References
- 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.
- 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.
- Harlan JM, Thompson 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.
- Jones A, Geczy CL. Thrombin and factor Xa enhance the production of interleukin-1. Immunology 1990;71:236–241.
- 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.
- McNamara CA, Sarembock IJ, Gimple LW, Fenton JW 2nd, Coughlin SR, Owens GK. Thrombin stimulates proliferation of cultured rat aortic smooth muscle cells by a proteolytically activated receptor. J Clin Invest 1993;91:94–98.
- Carney DH, Glenn KC, Cunningham DD. Conditions which affect initiation of animal cell division by trypsin and thrombin. J Cell Physiol 1978;95:13–22.
- Wiley MR, Fisher MJ. Small molecules direct thrombin inhibitors. Exp Opin Ther Pat 1997;7:1265–1282.
- 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.
- Sanderson PE, Cutrona KJ, Dorsey BD, Dyer DL, McDonough CM, Naylor-Olsen AM et al. L-374,087, an efficacious, orally bioavailable, pyridinone acetamide thrombin inhibitor. Bioorg Med Chem Lett 1998;8:817–822.
- Sanderson PE, Lyle TA, Cutrona KJ, Dyer DL, Dorsey BD, McDonough CM et al. Efficacious, orally bioavailable thrombin inhibitors based on 3-aminopyridinone or 3-aminopyrazinone acetamide peptidomimetic templates. J Med Chem 1998;41:4466–4474.
- 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.
- 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.
- 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.
- 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.
- Coop A, MacKerell AD. The future of opioid analgesics. Am J Pharm Educ 2002;66:153–156.
- Hansch C, Leo A. QSAR of nonspecific toxicity. In: Heller SR, ed. Exploring QSAR: Fundamentals and Applications in Chemistry and Biology. Washington, DC: American Chemical Society, 1995, pp. 169–221.
- Krogsgaard-Larsen P, Liljerfors T, Madsen U. Textbook of Drug Design and Discovery. New York, USA: Taylor & Francis, CRC Press, 2002.
- Todeschini R, Consonni V. Handbook of Molecular Descriptors. Weinheim, Germany: Wiley-VCH, 2000.
- Karelson M. Molecular Descriptors in QSAR/QSPR. New York, USA: Wiley-Interscience, 2000.
- 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.
- 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.
- Bonachéra F, Horvath D. Fuzzy tricentric pharmacophore fingerprints. 2. Application of topological fuzzy pharmacophore triplets in quantitative structure–activity relationships. J Chem Inf Model 2008;48:409–425.
- Xu L, Zhang WJ. Comparison of different methods for variable selection. Anal Chem Acta 2001;446:475–481.
- Schneider G, Wrede P. Artificial neural networks for computer-based molecular design. Prog Biophys Mol Biol 1998;70:175–222.
- Ramírez-Galicia G, Garduño-Juárez R, Deeb O, Hemmateenejad B. MLR-ANN and RTO approach to mu-opioid receptor-binding affinity. Pooling data from different sources. Chem Biol Drug Des 2008;71:260–270.
- 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.
- 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.
- 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 flexible ligand–protein interactions. Biopolymers 2010;93:161–170.
- 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.
- 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.
- Blaney JM, Dixon JS. A good ligand is hard to find: automated docking methods. Perspect Drug Discov Design 1993;1:301–319.
- Kuntz ID, Meng EC, Shoichet BK. Structure-based molecular design. Acc Chem Res 1994;27:117–123.
- 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.
- HyperChem™ [computer program]. Release 7.1 for Windows. Gainesville, FL: Hypercube, Inc., 2002.
- Stewart JJP. Optimization of parameters for semiempirical methods I. Method. J Comp Chem 1989;10:209–220.
- Stewart JPP. MOPAC 6.0 QCPE Program No 455. Chemistry Department, Indiana University, Bloomington, IN, 1989.
- Baker J. An algorithm for the location of transition states. J Compt Chem 1993;7:385–395.
- Todeschini R, Consonni V, Pavan M. Dragon Software version 2.1-2002 Pisani 13, Milano, Italy. Dragon Software and references therein, 2002.
- Guha R, Jurs PC. Determining the validity of a QSAR model—a classification approach. J Chem Inf Model 2005;45:65–73.
- Topliss JG, Costello RJ. Change correlations in structure–activity studies using multiple regression analysis. J Med Chem 1972;15:1066–1068.
- Topliss JG, Edwards RP. Chance factors in studies of quantitative structure–activity relationships. J Med Chem 1979;22:1238–1244.
- 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.
- Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J Mol Graph 1996;14:33–8, 27.
- Hoffman R, Minkin VI, Carpenter BK. Ockham’s razor and chemistry. HYLE Int J Phil Chem 1997;3:3–28.
- Walker CA, Owasoyo JO. The influence 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.
- Golbraikh A, Tropsha A. Beware of q2! J Mol Graph Model 2002;20:269–276.
- Akaike H. A new look at the statistical model identification. IEEE Trans Automat Contr AC-19 1974;716–723.
- Kubinyi H. Variable selection in QSAR studies 2: a highly efficient combination of systematic search and evolution. QSAR 1994;13:393–401.
- Anderson MJ, Legendre P. An empirical comparison of permutation methods for test of partial regression coefficients in a linear model. J Stat Comput Simul 1999;62:271–303.
- Basak SC, Balaban AT, Grunwald GD, Gute BD. Topological indices: their nature and mutual relatedness. J Chem Inf Comput Sci 2000;40:891–898.
- Broto P, Moreau G, Vandycke C. Molecular structures perception, autocorrelation descriptor and SAR studies. Eur J Med Chem 1984;19:66–70.
- 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.
- Brandstetter H, Turk D, Hoeffken HW, Grosse D, Stürzebecher J, Martin PD et al. Refined 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.
- 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.
- Nishi H, Ota M. Amino acid substitutions at protein–protein interfaces that modulate the oligomeric state. Proteins 2010;78:1563–1574.
- 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.