In Silico Analysis of Anti-Inflammatory and Antioxidant Properties of Bioactive Compounds from Crescentia cujete L.
Abstract
:1. Introduction
2. Results
2.1. ADME Prediction
2.2. Molecular Docking
3. Materials and Methods
3.1. ADME Prediction
3.2. Molecular Docking
3.3. Retrieval of Protein Structure
3.4. Retrieval of Ligands
3.5. Grid Preparation and Molecular Docking
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Sample Availability
References
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1CB4 | 2CAG | 2P31 | ||||
---|---|---|---|---|---|---|
Ligand | Naringenin | Ascorbic Acid | Naringenin | Ascorbic Acid | Pinocembrin | Ascorbic Acid |
binding energy | −10.32 | −3.46 | −11.87 | −3.64 | −10.85 | −4.49 |
ligand efficiency | −0.52 | −0.31 | −0.59 | −0.33 | −0.57 | −0.41 |
inhib constant | 27.26 | 2.93 | 1.99 | 2.16 | 11.08 | 512.61 |
inhib constant units | nM | mM | nM | mM | nM | uM |
intermol energy | −11.21 | −4.65 | −12.77 | −5.13 | −11.45 | −5.68 |
vdw hb desolv energy | −11.21 | −4.42 | −12.77 | −4.93 | −11.45 | −5.48 |
electrostatic energy | 0 | −0.23 | 0 | −0.2 | 0 | −0.21 |
total internal | −0.08 | −1.67 | −0.06 | −1.68 | −0.3 | −1.64 |
torsional energy | 0.89 | 1.19 | 0.89 | 1.49 | 0.6 | 1.19 |
unbound energy | −0.08 | −1.67 | −0.06 | −1.68 | −0.3 | −1.64 |
cIRMS | 0 | 0 | 0 | 0 | 0 | 0 |
refRMS | 69.76 | 72.15 | 58.64 | 63.49 | 28.98 | 28.06 |
rseed1 | none | none | none | none | none | none |
rseed2 | none | none | none | none | none | none |
H-bond formed | 2 | 3 | 2 | 0 | 0 | 2 |
3V99 | 4L9S | 3LN0 | ||||
---|---|---|---|---|---|---|
Ligand | Pinocembrin | Indomethacin | Eriodictyol | Indomethacin | Naringenin | Indomethacin |
binding energy | −11.29 | −8.31 | −10.39 | −9.47 | −11.96 | −11.22 |
ligand efficiency | −0.59 | −0.33 | −0.49 | −0.38 | −0.6 | −0.45 |
inhib constant | 5.29 | 804.47 | 24.39 | 113.87 | 1.72 | 6.01 |
inhib constant units | nM | nM | nM | nM | nM | nM |
intermol energy | −11.89 | −9.51 | −11.88 | −10.67 | −12.85 | −12.41 |
vdw hb desolv energy | −11.89 | −9.51 | −11.88 | −10.67 | −12.85 | −12.41 |
electrostatic energy | 0 | 0 | 0 | 0 | 0 | 0 |
total internal | −0.3 | −1.54 | 14.93 | −1.45 | −0.08 | −1.25 |
torsional energy | 0.6 | 1.19 | 1.49 | 1.19 | 0.89 | 1.19 |
unbound energy | −0.3 | −1.54 | 14.93 | −1.45 | −0.08 | −1.25 |
cIRMS | 0 | 0 | 0.25 | 0 | 0 | 0 |
refRMS | 90.94 | 73.39 | 30.16 | 38.62 | 72.45 | 90.14 |
rseed1 | none | none | none | none | none | none |
rseed2 | none | none | none | none | none | none |
H-bond formed | 2 | 2 | 4 | 4 | 2 | 0 |
Drug/Ligand | Structure | Molecular Weight (g/mol) |
---|---|---|
Ascorbic Acid | 176.12 | |
Indomethacin | 357.79 | |
Luteolin | 286.24 | |
Eriodictyol | 288.25 | |
Pinocembrin | 256.25 | |
Naringenin | 272.25 | |
Quercetin | 302.24 | |
Apigenin | 270.24 | |
Ferulic Acid | 194.18 |
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Gonzales, A.L.; Huang, S.K.-H.; Sevilla, U.T.A.; Hsieh, C.-Y.; Tsai, P.-W. In Silico Analysis of Anti-Inflammatory and Antioxidant Properties of Bioactive Compounds from Crescentia cujete L. Molecules 2023, 28, 3547. https://doi.org/10.3390/molecules28083547
Gonzales AL, Huang SK-H, Sevilla UTA, Hsieh C-Y, Tsai P-W. In Silico Analysis of Anti-Inflammatory and Antioxidant Properties of Bioactive Compounds from Crescentia cujete L. Molecules. 2023; 28(8):3547. https://doi.org/10.3390/molecules28083547
Chicago/Turabian StyleGonzales, Alecsanndra L., Steven Kuan-Hua Huang, Ureah Thea A. Sevilla, Cheng-Yang Hsieh, and Po-Wei Tsai. 2023. "In Silico Analysis of Anti-Inflammatory and Antioxidant Properties of Bioactive Compounds from Crescentia cujete L." Molecules 28, no. 8: 3547. https://doi.org/10.3390/molecules28083547