Insights into molecular docking and dynamics to reveal therapeutic potential of natural compounds against P53 protein

Abstract

P53 is eminent tumour suppressor protein that plays a prominent role in cell cycle arrest, DNA repair, senescence, differentiation and initiation of apoptosis. P53 is an attractive drug target and the high toxicity of some cancer chemotherapy drugs increase the demand for new anti-cancer drugs from natural products. In this current scenario, identification of promising anticancer compounds from natural sources by repurposing approach is still relevant for the early prevention and effective management of cancer. In present study, we docked natural compounds like podophyllotoxin, quercetin and rutin along standard drugs (MG-132 and Bay 61-3606) against p53 protein. ADME/T analysis predicted toxicity of phytochemicals and drugs. In silico docking analysis of podophyllotoxin, quercetin and rutin gave HDOCK docking scores of −187.87, −148. 97 and −143.85, whereas control drugs MG-132 and Bay 61-3606 showed docking scores of −159.59 and −140.71 against p53 respectively. AutoDock analysis of rutin and MG-132 showed highest binding affinity scores of −7.3 and −6.8 kcal/mol against p53. Molecular dynamic simulation for p53 protein displayed stable conformation and convergence. In this study, P53-rutin complex showed free binding energy score of 11.84 kcal/mol and P53-MG-132 complex reported free energy score of 16.3 kcal/mol. Protein contacts atlas gives non-covalent contacts framework by exploring interfaces of individual subunits and protein-ligand interactions. STRING tool predicts physical and functional interactions between proteins. The results of this study revealed that rutin and MG-132 could be promising inhibitors against targeted p53 protein and this could prove detrimental for molecular therapeutics and drug-designing strategies.

Communicated by Ramaswamy H. Sarma

Keywords:

• P53
• ADMET
• docking
• simulation
• MM/PB (GB)SA
• protein contacts atlas
• STRING

Disclosure statement

The authors have read the manuscript and have no conflict of interest.

Institutional Review Board Statement

Not applicable.

Authors’ contribution

Conceptualization, A.A., B.A.M., M.U.R Methodology, A.A, Software, A.A., Validation, A.A., Formal analysis, A.A., B.A.M., Investigation, A.A., B.A.M., Writing – original draft preparation, A.A., B.A.M., I.M., Writing – review and editing., A.A., B.A.M., M.U.R., N.A.D., S.B.A., R.M.A visualisation., A.A., Supervision, M.U.R., N.A.D., S.B.A. All authors have read and agreed to the published manuscript version.

Data availability statement

All the data generated have been published in this manuscript.

Additional information

Funding

This research did not receive any funding or grant from any funding agency.