Molecular Docking Study of Antibiotics, Anti-Inflammatory Drugs and [Eu(TTA)₃⋅AMX] Complex as COVID-19 Biomarker through Interaction of Its Main Protease (M^pro)

Abstract

Coronavirus Acute Respiratory Syndrome (SARS-CoV-2) is a very recent viral infection and has generated one of the world’s biggest problems of all time. There is no scientific evidence and clinical trials to indicate that possible therapies have shown results in suspected or confirmed patients other than the use of immunizations. Given the above, some substances are being studied to be applied to contain their spread and further damage. This work aims to perform an in silico study of amoxicillin, widely known as an antibiotic and used to prevent bacterial infections and a possible biomarker made from a complex with Europium (Eu). It was shown to have the ability to interact with the COVID-19 protein in Mpro protease as ligands. The study was conducted using the AutoDock Vina with Lamarckian genetic model algorithm (GA) combined with the estimation of grid-based energy in rigid and flexible conformation. Compared to affinity energy, amoxicillin presented [Formula: see text][Formula: see text]kcal/mol, which was better than its co-crystallized ligand in the study. The Europium complex, where its synthesis was also demonstrated in this work, presented energy of [Formula: see text][Formula: see text]kcal/mol with hydrogen bonds and possible color change when UV light was applied. For the choice of the best poses in the simulation, the neural network parameter, NNScore2, was used. It can be affirmed that this study is still introductory but promising both in the treatment and identification of the virus.

Electrostatics in Computational Biophysics and Its Implications for Disease Effects

“…Similarly, inhibitors against cyclin G-associated kinase involved in hepatitis C virus entry into host cells were studied, and short-range interactions were analyzed [ 34 ]. The importance of hydrogen bonds was demonstrated in a study of amoxicillin, widely known as an antibiotic, to bind to COVID-19 protein in Mpro protease [ 37 ]. Another study focused on the observation that SARS-CoV-2 entrance into the host cells occurs via interactions between the receptor binding domain (RBD) of the spike (S) protein on the virus with the angiotensin-converting enzyme 2 (ACE2) receptor.…”

“…The last section is about drug discovery, and we focus on computational works that indicate the role of salt bridges and hydrogen bonds [ 30 , 31 , 32 , 33 ] to identify efficient drugs. This includes inhibitor screening methods for hepatitis C virus [ 34 , 35 ], insulin amyloid fibril [ 36 ], and antibiotics against SARS-CoV-2 [ 37 , 38 ]. The goal of this review is to highlight the role of electrostatics in the field of computational biophysics and related disease mechanisms.…”