High-energy Intermediates Research Articles

Identification of a Hidden, Highly Aggregation-Prone Intermediate of Full-Length TDP-43 That Triggers its Misfolding and Amyloid Aggregation.

In cells, TDP-43 is a crucial protein that can form harmful amyloid aggregates linked to fatal and incurable human neurodegenerative disorders. Normally, TDP-43 exists in a smaller soluble native state that prevents aggregation. However, aging and stress can destabilize this native state, leading to the formation of disease-causing amyloid aggregates via the formation of partially unfolded, high-energy intermediates with a greater tendency to aggregate. These intermediates are crucial in the early stages of amyloid formation and are challenging to study due to their low stability. Understanding the structure of these early aggregation-prone states of TDP-43 is essential for designing effective treatments for TDP-43 proteinopathies. Targeting these initial intermediates could be more effective than focusing on fully formed amyloid aggregates. By disrupting the aggregation process at this early stage, we may be able to prevent the progression of diseases related to TDP-43 aggregation. Hence, we decided to uncover the hidden, high-energy intermediates in equilibrium with the native states of TDP-43 by modulating the thermodynamic stability of the soluble native dimer (N form) and monomeric molten globular state (MG form) of full-length TDP-43. The thermodynamic modulation performed in the current study successfully revealed the highly aggregation-prone intermediate of full-length TDP-43, i.e., PUF. Moreover, we observed that along with high aggregation propensity, the aggregation kinetics and mechanisms of PUF differ from previously identified intermediates of full-length TDP-43 (the MG and I forms). The information regarding the initial aggregation-prone state of full-length TDP-43 could lead to therapies for amyloid diseases by halting early protein aggregation.

Disorder-to-order active site capping regulates the rate-limiting step of the inositol pathway

Myo-inositol-1-phosphate synthase (MIPS) catalyzes the NAD+-dependent isomerization of glucose-6-phosphate (G6P) into inositol-1-phosphate (IMP), controlling the rate-limiting step of the inositol pathway. Previous structural studies focused on the detailed molecular mechanism, neglecting large-scale conformational changes that drive the function of this 240 kDa homotetrameric complex. In this study, we identified the active, endogenous MIPS in cell extracts from the thermophilic fungus Thermochaetoides thermophila. By resolving the native structure at 2.48 Å (FSC = 0.143), we revealed a fully populated active site. Utilizing 3D variability analysis, we uncovered conformational states of MIPS, enabling us to directly visualize an order-to-disorder transition at its catalytic center. An acyclic intermediate of G6P occupied the active site in two out of the three conformational states, indicating a catalytic mechanism where electrostatic stabilization of high-energy intermediates plays a crucial role. Examination of all isomerases with known structures revealed similar fluctuations in secondary structure within their active sites. Based on these findings, we established a conformational selection model that governs substrate binding and eventually inositol availability. In particular, the ground state of MIPS demonstrates structural configurations regardless of substrate binding, a pattern observed across various isomerases. These findings contribute to the understanding of MIPS structure-based function, serving as a template for future studies targeting regulation and potential therapeutic applications.

Chemiexcitation-Triggered Photosensitizer Activation for Photooxidation of Aβ1-42 Aggregates.

Oxidative degradation of the pathogenic amyloid-β-peptide (Aβ) aggregation is an effective and promising method to treat Alzheimer's disease under light irradiation. However, the limited penetration of external light sources into deep tissues has hindered the development of this treatment. Therefore, we have designed an unprecedented chemiluminescence-initiated photodynamic therapy system to replace external laser irradiation, primarily composed of d-glucose-based polyoxalate (G-poly(oxalate)), the novel photosensitizer (BD-Se-QM), and bis [2,4,5-trichloro-6-(pentoxy-carbonyl) phenyl] ester. BD-Se-QM possesses excellent singlet oxygen (1O2) generation efficiency and the ability to photooxidize Aβ1-42 aggregates under white light. G-poly(oxalate) not only helps the nanosystem to cross the blood-brain barrier but also has sufficient oxalate ester groups to significantly enhance the efficiency of chemiluminescence resonance energy transfer. The oxalate ester groups in BD-Se-QM/NPs can chemically react with H2O2 to produce high-energy intermediates that activate BD-Se-QM, which can generate 1O2 to inhibit Aβ1-42 aggregates and also promote microglial uptake of Aβ1-42, reducing the Aβ1-42-induced neurotoxicity. The chemically stimulated nanoplatform not only solves the drug delivery problem but also eliminates the need for external light sources. We anticipate that this chemically excited nanosystem could also be used for targeted delivery of other small molecule drugs.

Single-electron transfer between sulfonium and tryptophan enables site-selective photo crosslinking of methyllysine reader proteins.

The identification of readers, an important class of proteins that recognize modified residues at specific sites, is essential to uncover the biological roles of post-translational modifications. Photoreactive crosslinkers are powerful tools for investigating readers. However, existing methods usually employ synthetically challenging photoreactive warheads, and their high-energy intermediates generated upon irradiation, such as nitrene and carbene, may cause substantial non-specific crosslinking. Here we report dimethylsulfonium as a methyllysine mimic that binds to specific readers and subsequently crosslinks to a conserved tryptophan inside the binding pocket through single-electron transfer under ultraviolet irradiation. The crosslinking relies on a protein-templated σ-π electron donor-acceptor interaction between sulfonium and indole, ensuring excellent site selectivity for tryptophan in the active site and orthogonality to other methyllysine readers. This method could escalate the discovery of methyllysine readers from complex cell samples. Furthermore, this photo crosslinking strategy could be extended to develop other types of microenvironment-dependent conjugations to site-specific tryptophan.

The Hydrogen Evolution Reaction: Using Molecular Design in Transition Metal Complexes to Control Catalytic Microenvironments on Electrode Surfaces

AbstractHydrogen gas and its production from renewable power sources will be an important part of decreasing global reliance on fossil fuels and developing a sustainable energy economy. Efficient electrocatalysis, however, relies on the delivery of both protons and electrons; ideally in a concerted fashion to avoid high energy intermediates, prevent charge build‐up, and circumvent large kinetic barriers. While this can be achieved using ligand design in homogenous molecular transition metal catalysts (specifically incorporating proton shuttles in the secondary coordination sphere), heterogeneous systems are more desirable from an industrial perspective due to their ease of use and enhanced durability. Supporting transition metal catalysts on electrode surfaces is therefore a promising approach for developing next generation electrocatalysts that retain molecular level control in interfacial environments. This review will first cover key design principles from natural systems, such as hydrogenase enzymes, and then survey some representative examples of synthetic homogeneous hydrogen evolution electrocatalysts that incorporate these important features. We will then discuss transition metal species that have been supported on electrode materials, with a focus on recent advances in the field, and the major challenges that remain.

Unlocking carbene reactivity by metallaphotoredox α-elimination.

The ability to tame high-energy intermediates is important for synthetic chemistry, enabling the construction of complex molecules and propelling advances in the field of synthesis. Along these lines, carbenes and carbenoid intermediates are particularly attractive, but often unknown, high-energy intermediates1,2. Classical methods to access metal carbene intermediates exploit two-electron chemistry to form the carbon-metal bond. However, these methods are usually prohibitive because of reagent safety concerns, limiting their broad implementation in synthesis3-6. Mechanistically, an alternative approach to carbene intermediates that could circumvent these pitfalls would involve two single-electron steps: radical addition to metal to forge the initial carbon-metal bond followed by redox-promoted α-elimination to yield the desired metal carbene intermediate. Here we realize this strategy through a metallaphotoredox platform that exploits iron carbene reactivity using readily available chemical feedstocks as radical sources and α-elimination from six classes of previously underexploited leaving groups. These discoveries permit cyclopropanation and σ-bond insertion into N-H, S-H and P-H bonds from abundant and bench-stable carboxylic acids, amino acids and alcohols, thereby providing a general solution to the challenge of carbene-mediated chemical diversification.

Analysis of Altitude and Ambient Temperature Effects on the Reactivity of Oxidation Catalysts in the Presence of H2

Worldwide emission standards are now required to cover engine operation under extreme ambient conditions, which affect the raw emissions and the efficiency of the exhaust aftertreatment systems. These regulations also target new combustion technologies for decarbonization, such as neat hydrogen (H2) combustion or dual-fuel strategies, which involve a challenge to the analysis of exhaust aftertreatment system requirements and performance. This work addresses the impact of high altitude and low ambient temperature conditions on the reactivity of an oxidation catalyst in the presence of H2. A reaction mechanism is proposed to cover the main conversion paths of CO, HC, and H2, including the formation and consumption of high-energy surface reaction intermediates. The mechanism has been implemented into a faster-than-real-time reduced-order model for multi-layer washcoat honeycomb catalytic converters. The model was utilized to investigate the effect of H2 concentration on the reactivity of CO and HC within the catalyst under various operating and ambient conditions. By applying the model and examining the selectivity towards different reaction pathways in the presence of H2, insights into surface intermediates and reactivity across different cross-sections of the monolith were obtained. This analysis discusses the underlying causes of reactivity changes promoted by H2 and its relative importance as a function of driving boundary conditions.

Complex I activity in hypoxia: implications for oncometabolism.

Certain cancer cells within solid tumors experience hypoxia, rendering them incapable of oxidative phosphorylation (OXPHOS). Despite this oxygen deficiency, these cells exhibit biochemical pathway activity that relies on NAD+. This mini-review scrutinizes the persistent, residual Complex I activity that oxidizes NADH in the absence of oxygen as the electron acceptor. The resulting NAD+ assumes a pivotal role in fueling the α-ketoglutarate dehydrogenase complex, a critical component in the oxidative decarboxylation branch of glutaminolysis - a hallmark oncometabolic pathway. The proposition is that through glutamine catabolism, high-energy phosphate intermediates are produced via substrate-level phosphorylation in the mitochondrial matrix substantiated by succinyl-CoA ligase, partially compensating for an OXPHOS deficiency. These insights provide a rationale for exploring Complex I inhibitors in cancer treatment, even when OXPHOS functionality is already compromised.

Phosphorane-Promoted C-C Coupling during Aryne Annulations.

Arynes are fleeting, high-energy intermediates that undergo myriad trapping reactions by nucleophiles. Their unusual reactivity compared to other electrophiles can spur unexpected mechanistic pathways enroute to the formation of benzenoid products. Herein we explore a particularly unique case of thermally generated arynes reacting with phosphoranes to form helical dibenzothiophenes and -selenophenes. Multiple new helical polycyclic aromatic products are reported. DP4+ and X-ray crystallographic analysis were used in tandem to confirm the structural topologies of selected products and to demonstrate the utility of DP4+ for distinguishing between isomeric polycyclic aromatic compounds. Lastly, we discuss a plausible mechanism consistent with DFT computations that accounts for the product formation; namely, ligand coupling (i.e., reductive elimination) within a hypervalent, pentacarbon-ligated σ-phosphorane furnishes the dibenzothio- or dibenzoselenophene.

Efficient Discrimination of Hazardous Organophosphate Flame Retardants via Cataluminescence-Based Multidimensional Ratiometric Sensing.

Emerging contaminants have recently evolved into a severe worldwide environmental issue. Organophosphate flame retardants (OPFRs) with neurotoxicity, genotoxicity, and reproductive and developmental toxicity are a class of notorious emerging contaminants that cause great concern. The development of high-efficiency and portable sensors for rapid online monitoring of OPFRs has become the primary demand for the exploration of the environmental migration and transformation of OPFRs. In this work, interestingly, the cataluminescence (CTL) phenomenon of OPFRs is first observed, and an ingenious multidimensional ratiometric CTL sensing strategy is developed for the recognition of multiple OPFRs. Three characteristic ratios are extracted from the multipeak CTL spectral curves based on energy transfer of single Tb/Eu-modified MgO sensing material, and thus a novel three-dimensional (3D) code recognition could be mapped out. This obtained 3D coordinate is found to be a unique characteristic for a given OPFR, just like an exclusive person's ID number, which can successfully discriminate and detect 10 kinds of OPFR vapors, including homologous series and isomers. More importantly, CTL mechanism investigations for OPFRs demonstrate that OPFRs undergo a series of chemical reaction processes, e.g., oxidative pyrolysis and hydroxylation, and different high-energy excited intermediates are generated, which trigger discrepant energy-transfer efficiency toward rare earth ions, leading to multipeak spectral profiles. Briefly, this proposed CTL analytical platform for OPFRs recognition initiates a new sensing principle for the efficient identification of emerging contaminants and shows significant prospects on rapid on-site detection.

Improving the Quality of Bio-oil Using the Interaction of Plastics and Biomass through Copyrolysis Coupled with Nonthermal Plasma Processing.

Bio-oil produced from the pyrolysis of biomass is chemically complex, viscous, highly acidic, and highly oxygenated. Copyrolysis of biomass and plastics can enhance oil quality by raising the H/C ratio, leading to improved biofuel properties. In this work, copyrolysis of polystyrene and biomass was passed to a second-stage dielectric barrier discharge nonthermal plasma reactor with the aim to further improve the product bio-oil. Pyrolysis of the polystyrene and biomass produces volatiles that pass to the second stage to undergo cracking and autohydrogenation reactions under nonthermal plasma conditions. There was a synergistic interaction between biomass and polystyrene in terms of overall oil and gas yield and composition even in the absence of the nonthermal plasma. However, the introduction of the nonthermal plasma produced a marked increase in monocyclic aromatic hydrocarbons (e.g., ethylbenzene), whereas polycyclic aromatic compounds decreased in concentration. Most notably, the influence of the plasma markedly reduced the quantity of oxygenated compounds in the product oil. It is suggested that the unique reactive environment produced by the plasma involving high-energy electrons, excited radicals, ions, and intermediates increases the interaction of the polystyrene and biomass pyrolysis volatiles. Increasing input plasma power from 50 to 70 W further enhanced the effects of the nonthermal plasma.

Potassium ion efflux induces exaggerated mitochondrial damage and non-pyroptotic necrosis when energy metabolism is blocked

Damage-associated molecular patterns (DAMPs) such as extracellular ATP and nigericin (a bacterial toxin) not only act as potassium ion (K+) efflux inducers to activate NLRP3 inflammasome, leading to pyroptosis, but also induce cell death independently of NLRP3 expression. However, the roles of energy metabolism in determining NLRP3-dependent pyroptosis and -independent necrosis upon K+ efflux are incompletely understood. Here we established cellular models by pharmacological blockade of energy metabolism, followed by stimulation with a K+ efflux inducer (ATP or nigericin). Two energy metabolic inhibitors, namely CPI-613 that targets α-ketoglutarate dehydrogenase and pyruvate dehydrogenase (a rate-limiting enzyme) and 2-deoxy-d-glucose (2-DG) that targets hexokinase, are recruited in this study, and Nlrp3 gene knockout macrophages were used. Our data showed that CPI-613 and 2-DG dose-dependently inhibited NLRP3 inflammasome activation, but profoundly increased cell death in the presence of ATP or nigericin. The cell death was K+ efflux-induced but NLRP3-independent, which was associated with abrupt reactive oxygen species (ROS) production, reduction of mitochondrial membrane potential, and oligomerization of mitochondrial proteins, all indicating mitochondrial damage. Notably, the cell death induced by K+ efflux and blockade of energy metabolism was distinct from pyroptosis, apoptosis, necroptosis or ferroptosis. Furthermore, fructose 1,6-bisphosphate, a high-energy intermediate of glycolysis, significantly suppressed CPI-613+nigericin-induced mitochondrial damage and cell death. Collectively, our data show that energy deficiency diverts NLRP3 inflammasome activation-dependent pyroptosis to Nlrp3-independent necrosis upon K+ efflux inducers, which can be dampened by high-energy intermediate, highlighting a critical role of energy metabolism in cell survival and death under inflammatory conditions.

Chemiluminescence of a Firefly Luciferin Analogue Reveals that Formation of the Key Intermediate Responsible for Excited State Generation Occurs on a Fully Concerted Step.

The chemiluminescence (CL) reaction of eight different 2-(4-hydroxyphenyl)-4,5-dihydrothiazole-4-carboxylate esters with an organic superbase and oxygen was investigated through a kinetic and computational study. These esters are all analogues to the luciferin substrate involved in efficient firefly bioluminescence. The kinetic data obtained from CL emission and light absorption assays were used in the context of linear free energy relationships (LFER); we obtained the Hammett reaction constant ρ = +1.62 ± 0.09 and the Brønsted constant βlg = -0.39 ± 0.04. These observations from LFER, together with activation parameters obtained from Arrhenius plots, suggest that the formation of the high-energy intermediate (HEI) 1,2-dioxetanone occurs via a concerted mechanism during the rate-determining step of the reaction. Calculations performed using density functional theory support a late transition state for HEI formation within the reaction mechanism pathway, which was described considering geometric parameters, Wiberg bond indices from natural bond order analysis, and the atomic charges derived from the electrostatic potential.

Correlating Conformational Equilibria with Catalysis in the Electron Bifurcating EtfABCX of Thermotoga maritima.

Electron bifurcation (BF) is an evolutionarily ancient energy coupling mechanism in anaerobes, whose associated enzymatic machinery remains enigmatic. In BF-flavoenzymes, a chemically high-potential electron forms in a thermodynamically favorable fashion by simultaneously dropping the potential of a second electron before its donation to physiological acceptors. The cryo-EM and spectroscopic analyses of the BF-enzyme Fix/EtfABCX from Thermotoga maritima suggest that the BF-site contains a special flavin-adenine dinucleotide and, upon its reduction with NADH, a low-potential electron transfers to ferredoxin and a high-potential electron reduces menaquinone. The transfer of energy from high-energy intermediates must be carefully orchestrated conformationally to avoid equilibration. Herein, anaerobic size exclusion-coupled small-angle X-ray scattering (SEC-SAXS) shows that the Fix/EtfAB heterodimer subcomplex, which houses BF- and electron transfer (ET)-flavins, exists in a conformational equilibrium of compacted and extended states between flavin-binding domains, the abundance of which is impacted by reduction and NAD(H) binding. The conformations identify dynamics associated with the T. maritima enzyme and also recapitulate states identified in static structures of homologous BF-flavoenzymes. Reduction of Fix/EtfABCX's flavins alone is insufficient to elicit domain movements conducive to ET but requires a structural "trigger" induced by NAD(H) binding. Models show that Fix/EtfABCX's superdimer exists in a combination of states with respect to its BF-subcomplexes, suggesting a cooperative mechanism between supermonomers for optimizing catalysis. The correlation of conformational states with pathway steps suggests a structural means with which Fix/EtfABCX may progress through its catalytic cycle. Collectively, these observations provide a structural framework for tracing Fix/EtfABCX's catalysis.

Biasing the Formation of Solution-Unstable Intermediates in Coordination Self-Assembly by Mechanochemistry.

Due to the reversible nature of coordination bonds and solvation effect, coordination self-assembly pathways are often difficult to elucidate experimentally in solution, as intermediates and products are in constant equilibration. The present study shows that some of these transient and high-energy self-assembly intermediates can be accessed by means of ball-milling approaches. Among them, highly aqueous-unstable Pd3 L11 and Pd6 L14 open-cage intermediates of the framed Fujita Pd6 L14 cage and Pd2 L22 , Pd3 L21 and Pd4 L22 intermediates of Mukherjee Pd6 L24 capsule are successfully trapped in solid-state, where Pd=tmedaPd2+ , L1=2,4,6-tris(4-pyridyl)-1,3,5-triazine and L2=1,3,5-tris(1-imidazolyl)benzene). Their structures are assigned by a combination of solution-based characterization tools such as standard NMR spectroscopy, DOSY NMR, ESI-MS and X-ray diffraction. Collectively, these results highlight the opportunity of using mechanochemistry to access unique chemical space with vastly different reactivity compared to conventional solution-based supramolecular self-assembly reactions.

Recent Advances in Photochemical Asymmetric Three-Component Reactions.

Over the past decades, asymmetric photochemical synthesis has garnered significant attention for its sustainability and unique ability to generate enantio-enriched molecules through distinct reaction pathways. Photochemical asymmetric three-component reactions have demonstrated significant potential for the rapid construction of chiral compounds with molecular diversity and complexity. However, noteworthy challenges persist, including the participation of high-energy intermediates such as radical species, difficulties in precise control of stereoselectivity, and the presence of competing background and side reactions. Recent breakthroughs have led to the development of sophisticated strategies in this field. This review explores the intricate mechanisms, synthetic applications, and limitations of these methods. We anticipate that it will contribute towards advancing asymmetric catalysis, photochemical synthesis, and green chemistry.

A photochemical method to evidence directional molecular motions

Light driven synthetic molecular motors represent crucial building blocks for advanced molecular machines and their applications. A standing challenge is the development of very fast molecular motors able to perform rotations with kHz, MHz or even faster frequencies. Central to this challenge is the direct experimental evidence of directionality because analytical methods able to follow very fast motions rarely deliver precise geometrical insights. Here, a general photochemical method for elucidation of directional motions is presented. In a macrocyclization approach the molecular motor rotations are restricted and forced to proceed in two separate ~180° rotation-photoequilibria. Therefore, all four possible photoinduced rotation steps (clockwise and counterclockwise directions) can be quantified. Comparison of the corresponding quantum yields to the unrestricted motor delivers direct evidence for unidirectionality. This method can be used for any ultrafast molecular motor even in cases where no high energy intermediates are present during the rotation cycle.

Small-Molecule Organocatalysis Facilitates In Situ Nucleotide Activation and RNA Copying.

A key challenge in origin-of-life research is the identification of plausible conditions that facilitate multiple steps along the pathway from chemistry to biology. The incompatibility of nucleotide activation chemistry and nonenzymatic template-directed RNA copying has hindered attempts to define such a pathway. Here, we show that adding heteroaromatic small molecules to the reaction network facilitates in situ nucleotide phosphate activation under conditions compatible with RNA copying, allowing both reactions to take place in the same mixture. This is achieved using Passerini-type phosphate activation in concert with nucleophilic organocatalysts that intercept high-energy reactive intermediates; this sequence ultimately affords 5',5'-imidazolium-bridged dinucleotides─the active species in template-directed RNA polymerization. Our results suggest that mixtures of prebiotically relevant heteroaromatic small molecules could have played a key role in the transition from chemistry to biology.

Dual-Hydrogen-Bond Donor and Brønsted Acid Cocatalysis Enables Highly Enantioselective Protio-Semipinacol Rearrangement Reactions.

A catalytic protio-semipinacol ring-expansion reaction has been developed for the highly enantioselective conversion of tertiary vinylic cyclopropyl alcohols into cyclobutanone products bearing α-quaternary stereogenic centers. The method relies on the cocatalytic effect of a chiral dual-hydrogen-bond donor (HBD) with hydrogen chloride. Experimental evidence is provided for a stepwise mechanism where protonation of the alkene generates a short-lived, high-energy carbocation, which is followed by C-C bond migration to deliver the enantioenriched product. This research applies strong acid/chiral HBD cocatalysis to weakly basic olefinic substrates and lays the foundation for further investigations of enantioselective reactions involving high-energy cationic intermediates.

Activatable Sonoafterglow Nanoprobes for T cell Imaging.

Real-time imaging of immune system benefits early diagnosis of disease and precision immunotherapy; however, most existing imaging probes either have "always-on" signals with poor correlation to immune responses, or rely on light excitation with limited imaging depth. Herein, an ultrasound-induced afterglow (sonoafterglow) nanoprobe is developed to specifically detect granzyme B for accurate imaging of T cell immunoactivation in vivo. The sonoafterglow nanoprobe (Q-SNAP) consists of sonosensitizers, afterglow substrates, and quenchers. Upon ultrasound irradiation, sonosensitizers generate singlet oxygen, which converts substrates to high-energy dioxetane intermediates that slowly release energy after ultrasound cessation. Due to the proximity, energy from substrates can be transferred to quenchers, leading to afterglow quenching. Only in the presence of granzyme B, quenchers are liberated from Q-SNAP, resulting in bright afterglow emission with an LOD (2.1nM) much lower than most existing fluorescent probes. Due to the deep tissue-penetrating ultrasound, sonoafterglow can be induced through tissue of 4cm thickness. Based on the correlation between sonoafterglow and granzyme B, Q-SNAP not only distinguishes autoimmune hepatitis from healthy liver as early as 4 hours after probe injection, but also effectively monitoring the cyclosporin A-mediated reversal of T cell hyperactivation. Q-SNAP thus offers the possibilities for dynamic monitoring of T cell dysfunction and evaluation of prophylactic immunotherapy in deep-seated lesions. This article is protected by copyright. All rights reserved.