Identification of promising antiviral drug candidates against non-structural protein 15 (NSP15) from SARS-CoV-2: an in silico assisted drug-repurposing study

Abstract

The recent COVID-19 pandemic caused by SARS-CoV-2 has recorded a high number of infected people across the globe. The virulent nature of the virus makes it necessary for us to identify promising therapeutic agents in a time-sensitive manner. The current study utilises an in silico based drug repurposing approach to identify potential anti-viral drug candidates targeting non-structural protein 15 (NSP15), i.e. a uridylate specific endoribonuclease of SARS-CoV-2 which plays an indispensable role in RNA processing and viral immune evasion from the host immune system. The NSP15 protein was screened against an in-house library of 123 antiviral drugs obtained from the DrugBank database from which three promising drug candidates were identified based on their estimated binding affinities (ΔG), estimated inhibition constants (Ki), the orientation of drug molecules in the active site and the key interacting residues of NSP15. Molecular dynamics (MD) simulations were performed for the screened drug candidates in complex with NSP15 as well as the apo form of NSP15 to mimic their physiological states. Based on the stable MD simulation trajectories, the binding free energies of the screened NSP15-drug complexes were calculated using the MM/PBSA approach. Two candidate drugs, Simeprevir and Paritaprevir, achieved the lowest binding free energies for NSP15, with a value of −259.522 ± 17.579 and −154.051 ± 33.628 kJ/mol, respectively. In addition, their complexes with NSP15 also exhibited the strongest structural stabilities. Taken together, we propose that Simeprevir and Paritaprevir are promising drug candidates to inhibit NSP15 and may act as potential therapeutic agents against SARS-CoV-2.

Communicated by Ramaswamy H. Sarma

Graphical Abstract

Keywords:

• Drug repurposing
• SARS-CoV-2
• NSP15
• Molecular Docking
• MD simulation
• MM/PBSA

Acknowledgements

Dr. Amit Kumar Singh thanks the Department of Science and Technology (DST), Indian National Science Academy (INSA), Indian Council of Medical Research (ICMR), New Delhi, India. Gizachew Muluneh Amera thanks the College of Natural Science, Wollo University, Dessie, Ethiopia for the sponsorship. The authors thank Sharda University, Greater Noida, India for support.

Disclosure statement

No potential conflict of interest was reported by the authors.