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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 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Applying the ATOM drug discovery platform to small-molecule antivirals (Annual Report)

The objective of this project is to advance our understanding of the ML approaches needed to find the most potent inhibitor through an AI guided search that simultaneously optimizes for limited off-target safety activity and desirable pharmacokinetics (PK) properties. The methods will be tested for inhibiting SARS-CoV-2 activity through inhibition of the main protease as a demonstration, but the methodology will be developed to apply to any biothreat target using a small-molecule protein binding-based intervention, with limited experimental data. Computational experiments are conducted using our ATOM generative molecular design (GMD) loop software, which is the implementation of our AI/ML drug design pipeline.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Donor End-Capped Alkyl Chain Length Dependent Non-Radiative Energy Loss in All-Small-Molecule Organic Solar Cells

A critical bottleneck for further efficiency breakthroughs in organic solar cells (OSCs) is to minimize the non-radiative energy loss (eΔV nr ) while maximizing the charge generation. With the development of highly emissive low-bandgap non-fullerene acceptors, the design of high-performance donors becomes critical to enable the blend with the electroluminescence quantum efficiency to approach or surpass the pristine acceptor. Herein, by shortening the end-capped alkyl chains of the small-molecular donors from hexyl (MPhS-C6) to ethyl (MPhS-C2), the material obtained aggregation that was insensitive to thermal annealing (TA) along with condensed packing simultaneously. The former leads to small phase separation and suppressed upshifts of the highest occupied molecular orbital energy level during TA, and the latter facilitates its efficient charge-transport at aggregation-less packing. Hence, the ΔV nr decreases from 0.242 to 0.182 V, from MPhS-C6 to MPhS-C2 based OSCs. An excellent PCE of 17.11% is obtained by 1,8-diiodoctane addition due to almost unchanged high J sc (26.6 mA cm –2 ) and V oc (0.888 V) with improved fill factor, which is the record efficiency with the smallest energy loss (0.497 eV) and ΔV nr (0.192 V) in all-small-molecule OSCs. Finally, these results emphasize the potential material design direction of obtaining concurrent TA-insensitive aggregation and condensed packing to maximize the device performances with a super low ΔV nr .

36 MATERIALS SCIENCE↗
DOE OSTI2023

Identification of small-molecule protein–protein interaction inhibitors for NKG2D

NKG2D (natural-killer group 2, member D) is a homodimeric transmembrane receptor that plays an important role in NK, γδ + , and CD8 + T cell-mediated immune responses to environmental stressors such as viral or bacterial infections and oxidative stress. However, aberrant NKG2D signaling has also been associated with chronic inflammatory and autoimmune diseases, and as such NKG2D is thought to be an attractive target for immune intervention. Here, in this study, we describe a comprehensive small-molecule hit identification strategy and two distinct series of protein–protein interaction inhibitors of NKG2D. Although the hits are chemically distinct, they share a unique allosteric mechanism of disrupting ligand binding by accessing a cryptic pocket and causing the two monomers of the NKG2D dimer to open apart and twist relative to one another. Leveraging a suite of biochemical and cell-based assays coupled with structure-based drug design, we established tractable structure–activity relationships with one of the chemical series and successfully improved both the potency and physicochemical properties. Together, we demonstrate that it is possible, albeit challenging, to disrupt the interaction between NKG2D and multiple protein ligands with a single molecule through allosteric modulation of the NKG2D receptor dimer/ligand interface.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Discovery of potent small-molecule inhibitors of lipoprotein(a) formation

Lipoprotein(a) (Lp(a)), an independent, causal cardiovascular risk factor, is a lipoprotein particle that is formed by the interaction of a low-density lipoprotein (LDL) particle and apolipoprotein(a) (apo(a)). Apo(a) first binds to lysine residues of apolipoprotein B-100 (apoB-100) on LDL through the Kringle IV (K IV ) 7 and 8 domains, before a disulfide bond forms between apo(a) and apoB-100 to create Lp(a). Here we show that the first step of Lp(a) formation can be inhibited through small-molecule interactions with apo(a) K IV 7–8. We identify compounds that bind to apo(a) K IV 7–8, and, through chemical optimization and further application of multivalency, we create compounds with subnanomolar potency that inhibit the formation of Lp(a). Oral doses of prototype compounds and a potent, multivalent disruptor, LY3473329 (muvalaplin), reduced the levels of Lp(a) in transgenic mice and in cynomolgus monkeys. Although multivalent molecules bind to the Kringle domains of rat plasminogen and reduce plasmin activity, species-selective differences in plasminogen sequences suggest that inhibitor molecules will reduce the levels of Lp(a), but not those of plasminogen, in humans. These data support the clinical development of LY3473329—which is already in phase 2 studies—as a potent and specific orally administered agent for reducing the levels of Lp(a).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Fast event-based electron counting for small-molecule structure determination by MicroED

Electron counting helped realize the resolution revolution in single-particle cryoEM and is now accelerating the determination of MicroED structures. Its advantages are best demonstrated by new direct electron detectors capable of fast (kilohertz) event-based electron counting (EBEC). This strategy minimizes the inaccuracies introduced by coincidence loss (CL) and promises rapid determination of accurate structures. We used the Direct Electron Apollo camera to leverage EBEC technology for MicroED data collection. Given its ability to count single electrons, the Apollo collects high-quality MicroED data from organic small-molecule crystals illuminated with incident electron beam flux densities as low as 0.01–0.045 e − /Å 2 /s. Under even the lowest flux density (0.01 e − /Å 2 /s) condition, fast EBEC data produced ab initio structures of a salen ligand (268 Da) and biotin (244 Da). Each structure was determined from a 100° wedge of data collected from a single crystal in as few as 50 s, with a delivered fluence of only ∼0.5 e − /Å 2 . Fast EBEC data collected with a fluence of 2.25 or 3.33 e − /Å 2 also facilitated a 1.5 Å structure of thiostrepton (1665 Da). While refinement of these structures appeared unaffected by CL, a CL adjustment applied to EBEC data further improved the distribution of intensities measured from the salen ligand and biotin crystals. However, CL adjustment only marginally improved the refinement of their corresponding structures, signaling the already high counting accuracy of detectors with counting rates in the kilohertz range. Overall, by delivering low-dose structure-worthy data, fast EBEC collection strategies open new possibilities for high-throughput MicroED.

EBEC↗
DOE OSTI2024

Identification and characterization of small molecule inhibitors of the LINE-1 retrotransposon endonuclease

The long interspersed nuclear element-1 (LINE-1 or L1) retrotransposon is the only active autonomously replicating retrotransposon in the human genome. L1 harms the cell by inserting new copies, generating DNA damage, and triggering inflammation. Therefore, L1 inhibition could be used to treat many diseases associated with these processes. Previous research has focused on inhibition of the L1 reverse transcriptase due to the prevalence of well-characterized inhibitors of related viral enzymes. Here we present the L1 endonuclease as another target for reducing L1 activity. We characterize structurally diverse small molecule endonuclease inhibitors using computational, biochemical, and biophysical methods. We also show that these inhibitors reduce L1 retrotransposition, L1-induced DNA damage, and inflammation reinforced by L1 in senescent cells. These inhibitors could be used for further pharmacological development and as tools to better understand the life cycle of this element and its impact on disease processes.

60 APPLIED LIFE SCIENCES↗
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 OSTI2022

Targeted protein degradation: from small molecules to complex organelles—a Keystone Symposia report

Targeted protein degradation is critical for proper cellular function and development. Protein degradation pathways, such as the ubiquitin proteasomes system, autophagy, and endosome–lysosome pathway, must be tightly regulated to ensure proper elimination of misfolded and aggregated proteins and regulate changing protein levels during cellular differentiation, while ensuring that normal proteins remain unscathed. Protein degradation pathways have also garnered interest as a means to selectively eliminate target proteins that may be difficult to inhibit via other mechanisms. Additionally, on June 7 and 8, 2021, several experts in protein degradation pathways met virtually for the Keystone eSymposium “Targeting protein degradation: from small molecules to complex organelles.” The event brought together researchers working in different protein degradation pathways in an effort to begin to develop a holistic, integrated vision of protein degradation that incorporates all the major pathways to understand how changes in them can lead to disease pathology and, alternatively, how they can be leveraged for novel therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Identification of novel small molecule inhibitors of twin arginine translocation (Tat) pathway and their effect on the control of Campylobacter jejuni in chickens

Introduction Control ofCampylobacterfrom farm to fork is challenging due to the frequent emergence of antimicrobial-resistant isolates. Furthermore, poultry production systems are known reservoirs ofCampylobacter. The twin-arginine translocation (Tat) pathway is a crucial bacterial secretion system that allowsCampylobacterto colonize the host intestinal tract by using formate as the main source of energy. However, Tat pathway is also a major contributing factor for resistance to copper sulfate (CuSO 4 ). Methods Since mammals and chickens do not have proteins or receptors that are homologous to bacterial Tat proteins, identification of small molecule (SM) inhibitors targeting the Tat system would allow the development of safe and effective control methods to mitigateCampylobacterin infected or colonized hosts in both pre-harvest and post-harvest. In this study, we screened 11 commercial libraries (n = 50,917 SM) for increased susceptibility to CuSO 4 (1 mM) inC. jejuni81–176, a human isolate which is widely studied. Results Furthermore, we evaluated 177 SM hits (2.5 μg/mL and above) that increased the susceptibility to CuSO 4 for the inhibition of formate dehydrogenase (Fdh) activity, a Tat-dependent substrate. Eight Tat-dependent inhibitors (T1–T8) were selected for further studies. These selected eight Tat inhibitors cleared all testedCampylobacterstrains (n = 12) at >10 ng/mL in the presence of 0.5 mM CuSO 4 in vitro. These selected SMs were non-toxic to colon epithelial (Caco-2) cells when treated with 50 μg/mL for 24 h and completely cleared intracellularC. jejunicells when treated with 0.63 μg/mL of SM for 24 h in the presence of 0.5 mM of CuSO 4 . Furthermore, 3 and 5-week-old chicks treated with SM candidates for 5 days had significantly decreased cecal colonization (up to 1.2 log;p < 0.01) with minimal disruption of microbiota.In silicoanalyses predicted that T7 has better drug-like properties than T2 inhibitor and might target a key amino acid residue (glutamine 165), which is located in the hydrophobic core of TatC protein. Discussion Thus, we have identified novel SM inhibitors of the Tat pathway, which represent a potential strategy to controlC. jejunispread on farms.

Microbiology↗
DOE OSTI2020

Effect of the chlorine substitution position of the end-group on intermolecular interactions and photovoltaic performance of small molecule acceptors

The structure–property relationships of small molecular acceptors (SMAs) are a key issue in the molecular design of new-generation acceptor materials for further improving the device efficiencies of polymer solar cells (PSCs). Herein, three couples of SMA isomers were synthesized, based on three central fused ring units and two 1,1-dicyanomethylene-3-indanone (IC) isomer electron-withdrawing terminal units with chlorine substitutions in different positions of its benzene ring: Cl-1 with chlorine on the same side as a C=O group of IC and Cl-2 with chlorine on the same side as the CN groups of IC. Through systematical investigation, we found that the chlorine substitution position of the terminal groups has a regular and significant influence on the molecular packing and photovoltaic performance of the SMAs. The molecular packing behavior of the SMAs is closely related to and determined by the configuration of their terminal groups, no matter which central fused ring of the SMAs is used. In particular, the Cl-1-based SMAs possess a stronger crystallinity with long range ordering packing in their molecular plane direction, while the more abundant and stereoscopic π–π intermolecular interaction in the Cl-2-based SMAs promotes the molecules to form three-dimensional charge transporting channels and leads to their red-shifted absorption and higher electron mobilities. Therefore, the Cl-2-based PSCs exhibit a higher power conversion efficiency (PCE) compared to that of the Cl-1-based devices, and the best PCE of a Cl-2 SMA-based PSC reached 16.42%. These results highlight the importance of the investigation of intermolecular interactions, packing and the arrangement of the SMAs in the solid-state, which may provide direct insights for exploring the relationship between the molecular structure and property of the photovoltaic materials. Moreover, we envision that if fragments such as end groups or side chains with more diverse molecular interactions are added into the design and the subsequent synthesis of the SMAs, this may be beneficial to promoting molecular π–π accumulation and further improving the molecular order, forming suitable molecular packing and morphology in the resulting blend films, and finally affecting the efficiency of the PSCs.

14 SOLAR ENERGY↗
DOE OSTI2025

Q -score as a reliability measure for protein, nucleic acid and small-molecule atomic coordinate models derived from 3DEM maps

Atomic coordinate models are important for the interpretation of 3D maps produced with cryoEM and cryoET (3D electron microscopy; 3DEM). In addition to visual inspection of such maps and models, quantitative metrics can inform about the reliability of the atomic coordinates, in particular how well the model is supported by the experimentally determined 3DEM map. A recently introduced metric, Q-score, was shown to correlate well with the reported resolution of the map for well fitted models. Here, we present new statistical analyses of Q-score based on its application to ∼10 000 maps and models archived in the EMDB (Electron Microscopy Data Bank) and PDB (Protein Data Bank). Further, we introduce two new metrics based on Q-score to represent each map and model relative to all entries in the EMDB and those with similar resolution. We explore through illustrative examples of proteins, nucleic acids and small molecules how Q-scores can indicate whether the atomic coordinates are well fitted to 3DEM maps and also whether some parts of a map may be poorly resolved due to factors such as molecular flexibility, radiation damage and/or conformational heterogeneity. These examples and statistical analyses provide a basis for how Q-scores can be interpreted effectively in order to evaluate 3DEM maps and atomic coordinate models prior to publication and archiving.

B factors↗
DOE OSTI2023

The co-crystal structure of Cbl-b and a small-molecule inhibitor reveals the mechanism of Cbl-b inhibition

Cbl-b is a RING-type E3 ubiquitin ligase that is expressed in several immune cell lineages, where it negatively regulates the activity of immune cells. Cbl-b has specifically been identified as an attractive target for cancer immunotherapy due to its role in promoting an immunosuppressive tumor environment. A Cbl-b inhibitor, Nx-1607, is currently in phase I clinical trials for advanced solid tumor malignancies. Using a suite of biophysical and cellular assays, we confirm potent binding of C7683 (an analogue of Nx-1607) to the full-length Cbl-b and its N-terminal fragment containing the TKBD-LHR-RING domains. To further elucidate its mechanism of inhibition, we determined the co-crystal structure of Cbl-b with C7683, revealing the compound’s interaction with both the TKBD and LHR, but not the RING domain. Here, we provide structural insights into a novel mechanism of Cbl-b inhibition by a small-molecule inhibitor that locks the protein in an inactive conformation by acting as an intramolecular glue.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Synergy of Liquid-Crystalline Small-Molecule and Polymeric Donors Delivers Uncommon Morphology Evolution and 16.6% Efficiency Organic Photovoltaics

Achieving an ideal morphology is an imperative avenue for enhancing key parameters toward high-performing organic solar cells (OSCs). Among a myriad of morphological-control methods, the strategy of incorporating a third component with structural similarity and crystallinity difference to construct ternary OSCs has emerged as an effective approach to regulate morphology. A nematic liquid-crystalline benzodithiophene terthiophene rhodamine (BTR) molecule, which possesses the same alkylthio-thienyl-substituted benzo moiety but obviously stronger crystallinity compared to classical medium-bandgap polymeric donor PM6, is employed as a third component to construct ternary OSCs based on a PM6:BTR:Y6 system. The doping of BTR (5 wt%) is found to be enough to improve the OSC morphology—significantly enhancing the crystallinity of the photoactive layer while slightly reducing the donor/acceptor phase separation scale simultaneously. Rarely is such a morphology evolution reported. It positively affects the electronic properties of the device—prolongs the carrier lifetime, shortens the photocurrent decay time, facilitates exciton dissociation, charge transport, and collection, and ultimately boosts the power conversion efficiency from 15.7% to 16.6%. This result demonstrates that the successful synergy of liquid-crystalline small-molecule and polymeric donors delicately adjusts the active-layer morphology and refines device performance, which brings vibrancy to the OSC research field.

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

Conjugated Polymer Controlled Morphology and Charge Transport of Small-Molecule Organic Semiconductors

In this study, we report an efective approach to tune the crystallization, microstructure and charge transport of solution-processed organic semiconductors by blending with a conjugated polymer additive poly(3-hexylthiophene) (P3HT). When 6,13-bis(triisopropylsilylethynyl) pentacene (TIPS pentacene) was used as a model semiconductor material to mix with diferent amount of P3HT, their intermolecular interactions led to distinctive TIPS pentacene flm morphologies, including randomly-oriented crystal ribbons, elongated needles with enhanced long-range order, and grasslike curved microwires with interlinkages. Each type of morphology was found to further correlate to considerably diferent charge transport and device performance. As compared to pristine TIPS pentacene devices, bottom-gate, top-contact OTFTs with 2% in weight P3HT additive showed a 2-fold and 5-fold improvement of average feld-efect mobility and performance consistency (defned as the ratio of average mobility to the standard deviation), respectively. The improvement in transistor electrical performance can be attributed to the combined efect of enhanced crystal orientation and uniformity, as well as increased areal coverage. This work can be applied beyond the particular example demonstrated in this study and to tune the charge transport of other small-molecule organic semiconductors in general.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Probing the Behavior of Composition‐Tunable Ultrathin PtNi Nanowires for CO Oxidation and Small‐Molecule Electrocatalytic Reactions

We have successfully synthesized ultrathin nanowires of pure Pt, Pt 99 Ni 1 , Pt 9 Ni 1 , and Pt 7 Ni 3 using a modified room-temperature soft-template method. Analysis of both methanol oxidation reaction (MOR) and ethanol oxidation reaction (EOR) results found that the Pt 7 Ni 3 samples yielded the best performance with specific activities of 0.36 and 0.34 mA/cm 2 respectively. Additionally, formic acid oxidation reaction (FAOR) tests noted that both Pt and PtNi nanowires oxidize small organic molecules (SOMs) via an indirect pathway. CO oxidation data suggests little measurable performance without any pre-reduction treatment; however, after annealing in H 2 , we detected significantly improved CO 2 formation for both Pt 9 Ni 1 and Pt 7 Ni 3 motifs. These observations highlight the importance of pre-treating these nanowires under a reducing atmosphere to enhance their performance for CO oxidation. To explain these findings, we collected extended x-ray adsorption fine structure (EXAFS) spectroscopy data, consistent with the presence of partial alloying with a tendency for Pt and Ni to segregate, thereby implying the formation of a Pt-rich shell coupled with a Ni-rich core. Here, we also observed that the degree of alloying within the nanowires increased after annealing in a reducing atmosphere, a finding deduced through analysis of the coordination numbers and calculations of Cowley's short range order parameters.

36 MATERIALS SCIENCE↗
NASA NTRS1986

Current status of the prebiotic synthesis of small molecules

Experiments designed to simulate conditions on the primitive earth and to demonstrate how the organic compounds that made up the first living organisms were synthesized are described. Simulated atmospheres with CH4, N2, NH3, and H2O were found to be most effective for synthesis of small prebiotic molecules, although atmospheres with H2, CO, N2, and H2O, and with H2, CO2, N2, and H2O also give good yields of organic compounds provided the H2/CO and H2/CO2 ratios are above 1 and 2, respectively. The spark discharge (which is a good source of HCN) and UV light are also important. Reasonable prebiotic syntheses were worked out for the amino acids that occur in proteins (with the exception of lysine, arginine, and histidine), and for purines, pyrimidines, sugars, and nicotinic acid. Many of the molecules that have been produced in these simulated primitive-earth experiments are found in carbonaceous chondrites.

Miller, Stanley L.↗