Exploring the in-silico approach for assessing the potential of natural compounds as a SARS-CoV-2 main protease inhibitors

Abstract

The SARS-CoV-2 virus emerged as a major cause of the COVID-19 pandemic in December 2019. Many attempts have been made to block the viral infection by targeting various processes like its entry, uncoating, replication, activating T cells response, and rising antibody titer. Also, many drugs are repurposed like remdesivir, dexamethasone, tocilizumab, hydroxychloroquine based on their established therapeutic efficacy against other viruses in the past. Natural products (NP) consist of a promising candidate and are needed to evaluate those molecules with molecular docking for preliminary screening and in vitro studies. Therefore, in the present study, a total of 12 active constituents from natural products like Ashwagandha, Tinospora cordifolia, Tea, Neem and lemon balm were docked, using the Autodock tool, onto the crystal structure of SARS CoV-2 main protease (PDB ID-5R80), to study their capability to act as main protease (Mpro) COVID-19 inhibitors. All NPs derivatives displayed good binding energies (ΔG) ranging from -8.8 to -5.2 kcal/mol, but berberine, epicatechin, and rosmarinic acid were found most potent, among others. Therefore, good binding energy, drug-likeness, and efficient pharmacokinetics suggest the potential of NPs derivatives as SARS-CoV-2 main protease (Mpro) inhibitors. However, further research is necessary to investigate the ability of these compounds as COVID-19 inhibitors.

Antiviral Potential of Melissa officinalis L.: A Literature Review

“…Three plant compounds in Melissa officinalis extract, including luteolin-7-glucoside-3′-glucuronide, Metric acid-A and Quadranoside-III are known to be able to bind to these 2 proteins and deactivate them, thus showing antiviral activity. 32 , 34 , 120 …”

“… 32 Research has shown that 3 phytoconstituents from Melissa officinalis , including, Luteolin-7-glucoside- 3′-glucuronide, Metric acid-A, and Quadranoside-III have revealed better fusion affinity and solidity with the targets of SARS-CoV-2 main protease and spike protein. 33 , 34 …”

In silico design of quadruplex aptamers against the spike protein of SARS-CoV-2

“…In silico methods have been used in molecular biology for various analysis such as studying different receptors and ligands. By emerging of a global epidemic, many researchers sought to make it effective prevention and treatment strategies against COVID-19 using in silico , in vitro, and in vivo studies [ 25 ]. Regarding this pandemics, in silico methods have been used in different studies for analyzing the molecular structures of SARS-CoV-2 and even introducing potential therapeutic agents [ 26 , 27 ].…”