The Interaction Mechanism Between C14-Polyacetylene Compounds and the Rat TRPA1 Receptor: An In Silico Study
Abstract
1. Introduction
2. Results
2.1. Identification of Binding Sites
2.2. Interaction Analysis
2.3. Molecular Properties
3. Discussion
4. Materials and Methods
4.1. Structure Preparation and Binding Site Prediction
4.2. Molecular Dynamics Simulation and Binding Energy Calculation
4.3. Interaction Analysis
4.4. Molecular Property Calculation and Correlation Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Ligand | [Uel]P-L | [Uvdw]P-L | [Uel]L-Rest | [Uvdw]L-Rest | [Uel]L-water | [Uvdw]L-water | ΔGbind | ΔGEXP | γ/ΔGbind |
---|---|---|---|---|---|---|---|---|---|
Ⅱ-D | −54.2478 ± 2.3 | −103.834 ± 2.5 | −16.0441 ± 2.8 | −19.4748 ± 1.3 | −73.246 ± 0.051 | −74.9464 ± 0.095 | −24.506 | −23.320 | 69.465% |
Ⅱ-B | −37.1776 ± 2.9 | −82.3549 ± 5.8 | −36.6222 ± 1.9 | −32.7639 ± 3.7 | −72.6516 ± 0.052 | −75.9172 ± 0.095 | −24.612 | −25.439 | 69.166% |
Ⅱ-A | −29.4323 ± 3.0 | −133.438 ± 2.2 | −33.4841 ± 3.2 | −5.97493 ± 1.3 | −71.5446 ± 0.045 | −77.2402 ± 0.180 | −24.566 | −24.926 | 69.295% |
Residue ID | 606 | 611 | 613 | 621 | 622 | 623 | 624 | 638 | 663 | 664 | 666 | 667 |
---|---|---|---|---|---|---|---|---|---|---|---|---|
(a) | GLN | PHE | PRO | |||||||||
(b) | PHE | ARG | CYS | PRO | ILE | LEU | TYR | LEU | CYS | PRO | ||
(c) | TRP | GLN | PHE | ILE | PRO | |||||||
Residue ID | 668 | 669 | 670 | 671 | 677 | 680 | 681 | 682 | 686 | 687 | 690 | 990 |
(a) | LEU | MET | THR | THR | TYR | GLU | ||||||
(b) | LEU | VAL | ILE | THR | ILE | VAL | ||||||
(c) | SER | VAL | ILE | TYR |
Molecule | Echinophorin D | Echinophorin B | Echinophorin A |
---|---|---|---|
HOMO (eV) | −8.315 | −6.543 | −7.861 |
LUMO (eV) | −3.784 | −4.166 | −4.264 |
Difference (eV) | 4.531 | 2.377 | 3.597 |
VIP (kcal mol−1) | 223.44 | 190.688 | 222.778 |
VEA (kcal mol−1) | 55.672 | 54.917 | 77.785 |
Potency EC50 μM | 30.9 ± 2.8 | 25.0 ± 3.0 | 20.3 ± 3.2 |
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Yu, H.; Gao, D.; Yang, Y.; Liu, L.; Zhao, X.; Na, R. The Interaction Mechanism Between C14-Polyacetylene Compounds and the Rat TRPA1 Receptor: An In Silico Study. Int. J. Mol. Sci. 2024, 25, 11290. https://doi.org/10.3390/ijms252011290
Yu H, Gao D, Yang Y, Liu L, Zhao X, Na R. The Interaction Mechanism Between C14-Polyacetylene Compounds and the Rat TRPA1 Receptor: An In Silico Study. International Journal of Molecular Sciences. 2024; 25(20):11290. https://doi.org/10.3390/ijms252011290
Chicago/Turabian StyleYu, Hui, Denghui Gao, Ying Yang, Lu Liu, Xi Zhao, and Risong Na. 2024. "The Interaction Mechanism Between C14-Polyacetylene Compounds and the Rat TRPA1 Receptor: An In Silico Study" International Journal of Molecular Sciences 25, no. 20: 11290. https://doi.org/10.3390/ijms252011290
APA StyleYu, H., Gao, D., Yang, Y., Liu, L., Zhao, X., & Na, R. (2024). The Interaction Mechanism Between C14-Polyacetylene Compounds and the Rat TRPA1 Receptor: An In Silico Study. International Journal of Molecular Sciences, 25(20), 11290. https://doi.org/10.3390/ijms252011290