Md. Nabil1, Rafat Alam2*, Quazi Ashiqur Rahman3, Md.Mahabub Ul Islam4 and Md. Ali Asif Noor5
Background: Coronavirus Disease 2019 (COVID 19) is a disease caused by Sars-Cov-2 virus which has been announced as a pandemic and a global emergency health concern by WHO. It has already affected millions of people across the world. A lot of people have succumbed to this virus as well. The virus was originated in a small town of China (Wuhan) in December, 2019 and spread throughout the world very fast. A number of research works have been conducted to find an effective treatment for this deadly disease. The invention of a medicine through the conventional way against a virus is huge time consuming and extravagantly costly. Therefore, we have conducted a molecular docking study with a number of existing antiviral drugs available in the market for the treatment of different viral diseases, two vitamins (Vitamin C and D) and phytochemical components (Thymoquinone and Carvacrol, two major constituents of Nigella sativa) in search of an effective inhibitor of RNA dependent RNA polymerase enzyme of Sars-Cov-2 virus.
Materials and Methods: Molecular docking was conducted using the software Autodock Vina which is available in the MGLtools website. We also analyzed the amino acid interactions of the ligands by using Discovery Studio.
Results & Conclusion: Out of 20 ligands we sorted out Paritaprevir, Elvitegravir, Ledipasvir, Ribavirin and Favipiravir as top five ligands based on the binding affinity, ( -9.7, -6.5, -9.4, -5.8 and -5.8 KJ/mol respectively) RMSD values (2.19, 2.05, 2.24, 1.93 and 2.14 respectively) and amino acid interaction patterns (all five ligands possessed considerable number of interactions with hydrophobic and hydrogen bonds without any unfavorable bumps) to suggest for further study in pursuit of finding an inhibitor of RNA dependent RNA polymerase enzyme of Sars-Cov-2 virus.
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