SQ: A program for rapidly producing pharmacophorically relevent molecular superpositions

Journal of Medicinal Chemistry

Volumn 42, Issue 9, 1999, Pages 1505-1514

  Miller, Michael D ^a   Sheridan, Robert P ^a   Kearsley, Simon K ^a  

^a MERCK RESEARCH LABORATORIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANGIOTENSIN; ANGIOTENSIN 2 RECEPTOR ANTAGONIST; ANTIDIABETIC AGENT; INDINAVIR; PARACETAMOL; PROTEINASE INHIBITOR; RENIN INHIBITOR; THROMBIN INHIBITOR; THROMBOCYTE ACTIVATING FACTOR ANTAGONIST;

ALGORITHM; ARTICLE; AUTOANALYSIS; DRUG CONFORMATION; DRUG RECEPTOR BINDING; DRUG SCREENING; MOLECULAR DYNAMICS; MOLECULAR PROBE; PHARMACOPHORE;

ALGORITHMS; ANGIOTENSIN II; ANIMALS; ASPARTIC ENDOPEPTIDASES; CATTLE; DATABASES, FACTUAL; HIV PROTEASE INHIBITORS; HUMANS; LIGANDS; MODELS, MOLECULAR; STRUCTURE-ACTIVITY RELATIONSHIP; TETRAHYDROFOLATE DEHYDROGENASE; THERMOLYSIN; THROMBIN; TRYPSIN;

EID: 0033529045     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm9806143     Document Type: Article

References (27)

1. Lemmen, C.; Hiller, C.; Lengauer, T. RigFit: a new approach to superimposing ligand molecules. J. Comput.-Aided Mol. Des. 1998, 12, 491-502.
2. Masek, B. B.; Merchant, A.; Matthew, J. B. Molecular skins, a new concept for qualitative shape matching of a protein with its small molecule mimics. Proteins 1993, 17, 193-202.
3. Perkins, T. D. J.; Dean, P. M. An exploration of a novel strategy for superposing several flexible molecules. J. Comput.-Aided Mol. Des. 1993, 7, 155-172.
4. Kearsley, S. K.; Smith, G. M. An alternative method for the alignment of molecular structures: maximizing electrostatic and steric overlap. Tetrahedron Comput. Methodol. 1990, 3, 615-633.
5. Klebe, G.; Meitzner, T.; Weber, F. Different approaches toward an automatic structural alignment of drug molecules: Applications to sterol mimics, thrombin and thermolysin inhibitors. J. Comput.-Aided Mol. Des. 1994, 8, 751-778.
6. Perry, N. C.; van Geerstein, V. J. Database searching on the basis of three-dimensional molecular similarity using the SPERM program. J. Chem. Inf. Comput. Sci. 1992, 32, 607-616.
7. Thorner, D. A.; Willett, P.; Wright, P. M.; Taylor, R. Similarity searching in files of three-dimensional chemical structures: representation and searching of molecular electrostatic potentials using field-graphs. J. Comput.-Aided Mol. Des. 1997, 11, 163-174.
8. Jones, G.; Willett, P.; Glen, R. C. A genetic algorithm for flexible molecular overlay and pharmacophore elucidation. J. Comput.-Aided Drug Des. 1995, 9, 532-549.
9. McMartin, C.; Bohacek, R. S. QXP: Powerfull, rapid computer algorithms for structure-based drug design. J. Comput.-Aided Mol. Des. 1997, 11, 333-334.
10. Handschuh, S.; Wagener, M.; Gasteiger, J. "Superposition of three-dimensional chemical structures allowing for conformational flexibility by a hybrid method. J. Chem. Inf. Comput. Sci. 1998, 38, 220-232.
11. Martin, Y. C.; Bures, M. G.; Danaher, E. A.; DeLazzer, J.; Lico, I.; Pavlik, P. A. A fast new approach to pharmacophore mapping and its application to dopaminergic and benzodiazepine agonists. J. Comput.-Aided Mol. Des. 1993, 7, 83-102.
12. Artymiuk, P. J.; Bath, P. A.; Grindley, H. M.; Pepperrell, C. A.; Poirrette, A. R.; Rice, D. W.; Thorner, D. A.; Wild, D. J.; Willett, P.; Allen, F. H.; Taylor, R. Similarity searching in databases of three-dimensional molecules and macromolecules. J. Chem. Inf. Comput. Sci. 1992, 32, 617-630.
13. Lemmen, C.; Lengauer, T.; Klebe, G. FLEXS: a method for fast flexible ligand superposition. J. Med. Chem. 1998, 41, 4502-4520.
14. Jain, A. N.; Deitterich, T. G.; Lathrop, R. H.; Chapman, D.; Critchlow, R. E., Jr.; Bauer, B. E.; Webster, T. A.; Lozano-Perez, T. Compass: a shape-base machine learning tool for drug design. J. Comput.-Aided Mol. Des. 1994, 8, 635-652.
15. Mestres, J.; Rohrer, D. C.; Maggiora, G. M. A molecular field-based similarity approach to pharmacophoric pattern recognition. J. Mol. Graph. Modelling 1997, 15, 114-121.
16. Kearsley, S. K.; Sallamack, S.; Fluder, E. M.; Andose, J. D.; Mosley, R. T.; Sheridan, R. P. Chemical similarity using physiochemical property descriptors. J. Chem. Inf. Comput. Sci. 1996, 36, 118-127.
17. Sheridan, R. P.; Miller, M. D.; Underwood, D. J.; Kearsley, S. K. Chemical similarity using geometric atom pair descriptors. J. Chem. Inf. Comput. Sci. 1996, 36, 128-136.
18. Kearsley, S. K.; Underwood, D. J.; Sheridan, R. P.; Miller, M. D. Flexibases: A way to enhance the use of molecular docking methods. J. Comput.-Aided Mol. Des. 1994, 8, 565-582.
19. Miller, M. D.; Kearsley, S. K.; Underwood, D. J.; Sheridan, R. P. FLOG: a system to select quasi-flexlible ligands complementary to a receptor of known three-dimensional structure. J. Comput.-Aided Mol. Des. 1994, 8, 153-174.
20. Bush, B. L.; Sheridan, R. P. PATTY: a programmable atom typer and language for automatic classification of atoms in molecular databases. J. Chem. Inf. Comput. Sci. 1993, 33, 756-762.
21. Shoichet, B. K.; Kuntz, I. D. Matching chemistry and shape in molecular docking. Protein Eng. 1993, 6, 723-732.
22. Bernstein, F. C.; Koetzle, T. F.; Williams, G. J. B.; Meyer, E. F., Jr.; Brice, M. D.; Rodgers, J. R.; Kennard, O.; Shimanouchi, T.; Tasumi, M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 1977, 112, 535-542.
23. MACCS-II Drug Data Report, MDDR V97.2; Molecular Design Ltd.: San Leandro, CA, 1997.
24. Banner, D. W.; Hadvary, P. Crystallographic analysis at 3.0 Angstrom resolution of the binding to human thrombin of four active site-directed inhibitors. J. Biol. Chem. 1991, 266, 20085-20093.
25. Chen, Z.; Li, Y.; Chen, E.; Hall, D. L.; Darke, P. L.; Culberson, C.; Shafer, J. A.; Kuo, L. C. Crystal structure at 1.9 Angstrom resolution of human immunodeficiency virus (HIV) protease complexed with L-735,524, an orally bioavailable inhibitor of HIV proteases. J. Biol. Chem. 1994, 269, 26344-26348.
26. Beach, M. D.; Chasman, D.; Murphy, R. B.; Halgren, T. A.; Friesner, R. A. Accurate ab initio quantum chemical determination of the relative energetics of peptide conformations and assessment of empirical force fields. J. Am. Chem. Soc. 1997, 119, 5908-5920.
27. Prendergast, K.; Adams, K.; Greenlee, W. J.; Nachbar, R. B.; Patchett, A. A.; Underwood, D. J. Derivation of a 3D pharmacophore model for the angiotensin-II site one receptor. J. Comput.-Aided Mol. Des. 1994, 8, 491-512.