Chalcogen Bond as a Factor Stabilizing Ligand Conformation in the Binding Pocket of Carbonic Anhydrase IX Receptor Mimic
Abstract
:1. Introduction
2. Results and Discussion
2.1. Metric and Spectroscopic Signatures of Non-Covalent Interactions
2.1.1. Car–Parrinello Molecular Dynamics Description of the AZM ligand and Its Complexes with Amino Acids
2.1.2. Nuclear Quantum Effects: Car-Parrinello vs. Path Integral Molecular Dynamics
2.1.3. Free Energy Landscapes Derived from CPMD-Based Metadynamics
2.2. Electronic Structure Evidences of the Non-Covalent Network of Intra- and Intermolecular Interactions
2.3. Non-Covalent Interactions Analysis Based on the NCI Index
2.4. Atoms in Molecules Analysis of Intra- and Intermolecular Non-Covalent Bonds
2.5. Partitioning of the Interaction Energy
3. Materials and Methods
3.1. First-Principle Molecular Dynamics and Metadynamics Methods
3.1.1. Car–Parrinello Molecular Dynamics (CPMD)
3.1.2. Path Integral Molecular Dynamics (PIMD)
3.1.3. Metadynamics (METD)
3.1.4. Post-Processing of the Results Based on Time-Evolution Methods
3.2. Density Functional Theory (DFT) and Post-Hartree–Fock Methods
3.3. Symmetry-Adapted Perturbation Theory (SAPT)
- Extracted from the Carbonic Anhydrase IX mimic–AZM complex (PDB deposit 3DC3) and
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
AZM | Acetazolamide |
FPMD | First-Principle Molecular Dynamics |
METD | Metadynamics |
DFT | Density Functional Theory |
NCI | Non-Covalent Interaction |
NBO | Natural Bond Orbital |
AIM | Atoms In Molecules |
SAPT | Symmetry-Adapted Perturbation Theory |
CPMD | Car–Parrinello Molecular Dynamics |
PIMD | Path Integral Molecular Dynamics |
HB | Hydrogen bond |
EDA | Energy Decomposition Analysis |
PDB | Protein Data Bank |
CV | Collective Variable |
PES | Potential Energy Surface |
BCP | Bond Critical Point |
RCP | Ring Critical Point |
MEP | Molecular Electrostatic Potential |
BSSE | Basis Set Superposition Error |
NQE | Nuclear Quantum Effects |
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Complex | Origin | VCP | GCP | E1 | E2 | ||
---|---|---|---|---|---|---|---|
AZM | DFT | 0.020 | 0.066 | −0.014 | 0.015 | 4.478 | 4.132 |
CPMD | 0.045 | 0.152 | −0.040 | 0.039 | 12.490 | 10.486 | |
AZM-T | DFT | 0.020 | 0.065 | −0.014 | 0.015 | 4.426 | 4.086 |
CPMD | 0.049 | 0.163 | −0.045 | 0.043 | 14.018 | 11.490 | |
AZM-TT | DFT | 0.021 | 0.067 | −0.015 | 0.016 | 4.568 | 4.210 |
CPMD | 0.053 | 0.173 | −0.049 | 0.046 | 15.249 | 12.370 | |
AZM-TTL | DFT | 0.022 | 0.071 | −0.016 | 0.017 | 4.940 | 4.520 |
CPMD | 0.052 | 0.164 | −0.047 | 0.044 | 14.605 | 11.773 | |
AZM-TTLH | DFT | 0.022 | 0.072 | −0.016 | 0.017 | 4.953 | 4.533 |
CPMD | 0.054 | 0.170 | −0.049 | 0.046 | 15.445 | 12.341 |
Complex | Electrostatics | Exchange | Induction | Dispersion | SAPT0 | SAPT2 |
---|---|---|---|---|---|---|
Experimental structure | ||||||
AZM-T | −5.846 | 13.985 | −2.603 | −7.157 | −2.979 | −1.621 |
AZM-TT | −9.853 | 19.973 | −4.291 | −11.171 | −6.599 | −5.342 |
AZM-TTL | −18.854 | 30.558 | −8.371 | −20.057 | −19.657 | −16.723 |
AZM-TTLH, SAPT0 | −12.516 | 29.249 | −8.447 | −22.552 | −14.266 | – |
Optimized structure | ||||||
AZM-T | −22.738 | 26.825 | −8.096 | −13.031 | −20.543 | −17.040 |
AZM-TT | −40.280 | 51.954 | −15.134 | −26.006 | −36.737 | −29.465 |
AZM-TTL | −40.443 | 51.785 | −15.710 | −30.315 | −41.111 | −34.684 |
AZM-TTLH, SAPT0 | −68.386 | 69.536 | −26.657 | −40.273 | −65.780 | – |
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Wojtkowiak, K.; Michalczyk, M.; Zierkiewicz, W.; Jezierska, A.; Panek, J.J. Chalcogen Bond as a Factor Stabilizing Ligand Conformation in the Binding Pocket of Carbonic Anhydrase IX Receptor Mimic. Int. J. Mol. Sci. 2022, 23, 13701. https://doi.org/10.3390/ijms232213701
Wojtkowiak K, Michalczyk M, Zierkiewicz W, Jezierska A, Panek JJ. Chalcogen Bond as a Factor Stabilizing Ligand Conformation in the Binding Pocket of Carbonic Anhydrase IX Receptor Mimic. International Journal of Molecular Sciences. 2022; 23(22):13701. https://doi.org/10.3390/ijms232213701
Chicago/Turabian StyleWojtkowiak, Kamil, Mariusz Michalczyk, Wiktor Zierkiewicz, Aneta Jezierska, and Jarosław J. Panek. 2022. "Chalcogen Bond as a Factor Stabilizing Ligand Conformation in the Binding Pocket of Carbonic Anhydrase IX Receptor Mimic" International Journal of Molecular Sciences 23, no. 22: 13701. https://doi.org/10.3390/ijms232213701