Investigations of FAK inhibitors: a combination of 3D-QSAR, docking, and molecular dynamics simulations studies

References

• Andersen, H. C. (1983). Rattle: A “velocity” version of the shake algorithm for molecular dynamics calculations. Journal of Computational Physics, 52, 24–34.10.1016/0021-9991(83)90014-1
   Web of Science ®Google Scholar
• Athar, M., Lone, M. Y., Khedkar, V. M., & Jha, P. C. (2016). Pharmacophore model prediction, 3D-QSAR and molecular docking studies on vinyl sulfones targeting Nrf2-mediated gene transcription intended for anti-Parkinson drug design. Journal of Biomolecular Structure and Dynamics, 34, 1282–1297.10.1080/07391102.2015.1077343
   PubMed Web of Science ®Google Scholar
• Badhani, B., & Kakkar, R. (2016). In silico studies on potential MCF-7 inhibitors: A combination of pharmacophore and 3D-QSAR modeling, virtual screening, molecular docking, and pharmacokinetic analysis. Journal of Biomolecular Structure and Dynamics, 1–18. doi: 10.1080/07391102.2016.1202863
   PubMed Web of Science ®Google Scholar
• Benlimame, N., He, Q., Jie, S., Xiao, D. Z., Xu, Y. J., Loignon, M., … Alaoui-Jamali, M. A. (2005). FAK signaling is critical for ErbB-2/ErbB-3 receptor cooperation for oncogenic transformation and invasion. The Journal of Cell Biology, 171, 505–516.10.1083/jcb.200504124
   PubMed Web of Science ®Google Scholar
• Béraud, C., Dormoy, V., Danilin, S., Lindner, V., Béthry, A., Hochane, M., … Coquard, Catherine (2015). Targeting FAK scaffold functions inhibits human renal cell carcinoma growth. International Journal of Cancer, 137, 1549–1559.10.1002/ijc.29522
   PubMed Web of Science ®Google Scholar
• Case, D. A., Cheatham, T. E., Darden, T., Gohlke, H., Luo, R., Merz, K. M., … Woods, R. J. (2005). The Amber biomolecular simulation programs. Journal of Computational Chemistry, 26, 1668–1688.10.1002/(ISSN)1096-987X
   PubMed Web of Science ®Google Scholar
• Chen, I. H., Shih, H. C., Hsieh, P. W., Chang, F. R., Wu, Y. C., & Wu, C. C. (2015). HPW-RX40 restores anoikis sensitivity of human breast cancer cells by inhibiting integrin/FAK signaling. Toxicology and Applied Pharmacology, 289, 330–340.10.1016/j.taap.2015.09.011
   PubMed Web of Science ®Google Scholar
• Clark, M., Cramer, R. D., & Van Opdenbosch, N. (1989). Validation of the general purpose tripos 5.2 force field. Journal of Computational Chemistry, 10, 982–1012.10.1002/(ISSN)1096-987X
   Web of Science ®Google Scholar
• Cornell, W. D., Cieplak, P., Bayly, C. I., & Kollmann, P. A. (1993). Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation. Journal of the American Chemical Society, 115, 9620–9631.10.1021/ja00074a030
   Web of Science ®Google Scholar
• Da Silva, C. H., & Taft, C. A. (2016). 3D descriptors calculation and conformational search to investigate potential bioactive conformations, with application in 3D-QSAR and virtual screening in drug design. Journal of Biomolecular Structure and Dynamics, 1–9. doi: 10.1080/07391102.2016.1237382
   PubMed Web of Science ®Google Scholar
• Dao, P., Jarray, R., Le Coq, J., Lietha, D., Loukaci, A., Lepelletier, Y., … Chen, H. (2013). Synthesis of novel diarylamino-1,3,5-triazine derivatives as FAK inhibitors with anti-angiogenic activity. Bioorganic & Medicinal Chemistry Letters, 23, 4552–4556.10.1016/j.bmcl.2013.06.038
   PubMed Web of Science ®Google Scholar
• Dao, P., Jarray, R., Smith, N., Lepelletier, Y., Le Coq, J., Lietha, D., … Chen, H. (2014). Inhibition of both focal adhesion kinase and fibroblast growth factor receptor 2 pathways induces anti-tumor and anti-angiogenic activities. Cancer Letters, 348, 88–99.10.1016/j.canlet.2014.03.007
   PubMed Web of Science ®Google Scholar
• Dao, P., Smith, N., Tomkiewicz-Raulet, C., Yen-Pon, E., Camacho-Artacho, M., Lietha, D., … Chen, H. (2015). Design, synthesis, and evaluation of novel imidazo[1,2-a][1,3,5]triazines and their derivatives as focal adhesion kinase inhibitors with antitumor activity. Journal of Medicinal Chemistry, 58, 237–251.10.1021/jm500784e
   PubMed Web of Science ®Google Scholar
• Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems. The Journal of Chemical Physics, 98, 10089–10092.10.1063/1.464397
   Web of Science ®Google Scholar
• Diniz, E. M., Tomich de Paula da Silva, C. H., Gómez-Perez, V., Federico, L. B., & Campos Rosa, J. M. (2016). GRIND2-based 3D-QSAR and prediction of activity spectra for symmetrical bis-pyridinium salts with promastigote antileishmanial activity. Journal of Biomolecular Structure and Dynamics, 1–11. doi: 10.1080/07391102.2016.1221364
   PubMed Web of Science ®Google Scholar
• Fashena, S. J., & Thomas, S. M. (2000). Signalling by adhesion receptors. Nature Cell Biology, 2, E225–E229.10.1038/35046654
   PubMedGoogle Scholar
• Friesner, R. A., Murphy, R. B., Repasky, M. P., Frye, L. L., Greenwood, J. R., Halgren, T. A., … Mainz, D. T. (2006). Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. Journal of Medicinal Chemistry, 49, 6177–6196.10.1021/jm051256o
   PubMed Web of Science ®Google Scholar
• Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., … Fox, D. J. (2009). GAUSSIAN 09 (revision B.01). Wallingford, CT: Gaussian.
   Google Scholar
• Genheden, S., Kongsted, J., Söderhjelm, P., & Ryde, U. (2010). Nonpolar solvation free energies of protein−ligand complexes. Journal of Chemical Theory and Computation, 6, 3558–3568.10.1021/ct100272s
   PubMed Web of Science ®Google Scholar
• Homeyer, N., Horn, A. H. C., Lanig, H., & Sticht, H. (2006). AMBER force-field parameters for phosphorylated amino acids in different protonation states: phosphoserine, phosphothreonine, phosphotyrosine, and phosphohistidine. Journal of Molecular Modeling, 12, 281–289.10.1007/s00894-005-0028-4
   PubMed Web of Science ®Google Scholar
• Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., & Simmerling, C. (2006). Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins-Structure Function and Bioinformatics, 65, 712–725.10.1002/prot.v65:3
   PubMed Web of Science ®Google Scholar
• Hou, T. J., Wang, J. M., Li, Y. Y., & Wang, W. (2011). Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking. Journal of Computational Chemistry, 32, 866–877.10.1002/jcc.v32.5
   PubMed Web of Science ®Google Scholar
• Kumar, A., Roy, S., Tripathi, S., & Sharma, A. (2016). Molecular docking based virtual screening of natural compounds as potential BACE1 inhibitors: 3D QSAR pharmacophore mapping and molecular dynamics analysis. Journal of Biomolecular Structure & Dynamics, 34, 239–249.10.1080/07391102.2015.1022603
   PubMed Web of Science ®Google Scholar
• Kuo, C. L., Assefa, H., Kamath, S., Brzozowski, Z., Slawinski, J., Saczewski, F., … Neamati, N. (2004). Application of CoMFA and CoMSIA 3D-QSAR and docking studies in optimization of mercaptobenzenesulfonamides as HIV-1 integrase inhibitors. Journal of Medicinal Chemistry, 47, 385–399.10.1021/jm030378i
   PubMed Web of Science ®Google Scholar
• Lebrun, P., Mothe-Satney, I., Delahaye, L., Van Obberghen, E., & Baron, V. (1998). Insulin receptor substrate-1 as a signaling molecule for focal adhesion kinase pp125(FAK) and pp60(src). Journal of Biological Chemistry, 273, 32244–32253.10.1074/jbc.273.48.32244
   PubMed Web of Science ®Google Scholar
• Lim, S. T., Mikolon, D., Stupack, D. G., & Schlaepfer, D. D. (2008). FERM control of FAK function – implications for cancer therapy. Cell Cycle, 7, 2306–2314.10.4161/cc.6367
   PubMed Web of Science ®Google Scholar
• Liu, T. J., LaFortune, T., Honda, T., Ohmori, O., Hatakeyama, S., Meyer, T., … Yung, W. K. (2007). Inhibition of both focal adhesion kinase and insulin-like growth factor-I receptor kinase suppresses glioma proliferation in vitro and in vivo. Molecular Cancer Therapeutics, 6, 1357–1367.10.1158/1535-7163.MCT-06-0476
   PubMed Web of Science ®Google Scholar
• Lu, X. Y., Lv, M., Huang, K., Ding, K., & You, Q. D. (2012). Pharmacophore and molecular docking guided 3D-QSAR study of bacterial enoyl-ACP reductase (FabI) inhibitors. International Journal of Molecular Sciences, 13, 6620–6638.10.3390/ijms13066620
   PubMed Web of Science ®Google Scholar
• Mark, P., & Nilsson, L. (2001). Structure and dynamics of the TIP3P, SPC, and SPC/E water models at 298 K. The Journal of Physical Chemistry A, 105, 9954–9960.10.1021/jp003020w
   Web of Science ®Google Scholar
• Mitra, S. K., Mikolon, D., Molina, J. E., Hsia, D. A., Hanson, D. A., Chi, A., & Lim, S-T (2006). Intrinsic FAK activity and Y925 phosphorylation facilitate an angiogenic switch in tumors. Oncogene, 25, 5969–5984.10.1038/sj.onc.1209588
   PubMed Web of Science ®Google Scholar
• O’Neil, R. H., Lilien, R. H., Donald, B. R., Stroud, R. M., & Anderson, A. C. (2003). Phylogenetic classification of protozoa based on the structure of the linker domain in the bifunctional enzyme, dihydrofolate reductase-thymidylate synthase. Journal of Biological Chemistry, 278, 52980–52987.10.1074/jbc.M310328200
   PubMed Web of Science ®Google Scholar
• Park, S. A., Kim, M. J., Park, S. Y., Kim, J. S., Lim, W., Nam, J. S., & Sheen, Y. Y. (2015). TIMP-1 mediates TGF-β-dependent crosstalk between hepatic stellate and cancer cells via FAK signaling. Scientific Reports, 5, 16492.10.1038/srep16492
   PubMed Web of Science ®Google Scholar
• Parsons, J. T. (2003). Focal adhesion kinase: the first ten years. Journal of Cell Science, 116, 1409–1416.10.1242/jcs.00373
   PubMed Web of Science ®Google Scholar
• Punkvang, A., Hannongbua, S., Saparpakorn, P., & Pungpo, P. (2016). Insight into the structural requirements of aminopyrimidine derivatives for good potency against both purified enzyme and whole cells of M-tuberculosis: combination of HQSAR, CoMSIA, and MD simulation studies. Journal of Biomolecular Structure & Dynamics, 34, 1079–1091.10.1080/07391102.2015.1068711
   PubMed Web of Science ®Google Scholar
• Qi, J. H., & Claesson-Welsh, L. (2001). VEGF-induced activation of phosphoinositide 3-kinase is dependent on focal adhesion kinase. Experimental Cell Research, 263, 173–182.10.1006/excr.2000.5102
   PubMed Web of Science ®Google Scholar
• Rastelli, G., Del Rio, A., Degliesposti, G., & Sgobba, M. (2010). Fast and accurate predictions of binding free energies using MM-PBSA and MM-GBSA. Journal of Computational Chemistry, 31, 797–810.
   PubMed Web of Science ®Google Scholar
• Roberts, W. G., Ung, E., Whalen, P., Cooper, B., Hulford, C., Autry, C., … Vajdos, F. (2008). antitumor activity and pharmacology of a selective focal adhesion kinase inhibitor, PF-562,271. Cancer Research, 68, 1935–1944.10.1158/0008-5472.CAN-07-5155
   PubMed Web of Science ®Google Scholar
• Rodriguez-Fernandez, J. L., & Rozengurt, E. (1998). Bombesin, vasopressin, lysophosphatidic acid, and sphingosylphosphorylcholine induce focal adhesion kinase activation in intact Swiss 3T3 Cells. Journal of Biological Chemistry, 273, 19321–19328.10.1074/jbc.273.30.19321
   PubMed Web of Science ®Google Scholar
• Schwartz, M. A. (1993). Signaling by integrins: implications for tumorigenesis. Cancer Research, 53, 1503–1506.
   PubMed Web of Science ®Google Scholar
• Schwartz, M. A., & Ginsberg, M. H. (2002). Networks and crosstalk: integrin signalling spreads. Nature Cell Biology, 4, E65–E68.10.1038/ncb0402-e65
   PubMed Web of Science ®Google Scholar
• Sitkoff, D., Sharp, K. A., & Honig, B. (1994). Accurate calculation of hydration free energies using macroscopic solvent models. The Journal of Physical Chemistry, 98, 1978–1988.10.1021/j100058a043
   Web of Science ®Google Scholar
• Tancioni, I., Miller, N. L. G., Uryu, S., Lawson, C., Jean, C., Chen, X. L., … Schlaepfer, D. D. (2015). FAK activity protects nucleostemin in facilitating breast cancer spheroid and tumor growth. Breast Cancer Research, 17, 9.10.1186/s13058-015-0551-x
   PubMed Web of Science ®Google Scholar
• Tomich de Paula da Silva, C. H., Campos Bernardes, L. S., da Silva, V. B., Zani, C. L., & Carvalho, I. (2012). Novel aryl beta-aminocarbonyl derivatives as inhibitors of Trypanosoma cruzi trypanothione reductase: binding mode revised by docking and GRIND2-based 3D-QSAR procedures. Journal of Biomolecular Structure & Dynamics, 29, 702–716.
   PubMed Web of Science ®Google Scholar
• Tripuraneni, N. S., & Azam, M. A. (2016). A combination of pharmacophore modeling, atom-based 3D-QSAR, molecular docking and molecular dynamics simulation studies on PDE4 enzyme inhibitors. Journal of Biomolecular Structure and Dynamics, 34, 2481–2492.10.1080/07391102.2015.1119732
   PubMed Web of Science ®Google Scholar
• Tsai, K. C., Chen, Y. C., Hsiao, N. W., Wang, C. L., Lin, C. L., Lee, Y. C., … Wang, B. H. (2010). A comparison of different electrostatic potentials on prediction accuracy in CoMFA and CoMSIA studies. European Journal of Medicinal Chemistry, 45, 1544–1551.10.1016/j.ejmech.2009.12.063
   PubMed Web of Science ®Google Scholar
• Wang, J. M., Cieplak, P., & Kollman, P. A. (2000). How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? Journal of Computational Chemistry, 21, 1049–1074.10.1002/(ISSN)1096-987X
   Web of Science ®Google Scholar
• Wang, J. M., Wolf, R. M., Caldwell, J. W., Kollman, P. A., & Case, D. A. (2004). Development and testing of a general amber force field. Journal of Computational Chemistry, 25, 1157–1174.10.1002/(ISSN)1096-987X
   PubMed Web of Science ®Google Scholar
• Wang, X., Xu, X., Ma, M., Zhou, W., Wang, Y., & Yang, L. (2012). pH-dependent channel gating in connexin26 hemichannels involves conformational changes in N-terminus. Biochimica et Biophysica Acta (BBA) - Biomembranes, 1818, 1148–1157.10.1016/j.bbamem.2011.12.027
   PubMed Web of Science ®Google Scholar
• Wang, J., Li, Y., Yang, Y., Zhang, S., & Yang, L. (2013). Profiling the structural determinants of heteroarylnitrile scaffold-based derivatives as falcipain-2 inhibitors by in silico methods. Current Medicinal Chemistry, 20, 2032–2042.10.2174/0929867311320150008
   PubMed Web of Science ®Google Scholar
• Wang, F., Yang, W., Shi, Y., & Le, G. (2015). 3D-QSAR, molecular docking and molecular dynamics studies of a series of RORγt inhibitors. Journal of Biomolecular Structure & Dynamics, 33, 1929–1940.10.1080/07391102.2014.980321
   PubMed Web of Science ®Google Scholar
• Wang, J., Yang, Y., Li, Y., & Wang, Y. (2016). Computational study exploring the interaction mechanism of benzimidazole derivatives as potent cattle bovine viral diarrhea virus inhibitors. Journal of Agricultural and Food Chemistry, 64, 5941–5950.10.1021/acs.jafc.6b01067
   PubMed Web of Science ®Google Scholar
• van de Waterbeemd, H., & Gifford, E. (2003). ADMET in silico modelling: towards prediction paradise? Nature Reviews Drug Discovery, 2, 192–204.10.1038/nrd1032
   PubMed Web of Science ®Google Scholar
• Xu, X., Li, R., Ma, M., Wang, X., Wang, Y., & Zou, H. (2012). Multidrug resistance protein P-glycoprotein does not recognize nanoparticle C60: experiment and modeling. Soft Matter, 8, 2915–2923.10.1039/c2sm06811g
   Web of Science ®Google Scholar
• Xu, X., Wang, X., Li, Y., Wang, Y., & Yang, L. (2012). A large-scale association study for nanoparticle C60 uncovers mechanisms of nanotoxicity disrupting the native conformations of DNA/RNA. Nucleic Acids Research, 40, 7622–7632.10.1093/nar/gks517
   PubMed Web of Science ®Google Scholar
• Xu, L., Sun, H. Y., Li, Y. Y., Wang, J. M., & Hou, T. J. (2013). Assessing the performance of MM/PBSA and MM/GBSA methods. 3. The impact of force fields and ligand charge models. The Journal of Physical Chemistry B, 117, 8408–8421.
   PubMed Web of Science ®Google Scholar
• Yang, Y., Qin, J., Liu, H., & Yao, X. (2011). Molecular dynamics simulation, free energy calculation and structure-based 3D-QSAR studies of B-RAF kinase inhibitors. Journal of Chemical Information and Modeling, 51, 680–692.10.1021/ci100427j
   PubMed Web of Science ®Google Scholar
• Zhang, H. X., Li, Y., Wang, X., Xiao, Z. T., & Wang, Y. H. (2011). Insight into the structural requirements of benzothiadiazine scaffold-based derivatives as hepatitis C virus NS5B polymerase inhibitors using 3D-QSAR, molecular docking and molecular dynamics. Current Medicinal Chemistry, 18, 4019–4028.10.2174/092986711796957220
   PubMed Web of Science ®Google Scholar
• Zhou, S., Fang, D., Tan, S., Lin, W., Wu, W., & Zheng, K. (2016). Investigating the binding mechanism of novel 6-aminonicotinate-based antagonists with P2Y12 by 3D-QSAR, docking and molecular dynamics simulations. Journal of Biomolecular Structure and Dynamics, 1–28. doi: 10.1080/07391102.2016.1237381
   Web of Science ®Google Scholar