Research Article Molecular Dynamics Simulation of Ligands from Anredera cordifolia (Binahong)totheMainProtease(M pro )ofSARS-CoV-2 Jaka Fajar Fatriansyah , 1 Ara Gamaliel Boanerges, 1 Syarafina Ramadhanisa Kurnianto, 1 Agrin Febrian Pradana, 1 Fadilah , 2 and Siti Norasmah Surip 3 1 Department of Metallurgical and Materials Engineering, Faculty of Engineering, University of Indonesia, Depok, Jawa Barat 16424, Indonesia 2 Department of Medicinal Chemistry, Faculty of Medicine, Universitas Indonesia, Salemba Raya, Jakarta 10430, Indonesia 3 Faculty of Applied Sciences, Universiti Teknologi MARA, 40450 Shah Alam, Selangor, Malaysia Correspondence should be addressed to Jaka Fajar Fatriansyah; jakafajar@ui.ac.id Received 6 October 2022; Revised 8 November 2022; Accepted 11 November 2022; Published 22 November 2022 Academic Editor: Lawrence Sheringham Borquaye Copyright©2022JakaFajarFatriansyahaetal.TisisanopenaccessarticledistributedundertheCreativeCommonsAttribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. COVID•19 in Indonesia is considered to be entering the endemic phase, and the population is expected to live side by side with the SARS•CoV 2 viruses and their variants. In this study, procyanidin, oleic acid, methyl linoleic acid, and vitexin, four compounds from binahong leaves•tropical/subtropical plant, were examined for their interactions with the major protease (Mpro) of the SARS•CoV 2 virus. Molecular dynamics simulation shows that procyanidin and vitexin have the best docking scores of −9.132and −8.433, respectively. Molecular dynamics simulation also shows that procyanidin and vitexin have the best Root Mean Square Displacement (RMSD) and Root Mean Square Fluctuation (RMSF) performance due to dominant hydrogen, hydrophobic, and water bridge interactions. However, further strain energy calculation obtained from ligand torsion analyses, procyanidin and vitexin do not conform as much as quercetin as ligand control even though these two ligands have good performance in terms of interaction with the target protein. 1. Introduction Coronavirus disease (COVID•19) is an infectious disease caused by the SARS•CoV 2 virus. Tis disease was frst reported to have spread in Wuhan, China, on December 31st, 2019. Less than three months later, on March 9th, 2020, COVID•19 was declared a pandemic by the WHO (World Health Organization). Until now, in August 2021, the total number of cases of this disease reached 601 million around the world, resulting in the deaths of approximately 6.49 million victims. Indonesia is one of the countries most af• fected by COVID•19. In Indonesia alone, 6.35 million cases have occurred since the pandemic started on February 2020, and it took 158 thousand lives in Indonesia [1]. Although in Jakarta, the Indonesian capital, COVID•19 was considered to be entering the endemic phase, where mortality is low [2], the countryside is still afected, and the population is expected to live side by side with the existence of the SARS• CoV 2 viruses and their variants [3]. Tere are two most common methods to explore COVID•19 antiviral medications, mainly through experi• ments and simulations. Experimental methods can be car• ried out in two ways: in vivo and in vitro. Meanwhile, the simulation method is called in silico. While experimental methods play a signifcant role in drug discovery, they can be time•consuming and costly [4]. Particularly when they are repeatedly employing the trial and error approach. To simulate the performance and efcacy of medications in treating COVID•19, the in silico method may be a pre• liminary step and can be very important to speed up drug discovery [5–9]. Tropical countries have abundant medicinal plant re• sources which have yet to be discovered [10–12]. Te binahong (Anredera cordifolia) is a plant native to tropical Hindawi Journal of Tropical Medicine Volume 2022, Article ID 1178228, 13 pages https://doi.org/10.1155/2022/1178228