In Silico Analyses of a Promising Drug Candidate for the Treatment of Amyotrophic Lateral Sclerosis Targeting Superoxide Dismutase I Protein
Abstract
:1. Introduction
2. Materials and Methods
2.1. Data Retrieval
2.2. Molecular Dynamics Simulations
2.3. Trajectory Analysis
2.4. In Silico Pharmacokinetics and Toxicological Assessment
3. Results and Discussion
3.1. Data Retrieval
3.2. Molecular Dynamics Simulations
3.3. In Silico Pharmacokinetics and Toxicological Assessment
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Protein | π-Stacking 1 | Cation-π 1 | Hydrophobic Contacts 1 | Minimum Distance 2 |
---|---|---|---|---|
wild-type | 9.02% | 3.8% | 36.13% | 0.37 ± 0.10 nm |
A4V | 16.88% | 38.46% | 89.55% | 0.26 ± 0.03 nm |
D90A | 15.76% | 10.12% | 49.25% | 0.34 ± 0.08 nm |
Protein | Hydrogen Bonds 1 | Hydrophobic Contacts 1 | Ionic Bonds 2 | Cation-π 2 |
---|---|---|---|---|
WT | 2.42 ± 1.07 | 10.07 ± 5.69 | 72.72% | 19.92% |
A4V | 1.98 ± 1.25 | 11.81 ± 7.63 | 57.34% | 55.51% |
D90A | 1.78 ± 0.91 | 8.91 ± 5.88 | 48.39% | 13.61% |
Protein | Lys23 | Glu21 | Pro28 | Glu100 |
---|---|---|---|---|
WT | 18.23% | 46.76% | 5.21% | 93.67% |
A4V | 12.15% | 71.51% | 1.38% | 51.09% |
D90A | 18.83% | 35.74% | 6.85% | 70.99% |
Protein | ΔE Polar (kJ/mol) | ΔE Apolar (kJ/mol) | ΔE MM (kJ/mol) | Binding Energy (kJ/mol) |
---|---|---|---|---|
WT | 229 ± 35 | −9.41 ± 1.27 | −349 ± 65 | −129 ± 42 |
A4V | 205 ± 85 | −8.80 ± 2.27 | −409 ± 118 | −209 ± 52 |
D90A | 240 ± 31 | −9.22 ± 1.20 | −377 ± 61 | −146 ± 39 |
Model | ADMET Risk | Absn Risk | CYP Risk | Tox Risk | MutRisk | Mutx Risk | Vd & Fu | Lipinski’s Rule | Repro Tox | CYP Inhibition |
---|---|---|---|---|---|---|---|---|---|---|
Penalty | 2.5 | 0.5 | 1 | 1 | 1.2 | 0.64 | 0 | 0 | _ | _ |
Violation | HBD; MUT; 2D6 | HBD | 2D6 | MUT | S_97; NIHS | S_97; NIHS | No | No | No | CYP1A2, CYP2D6, CYP3A4 |
Cut-off | ≤7 | ≤4 | ≤2 | ≤2 | ≤1 | ≤1 | _ | ≤2 | _ | _ |
Module | Model | Parameter Value | Classification | Reference Value |
---|---|---|---|---|
DrugSafetyprofiling | Mutagenicity | 0.35 | Undefined | ≤0.33 |
hERG inhibition | 0.31 | Non-inhibitor | ≤0.33 | |
CYP inhibition | 0.33–0.64 | Undefined (3A4, 2D6, 2C19, 1A2); Non-inhibitor (2C9) | ≤0.33 | |
Acute Toxicity | _ | No hazardous fragment | No hazardous fragment | |
PhysChem profiling | Lipinski’s Rule | 0 violations | Optimal | _ |
Lead-like Rule | 0 violations | Optimal | _ | |
Solubility | 33.9 mg/mL | Soluble | ≥10 mg/mL | |
Rotatable bonds | 5 | Optimal | ≤10 | |
Nº of rings | 3 | Optimal | ≤4 | |
ADME profiling | Bioavailability | 96% | High | ≥70% |
Caco-2 | 16 × 10−6 cm/s | High | ≥7 × 10−6 cm/s | |
HIA | 100% | High | ≥70% | |
PPB | 81% | High | ≥40% & ≤80% | |
Metabolic Stability | 0.49 | Undefined | ≤0.33 | |
CNS-Access | −2.93 | Sufficient for CNS activity | >3 |
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Pereira, G.R.C.; Abrahim-Vieira, B.d.A.; de Mesquita, J.F. In Silico Analyses of a Promising Drug Candidate for the Treatment of Amyotrophic Lateral Sclerosis Targeting Superoxide Dismutase I Protein. Pharmaceutics 2023, 15, 1095. https://doi.org/10.3390/pharmaceutics15041095
Pereira GRC, Abrahim-Vieira BdA, de Mesquita JF. In Silico Analyses of a Promising Drug Candidate for the Treatment of Amyotrophic Lateral Sclerosis Targeting Superoxide Dismutase I Protein. Pharmaceutics. 2023; 15(4):1095. https://doi.org/10.3390/pharmaceutics15041095
Chicago/Turabian StylePereira, Gabriel Rodrigues Coutinho, Bárbara de Azevedo Abrahim-Vieira, and Joelma Freire de Mesquita. 2023. "In Silico Analyses of a Promising Drug Candidate for the Treatment of Amyotrophic Lateral Sclerosis Targeting Superoxide Dismutase I Protein" Pharmaceutics 15, no. 4: 1095. https://doi.org/10.3390/pharmaceutics15041095
APA StylePereira, G. R. C., Abrahim-Vieira, B. d. A., & de Mesquita, J. F. (2023). In Silico Analyses of a Promising Drug Candidate for the Treatment of Amyotrophic Lateral Sclerosis Targeting Superoxide Dismutase I Protein. Pharmaceutics, 15(4), 1095. https://doi.org/10.3390/pharmaceutics15041095