Selenium Organic Content Prediction in Jengkol (Archidendron pauciflorum) and Its Molecular Interaction with Cardioprotection Receptors PPAR-γ, NF-κB, and PI3K
Abstract
:1. Introduction
2. Results
2.1. Jengkol Se Content Analysis
2.2. Separation of the Jengkol Extract Using HPLC Combined with Fluorometry
2.3. Characterization of Organic Se Using LC-MS
2.4. Docking Simulation of Organic Se in Jengkol to Cardioprotection Receptor
2.5. Molecular Dynamic Simulation
2.5.1. Root Mean Square Deviation (RMSD) and Root Mean Square Fluctuation (RMSF) Analysis of the Ligand–Receptor Complex
2.5.2. Solvent-Accessible Surface Area (SASA) Analysis
2.5.3. Radius Gyration (Rg) Analysis
2.5.4. MM-PBSA Binding Free Energy Calculations
3. Discussion
3.1. Analysis of the Se Content in Jengkol
3.2. Separation of the Jengkol Extract and Characterization of Organic Se
3.3. Docking Simulation of Organic Se in Jengkol to a Cardioprotective Receptor
3.3.1. Preparation of Protein Receptor and Validation
3.3.2. Docking Simulation
3.4. Molecular Dynamic Simulation
4. Materials and Methods
4.1. Materials
4.2. Standard and Sample Preparation
4.3. Analysis of the Se Content in Jengkol
4.4. Separation of the Jengkol Extract Using HPLC Combined with the Fluorometric Method
4.5. Characterization of Organic Se Using LC-MS
4.6. Docking Simulation of Organic Se in Jengkol
4.6.1. Preparation of the Ligand Structure
4.6.2. Preparation of the Protein Receptor
4.6.3. Validation of the Molecular Docking Method
4.6.4. Docking Simulation
4.7. Molecular Dynamic Simulation
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Sample Availability
References
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City or Regency | Se Content (ng/g) | SD |
---|---|---|
Kabupaten Bandung Barat | 48 | 24.1 |
Kabupaten Kuningan | 44.1 | 10.9 |
Kota Banjar | 246.9 | 19 |
Kota Bogor | 27.3 | 23.9 |
Kabupaten Purwakarta | 264 | 31.1 |
Kabupaten Subang | 498 | 66.6 |
Kabupaten Sukabumi | 298.2 | 15.2 |
Kabupaten Garut | 161.8 | 25.6 |
Kota Cimahi | 35.0 | 6.5 |
Kota Bandung | 92.1 | 9.7 |
Kota Tasikmalaya | 74.9 | 51.2 |
Kabupaten Tasikmalaya | 341.4 | 3.3 |
Kabupaten Bekasi | 133.9 | 44.7 |
Kabupaten Sumedang | 187.7 | 86.0 |
Code | Fraction | Intensity | Se Concentration (µmol/L) |
---|---|---|---|
0 | 0–10 | 19,280 | 0.09648 |
A | 10–20 | 31,105 | 0.45070 |
B | 20–30 | 40,453 | 0.70181 |
C | 30–40 | 15,393 | −0.02825 |
Fraction | Molecular Weight (m/z) | Retention Time | Molecular Formula | Organic Se | Reference |
---|---|---|---|---|---|
A | 198 | 0.95 | C5 H12NO2Se | selenomethionine (C5H12O2Nse+) | [27,38] |
313 | 19.14 | (−) | gamma-GluMetSeCys (C9H17O5N2Se+) | [27] | |
609 | 16.36 | C26H53N6O5Se | (−) | ||
475 | 16.36 | C18 H43N4O5Se | C13H23O8N4Sse+ | [27] | |
B1 | 181 | 1.31 | C3H9N4Se | C5H9O2Se+ | [27] |
223 | 1.31 | C5H11N4Ose | C6H10NO3Se+ | [35] | |
267 | 2.3 | C12H15N2Se | (−) | ||
B2 | 384 | 1.05 | C13H5N4O9Se | (−) | |
265 | 1.05 | C2H13N6O4Se | (−) | ||
779 | 6.88 | C34H63N14O2Se | (−) | ||
761 | 7.24 | C38H64N7O4Se | (−) |
Code | Compound | Binding Energy (kkal/mol) | Hydrogen Bond Distance (Ǻ) | H-Bond Interactions | Nearest Amino Acid Residue(s) | Other Interactions |
---|---|---|---|---|---|---|
N | Native ligand | −9.37 | 2.17, 1.94, and 2.20 | CYS285, SER289, and HIS323 | SER289, CYS285, HIS323, ARG288 | PHE282, PHE363, GLY284, TYR327, TYR473, LYS367, LEU330, LEU453, LEU465, LEU469, GLN286, HIS323, HIS449, ILE326, ALA292, ARG288, MET364 |
Se01 | Selenomethionine | −3.99 | 2.11, 2.48, and 2.83 | TYR327, MET364, and LYS367 | TYR327, MET364, LYS367, PHE282 | LEU330, LEU 469, GLN286, PHE282, PHE363, SER289, HIS323, HIS449, CYS285 |
Se02 | Gamma-GluMetSeCys | −4.4 | 3.32 | HIS449 | HIS323, HIS449 | LEU330, LEU453, LEU465, LEU469, PHE282, PHE363, TYR327, TYR473, HIS323, CYS285, SER289, GLN286, ARG288, ILE326, LYS367 |
Se03 | Se-S conjugate of the cysteine-selenoglutathione | −3.32 | 1.96, 1.96, 2.12, and 2.70 | GLY284, SER342, ILE326, SER289 | GLY284, SER342, ILE326, SER289, CYS285 | ILE325, ILE341, LEU330, LEU333, LEU340, MET329, MET334, MET364, PHE363, LYS367, TYR327, GLN286, VAL339, CYS285, ALA292, ARG288 |
Code | Compound | Binding Energy (kkal/mol) | Hydrogen Bond Distance (Ǻ) | H-Bond Interactions | Nearest Amino Acid Residue (s) | Other Interactions |
---|---|---|---|---|---|---|
N | Native ligand | −8.7 | 1.82 | VAL882 | VAL882, TYR867 | MET804, ILE831, TYR867, ILE879, ILE963MET953 |
Se01 | Selenomethionine | −4.5 | 2.65 and 1.59 | LYS807 and ASP950 | SER806, LYS807, and ASP950 | MET804, ALA805, SER806, PRO810, ASN951 |
Se02 | Gamma-GluMetSeCys | −5.04 | 2.06, 1.70, 1.77 | THR887, LYS890, and ASP950 | THR887, LYS890, ASP950, and ILE831 | MET804, SER806, LYS807, TRP812, ILE831, ILE879, ASN951, MET958, ILE963 |
Se03 | Se-S conjugate of cysteine-selenoglutathione | −4.67 | 2.47, 1.93, and 1.83 | MET804, LYS890, and ASP950 | ASP950, LYS890, MET804, LYS833 | SER806, PRO810, TRP812, ILE831, LYS833, ILE879, THR887, ILE963 |
Code | Compound | Binding Energy (kkal/mol) | Hydrogen Bond Distance (Ǻ) | Interactions H-Bond | Nearest Amino Acid Residue(s) | Other Interactions |
---|---|---|---|---|---|---|
N | Native ligand | −9.71 | 1.86 and 1.82 | GLU440 and GLU470 | GLU440, GLU470, ILE467 | PHE535, LYS429, CYS444, ILE467, LEU522, VAL414, CYS533, LEU472, PRO454, VAL453, ALA427, LEU471, GLY536, GLY475, GLY409, ASP534, ARG408, SER476 |
Se01 | Selenomethionine | −4.86 | 2.00, 1.78, and 2.19 | LEU406, ARG408, and ARG416 | ALA427, ARG408, LEU406, ARG416 | GLY 407, HIS415, ARG405, VAL414, LEU472, ALA427, LEU471 |
Se02 | Gamma-GluMetSeCys | −5.27 | 3.07, 1.85, and 2.85 | ARG416, LEU472, and CYS533 | LEU472, CYS533, ARG416, ARG408 | ALA427, VAL414, LEU471, HIS415, LEU406, GLY475, MET469, LEU522, VAL453, ARG405, ARG408 |
Se03 | Se-S conjugate of cysteine-selenoglutathione | −5.56 | 1.99, 3.32, 1.99, 2.62, 2.10, and 2.36 | GLU470, CYS533, ASN520, ASP519, GLN479, and ARG408 | ASN520, GLU470, GLN479 | VAL 453, MET 469, ALA427, GLY475, LEU522, LEU472, ARG416, GLU413, ASP534, SER410, LEU471, SER476, GLY409, VAL414 |
Receptor | Ligand | Van Der Waals Energy (KJ/mol) | Electrostatic Energy (KJ/mol) | Polar Solvation Energy (KJ/mol) | SASA Energy (KJ/mol) | Total Binding Energy (KJ/mol) |
---|---|---|---|---|---|---|
PPAR-γ | Native ligand | −139.618 ± 11.007 | −34.531 ± 25.211 | 120.493 ± 26.547 | −15.909 ± 0.639 | −69.565 ± 13.830 |
Se02 | −255.404 ± 11.487 | −50.584 ± 9.711 | 201.318 ± 17.740 | −25.249 ± 0.837 | −129.919 ± 17.381 | |
PI3K | Native ligand | −85.492 ± 18.675 | −98.064 ± 57.119 | 176.346 ± 74.158 | −12.801 ± 2.094 | −20.011 ± 23.103 |
Se02 | −182.499 ± 19.445 | −30.823 ± 24.734 | 150.574 ± 47.547 | −20.019 ± 1.483 | −82.767 ± 21.369 | |
NF-ΚB | Native ligand | −139.618 ± 11.007 | −34.531 ± 25.211 | 120.493 ± 26.547 | −15.909 ± 0.639 | −69.565 ± 13.830 |
Se03 | −238.397 ± 15.323 | −55.390 ± 18.886 | 219.017 ± 26.684 | −24.322 ± 1.095 | −99.091 ± 17.208 |
T (min) | % ACN | % Water | Gradient Steepness (%/min) |
---|---|---|---|
0 | 5 | 95 | 1 |
5 | 5 | 95 | 1 |
30 | 95 | 5 | 1 |
35 | 95 | 5 | 1 |
38 | 5 | 95 | 1 |
40 | 5 | 95 | 1 |
No. | IUPAC Name | Structure |
---|---|---|
1. | Compound Se01 Selenomethionine (SeMet) | |
2. | Compound Se02 Glutamyl-glycinyl-N-2,3-DHP-selenocysteine (Gamma-Glu-MetSeCys) | |
3. | Compound Se03 Se-S conjugate of cysteine-selenoglutathione |
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Shalihat, A.; Lesmana, R.; Hasanah, A.N.; Mutakin, M. Selenium Organic Content Prediction in Jengkol (Archidendron pauciflorum) and Its Molecular Interaction with Cardioprotection Receptors PPAR-γ, NF-κB, and PI3K. Molecules 2023, 28, 3984. https://doi.org/10.3390/molecules28103984
Shalihat A, Lesmana R, Hasanah AN, Mutakin M. Selenium Organic Content Prediction in Jengkol (Archidendron pauciflorum) and Its Molecular Interaction with Cardioprotection Receptors PPAR-γ, NF-κB, and PI3K. Molecules. 2023; 28(10):3984. https://doi.org/10.3390/molecules28103984
Chicago/Turabian StyleShalihat, Ayu, Ronny Lesmana, Aliya Nur Hasanah, and Mutakin Mutakin. 2023. "Selenium Organic Content Prediction in Jengkol (Archidendron pauciflorum) and Its Molecular Interaction with Cardioprotection Receptors PPAR-γ, NF-κB, and PI3K" Molecules 28, no. 10: 3984. https://doi.org/10.3390/molecules28103984