Investigation of the New Inhibitors by Sulfadiazine and Modified Derivatives of α-D-glucopyranoside for White Spot Syndrome Virus Disease of Shrimp by In Silico: Quantum Calculations, Molecular Docking, ADMET and Molecular Dynamics Study
Abstract
:1. Introduction
2. Computational Details of Procedure
2.1. Optimization and Ligand Preparation
2.2. Protein Preparation and Collection
2.3. Molecular Docking and Visualization of Docking
2.4. Pharmacokinetics and ADMET Studies
2.5. Lipinski Rule and Pharmacokinetics
2.6. Molecular Dynamic
2.7. White Spot Trial Procedure
3. Results and Discussions
3.1. Optimized Structure
3.2. HOMO, LUMO, and Chemical Reactivity Descriptors
3.3. Frontier Molecular Orbital: HOMO and LUMO
3.4. Molecular Docking
3.5. Protein-Ligand Interaction
3.6. Pharmacokinetics and Drug-Likeness Study
3.7. Pharmacokinetics and ADMET Studies
3.8. Aquatic and Non-Aquatic Toxicity
3.9. Protein-Ligand Interaction
3.10. Molecular Dynamics
3.11. Trial Results
4. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Title | PDB ID: 2ED6 | PDB ID: 2GJ2 | PDB ID: 2GJI | PDB ID: 2EDM |
---|---|---|---|---|
Organism | Shrimp white spot syndrome virus | Shrimp white spot syndrome virus | Shrimp white spot syndrome virus | Shrimp white spot syndrome virus |
Resolution | 2.00 Å | 2.35 Å | N/A | 2.20 Å |
R-Value Free | 0.281 | 0.275 | N/A | 0.278 |
References | [38] | [39] | [39] | [38] |
Protein Name with PDB ID | Grid Box Size | |
---|---|---|
Center | Dimension (Å) | |
Envelope Protein WSSV (PDB 2ED6) | X = 28.2583 | X = 38.9011 |
Y = 106.048 | Y = 67.0482 | |
Z = 92.9776 | Z = 45.525 | |
White Spot Syndrome Virus (PDB 2GJI) | X = −8.6514 | X = 32.888 |
Y = 15.6227 | Y = 33.828 | |
Z = −5.5754 | Z = 43.396 | |
White Spot Syndrome Virus (PDB 2EDM) | X= 37.1819 | X= 39.3455 |
Y= 35.3181 | Y= 44.655 | |
Z= 92.9466 | Z= 61.178 | |
White Spot Syndrome Virus (PDB 2GJ2) | X = 36.2550 | X = 34.8480 |
Y = 1.4367 | Y = 37.8846 | |
Z = −6.1508 | Z= 28.8952 |
Ligand. | LUMO | HOMO | A = −LUMO | I = −HOMO | Energy Gap = I − A | Hardness | Electrophilicity | |||
---|---|---|---|---|---|---|---|---|---|---|
L01 | −1.685 | −8.445 | 1.685 | 8.445 | 6.760 | −5.065 | 3.38 | 5.065 | 0.2959 | 3.7950 |
L02 | −1.550 | −8.528 | 1.550 | 8.528 | 6.978 | −5.039 | 3.489 | 5.039 | 0.2866 | 3.6388 |
L03 | −1.413 | −8.159 | 1.413 | 8.159 | 6.746 | −4.786 | 3.373 | 4.786 | 0.3965 | 3.3955 |
L04 | −1.647 | −8.896 | 1.647 | 8.896 | 7.249 | −5.2715 | 3.6245 | 5.271 | 0.2759 | 3.8335 |
L05 | −1.594 | −8.837 | 1.594 | 8.837 | 7.243 | −5.2155 | 3.6215 | 5.215 | 0.2761 | 3.7555 |
L06 | −1.701 | −8.605 | 1.701 | 8.605 | 6.904 | −5.1530 | 3.452 | 5.153 | 0.2897 | 3.8461 |
L07 | −1.580 | −8.573 | 1.580 | 8.573 | 6.993 | −5.0765 | 3.4965 | 5.076 | 0.2860 | 3.6852 |
L08 | −1.624 | −8.909 | 1.624 | 8.909 | 7.285 | −5.2665 | 3.6425 | 5.266 | 0.2745 | 3.8073 |
L09 | −0.68 | −8.673 | 0.68 | 8.673 | 7.993 | −4.6765 | 3.9965 | 4.6765 | 0.2503 | 2.7361 |
L10 | −1.240 | −7.877 | 1.240 | 7.877 | 6.637 | −4.5585 | 3.3185 | 4.5585 | 0.3013 | 3.1309 |
L11 | −2.163 | −9.146 | 2.163 | 9.146 | 6.983 | −5.6545 | 3.4915 | 5.6545 | 0.2864 | 4.5787 |
L12 | −1.745 | −8.464 | 1.745 | 8.464 | 6.719 | −5.1045 | 3.3595 | 5.1045 | 0.2977 | 3.8779 |
Ligands | Envelope Protein WSSV (PDB ID: 2ED6) | Main Protease of WSSV (PDB ID: 2GJ2) | Main Protease of WSSV (PDB ID: 2GJI) | Main Protease of WSSV (PDB ID: 2EDM) |
---|---|---|---|---|
L01 | −6.4 | −6.20 | −6.2 | −7.0 |
L02 | −5.6 | −6.30 | −6.0 | −6.4 |
L03 | −6.5 | −6.90 | −6.1 | −6.6 |
L04 | −6.6 | −6.20 | −5.7 | −6.3 |
L05 | −5.6 | −6.20 | −5.7 | −6.0 |
L06 | −6.2 | −5.80 | −5.5 | −6.1 |
L07 | −5.6 | −5.80 | −5.0 | −5.7 |
L08 | −5.5 | −5.10 | −4.7 | −5.5 |
L09 | −5.6 | −6.54 | −5.9 | −5.7 |
L10 | −5.7 | −6.74 | −5.6 | −5.4 |
L11 | −6.1 | −6.4 | −6.4 | −6.4 |
L12 | −5.5 | −5.4 | −5.1 | −5.8 |
Ligand | Inhibitor Constant (µM) | Ligand Efficiency (kcal/mol) | Internal Energy (kcal/mol) | Electrostatic Energy (kcal/mol) | Total Internal Energy (kcal/mol) | Torsional Energy (kcal/mol) | Unbound Energy (kcal/mol) |
---|---|---|---|---|---|---|---|
L01 | 40.00 | −0.19 | −7.37 | −0.15 | −2.60 | 1.79 | −2.60 |
L02 | 36.00 | −0.17 | −8.44 | −0.24 | −2.73 | 2.39 | −2.73 |
L03 | 10.28 | −0.15 | −9.06 | −0.09 | −4.49 | 2.68 | −4.49 |
L04 | 16.21 | −0.38 | −7.43 | −1.40 | −1.58 | 0.89 | −1.58 |
L05 | 11.43 | −0.40 | −7.64 | −1.37 | −0.27 | 0.89 | −0.27 |
L06 | 17.18 | −0.43 | −6.88 | −0.46 | −3.71 | 2.45 | −2.08 |
L07 | 17.25 | −0.36 | −6.69 | −0.64 | −4.10 | 2.32 | −1.94 |
L08 | 18.66 | −0.32 | −6.51 | −0.69 | −3.98 | 2.11 | −1.96 |
L09 | 22.23 | −0.22 | −6.34 | −0.71 | −3.78 | 2.67 | −1.76 |
L10 | 21.23 | −0.24 | −6.10 | −0.88 | −3.67 | 3.20 | −2.44 |
L11 | 20.01 | −0.26 | −5.90 | −0.81 | −4.20 | 2.45 | −2.87 |
L12 | 18.56 | −0.28 | −6.10 | −0.96 | −4.36 | 2.98 | 2.62 |
Ligands | NBR | HBA | HBD | TPSA, Ų | Consensus Log Po/w | Log Kp (Skin Permeation), cm/s | Lipinski Rule | MW | Bioavailability Score | GI Absorption | |
---|---|---|---|---|---|---|---|---|---|---|---|
Result | Violation | ||||||||||
L01 | 05 | 07 | 01 | 83.45 | 3.16 | −6.69 | Yes | 00 | 455.29 | 0.55 | High |
L02 | 08 | 08 | 0 | 89.52 | 4.23 | −5.81 | No | 01 | 539.40 | 0.55 | High |
L03 | 09 | 08 | 0 | 89.52 | 5.64 | −4.90 | No | 02 | 615.50 | 0.17 | Low |
L04 | 07 | 08 | 00 | 89.52 | 3.37 | −6.54 | Yes | 00 | 497.32 | 0.55 | High |
L05 | 10 | 08 | 00 | 89.52 | 4.47 | −5.83 | Yes | 01 | 539.40 | 0.55 | High |
L06 | 11 | 08 | 00 | 89.52 | 4.75 | −5.53 | Yes | 01 | 553.43 | 0.55 | High |
L07 | 06 | 07 | 00 | 80.29 | 7.79 | −2.93 | No | 02 | 649.65 | 0.17 | Low |
L08 | 19 | 08 | 00 | 89.52 | 7.56 | −3.13 | No | 02 | 665.64 | 0.17 | Low |
L09 | 03 | 06 | 02 | 109.47 | −0.26 | −8.16 | Yes | 0 | 260.36 | 0.55 | High |
L10 | 03 | 04 | 01 | 119.13 | 1.18 | −7.41 | Yes | 0 | 267.33 | 0.55 | High |
L11 | 02 | 10 | 07 | 201.85 | −1.04 | −9.62 | No | 02 | 460.43 | 0.11 | Low |
L12 | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | 528.16 | N/A | N/A |
Ligands. | Caco-2 Permeability | Blood Brain Barrier Permeant | P-I Glycoprotein Inhibitor | P-Glycoprotein Substrate | Total Clearance | CYP2C9 Inhibitor | CYP 1A2 Inhibitor |
---|---|---|---|---|---|---|---|
L01 | 1.47 | No | Yes | No | 0.595 | No | No |
L02 | 1.807 | No | Yes | No | 0.431 | No | No |
L03 | 1.878 | No | Yes | No | 0.424 | Yes | No |
L04 | 1.70 | No | Yes | No | 0.561 | No | No |
L05 | 0.747 | No | No | No | 0.711 | No | Yes |
L06 | 1.778 | No | Yes | No | 0.627 | Yes | Yes |
L07 | 1.758 | No | Yes | No | 0.705 | No | No |
L08 | 1.59 | No | Yes | No | 0.873 | No | No |
L09 | −0.018 | No | No | No | 0.642 | No | No |
L10 | 1.296 | No | No | No | −0.112 | No | No |
L11 | −0.538 | No | No | Yes | 0.456 | No | No |
L12 | −0.595 | N/A | No | Yes | 0.225 | No | No |
Ligands | Max Tolerated Dose (mg/kg/day) | Oral Rat Chronic Toxicity ((LOAEL) | Hepatotoxicity | AMES Toxicity | Water Solubility, Log S | Oral Rat Acute Toxicity (LD50) (mol/kg) | T. Pyriformis Toxicity (log μg/L) |
---|---|---|---|---|---|---|---|
L01 | 0.581 | 1.556 | No | No | −4.658 | 2.746 | 0.285 |
L02 | 0.674 | 1.530 | No | No | −4.219 | 3.034 | 0.285 |
L03 | 0.590 | 1.113 | No | No | −3.698 | 2.910 | 0.285 |
L04 | 0.822 | 1.522 | No | No | −4.674 | 3.264 | 0.285 |
L05 | 0.438 | 10.30 | No | Yes | −2.892 | 2.482 | 0.285 |
L06 | 0.763 | 1.524 | No | No | −5.509 | 3.148 | 0.285 |
L07 | 0.525 | 1.396 | No | No | −4.321 | 2.302 | 0.285 |
L08 | 0.700 | 1.497 | No | No | −5.021 | 2.621 | 0.285 |
L09 | 1.156 | 1.97 | Yes | No | −2.954 | 2.234 | 0.285 |
L10 | 1.014 | 1.838 | Yes | No | −3.076 | 2.348 | 0.285 |
L11 | 1.136 | 5.156 | No | No | −2.528 | 5.156 | 0.285 |
L12 | 1.045 | 4.524 | No | No | −2.497 | 2.456 | 0.285 |
S.L. No. | Name of the Drugs | Dose | Cure Rate |
---|---|---|---|
1 | Oxytetracycline (OTC) 50% with vitamin C | OTC-10 g/kg feed for 7 days and VC 10 g/kg feed for 10 days | 40–45% |
2 | Sulfadiazine (SFD) | 10 g/kg feed for 7 days | 5–7% |
3 | Oxytetracycline dehydrate (OTCD) | 10 g/kg feed for 7 days | 10–15% |
4 | p-Mercapto-Sulfadiazine (p-M-SFD) | 10 g/kg feed for 7 days | 00% |
5 | Oxytetracycline 50%+ sulfadiazine | OTC-5 g and SFD-5 g/kg feed for 7 days | 30–35% |
6 | Sulfadiazine with vitamin | SFD-10 g/kg feed and VC 10 g/kg feed for 7 days | 3–5% |
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Kumer, A.; Chakma, U.; Rana, M.M.; Chandro, A.; Akash, S.; Elseehy, M.M.; Albogami, S.; El-Shehawi, A.M. Investigation of the New Inhibitors by Sulfadiazine and Modified Derivatives of α-D-glucopyranoside for White Spot Syndrome Virus Disease of Shrimp by In Silico: Quantum Calculations, Molecular Docking, ADMET and Molecular Dynamics Study. Molecules 2022, 27, 3694. https://doi.org/10.3390/molecules27123694
Kumer A, Chakma U, Rana MM, Chandro A, Akash S, Elseehy MM, Albogami S, El-Shehawi AM. Investigation of the New Inhibitors by Sulfadiazine and Modified Derivatives of α-D-glucopyranoside for White Spot Syndrome Virus Disease of Shrimp by In Silico: Quantum Calculations, Molecular Docking, ADMET and Molecular Dynamics Study. Molecules. 2022; 27(12):3694. https://doi.org/10.3390/molecules27123694
Chicago/Turabian StyleKumer, Ajoy, Unesco Chakma, Md Masud Rana, Akhel Chandro, Shopnil Akash, Mona M. Elseehy, Sarah Albogami, and Ahmed M. El-Shehawi. 2022. "Investigation of the New Inhibitors by Sulfadiazine and Modified Derivatives of α-D-glucopyranoside for White Spot Syndrome Virus Disease of Shrimp by In Silico: Quantum Calculations, Molecular Docking, ADMET and Molecular Dynamics Study" Molecules 27, no. 12: 3694. https://doi.org/10.3390/molecules27123694