Mechanism Of Adduct Formation Research Articles

Primary Antioxidant Power and Mpro SARS-CoV-2 Non-Covalent Inhibition Capabilities of Miquelianin.

The antioxidant power of quercetin-3-O-glucuronide (miquelianin) has been studied, at the density functional level of theory, in both lipid-like and aqueous environments. In the aqueous phase, the computed pKa equilibria allowed the identification of the neutral and charged species present in solution that can react with the ⋅OOH radical. The Hydrogen Atom Transfer (HAT), Single Electron Transfer (SET) and Radical Adduct Formation (RAF) mechanisms were considered, and the individual, total and fraction corrected rate constants were obtained. Potential non-covalent inhibition of Mpro from SARS-CoV-2 by miquelianin has been also evaluated.

Effect of hydroxyl position on antioxidant ability of hydroxycoumarin derivatives: A theoretical investigation

Effect of the OH group position on the antioxidant ability of hydroxycoumarin derivatives (HOC) was investigated by quantum chemical computation. Frontier molecular orbitals, molecular electrostatic potential, and thermodynamic parameters were analyzed in detail. The results indicate that 3-HOC, 6-HOC, and 7-HOC exhibit as the best reactants with free radicals through analysis of global reactivity descriptor values, meanwhile H (in OH groups) of 4-HOC, 5-HOC, 6-HOC, and 7-HOC molecules are the most preferable sites for nucleophilic attacks. Besides, thermodynamic and kinetic studies reveal hydrogen atomic transfer is the primary mechanism when hydroxycoumarin derivatives react with HOO• free radical in the gas phase and pentyl ethanoate. Hydrogen atomic transfer products account for over 97 % of the total products of hydrogen atomic transfer and radical adduct formation mechanisms. According to the study, 6-HOC is the most effective scavenger of free radicals when compared to other derivatives, with a rate constant of 1.38 × 104 M−1s−1 in the gas phase and 6.5 × 103 M−1s−1 in pentyl ethanoate. The interaction of O20∙∙∙H21 in the transition state of 6-HOC is crucial in stabilizing its structure. This finding suggests that 6-HOC can be a potential candidate for developing antioxidants for various applications in the medical and industrial fields. The results of this study provide valuable insights into the mechanisms by which antioxidants can scavenge free radicals and protect against oxidative stress.

Radical adducts formation mechanism of CH3CO2∙ and CH3CO3∙ realized decomposition of chitosan by plasma catalyzed peracetic acid

High-molecular-weight chitosan has limited applications due to unsatisfactory solubility and hydrophilicity. Discharge plasma coupled with peracetic acid (PAA) oxidation (“plasma+PAA”) realized fast depolymerization of high-molecular-weight chitosan in this study. The molecular weight of chitosan rapidly declined to 81.1 kDa from initial 682.5 kDa within 60 s of “plasma+PAA” treatment, and its reaction rate constant was 12-fold higher than single plasma oxidation. Compared with 1O2, ∙CH3, CH3O2·, and O2∙−, CH3CO2∙ and CH3CO3∙ played decisive roles in the chitosan depolymerization in the plasma+PAA system through mechanisms of radical adduct formation. The attacks of CH3CO2∙ and CH3CO3∙ destroyed the β-(1,4) glycosidic bonds and hydrogen bonds of chitosan, leading to generation of low-molecular-weight chitosan; the main chain structure of chitosan was not changed during the depolymerization process. Furthermore, the generated low-molecular-weight chitosan exhibited greater antioxidant activities than original chitosan. Overall, this study revealed the radical adduct formation mechanisms of CH3CO2∙ and CH3CO3∙ for chitosan decomposition, providing an alternative for fast depolymerization of high-molecular-weight chitosan.

An unprecedented free radical mechanism for the formation of DNA adducts by the carcinogenic N-sulfonated metabolite of aristolochic acids

The carcinogenicity of aristolochic acids (AAs) has been attributed mainly to the formation of stable DNA-aristolactam (DNA-AL) adducts by its reactive N-sulfonated metabolite N-sulfonatooxyaristolactam (N–OSO3--AL). The most accepted mechanism for such DNA-AL adduct formation is via the postulated but never unequivocally-confirmed aristolactam nitrenium ion. Here we found that both sulfate radical and two ALI-derived radicals (N-centered and C-centered spin isomers) were produced by N–OSO3--ALI, which were detected and unequivocally identified by complementary applications of ESR spin-trapping, HPLC-MS coupled with deuterium-exchange methods. Both the formation of the three radical species and DNA-ALI adducts can be significantly inhibited (up to 90%) by several well-known antioxidants, typical radical scavengers, and spin-trapping agents. Taken together, we propose that N–OSO3--ALI decomposes mainly via a new N–O bond homolysis rather than the previously proposed heterolysis pathway, yielding reactive sulfate and ALI-derived radicals, which are together and in concert responsible for forming DNA-ALI adducts. This study presents strong and direct evidence for the production of free radical intermediates during N–OSO3--ALI decomposition, providing an unprecedented free radical perspective and conceptual breakthrough, which can better explain and understand the molecular mechanism for the formation of DNA-AA adducts, the carcinogenicity of AAs and their potential prevention.

Radical Scavenging Mechanisms of 1-Arylhydrazone Benzimidazole Hybrids with Neuroprotective Activity.

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.

Theoretical and Experimental Investigation of the Antioxidation Mechanism of Loureirin C by Radical Scavenging for Treatment of Stroke

Recent pharmacological studies have shown that dragon's blood has an anti-cerebral ischemia effect. Loureirin C (LC), a kind of dihydrochalcone compound in dragon's blood, is believed to be play an important role in the treatment of ischemia stroke, but fewer studies for LC have been done. In this paper, we report the first experimental and theoretical studies on the antioxidation mechanism of LC by radical scavenging. The experimental studies show that LC has almost no effect on cell viability under 15 μM for the SH-SY5Y cells without any treatments. For the SH-SY5Y cells with oxygen and glucose deprivation-reperfusion (OGD/R) treatment, LC increased the viability of SH-SY5Y cells. The results of 2',7'-Dichlorodihydrofluorescein diacetate (DCFH-DA) and MitoSox Red experiments indicate that LC is very efficient in inhibiting the generation of the intracellular/mitochondrial reactive oxygen species (ROS) or removing these two kinds of generated ROS. The density functional theory (DFT) calculations allowed us to elucidate the antioxidation mechanisms of LC. Fukui function analysis reveals the radical scavenging of LC by hydrogen abstraction mechanism, the complex formation by e-transfer, and radical adduct formation (RAF) mechanism. Among the H-abstraction, the complex formation by e-transfer, and radical adduct formation (RAF) reactions on LC, the H-abstraction at O-H35 position by OH• is favorable with the smallest energy difference between the product and two reactants of the attack of OH• to LC of -0.0748 Ha. The bond dissociation enthalpies (BDE), proton affinities (PA), ionization potential (IP), proton dissociation enthalpy (PDE), and electron transfer enthalpy (ETE) were calculated to determine thermodynamically preferred reaction pathway for hydrogen abstraction mechanism. In water, IP and the lowest PDE value at O3-H35 position are lower than the lowest BDE value at O3-H35 position; 41.8986 and 34.221 kcal/mol, respectively, indicating that SEPT mechanism is a preferred one in water in comparison with the HAT mechanism. The PA value of O3-H35 of LC in water is -17.8594 kcal/mol, thus the first step of SPLET would occur spontaneously. The minimum value of ETE is higher than the minimum value of PDE at O3-H35 position and IP value, 14.7332 and 22.4108 kcal/mol, respectively, which suggests that the SEPT mechanism is a preferred one in water in comparison with the SPLET mechanism. Thus, we can draw a conclusion that the SEPT mechanism of is the most favorite hydrogen abstraction mechanism in water, and O-H35 hydroxyl group has the greatest ability to donate H-atoms.

Mechanistic aspects of reactive metabolite formation in clomethiazole catalyzed biotransformation by cytochrome P450 enzymes.

Clomethiazole (CLM), a sedative and anticonvulsant drug, is commonly employed for the treatment of alcohol withdrawal syndromebecause it suppresses cytochrome P450 (P450) activity associated with the generation of free radicals and liver damage. The catalyzed biotransformation of thiazole-containing drugs by P450 is known to afford reactive metabolites. These metabolites can alter the biological functions of macromolecules and result in toxicity and adverse drug interactions. Multitargeted molecular modeling and quantum chemical DFT calculations were performed to explore the binding modes and molecular mechanisms underlying the mechanism-based inactivation (MBI) of P450 by CLM. The mechanistic details associated with reactive metabolite formation from further metabolic processes were extensively assessed. Seven possible routes were proposed for CLM-P450 biotransformation including CLM hydroxylation, sulfoxidation, N-oxidation, CN epoxidation (oxaziridine formation), and CC epoxidation. The results revealed a degree of preference for the C-N epoxidation pathway because of the low energy requirements of its rate-determining step (8.74 and 10.07 kcal mol-1 for LS and HS states, respectively). A kinetic competition for the CLM-methyl hydroxylation pathway was detected because the H-abstraction energy barrier was relatively comparable to the thermodynamically prevailing oxaziridine formation rate-determining step (12.58 and 14.52 kcal mol-1 for quartet and doublet states, respectively). Our studies assessed the mechanisms of covalent nucleophilic epoxide adduct formation through nucleophilic addition, hydrolysis of epoxidation products, and nonenzymatic degradation. CLM was shown to display P450-inhibitory activity by forming covalent adducts rather than further metabolization to reactive metabolites. The outcomes of molecular docking allowed assessing the binding profile of CLM with three human P450 isozymes, namely, CYP2E1, CYP3A4, and CYP2D6.

Elucidation of reactive oxygen species scavenging pathways of norbergenin utilizing DFT approaches.

Bergenin is a polyphenolic compound that contains isocoumarin skeletal derived from C-glycosylated 4-O-methylgallic acid. The biological activities of this compound and its derivatives are quite diverse. Recent studies reveal neuroprotective effects in vitro and in vivo in Alzheimer's. Norbergenin is a demethylated form of bergenin, known for better antioxidant capacity and associated with neuroprotective properties through oxidative stress inhibition. This study focused on investigating the scavenging mechanism of norbergenin with the •OH, •OOH, and as a radical model under physiological and lipid environments. The thermodynamic and kinetic parameters of the hydrogen transfer (HT), single electron transfer (SET), sequential proton lost-electron transfer (SPLET) and radical adduct formation (RAF) mechanisms were determined theoretically by the density functional theory (DFT) at M06-2X/6-311 + + G(d,p) level of theory. Based on the computational results, this compound has proved as an excellent •OOH and •OH scavenger under physiological conditions better than Trolox and vitamin C, whereas its radical demonstrated as an efficient scavenger.

Antioxidant activity of caffeic acid: thermodynamic and kinetic aspects on the oxidative degradation pathway

Caffeic acid is a phenolic secondary metabolite from plants, which is known for its antioxidant properties. The effective mitigation of methanol-induced oxidative stress by caffeic acid depends on the direct radical scavenging as well as the formation of new metabolites via oxidative degradation. Herein, thermodynamic and kinetic aspects of the oxidative degradation pathway of caffeic acid in the presence of radical CH3O• and its isomer, •CH2OH are discussed for the first time, employing density functional theory (DFT). The direct radical scavenging activity of caffeic acid against these radicals is verified via hydrogen atom transfer (HAT) and radical adduct formation (RAF) mechanisms. HAT is predicted to be more feasible than RAF mechanism as per the computed data. Additionally, energetic details of the proposed oxidative degradation pathway of radical adduct intermediates toward the formation of a cyclic metabolite is analyzed. Kinetic studies indicated a significant tunneling contribution to the H abstraction pathways having high activation barriers. Further, our results imply that the newly formed metabolites exhibit comparable antioxidant activity with that of caffeic acid.

Retrospective detection for V-type OPNAs exposure via phosphonylation and disulfide adducts in albumin

Organophosphorus nerve agents (OPNAs) that damage the central nervous system by inhibiting acetylcholinesterase activity, pose severe threats to human health and life security. Reliable biomarkers that quickly and accurately detect OPNAs exposure are urgently needed to help diagnose quickly and treat in time. Albumins that covalently bind to OPNAs could serve as important targets for retrospective verification of OPNAs exposure. The goal of this study is to explore the potential biomarkers in albumins with high reactivity and good stability and expand the group of potential biomarkers in different species for detecting the exposure of V-type OPNAs including O-ethyl S-(2-(diisopropylamino)ethyl) methylphosphonothioate (VX), O-isobutyl S-(2(diethylamino)ethyl) methylphosphonothioate (VR), and O-butyl S-(2-(diethylamino)ethyl) methylphosphonothioate (Vs). Taking human serum albumin (HSA), bovine serum albumin (BSA) and rabbit serum albumin (RSA) as the research objectives, multiple active sites including phosphonylation and disulfide adduct sites were observed in albumins from different species. Numerous phosphonylation sites labeled by all agents in one type of albumin were found. Among the different species, four shared phosphonylation sites with high reactivity include K499, K549, K249, and Y108. In addition, Y108 on ETY*GEMADCCAK, Y287 on Y*ICENQDSISSK, Y377 on TY*ETTLEK and Y164 on YLY*EIAR in HSA were stably phosphonylated by all agents in gradient concentration, making them stable and suitable potential biomarkers for V-type OPNAs exposure. Notably, Y108 on ETY*GEMADCCAK in HSA, on DTY*GDVADCCEK in RSA, and on ETY*GDMADCCEK in BSA were highly reactive to all V-type agents, regardless of species. It was also successfully labeled in HSA exposed to class V agents in gradient concentration. Y108 is expected to be used to screen and identify the exposure of V-type agents in the retrospective research. Disulfide adducts sites, consisted of four sites in HSA and two sites in BSA were also successfully labeled by V-type agents, and characteristic ion fragments from these disulfide adducts were also identified by secondary mass spectrometry. Molecular simulation of the stably modified sites were conducted to discover the promoting factors of covalent adduct formation, which help further clarify formation mechanism of albumin adducts at active sites.

Metabolism and DNA Adduct Formation of Tobacco-Specific N-Nitrosamines.

The tobacco-specific N-nitrosamines 4-(N-nitrosomethylamino)-1-(3-pyridyl)-1-butanone (NNK) and N′-nitrosonornicotine (NNN) always occur together and exclusively in tobacco products or in environments contaminated by tobacco smoke. They have been classified as “carcinogenic to humans” by the International Agency for Research on Cancer. In 1998, we published a review of the biochemistry, biology and carcinogenicity of tobacco-specific nitrosamines. Over the past 20 years, considerable progress has been made in our understanding of the mechanisms of metabolism and DNA adduct formation by these two important carcinogens, along with progress on their carcinogenicity and mutagenicity. In this review, we aim to provide an update on the carcinogenicity and mechanisms of the metabolism and DNA interactions of NNK and NNN.

UV Photolysis Study of Para-Aminobenzoic Acid Using Parahydrogen Matrix Isolated Spectroscopy

Many sunscreen chemical agents are designed to absorb UVB radiation (and in some cases UVA) to protect the skin from sunlight, but UV absorption is often accompanied by photodissociation of the chemical agent, which may reduce its UV absorption capacity. Therefore, it is important to understand the photochemical processes of sunscreen agents. In this study, the photolysis of para-aminobenzoic acid (PABA), one of the original sunscreen chemical agents, at three different UV ranges (UVA: 355 nm, UVB: >280 nm, and UVC: 266 nm and 213 nm) was investigated using parahydrogen (pH2) matrix isolation Fourier-Transform Infrared (FTIR) Spectroscopy. PABA was found to be stable under UVA (355 nm) irradiation, while it dissociated into 4-aminylbenzoic acid (the PABA radical) through the loss of an amino hydrogen atom under UVB (>280 nm) and UVC (266 nm and 213 nm) irradiation. The radical production supports a proposed mechanism of carcinogenic PABA-thymine adduct formation. The infrared spectrum of the PABA radical was analyzed by referring to quantum chemical calculations, and two conformers were found in solid pH2. The PABA radicals were stable in solid pH2 for hours after irradiation. The trans-hydrocarboxyl (HOCO) radical was also observed as a minor secondary photoproduct of PABA following 213 nm irradiation. This work shows that pH2 matrix isolation spectroscopy is effective for photochemical studies of sunscreen agents.

Sodium adduct formation with graph-based machine learning can aid structural elucidation in non-targeted LC/ESI/HRMS

Non-targeted screening with LC/ESI/HRMS aims to identify the structure of the detected compounds using their retention time, exact mass, and fragmentation pattern. Challenges remain in differentiating between isomeric compounds. One untapped possibility to facilitate identification of isomers relies on different ionic species formed in electrospray. In positive ESI mode, both protonated molecules and adducts can be formed; however, not all isomeric structures form the same ionic species. The complicated mechanism of adduct formation has hindered the use of this molecular characteristic in the structural elucidation in non-targeted screening. Here, we have studied the adduct formation for 94 small molecules with ion mobility spectra and compared collision cross-sections of the respective ions. Based on the results we developed a fast support vector machine classifier with polynomial kernels for accurately predicting the sodium adduct formation in ESI/HRMS. The model is trained on five independent data sets from different laboratories and uses the graph-based connectivity of functional groups and PubChem fingerprints to predict the sodium adduct formation in ESI/HRMS. The validation of the model showed an accuracy of 74.7% (balanced accuracy 70.0%) on a dataset from an independent laboratory, which was not used in the training of the model. Lastly, we applied the classification algorithm to the SusDat database by NORMAN network to evaluate the proportion of isomeric compounds that could be distinguished based on predicted sodium adduct formation. It was observed that sodium adduct formation probability can provide additional selectivity for about one quarter of the exact masses and, therefore, shows practical utility for structural assignment in non-targeted screening.

Theoretical Calculation on the Reaction Mechanisms, Kinetics and Toxicity of Acetaminophen Degradation Initiated by Hydroxyl and Sulfate Radicals in the Aqueous Phase.

The •OH and SO4•− play a vital role on degrading pharmaceutical contaminants in water. In this paper, theoretical calculations have been used to discuss the degradation mechanisms, kinetics and ecotoxicity of acetaminophen (AAP) initiated by •OH and SO4•−. Two significant reaction mechanisms of radical adduct formation (RAF) and formal hydrogen atom transfer (FHAT) were investigated deeply. The results showed that the RAF takes precedence over FHAT in both •OH and SO4•− with AAP reactions. The whole and branched rate constants were calculated in a suitable temperature range of 198–338 K and 1 atm by using the KiSThelP program. At 298 K and 1 atm, the total rate constants of •OH and SO4•− with AAP were 3.23 × 109 M−1 s−1 and 4.60 × 1010 M−1 s−1, respectively, considering the diffusion-limited effect. The chronic toxicity showed that the main degradation intermediates were harmless to three aquatic organism, namely, fish, daphnia, and green algae. From point of view of the acute toxicity, some degradation intermediates were still at harmful or toxic level. These results provide theoretical guidance on the practical degradation of AAP in the water.

Anticancer activity and cell death mechanism of Pt(II) complexes: Their in vitro bio-transformation to Pt(II)-DNA adduct formation and BSA binding study by spectroscopic method

Pt(II) complex cis-[Pt(PEA)(OH2)2] X2, C-2 (where, PEA = 2-Pyridylethylamine and X = ClO4− or NO3–) was synthesized by hydrolysis of cis-[Pt(PEA)Cl2] C-1. Glutathione (GSH) and DL-penicilamine (DL-pen) substituted complexes cis-[Pt(PEA)(GSH)],C-3 and cis-[Pt(PEA)DL-pen)]X C-4 were synthesized and characterized by spectroscopic methods. Kinetic studies were traced on complex C-2 with the thiols, GSH and DL-pen. Pt(II)-Sulfur adduct formation mechanisms of the substituted products C-3 and C-4 were established from the kinetic investigation. At pH 4.0, C-2 - thiols interactions follow two consecutive steps: the first step is dependent, and the second is independent of [thiol]. The association equilibrium constant (KE), substitution rate constants for both steps (k1 & k2), and activation parameters (ΔH‡ and ΔS‡) have been assessed to propose the mechanism. Agarose gel electrophoresis mobilization pattern of DNA with complexes was performed to visualize the interaction nature. CT-DNA and BSA binding activities of the complexes have been executed by electronic, fluorescence spectroscopy, and viscometric titration methods. Evaluation of thermodynamic parameters (ΔH0, ΔS0, and ΔG0) from BSA binding constants was executed to propose the driving forces of interaction between these species. A molecular docking study was performed to evaluate the binding mode of complexes with BDNA strands. Anticancer activity of the complexes C-1 to C-4 was explored on both A549 and HEp-2 cell lines, compared with approved anticancer drugs cisplatin, carboplatin, and oxaliplatin. All these complexes were tested by NBT assay on normal cell line skeletal muscle cells (L6 myotubes) to observe the adverse effects compared to recognized anticancer medications. The ultimate aim is to explore the role of anticancer agents on cell death mechanism, which has been performed by flow-cytometer on HEp-2 cell lines.

New Insight into the Protein‐based Cofactor of Mycobacterium tuberculosis KatG: Toward Better Understanding an Unusual Catalase Mechanism

Catalase-peroxidases (KatG) has been engineered by nature to exhibit dual functionalism of catalase and peroxidase mechanisms, serving to protect the organisms that carry it against peroxide-dependent oxidative damage. Despite bearing no resemblance to monofunctional (i.e., typical) catalases, KatGs have robust catalase activity due at least in part to a novel covalent linkage between three side chains (by Mycobacterium tuberculosis KatG [MtKatG] numbering, Met-255, Tyr-229, and Trp-107) (MYW). This MYW cofactor redox cycles between its radical (MYW•+) and fully covalent states, enabling KatG to leverage heme intermediates for catalatic O2 production. However, the molecular mechanism by which the adduct is formed and how this unique structure contributes to overall catalytic mechanism of KatG is yet to be explored. Here, optical stopped-flow spectrophotometry, rapid freeze-quench EPR spectroscopy and mutagenesis have been used to investigate the mechanism of MYW adduct formation. We have expressed and purified MtKatG lacking heme and reconstituted with the cofactor after purification. This produces KatG lacking the MYW crosslink, allowing us to monitor its formation upon reaction with peroxides. Under multiple-turnover conditions using H2O2, optical stopped-flow experiments showed an initial appearance of a high-valent ferryl-like (FeIV=O) intermediate instead of the typical FeIII-O2•- -like steady-state intermediate of KatG's catalase activity. Nevertheless, in contrast to catalase-negative canonical heme peroxidases, full catalase H2O2 decomposition did emerge, returning the enzyme to its FeIII state. EPR experiments revealed that an admixture of radical species appeared before MYW cofactor radical intermediate, suggestive of the preferred site of crosslink initiation. In addition to that, KatG variants lacking the MYW adduct (M255I, Y229F and W107F) were also constructed, expressed, purified, and reconstituted with heme. Stopped flow and UV-vis analysis of these variants showed disrupted catalase activities and incomplete catalatic turnover. These observations strongly suggest that, these distal side residues actively participate in intramolecular electron transfer, thereby fulfilling a mechanistic role in KatG catalase mechanism. Our reconstituted KatG proteins may permit investigation of radical transfer reactions leading to formation of KatG's novel MYW cofactor as well as the influence of other protein radical transfer reactions on that process.

Antiradical Activity of Beetroot (Beta vulgaris L.) Betalains.

Flavonoids, phenolic acids, and anthocyanidins are widely studied polyphenolics owing to their antiradical activity. Recently, beetroot dyes have drawn an attention as possible radical scavengers, but scant information can be found on this topic. In this study selected compounds were investigated using computational chemistry methods. Implicit water at physiological pH was chosen as the environment of interest. Betalains’ dissociation process and electronic structure were examined, as well as the reactivity in six pathways against some common radicals, such as hydroxyl, hydroperoxide, superoxide, and nitric oxide. The study showed that all carboxyl groups are dissociated in the given conditions. The dissociation process impacts the electronic structure, which has consequences for the overall activity. Highly stabilized conjugated structures favor the electron–accepting type of scavenging reactions, primarily by a radical adduct formation mechanism. Betanidin and indicaxanthin were found to be the most promising of the compounds studied. Nevertheless, the study established the role of betalains as powerful antiradical dietary agents.

Identification of the DPPH radical scavenging reaction adducts of ferulic acid and sinapic acid and their structure-antioxidant activity relationship

Phenolic acids may provide health benefits as antioxidants and have potential applications in food and pharmaceutical science. The antioxidant activity and mechanism of sinapic acid (SA), ferulic acid (FA), disinapic acids (DSA) and diferulic acids (DFA) were evaluated by experiments and theoretical calculation. DSA-1–3 and DFA-1–3 were synthesized and identified by HPLC–MS and nuclear magnetic resonance. DSA-1 and DFA-1 (8-8′-dilactone dimers) were identified as adducts in the SA-/FA-DPPH system for the first time, which confirmed the mechanism of radical adduct formation. The orders of their antioxidant activities by DPPH and FRAP assays were consistent with theoretical calculation based on density functional theory, e.g., DSA-3 > DSA-2 > SA > DSA-1, DFA-3 > DFA-2 > FA > DFA-1, and SA group > FA group. These phenolic acids were more likely to occur the HAT mechanism in the gas phase, while occur SETPT and SPLET mechanisms in polar solvents. Moreover, the active phenolic hydroxyls of DSA-2 (4-OH) and DFA-2 (4′-OH) were opposite according to the bond dissociation energy and HOMO distribution. Methoxyl on the benzene rings may play a crucial role in the formation of DSA and DFA, as well as the antioxidant activity and phenolic hydroxyl active center.

Investigation of 2′-Deoxyadenosine-Derived Adducts Specifically Formed in Rat Liver and Lung DNA by N′-Nitrosonornicotine Metabolism

The International Agency for Research on Cancer has classified the tobacco-specific nitrosamines N'-nitrosonornicotine (NNN) and 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) as "carcinogenic to humans" (Group 1). To exert its carcinogenicity, NNN requires metabolic activation to form reactive intermediates which alkylate DNA. Previous studies have identified cytochrome P450-catalyzed 2'-hydroxylation and 5'-hydroxylation of NNN as major metabolic pathways, with preferential activation through the 5'-hydroxylation pathway in some cultured human tissues and patas monkeys. So far, the only DNA adducts identified from NNN 5'-hydroxylation in rat tissues are 2-[2-(3-pyridyl)-N-pyrrolidinyl]-2'-deoxyinosine (Py-Py-dI), 6-[2-(3-pyridyl)-N-pyrrolidinyl]-2'-deoxynebularine (Py-Py-dN), and N6-[4-hydroxy-1-(pyridine-3-yl)butyl]-2'-deoxyadenosine (N6-HPB-dAdo) after reduction. To expand the DNA adduct panel formed by NNN 5'-hydroxylation and identify possible activation biomarkers of NNN metabolism, we investigated the formation of dAdo-derived adducts using a new highly sensitive and specific liquid chromatography-nanoelectrospray ionization-high-resolution tandem mass spectrometry method. Two types of NNN-specific dAdo-derived adducts, N6-[5-(3-pyridyl)tetrahydrofuran-2-yl]-2'-deoxyadenosine (N6-Py-THF-dAdo) and 6-[2-(3-pyridyl)-N-pyrrolidinyl-5-hydroxy]-2'-deoxynebularine (Py-Py(OH)-dN), were observed for the first time in calf thymus DNA incubated with 5'-acetoxyNNN. More importantly, Py-Py(OH)-dN was also observed in relatively high abundance in the liver and lung DNA of rats treated with racemic NNN in the drinking water for 3 weeks. These new adducts were characterized using authentic synthesized standards. Both NMR and MS data agreed well with the proposed structures of N6-Py-THF-dAdo and Py-Py(OH)-dN. Reduction of Py-Py(OH)-dN by NaBH3CN led to the formation of Py-Py-dN both in vitro and in vivo, which was confirmed by its isotopically labeled internal standard [pyridine-d4]Py-Py-dN. The NNN-specific dAdo adducts Py-THF-dAdo and Py-Py(OH)-dN formed by NNN 5'-hydroxylation provide a more comprehensive understanding of the mechanism of DNA adduct formation by NNN.

An insight into the interaction between α-ketoamide- based inhibitor and coronavirus main protease: A detailed in silico study

The search for therapeutic drugs that can neutralize the effects of COVID-2019 (SARS-CoV-2) infection is the main focus of current research. The coronavirus main protease (Mpro) is an attractive target for anti-coronavirus drug design. Further, α-ketoamide is proved to be very effective as a reversible covalent-inhibitor against cysteine proteases. Herein, we report on the non-covalent to the covalent adduct formation mechanism of α-ketoamide-based inhibitor with the enzyme active site amino acids by QM/SQM model (QM = quantum mechanical, SQM = semi-empirical QM). To uncover the mechanism, we focused on two approaches: a concerted and a stepwise fashion. The concerted pathway proceeds via deprotonation of the thiol of cysteine (here, Cys145 SγH) and simultaneous reversible nucleophilic attack of sulfur onto the α-ketoamide warhead. In this work, we propose three plausible concerted pathways. On the contrary, in a traditional two-stage pathway, the first step is proton transfer from Cys145 SγH to His41 Nδ forming an ion pair, and consecutively, in the second step, the thiolate ion attacks the α-keto group to form a thiohemiketal. In this reaction, we find that the stability of the tetrahedral intermediate oxyanion/hydroxyl group plays an important role. Moreover, as the α-keto group has two faces Si or Re for the nucleophilic attack, we considered both possibilities of attack leading to S- and R-thiohemiketal. We computed the structural, electronic, and energetic parameters of all stationary points including transition states via ONIOM and pure DFT method. Additionally, to characterize covalent, weak noncovalent interaction (NCI) and hydrogen-bonds, we applied NCI-reduced density gradient (NCI-RDG) methods along with Bader's Quantum Theory of Atoms-in-Molecules (QTAIM) and natural bonding orbital (NBO) analysis