Computational-guided approach for identification of PI3K alpha inhibitor in the treatment of hepatocellular carcinoma by virtual screening and water map analysis

References

• Abel, R., Young, T., Farid, R., Berne, B. J., & Friesner, R. A. (2008). Role of the active-site solvent in the thermodynamics of factor Xa ligand binding. Journal of the American Chemical Society, 130(9), 2817–2831. https://doi.org/10.1021/ja0771033
   PubMed Web of Science ®Google Scholar
• Abohassan, M., Alshahrani, M., Alshahrani, M. Y., & Rajagopalan, P. (2022). Insilco and Invitro approaches identify novel dual PI3K/AKT pathway inhibitors to control acute myeloid leukemia cell proliferations. Medical Oncology, 39(12), 249. https://doi.org/10.1007/s12032-022-01846-1
   PubMed Web of Science ®Google Scholar
• Bhaskar, B. V., Rammohan, A., Babu, T. M., Zheng, G. Y., Chen, W., Rajendra, W., Zyryanov, G. V., & Gu, W. (2021). Molecular insight into isoform specific inhibition of PI3K-α and PKC-η with dietary agents through an ensemble pharmacophore and docking studies. Scientific Reports, 11(1), 12150. https://doi.org/10.1038/s41598-021-90287-3
   PubMed Web of Science ®Google Scholar
• Biswal, J., Jayaprakash, P., Rayala, S. K., Venkatraman, G., Rangaswamy, R., & Jeyaraman, J. (2021). WaterMap and Molecular Dynamic Simulation-Guided Discovery of Potential PAK1 Inhibitors Using Repurposing Approaches. ACS Omega, 6(41), 26829–26845. https://doi.org/10.1021/acsomega.1c02032
   PubMed Web of Science ®Google Scholar
• Bodige, S., Ravula, P., Gulipalli, K. C., Endoori, S., Chandra, J. N. N. S., Cherukumalli, P. K. R., Vanaja, G., & Seelam, N. (2018). Design, synthesis and biological evaluation of novel urea and thiourea bearing thieno[3,2-d]-pyrimidines as PI3 kinase inhibitors. Anti-Cancer Agents in Medicinal Chemistry, 18(6), 891–902. https://doi.org/10.2174/1871520618666180209151018
   PubMed Web of Science ®Google Scholar
• Cheng, H., Orr, S. T. M., Bailey, S., Brooun, A., Chen, P., Deal, J. G., Deng, Y. L., Edwards, M. P., Gallego, G. M., Grodsky, N., Huang, B., Jalaie, M., Kaiser, S., Kania, R. S., Kephart, S. E., Lafontaine, J., Ornelas, M. A., Pairish, M., Planken, S., … Kath, J. C. (2021). Structure-based drug design and synthesis of PI3Kα-selective inhibitor (PF-06843195). Journal of Medicinal Chemistry, 64(1), 644–661. https://doi.org/10.1021/acs.jmedchem.0c01652
   PubMed Web of Science ®Google Scholar
• Daina, A., Michielin, O., & Zoete, V. (2014). ILOGP: A simple, robust, and efficient description of n-octanol/water partition coefficient for drug design using the GB/SA approach. Journal of Chemical Information and Modeling, 54(12), 3284–3301. https://doi.org/10.1021/CI500467K
   PubMed Web of Science ®Google Scholar
• Daina, A., Michielin, O., & Zoete, V. (2017). SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific Reports, 7(1), 42717. https://doi.org/10.1038/srep42717
   PubMed Web of Science ®Google Scholar
• Drullinsky, P. R., & Hurvitz, S. A. (2020). Mechanistic basis for PI3K inhibitor antitumor activity and adverse reactions in advanced breast cancer. Breast Cancer Research and Treatment, 181(2), 233–248. https://doi.org/10.1007/s10549-020-05618-1
   PubMed Web of Science ®Google Scholar
• Duan, B., Huang, C., Bai, J., Zhang, Y. L., Wang, X., Yang, J., & Li, J. (2019). Multidrug Resistance in Hepatocellular Carcinoma. In Hepatocellular carcinoma. (pp. 141–158). Codon Publications. https://doi.org/10.15586/hepatocellularcarcinoma.2019.ch8
   Google Scholar
• Friesner, R. A., Banks, J. L., Murphy, R. B., Halgren, T. A., Klicic, J. J., Mainz, D. T., Repasky, M. P., Knoll, E. H., Shelley, M., Perry, J. K., Shaw, D. E., Francis, P., & Shenkin, P. S. (2004). Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. Journal of Medicinal Chemistry, 47(7), 1739–1749. https://doi.org/10.1021/jm0306430
   PubMed Web of Science ®Google Scholar
• Friesner, R. A., Murphy, R. B., Repasky, M. P., Frye, L. L., Greenwood, J. R., Halgren, T. A., Sanschagrin, P. C., & 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(21), 6177–6196. https://doi.org/10.1021/jm051256o
   PubMed Web of Science ®Google Scholar
• Haider, K., Ahmad, K., Najmi, A. K., Das, S., Joseph, A., & Shahar Yar, M. (2022). Design, synthesis, biological evaluation, and in silico studies of 2‐aminobenzothiazole derivatives as potent PI3Kα inhibitors. Archiv Der Pharmazie, 355(10), e2200146. https://doi.org/10.1002/ardp.202200146
   PubMed Web of Science ®Google Scholar
• Halder, D., Das, S., & Jeyaprakash, R. S. (2023). Identification of natural product as selective PI3Kα inhibitor against NSCLC: Multi-ligand pharmacophore modeling, molecular docking, ADME, DFT, and MD simulations. Molecular Diversity, https://doi.org/10.1007/s11030-023-10727-2
   PubMed Web of Science ®Google Scholar
• Halder, D., Das, S., A, R., & J, R. S. (2022). Molecular docking and dynamics based approach for the identification of kinase inhibitors targeting PI3Kα against non-small cell lung cancer: A computational study. RSC Advances, 12(33), 21452–21467. https://doi.org/10.1039/D2RA03451D
   PubMed Web of Science ®Google Scholar
• Halder, D., Das, S., Joseph, A., & Jeyaprakash, R. S. (2022). Molecular docking and dynamics approach to in silico drug repurposing for inflammatory bowels disease by targeting TNF alpha. Journal of Biomolecular Structure & Dynamics, 41(8), 3462–3475. https://doi.org/10.1080/07391102.2022.2050948
   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. Enrichment factors in database screening. Journal of Medicinal Chemistry, 47(7), 1750–1759. https://doi.org/10.1021/jm030644s
   PubMed Web of Science ®Google Scholar
• Heffron, T. P., Heald, R. A., Ndubaku, C., Wei, B., Augistin, M., Do, S., Edgar, K., Eigenbrot, C., Friedman, L., Gancia, E., Jackson, P. S., Jones, G., Kolesnikov, A., Lee, L. B., Lesnick, J. D., Lewis, C., McLean, N., Mörtl, M., Nonomiya, J., … Olivero, A. G. (2016). The rational design of selective benzoxazepin inhibitors of the α-isoform of phosphoinositide 3-kinase culminating in the identification of (S) -2-((2-(1-Isopropyl-1 H -1,2,4-triazol-5-yl)-5,6-dihydrobenzo [f] imidazo[1,2- d] [1,4]oxazepin-9-yl)oxy)propa. Journal of Medicinal Chemistry, 59(3), 985–1002. https://doi.org/10.1021/acs.jmedchem.5b01483
   PubMed Web of Science ®Google Scholar
• Hevener, K. E., Zhao, W., Ball, D. M., Babaoglu, K., Qi, J., White, S. W., & Lee, R. E. (2009). Validation of molecular docking programs for virtual screening against dihydropteroate synthase. Journal of Chemical Information and Modeling, 49(2), 444–460. https://doi.org/10.1021/ci800293n
   PubMed Web of Science ®Google Scholar
• Jia, W., Luo, S., Zhao, W., Xu, W., Zhong, Y., & Kong, D. (2022). Discovery of novel PI3Kδ inhibitors based on the p110δ crystal structure. Molecules, 27(19), 6211. https://doi.org/10.3390/molecules27196211
   PubMed Web of Science ®Google Scholar
• Kumar, A., Rathi, E., & Kini, S. G. (2019). E-pharmacophore modelling, virtual screening, molecular dynamics simulations and in-silico ADME analysis for identification of potential E6 inhibitors against cervical cancer. Journal of Molecular Structure, 1189, 299–306. https://doi.org/10.1016/j.molstruc.2019.04.023
   Web of Science ®Google Scholar
• LigPrep 3.6. (2015). Schrödinger Press, 1–79.
   Google Scholar
• Liu, W., Zheng, L., Zhang, R., Hou, P., Wang, J., Wu, L., & Li, J. (2022). Circ-ZEB1 promotes PIK3CA expression by silencing miR-199a-3p and affects the proliferation and apoptosis of hepatocellular carcinoma. Molecular Cancer, 21(1), 72. https://doi.org/10.1186/s12943-022-01529-5
   PubMed Web of Science ®Google Scholar
• Llovet, J. M., Kelley, R. K., Villanueva, A., Singal, A. G., Pikarsky, E., Roayaie, S., Lencioni, R., Koike, K., Zucman-Rossi, J., & Finn, R. S. (2021). Hepatocellular carcinoma. Nature Reviews Disease Primers, 7(1), 6. https://doi.org/10.1038/s41572-020-00240-3
   PubMed Web of Science ®Google Scholar
• Lyne, P. D. (2002). Structure-based virtual screening: An overview. Drug Discovery Today, 7(20), 1047–1055. https://doi.org/10.1016/S1359-6446(02)02483-2
   PubMed Web of Science ®Google Scholar
• Madhavi Sastry, G., Adzhigirey, M., Day, T., Annabhimoju, R., & Sherman, W. (2013). Protein and ligand preparation: Parameters, protocols, and influence on virtual screening enrichments. Journal of Computer-Aided Molecular Design, 27(3), 221–234. https://doi.org/10.1007/s10822-013-9644-8
   PubMed Web of Science ®Google Scholar
• Mohamed, A. R., El Kerdawy, A. M., George, R. F., Georgey, H. H., & Abdel Gawad, N. M. (2021). Design, synthesis and in silico insights of new 7,8-disubstituted-1,3-dimethyl-1H-purine-2,6(3H,7H)-dione derivatives with potent anticancer and multi-kinase inhibitory activities. Bioorganic Chemistry, 107(December 2020), 104569. https://doi.org/10.1016/j.bioorg.2020.104569
   PubMedGoogle Scholar
• Prime 4.0 User Manual. (2015). Schrödinger Press, 1–133.
   Google Scholar
• PubChem Compound Summary for CID 56649450. (2022). Alpelisib" PubChem. https://pubchem.ncbi.nlm.nih.gov/compound/Alpelisib
   Google Scholar
• Roos, K., Wu, C., Damm, W., Reboul, M., Stevenson, J. M., Lu, C., Dahlgren, M. K., Mondal, S., Chen, W., Wang, L., Abel, R., Friesner, R. A., & Harder, E. D. (2019). OPLS3e: extending force field coverage for drug-like small molecules. Journal of Chemical Theory and Computation, 15(3), 1863–1874. https://doi.org/10.1021/acs.jctc.8b01026
   PubMed Web of Science ®Google Scholar
• Schrödinger Release 2021-4: Desmond Molecular Dynamics System, D. E. Shaw Research. (2021). New York, NY, 2021. Maestro-Desmond Interoperability Tools, Schrödinger, New York, NY, 2021
   Google Scholar
• Schrödinger Release 2021-4: Glide, Schrödinger, LLC. (2021). New York, NY, 2021
   Google Scholar
• Schrödinger Release 2021-4: Jaguar, Schrödinger, LLC. (2021). New York, NY, 2021
   Google Scholar
• Schrödinger Release 2021-4: LigPrep, Schrödinger, LLC. (2021). New York, NY, 2021
   Google Scholar
• Schrödinger Release 2021-4: Protein Preparation Wizard; Epik, Schrödinger, LLC. (n.d)., New York, NY, 2021; Impact, SchrödingerLLCNew YorkNY; Prime, Schrödinger, LLC, New York, NY, 2021
   Google Scholar
• Schrödinger Release 2021-4: QikProp, Schrödinger, LLC. (2021). New York, NY, 2021
   Google Scholar
• Schrödinger Release 2022-4: LigPrep, Schrödinger, LLC. (2021). New York, NY, 2021
   Google Scholar
• Schrödinger Release 2023-1: Glide, Schrödinger, LLC. (2021). New York, NY, 2021
   Google Scholar
• Schrödinger Release 2023-1: Prime, Schrödinger, LLC. (2021). New York, NY, 2021
   Google Scholar
• Sobhia, M. E., Ghosh, K., Sivangula, S., Kumar, S., & Singh, H. (2020). Identification of potential SARS-CoV-2 Mpro inhibitors integrating molecular docking and water thermodynamics. Journal of Biomolecular Structure & Dynamics, 40(11), 5079–5089. https://doi.org/10.1080/07391102.2020.1867642
   Web of Science ®Google Scholar
• Sobhia, M. E., Kumar, G. S., Sivangula, S., Ghosh, K., Singh, H., Haokip, T., & Gibson, J. (2021). Rapid structure-based identification of potential SARS-CoV-2 main protease inhibitors. Future Medicinal Chemistry, 13(17), 1435–1450. https://doi.org/10.4155/fmc-2020-0264
   PubMed Web of Science ®Google Scholar
• Srivastava, S., Vengamthodi, A., Singh, I., Choudhary, B. S., Sharma, M., & Malik, R. (2019). Determination of comprehensive in silico determinants as a strategy for identification of novel PI3Kα inhibitors. Structural Chemistry, 30(5), 1761–1778. https://doi.org/10.1007/s11224-019-01303-2
   Web of Science ®Google Scholar
• Sun, E. J., Wankell, M., Palamuthusingam, P., McFarlane, C., & Hebbard, L. (2021). Targeting the PI3K/Akt/mTOR pathway in hepatocellular carcinoma. Biomedicines, 9(11), 1639. https://doi.org/10.3390/biomedicines9111639
   PubMed Web of Science ®Google Scholar
• Tian, L.-Y., Smit, D. J., & Jücker, M. (2023). The role of PI3K/AKT/mTOR signaling in hepatocellular carcinoma metabolism. International Journal of Molecular Sciences, 24(3), 2652. https://doi.org/10.3390/ijms24032652
   PubMed Web of Science ®Google Scholar
• Yang, J., Nie, J., Ma, X., Wei, Y., Peng, Y., & Wei, X. (2019). Targeting PI3K in cancer: Mechanisms and advances in clinical trials. Molecular Cancer, 18(1), 26. https://doi.org/10.1186/s12943-019-0954-x
   PubMed Web of Science ®Google Scholar
• Zhou, Q., Lui, V. W., & Yeo, W. (2011). Targeting the PI3K/Akt/mTOR pathway in hepatocellular carcinoma. Future Oncology (London, England), 7(10), 1149–1167. https://doi.org/10.2217/fon.11.95
   PubMed Web of Science ®Google Scholar