Binding Affinity and Mechanisms of Potential Antidepressants Targeting Human NMDA Receptors
Abstract
:1. Introduction
2. Results and Discussion
3. Method
3.1. Protein Structures
3.2. Compounds Selection
3.3. Ligand–Protein Docking
3.4. Molecular Dynamic Simulation
3.5. Binding Free Energy Calculation
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Sample Availability
References
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Ro 25-6981 | S-ketamine | R-ketamine | ifenprodil |
C22H29NO2 | C13H16ClNO | C13H17Cl2NO | C21H27NO2 |
CID: 6604887 | CID: 182137 | CID: 9838417 | CID: 3689 |
traxoprodil | memantine | lanicemine | dextromethorphan |
C20H25NO3 | C12H21N | C13H14N2 | C18H25NO |
CID: 219101 | CID:4054 | CID:9794203 | CID: 5360696 |
Conformations | Egas | Esolv | Etotal | Snmode | Gbind |
---|---|---|---|---|---|
Ro 25-6981 | −63.116 | 12.923 | −50.193 | −20.762 | −29.431 |
R-ketamine | −37.565 | 9.795 | −27.770 | −12.809 | −14.961 |
S-ketamine | −36.777 | 8.675 | −28.102 | −16.179 | −11.922 |
ifenprodil | −32.952 | 5.366 | −27.587 | −20.751 | −6.835 |
Traxoprodil | −30.773 | 9.995 | −20.777 | −17.271 | −3.506 |
Memantine | −22.044 | 4.409 | −17.635 | −14.673 | −2.962 |
Dextromethorphan | −13.273 | 3.056 | −10.217 | −12.206 | 1.989 |
Lanicemine | −19.317 | 7.180 | −12.136 | −15.054 | 2.918 |
Conformations | Important Residues | ||||
---|---|---|---|---|---|
1 | 2 | 3 | 4 | 5 | |
S-ketamine | Phe88 | Asn160 | Leu92 | Tyr157 | Trp93 |
R-ketamine | Met63 | Ile64 | Leu124 | Ile153 | Tyr157 |
ifenprodil | Leu77 | Thr70 | Thr158 | Leu73 | Ala74 |
traxoprodil | Ile152 | Ala155 | Leu77 | Leu92 | Met151 |
Ro 25-6981 | Leu124 | Met63 | Asn45 | Val103 | Val42 |
memantine | Met36 | Val15 | Trp12 | Val19 | Trp40 |
dextromethorphan | Val96 | Phe149 | Trp146 | Arg81 | Val154 |
lanicemine | Ala155 | Leu73 | Met151 | Leu77 | Val154 |
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Ye, S.; Han, Y.; Wei, Z.; Li, J. Binding Affinity and Mechanisms of Potential Antidepressants Targeting Human NMDA Receptors. Molecules 2023, 28, 4346. https://doi.org/10.3390/molecules28114346
Ye S, Han Y, Wei Z, Li J. Binding Affinity and Mechanisms of Potential Antidepressants Targeting Human NMDA Receptors. Molecules. 2023; 28(11):4346. https://doi.org/10.3390/molecules28114346
Chicago/Turabian StyleYe, Simin, Yanqiang Han, Zhiyun Wei, and Jinjin Li. 2023. "Binding Affinity and Mechanisms of Potential Antidepressants Targeting Human NMDA Receptors" Molecules 28, no. 11: 4346. https://doi.org/10.3390/molecules28114346