Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Active target”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 451 records · Page 25
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Production of Radioisotopes of Scandium for Imaging and Therapy (Final Report)

The theranostic approach is a powerful technique that enables scientists and physicians to diagnose and treat diseases using the same targeting moiety labeled with radionuclides for imaging and therapy. A challenge behind synthesizing and evaluating these theranostic radiopharmaceuticals lies in the production of suitable radionuclides. This study aimed to investigate the production of high radionuclidic purity 43 Sc from enriched [ 46 Ti]TiO 2 for Positron Emission Tomography (PET) and 47 Sc from enriched [ 50 Ti]TiO 2 for targeted radiotherapy, as well as establish a target recycling technique for continued production of these radionuclides. Methods: Targets were prepared with 100 mg of either enriched [ 46 Ti]TiO 2 or [ 50 Ti]TiO 2 , pressed into pellets, and placed into Ta target holders with a 0.127 mm natTi cover foil. The 46 Ti targets were bombarded with 18 MeV protons at 20 µA for 1.5 h, while 50Ti targets were bombarded with 24 MeV protons at 20 µA for 4 or 8 h. The radioscandium nuclides were purified using branched N, N, N’, N’ -tetra-2-ethylhexyldiglycolamide (DGA) resin. The titanium targets were recycled by precipitating the dissolved Ti collected from the column effluent and wash streams, pH adjustment, vacuum filtration, and then drying the solid at 250 °C prior to reforming the target for the subsequent bombardment. The apparent molar activity of the isolated radioscandiums was analyzed by titration with 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA). The relative imaging performance of 18 F, 43 Sc, and 68 Ga were analyzed with PET images acquired with 30-min static scans. Results: The average radioscandium recovery for 43Sc was 91.7 ± 7.4 %, with a radionuclidic purity of 98.8 %. The average recovery of 47Sc was 89.9 ± 3.9 %, with a radionuclidic purity of 90.8%. The average recovery of enriched TiO2 was 96 ± 4.0 %. The highest apparent molar activity for [43Sc]Sc-DOTA was 23.2 GBq/µmol and 3.39 GBq/µmol for [ 47 Sc]Sc-DOTA. The order of PET resolution from highest to lowest was 18 F > 43 Sc > 68 Ga. Conclusions: This work demonstrates the feasibility of using enriched recycled [ 46 Ti]TiO 2 and [ 50 Ti]TiO 2 targets for the production of the 43 Sc and 47 Sc theranostic isotope pair in high purity.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2020

Overcoming challenges to support US resumption of high specific activity cobalt-60

Domestic production of high specific activity 60 Co was halted after a target rupture in 2012 at the Advanced Test Reactor (ATR). The Isotope Program (IP) within the US Department of Energy (DOE) Office of Science tasked a multilaboratory team of researchers and managers from Oak Ridge and Idaho National Laboratories with the redesign the radioisotope capsule. The objective of this effort was to create a more robust and reliable design, compared to the pre-2012 target. The team successfully completed this task to produce the DOE-IP cobalt (Co) production capsule design. Furthermore, 66 capsules were successfully fabricated by Oak Ridge National Laboratory (ORNL) and delivered to Idaho National Laboratory (INL) for irradiation in the ATR between January 2014 and October 2016. This paper describes the efforts of the team to prepare and disposition the two initial DOE-IP Co production capsules that were processed in March 2020. These efforts include performing accurate production predictions, experimentally validating predictions with assay measurements, shipping with the Orano-furnished Battelle Energy Alliance Research Reactor shipping package, and disassembling capsules at the isotope vendor site.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2022

How do super concentrated electrolytes push the Li-ion batteries and supercapacitors beyond their thermodynamic and electrochemical limits?

Increasing the energy density of energy storage devices is currently the key target of many battery and supercapacitor research activities. For both types of devices, the electrochemical stability window (ESW) determines the effective energy density of the device. ESWs are defined by the effective oxidation and reduction potentials of the electrolyte, which are controlled by many various factors, including the HOMO/LUMO (highest/lowest unoccupied molecular orbital) energies of the electrolyte molecules, the nature of the electrode/electrolyte interphases, and other physicochemical properties. The concentration of the electrolyte would affect the HOMO/ LUMO levels thus also change the ESW. A higher concentration of salt induces specific arrangements among the anion, cation, and solvent molecules of an electrolyte, altering the bulk behavior of the electrolyte, resulting in drastic change in the electrode interfaces. These uniquely modified physicochemical properties extend the ESW in several different ways, including the enhancement in the kinetic stability of the electrodes, as well as the thermodynamic and Nernst shifts of the oxidation/reduction potentials of the electrolyte. For organic electrolytes, it is the reduced amount of free solvent molecules that plays the key role in such changes; whereas for aqueous electrolytes, it is the scarcity of free water molecules and the reduced water activity that control the key properties of the electrolyte. Here, we focus on elucidating the fundamental structural changes occurring within an electrolyte system with increasing salt concentrations. The underlying mechanisms which not only facilitates the extension of the ESW, but also enables higher rate capabilities and mitigates aluminum dissolution for batteries with organic electrolytes, are meticulously explained. Further, we thoroughly discuss the importance of high-voltage stability in aqueous battery systems by exploiting the changed properties observed with higher concentrations of salts. To finish, high-voltage supercapacitors enabled by superconcentrated electrolytes are also explored.

25 ENERGY STORAGE↗
DOE OSTI2024

Diverse array of neutralizing antibodies elicited upon Spike Ferritin Nanoparticle vaccination in rhesus macaques

The repeat emergence of SARS-CoV-2 variants of concern (VoC) with decreased susceptibility to vaccine-elicited antibodies highlights the need to develop next-generation vaccine candidates that confer broad protection. Here we describe the antibody response induced by the SARS-CoV-2 Spike Ferritin Nanoparticle (SpFN) vaccine candidate adjuvanted with the Army Liposomal Formulation including QS21 (ALFQ) in non-human primates. By isolating and characterizing several monoclonal antibodies directed against the Spike Receptor Binding Domain (RBD), N-Terminal Domain (NTD), or the S2 Domain, we define the molecular recognition of vaccine-elicited cross-reactive monoclonal antibodies (mAbs) elicited by SpFN. We identify six neutralizing antibodies with broad sarbecovirus cross-reactivity that recapitulate serum polyclonal antibody responses. In particular, RBD mAb WRAIR-5001 binds to the conserved cryptic region with high affinity to sarbecovirus clades 1 and 2, including Omicron variants, while mAb WRAIR-5021 offers complete protection from B.1.617.2 (Delta) in a murine challenge study. Our data further highlight the ability of SpFN vaccination to stimulate cross-reactive B cells targeting conserved regions of the Spike with activity against SARS CoV-1 and SARS-CoV-2 variants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structural basis of sequence-specific cytosine deamination by double-stranded DNA deaminase toxin DddA

The interbacterial deaminase toxin DddA catalyzes cytosine-to-uracil conversion in double-stranded (ds) DNA and enables CRISPR-free mitochondrial base editing, but the molecular mechanisms underlying its unique substrate selectivity have remained elusive. Here, we report crystal structures of DddA bound to a dsDNA substrate containing the 5'-TC target motif. These structures show that DddA binds to the minor groove of a sharply bent dsDNA and engages the target cytosine extruded from the double helix. DddA Phe1375 intercalates in dsDNA and displaces the 5' (-1) thymine, which in turn replaces the target (0) cytosine and forms a noncanonical T–G base pair with the juxtaposed guanine. This tandem displacement mechanism allows DddA to locate a target cytosine without flipping it into the active site. Biochemical experiments demonstrate that DNA base mismatches enhance the DddA deaminase activity and relax its sequence selectivity. On the basis of the structural information, we further identified DddA mutants that exhibit attenuated activity or altered substrate preference. Our studies may help design new tools useful in genome editing or other applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

A curated benchmark for cofolding models on kinase conformational states

Abstract Protein kinases are critical drug targets, requiring therapeutics that can modulate their active and inactive conformational states. While cofolding models can generate global folds directly from kinase sequences and ligand SMILES strings, these models have not yet been tested on their ability to recover ligand-induced-fit conformational states of the kinase proteins. Here, we introduce KinConfBench, a curated benchmark of 2225 high-quality human kinase chains to evaluate the ability of four state-of-the-art cofolding models—Boltz-2, Chai-1, Protenix, and RoseTTAFold-All-Atom—to recover both canonical and rare conformational states. We show that geometric success metrics of a ligand pose in the active site do not correlate strongly with the correct kinase conformational state, motivating a new set of dynamical benchmarks for assessing cofolding models. While all four cofolding models achieve ~60–80% prediction accuracy for kinase conformational classification, they exhibit severe mode collapse when performing multiple inferences, show negligible structural diversity in sampling induced-fit motions, and display a prevalent “apo-drift” in which most cofolding models predominantly predict the kinase to be in its ligand-free state. Our results highlight that capturing ligand-induced protein conformational diversity, not just geometric fit, is critical for next-generation structure-based drug discovery.

Sun, Kunyang↗
DOE OSTI2021

GHB analogs confer neuroprotection through specific interaction with the CaMKIIα hub domain

Ca 2+ /calmodulin-dependent protein kinase II alpha subunit (CaMKIIα) is a key neuronal signaling protein and an emerging drug target. The central hub domain regulates the activity of CaMKIIα by organizing the holoenzyme complex into functional oligomers, yet pharmacological modulation of the hub domain has never been demonstrated. Here, using a combination of photoaffinity labeling and chemical proteomics, we show that compounds related to the natural substance γ-hydroxybutyrate (GHB) bind selectively to CaMKIIα. By means of a 2.2-Å x-ray crystal structure of ligand-bound CaMKIIα hub, we reveal the molecular details of the binding site deep within the hub. Furthermore, we show that binding of GHB and related analogs to this site promotes concentration-dependent increases in hub thermal stability believed to alter holoenzyme functionality. Selectively under states of pathological CaMKIIα activation, hub ligands provide a significant and sustained neuroprotection, which is both time and dose dependent. This is demonstrated in neurons exposed to excitotoxicity and in a mouse model of cerebral ischemia with the selective GHB analog, HOCPCA (3-hydroxycyclopent-1-enecarboxylic acid). Together, our results indicate a hitherto unknown mechanism for neuroprotection by a highly specific and unforeseen interaction between the CaMKIIα hub domain and small molecule brain-penetrant GHB analogs. This establishes GHB analogs as powerful tools for investigating CaMKII neuropharmacology in general and as potential therapeutic compounds for cerebral ischemia in particular.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structural insights reveal interplay between LAG-3 homodimerization, ligand binding, and function

Lymphocyte activation gene-3 (LAG-3) is an inhibitory receptor expressed on activated T cells and an emerging immunotherapy target. Domain 1 (D1) of LAG-3, which has been purported to directly interact with major histocompatibility complex class II (MHCII) and fibrinogen-like protein 1 (FGL1), has been the major focus for the development of therapeutic antibodies that inhibit LAG-3 receptor-ligand interactions and restore T cell function. Here, we present a high-resolution structure of glycosylated mouse LAG-3 ectodomain, identifying that cis-homodimerization, mediated through a network of hydrophobic residues within domain 2 (D2), is critically required for LAG-3 function. Additionally, we found a previously unidentified key protein-glycan interaction in the dimer interface that affects the spatial orientation of the neighboring D1 domain. Mutation of LAG-3 D2 residues reduced dimer formation, dramatically abolished LAG-3 binding to both MHCII and FGL1 ligands, and consequentially inhibited the role of LAG-3 in suppressing T cell responses. Intriguingly, we showed that antibodies directed against D1, D2, and D3 domains are all capable of blocking LAG-3 dimer formation and MHCII and FGL-1 ligand binding, suggesting a potential allosteric model of LAG-3 function tightly regulated by dimerization. Furthermore, our work reveals unique epitopes, in addition to D1, that can be targeted for immunotherapy of cancer and other human diseases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Insights into the molecular mechanism of translation inhibition by the ribosome-targeting antibiotic thermorubin

Thermorubin (THR) is an aromatic anthracenopyranone antibiotic active against both Gram-positive and Gram-negative bacteria. It is known to bind to the 70S ribosome at the intersubunit bridge B2a and was thought to inhibit factor-dependent initiation of translation and obstruct the accommodation of tRNAs into the A site. Here, we show that thermorubin causes ribosomes to stall in vivo and in vitro at internal and termination codons, thereby allowing the ribosome to initiate protein synthesis and translate at least a few codons before stalling. Our biochemical data show that THR affects multiple steps of translation elongation with a significant impact on the binding stability of the tRNA in the A site, explaining premature cessation of translation. Our high-resolution crystal and cryo-EM structures of the 70S-THR complex show that THR can co-exist with P- and A-site tRNAs, explaining how ribosomes can elongate in the presence of the drug. Remarkable is the ability of THR to arrest ribosomes at the stop codons. Our data suggest that by causing structural re-arrangements in the decoding center, THR interferes with the accommodation of tRNAs or release factors into the ribosomal A site.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Crystal structure of a seven-substitution mutant of hydroxynitrile lyase from rubber tree

The α/β-hydrolase fold superfamily includes esterases and hydroxynitrile lyases which, despite catalyzing different reactions, share a Ser–His–Asp catalytic triad. We report a 1.99 Å resolution crystal structure of HNL6V, an engineered variant of hydroxynitrile lyase fromHevea brasiliensis(HbHNL) containing seven amino-acid substitutions (T11G, E79H, C81L, H103V, N104A, G176S and K236M). The structure reveals that HNL6V maintains the characteristic α/β-hydrolase fold while exhibiting systematic shifts in backbone and catalytic atom positions. Compared with wild-typeHbHNL, the C α positions in HNL6V differ by a mean of 0.2 ± 0.1 Å, representing a statistically significant displacement. Importantly, the catalytic triad and oxyanion-hole atoms have moved 0.2–0.8 Å closer to their corresponding positions in SABP2, although they remain 0.3–1.1 Å from fully achieving the configuration of SABP2. The substitutions also increase local flexibility, particularly in the lid domain covering the active site. This structural characterization demonstrates that targeted amino-acid substitutions can systematically shift catalytic geometries towards those of evolutionarily related enzymes.

Biochemistry & Molecular Biology↗
DOE OSTI2025

FY24 Task 5: Leachate Disposition

Directly feeding sludge solids to the high-level waste (HLW) Waste Treatment Plant represents an alternative flowsheet seeking to initiate sludge processing as soon as possible. Key processing functions previously captured during baseline pretreatment operations include leaching and washing prior to solids concentration. These operations should be considered in the potential direct feed flowsheets to maximize waste feed loading, minimize HLW volume, and mitigate corrosion challenges associated with vitrification of high phosphate and fluoride concentrations. Additionally, single-shell tank (SST) retrievals and waste transfers to double-shell tanks (DSTs) in a direct feed flowsheet would likely also benefit from some level of leaching, washing, and solids concentration in order to reduce DST space and mission duration. These operations could occur in a new facility or potentially in available DSTs. If washing and leaching are utilized, an effective disposition pathway for the wash water and leachate solutions are needed. Three target species that benefit significantly from leaching and washing are phosphate, fluoride and aluminum. Phosphate (PO 4 3- ) and fluoride (F - ) can contribute substantially to the amount of carrier fluid needed for dissolution, and the resulting volume of liquid generated. Disposition of this retrieval solution should be evaluated in order to prevent crystallization of these anions throughout system processing. Since there is a high probability that any retrieval solutions will be at or near their PO 4 3- and F - solubility limits, evaporation or blending with a high Na supernate (>3.5 M) is not recommended for the wash water streams without a method to remove precipitants prior to solution disposal. Additionally, aluminum present in the southeast quadrant of the Hanford site represents roughly 60% of the waste solids in the initial processing tanks. These aluminum solids are in the form of gibbsite (Al(OH) 3 ) and can pose significant challenges for processing due to the fast-settling times and high solids loading associated with these materials. Easily remediated by caustic addition to the solids, these wash solutions could be processed through crystalline silicotitanate (CST) ion exchange columns to prepare the supernate solutions for disposition. The current target for feed conditions to the Low Activity Waste (LAW) melter are waste streams that contain nominally 5-6 M Na. Fractions within the tanks contain upwards of 0.2 M phosphate and fluoride in solution at 3.5 M Na. Concentrating these solutions above 5 M Na would result in an exceedance of the solubility limits, and potential for uncontrolled precipitation of the phosphate and fluoride crystal material. The resulting crystalline salt material is typically sodium fluoride phosphate, also referred to as natrophosphate (Na 7 FPO 4 ·19H 2 O). Salt phases are of importance in tank waste due to their chemical reactivity, which can result in precipitation, dissolution, or transformation, impacting any downstream processes (Bolling et al. 2020, Russell, Snow, and Peterson 2010). Salt generation and precipitation could pose challenges by causing system plugging and melter corrosion if left in the supernate stream, or limit sodium molarity of the supernate that would be accepted without incident in waste operations. To understand the impact of this salt generation, the crystallization of natrophosphate in multiple simulant feed matrices was studied to understand the implications of various tank waste supernate chemistries. Three matrices were examined: high PO 4 3- /low F - , low PO 4 3- /high F - , and an average matrix. Subsequent testing was performed with the average matrix with the inclusion of CsNO 3 , and a final run with the average matrix including CsNO 3 and a 137 Cs spike for tracer purposes.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2022

Production of GMP-Compliant Clinical Amounts of Copper-61 Radiopharmaceuticals from Liquid Targets

PET imaging has gained significant momentum in the last few years, especially in the area of oncology, with an increasing focus on metal radioisotopes owing to their versatile chemistry and favourable physical properties. Copper-61 (t1/2 = 3.33 h, 61% β+, Emax = 1.216 MeV) provides unique advantages versus the current clinical standard (i.e., gallium-68) even though, until now, no clinical amounts of 61Cu-based radiopharmaceuticals, other than thiosemicarbazone-based molecules, have been produced. This study aimed to establish a routine production, using a standard medical cyclotron, for a series of widely used somatostatin analogues, currently labelled with gallium-68, that could benefit from the improved characteristics of copper-61. We describe two possible routes to produce the radiopharmaceutical precursor, either from natural zinc or enriched zinc-64 liquid targets and further synthesis of [61Cu]Cu-DOTA-NOC, [61Cu]Cu-DOTA-TOC and [61Cu]Cu-DOTA-TATE with a fully automated GMP-compliant process. The production from enriched targets leads to twice the amount of activity (3.28 ± 0.41 GBq vs. 1.84 ± 0.24 GBq at EOB) and higher radionuclidic purity (99.97% vs. 98.49% at EOB). Our results demonstrate, for the first time, that clinical doses of 61Cu-based radiopharmaceuticals can easily be obtained in centres with a typical biomedical cyclotron optimised to produce 18F-based radiopharmaceuticals.

Fonseca, Alexandra I. (ORCID:000000031924178X)↗
DOE OSTI2021

Selective Photoswitchable Allosteric Agonist of a G Protein-Coupled Receptor

G protein-coupled receptors (GPCRs) are the most common targets of drug discovery. However, the similarity between related GPCRs combined with the complex spatiotemporal dynamics of receptor activation in vivo has hindered drug development. Photopharmacology offers the possibility of using light to control the location and timing of drug action by incorporating a photoisomerizable azobenzene into a GPCR ligand, enabling rapid and reversible switching between an inactive and active configuration. Recent advances in this area include (i) photoagonists and photoantagonists that directly control receptor activity but are nonselective because they bind conserved sites, and (ii) photoallosteric modulators that bind selectively to nonconserved sites but indirectly control receptor activity by modulating the response to endogenous ligand. In this study, we designed a photoswitchable allosteric agonist that targets a nonconserved allosteric site for selectivity and activates the receptor on its own to provide direct control. This work culminated in the development of aBINA, a photoswitchable allosteric agonist that selectively activates the G i/o -coupled metabotropic glutamate receptor 2 (mGluR2). aBINA is the first example of a new class of precision drugs for GPCRs and other clinically important signaling proteins.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

High efficiency continuous-flow production of radioisotopes

Methods and systems are provided for continuous-flow production of radioisotopes with high specific activity. Radioisotopes with high specific activity produced according to the methods described are also provided. The methods can include causing a liquid capture matrix to contact a target containing a target nuclide; irradiating the target with radiation, ionizing radiation, particles, or a combination thereof to produce the radionuclides that are ejected from the target and into the capture matrix; and causing the liquid capture matrix containing the radionuclides to flow from the target to recover the capture matrix containing the radionuclides with high specific activity. The methods are suitable for the production of a variety of radionuclides. For example, in some aspects the target nuclide is 237Np, and the radionuclide is 238Np that decays to produce 238Pu. In other aspects, the target nuclide is 98Mo, and the radionuclide is Mo that decays to produce 99mTc.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2023

Structure and epitope of a neutralizing monoclonal antibody that targets the stem helix of β coronaviruses

Monoclonal antibodies that retain neutralizing activity against multiple coronavirus (CoV) lineages and variants of concern (VoC) must be developed to protect against future pandemics. These broadly neutralizing MAbs (BNMAbs) may be used as therapeutics and/or to assist in the rational design of vaccines that induce BNMAbs. 1249A8 is a BNMAb that targets the stem helix (SH) region of CoV spike (S) protein and neutralizes Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) original strain, delta, and omicron VoC, Severe Acute Respiratory Syndrome CoV (SARS-CoV), and Middle East Respiratory Syndrome CoV (MERS-CoV). To understand its mechanism of action, the crystal structure of 1249A8 bound to a MERS-CoV SH peptide was determined at 2.1 Å resolution. BNMAb 1249A8 mimics the SARS-CoV-2 S loop residues 743–749, which interacts with the N-terminal end of the SH helix in the S post-fusion conformation. The conformation of 1249A8-bound SH is distinct from the SH conformation observed in the post-fusion SARS-CoV-2 S structure, suggesting 1249A8 disrupts the secondary structure and refolding events required for CoV post-fusion S to initiate membrane fusion and ultimately infection. This study provides novel insights into the neutralization mechanisms of SH-targeting CoV BNMAbs that may inform vaccine development and the design of optimal BNMAb therapeutics.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Structure–activity relationship-based chemical classification of highly imbalanced Tox21 datasets

Abstract The specificity of toxicant-target biomolecule interactions lends to the very imbalanced nature of many toxicity datasets, causing poor performance in Structure–Activity Relationship (SAR)-based chemical classification. Undersampling and oversampling are representative techniques for handling such an imbalance challenge. However, removing inactive chemical compound instances from the majority class using an undersampling technique can result in information loss, whereas increasing active toxicant instances in the minority class by interpolation tends to introduce artificial minority instances that often cross into the majority class space, giving rise to class overlapping and a higher false prediction rate. In this study, in order to improve the prediction accuracy of imbalanced learning, we employed SMOTEENN, a combination of Synthetic Minority Over-sampling Technique (SMOTE) and Edited Nearest Neighbor (ENN) algorithms, to oversample the minority class by creating synthetic samples, followed by cleaning the mislabeled instances. We chose the highly imbalanced Tox21 dataset, which consisted of 12 in vitro bioassays for > 10,000 chemicals that were distributed unevenly between binary classes. With Random Forest (RF) as the base classifier and bagging as the ensemble strategy, we applied four hybrid learning methods, i.e., RF without imbalance handling (RF), RF with Random Undersampling (RUS), RF with SMOTE (SMO), and RF with SMOTEENN (SMN). The performance of the four learning methods was compared using nine evaluation metrics, among which F 1 score, Matthews correlation coefficient and Brier score provided a more consistent assessment of the overall performance across the 12 datasets. The Friedman’s aligned ranks test and the subsequent Bergmann-Hommel post hoc test showed that SMN significantly outperformed the other three methods. We also found that a strong negative correlation existed between the prediction accuracy and the imbalance ratio (IR), which is defined as the number of inactive compounds divided by the number of active compounds. SMN became less effective when IR exceeded a certain threshold (e.g., > 28). The ability to separate the few active compounds from the vast amounts of inactive ones is of great importance in computational toxicology. This work demonstrates that the performance of SAR-based, imbalanced chemical toxicity classification can be significantly improved through the use of data rebalancing.

Idakwo, Gabriel↗
DOE OSTI2021

The UPR regulator IRE1 promotes balanced organ development by restricting TOR-dependent control of cellular differentiation in Arabidopsis

Proteostasis of the endoplasmic reticulum (ER) is controlled by sophisticated signaling pathways that are collectively called the unfolded protein response (UPR) and are initiated by specialized ER membrane-associated sensors. The evidence that complete loss-of-function mutations of the most conserved of the UPR sensors, inositol-requiring enzyme 1 (IRE1), dysregulates tissue growth and development in metazoans and plants raises the fundamental question as to how IRE1 is connected to organismal growth. To address this question, we interrogated the Arabidopsis primary root, an established model for organ development, using the tractable Arabidopsis IRE1 mutant ire1a ire1b, which has marked root development defects in the absence of exogenous stress. We demonstrate that IRE1 is required to reach maximum rates of cell elongation and root growth. We also established that in the actively growing ire1a ire1b mutant root tips the Target of Rapamycin (TOR) kinase, a widely conserved pro-growth regulator, is hyperactive, and that, unlike cell proliferation, the rate of cell differentiation is enhanced in ire1a ire1b in a TOR-dependent manner. By functionally connecting two essential growth regulators, these results underpin a novel and critical role of IRE1 in organ development and indicate that, as cells exit an undifferentiated state, IRE1 is required to monitor TOR activity to balance cell expansion and maturation during organ biogenesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Structural Mechanism of an Efficacy Photoswitch Targeting the β 2 ‐adrenergic Receptor

The field of photopharmacology develops light-responsive drugs that can modulate protein activity, enabling precise and dynamic investigations of their roles in health and disease. Adrenergic receptors are prominent targets for this approach because they are prototypical G protein-coupled receptors with high clinical relevance in bronchial and cardiovascular diseases. Here, we employed the azobenzene-based compound photoazolol-1 in combination with time-resolved serial crystallography at X-ray free-electron lasers to resolve the molecular mechanisms by which photoswitchable β-blockers modulate activity of the β 2 -adrenoceptor (β 2 AR). Time-resolved structures of the receptor bound to trans-photoazolol-1 (pre-photoconversion), a strained intermediate in the nanosecond range, and the fully photoisomerized cis-photoazolol-1 reveal how isomerization of the azobenzene moiety induces distinct conformational changes within the orthosteric ligand binding pocket. Within seconds, light-excited photoazolol-1 adopts a new binding pose, altering interactions with extracellular loop 2 and shifting the positions of transmembrane helices 5, 6, and 7. Functional assays of β 2 AR in cellular membranes show that photoazolol-1 acts as an efficacy photoswitch, changing from an inverse agonist to a neutral antagonist upon isomerization without leaving the binding pocket. In combination, these findings suggest a molecular mechanism for activity modulation via efficacy photoswitches and provide a framework for designing ligands that exploit light-driven transitions within the binding pocket to achieve spatiotemporal control of receptor function.

G protein-coupled receptors↗