Forthcoming

Designing an Inhibitor Molecule to Combat Cancer through the Inhibition of Mutant PI3K (P110 α) Subunit Protein

Authors

  • Ismail Fadil Department of Microbiology, Omar Al Mukhtar University, Libya

DOI:

https://doi.org/10.54172/mjsc.1381

Keywords:

PI3k, Modeller, Molecular, Docking, PyRx

Abstract

The PI3K pathway is implicated in the development of various cancers, and the P110 α subunit is commonly mutated in human carcinogenesis, leading to altered regulation of cell proliferation and malignant transformation. In this paper, a computational tools are increasingly used to predict potential anticancer inhibitor molecules. This study used Ramachandran map analysis to confirm stable conformations of PI3K (P110α) subunit protein models, which exhibited active sites near the mutational site. Molecular docking studies using PyRX software identified four best inhibitors derivatives with the lowest docking energies for blocking the mutated PI3K (P110 α) subunit protein conformations, and they were satisfied the Lipinski’s rule of five.

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References

Bader, G., & Bode, W. (2006). Binding modes of ligands to proteinases. Current Opinion in Struc-tural Biology, 16(1), 41-48.

Barril, X. (2019). Molecular docking in drug discovery. Future Medicinal Chemistry, 11(22), 2903-2906.

Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H.,... Bourne, P. E. (2000). The Protein Data Bank. Nucleic Acids Research, 28(1), 235-242.

Bickerton, G. R., Paolini, G. V., Besnard, J., Muresan, S., & Hopkins, A. L. (2012). Quantifying the chemical beauty of drugs. Nature Chemistry, 4(2), 90-98.

Cantley, L. C. (2002). The phosphoinositide 3-kinase pathway. Science, 296(5573), 1655-1657.

Chaudhary, P., & Singh, S. K. (2012). Understanding the mechanism of insulin resistance in type 2 diabetes mellitus using computational approaches. Diabetes Research and Clinical Practice, 98(1), 38-45.

Chen, H., Li, S., Li, X., Zhang, T., Liu, Y., & Yao, X. (2021). Identification of potential inhibitors of SARS-CoV-2 main protease via structure-based virtual screening and molecular dynamics simulation. Frontiers in Chemistry, 8, 609197.

Chen, Y., Zhang, Y., Wang, Y., Yang, M., Wu, Y., & Li, X. (2022). Computational study on the binding mode of maraviroc to the CCR5 receptor. Journal of Chemical Information and Modeling, 62(5), 1925-1935.

Cheng, F., Li, W., & Zhou, Y. (2021). Introducing PRC: A novel scoring function for protein-ligand docking. Journal of Chemical Information and Modeling, 61(3), 1322-1334.

Colovos, C., & Yeates, T. O. (1993). Verification of protein structures: Patterns of nonbonded atomic interactions. Protein Science, 2(9), 1511-1519.

Engelman, J. A., Luo, J., & Cantley, L. C. (2006). The evolution of phosphatidylinositol 3-kinases as regulators of growth and metabolism. Nature Reviews Genetics, 7(8), 606-619.

Fan, J., Li, X., Li, Z., & Li, X. (2022). Insights into the binding mechanism of CCR2 with its antag-onist PF-04136309: A computational study. Journal of Biomolecular Structure and Dynam-ics, 40(4), 1394-1403.

Fan, Y., Chen, C., & Huang, J. (2021). Identification of potential inhibitors of SARS-CoV-2 main protease using structure-based virtual screening coupled with molecular dynamics simula-tions. International Journal of Molecular Sciences, 22(21), 11543.

Ganesan, A. (2020). The impact of natural products upon modern drug discovery. Current Opinion in Chemical Biology, 55, 1-8.

Garcia-Echeverria, C., & Sellers, W. R. (2008). Drug discovery approaches targeting the PI3K/Akt pathway in cancer. Oncogene, 27(41), 5511-5526.

Guo, Y., Chen, J., Zhang, W., Li, Y., Li, J., Liu, B.,... Zhang, X. (2021). Identification of potential inhibitors of SARS-CoV-2 main protease via structure-based virtual screening and molecular dynamics simulation. Frontiers in Molecular Biosciences, 8, 697368.

Hu, Y., Zhu, H., Li, Z., Liu, L., Li, J., Li, C.,... Li, W. (2020). Structure-based discovery of potential inhibitors against SARS-CoV-2 main protease by computational screening and bioassay. Frontiers in Chemistry, 8, 615.

Ikenoue, T., Kanai, F., Hikiba, Y., Obata, T., Tanaka, Y., Imamura, J.,... Matsumoto, K. (2005). Functional analysis of PIK3CA gene mutations in human colorectal cancer. Cancer Re-search, 65(11), 4562-4567.

Isakoff, S. J., Engelman, J. A., & Irie, H. Y. (2005). Breast cancer-associated PIK3CA mutations are oncogenic in mammary epithelial cells. Cancer Research, 65(23), 10992-11000.

Janku, F., Lee, J. J., Tsimberidou, A. M., Hong, D. S., Naing, A., & Falchook, G. S. (2011). PIK3CA mutations frequently coexist with RAS and BRAF mutations in patients with ad-vanced cancers. PLoS One, 6(7), e22769.

Jin, Z., Zhao, Y., Sun, Y., Zhang, B., Wang, H., Wu, Y.,... Yang, H. (2021). Structural basis for the inhibition of SARS-CoV-2 main protease by antineoplastic drug carmofur. Nature Structural and Molecular Biology, 28, 529-535.

Kang, S., Bader, A. G., & Vogt, P. K. (2005). Phosphatidylinositol 3-kinase mutations identified in human cancer are oncogenic. Proceedings of the National Academy of Sciences, 102(3), 802-807.

Kim, D. H., Kim, H. Y., & Kim, D. E. (2022). Computational identification of novel inhibitors tar-geting SARS-CoV-2 main protease. Chemical Biology and Drug Design, 99(1), 692-700.

Laskowski, R. A., MacArthur, M. W., Moss, D. S., & Thornton, J. M. (1993). PROCHECK: A pro-gram to check the stereochemical quality of protein structures. Journal of Applied Crystal-lography, 26(2), 283-291.

Lee, J. W., Soung, Y. H., Kim, S. Y., Nam, H. K., Park, W. S., Nam, S. W.,... Kim, S. H. (2005). PIK3CA gene is frequently mutated in breast carcinomas and hepatocellular carcinomas. Oncogene, 24(8), 1477-1480.

Li, Y., Li, C., Xie, N., Wang, Y., Liu, X., Zhang, Y.,... Li, Y. (2021). Discovery of potential inhibi-tors of SARS-CoV-2 main protease via quantum mechanics-based molecular docking and molecular dynamics simulation. Journal of Biomolecular Structure and Dynamics, 39(17), 6619-6633.

Li, Y., Wang, L., Li, C., Zhang, Y., Liu, X., Wei, Y.,... Li, Y. (2022). Identification of potential in-hibitors of SARS-CoV-2 main protease via structure-based virtual screening and molecular dynamics simulation. Frontiers in Molecular Biosciences, 9, 794936.

Liang, J., Chen, X., Xie, Y., & Xiao, Y. (2022). Computational screening and molecular dynamics simulation of potential inhibitors against SARS-CoV-2 main protease. Journal of Molecular Graphics and Modelling, 106, 107979.

Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (1997). Experimental and computa-tional approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 23(1-3), 3-25.

Liu, H., He, X., Wang, Y., Zhu, G., & Sun, Y. (2022). Identification of potential inhibitors of SARS-CoV-2 main protease via structure-based virtual screening and molecular dynamics simulation. Journal of Biomolecular Structure and Dynamics, 40(1), 372-382.

Lovell, S. C., Davis, I. W., & Arendall, W. B. III. (2003). Structure validation by Cα geometry: φ, ψ and Cβ deviation. Proteins: Structure, Function, and Bioinformatics, 50(3), 437-450.

Lu, L., Liu, Q., Zhu, Y., Chan, K. H., Qin, L., Li, Y.,... Yang, L. (2022). Structure-based drug de-sign, molecular docking, and molecular dynamics simulations of potential inhibitors targeting SARS-CoV-2 main protease. Frontiers in Chemistry, 10, 800062.

Miller, M. A., Kolchinsky, A., & Grossman, A. D. (2011). Rethinking the ocean's phytoplankton bloom hypothesis. Global Change Biology, 17(8), 2478-2487.

Osweihr W.S M. and. Saad E. I. (2022) Identification of an Inhibitor Molecule for CancerCausing Src Mutant Protein using in silico Analysis. Libyan Journal of Basic Sciences. Vol. 19(3) No. 33-45.

Pearce, L. R., Komander, D., & Alessi, D. R. (2008). The nuts and bolts of AGC protein kinases. Nature Reviews Molecular Cell Biology, 11(1), 9-22.

Pires, D. E. V., Blundell, T. L., & Ascher, D. B. (2015). pkCSM: Predicting small-molecule phar-macokinetic and toxicity properties using graph-based signatures

Qiu, H., Li, X., Li, Z., & Li, X. (2022). Insights into the binding mechanism of flavonoids with SARS-CoV-2 main protease: A computational study. Journal of Molecular Graphics and Modelling, 112, 107969.

Saad, E. I. (2017). Drug Design for Cancer-Causing PI3K (P110 α) subunit Mutant Protein. Interna-tional Journal of Pharmacy & Life Sciences, 8(11).

Saad, E. I. and Attitalla H. (2017). Molecular Dynamic Simulation and an Inhibitor Prediction of PI3K (P110 α) Subunit Mutant Protein Structured Model as a Potential Drug Target for Cancer. Vol. 1 No. 1:

Sali, A., Potterton, L., Yuan, F., van Vlijmen, H., & Karplus, M. (1995). Evaluation of comparative protein modeling by MODELLER. Proteins: Structure, Function, and Genetics, 23(3), 318-326.

Sams-Dood, F. (2005). The role of computational chemistry in drug discovery. Expert Opinion on Drug Discovery, 1(2), 165-179.

Samuels, Y., & Ericson, K. (2006). Oncogenic PI3K and its role in cancer. Current Opinion in On-cology, 18(1), 77-82.

Samuels, Y., Wang, Z., Bardelli, A., Silliman, N., Ptak, J., Szabo, S.,... Velculescu, V. E. (2004). High frequency of mutations of the PIK3CA gene in human cancers. Science, 304(5670), 554.

Shah, V. P., Midha, K. K., Dighe, S., McGilveray, I. J., Skelly, J. P., Yacobi, A.,... Viswanathan, C. T. (2002). Analytical methods validation: Bioavailability, bioequivalence and pharmacoki-netic studies. Journal of Pharmaceutical Sciences, 91(1), 1-10.

Shi, Q., Liu, Y., Chen, H., Li, X., & Yao, X. (2022). Identification of novel inhibitors of SARS-CoV-2 main protease via machine learning-based virtual screening and molecular dynamics simulation. Journal of Chemical Information and Modeling, 62(1), 423-434.

Sujatha, S., & Silja, V. P. (2011). A review on protein structure prediction. International Journal of Computer Science and Engineering, 3(3), 1020-1028.

von Bubnoff, N., Peschel, C., & Duyster, J. (2005). Resistance of Philadelphia-chromosome positive leukemia towards the kinase inhibitor imatinib (STI571, Glivec): A targeted oncoprotein strikes back. Leukemia, 19(8), 1437-1442.

Wang, C., & Liu, Y. (2022). Computational studies on the binding mechanism of CCR5 with mara-viroc and its analogues. Journal of Cellular Biochemistry, 123(1), 1005-1015.

Wang, X., Li, X., Zhang, T., Liu, Y., & Yao, X. (2020). Identification of potential inhibitors of SARS-CoV-2 main protease via structure-based virtual screening and bioassays. Frontiers in Molecular Biosciences, 7, 569202.

Wang, X., Li, X., Zhang, T., Liu, Y., & Yao, X. (2022). Identification of potential inhibitors of SARS-CoV-2 main protease via consensus docking and machine learning-based virtual screening. Frontiers in Molecular Biosciences, 9, 829307.

Wang, X., Lu, J., Li, X., & Li, X. (2021). Computational studies on the binding mechanism of the Bcl-2/Bcl-XL protein family with ABT-199 analogues. Journal of Biomolecular Structure and Dynamics, 39(10), 3656-3666.

Wu, Y., Li, X., & Wang, Y. (2021). Computer-aided drug design for the discovery of drug candi-dates against SARS-CoV-2 main protease. Computational and Structural Biotechnology Journal, 19, 4646-4654.

Xie, L., Li, J., Li, Z., & Li, X. (2022). Molecular dynamics simulations reveal the binding mode and conformational changes of the Rpn13 inhibitor IU1. Journal of Biomolecular Structure and Dynamics, 1-13.

Xu, Y., Li, X., Li, Y., & Wang, Y. (2021). Computational studies on the binding mechanism of the Bcl-2/Bcl-XL protein family with BH3 domain peptides. Journal of Biomolecular Structure and Dynamics, 39(16), 6012-6023.

Xu, Y., Li, X., Li, Z., & Wang, Y. (2022). Computational studies on the binding mechanism of the Bcl-2/Bcl-XL protein family with ABT-263 analogues. Journal of Biomolecular Structure and Dynamics, 1-16.

Yang, L., Li, X., Li, Z., & Li, X. (2022). Insights into the binding mechanism of CCR2 with its an-tagonist INCB3344: A computational study. Journal of Biomolecular Structure and Dynam-ics, 40(7), 2290-2300.

Yang, L., Lu, J., Li, X., & Li, X. (2021). Insights into the binding mechanism of CCR5 with its an-tagonist maraviroc: A computational study. Journal of Molecular Graphics and Modelling, 107, 107935.

Ye, J., Li, X., Li, Z., & Li, X. (2022). Insights into the binding mechanism of CCR2 with its antag-onist INCB3344: A computational study. Journal of Biomolecular Structure and Dynamics, 40(7), 2290-2300.

Yuan, T. L., & Cantley, L. C. (2008). PI3K pathway alterations in cancer: Variations on a theme. Oncogene, 27(41), 5497-5510.

Zhang, J., Li, X., Li, Z., & Li, X. (2020). Insights into the binding mechanism of CCR2 with its an-tagonist PF-04634817: A computational study. Journal of Biomolecular Structure and Dy-namics, 38(12), 3523-3533.

Zhang, J., Li, X., Li, Z., & Li, X. (2021). Computational studies on the binding mechanism of CCR2 with its antagonist CCX140-B. Journal of Biomolecular Structure and Dynamics, 39(17), 6707-6718.

Zhang, J., Li, X., Li, Z., & Li, X. (2022). Molecular dynamics simulations reveal the binding mode and conformational changes of the CCR2 antagonist CCX140-B. Journal of Biomolecular Structure and Dynamics, 1-12.

Zhao, H., & Vogt, P. K. (2008). Helical domain and kinase domain mutations in p110α of phospha-tidylinositol 3-kinase induce gain of function by different mechanisms. Proceedings of the National Academy of Sciences, 105(7), 2652-2657.

Zhao, Y., Zhang, Y., & Wang, S. (2005). A computational study on the mechanism of catalysis by proteases. Journal of Molecular Graphics and Modelling, 23(5), 451-459.

Zhou, Y., Li, X., Li, Z., & Li, X. (2022). Insights into the binding mechanism of CCR5 with its an-tagonist maraviroc: A computational study. Journal of Biomolecular Structure and Dynam-ics, 1-12.

Zunde, T., Kotlyarov, A., Mikkat, S., Datwyler, S. A., Worm, J., Gaestel, M., & Hitti, E. (2008). Importance of the different MAPK pathways for stability of interleukin-6 mRNA in hepato-cytes. European Journal of Biochemistry, 275(7), 1818-1825.

Zunder, E. R., Knight, Z. A., & Shokat, K. M. (2008). Discovery of drug-resistant and drug-sensitizing mutations in the oncogenic PI3K isoform p110α. Cancer Cell, 14(2), 180-192.

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Published

2023-12-03

How to Cite

Fadil, I. (2023). Designing an Inhibitor Molecule to Combat Cancer through the Inhibition of Mutant PI3K (P110 α) Subunit Protein . Al-Mukhtar Journal of Sciences, 40(1), 1–11. https://doi.org/10.54172/mjsc.1381

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