All-atom MD simulation studies suggested complex stability of Mpro in the presence of both compounds with minimal structural changes

All-atom MD simulation studies suggested complex stability of Mpro in the presence of both compounds with minimal structural changes. Funding This work is funded by the Indian Council of Medical Research. Ethical approval This article does not contain any studies with human participants or animals performed by Eliglustat any of the authors. CRediT authorship contribution statement Taj Mohammad: Conceptualization, Methodology, Software, Investigation, Data curation, Writing – original draft, Visualization. on the basis of their molecular formula. It uses multilevel neighbors of atoms (MNA) descriptors, suggesting the biological activity of a compound is the function of its chemical structure. It defines the prediction of biological properties of a compound based on the ratio of probability to be active (Pa) and probability to be inactive (Pi). Higher the Pa value for a prediction means the compound is having more probability to be active under that particular activity or biological property. Here, we selected only those compounds showing antiviral properties and protease inhibitory potential and subsequently discussed their analog properties with parent compounds. 2.3. Eliglustat MD simulations MD simulations were performed on three systems, one, the apo- SARS-CoV-2 Mpro and the other two with the selected ligands, 10428963 and 71481120 for 50?ns at the molecular mechanics level using GROMOS 54A7 force-field in GROMACS 5.1.2 at 300?K. Compounds 10428963 and 71481120 were extracted out from the docked complexes; subsequently, their topology and force-field parameters were produced through the PRODRG webserver and then combined into the Mpro topology to make the Gromacs complexed systems. All three systems were soaked in the Simple Point Charge (spc216) model for solvation and energy minimized using steepest descent approach under 1500 steps. Final MD run was performed for 50,000?ps (50?ns) for each system and the generated trajectories were analyzed using the inbuilt tools of GROMACS as described in our preceding communications (Mohammad et al., 2019; Naqvi et al., 2018). 2.4. Principal component analysis To study the conformational sampling and atomic motions of Mpro and its docked complexes, principal component (PC) and free energy landscape (FEL) analyses were performed using the essential dynamics approach employing the calculation of the covariance matrix (Altis et al., 2008). The covariance matrix was calculated while using the following formula: Cij = (xi – xi ) (xj – xj ) where xi/xj is the coordinate of the ith/jth atom of the systems, and – in the ensemble average. The FELs of a protein can be attained using the conformational sampling approach that allows exploring the protein conformations near the native state (Papaleo et al., 2009). FELs were generated to investigate the Tnf stability and native states of SARS-CoV-2 Mpro, before and after compounds binding. The FELs were generated as: ln is the temperature of simulation, and values as 2.22?nm, 2.21?nm, and 2.20?nm, respectively. The analysis shows a minor decrease in the values when in the bound states with the selected compounds. A little decrease in is showing higher compactness of Mpro while its binding pocket is occupied by 10428963 and 71481120. However, initially up to 10?ns, the Mpro in presence of 71481120 was found with an increased which suggesting initial adjustment of Mpro binding pocket occupied with the ligand. Here, no structural shift was observed in Mpro in the presence of the compounds where the is attaining a stable equilibrium, suggests stability of protein-ligand complexes during the entire simulation (Fig. 4C). The solvent-accessible surface area is calculated as an interface surrounded by a Eliglustat solvent (Ausaf Ali et al., 2014; Rodier et al., 2005). This solvent behaves differently with varying conditions and thus a useful parameter to study the conformational dynamics of a protein in the solvent environment. To investigate the conformational behavior of Mpro before and after the binding of 71481120 and 10428963, we have computed the SASA of all three systems. The average SASA values for apo Mpro, Mpro-10428962 and Mpro-71481120 were found as 148.47?nm2, 149.75?nm2, and 149.04?nm2, respectively. A minor increase.