Modeling robust QSAR. 1. Coding molecules in 3D-QSAR - From a point to surface sectors and molecular volumes

Journal of Chemical Information and Modeling

Volumn 45, Issue 5, 2005, Pages 1447-1455

  Gieleciak, Rafal ^a   Magdziarz, Tomasz ^a   Bak, Andrzej ^a   Polanski, Jaroslaw ^a  

^a UNIVERSITY OF SILESIA   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

AROMATIC COMPOUNDS; ENZYME INHIBITION; FUNCTIONS; FUNGI; MATHEMATICAL MODELS; SURFACE PHENOMENA;

CODING MOLECULES; COMPARATIVE MOLECULAR SURFACE ANALYSIS (COMSA); MOLECULAR DESCRIPTORS; MOLECULAR VOLUMES;

MOLECULAR ORIENTATION;

ACYLTRANSFERASE; ANTIFUNGAL AGENT; ANTILIPEMIC AGENT; ANTITHROMBOCYTIC AGENT; GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE; PROTEIN N MYRISTOYLTRANSFERASE;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; COMPUTER SIMULATION; DRUG ANTAGONISM; DRUG DESIGN; METABOLISM; QUANTITATIVE STRUCTURE ACTIVITY RELATION;

ACYLTRANSFERASES; ANTIFUNGAL AGENTS; ANTILIPEMIC AGENTS; COMPUTER SIMULATION; DRUG DESIGN; MOLECULAR STRUCTURE; PLATELET AGGREGATION INHIBITORS; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; SOFTWARE;

EID: 26944432634     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci0501488     Document Type: Article

References (43)

1. Kolb, H. C.; Finn, M. G.; Sharpless, K. B. Click Chemistry: Diverse Chemical Function from a Few Good Reactions. Angew. Chem., Int. Ed. 2001, 40, 2004-2021.
2. Kubinyi, H. QSAR: Hansch Analysis and Related Approaches. In Methods and Principles in Medicinal Chemistry; Mannhold, R., Krogsgaard-Larsen, P., Timmerman, H., Eds.; VCH: Weinheim, 1993.
3. Wermuth, C. G. The impact of QSAR and CADD methods on drug discovery. In Rational Approaches to Drug Design - Proceedings of the 13th European Symposium on Quantitative Structure - Activity Relationships; Holtje, H.-D., Sippl, W., Eds.; Prous: Barcelona, 2001; pp 3-20.
4. Doweyko, A. M. 3D-QSAR illusions. J. Comput.-Aided. Mol. Des. 2004, 18, 587-96.
5. Korhonen, S.-P.; Tuppurainen, K.; Laatikainen, R.; Peräkylä, M. FLUFF-BALL, A template-based grid-independent superposition and QSAR technique: Validation using a benchmark steroid data set. J. Chem. Inf. Comput. Sci. 2003, 43, 1780-1793.
6. Polanski, J.; Gieleciak, R.; Wyszomirski, M. Mapping dye pharmacophores by the comparative molecular surface analysis (CoMSA): application to heterocyclic monoazo dyes. Dyes Pigm. 2004, 62, 63-78.
7. Polanski, J. Self-organizing neural networks for pharmacophore mapping. Adv. Drug Deliv. Rev. 2003, 55, 1149-1162.
8. Polanski, J.; Bak, A.; Gieleciak, R.; Magdziarz, T. Self-organizing neural networks for modeling robust 3D and 4D QSAR: Application to dihydrofolate reductase inhibitors. Molecules 2004, 9, 1148.
9. Cramer, III, R. D.; Patterson, D. E.; Bunce, J. D. Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding steroids to carrier proteins. J. Am. Chem. Soc. 1988, 110, 5959-5967.
10. Melville, J.; Hirst, J. D. On the stability of CoMFA models. J. Chem. Inf. Comput. Sci. 2004, 44, 1294-1300.
11. Jain, A. N.; Koile, K.; Chapman, D. Compass: Predicting biological activities from molecular surface properties. Performance comparisons on a steroid benchmark. J. Med. Chem. 1994, 37, 2315-2327.
12. Ivanciuc, O.; Ivanciuc, T.; Cabrol-Bass, D. 3D QSAR with CoRSA. Comparative receptor surface analysis. Application to calcium channel agonists. Analusis 2000, 28, 637-642.
13. Polanski, J. Molecular shape analysis. In Handbook of chemoinformatics; Gasteiger, J., Ed.; Wiley-VCH: Verlag: Weinheim, 2003; pp 302-319.
14. Hofbauer, C.; Aszodi, A. SH2 Binding site comparison: A new application of the SURFCOMP method. J. Chem. Inf. Model. 2005, 45, 414-421.
15. Polanski, J.; Gieleciak, R.; Magdziarz, T. The grid formalism for the comparative molecular surface analysis: application to the CoMFA benchmark steroids, azo dyes and HEPT derivatives. J. Chem. Inf. Comput. Sci. 2004, 44, 1423-1435.
16. Anzali, S.; Gasteiger, J.; Holzgrabe, U.; Polanski, J.; Teckentrup, A.; Wagener, M. The use of self-organizing neural networks in drug design. Perspect. Drug Discovery Des. 1998, 9/10/11, 273-299.
17. Polanski, J.; Walczak, B. The comparative molecular surface analysis (CoMSA): a novel tool for molecular design. Comput. Chem. 2000, 24, 615-625.
18. a values of benzoic and alkanoic acids. J. Chem. Inf. Comput. Sci. 2002, 42, 184-191.
19. Polanski, J.; Gieleciak, R. The comparative molecular surface analysis (CoMSA) with modified uninformative variable elimination-PLS (UVE-PLS) method: application to the steroids binding the aromatase enzym. J. Chem. Inf. Comput. Sci. 2003, 43, 656-666.
20. Polanski, J.; Gieleciak, R.; Wyszomirski, M. Comparative molecular surface analysis (CoMSA) for modeling dye-fiber affinities of the azo and antraquinone dyes. J. Chem. Inf. Comput. Sci. 2003, 43, 1754-1762.
21. Polanski, J.; Gieleciak, R. Comparative molecular surface analysis: a novel tool for drug design and molecular diversity studies. Mol. Diversity 2003, 7, 45-59.
22. Polanski, J.; Gieleciak, R.; Bak, A. Probability issues in molecular design: Predictive and modeling ability in 3D-QSAR schemes. Comb. Chem. High Throughput Screening 2004, 7, 793-807.
23. Hopfinger, A. J.; Wang, S.; Tokarski, J. S.; Jin, B.; Albuquerque, M.; Madhav, P. J.; Duraiswami, C. Construction of 3D QSAR models using the 4D QSAR analysis formalism. J. Am. Chem. Soc. 1997, 119, 10509-10524.
24. a values and steroid CBG binding affinities. J. Chem. Inf. Comput. Sci. 2003, 43, 2081-2092.
25. Chilmonczyk, Z.; Siluk, D.; Kaliszan, R.; Lozowicka, B.; Poplawski, J.; Filipek, S. New chemical structures of hypolipidemic and antiplatelet activity. Pure Appl. Chem. 2001, 73, 1445-1458.
26. Hasegawa, K.; Morikami, K.; Shiratori, Y.; Ohtsuka, T.; Aoki, Y.; Shimma, N. 3D-QSAR study of antifungal N-myristoyltransferase inhibitors by comparative molecular surface analysis. Chemom. Intell. Lab. Syst. 2003, 69, 51-59.
27. Match3D program package, available from Professor J. Gasteiger, Computer-Chemie-Centrum, University Erlangen-Nurnberg, Germany. See: http://www2.ccc.uni-erlangen.de.
28. Hasegawa, K.; Matsuoka, S.; Arakawa, M.; Funatsu, K. New molecular surface-based 3D-QSAR method using Kohonen neural network and 3-Way PLS. Comput. Chem. 2002, 26, 583-589.
29. Hasegawa, K.; Matsuoka, S.; Arakawa, M.; Funatsu, K. Multi-way PLS modeling of structure-activity data by incorporating electrostatic and lipophilic potentials on molecular surface. Comput. Biol. Chem. 2003, 27, 381-386.
30. MATLAB 5.0 program, available from: The Mathworks Inc., Natick, MA. http://www.mathworks.com.
31. Centner, V.; Massart, D. L.; de Noord, O. E.; de Jong, S.; Vandeginste, B. M. V.; Sterna, C. Elimination of uninformative variables for multivariate calibration. Anal. Chem. 1996, 68, 3851-3858.
32. Testa, B.; Purcell, W. P. A QSAR study of sulfonamide binding to carbonic anhydrase as test of steric models. Eur. J. Med. Chem. 1978, 13, 509-514.
33. Eghdamian, B.; Ghose, K. Mode of action and adverse effects of lipid lowering drugs. Drugs Today 1998, 34, 943-956.
34. Farmer, J. A.; Gotto, A., Jr. Current and future therapeutic approaches to hyperlipidemia. Adv. Pharmacol. 1996, 35, 79-114.
35. Chamorro, G.; Garduno, L.; Sanchez, A.; Labarrios, F.; Salazar, M.; Martinez, E.; Diaz, F.; Tamariz, J. Hypolipemic activity of dimethoxy unconjugated propenyl side-chain analogues of alpha-asarone in mice. Drug Dev. Res. 1998, 43, 105-108.
36. Labarrios, F.; Garduno, L.; Vidal, M.; Garcia, R.; Salazar, M.; Martinez, E.; Diaz, F.; Chamorro, G.; Tamariz, J. Synthesis and hypolipidaemic evaluation of a series of alpha-asarone analogues related to clofibrate in mice. J. Pharm. Pharmacol. 1999, 51, 1-7.
37. Dandiya, P. C.; Sharma, J. D. Studies on Acorus calamus. V. Pharmacological actions of asarone and beta-asarone on central nervous system. Indian J. Med. Res. 1962, 50, 46-60.
38. Dandiya, P. C.; Menon, M. K. Effects of asarone and beta-asarone on conditioned responses, fighting behaviour and convulsions. Br. Pharm. Chemother. 1963, 20, 436-442.
39. Belova, L.; Alibekov, S.; Baginskaya, A.; Sokolov, S.; Pokrovskaya, G.; Stikhin, V.; Trumpe, T.; Gorodnyuk, T. Asarone and its biological properties. Farmak. Toksikol. 1985, 48, 17-20.
40. Salazar, M.; Salazar, S.; Ulloa, V.; Mendoza, T.; Pages, N.; Chamorro, G. Teratogenic action of alpha-asarone in the mouse. J. Toxicol. Clin. Exp. 1992, 12, 149-154.
41. Filipek, S.; Lozowicka, B. Alpha-asarone congeners as hypolipidemic agents. Pseudoreceptor versus minireceptor modeling. Acta Pol. Pharm. 2000, 57, 106-109.
42. Cruz, M.; Salazar, M.; Garciafigueroa, Y.; Hernandez, D.; Diaz, F.; Chamorro, G.; Tamariz, J. Hypolipidemic activity of new phenoxy-acetic derivatives related to alpha asarone with minimal pharmacophore features Drug. Dev. Res. 2003, 60, 186-190.
43. Magdziarz, T.; Lozowicka, B.; Gieleciak, R.; Bak, A.; Polanski, J.; Chilmonczyk, Z. The 3D QSAR study of hypolipidemic asarones by comparative molecular surface analysis. Bioorg. Med. Chem. submitted.