PMC:7441777 / 23528-28835 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7441777","sourcedb":"PMC","sourceid":"7441777","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7441777","text":"3.2.1. Thermodynamic stability and flexibility analysis\nThe 150 ns production simulations carried out for nine systems (complex of remdesivir, EGCG, TF1, TF2a, TF2b, TF3, hesperidin, myricetin, and quercetagetin with the SARS-CoV-2 RdRp) were stable on the basis of the potential energy and total energy (data not shown) of those complexes. Subsequently, the root-mean-square deviations (RMSDs) of backbone atoms relative to their respective initial positions were calculated for each complex and are shown in Figure 3(A). It is evident from Figure 3(A) that all the nine studied systems drifted from their initial positions during the first 50 ns, and after that, they reached equilibrium. The average RMSD values were estimated to be 2.30 Å, 2.45 Å, 1.87 Å, 2.28 Å, 1.68 Å, 2.47 Å, 1.90 Å, 2.03 Å and 1.88 Å for RdRp/remdesivir, RdRp/EGCG, RdRp/TF3, RdRp/TF2b, RdRp/TF2a, RdRp/myricetin, RdRp/quercetagetin, RdRp/hesperidin, and RdRp/TF1 complexes, respectively (Table 3). The least deviation was observed for RdRp/TF2a, while RdRp/myricetin displayed the highest deviation. We also investigated structural variations in the binding site, including all amino acids that fall within a radius of 5 Å from the inhibitor, and the same trend was observed (Figure S2A in the Supplementary Information). Overall, this suggests the convergence of our simulations.\nFigure 3. (A) Time evolution of root-mean-square deviations (RMSDs) of backbone atoms and (B) the root-mean-square fluctuations (RMSFs) of Cα atoms of nine complexes relative to their respective energy minimized structure.\nTable 3. The average backbone RMSD, radius of gyration (RoG), and solvent accessible surface area (SASA) for all nine complexes. The data are reported as average ± standard error of the mean (SEM).\nSystem RMSD (Å) RoG (Å) SASA (Å2)\nRdRp/Remdesivir 2.30 ± 0.03 29.96 ± 0.02 34973.20 ± 91.56\nRdRp/EGCG 2.45 ± 0.05 29.52 ± 0.06 35026.03 ± 63.52\nRdRp/TF3 1.87 ± 0.02 29.60 ± 0.01 34080.16 ± 53.41\nRdRp/TF2b 2.28 ± 0.01 29.86 ± 0.02 35462.92 ± 50.40\nRdRp/TF2a 1.68 ± 0.02 29.75 ± 0.02 34312.55 ± 112.89\nRdRp/Myricetin 2.47 ± 0.03 29.88 ± 0.01 35395.35 ± 104.67\nRdRp/Quercetagetin 1.90 ± 0.03 29.84 ± 0.01 34618.65 ± 51.25\nRdRp/Hesperidin 2.03 ± 0.04 29.74 ± 0.02 34554.08 ± 47.25\nRdRp/TF1 1.88 ± 0.03 29.86 ± 0.01 34420.69 ± 56.90 Next, we investigated the structural stability of remdesivir and eight polyphenols by estimating the temporal RMSDs of heavy atoms relative to their respective initial coordinates (see Figure S2B in the Supplementary Information). It is evident from Figure S2B that EGCG, myricetin, quercetagetin, TF1, TF3 displayed a rigid behavior in the bound form with an average RMSD of \u003c 1.0 Å. However, remdesivir, TF2a, TF2b and hesperidin showed higher fluctuations as compared to the abovementioned polyphenols, and an average RMSD of \u003e 2.0 Å was noted.\nTo identify the regions which are flexible, the root-mean-square fluctuations (RMSFs) of Cα atoms of each residue are calculated and shown in Figure 3(B). From this analysis, we can get a better insight into what extent the binding of remdesivir and natural polyphenols affects the residual flexibility of RdRp (mainly Nsp12). Figure 3(B) indicates that RdRp/remdesivir and RdRp-polyphenols shared a similar RMSF pattern. Notable dynamic fluctuations were located in the non-active site domain, including both N-terminals and C-terminal. Regions around Asn150, Asp260, Arg305, Asn360, and Phe440 are found to be more flexible compared to the other area for all complexes. The binding pocket residues, such as Asp452, Lys545, Lys551, Tyr455, Arg553, Ala554, Arg555, Thr556, Asp618, Tyr619, pro620, Lys621, Cys622, Asp623 Arg624, Asn691, Asp760, Asp761, Phe793, Met794, Ser795, Lys798, Trp800, Glu811, Phe812, and Ser814 exhibited considerably low fluctuations for all the RdRp-inhibitor complexes. In the case of RdRp/TF3 and RdRp/TF2a, the binding site residues displayed lesser fluctuations compared to the other RdRp-polyphenol complexes. This suggests that TF3 and TF2a are likely to be bound to RdRp more strongly than the other polyphenols.\nSince the radius of gyration (RoG) helps us to understand the protein structural compactness, RoG of each complex was monitored and represented in Figure S3A in the Supplementary Information. The average values of RoG are 29.96 Å, 29.52 Å, 29.60 Å, 29.86 Å, 29.75 Å, 29.88 Å, 29.84 Å, 29.74 Å and 29.86 Å for RdRp complexed with remdesivir, EGCG, TF3, TF2b, TF2a, myricetin, quercetagetin, hesperidin and TF1 respectively (Table 3). This suggests that the structural compactness remained unchanged during simulations. Finally, the solvent-accessible surface area (SASA) was also explored, and the time evolution of SASA for four RdRp-polyphenol complexes are shown in Figure S3B in the Supplementary Information. The average values of SASA are reported in Table 3. Binding of an inhibitor to the substrate changes SASA and sometimes could greatly affect the protein structure. Here, a relatively higher SASA value was obtained for RdRp/TF2b (35462.9 Å2) compared to the other RdRp/inhibitor complexes. On the other hand, the lowest SASA value was noted for RdRp/TF3 (34080.2 Å2). Thus, it can be suggested that the binding of TF3 could potentially reduce protein 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