EXPLORING THE ANTI-CANCER POTENTIAL OF PHYTOCHEMICALS FROM SPECIFIC PLANTS: EXAMINING AND VALIDATING THROUGH MOLECULAR DOCKING AND MD SIMULATIONS
DOI:
https://doi.org/10.56588/iabcd.v3i1.198Keywords:
Combretaceae family plants, Phytochemicals, Molecular docking, Molecular Dynamic SimulationAbstract
Worldwide, cancer is the leading cause of death. Anti-cancer medications frequently induce side effects and multidrug resistance (MDR), which continues to be a key obstacle to effective cancer therapy. Essential nutrients and functionally bioactive substances can both be found in abundance in plants. The phytochemical components have great promise for treating both plant and human ailments. This study is designed to conduct an in-silico analysis on phytochemicals derived from Combretaceae family plants for targeting the proteins 4UWH, 5LWM, and 6P3D. The Combretaceae family has demonstrated pharmacological benefits such as anti-leishmanial, cytotoxic, antibacterial, antidiabetic, antiprotozoal, anticancer, and antifungal qualities. To conduct experiments with the natural phytochemicals against the proteins, computerized tools, online servers, and online databases were used. 196 natural compounds were used for virtual screening out of the top 5 best-docked compounds selected based on their binding energy. The best-selected phytochemicals possessed potential results in 10ns molecular dynamic simulation. So, it is convincible based on in-silico research this selected phytochemical has the potential to serve as a promising lead compound against cancer.
References
Ai, D. et al. (2021) ‘TRPS1: a highly sensitive and specific marker for breast carcinoma, especially for triple-negative breast cancer’, Modern Pathology, 34(4), pp. 710–719. doi: 10.1038/s41379-020-00692-8.
Allouche, A. (2012) ‘Software News and Updates Gabedit — A Graphical User Interface for Computational Chemistry Softwares’, Journal of computational chemistry, 32, pp. 174–182. doi: 10.1002/jcc.
Altomare, D. A. and Testa, J. R. (2005) ‘Perturbations of the AKT signaling pathway in human cancer’, Oncogene, 24(50), pp. 7455–7464. doi: 10.1038/sj.onc.1209085.
Anderson, K. E. et al. (2021) ‘Reports of Forgone Medical Care among US Adults during the Initial Phase of the COVID-19 Pandemic’, JAMA Network Open, 4(1), pp. 1–11. doi: 10.1001/jamanetworkopen.2020.34882.
Balupuri, A., Balasubramanian, P. K. and Cho, S. J. (2020) ‘3D-QSAR, docking, molecular dynamics simulation and free energy calculation studies of some pyrimidine derivatives as novel JAK3 inhibitors’, Arabian Journal of Chemistry, 13(1), pp. 1052–1078. doi: 10.1016/j.arabjc.2017.09.009.
Bartholomeusz, C. and Gonzalez-Angulo, A. M. (2012) ‘Targeting the PI3K signaling pathway in cancer therapy’, Expert Opinion on Therapeutic Targets, 16(1), pp. 121–130. doi: 10.1517/14728222.2011.644788.
Corcoran, R. B. et al. (2015) ‘Combined BRAF and MEK inhibition with dabrafenib and trametinib in BRAF V600-Mutant colorectal cancer’, Journal of Clinical Oncology, 33(34), pp. 4023–4031. doi: 10.1200/JCO.2015.63.2471.
Courtney, K. D., Corcoran, R. B. and Engelman, J. A. (2010) ‘The PI3K pathway as drug target in human cancer’, Journal of Clinical Oncology, 28(6), pp. 1075–1083. doi: 10.1200/JCO.2009.25.3641.
Eloff, J. N., Katerere, D. R. and McGaw, L. J. (2008) ‘The biological activity and chemistry of the southern African Combretaceae’, Journal of Ethnopharmacology, 119(3), pp. 686–699. doi: 10.1016/j.jep.2008.07.051.
Factor, I. (2022) ‘Herbal Plants: A Study of Phytochemicals’, (111), pp. 111–114.
Fanelli, G. N. et al. (2020) ‘The heterogeneous clinical and pathological landscapes of metastatic Braf-mutated colorectal cancer’, Cancer Cell International, 20(1), pp. 1–12. doi: 10.1186/s12935-020-1117-2.
Fumarola, C. et al. (2014) ‘Targeting PI3K/AKT/mTOR pathway in non small cell lung cancer’, Biochemical Pharmacology, 90(3), pp. 197–207. doi: 10.1016/j.bcp.2014.05.011.
Ghoshal, S. et al. (2022) ‘Institutional Surgical Response and Associated Volume Trends Throughout the COVID-19 Pandemic and Postvaccination Recovery Period’, JAMA Network Open, 5(8), p. E2227443. doi: 10.1001/jamanetworkopen.2022.27443.
Hanahan, D. (2022) ‘Hallmarks of Cancer: New Dimensions’, Cancer Discovery, 12(1), pp. 31–46. doi: 10.1158/2159-8290.CD-21-1059.
Hong, D. S. et al. (2012) ‘BRAF(V600) inhibitor GSK2118436 targeted inhibition of mutant BRAF in cancer patients does not impair overall immune competency’, Clinical Cancer Research, 18(8), pp. 2326–2335. doi: 10.1158/1078-0432.CCR-11-2515.
Hou, P., Liu, D. and Xing, M. M. (2007) ‘Functional characterization of the T1799-1801del and A1799-1816ins BRAF mutations in papillary thyroid cancer’, Cell Cycle, 6(3), pp. 377–379. doi: 10.4161/cc.6.3.3818.
Hu, X. et al. (2021) ‘The JAK/STAT signaling pathway: from bench to clinic’, Signal Transduction and Targeted Therapy, 6(1). doi: 10.1038/s41392-021-00791-1.
Jeong, E. G. et al. (2008) ‘Somatic mutations of JAK1 and JAK3 in acute leukemias and solid cancers’, Clinical Cancer Research, 14(12), pp. 3716–3721. doi: 10.1158/1078-0432.CCR-07-4839.
Keute, M. et al. (2019) ‘No modulation of pupil size and event-related pupil response by transcutaneous auricular vagus nerve stimulation (taVNS)’, Scientific Reports, 9(1), pp. 1–10. doi: 10.1038/s41598-019-47961-4.
Kim, B. H. et al. (2020) ‘STAT3 Inhibitor ODZ10117 Suppresses Glioblastoma Malignancy and Prolongs Survival in a Glioblastoma Xenograft Model’, Cells, 9(3), pp. 1–16. doi: 10.3390/cells9030722.
Krieger, E. and Vriend, G. (2015) ‘New ways to boost molecular dynamics simulations’, Journal of Computational Chemistry, 36(13), pp. 996–1007. doi: 10.1002/jcc.23899.
Lin, K. et al. (2010) ‘The role of B-RAF mutations in melanoma and the induction of EMT via dysregulation of the NF-κB/snail/RKIP/PTEN circuit’, Genes and Cancer, 1(5), pp. 409–420. doi: 10.1177/1947601910373795.
Liu, K., Watanabe, E. and Kokubo, H. (2017) ‘Exploring the stability of ligand binding modes to proteins by molecular dynamics simulations’, Journal of Computer-Aided Molecular Design, 31(2), pp. 201–211. doi: 10.1007/s10822-016-0005-2.
Massarotti, A. et al. (2012) ‘The tubulin colchicine domain: A molecular modeling perspective’, ChemMedChem, 7(1), pp. 33–42. doi: 10.1002/cmdc.201100361.
Nairismägi, M. L. et al. (2018) ‘Oncogenic activation of JAK3-STAT signaling confers clinical sensitivity to PRN371, a novel selective and potent JAK3 inhibitor, in natural killer/T-cell lymphoma’, Leukemia, 32(5), pp. 1147–1156. doi: 10.1038/s41375-017-0004-x.
Patel, C. N. et al. (2021) ‘Pinpointing the potential hits for hindering interaction of SARS-CoV-2 S-protein with ACE2 from the pool of antiviral phytochemicals utilizing molecular docking and molecular dynamics (MD) simulations’, Journal of Molecular Graphics and Modelling, 105(February 2020), p. 107874. doi: 10.1016/j.jmgm.2021.107874.
Pinzi, L. and Rastelli, G. (2019) ‘Metode berbasis struktur bergantung pada informasi yang diperoleh dari pengetahuan tentang struktur 3D target yang menarik, dan mereka memungkinkan database peringkat molekul sesuai dengan struktur dan komplementaritas elektronik ligan ke target tertentu’, igms in drug discovery. InternatInPinzi, L., & Rastelli, G. (2019). Molecular docking: Shifting paradional Journal of Molecular Sciences, 20(18). https://doi.org/10.3390/ijms20184331ternational Journal of Molecular Sciences, 20(18), pp. 1–23.
Prajapati, P. et al. (2023) ‘Computational Analysis of Transcription Factors As Cancer Drug Targets With Potential Inhibitors From the Npact Database’, International Association of Biologicals and Computational Digest, 2(2), pp. 14–26. doi: 10.56588/iabcd.v2i2.97.
Surveillance Epidemiology (2019) ‘Colorectal Cancer - Cancer Stat Facts’, SEER Cancer Stat Facts: Colorectal Cancer, 9(1), p. 2. Available at: https://seer.cancer.gov/statfacts/html/colorect.html.
Trayes, K. P. and Cokenakes, S. E. . (2021) ‘Treatment Cancer Breast’, Am Fam Physician, 104(2), pp. 171–178.
Velavan, S. (2016) ‘Phytochemical Techniques - A Review’, World Journal of Science and Research, 1(3), pp. 80–91.
Wong, K. K., Engelman, J. A. and Cantley, L. C. (2010) ‘Targeting the PI3K signaling pathway in cancer’, Current Opinion in Genetics and Development, 20(1), pp. 87–90. doi: 10.1016/j.gde.2009.11.002.