In-silico evaluation of bioactive compounds from tea as potential SARS-CoV-2 nonstructural protein 16 inhibitors

Rahul Singh; Vijay Kumar Bhardwaj; Jatin Sharma; Rituraj Purohit; Sanjay Kumar

doi:10.1016/j.jtcme.2021.05.005

In-silico evaluation of bioactive compounds from tea as potential SARS-CoV-2 nonstructural protein 16 inhibitors

J Tradit Complement Med. 2022 Jan;12(1):35-43. doi: 10.1016/j.jtcme.2021.05.005. Epub 2021 Jun 3.

Authors

Rahul Singh^{1

2}, Vijay Kumar Bhardwaj^{1

2

3}, Jatin Sharma^{1

2}, Rituraj Purohit^{1

2

3}, Sanjay Kumar²

Affiliations

¹ Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India.
² Biotechnology Division, CSIR-IHBT, Palampur, HP, 176061, India.
³ Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India.

Abstract

Background and aim: A novel coronavirus, called the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been found to cause COVID-19 in humans and some other mammals. The nonstructural protein 16 (NSP16) of SARS-CoV-2 plays a significant part in the replication of viruses and suppresses the ability of innate immune system to detect the virus. Therefore, inhibiting NSP16 can be a secure path towards identifying a potent medication against SARS-CoV-2. Tea (Camellia sinensis) polyphenols have been reported to exhibit potential treatment options against various viral diseases.

Methods: We conducted molecular docking and structural dynamics studies with a set of 65 Tea bioactive compounds to illustrate their ability to inhibit NSP16 of SARS-CoV-2. Moreover, post-simulations end state thermodynamic free energy calculations were estimated to strengthen our results.

Results and conclusion: Six bioactive tea molecules showed better docking scores than the standard molecule sinefungin. These results were further validated by MD simulations, where Theaflavin compound demonstrated lower binding free energy in comparison to the standard molecule sinefungin. The compound theaflavin could be considered as a novel lead compound for further evaluation by in-vitro and in-vivo studies.

Keywords: COVID-19; MD simulations; MM-PBSA; Methyltransferase; NSP16; SARS-CoV-2.