Search Results (114)

Cytochrome P450 (CYP450) enzymes play an essential role in the metabolism of drugs, particularly in phase I metabolic reactions. In this article, we present a comprehensive review of fifteen selected enzymes belonging to the CYP450 family. The enzymes included in this analysis are CYP7A1, CYP3A4, CYP3A5, CYP2D6, CYP2E1, CYP2C8, CYP2C18, CYP2C9, CYP2C19, CYP2B6, CYP2A6, CYP2A13, CYP1B1, CYP1A1, and CYP1A2. We examined the influence of natural, polymorphic variations within their primary amino acid sequences on their enzymatic function and mechanisms of action. To begin, we compiled a dataset of naturally occurring polymorphic variants for these enzymes. This was achieved through a detailed analysis of entries in the UniProt database, as well as an extensive review of the current scientific literature. For each variant, we included commentary regarding its potential impact on enzyme activity or drug response, based on evidence observed in in vitro experiments, in vivo studies, or clinical trials. Particular emphasis was placed on how such polymorphisms might alter the metabolism of xenobiotics, thereby potentially affecting pharmacological outcomes. In this respect, the work represents the first comprehensive source in the scientific literature that systematically gathers and organizes data on CYP450 polymorphisms, including an assessment of their potential significance in processes mediated by these enzymes. A more detailed comparison of the polymorphism-related in vitro studies is devoted to CYP3A4, an enzyme that displays the largest fraction of clinically significant polymorphs. Secondly, we aimed to establish possible molecular explanations for why specific polymorphisms exhibit clinically or experimentally observable effects. To explore this, we performed a qualitative structural analysis of the enzymes, focusing on shared structural characteristics among the examined members of the CYP450 family. The results of this analysis demonstrate that there is no single universal mechanism by which polymorphisms influence the function of CYP450 enzymes. Instead, the mechanisms vary and may include alterations in the orientation of the enzyme within the lipid membrane, changes affecting the association or dissociation of substrates and products at the active site, structural stabilization or destabilization of the enzyme’s reactive centers, modifications in the way the enzyme interacts with its ligand, or alterations in the character of the interface involved in contact with its redox partner (electron transfer protein). Furthermore, among the polymorphisms that significantly impact enzyme function, mutations involving the substitution of arginine residues for other amino acids appear to be overrepresented. Full article

Plastic waste, particularly poly(ethylene terephthalate) (PET), negatively impacts the environment and human health. Biotechnology could become an alternative to managing PET waste if enzymes ensure the recovery of terephthalic acid with efficiencies comparable to those of chemical treatments. Recent research has highlighted the potential of fungal cutinases, such as wild-type ANCUT1 (ANCUT1^wt) from Aspergillus nidulans, in achieving PET depolymerization. Fungal cutinases’ structures differ from those of bacterial cutinases, while their PET depolymerization mechanism has not been well studied. Here, a reliable model of the ANCUT1^wt was obtained using AlphaFold 2.0. Computational chemistry revealed potential cation-binding sites, which had not been described regarding enzymatic activation in fungal cutinases. Moreover, it allowed the prediction of residues with the ability to interact with a PET trimer that were mutation candidates to engineer the substrate binding cleft, seeking enhancements of PET hydrolysis. Enzyme kinetics revealed that both ANCUT1^wt and ANCUT1^N73V/L171Q (DM) were activated by MgCl₂, increasing the dissociation constant of the substrate and maximal reaction rate. We found that in the presence of MgCl₂, DM hydrolyzed different PET samples and released 9.1-fold more products than ANCUT1^wt. Scanning Electron Microscopy revealed a different hydrolysis mode of these enzymes, influenced by the polymer’s crystallinity and structure. Full article

We synthesized 16 representatives of a new class of tetraene macrodiolides with two pharmacophore cis,cis-1,5-diene fragments of the molecule in their structure in rather high yields (from 67 to 84%), which, in turn, were synthesized by a catalytic intermolecular cyclocondensation reaction of α,ω-alka-nZ,(n+4)Z-diendiols with α,ω-alka-nZ,(n+4)Z-diendioic acids using Hf(OTf)₄. The synthesis of starting substrates with 1Z,5Z-diene moieties with a high degree of stereoselectivity was carried out using the authors’ original reaction of catalytic homo-cyclomagnesiation of O-containing allenes. The cytotoxic potential of the examined compounds was assessed using the following cell lines: Jurkat, K562, U937, HL60, HEK293, and Wi-38 (fibroblasts). Biological tests of the synthesized compounds showed a direct effect on mitochondrial biogenesis by the dissociation of oxidation and phosphorylation and the release of cytochrome P450 into the cell cytosol, as well as the induction of mitochondrial apoptosis. The selectivity index demonstrates significant variability, ranging from approximately 2.5 to 5.3 for Jurkat cells and from 3.0 to 5.8 for the other cell lines. Full article

Hydrogen (H₂) has become a more important alternative source in the current energy transition process. Beyond its role in clean energy production, it also serves as a key reactant in a wide range of industrial chemical transformations, such as hydrogenation and hydroprocessing. A fundamental step in many of these processes is the dissociation of hydrogen on catalyst surfaces. This short review provides an overview of the fundamental mechanisms involved in hydrogen dissociation over catalysts, with a specific emphasis on heterolytic pathways. Meanwhile, the influence of surface coordination environments on hydrogen activation is discussed, focusing on key factors—Lewis acid–base pairs, lattice oxygen and oxygen vacancies, and metal–support interfaces. With recognizing the significance of understanding the reaction mechanisms, we provide a critical review of experimental techniques, including spectroscopy, temperature-programmed methods, and kinetic analysis, that have been successfully applied or appear promising for probing active sites, reaction dynamics, chemisorbed intermediates, and elementary steps. Our goal is to highlight how these techniques contribute to a mechanistic understanding and to outline future directions, making this review a valuable resource for both new and experienced researchers. Full article

The degradation of polystyrene (PS) represents a significant challenge in plastic waste management due to its chemical stability and low biodegradability. In this study, the catalytic degradation mechanisms of PS were investigated by density functional theory (DFT)-based calculations using the hybrid functional B3LYP and the 6-311G++(d,p) basis in Gaussian 16. The influence of acidic (AlCl₃, Fe₂(SO₄)₃) and basic (CaO) catalysts was evaluated in terms of activation energy, reaction mechanisms, and degradation products. The results revealed that acid catalysts induce PS fragmentation through the formation of carbocationic intermediates, promoting the selective cleavage of C-C bonds in branched chains with bond dissociation energies (BDE) of 176.8 kJ/mol (C1-C7) and 175.2 kJ/mol (C3-C8). In contrast, basic catalysts favor β-scission by stabilizing carbanions, reducing the BDE to 151.6 kJ/mol (C2-C3) and 143.9 kJ/mol (C3-C4), which facilitates the formation of aromatic products such as styrene and benzene. Fe₂(SO₄)₃ was found to significantly decrease the activation barriers to 328.12 kJ/mol, while the basic catalysts reduce the energy barriers to 136.9 kJ/mol. Gibbs free energy (ΔG) calculations confirmed the most favorable routes, providing key information for the design of optimized catalysts in PS valorization. This study highlights the usefulness of computational modeling in the optimization of plastic recycling strategies, contributing to the development of more efficient and sustainable methods. Full article

The search for alternative sources of, and substitutes for, chemicals derived from fossil-based feedstocks encourages studies of heterogeneous catalysts to increase the feasibility of sustainable production of biomass derivatives, such as γ-valerolactone, among others. In this context, first, the performance of a titania-supported nickel catalyst (a non-noble catalyst) was evaluated in the reaction of hydrogenation of levulinic acid to γ-valerolactone in water using molecular hydrogen. The methods used included the synthesis of titania via the solgel method and nickel deposition by deposition–precipitation via removal of the complexing agent. The nickel was activated in a flow of hydrogen; the temperature of reduction and the calcination step were investigated with experiments at reaction conditions to study the catalyst’s stability. Then, after a statistical evaluation of several proposed kinetic models, the kinetics of the reaction was found to be best represented by a model obtained considering that the reaction over the surface was the determinant step, followed by the non-dissociative adsorption of hydrogen and the competitive adsorption among hydrogen, levulinic acid, and γ-valerolactone. With that model, the activation energy of the levulinic acid to 4-hydroxypentanoic acid step was (47.0 ± 1.2) kJ mol⁻¹, since the determinant step was the hydrogenation reaction of the levulinic acid to 4-hydroxypentanoic acid. It was also concluded that the catalyst prepared was stable, active, and selective to γ-valerolactone. Full article

This study demonstrates, for the first time, the formation of a hemiester of carbonic acid on self-assembled monolayers using voltammetric techniques and redox probes. A gold electrode (GE) was modified with 2-mercaptoethanol (ME) through self-assembly. With this modified electrode (GE-ME), a well-defined peak was observed by differential pulse voltammetry (DPV) for the negatively charged redox probe, ferricyanide/ferrocyanide, [Fe(CN)₆]³⁻/⁴⁻, in sodium acetate as an electrolyte adjusted to pH 8.2. In the presence of dissolved CO₂ in equilibrium with bicarbonate, there is a decrease in the ferrocyanide peak current with time (~30% in 60 min), attributed to the formation of hemiester 2-mercapto ethyl carbonate at the GE-ME/solution interface. Similarly, dissolved CO₂ and bicarbonate also affect the electrochemical impedance measurements by increasing resistance to the charge transfer process with time (elevation of Rct values), compatible with the formation of the hemiester. The addition of barium salt led to the displacement of the equilibrium towards BaCO₃ precipitation and consequent dissociation of the hemiester, attested by the recovery of the initial ferricyanide DPV signal. With the positively charged redox probe [Ru(NH₃)₆]²⁺, no decrease in the DPV peak was observed during the formation of the hemiester by reaction with bicarbonate. The repulsion of [Fe(CN)₆]³⁻, but not of [Ru(NH3)₆]²⁺, suggests that the formed species is the negatively charged 2-mercapto-ethyl carbonate, i.e., the hemiester with a dissociated proton. Due to the lack of a voltammetric signal from the hemiester itself, the formation of a self-assembled layer of thio-alcohol followed by the gradual formation of the corresponding carbonic acid hemiester allowed us to reach an elegant way of electrochemically demonstrating the formation of these species. Full article

3,4-Dihydroxy-L-phenylalanine (DOPA) is a promising noncanonical amino acid (ncAA) that introduces novel catechol chemical features into proteins, expanding their functional potential. However, the most common approach to incorporating ncAAs into proteins relies on stop codon suppression, which is often limited by the competition of endogenous translational termination machinery. Here, we employed a special in vitro protein expression system that facilitates the efficiency of DOPA incorporation into proteins by removing essential Class I peptide release factors through targeted degradation. In the absence of both RF1 and RF2, we successfully demonstrated DOPA incorporation at all three stop codons (TAG, TAA, and TGA). By optimizing the concentration of engineered DOPA-specific aminoacyl-tRNA synthetase (DOPARS), DOPA, and DNA template, we achieved a synthesis yield of 2.24 µg of sfGFP with 100% DOPA incorporation in a 20 μL reaction system. DOPARS exhibited a dissociation constant (Kd) of 11.7 μM for DOPA but showed no detectable binding to its native counterpart, tyrosine. Additionally, DOPA was successfully incorporated into a reverse transcriptase, which interfered with its activity. This system demonstrates a fast and efficient approach for precise DOPA incorporation into proteins, paving the way for advanced protein engineering applications. Full article

Frequent removal and reapplication of wound dressings can cause mechanical disruption to the healing process and significant physical discomfort for patients. In response to this challenge, a dynamic covalent hydrogel has been developed to advance wound care strategies. This system comprises aldehyde functionalized chondroitin sulfate (CS-CHO) and thiolated hyaluronic acid (HA-SH), with the distinct ability to form in situ via thiol–aldehyde addition and dissolve on-demand via the thiol–hemithioacetal exchange reaction. Although rarely reported, the dynamic covalent reaction of thiol–aldehyde addition holds great promise for the preparation of dynamic hydrogels due to its rapid reaction kinetics and easy reversible dissociation. The thiol–aldehyde addition chemistry provides the hydrogel system with highly desirable characteristics of rapid gelation (within seconds), self-healing, and on-demand dissolution (within 30 min). The mechanical and dissolution properties of the hydrogel can be easily tuned by utilizing CS-CHO materials of different aldehyde functional group contents. The chemical structure, rheology, self-healing, swelling profile, degradation rate, and cell biocompatibility of the hydrogels are characterized. The hydrogel possesses excellent biocompatibility and proves to be significant in promoting cell proliferation in vitro when compared to a commercial hydrogel (HyStem^® Cell Culture Scaffold Kit). This study introduces the simple fabrication of a new dynamic hydrogel system that can serve as an ideal platform for biomedical applications, particularly in wound care treatments as an on-demand dissolvable wound dressing. Full article

β C-S lyases (β-CSLs; EC 4.4.1.8) are enzymes catalyzing the dissociation of β carbon–sulfur bonds of cysteine S-conjugates to produce odorant metabolites with a free thiol group. These enzymes are increasingly studied for their role in flavor generation in a variety of food products, whether these processes occur directly in plants, by microbial β-CSLs during fermentation, or in the mouth under the action of the oral microbiota. Microbial β-CSLs react with sulfur aroma precursors present in beverages, vegetables, fruits, or aromatic herbs like hop but also potentially with some precursors formed through Maillard reactions in cooked foods such as meat or coffee. β-CSLs from microorganisms like yeasts and lactic acid bacteria have been studied for their role in the release of polyfunctional thiols in wine and beer during fermentation. In addition, β-CSLs from microorganisms of the human oral cavity were shown to metabolize similar precursors and to produce aroma in the mouth with an impact on retro-olfaction. This review summarizes the current knowledge on β-CSLs involved in flavor generation with a focus on enzymes from microbial species present either in the fermentative processes or in the oral cavity. This paper highlights the importance of this enzyme family in the food continuum, from production to consumption, and offers new perspectives concerning the utilization of β-CSLs as a flavor enhancer. Full article

(1) Background: DNA damage is of great importance in the understanding of the effects of ionizing radiation. Various types of DNA damage can result from exposure to ionizing radiation, with clustered types considered the most important for radiobiological effects. (2) Methods: The code RITRACKS (Relativistic Ion Tracks), a program that simulates stochastic radiation track structures, was used to simulate DNA damage by photons and ions spanning a broad range of linear energy transfer (LET) values. To perform these simulations, the transport code was modified to include cross sections for the interactions of ions or electrons with DNA and amino acids for ionizations, dissociative electron attachment, and elastic collisions. The radiochemistry simulations were performed using a step-by-step algorithm that follows the evolution of all particles in time, including reactions between radicals and DNA structures and amino acids. Furthermore, detailed DNA damage events, such as base pair positions, DNA fragment lengths, and fragment yields, were recorded. (3) Results: We report simulation results using photons and the ions ¹H⁺, ⁴He²⁺, ¹²C⁶⁺, ¹⁶O⁸⁺, and ⁵⁶Fe²⁶⁺ at various energies, covering LET values from 0.3 to 164 keV/µm, and performed a comparison with other codes and experimental results. The results show evidence of DNA protection from damage at its points of contacts with histone proteins. (4) Conclusions: RITRACKS can provide a framework for studying DNA damage from a variety of ionizing radiation sources with detailed representations of DNA at the atomic scale, DNA-associated proteins, and resulting DNA damage events and statistics, enabling a broader range of future comparisons with experiments such as those based on DNA sequencing. Full article

In lactic acid bacteria, the global transcriptional regulator CcpA regulates carbon metabolism by repressing and activating the central carbon metabolism pathway, thus decreasing or increasing the yield of certain metabolites to maximize carbon flow. However, there are no reports on the deregulation of the inhibitory effects of CcpA on the metabolism of secondary metabolites. In this study, we identified a single-base mutant strain of Lactococcus lactis N8-2 that is capable of metabolizing 2,3-butanediol. It has been established that CcpA dissociates from the catabolite responsive element (cre) site due to a mutation, leading to the activation of derepression and expression of the 2,3-butanediol dehydrogenase gene cluster (butB and butA). Transcriptome analysis and quantitative polymerase chain reaction (Q-PCR) results showed significant upregulation of transcription of butB and butA compared to the unmutated strain. Furthermore, micro-scale thermophoresis experiments confirmed that CcpA did not bind to the mutated cre. Furthermore, in a bacterial two-plasmid fluorescent hybridization system, it was similarly confirmed that the dissociation of CcpA from cre eliminated the repressive effect of CcpA on downstream genes. Finally, we investigated the differing catalytic capacities of the 2,3-butanediol dehydrogenase gene cluster in L. lactis N8-1 and L. lactis N8-2 for 2,3-butanediol. This led to increased expression of butB and butA, which were deregulated by CcpA repression. This is the first report on the elimination of the deterrent effect of CcpA in lactic acid bacteria, which changes the direction of enzymatic catalysis and alters the direction of carbon metabolism. This provides new perspectives and strategies for metabolizing 2,3-butanediol using bacteria in synthetic biology. Full article

Lithium is a significant energy metal. This study focuses on the extraction of lithium from lithium-bearing clay minerals utilizing calcination combined with oxalic acid leaching. The relevant important parameters, leaching kinetics analysis, and the lithium extraction mechanism were deeply investigated. The results demonstrate that a high lithium recovery of 91.35% could be achieved under the optimal conditions of calcination temperature of 600 °C, calcination time of 60 min, leaching temperature of 80 °C, leaching time of 180 min, oxalic acid concentration of 1.2 M, and liquid-to-solid ratio of 8:1. According to the shrinkage core model, the leaching kinetics of lithium using oxalic acid followed a chemical reaction-controlled process. XRD, TG, and SEM analysis showed that the kaolinite, boehmite, and diaspore phases in raw ore transformed into corundum, quartz, and muscovite phase in calcination products when the calcination temperature was higher than 600 °C. Moreover, the expansion of the interlayer spacing of minerals during the calcination process could promote the lithium release. During the leaching process, lithium present in the layered silicates was efficiently recovered through ion exchange with the dissociated H⁺ from oxalic acid. This study could provide a promising guide for lithium extraction from lithium-bearing clay minerals. Full article

Major Depressive Disorder (MDD) is a complex mental disorder that involves alterations in signal transmission across multiple scales and structural abnormalities. The development of effective antidepressants (ADs) has been hindered by the dominance of monoamine hypothesis, resulting in slow progress. Traditional ADs have undesirable traits like delayed onset of action, limited efficacy, and severe side effects. Recently, two categories of fast-acting antidepressant compounds have surfaced, dissociative anesthetics S-ketamine and its metabolites, as well as psychedelics such as lysergic acid diethylamide (LSD). This has led to structural research and drug development of the receptors that they target. This review provides breakthroughs and achievements in the structure of depression-related receptors and novel ADs based on these. Cryo-electron microscopy (cryo-EM) has enabled researchers to identify the structures of membrane receptors, including the N-methyl-D-aspartate receptor (NMDAR) and the 5-hydroxytryptamine 2A (5-HT_2A) receptor. These high-resolution structures can be used for the development of novel ADs using virtual drug screening (VDS). Moreover, the unique antidepressant effects of 5-HT_1A receptors in various brain regions, and the pivotal roles of the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) and tyrosine kinase receptor 2 (TrkB) in regulating synaptic plasticity, emphasize their potential as therapeutic targets. Using structural information, a series of highly selective ADs were designed based on the different role of receptors in MDD. These molecules have the favorable characteristics of rapid onset and low adverse drug reactions. This review offers researchers guidance and a methodological framework for the structure-based design of ADs. Full article

Lignocellulosic biomass can uptake CO₂ during growth, which can then be pyrolysed into three major products, biochar (BC), syngas, and bio-oil. Due to the presence of oxygenated organic compounds, the produced bio-oil is not suitable for direct use as a fuel and requires upgrading via hydrodeoxygenation (HDO) and hydrogenation. This is typically carried out over a supported metal catalyst. Regarding circular economy and sustainability, the BC from the pyrolysis step can potentially be activated and used as a novel catalyst support, as reported here. A 15 wt% Ni/BC catalyst was developed by chemically modifying BC with sulfuric acid to improve mesoporous structure and surface area. When compared to the pristine Ni/BC catalyst, sulfuric activated Ni/BC catalyst has excellent mesopores and a high surface area, which increases the dispersion of Ni nanoparticles and hence improves the adsorptive effect and thus catalytic performance. A liquid phase hydrogenation of furfural to 2-methylfuran was performed over the developed 15 wt% Ni/BC catalyst. Langmuir–Hinshelwood–Hougen–Watson (LHHW) kinetic type models for adsorption of dissociative H₂ were screened based on an R² value greater than 99%, demonstrating that the experimental data satisfactorily fit to three plausible models: competitive (Model I), competitive at only one type of adsorption site (Model II), and non-competitive with two types of adsorption sites (Model III). With a correlation coefficient greater than 99% between the experimental rates and the predicted rate, Model III, which is a dual-site adsorption mechanism involving furfural adsorption and hydrogen dissociative adsorption and surface reaction, is the best fit. The Ni/BC catalyst demonstrated comparative performance and significant cost savings over previous catalysts; a value of 24.39 kJ mol⁻¹ was estimated for activation energy, −11.43 kJ mol⁻¹ for the enthalpy of adsorption for H₂, and −5.86 kJ mol⁻¹ for furfural. The developed Ni/BC catalyst demonstrated excellent stability in terms of conversion of furfural (96%) and yield of 2-methylfuran (54%) at the fourth successive experiments. Based on furfural conversion and yield of products, it appears that pores are constructed slowly during sulfuric acid activation of the biochar. Full article