ISSN print edition: 0366-6352 ISSN electronic edition: 1336-9075 Registr. No.: MK SR 9/7 Published monthly

An insight into the inhibitory mechanism of phytochemicals and FDA-approved drugs on the ACE2–Spike complex of SARS-CoV-2 using computational methods

Vinod Jani, Shruti Koulgi, V. N. Mallikarjunachari Uppuladinne, Uddhavesh Sonavane, and Rajendra Joshi

High Performance Computing-Medical and Bioinformatics Applications Group, Centre for Development of Advanced Computing, Pune, India

E-mail: rajendra@cdac.in

Received: 3 January 2021  Accepted: 24 April 2021

Abstract:

The S-glycoprotein (Spike) of the SARS-CoV-2 forms a complex with the human transmembrane protein angiotensin-converting enzyme 2 (ACE2) during infection. It forms the first line of contact with the human cell. The FDA-approved drugs and phytochemicals from Indian medicinal plants were explored. Molecular docking and simulations of these molecules targeting the ACE2–Spike complex were performed. Rutin DAB10 and Swertiapuniside were obtained as the top-scored drugs as per the docking protocol. The MD simulations of ligand-free, Rutin DAB10-bound, and Swertiapuniside-bound ACE2–Spike complex revealed abrogation of the hydrogen bonding network between the two proteins. The principal component and dynamic cross-correlation analysis pointed out conformational changes in both the proteins unique to the ligand-bound systems. The interface residues, His34, and Lys353 from ACE2 and Arg403, and Tyr495 from the Spike protein formed significant strong interactions with the ligand molecules, inferring the inhibition of ACE2–Spike complex. Few novel interactions specific to Rutin-DAB10 and Swertiapuniside were also identified. The conformational flexibility of the drug-binding pocket was captured using the RMSD-based clustering of the ligand-free simulations. Ensemble docking was performed wherein the FDA-approved database and phytochemical dataset were docked on each of the cluster representatives of the ACE2–Spike. The phytochemicals identified belonged to Withania somnifera, Swertia chirayita, Tinospora cordifolia and Rutin DAB10, fulvestrant, elbasvir from FDA.

Keywords: Spike protein; ACE2; FDA; Phytochemicals; Molecular dynamics

Full paper is available at www.springerlink.com.

DOI: 10.1007/s11696-021-01680-1

Chemical Papers 75 (9) 4625–4648 (2021)