In silico approach: Anthocyanin derivatives as potential inhibitors of the COVID-19 main protease

  1. Muhammad Ikhlas AbdjanORCID Logo,
  2. Khusna Arif Rakhman,
  3. Sri Handayani,
  4. Chairil Anjasmara Robo Putra and
  5. Imam Siswanto

Submitting author affiliation: Universitas Airlangga, Surabaya, Indonesia

Beilstein Arch. 2020, 2020106. https://doi.org/10.3762/bxiv.2020.106.v1

Published 15 Sep 2020

  • Preprint

Abstract

In silico approach has been carried out for the determination of drug candidates from anthocyanin derivative as inhibitors of the COVID-19 main protease. Geometry optimization has performed using the DFT/B3LYP/6-31G(d,p) method as an initial step to prepare candidate ligand. The results of molecular docking showed that candidates C5 and C6 had promising results with a grid score smaller than the ligand reference (X77) with a flexible conformation type. Studies on absorption, distribution, metabolism, excretion, and toxicity of C5 and C6 candidates were conducted to study the physicochemical properties of drug candidates and to show good predictive results as drugs. Molecular dynamic simulation uses the ffSB14 force field for 200 ns to study the interaction between ligand and receptor, the system stability, solvent accessibility, energy interactions, and hydrogen bonds. The results show good interaction stability on the C5 complex compared to the reference ligand which is characterized by the binding free energy value of C5 was -42.77 ± 0.37 kcal/mol and X77 was -42.37 ± 0.41 kcal/mol.

Keywords: anthocyanin; COVID-19 main protease; molecular docking; molecular dynamic simulation

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Abdjan, M. I.; Rakhman, K. A.; Handayani, S.; Putra, C. A. R.; Siswanto, I. Beilstein Arch. 2020, 2020106. doi:10.3762/bxiv.2020.106.v1

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