Date of Completion

7-2021

Document Type

Thesis

Degree Name

Bachelor of Science in Biochemistry

Keywords

Plant Secondary Metabolites, SARS-CoV-2, RdRp, Molecular Docking, In silico

Abstract

The rising cases of COVID-19 brought upon by SARS-CoV-2 urged the scientific community to develop possible treatments for the disease. Molecular docking methods have been utilized in order to screen possible compounds which can inhibit the virus replication. With the use of AutoDock Vina and AutoDock Tools, selected secondary metabolites from the plant Coleus aromaticus and the reference ligand, remdesivir, have been docked to the SARS-CoV-2 RNAdirected RNA polymerase (RdRp) a key enzyme in the virus replication. The results in this study showed that the five compounds with the highest binding affinity for RdRp were rutin (–8.6 kcal/mol), cirsimarin (–8.0 kcal/mol), rosmarinic acid (–7.3 kcal/mol), salvianolic acid (–7.3 kcal/mol), and chlorogenic acid (–7.0 kcal/mol), while docking with remdesivir gave a binding affinity of –6.4 kcal/mol. The five compounds and remdesivir were then assessed for their possible ADME and toxicity properties. Four of the compounds, except rutin, have shown drug-likeness based on Lipinski’s Rule of Five. Toxicity results show that all five compounds exhibited no possible toxicity properties. In terms of binding affinity and predicted toxicity properties, the best drug candidate among the 35 compounds is rutin. However, the top ligands should be subjected to molecular dynamics simulation to verify the binding affinities. Since these data cannot confirm that these compounds may be developed as a drug against SARS-CoV-2, in vitro and in vivo studies may be conducted to establish the inhibiting properties of the compounds

First Advisor

Margel C. Bonifacio, PhD

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