| Literature DB >> 35480831 |
Nguyen Minh Tam1,2, Minh Quan Pham3,4, Huy Truong Nguyen5, Nam Dao Hong6, Nguyen Khoa Hien3,7, Duong Tuan Quang8, Huong Thi Thu Phung9, Son Tung Ngo2,10.
Abstract
Preventing the biological activity of SARS-CoV-2 main protease using natural compounds is of great interest. In this context, using a combination of AutoDock Vina and fast pulling of ligand simulations, eleven marine fungi compounds were identified that probably play as highly potent inhibitors for preventing viral replication. In particular, four compounds including M15 (3-O-(6-O-α-l-arabinopyranosyl)-β-d-glucopyranosyl-1,4-dimethoxyxanthone), M8 (wailupemycins H), M11 (cottoquinazolines B), and M9 (wailupemycins I) adopted the predicted ligand-binding free energy of -9.87, -9.82, -9.62, and -9.35 kcal mol-1, respectively, whereas the other adopted predicted ligand-binding free energies in the range from -8.54 to -8.94 kcal mol-1. The results were obtained using a combination of Vina and FPL simulations. Notably, although, AutoDock4 adopted higher accurate results in comparison with Vina, Vina is proven to be a more suitable technique for rapidly screening ligand-binding affinity with a large database of compounds since it requires much smaller computing resources. Furthermore, FPL is better than Vina to classify inhibitors upon ROC-AUC analysis. This journal is © The Royal Society of Chemistry.Entities:
Year: 2021 PMID: 35480831 PMCID: PMC9034196 DOI: 10.1039/d1ra03852d
Source DB: PubMed Journal: RSC Adv ISSN: 2046-2069 Impact factor: 4.036
Fig. 1Computational scheme including molecular docking and steered-molecular dynamics simulations. (A) Molecular docking using AutoDock approaches. (B) and (C) FPL initial conformation of SARS-CoV-2 Mpro + M15 in a different perspective. (D) The protonation states of His41 and Cys145.
The obtained values of the docking simulations
| No. | Compound | Δ | Δ | Δ | Δ | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Short | Medium | Long | Short | Medium | Long | Short | Medium | Long | |||
| 1 | Atazanavir | −7.61 | −10.46 | −14.41 | −4.55 | −9.50 | −8.48 | −8.30 | −8.20 | −8.20 | −8.64 |
| 2 | Candesartan cilexetil | −8.22 | −11.19 | −11.56 | −7.90 | −10.88 | −11.22 | −8.10 | −8.10 | −8.10 | −9.23 |
| 3 | Chloroquine | −7.41 | −8.11 | −8.35 | −6.79 | −7.46 | −7.78 | −6.10 | −6.10 | −6.10 | −8.56 |
| 4 | Cimetidine | −6.08 | −6.97 | −7.32 | −5.6 | −6.00 | −6.14 | −6.10 | −5.80 | −6.10 | −7.51 |
| 5 | Maribavir | −8.59 | −10.36 | −10.43 | −6.82 | −7.42 | −7.7 | −6.60 | −6.60 | −6.60 | −7.51 |
| 6 | Omeprazole | −8.02 | −8.28 | −8.54 | −7.06 | −7.91 | −8.09 | −7.70 | −7.80 | −7.70 | −8.03 |
| 7 | Oxytetracycline | −10.06 | −10.38 | −10.85 | −8.77 | −8.56 | −8.58 | −8.20 | −8.20 | −8.30 | −8.22 |
| 8 | Roxatidine acetate hydrochloride | −7.02 | −8.11 | −9.47 | −5.74 | −6.48 | −7.13 | −7.10 | −7.10 | −7.10 | −8.05 |
| 9 | Sulfacetamide | −5.53 | −5.95 | −5.96 | −5.28 | −5.88 | −5.89 | −5.80 | −5.80 | −5.80 | −7.51 |
| 10 | Valacyclovir hydrochloride | −6.08 | −8.18 | −9.66 | −5.58 | −5.03 | −5.35 | −6.50 | −6.60 | −6.40 | −8.16 |
The experimental binding free energy was obtained through inhibition constant ki.[66] The units of energy and force are in kcal mol−1 and pN, respectively.
Fig. 2The Pearson correlation coefficient between docking and experimental data. The docking results were obtained using AD4 and Vina in various docking options.
Fig. 3Comparison between the mean of binding free energy providing by docking and experimental approaches. The docking results were obtained by AD4 and Vina via various options.
Fig. 4Contribution of docking energy of marine fungi compounds targeting SARS-CoV-2 Mpro.
Fig. 5Comparison between docked (green) and MD-refined (gray) structures of SARS-CoV-2 Mpro + M15. Black texts represent residues, which form HBs to both docked and MD-refined structures. Gray texts represent residues, which only form HBs to MD-refined structure. Green texts mention residues, which only form HBs to the docked ligand.
Fig. 6The pulling force in displacement dependence over FPL simulations. The results were obtained via 8 independent FPL trajectories.
The computational values using molecular docking and FPL simulations
| No. | Compound | Δ |
|
| Δ | Predicted ICPre50 range |
|---|---|---|---|---|---|---|
| 1 | M15 | −9.4 | 692.8 ± 26.7 | 77.7 ± 3.7 | −9.87 | High-nanomolar |
| 2 | M8 | −9.7 | 636.4 ± 37.9 | 77.0 ± 3.1 | −9.82 | High-nanomolar |
| 3 | M11 | −9.6 | 764.9 ± 32.0 | 73.4 ± 3.6 | −9.62 | High-nanomolar |
| 4 | M9 | −9.7 | 601.5 ± 30.2 | 68.5 ± 2.7 | −9.35 | High-nanomolar |
| 5 | M2 | −10.2 | 579.2 ± 49.4 | 60.5 ± 4.6 | −8.90 | Sub-micromolar |
| 6 | M13 | −9.5 | 587.9 ± 37.6 | 59.4 ± 5.3 | −8.84 | Sub-micromolar |
| 7 | M3 | −9.9 | 593.1 ± 35.3 | 59.0 ± 2.5 | −8.82 | Sub-micromolar |
| 8 | M5 | −9.8 | 595.8 ± 30.1 | 58.4 ± 2.1 | −8.78 | Sub-micromolar |
| 9 | M4 | −9.9 | 549.1 ± 32.3 | 56.6 ± 3.9 | −8.68 | Sub-micromolar |
| 10 | M16 | −9.4 | 587.5 ± 37.4 | 54.6 ± 3.8 | −8.57 | Sub-micromolar |
| 11 | M6 | −9.8 | 551.1 ± 24.7 | 54.0 ± 3.0 | −8.54 | Sub-micromolar |
| 12 | M1 | −10.6 | 530.2 ± 20.0 | 50.8 ± 2.4 | −8.36 | Micromolar |
| 13 | M12 | −9.6 | 512.9 ± 28.0 | 44.1 ± 1.3 | −7.98 | Micromolar |
| 14 | M14 | −9.4 | 447.9 ± 19.0 | 40.7 ± 2.5 | −7.79 | Micromolar |
| 15 | M7 | −9.7 | 418.8 ± 30.2 | 37.7 ± 2.9 | −7.62 | Micromolar |
| 16 | M10 | −9.6 | 428.9 ± 20.3 | 34.3 ± 1.8 | −7.43 | Micromolar |
The predicted binding affinity ΔGPreFPL = −0.056 × W − 5.512.[59]
The predicted ICPre50 was calculated via formula with assumption that IC50 equals to inhibition constant ki. The computed error is the standard error of the mean. The unit of force and energy in pN and kcal mol−1, respectively.
Fig. 7Highly potent inhibitors for SARS-CoV-2 Mpro estimated by molecular docking and FPL simulations from marine fungi compounds. The ADME estimation was reported in Table S5 of the ESI,† in which all properties are appropriate.
Fig. 8The collective-variable FEL exposing the unbinding pathway of M15 out of SARS-CoV-2 Mpro cavity.