Quantized Surface Complementarity Diversity (QSCD): A model based oil small molecule-target complementarity

Journal of Medicinal Chemistry

Volumn 43, Issue 10, 2000, Pages 1993-2006

  Wintner, Edward A ^a   Moallemi, Ciamac C ^a  

^a NeoGenesis Drug Discovery   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANGIOTENSIN RECEPTOR ANTAGONIST;

ANALYTIC METHOD; ARTICLE; CRYSTAL STRUCTURE; DNA LIBRARY; MOLECULAR RECOGNITION; QUANTITATIVE ASSAY; STRUCTURE ANALYSIS; TARGET CELL; X RAY CRYSTALLOGRAPHY;

CHEMISTRY, PHYSICAL; COMBINATORIAL CHEMISTRY TECHNIQUES; HYDROGEN BONDING; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MOLECULAR STRUCTURE; STRUCTURE-ACTIVITY RELATIONSHIP; THERMODYNAMICS;

EID: 0034093179     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm990504b     Document Type: Article

References (50)

1. Tan, D. S.; Foley, M. A.; Shair, M. D.; Schreiber, S. L. Stereo-selective synthesis of over two million compounds having structural features both reminiscent of natural products and compatible with miniaturized cell-based assays. J. Am. Chem. Soc. 1998, 120, 8565-8566.
2. Boger, D. L.; Jiang, W.; Goldberg, J. Convergent solution-phase combinatorial synthesis with multiplication of diversity through rigid biaryl and diarylacetylene couplings. J. Org. Chem. 1999, 64, 7094-7100.
3. Carell, T.; Wintner, E. A.; Sutherland, A. J.; Dunayevskiy, Y.; Vouros, P.; Rebek, J., Jr. New promise in combinatorial chemistry: Synthesis, characterization, and screening of small molecule libraries in solution. Chem. Biol. 1995, 2, 171-183.
4. An, H.; Cummins, L. L.; Griffey, R. H.; Bharadwaj, R.; Haly, B. D.; Fraser, A. S.; Wilson-Lingardo, L.; Risen, L. M.; Wyatt, J. R.; Cook, P. D. Solution phase combinatorial chemistry. Discovery of novel polyazapyridinophanes with potent antibacterial activity by a solution phase simultaneous addition of functionalities approach. J. Am. Chem. Soc. 1997, 119, 3696-3708.
5. Mitchison, T. J. Towards a pharmacological Genetics. Chem. Biol. 1994, 1, 3-6.
6. Bartlett, P. A.; Joyce, G. F. Combinatorial chemistry: The search continues. Curr. Opin. Chem. Biol. 1999, 3, 253-255.
7. Drews, J. Genomic sciences and the medicine of tomorrow. Nat. Biotechnol. 1996, 14, 1516-1518.
8. Ghose, A. K.; Viswanadhan, V. N.; Wendoloski, J. J. A knowledge-based approach in designing combinatorial or medicinal chemistry libraries for drug discovery. 1. A qualitative and quantitative characterization of known drug databases. J. Comb. Chem. 1999, 1, 55-68.
9. Gaasterland, T. Structural genomics: Bioinformatics in the driver's seat. Nat. Biotechnol. 1998, 16, 625-627.
10. Kauvar, L. M.; Laborde, E. The diversity challenge in combinatorial chemistry. Curr. Opin. Drug Discov. Dev. 1998, 1, 66-70.
11. Matter, H. Selecting optimally diverse compounds from structure databases: A validation study of two-dimensional and three-dimensional molecular descriptors. J. Med. Chem. 1997, 40, 1219-1229.
12. Patterson, D. E.; Cramer, R. D.; Ferguson, A. M.; Clark, R. D.; Weinberge, L. E. Neighborhood behavior: A useful concept for validation of "molecular diversity" descriptors. J. Med. Chem. 1996, 39, 3049-3059.
13. Polinsky, A. Combichem and cheminformatics. Curr. Opin. Drug Discov. Dev. 1999, 2, 197-203.
14. Ajay; Murcko, M. A. Computational methods to predict binding free energy in ligand-receptor complexes. J. Med. Chem. 1995, 38, 4953-4967.
15. Klebe, G.; Böhm, H.-J. Energetic and entropic factors determining binding affinity in protein-ligand complexes. J. Recept. Signal Transduction Res. 1997, 17, 459-473.
16. Fersht, A. R. The hydrogen bond in molecular recognition. Trends Biochem. Sci. 1987, 12, 301-304.
17. Tokarski, J. S.; Hopfinger, A. J. Prediction of ligand-receptor binding thermodynamics by free energy force field (FEFF) 3D-QSAR analysis: application to a set of peptidomimetic renin inhibitors. J. Chem. Inf. Comput. Sci. 1997, 37, 792-811.
18. Creighton, T. E. Proteins: Structures and Molecular Properties; W. H. Freeman and Co.: New York, 1984.
19. Mecozzi, S.; Rebek, J., Jr. The 55% solution: A formula for molecular recognition in the liquid state. Chem. Eur. J. 1998, 4, 1016-1022.
20. So, S.-S.; Karplus, M. A comparative study of ligand-receptor complex binding affinity prediction methods based on glycogen phosphorylase inhibitors. J. Comput.-Aided Mol. Des. 1999, 13, 243-258.
21. Muegge, I.; Martin, Y. C. A general and fast scoring function for protein-ligand interactions: A simplified potential approach. J. Med. Chem. 1999, 42, 791-804.
22. Burkhard, P.; Taylor, P.; Walkinshaw, M. D. An example of a protein ligand found by database mining: Description of the docking method and its verification by a 2.3 Å X-ray structure of a thrombin-ligand complex. J. Mol. Biol. 1998, 277, 449-466.
23. Norel, R.; Petrey, D.; Wolfson, H. J.; Nussinov, R. Examination of shape complementarity in docking of unbound proteins. Proteins 1999, 36, 307-317.
24. Liang, J.; Edelsbrunner, H.; Woodward, C. Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design. Protein Sci. 1998, 7, 1884-1897.
25. Mason, J. S.; Hermsmeier, M. A. Diversity assessment. Curr. Opin. Chem. Biol. 1999, 3, 342-349.
26. Warr, W. A. Commercial software systems for diversity analysis. Perspect. Drug Discovery Des. 1997, 7/8, 115-130.
27. University of Texas. DiverseSolutions User's Manual version 3.0.2; Laboratory for Molecular Graphics and Theoretical Modeling, Distributed by Tripos, Inc.: 1699 S. Hanley Rd., St. Louis, MO 63144, 1997.
28. Pearlman, R. S.; Smith, K. M. Novel software tools for chemical diversity. Perspect. Drug Discovery Des. 1998, 9, 339-353.
29. Menard, P. R.; Mason, J. S.; Morize, I.; Bauerschmidt, S. Chemistry space metrics in diversity analysis, library design, and compound selection. J. Chem. Inf. Comput. Sci. 1998, 38, 1204-1213.
30. Mason, J. S.; Morize, I.; Menard, P. R.; Cheney, D. L.; Hulme, C.; Labaudiniere, R. F. New 4-point pharmacophore method for molecular similarity and diversity applications: Overview of the method and applications, including a novel approach to the design of combinatorial libraries containing privileged substructures. J. Med. Chem. 1999, 42, 3251-3264.
31. Good, A. C.; Lewis, R. A. New methodology for profiling combinatorial libraries and screening sets: Cleaning up the design process with HARPick. J. Med. Chem. 1997, 40, 3926-3936.
32. Pickett, S. D.; Mason, J. S.; McLay, I. M. Diversity profiling and design using 3D pharmacophores: Pharmacophore derived queries (PDQ). J. Chem. Inf. Comput. Sci. 1996, 36, 1204-1213.
33. Parks, C. A.; Crippen, G. M.; Topliss, J. G. The measurement of molecular diversity by receptor site interaction simulation. J. Comput.-Aided Mol. Des. 1998, 12, 441-449.
34. Chem-X software; Oxford Molecular: Medawar Center, Oxford Science Park, Oxford OX4 4GA, England.
35. Kauvar, L. M.; Higgins, D. L.; Villar, H. O.; Sportsman, J. R.; Engqvist-Goldstein, Å.; Bukar, R.; Bauer, K. E.; Dilley, H.; Rocke, D. M. Predicting ligand binding to proteins by affinity fingerprinting. Chem. Biol. 1995, 2, 107-118.
36. Dixon, S. L.; Villar, H. O. Bioactive diversity and screening library selection via affinity fingerprinting. J. Chem. Inf. Comput. Sci. 1998, 38, 1192-1203.
37. Briem, H.; Kuntz, I. D. Molecular similarity based on DOCK-generated fingerprints. J. Med. Chem. 1996, 39, 3401-3408.
38. Bures, M. G.; Martin, Y. C. Computational methods in molecular diversity and combinatorial chemistry. Curr. Opin. Chem. Biol. 1998, 2, 376-380.
39. Dixon, S. L.; Koehler, R. T. The hidden component of size in two-dimensional fragment descriptors: Side effects on sampling in bioactive libraries. J. Med. Chem. 1999, 42, 2887-2900.
40. Johnson, M.; Maggiora, G. M. Concepts and Applications of Molecular Similarity; Wiley: New York, 1990.
41. Jiang, F.; Kim, S. H. "Soft Docking": Matching of molecular surface cubes. J. Mol. Biol. 1991, 219, 79-102.
42. Bemis, G. W.; Murcko, M. A. The properties of known drugs: 1. Molecular frameworks. J. Med. Chem. 1996, 39, 2887-2893.
43. Mount, J.; Ruppert, J.; Welch, W.; Jain, A. N. IcePick: A flexible surface-based system for molecular diversity. J. Med. Chem. 1999, 42, 60-66.
44. Marx, M. A.; Grillot, A.-L.; Louer, C. T.; Beaver, K. A.; Bartlett, P. A. Synthetic design for combinatorial chemistry. Solution and polymer supported synthesis of polycyclic lactams by intramolecular cyclization of azomethine ylides. J. Am. Chem. Soc. 1997, 119, 6153-6167.
45. Boojamra, C. G.; Burrow, K. M.; Thompson, L. A.; Ellman, J. A. Solid-phase synthesis of 1,4-benzodiazepine-2,5-diones. Library preparation and demonstration of synthesis generality. J. Org. Chem. 1997, 62, 1240-1256.
46. Wallace, A. C.; Borkakoti, N.; Thornton, J. M. TESS: A geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites. Protein Sci. 1997, 6, 2308-2323.
47. MacBeath, G.; Koehler, A. N.; Schreiber, S. L. Printing small molecules as microarrays and detecting protein-ligand interactions en masse. J. Am. Chem. Soc. 1999, 121, 7967-7968.
48. Lam, K. S.; Lebl, M.; Krchňák, V. The "one-bead-one-compound" combinatorial library method. Chem. Rev. 1997, 97, 411-448.
49. 1 antagonists: Confomationally constrained heterocyclic bioisosteres of the ester linkage. J. Med. Chem. 1995, 38, 923-933.
50. Depreux, P.; Lesieur, D.; Mansour, H. A.; Morgan, P.; Howell, H. E.; Renard, P.; Caignard, D.-H.; Pfeiffer, B.; Delagrange, P.; Guardiola, B.; Yous, S.; Demarque, A.; Adam, G.; Andrieux, J. Synthesis and structure-activity relationships of novel naphthalenic and bioisosteric related amidic derivatives as melatonin receptor ligands. J. Med. Chem. 1994, 37, 3231-3239.