In sillico binding affinity studies of microbial enzymatic degradation of plastics

In Silico Screening of Active Compounds in Garri for the Inhibition of Key Enzymes Linked to Diabetes Mellitus

“…The downloaded enzymes had resolutions of 3.20 and 2.00 Å, respectively, and without mutations. The protein structures were cleaned by removing additional chains, water molecules were removed, Gasteiger charges computed, polar hydrogens added, and nonpolar hydrogens merged using AutoDock4.2.1 . The active sites chosen were the binding sites of the cocrystallized ligands.…”

“…The protein structures were cleaned by removing additional chains, water molecules were removed, Gasteiger charges computed, polar hydrogens added, and nonpolar hydrogens merged using AutoDock4.2.1. 24 The active sites chosen were the binding sites of the cocrystallized ligands. The description of the enzymes is presented in Table 1.…”

“…25 A negative free binding energy, ΔG derived from the docking procedure, is often what distinguishes an effective enzyme−inhibitor interaction. 24 This is comparable to the reaction free energy, which is frequently used to describe chemical reactions in QM theory. Therefore, the most straightforward strategy to find new effective medication ingredients and to change the existing pharmaceuticals would likely be to maximize the enzyme− substrate negative interaction energy under control of classical QM methods, ab initio or density functional theory (DFT).…”

“…Prediction of the ligand structure, as well as its placement and orientation inside these sites (often referred to as pose) and evaluation of the binding affinity, are the two fundamental processes in the docking process . A negative free binding energy, Δ G derived from the docking procedure, is often what distinguishes an effective enzyme–inhibitor interaction . This is comparable to the reaction free energy, which is frequently used to describe chemical reactions in QM theory.…”

“…The molecular docking method allows us to define how tiny molecules behave in the binding site of target proteins and to better understand basic biological processes by modeling the atomic-level interaction between a small chemical and a protein. 24 Prediction of the ligand structure, as well as its placement and orientation inside these sites (often referred to as pose) and evaluation of the binding affinity, are the two fundamental processes in the docking process. 25 A negative free binding energy, ΔG derived from the docking procedure, is often what distinguishes an effective enzyme−inhibitor interaction.…”