Nguyen Minh Tamab,
Pham Cam Namc,
Duong Tuan Quangd,
Nguyen Thanh Tungef,
Van V. Vug and
Son Tung Ngo*bh
aComputational Chemistry Research Group, Ton Duc Thang University, Ho Chi Minh City, Vietnam
bFaculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
cDepartment of Chemistry, The University of Danang, University of Science and Technology, Danang, Vietnam
dUniversity of Education, Hue University, Vietnam
eInstitute of Materials Science, Vietnam Academy of Science and Technology, Hanoi, Vietnam
fGraduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
gNTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
hLaboratory of Theoretical and Computational Biophysics, Ton Duc Thang University, Ho Chi Minh City, Vietnam. E-mail: ngosontung@tdtu.edu.vn
First published on 13th January 2021
SARS-CoV-2 rapidly infects millions of people worldwide since December 2019. There is still no effective treatment for the virus, resulting in the death of more than one million patients. Inhibiting the activity of SARS-CoV-2 main protease (Mpro), 3C-like protease (3CLP), is able to block the viral replication and proliferation. In this context, our study has revealed that in silico screening for inhibitors of SARS-CoV-2 Mpro can be reliably done using the monomeric structure of the Mpro instead of the dimeric one. Docking and fast pulling of ligand (FPL) simulations for both monomeric and dimeric forms correlate well with the corresponding experimental binding affinity data of 24 compounds. The obtained results were also confirmed via binding pose and noncovalent contact analyses. Our study results show that it is possible to speed up computer-aided drug design for SARS-CoV-2 Mpro by focusing on the monomeric form instead of the larger dimeric one.
Coronaviruses genomes occupy ca. 26–32 kb in length which is the largest sequence among RNA viruses.8,9 The SARS-CoV-2 genome encodes more than 20 various structural and non-structural proteins. Particularly, the SARS-CoV-2 main protease (Mpro), 3C-like protease (3CLP), is one of the most important viral enzymes, having more than 96% similarity with SARS-CoV 3CLP.9,10 SARS-CoV-2 Mpro cleaves nascent polyproteins, which are produced by the translation of the viral RNA. During this process, 11 non-structural polyproteins are auto-cleaved to become polypeptides, which are required for the viral replication and transcription.9 Therefore, SARS-CoV-2 Mpro turns out to be an attractive target for antiviral drug development since blocking viral protease can inhibit viral replication and proliferation.10,11 Numerous investigations following this strategy have been carried out and shown some initial success.12–21 However, unfortunately, an effective drug for COVID-19 is still unavailable.
Currently, it should be noted that the time and cost to advance a drug has been significantly decreased by using the power of computational approaches.22–25 Generally, the binding free energy, ΔG, between a ligand and an enzyme can be probed via computational approaches. The ΔG is associated with the experimental inhibition constant, ki, via formula ΔGbind = RTln(ki), where R is gas constant, T is absolute temperature, and ki is a critical metric revealing the nature of binding between two biomolecules.22 Accurate assessment of the ligand-binding free energy is very important in computer-aided drug design (CADD) problem.26
In addition, it should be noted that the dimer was shown to be the biologically active form of the SARS-CoV Mpro instead of the monomeric one.27 Moreover, the SARS-CoV-2 Mpro possibly acts like the SARS-CoV Mpro due to the dissimilitude of only is 12 of 306 amino acids. However, fortunately, the interface of SARS-CoV-2 Mpro does not contain a ligand-binding pocket,14 the computational screening potential inhibitors for SARS-CoV-2 Mpro are thus possible to carry out based on the monoclinic structure.28,29 However, an important question is raised that what is the difference when we use the monomeric form of SARS-CoV-2 Mpro as inhibitor-screening target instead of the dimeric one to reduce CPU time consumption? In this context, the binding affinity of available inhibitors12–21 to the monomeric and dimeric SARS-CoV-2 Mpro was examined via docking and FPL schemes. The affinity of the some inhibitors of SARS-CoV-2 to the Mpro was also evaluated. The high correlation coefficients between computational values of monomeric and dimeric systems suggests that we can use the monomeric form of SARS-CoV-2 Mpro as CADD target instead of the dimeric form. Moreover, the similar of Pearson correlation between computed and experimental metrics of SARS-CoV-2 Mpro monomer and dimer was observed. The obtained results can be beneficial to the COVID-19 therapy by speeding up CADD progression.
Fig. 1 Computational scheme for evaluation of the ligand-binding affinity to the monomeric and dimeric SARS-CoV-2 Mpro. |
The atomistic simulation was performed utilizing the parameters referred to the prior works.36,37 Particularly, the MD time step is 2 fs. The noncovalent pair was affected within a radius of 0.9 nm. The electrostatics interaction was assessed implementing the fast particle-mesh Ewald electrostatics scheme.43 The SARS-CoV-2 + inhibitor was then optimized and equalized throughout the EM, NVT, and NPT imitations. The NVT and NPT imitations were operated during intervals of 0.1 and 2.0 ns, correspondingly. Moreover, the SARS-CoV-2 Mpro Cα atoms were restrained during these imitations via a small harmonic force with a value of 1000 kJ mol−1 nm−2 per proportions. The relaxed conformation of the SARS-CoV-2 Mpro + inhibitor was then employed as initial structure of FPL simulation. During which, the inhibitor was pulled out of the binding cleft under effect of an externally harmonic force with parameters of k = 0.005 nm ps−1 and v = 600 kJ mol−1 nm−2 for pulling speed and cantilever spring constant (cf. Fig. 1), respectively.37 Totally, 8 independent trajectories were carried out to assess the ligand-binding affinity.
No. | Name | ΔGMonomerDock | ΔGDimerDock | ΔGEXPa | ||||
---|---|---|---|---|---|---|---|---|
Short | Medium | Long | Short | Medium | Long | |||
a The experimental binding free energies were gained based on IC50 value,12–18 approximating that the one equals to the inhibition constant ki. The unit is of kcal mol−1. | ||||||||
1 | 7j | −7.2 | −7.4 | −7.2 | −7.6 | −7.4 | −7.3 | −8.69 |
2 | 11a | −7.5 | −7.6 | −7.6 | −7.2 | −7.1 | −7.1 | −9.96 |
3 | 11b | −8.0 | −8.1 | −8.0 | −7.3 | −7.4 | −7.4 | −10.13 |
4 | 11r | −6.7 | −6.4 | −6.3 | −7.9 | −8.1 | −8.3 | −9.23 |
5 | 13a | −7.6 | −7.6 | −7.6 | −8.0 | −7.8 | −7.8 | −7.70 |
6 | 13b | −7.6 | −7.8 | −7.8 | −7.6 | −7.1 | −7.8 | −8.45 |
7 | Calpain inhibitor I | −5.2 | −5.2 | −5.2 | −5.4 | −5.4 | −5.6 | −6.94 |
8 | Calpain inhibitor II | −5.3 | −5.5 | −5.5 | −5.5 | −5.7 | −5.6 | −8.23 |
9 | Calpain inhibitor XII | −6.2 | −6.3 | −6.3 | −7.3 | −7.3 | −7.2 | −8.69 |
10 | Calpeptin | −5.8 | −5.5 | −6.1 | −6.1 | −6.4 | −6.3 | −6.81 |
11 | Candesartan cilexetil | −7.5 | −7.4 | −7.9 | −7.9 | −8.4 | −8.4 | −7.60 |
12 | Carmofur | −5.2 | −5.5 | −5.6 | −5.7 | −5.8 | −6.1 | −7.86 |
13 | Chloroquine | −5.0 | −5.3 | −5.1 | −6.6 | −6.6 | −6.6 | −7.41 |
14 | Dipyridamole | −6.5 | −6.5 | −6.6 | −6.7 | −6.6 | −6.6 | −8.52 |
15 | Disulfiram | −3.9 | −3.8 | −3.9 | −4.3 | −4.1 | −4.1 | −6.89 |
16 | GC-373 | −7.0 | −7.0 | −7.1 | −6.5 | −6.8 | −7.0 | −8.76 |
17 | Hydroxychloroquine | −5.8 | −6.3 | −6.2 | −6.1 | −6.2 | −6.5 | −7.58 |
18 | MG-115 | −5.7 | −5.7 | −5.5 | −5.7 | −5.7 | −6.1 | −7.53 |
19 | MG-132 | −5.6 | −6.2 | −6.2 | −6.1 | −5.8 | −6.2 | −7.41 |
20 | Narlaprevir | −7.8 | −7.5 | −7.4 | −6.5 | −6.9 | −6.8 | −7.18 |
21 | Omeprazole | −6.6 | −6.6 | −6.6 | −6.8 | −6.8 | −6.8 | −6.40 |
22 | Oxytetracycline | −7.3 | −7.3 | −7.3 | −6.7 | −6.7 | −6.7 | −6.60 |
23 | PX-12 | −3.8 | −3.8 | −3.8 | −4.1 | −4.2 | −4.5 | −6.39 |
24 | Shikonin | −6.1 | −6.1 | −6.1 | −7.0 | −6.9 | −6.9 | −6.58 |
Fig. 2 Correlation between docking results of ligands to monomeric and dimeric forms of SARS-CoV-2 Mpro. Computational results were obtained using Autodock Vina. The computed error was attained via 1000 rounds of the bootstrapping method.44 |
Furthermore, the binding pose of inhibitors to the monomeric and dimeric SARS-CoV-2 Mpro is in good agreement together since espousing the root-mean-square deviation (RMSD) of 0.21 ± 0.02 nm (cf. Fig. 3 and Table S1 of the ESI†). It should be noted that the RMSD of the ligand-binding poses, which is smaller than 0.20 nm, normally counted as the conformations locating in the same cluster.35,46 The difference in docking poses probably causes the uncorrelation between docking energies of monomeric and dimeric systems. The structural observation is thus confirmed the obtained docking energy above.
The molecular docking with larger exhaustiveness, which selected as 56 and 400 according to the previous study,35 were also performed in order to validate the convergence of the docking scheme. In total we used three different values of exhaustiveness including 400, 56, and 8 which are denoted as long, medium, and short options, respectively. The associations of the docking simulations for monomer and dimer with respect to experiment are shown in Table 1. Interestingly, changing the docking exhaustiveness parameter from short to medium and/or long does not have a significant impact on the correlation coefficient and RMSE, which is consistent with the prior benchmark.35 In particular, the correlation coefficients slightly change to RMonomerDock = 0.53 ± 0.14 and RDimerDock = 0.49 ± 0.13 matching with the medium option. The metrics are of RMonomerDock = 0.50 ± 0.15 and RDimerDock = 0.50 ± 0.12 resembling the long option. Moreover, the calculated accuracy is also associated with the RMSE value. Absolutely, within computed error, the RMSE was unchanged over the docking options short, medium, and long with amounts of RMSEDimerDock = 1.65 ± 0.17, RMSEDimerDock = 1.65 ± 0.17, and RMSEDimerDock = 1.55 ± 0.18 kcal mol−1 for the dimeric system and RMSEMonomerDock = 1.89 ± 0.15, RMSEMonomerDock = 1.81 ± 0.17, and RMSEMonomerDock = 1.81 ± 0.16 kcal mol−1 for the monomeric system, respectively. Furthermore, the docking outcomes of ligands to monomeric and dimeric shapes of SARS-CoV-2 Mpro well correlate each other with RMonomer–DimerDock = 0.83 ± 0.08 and RMonomer–DimerDock = 0.85 ± 0.09 corresponding to medium and long options (Fig. 4), respectively. Consequently, the RMSE between docking results unchange with values of RMSEMonomer–DimerDock = 0.67 ± 0.10 and RMSEMonomer–DimerDock = 0.67 ± 0.13 kcal mol−1 respecting to the docking option medium and long (Fig. 4), respectively. Overall, the docking simulations provide similar results when ligands docked to monomeric and dimeric systems and the default option of Autodock Vina is appropriate for performing docking simulations.
Fig. 4 Correlation and RMSE values between docking binding affinity of ligands to monomeric and dimeric forms of SARS-CoV-2 Mpro. |
The computed values of the rupture force and pulling work were shown in Table 2. The denoted pulling force and work profiles were described in Tables S2 and S3 of the ESI file.† The shape of both pulling force and work appear reliable when compared to the previous exertion.50,51 In particular, starting at zero, the pulling force quickly increases to the maximum value, then suddenly drops to zero due to the loss the non-covalent bond contact to the receptor. During this process, recorded-pulling work speedily rises from zero value to a stable value, corresponding to the distance at which the contact between protein and inhibitor is vanished. Moreover, the rupture force FMonomerMax of monomeric Mpros diffuses in the range from 295.0 to 977.6 pN corresponding with the spreading of pulling work WMonomer from 13.7 to 106.1 kcal mol−1. Besides that, the matching metrics of dimeric Mpros forms in the range from 307.7 to 860.2 pN and 22.4 to 85.7 kcal mol−1, correspondingly. It should be noted that the computed works are significantly larger than the magnitude of experimental binding affinity, which diffuses in the range from 6.39 to 10.13 kcal mol−1, since applied large cantilever and high pulling velocity.50 Although the discrepancy can be reduced to zero by using a small cantilever and an extremely low pulling velocity, it is not appropriate since it requires to perform several trajectories with hundred nanoseconds each.52 Furthermore, previous investigations revealed that although reducing the magnitude of cantilever spring constant and pulling velocity was able to enlarge the accuracy of the estimations, the observed results are approximately the equivalent as those at high pulling velocity.50
No. | Name | FMonomerMax | WMonomer | FDimerMax | WDimer | ΔGEXPa |
---|---|---|---|---|---|---|
a The experimental binding free energies were gained based on IC50 value,12–18 approximating that the one equals to the inhibition constant ki. The unit of force and energy/work are in pN and kcal mol−1, respectively. | ||||||
1 | 7j | 575.3 ± 32.3 | 57.9 ± 3.9 | 583.6 ± 33.8 | 60.5 ± 4.2 | −8.69 |
2 | 11a | 761.0 ± 27.0 | 73.8 ± 3.3 | 860.2 ± 31.3 | 95.7 ± 3.9 | −9.96 |
3 | 11b | 735.4 ± 40.5 | 74.2 ± 3.9 | 814.0 ± 52.5 | 80.7 ± 4.9 | −10.13 |
4 | 11r | 724.8 ± 57.7 | 77.6 ± 7.1 | 636.6 ± 28.2 | 71.5 ± 2.9 | −9.23 |
5 | 13a | 526.9 ± 56.4 | 54.4 ± 7.3 | 769.6 ± 16.3 | 84.7 ± 3.2 | −7.70 |
6 | 13b | 977.6 ± 33.7 | 106.1 ± 4.6 | 739.1 ± 28.4 | 81.6 ± 3.0 | −8.45 |
7 | Calpain inhibitor I | 625.0 ± 26.3 | 57.9 ± 2.7 | 683.2 ± 34.1 | 63.4 ± 2.5 | −6.94 |
8 | Calpain inhibitor II | 592.5 ± 31.5 | 54.4 ± 3.5 | 497.4 ± 29.1 | 44.6 ± 4.3 | −8.23 |
9 | Calpain inhibitor XII | 491.6 ± 20.5 | 46.0 ± 2.3 | 693.6 ± 50.7 | 63.5 ± 4.8 | −8.69 |
10 | Calpeptin | 446.8 ± 16.9 | 33.4 ± 2.2 | 662.7 ± 32.5 | 62.5 ± 3.6 | −6.81 |
11 | Candesartan cilexetil | 547.2 ± 38.0 | 51.4 ± 5.3 | 510.7 ± 39.3 | 49.7 ± 3.4 | −7.60 |
12 | Carmofur | 485.5 ± 34.2 | 36.2 ± 2.7 | 436.9 ± 16.3 | 33.6 ± 1.8 | −7.86 |
13 | Chloroquine | 363.4 ± 32.1 | 28.5 ± 2.8 | 410.9 ± 12.5 | 36.0 ± 1.6 | −7.41 |
14 | Dipyridamole | 547.2 ± 38.0 | 51.4 ± 5.3 | 507.5 ± 18.7 | 51.0 ± 2.4 | −8.52 |
15 | Disulfiram | 364.7 ± 24.7 | 22.7 ± 1.9 | 526.2 ± 30.3 | 40.1 ± 1.9 | −6.89 |
16 | GC-373 | 616.9 ± 34.0 | 58.2 ± 4.4 | 557.3 ± 39.9 | 52.0 ± 5.2 | −8.76 |
17 | Hydroxychloroquine | 392.0 ± 27.2 | 30.2 ± 3.1 | 307.7 ± 24.9 | 22.4 ± 2.9 | −7.58 |
18 | MG-115 | 564.8 ± 26.4 | 56.6 ± 2.5 | 708.8 ± 31.1 | 70.6 ± 3.5 | −7.53 |
19 | MG-132 | 543.2 ± 22.2 | 49.8 ± 2.1 | 505.7 ± 41.1 | 47.5 ± 6.0 | −7.41 |
20 | Narlaprevir | 601.8 ± 31.9 | 64.8 ± 2.8 | 522.0 ± 38.3 | 54.7 ± 4.3 | −7.18 |
21 | Omeprazole | 478.6 ± 24.0 | 38.1 ± 2.2 | 413.3 ± 33.1 | 31.7 ± 3.2 | −6.40 |
22 | Oxytetracycline | 447.2 ± 21.6 | 37.0 ± 2.9 | 432.4 ± 49.6 | 37.7 ± 4.8 | −6.60 |
23 | PX-12 | 295.0 ± 17.4 | 13.7 ± 1.2 | 382.0 ± 25.5 | 27.2 ± 2.0 | −6.39 |
24 | Shikonin | 321.8 ± 29.7 | 19.7 ± 3.0 | 504.5 ± 22.8 | 39.1 ± 1.2 | −6.58 |
In practice, the rupture force has been used as a predictor of ligand-binding affinity based on the assumption that a ligand binds with a higher affinity requires a stronger pulling force to dissociate it from binding cleft.53 Using the rupture force as a proxy to ligand-binding affinity, numerous investigations were successful in predicting the ligand-binding affinity to various targets.53,54 Here, the average of rupture forces were estimated over 8 independent FPL trajectories (cf. Table 2). The correlation coefficient to experiments, obtained results of monomeric systems, is RMonomerForce = −0.69 ± 0.10; while the analogous value of dimeric forms is RDimerForce = −0.60 ± 0.15. Because the correlation coefficients appear to be the same within the error range, we may conclude that there is no difference when using monomer or dimer as a CADD target. Moreover, the correlation between rupture forces obtained over SARS-CoV-2 Mpro monomer and dimer is appropriate with a value of RMonomer–DimerForce = 0.67 ± 0.10 (cf. Fig. 5). It may be argued that the recorded rupture forces of the SARS-CoV-2 Mpro monomer is quite similar to the dimeric one, although the correlation is smaller than obtained values via docking approach.
Fig. 5 Relationship between rupture forces of the SARS-CoV-2 Mpro monomer and dimer. Rupture forces were obtained via FPL calculations. The computed error was attained via 1000 rounds of the bootstrapping method.44 |
The work of pulling force was assessed via formula , where v is pulling velocity and F(t) is pulling force. In isothermal–isobaric simulations, W is related to the experimental binding affinity via Jarzynski equality.55 Therefore, utilizing W to estimate the ligand-binding affinity commonly acquires a better accurate result in comparison to rupture force.47,50,54 The obtained results reaffirmed this statement. The correlation coefficients of the monomeric and dimeric SARS-CoV-2 Mpro are RMonomerWork = −0.69 ± 0.09 and RDimerWork = −0.65 ± 0.13, respectively. Although, the computational accuracy targeting the SARS-CoV-2 Mpro monomer is slightly larger than that of the dimeric system, the difference in correlation coefficients is insignificant implying that the monomeric form of SARS-CoV-2 Mpro can be used as CADD target instead of the dimeric one. Moreover, it should be noted that FPL outcomes based on the short NPT simulation of only 2.0 ns. The results possibly limited since the complex may not gain the equilibrium states as reported in the recent work.45
The association of computed pulling works of the monomeric and dimeric SARS-CoV-2 Mpro was probed and shown in Fig. 6. Over the bootstrapping examination, the correlation coefficient is RMonomer–DimerWork = 0.78 ± 0.06 confirming the observation above. The non-enhancement of FPL outcomes compared with docking results possibly occurs due to the increase of the different binding poses to various targets, which was described below. Overall, it may be concluded that we can perform the inhibitor screening for SARS-CoV-2 Mpro with smaller computing resources since targeting the monomeric form.
Fig. 6 Association between calculated pulling work of the monomeric and dimeric SARS-CoV-2 Mpro. The computed error was attained via 1000 rounds of the bootstrapping method.44 |
In addition, the MD-refined ligand-binding affinity results are confirmed since the RMSD between ligand-binding poses to the monomeric and dimeric forms is of 0.23 ± 0.02 nm only. It should be noted that the RMSD metrics were calculated based on the last snapshot of NPT simulations, which were utilized for the binding free energy prediction via the FPL scheme. Moreover, the RMSD of MD-refined structure was slightly larger than docking results due to the effects of the conformational entropy. Moreover, the intermolecular hydrogen bond analyses suggests that three residues including Thr25, Asn142, Gly143, and Glu166 are critical residues controlling the binding mechanism of the inhibitors to both monomeric and dimeric SARS-CoV-2 Mpro (cf. Table S4 of the ESI†).
No. | Name | ΔGMonomerDock | ΔGDimerDock | FMonomerMax | WMonomer | FDimerMax | WDimer | ΔGEXPa | ||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Short | Medium | Long | Short | Medium | Long | |||||||
a The experimental binding free energies were gained based on IC50 value,20,21 approximating that the one equals to the inhibition constant ki. The unit of force and energy/work are in pN and kcal mol−1, respectively. | ||||||||||||
1 | Bazedoxifene | −7.4 | −7.5 | −7.4 | −7.4 | −7.4 | −7.5 | 460.3 ± 26.0 | 41.2 ± 3.1 | 471.1 ± 20.0 | 47.5 ± 3.6 | −7.48 |
2 | Cyclosporine | −5.8 | −5.7 | −5.7 | −5.4 | −5.4 | −5.4 | 638.8 ± 33.4 | 67.7 ± 5.4 | 426.5 ± 41.6 | 44.1 ± 4.7 | −7.17 |
3 | Digitoxin | −8.1 | −8.1 | −8.2 | −7.0 | −7.0 | −7.2 | 667.4 ± 17.7 | 70.9 ± 2.1 | 502.6 ± 65 | 55.3 ± 8.3 | −9.09 |
4 | Digoxin | −8.1 | −8.1 | −8.1 | −7.1 | −7.2 | −7.2 | 637.0 ± 30.3 | 75.0 ± 2.5 | 573.1 ± 42.3 | 59.4 ± 4.9 | −9.20 |
5 | Dihydrogambogic acid | −7.0 | −7.0 | −7.0 | −7.2 | −7.2 | −7.2 | 542.8 ± 37.7 | 59.6 ± 3.2 | 487.5 ± 29.9 | 44.0 ± 3.3 | −6.67 |
6 | Ebastine | −5.7 | −6.5 | −6.1 | −6.5 | −6.3 | −6.4 | 447.5 ± 40.1 | 40.2 ± 3.5 | 389.8 ± 25.0 | 32.8 ± 2.8 | −7.06 |
7 | Favipiravir | −4.5 | −4.8 | −4.8 | −5.0 | −5.0 | −5.0 | 364.9 ± 26.2 | 21.3 ± 2.9 | 336.1 ± 19.1 | 20.5 ± 2.5 | −4.52 |
8 | Fluspirilene | −6.9 | −7.2 | −7.3 | −8.0 | −7.7 | −7.6 | 490.1 ± 23.6 | 43.8 ± 2.0 | 544.6 ± 36.3 | 58.0 ± 3.2 | −7.53 |
9 | Isoosajin | −7.7 | −7.7 | −7.7 | −8.0 | −8.0 | −8.0 | 393.1 ± 32.8 | 28.9 ± 3.2 | 454.4 ± 19.7 | 40.4 ± 2.5 | −7.52 |
10 | Ivacaftor | −6.7 | −6.7 | −6.7 | −7.2 | −7.6 | −7.5 | 347.9 ± 34.8 | 22.3 ± 4.4 | 477.5 ± 22.1 | 41.0 ± 2.1 | −7.10 |
11 | Lusutrombopag | −6.2 | −6.1 | −6.8 | −6.4 | −6.5 | −6.3 | 540.6 ± 37.5 | 59.1 ± 3.7 | 396.8 ± 24.3 | 41.8 ± 2.2 | −7.42 |
12 | Mefloquine | −6.5 | −6.5 | −6.5 | −7.6 | −7.7 | −7.6 | 523.7 ± 23.5 | 41.5 ± 2.3 | 509.6 ± 43.3 | 46.3 ± 3.3 | −7.34 |
13 | Mequitazine | −6.6 | −6.6 | −6.6 | −6.3 | −6.3 | −6.3 | 392.5 ± 51.3 | 29.5 ± 4.0 | 384.9 ± 24.4 | 29.0 ± 2.2 | −7.03 |
14 | Osajin | −6.8 | −6.9 | −6.8 | −7.6 | −8.0 | −8.0 | 367.9 ± 20.4 | 30.8 ± 2.9 | 471.4 ± 23.9 | 39.8 ± 1.8 | −7.41 |
15 | Oxyclozanide | −6.4 | −6.4 | −6.4 | −6.7 | −6.7 | −6.7 | 463.7 ± 31.7 | 33.6 ± 3.2 | 468.1 ± 13.3 | 39.2 ± 3.5 | −7.44 |
16 | Penfluridol | −7.0 | −6.9 | −6.9 | −8.0 | −8.2 | −8.2 | 542.3 ± 33.1 | 53.3 ± 2.7 | 444.5 ± 25.0 | 48.0 ± 3.9 | −7.26 |
17 | Phenazopyridine | −6.0 | −6.0 | −6.0 | −6.0 | −6.0 | −6.0 | 391.7 ± 36.2 | 25.6 ± 2.8 | 384.8 ± 22.7 | 32.4 ± 1.4 | −6.23 |
18 | Proscillaridin | −7.7 | −7.7 | −7.7 | −6.8 | −7.3 | −7.3 | 485.6 ± 37.2 | 45.8 ± 3.3 | 512.8 ± 18.9 | 58.0 ± 1.6 | −7.79 |
19 | Tetrandrine | −6.6 | −6.6 | −6.6 | −6.8 | −6.8 | −6.8 | 485.6 ± 37.2 | 45.8 ± 3.3 | 401.5 ± 18.5 | 31.6 ± 1.8 | −7.56 |
The obtained computational values of the monomeric and dimeric SARS-CoV-2 Mpro correlate to experiments in similar amounts. The docking approach formed a Pearson correlation of ca. RDock = 0.50 to both targets. FPL approach enhanced the accuracy of the calculated ligand-binding affinity since a correlation is ca. RWork ≈ −0.65 over both receptors. The accuracy of FPL simulations probably increases due to extending the NPT simulation time as reported in the recent work.45
In addition, in good agreement with the previous observation,35 the molecular docking by Vina package rapidly converged since the correlation coefficient between computed and experimental values did not change when the docking option was altered. The RMSE of docking results also unchanged upon these alterations. Finally, it may be concluded that for SARS-CoV-2 Mpro system the pulling work is better than rupture force in predicting the ligand-binding affinity. It is well compatible with earlier probe various protein–ligand complexes.47,50,54
Footnote |
† Electronic supplementary information (ESI) available: The binding pose of ligands to SARS-CoV-2 Mpro, pulling forces and works over 8 independent trajectories of SMD simulations, interaction diagram between inhibitors and SARS-CoV-2 Mpro, the binding pose of other inhibitors to SARS-CoV-2 Mpro, the pulling force and pulling work of other inhibitors to SARS-CoV-2 Mpro. See DOI: 10.1039/d0ra09858b |
This journal is © The Royal Society of Chemistry 2021 |