Molecular docking, X-ray crystallography, Hirshfeld surface and computational studies of N-((2,3-dichlorophenyl)(ethoxy)methyl)-2-methoxy-4-nitrobenzenamine

Abstract

In this study, we report the synthesis, characterization and theoretical study of an organic compound namely N-((2,3-dichlorophenyl)(ethoxy)methyl)-2-methoxy-4-nitrobenzenamine (L) as potential drug candidate against SARS-CoV-2 main protease. Structural and Hirshfeld surface analysis was carried out on the organic compound (L). The potential application was also assessed through molecular docking and 3-D visualizations of intermolecular interactions with two very important crucial proteins of SARS-CoV-2 (M^Pro-7C6U & 7C6S). Molecular docking calculations exhibited high binding energy and inhibition constant of −7.4 kcal/mol and 2.413 µM with SARS-CoV-2 M^Pro. Besides this, an ADMET prediction was also studied. This study provides an alternative and viable therapeutic agent for SARS-CoV-2 virus.

Keywords:

• Hirshfeld surface analysis
• molecular docking
• organic compound
• SARS-CoV-2
• X-ray diffraction study

Acknowledgments

The author is thankful to the Sophisticated Analytical Instrument Facility (SAIF), IIT Madras, India for single crystal data collection of organic ligand (L). For computer time, this research used the resources of the computational facility at the Department of Chemistry, NIT Patna, India.

Author’s contribution

Sunil Kumar ([email protected]):Writing-original draft, Writing-review & editing. Mukesh Choudhary ([email protected]):Supervision, Conceptualization, Data curation, Formal analysis, Investigation, Methodology.

Declaration of competing interest

The authors declare no conflict of interest.