1st International and 10th National Iranian Conference on Bioinformatics
Home Accepted Papers
Investigation of some natural extract compounds against COVID-19 by Molecular Docking study
Paper ID : 1076-ICB10
Authors:
Akbar Vaseghi *1, Sanaz Soltangheis2, Reza Ashrafi Parchin3, Kosar Rezaee chamani4, Majid Sadeghizadeh5
1Nanobiotechnology, biological science, Tarbaiat Modars University, Tehran, Iran
2Department of Chemical engineering, University of Mohaghegh, Ardabil, Iran
3Excir Faravaran Sabalan company, Ardabil Science and Technology Park, Ardabil, Iran
4Department of Biology, Faculty of Science, University of Guilan, Rasht, Iran
5Demarteman of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
Abstract:
We used the molecular docking technique on the ACE2, Heat Shock Protein A5 substrate-binding domain b (HSPA5 SBDb), proteins in the human body, and the main protease (PDB6LU7) protein of SARS-CoV-2. We describe from silico studies on the host-cell receptor recognized by the viral spike protein that leads to an essential foundation about SARS-CoV-2 resistance of individual compounds. In this study, 11 natural compounds, which have antiviral properties according to previous studies, have been selected as small molecules candidates in the molecular docking study of spike and PDB6LU7 proteins of SARS‑CoV2 and also ACE2, TMPRSS2, and HSPA5 proteins in human cells. Binding constants of CAPE, Apigenin, Acacetin, Rutin, Chrysin, Galangin, Kaempferol, Quercetin, Artepillin c, Cinnamic acid, Prenyl caffeate, and three drugs as conventional antivirus include Oseltamivir, Heparan sulfate, and Acyclovir were measured using the AutoDock 4.2 molecular docking program. The results showed a high binding affinity for the Rutin, Galangin, and Quercetin to the ACE2, HSPA5, TMPRSS2, and 6LU7 protein from -8.1 to -10.7 kcal/mol. Also, Chrysin had the best inhibition potentials among the studied molecules with high binding energy -9.4 kcal/mol from S protein. Our studies showed that rutin had the best inhibition potentials among the studied molecules with high binding energy again ACE2, HSPA5, TMPRSS2, 6LU7, and S protein. Among these compounds, Rutin might compete with Covid-19 for ACE2, HSPA5, TMPRSS2, 6LU7, and S proteins and might prevent or delay the entry of Covid-19 into the cell. It is followed by myricetin, caffeic acid phenethyl ester, hesperetin, and pinocembrin. In conclusion, the high potential of polyphenolic agents and flavonoids in propolis to bind to human and viral proteins associated with the SARS-CoV-2 pandemic indicates that has high potential in the treatment of Covid-19.
Keywords:
SARS-CoV-2, natural compounds, Molecular Docking
Status : Paper Accepted (Poster Presentation)