Design and screening of FAK, CDK 4/6 dual inhibitors by pharmacophore model, molecular docking, and molecular dynamics simulation

Reference

• Béraud, C., Dormoy, V., Danilin, S., Lindner, V., Béthry, A., Hochane, M., Coquard, C., Barthelmebs, M., Jacqmin, D., Lang, H., & Massfelder, T. (2015). Targeting FAK scaffold functions inhibits human renal cell carcinoma growth. International Journal of Cancer, 137(7), 1549–1559. https://doi.org/https://doi.org/10.1002/ijc.29522
   PubMed Web of Science ®Google Scholar
• Cai, C., Wu, Q., Luo, Y., Ma, H., Shen, J., Zhang, Y., Yang, L., Chen, Y., Wen, Z., & Wang, Q. (2017). In silico prediction of ROCK II inhibitors by different classification approaches. Molecular Diversity, 21(4), 791–717. https://doi.org/https://doi.org/10.1007/s11030-017-9772-5
   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(2), 330–340. https://doi.org/https://doi.org/10.1016/j.taap.2015.09.011
   PubMed Web of Science ®Google Scholar
• Fashena, S. J., & Thomas, S. M. (2000). Signalling by adhesion receptors. Nature Cell Biology, 2(12), E225–E229. https://doi.org/https://doi.org/10.1038/35046654
   PubMedGoogle Scholar
• Frame, M. C., Hitesh, P., Bryan, S., Daniel, L., & Eck, M. J. (2010). The FERM domain: Organizing the structure and function of FAK. Nature Reviews. Molecular Cell Biology, 11(11), 802–814. https://doi.org/https://doi.org/10.1038/nrm2996
   PubMed Web of Science ®Google Scholar
• Fry, D. W., Harvey, P. J., Keller, P. R., Elliott, W. L., Meade, M., Trachet, E., Albassam, M., Zheng, X., Leopold, W. R., Pryer, N. K., & Toogood, P. L. (2004). Specific inhibition of cyclin-dependent kinase 4/6 by PD 0332991 and associated antitumor activity in human tumor xenografts. Molecular Cancer Therapeutics, 3(11), 1427–1438.
   PubMed Web of Science ®Google Scholar
• Gelbert, L. M., Cai, S., Lin, X., Sanchez-Martinez, C., Del Prado, M., Lallena, M. J., Torres, R., Ajamie, R. T., Wishart, G. N., Flack, R. S., Neubauer, B. L., Young, J., Chan, E. M., Iversen, P., Cronier, D., Kreklau, E., & de Dios, A. (2014). Preclinical characterization of the CDK4/6 inhibitor LY2835219: In-vivo cell cycle-dependent/independent anti-tumor activities alone/in combination with gemcitabine. Investigational New Drugs, 32(5), 825–837. https://doi.org/https://doi.org/10.1007/s10637-014-0120-7
   PubMed Web of Science ®Google Scholar
• Hess, B., Kutzner, C., David, V. D. S., & Lindahl, E. (2008). Gromacs 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation, 4(3), 435–447. https://doi.org/https://doi.org/10.1021/ct700301q
   PubMed Web of Science ®Google Scholar
• Kang, Y., Hu, W., Ivan, C., Dalton, H. J., Miyake, T., Pecot, C. V., Zand, B., Liu, T., Huang, J., Jennings, N. B., Rupaimoole, R., Taylor, M., Pradeep, S., Wu, S. Y., Lu, C., Wen, Y., Huang, J., Liu, J., & Sood, A. K. (2013). Role of focal adhesion kinase in regulating YB-1-mediated paclitaxel resistance in ovarian cancer. JNCI: Journal of the National Cancer Institute, 105(19), 1485–1495. https://doi.org/https://doi.org/10.1093/jnci/djt210
   PubMedGoogle Scholar
• Katsumi, Y., Iehara, T., Miyachi, M., Yagyu, S., Tsubai-Shimizu, S., Kikuchi, K., Tamura, S., Kuwahara, Y., Tsuchiya, K., Kuroda, H., Sugimoto, T., Houghton, P., & Hosoi, H. (2011). Sensitivity of malignant rhabdoid tumor cell lines to PD 0332991 is inversely correlated with p16 expression. Biochemical and Biophysical Research Communications, 413(1), 62–68. https://doi.org/https://doi.org/10.1016/j.bbrc.2011.08.047
   PubMed Web of Science ®Google Scholar
• Kheder, N. A. (2016). Hydrazonoyl chlorides as precursors for synthesis of novel bis-pyrrole derivatives. Molecules (Basel, Switzerland), 21(3), 326. https://doi.org/https://doi.org/10.3390/molecules21030326
   PubMed Web of Science ®Google Scholar
• Ku, B. M., Yi, S. Y., Koh, J., Bae, Y. H., Sun, J., Le, e S. H., Ahn, J. S., Park, K., & Ahn, M. J. (2016). The CDK4/6 inhibitor LY2835219 has potent activity in combination with mTOR inhibitor in head and neck squamous cell carcinoma. Oncotarget, 7(12), 14803–14813. https://doi.org/https://doi.org/10.18632/oncotarget.7543
   PubMedGoogle Scholar
• Kwapisz, D. (2017). Cyclin-dependent kinase 4/6 inhibitors in breast cancer: Palbociclib, ribociclib, and abemaciclib. Breast Cancer Research and Treatment, 166(1), 41–54. https://doi.org/https://doi.org/10.1007/s10549-017-4385-3
   PubMed Web of Science ®Google Scholar
• Lietha, D., & Eck, M. J. (2008). Crystal structures of the FAK kinase in complex with TAE226 and related bis-anilino pyrimidine inhibitors reveal a helical DFG conformation. PLoS One, 3(11), e3800. https://doi.org/https://doi.org/10.1371/journal.pone.0003800
   PubMed Web of Science ®Google Scholar
• Rader, J., Russell, M. R., Hart, L. S., Nakazawa, M. S., Belcastro, L. T., Martinez, D., Li, Y., Carpenter, E. L., Attiyeh, E. F., Diskin, S. J., Kim, S., Parasuraman, S., Caponigro, G., Schnepp, R. W., Wood, A. C., Pawel, B., Cole, K. A., & Maris, J. M. (2013). Dual CDK4/CDK6 inhibition induces cell-cycle arrest and senescence in neuroblastoma. Clinical Cancer Research, 19(22), 6173–6182. https://doi.org/https://doi.org/10.1158/1078-0432.CCR-13-1675
   PubMed Web of Science ®Google Scholar
• Sánchez-Martínez, C., Gelbert, L. M., Lallena, M. J., & de Dios, A. (2015). DiosCyclin dependent kinase (CDK) inhibitors as anticancer drugs. Bioorganic & Medicinal Chemistry Letters, 25(17), 3420–3435. https://doi.org/https://doi.org/10.1016/j.bmcl.2015.05.100
   PubMed Web of Science ®Google Scholar
• Schaller, M. D. (2010). Cellular functions of FAK kinases: Insight into molecular mechanisms and novel functions. Journal of Cell Science, 123(Pt 7), 1007–1013. https://doi.org/https://doi.org/10.1242/jcs.045112
   PubMed Web of Science ®Google Scholar
• Schüttelkopf, A. W., & van Aalten, D. M. F. V. (2004). PRODRG: A tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallographica. Section D, Biological Crystallography, 60(Pt 8), 1355–1363. https://doi.org/https://doi.org/10.1107/S0907444904011679
   PubMedGoogle Scholar
• Schwartz, M. A., & Ginsberg, M. H. (2002). Networks and crosstalk: Integrin signalling spreads. Nature Cell Biology, 4(4), E65–68. https://doi.org/https://doi.org/10.1038/ncb0402-e65
   PubMed Web of Science ®Google Scholar
• Stocker, U., & Gunsteren, W. F. (2000). Molecular dynamics simulation of hen egg white lysozyme: A test of the gromos96 force field against nuclear magnetic resonance data. Proteins: Structure, Function, and Genetics, 40(1), 145–153. https://doi.org/https://doi.org/10.1002/(SICI)1097-0134(20000701)40:1<145::AID-PROT160>3.0.CO;2-Y
   PubMed Web of Science ®Google Scholar
• Tanjoni, I., Walsh, C., Uryu, S., Tomar, A., Nam, J., Mielgo, A., Lim, S., Liang, C., Koenig, M., Sun, C., Patel, N., Kwok, C., McMahon, G., Stupack, D. G., & Schlaepfer, D. D. (2010). PND-1186 FAK inhibitor selectively promotes tumor cell apoptosis in three-dimensional environments. Cancer Biology & Therapy, 9(10), 764–777. https://doi.org/https://doi.org/10.4161/cbt.9.10.11434
   PubMed Web of Science ®Google Scholar
• VanArsdale, T., Boshoff, C., Arndt, K. T., & Abraham, R. T. (2015). Molecular pathways: Targeting the cyclin D-CDK4/6 axis for cancer treatment. Clinical Cancer Research, 21(13), 2905–2910. https://doi.org/https://doi.org/10.1158/1078-0432.CCR-14-0816
   PubMed Web of Science ®Google Scholar
• Wang, C., Chang, S., & Gong, X. (2012). Progress in the scoring functions of protein-protein docking. Acta Physico-Chimica Sinica, 28, 751–758.
   Web of Science ®Google Scholar
• Yadav, V., Burke, T. F., Huber, L., Van, H. R. D., Zhang, Y., Buchanan, S. G., Chan, E. M., Starling, J. J., Beckmann, R. P., & Peng, S. B. (2014). The CDK4/6 inhibitor LY2835219 overcomes vemurafenib resistance resulting from MAPK reactivation and cyclin D1 upregulation. Molecular Cancer Therapeutics, 13(10), 2253–2263. https://doi.org/https://doi.org/10.1158/1535-7163.MCT-14-0257
   PubMed Web of Science ®Google Scholar
• Yang, Z. R., & Chou, K. C. (2004). Bio-support vector machines for computational proteomics. Bioinformatics (Oxford, England), 20(5), 735–741. https://doi.org/https://doi.org/10.1093/bioinformatics/btg477
   PubMed Web of Science ®Google Scholar
• Zhang, C., Stockwell, S. R., Elbanna, M., Ketteler, R., Freeman, J., Al-Lazikani, B., Eccles, S., De Haven Brandon, A., Raynaud, F., Hayes, A., Clarke, P. A., Workman, P., & Mittnacht, S. (2019). Signalling involving MET and FAK supports cell division independent of the activity of the cell cycle-regulating CDK4/6 kinases. Oncogene, 38(30), 5905–5920. https://doi.org/https://doi.org/10.1038/s41388-019-0850-2
   PubMed Web of Science ®Google Scholar