Theoretical Studies for the Discovery of Potential Sucrase-Isomaltase Inhibitors from Maize Silk Phytochemicals: An Approach to Treatment of Type 2 Diabetes
Abstract
:1. Introduction
2. Results
2.1. Structural Optimization of Ligands
2.2. Molecular Docking Analysis between Ligands, ACA, MAY, and LUT, with the Sucrase-Isomaltase Domain B and D
2.3. Molecular Dynamics Simulation Analysis
2.4. Chemical Reactivity Parameters and Charge Transfer Descriptor
3. Discussion
4. Methods
4.1. Structural Optimization
4.2. Molecular Docking Calculations
4.3. Molecular Dynamics Simulations
4.4. Binding Free Energy Calculations
4.5. Chemical Reactivity and Charge Transfer Calculations
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Sample Availability
Appendix A
ID Compound | vdW | elec | PB | SA | Ggas | Gsol | Gbind |
---|---|---|---|---|---|---|---|
ACA | −17.42 | −105.35 | 110.22 | −2.97 | −122.77 | 107.25 | −15.52 |
MAY | −27.61 | −58.28 | 75.05 | −3.26 | −85.89 | 71.79 | −14.09 |
LUT | −18.85 | −53.90 | 66.27 | −2.85 | −72.75 | 63.43 | −9.32 |
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Conformer | Difference in Relative Energy and Structure | |
---|---|---|
ACA | MAY | |
Global minimum | 0.0 | 0.0 |
Conformer 1 | 2.8 | 3.5 |
Conformer 2 | 7.1 | 5.0 |
Conformer 3 | 8.4 | 7.4 |
Conformer 4 | NA | 9.7 |
Ligand | Domain | Binding Free Energy (Kcal/mol) | Binding Site Residues |
---|---|---|---|
ACA | B | −7.8 | TRP327, ASN328, LYS330, ILE356, TRP435 (H-bond), TRP470, ASP472 (H-bond), MET473, ARG555, ASP571 (H-bond), PHE604, HIS629, and ASP632 |
D | −8.8 | ASN43 (H-bond), ILE45, PRO46, GLU47, GLN48, PHE49 (H-bond), PRO50, SER68, LEU69, THR224, PHE272, ARG282, and LYS594 | |
MAY | B | −8.0 | ASP231, LEU233, TRP327, ASP355 (H-bond), ILE356, TRP435 (π–π interaction), TRP470, ASP472, MET473, SER477, PHE479, LYS509 (H-bond), HIS629 (H-bond), and SER631 |
D | −7.5 | ASP231, GLN232, LEU233, TRP327, ASP355 (H-bond), ILE392, TRP435, TRP470, and LYS509 | |
LUT | B | −8.6 | ASP231 (H-bond), TRP327, ASP355 (H-bond), ILE392, TRP435, TRP470, ASP472, PHE479, LYS509 (H-bond), ASP571, PHE600, and SER631 |
D | −7.4 | LEU311, ALA313, ARG549, ARG563, HIS629, and LYS805 (π–π interaction) |
Ligand | Molecular Interactions | ||
---|---|---|---|
H-Bonds (Occupancy in %) | π–π Interaction | Aromatic H-Bond | |
ACA | ASP472 (55.43), ASP571 (40.72) ASP632 (15.17) | NA | NA |
MAY | ASP355 (87.89) | TRP435 | TRP327 |
LUT | ASP472 (88.61), SER631 (17.29) | TRP327 | NA |
Ligand | EA | IP | η | χ | ω | μ |
---|---|---|---|---|---|---|
ACA | 0.01 | 6.12 | 3.05 | 3.07 | 1.54 | −3.07 |
MAY | 1.95 | 5.83 | 1.94 | 3.89 | 3.90 | −3.89 |
LUT | 1.74 | 5.88 | 2.07 | 3.81 | 3.50 | −3.81 |
Ligand | Residue Active Site | η | µ | ΔN |
---|---|---|---|---|
ACA | TRP327-ASN328 | 2.15 | −3.23 | −0.016 |
LYS330 | 3.06 | −3.68 | −0.050 | |
ILE356 | 2.97 | −3.52 | −0.037 | |
TRP435 | 2.24 | −3.08 | −0.001 | |
TRP470 | 2.25 | −2.87 | 0.018 | |
ASP472-MET473 | 2.73 | −3.27 | −0.018 | |
TRP568 | 2.27 | −3.04 | 0.002 | |
ASP571 | 2.72 | −3.21 | −0.013 | |
PHE604 | 2.80 | −3.45 | −0.033 | |
ASP632 | 2.67 | −3.33 | −0.023 | |
MAY | ASP231 | 2.71 | −3.41 | 0.052 |
TRP327-ASN328 | 2.07 | −3.09 | 0.100 | |
ASP355-ILE356-ASP357 | 2.83 | −3.03 | 0.090 | |
ILE392 | 3.07 | −3.55 | 0.034 | |
TRP435 | 2.28 | −3.03 | 0.102 | |
MET473 | 2.52 | −3.14 | 0.084 | |
PHE479 | 2.80 | −3.53 | 0.038 | |
LYS509 | 3.01 | −3.65 | 0.024 | |
LUT | LEU233 | 3.04 | −3.65 | 0.016 |
TRP327 | 2.30 | −3.12 | 0.078 | |
ILE356 | 3.06 | −3.44 | 0.036 | |
ILE392 | 3.14 | −3.54 | 0.026 | |
TRP470 | 2.19 | −3.04 | 0.090 | |
ASP472-MET473 | 2.64 | −3.25 | 0.060 | |
ASP571 | 2.76 | −3.10 | 0.074 | |
PHE604-VAL605 | 2.70 | −3.45 | 0.037 | |
SER631 | 2.96 | −3.89 | −0.008 |
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Landeros-Martínez, L.-L.; Campos-Almazán, M.I.; Sánchez-Bojorge, N.-A.; Flores, R.; Palomares-Báez, J.P.; Rodríguez-Valdez, L.M. Theoretical Studies for the Discovery of Potential Sucrase-Isomaltase Inhibitors from Maize Silk Phytochemicals: An Approach to Treatment of Type 2 Diabetes. Molecules 2023, 28, 6778. https://doi.org/10.3390/molecules28196778
Landeros-Martínez L-L, Campos-Almazán MI, Sánchez-Bojorge N-A, Flores R, Palomares-Báez JP, Rodríguez-Valdez LM. Theoretical Studies for the Discovery of Potential Sucrase-Isomaltase Inhibitors from Maize Silk Phytochemicals: An Approach to Treatment of Type 2 Diabetes. Molecules. 2023; 28(19):6778. https://doi.org/10.3390/molecules28196778
Chicago/Turabian StyleLanderos-Martínez, Linda-Lucila, Mara Ibeth Campos-Almazán, Nora-Aydeé Sánchez-Bojorge, Raul Flores, Juan Pedro Palomares-Báez, and Luz María Rodríguez-Valdez. 2023. "Theoretical Studies for the Discovery of Potential Sucrase-Isomaltase Inhibitors from Maize Silk Phytochemicals: An Approach to Treatment of Type 2 Diabetes" Molecules 28, no. 19: 6778. https://doi.org/10.3390/molecules28196778
APA StyleLanderos-Martínez, L. -L., Campos-Almazán, M. I., Sánchez-Bojorge, N. -A., Flores, R., Palomares-Báez, J. P., & Rodríguez-Valdez, L. M. (2023). Theoretical Studies for the Discovery of Potential Sucrase-Isomaltase Inhibitors from Maize Silk Phytochemicals: An Approach to Treatment of Type 2 Diabetes. Molecules, 28(19), 6778. https://doi.org/10.3390/molecules28196778