New insights in the mechanism of the SARS-CoV-2 M inhibition by benzisoselenazolones and diselenides.

Although global vaccination campaigns alleviated the SARS-CoV-2 pandemic in terms of morbidity and mortality, the ability of the virus to originate mutants may reduce the efficacy of vaccines, posing a serious risk of a renewed pandemic. There is therefore a need to develop small molecules capable of targeting conserved viral targets, such as the main protease (M). Here, a series of benzisoselenazolones and diselenides were tested for their ability to inhibit M; then the most potent compounds were measured for antiviral activity in vitro, and the mechanism of action was investigated.

50 Years of Organoselenium Chemistry, Biochemistry and Reactivity: Mechanistic Understanding, Successful and Controversial Stories.

In 1973, two major discoveries changed the face of selenium chemistry: the identification of the first mammal selenoenzyme, glutathione peroxidase 1, and the discovery of the synthetic utility of the so-called selenoxide elimination. While the chemical mechanism behind the catalytic activity of glutathione peroxidases appears to be mostly unveiled, little is known about the mechanisms of other selenoproteins and, for some of them, even the function lies in the dark. In chemistry, the capacity of organoselenides of catalyzing hydrogen peroxide activation for the practical manipulation of organic functional groups has been largely explored, and some mechanistic details have been clearly elucidated.

Antioxidant activity of Zuccagnia-type propolis: A combined approach based on LC-HRMS analysis of bioanalytical-guided fractions and computational investigation.

This study reports a combined approach to assess the antioxidant activity of Zuccagnia-type propolis. Fractions exhibiting the highest antioxidant activities evidenced by DPPH, a β-carotene bleaching and superoxide radical scavenging activity-non-enzymatic assays, were processed by LC-HRMS/MS to characterize the relevant chemical compounds. A computational protocol based on the DFT calculations was used to rationalize the main outcomes.

Five Hypotheses on the Origins of Temperature Dependence of Se NMR Shifts in Diselenides.

Notable thermal shifts in diselenides have been documented in Se NMR for more than 50 years, but no satisfactory explanation has been found. Here, five hypotheses are considered as possible explanations for the large temperature dependence of the Se chemical shifts of diaryl and dialkyl diselenides compared to monoselenides and selenols. Density functional theory calculations are provided to bolster hypotheses and better understand the effects of barrier height and dipole energies.

Antioxidant Chimeric Molecules: Are Chemical Motifs Additive? The Case of a Selenium-Based Ligand.

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.

Indole-5,6-quinones display hallmark properties of eumelanin.

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.

Diphenyl Diselenide and SARS-CoV-2: Exploration of the Mechanisms of Inhibition of Main Protease (M) and Papain-like Protease (PL).

The SARS-CoV-2 pandemic has prompted global efforts to develop therapeutics. The main protease of SARS-CoV-2 (M) and the papain-like protease (PL) 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) which is an archetypal model of diselenides and a renowned potential therapeutic agent.

Radical Scavenging Potential of Ginkgolides and Bilobalide: Insight from Molecular Modeling.

The reactive oxygen species (ROS) scavenging capacities of ginkgolides and bilobalide, which are the peculiar constituents of the extract of , 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.

analysis of the antidepressant fluoxetine and similar drugs as inhibitors of the human protein acid sphingomyelinase: a related SARS-CoV-2 inhibition pathway.

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.

ROS-Scavenging Selenofluoxetine Derivatives Inhibit Serotonin Reuptake.

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 () carries the ability to inhibit serotonin reuptake in mice.

Parameter free evaluation of S2 reaction rates for halide substitution in halomethane.

We estimate the kinetic constants of a series of archetypal S2 reactions, , the nucleophilic substitutions of halides in halomethane. A parameter free, multiscale approach recently developed [Campeggio , , 2020, , 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.

Drug Design: Where We Are and Future Prospects.

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.

Methylmercury Can Facilitate the Formation of Dehydroalanine in Selenoenzymes: Insight from DFT Molecular Modeling.

Experimental studies have indicated that electrophilic mercury forms (e.g., methylmercury, MeHg) can accelerate the breakage of selenocysteine .

Selenoxide Elimination Triggers Enamine Hydrolysis to Primary and Secondary Amines: A Combined Experimental and Theoretical Investigation.

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.

Effect of Methylmercury Binding on the Peroxide-Reducing Potential of Cysteine and Selenocysteine.

Methylmercury (CHHg) 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, CHHg binding to the selenocysteine of thioredoxin reductase has been directly observed [Pickering, I. J.

Radical scavenging activity of natural antioxidants and drugs: Development of a combined machine learning and quantum chemistry protocol.

Many natural substances and drugs are radical scavengers that prevent the oxidative damage to fundamental cell components. This process may occur via different mechanisms, among which, one of the most important, is hydrogen atom transfer. The feasibility of this process can be assessed in silico using quantum mechanics to compute ΔG .

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.

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.

Chalcogen-mercury bond formation and disruption in model Rabenstein's reactions: A computational analysis.

Methylmercury is a highly toxic compound and human exposure is mainly related to consumption of polluted fish and seafood. The inactivation of thiol-based enzymes, promoted by the strong affinity binding of electrophilic mercuric ions to thiol and selenol groups of proteins, is likely an important factor explaining its toxicity. A key role is played by the chemistry and reactivity of the mercury-chalcogens bond, particularly HgS and HgSe, which is the focus of this computational work (level of theory: (COSMO)-ZORA-BLYP-D3(BJ)/TZ2P).

Fluoxetine scaffold to design tandem molecular antioxidants and green catalysts.

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.

Multiscale modeling of reaction rates: application to archetypal S2 nucleophilic substitutions.

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.

Human elastin-like polypeptides as a versatile platform for exploitation of ultrasensitive bilirubin detection by UnaG.

A new, bifunctional recombinant protein was expressed as the fusion product of human elastin-like polypeptide (HELP) and the bilirubin-binding protein UnaG. The engineered product displays both the HELP-specific property of forming a functional hydrogel matrix and the UnaG-specific capacity of emitting green fluorescence upon ligand binding. The new fusion protein has been proven to be effective at detecting bilirubin in complex environments with high background noise.

The Te Chemical Shift of Diphenyl Ditelluride: Chasing Conformers over a Flat Energy Surface.

The interest in diphenyl ditelluride (Ph₂Te₂) is related to its strict analogy to diphenyl diselenide (Ph₂Se₂), whose capacity to reduce organic peroxides is largely exploited in catalysis and green chemistry. Since the latter is also a promising candidate as an antioxidant drug and mimic of the ubiquitous enzyme glutathione peroxidase (GPx), the use of organotellurides in medicinal chemistry is gaining importance, despite the fact that tellurium has no recognized biological role and its toxicity must be cautiously pondered. Both Ph₂Se₂ and Ph₂Te₂ exhibit significant conformational freedom due to the softness of the inter-chalcogen and carbon⁻chalcogen bonds, preventing the existence of a unique structure in solution.

Psychiatric Disorders and Oxidative Injury: Antioxidant Effects of Zolpidem Therapy disclosed .

Zolpidem (,-Dimethyl-2-[6-methyl-2-(4-methylphenyl)imidazo[1,2-]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.

Nature and strength of chalcogen-π bonds.

Chalcogen-π interactions occur between a covalently bound chalcogen atom that enters into a non-covalent interaction with an unsaturated moiety, a bonding motif found in various structures, such as, proteins. In this work, we have systematically explored and analyzed chalcogen-π interactions in model systems X2DA (with D = O, S, Se, Te; X = halogen; A = acetylene, ethylene and 2-butyne), using relativistic density functional theory (DFT). The nature and trends in stability of the chalcogen-π bonds are analyzed and interpreted in terms of quantitative MO theory in combination with a matching canonical energy decomposition analysis (EDA) scheme.