The fundamentals of pharmacophore modeling in combinatorial chemistry

Journal of Receptors and Signal Transduction

Volumn 21, Issue 4, 2001, Pages 357-375

  Ghose, Arup K ^a   Viswanadhan, Vellarkad N ^a   Wendoloski, John J ^b  

^a AMGEN INC   (United States)

^b ASTRAZENECA   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING SITE; CHEMICAL MODEL; COMBINATORIAL CHEMISTRY; DRUG DESIGN; PROTEIN BINDING; QUANTITATIVE STRUCTURE ACTIVITY RELATION; REVIEW;

BINDING SITES; COMBINATORIAL CHEMISTRY TECHNIQUES; DRUG DESIGN; MODELS, CHEMICAL; PROTEIN BINDING; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 0035523853     PISSN: 10799893     EISSN: 15324281     Source Type: Journal    
DOI: 10.1081/RRS-100107923     Document Type: Article

References (42)

1. Ehrlich, P. Über den jetzigen Stand der Chemotherapie. Chem. Ber. 1909, 42, 17.
2. Ghose, A. K.; Logan, M. E.; Treasurywala, A. M.; Wang, H.; Wahl, R. C.; Tomczuk, B.; Gowravaram, M.; Jaeger, E. P.; Wendoloski, J. J. Determination of pharmacophoric geometry for collagenase inhibitors using a novel computational method and its verification using molecular dynamics, NMR and X-ray crystallography. J. Am. Chem. Soc. 1995, 117, 4671-4682.
3. Ghose, A. K.; Wendoloski, J. Pharmacophore modeling: methods, experimental verifications and applications. In 3D QSAR in Drug Design: Theory, Methods, and Applications; Kubinyi, H., Folker, G., Martin, Y. C., Eds.; Kluwer: Dordrecht, 1997.
4. Gund P. Pharmacophoric pattern searching and receptor mapping. Ann. Rep. Med. Chem. 1979, 14, 299-308.
5. Humblet, C; Marshall, G. R. Pharmacophore identification and receptor mapping. Ann. Rep. Med. Chem. 1980, 15, 267-276.
6. Klebe, G. Structural alignment of molecules. In 3D QSAR in Drug Design: Theory, Methods and Applications; Kubinyi, H., Ed.; ESCOM: Leiden, 1993; pp. 173-199.
7. Martin, Y. C. Pharmacophore mapping. In Designing Bioactive Molecules; Martin, Y. C., Willett, P., Eds.; American Chemical Society: Washington, DC, 1997; pp. 121-148.
8. MDL Information Systems 1. ISIS; v 2.0.2 ed. San Leandro, CA, 1997.
9. Pullman, A. Compt. Rend. 1945, 221, 140.
10. Coulson, CA. Adv. Cancer. Res. 1953, 1, 1.
11. Kier, L. B. Molecular Orbital Theory in Drug Research; Academic Press: New York, 1971.
12. Crippen, GM. Rapid calculation of coordinates from distance matrices. J. Comput. Phys. 1977, 26, 449-452.
13. Crippen, G. M. Quantitative structure-activity relationships by distance geometry: systematic analysis of dihydrofolate reductase inhibitors. J. Med. Chem. 1980, 23, 599-606. (Pubitemid 11237813)
14. Crippen, G. M. Why energy embedding works. J. Phys. Chem. 1987, 91, 6341-6343.
15. Ghose, A. K.; Crippen, G. M. Geometrically feasible binding modes of the flexible ligand molecule at the receptor site. J. Comput. Chem. 1985, 6, 350-359.
16. Motoc, I.; Dammkoehler, R. A.; Marshall, G. R. Three-dimensional structure activity relationships and biological receptor mapping. In Mathematical and Computational Concepts in Chemistry; Trinajstic, N., Ed.; Ellis Horwood: Chichester, 1986; pp. 222-251.
17. Sheridan, R. P.; Nilakantan, R.; Dixon, J. S.; Venkataraghavan, R. The ensemble distance geometry: application to the nicotinic pharmacophore. J. Med. Chem. 1986, 29, 899-906. (Pubitemid 16068795)
18. Payne, A. W.; Glen, R. C. Molecular recognition using a binary genetic search algorithm. J. Mol. Graphics. 1993, 11, 74-91.
19. Willett, P. Similarity and Clustering in Chemical Information Systems; Research Studies Press: Letchworth, 1986.
20. Hahn, M. Three-dimensional shape-based searching of conformationally flexible compounds. J. Chem. Inf. Comput. Sci. 1997, 33, 80-86. (Pubitemid 127601581)
21. Ghose, A. K.; Crippen, G. M. Atomic physicochemical parameters for three-dimensional structure directed quantitative structure-activity relationships. I. Partition coefficients as a measure of hydrophobicity. J. Comput. Chem. 1986, 7, 565-577.
22. Ghose, A. K.; Viswanadhan, V. N.; Wendoloski, J. J. Prediction of hydrophobic properties of small organic molecules using fragmental methods: an analysis of ALOGP and CLOGP methods. J. Phys. Chem. 1998, 102, 3762-3772. (Pubitemid 128611348)
23. Ghose, A. K.; Crippen, G. M.; Revankar, G. R.; McKernan, P. A.; Smee, D. F.; Robins, R. K. Analysis of the in vitro antiviral activity of certain ribonucleosides against parainfluenza virus using a novel computer aided receptor modeling procedure. J. Med. Chem. 1989, 32, 746-756. (Pubitemid 19100186)
24. Viswanadhan, V. N.; Ghose, A. K.; Revankar, G. R.; Robins, R. K. Atomic physico-chemical parameters for three-dimensional structure directed quantitative structure-activity relationships. 4. Additional parameters for hydrophobic and dispersive interactions and their application for an automated superposition of certain naturally occurring nucleoside antibiotics. J. Chem. Inf. Comput. Sci. 1989, 29, 163-172.
25. Ghose, A. K.; Crippen, G. M. Atomic physicochemical parameters for three-dimensional structure-directed quantitative structure-activity relationships. 2. Modeling dispersive and hydrophobic interactions. J. Chem. Inf. Comp. Sci. 1987, 27, 21-35.
26. AM-Technologies. Galaxy v2.6. Manual Vol. 2, San Antonio, TX, 1999. www.amtech.com
27. Ghose, A. K.; Viswanadhan, V. N.; Sanghvi, Y. S.; Nord, L. D.; Willis, R. C.; Revankar, G. R.; Robins, R. K. Structural mimicry of adenosine by the antitumor agents 4-methoxy-and 4-amino-8-(β-D-ribofuranosylamino) pyrimido[5, 4-d]pyrimidine as viewed by a molecular modeling method. Proc. Nat. Acad. Sci. USA 1989, 86, 8242-8246. (Pubitemid 19286035)
28. 1H NMR and theoretical methods. J. Am. Chem. Soc. 1990, 112, 3622-3628. (Pubitemid 20305706)
29. DesJarlais, R.; Sheridan, R. P.; Seibel, G. L.; Dixon, J. S.; Kuntz, I. D.; Venkataraghavan, R. Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure. J. Med. Chem. 1988, 31, 722-729. (Pubitemid 18097087)
30. Miranker, A.; Karplus, M. Functionality maps of binding sites: a multiple copy simultaneous search method. Proteins 1991, 11, 29-34.
31. Bohm, H.-J. The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure. J. CAD Mol. Des. 1994, 8, 243-256.
32. Goodsell, D. S.; Olson, AJ. Automated docking of substrates to proteins by simulated annealing. Proteins Str. Func. Genet. 1990, 8, 195-202. (Pubitemid 20363304)
33. Gillet, V. J.; Johnson, A. P. Structure generation for de novo design. In Designing Bioactive Molecules; Martin, Y. C., Willett, P., Eds.; American Chemical Society: Washington, DC, 1997; pp. 149-174.
34. Ghose, A. K.; Viswanadhan VN.; Wendoloski, JJ. Adapting structure-based drug design in the paradigm of combinatorial chemistry and high-throughput screening: an overview and new examples with important caveats for newcomers to combinatorial library design using pharmacophore models or multiple copy simultaneous search fragments. In Rational Drug Design: Novel Methodology and Practical Applications; Parrill, A. L., Reddy, M. R., Eds.; American Chemical Society: Washington, DC, 1999; pp. 226-238. (Pubitemid 129547003)
35. Livnah, O.; Stura, E. A.; Johnson, D. L.; Middleton, S. A.; Mulcahy, L. S.; Wrighton, N. C; Dower, W. J.; Joliffe, L. K.; Wilson, I. A. Functional mimicry of a protein hormone by a peptide agonist: the EPO receptor complex at 2.8 A. Science 1996, 273, 464-471. (Pubitemid 26286442)
36. Nicklaus, M. C., Wang, S.; Driscol, J. S.; Milne, G. W. Conformational changes of small molecules binding to proteins. Bioorg. Med. Chem. 1995, 3, 411-428.
37. Bartlett, PA.; Shea, J. T.; Telfer, S. J.; Waterman, S. Molecular recognition in chemical and biological problems. In CAVEAT: A Program to Facilitate the Structure-derived Design of Biologically Active Molecules, Special publication 78; Royal Chemical Society, 1989; pp. 182-196.
38. Tschinke, V; Cohen, N. C. The NEWLEAD program: a new method for the design of candidate structures from pharmacophoric hypotheses. J. Med. Chem. 1993, 36, 3863-3870. (Pubitemid 24006717)
39. Gillet, V; Johnson, A. P; Mata, P.; Sike, S.; Williams, P. SPROUT: a program for structure generation. J. CAD Mol. Des. 1993, 7, 127-153.
40. Eisen, M. B.; Wiley, D. C.; Karplus, M.; Hubbard RE. HOOK: a program for finding novel molecular architectures that satisfy the chemical and steric requirements of a macro-molecule binding site. Proteins 1994, 19, 199-221. (Pubitemid 24215048)
41. Eck, M. J.; Pulskey, S.; Trub, T; Harrison, S. C.; Shoelson, S. E. Spatial constraints on the recognition of phosphoproteins by the tandem SH2 domains of the phosphate SHPTP2. Nature 1996, 379, 277-280.
42. Lunney, E. A.; Para, K. S.; Rubin, J. R.; Humblet, C; Fergus, J. H.; Marks, J. S.; Sawyer, T. K. Structure-based design of a novel series of nonpeptide ligands that bind to the pp60 SRC SH2 domain. J. Am. Chem. Soc. 1997, 119, 12471.