KEMAMPUAN SENYAWA PATELAMIDA E DARI PROCHLORON DIDEMNI ASAL TELUK MANADO SEBAGAI INHIBITOR REPLIKASI SARS-CoV-2 BERDASARKAN KAJIAN PENAMBATAN MOLEKULER DENGAN AUTODOCK

Abstract

The COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has lead to a global health emergency. The outbreak of COVID-19 to date indicates an urgency to find and develop effective therapeutic agents. One alternative that needs to be explored is to design drug candidates from marine fauna. Marine microbes have promising molecular potential as a source of pharmaceutical biomaterials, including Prochloron didemni which associated with Ascidiacea belongs to the invertebrate subphylum Tunicata in Manado Bay, North Sulawesi. This microbe has been isolated from its host Lissoclinum patella and cultivated in the laboratory. P. didemni has been reported to produce several cyclic peptides including patelamide E compound. One approach to develop this compound as antiviral drug is in silico analysis using AutoDock. This analysis aims to predict the ability of patelamide E compounds to inhibit the activity of the non-structural protein (nsp13) SARS-CoV-2 which is known to play an important role in the viral replication. Its molecular structure was downloaded from the RCSB Protein Database with ID 6ZSL. As ligands, the molecular structure of patelamide E and the recommended drugs for COVID-19 (ivermectin, remdesivir, malnupiravir, favipiravir and oseltamivir) were downloaded from https://pubchem.ncbi.nlm.nih.gov/. The binding affinity between the protein and the ligand was assessed using AutoDock and visualized by PyMol. The results show that the free energy (∆G) value of -15.4 kcal/mol was obtained for binding affinity of patelamide E towards nsp13 SARS-CoV-2, indicating that this compound could inhibit the viral replication. The inhibitory ability of patelamide E is stronger than the recommended drugs (ivermectin, remdesivir, malnupiravir, favipiravir and oseltamivir) with ∆G values ranged from -6.7 to -13.7 kcal/mol. This analysis is obviously necessary to accomplish with further computer simulation for assesing the binding stability. The potential of patelamide E as an anti-SARS-CoV-2 drug candidate should be more clinically assayed after in vitro and in vivo analyses.Keywords: Molecular docking, nsp 13, patellamide E, SARS-CoV-2, marine microbes