Oxidative Stress and Antioxidants in Computational Chemistry

A special issue of Antioxidants (ISSN 2076-3921). This special issue belongs to the section "Health Outcomes of Antioxidants and Oxidative Stress".

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 6125

Special Issue Editor

Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Av. Ferrocarril San Rafael Atlixco 186, Col. Leyes de Reforma 1A Sección, Mexico City 09310, Mexico
Interests: antioxidant activity; oxidative stress; free radicals; reaction mechanisms; kinetics; thermochemistry; computational chemistry; theoretical chemistry; multifunctional antioxidants; rational design of medical drugs

Special Issue Information

Dear Colleagues,

Oxidative stress (OS) has long been recognized as a risk to human health. It is associated with the onset and development of numerous diseases. Antioxidants, on the other hand, contribute to ameliorate the deleterious effects of OS, and have been proven to be beneficial in the treatment of many OS-related diseases. They are both of a multifaceted nature, and can be mediated by enzymatic and chemical processes. Their complexity arises from different factors. Some of them are as follows: (i) the wide variety of chemical species that may be involved in competing, simultaneous or consecutive reactions; (ii) the presence of other species in the environment, such as redox metals, that influence oxidant and antioxidant actions; (iii) the dual behavior of some chemicals that can act as antioxidants as well as pro-oxidants; (iv) the myriad of reaction mechanisms and sites that might be involved in such processes. Thus, investigating oxidative stress and antioxidant activity is a challenging task, regardless of whether it is faced experimentally or theoretically.

This Special Issue will focus on the later, and intends to provide a collection of novel insights into oxidative damage and antioxidant protection from experts on the subjects. Original researches and reviews are equally welcome.

Prof. Dr. Annia Galano
Guest Editor

Manuscript Submission Information

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Keywords

  • oxidative stress
  • antioxidants
  • reaction mechanisms
  • kinetics
  • pro-oxidant
  • reactivity

Published Papers (5 papers)

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Research

21 pages, 1690 KiB  
Article
Cysteine Is the Only Universally Affected and Disfavored Proteomic Amino Acid under Oxidative Conditions in Animals
by Mario Schindeldecker and Bernd Moosmann
Antioxidants 2024, 13(3), 267; https://doi.org/10.3390/antiox13030267 - 22 Feb 2024
Viewed by 1198
Abstract
Oxidative modifications of amino acid side chains in proteins are a hallmark of oxidative stress, and they are usually regarded as structural damage. However, amino acid oxidation may also have a protective effect and may serve regulatory or structural purposes. Here, we have [...] Read more.
Oxidative modifications of amino acid side chains in proteins are a hallmark of oxidative stress, and they are usually regarded as structural damage. However, amino acid oxidation may also have a protective effect and may serve regulatory or structural purposes. Here, we have attempted to characterize the global redox role of the 20 proteinogenic amino acids in animals by analyzing their usage frequency in 5 plausible evolutionary paradigms of increased oxidative burden: (i) peroxisomal proteins versus all proteins, (ii) mitochondrial proteins versus all proteins, (iii) mitochondrially encoded respiratory chain proteins versus all mitochondrial proteins, (iv) proteins from long-lived animals versus those from short-lived animals, and (v) proteins from aerobic, free-living animals versus those from facultatively anaerobic animals. We have found that avoidance of cysteine in the oxidative condition was the most pronounced and significant variation in the majority of comparisons. Beyond this preeminent pattern, only local signals were observed, primarily increases in methionine and glutamine as well as decreases in serine and proline. Hence, certain types of cysteine oxidation appear to enforce its proteome-wide evolutionary avoidance despite its essential role in disulfide bond formation and metal ligation. The susceptibility to oxidation of all other amino acids appears to be generally unproblematic, and sometimes advantageous. Full article
(This article belongs to the Special Issue Oxidative Stress and Antioxidants in Computational Chemistry)
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17 pages, 2368 KiB  
Article
Mechanism of Antiradical Activity of Coumarin-Trihydroxybenzohydrazide Derivatives: A Comprehensive Kinetic DFT Study
by Žiko Milanović, Dušan Dimić, Edina H. Avdović, Dušica M. Simijonović, Đura Nakarada, Vladimir Jakovljević, Radiša Vojinović and Zoran S. Marković
Antioxidants 2024, 13(2), 143; https://doi.org/10.3390/antiox13020143 - 24 Jan 2024
Viewed by 765
Abstract
As part of this study, the mechanisms of the antioxidant activity of previously synthesized coumarin–trihydrobenzohydrazine derivatives were investigated: (E)-2,4-dioxo-3-(1-(2-(2″,3″,4″-trihydroxybenzoyl)hydrazineyl)ethylidene)chroman-7-yl acetate (1) and (E)-2,4-dioxo-3-(1-(2-(3″,4″,5″-trihydroxybenzoyl)hydrazineyl)ethylidene)chroman-7-yl acetate (2). The capacity of the compounds to neutralize HO was [...] Read more.
As part of this study, the mechanisms of the antioxidant activity of previously synthesized coumarin–trihydrobenzohydrazine derivatives were investigated: (E)-2,4-dioxo-3-(1-(2-(2″,3″,4″-trihydroxybenzoyl)hydrazineyl)ethylidene)chroman-7-yl acetate (1) and (E)-2,4-dioxo-3-(1-(2-(3″,4″,5″-trihydroxybenzoyl)hydrazineyl)ethylidene)chroman-7-yl acetate (2). The capacity of the compounds to neutralize HO was assessed by EPR spectroscopy. The standard mechanisms of antioxidant action, Hydrogen Atom Transfer (HAT), Sequential Proton Loss followed by Electron Transfer (SPLET), Single-Electron Transfer followed by Proton Transfer (SET-PT), and Radical Adduct/Coupling Formation (RAF/RCF) were examined using the QM-ORSA methodology. It was estimated that the newly synthesized compounds, under physiological conditions, exhibited antiradical activity via SPLET and RCF mechanisms. Based on the estimated overall rate constants (koverall), it can be concluded that 2 exhibited a greater antiradical capacity. The obtained values indicated a good correlation with the EPR spectroscopy results. Both compounds exhibit approximately 1.5 times more activity in comparison to the precursor compound used in the synthesis (gallic acid). Full article
(This article belongs to the Special Issue Oxidative Stress and Antioxidants in Computational Chemistry)
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17 pages, 2782 KiB  
Article
Quinoline Derivatives: Promising Antioxidants with Neuroprotective Potential
by Luis Felipe Hernández-Ayala, Eduardo Gabriel Guzmán-López and Annia Galano
Antioxidants 2023, 12(10), 1853; https://doi.org/10.3390/antiox12101853 - 12 Oct 2023
Cited by 2 | Viewed by 1463
Abstract
Quinoline has been proposed as a privileged molecular framework in medicinal chemistry. Although by itself it has very few applications, its derivatives have diverse biological activities. In this work, 8536 quinoline derivatives, strategically designed using the CADMA-Chem protocol, are presented. This large chemical [...] Read more.
Quinoline has been proposed as a privileged molecular framework in medicinal chemistry. Although by itself it has very few applications, its derivatives have diverse biological activities. In this work, 8536 quinoline derivatives, strategically designed using the CADMA-Chem protocol, are presented. This large chemical space was sampled, analyzed and reduced using selection and elimination scores that combine their properties of bioavailability, toxicity and manufacturability. After applying several filters, 25 derivatives were selected to investigate their acid–base, antioxidant and neuroprotective properties. The antioxidant activity was predicted based on the ionization potential and bond dissociation energies, parameters directly related to the transfer of hydrogen atoms and of a single electron, respectively. These two mechanisms are typically involved in the radical scavenging processes. The antioxidant efficiency was compared with reference compounds, and the most promising antioxidants were found to be more efficient than Trolox but less efficient than ascorbate. In addition, based on molecular docking simulations, some derivatives are expected to act as inhibitors of catechol-O methyltransferase (COMT), acetylcholinesterase (AChE) and monoamine oxidase type B (MAO-B) enzymes. Some structural insights about the compounds were found to enhance or decrease the neuroprotection activity. Based on the results, four quinoline derivatives are proposed as candidates to act as multifunctional antioxidants against Alzheimer’s (AD) and Parkinson’s (PD) diseases. Full article
(This article belongs to the Special Issue Oxidative Stress and Antioxidants in Computational Chemistry)
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13 pages, 1945 KiB  
Article
To Prevent Oxidative Stress, What about Protoporphyrin IX, Biliverdin, and Bilirubin?
by Ana Martínez, Isabel López-Rull and Juan A. Fargallo
Antioxidants 2023, 12(9), 1662; https://doi.org/10.3390/antiox12091662 - 23 Aug 2023
Cited by 2 | Viewed by 923
Abstract
The pigments responsible for eggshell color and patterning in birds are protoporphyrin IX (PP) and biliverdin (BV). Both are involved in the catalytic degradation of the hemo group. Bilirubin (BR), another pigment, is produced when BV is broken down. PP, BV, and BR [...] Read more.
The pigments responsible for eggshell color and patterning in birds are protoporphyrin IX (PP) and biliverdin (BV). Both are involved in the catalytic degradation of the hemo group. Bilirubin (BR), another pigment, is produced when BV is broken down. PP, BV, and BR are free radical scavengers. In this study, we theoretically investigated the antioxidant capacities of these three biological meaningful molecules using Density Functional Theory calculations. First, two antioxidant mechanisms were analyzed for PP, BV, and BR: electron transfer and Hydrogen Atom Transfer. Second, since PP and BV interact with the calcium carbonate matrix of the eggshell, we analyzed the interaction of these pigments with Ca2+ and investigated their chelate compounds. Third, we explored the pro-oxidant properties of PP and BV, which have been proposed for PP when photoactivated to the triplet state, but not for BV. Our results show that PP, BV, and BR are just as good antiradical as other important natural pigments (carotenoids). Neither the antiradical properties of PP and BV nor the UV-visible spectra change due to the presence of calcium, suggesting that the signaling function of these pigments is not affected by the link with Ca2+. Finally, we found that both PP and BV (alone and when linked to Ca2+) can transfer energy from its triplet state to molecular-oxygen-producing singlet oxygen, indicating their pro-oxidant capacity. This investigation answers important questions about the function of these pigments, which may help to understand their influence on the reproductive success of birds. Full article
(This article belongs to the Special Issue Oxidative Stress and Antioxidants in Computational Chemistry)
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15 pages, 2658 KiB  
Article
The Synergy between Glutathione and Phenols—Phenolic Antioxidants Repair Glutathione: Closing the Virtuous Circle—A Theoretical Insight
by Mirzam Carreon-Gonzalez and Juan Raúl Alvarez-Idaboy
Antioxidants 2023, 12(5), 1125; https://doi.org/10.3390/antiox12051125 - 19 May 2023
Cited by 1 | Viewed by 1247
Abstract
Glutathione (GSH) and phenols are well-known antioxidants, and previous research has suggested that their combination can enhance antioxidant activity. In this study, we used Quantum Chemistry and computational kinetics to investigate how this synergy occurs and elucidate the underlying reaction mechanisms. Our results [...] Read more.
Glutathione (GSH) and phenols are well-known antioxidants, and previous research has suggested that their combination can enhance antioxidant activity. In this study, we used Quantum Chemistry and computational kinetics to investigate how this synergy occurs and elucidate the underlying reaction mechanisms. Our results showed that phenolic antioxidants could repair GSH through sequential proton loss electron transfer (SPLET) in aqueous media, with rate constants ranging from 3.21 × 106 M−1 s−1 for catechol to 6.65 × 108 M−1 s−1 for piceatannol, and through proton-coupled electron transfer (PCET) in lipid media with rate constants ranging from 8.64 × 106 M−1 s−1 for catechol to 5.53 × 107 M−1 s−1 for piceatannol. Previously it was found that superoxide radical anion (O2•−) can repair phenols, thereby completing the synergistic circle. These findings shed light on the mechanism underlying the beneficial effects of combining GSH and phenols as antioxidants. Full article
(This article belongs to the Special Issue Oxidative Stress and Antioxidants in Computational Chemistry)
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