Conformational perturbation of SARS-CoV-2 spike protein using N-acetyl cysteine: an exploration of probable mechanism of action to combat COVID-19

Abstract

The infection caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) resulted in a pandemic with huge death toll and economic consequences. The virus attaches itself to the human epithelial cells through noncovalent bonding of its spike protein with the angiotensin-converting enzyme-2 (ACE2) receptor on the host cell. Based on in silico studies we hypothesized that perturbing the functionally active conformation of spike protein through the reduction of its solvent accessible disulfide bonds, thereby disintegrating its structural architecture, may be a feasible strategy to prevent infection by reducing the binding affinity towards ACE2 enzyme. Proteomics data showed that N-acetyl cysteine (NAC), an antioxidant and mucolytic agent been widely in use in clinical medicine, forms covalent conjugates with solvent accessible cysteine residues of spike protein that were disulfide bonded in the native state. Further, in silico analysis indicated that the presence of the selective covalent conjugation of NAC with Cys525 perturbed the stereo specific orientations of the interacting key residues of spike protein that resulted in threefold weakening in the binding affinity of spike protein with ACE2 receptor. Interestingly, almost all SARS-CoV-2 variants conserved cystine residues in the spike protein. Our finding results possibly provides a molecular basis for identifying NAC and/or its analogues for targeting Cys-525 of the viral spike protein as fusion inhibitor and exploring in vivo pharmaco-preventive and its therapeutic potential activity for COVID-19 disease. However, in-vitro assay and animal model-based experiment are required to validate the probable mechanism of action.

Communicated by Ramaswamy H. Sarma

Spike protein is used to target human ACE2 receptor for viral fusion into the human cell. N-acetyl cysteine can interestingly inhibit this viral fusion process by increasing the probability of structural deformation of this viral spike protein. This process may indirectly reduce the intermolecular binding affinity between two enzymes

Keywords:

• SARS-CoV-2
• spike protein
• disulfide bonds
• N-acetyl cysteine (NAC)
• angiotensin-converting enzyme 2 (ACE2)
• mass spectrometry
• proteomics
• molecular docking
• MD simulation

Acknowledgements

We thank IISER-Kolkata, CSIR-Central Drug Research Institute, Lucknow, India and UPES-Dehradun for giving financial and infrastructural support to perform this experiment.

Authors’ contribution

UD designed and executed the experiments, analyzed data, and wrote the paper. AM performed protein modifications and executed enzyme digestion, designed the mass spectrometry-based experiments, and wrote the paper. VD has done MD simulation experiment. YSP has helped in designing MD simulation work and provided critical comments during manuscript preparation. RT, KK, PW and UV executed the mass spectrometry-based experiments and analyzed the data. AVK and PSB and AB provided critical comments to write the paper. AKM conceived the idea, designed the experiments, analyzed data and wrote the paper.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

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