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At least 415 records · Page 23

The PTPN2/PTPN1 inhibitor ABBV-CLS-484 unleashes potent anti-tumour immunity

Immune checkpoint blockade is effective for some patients with cancer, but most are refractory to current immunotherapies and new approaches are needed to overcome resistance. The protein tyrosine phosphatases PTPN2 and PTPN1 are central regulators of inflammation, and their genetic deletion in either tumour cells or immune cells promotes anti-tumour immunity. However, phosphatases are challenging drug targets; in particular, the active site has been considered undruggable. Here we present the discovery and characterization of ABBV-CLS-484 (AC484), a first-in-class, orally bioavailable, potent PTPN2 and PTPN1 active-site inhibitor. AC484 treatment in vitro amplifies the response to interferon and promotes the activation and function of several immune cell subsets. In mouse models of cancer resistant to PD-1 blockade, AC484 monotherapy generates potent anti-tumour immunity. We show that AC484 inflames the tumour microenvironment and promotes natural killer cell and CD8 + T cell function by enhancing JAK–STAT signalling and reducing T cell dysfunction. Inhibitors of PTPN2 and PTPN1 offer a promising new strategy for cancer immunotherapy and are currently being evaluated in patients with advanced solid tumours (ClinicalTrials.gov identifier NCT04777994). More broadly, our study shows that small-molecule inhibitors of key intracellular immune regulators can achieve efficacy comparable to or exceeding that of antibody-based immune checkpoint blockade in preclinical models. Finally, to our knowledge, AC484 represents the first active-site phosphatase inhibitor to enter clinical evaluation for cancer immunotherapy and may pave the way for additional therapeutics that target this important class of enzymes.

60 APPLIED LIFE SCIENCES↗

Revealing protonation states and tracking substrate in serine hydroxymethyltransferase with room-temperature X-ray and neutron crystallography

Pyridoxal 5’-phosphate (PLP)-dependent enzymes utilize a vitamin B 6 -derived cofactor to perform a myriad of chemical transformations on amino acids and other small molecules. Some PLP-dependent enzymes, such as serine hydroxymethyltransferase (SHMT), are promising drug targets for the design of small-molecule antimicrobials and anticancer therapeutics, while others have been used to synthesize pharmaceutical building blocks. Understanding PLP-dependent catalysis and the reaction specificity is crucial to advance structure-assisted drug design and enzyme engineering. Here we report the direct determination of the protonation states in the active site of Thermus thermophilus SHMT (TthSHMT) in the internal aldimine state using room-temperature joint X-ray/neutron crystallography. Conserved active site architecture of the model enzyme TthSHMT and of human mitochondrial SHMT (hSHMT2) were compared by obtaining a room-temperature X-ray structure of hSHMT2, suggesting identical protonation states in the human enzyme. The amino acid substrate serine pathway through the TthSHMT active site cavity was tracked, revealing the peripheral and cationic binding sites that correspond to the pre-Michaelis and pseudo-Michaelis complexes, respectively. At the peripheral binding site, the substrate is bound in the zwitterionic form. By analyzing the observed protonation states, Glu53, but not His residues, is proposed as the general base catalyst, orchestrating the retro-aldol transformation of L-serine into glycine.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Unraveling Dimensional Tuning: From 2D to 3D in Covalent Organic Frameworks for Enhanced 2e – Oxygen Reduction Reaction

Covalent organic frameworks (COFs) with a two-dimensional (2D) topology have recently emerged as promising catalyst systems for the electrosynthesis of hydrogen peroxide (H 2 O 2 ) from oxygen (O 2 ). However, designing 2D catalysts to achieve higher H 2 O 2 selectivity presents a significant challenge because of the extensive layer stacking and the aggregated active sites located in the basal planes. It results in lower atom utilization, which requires attention. In this study, we present two functionally similar COFs: one with a 2D rhombus topology (2D@BT_TPA-COF) and another with a three-dimensional (3D) noninterpenetrated pts topology (3D@BT_TPA-COF). Both COFs were utilized for the 2e – oxygen reduction reaction (2e – ORR). Tunning the dimensionality from 2D to 3D resulted in an increase in H 2 O 2 selectivity from approximately ~56% to approximately ~96% (at 0.4 V) and a rise in the turnover frequency (TOF) from 0.05 to 0.08 s –1 at 0.3 V. Nonaggregated active site distribution over 3D topology, featuring higher active site exposure, provides better access to the O 2 /electrolyte and facilitates electron transfer leading to higher 2e – ORR activity and selectivity compared to the 2D counterpart.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

An RNA aptamer exploits exosite-dependent allostery to achieve specific inhibition of coagulation factor IXa

Hemostasis relies on a reaction network of serine proteases and their cofactors to form a blood clot. Coagulation factor IXa (protease) plays an essential role in hemostasis as evident from the bleeding disease associated with its absence. RNA aptamers specifically targeting individual coagulation factors have potential as anticoagulants and as probes of the relationship between structure and function. Here, we report X-ray structures of human factor IXa without a ligand bound to the active site either in the apo-form or in complex with an inhibitory aptamer specific for factor IXa. The aptamer binds to an exosite in the catalytic domain and allosterically distorts the active site. Our studies reveal a conformational ensemble of IXa states, wherein large movements of Trp 215 near the active site drive functional transitions between the closed (aptamer-bound), latent (apo), and open (substrate-bound) states. The latent state of the apo-enzyme may bear on the uniquely poor catalytic activity of IXa compared to other coagulation proteases. The exosite, to which the aptamer binds, has been implicated in binding VIIIa and heparin, both of which regulate IXa function. Our findings reveal the importance of exosite-driven allosteric modulation of IXa function and new strategies to rebalance hemostasis for therapeutic gain.

Science & Technology - Other Topics↗

High-Resolution XFEL Structure of the Soluble Methane Monooxygenase Hydroxylase Complex with its Regulatory Component at Ambient Temperature in Two Oxidation States

Soluble methane monooxygenase (sMMO) is a multicomponent metalloenzyme that catalyzes the conversion of methane to methanol at ambient temperature using a nonheme, oxygen-bridged dinuclear iron cluster in the active site. Structural changes in the hydroxylase component (sMMOH) containing the diiron cluster caused by complex formation with a regulatory component (MMOB) and by iron reduction are important for the regulation of O 2 activation and substrate hydroxylation. Structural studies of metalloenzymes using traditional synchrotron-based X-ray crystallography are often complicated by partial X-ray-induced photoreduction of the metal center, thereby obviating determination of the structure of the enzyme in pure oxidation states. Here, microcrystals of the sMMOH:MMOB complex from Methylosinus trichosporium OB3b were serially exposed to X-ray free electron laser (XFEL) pulses, where the ≤35 fs duration of exposure of an individual crystal yields diffraction data before photoreduction-induced structural changes can manifest. Merging diffraction patterns obtained from thousands of crystals generates radiation damage-free, 1.95 Å resolution crystal structures for the fully oxidized and fully reduced states of the sMMOH:MMOB complex for the first time. The results provide new insight into the manner by which the diiron cluster and the active site environment are reorganized by the regulatory protein component in order to enhance the steps of oxygen activation and methane oxidation. Furthermore, this study also emphasizes the value of XFEL and serial femtosecond crystallography (SFX) methods for investigating the structures of metalloenzymes with radiation sensitive metal active sites.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Atomically dispersed metal–nitrogen–carbon catalysts for fuel cells: advances in catalyst design, electrode performance, and durability improvement

The urgent need to address the high-cost issue of proton-exchange membrane fuel cell (PEMFC) technologies, particularly for transportation applications, drives the development of simultaneously highly active and durable platinum group metal-free (PGM-free) catalysts and electrodes. The past decade has witnessed remarkable progress in exploring PGM-free cathode catalysts for the oxygen reduction reaction (ORR) to overcome sluggish kinetics and catalyst instability in acids. Among others, scientists have identified the newly emerging atomically dispersed transition metal (M: Fe, Co, or/and Mn) and nitrogen co-doped carbon (M–N–C) catalysts as the most promising alternative to PGM catalysts. Here, we provide a comprehensive review of significant breakthroughs, remaining challenges, and perspectives regarding the M–N–C catalysts in terms of catalyst activity, stability, and membrane electrode assembly (MEA) performance. A variety of novel synthetic strategies demonstrated effectiveness in improving intrinsic activity, increasing active site density, and attaining optimal porous structures of catalysts. Rationally designing and engineering the coordination environment of single metal MN x sites and their local structures are crucial for enhancing intrinsic activity. Increasing the site density relies on the innovative strategies of restricting the migration and agglomeration of single metal sites into metallic clusters. Relevant understandings provide the correlations among the nature of active sites, nanostructures, and catalytic activity of M–N–C catalysts at the atomic scale through a combination of experimentation and theory. Current knowledge of the transferring catalytic properties of M–N–C catalysts to MEA performance is limited. Rationally designing morphologic features of M–N–C catalysts play a vital role in boosting electrode performance through exposing more accessible active sites, realizing uniform ionomer distribution, and facilitating mass/proton transports. We outline future research directions concerning the comprehensive evaluation of M–N–C catalysts in MEAs. The most considerable challenge of current M–N–C catalysts is the unsatisfied stability and rapid performance degradation in MEAs. Therefore, we further discuss practical methods and strategies to mitigate catalyst and electrode degradation, which is fundamentally essential to make M–N–C catalysts viable in PEMFC technologies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Monobody Inhibitor Selective to the Phosphatase Domain of SHP2 and its Use as a Probe for Quantifying SHP2 Allosteric Regulation

SHP2 is a phosphatase/adaptor protein that plays an important role in various signaling pathways. Its mutations are associated with cancers and developmental diseases. SHP2 contains a protein tyrosine phosphatase (PTP) and two SH2 domains. Selective inhibition of these domains has been challenging due to the multitude of homologous proteins in the proteome. Here, we developed a monobody, synthetic binding protein, that bound to and inhibited the SHP2 PTP domain. It was selective to SHP2 PTP over close homologs. A crystal structure of the monobody-PTP complex revealed that the monobody bound both highly conserved residues in the active site and less conserved residues in the periphery, rationalizing its high selectivity. Its epitope overlapped with the interface between the PTP and N-terminal SH2 domains that is formed in auto-inhibited SHP2. By using the monobody as a probe for the accessibility of the PTP active site, we developed a simple, nonenzymatic assay for the allosteric regulation of SHP2. The assay showed that, in the absence of an activating phospho-Tyr ligand, wild-type SHP2 and the “PTP-dead” C459E mutant were predominantly in the closed state in which the PTP active site is inaccessible, whereas the E76K and C459S mutants were in the open, active state. It also revealed that previously developed monobodies to the SH2 domains, ligands lacking a phospho-Tyr, weakly favored the open state. These results provide corroboration for a conformational equilibrium underlying allosteric regulation of SHP2, provide powerful tools for characterizing and controlling SHP2 functions, and inform drug discovery against SHP2.

59 BASIC BIOLOGICAL SCIENCES↗

Atomically dispersed supported metal species as catalysts for alcohol conversion, and hydrogen and chemicals production

Supported single metal atoms are a new class of catalyst in which precious metals can be used at the ultimate limit of atom efficiency. While great strides have been made in demonstrating the potential of single-atom catalysts for many industrial reactions, there remains much debate in the literature over the nature of the active sites and the reaction mechanisms. The major goal of this project was to elucidate how atomic dispersions of metals on oxide supports enable catalytic reactions and how to stabilize such active sites for practical catalyst development. This is particularly important for the reactions of interest to fuel reforming for hydrogen generation in which atomically-dispersed metal ions on various oxide surfaces have been identified as the active sites. Working with trace amounts of precious metals is both fundamentally intriguing and of great practical interest in our continual search for low-cost, efficient and stable catalysts for the conversion of fuels to hydrogen under highly demanding operating conditions. A second major goal of the project was to rationally design and prepare single atom alloy (SAA) catalyst compositions based on information gathered from surface science studies on model catalysts and by catalytic evaluation of nanoparticle SAA analogs under realistic conditions. The overarching goal was to use the knowledge garnered from this project to design and develop new catalysts at the single atom limit, which can be applied to selective hydrogenation reactions (alkynes and dienes to alkenes) and the dehydrogenation of methanol and ethanol to value-added products at near-ambient conditions. Detailed information about the results of the project are given below.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Self-inhibited State of Venezuelan Equine Encephalitis Virus (VEEV) nsP2 Cysteine Protease: A Crystallographic and Molecular Dynamics Analysis

The Venezuelan equine encephalitis virus (VEEV) belongs to the Togaviridae family and is pathogenic to both humans and equines. The VEEV non-structural protein 2 (nsP2) is a cysteine protease (nsP2pro) that processes the polyprotein and thus it is a drug target for inhibitor discovery. The atomic structure of the VEEV nsP2 catalytic domain was previously characterized by both X-ray crystallography and computational studies. A modified nsP2pro harboring a N475A mutation in the N terminus was observed to exhibit an unexpected conformation: the N-terminal residues bind to the active site, mimicking binding of a substrate. The large conformational change of the N terminus was assumed to be induced by the N475A mutation, as N475 has an important role in stabilization of the N terminus and the active site. This conformation was first observed in the N475A mutant, but we also found it while determining a crystal structure of the catalytically active nsP2pro containing the wild-type N475 active site residue and K741A/K767A surface entropy reduction mutations. This suggests that the N475A mutation is not a prerequisite for self-inhibition. Here, we describe a high resolution (1.46 Å) crystal structure of a truncated nsP2pro (residues 463–785, K741A/K767A) and analyze the structure further by molecular dynamics to study the active and self-inhibited conformations of nsP2pro and its N475A mutant. A comparison of the different conformations of the N-terminal residues sheds a light on the interactions that play an important role in the stabilization of the enzyme.

59 BASIC BIOLOGICAL SCIENCES↗

Kβ X-ray Emission Spectroscopy of Cu(I)-Lytic Polysaccharide Monooxygenase: Direct Observation of the Frontier Molecular Orbital for H 2 O 2 Activation

Lytic polysaccharide monooxygenases (LPMOs) catalyze the degradation of recalcitrant carbohydrate polysaccharide substrates. These enzymes are characterized by a mononuclear Cu(I) active site with a three-coordinate T-shaped “His-brace” configuration including the N-terminal histidine and its amine group as ligands. Here, this study explicitly investigates the electronic structure of the d 10 Cu(I) active site in a LPMO using Kβ X-ray emission spectroscopy (XES). The lack of inversion symmetry in the His-brace site enables the 3d/p mixing required for intensity in the Kβ valence-to-core (VtC) XES spectrum of Cu(I)-LPMO. These Kβ XES data are correlated to density functional theory (DFT) calculations to define the bonding, and in particular, the frontier molecular orbital (FMO) of the Cu(I) site. These experimentally validated DFT calculations are used to evaluate the reaction coordinate for homolytic cleavage of the H 2 O 2 O–O bond and understand the contribution of this FMO to the low barrier of this reaction and how the geometric and electronic structure of the Cu(I)-LPMO site is activated for rapid reactivity with H 2 O 2 .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Facet Preferencing by Chemical Substitution Controls Semi-Hydrogenation Selectivity in Ternary Pyrite-Type Intermetallic Compounds

Intermetallic compounds serve as model catalysts for selective hydrogenation reactions, offering precise control over the active site composition(s), geometric and electronic structure. The addition of a third element to form a ternary intermetallic alters the exposed crystal facet(s), demonstrating a strategy to impart improved catalytic behavior in intermetallic catalysts. The site-specific substitution of a small fraction of Pd atoms with Au in pyrite-type PdSb 2 results in the preferential exposure of the (100) facet over the (111) facet. Electron back scattered diffraction and density functional theory calculations confirm the facet change upon the substitution of Pd with Au to form the ternary Pd 1−x Au x Sb 2 (0.075 ≤ x ≤ 0.25). The (100) facet demonstrates higher net alkene selectivity due to significantly weaker alkene binding compared to the (111) facet. Distinct from our prior work on chemical substitution to directly alter the active site composition, this work demonstrates the indirect modification of active sites via preferential facet exposure.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

The structure of the RCAN1:CN complex explains the inhibition of and substrate recruitment by calcineurin

Regulator of calcineurin 1 (RCAN1) is an endogenous inhibitor of the Ser/Thr phosphatase calcineurin (CN). It has been shown that excessive inhibition of CN is a critical factor for Down syndrome and Alzheimer’s disease. Here, we determined RCAN1’s mode of action. Using a combination of structural, biophysical, and biochemical studies, we show that RCAN1 inhibits CN via multiple routes: first, by blocking essential substrate recruitment sites and, second, by blocking the CN active site using two distinct mechanisms. We also show that phosphorylation either inhibits RCAN1-CN assembly or converts RCAN1 into a weak inhibitor, which can be reversed by CN via dephosphorylation. This highlights the interplay between posttranslational modifications in regulating CN activity. Last, this work advances our understanding of how active site inhibition of CN can be achieved in a highly specific manner. Together, these data provide the necessary road map for targeting multiple neurological disorders.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

M379A Mutant Tyrosine Phenol–lyase from Citrobacter freundii Has Altered Conformational Dynamics

The M379A mutant of Citrobacter freundii tyrosine phenol-lyase (TPL) has been prepared. M379A TPL is a robust catalyst to prepare a number of tyrosines substituted at the 3-position with bulky groups that cannot be made with wild type TPL. The three dimensional structures of M379A TPL complexed with L-methionine and 3-bromo-DL-phenylalanine have been determined by X-ray crystallography. Methionine is bound as a quinonoid complex in a closed active site in 3 of 4 chains of homotetrameric M379A TPL. M379A TPL reacts with L-methionine about 8-fold slower than wild type TPL. The temperature dependence shows that the slower reaction is due to less positive activation entropy. The structure of the M379A TPL complex of 3-bromo-DL-phenylalanine has a quinonoid complex in two subunits, with an open active site conformation. The effects of the M379A mutation on TPL suggest that the mutant enzyme has altered the conformational dynamics of the active site.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Engineering Active Fe Sites on Nickel–Iron Layered Double Hydroxide through Component Segregation for Oxygen Evolution Reaction

Nickel-iron layered double hydroxide (NiFe LDH) is a promising oxygen evolution reaction (OER) electrocatalyst under alkaline conditions. Much research has been performed to understand the structure-activity relationship of NiFe LDH under OER conditions. However, the specific role of the Fe species remains unclear and under debate. Herein, based on DFT calculations, it was discovered that the edge Fe sites show higher activity towards OER than either the edge Ni sites or lattice sites. Therefore, a facile acid-etching method was proposed to controllably induce the formation of edge Fe sites in NiFe LDH, and the obtained sample exhibited higher OER activity. X-ray absorption near edge structure and extended X-ray absorption fine structure analyses further revealed that the interaction of the edge Fe species with Ni is believed to contribute to the enhancement of the OER performance. This work provides a new understanding of the structure-activity relationship in NiFe LDH and offers a facile method for the design of efficient electrocatalysts in an alkaline environment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Iron-Imprinted Single-Atomic Site Catalyst-Based Nanoprobe for Detection of Hydrogen Peroxide in Living Cells

Fe-based single-atomic site catalysts (SASCs), with the natural metalloproteases-like active site structure, have attracted widespread attention in biocatalysis and biosensing. Precisely, controlling the isolated single-atom Fe-N-C active site structure is crucial to improve the SASCs’ performance. In this work, we use a facile ion-imprinting method (IIM) to synthesize isolated Fe-N-C single-atomic site catalysts (IIM-Fe-SASC). With this method, the ion-imprinting process can precisely control ion at the atomic level and form numerous well-defined single-atomic Fe-N-C sites. The IIM-Fe-SASC shows better peroxidase-like activities than that of non-imprinted references. Due to its excellent properties, IIM-Fe-SASC is an ideal nanoprobe used in the colorimetric biosensing of hydrogen peroxide (H 2 O 2 ). Using IIM-Fe-SASC as the nanoprobe, in situ detection of H 2 O 2 generated from MDA-MB-231 cells has been successfully demonstrated with satisfactory sensitivity and specificity. This work opens a novel and easy route in designing advanced SASC and provides a sensitive tool for intracellular H 2 O 2 detection.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Tuning Structural and Electronic Configuration of FeN 4 via External S for Enhanced Oxygen Reduction Reaction

The Fe–N–C material represents an attractive oxygen reduction reaction electrocatalyst, and the FeN 4 moiety has been identified as a very competitive catalytic active site. Fine tuning of the coordination structure of FeN 4 has an essential impact on the catalytic performance. Herein, we construct a sulfur‐modified Fe–N–C catalyst with controllable local coordination environment, where the Fe is coordinated with four in‐plane N and an axial external S. The external S atom affects not only the electron distribution but also the spin state of Fe in the FeN 4 active site. The appearance of higher valence states and spin states for Fe demonstrates the increase in unpaired electrons. With the above characteristics, the adsorption and desorption of the reactants at FeN 4 active sites are optimized, thus promoting the oxygen reduction reaction activity. This work explores the key point in electronic configuration and coordination environment tuning of FeN 4 through S doping and provides new insight into the construction of M–N–C‐based oxygen reduction reaction catalysts.

25 ENERGY STORAGE↗

Toho-1 β-lactamase: backbone chemical shift assignments and changes in dynamics upon binding with avibactam

Backbone chemical shift assignments for the Toho-1 β-lactamase (263 amino acids, 28.9 kDa) are reported based on triple resonance solution-state NMR experiments performed on a uniformly 2 H, 13 C, 15 N-labeled sample. These assignments allow for subsequent site-specific characterization at the chemical, structural, and dynamical levels. At the chemical level, titration with the non-β-lactam β-lactamase inhibitor avibactam is found to give chemical shift perturbations indicative of tight covalent binding that allow for mapping of the inhibitor binding site. At the structural level, protein secondary structure is predicted based on the backbone chemical shifts and protein residue sequence using TALOS-N and found to agree well with structural characterization from X-ray crystallography. At the dynamical level, model-free analysis of 15 N relaxation data at a single field of 16.4 T reveals well-ordered structures for the ligand-free and avibactam-bound enzymes with generalized order parameters of ~0.85. Complementary relaxation dispersion experiments indicate that there is an escalation in motions on the millisecond timescale in the vicinity of the active site upon substrate binding. The combination of high rigidity on short timescales and active site flexibility on longer timescales is consistent with hypotheses for achieving both high catalytic efficiency and broad substrate specificity: the induced active site dynamics allows variously sized substrates to be accommodated and increases the probability that the optimal conformation for catalysis will be sampled.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Coordination and activation of nitrous oxide by iron zeolites

Iron-containing zeolites are heterogeneous catalysts that exhibit remarkable activity in the selective oxidation of inert hydrocarbons and catalytic decomposition of nitrous oxide (N 2 O). The reduction of N 2 O is critical to both these functions, but experimental data tracking the iron active sites during N 2 O binding and activation are limited. Here, the N 2 O-ligated Fe(ii) active site in iron-exchanged zeolite beta is isolated and characterized by variable-temperature Mössbauer, diffuse reflectance UV-vis-NIR and Fourier transform infrared spectroscopy. N 2 O binds through the terminal nitrogen atom with substantial backbonding from the Fe(ii) centre at low temperature. At higher temperatures, the Fe–N 2 O interaction is weakened, facilitating isomerization to the O-bound form, which is competent in O-atom transfer. Density functional theory calculations show the geometric and electronic structure requirements for N 2 O binding and activation. A geometric distortion imposed by the zeolite lattice plays an important role in activating N 2 O. As a result, this highlights a mechanism for structural control over function in Fe-zeolite catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗