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Rusdipoetra RA, Suwito H, Puspaningsih NNT, Haq KU. Theoretical insight of reactive oxygen species scavenging mechanism in lignin waste depolymerization products. RSC Adv 2024; 14:6310-6323. [PMID: 38380240 PMCID: PMC10877321 DOI: 10.1039/d3ra08346b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 01/31/2024] [Indexed: 02/22/2024] Open
Abstract
Apart from natural products and synthesis, phenolic compounds can be produced from the depolymerization of lignin, a major waste in biofuel and paper production. This process yields a plethora of aryl propanoid phenolic derivatives with broad biological activities, especially antioxidant properties. Due to its versatility, our study focuses on investigating the antioxidant mechanisms of several phenolic compounds obtained from renewable and abundant resources, namely, syringol (Hs), 4-allylsyringol (HAs), 4-propenylsyringol (HPns), and 4-propylsyringol (HPs). Employing the density functional theory (DFT) approach in conjunction with the QM-ORSA protocol, we aim to explore the reactivity of these compounds in neutralizing hydroperoxyl radicals in physiological and non-polar media. Kinetic and thermodynamic parameter calculations on the antioxidant activity of these compounds were also included in this study. Additionally, our research utilizes the activation strain model (ASM) for the first time to explain the reactivity of the HT and RAF mechanisms in the peroxyl radical scavenging process. It is predicted that HPs has the best rate constant in both media (1.13 × 108 M-1 s-1 and 1.75 × 108 M-1 s-1, respectively). Through ASM analysis, it is observed that the increase in the interaction energy due to the formation of intermolecular hydrogen bonds during the reaction is an important feature for accelerating the hydrogen transfer process. Furthermore, by examining the physicochemical and toxicity parameters, only Hs is not suitable for further investigation as a therapeutic agent because of potential toxicity and mutagenicity. However, overall, all compounds are considered potent HOO˙ scavengers in lipid-rich environments compared to previously studied antioxidants.
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Affiliation(s)
- Rahmanto Aryabraga Rusdipoetra
- Bioinformatic Research Group, Research Centre of Bio-Molecule Engineering (BIOME), Airlangga University Jl. Ir. H. Soekarno Mulyorejo Surabaya Indonesia
- Department of Chemistry, Faculty of Science and Technology, Airlangga University Jl. Ir. H. Soekarno Mulyorejo Surabaya Indonesia
| | - Hery Suwito
- Department of Chemistry, Faculty of Science and Technology, Airlangga University Jl. Ir. H. Soekarno Mulyorejo Surabaya Indonesia
| | - Ni Nyoman Tri Puspaningsih
- Department of Chemistry, Faculty of Science and Technology, Airlangga University Jl. Ir. H. Soekarno Mulyorejo Surabaya Indonesia
- Proteomic Research Group, Research Centre of Bio-Molecule Engineering (BIOME), Airlangga University Jl. Ir. H. Soekarno Mulyorejo Surabaya Indonesia
| | - Kautsar Ul Haq
- Bioinformatic Research Group, Research Centre of Bio-Molecule Engineering (BIOME), Airlangga University Jl. Ir. H. Soekarno Mulyorejo Surabaya Indonesia
- Department of Chemistry, Faculty of Science and Technology, Airlangga University Jl. Ir. H. Soekarno Mulyorejo Surabaya Indonesia
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Walton-Raaby M, Floen T, García-Díez G, Mora-Diez N. Calculating the Aqueous pK a of Phenols: Predictions for Antioxidants and Cannabinoids. Antioxidants (Basel) 2023; 12:1420. [PMID: 37507958 PMCID: PMC10376140 DOI: 10.3390/antiox12071420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/30/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
We aim to develop a theoretical methodology for the accurate aqueous pKa prediction of structurally complex phenolic antioxidants and cannabinoids. In this study, five functionals (M06-2X, B3LYP, BHandHLYP, PBE0, and TPSS) and two solvent models (SMD and PCM) were combined with the 6-311++G(d,p) basis set to predict pKa values for twenty structurally simple phenols. None of the direct calculations produced good results. However, the correlations between the calculated Gibbs energy difference of each acid and its conjugate base, ΔGaq(BA)°=ΔGaqA-°-ΔGaq(HA)°, and the experimental aqueous pKa values had superior predictive accuracy, which was also tested relative to an independent set of ten molecules of which six were structurally complex phenols. New correlations were built with twenty-seven phenols (including the phenols with experimental pKa values from the test set), which were used to make predictions. The best correlation equations used the PCM method and produced mean absolute errors of 0.26-0.27 pKa units and R2 values of 0.957-0.960. The average range of predictions for the potential antioxidants (cannabinoids) was 0.15 (0.25) pKa units, which indicates good agreement between our methodologies. The new correlation equations could be used to make pKa predictions for other phenols in water and potentially in other solvents where they might be more soluble.
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Affiliation(s)
- Max Walton-Raaby
- Department of Chemistry, Thompson Rivers University, Kamloops, BC V2C 0C8, Canada
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Tyler Floen
- Department of Chemistry, Thompson Rivers University, Kamloops, BC V2C 0C8, Canada
| | | | - Nelaine Mora-Diez
- Department of Chemistry, Thompson Rivers University, Kamloops, BC V2C 0C8, Canada
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Georgieva MK, Anastassova N, Stefanova D, Yancheva D. Radical Scavenging Mechanisms of 1-Arylhydrazone Benzimidazole Hybrids with Neuroprotective Activity. J Phys Chem B 2023; 127:4364-4373. [PMID: 37163390 DOI: 10.1021/acs.jpcb.2c05784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Benzimidazole-arylhydrazone hybrids showed promising potential as multifunctional drugs for the treatment of neurodegenerative disorders. The neuroprotection studies conducted using an in vitro model of H2O2-induced oxidative stress on the SH-SY5Y cell line revealed a remarkable activity of the compound possessing a vanilloid structural fragment. The cell viability was preserved up to 84% and this effect was significantly higher than the one exerted by the reference compounds melatonin and rasagiline. Another compound with a catecholic moiety demonstrated the second-best neuroprotective activity. Computational studies were further conducted to characterize in depth the antioxidant properties of both compounds. The possible radical scavenging mechanisms were estimated as well as the most reactive sites through which the compounds may deactivate a variety of free radicals. Both of the compounds are able to deactivate not only the highly reactive hydroxyl radicals but also alkoxyl and hydroperoxyl radicals, following hydrogen atom transfer or radical adduct formation mechanism. In nonpolar medium, 3e is predicted to react slightly faster than 3a with alkoxyl radicals and around two orders of magnitude faster than 3a with hydroperoxyl radicals. The most reactive sites for formal hydrogen atom transfer in 3a are the meta-hydroxy group in the phenyl ring in water and the amide N-H group in benzene; in 3e, the amide N-H group is more reactive in both solvents. The radical adduct formation can occur at several positions in 3a and 3e, the most active being C4, C6, and C14. The stability of the formed radicals was estimated by NBO calculations. The NBO calculations indicated that the spin density in the radicals formed by the abstraction of a hydrogen atom from the amide groups of both compounds is delocalized over the phenyl ring and the hydrazone chain. The obtained theoretical data for the better radical scavenging ability of the vanilloid hybrid corroborate its experimentally established better neuroprotective activity.
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Affiliation(s)
- Miglena K Georgieva
- LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Neda Anastassova
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Building 9, 1113 Sofia, Bulgaria
| | - Denitsa Stefanova
- Laboratory of Drug Metabolism and Drug Toxicity, Department of Pharmacology, Pharmacotherapy and Toxicology, Faculty of Pharmacy, Medical University-Sofia, 2 Dunav Str., 1000 Sofia, Bulgaria
| | - Denitsa Yancheva
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Building 9, 1113 Sofia, Bulgaria
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Chen M, Li Z, Sun G, Jin S, Hao X, Zhang C, Liu L, Zhang L, Liu H. Theoretical study on the free radical scavenging potency and mechanism of natural coumestans: Roles of substituent, noncovalent interaction and solvent. PHYTOCHEMISTRY 2023; 207:113580. [PMID: 36587886 DOI: 10.1016/j.phytochem.2022.113580] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/19/2022] [Accepted: 12/28/2022] [Indexed: 06/17/2023]
Abstract
The free radical scavenging potency and mechanisms of seven representative natural coumestans were systematically evaluated using density functional theory (DFT) approach. Thermodynamic feasibility of different mechanisms was assessed by various physio-chemical descriptors involved in the double (2H+/2e‒) radical-trapping processes. Energy diagram and related transition state structures of the reaction between wedelolactone (WEL) and hydroperoxyl radical were constructed to further uncover the radical-trapping details. Results showed that the studied coumestans prefer to scavenge radicals via formal hydrogen atom transfer (fHAT) mechanism in the gas phase and non-polar environment, whereas sequential proton loss electron transfer (SPLET) is favored in polar media. Moreover, the feasibility of second fHAT and SPLET processes was also revealed. Sequential double proton loss double electron transfer (SdPLdET) mechanism represents the preferred pathway in aqueous solution at physiological pH. Our findings highlight the essential role of ortho-dihydroxyl group, noncovalent interaction and solvents on radical-trapping potency. 4'-OH in D-ring was found to be the most favorable site to trap radical for most of the studied coumestans, whereas 3-OH in A-ring for lucernol (LUN).
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Affiliation(s)
- Mohan Chen
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, No.209, Tongshan Road, Xuzhou, Jiangsu, 221004, China
| | - Zheng Li
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, No.209, Tongshan Road, Xuzhou, Jiangsu, 221004, China
| | - Gang Sun
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, No.209, Tongshan Road, Xuzhou, Jiangsu, 221004, China
| | - Shuang Jin
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, No.209, Tongshan Road, Xuzhou, Jiangsu, 221004, China
| | - Xiyue Hao
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, No.209, Tongshan Road, Xuzhou, Jiangsu, 221004, China
| | - Chi Zhang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, No.209, Tongshan Road, Xuzhou, Jiangsu, 221004, China
| | - Ling Liu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, No.209, Tongshan Road, Xuzhou, Jiangsu, 221004, China
| | - Ling Zhang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, No.209, Tongshan Road, Xuzhou, Jiangsu, 221004, China
| | - Hongli Liu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, No.209, Tongshan Road, Xuzhou, Jiangsu, 221004, China.
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Cam Nam P, Van Bay M, Vo QV, Mechler A, Minh Thong N. Tautomerism and antioxidant power of sulfur-benzo[h]quinoline: DFT and molecular docking studies. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Milanović Ž, Tošović J, Marković S, Marković Z. Comparison of the scavenging capacities of phloroglucinol and 2,4,6-trihydroxypyridine towards HO˙ radical: a computational study. RSC Adv 2020; 10:43262-43272. [PMID: 35519718 PMCID: PMC9058218 DOI: 10.1039/d0ra08377a] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/21/2020] [Indexed: 01/06/2023] Open
Abstract
In this work the scavenging capacities of biologically active phloroglucinol (1,3,5-trihydroxybenzene, THB–OH) and structurally similar 2,4,6-trihydroxypyridine (THP–OH) towards HO˙ were examined. This task was realized by means of density functional theory, through investigation of all favorable antioxidative pathways in two solvents of different polarity: benzene and water. It was found that in benzene both compounds conform to the hydrogen atom transfer (HAT) and radical adduct formation (RAF) mechanisms. In water, the mechanisms of antioxidative action of the investigated compounds are far more complex, especially those of THB–OH. This compound and HO˙ undergo all four investigated mechanisms: HAT, RAF, sequential proton loss electron transfer (SPLET), and single electron transfer-proton transfer (SET-PT). HAT, RAF and SPLET are operative mechanisms in the case of THP–OH. Independently of solvent polarity, both investigated compounds are more reactive towards HO˙ in comparison to Trolox. Our final remark is as follows: the electron-withdrawing effect of the nitrogen is stronger than the electron-donating effect of the OH groups in the molecule of THP–OH. As a consequence, THB–OH is more powerful antioxidant than THP–OH, thus implying that the presence of nitrogen decreases the scavenging capacity of the respective compound. The scavenging capacities of biologically active phloroglucinol (1,3,5-trihydroxybenzene, THB–OH) and structurally similar 2,4,6-trihydroxypyridine (THP–OH) towards HO˙ were elucidated.![]()
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Affiliation(s)
- Žiko Milanović
- Department of Chemistry, Faculty of Science, University of Kragujevac 12 Radoja Domanovića 34000 Kragujevac Serbia
| | - Jelena Tošović
- Department of Chemistry, Faculty of Science, University of Kragujevac 12 Radoja Domanovića 34000 Kragujevac Serbia
| | - Svetlana Marković
- Department of Chemistry, Faculty of Science, University of Kragujevac 12 Radoja Domanovića 34000 Kragujevac Serbia
| | - Zoran Marković
- Department of Science, Institute for Information Technologies, University of Kragujevac Jovana Civijića bb 34000 Kragujevac Serbia
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Antioxidative Action of Ellagic Acid-A Kinetic DFT Study. Antioxidants (Basel) 2020; 9:antiox9070587. [PMID: 32640518 PMCID: PMC7402119 DOI: 10.3390/antiox9070587] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/02/2020] [Accepted: 07/03/2020] [Indexed: 12/15/2022] Open
Abstract
Although one can find numerous studies devoted to the investigation of antioxidative activity of ellagic acid (EA) in the scientific literature, the mechanisms of its action have not yet been fully clarified. Therefore, further kinetic studies are needed to understand its antioxidative capacity completely. This work aims to reveal the underlying molecular mechanisms responsible for the antioxidative action of EA. For this purpose, its reactions with HO• and CCl3OO• radicals were simulated at physiological conditions using the quantum mechanics-based test for overall free-radical scavenging activity. The density functional theory in combination with the conductor-like polarizable continuum solvation model was utilized. With HO• radical EA conforms to the hydrogen atom transfer and radical adduct formation mechanisms, whereas sequential proton loss electron transfer mechanism is responsible for scavenging of CCl3OO• radical. In addition, compared to trolox, EA was found more reactive toward HO•, but less reactive toward CCl3OO•. The calculated rate constants for the reactions of EA with both free radicals are in a very good agreement with the corresponding experimental values.
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