Efficacy of defensins as neutralizing agents against the deadly SARS-CoV-2

Abstract

SARS-CoV-2 infection causes asymptomatic to severe human respiratory diseases. Vaccinations are effective only to a certain extent, and the disease recurs with milder symptoms even after booster doses. Hence, we hypothesize that antiviral therapy in conjunction with vaccination is the need of the hour for containing the disease. SARS-CoV-2 enters the host cell through interaction between viral spike (S) protein and human Angiotensin II converting enzyme2 (ACE2). So, any S-protein neutralizing molecule could be a potential antiviral moiety. The interaction-interface architecture indicates that cationic peptides effectively bind to anionic interface residues of S protein-receptor binding domain (S-RBD). Subsequently, we adopted molecular docking and simulation approaches to examine the binding affinity of cationic human α and β defensins, HNP1 and HBD2 with S-RBD. We observed strong hydrogen bonds, electrostatic, salt bridge, and hydrophobic interactions between these defensins and S-RBD with binding energy (BE) of −10.7 kcal/mol. Interestingly, defensins from Zea mays (ZmD32), Solanum lycopersicum (TPP3), and Sorghum bicolor (DEF1_SORBI) exhibited approximately similar BE of −11.1 kcal/mol, −11.9 kcal/mol, and −12.6 kcal/mol respectively, comparable to ACE2 (BE= −11.9 kcal/mol). Molecular dynamics simulation of S-RBD complexes formed with HBD2, ZmD32 and TPP3, showed stable associations for 100 ns. Results of in-silico studies demonstrated higher binding affinity of more positively-charged peptides with S-RBD, suggesting the potential of plant defensins to block ACE2 binding of S-RBD. These results warrant experimental validation. However these findings indicate the usefulness of plant defensin homologues as neutralizing antiviral agents for use as ideal prophylactic and therapeutic drugs for COVID-19.

Communicated by Ramaswamy H. Sarma

Graphical Abstract

Keywords:

• COVID-19 treatment
• phytochemicals
• angiotensin-II converting enzyme
• in-silico study
• spike-protein
• defensin

Disclosure statement

The authors declare no conflict of interest in publishing this manuscript in the journal, Journal of Biomolecular Structure and Dynamics.

Additional information

Funding

The work is financed by the Department of Higher Education, and Department of Health and Family Welfare, Govt. of Kerala. VD is a recipient of Indian Council for Medical Research, Govt. of India, Research Associateship (No. 3/1/13/Neuro/139/2020-NCD-I).