Date of Completion

7-2021

Document Type

Thesis

Degree Name

Bachelor of Science in Biochemistry

Keywords

Computer Simulation, Sonchus, SARS-CoV-2

Abstract

The global pandemic caused by the novel coronavirus calls for urgent and efficacious therapeutic strategies. Although there have already been a lot of drug development programs for COVID-19, the FDA continues to seek further treatments. This study assessed and evaluated the potential of the secondary metabolites of Sonchus oleraceus Linn. in treating viral infection through in silico studies particularly by docking the ligands against the SARS-CoV-2 Main Protease (Mpro). In the screening process, 8 out of 30 secondary metabolites stood out as potential inhibitors of Mpro wherein 15-O-N-glucopyranosyl-11-B-13-dihydrourospermal had the most negative docking score of -6.7 kcal/mol while the reference drugs namely remdesivir and favipiravir had -3.4 kcal/mol and -2.8 kcal/mol respectively. Results also suggested a resemblance of the amino acid residues interacting with the secondary metabolites and the reference drugs. Meanwhile, based on in silico ADMET analysis, four of the top secondary metabolites gave positive absorption and distribution results including 7-hydroxycoumarin, coumarin, 3,4-dihydrocoumarin and triterpenoid. It is predicted to have good solubility, physicochemical and pharmacokinetic properties and obey Lipinski's rule. However, manifested hepatotoxicity and had low MTRD. The study therefore concludes that 15-O-N-glucopyranosyl-11-B-13-dihydrourospermal has the greatest potential in inhibiting Mpro and a promising compound for biochemical and cell-based assays considering its high binding affinity, good bioavailability and its non toxic characteristic. Use of other ligands from plants of the same species, molecular dynamics simulation to avoid false-positive results and conduct of in vivo and in vitro experiments are highly recommended.

First Advisor

Margel C. Bonifacio

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