Biophysical, Biochemical, and Molecular Docking Investigations of Anti-Glycating, Antioxidant, and Protein Structural Stability Potential of Garlic
Abstract
:1. Introduction
2. Results
2.1. Biochemical Analysis
Phytochemical Screening
2.2. Antioxidant and Free Radical Scavenging Activities of Garlic Extract
2.2.1. Assay for Ferric Reducing Antioxidant Power (FRAP)
2.2.2. 2,2-Diphenyl-1-Picrylhydrazyl (DPPH) Radical Scavenging Assay
2.3. Inhibition of Structural Changes by Garlic Extract
2.3.1. Protein Denaturation Inhibition
2.3.2. Protein Browning Inhibition
2.3.3. Inhibition in Protein Aggregate Formation
2.3.4. Amyloid Structure Inhibition
2.3.5. Spectral Studies
2.3.6. Circular Dichroism
2.4. Molecular Docking Studies for Potential Natural Product Metabolites as Inhibitors of Glycation
3. Discussion
4. Materials and Methods
4.1. Materials
4.2. Chemical and Biological Studies
4.2.1. Preparation of Aqueous Solution of Garlic Extract
4.2.2. Qualitative and Quantitative Analysis for Flavonoids and Phenolics
4.2.3. Antioxidant and Free Radical Scavenging Activities of Extract
4.3. Modification of HSA by Glucose
4.4. Protein Denaturation Inhibition by Garlic Extract
4.5. Measurement of Browning in Glycated Samples
4.6. Effect of Garlic Extract on Protein Aggregation Index
4.7. Spectral Studies
4.8. Circular Dichroism
4.9. Structural Details of Potential Natural Product Ligands/Inhibitors of HSA Glycation
4.10. Molecular Docking and Scoring of Ligand Poses
4.11. Statistical Analysis
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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Preliminary Screening | Garlic Extract |
---|---|
Weight of dry powder | 50 g |
Yield | 5.19% |
Extract | Aqueous |
Flavonoids | + |
Polyphenolic compounds | + |
Total phenolic compounds | 21.45 ± 0.02 mg gallic acid equivalent/g dry weight of extract |
Total flavonoid content | 16.58 ± 0.03 mg quercetin equivalent/g dry weight of the extract |
Conformation | N-HSA | G-HSA | G-HSA with Garlic Extracts (μg/mL) | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
- | 0.78 | 1.56 | 3.12 | 6.25 | 12.5 | 25 | 50 | 100 | AG | ||
α-helix | 42.7 ± 0.6 | 38.2 ± 0.3 (−10.5%) | 38.2 ± 0.3 (−10.5%) | 38.3 ± 0.3 (−10.3%) | 38.4 ± 0.3 (−10.0%) | 38.8 ± 0.3 (−9.1%) | 39.8 ± 0.3 * (−6.8%) | 40.5 ± 0.3 * (−5.2%) | 40.9 ± 0.3 ** (−4.2%) | 41.5 ± 0.3 *** (−2.8%) | 40.8 ± 0.3 ** (−4.4%) |
β-sheet | 26.2 ± 0.5 | 30.1 ± 0.2 (+14.9%) | 30.1 ± 0.2 (+14.9%) | 30.0 ± 0.2 (+14.5%) | 29.9 ± 0.2 (+14.1%) | 29.6 ± 0.2 (+13.0%) | 28.8 ± 0.2 * (+9.9%) | 28.1 ± 0.2 ** (+7.3%) | 27.9 ± 0.2 ** (+6.5%) | 27.4 ± 0.2 *** (+4.6%) | 27.8 ± 0.2 ** (+6.1%) |
β-turn | 18.5 ± 0.2 | 19.4 ± 0.3 (+4.9%) | 19.4 ± 0.3 (+4.9%) | 19.4 ± 0.3 (+4.9%) | 19.4 ± 0.3 (+4.9%) | 19.2 ± 0.3 (+4.3%) | 19.1 ± 0.3 * (+3.2%) | 19.0 ± 0.3 ** (+2.7%) | 18.8 ± 0.3 ** (+1.6%) | 18.6 ± 0.3 ** (+0.5%) | 19.0 ± 0.3 ** (+2.7%) |
Random coil | 12.6 ± 0.5 | 12.3 ± 0.4 (−2.4%) | 12.3 ± 0.4 (−2.4%) | 12.3 ± 0.4 (−2.4%) | 12.3 ± 0.4 (−2.4%) | 12.3 ± 0.4 (−2.4%) | 12.3 ± 0.4 (−2.4%) | 12.4 ± 0.4 * (−1.6%) | 12.4 ± 0.4 * (−1.6%) | 12.5 ± 0.4 *** (−0.8%) | 12.4 ± 0.4 * (−1.6%) |
Ligand/Inhibitor Name (Common Name) | IUPAC Name, Mol Formula, and PubChem ID | Binding Affinity Kcal/Mol | Number of Hydrogen Bonds | Other Interactions * |
---|---|---|---|---|
Glucose (Cyclic form) | (3R,4S,5S,6R)-6-(hydroxymethyl)oxane-2,3,4,5-tetrol Mol formula: C6H12O6 PubChem ID: 5793 | −6.2 | 6 (3 × Arg257, 1 × Arg221, 1 × Tyr150, 1 × His242) | 1 (1 × Lys199) Leu238 and Ala291 (Hydrophobic interactions) |
Catechin | (2S,3R)-2-(3,4-dihydroxyphenyl)-3,4-dihydro-2H-chromene-3,5,7-triol Mol formula: C15H14O6 PubChem ID: 73160 | −6.7 | 1 (1 × His 288) | 13 (1 × Arg 257, 1 × His 288, 1 × Glc 602, 1 × Ala 291, 1 × Tyr 150, 1 × Glu 153, 1 × Glu 292, 1 × Lys 195, 1 × Ala 191, 1 × Phe 157, 1 × Ser 192, 1 × Lys 436, 1 × Glu 188 Carbon H Bond) |
Caffeic Acid | (E)-3-(3,4-dihydroxyphenyl) prop-2-enoic acid Mol formula: C9H8O4 PubChem ID:689043 | −6.6 | 3 (1 × Arg 222, 2 × Ser 192) | 12 (1 × Arg 218, 1 × Po 4603, 1 × Glc 602, 1 × Leu 238, 1 × Tyr 150, 1 × Lys 195, 1 × Glu 153, 1 × Ala 291, 1 × His 288, 1 × Phe 157,1 × Gln 196, 1 × Lys 199) |
Gallic Acid | 3,4,5-trihydroxybenzoic acid Mol formula: C7H6O5 PubChem ID: 370 | −6.4 | 4 (2 × Lys 199, 1 × Gln 196, 1 × Glu 153) | 10 (1 × His 242, 1 × Gln 196, 1 × Ser 192, 1 × Lys 195, 1 × Tyr 150, 1 × Ala 291, 1 × Phe 157, 1 × His 288, 1 × Glu 292, 1 × Arg 257) |
m-Coumaric Acid | E)-3-(3-hydroxyphenyl)prop-2-enoic acid Mol formula: C9H8O3 PubChem ID: 637541 | −6.3 | 4 (1 × Arg 222, 1 × PO 4603, 1 × Glc 602, 1 × Ser 192) | 6 (1 × Arg 222, 1 × PO 4603, 1 × Glc 602, 1 × Ser 192, 1 × Gln 196 Unfavorable donor–donor, 1 × Gln 196 Unfavorable donor–donor) |
Quercetin | 2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxychromen-4-one Mol formula: C15H10O7 PubChem ID: 5280343 | −8.1 | 4 (1 × Ser 192, 1 × Lys 199, 1 × Arg 257, 1 × Arg 222) | 17 (1 × Lys 195, 1 × Lys 199, 1 × Gln 196, 1 × His 242, 1 × Tyr 150, 3 × Ala 291, 2 × Leu 238, 1 × Leu 260, 1 × Ala 261, 1 × Ser 287, 1 × Ile 290, 1 × Leu 219,1 × Arg 222, 1 × Glu 153) |
Pyrogallol | benzene-1,2,3-triol Mol formula: C6H6O3 PubChem ID: 1057 | −5.4 | 3 (2 × Ser 192, 1 × Gln 196) | 8 (1 × Tyr 150, 1 × Glu 153, 1 × Phe 157, 1 × Lys 199, 1 × Ala 291, 1 × Lys 195, 1 × His 242, 1 × Arg 257) |
Dihydroxybenzoic acid | 2,3-dihydroxybenzoic acid Mol formula: C7H6O4 PubChem ID: 19 | −6.2 | 3 (1 × Arg 222, 1 × Ser 287, 1 × Arg 257) | 9 (1 × Leu 260, 1 × Ile 290, 1 × Leu 238, 1 × Ala 291, 1 × Arg 257, 1 × Leu 219, 1 × Ile 264, 1 × Ala 261, 1 × Tyr 150) |
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Khan, M.W.A.; Otaibi, A.A.; Alsukaibi, A.K.D.; Alshammari, E.M.; Al-Zahrani, S.A.; Sherwani, S.; Khan, W.A.; Saha, R.; Verma, S.R.; Ahmed, N. Biophysical, Biochemical, and Molecular Docking Investigations of Anti-Glycating, Antioxidant, and Protein Structural Stability Potential of Garlic. Molecules 2022, 27, 1868. https://doi.org/10.3390/molecules27061868
Khan MWA, Otaibi AA, Alsukaibi AKD, Alshammari EM, Al-Zahrani SA, Sherwani S, Khan WA, Saha R, Verma SR, Ahmed N. Biophysical, Biochemical, and Molecular Docking Investigations of Anti-Glycating, Antioxidant, and Protein Structural Stability Potential of Garlic. Molecules. 2022; 27(6):1868. https://doi.org/10.3390/molecules27061868
Chicago/Turabian StyleKhan, Mohd W. A., Ahmed A. Otaibi, Abdulmohsen K. D. Alsukaibi, Eida M. Alshammari, Salma A. Al-Zahrani, Subuhi Sherwani, Wahid A. Khan, Ritika Saha, Smita R. Verma, and Nessar Ahmed. 2022. "Biophysical, Biochemical, and Molecular Docking Investigations of Anti-Glycating, Antioxidant, and Protein Structural Stability Potential of Garlic" Molecules 27, no. 6: 1868. https://doi.org/10.3390/molecules27061868
APA StyleKhan, M. W. A., Otaibi, A. A., Alsukaibi, A. K. D., Alshammari, E. M., Al-Zahrani, S. A., Sherwani, S., Khan, W. A., Saha, R., Verma, S. R., & Ahmed, N. (2022). Biophysical, Biochemical, and Molecular Docking Investigations of Anti-Glycating, Antioxidant, and Protein Structural Stability Potential of Garlic. Molecules, 27(6), 1868. https://doi.org/10.3390/molecules27061868