Computational investigation of imidazopyridine analogs as protein kinase B (Akt1) allosteric inhibitors by using 3D-QSAR, molecular docking and molecular dynamics simulations

References

• Abbasi, M., Sadeghi-Aliabadi, H., & Amanlou, M. (2018). 3D-QSAR, molecular docking, and molecular dynamic simulations for prediction of new Hsp90 inhibitors based on isoxazole scaffold. Journal of Biomolecular Structure and Dynamics, 36(6), 1463–1478.
   PubMed Web of Science ®Google Scholar
• Ashwell, M. A., Lapierre, J.-M., Brassard, C., Bresciano, K., Bull, C., Cornell-Kennon, S., … Chan, T. C. K. (2012). Discovery and optimization of a series of 3-(3-phenyl-3H-imidazo[4,5-b]pyridin-2-yl)pyridin-2-amines: Orally bioavailable, selective, and potent ATP-independent Akt inhibitors. Journal of Medicinal Chemistry, 55(11), 5291–5310. doi:10.1021/jm300276x
   PubMed Web of Science ®Google Scholar
• Balasubramanian, P. K., Balupuri, A., Bhujbal, S. P., & Cho, S. J. (2019). 3D-QSAR-aided design of potent c-Met inhibitors using molecular dynamics simulation and binding free energy calculation. Journal of Biomolecular Structure and Dynamics, 37(8), 2165–2178. doi:10.1080/07391102.2018.1479309
   PubMed Web of Science ®Google Scholar
• Bhutani, J., Sheikh, A., & Niazi, A. (2013). Akt inhibitors: Mechanism of action and implications for anticancer therapeutics. Infectious agents and Cancer, 8 (1), 49. doi:10.1186/1750-9378-8-49
   PubMedGoogle Scholar
• Cecconi, S., Mauro, A., Cellini, V., & Patacchiola, F. (2012). The role of Akt signalling in the mammalian ovary. The International Journal of Developmental Biology, 56 (10–12), 809–817. doi:10.1387/ijdb.120146sc
   PubMed Web of Science ®Google Scholar
• Cheng, P., Li, J., Wang, J., Zhang, X., & Zhai, H. (2018). Investigations of FAK inhibitors: A combination of 3D-QSAR, docking, and molecular dynamics simulations studies. Journal of Biomolecular Structure and Dynamics, 36(6), 1529–1549. doi:10.1080/07391102.2017.1329095
   PubMed Web of Science ®Google Scholar
• Chohan, T. A., Chen, J. J., Qian, H. Y., Pan, Y. L., & Chen, J. Z. (2016). Molecular modeling studies to characterize N-phenylpyrimidin-2-amine selectivity for CDK2 and CDK4 through 3D-QSAR and molecular dynamics simulations. Molecular Biosystems, 12(4), 1250–1268. doi:10.1039/C5MB00860C
   PubMedGoogle Scholar
• Chu, N., Salguero, A. L., Liu, A. Z., Chen, Z., Dempsey, D. R., Ficarro, S. B., … Cole, P. A. (2018). Akt Kinase Activation Mechanisms Revealed Using Protein Semisynthesis. Cell, 174(4), 897–907. e814. doi:10.1016/j.cell.2018.07.003
   PubMed Web of Science ®Google Scholar
• Craig, W. L. (2010). The Akt/PKB family of protein kinases: A review of small molecule inhibitors and progress towards target validation: A 2009 update. Current Topics in Medicinal Chemistry, 10(4), 458–477. doi: http://dx.doi.org/10.2174/156802610790980602.
   PubMed Web of Science ®Google Scholar
• Dong, X., Zhou, X., Jing, H., Chen, J., Liu, T., Yang, B., … Hu, Y. (2011). Pharmacophore identification, virtual screening and biological evaluation of prenylated flavonoids derivatives as PKB/Akt1 inhibitors. European Journal of Medicinal Chemistry, 46(12), 5949–5958. doi:10.1016/j.ejmech.2011.10.006
   PubMed Web of Science ®Google Scholar
• Eathiraj, S., Palma, R., Volckova, E., Hirschi, M., France, D. S., Ashwell, M. A., & Chan, T. C. K. (2011). Discovery of a novel mode of protein kinase inhibition characterized by the mechanism of inhibition of human mesenchymal-epithelial transition factor (c-Met) protein autophosphorylation by ARQ 197. Journal of Biological Chemistry, 286(23), 20666–20676. doi:10.1074/jbc.M110.213801
   PubMed Web of Science ®Google Scholar
• Farahnaz, R. M., & Jahan, B. G. (2018). Combating Diseases with Computational Strategies Used for Drug Design and Discovery. Current Topics in Medicinal Chemistry, 18(32), 2743–2773. doi:10.2174/1568026619666190121125106.
   PubMed Web of Science ®Google Scholar
• Genheden, S., & Ryde, U. (2015). The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert opinion on drug Discovery, 10 (5), 449–413. doi:10.1517/17460441.2015.1032936
   PubMed Web of Science ®Google Scholar
• Halgren, T. A., Murphy, R. B., Friesner, R. A., Beard, H. S., Frye, L. L., Pollard, W. T., & Banks, J. L. (2004). Glide: A new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. Journal of Medicinal Chemistry, 47(7), 1750–1759. doi:10.1021/jm030644s
   PubMed Web of Science ®Google Scholar
• Hsu, J.-H., Shi, Y., Hu, L., Fisher, M., Franke, T., & Lichtenstein, A. (2002). Role of the AKT kinase in expansion of multiple myeloma clones: effects on cytokine-dependent proliferative and survival responses. Oncogene, 21 (9), 1391–1400. doi:10.1038/sj.onc.1205194
   PubMed Web of Science ®Google Scholar
• Jetzt, A., Howe, J.A., Horn, M.T., Maxwell, E., Yin, Z., Johnson, D., & Chandra Kumar, C. (2003). Adenoviral-mediated expression of a kinase-dead mutant of Akt induces apoptosis selectively in tumor cells and suppresses tumor growth in mice. Cancer Research, 63 (20), 6697–6706.
   PubMed Web of Science ®Google Scholar
• Jujjavarapu, S. E., & Dhagat, S. (2018). In silico discovery of novel ligands for antimicrobial lipopeptides for computer-aided drug design. Probiotics and Antimicrobial Proteins, 10(2), 129–141. doi:10.1007/s12602-017-9356-9
   PubMed Web of Science ®Google Scholar
• Kayikci, M., Venkatakrishnan, A. J., Scott-Brown, J., Ravarani, C. N. J., Flock, T., & Babu, M. M. (2018). Visualization and analysis of non-covalent contacts using the Protein Contacts Atlas. Nature Structural & Molecular Biology, 25(2), 185–194. doi:10.1038/s41594-017-0019-z
   PubMed Web of Science ®Google Scholar
• Kenney, I. M., Beckstein, O., & Iorga, B. I. (2016). Prediction of cyclohexane-water distribution coefficients for the SAMPL5 data set using molecular dynamics simulations with the OPLS-AA force field. Journal of Computer-Aided Molecular Design, 30(11), 1045–1058. doi:10.1007/s10822-016-9949-5
   PubMed Web of Science ®Google Scholar
• Kuriyan, J., Calleja, V., Alcor, D., Laguerre, M., Park, J., Vojnovic, B., … Larijani, B. (2007). Intramolecular and intermolecular interactions of protein kinase b define its activation in vivo. PLoS Biology, 5(4) doi:10.1371/journal.pbio.0050095
   Web of Science ®Google Scholar
• Lapierre, J.-M., Eathiraj, S., Vensel, D., Liu, Y., Bull, C. O., Cornell-Kennon, S., … Schwartz, B. (2016). Discovery of 3-(3-(4-(1-Aminocyclobutyl)phenyl)-5-phenyl-3H-imidazo[4,5-b]pyridin-2-yl)pyridin -2-amine (ARQ 092): An orally bioavailable, selective, and potent allosteric AKT inhibitor. Journal of Medicinal Chemistry, 59(13), 6455–6469. doi:10.1021/acs.jmedchem.6b00619
   PubMed Web of Science ®Google Scholar
• Liu, H., Radisky, D. C., Nelson, C. M., Zhang, H., Fata, J. E., Roth, R. A., & Bissell, M. J. (2006). Mechanism of Akt1 inhibition of breast cancer cell invasion reveals a protumorigenic role for TSC2. Proceedings of the National Academy of Sciences of Sciences, 103(11), 4134–4139. doi:10.1073/pnas.0511342103
   PubMed Web of Science ®Google Scholar
• Macalino, S. J., Gosu, V., Hong, S., & Choi, S. (2015). Role of computer-aided drug design in modern drug discovery. Archives of pharmacal Research, 38(9), 1686-1701. doi:10.1007/s12272-015-0640-5
   Web of Science ®Google Scholar
• Manning, B. D., & Cantley, L. C. (2007). AKT/PKB signaling: Navigating downstream. Cell, 129(7), 1261–1274. doi:10.1016/j.cell.2007.06.009
   PubMed Web of Science ®Google Scholar
• Marsh, R. D W., Lima, C. M. R., Levy, D. E., Mitchell, E. P., Rowland, K. M., & Benson, A. B. (2007). A phase II trial of perifosine in locally advanced, unresectable, or metastatic pancreatic adenocarcinoma. American Journal of Clinical Oncology, 30(1), 26–31. doi:10.1097/01.coc.0000251235.46149.43
   PubMed Web of Science ®Google Scholar
• Nitulescu, G. M., Margina, D., Juzenas, P., Peng, Q., Olaru, O. T., Saloustros, E., … Tsatsakis, A. M. (2016). Akt inhibitors in cancer treatment: The long journey from drug discovery to clinical use (Review). International Journal of Oncology, 48(3), 869–885. doi:10.3892/ijo.2015.3306
   PubMed Web of Science ®Google Scholar
• Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., … Schulten, K. (2005). Scalable molecular dynamics with NAMD. Journal of Computational Chemistry, 26(16), 1781–1802. doi:10.1002/jcc.20289
   PubMed Web of Science ®Google Scholar
• Ramharack, P., & Soliman, M. E. S. (2018). Zika virus NS5 protein potential inhibitors: An enhanced in silico approach in drug discovery. Journal of Biomolecular Structure and Dynamics, 36(5), 1118–1133. doi:10.1080/07391102.2017.1313175
   PubMed Web of Science ®Google Scholar
• Timothy, J. C., Mark, D. M., & Robert, A. S. (2011). High content pharmacophores from molecular fields: a biologically relevant method for comparing and understanding ligands. Current Computer-Aided Drug Design, 7(3), 190–205. doi:10.2174/157340911796504314.
   PubMed Web of Science ®Google Scholar
• Ul-Haq, Z., Ashraf, S., & Bkhaitan, M. M. (2019). Molecular dynamics simulations reveal structural insights into inhibitor binding modes and mechanism of casein kinase II inhibitors. Journal of Biomolecular Structure and Dynamics, 37(5), 1120–1135. doi:10.1080/07391102.2018.1450166
   PubMed Web of Science ®Google Scholar
• Wang, Y., Feng, S., Gao, H., & Wang, J. (2019). Computational investigations of gram-negative bacteria phosphopantetheine adenylyltransferase inhibitors using 3D-QSAR, molecular docking and molecular dynamic simulations. Journal of Biomolecular Structure and Dynamics, 30, 1–13. doi:10.1080/07391102.2019.1608305
   Google Scholar
• Wang, M., Wang, Y., Kong, D., Jiang, H., Wang, J., & Cheng, M. (2018). In silico exploration of aryl sulfonamide analogs as voltage-gated sodium channel 1.7 inhibitors by using 3D-QSAR, molecular docking study, and molecular dynamics simulations. Computational Biology and Chemistry, 77, 214–225. doi:10.1016/j.compbiolchem.2018.10.009
   PubMed Web of Science ®Google Scholar
• Wang, Z. Z., Yang, J., Sun, X. D., Ma, C. Y., Gao, Q. B., Ding, L., & Liu, H. M. (2019). Probing the binding mechanism of substituted pyridine derivatives as effective and selective lysine-specific demethylase 1 inhibitors using 3D-QSAR, molecular docking and molecular dynamics simulations. Journal of Biomolecular Structure and Dynamics, 37(13), 3482–3495. doi:10.1080/07391102.2018.1518158
   PubMed Web of Science ®Google Scholar
• Wang, T., Yuan, X. S., Wu, M. B., Lin, J. P., & Yang, L. R. (2017). The advancement of multidimensional QSAR for novel drug discovery - where are we headed?. Expert Opinion on Drug Discovery, 12(8), 769–784. doi:10.1080/17460441.2017.1336157
   PubMed Web of Science ®Google Scholar
• Zhang, J., Liu, X., Wang, S. Q., Liu, G. Y., Xu, W. R., Cheng, X. C., & Wang, R. L. (2017). Identification of dual ligands targeting angiotensin II type 1 receptor and peroxisome proliferator-activated receptor-gamma by core hopping of telmisartan. J Biomol Struct Dyn, 35(12), 2665–2680. doi:10.1080/07391102.2016.1227726
   PubMed Web of Science ®Google Scholar