In Silico Molecular Docking Study of Isolated Compounds from Clusiaceae Family as SARS-COV2 Main Protease Inhibitor Neneng Siti Silfi Ambarwati (a), Islamudin Ahmad (b*)
a) Department of Cosmetology, Faculty of Engineering, Universitas Negeri Jakarta, Jl. Rawamangun Muka, East Jakarta 13220, Indonesia
b) Department of Pharmaceutical Sciences, Faculty of Pharmacy, Mulawarman University, Jl. Kuaro Gn. Kelua, Samarinda 75119, East Kalimantan, Indonesia
Abstract
Clusiaceae Family are plants that are commonly found in Indonesia, 33 isolates of compounds from these plants have been obtained. These compounds can be developed and utilized to deal with the COVID-19 pandemic with an in silico molecular docking study approach. Therefore, this study aims to predict the activity of SARS-CoV-2 main protease inhibitor from isolated compounds from plant compounds Clusiaceae species by in silico molecular docking study. Molecular docking was performed using autodocktools on the macromolecule SARS-CoV-2 main protease (PDB 6LU7, resolution 2.16 Angstrom). The docking simulation was performed using Lamarckian parameters including the mutation rate of 0.02, elitisim of 1, the population size of 150, the crossover rate of 0.80 , and 2500000 energy evaluations. The grid box used for the 4ym9 receptor consists of 36 x 62 x 40 centered on the active site X = -9,732- Y= 11.403- Z= 68,483 (XYZ-coordinates). The results showed that based on the binding energy value, there were only 4 compounds that had a lower binding energy than the native ligand, namely amentoflavone compounds (-11.53 kcal/mol), fukugiside (-10.91 kcal/mol), ananixanthone (-10, 38 kcal/mol) and canophyllol (-9.88 kcal/mol). Meanwhile, based on conformational interactions with the active site of the receptor, only amentoflavone and ananixanthone compounds have direct interactions with the active site of the receptor on residues of His 41 and Cys 145. Therefore, it can be concluded that amentoflavone and ananixanthone compounds have very good potential for further development as major protease inhibitors of SARS-CoV-2.
Keywords: Amentoflavone- Clusiaceae- SARS-COV2- in silico- molecular docking
