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PMC:7441777 / 23486-40997 JSONTXT 10 Projects

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Id Subject Object Predicate Lexical cue
T228 0-4 Sentence denotes 3.2.
T229 6-40 Sentence denotes Molecular dynamics (MD) simulation
T230 42-48 Sentence denotes 3.2.1.
T231 50-98 Sentence denotes Thermodynamic stability and flexibility analysis
T232 99-383 Sentence denotes The 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.
T233 384-565 Sentence denotes 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).
T234 566-733 Sentence denotes 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.
T235 734-1017 Sentence denotes 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).
T236 1018-1119 Sentence denotes The least deviation was observed for RdRp/TF2a, while RdRp/myricetin displayed the highest deviation.
T237 1120-1341 Sentence denotes 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).
T238 1342-1400 Sentence denotes Overall, this suggests the convergence of our simulations.
T239 1401-1624 Sentence denotes Figure 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.
T240 1625-1633 Sentence denotes Table 3.
T241 1635-1754 Sentence denotes The average backbone RMSD, radius of gyration (RoG), and solvent accessible surface area (SASA) for all nine complexes.
T242 1755-1823 Sentence denotes The data are reported as average ± standard error of the mean (SEM).
T243 1824-1860 Sentence denotes System RMSD (Å) RoG (Å) SASA (Å2)
T244 1861-1921 Sentence denotes RdRp/Remdesivir 2.30 ± 0.03 29.96 ± 0.02 34973.20 ± 91.56
T245 1922-1976 Sentence denotes RdRp/EGCG 2.45 ± 0.05 29.52 ± 0.06 35026.03 ± 63.52
T246 1977-2030 Sentence denotes RdRp/TF3 1.87 ± 0.02 29.60 ± 0.01 34080.16 ± 53.41
T247 2031-2085 Sentence denotes RdRp/TF2b 2.28 ± 0.01 29.86 ± 0.02 35462.92 ± 50.40
T248 2086-2141 Sentence denotes RdRp/TF2a 1.68 ± 0.02 29.75 ± 0.02 34312.55 ± 112.89
T249 2142-2202 Sentence denotes RdRp/Myricetin 2.47 ± 0.03 29.88 ± 0.01 35395.35 ± 104.67
T250 2203-2266 Sentence denotes RdRp/Quercetagetin 1.90 ± 0.03 29.84 ± 0.01 34618.65 ± 51.25
T251 2267-2327 Sentence denotes RdRp/Hesperidin 2.03 ± 0.04 29.74 ± 0.02 34554.08 ± 47.25
T252 2328-2612 Sentence denotes RdRp/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).
T253 2613-2766 Sentence denotes 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 < 1.0 Å.
T254 2767-2929 Sentence denotes However, remdesivir, TF2a, TF2b and hesperidin showed higher fluctuations as compared to the abovementioned polyphenols, and an average RMSD of > 2.0 Å was noted.
T255 2930-3084 Sentence denotes To 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).
T256 3085-3256 Sentence denotes 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).
T257 3257-3351 Sentence denotes Figure 3(B) indicates that RdRp/remdesivir and RdRp-polyphenols shared a similar RMSF pattern.
T258 3352-3467 Sentence denotes Notable dynamic fluctuations were located in the non-active site domain, including both N-terminals and C-terminal.
T259 3468-3601 Sentence denotes Regions around Asn150, Asp260, Arg305, Asn360, and Phe440 are found to be more flexible compared to the other area for all complexes.
T260 3602-3926 Sentence denotes 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.
T261 3927-4070 Sentence denotes In the case of RdRp/TF3 and RdRp/TF2a, the binding site residues displayed lesser fluctuations compared to the other RdRp-polyphenol complexes.
T262 4071-4175 Sentence denotes This suggests that TF3 and TF2a are likely to be bound to RdRp more strongly than the other polyphenols.
T263 4176-4367 Sentence denotes Since 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.
T264 4368-4608 Sentence denotes 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).
T265 4609-4693 Sentence denotes This suggests that the structural compactness remained unchanged during simulations.
T266 4694-4888 Sentence denotes 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.
T267 4889-4940 Sentence denotes The average values of SASA are reported in Table 3.
T268 4941-5052 Sentence denotes Binding of an inhibitor to the substrate changes SASA and sometimes could greatly affect the protein structure.
T269 5053-5177 Sentence denotes Here, a relatively higher SASA value was obtained for RdRp/TF2b (35462.9 Å2) compared to the other RdRp/inhibitor complexes.
T270 5178-5255 Sentence denotes On the other hand, the lowest SASA value was noted for RdRp/TF3 (34080.2 Å2).
T271 5256-5349 Sentence denotes Thus, it can be suggested that the binding of TF3 could potentially reduce protein expansion.
T272 5351-5357 Sentence denotes 3.2.2.
T273 5359-5387 Sentence denotes Binding free energy analysis
T274 5388-5621 Sentence denotes We predicted the binding free energy of all nine complexes by utilizing the MM-PBSA scheme, and four polyphenols, namely EGCG, TF3, TF2b, and TF2a, displayed a higher estimated affinity compared to remdesivir as depicted in Figure 4.
T275 5622-5721 Sentence denotes Various components of the binding free energy of EGCG, TF3, TF2b, and TF2a are reported in Table 4.
T276 5722-5864 Sentence denotes The remaining four polyphenols which showed lower estimated affinity compare to remdesivir are shown in Table S2 in Supplementary Information.
T277 5865-6090 Sentence denotes It can be noted from Figure 4 that the intermolecular van der Waals (ΔEvdW) and electrostatic (ΔEelec) terms are favorable for the ligand binding, whereas the desolvation of polar groups (ΔGpol) opposes the complex formation.
T278 6091-6172 Sentence denotes Non-polar solvation free energy (ΔGnp) is favorable to the binding for all cases.
T279 6173-6256 Sentence denotes A similar trend was observed in our earlier study (Sk, Roy, Jonniya, et al., 2020).
T280 6257-6266 Sentence denotes Figure 4.
T281 6268-6555 Sentence denotes Energy components (kcal/mol) for the binding of remdesivir and four polyphenols to RdRp receptor. ΔEvdW, van der Waals interaction; ΔEele, electrostatic interaction in the gas phase; ΔGpol, polar solvation energy; ΔGnp, non-polar solvation energy, and ΔGbind, estimated binding affinity.
T282 6556-6564 Sentence denotes Table 4.
T283 6566-6690 Sentence denotes Energetic components of the binding free energy of RdRp and natural polyphenols along with remdesivir complexes in kcal/mol.
T284 6691-6729 Sentence denotes Data are represented as average ± SEM.
T285 6730-6775 Sentence denotes Components Remdesivir EGCG TF3 TF2b TF2a
T286 6776-6856 Sentence denotes ΔEvdW −31.85 ± 0.15 −25.11 ± 0.18 −37.82 ± 0.21 −30.66 ± 0.23 −22.55 ± 0.19
T287 6857-6939 Sentence denotes ΔEelec −98.40 ± 0.70 −69.38 ± 0.73 −123.63 ± 0.88 −47.18 ± 0.64 −95.28 ± 1.27
T288 6940-7017 Sentence denotes ΔGpol 109.97 ± 0.57 71.62 ± 0.48 124.47 ± 0.58 55.01 ± 0.49 94.94 ± 1.10
T289 7018-7092 Sentence denotes ΔGnp −4.29 ± 0.01 −4.15 ± 0.01 −5.29 ± 0.01 −3.91 ± 0.01 −4.28 ± 0.02
T290 7093-7171 Sentence denotes aΔGsolv 105.68 ± 0.57 67.47 ± 0.48 119.18 ± 0.58 51.1 ± 0.49 90.66 ± 1.10
T291 7172-7252 Sentence denotes bΔGpol + elec 11.57 ± 0.90 2.24 ± 0.87 0.84 ± 1.05 7.83 ± 0.80 −0.34 ± 1.68
T292 7253-7336 Sentence denotes cΔEMM −130.25 ± 0.71 −94.49 ± 0.75 −161.45 ± 0.90 −77.84 ± 0.68 −117.83 ± 1.28
T293 7337-7421 Sentence denotes ΔGbindSim −24.57 ± 0.91 −27.02 ± 0.89 −42.27 ± 1.07 −26.74 ± 0.83 −27.17 ± 1.69
T294 7422-7447 Sentence denotes a ΔGsolv = ΔGnp + ΔGpol,
T295 7448-7481 Sentence denotes b ΔGpol + elec = ΔEelec + ΔGpol,
T296 7482-7507 Sentence denotes c ΔEMM = ΔEvdW + ΔEelec.
T297 7508-7677 Sentence denotes It is evident from Table 4 that for all complexes, ΔEvdW varies between −22.55 kcal/mol and −37.82 kcal/mol while ΔEelec ranges from −47.18 kcal/mol to −123.63 kcal/mol.
T298 7678-8124 Sentence denotes Furthermore, in the cases of RdRp/remdesivir, RdRp/EGCG, RdRp/TF3, and RdRp/TF2b, ΔEele is over-compensated by the desolvation energy (ΔGpol), indicating that the sum of these two components, ΔGpol + elec, is unfavorable to the binding and varies between 0.84 kcal/mol and 11.57 kcal/mol (see Table 4) and similar results are found for RdRp/myricetin, RdRp/quercetagetin, RdRp/hesperidin, and RdRp/TF1 (see Table S2 in Supplementary Information).
T299 8125-8243 Sentence denotes In contrast, in the case of RdRp/TF2a, ΔGpol + elec, is favorable to the complexation (ΔGpol + elec = −0.34 kcal/mol).
T300 8244-8396 Sentence denotes Overall, this suggests that the complex formation is mainly driven by the van der Waals interactions between polyphenols as well as remdesivir and RdRp.
T301 8397-8501 Sentence denotes Therefore, hydrophobic residues in the binding pocket played a crucial role in the complexation process.
T302 8502-8818 Sentence denotes The estimated binding free energy (ΔGbind) of remdesivir, EGCG, TF3, TF2b, and TF2a were −24.57, −27.02, −42.27, −26.74 and −27.17 kcal/mol, respectively (Table 4) and myricetin, quercetagetin, hesperidin and TF1 show lower binding affinity compared to that of remdesivir (Table S2 in the Supplementary Information).
T303 8819-8908 Sentence denotes This suggests that polyphenol TF3 binds most strongly to RdRp, followed by TF2a and EGCG.
T304 8909-9016 Sentence denotes The potency of the five inhibitors decreases in the following order: TF3 > TF2a > EGCG > TF2b > remdesivir.
T305 9017-9146 Sentence denotes TF3 binds most strongly to RdRp because both ΔEvdW and ΔEelec are more favorable to the binding compared to the other inhibitors.
T306 9147-9407 Sentence denotes Similarly, TF2a binds more strongly to RdRp compared to EGCG or TF2b because ΔGpol + elec is favorable for TF2a (ΔGpol + elec = −0.34 kcal/mol) while it is found to be unfavorable for EGCG (ΔGpol + elec = 2.24 kcal/mol) and TF2b (ΔGpol + elec = 7.83 kcal/mol).
T307 9409-9415 Sentence denotes 3.2.3.
T308 9417-9459 Sentence denotes Essential residues for polyphenols binding
T309 9460-9669 Sentence denotes Further, to gain a deeper insight into the best four RdRp/polyphenols and remdesivir interaction pattern, the total binding free energy was decomposed into polyphenols-residue pair based on the MM-GBSA scheme.
T310 9670-9860 Sentence denotes The approach of per-residue based contributions is useful to determine the binding mechanisms of an inhibitor at an atomistic level, and it also reveals the individual residue contributions.
T311 9861-9989 Sentence denotes The different energy contributions from the backbone and side-chain of each residue are shown in Figure 5 and listed in Table 5.
T312 9990-9999 Sentence denotes Figure 5.
T313 10001-10147 Sentence denotes Decomposition of the binding free energy into contributions from individual residues for RdRp complexed with remdesivir, EGCG, TF3, TF2b and TF2a.
T314 10148-10156 Sentence denotes Table 5.
T315 10158-10294 Sentence denotes Per-residue based decomposition of binding free energy for the complex of remdesivir, EGCG, TF3, TF2a and TF2b with the SARS-CoV-2 RdRp.
T316 10295-10358 Sentence denotes Residue TvdW Telec Tpol Tnp Tside_chain Tbackbone Ttotal
T317 10359-10374 Sentence denotes RdRp/Remdesivir
T318 10375-10430 Sentence denotes Asp761 1.05 −21.73 18.81 −0.14 −1.82 −0.19 −2.01
T319 10431-10484 Sentence denotes Lys798 −2.74 −4.28 5.74 −0.47 −1.76 0.01 −1.75
T320 10485-10539 Sentence denotes Pro620 −1.42 −1.15 1.16 −0.18 −1.26 −0.33 −1.59
T321 10540-10594 Sentence denotes Asp760 −0.57 −4.27 4.24 −0.12 −0.20 −0.52 −0.72
T322 10595-10648 Sentence denotes Arg553 −2.07 −3.71 5.61 −0.51 −0.76 0.08 −0.68
T323 10649-10658 Sentence denotes RdRp/EGCG
T324 10659-10712 Sentence denotes Asp452 1.65 −16.48 9.85 −0.08 −5.15 0.09 −5.06
T325 10713-10766 Sentence denotes Arg553 −3.83 −4.84 6.59 −0.59 −2.68 0.01 −2.67
T326 10767-10821 Sentence denotes Pro620 −1.64 −0.41 0.51 −0.33 −1.62 −0.25 −1.87
T327 10822-10875 Sentence denotes Asp618 0.49 −8.14 6.66 −0.09 −1.13 −0.05 −1.08
T328 10876-10930 Sentence denotes Lys621 −2.26 −5.12 6.92 −0.50 −0.87 −0.09 −0.96
T329 10931-10939 Sentence denotes RdRp/TF3
T330 10940-10995 Sentence denotes Asp761 2.52 −30.13 22.11 −0.25 −5.54 −0.21 −5.75
T331 10996-11052 Sentence denotes Arg836 −0.83 −14.95 12.29 −0.37 −3.85 −0.01 −3.86
T332 11053-11107 Sentence denotes Arg555 −5.80 −4.00 7.29 −0.70 −2.98 −0.23 −3.21
T333 11108-11162 Sentence denotes Thr556 −0.20 −3.96 2.44 −0.13 −0.21 −1.64 −1.85
T334 11163-11217 Sentence denotes Ile548 −1.03 −0.08 0.12 −0.13 −0.65 −0.47 −1.12
T335 11218-11271 Sentence denotes Ser814 −1.67 0.09 0.78 −0.08 −0.48 −0.40 −0.88
T336 11272-11326 Sentence denotes Val557 −0.65 −0.16 0.17 −0.24 −0.65 −0.23 −0.88
T337 11327-11336 Sentence denotes RdRp/TF2b
T338 11337-11391 Sentence denotes His816 −3.00 −0.81 1.69 −0.32 −1.63 −0.81 −2.44
T339 11392-11446 Sentence denotes Asp833 −1.29 −0.23 0.46 −0.18 −0.21 −1.03 −1.24
T340 11447-11501 Sentence denotes Tyr877 −0.92 −2.06 2.06 −0.27 −0.43 −0.76 −1.19
T341 11502-11554 Sentence denotes Glu811 0.22 −9.24 8.11 −0.13 −2.07 1.03 −1.04
T342 11555-11609 Sentence denotes His810 −1.88 −0.41 1.66 −0.34 −0.10 −0.85 −0.95
T343 11610-11664 Sentence denotes Tyr831 −1.51 −0.36 1.19 −0.13 −0.21 −0.60 −0.81
T344 11665-11719 Sentence denotes Asn815 −0.60 −0.27 0.09 −0.01 −0.25 −0.54 −0.79
T345 11720-11729 Sentence denotes RdRp/TF2a
T346 11730-11785 Sentence denotes Asp618 2.63 −20.71 13.40 −0.17 −4.84 −0.01 −4.85
T347 11786-11840 Sentence denotes Arg553 −3.80 −6.52 7.55 −0.69 −2.68 −0.78 −3.46
T348 11841-11895 Sentence denotes Lys551 −2.23 −0.80 2.23 −0.45 −0.84 −0.41 −1.25
T349 11896-11950 Sentence denotes Arg555 −1.33 −0.62 1.05 −0.27 −1.12 −0.05 −1.17
T350 11951-12233 Sentence denotes Glu167 0.42 −6.82 5.92 −0.12 −0.61 0.01 −0.60 As shown in Figure 5, it was observed that residues favoring the binding of the polyphenols with RdRp include Asp452, Arg553, Arg555, Val557, Asp618, Pro620, Lys621, Asp623, Arg624, Asp760, Asp761, and Glu811, Asp833, and Arg836.
T351 12234-12358 Sentence denotes Most of these residues are located in the binding site of RdRp and can form direct contacts with polyphenols and remdesivir.
T352 12359-12735 Sentence denotes Figure 5 shows that amino acids Pro620, Asp761 and Lys798 for RdRp/remdesivir; Asp452, Arg553, Pro620 and Lys621 for RdRp/EGCG; Ile548, Arg555, Thr556, Asp761 and Arg836 for RdRp/TF3; Glu811, His816, Asp833 and Tyr877 for RdRp/TF2b; Lys551, Arg553, Arg555 and Asp618 for RdRp/TF2a contributed more favorably towards the binding by contributing more than −1.0 kcal/mol in size.
T353 12736-12916 Sentence denotes To complement the energetic analysis, we performed MD trajectory-based hydrogen bond (h-bond) analysis for all five complexes, and the h-bonds with occupancy are listed in Table 6.
T354 12917-13025 Sentence denotes The h-bonds were determined by setting the acceptor-donor distance of ≤ 3.5 Å, and the angle cut off ≥ 1200.
T355 13026-13090 Sentence denotes Important h-bonds between RdRp-inhibitors are shown in Figure 6.
T356 13091-13214 Sentence denotes In the case of RdRp/remdesivir, key residues involved in the hydrogen bonding are Asp761, Asp760, and Ser759, respectively.
T357 13215-13372 Sentence denotes Asp760 is found to form two h-bonds with remdesivir (Asp760@OD2 - Lig@O7, Asp760@OD2 - Lig@O6) with an occupancy of more than 15% (see Table 6 and Figure 6).
T358 13373-13505 Sentence denotes In the case of RdRp/EGCG, both Asp618 and Asp760 form two h-bonds with the ligand with an occupancy in the range of 16.09 to 30.17%.
T359 13506-13753 Sentence denotes On the other hand, Asp761 form an h-bond with TF3 (Asp761@OD1 - Lig@O11) with an occupancy of 69.84%, while Arg836 forms two h-bonds with the ligand (Arg836@NH2 - Lig@O14, Arg836@NE - Lig@O14) with an occupancy of 52.66%, and 48.70%, respectively.
T360 13754-13906 Sentence denotes Glu811, Thr556 and Asp761 also formed h-bonds with the ligand during our simulations with an occupancy varying in the range of 44% to 58% (see Table 6).
T361 13907-14088 Sentence denotes In the case of RdRp/TF2b, Glu811 is found to form two strong h–bonds with the ligand (Glu811@OE1 – Lig@O7, Glu811@OE2 – Lig@O7) with an occupancy of 22.45% and 18.89%, respectively.
T362 14089-14258 Sentence denotes On the other hand, it can be observed from Table 6 that Pro832 and Tyr877 form strong h-bonds (Pro832@O -Lig@O8 and Lig@O10 -Tyr877@OH) with increased occupancy (> 24%).
T363 14259-14449 Sentence denotes Finally, in the case of RdRp/TF2a, Asp618 is found to form two strong h-bonds with the TF2a (Asp618@OD1 – Lig@O10, Asp618@OD1 – Lig@O11) with an occupancy of 38.68% and 38.38%, respectively.
T364 14450-14526 Sentence denotes Asp760 also forms a h-bond (Asp760@O – Lig@O11) with an occupancy of 20.83%.
T365 14527-14536 Sentence denotes Figure 6.
T366 14538-14600 Sentence denotes Five main hydrogen bond interactions between ligands and RdRp.
T367 14601-14609 Sentence denotes Table 6.
T368 14611-14824 Sentence denotes Main hydrogen bond interactions formed by RdRp with remdesivir and polyphenols along with the corresponding average distance and percentage of occupancy determined using the trajectories of production simulations.
T369 14825-14846 Sentence denotes Acceptor Donor Avg.
T370 14847-14874 Sentence denotes Distance (Å) Occupancy (%)
T371 14875-14890 Sentence denotes RdRp/Remdesivir
T372 14891-14922 Sentence denotes Asp760@OD2 Lig@O7 2.66 19.46
T373 14923-14954 Sentence denotes Asp761@OD1 Lig@O7 2.65 17.70
T374 14955-14986 Sentence denotes Asp761@OD2 Lig@O6 2.63 16.86
T375 14987-15018 Sentence denotes Asp760@OD2 Lig@O6 2.65 16.65
T376 15019-15049 Sentence denotes Lig@O6 Ser759@OG 2.80 11.63
T377 15050-15081 Sentence denotes Asp760@OD1 Lig@O7 2.66 10.59
T378 15082-15091 Sentence denotes RdRp/EGCG
T379 15092-15123 Sentence denotes Asp618@OD1 Lig@O5 2.61 30.13
T380 15124-15155 Sentence denotes Asp618@OD1 Lig@O6 2.61 29.28
T381 15156-15187 Sentence denotes Asp618@OD2 Lig@O5 2.61 18.25
T382 15188-15219 Sentence denotes Asp618@OD2 Lig@O6 2.61 17.38
T383 15220-15251 Sentence denotes Asp760@OD1 Lig@O5 2.63 16.09
T384 15252-15283 Sentence denotes Tyr455@OH Lig@O11 2.83 10.97
T385 15284-15292 Sentence denotes RdRp/TF3
T386 15293-15325 Sentence denotes Asp761@OD1 Lig@O11 2.61 69.84
T387 15326-15356 Sentence denotes Glu811@O Lig@O10 2.76 58.43
T388 15357-15386 Sentence denotes Thr556@O Lig@O3 2.72 56.95
T389 15387-15419 Sentence denotes Lig@O14 Arg836@NH2 2.83 52.66
T390 15420-15451 Sentence denotes Lig@O14 Arg836@NE 2.86 48.70
T391 15452-15484 Sentence denotes Asp761@OD2 Lig@O20 2.62 44.51
T392 15485-15494 Sentence denotes RdRp/TF2b
T393 15495-15524 Sentence denotes Pro832@O Lig@O8 2.77 26.31
T394 15525-15556 Sentence denotes Lig@O11 Tyr877@OH 2.75 24.39
T395 15557-15588 Sentence denotes Glu811@OE1 Lig@O7 2.65 22.45
T396 15589-15620 Sentence denotes Glu811@OE2 Lig@O7 2.65 18.89
T397 15621-15652 Sentence denotes Asp833@OD2 Lig@O8 2.65 12.01
T398 15653-15684 Sentence denotes Asn874@OD1 Lig@O11 2.68 8.58
T399 15685-15694 Sentence denotes RdRp/TF2a
T400 15695-15727 Sentence denotes Asp618@OD1 Lig@O10 2.59 38.68
T401 15728-15760 Sentence denotes Asp618@OD1 Lig@O11 2.62 38.38
T402 15761-15791 Sentence denotes Asp760@O Lig@O11 2.70 20.83
T403 15792-15824 Sentence denotes Asp618@OD2 Lig@O11 2.62 16.59
T404 15825-15857 Sentence denotes Asp618@OD2 Lig@O10 2.58 16.49
T405 15858-16113 Sentence denotes Asp618@OD1 Lig@O15 2.67 16.37 Finally, we supplemented the above results by analyzing the final conformation of each production simulation with the help of 2D LigPlot+ software, and different h-bonds and hydrophobic interactions were shown in Figure 7.
T406 16114-16236 Sentence denotes Hydrogen bonds are depicted in green dotted lines, while red semicircle residues are involved in hydrophobic interactions.
T407 16237-16402 Sentence denotes For the RdRp/remdesivir complex, Figure 7(A) displayed nine hydrophobic interactions with Lys545, Ala547, Ser549, Arg553, Val557, Asp684, Ser759, Ser814, and Arg836.
T408 16403-16516 Sentence denotes This large number of interactions account for the high stability and good binding affinity of remdesivir to RdRp.
T409 16517-16613 Sentence denotes EGCG formed hydrophobic interactions with Lys551, Ala554, Arg553, Arg624, Pro620, (Figure 7(B)).
T410 16614-16775 Sentence denotes In the case of TF3, eight hydrophobic interactions with His439, Ile548, Ser814, Phe812, Val557, Ser549, Tyr619 and Arg555 were formed as revealed by Figure 7(C).
T411 16776-16919 Sentence denotes Figure 7(D) shows that seven hydrophobic interactions with Asp833, His816, Pro832, Gln815, His872, His810 and Ser434 were formed for RdRp/TF2b.
T412 16920-17025 Sentence denotes Finally, Figure 7(E) shows that RdRp/TF2a formed hydrophobic interactions with Arg555, Ala554 and Lys551.
T413 17026-17192 Sentence denotes Overall, TF3 has a higher binding affinity toward RdRp compared to the other polyphenols due to a larger number of stable hydrogen bonds and hydrophobic interactions.
T414 17193-17202 Sentence denotes Figure 7.
T415 17204-17327 Sentence denotes The RdRp-ligands interaction profile for (A) RdRp/remdesivir, (B) RdRp/EGCG, (C) RdRp/TF3, (D) RdRp/TF2b and (E) RdRp/TF2a.
T416 17328-17389 Sentence denotes The polyphenols and remdesivir are shown in balls and sticks.
T417 17390-17511 Sentence denotes Hydrogen bonds are depicted in green dotted lines, and red semicircles residues are involved in hydrophobic interactions.