Computational Identification of Dithymoquinone as a Potential Inhibitor of Myostatin and Regulator of Muscle Mass
Abstract
:1. Introduction
2. Results
3. Discussion
4. Materials and Methods
4.1. Natural Compounds Library Preparation
4.2. Pharmacokinetics Properties of the Selected Compound
4.3. BioTransformer
4.4. Preparation of the Receptor Structure and Interaction Study
4.5. Protein–Protein Interaction Study
4.6. Molecular Dynamics Simulation
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Sample Availability
Abbreviations
References
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Properties | Dithymoquinone (DTQ) | Calycosin | Limonin | Nigellidine | |
---|---|---|---|---|---|
Physicochemical properties | Formula | C20H24O4 | C16H12O5 | C26H30O8 | C18H18N2O2 |
Molecular weight (g/mol) | 328.40 | 284.26 | 470.51 | 294.35 | |
H-bond acceptors | 4 | 5 | 8 | 2 | |
H-bond donors | 0 | 2 | 0 | 1 | |
TPSA (Å2) | 68.28 | 79.90 | 104.57 | 47.16 Å | |
Pharmacokinetics | GIA | high | High | High | High |
BBB | Yes | No | No | Yes | |
Drug-likeness | Lipinski Rule | Yes | Yes | Yes | Yes |
Ghose Rule | Yes | Yes | Yes | Yes | |
Veber Rule | Yes | Yes | Yes | Yes | |
Egan Rule | Yes | Yes | Yes | Yes | |
Muegge Rule | Yes | Yes | Yes | Yes |
Property | Parameters | Dithymoquinone (DTQ) | Calycosin | Limonin | Nigellidine |
---|---|---|---|---|---|
Absorption | Water solubility (log mol/L) | −3.654 | −3.423 | −4.041 | −3.651 |
Caco2 permeability (log Papp in 10–6 cm/s) | 1.367 | 0.96 | 0.922 | 1.304 | |
Intestinal absorption (human) (% Absorbed) | 100 | 95.098 | 100 | 95.368 | |
Skin permeability (log Kp) | −3.189 | −2.747 | −2.832 | −2.916 | |
P-glycoprotein substrate (Yes/No) | No | Yes | No | No | |
P-glycoprotein I inhibitor (Yes/No) | Yes | No | Yes | Yes | |
P-glycoprotein II inhibitor (Yes/No) | No | No | No | No | |
Distribution | VDss (human) (log L/kg) | −0.026 | −0.326 | 0.265 | 0.508 |
Fraction unbound (human) (Fu) | 0.188 | 0.057 | 0.145 | 0.123 | |
BBB permeability (log BB) | −0.118 | −0.315 | −0.844 | −0.104 | |
CNS permeability (log PS) | −2.719 | −2.24 | −3.07 | −2.16 | |
Metabolism | CYP2D6 substrate (Yes/No) | No | No | No | No |
CYP3A4 substrate (Yes/No) | Yes | Yes | Yes | Yes | |
CYP1A2 inhibitor (Yes/No) | No | Yes | No | No | |
CYP2C19 inhibitor (Yes/No) | No | Yes | No | Yes | |
CYP2C9 inhibitor (Yes/No) | No | Yes | No | No | |
CYP2D6 inhibitor (Yes/No) | No | No | No | No | |
CYP3A4 inhibitor (Yes/No) | No | Yes | No | No | |
Excretion | Total clearance (log ml/min/kg) | −0.016 | 0.18 | 0.088 | 0.511 |
Renal OCT2 substrate (Yes/No) | Yes | No | No | Yes | |
Toxicity | AMES toxicity (Yes/No) | Yes | Yes | No | No |
Max. tolerated dose (human) (log mg/kg/day) | 0.534 | 0.141 | −0.508 | −0.425 | |
hERG I inhibitor (Yes/No) | No | No | No | No | |
hERG II inhibitor (Yes/No) | No | No | No | No | |
Oral Rat Acute Toxicity (LD50) (mol/kg) | 1.649 | 2.127 | 3.452 | 2.423 | |
Oral Rat Chronic Toxicity (LOAEL) (log mg/kg_bw/day) | 1.53 | 1.796 | 1.911 | 1.081 | |
Hepatotoxicity (Yes/No) | No | No | No | Yes | |
Skin sensitization (Yes/No) | No | No | No | No | |
T. pyriformis toxicity (log ug/L) | 0.445 | 0.521 | 0.286 | 1.437 | |
Minnow toxicity (log mM) | 1.323 | 0.397 | 0.446 | 1.17 |
Target | Ligands Name | AutoDock Binding Energy (kcal/mol) | PyRx Binding Energy (kcal/mol) | Molecular Docking Server (kcal/mol) | SWISS Dock Binding Energy | |
---|---|---|---|---|---|---|
ΔG (kcal/mol) | Full Fitness Score (kcal/mol) | |||||
MSTN | Dithymoquinone (DTQ) | −7.40 | −6.60 | −6.23 | −6.47 | −444.64 |
Calycosin | −6.60 | −6.88 | −6.85 | −6.65 | −625.45 | |
Limonin | −6.85 | −6.30 | −6.35 | −6.30 | −643.54 | |
Nigellidine | −6.82 | −6.65 | −6.22 | −6.45 | −554.53 |
Target Name | Compound Name | H-Bond | H-Bond Distance (Å) |
---|---|---|---|
MSTN | Dithymoquinone (DTQ) | TYR38:OH-DTQ:O24 | 3.18 |
TYR38:OH-DTQ:O23 | 3.18 | ||
CYS43:N-DTQ:O19 | 3.21 | ||
VAL103:N-DTQ:O2 | 3.1 | ||
DTQ:O2-ALA40:O | 2.81 | ||
DTQ:O2-MET101:O | 3.28 | ||
DTQ:O3-CYS43:SG | 3.69 | ||
DTQ:O9-ASN41:O | 3.12 | ||
DTQ:O22-CYS43:O | 2.86 | ||
PRO76:CD-DTQ:O21 | 3.35 |
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Ahmad, S.S.; Ahmad, K.; Lee, E.J.; Shaikh, S.; Choi, I. Computational Identification of Dithymoquinone as a Potential Inhibitor of Myostatin and Regulator of Muscle Mass. Molecules 2021, 26, 5407. https://doi.org/10.3390/molecules26175407
Ahmad SS, Ahmad K, Lee EJ, Shaikh S, Choi I. Computational Identification of Dithymoquinone as a Potential Inhibitor of Myostatin and Regulator of Muscle Mass. Molecules. 2021; 26(17):5407. https://doi.org/10.3390/molecules26175407
Chicago/Turabian StyleAhmad, Syed Sayeed, Khurshid Ahmad, Eun Ju Lee, Sibhghatulla Shaikh, and Inho Choi. 2021. "Computational Identification of Dithymoquinone as a Potential Inhibitor of Myostatin and Regulator of Muscle Mass" Molecules 26, no. 17: 5407. https://doi.org/10.3390/molecules26175407
APA StyleAhmad, S. S., Ahmad, K., Lee, E. J., Shaikh, S., & Choi, I. (2021). Computational Identification of Dithymoquinone as a Potential Inhibitor of Myostatin and Regulator of Muscle Mass. Molecules, 26(17), 5407. https://doi.org/10.3390/molecules26175407