Structural and theoretical investigations, Hirshfeld surface analysis and anti-SARS CoV-2 of nickel (II) coordination complex

Abstract

A nickel(II) Schiff base complex, [Ni(L)(DMF)](1), was synthesized by treating NiCl₂.6H₂O with an ONS-donor Schiff base ligand(H₂L) derived from the condensation 3,5-Dichlorosalicylaldehyde and 4,4-Dimethyl-3-thiosemicarbazide in DMF. The geometry around the center metal ion in [Ni(L)(DMF)](1) was square planar as revealed by the data collection from diffraction studies. DFT calculations were performed on the complex to get a structure-property relationship. Hirshfeld surface analysis was also carried out in the crystal structure of nickel (II) Schiff base complex. Additionally, inspiring from recent developments to find a potential inhibitor for SARS-CoV-2 virus, we have also performed molecular docking study of [Ni(L)(DMF)](1) to see if our novel complex show affinity for main protease (M^pro) of SARS-CoV-2 M^pro (PDB ID: 6LZE). Interestingly, the results are found quite encouraging where the binding affinity and inhibition constant was found to be −6.6 kcal/mol and 2.358 µM, respectively, for the best docked confirmation of complex [Ni(L)(DMF)](1) with M^pro protein. This binding affinity is reasonably well as compared to recently known antiviral drugs. For instance, the binding affinity of complex [Ni(L)(DMF)](1) is found to be better than that of recently docking results of anti-SARS-CoV-2 drugs like chloroquine (-6.293 kcal/mol), hydroxychloroquine (-5.573 kcal/mol) and remdesivir (-6.352 kcal/mol) when targeted to the active-site of SARS-CoV-2 M^pro. Besides this, molecular docking against G25K GTP-nucleotide binding protein (PDB ID: 1A4R) was also studied. We believe that current results can intrigue not only for the biomedical community but also for the materials chemists who are engaged to explore the application coordination complexes.

Communicated by Ramaswamy H. Sarma

Keywords:

• Nickel complex
• ONS-donor Schiff base
• diffraction study
• SARS-CoV-2
• molecular docking
• Hirshfeld surface analysis

Acknowledgments

The author is thankful to the Sophisticated Analytical Instrument Facility (SAIF), IIT Madras, India for single crystal data collection of nickel(II) complex [Ni(L)(DMF)](1). The authors thank to the SAIF, IIT(ISM), India for HRMS analysis. For computer time, this research used the resources of the computational facility at Department of Chemistry, NIT Patna, India.

Disclosure statement

The authors declare no conflict of interest.

Credit authorship contribution statement

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

Funding

The author(s) reported there is no funding associated with the work featured in this article.