Imidazole-Based Alkaloids from Marine Sponges (Leucetta and Clathrina) as Potential Inhibitors Targeting SARS-CoV-2 Main Protease: An In Silico Approach

Abstract

Imidazole-based compounds form a prominent class of heterocyclic compounds, displaying diverse applications, especially with regards to its biological and pharmacological activities. Molecular docking, simulations, and drug-likeness prediction were performed on 45 imidazole-based alkaloids from two species of marine sponges (Leucetta and Clathrina). The study seeks to identify possible inhibitors of the SARS-CoV-2 Main Protease in an effort to battle the prevailing pandemic which has been caused by the widespread infections of the SAR-CoV-2 virus in its varied mutated forms. Computational analysis with MOE 2015.10 program reveals that, among the imidazole-based alkaloids, Naamidines have a high affinity for the target protein (PDB ID:6W63), even interacting with the catalytic dyad, as compared to its non-covalent inhibitor X77. Among all the top-scoring ligands, Naamidine H produced the highest binding score of −8.87078 kcal/mol. MD simulation studies with NAMD confirms the stability of the interactions of Naamidines with the target protein. MM-GBSA calculations were performed on the top binding ligands which further confirms the binding affinity of the top-scoring ligands. Computational and pharmacological investigations in this study proposes Naamidines, as effective inhibitors of Mpro. Naamidine I, Naamidine E, and Pyronaamidine could be potential anti-viral candidates against SAR-CoV-2.

Keywords:

• SARS-CoV-2 main protease
• molecular docking
• marine sponges
• anti-viral drug
• MM/GBSA

Acknowledgments

Authors are thankful to the St. Joseph’s College (autonomous) Jakhama and St. Joseph University, Dimapur for the facilities and infrastructure.

Disclosure statement

No potential conflict of interest was reported by the author(s).