Crystal structure, chemical reactivity, kinetic and thermodynamic studies of new ligand derived from 4-hydroxycoumarin: Interaction with SARS-CoV-2

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ChafiaAitRamdaneTerbouche^aHasniaAbdeldjebar^aAchourTerbouche^aHouriaLakhdari^aKhaldounBachari^aThierryRoisnel^bDidierHauchard^c

^aCentre de Recherche Scientifique et Technique en Analyses Physico-chimiques(CRAPC), BP384, Bou-Ismail, RP 42004, Tipasa, Algeria^bUniv Rennes^, CNRS^, ISCR (Institut des Sciences Chimiques de Rennes)-UMR 6226^, F-35000^, Rennes^, France^cUniv Rennes^, Ecole Nationale Supérieure de Chimie de Rennes^, CNRS^, ISCR (Institut des Sciences Chimiques de Rennes)-UMR 6226^, F-35000 Rennes^, France

Received 12 May 2020, Revised 30 June 2020, Accepted 15 July 2020, Available online 16 July 2020.

Abstract

Currently, Covid-19 pandemic infects staggering number of people around the globe and causes a high rate of mortality. In order to fight this disease, a new coumarin derivative ligand (4-[(pyridin-3-ylmethyl) amino]-2H-chromen-2-one) (L_TA) has been synthesized and characterized by single-crystal X-ray diffraction, NMR, ATR, UV-Visible and cyclic voltammetry. Chemical reactivity, kinetic and thermodynamic studies were investigated using DFT method. The possible binding mode between L_TA and Main protease (Mpro) of SARS-CoV-2 and their reactivity were studied using molecular docking simulation.

Single crystal X-ray diffraction showed that L_TA crystallizes in a monoclinic system with P2₁ space group.

The reactivity descriptors such as nucleophilic index confirm that L_TA is more nucleophile, inducing complexation with binding species like biomolecules. The kinetic and thermodynamic parameters showed that the mechanism of crystal formation is moderately exothermic.

The binding energy of the SARS-CoV-2/Mpro-L_TA complex and the calculated inhibition constant using docking simulation showed that the active L_TA molecule has the ability to inhibit SARS-CoV-2.