In Silico Evaluation of Different Flavonoids from Medicinal Plants for Their Potency against SARS-CoV-2
Abstract
:1. Introduction
2. Results and Discussion
2.1. Molecular Docking
2.2. ADMET Properties and Drug-Likeness Model Score
2.3. Molecular Dynamic Simulation (MD)
2.3.1. Root Mean Square Deviation (RMSD)
2.3.2. Root Mean Square Fluctuation (RMSF)
2.3.3. Hydrogen Bonds Analysis
2.4. MM-PBSA Binding Free Energy
3. Materials and Methods
3.1. Ligand and Protein Preparation
3.2. Assessment of Pharmacokinetics and Pharmacological Properties
3.3. Molecular Docking Analysis and Binding Energy Estimation
3.4. Molecular Dynamic (MD) Simulation
3.5. MM-PBSA Calculation
4. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Compounds | Interactions | |||||
---|---|---|---|---|---|---|
H-Bonds | Hydrophobic | |||||
Binding Energy | Number | Residue | Distance (Å) | Number | Residue | |
Anthranol | −10.22 | 1 | GLU 189 | 2.11 | 2 | MET 165, MET 49 |
Apigenin | −12.32 | 2 | PHE 185, ASN 180 | 2.07, 2.22 | 2 | PHE 181, PHE 134 |
Cannflavin | −10.88 | 2 | ARG 188, THR 25 | 2.27, 2.58 | 2 | CYS 44, MET 49 |
Derrisin | −11.44 | 2 | ARG 188, GLU 166 | 2.44, 2.55 | 3 | MET 165, HIS 41, CYS 145 |
Jaceidin | −9.66 | 1 | LYS 137 | 2.06 | 2 | TYR 126, GLU 290 |
Lupiwighteone | −11.02 | 2 | ARG 188, ASN 142 | 2.07, 2.18 | 2 | PRO 168, MET 49 |
Luteolin | −13.97 | 6 | TYR 239, LEU 287 GLU 288, ASP 289 LYS 137, ARG 131 | 2.56, 2.02 2.17, 2.44 2.11, 2.27 | 1 | ASP 289 |
Methylglovanon | −9.66 | - | - | - | 2 | PHE 134, GLU 240 |
Mundulinol | −13.12 | 2 | ARG 188, GLU 55 | 2.29, 2.01 | 4 | PHE 181, VAL 186, PRO 52, TYR 54 |
Naringenin | −12.72 | 4 | ASP 33, TYR 101 GLN 83, LYS 88 | 2.36, 2.18 2.19, 2.26 | 1 | PHE 103 |
Rhamnetin | −10.15 | 1 | LEU 287 | 1.88 | 1 | TYR 239 |
Tamarixetin | −11.13 | 2 | PHE 103, TYR 101 | 2.11, 2.03 | 2 | LYS 102, GLU 178 |
Favipiravir | −13.02 | 3 | ASP 33, TYR 101 LYS 88 | 2.38, 2.16 2.24 | 2 | PHE 103, TYR 239 |
Lopinavir | −12.98 | 2 | GLU 288, ASP 289 | 2.11, 2.32 | 2 | PHE 181, VAL 186 |
Hydroxychloroquine | −12.45 | 2 | ARG 188, GLU 166 | 2.25, 2.34 | 3 | VAL 186, PRO 52, TYR 54 |
Compounds | Interactions | |||||
---|---|---|---|---|---|---|
H-Bonds | Hydrophobic Bonds | |||||
Binding Energy | Number | Residue | Distance (Å) | Number | Residue | |
Anthranol | −9.08 | 1 | THR 315 | 2.11 | 2 | CYS 301, ALA 292 |
Apigenin | −10.09 | 5 | MET 731, LYS 733 SER 730, HIS 1058 ASP 867 | 2.15, 2.26 2.27, 2.31 2.40 | 2 | VAL 860, PRO 863 |
Cannflavin | −9.11 | 1 | THR 315 | 2.46 | 2 | CYS 301, ALA 292 |
Derrisin | −11.04 | 2 | ARG 319, ASN 317 | 2.38, 2.49 | 2 | PHE 318, VAL 595 |
Jaceidin | −10.54 | 2 | LEU 48, ASN 856 | 2.14, 2.28 | 2 | LEU 966, SER 967 |
Lupiwighteone | −9.92 | 1 | PRO 665 | 2.46 | 3 | ILE 312, LEU 303, TYR 313 |
Luteolin | −10.92 | 2 | ASN 544, GLY 545 | 2.32, 2.16 | 3 | ALA 522, HIS 519 |
Methylglovanon | −9.43 | 1 | LYS 964 | 2.56 | 1 | LEU 303 |
Mundulinol | −11.08 | 2 | ASN 969, ASP 867 | 2.33, 2.39 | 1 | PHE 970 |
Naringenin | −10.12 | 2 | LEU 517 ASN 544 | 2.31 2.26 | 2 | ALA 522, ASN 544 |
Rhamnetin | −10.15 | 2 | GLN 516 ALA 520 | 2.28 2.19 | 2 | LEU 546, HIS 519 |
Tamarixetin | −10.33 | 2 | ARG 765, GLN 762 | 2.15, 2.23 | 2 | ALA 766 |
Favipiravir | −10.76 | 2 | ASN 969, THR 315 | 2.24, 2.56 | 2 | PHE 318, ALA 292 |
Lopinavir | −10.72 | 2 | MET 731, LYS 733 | 2.19, 2.38 | 1 | SER 967 |
Hydroxychloroquine | −10.35 | 1 | GLY 545 | 2.33 | 1 | ASN 544 |
Compounds | Estimated Solubility Log Score | Estimated Solubility Class | GIT Absorption | Caco-2 Permeability | BBB Penetration | Lipinski Violations | Toxicity | Carcinogenicity |
---|---|---|---|---|---|---|---|---|
Anthranol | −2.63 | High soluble | High | 1.14 | No | 0 | Non-toxic | Non-carcinogenic |
Apigenin | −2.74 | High Soluble | High | 1.01 | No | 0 | Non-toxic | Non-carcinogenic |
Cannflavin | −5.47 | Moderately soluble | High | 1.21 | No | 0 | Non-toxic | Non-carcinogenic |
Derrisin | −2.72 | Hight Soluble | High | 1.03 | No | 0 | Non-toxic | Non-carcinogenic |
Jaceidin | −5.11 | Moderately soluble | High | 1.28 | No | 0 | Non-toxic | Non-carcinogenic |
Lupiwighteone | −3.71 | High Soluble | High | 0.79 | No | 0 | Non-toxic | Non-carcinogenic |
Luteolin | −3.04 | high soluble | High | 0.69 | No | 0 | Non-toxic | Non-carcinogenic |
Methylglovanon | −5.86 | Moderately soluble | High | 1.25 | No | 0 | Non-toxic | Non-carcinogenic |
Mundulinol | −1.49 | High Soluble | High | 0.46 | No | 0 | Non-toxic | Non-carcinogenic |
Naringenin | −2.88 | High Soluble | High | 1.07 | No | 0 | Non-toxic | Non-carcinogenic |
Rhamnetin | −4.54 | Moderately soluble | High | 1.12 | No | 0 | Non-toxic | Non-carcinogenic |
Tamarixetin | −4.63 | Moderately soluble | High | 1.15 | No | 0 | Non-toxic | Non-carcinogenic |
Compounds | Drug-Likeness Model Score |
---|---|
Anthranol | 0.60 |
Apigenin | 0.98 |
Cannflavin | 0.67 |
Derrisin | −1.08 |
Jaceidin | 0.25 |
Lupiwighteone | 0.36 |
Luteolin | 0.95 |
Methylglovanon | 0.18 |
Mundulinol | 0.92 |
Naringenin | 0.90 |
Rhamnetin | −0.50 |
Tamarixetin | 0.27 |
Complexes | ΔEElectrostatic (kJ/mol) | ΔEVan derWaal (kJ/mol) | ΔEpolar (kJ/mol) | SASA (kJ/mol) | ΔEbinding (kJ/mol) |
---|---|---|---|---|---|
Mundulinol + 6W63 | −114.54 ± 1.33 | −33.65 ± 2.18 | 35.55 ± 2.16 | −36.32 ± 2.18 | −148.96 ± 3.55 |
Luteolin + 6W63 | −117.54 ± 2.06 | −33.65 ± 2.36 | 35.55 ± 2.65 | −35.32 ± 3.34 | −150.96 ± 2.64 |
Mundulinol + 6VYB | −115.54 ± 2.32 | −37.65 ± 2.98 | 38.55 ± 2.39 | −37.32 ± 4.05 | −151.96 ± 3.55 |
Luteolin + 6VYB | −125.21 ± 2.64 | −36.23 ± 3.49 | 35.15 ± 2.18 | −37.65 ± 3.54 | −163.94 ± 2.63 |
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El-Mageed, H.R.A.; Abdelrheem, D.A.; Rafi, M.O.; Sarker, M.T.; Al-Khafaji, K.; Hossain, M.J.; Capasso, R.; Emran, T.B. In Silico Evaluation of Different Flavonoids from Medicinal Plants for Their Potency against SARS-CoV-2. Biologics 2021, 1, 416-434. https://doi.org/10.3390/biologics1030024
El-Mageed HRA, Abdelrheem DA, Rafi MO, Sarker MT, Al-Khafaji K, Hossain MJ, Capasso R, Emran TB. In Silico Evaluation of Different Flavonoids from Medicinal Plants for Their Potency against SARS-CoV-2. Biologics. 2021; 1(3):416-434. https://doi.org/10.3390/biologics1030024
Chicago/Turabian StyleEl-Mageed, H. R. Abd, Doaa A. Abdelrheem, Md. Oliullah Rafi, Md. Takim Sarker, Khattab Al-Khafaji, Md. Jamal Hossain, Raffaele Capasso, and Talha Bin Emran. 2021. "In Silico Evaluation of Different Flavonoids from Medicinal Plants for Their Potency against SARS-CoV-2" Biologics 1, no. 3: 416-434. https://doi.org/10.3390/biologics1030024