Exploring QSARs for inhibitory effect of a set of heterocyclic thrombin inhibitors by multilinear regression refined by artificial neural network and molecular docking simulations

Journal of Enzyme Inhibition and Medicinal Chemistry

Volumn 27, Issue 2, 2012, Pages 174-186

  Ramrez Galicia, Guillermo ^a   Garduo Juárez, Ramn ^b   Correa Basurto, José ^c   Deeb, Omar ^d  

^a UNIVERSIDAD DEL PAPALOAPAN   (Mexico)

^b INSTITUTO DE CIENCIAS FÍSICAS   (Mexico)

^c INSTITUTO POLITÉCNICO NACIONAL   (Mexico)

^d AL QUDS UNIVERSITY   (Palestine)

Author keywords

Artificial neuron network; Docking; Heterocyclic thrombin inhibitors; Quantitative structureactivity relationship

Indexed keywords

BENZIMIDAZOLE; LIGAND; THROMBIN; THROMBIN INHIBITOR;

ARTICLE; ARTIFICIAL NEURAL NETWORK; CHEMICAL STRUCTURE; HYDROGEN BOND; IC 50; LIGAND BINDING; METHODOLOGY; MOLECULAR DOCKING; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; QUANTITATIVE STRUCTURE ACTIVITY RELATION; SIMULATION;

ANTICOAGULANTS; BINDING SITES; COMPUTER SIMULATION; DRUG DESIGN; HETEROCYCLIC COMPOUNDS; HYDROGEN BONDING; MODELS, MOLECULAR; MOLECULAR STRUCTURE; NEURAL NETWORKS (COMPUTER); QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; THROMBIN;

EID: 84858141785     PISSN: 14756366     EISSN: 14756374     Source Type: Journal    
DOI: 10.3109/14756366.2011.582467     Document Type: Article

References (57)

1. Berndt M, Phillips D. Platelet membrane proteins: composition and receptor function. In: Gordon J, ed. Platelet in Biology and Pathology. North Holland, Amsterdam: Elsevier, 1981, pp. 43-74.
2. Bar-Shavit R, Kahn A, Fenton JW 2nd, Wilner GD. Receptor-mediated chemotactic response of a macrophage cell line (J774) to thrombin. Lab Invest 1983;49:702-707.
3. Harlan JM, Tompson PJ, Ross RR, Bowen-Pope DF. Alpha-thrombin induces release of platelet-derived growth factor-like molecule(s) by cultured human endothelial cells. J Cell Biol 1986;103:1129-1133. (Pubitemid 17177359)
4. Jones A, Geczy CL. Trombin and factor Xa enhance the production of interleukin-1. Immunology 1990;71:236-241. (Pubitemid 20341224)
5. Okazaki H, Majesky MW, Harker LA, Schwartz SM. Regulation of platelet-derived growth factor ligand and receptor gene expression by alpha-thrombin in vascular smooth muscle cells. Circ Res 1992;71:1285-1293.
6. McNamara CA, Sarembock IJ, Gimple LW, Fenton JW 2nd, Coughlin SR, Owens GK. Trombin stimulates proliferation of cultured rat aortic smooth muscle cells by a proteolytically activated receptor. J Clin Invest 1993;91:94-98. (Pubitemid 23037258)
7. Carney DH, Glenn KC, Cunningham DD. Conditions which afect initiation of animal cell division by trypsin and thrombin. J Cell Physiol 1978;95:13-22. (Pubitemid 9115634)
8. Wiley MR, Fisher MJ. Small molecules direct thrombin inhibitors. Exp Opin Ter Pat. 1997; 7: 1265-1282. (Pubitemid 27478977)
9. Sanderson PEJ, Dyer DL, Naylon-Olsen AM, Vacca JP, Gardell SJ, Lewis SD et al. L-373,890: an achiral, noncovalent, subnanomolar thrombin inhibitor. Bioorg Med Chem Lett 1997;7:1497-1500. (Pubitemid 27250199)
10. Sanderson PE, Cutrona KJ, Dorsey BD, Dyer DL, McDonough CM, Naylor-Olsen AM et al. L-374,087, an efcacious, orally bioavailable, pyridinone acetamide thrombin inhibitor. Bioorg Med Chem Lett 1998;8:817-822. (Pubitemid 28160046)
11. Sanderson PE, Lyle TA, Cutrona KJ, Dyer DL, Dorsey BD, McDonough CM et al. Efcacious, orally bioavailable thrombin inhibitors based on 3-aminopyridinone or 3-aminopyrazinone acetamide peptidomimetic templates. J Med Chem 1998;41:4466-4474. (Pubitemid 28516445)
12. Tamura SY, Semple JE, Reiner JE, Goldman EA, Brunck TK, Lim-Wilby MS et al. Design and synthesis of a novel class of thrombin inhibitors incorporating heterocyclic dipeptide surrogates. Bioorg Med Chem Lett 1997;7:1543-1548. (Pubitemid 27250208)
13. Iwanowicz EJ, Lau WF, Lin J, Roberts DGM, Seiler SM. Derivatives of 5-amide indole as inhibitor of thrombin catalytic activity. Bioorg Med Chem Lett 1996;6:1339-1344. (Pubitemid 26199245)
14. Ries UJ, Priepke HW, Hauel NH, Haaksma EE, Stassen JM, Wienen W et al. Heterocyclic thrombin inhibitors. Part 1: design and synthesis of amidino-phenoxy quinoline derivatives. Bioorg Med Chem Lett 2003;13:2291-2295. (Pubitemid 36724968)
15. Ries UJ, Priepke HW, Hauel NH, Handschuh S, Mihm G, Stassen JM et al. Heterocyclic thrombin inhibitors. Part 2: quinoxalinone derivatives as novel, potent antithrombotic agents. Bioorg Med Chem Lett 2003;13:2297-2302. (Pubitemid 36724969)
16. Coop A, MacKerell AD. Te future of opioid analgesics. Am J Pharm Educ 2002;66:153-156.
17. Hansch C, Leo A. QSAR of nonspecifc toxicity. In: Heller SR, ed. Exploring QSAR: Fundamentals and Applications in Chemistry and Biology. Washington, DC: American Chemical Society, 1995, pp. 169-221.
18. Krogsgaard-Larsen P, Liljerfors T, Madsen U. Textbook of Drug Design and Discovery. New York, USA: Taylor & Francis, CRC Press, 2002.
19. Todeschini R, Consonni V. Handbook of Molecular Descriptors. Weinheim, Germany: Wiley-VCH, 2000.
20. Karelson M. Molecular Descriptors in QSAR/QSPR. New York, USA: Wiley-Interscience, 2000.
21. Nicolotti O, Miscioscia TF, Carotti A, Leonetti F, Carotti A. An integrated approach to ligand-and structure-based drug design: development and application to a series of serine protease inhibitors. J Chem Inf Model 2008;48:1211-1226.
22. Fukunishi H, Teramoto R, Shimada J. Hidden active information in a random compound library: extraction using a pseudo-structure-activity relationship model. J Chem Inf Model 2008;48:575-582. (Pubitemid 351535425)
23. Bonachéra F, Horvath D. Fuzzy tricentric pharmacophore fngerprints. 2. Application of topological fuzzy pharmacophore triplets in quantitative structure-activity relationships. J Chem Inf Model 2008;48:409-425. (Pubitemid 351473043)
24. Xu L, Zhang WJ. Comparison of diferent methods for variable selection. Anal Chem Acta 2001;446:475-481.
25. Schneider G, Wrede P. Artifcial neural networks for computer-based molecular design. Prog Biophys Mol Biol 1998;70:175-222. (Pubitemid 28487613)
26. Ramírez-Galicia G, Garduño-Juárez R, Deeb O, Hemmateenejad B. MLR-ANN and RTO approach to mu-opioid receptor-binding afnity. Pooling data from diferent sources. Chem Biol Drug Des 2008;71:260-270. (Pubitemid 351208192)
27. Ramírez-Galicia G, Garduño-Juarez R, Hemmateenejad B, Deeb O, Estrada-Soto S. QSAR study on the relaxant agents from some Mexican medicinal plants and synthetic related organic compounds. Chem Biol Drug Des 2007;70:143-153. (Pubitemid 47228654)
28. Ramírez-Galicia G, Garduño-Juárez R, Hemmateenejad B, Deeb O, Deciga-Campos M, Moctezuma-Eugenio JC. QSAR study on the antinociceptive activity of some morphinans. Chem Biol Drug Des 2007;70:53-64. (Pubitemid 47057421)
29. Deeb O, Rosales-Hernández MC, Gómez-Castro C, Garduño-Juárez R, Correa-Basurto J. Exploration of human serum albumin binding sites by docking and molecular dynamics fexible ligand-protein interactions. Biopolymers 2010;93:161-170.
30. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart E, Belew RK et al. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 1998;19:1639-1662. (Pubitemid 128590223)
31. Chen Z, Li HL, Zhang QJ, Bao XG, Yu KQ, Luo XM et al. Pharmacophore-based virtual screening versus docking-based virtual screening: a benchmark comparison against eight targets. Acta Pharmacol Sin 2009;30:1694-1708.
32. Blaney JM, Dixon JS. A good ligand is hard to fnd: automated docking methods. Perspect Drug Discov Design 1993;1:301-319.
33. Kuntz ID, Meng EC, Shoichet BK. Structure-based molecular design. Acc Chem Res 1994;27:117-123. (Pubitemid 24972237)
34. Hauel NH, Nar H, Priepke H, Ries U, Stassen JM, Wienen W. Structure-based design of novel potent nonpeptide thrombin inhibitors. J Med Chem 2002;45:1757-1766. (Pubitemid 34415371)
35. ™ [computer program]. Release 7.1 for Windows. Gainesville, FL: Hypercube, Inc. 2002.
36. Stewart JJP. Optimization of parameters for semiempirical methods 1. Method. J Comp Chem 1989;10:209-220.
37. Stewart JPP. MOPAC 6.0 QCPE Program No 455. Chemistry Department, Indiana University, Bloomington, IN, 1989.
38. Baker J. An algorithm for the location of transition states. J Compt Chem 1993;7:385-395.
39. Todeschini R, Consonni V, Pavan M. Dragon Software version 2.1-2002 Pisani 13, Milano, Italy. Dragon Software and references therein, 2002.
40. Guha R, Jurs PC. Determining the validity of a QSAR model-a classifcation approach. J Chem Inf Model 2005;45:65-73. (Pubitemid 40736957)
41. Topliss JG, Costello RJ. Change correlations in structure-activity studies using multiple regression analysis. J Med Chem 1972;15:1066-1068.
42. Topliss JG, Edwards RP. Chance factors in studies of quantitative structure-activity relationships. J Med Chem 1979;22:1238-1244. (Pubitemid 10237430)
43. Fernández M, Caballero J. QSAR models for predicting the activity of non-peptide luteinizing hormone-releasing hormone (LHRH) antagonists derived from erythromycin A using quantum chemical properties. J Mol Model 2007;13:465-476. (Pubitemid 46404030)
44. Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J Mol Graph 1996;14:33-8, 27.
45. Hofman R, Minkin VI, Carpenter BK. Ockham's razor and chemistry. HYLE Int J Phil Chem 1997;3:3-28.
46. Walker CA, Owasoyo JO. Te infuence of serotonin, GABA and dl-dopa on the circadian rhythm in the toxicity of picrotoxin, pentylenetetrazol and phenobarbital in mice. Int J Chronobiol 1974;2:125-130.
47. Golbraikh A, Tropsha A. Beware of q2! J Mol Graph Model 2002;20:269-276.
48. Akaike H. A new look at the statistical model identifcation. IEEE Trans Automat Contr AC-19 1974;716-723.
49. Kubinyi H. Variable selection in QSAR studies 2: a highly efcient combination of systematic search and evolution. QSAR 1994;13:393-401.
50. Anderson MJ, Legendre P. An empirical comparison of permutation methods for test of partial regression coefcients in a linear model. J Stat Comput Simul 1999;62:271-303.
51. Basak SC, Balaban AT, Grunwald GD, Gute BD. Topological indices: their nature and mutual relatedness. J Chem Inf Comput Sci 2000;40:891-898.
52. Broto P, Moreau G, Vandycke C. Molecular structures perception, autocorrelation descriptor and SAR studies. Eur J Med Chem 1984;19:66-70. (Pubitemid 14156801)
53. Frédérick R, Robert S, Charlier C, Wouters J, Masereel B, Pochet L. Mechanism-based thrombin inhibitors: design, synthesis, and molecular docking of a new selective 2-oxo-2H-1-benzopyran derivative. J Med Chem 2007;50:3645-3650. (Pubitemid 47195469)
54. Brandstetter H, Turk D, Hoefken HW, Grosse D, Stürzebecher J, Martin PD et al. Refned 2.3 A X-ray crystal structure of bovine thrombin complexes formed with the benzamidine and arginine-based thrombin inhibitors NAPAP, 4-TAPAP and MQPA. A starting point for improving antithrombotics. J Mol Biol 1992;226:1085-1099.
55. Banner DW, Hadváry P. Crystallographic analysis at 3.0-A resolution of the binding to human thrombin of four active site-directed inhibitors. J Biol Chem 1991;266:20085-20093. (Pubitemid 21908430)
56. Nishi H, Ota M. Amino acid substitutions at protein-protein interfaces that modulate the oligomeric state. Proteins 2010;78:1563-1574.
57. Hemmateenejad B, Javadnia K, Elyasi M. Quantitative structure-retention relationship for the Kovats retention indices of a large set of terpenes: a combined data splitting-feature selection strategy. Anal Chim Acta 2007;592:72-81. (Pubitemid 46702097)