QM-CSA: A Novel Quantum Mechanics-Based Protocol for Evaluation of the Carcinogen-Scavenging Activity of Polyphenolic Compounds
Abstract
:1. Introduction
2. Computational Methods
- The identification of the main molecular mechanism of alkylation reactions between nine chemical carcinogens and polyphenolic compounds at physiological conditions (pH 7.4 and an aqueous environment).
- Two scales for the quantification of CSA: the absolute scale based on the comparison of the calculated activation-free energies for alkylation reactions of polyphenols with guanine and the relative scale using glutathione as a reference compound.
- The establishment of the order of CSA in a series of polyphenolic compounds at physiological conditions.
- The identification of the most effective scavengers of chemical carcinogens of the epoxy type and the structural features responsible for their activity.
2.1. Investigation of Molecular Mechanisms of Alkylation Reactions of Guanine, Glutathione, and Polyphenolic Compounds with Chemical Carcinogens at Physiological Conditions
2.2. The Determination of an Appropriate Combination of Density Functional, Flexible Basis Set, and Implicit Solvation Model
2.3. Determination of Anticarcinogenic Potential of Various Polyphenolic Compounds as Scavengers of Nine Investigated Chemical Carcinogens of the Epoxy Type Using QM-CSA Methodology
2.4. Evaluation of the CSA of Polyphenolic Compounds by Applying Two Scales
3. Results and Discussion
3.1. Validation of the Developed QM-CSA Protocol
3.2. Application of the QM-CSA Protocol: Mechanistic Insights into Alkylation Reactions of Nine Investigated Chemical Carcinogens with EGCG, EGC, and (+)-Catechin
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Appendix A
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Functional/Solvation Model | (kcal/mol) a | ωTS (i cm−1) b | ωR (cm−1) c | dTS (Å) d | dR (Å) e | (kcal/mol) f | (/) g | (kcal/mol) h |
---|---|---|---|---|---|---|---|---|
Styrene Oxide | ||||||||
M11-L/SMD | 27.16 | 640.08 | 17.63 | 1.94 | 3.34 | 0.66 | 0.02 | 26.5 |
MN12-L/SMD | 25.50 | 577.35 | 22.26 | 1.94 | 3.13 | 1.00 | 0.04 | 26.5 |
Propylene Oxide | ||||||||
M11-L/SMD | 26.34 | 629.23 | 29.99 | 2.06 | 3.82 | 0.94 | 0.04 | 25.4 |
MN12-L/SMD | 25.45 | 569.04 | 30.07 | 2.05 | 3.17 | 0.05 | 0.002 | 25.4 |
Ethylene Oxide | ||||||||
M11-L/SMD | 24.08 | 613.17 | 11.77 | 2.07 | 2.79 | 0.62 | 0.02 | 24.7 |
MN12-L/SMD | 23.29 | 580.76 | 8.28 | 2.06 | 3.24 | 1.41 | 0.05 | 24.7 |
Glycidamide | ||||||||
M11-L/SMD | 23.76 | 654.07 | 24.06 | 2.08 | 3.70 | 0.96 | 0.04 | 22.8 |
MN12-L/SMD | 23.35 | 598.03 | 24.22 | 2.06 | 3.26 | 0.55 | 0.02 | 22.8 |
Vinyl Carbamate Epoxide | ||||||||
M11-L/SMD | 20.65 | 543.75 | 29.15 | 2.15 | 3.49 | 1.75 | 0.08 | 22.4 |
MN12-L/SMD | 20.95 | 515.44 | 25.84 | 2.13 | 3.36 | 1.45 | 0.06 | 22.4 |
Beta-propiolactone | ||||||||
M11-L/SMD | 21.11 | 583.95 | 16.85 | 2.13 | 3.57 | 0.31 | 0.01 | 20.8 |
MN12-L/SMD | 21.34 | 562.69 | 17.17 | 2.13 | 3.39 | 0.54 | 0.03 | 20.8 |
Chloroethylene Oxide | ||||||||
M11-L/SMD | 18.35 | 539.26 | 23.65 | 2.19 | 3.59 | 1.15 | 0.06 | 19.5 |
MN12-L/SMD | 17.64 | 515.29 | 36.83 | 2.16 | 3.19 | 1.86 | 0.09 | 19.5 |
2-Cyanoethylene Oxide | ||||||||
M11-L/SMD | 20.65 | 646.51 | 20.00 | 2.10 | 3.32 | 1.45 | 0.08 | 19.2 |
MN12-L/SMD | 20.57 | 616.92 | 45.33 | 2.08 | 3.50 | 1.37 | 0.07 | 19.2 |
AFB1 Exo-8.9-Epoxide | ||||||||
M11-L/SMD | 16.99 | 225.87 | 21.53 | 2.12 | 4.21 | 1.89 | 0.12 | 15.1 |
MN12-L/SMD | 16.88 | 207.05 | 26.03 | 2.12 | 4.14 | 1.78 | 0.12 | 15.1 |
Functional/Solvation Model M11-L/SMD | (kcal/mol) a | ωTS (i cm−1) b | ωR (cm−1) c | dTS (Å) d | dR (Å) e | r (/) f | (kcal/mol) g |
---|---|---|---|---|---|---|---|
Styrene Oxide | |||||||
EGCG | 25.65 | 585.16 | 10.48 | 1.99 | 3.35 | 1.53 | 27.16 |
EGC | 19.80 | 577.89 | 6.19 | 2.04 | 3.67 | 1.18 | 27.16 |
(+)-Catechin | 20.32 | 591.12 | 11.05 | 2.03 | 3.14 | 1.21 | 27.16 |
Glutathione | 16.81 | 677.09 | 15.61 | 2.60 | 4.14 | 1.00 | 27.16 |
Propylene Oxide | |||||||
EGCG | 25.71 | 566.03 | 14.46 | 2.00 | 3.25 | 1.52 | 26.34 |
EGC | 20.73 | 581.61 | 25.13 | 2.03 | 3.41 | 1.23 | 26.34 |
(+)-Catechin | 18.85 | 555.36 | 16.31 | 2.02 | 3.35 | 1.12 | 26.34 |
Glutathione | 16.87 | 663.75 | 22.00 | 2.58 | 3.47 | 1.00 | 26.34 |
Ethylene Oxide | |||||||
EGCG | 24.27 | 566.56 | 14.55 | 2.01 | 3.73 | 1.70 | 24.08 |
EGC | 22.12 | 586.59 | 27.95 | 2.05 | 3.85 | 1.55 | 24.08 |
(+)-Catechin | 17.37 | 574.66 | 21.41 | 2.03 | 3.36 | 1.22 | 24.08 |
Glutathione | 14.25 | 675.23 | 27.41 | 2.60 | 3.69 | 1.00 | 24.08 |
Glycidamide | |||||||
EGCG | 22.07 | 552.28 | 16.34 | 2.02 | 4.48 | 1.09 | 23.76 |
EGC | 19.35 | 562.81 | 8.97 | 2.06 | 4.64 | 0.95 | 23.76 |
(+)-Catechin | 19.46 | 583.34 | 11.72 | 2.05 | 3.48 | 0.96 | 23.76 |
Glutathione | 20.30 | 694.05 | 9.16 | 2.57 | 4.13 | 1.00 | 23.76 |
Vinyl Carbamate Epoxide | |||||||
EGCG | 17.64 | 564.04 | 10.75 | 2.10 | 3.58 | 1.47 | 20.65 |
EGC | 11.64 | 591.42 | 11.13 | 2.13 | 3.54 | 0.97 | 20.65 |
(+)-Catechin | 13.61 | 590.77 | 21.98 | 2.12 | 3.70 | 1.14 | 20.65 |
Glutathione | 11.97 | 655.05 | 14.84 | 2.65 | 4.82 | 1.00 | 20.65 |
Beta-propiolactone | |||||||
EGCG | 16.97 | 581.69 | 12.28 | 2.09 | 3.06 | 1.20 | 21.11 |
EGC | 12.85 | 615.41 | 17.64 | 2.10 | 3.23 | 0.91 | 21.11 |
(+)-Catechin | 10.65 | 630.25 | 16.37 | 2.08 | 3.24 | 0.75 | 21.11 |
Glutathione | 14.19 | 653.94 | 12.49 | 2.62 | 3.65 | 1.00 | 21.11 |
Chloroethylene Oxide | |||||||
EGCG | 15.70 | 580.33 | 15.14 | 2.14 | 3.82 | 1.68 | 18.35 |
EGC | 12.86 | 607.74 | 17.61 | 2.16 | 3.52 | 1.37 | 18.35 |
(+)-Catechin | 8.02 | 591.69 | 9.26 | 2.15 | 3.47 | 0.86 | 18.35 |
Glutathione | 9.36 | 633.79 | 23.68 | 2.74 | 3.69 | 1.00 | 18.35 |
2-Cyanoethylene Oxide | |||||||
EGCG | 20.01 | 612.51 | 6.30 | 2.04 | 3.30 | 1.43 | 20.65 |
EGC | 17.97 | 634.52 | 5.88 | 2.07 | 3.37 | 1.29 | 20.65 |
(+)-Catechin | 13.95 | 644.96 | 3.85 | 2.05 | 3.45 | 0.99 | 20.65 |
Glutathione | 13.99 | 712.15 | 9.04 | 2.63 | 3.68 | 1.00 | 20.65 |
AFB1 Exo-8.9-Epoxide | |||||||
EGCG | 17.15 | 156.05 | 14.12 | 2.40 | 3.81 | 1.33 | 16.99 |
EGC | 13.15 | 204.14 | 10.80 | 2.68 | 3.40 | 1.02 | 16.99 |
(+)-Catechin | 14.37 | 143.49 | 10.84 | 2.39 | 3.32 | 1.11 | 16.99 |
Glutathione | 12.92 | 245.54 | 8.88 | 3.06 | 3.77 | 1.00 | 16.99 |
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Furlan, V.; Tošović, J.; Bren, U. QM-CSA: A Novel Quantum Mechanics-Based Protocol for Evaluation of the Carcinogen-Scavenging Activity of Polyphenolic Compounds. Foods 2024, 13, 2708. https://doi.org/10.3390/foods13172708
Furlan V, Tošović J, Bren U. QM-CSA: A Novel Quantum Mechanics-Based Protocol for Evaluation of the Carcinogen-Scavenging Activity of Polyphenolic Compounds. Foods. 2024; 13(17):2708. https://doi.org/10.3390/foods13172708
Chicago/Turabian StyleFurlan, Veronika, Jelena Tošović, and Urban Bren. 2024. "QM-CSA: A Novel Quantum Mechanics-Based Protocol for Evaluation of the Carcinogen-Scavenging Activity of Polyphenolic Compounds" Foods 13, no. 17: 2708. https://doi.org/10.3390/foods13172708