O estudo da docagem e dinâmica molecular de potenciais fármacos: rodatina, scedapina C e cequinadolina A, utilizados no tratamento da SARS-COV-2

Abstract

Due to the study of new drugs to combat the SARS-COV-2 virus, which is causing the COVID-19 pandemic. In this work, we address the use of three drugs (Rhodatin, Scedapin C and Scequinadoline A) as possible inhibitors of SARS-CoV-2, as they have several interactive properties, showing potential to be used in the treatment of COVID19 disease. Molecular docking provided information about the affinity energy which was -8.186, -9.617, -7.866, -7.601, -7.527 kcal/mol, for the best conformations with Scequinadoline A. Molecular couplings and affinity energy showed the residues of the site macrostructures, and analyzed the electrostatic potential map to predict some promising candidates for virus antagonists. Molecular dynamics techniques were used, where the targets were the external structures of the virus, but specifically the envelope protein, main protease, Spike glycoprotein. Using the GROMACS 2021.2 modules, the results showed that the ligands have characteristics of interaction over time. Molecular dynamics provided values between 1.5 and 4.5Å for the mean square deviation of atomic positions. Among the results obtained through molecular dynamics, it was noted that the hydrogen bonds, when compared to the calculation of the square root of the mean square deviation, underwent a change in the amount of hydrogen bonds in the bonding process, according to the proximity of the ligand used to filter out unrealistic poses in the snap, and also improved the accuracy of binding energy calculation. Analysis of molecular couplings showed that the S-gly active site residues strongly interacted with the three drugs. The reuse of these drugs in the fight against SARSCoV-2 may be candidates via virus antagonists, which if confirmed through experimental approaches, can contribute to the resolution of the global crisis of the COVID-19 pandemic.