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In silico analysis of the antidepressant fluoxetine and similar drugs as inhibitors of the human protein acid sphingomyelinase: a related SARS-CoV-2 inhibition pathway. J Biomol Struct Dyn 2023; 41:9562-9575. [PMID: 36447407 DOI: 10.1080/07391102.2022.2148124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 10/29/2022] [Indexed: 12/05/2022]
Abstract
Acid Sphingomyelinase (ASM) is a human phosphodiesterase that catalyzes the metabolism of sphingomyelin (SM) to ceramide and phosphocholine. ASM is involved in the plasma membrane cell repair and is associated with the lysosomal inner lipid membrane by nonbonding interactions. The disruption of those interaction would result in ASM release into the lysosomal lumen and consequent degradation of its structure. Furthermore, SARS-CoV-2 infection has been linked with ASM activation and with a ceramide domain formation in the outer leaflet of the plasma membrane that is thought to be crucial for the viral particles recognition by the host cells. In this study, we have explored in silico the behavior of fluoxetine and related drugs as potential inhibitors of ASM. Theoretically, these drugs would be able to overpass lysosomal membrane and reach the interactions that sustain ASM structure, breaking them and inhibiting the ASM. The analyses of docking data indicated that fluoxetine allocated mainly in the N-terminal saposin domain via nonbonding interactions, mostly of hydrophobic nature. Similar results were obtained for venlafaxine, citalopram, atomoxetine, nisoxetine and fluoxetine's main metabolite norfluoxetine. In conclusion, it was observed that the saposin allocation may be a good indicative of the drugs inhibition mechanism, once this domain is responsible for the binding of ASM to lysosomal membrane and some of those drugs have previously been reported to inhibit the phosphodiesterase by releasing its structure in the lysosomal lumen. Our MD data also provides some insight about natural ligand C18 sphingomyelin conformations on saposin.Communicated by Ramaswamy H. Sarma.
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Antioxidant Chimeric Molecules: Are Chemical Motifs Additive? The Case of a Selenium-Based Ligand. Int J Mol Sci 2023; 24:11797. [PMID: 37511560 PMCID: PMC10380222 DOI: 10.3390/ijms241411797] [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: 07/02/2023] [Revised: 07/18/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
We set up an in silico experiment and designed a chimeric compound integrating molecular features from different efficient ROS (Reactive Oxygen Species) scavengers, with the purpose of investigating potential relationships between molecular structure and antioxidant activity. Furthermore, a selenium centre was inserted due to its known capacity to reduce hydroperoxides, acting as a molecular mimic of glutathione peroxidase; finally, since this organoselenide is a precursor of a N-heterocyclic carbene ligand, its Au(I) carbene complex was designed and examined. A validated protocol based on DFT (Density Functional Theory) was employed to investigate the radical scavenging activity of available sites on the organoselenide precursor ((SMD)-M06-2X/6-311+G(d,p)//M06-2X/6-31G(d)), as well as on the organometallic complex ((SMD)-M06-2X/SDD (Au), 6-311+G(d,p)//ZORA-BLYP-D3(BJ)/TZ2P), considering HAT (Hydrogen Atom Transfer) and RAF (Radical Adduct Formation) regarding five different radicals. The results of this case study suggest that the antioxidant potential of chemical motifs should not be considered as an additive property when designing a chimeric compound, but rather that the relevance of a molecular topology is derived from a chemical motif combined with an opportune chemical space of the molecule. Thus, the direct contributions of single functional groups which are generally thought of as antioxidants per se do not guarantee the efficient radical scavenging potential of a molecular species.
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Indole-5,6-quinones display hallmark properties of eumelanin. Nat Chem 2023:10.1038/s41557-023-01175-4. [PMID: 37037912 DOI: 10.1038/s41557-023-01175-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 03/07/2023] [Indexed: 04/12/2023]
Abstract
Melanins are ubiquitous biopolymers produced from phenols and catechols by oxidation. They provide photoprotection, pigmentation and redox activity to most life forms, and inspire synthetic materials with desirable optical, electronic and mechanical properties. The chemical structures of melanins remain elusive, however, creating uncertainty about their roles, and preventing the design of synthetic mimics with tailored properties. Indole-5,6-quinone (IQ) has been implicated as a biosynthetic intermediate and structural subunit of mammalian eumelanin pigments, but its instability has prevented its isolation and unambiguous characterization. Here we use steric shielding to stabilize IQ and show that 'blocked' derivatives exhibit eumelanin's characteristic ultrafast nonradiative decay and its ability to absorb light from the ultraviolet to the near-infrared. These new compounds are also redox-active and a source of paramagnetism, emulating eumelanin's unique electronic properties, which include persistent radicals. Blocked IQs are atomistically precise and tailorable molecules that can offer a bottom-up understanding of emergent properties in eumelanin and have the potential to advance the rational design of melanin-inspired materials.
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Diphenyl Diselenide and SARS-CoV-2: in silico Exploration of the Mechanisms of Inhibition of Main Protease (M pro) and Papain-like Protease (PL pro). J Chem Inf Model 2023; 63:2226-2239. [PMID: 36952618 PMCID: PMC10091420 DOI: 10.1021/acs.jcim.3c00168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
The SARS-CoV-2 pandemic has prompted global efforts to develop therapeutics. The main protease of SARS-CoV-2 (Mpro) and the papain-like protease (PLpro) are essential for viral replication and are key targets for therapeutic development. In this work, we investigate the mechanisms of SARS-CoV-2 inhibition by diphenyl diselenide (PhSe)2 which is an archetypal model of diselenides and a renowned potential therapeutic agent. The in vitro inhibitory concentration of (PhSe)2 against SARS-CoV-2 in Vero E6 cells falls in the low micromolar range. Molecular dynamics (MD) simulations and density functional theory (DFT) calculations [level of theory: SMD-B3LYP-D3(BJ)/6-311G(d,p), cc-pVTZ] are used to inspect non-covalent inhibition modes of both proteases via π-stacking and the mechanism of covalent (PhSe)2 + Mpro product formation involving the catalytic residue C145, respectively. The in vitro CC50 (24.61 μM) and EC50 (2.39 μM) data indicate that (PhSe)2 is a good inhibitor of the SARS-CoV-2 virus replication in a cell culture model. The in silico findings indicate potential mechanisms of proteases' inhibition by (PhSe)2; in particular, the results of the covalent inhibition here discussed for Mpro, whose thermodynamics is approximatively isoergonic, prompt further investigation in the design of antiviral organodiselenides.
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Radical Scavenging Potential of Ginkgolides and Bilobalide: Insight from Molecular Modeling. Antioxidants (Basel) 2023; 12:antiox12020525. [PMID: 36830083 PMCID: PMC9952587 DOI: 10.3390/antiox12020525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/12/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
The reactive oxygen species (ROS) scavenging capacities of ginkgolides and bilobalide, which are the peculiar constituents of the extract of Ginkgo biloba, are investigated in silico (level of theory: (SMD)-M06-2X/6-311+G(d,p)//M06-2X/6-31G(d)). Unlike other popular antioxidant natural substances, the carbon backbones of these compounds are entirely aliphatic and exclusively single C-C bonds are present. The selectivity for alkoxyl radicals via hydrogen-atom transfer (HAT) is assessed; importantly, the scavenging of peroxyl radicals is also possible from a peculiar site, here labeled C10 both for ginkgolides and bilobalide. The energetics are described in detail, and the analysis discloses that the studied compounds are powerful scavengers, with thermodynamic and kinetic properties similar to those of Trolox and melatonin, and that, in addition, they display selectivity for peroxyl radicals. These are all chemical-reactivity features contributing to the therapeutic action of the extract of G. biloba.
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Swine manure treatment technologies as drivers for circular economy in agribusiness: A techno-economic and life cycle assessment approach. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159494. [PMID: 36257411 DOI: 10.1016/j.scitotenv.2022.159494] [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: 07/13/2022] [Revised: 09/27/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
Anaerobic digestion has been employed as a technology capable of adding value to waste coupled with environmental impact mitigation. However, many issues need to be elucidated to ensure the systems viability based on this technology. In this sense, the present study evaluated technically, environmentally, and economically, four configurations of swine waste treatment systems focused on the promotion of decarbonization and circularity of the swine chain. For this, a reference plant, based on a compact treatment process named SISTRATES® (Portuguese acronym for swine effluent treatment system) was adopted to serve as a model for comparison and validation. The results showed the importance of prioritization of the energy recuperation routes through anaerobic digestion, providing increased economic benefits and minimizing environmental damage. Thus, the SISTRATES® configuration was the one that presented the best designs in a circular context, maximizing the recovery of energy and nutrients, along with the reduction of greenhouse gas emissions, ensuring the sustainability of the pig production chain.
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Thiol modifier effects of diphenyl diselenides: insight from experiment and DFT calculations. NEW J CHEM 2023. [DOI: 10.1039/d2nj05976b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
A combination of spectroscopic, chromatographic and computational approaches was employed to investigate the reaction of several diselenides of formula (R-PhSe)2 (R= CH3O, CH3, H, Cl, CF3) with a thiolate nucleophile,...
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The Potential of Ebselen Against Bipolar Disorder: a Perspective on the Interaction with Inositol Monophosphatase (IMPase). CURR ORG CHEM 2022. [DOI: 10.2174/1385272827666221130122416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Abstract:
Despite its narrow therapeutic index and the toxicity issues related to renal injuries, lithium is still a first-line choice for the treatment of mania and for preventing recurrences in bipolar disorder. Nevertheless, side effects and limited efficacy in some of the cases push the search for novel tools to ameliorate these conditions, which still represent a social burden, and great efforts are being made toward the identification of alternative therapeutic options. In this context, rational drug design, drug repurposing, and computer-aided drug discovery represent time-saving and efficient strategies to pursue this goal.
Inositol monophosphatase (IMPase) represents the molecular target of lithium which acts as an uncompetitive inhibitor. In this context, a screening on NIH Clinical Collection of drug-like compounds highlighted the polypharmacological drug ebselen (2-phenyl-1,2-benzisoselenazol-3(2H)-one) as a non-competitive, irreversible IMPase inhibitor, suggesting that this molecule could represent a valid therapeutic alternative.
In this perspective article, we aim at providing a historical overview of the uses of ebselen with particular attention to its potential use as lithium-mimetic. We critically analyse this aspect by investigating in silico the molecular mechanism leading to the formation of the Se-S bond between IMPase Cys141 and ebselen. Evidence of the bond formation is supported by the crystallographic data recently reported by Fenn et al Acta Cryst. 2020. We hypothesize that the IMPase-ebselen complex promotes the association with other IMPase chains, improving the formation of the tetramer adduct, suggesting that ebselen may stabilize the human IMPase in a form that could be less active, resulting in a decreased enzymatic activity.
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In silico studies of M pro and PL pro from SARS-CoV-2 and a new class of cephalosporin drugs containing 1,2,4-thiadiazole. Struct Chem 2022; 33:2205-2220. [PMID: 36106095 PMCID: PMC9463509 DOI: 10.1007/s11224-022-02036-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 08/09/2022] [Indexed: 11/29/2022]
Abstract
The SARS-CoV-2 proteases Mpro and PLpro are important targets for the development of antivirals against COVID-19. The functional group 1,2,4-thiadiazole has been indicated to inhibit cysteinyl proteases, such as papain and cathepsins. Of note, the 1,2,4-thiadiazole moiety is found in a new class of cephalosporin FDA-approved antibiotics: ceftaroline fosamil, ceftobiprole, and ceftobiprole medocaril. Here we investigated the interaction of these new antibiotics and their main metabolites with the SARS-CoV-2 proteases by molecular docking, molecular dynamics (MD), and density functional theory (DFT) calculations. Our results indicated the PLpro enzyme as a better in silico target for the new antibacterial cephalosporins. The results with ceftaroline fosamil and the dephosphorylate metabolite compounds should be tested as potential inhibitor of PLpro, Mpro, and SARS-CoV-2 replication in vitro. In addition, the data here reported can help in the design of new potential drugs against COVID-19 by exploiting the S atom reactivity in the 1,2,4-thiadiazole moiety. Supplementary Information The online version contains supplementary material available at 10.1007/s11224-022-02036-5.
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Model Study on the Catalytic Cycle of Glutathione Peroxidase Utilizing Selenocysteine-Containing Tripeptides: Elucidation of the Protective Bypass Mechanism Involving Selenocysteine Selenenic Acids. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2022. [DOI: 10.1246/bcsj.20220156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Parameter free evaluation of S N2 reaction rates for halide substitution in halomethane. Phys Chem Chem Phys 2022; 24:7474-7480. [PMID: 35274635 DOI: 10.1039/d1cp05220a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We estimate the kinetic constants of a series of archetypal SN2 reactions, i.e., the nucleophilic substitutions of halides in halomethane. A parameter free, multiscale approach recently developed [Campeggio et al., Phys. Chem. Chem. Phys., 2020, 22, 3455] is employed. The protocol relies on quantum mechanical calculations for the description of the energy profile along the intrinsic reaction coordinate, which is then mapped onto a reaction coordinate conveniently built for the reactive process. A Kramers-Klein equation is used to describe the stochastic time evolution of the reaction coordinate and its velocity; friction is parameterized using a hydrodynamic model and Kramers theory is used to derive the rate constant of the reaction. The method is here applied to six SN2 reactions in water at 295.15 K, which differ in the nucleophile and the leaving group. The computed reaction rates are in good agreement with the experimental data and correlate well with the trends observed for the activation energies.
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ROS-Scavenging Selenofluoxetine Derivatives Inhibit In Vivo Serotonin Reuptake. ACS OMEGA 2022; 7:8314-8322. [PMID: 35309454 PMCID: PMC8928538 DOI: 10.1021/acsomega.1c05567] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/31/2021] [Indexed: 06/14/2023]
Abstract
While the neurochemistry that underpins the behavioral phenotypes of depression is the subject of many studies, oxidative stress caused by the inflammation comorbid with depression has not adequately been addressed. In this study, we described novel antidepressant-antioxidant agents consisting of selenium-modified fluoxetine derivatives to simultaneously target serotonin reuptake (antidepressant action) and oxidative stress. Excitingly, we show that one of these agents (1-F) carries the ability to inhibit serotonin reuptake in vivo in mice. We therefore present a frontier dual strategy that paves the way for the future of antidepressant therapies.
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Abstract
Medicinal chemistry is facing new challenges in approaching precision medicine. Several powerful new tools or improvements of already used tools are now available to medicinal chemists to help in the process of drug discovery, from a hit molecule to a clinically used drug. Among the new tools, the possibility of considering folding intermediates or the catalytic process of a protein as a target for discovering new hits has emerged. In addition, machine learning is a new valuable approach helping medicinal chemists to discover new hits. Other abilities, ranging from the better understanding of the time evolution of biochemical processes to the comprehension of the biological meaning of the data originated from genetic analyses, are on their way to progress further in the drug discovery field toward improved patient care. In this sense, the new approaches to the delivery of drugs targeted to the central nervous system, together with the advancements in understanding the metabolic pathways for a growing number of drugs and relating them to the genetic characteristics of patients, constitute important progress in the field.
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Methylmercury Can Facilitate the Formation of Dehydroalanine in Selenoenzymes: Insight from DFT Molecular Modeling. Chem Res Toxicol 2021; 34:1655-1663. [PMID: 34077192 DOI: 10.1021/acs.chemrestox.1c00073] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Experimental studies have indicated that electrophilic mercury forms (e.g., methylmercury, MeHg+) can accelerate the breakage of selenocysteine in vitro. Particularly, in 2009, Khan et al. (Environ. Toxicol. Chem. 2009, 28, 1567-1577) proposed a mechanism for the degradation of a free methylmercury selenocysteinate complex that was theoretically supported by Asaduzzaman et al. (Inorg. Chem. 2010, 50, 2366-2372). However, little is known about the fate of methylmercury selenocysteinate complexes embedded in an enzyme, especially in conditions of oxidative stress in which methylmercury target enzymes operate. Here, an accurate computational study on molecular models (level of theory: COSMO-ZORA-BLYP-D3(BJ)/TZ2P) was carried out to investigate the formation of dehydroalanine (Dha) in selenoenzymes, which irreversibly impairs their function. Methylselenocysteine as well as methylcysteine and methyltellurocysteine were included to gain insight on the peculiar behavior of selenium. Dha forms in a two-step process, i.e., the oxidation of the chalcogen nucleus followed by a syn-elimination leading to the alkene and the chalcogenic acid. The effect of an excess of hydrogen peroxide, which may lead to the formation of chalcogenones before the elimination, and of MeHg+, a severe toxicant targeting selenoproteins, which leads to the formation of methylmercury selenocysteinate, are also studied with the aim of assessing whether these pathological conditions facilitate the formation of Dha. Indeed, elimination occurs after chalcogen oxidation and MeHg+ facilitates the process. These results indicate a possible mechanism of toxicity of MeHg+ in selenoproteins.
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Selenoxide Elimination Triggers Enamine Hydrolysis to Primary and Secondary Amines: A Combined Experimental and Theoretical Investigation. Molecules 2021; 26:2770. [PMID: 34066723 PMCID: PMC8125833 DOI: 10.3390/molecules26092770] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/03/2021] [Accepted: 05/05/2021] [Indexed: 11/18/2022] Open
Abstract
We discuss a novel selenium-based reaction mechanism consisting in a selenoxide elimination-triggered enamine hydrolysis. This one-pot model reaction was studied for a set of substrates. Under oxidative conditions, we observed and characterized the formation of primary and secondary amines as elimination products of such compounds, paving the way for a novel strategy to selectively release bioactive molecules. The underlying mechanism was investigated using NMR, mass spectrometry and density functional theory (DFT).
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Essentials for Combined Experimental and Computational 77Se NMR of Organoselenium Catalysts and Bioinspired Antioxidants. MINI-REV ORG CHEM 2021. [DOI: 10.2174/1570193x17999200523152708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The importance of selenium in biology, in organic catalysis, and green chemistry is well
established. Selenoproteins, among which are ubiquitous Glutathione Peroxidases (GPx), play a key
role in mitigating oxidative stress by reducing H2O2 and hydroperoxides using glutathione as a cofactor.
Organoselenides, particularly diphenyl diselenide, in the presence of H2O2, are efficient and
often green oxygen transfer agents in important organic reactions, such as Baeyer-Villiger oxidations
of ketones/aldehydes, the conversion of alkenes into epoxides, and the oxidations of alcohols and nitrogen-
containing compounds. NMR spectroscopy can facilitate the investigation of the properties of
this element in a biological environment and the characterization of the peculiar species of its chemistry.
In this short review, a brief overview of the experimental and computational 77Se NMR-based
techniques is outlined, with a particular focus on their applications to the study of biologically relevant
organoselenium compounds and bio-mimetic systems. Experimental protocols, together with
computational methods used in different contexts, are presented and their potential as efficient investigation
tools is critically discussed. It emerges that while the 77Se NMR measurement is a consolidated
technique, no standard computational protocol is available to compute the shielding constant of
the chalcogen nucleus with accuracy and the optimal approach combines molecular dynamics in solution
and quantum chemistry calculations to take into account the conformational freedom.
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Effect of Methylmercury Binding on the Peroxide-Reducing Potential of Cysteine and Selenocysteine. Inorg Chem 2021; 60:4646-4656. [PMID: 33587617 PMCID: PMC8763373 DOI: 10.1021/acs.inorgchem.0c03619] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Indexed: 01/09/2023]
Abstract
Methylmercury (CH3Hg+) binding to catalytically fundamental cysteine and selenocysteine of peroxide-reducing enzymes has long been postulated as the origin of its toxicological activity. Only very recently, CH3Hg+ binding to the selenocysteine of thioredoxin reductase has been directly observed [Pickering, I. J. Inorg. Chem., 2020, 59, 2711-2718], but the precise influence of the toxicant on the peroxide-reducing potential of such a residue has never been investigated. In this work, we employ state-of-the-art density functional theory calculations to study the reactivity of molecular models of the free and toxified enzymes. Trends in activation energies are discussed with attention to the biological consequences and are rationalized within the chemically intuitive framework provided by the activation strain model. With respect to the free, protonated amino acids, CH3Hg+ binding promotes oxidation of the S or Se nucleus, suggesting that chalcogenoxide formation might occur in the toxified enzyme, even if the actual rate of peroxide reduction is almost certainly lowered as suggested by comparison with fully deprotonated amino acids models.
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Radical scavenging activity of natural antioxidants and drugs: Development of a combined machine learning and quantum chemistry protocol. J Chem Phys 2020; 153:114117. [DOI: 10.1063/5.0013278] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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Antioxidant Potential of Psychotropic Drugs: From Clinical Evidence to In Vitro and In Vivo Assessment and toward a New Challenge for in Silico Molecular Design. Antioxidants (Basel) 2020; 9:E714. [PMID: 32781750 PMCID: PMC7465375 DOI: 10.3390/antiox9080714] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/02/2020] [Accepted: 08/04/2020] [Indexed: 12/13/2022] Open
Abstract
Due to high oxygen consumption, the brain is particularly vulnerable to oxidative stress, which is considered an important element in the etiopathogenesis of several mental disorders, including schizophrenia, depression and dependencies. Despite the fact that it is not established yet whether oxidative stress is a cause or a consequence of clinic manifestations, the intake of antioxidant supplements in combination with the psychotropic therapy constitutes a valuable solution in patients' treatment. Anyway, some drugs possess antioxidant capacity themselves and this aspect is discussed in this review, focusing on antipsychotics and antidepressants. In the context of a collection of clinical observations, in vitro and in vivo results are critically reported, often highlighting controversial aspects. Finally, a new challenge is discussed, i.e., the possibility of assessing in silico the antioxidant potential of these drugs, exploiting computational chemistry methodologies and machine learning. Despite the physiological environment being incredibly complex and the detection of meaningful oxidative stress biomarkers being all but an easy task, a rigorous and systematic analysis of the structural and reactivity properties of antioxidant drugs seems to be a promising route to better interpret therapeutic outcomes and provide elements for the rational design of novel drugs.
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Chalcogen–mercury bond formation and disruption in model Rabenstein's reactions: A computational analysis. J Comput Chem 2020; 41:2045-2054. [DOI: 10.1002/jcc.26371] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/08/2020] [Accepted: 06/08/2020] [Indexed: 12/11/2022]
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Multiscale modeling of reaction rates: application to archetypal S N2 nucleophilic substitutions. Phys Chem Chem Phys 2020; 22:3455-3465. [PMID: 31984980 DOI: 10.1039/c9cp03841h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We propose an approach to the evaluation of kinetic rates of elementary chemical reactions within Kramers' theory based on the definition of the reaction coordinate as a linear combination of natural, pseudo Z-matrix, internal coordinates of the system. The element of novelty is the possibility to evaluate the friction along the reaction coordinate, within a hydrodynamic framework developed recently [J. Campeggio et al., J. Comput. Chem. 2019, 40, 679-705]. This, in turn, allows to keep into account barrier recrossing, i.e. the transmission coefficient that is employed in correcting transition state theory evaluations. To test the capabilities and the flaws of the approach we use as case studies two archetypal SN2 reactions. First, we consider to the standard substitution of chloride ion to bromomethane. The rate constant at 295.15 K is evaluated to k/c⊖ = 2.7 × 10-6 s-1 (with c⊖ = 1 M), which compares well to the experimental value of 3.3 × 10-6 s-1 [R. H. Bathgate and E. A. Melwyn-Hughes, J. Chem. Soc 1959, 2642-2648]. Then, the method is applied to the SN2 reaction of methylthiolate to dimethyl disulfide in water. In biology, such an interconversion of thiols and disulfides is an important metabolic topic still not entirely rationalized. The predicted rate constant is k/c⊖ = 7.7 × 103 s-1. No experimental data is available for such a reaction, but it is in accord with the fact that the alkyl thiolates to dialkyl disulfides substitutions in water have been found to be fast reactions [S. M. Bachrach, J. M. Hayes, T. Dao and J. L. Mynar, Theor. Chem. Acc. 2002, 107, 266-271].
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Fluoxetine scaffold to design tandem molecular antioxidants and green catalysts. RSC Adv 2020; 10:18583-18593. [PMID: 35518299 PMCID: PMC9053872 DOI: 10.1039/d0ra03509b] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 05/07/2020] [Indexed: 12/12/2022] Open
Abstract
Fluoxetine finds application in the treatment of depression and mood disorders. This selective serotonin-reuptake inhibitor (SSRI) also contrasts oxidative stress by direct ROS scavenging, modulation of the endogenous antioxidant defense system, and/or enhancement of the serotonin antioxidant capacity. We synthesised some fluoxetine analogues incorporating a selenium nucleus, thus expanding its antioxidant potential by enabling a hydroperoxides-inactivating, glutathione peroxidase (GPx)-like activity. Radical scavenging and peroxidatic activity were combined in a water-soluble, drug-like, tandem antioxidant molecule. Selenofluoxetine derivatives were reacted with H2O2 in water, and the mechanistic details of the reaction were unravelled combining nuclear magnetic resonance (NMR), electrospray ionisation-mass spectrometry (ESI-MS) and quantum chemistry calculations. The observed oxidation–elimination process led to the formation of seleninic acid and cinnamylamine in a trans-selective manner. This mechanism is likely to be extended to other substrates for the preparation of unsaturated cinnamylamines. We modified fluoxetine by incorporating a selenium nucleus enabling a hydroperoxide-inactivating, glutathione peroxidase (GPx)-like activity and paving the way for its use as green catalyst.![]()
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Sequential oxidations of phenylchalcogenides by H2O2: insights into the redox behavior of selenium via DFT analysis. NEW J CHEM 2020. [DOI: 10.1039/c9nj06449d] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The biological activity of sulfur and selenium, despite their similarity, shows some remarkable differences that have been recognized in many different scenarios.
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Modelling of Ca2+-promoted structural effects in wild type and post-translationally modified Connexin26. MOLECULAR SIMULATION 2019. [DOI: 10.1080/08927022.2019.1690653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Oxidation of organic diselenides and ditellurides by H 2O 2 for bioinspired catalyst design. Phys Chem Chem Phys 2019; 20:20874-20885. [PMID: 30066704 DOI: 10.1039/c8cp02748j] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The reactivity of diselenides and ditellurides of general formula (RX)2 (X = Se, Te; R = H, CH3, Ph) toward hydrogen peroxide was studied through a computational approach based on accurate Density Functional Theory (DFT) calculations. The aliphatic and aromatic dichalcogenides have been chosen in light of their activity in glutathione peroxidase (GPx)-like catalytic cycles and their promising features as efficient antioxidant compounds. The reaction products, the energetics and the mechanistic details of these oxidations are discussed. Analogous disulfides are included in our analysis for completeness. We find that the barrier for oxidation of dichalcogenides decreases from disulfides to diselenides to ditellurides. On the other hand, variation of the substituents at the chalcogen nucleus has relatively little effect on the reactivity.
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Psychiatric Disorders and Oxidative Injury: Antioxidant Effects of Zolpidem Therapy disclosed In Silico. Comput Struct Biotechnol J 2019; 17:311-318. [PMID: 30867894 PMCID: PMC6396081 DOI: 10.1016/j.csbj.2019.02.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 02/01/2019] [Accepted: 02/02/2019] [Indexed: 01/09/2023] Open
Abstract
Zolpidem (N,N-Dimethyl-2-[6-methyl-2-(4-methylphenyl)imidazo[1,2-a]pyridin-3-yl]acetamide) is a well-known drug for the treatment of sleeping disorders. Recent literature reports on positive effects of zolpidem therapy on improving renal damage after cisplatin and on reducing akinesia without sleep induction. This has been ascribed to the antioxidant and neuroprotective capacity of this molecule, and tentatively explained according to a generic structural similarity between zolpidem and melatonin. In this work, we investigate in silico the antioxidant potential of zolpidem as scavenger of five ROSs, acting via hydrogen atom transfer (HAT) mechanism; computational methodologies based on density functional theory are employed. For completeness, the analysis is extended to six metabolites. Thermodynamic and kinetic results disclose that indeed zolpidem is an efficient radical scavenger, similarly to melatonin and Trolox, supporting the biomedical evidence that the antioxidant potential of zolpidem therapy may have a beneficial effect against oxidative injury, which is emerging as an important etiopathogenesis in numerous severe diseases, including psychiatric disorders.
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Key Words
- Antioxidant activity
- DFT calculations
- DFT, Density Functional Theory
- HAT, Hydrogen Atom Transfer (mechanism)
- M06-2X, Minnesota Hybrid functional with 54% Hartree-Fock exchange
- NBO, Natural Bond Orbitals
- NPA, Natural Population Analysis
- Oxidative stress
- PC, Product Complex
- Psychiatric disorders
- RAF, Radical Adduct Formation (mechanism)
- RC, Reactant Complex
- ROS, Reactive Oxygen Species
- Radical scavenging
- SMD, Solvation Model based on Density
- TS, Transition State
- Zolpidem
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Abstract
We have analyzed the chalcogen–π bonding mechanism in a systematic series of model systems through Kohn–Sham molecular orbital theory and a quantitative energy decomposition scheme.
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Front Cover: Role of the Chalcogen (S, Se, Te) in the Oxidation Mechanism of the Glutathione Peroxidase Active Site (ChemPhysChem 21/2017). Chemphyschem 2017. [DOI: 10.1002/cphc.201701129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Role of the Chalcogen (S, Se, Te) in the Oxidation Mechanism of the Glutathione Peroxidase Active Site. Chemphyschem 2017; 18:2990-2998. [DOI: 10.1002/cphc.201700743] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Indexed: 12/23/2022]
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Mechanistic Insight into the Oxidation of Organic Phenylselenides by H 2 O 2. Chemistry 2017; 23:2405-2422. [PMID: 27935210 DOI: 10.1002/chem.201604915] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Indexed: 12/24/2022]
Abstract
The oxidation of organic phenylselenides by H2 O2 is investigated in model compounds, namely, n-butyl phenyl selenide (PhSe(nBu)), bis(phenylselanyl)methane (PhSeMeSePh), diphenyl diselenide (PhSeSePh), and 1,2-bis(phenylselanyl)ethane (PhSeEtSePh). Through a combined experimental (1 H and 77 Se NMR) and computational approach, we characterize the direct oxidation of monoselenide to selenoxide, the stepwise double oxidation of PhSeMeSePh that leads to different diastereomeric diselenoxides, the complete oxidation of the diphenyldiselenide that leads to selenium-selenium bond cleavage, and the subsequent formation of the phenylseleninic product. The oxidation of PhSeEtSePh also results in the formation of phenylseleninic acid along with 1-(vinylseleninyl)benzene, which is derived from a side elimination reaction. The evidence of a direct mechanism, in addition to an autocatalytic mechanism that emerges from kinetic studies, is discussed. By considering our observations of diselenides with chalcogen atoms that are separated by alkyl spacers of different length, a rationale for the advantage of diselenide versus monoselenide catalysts is presented.
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Addition-Elimination or Nucleophilic Substitution? Understanding the Energy Profiles for the Reaction of Chalcogenolates with Dichalcogenides. J Chem Theory Comput 2016; 12:2752-61. [PMID: 27096625 DOI: 10.1021/acs.jctc.6b00253] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We have quantum chemically explored the mechanism of the substitution reaction between CH3X(-) and the homo- and heterodichalcogenides CH3X'X″CH3 (X, X', X″ = S, Se, Te) using relativistic density functional theory at ZORA-OLYP/TZ2P and COSMO for simulating the effect of aqueous solvation. In the gas phase, all substitution reactions proceed via a triple-well addition-elimination mechanism that involves a stable three-center intermediate. Aqueous solvation, in some cases, switches the character of the mechanism to double-well SN2 in which the stable three-center intermediate has become a labile transition state. We rationalize reactivity trends and some puzzling aspects of these elementary reactions, in particular, vanishing activation energies and ghost three-center intermediates, using the activation strain model (ASM).
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Abstract
BACKGROUND Originally introduced for cutaneous T-cell lymphomas and autoimmune diseases, extracorporeal photopheresis (ECP) has been proven effective to reverse allograft rejection. The aim of the present work was to show the results of a single-center experience with ECP for the treatment of biopsy-proven rejection in selected liver transplant (LT) recipients. PATIENTS AND METHODS A retrospective review of five LT patients (M:F=4:1; median age 51 years) undergoing ECP for biopsy-proven allograft rejection between January 1996 and December 2003. In this period 476 LT were performed on 441 patients. RESULTS The indications for LT were three cases of HCV-related cirrhosis, complicated by hepatocellular carcinoma in two; one HBV-HDV-alcoholic cirrhosis; and one fulminant HBV hepatitis. All patients received calcineurin-inhibitor (CNI)-based immunosuppression with induction using anti-IL2R monoclonal antibodies. Indications for ECP were: ductopenic rejection in one patient with HCV recurrence; steroid-resistant acute rejection in two; acute rejection in a major ABO-mismatched liver graft; and one acute rejection in a patient with a proven allergy to steroids. The median interval from LT to inception of ECP was 43 days. The median number of ECP sessions per patient was 20. During the course of ECP, two patients tested positive for CMV antigenemia, associated in one case with bacterial pneumonia. All patients tolerated ECP and there were no procedure-related complications. At a median follow-up of 7.9 months after start of ECP, neither rejection relapses nor HCV/HBV recurrences have been observed. Three patients are off ECP with complete reversal and low-dose immunosuppression. Two patients are still receiving ECP with full-dose immunosuppression: one has achieved normal liver function but ECP is indicated due to a major ABO-incompatible liver graft, while the other patient's liver functions have not yet returned to baseline values.
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Abstract
We describe a case of polyradiculoneuropathy (PRN) following living donor kidney transplantation, without clinical evidence of preexisting infection. In this study plasma exchange treatment resulted 6 days later in improvement in extremity weakness and paresthesias in the upper and lower extremities. Total neurological recovery was obtained 3 months after the onset of symptoms.
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