A Molecular Modeling Investigation of the Therapeutic Potential of Marine Compounds as DPP-4 Inhibitors
Abstract
:1. Introduction
2. Results and Discussion
3. Materials and Methods
3.1. Target Selection and Protein Preparation
3.2. Receptor Grid Generation
3.3. Ligand Preparation
3.4. Virtual Screening and Free Energy of Binding
3.5. Molecular Dynamics
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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DPP-4 PDB ID | Docked Molecule | XP GlideScore (kcal/mol) | MM-GBSA Binding Energy (kcal/mol) | Hydrogen Bonds | Hydrophobic Interactions | π-π Interactions | π-Cation Interactions | Salt Bridges |
---|---|---|---|---|---|---|---|---|
6B1E | CMNPD17868 | −13.45 | −73.08 | Tyr547, Arg669, Glu205, Glu206 | Tyr547, Phe357, Val207, Tyr666, Tyr662, Trp659, Val656, Val711, Tyr631, Trp629 | Phe357 | Tyr666 | Arg125, Glu205, Glu206 |
CMNPD13046 | −13.35 | −74.92 | Arg125, Glu206, Val207, Ser630, Asp739 | Trp124, Val207, Phe357, Tyr547, Trp629, Tyr631, Val656, Trp659, Tyr662, Tyr666, Val711, Ala743 | Tyr666, His740 | Glu205, Glu206 | ||
Vildagliptin | −6.11 | −53.57 | Glu205, Glu206, Asn710 | Phe357, Tyr547, Tyr631, Val656, Trp659, Tyr662, Tyr666, Val711 | ||||
5I7U | CMNPD17868 | −11.68 | −73.82 | Glu206, Tyr662, Arg669 | Val207, Phe357, Val546, Tyr547, Trp629, Tyr631, Val656, Trp659, Tyr662, Tyr666, Val711 | Tyr666 | Glu205, Glu206 | |
CMNPD13046 | −12.79 | −70.77 | Arg125, His126, Glu205, Glu206, Tyr662, Asp739 | Tyr547, Tyr631, Val656, Trp659, Tyr662, Tyr666, Val711, Ala743 | Tyr666 | Glu205, Glu206 | ||
Vildagliptin | −7.05 | −56.35 | Glu205, Glu206 | Phe357, Tyr547, Tyr631, Val656, Tyr662, Tyr666, Val711 | ||||
5T4E | CMNPD17868 | −11.54 | −82.49 | Glu206, Ser209, Lys554 | Val546, Tyr547, Trp629, Tyr631, Val656, Trp659, Tyr662, Tyr666, Val711 | Arg125, Tyr666 | Glu205, Glu206, Lys554 | |
CMNPD13046 | −11.4 | −79.27 | Lys122, Glu205, Glu206, Asp545, Tyr631 | Trp124, Phe357, Val546, Tyr547, Trp627, Trp629, Tyr631, Tyr666, Ala743, Tyr752 | Lys554 | |||
Vildagliptin | −6.37 | −50.96 | Glu205, Glu206 | Val207, Phe357, Tyr547, Tyr631, Trp659, Tyr662, Tyr666 |
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Antony, P.; Baby, B.; Aleissaee, H.M.; Vijayan, R. A Molecular Modeling Investigation of the Therapeutic Potential of Marine Compounds as DPP-4 Inhibitors. Mar. Drugs 2022, 20, 777. https://doi.org/10.3390/md20120777
Antony P, Baby B, Aleissaee HM, Vijayan R. A Molecular Modeling Investigation of the Therapeutic Potential of Marine Compounds as DPP-4 Inhibitors. Marine Drugs. 2022; 20(12):777. https://doi.org/10.3390/md20120777
Chicago/Turabian StyleAntony, Priya, Bincy Baby, Hamda Mohammed Aleissaee, and Ranjit Vijayan. 2022. "A Molecular Modeling Investigation of the Therapeutic Potential of Marine Compounds as DPP-4 Inhibitors" Marine Drugs 20, no. 12: 777. https://doi.org/10.3390/md20120777