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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.

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At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Viral Nuclease Inhibitors: Small molecule disruptors of the UL12 alkaline nuclease display broad anti-herpes virus activity

Herpes simplex virus 1 (HSV-1) UL12 encodes a highly conserved 5′ → 3′ alkaline exonuclease that is essential for the production of infectious virus. Together with the viral single-stranded DNA-binding/annealing protein ICP8, UL12 functions as a two-component recombinase that mediates recombination-dependent viral DNA replication. Here, we present the crystal structure of the catalytic domain of the HSV alkaline nuclease (UL12), which provides the first view of an α-herpesvirus alkaline nuclease. Using this structure, we optimized a series of small-molecule viral nuclease inhibitors (VNIs) that target the UL12 active site and potently inhibit UL12 exonuclease activity in vitro. We have thus established a robust platform for structure-based docking, SAR analysis and rational inhibitor design. Because UL12 orthologs are conserved across all human herpesviruses, we examined the activity of these compounds against the β- and γ-herpesvirus alkaline nucleases UL98 and SOX and found that they inhibit all three enzymes. The VNIs also exhibit antiviral activity against HSV-1 and HCMV in cell culture. EC 50 and IC 50 values were in the nanomolar to low micromolar range. Together, these findings establish herpesvirus alkaline nucleases as conserved, druggable antiviral targets and provide a foundation for the development of broad-spectrum anti-herpesvirus therapeutics, either as standalone agents or in combination with existing nucleoside analogs.

Sharma, Nidhi↗
DOE OSTI2023

Genetic interactions between polycystin-1 and Wwtr1 in osteoblasts define a novel mechanosensing mechanism regulating bone formation in mice

Molecular mechanisms transducing physical forces in the bone microenvironment to regulate bone mass are poorly understood. Here, we used mouse genetics, mechanical loading, and pharmacological approaches to test the possibility that polycystin-1 and Wwtr1 have interdependent mechanosensing functions in osteoblasts. We created and compared the skeletal phenotypes of control Pkd1 flox/+ ;Wwtr1 flox/+ , Pkd1 Oc-cKO , Wwtr1 Oc-cKO , and Pkd1/Wwtr1 Oc-cKO mice to investigate genetic interactions. Consistent with an interaction between polycystins and Wwtr1 in bone in vivo, Pkd1/Wwtr1 Oc-cKO mice exhibited greater reductions of BMD and periosteal MAR than either Wwtr1 Oc-cKO or Pkd1 Oc-cKO mice. Micro-CT 3D image analysis indicated that the reduction in bone mass was due to greater loss in both trabecular bone volume and cortical bone thickness in Pkd1/Wwtr1 Oc-cKO mice compared to either Pkd1 Oc-cKO or Wwtr1 Oc-cKO mice. Pkd1/Wwtr1 Oc-cKO mice also displayed additive reductions in mechanosensing and osteogenic gene expression profiles in bone compared to Pkd1 Oc-cKO or Wwtr1 Oc-cKO mice. Moreover, we found that Pkd1/Wwtr1 Oc-cKO mice exhibited impaired responses to tibia mechanical loading in vivo and attenuation of load-induced mechanosensing gene expression compared to control mice. Finally, control mice treated with a small molecule mechanomimetic, MS2 that activates the polycystin complex resulted in marked increases in femoral BMD and periosteal MAR compared to vehicle control. In contrast, Pkd1/Wwtr1 Oc-cKO mice were resistant to the anabolic effects of MS2. These findings suggest that PC1 and Wwtr1 form an anabolic mechanotransduction signaling complex that mediates mechanical loading responses and serves as a potential novel therapeutic target for treating osteoporosis.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Ligand effects on electronic structure and bonding in U(iii) coordination complexes: a combined MCD, EPR and computational study

The trivalent oxidation state of uranium has been shown to undergo unique reactivity, from its ability to activate a variety of small molecules to its role in the catalytic reduction of ethene to ethane amongst others. Central to this unique reactivity and ability to rationally design ligands for isotope separation is the underlying uranium electronic structure. While electronic structure studies of U(IV), U(V), and U(VI) have been extensive, by comparison, analogous studies of more reduced oxidation states such as U(III) remains underdeveloped. Herein we report a combined MCD and EPR spectroscopic approach along with density functional theory and multireference wavefunction calculations to elucidate the effects of ligand perturbation in three uranium(III) Tp* complexes. Overall, the experimental and computational insight suggests that the change in ligand environment across this series of U(III) complexes resulted in only minor perturbations in the uranium electronic structure. This combined approach was also used to redefine the electronic ground state of a U(III) complex with a redox non-innocent Bipy - ligand. Overall, these studies demonstrate the efficacy of the combined experimental and theoretical approach towards evaluating electronic structure and bonding in U(III) complexes and provide important insight into the challenges in altering ligand environments to modify bonding and reactivity in uranium coordination chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Theoretical Investigations on the Plasmon-Mediated Dissociation of Small Molecules in the Presence of Silver Atomic Wires

Plasmonic nanoparticles can promote bond activation in adsorbed molecules under relatively benign conditions via excitation of the nanoparticle’s plasmon resonance. As the plasmon resonance often falls within the visible light region, plasmonic nanomaterials are a promising class of catalysts. However, the exact mechanisms through which plasmonic nanoparticles activate the bonds of nearby molecules are still unclear. Herein, we evaluate Ag 8 –X 2 (X = N, H) model systems via real-time time-dependent density functional theory (RT-TDDFT), linear response time-dependent density functional theory (LR-TDDFT), and Ehrenfest dynamics in order to better understand the bond activation processes of N 2 and H 2 facilitated by the presence of the atomic silver wire under excitation at the plasmon resonance energies. We find that dissociation is possible for both small molecules at high electric field strength. Activation of each adsorbate is symmetry- and electric field-dependent, and H 2 activates at lower electric field strengths than N 2 . Furthermore, this work serves as a step toward understanding the complex time-dependent electron and electron–nuclear dynamics between plasmonic nanowires and adsorbed small molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Increased Static Charge–Induced Threshold Voltage Shifts and Memristor Activity in Pentacene OFETs Comprising Polystyrene–Based Gate Dielectrics Containing Electroactive Small Molecule Crystallites

Top-contact bottom-gate pentacene OFETs are fabricated with single layer dielectrics comprised of either polystyrene (PS), poly(4-methylstyrene) (P4MS), or poly(4-tert-butylstyrene) (P4TBS). The polystyrenes are blended with varying concentrations of two different small molecules, dibenzotetrathiafulvalene (DBTTF) and 2,8-difluoro-5,11-bis(triethylsilylethynyl)anthradithiophene (diF-TES-ADT), to form small, separated crystallites contained throughout the polymer dielectric layer. The OFET characteristics of these devices are investigated and their threshold voltage shifts are measured after –70 V static charging for 5 min. Two-terminal measurements are conducted using multiple different gate biases in the range of –50 to +50 V to investigate memristor behavior in the devices. OFETs containing DBTTF exhibited ΔVth increases as large as 330% relative to control OFETs containing no DBTTF, while OFETs containing at least 7.5 wt.% DBTTF exhibited memristor activity, with currents ranging from 20 nA to 44 µA depending on the applied bias. Furthermore, this work demonstrates that including small, separated crystallites in polymer dielectrics enhances their charge storage ability and can be promising for creating nonbinary memory devices for data processing. Additionally, the observed memristor activity indicates the OFETs in this work can be used in development of neuromorphic systems that aim to mimic the synaptic behavior of the human nervous system.

25 ENERGY STORAGE↗
DOE OSTI2021

Molecular mechanism and structural basis of small-molecule modulation of the gating of acid-sensing ion channel 1

Acid-sensing ion channels (ASICs) are proton-gated cation channels critical for neuronal functions. Studies of ASIC1, a major ASIC isoform and proton sensor, have identified acidic pocket, an extracellular region enriched in acidic residues, as a key participant in channel gating. While binding to this region by the venom peptide psalmotoxin modulates channel gating, molecular and structural mechanisms of ASIC gating modulation by small molecules are poorly understood. Here, combining functional, crystallographic, computational and mutational approaches, we show that two structurally distinct small molecules potently and allosterically inhibit channel activation and desensitization by binding at the acidic pocket and stabilizing the closed state of rat/chicken ASIC1. Our work identifies a previously unidentified binding site, elucidates a molecular mechanism of small molecule modulation of ASIC gating, and demonstrates directly the structural basis of such modulation, providing mechanistic and structural insight into ASIC gating, modulation and therapeutic targeting.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Defining the S-Glutathionylation Proteome by Biochemical and Mass Spectrometric Approaches

Protein S-glutathionylation (SSG) is a reversible post-translational modification (PTM) featuring the conjugation of glutathione to a protein cysteine thiol. SSG can alter protein structure, activity, subcellular localization, and interaction with small molecules and other proteins. Thus, it plays a critical role in redox signaling and regulation in various physiological activities and pathological events. In this review, we summarize current biochemical and analytical approaches for characterizing SSG at both the proteome level and at individual protein levels. To illustrate the mechanism underlying SSG-mediated redox regulation, we highlight recent examples of functional and structural consequences of SSG modifications. Finally, we discuss the analytical challenges in characterizing SSG and the thiol PTM landscape, future directions for understanding of the role of SSG in redox signaling and regulation and its interplay with other PTMs, and the potential role of computational approaches to accelerate functional discovery.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Interplays of electron and nuclear motions along CO dissociation trajectory in myoglobin revealed by ultrafast X-rays and quantum dynamics calculations

Significance In this multidisciplinary study, we investigated local and global structural responses upon carbon monoxide (CO) dissociation from the heme iron(II) in myoglobin in solution using ultrafast X-ray absorption and scattering. CO dissociation was optically triggered and pulsed X-rays probed structural and electronic changes as a function of time, revealing an iron(II) spin state transition and nuclear motions propagating from the active site throughout the entire protein. Quantum mechanical computational results were used to assign the iron K-edge absorption features, and to map out electronic and nuclear trajectories during Fe–CO bond elongation and heme macrocycle doming. The study has important implications for heme–protein function and the interaction of small molecule substrates with the metal active centers in enzymes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

A hidden cysteine in Fis1 targeted to prevent excessive mitochondrial fission and dysfunction under oxidative stress

Fis1-mediated mitochondrial localization of Drp1 and excessive mitochondrial fission occur in human pathologies associated with oxidative stress. However, it is not known how Fis1 detects oxidative stress and what structural changes in Fis1 enable mitochondrial recruitment of Drp1. We find that conformational change involving α1 helix in Fis1 exposes its only cysteine, Cys41. In the presence of oxidative stress, the exposed Cys41 in activated Fis1 forms a disulfide bridge and the Fis1 covalent homodimers cause increased mitochondrial fission through increased Drp1 recruitment to mitochondria. Our discovery of a small molecule, SP11, that binds only to activated Fis1 by engaging Cys41, and data from genetically engineered cell lines lacking Cys41 strongly suggest a role of Fis1 homodimerization in Drp1 recruitment to mitochondria and excessive mitochondrial fission. The structure of activated Fis1-SP11 complex further confirms these insights related to Cys41 being the sensor for oxidative stress. Importantly, SP11 preserves mitochondrial integrity and function in cells during oxidative stress and thus may serve as a candidate molecule for the development of treatment for diseases with underlying Fis1-mediated mitochondrial fragmentation and dysfunction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Characterization of Sequentially Extracted Soil Organic Matter by Electrospray Ionization and Atmospheric Pressure Photoionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

Soil organic matter (SOM) is a complex mixture of small molecules and biopolymers that are active in various biogeochemical processes. However, the chemical diversity of biopolymer-derived SOM remains poorly explored. Identifying this diversity is important because global environmental changes may well alter SOM chemistry, as field experiments are beginning to show. Here, organic solvent-extractable (DcMe-SOM), base-hydrolyzable (KOH Hy -SOM), and CuO-oxidizable (CuO Ox -SOM) SOM fractions from a forest with a long-term nitrogen addition experiment were sequentially extracted and characterized by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) coupled with negative-ion electrospray ionization (ESI) or atmospheric pressure photoionization (APPI). From DcMe-SOM to CuO Ox -SOM, the total number of assigned formulas, average O/C ratio, aromaticity, and unsaturation degree of SOM continuously increased, while the average m/z and H/C ratio decreased. Moreover, the dominant chemical category shifted from lipid-like components to phytochemical- and protein-like components. Complementary to ESI, APPI effectively facilitated detection of additional compounds with low polarity. With long-term nitrogen addition, the average m/z, unsaturation degree, aromaticity, and oxidation state of SOM increased, and more aromatic nitrogen-containing formulas were detected in CuOOx-SOM. Our study demonstrates that chronic nitrogen deposition in forests alters both the small molecules and biopolymers of SOM fundamentally.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Novel small molecule FGF 23 inhibitors increase serum phosphate and improve skeletal abnormalities in Hyp mice

We report that excess fibroblast growth factor 23 (FGF23) causes hereditary hypophosphatemic rickets, such as X-linked hypophosphatemia (XLH) and tumor induced osteomalacia (TIO). A small molecule that specifically binds to FGF23 to prevent activation of the FGFR/a-Klotho complex has potential advantages over the currently approved systemically administered FGF23 blocking antibody. Using structure-based drug design we previously identified ZINC13407541 (N-[[2-(2-phenylethenyl)cyclopenten-1-yl]methylidene]hydroxylamine) as a small molecule antagonist for FGF23. Additional structure-activity studies developed a series of ZINC13407541 analogues with enhanced drug-like properties. In this study, we tested in a pre-clinical Hyp mouse homologue of XLH a direct connect analogue (8n) [(E)-2-(4-(tert-butyl)phenyl)cyclopent-1-ene-1-carbaldehyde oxime] that exhibited the greatest stability in microsomal assays, and 13a [(E)-2-((E)-4-methylstyryl)benzaldehyde oxime] that exhibited increased in vitro potency. Using cryo-electron microscopy (Cryo-EM) structure and computational docking, we identified a key binding residue (Q156) of the FGF23 antagonists, ZINC13407541 and its analogues (8n and 13a) in the N-terminal domain of FGF23 protein. Site-directed mutagenesis and bimolecular fluorescence complementation (BiFC)-fluorescence resonance energy transfer (FRET) assay confirmed the binding site of these three antagonists. We found that pharmacological inhibition of FGF23 with either of these compounds blocked FGF23 signaling and increased serum phosphate and 1,25(OH)2D concentrations in Hyp mice. Long-term parenteral treatment with 8n or 13a also enhanced linear bone growth, increased mineralization of bone, and narrowed the growth plate in Hyp mice. The more potent 13a compound had greater therapeutic effects in Hyp mice. Further optimization of these FGF23 inhibitors may lead to versatile drugs to treat excess FGF23-mediated disorders.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Molecular packing modulation enabling optimized blend morphology and efficient all small molecule organic solar cells

The molecular planarity of a small molecule donor is one of the key factors affecting its molecular packing behavior, the morphology of the related active blend and thus the photovoltaic properties of all small molecule organic solar cells (ASM-OSCs). Here, a series of new benzodithiophene (BDT)-based A-π-D-π-A type small molecules were developed, namely SD1, SD2 and SD3, by combining the chemical modification of side chain (sulfuration), π-bridge (alkoxy groups introducing) and end group (different type or different alkyl chain). The sulfuration of the BDT side chains and introducing alkoxy group to the π-bridge could induce intermolecular S … S and intramolecular S … O non-covalent interactions for higher planarity of these small molecules. The rhodanine and cyanoacetate end groups showed less effect on the optical and electronic properties but significantly affected the molecular packing behavior and blend morphology. From SD1:Y6-T to SD2:Y6-T and SD3:Y6-T, the face-to-face packing was gradually reduced, while the face-to-edge packing was increased, which resulted in lowered exciton dissociation efficiency, further decreased the device performance. SD1:Y6-T blend exhibited more favorable face-to-face packing and ideal morphology for efficient charge dissociation and transport, contributing to a champion PCE of 10.12%. This work provided a deep insight of the donor and acceptor packing behavior effect on the photovoltaic property by molecular design.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Exploring the Effects of Intersubunit Interface Mutations on Virus-Like Particle Structure and Stability

Virus-like particles (VLPs) from bacteriophage MS2 provide a platform to study protein self-assembly and create engineered systems for drug delivery. Here, we aim to understand the impact of intersubunit interface mutations on the local and global structure and function of MS2-based VLPs. In previous work, our lab identified locally supercharged double mutants [T71K/G73R] that concentrate positive charge at capsid pores, enhancing uptake into mammalian cells. To study the effects of particle size on cellular internalization, we combined these double mutants with a single point mutation [S37P] that was previously reported to switch particle geometry from T = 3 to T = 1 icosahedral symmetry. These new variants retained their enhanced cellular uptake activity and could deliver small-molecule drugs with efficacy levels similar to our first-generation capsids. Surprisingly, these engineered triple mutants exhibit increased thermostability and unexpected geometry, producing T = 3 particles instead of the anticipated T = 1 assemblies. Transmission electron microscopy revealed various capsid assembly states, including wild-type (T = 3), T = 1, and rod-like particles, that could be accessed using different combinations of these point mutations. Molecular dynamics experiments recapitulated the structural rationale in silico for the single point mutation [S37P] forming a T = 1 virus-like particle and showed that this assembly state was not favored when combined with mutations that favor rod-like architectures. Through this work, we investigated how interdimer interface dynamics influence VLP size and morphology and how these properties affect particle function in applications such as drug delivery.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Ultrafast Reaction Mechanisms in Perovskite Based Photocatalytic C–C Coupling

Solar driven carbon-carbon (C-C) bond formation is a new direction in solar energy utilization. Earth abundant nanocrystal based photocatalysts are highly sought after as they can potentially eliminate expensive noble metal catalysts. A detailed understanding of the underlying reaction mechanisms could provide guidance in designing new systems that can activate a larger class of small molecules. Here, we employ transient absorption spectroscopy to study a model C-C bond formation reaction, i.e., a-alkylation of aldehydes catalyzed by colloidal CsPbBr3 nanocrystals (NCs). We find that both electrons and holes undergo ultrafast charge transfer (~50 ps) from photoexcited perovskite NCs to reactant molecules. A charge separated state lives for more than 0.8 µs, enabling a radical mechanism to form the C-C bonds. We discuss the differences between the NCs photoredox catalysts and the molecular catalyst.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Ligand‐induced CaMKIIα hub Trp403 flip, hub domain stacking, and modulation of kinase activity

Abstract γ‐Hydroxybutyric acid (GHB) analogs are small molecules that bind competitively to a specific cavity in the oligomeric CaMKIIα hub domain. Binding affects conformation and stability of the hub domain, which may explain the neuroprotective action of some of these compounds. Here, we describe molecular details of interaction of the larger‐type GHB analog 2‐(6‐(4‐chlorophenyl)imidazo[1,2‐b]pyridazine‐2‐yl)acetic acid (PIPA). Like smaller‐type analogs, PIPA binding to the CaMKIIα hub domain promoted thermal stability. PIPA additionally modulated CaMKIIα activity under sub‐maximal CaM concentrations and ultimately led to reduced substrate phosphorylation. A high‐resolution X‐ray crystal structure of a stabilized CaMKIIα (6x mutant) hub construct revealed details of the binding mode of PIPA, which involved outward placement of tryptophan 403 (Trp403), a central residue in a flexible loop close to the upper hub cavity. Small‐angle X‐ray scattering (SAXS) solution structures and mass photometry of the CaMKIIα wild‐type hub domain in the presence of PIPA revealed a high degree of ordered self‐association (stacks of CaMKIIα hub domains). This stacking neither occurred with the smaller compound 3‐hydroxycyclopent‐1‐enecarboxylic acid (HOCPCA), nor when Trp403 was replaced with leucine (W403L). Additionally, CaMKIIα W403L hub was stabilized to a larger extent by PIPA compared to CaMKIIα hub wild type, indicating that loop flexibility is important for holoenzyme stability. Thus, we propose that ligand‐induced outward placement of Trp403 by PIPA, which promotes an unforeseen mechanism of hub domain stacking, may be involved in the observed reduction in CaMKIIα kinase activity. Altogether, this sheds new light on allosteric regulation of CaMKIIα activity via the hub domain.

Biochemistry & Molecular Biology↗