Abstract
The current pandemic, caused by SARS-CoV-2 virus, is a severe challenge for human health and the world economy. There is an urgent need for development of drugs that can manage this pandemic, as it has already infected 19 million people and led to the death of around 711,277 people worldwide. At this time, in-silico studies are providing lots of preliminary data about potential drugs, which can be a great help in further in-vitro and in-vivo studies. Here, we have selected three polyphenolic compounds, mangiferin, glucogallin, and phlorizin. These compounds are isolated from different natural sources but share structural similarities and have been reported for their antiviral activity. The objective of this study is to analyze and predict the anti-protease activity of these compounds on SARS-CoV-2main protease (Mpro) and TMPRSS2 protein. Both the viral protein and the host protein play an important role in the viral life cycle, such as post-translational modification and viral spike protein priming. This study has been performed by molecular docking of the compounds using PyRx with AutoDock Vina on the two aforementioned targets chosen for this study, i.e., SARS-CoV-2 Mpro and TMPRSS2. The compounds showed good binding affinity and are further analyzed by (Molecular dynamic) MD and Molecular Mechanics Poisson-Boltzmann Surface Area MM-PBSA study. The MD-simulation study has predicted that these natural compounds will have a great impact on the stabilization of the binding cavity of the Mpro of SARS-CoV-2. The predicted pharmacokinetic parameters also show that these compounds are expected to have good solubility and absorption properties. Further predictions for these compounds also showed no involvement in drug-drug interaction and no toxicity.
Highlights
The current COVID-19 pandemic is the most serious global outbreak to have occurred in recent times
SWISS-MODEL server has developed three different models of TMPRSS2, out of which we have selected the best model for molecular docking based upon the QMEANS score
The models were built depending on the template-target alignment utilizing the ProMod3
Summary
The current COVID-19 pandemic is the most serious global outbreak to have occurred in recent times. Researchers from different fields are trying to understand it by different approaches [1]. Until now, no medication or any established therapy has been established. Natural compounds always offer a great promise in the cure of critical diseases. Polyphenolic compounds are naturally occurring phenolic compounds that contain more than one phenol group. Polyphenols are found largely in the fruits, vegetables, cereals. It has been observed that fruits such as apples, pears, grapes, and cherries
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