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Este artigo tem o objetivo de realizar um levantamento da produção bibliográfica relativa ao tema “Trabalho prisional”, que vem ganhando espaço na área de estudos organizacionais. Para tanto, foi realizada uma consulta ao Portal Capes, Scielo, Spell e Anpad, sendo incluídos artigos de revistas, bancos de dissertações, teses, notícias de jornais, livros, capítulos de livros e monografias, todos escritos e publicados nas Ciências Sociais aplicadas. Após os recortes empíricos, restaram 27 artigos para analisar e para compreender o trabalho prisional em sua totalidade. Na tentativa de apresentar os sentidos do labor encarcerado, o tema foi reorganizado em subtemas, quais sejam: o trabalho como meio de sobrevivência, o binômio da educação e trabalho, os egressos e o mercado de trabalho, e, por fim, os trabalhadores do sistema prisional brasileiro. A revisão da literatura permite concluir que a produção acadêmica, voltada para a compreensão dos significados do trabalho dentro do sistema prisional, destaca três elementos bastante proeminentes na teoria marxista: a humanização, a exploração e a alienação dos trabalhadores

Aux Antilles françaises, la pollution des sols et des ressources en eau par la chlordécone, un pesticide organochloré longtemps utilisé dans les bananeraies, représente un problème environnemental, sanitaire et socio-économique majeur pour les pouvoirs publics. En effet, aucune méthode simple et efficace de dépollution n'existe actuellement face à cette molécule résistante. Focus sur une solution agroécologique alternative à la dépollution : la séquestration des pesticides dans le sol par ajout de matière organique.

Global plastic production exceeded 400 million tons in 2022, urgently demanding improved waste management and recycling strategies for a circular plastic economy. While the enzymatic hydrolysis of polyethylene terephthalate (PET) has become feasible on industrial scales, efficient enzymes targeting other hydrolysable plastic types such as polyurethanes (PURs) are lacking. Recently, enzymes of the amidase signature (AS) family, capable of cleaving urethane bonds in a polyether-PUR analog and a linear polyester-PUR, have been identified. Herein, we present high-resolution crystal structures of the AS enzyme UMG-SP3 in three states: ligand-free, bound with a suicidal inhibitor mimicking the transition state, and bound with a monomeric PUR degradation product. Besides revealing the conserved core and catalytic triad akin to other AS family members, the UMG-SP3 structures show remarkable flexibility of loop regions. Particularly, Arg209 in loop 3 adopts two induced-fit conformations upon ligand binding. Through structure-guided kinetic studies and enzyme engineering, we mapped structural key elements that determine the enhanced hydrolysis of urethane and amide bonds in various small molecules including a linear PUR fragment analog. Our findings contribute critical insights into urethanase activity, aiding PUR degradation campaigns and sustainable plastic recycling efforts in the future., (© 2024 Wiley‐VCH GmbH.)

Nucleic acid mimics (NAMs) have demonstrated high potential as antibacterial drugs. However, very few studies have assessed their possible diffusion across the bacterial envelope. In this work, we studied NAMs' diffusion in lipid bilayer systems that mimic the bacterial outer membrane using molecular dynamics (MD) simulations. Additionally, we examined the interactions of a NAM sequence with lipid membranes and ascertained the partition constants ( K p ) through MD and spectroscopic investigations. The NAM sequences were composed of locked nucleic acid (LNA) and 2'-O-methyl (2'-OMe) residues, whereas the membrane models were composed of 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC) or 1-palmitoyl-2-oleoyl- sn -glycero-3-phospho-(1'-rac-glycerol) (POPG) phospholipids. The parametrization protocol followed was validated against literature data and demonstrated the reliability of our approach for simulating NAM sequences. Investigation into the interaction of the sequences with zwitterionic and anionic membranes revealed a preference for hydrogen bond formation with the anionic model over the zwitterionic one. Additionally, potential of mean force (PMF) calculations unveiled a lower free energy barrier for translocation across the zwitterionic bilayer model. Contrarily, the partition constants derived suggested a slightly higher partitioning within the anionic membrane, emphasizing a nuanced interplay of factors. Finally, spectroscopic partition measurements with liposomes presented challenges in quantifying the partition of NAMs due to minimal signal variations. However, a tendency for quenching in anionic vesicles suggested a potential, albeit small, partitioning effect that warrants further investigation. In summary, our study revealed that NAMs will not, in principle, be able to cross an intact bacterial outer membrane by passive diffusion.

Fatty acid synthase (FAS) multienzymes are responsible for de novo fatty acid biosynthesis and crucial in primary metabolism. Despite extensive research, the molecular details of the FAS catalytic mechanisms are still poorly understood. For example, the b-ketoacyl synthase (KS) catalyzes the fatty acid elongating carbon-carbon-bond formation, which is the key catalytic step in biosynthesis, but factors that determine the speed and accuracy of his reaction are still unclear. Here, we report enzyme kinetics of the KS-mediated carbon-carbon bond formation, enabled by a continuous fluorometric activity assay. We observe that the KS is likely rate-limiting to the fatty acid biosynthesis, its kinetics are adapted to the length of the bound fatty acyl chain, and that the KS is also responsible for the fidelity of biosynthesis by preventing intermediates from undergoing KS-mediated elongation. To provide mechanistic insight into KS selectivity, we performed computational molecular dynamics (MD) simulations. We identify positive cooperativity of the KS dimer, which we suggest to affect the conformational variability of the multienzyme. Advancing our knowledge about the KS molecular mechanism will pave the ground for engineering FAS for biotechnology applications and the design of new therapeutics targeting the fatty acid metabolism., (© 2024 Wiley‐VCH GmbH.)

Snakebite envenoming claims 81-138 thousand lives annually, with vipers responsible for many of those. Phospholipase A 2 (PLA 2 ) enzymes and PLA 2 -like proteins are among the most important viper venom toxins. The latter are particularly intriguing, as three decades after their discovery, their molecular mechanism of toxicity is still poorly understood at best. PLA 2 -like proteins destabilize eukaryotic cell membranes through an unknown mechanism, causing an uncontrolled influx of Ca 2+ ions and ultimately triggering cell death. It is now clear that the C-terminal segment is fundamental to the toxicity, as 13-mer peptides with the same sequence exhibit most or all of the activities of the complete PLA 2 -like proteins. To finally clarify the mechanism of toxicity of these venom peptides, we have simulated their interaction with model cell membranes. Molecular dynamics simulations showed that peptides initially dispersed across the cell membrane quickly and spontaneously migrated, aggregated, induced membrane thinning, and formed clear and transient membrane pores. We calculated the potentials of the mean force for Ca 2+ transfer across the cell membranes through the transient pores. The pores significantly lower the free energy barrier for Ca 2+ translocation, an effect that grows with the size of the peptide aggregates and, thus, with the pore radius. Ca 2+ flowed across the membrane through the largest pores with almost no barrier. The permeability of Ca 2+ through the largest pores exceeded the permeability of pharmaceutical drugs by 4 orders of magnitude, revealing the easiness by which Ca 2+ overflows the intracellular medium. These results elucidate the illusive molecular origin of the toxicity of this famous class of snake venom-derived peptides., Competing Interests: The authors declare no competing financial interest., (© 2024 The Authors. Published by American Chemical Society.)

We have studied the hydroxylation mechanism of l-Tyr by the heme-dependent enzyme CYP76AD1 from the sugar beet ( Beta vulgaris ). This enzyme has a promising biotechnological application in modified yeast strains to produce medicinal alkaloids, an alternative to the traditional opium poppy harvest. A generative machine learning software based on AlphaFold was used to build the structure of CYP76AD1 since there are no structural data for this specific enzyme. After model validation, l-Tyr was docked in the active site of CYP76AD1 to assemble the reactive complex, whose catalytic distances remained stable throughout the 100 ns of MD simulation. Subsequent QM/MM calculations elucidated that l-Tyr hydroxylation occurs in two steps: hydrogen abstraction from l-Tyr by CpdI, forming an l-Tyr radical, and subsequent radical rebound, corresponding to a rate-limiting step of 16.0 kcal·mol -1 . Our calculations suggest that the hydrogen abstraction step should occur in the doublet state, while the radical rebound should happen in the quartet state. The clarification of the reaction mechanism of CYP76AD1 provides insights into the rational optimization of the biosynthesis of alkaloids to eliminate the use of opium poppy.

"Purple Drank", a soft drink containing promethazine (PMZ) and codeine (COD), has gained global popularity for its hallucinogenic effects. Consuming large amounts of this combination can lead to potentially fatal events. The binding of these drugs to plasma proteins can exacerbate the issue by increasing the risk of drug interactions, side effects, and/or toxicity. Herein, the binding affinity to human serum albumin (HSA) of PMZ and its primary metabolites [N-desmethyl promethazine (DMPMZ) and promethazine sulphoxide (PMZSO)], along with COD, was investigated by high-performance affinity chromatography (HPAC) though zonal approach. PMZ and its metabolites exhibited a notable binding affinity for HSA (%b values higher than 80%), while COD exhibited a %b value of 65%. To discern the specific sites of HSA to which these compounds were bound, displacement experiments were performed using warfarin and (S)-ibuprofen as probes for sites I and II, respectively, which revealed that all analytes were bound to both sites. Molecular docking studies corroborated the experimental results, reinforcing the insights gained from the empirical data. The in silico data also suggested that competition between PMZ and its metabolites with COD can occur in both sites of HSA, but mainly in site II. As the target compounds are chiral, the enantioselectivity for HSA binding was also explored, showing that the binding for these compounds was not enantioselective., (© 2024. The Author(s).)

Trypsin is a serine protease, an important digestive enzyme that digests the proteins in the small intestine. In the present study, we have investigated the interaction of safranal, a major saffron metabolite, with trypsin using spectroscopic and molecular docking analyses. Fluorescence emission spectra of trypsin were largely affected by the inner filter effect from safranal; that's why these were corrected using the standard procedure. The corrected fluorescence spectra have shown that the safranal quenched the intrinsic fluorescence of trypsin with a blue shift in the wavelength of emission maximum, which revealed that the microenvironment of the fluorophore became more hydrophobic. There was approximately 1: 1 fair binding between them, which increased with a rise in temperature. The interaction was favored, principally, by hydrophobic forces, and there was an efficient energy transfer from the fluorophore to the safranal. Synchronous fluorescence spectra suggested that the tryptophan residues were the major ones taking part in the fluorescence quenching of trypsin. Safranal also influenced the secondary structure of trypsin and caused partial unfolding. Molecular Docking and the Molecular Dynamics simulation of the free and complexed trypsin was also carried out. Safranal formed a stable, non-covalent complex within the S2'-S5' subsite. Moreover, two nearby tyrosine residues (Tyr39 and Tyr151) stabilized safranal through π-π interactions. Additionally, the presence of safranal led to changes in the protein flexibility and compactness, which could indicate changes in the surrounding of tryptophan residues, impacting their fluorescence. Furthermore, a loss in compactness is in line with the partial unfolding observed experimentally. Thus, both experimental and computational studies were in good agreement with each other., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Due to its detrimental impact on human health and the environment, regulations demand ultralow sulfur levels on fossil fuels, in particular in diesel. However, current desulfurization techniques are expensive and cannot efficiently remove heteroaromatic sulfur compounds, which are abundant in crude oil and concentrate in the diesel fraction after distillation. Biodesulfurization via the four enzymes of the metabolic 4S pathway of the bacterium Rhodococcus erythropolis (DszA-D) is a possible solution. However, the 4S pathway needs to operate at least 500 times faster for industrial applicability, a goal currently pursued through enzyme engineering. In this work, we unveil the catalytic mechanism of the flavin monooxygenase DszA. Surprisingly, we found that this enzyme follows a recently proposed atypical mechanism that passes through the formation of an N 5 OOH intermediate at the re side of the cofactor, aided by a well-defined, predominantly hydrophobic O 2 pocket. Besides clarifying the unusual chemical mechanism of the complex DszA enzyme, with obvious implications for understanding the puzzling chemistry of flavin-mediated catalysis, the result is crucial for the rational engineering of DszA, contributing to making biodesulfurization attractive for the oil refining industry.

Secreted phospholipase A2 (sPLA2) is a Ca 2+ -dependent, widely distributed enzyme superfamily in almost all mammalian tissues and bacteria. It is also a critical component of the venom of nearly all snakes, as well as many invertebrate species. In non-venomous contexts, sPLA2 assumes significance in cellular signaling pathways by binding cell membranes and catalyzing ester bond hydrolysis at the sn-2 position of phospholipids. Elevated levels of GIIA sPLA2 have been detected in the synovial fluid of arthritis patients, where it exhibits a pro-inflammatory function. Consequently, identifying sPLA2 inhibitors holds promise for creating highly effective pharmaceutical treatments. Beyond arthritis, the similarities among GIIA sPLA2s offer an opportunity for developing treatments against snakebite envenoming, the deadliest neglected tropical disease. Despite decades of study, the details of PLA2 membrane-binding, substrate-binding, and reaction mechanism remain elusive, demanding a comprehensive understanding of the sPLA2 catalytic mechanism. This study explores two reaction mechanism hypotheses, involving one or two water molecules, and distinct roles for the Ca 2+ cofactor. Our research focuses on the human synovial sPLA2 enzyme bound to lipid bilayers of varying phospholipid compositions, and employing adiabatic QM/MM and QM/MM MD umbrella sampling methods to energetically and geometrically characterize the structures found along both reaction pathways. Our studies demonstrate the higher frequency of productive conformations within the single-water pathway, also revealing a lower free energy barrier for hydrolyzing POPC. Furthermore, we observe that the TS of this concerted one-step reaction closely resembles transition state geometries observed in X-ray crystallography complexes featuring high-affinity transition state analogue inhibitors., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

Since the beginning of the XXI century, Leishmaniasis has been integrated into the World Health Organization's list of the 20 neglected tropical diseases, being considered a public health issue in more than 88 countries, especially in the tropics, subtropics, and the Mediterranean area. Statistically, this disease presents a world prevalence of 12 million cases worldwide, with this number being expected to increase shortly due to the 350 million people considered at risk and the 2-2.5 million new cases appearing every year. The lack of an appropriate and effective treatment against this disease has intensified the interest of many research groups to pursue the discovery and development of novel treatments in close collaboration with the WHO, which hopes to eradicate it shortly. This paper intends to highlight the quinoline scaffold's potential for developing novel antileishmanial agents and provide a set of structural guidelines to help the research groups in the medicinal chemistry field perform more direct drug discovery and development programs. Thus, this review paper presents a thorough compilation of the most recent advances in the development of new quinoline-based antileishmanial agents, with a particular focus on structure-activity relationship studies that should be considerably useful for the future of the field.

Viper venom phospholipase A2 enzymes (vvPLA2s) and phospholipase A2-like (PLA2-like) proteins are two of the principal toxins in viper venom that are responsible for the severe myotoxic and neurotoxic effects caused by snakebite envenoming, among other pathologies. As snakebite envenoming is the deadliest neglected tropical disease, a complete understanding of these proteins' properties and their mechanisms of action is urgently needed. Therefore, we created a database comprising information on the holo-form, cofactor-bound 3D structure of 217 vvPLA2 and PLA2-like proteins in their physiologic environment, as well as 79 membrane-bound viper species from 24 genera, which we have made available to the scientific community to accelerate the development of new anti-snakebite drugs. In addition, the analysis of the sequenced, 3D structure of the database proteins reveals essential aspects of the anatomy of the proteins, their toxicity mechanisms, and the conserved binding site areas that may anchor universal interspecific inhibitors. Moreover, it pinpoints hypotheses for the molecular origin of the myotoxicity of the PLA2-like proteins. Altogether, this study provides an understanding of the diversity of these toxins and how they are conserved, and it indicates how to develop broad, interspecies, efficient small-molecule inhibitors to target the toxin's many mechanisms of action.

Divalent metal ions are essential micronutrients for many intercellular reactions. Maintaining their homeostasis is necessary for the survival of bacteria. In Streptococcus gordonii, one of the primary colonizers of the tooth surface, the cellular concentration of manganese ions (Mn 2+ ) is regulated by the manganese-sensing transcriptional factor ScaR which controls the expression of proteins involved in manganese homeostasis. To resolve the molecular mechanism through which the binding of Mn 2+ ions increases the binding affinity of ScaR to DNA, a variety of computational (QM and MD) and experimental (ITC, DSC, EMSA, EPR, and CD) methods were applied. The computational results showed that Mn 2+ binding induces a conformational change in ScaR that primarily affects the position of the DNA binding domains and, consequently, the DNA binding affinity of the protein. In addition, experimental results revealed a 1:4 binding stoichiometry between ScaR dimer and Mn 2+ ions, while the computational results showed that the binding of Mn 2+ ions in the primary binding sites is sufficient to induce the observed conformational change of ScaR., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023. Published by Elsevier B.V.)

Due to the emergence of antibiotic resistance, the need to explore novel antibiotics and/or novel strategies to counter antibiotic resistance is of utmost importance. In this work, we explored the molecular and mechanistic details of the degradation of a streptogramin B antibiotic by virginiamycin B (Vgb) lyase of Staphylococcus aureus using classical molecular dynamics simulations and multiscale quantum mechanics/molecular mechanics methods. Our results were in line with available experimental kinetic information. Although we were able to identify a stepwise mechanism, in the wild-type enzyme, the intermediate is short-lived, showing a small barrier to decay to the product state. The impact of point mutations on the reaction was also assessed, showing not only the importance of active site residues to the reaction catalyzed by Vgb lyase but also of near positive and negative residues surrounding the active site. Using molecular dynamics simulations, we also predicted the most likely protonation state of the 3-hydroxypicolinic moiety of the antibiotic and the impact of mutants on antibiotic binding. All this information will expand our understanding of linearization reactions of cyclic antibiotics, which are crucial for the development of novel strategies that aim to tackle antibiotic resistance.

By taking advantage of the outstanding intrinsic optoelectronic properties of perovskite-based photovoltaic materials, together with the strong near-infrared (NIR) absorption and electronic confinement in PbS quantum dots (QDs), sub-bandgap photocurrent generation is possible, opening the way for solar cell efficiencies surpassing the classical limits. The present study shows an effective methodology for the inclusion of high densities of colloidal PbS QDs in a MAPbI 3 (methylammonium lead iodide) perovskite matrix as a means to enhance the spectral window of photon absorption of the perovskite host film and allow photocurrent production below its bandgap. The QDs were introduced in the perovskite matrix in different sizes and concentrations to study the formation of quantum-confined levels within the host bandgap and the potential formation of a delocalized intermediate mini-band (IB). Pronounced sub-bandgap (in NIR) absorption was optically confirmed with the introduction of QDs in the perovskite. The consequent photocurrent generation was demonstrated via photoconductivity measurements, which indicated IB establishment in the films. Despite verifying the reduced crystallinity of the MAPbI 3 matrix with a higher concentration and size of the embedded QDs, the nanostructured films showed pronounced enhancement (above 10-fold) in NIR absorption and consequent photocurrent generation at photon energies below the perovskite bandgap.

Snake venom metalloproteinases (SVMPs) are important drug targets against snakebite envenoming, the neglected tropical disease with the highest mortality worldwide. Here, we focus on Russell's viper ( Daboia russelii ), one of the "big four" snakes of the Indian subcontinent that, together, are responsible for ca. 50,000 fatalities annually. The "Russell's viper venom factor X activator" (RVV-X), a highly toxic metalloproteinase, activates the blood coagulation factor X (FX), leading to the prey's abnormal blood clotting and death. Given its tremendous public health impact, the WHO recognized an urgent need to develop efficient, heat-stable, and affordable-for-all small-molecule inhibitors, for which a deep understanding of the mechanisms of action of snake's principal toxins is fundamental. In this study, we determine the catalytic mechanism of RVV-X by using a density functional theory/molecular mechanics (DFT:MM) methodology to calculate its free energy profile. The results showed that the catalytic process takes place via two steps. The first step involves a nucleophilic attack by an in situ generated hydroxide ion on the substrate carbonyl, yielding an activation barrier of 17.7 kcal·mol -1 , while the second step corresponds to protonation of the peptide nitrogen and peptide bond cleavage with an energy barrier of 23.1 kcal·mol -1 . Our study shows a unique role played by Zn 2+ in catalysis by lowering the p K a of the Zn 2+ -bound water molecule, enough to permit the swift formation of the hydroxide nucleophile through barrierless deprotonation by the formally much less basic Glu140. Without the Zn 2+ cofactor, this step would be rate-limiting.

Animal venoms and their chemical compounds have aroused both empirical and scientific attention for ages. However, there has been a significant increase in scientific investigations in recent decades, allowing the production of various formulations that are helping in the development of many important tools for biotechnological, diagnostic, or therapeutic use, both in human and animal health, as well as in plants. Venoms are composed of biomolecules and inorganic compounds that may have physiological and pharmacological activities that are not related to their principal actions (prey immobilization, digestion, and defense). Snake venom toxins, mainly enzymatic and non-enzymatic proteins, and peptides have been identified as potential prototypes for new drugs and/or models for the development of pharmacologically active structural domains for the treatment of cancer, cardiovascular diseases, neurodegenerative and autoimmune diseases, pain, and infectious-parasitic diseases. This minireview aims to provide an overview of the biotechnological potential of animal venoms, with a focus on snakes, and to introduce the reader to the fascinating world of Applied Toxinology, where animal biodiversity can be used to develop therapeutic and diagnostic applications for humans., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023. Published by Elsevier B.V.)

( S )-Norcoclaurine is synthesized in vivo through a metabolic pathway that ends with ( S )-norcoclaurine synthase (NCS). The former constitutes the scaffold for the biosynthesis of all benzylisoquinoline alkaloids (BIAs), including many drugs such as the opiates morphine and codeine and the semi-synthetic opioids oxycodone, hydrocodone, and hydromorphone. Unfortunately, the only source of complex BIAs is the opium poppy, leaving the drug supply dependent on poppy crops. Therefore, the bioproduction of ( S )-norcoclaurine in heterologous hosts, such as bacteria or yeast, is an intense area of research nowadays. The efficiency of ( S )-norcoclaurine biosynthesis is strongly dependent on the catalytic efficiency of NCS. Therefore, we identified vital NCS rate-enhancing mutations through the rational transition-state macrodipole stabilization method at the Quantum Mechanics/Molecular Mechanics (QM/MM) level. The results are a step forward for obtaining NCS variants able to biosynthesize ( S )-norcoclaurine on a large scale.

Snake venom-secreted phospholipase A 2 (svPLA 2 ) enzymes, both catalytically active and inactive, are a central component in envenoming. These are responsible for disrupting the cell membrane's integrity, inducing a wide range of pharmacological effects, such as the necrosis of the bitten limb, cardiorespiratory arrest, edema, and anticoagulation. Although extensively characterized, the reaction mechanisms of enzymatic svPLA 2 are still to be thoroughly understood. This review presents and analyses the most plausible reaction mechanisms for svPLA 2, such as the "single-water mechanism" or the "assisted-water mechanism" initially proposed for the homologous human PLA 2 . All of the mechanistic possibilities are characterized by a highly conserved Asp/His/water triad and a Ca 2+ cofactor. The extraordinary increase in activity induced by binding to a lipid-water interface, known as "interfacial activation," critical for the PLA 2 s activity, is also discussed. Finally, a potential catalytic mechanism for the postulated noncatalytic PLA 2 -like proteins is anticipated.

Leishmaniasis is one of the most neglected diseases in modern times, mainly affecting people from developing countries of the tropics, subtropics and the Mediterranean basin, with approximately 350 million people considered at risk of developing this disease. The incidence of human leishmaniasis has increased over the past decades due to failing prevention and therapeutic measures-there are no vaccines and chemotherapy, which is problematic. Acridine derivatives constitute an interesting group of nitrogen-containing heterocyclic compounds associated with numerous bioactivities, with emphasis to their antileishmanial potential. The present work builds on computational studies focusing on a specific enzyme of the parasite, S -adenosylmethionine decarboxylase (AdoMet DC), with several 1,2,3,4-tetrahydro-acridines emerging as potential inhibitors, evidencing this scaffold as a promising building block for novel antileishmanial pharmaceuticals. Thus, several 1,2,3,4-tetrahydroacridine derivatives have been synthesized, their activity against Leishmania (Leishmania) infantum promastigotes evaluated and a structure-activity relationship (SAR) study was developed based on the results obtained. Even though the majority of the 1,2,3,4-tetrahydroacridines evaluated presented high levels of toxicity, the structural information gathered in this work allowed its application with another scaffold (quinoline), leading to the obtention of N 1 , N 12 -bis(7-chloroquinolin-4-yl)dodecane-1,12-diamine ( 12 ) as a promising novel antileishmanial agent (IC 50 = 0.60 ± 0.11 μM, EC 50 = 11.69 ± 3.96 μM and TI = 19.48).

Mitochondrial targeting represents an attractive strategy for treating metabolic, degenerative and hyperproliferative diseases, since this organelle plays key roles in essential cellular functions. Triphenylphosphonium (TPP + ) moieties - the current "gold standard" - have been widely used as mitochondrial targeting vectors for a wide range of molecular cargo. Recently, further optimisation of the TPP + platform drew considerable interest as a way to enhance mitochondrial therapies. However, although the modification of this system appears promising, the core structure of the TPP + moiety remains largely unchanged. Thus, this study explored the use of aminophosphonium (PN + ) and phosphazenylphosphonium (PPN + ) main group frameworks as novel mitochondrial delivery vectors. The PPN + moiety was found to be a highly promising platform for this purpose, owing to its unique electronic properties and high lipophilicity. This has been demonstrated by the high mitochondrial accumulation of a PPN + -conjugated fluorophore relative to its TPP + -conjugated counterpart, and has been further supported by density functional theory and molecular dynamics calculations, highlighting the PPN + moiety's unusual electronic properties. These results demonstrate the potential of novel phosphorus-nitrogen based frameworks as highly effective mitochondrial delivery vectors over traditional TPP + vectors., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

Chronic inflammatory diseases are triggered by causal stimuli that might occur long before the appearance of the symptoms. Increasing evidence suggests that these stimuli are necessary but not always sufficient to induce the diseases. The murine model of type II collagen emulsified in Freund's incomplete adjuvant (collagen-induced arthritis) to induce rheumatoid arthritis (RA) follows this pattern as some animals do not develop the chronically inflamed phenotype. Considering that in the immune-pineal axis (IPA) theory adrenal-pineal cross-talk adjusts early phases of inflammatory processes, we investigated whether differences in IPA activation could explain why some animals are resistant (RES) while others develop RA. We observed a similar increase in 6-sulfatoxymelatonin (aMT6s) excretion from day 3 to 13 in both RES and RA animals, followed by a significant decrease in RA animals. This pattern of aMT6s excretion positively correlated with plasma corticosterone (CORT) in RES animals. Additionally, RA animals presented a lower aMT6s/CORT ratio than saline-injected or RES animals. Plasmatic levels of tumour necrosis factor were similar in both groups, but interleukin (IL)-1β and monocyte chemotactic protein 1 (MCP-1) levels were lower in RES compared to RA animals. IL-2 and IL-4 were decreased in RES animals compared to saline-injected animals. The aMT6s/CORT ratio inversely correlated with the paw thickness and the inflammatory score (levels of IL-1β, MCP-1, IL-2 and IL-4 combined). Thus, adrenocortical-pineal positive interaction is an early defence mechanism for avoiding inflammatory chronification. KEY POINTS: Immune-pineal axis imbalance is observed in early-phase rheumatoid arthritis development. Only resistant animals present a positive association between adrenal and pineal hormones. The 6-sulfatoxymelatonin/corticosterone ratio is decreased in animals that develop rheumatoid arthritis. The inflammatory score combining the levels of nocturnal interleukin (IL)-1β, monocyte chemotactic protein 1, IL-2 and IL-4 presents a very strong positive correlation with the size of inflammatory lesion. The 6-sulfatoxymelatonin/corticosterone ratio presents a strong negative correlation with the inflammatory score and paw oedema size., (© 2022 The Authors. The Journal of Physiology © 2022 The Physiological Society.)

Graphene oxide (GO), a nanomaterial with promising applications that range from water purification to enzyme immobilization, is actively present in scientific research since its discovery. GO studies with computational methodologies such as molecular dynamics are frequently reported in the literature; however, the models used often rely on approximations, such as randomly placing functional groups and the use of generalized force fields. Therefore, it is important to develop new MD models that provide a more accurate description of GO structures and their interaction with an aqueous solvent and other adsorbate molecules. In this paper, we derived new force field non-bonded parameters from linear-scaling density functional theory calculations of nanoscale GO sheets with more than 10,000 atoms through an atoms-in-molecules (AIM) partitioning scheme. The resulting GAFF2-AIM force field, derived from the bonded terms of GAFF2 parameterization, reproduces the solvent structure reported in ab initio MD simulations better than the force field nowadays widely used in the literature. Additionally, we analyzed the effect of the ionic strength of the medium and of the C/O ratio on the distribution of charges surrounding the GO sheets. Finally, we simulated the adsorption of natural amino acid molecules to a GO sheet and estimated their free energy of binding, which compared very favorably to their respective experimental values, validating the force field presented in this work.

We describe an approach to identify enzyme mutants with increased turnover using the enzyme DszC as a case study. Our approach is based on recalculating the barriers of alanine mutants through single-point energy calculations at the hybrid QM/MM level in the wild-type reactant and transition state geometries. We analyze the difference in the electron density between the reactant and transition state to identify sites/residues where electrostatic interactions stabilize the transition state over the reactants. We also assess the insertion of a unit probe charge to identify positions in which the introduction of charged residues lowers the barrier.

Objective: to compare cardiac anxiety symptoms in patients undergoing coronary artery bypass graft and valve surgery repair in the preoperative period, on the day of hospital discharge and on the first return visit after hospital discharge., Methods: an observational study, carried out in inpatient units and in outpatient clinic of a university hospital. Data were collected through interviews. Cardiac anxiety symptoms were assessed using the Cardiac Anxiety Questionnaire., Results: we observed the effect of time on cardiac anxiety symptoms of patients undergoing coronary artery bypass graft in the total score and in the "Avoidance" domain at discharge and at the first return visit. In patients undergoing valve repair surgery, the effect of time on symptoms was observed only in the first return visit, when compared with the preoperative period., Conclusion: the findings revealed increased cardiac anxiety symptoms in the postoperative period, discharge and first return, when compared to the preoperative period.

Hydrolysis of lignocellulosic biomass, composed of a lignin-carbohydrate-complex (LCC) matrix, is critical for producing bioethanol from glucose. However, current methods for LCC processing require costly and polluting processes. The fungal Thermothelomyces thermophila glucuronoyl esterase (TtGE) is a promising thermophilic enzyme that hydrolyses LCC ester bonds. This study describes the TtGE catalytic mechanism using QM/MM methods. Two nearly-degenerate rate-determining transition states were found, with barriers of 16 and 17 kcal ⋅ mol -1 , both with a zwitterionic nature that results from a proton interplay from His346 to either the Ser213-hydroxyl or the lignin leaving group and the rehybridisation of the ester moiety of the substrate to an alkoxide. An oxyanion hole, characteristic of esterases, was provided by the conserved Arg214 through its backbone and sidechain. Our work further suggests that a mutation of Glu267 to a non-negative residue will decrease the energetic barrier in ca. -5 kcal ⋅ mol -1 , improving the catalytic rate of TtGE., (© 2022 Wiley-VCH GmbH.)

Understanding the plasmonic coupling between a set of metallic nanoparticles (NPs) in a 2D array, and how a substrate affects such coupling, is fundamental for the development of optimized optoelectronic structures. Here, a simple semi-analytical procedure based on discrete dipole approximation (DDA) is reported to simulate the far-field and near-field properties of arrays of NPs, considering the coupling between particles, and the effect of the presence of a semiconductor substrate based on the image dipole approach. The method is validated for Ag NP dimers and single Ag NPs on a gallium nitride (GaN) substrate, a semiconductor widely used in optical devices, by comparison with the results obtained by the finite element method (FEM), indicating a good agreement in the weak coupling regime. Next, the method is applied to square and random arrays of Ag NPs on a GaN substrate. The increase in the surface density of NPs on a GaN substrate mainly results in a redshift of the dipolar resonance frequency and an increase in the near-field enhancement. This model, based on a single dipole approach, grants very low computational times, representing an advantage to predict the optical properties of large NP arrays on a semiconductor substrate for different applications.

Introduction: Implantable cardiac pacemakers or cardioverter defibrillators are alternatives for the treatment of arrhythmias, however, their use has caused changes in the emotional state of patients. The objective of this study was to compare the measures of anxiety and depression symptoms in individuals according to their sex, type of cardiac device, and diagnosis of Chagas disease., Methods: This is an observational and cross-sectional study conducted with adults with implantable cardiac pacemakers or cardioverter defibrillators. Data was collected using a sociodemographic and clinical questionnaire and the Hospital Anxiety and Depression Scale. We used the Student's t-test for independent samples and the Chi-squared test, with a significance level of 0.05., Results: Two hundred forty-four patients participated in the study, 168 with cardiac pacemakers and 76 with implantable cardioverter defibrillators; 104 had Chagas cardiomyopathy (85 with cardiac pacemakers and 19 with implantable cardioverter defibrillators). No statistically significant differences were found in measures of anxiety and depression symptoms according to device type (P=0.594 and P=0.071, respectively) and the presence of Chagas etiology (P=0.649 and P=0.354, respectively). Women had higher mean scores for anxiety (P=0.002) and depression symptoms (P<0.001)., Conclusion: In the comparison between the groups, according to the type of implanted device and the diagnosis of Chagas disease, no significant differences were found in the measures of anxiety and depression symptoms. Women showed higher means when compared to men, indicating the need to test and implement interventions to minimize these symptoms in this population.

We assessed enzyme:substrate conformational dynamics and the rate-limiting glycosylation step of a human pancreatic α-amylase:maltopentose complex. Microsecond molecular dynamics simulations suggested that the distance of the catalytic Asp197 nucleophile to the anomeric carbon of the buried glucoside is responsible for most of the enzyme active site fluctuations and that both Asp197 and Asp300 interact the most with the buried glucoside unit. The buried glucoside binds either in a 4 C 1 chair or 2 S O skew conformations, both of which can change to TS-like conformations characteristic of retaining glucosidases. Starting from four distinct enzyme:substrate complexes, umbrella sampling quantum mechanics/molecular mechanics simulations (converged within less than 1 kcal·mol -1 within a total simulation time of 1.6 ns) indicated that the reaction occurrs with a Gibbs barrier of 13.9 kcal·mol -1 , in one asynchronous concerted step encompassing an acid-base reaction with Glu233 followed by a loose S N 2-like nucleophilic substitution by the Asp197. The transition state is characterized by a 2 H 3 half-chair conformation of the buried glucoside that quickly changes to the E 3 envelope conformation preceding the attack of the anomeric carbon by the Asp197 nucleophile. Thermodynamic analysis of the reaction supported that a water molecule tightly hydrogen bonded to the glycosidic oxygen of the substrate at the reactant state (∼1.6 Å) forms a short hydrogen bond with Glu233 at the transition state (∼1.7 Å) and lowers the Gibbs barrier in over 5 kcal·mol -1 . The resulting Asp197-glycosyl was mostly found in the 4 C 1 conformation, although the more endergonic B 3, O conformation was also observed. Altogether, the combination of short distances for the acid-base reaction with the Glu233 and for the nucleophilic attack by the Asp197 nucleophile and the availability of water within hydrogen bonding distance of the glycosidic oxygen provides a reliable criteria to identify reactive conformations of α-amylase complexes.

The influence of the dynamical flexibility of enzymes on reaction mechanisms is a cornerstone in biological sciences. In this study, we aim to 1) study the convergence of the activation free energy by using the first step of the reaction catalysed by HIV-1 protease as a case study, and 2) provide further evidence for a mechanistic divergence in this enzyme, as two different reaction pathways were seen to contribute to this step. We used quantum mechanics/molecular mechanics molecular dynamics simulations, on four different initial conformations that led to different barriers in a previous study. Despite the sampling, the four activation free energies still spanned a range of 5.0 kcal ⋅ mol -1 . Furthermore, the new simulations did confirm the occurrence of an unusual mechanistic divergence, with two different mechanistic pathways displaying equivalent barriers. An active-site water molecule is proposed to influence the mechanistic pathway., (© 2022 Wiley-VCH GmbH.)

We employed QM/MM molecular dynamics (MD) simulations to characterize the rate-limiting step of the glycosylation reaction of pancreatic α-amylase with combined DFT/molecular dynamics methods (PBE/def2-SVP : AMBER). Upon careful choice of four starting active site conformations based on thorough reactivity criteria, Gibbs energy profiles were calculated with umbrella sampling simulations within a statistical convergence of 1-2 kcal ⋅ mol -1 . Nevertheless, Gibbs activation barriers and reaction energies still varied from 11.0 to 16.8 kcal ⋅ mol -1 and -6.3 to +3.8 kcal ⋅ mol -1 depending on the starting conformations, showing that despite significant state-of-the-art QM/MM MD sampling (0.5 ns/profile) the result still depends on the starting structure. The results supported the one step dissociative mechanism of Asp197 glycosylation preceded by an acid-base reaction by the Glu233, which are qualitatively similar to those from multi-PES QM/MM studies, and thus support the use of the latter to determine enzyme reaction mechanisms., (© 2022 Wiley-VCH GmbH.)

The fascination and fear of snakes dates back to time immemorial, with the first scientific treatise on snakebite envenoming, the Brooklyn Medical Papyrus, dating from ancient Egypt. Owing to their lethality, snakes have often been associated with images of perfidy, treachery and death. However, snakes did not always have such negative connotations. The curative capacity of venom has been known since antiquity, also making the snake a symbol of pharmacy and medicine. Today, there is renewed interest in pursuing snake-venom-based therapies. This Review focuses on the chemistry of snake venom and the potential for venom to be exploited for medicinal purposes in the development of drugs. The mixture of toxins that constitute snake venom is examined, focusing on the molecular structure, chemical reactivity and target recognition of the most bioactive toxins, from which bioactive drugs might be developed. The design and working mechanisms of snake-venom-derived drugs are illustrated, and the strategies by which toxins are transformed into therapeutics are analysed. Finally, the challenges in realizing the immense curative potential of snake venom are discussed, and chemical strategies by which a plethora of new drugs could be derived from snake venom are proposed., (© 2022. Springer Nature Limited.)

Ethnopharmacological Relevance: Traditional healers have used medicinal plants to treat snakebite envenomation worldwide; however, mostly without scientific validation. There have been many studies on the therapeutic potential of the natural products against snake envenomation., Aim of the Study: This review has highlighted snake venom inhibitory activity of bioactive compounds and peptides from plants that have found a traditional use in treating snakebite envenomation. We have systematically reviewed the scenario of different phases of natural snake venom inhibitors characterization covering a period from 1994 until the present and critically analysed the lacuna of the studies if any, and further scope for their translation from bench to bedside., Materials and Methods: The medicinal plant-derived compounds used against snakebite therapy were reviewed from the available literature in public databases (Scopus, MEDLINE) from 1994 till 2020. The search words used were 'natural inhibitors against snakebite,' 'natural products as therapeutics against snakebite,' 'natural products as antidote against snake envenomation,' ' snake venom toxin natural inhibitors,' 'snake venom herbal inhibitors'. However, the scope of this review does not include computational (in silico) predictions without any wet laboratory validation and snake venom inhibitory activity of the crude plant extracts. In addition, we have also predicted the ADMET properties of the identified snake venom inhibitors to highlight their valuable pharmacokinetics for future clinical studies., Results: The therapeutic application of plant-derived natural inhibitors to treat snakebite envenomation as an auxiliary to antivenom therapy has been gaining significant momentum. Pharmacological reassessment of the natural compounds derived from traditional medicinal plants has demonstrated inhibition of the principal toxic enzymes of snake venoms at various extents to curb the lethal and/or deleterious effects of venomous snakebite. Nevertheless, such molecules are yet to be commercialized for clinical application in the treatment of snakebite. There are many obstacles in the marketability of the plant-derived natural products as snake envenomation antidote and strategies must be explored for the translation of these compounds from drug candidates to their clinical application., Conclusion: In order to minimize the adverse implications of snake envenomation, strategies must be developed for the smooth transition of these plant-derived small molecule inhibitors from bench to bedside. In this article we have presented an inclusive review and have critically analysed natural products for their therapeutic potential against snake envenomation, and have proposed a road map for use of natural products as antidote against snakebite., (Copyright © 2022 Elsevier B.V. All rights reserved.)

Despite the development of vaccines against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, there is an urgent need for efficient drugs to treat infected patients. An attractive drug target is the human transmembrane protease serine 2 (TMPRSS2) because of its vital role in the viral infection mechanism of SARS-CoV-2 by activation of the virus spike protein (S protein). Having in mind that the information derived from quantum mechanics/molecular mechanics (QM/MM) studies could be an important tool in the design of transition-state (TS) analogue inhibitors, we resorted to adiabatic QM/MM calculations to determine the mechanism of the first step (acylation) of proteolytic cleavage of the S protein with atomistic details. Acylation occurred in two stages: (i) proton transfer from Ser441 to His296 concerted with the nucleophilic attack of Ser441 to the substrate's P1-Arg and (ii) proton transfer from His296 to the P1'-Ser residue concerted with the cleavage of the ArgP1-SerP1' peptide bond, with a Gibbs activation energy of 17.1 and 15.8 kcal mol -1 , relative to the reactant. An oxyanion hole composed of two hydrogen bonds stabilized the rate-limiting TS by 8 kcal mol -1 . An analysis of the TMPRSS2 interactions with the high-energy, short-lived tetrahedral intermediate highlighted the limitations of current clinical inhibitors and pointed out specific ways to develop higher-affinity TS analogue inhibitors. The results support the development of more efficient drugs against SARS-CoV-2 using a human target, free from resistance development.

Plant-derived natural compounds have been used for treating diseases since prehistorical times. The supply of many plant-derived natural compounds for medicinal purposes, such as thebaine, morphine, and codeine, is primarily dependent on opium poppy crop harvesting. This dependency adds an extra risk factor to ensuring the supply chain because crops are highly susceptible to environmental conditions. Emerging technologies, such as biocatalysis, might help to solve this problem by diversifying the sources of supply of these compounds. Here we review the first committed step in the production of alkaloid painkillers, the production of S-norcoclaurine, and the enzymes involved. The improvement of these enzymes can be carried out experimentally by directed evolution and rational design strategies, supported by computational methods, to create variants that produce the S-norcoclaurine precursor for alkaloid painkillers in heterologous organisms, meeting the pharmaceutical industry standards and needs without depending on opium poppy crops., (© 2021 Wiley-VCH GmbH.)