In silico study on spice-derived antiviral phytochemicals against SARS-CoV-2 TMPRSS2 target

Abstract

Corona Virus Disease (COVID-19) caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a pandemic that has claimed so far over half a million human life across the globe. Researchers all over the world are exploring various molecules including phytochemicals to get a potential anti-COVID-19 drug. Certain phytochemicals present in some spices are claimed to possess antiviral, anti-bacterial, and anti-fungal properties. Hence, an in-silico study was done by selecting eighteen well reported antiviral phytochemicals from some spices commonly used in Indian kitchen viz. Curcuma longa (Turmeric), Nigella sativa (Black cumin), Piper nigrum (Black pepper), Trachyspermum ammi (Carom) and Zingiber officinale (Ginger) to find out whether they can prevent SARS-CoV-2 infection. Firstly, we predicted the structure of TMPRSS2 (transmembrane protease serine 2), a host protein that truncates spike protein of SARS-CoV-2 thereby facilitating its endocytosis, and then docked against its catalytic domain the selected phytochemicals and camostat (a well-known synthetic inhibitor of TMPRSS2). Thereafter, stability of seven best docked phytochemicals and camostat were scrutinized by Molecular Dynamic Simulation (MDS). MDS analysis indicated bisdemethoxycurcumin (BDMC), carvacrol and thymol as better inhibitors than the camostat due to their stable binding with TMPRSS2 in its oxyanion hole and inducing subtle modification in the spatial arrangement of the catalytic triad residues. Among these three phytochemicals, carvacrol appeared to be the best inhibitor, followed by BDMC, whereas thymol was least effective.

Graphical Abstract

Highlights

• TMPRSS2 facilitate the entry of SARS-CoV-2 in the host cell

• Spices have numerous potent anti-viral phytochemicals

• The study identified the phytochemicals (BDMC, carvacrol and thymol) as potent inhibitor candidates of TMPRSS2

Communicated by Ramaswamy H. Sarma

Keywords:

• SARS-CoV-2
• COVID-19
• TMPRSS2 inhibitor
• spices
• antiviral phytochemical
• molecular dynamics simulation

Acknowledgments

Authors acknowledge Department of Biotechnology (DBT), Govt. of India for providing financial support to the Bioinformatics Centre of the University where this work was carried out, and also to the DBT electronic library consortium for providing access to the e-resources. First author thanks the DBT for providing Post-doctoral Fellowship. Critical suggestions during the finalization of the manuscript from Dr. K. C. Mishra, a faculty of the University are acknowledged.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work was funded by Department of Biotechnology, Ministry of Science and Technology.