Mechanistic Insights Research Articles

Mechanistic insight into heteroatom removal from vacuum gas oil blended with PMMA or PET waste.

This work analyzes vacuum gas oil (VGO) and hydrocracking products of feed blended with polymethylmethacrylate (PMMA) or polyethylene terephthalate (PET) in depth to clarify the oxygen, nitrogen, and sulfur removal pathways in these complex mixtures. Hydrocracking reactions are conducted in a semi-batch reactor with a Pt-Pd/HY bifunctional catalyst at 400 °C and 80 bar for 300 min with 10 wt% waste plastic using 0.1 catalyst/feed weight ratio. The samples are analyzed using various techniques, including high-resolution mass spectrometry, providing an improved, more detailed analytical representation. The results demonstrate the synergistic effect of cofeeding oxygenated plastics to the VGO, altering the preferential reaction pathways of heteroatom-containing species in the following order: nitrogen, oxygen, and sulfur. We assess the chemical structures from the gathered data, establish plausible reaction mechanisms, and evaluate the catalyst's role.

Tuberculosis-diabetes comorbidities: Mechanistic insights for clinical considerations and treatment challenges

Tuberculosis (TB) remains a leading cause of death among infectious diseases, particularly in poor countries. Viral infections, multidrug-resistant and ex-tensively drug-resistant TB strains, as well as the coexistence of chronic illnesses such as diabetes mellitus (DM) greatly aggravate TB morbidity and mortality. DM [particularly type 2 DM (T2DM)] and TB have converged making their control even more challenging. Two contemporary global epidemics, TB-DM behaves like a syndemic, a synergistic confluence of two highly prevalent diseases. T2DM is a risk factor for developing more severe forms of multi-drug resistant-TB and TB recurrence after preventive treatment. Since a bidirectional relationship exists between TB and DM, it is necessary to concurrently treat both, and promote recommendations for the joint management of both diseases. There are also some drug-drug interactions resulting in adverse treatment outcomes in TB-DM patients including treatment failure, and reinfection. In addition, autophagy may play a role in these comorbidities. Therefore, the TB-DM comorbidities present several health challenges, requiring a focus on multidisciplinary collaboration and integrated strategies, to effectively deal with this double burden. To effectively manage the comorbidity, further screening in affected countries, more suitable drugs, and better treatment strategies are required.

Caenorhabditis elegans Dicer acts with the RIG-I-like helicase DRH-1 and RDE-4 to cleave dsRNA.

Invertebrates use the endoribonuclease Dicer to cleave viral dsRNA during antiviral defense, while vertebrates use RIG-I-like Receptors (RLRs), which bind viral dsRNA to trigger an interferon response. While some invertebrate Dicers act alone during antiviral defense, Caenorhabditis elegans Dicer acts in a complex with a dsRNA binding protein called RDE-4, and an RLR ortholog called DRH-1. We used biochemical and structural techniques to provide mechanistic insight into how these proteins function together. We found RDE-4 is important for ATP-independent and ATP-dependent cleavage reactions, while helicase domains of both DCR-1 and DRH-1 contribute to ATP-dependent cleavage. DRH-1 plays the dominant role in ATP hydrolysis, and like mammalian RLRs, has an N-terminal domain that functions in autoinhibition. A cryo-EM structure indicates DRH-1 interacts with DCR-1's helicase domain, suggesting this interaction relieves autoinhibition. Our study unravels the mechanistic basis of the collaboration between two helicases from typically distinct innate immune defense pathways.

Uncovering the Role of Methylmercury on DNA Lesions at Cytotoxic Concentrations in Glutathione-Depleted Cells: Insights from Experimental and Computational Studies.

Organomercurials (RHg+), especially methylmercury (MeHg+) and ethylmercury (EtHg+), are considered to be more neurotoxic than the inorganic counterpart (Hg2+). They cause massive DNA damage in cells, especially in neurons, where cellular glutathione (GSH) levels are significantly low. However, the mechanism by which RHg+ exerts massive DNA damage at cytotoxic concentrations in brain cells remains obscure. In this study, we investigated the effect of RHg+ on the structural and electronic properties of nucleosides and its effects on DNA damage. The direct interaction of RHg+ with the nucleoside significantly weakens N-glycosidic bonds, decreases the C-H bond energy of sugar moieties, and increases the electrophilicity of the C8-center of purine bases. As a consequence, RHg+-conjugated DNA molecules are extremely labile and highly sensitive to any nucleophiles/radicals present in GSH-depleted cells and, thus, undergo enhanced oxidative and unusual alkylative DNA damage. We also report a functional model of organomercurial lyase, which showed excellent cytoprotective effect against RHg+-induced cytotoxicity; this reverses the activity of glutathione reductase inhibited by MeHgCl and ceases oxidative and alkylating DNA damage. This intriguing finding provides new mechanistic insight into the mode of action of organomercurials in GSH-depleted cells and their adverse effects on individuals with neurodegenerative disorders associated with oxidative stress.

Temperature dependence mechanism of high-temperature oxidation of transition metal silicide MoSi2.

Transition metal silicides represented by MoSi2 have excellent oxidation resistance and are widely used as high-temperature anti-oxidation coatings in hot end components of power equipment. However, the mechanism of temperature-dependent growth of MoSi2 oxidation products has not been revealed. Therefore, this study investigated the formation characteristics of oxide film and silicide-poor compound on MoSi2 at temperatures of 1000-1550℃ through high-temperature oxidation experiments, combined with microscopic Raman spectroscopy, SEM, and XRD characterizations. The result showed that MoSi2 underwent high-temperature selective oxidation reactions at 1000-1200℃, forming MoO2 and SiO2 oxide film on the substrate. As the oxidation temperature increased to 1550℃, after 100 hours of oxidation, along with the disappearance of MoO2 and the phase transformation of SiO2, a continuous Mo5Si3 layer with a thickness of approximately 47 μm was formed at the SiO2-MoSi2 interface. Thermodynamics and kinetic calculations further revealed the mechanism of temperature-dependent growth of oxidation products (MoO2 and Mo5Si3) during high-temperature oxidation process of MoSi2. As the temperature increased, the diffusion flux ratio of O and Si decreased, leading to a decrease in oxygen concentration at the interface and promoting the growth of the Mo5Si3 layer. Its thickness is an important indicator for evaluating the oxidation resistance of MoSi2 coatings during service. This study provides experimental and mechanistic insights into the temperature-dependent growth behavior of Mo5Si3 during the high-temperature oxidation of MoSi2 coating, and provides guidance for predicting the service life and improving the oxidation resistance of silicide coatings.

Potential Role and Mechanism of Mulberry Extract in Immune Modulation: Focus on Chemical Compositions, Mechanistic Insights, and Extraction Techniques

Potential Role and Mechanism of Mulberry Extract in Immune Modulation: Focus on Chemical Compositions, Mechanistic Insights, and Extraction Techniques

Structural and mechanistic insights into Quinolone Synthase to address its functional promiscuity

Quinolone synthase from Aegle marmelos (AmQNS) is a type III polyketide synthase that yields therapeutically effective quinolone and acridone compounds. Addressing the structural and molecular underpinnings of AmQNS and its substrate interaction in terms of its high selectivity and specificity can aid in the development of numerous novel compounds. This paper presents a high-resolution AmQNS crystal structure and explains its mechanistic role in synthetic selectivity. Additionally, we provide a model framework to comprehend structural constraints on ketide insertion and postulate that AmQNS’s steric and electrostatic selectivity plays a role in its ability to bind to various core substrates, resulting in its synthetic diversity. AmQNS prefers quinolone synthesis and can accommodate large substrates because of its wide active site entrance. However, our research suggests that acridone is exclusively synthesized in the presence of high malonyl-CoA concentrations. Potential implications of functionally relevant residue mutations were also investigated, which will assist in harnessing the benefits of mutations for targeted polyketide production. The pharmaceutical industry stands to gain from these findings as they expand the pool of potential drug candidates, and these methodologies can also be applied to additional promising enzymes.

Mechanistic and Electronic Insights into Efficient Carbon Dioxide Reduction Driven by Visible Light Using a Coordination Polymer

Mechanistic and Electronic Insights into Efficient Carbon Dioxide Reduction Driven by Visible Light Using a Coordination Polymer

Functional and antigenic characterization of SARS-CoV-2 spike fusion peptide by deep mutational scanning

The fusion peptide of SARS-CoV-2 spike protein is functionally important for membrane fusion during virus entry and is part of a broadly neutralizing epitope. However, sequence determinants at the fusion peptide and its adjacent regions for pathogenicity and antigenicity remain elusive. In this study, we perform a series of deep mutational scanning (DMS) experiments on an S2 region spanning the fusion peptide of authentic SARS-CoV-2 in different cell lines and in the presence of broadly neutralizing antibodies. We identify mutations at residue 813 of the spike protein that reduced TMPRSS2-mediated entry with decreased virulence. In addition, we show that an F823Y mutation, present in bat betacoronavirus HKU9 spike protein, confers resistance to broadly neutralizing antibodies. Our findings provide mechanistic insights into SARS-CoV-2 pathogenicity and also highlight a potential challenge in developing broadly protective S2-based coronavirus vaccines.

Electron transport chain capacity expands yellow fever vaccine immunogenicity.

Vaccination has successfully controlled several infectious diseases although better vaccines remain desirable. Host response to vaccination studies have identified correlates of vaccine immunogenicity that could be useful to guide development and selection of future vaccines. However, it remains unclear whether these findings represent mere statistical correlations or reflect functional associations with vaccine immunogenicity. Functional associations, rather than statistical correlates, would offer mechanistic insights into vaccine-induced adaptive immunity. Through a human experimental study to test the immunomodulatory properties of metformin, an anti-diabetic drug, we chanced upon a functional determinant of neutralizing antibodies. Although vaccine viremia is a known correlate of antibody response, we found that in healthy volunteers with no detectable or low yellow fever 17D viremia, metformin-treated volunteers elicited higher neutralizing antibody titers than placebo-treated volunteers. Transcriptional and metabolomic analyses collectively showed that a brief course of metformin, started 3 days prior to YF17D vaccination and stopped at 3 days after vaccination, expanded oxidative phosphorylation and protein translation capacities. These increased capacities directly correlated with YF17D neutralizing antibody titers, with reduced reactive oxygen species response compared to placebo-treated volunteers. Our findings thus demonstrate a functional association between cellular respiration and vaccine-induced humoral immunity and suggest potential approaches to enhancing vaccine immunogenicity.

Phosphomethylpyrimidine Synthase (ThiC): Trapping of Five Intermediates Provides Mechanistic Insights on a Complex Radical Cascade Reaction in Thiamin Biosynthesis

Phosphomethylpyrimidine Synthase (ThiC): Trapping of Five Intermediates Provides Mechanistic Insights on a Complex Radical Cascade Reaction in Thiamin Biosynthesis

Decennary Update on Oxidative-Rearrangement Involving 1,2-Aryl C-C Migration Around Alkenes: Synthetic and Mechanistic Insights.

In recent years, numerous methodologies on oxidative rearrangements of alkenes have been investigated, that produce multipurpose synthons and heterocyclic scaffolds of potential applications. The present review focused on recently established methodologies for oxidative transformation via 1,2-aryl migration in alkenes (2013-2023). Special emphasis has been placed on mechanistic pathways to understand the reactivity pattern of different substrates, challenges to enhance selectivity, the key role of different reagents, and effect of different substituents, and how they affect the rearrangement process. Moreover, synthetic limitations and future direction also have been discussed. We believe, this review offers new synthetic and mechanistic insight to develop elegant precursors and approaches to explore the utilization of alkene-based compounds for natural product synthesis and functional materials.

Mechanism Insights in Anticorrosion Performance of Waterborne Epoxy Coatings Reinforced by PEI-Functionalized Boron Nitride Nanosheets.

Functionalized hexagonal boron nitride nanosheets (BNNSs) have arisen as compelling anticorrosive additives, yet the precise mechanism of their corrosion resistance enhancement in coatings remains unclear. Here, polyethylenimine functionalized BNNSs (PEI-BNNSs) with approximately 6-11 layers were prepared through a "one-step" method. Then, the PEI-BNNSs/Waterborne epoxy (WEP) composite coatings were incorporated via the waterborne latex blending method for the anticorrosion of the Q235 substrate. The impedance modulus (|Z|f = 0.01 Hz) of 0.5 wt % PEI-BNNSs/WEP composite coating soaked in 3.5 wt % NaCl solution for 35 days increased by 4 orders of magnitude compared to pure WEP coating, exhibiting exceptional long-term resistance against corrosion. The positron annihilation lifetime spectroscopy and corrosion product analysis demonstrated that the reinforced anticorrosion capabilities are not solely ascribed to the "tortuous path effect" arising from BNNSs impermeability. These mechanisms also encompass the reduction in free volume fraction and radius of the free volume cavities within the composite coating brought about by the PEI molecules. Additionally, the increase in coating adhesion, promoted by PEI, plays an important role in augmenting the barrier properties against corrosive agents. This study provided a full comprehension of the role played by functionalized BNNSs in fortifying the anticorrosion attributes of WEP coatings.

Moving towards a mechanistic understanding of biostimulant impacts on soil properties and processes: a semi-systematic review

Biostimulants are gaining prominence in scientific research, with the potential to enhance plant productivity through benefits to crop yield/quality and tolerance to environmental stresses. Through possible improvements to nutrient use efficiency, they may also lessen the adverse environmental impacts of conventional inorganic fertilizer use in agriculture. The application of biostimulants is currently uncommon as a farming practice, with uncertain effectiveness in delivering these potential benefits. Current research focuses on biostimulant effects on plant physiological changes. There is little scientific evidence on the impact of biostimulants on soil properties (biological, physical, or chemical) or soil functions. This knowledge gap should be addressed considering the vital role of soil processes in the bioavailability of nutrients, as reflected in crop productivity. This review evaluates laboratory and field experimental work on the effectiveness of common, non-microbial biostimulants, with a focus on their modes of action within the soil matrix. Of 2,097 initial articles returned through the search strings, 10 were within the scope of this review. A common soil biostimulant mechanism emerges from this literature. This relates to the supply of nutrients provided by the biostimulants, which stimulate native soil microbiology in mineralizing organic material in the soil, thus producing more bioavailable nutrients for plant uptake. Additionally, some articles link biostimulant effects to soil physical and chemical changes, which in turn impact soil biology (and vice versa). However, there is inconsistent evidence to provide full support for these explanatory mechanisms. This review highlights the need for further research into the effect of biostimulants on the native soil microbiology and associated soil properties, to provide greater clarity on biostimulants’ modes of action and greater mechanistic insights into how they can be used to improve crop production.

Protonation of an Imine-linked Covalent Organic Framework for Efficient H2O2 Photosynthesis under Visible Light up to 700 nm.

Covalent organic frameworks (COFs) are promising photocatalysts for H2O2 production from water via oxygen reduction reactions (ORR). The design of COFs for efficient H2O2 production indubitably hinges on an in-depth understanding of their ORR mechanisms. In this work, taking an imine-linked COF as an example, we demonstrate that protonation of the functional units such as imine, amine, and triazine, is a highly efficient strategy to upgrade the activity levels for H2O2 synthesis. The protonation not only extends the light absorption of the COF but also provides proton sources that directly participate in H2O2 generation. Notably, the protonation simplifies the reaction pathways of ORR to H2O2, i.e. from an indirect superoxide radical ([[EQUATION]]) mediated route to a direct one-step two-electron route. Theoretical calculations confirm that the protonation favors H2O2 synthesis due to easy access of protons near the reaction sites that removes the energy barrier for generating *OOH intermediate. These findings not only extend the mechanistic insight into H2O2 photosynthesis but also provide a rational guideline for the design and upgradation of efficient COFs.

Crosstalk between degradation and bioenergetics: how autophagy and endolysosomal processes regulate energy production

Abstract Cells undergo metabolic reprogramming to adapt to changes In nutrient availability, cellular activity, and transitions in cell states. The balance between glycolysis and mitochondrial respiration is crucial for energy production, and metabolic reprogramming stipulates a shift in such balance to optimize both bioenergetic efficiency and anabolic requirements. Failure in switching bioenergetic dependence can lead to maladaptation and pathogenesis. While cellular degradation is known to recycle precursor molecules for anabolism, its potential role in regulating energy production remains less explored. The bioenergetic switch between glycolysis and mitochondrial respiration involves transcription factors and organelle homeostasis, which are both regulated by the cellular degradation pathways. A growing body of studies has demonstrated that both stem cells and differentiated cells exhibit bioenergetic switch upon perturbations of autophagic activity or endolysosomal processes. Here, we highlighted the current understanding of the interplay between degradation processes, specifically autophagy and endolysosomes, transcription factors, endolysosomal signaling, and mitochondrial homeostasis in shaping cellular bioenergetics. This review aims to summarize the relationship between degradation processes and bioenergetics, providing a foundation for future research to unveil deeper mechanistic insights into bioenergetic regulation.

Protonation of an Imine‐linked Covalent Organic Framework for Efficient H2O2 Photosynthesis under Visible Light up to 700 nm

Covalent organic frameworks (COFs) are promising photocatalysts for H2O2 production from water via oxygen reduction reactions (ORR). The design of COFs for efficient H2O2 production indubitably hinges on an in‐depth understanding of their ORR mechanisms. In this work, taking an imine‐linked COF as an example, we demonstrate that protonation of the functional units such as imine, amine, and triazine, is a highly efficient strategy to upgrade the activity levels for H2O2 synthesis. The protonation not only extends the light absorption of the COF but also provides proton sources that directly participate in H2O2 generation. Notably, the protonation simplifies the reaction pathways of ORR to H2O2, i.e. from an indirect superoxide radical ([[EQUATION]]) mediated route to a direct one‐step two‐electron route. Theoretical calculations confirm that the protonation favors H2O2 synthesis due to easy access of protons near the reaction sites that removes the energy barrier for generating *OOH intermediate. These findings not only extend the mechanistic insight into H2O2 photosynthesis but also provide a rational guideline for the design and upgradation of efficient COFs.

Quantum mechanics insights into melatonin and analogs binding to melatonin MT1 and MT2 receptors

Melatonin receptors MT1 and MT2 are G protein-coupled receptors that mediate the effects of melatonin, a hormone involved in circadian rhythms and other physiological functions. Understanding the molecular interactions between these receptors and their ligands is crucial for developing novel therapeutic agents. In this study, we used molecular docking, molecular dynamics simulations, and quantum mechanics calculation to investigate the binding modes and affinities of three ligands: melatonin (MLT), ramelteon (RMT), and 2-phenylmelatonin (2-PMT) with both receptors. Based on the results, we identified key amino acids that contributed to the receptor-ligand interactions, such as Gln181/194, Phe179/192, and Asn162/175, which are conserved in both receptors. Additionally, we described new meaningful interactions with Gly108/Gly121, Val111/Val124, and Val191/Val204. Our results provide insights into receptor-ligand recognition’s structural and energetic determinants and suggest potential strategies for designing more optimized molecules. This study enhances our understanding of receptor-ligand interactions and offers implications for future drug development.

Reaction Mechanism of Hydrogen Generation and Nitrogen Fixation at Carbon Nitride/Double Perovskite Heterojunctions

Photocatalytically active heterojunctions based on metal halide perovskites (MHPs) are drawing significant interest for their chameleon ability to foster several redox reactions. The lack of mechanistic insights into their performance, however, limits the ability of engineering novel and optimized materials. Herein, a report is made on a composite system including a double perovskite, Cs2AgBiCl6/g‐C3N4, used in parallel for solar‐driven hydrogen generation and nitrogen reduction, quantified by a rigorous analytical approach. The composite efficiently promotes the two reactions, but its activity strongly depends on the perovskite/carbon nitride relative amounts. Through advanced spectroscopic investigation and density function theory (DFT) modeling the H2 and NH3 production reaction mechanisms are studied, finding perovskite halide vacancies as the primary reactive sites for hydrogen generation together with a positive contribution of low loaded g‐C3N4 in reducing carrier recombination. For nitrogen reduction, instead, the active sites are g‐C3N4 nitrogen vacancies, and the heterojunction best performs at low perovskites loadings where the composites maximize light absorption and reduce carrier losses. It is believed that these insights are important add‐ons toward universal exploitation of MHPs in contemporary photocatalysis.

Impact of Combinatorial Histone Modifications on Acetyllysine Recognition by the ATAD2 and ATAD2B Bromodomains.

The ATPase family AAA+ domain containing 2 (ATAD2) protein and its paralog ATAD2B have a C-terminal bromodomain (BRD) that functions as a reader of acetylated lysine residues on histone proteins. Using a structure-function approach, we investigated the ability of the ATAD2/B BRDs to select acetylated lysine among multiple histone post-translational modifications. The ATAD2B BRD can bind acetylated histone ligands that also contain adjacent methylation or phosphorylation marks, while the presence of these modifications significantly weakened the acetyllysine binding activity of the ATAD2 BRD. Our structural studies provide mechanistic insights into how ATAD2/B BRD-binding pocket residues coordinate the acetyllysine group in the context of adjacent post-translational modifications. Furthermore, we investigated how sequence changes in amino acids of the histone ligands impact the recognition of an adjacent acetyllysine residue. Our study highlights how the interplay between multiple combinations of histone modifications influences the reader activity of the ATAD2/B BRDs, resulting in distinct binding modes.