Pharmacophore based 3D-QSAR modeling and free energy analysis of VEGFR-2 inhibitors

References

• Rahimi N. Vascular endothelial growth factor receptors: molecular mechanisms of activation and therapeutic potentials. Exp Eye Res 2006;83:1005–1016.
   PubMed Web of Science ®Google Scholar
• Iwata H, Imamura S, Hori A, Hixon MS, Kimura H, Miki H. Biochemical characterization of a novel type-II VEGFR2 kinase inhibitor: comparison of binding to non-phosphorylated and phosphorylated VEGFR2. Bioorg Med Chem 2011;19:5342–5351.
   PubMedGoogle Scholar
• Ferrara N, Gerber HP, LeCouter J. The biology of VEGF and its receptors. Nat Med 2003;9:669–676.
   PubMed Web of Science ®Google Scholar
• Schenone S, Bondavalli F, Botta M. Antiangiogenic agents: an update on small molecule VEGFR inhibitors. Curr Med Chem 2007;14:2495–2516.
   PubMed Web of Science ®Google Scholar
• Holmes K, Roberts OL, Thomas AM, Cross MJ. Vascular endothelial growth factor receptor-2: structure, function, intracellular signalling and therapeutic inhibition. Cell Signal 2007;19:2003–2012.
   PubMed Web of Science ®Google Scholar
• Manley PW, Bold G, Brüggen J, Fendrich G, Furet P, Mestan J et al. Advances in the structural biology, design and clinical development of VEGF-R kinase inhibitors for the treatment of angiogenesis. Biochim Biophys Acta 2004;1697:17–27.
   PubMed Web of Science ®Google Scholar
• Roskoski R Jr. VEGF receptor protein-tyrosine kinases: structure and regulation. Biochem Biophys Res Commun 2008;375:287–291.
   PubMed Web of Science ®Google Scholar
• Kendall RL, Rutledge RZ, Mao X, Tebben AJ, Hungate RW, Thomas KA. Vascular endothelial growth factor receptor KDR tyrosine kinase activity is increased by autophosphorylation of two activation loop tyrosine residues. J Biol Chem 1999;274:6453–6460.
   PubMed Web of Science ®Google Scholar
• Leppänen VM, Prota AE, Jeltsch M, Anisimov A, Kalkkinen N, Strandin T et al. Structural determinants of growth factor binding and specificity by VEGF receptor 2. Proc Natl Acad Sci USA 2010;107:2425–2430.
   PubMedGoogle Scholar
• Franklin MC, Navarro EC, Wang Y, Patel S, Singh P, Zhang Y et al. The structural basis for the function of two anti-VEGF receptor 2 antibodies. Structure 2011;19:1097–1107.
   PubMed Web of Science ®Google Scholar
• Miyazaki Y, Matsunaga S, Tang J, Maeda Y, Nakano M, Philippe RJ et al. Novel 4-amino-furo[2,3-d]pyrimidines as Tie-2 and VEGFR2 dual inhibitors. Bioorg Med Chem Lett 2005;15:2203–2207.
   PubMed Web of Science ®Google Scholar
• Hasegawa M, Nishigaki N, Washio Y, Kano K, Harris PA, Sato H et al. Discovery of novel benzimidazoles as potent inhibitors of TIE-2 and VEGFR-2 tyrosine kinase receptors. J Med Chem 2007;50:4453–4470.
   PubMed Web of Science ®Google Scholar
• Lee K, Jeong KW, Lee Y, Song JY, Kim MS, Lee GS et al. Pharmacophore modeling and virtual screening studies for new VEGFR-2 kinase inhibitors. Eur J Med Chem 2010;45:5420–5427.
   PubMed Web of Science ®Google Scholar
• Morabito A, De Maio E, Di Maio M, Normanno N, Perrone F. Tyrosine kinase inhibitors of vascular endothelial growth factor receptors in clinical trials: current status and future directions. Oncologist 2006;11:753–764.
   PubMed Web of Science ®Google Scholar
• Huang S, Li R, Connolly PJ, Xu G, Gaul MD, Emanuel SL et al. Synthesis and biological study of 4-aminopyrimidine-5-carboxaldehyde oximes as antiproliferative VEGFR-2 inhibitors. Bioorg Med Chem Lett 2006;16:6063–6066.
   PubMedGoogle Scholar
• Huang S, Li R, LaMontagne KR, Greenberger LM, Connolly PJ. 4-aminopyrimidine-5-carbaldehyde oximes as potent VEGFR-2 inhibitors. Part II. Bioorg Med Chem Lett 2011;21:1815–1818.
   PubMedGoogle Scholar
• Kubo K, Shimizu T, Ohyama S, Murooka H, Iwai A, Nakamura K et al. Novel potent orally active selective VEGFR-2 tyrosine kinase inhibitors: synthesis, structure-activity relationships, and antitumor activities of N-phenyl-N’-{4-(4-quinolyloxy)phenyl}ureas. J Med Chem 2005;48:1359–1366.
   PubMed Web of Science ®Google Scholar
• Dhanachandra Singh Kh, Karthikeyan M, Kirubakaran P, Nagamani S. Pharmacophore filtering and 3D-QSAR in the discovery of new JAK2 inhibitors. J Mol Graph Model 2011;30:186–197.
   PubMed Web of Science ®Google Scholar
• Dixon SL, Smondyrev AM, Rao SN. PHASE: a novel approach to pharmacophore modeling and 3D database searching. Chem Biol Drug Des 2006;67:370–372.
   PubMed Web of Science ®Google Scholar
• John S, Thangapandian S, Sakkiah S, Lee KW. Discovery of potential pancreatic cholesterol esterase inhibitors using pharmacophore modelling, virtual screening, and optimization studies. J Enzyme Inhib Med Chem 2011;26:535–545.
   PubMed Web of Science ®Google Scholar
• Ebalunode JO, Zheng W, Tropsha A. Application of QSAR and shape pharmacophore modeling approaches for targeted chemical library design. Methods Mol Biol 2011;685:111–133.
   PubMedGoogle Scholar
• Yang SY. Pharmacophore modeling and applications in drug discovery: challenges and recent advances. Drug Discov Today 2010;15:444–450.
   PubMed Web of Science ®Google Scholar
• Khedkar SA, Malde AK, Coutinho EC, Srivastava S. Pharmacophore modeling in drug discovery and development: an overview. Med Chem 2007;3:187–197.
   PubMed Web of Science ®Google Scholar
• Langer T, Wolber G. Pharmacophore definition and 3D searches. Drug Discov Today. 2004;1:203–207.
   Google Scholar
• Gilson MK, Zhou HX. Calculation of protein-ligand binding affinities. Annu Rev Biophys Biomol Struct 2007;36:21–42.
   PubMedGoogle Scholar
• Hu G, Wang D, Liu X, Zhang Q. A computational analysis of the binding model of MDM2 with inhibitors. J Comput Aided Mol Des 2010;24:687–697.
   PubMed Web of Science ®Google Scholar
• Stoica I, Sadiq SK, Coveney PV. Rapid and accurate prediction of binding free energies for saquinavir-bound HIV-1 proteases. J Am Chem Soc 2008;130:2639–2648.
   PubMed Web of Science ®Google Scholar
• Rastelli G, Del Rio A, Degliesposti G, Sgobba M. Fast and accurate predictions of binding free energies using MM-PBSA and MM-GBSA. J Comput Chem 2010;31:797–810.
   PubMed Web of Science ®Google Scholar
• Hou T, Wang J, Li Y, Wang W. Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations. J Chem Inf Model 2011;51:69–82.
   PubMed Web of Science ®Google Scholar
• Hu G, Zhang Q, Chen LY. Insights into scFv:drug binding using the molecular dynamics simulation and free energy calculation. J Mol Model 2011;17:1919–1926.
   PubMedGoogle Scholar
• Muthukumaran R, Sangeetha B, Amutha R, Mathur PP. Development of anti-HIV activity models of lysine sulfonamide analogs: a QSAR perspective. Curr Comput Aided Drug Des 2012;8:70–82.
   PubMed Web of Science ®Google Scholar
• Dixon SL, Smondyrev AM, Knoll EH, Rao SN, Shaw DE, Friesner RA. PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results. J Comput Aided Mol Des 2006;20:647–671.
   PubMed Web of Science ®Google Scholar
• Banks JL, Beard HS, Cao Y, Cho AE, Damm W, Farid R et al. Integrated Modeling Program, Applied Chemical Theory (IMPACT). J Comput Chem 2005;26:1752–1780.
   PubMed Web of Science ®Google Scholar
• Papakyriakou A, Katsarou ME, Belimezi M, Karpusas M, Vourloumis D. Discovery of potent vascular endothelial growth factor receptor-2 inhibitors. ChemMedChem 2010;5:118–129.
   PubMed Web of Science ®Google Scholar
• Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT et al. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 2004;47:1739–1749.
   PubMed Web of Science ®Google Scholar
• Case DA, Cheatham TE 3rd , Darden T, Gohlke H, Luo R, Merz KM Jr et al. The Amber biomolecular simulation programs. J Comput Chem 2005;26:1668–1688.
   PubMed Web of Science ®Google Scholar
• Hornak V, Abel R, Okur A, Strockbine B, Roitberg A, Simmerling C. Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins 2006;65:712–725.
   PubMed Web of Science ®Google Scholar
• Wang J, Wang W, Kollman PA, Case DA. Automatic atom type and bond type perception in molecular mechanical calculations. J Mol Graph Model 2006;25:247–260.
   PubMed Web of Science ®Google Scholar
• Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA. Development and testing of a general amber force field. J Comput Chem 2004;25:1157–1174.
   PubMed Web of Science ®Google Scholar
• Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Kleins ML. Comparison of simple potential functions for simulating liquid water. J Chem Phys 1983, 79, 926–993.
   Web of Science ®Google Scholar
• Darden T, York D, Pedersen L. Particle mesh Ewald: An N. log(N) method for Ewald sums in large systems. J Chem Phys 1993, 98, 10089–10092.
   Web of Science ®Google Scholar
• Ryckaert JP, Ciccotti G, Berendsen HJC. Numerical integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes. J Comput Phys 1977, 23, 327–341.
   Web of Science ®Google Scholar
• Gohlke H, Case DA. Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf. J Comput Chem 2004;25:238–250.
   PubMed Web of Science ®Google Scholar
• Onufriev A, Bashford D, Case DA. Exploring protein native states and large-scale conformational changes with a modified generalized born model. Proteins 2004;55:383–394.
   PubMed Web of Science ®Google Scholar