Analysis of the Setomimycin Biosynthetic Gene Cluster from Streptomyces nojiriensis JCM3382 and Evaluation of Its α-Glucosidase Inhibitory Activity Using Molecular Docking and Molecular Dynamics Simulations
Abstract
:1. Introduction
2. Results
2.1. Comparative Analysis of Biosynthetic Gene Clusters between Setomimycin Producing Microorganisms
2.2. Putative Setomimycin Biosynthetic Pathway
2.2.1. Minimal PKS
2.2.2. Ketoreduction and Cyclization
2.2.3. Chain Release
2.2.4. Dimerization
2.2.5. Concluding Remarks
2.3. α-Glucosidase Inhibitory Activity of Setomimycin and Streptomyces nojiriensis JCM3382
2.4. Chemoinformatic Analysis
2.5. Docking and Molecular Dynamics (MD) Simulations
2.5.1. Molecular Docking Simulation
2.5.2. Molecular Dynamics (MD) Simulation
3. Materials and Methods
3.1. Chemicals and Reagents
3.2. Fermentation and Extraction
3.3. Enzymatic Analysis
3.4. Chemoinformatic Analysis
3.5. Molecular Docking Simulation Analysis
3.6. Molecular Dynamics (MD) Simulations Analysis
3.7. Statistical Analyses
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Compounds | MW | HBA | HBD | RB | TPSA | Log p | MR | Lipinski’s Rule |
---|---|---|---|---|---|---|---|---|
Setomimycin | 580.58 | 9 | 5 | 3 | 169.43 | 3.476 | 160.66 | Yes; 1 violation: MW > 500 |
Acarbose | 645.60 | 5 | 3 | 9 | 90.90 | 3.307 | 136.69 | No; 3 violations: MW > 500, N or O > 10, NH or OH > 5 |
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Hyun, K.-A.; Liang, X.; Xu, Y.; Kim, S.-Y.; Boo, K.-H.; Park, J.-S.; Chi, W.-J.; Hyun, C.-G. Analysis of the Setomimycin Biosynthetic Gene Cluster from Streptomyces nojiriensis JCM3382 and Evaluation of Its α-Glucosidase Inhibitory Activity Using Molecular Docking and Molecular Dynamics Simulations. Int. J. Mol. Sci. 2024, 25, 10758. https://doi.org/10.3390/ijms251910758
Hyun K-A, Liang X, Xu Y, Kim S-Y, Boo K-H, Park J-S, Chi W-J, Hyun C-G. Analysis of the Setomimycin Biosynthetic Gene Cluster from Streptomyces nojiriensis JCM3382 and Evaluation of Its α-Glucosidase Inhibitory Activity Using Molecular Docking and Molecular Dynamics Simulations. International Journal of Molecular Sciences. 2024; 25(19):10758. https://doi.org/10.3390/ijms251910758
Chicago/Turabian StyleHyun, Kyung-A, Xuhui Liang, Yang Xu, Seung-Young Kim, Kyung-Hwan Boo, Jin-Soo Park, Won-Jae Chi, and Chang-Gu Hyun. 2024. "Analysis of the Setomimycin Biosynthetic Gene Cluster from Streptomyces nojiriensis JCM3382 and Evaluation of Its α-Glucosidase Inhibitory Activity Using Molecular Docking and Molecular Dynamics Simulations" International Journal of Molecular Sciences 25, no. 19: 10758. https://doi.org/10.3390/ijms251910758