemistry.

[39]  A. Baniahmad,et al.  Thyroid hormone receptors , 2002 .

[40]  V. Mikol,et al.  Crystal structures of the catalytic domain of HIV-1 integrase free and complexed with its metal cofactor: high level of similarity of the active site with other viral integrases. , 1998, Journal of molecular biology.

[41]  Hugo Kubinyi,et al.  3D QSAR in drug design : theory, methods and applications , 2000 .

[42]  A. Cavalli,et al.  A new class of nonsteroidal aromatase inhibitors: design and synthesis of chromone and xanthone derivatives and inhibition of the P450 enzymes aromatase and 17 alpha-hydroxylase/C17,20-lyase. , 2001, Journal of medicinal chemistry.

[43]  Ulf Norinder,et al.  Refinement of Catalyst hypotheses using simplex optimisation , 2000, J. Comput. Aided Mol. Des..

[44]  Mark Froimowitz,et al.  Homology modeling of the dopamine D2 receptor and its testing by docking of agonists and tricyclic antagonists. , 1994, Journal of medicinal chemistry.

[45]  Y. Pommier,et al.  Potent inhibitors of human immunodeficiency virus type 1 integrase: identification of a novel four-point pharmacophore and tetracyclines as novel inhibitors. , 1997, Molecular pharmacology.

[46]  L. Moore,et al.  Pharmacophore analysis of the nuclear oxysterol receptor LXRalpha. , 2001, Journal of medicinal chemistry.

[47]  A. Beck‐Sickinger Structural characterization and binding sites of G-protein-coupled receptors , 1996 .

[48]  J. Grembecka,et al.  Computer-aided design and activity prediction of leucine aminopeptidase inhibitors , 2000, J. Comput. Aided Mol. Des..

[49]  David S. Goodsell,et al.  Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function , 1998 .

[50]  P. Gund Three-Dimensional Pharmacophoric Pattern Searching , 1977 .