Comparative molecular docking analysis of the SARS CoV-2 Spike glycoprotein with the human ACE-2 receptors and thrombin.

Piyush Bhanu

doi:10.6026/97320630016532

Abstract

Comparative molecular docking and vixualization analysis of the human thrombin with the SARS CoV-2 Spike glycoprotein and the human ACE-2 receptors is of interest. The data shows that residues spanning positions 30-41 in the ACE-2 have interaction with the spike glycoprotein (UniProt ID: Q9BYF1). Results also shows that thrombin binds with SER494 in the spike protein, and GLU37 in the ACE2 receptor. SER494 in the viral receptor-binding domain provides support for hotspot-353 reported elsewhere. These preliminary data provide insights for further probe.

Highlights

[1] More than seventeen lakh people have been diagnosed from 213 countries, out of which 106,138 have died
There is another interaction with atom H25 of the ligand with OD1 of ASN459 in the protein with a bond length of 2.1 Å, and an interaction with atom H18 of the ligand and OG1 of THR364 in the protein with a bond length of 2.1Å

Summary

Introduction

A viral infection of second Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2), originated in China in December 2019, has spread across the world rapidly. [1] More than seventeen lakh people have been diagnosed from 213 countries, out of which 106,138 have died. [2] there is an urgent need to find a way to put an end to this pandemic outbreak. [4] SARS-CoV uses angiotensinconverting enzyme-2 (ACE-2) cell receptors to infect host cells, whereas MERS-CoV enters via CD26. [5] Receptor-binding domain (RBD) of SARS-CoV is structurally similar to the RBD of SARSCoV-2 based on molecular modelling studies. [13] We used MetaPocket [14] to identify the potential ligand binding sites in the protein on initializing the number of pockets to three. A grid box was set up around the binding site or the active site of the protein. It is an essential step to perform molecular docking of ligand and receptor. The further steps for docking were carried out using the protocol [16] and the resultant complex.pdb file was visualized using PYMOL [17] after which, pose with lower binding energy was selected

Objectives

Methods

Results