Prediction of SARS-CoV-2 Main Protease Inhibitors from Several Medicinal Plant Compounds by Drug Repurposing and Molecular Docking Approach.

Sayma Farabi, Nihar Ranjan Saha, Noushin Anika Khan, Md. Hasanuzzaman.

10.26434/chemrxiv.12440024.v1

Research curated

Abstract

Coronaviruses are endemic in humans and infections normally mild, such as the common cold but cross-species transmission has produced some unusually virulent strains which now causing viral pneumonia and in serious cases even acute respiratory distress syndrome and death. SARS-CoV-2 is the most threatening issue which leads the world to an uncertainty alongside thousands of regular death scenes. For this virus, death toll is increasing in. An effective vaccine to cure this virus is not yet available, thus requires concerted efforts at various scales. The viral Main Protease controls Coronavirus replication and is a proven drug discovery target for SARS-CoV-2. Here, comprehensive computational approaches including drug repurposing and molecular docking were employed to predict the efficacy of medicinal plant-based bioactive compounds against SARS-CoV-2 Mpro. Molecular docking was performed using PyRx-autodock vina to analyze the inhibition probability. MPP (6LU7) was docked with 90 phytochemical compounds and docking was analysed by PyRx-autodock vina, Pymol version 1.7.4.5 Edu, and Biovia Discovery Studio 4.5. Furthermore, ADME analysis along with analysis of toxicity was also investigated to check the pharmacokinetics and drug-likeness properties of the antiviral phytochemicals. Remdesivir and lopinavir were used as standards for comparison. Our analyses revealed that the top ten (Azadirachtin, -12.5kcal/mol; Rutin, -9 kcal/mol; Theaflavin, -9 kcal/mol; Astragalin, -8.8 kcal/mol; Isoquercitrin, -8.7 kcal/mol; Hyperoside, -8.6 kcal/mol; Baicalin, -8.4 kcal/mol; Saponin, -8.3 kcal/mol; Sennoside A, -8.3 kcal/mol; Aloin, -8.2 kcal/mol, while Remdesivir and Lopinavir showed -8.2 and -7.9 kcal/mol) hits might serve as potential anti-SARS-CoV-2 lead molecules for further optimization and drug development process to combat COVID-19.

Source: ChemRxiv

Related molecules

Name	Synonyms	Genes
Astragalin	Astraglin
Astragalin	Astraglin
Isoquercitrin	Isoquercetin
Hyperoside
Tieghemelin
Sennoside A
Theaflavin
Baicalin
3C-like protease	3CLpro, Mpro, SARS coronavirus main peptidase, 3CLpro-SARS-CoV-2	rep, ORF1a-1b
Rutin

Related interactions

Target	Drug	Type	Result
3C-like protease	Theaflavin	Computational	positive
3C-like protease	Astragalin	Computational	positive
3C-like protease	Isoquercitrin	Computational	positive
3C-like protease	Hyperoside	Computational	positive
3C-like protease	Baicalin	Computational	positive
3C-like protease	Tieghemelin	Computational	positive
3C-like protease	Sennoside A	Computational	positive
3C-like protease	Rutin	Computational	positive