In silico analysis of Alliin derivatives as potential antiviral compounds against COVID-19

Date of Completion

2022

Document Type

Thesis

Degree Name

Bachelor of Science in Biochemistry

Keywords

Computer Simulation, COVID-19, Antiviral Agents

Abstract

Since the viral outbreak that had originated in Wuhan China, SARS-CoV-2 infects millions of people worldwide by utilizing its receptor binding domain (RBD) to infect cells with the Angiotensin Converting Enzyme II protein. This allows the virus to enter and proliferate with the help of its main protease (Mpro).

Many researchers utilize organic compounds as potential viral inhibitors and modify their structures to yield better results. Alliin is an organic compounds present in Allium sativum that have inhibited Mpro activity. This study aims to create alliin derivatives as potential drug candidates to impede viral entry and viral replication of SARS-CoV-2 by inhibiting spike RBD and Mpro enzymes. It is important that the ACE2 enzyme does not get inhibited by the designed derivative. In order to do so, alliin is designed similar to the known Mpro inhibitor, nirmatrelvir and a spike inhibitor, bictegravir. To test its inhibition, molecular docking via USCF Chimera and AutoDock Vina was performed on proteins ACE2, Mpro and spike RBD. To determine the protein-ligand interactions, BIOVIA Discovery Studio Visualizer was utilized in order to check if active residues of the protein were inhibited by the alliin derivative. Swiss ADME determine the druglikeness, bioavailability and pharmacokinetics of the designed derivative. PASS Online was used to determine the adverse effects and toxicity of the compound.

Out of the 65 designed alliin derivatives, 10 derivatives were able to selectively inhibit Mpro than ACE2 with binding scores more negative than that of nirmatrelvir. These makes their binding affinity better than nirmatrelivir. Six alliin derivatives were chosen due to having more negative binding energies than the rest. All of these alliin derivatives were able to target the catalytic dyad His41 and Cys145 of Mpro. Thus, it is predicted that these derivatives inhibit Mpro proteolytic function which then inhibits viral replication within host cells. Alliin derivative 31 (A31) and alliin derivative 61 (A61) provide the most promising results as potential drug candidates based on their Swiss ADME and PASS Online results. With that in mind, these alliin derivatives can be utilized in future in-vivo and in-vitro studies.

First Advisor

Margel C. Bonifacio

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