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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 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Structural Insights into the Mechanisms and Pharmacology of K 2P Potassium Channels

Leak currents, defined as voltage and time independent flows of ions across cell membranes, are central to cellular electrical excitability control. The K 2P (KCNK) potassium channel class comprises an ion channel family that produces potassium leak currents that oppose excitation and stabilize the resting membrane potential in cells in the brain, cardiovascular system, immune system, and sensory organs. Due to their widespread tissue distribution, K 2P s contribute to many physiological and pathophysiological processes including anesthesia, pain, arrythmias, ischemia, hypertension, migraine, intraocular pressure regulation, and lung injury responses. Structural studies of six homomeric K 2P s have established the basic architecture of this channel family, revealed key moving parts involved in K 2P function, uncovered the importance of asymmetric pinching and dilation motions in the K 2P selectivity filter (SF) C-type gate, and defined two K 2P structural classes based on the absence or presence of an intracellular gate. Further, a series of structures characterizing K 2P :modulator interactions have revealed a striking polysite pharmacology housed within a relatively modestly sized (~70 kDa) channel. Binding sites for small molecules or lipids that control channel function are found at every layer of the channel structure, starting from its extracellular side through the portion that interacts with the membrane bilayer inner leaflet. This framework provides the basis for understanding how gating cues sensed by different channel parts control function and how small molecules and lipids modulate K 2P activity. Such knowledge should catalyze development of new K 2P modulators to probe function and treat a wide range of disorders.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

On the effects of quadrupolar relaxation in Earth’s field NMR spectra

There is growing interest in using low-field magnetic resonance experiments for routine chemical characterization. Earth’s field NMR is one such technique that can garner structural information and enable sample differentiation with low cost and highly portable designs. The resulting NMR spectra are primarily influenced by $J$-couplings, resulting in so-called $J$-coupled spectra (JCS). Many small molecules include atoms with NMR-active nuclei that are quadrupolar either at natural abundance or are often isotopically enriched (e.g., 2 H, 6 Li, 11 B, 14 N, 17 O, etc.) where the effects of quadrupolar J-couplings and relaxation on JCS of strongly- and weakly-coupled spin systems have not been explored to date. Herein, using a set of seven fluoropyridine samples with unique substitution and $J$-couplings, we demonstrate that the 14 N relaxation rates can induce drastic line-broadening in the JCS. This includes a previously unexplored unique line broadening mechanism enabled by strongly coupled spins at low-field. In conclusion, numerical simulations are used to model and refine the magnitudes and signs of $J$-couplings, as well as indirectly determine the 14 N relaxation rates in a single 1D experiment that has a higher fidelity than observed in high-field NMR experiments.

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

A small molecule inhibitor prevents gut bacterial genotoxin production

Abstract The human gut bacterial genotoxin colibactin is a possible key driver of colorectal cancer (CRC) development. Understanding colibactin’s biological effects remains difficult owing to the instability of the proposed active species and the complexity of the gut microbiota. Here, we report small molecule boronic acid inhibitors of colibactin biosynthesis. Designed to mimic the biosynthetic precursor precolibactin, these compounds potently inhibit the colibactin-activating peptidase ClbP. Using biochemical assays and crystallography, we show that they engage the ClbP binding pocket, forming a covalent bond with the catalytic serine. These inhibitors reproduce the phenotypes observed in a clbP deletion mutant and block the genotoxic effects of colibactin on eukaryotic cells. The availability of ClbP inhibitors will allow precise, temporal control over colibactin production, enabling further study of its contributions to CRC. Finally, application of our inhibitors to related peptidase-encoding pathways highlights the power of chemical tools to probe natural product biosynthesis.

Biochemistry & Molecular Biology↗
DOE OSTI2024

Selective CK1α degraders exert antiproliferative activity against a broad range of human cancer cell lines

Molecular-glue degraders are small molecules that induce a specific interaction between an E3 ligase and a target protein, resulting in the target proteolysis. The discovery of molecular glue degraders currently relies mostly on screening approaches. Here, we describe screening of a library of cereblon (CRBN) ligands against a panel of patient-derived cancer cell lines, leading to the discovery of SJ7095, a potent degrader of CK1α, IKZF1 and IKZF3 proteins. Through a structure-informed exploration of structure activity relationship (SAR) around this small molecule we develop SJ3149, a selective and potent degrader of CK1α protein in vitro and in vivo. The structure of SJ3149 co-crystalized in complex with CK1α + CRBN + DDB1 provides a rationale for the improved degradation properties of this compound. In a panel of 115 cancer cell lines SJ3149 displays a broad antiproliferative activity profile, which shows statistically significant correlation with MDM2 inhibitor Nutlin-3a. These findings suggest potential utility of selective CK1α degraders for treatment of hematological cancers and solid tumors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Small-Molecule Models of Hydrogen-Evolving MX 2 (M = Mo, W; X = S, Se) Bulk Solids: Composition–Activity Relationships

Triangular metal chalcogenide clusters of the form [M 3 Q 7 L 3 ]An (M = Mo or W; Q = S or Se; L = i Bu 2 NCS 2 – , (CF 3 CH 2 ) 2 NCS 2 – , i Bu 2 NCSe 2 – , or i Bu 2 PS 2 – ; An = Cl – or I – ) have been investigated as molecular analogues of layered metal dichalcogenide (MX 2 ) H 2 -evolution catalysts. These clusters have been evaluated for their relative H 2 -evolving ability under a common photolysis protocol implementing [Ru(bpy) 3 ] 2+ as chromophore and Et 3 N as sacrificial electron donor. With M constant as Mo and with constant supporting ligand, clusters with an all-sulfide core enable greater H 2 -TON than clusters with an all-selenide core. A more active catalyst is produced by [Mo 3 S 7 (S 2 CN i Bu 2 ) 3 ] + I – than its W 3 analogue with the same core sulfide composition and supporting dithiocarbamate ligands. Dichalcogenocarbamate ligands provide more active catalysts than dialkyldithiophosphate ligated clusters, and within the dichalcogenocarbamate set, greater H 2 -turnovers correlate with more-electron-donating ligands (i.e., i Bu 2 NCS 2 – > (CF 3 CH 2 ) 2 NCS 2 – > i Bu 2 NCSe 2 – ). Cluster cations with Cl – as counteranion are very similar in activity H 2 -evolving levels to identical clusters with I – , ruling out any significant interfering effect by I – upon the electron transfer relay between Et 3 N and catalyst. In the aggregate, observations are consistent with a mechanism for H 2 evolution that involves reductive extrusion of H 2 from a metal hydride intermediate.

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

Small molecule inhibitors for treatment of alpha viruses

An in vitro assay was designed to measure the activity of the alphavirus non-structural protein 2 (nsP2), which is the viral protease and is required for viral replication. By taking advantage of fluorescence-resonance energy transfer between two proteins, a protease cleavage assay was generated. This was utilized for high-throughput screening of 40,000 small molecules. Inhibitors were validated using cell-based assays to measure alphavirus infection and cytotoxicity. Certain compounds were then characterized for anti-viral efficacy in various cell lines in numerous assays. Compounds were tested against Chikungunya virus, Venezuelan Equine Encephalitis virus, Rift Valley Fever virus, and Zika virus. Three compounds (compounds I, II, and III) showed pan-alphavirus anti-viral efficacy at concentrations that did not result in cell toxicity. An additional compound, structure IV, showed broad spectrum inhibition of all viruses tested. Pharmaceutical preparations and methods of treatment including these compounds are provided herein.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Split aminoacyl-tRNA synthetases for proximity-induced stop codon suppression

Synthetic biology tools for regulating gene expression have many useful biotechnology and therapeutic applications. Most tools developed for this purpose control gene expression at the level of transcription, and relatively few methods are available for regulating gene expression at the translational level. Here, we design and engineer split orthogonal aminoacyl-tRNA synthetases (o-aaRS) as unique tools to control gene translation in bacteria and mammalian cells. Using chemically induced dimerization domains, we developed split o-aaRSs that mediate gene expression by conditionally suppressing stop codons in the presence of the small molecules rapamycin and abscisic acid. Furthermore, by activating o-aaRSs, these molecular switches induce stop codon suppression, and in their absence stop codon suppression is turned off. We demonstrate, in Escherichia coli and in human cells, that split o-aaRSs function as genetically encoded AND gates where stop codon suppression is controlled by two distinct molecular inputs. In addition, we show that split o-aaRSs can be used as versatile biosensors to detect therapeutically relevant protein–protein interactions, including those involved in cancer, and those that mediate severe acute respiratory syndrome-coronavirus-2 infection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Biocatalytic Membranes for Carbon Capture and Utilization

Innovative carbon capture technologies that capture CO 2 from large point sources and directly from air are urgently needed to combat the climate crisis. Likewise, corresponding technologies are needed to convert this captured CO 2 into valuable chemical feedstocks and products that replace current fossil-based materials to close the loop in creating viable pathways for a renewable economy. Biocatalytic membranes that combine high reaction rates and enzyme selectivity with modularity, scalability, and membrane compactness show promise for both CO 2 capture and utilization. This review presents a systematic examination of technologies under development for CO 2 capture and utilization that employ both enzymes and membranes. CO 2 capture membranes are categorized by their mode of action as CO 2 separation membranes, including mixed matrix membranes (MMM) and liquid membranes (LM), or as CO 2 gas–liquid membrane contactors (GLMC). Because they selectively catalyze molecular reactions involving CO 2 , the two main classes of enzymes used for enhancing membrane function are carbonic anhydrase (CA) and formate dehydrogenase (FDH). Small organic molecules designed to mimic CA enzyme active sites are also being developed. CO 2 conversion membranes are described according to membrane functionality, the location of enzymes relative to the membrane, which includes different immobilization strategies, and regeneration methods for cofactors. Parameters crucial for the performance of these hybrid systems are discussed with tabulated examples. Progress and challenges are discussed, and perspectives on future research directions are provided.

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

Structural mechanism of allosteric activation of TRPML1 by PI(3,5)P 2 and rapamycin

Transient receptor potential mucolipin 1 (TRPML1) is a Ca 2+ -permeable, nonselective cation channel ubiquitously expressed in the endolysosomes of mammalian cells and its loss-of-function mutations are the direct cause of type IV mucolipidosis (MLIV), an autosomal recessive lysosomal storage disease. TRPML1 is a ligand-gated channel that can be activated by phosphatidylinositol 3,5-bisphosphate [PI(3,5)P 2 ] as well as some synthetic small-molecule agonists. Recently, rapamycin has also been shown to directly bind and activate TRPML1. Interestingly, both PI(3,5)P 2 and rapamycin have low efficacy in channel activation individually but together they work cooperatively and activate the channel with high potency. To reveal the structural basis underlying the synergistic activation of TRPML1 by PI(3,5)P 2 and rapamycin, we determined the high-resolution cryoelectron microscopy (cryo-EM) structures of the mouse TRPML1 channel in various states, including apo closed, PI(3,5)P 2 -bound closed, and PI(3,5)P 2 /temsirolimus (a rapamycin analog)-bound open states. These structures, combined with electrophysiology, elucidate the molecular details of ligand binding and provide structural insight into how the TRPML1 channel integrates two distantly bound ligand stimuli and facilitates channel opening.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Cooperative actin filament nucleation by the Arp2/3 complex and formins maintains the homeostatic cortical array in Arabidopsis epidermal cells

Abstract Precise control over how and where actin filaments are created leads to the construction of unique cytoskeletal arrays within a common cytoplasm. Actin filament nucleators are key players in this activity and include the conserved actin-related protein 2/3 (Arp2/3) complex as well as a large family of formins. In some eukaryotic cells, these nucleators compete for a common pool of actin monomers and loss of one favors the activity of the other. To test whether this mechanism is conserved, we combined the ability to image single filament dynamics in the homeostatic cortical actin array of living Arabidopsis (Arabidopsis thaliana) epidermal cells with genetic and/or small molecule inhibitor approaches to stably or acutely disrupt nucleator activity. We found that Arp2/3 mutants or acute CK-666 treatment markedly reduced the frequency of side-branched nucleation events as well as overall actin filament abundance. We also confirmed that plant formins contribute to side-branched filament nucleation in vivo. Surprisingly, simultaneous inhibition of both classes of nucleator increased overall actin filament abundance and enhanced the frequency of de novo nucleation events by an unknown mechanism. Collectively, our findings suggest that multiple actin nucleation mechanisms cooperate to generate and maintain the homeostatic cortical array of plant epidermal cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Small-molecule modulation of β-arrestins

β-Arrestins are multifunctional regulators of G-protein-coupled receptor (GPCR) signalling and orchestrate diverse downstream signalling events and physiological responses across the GPCR superfamily. Although GPCR pharmacology has advanced to target orthosteric and allosteric sites, as well as G proteins and GPCR kinases, direct chemical tools to modulate β-arrestin activities have remained conspicuously absent. Here we report the identification of small-molecule inhibitors that selectively target β-arrestins and delineate their mechanism of action through integrated pharmacological, biochemical, biophysical and structural analyses. These inhibitors disrupt β-arrestin engagement with agonist-activated GPCRs, impairing desensitization, internalization and β-arrestin-dependent physiological functions while sparing G protein–receptor coupling. Cryo-electron microscopy, molecular dynamics simulations and structure-guided mutagenesis reveal that one modulator, Cmpd-5, engages a pocket within the central crest of β-arrestin1 formed by the middle, C and lariat loops, a critical receptor-binding interface, stabilizing a distinct conformation that is incompatible with full β-arrestin–receptor engagement. Together, these findings establish a mechanistic framework for β-arrestin modulation, reveal a novel allosteric site for structure-based drug design, and open new avenues for transducer-targeted, pathway-specific GPCR therapeutic agents.

Kahsai, Alem W. [Duke University, Durham, NC (Unit↗
DOE OSTI2024

Discovery of BBO-8520, a First-In-Class Direct and Covalent Dual Inhibitor of GTP-Bound (ON) and GDP-Bound (OFF) KRASG12C

Abstract Approved inhibitors of KRASG12C prevent oncogenic activation by sequestering the inactive, GDP-bound (OFF) form rather than directly binding and inhibiting the active, GTP-bound (ON) form. This approach provides no direct target coverage of the active protein. Expectedly, adaptive resistance to KRASG12C (OFF)-only inhibitors is observed in association with increased expression and activity of KRASG12C(ON). To provide optimal KRASG12C target coverage, we have developed BBO-8520, a first-in-class, direct dual inhibitor of KRASG12C(ON) and (OFF) forms. BBO-8520 binds in the Switch-II/Helix3 pocket, covalently modifies the target cysteine, and disables effector binding to KRASG12C(ON). BBO-8520 exhibits potent signaling inhibition in growth factor–activated states, in which current (OFF)-only inhibitors demonstrate little measurable activity. In vivo, BBO-8520 demonstrates rapid target engagement and inhibition of signaling, resulting in durable tumor regression in multiple models, including those resistant to KRASG12C(OFF)-only inhibitors. BBO-8520 is in phase 1 clinical trials in patients with KRASG12C non–small cell lung cancer. Significance: BBO-8520 is a first-in-class direct, small molecule covalent dual inhibitor that engages KRASG12C in the active (ON) and inactive (OFF) conformations. BBO-8520 represents a novel mechanism of action that allows for optimal target coverage and delays the emergence of adaptive resistance seen with (OFF)-only inhibitors in the clinic. See related commentary by Zhou and Westover, p. 455

Oncology↗
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

The synthesis and versatile reducing power of low-valent uranium complexes

This Perspective provides a detailed overview of the chemistry of low-valent (di- and trivalent) uranium. The reactivity of uranium(II) and uranium(III) complexes is discussed both to illustrate the general types of reactions that might be expected and to highlight the many unusual modes of reactivity observed with this element. A particular emphasis is given to redox reactions with uranium(III) species, including reduction of small molecules, multi-electron reductions involving redox-active ligands, and formation of uranium–ligand multiple bonds. Redox-neutral adduct formation with uranium(III) complexes as well as the current state of the young field of uranium(II) redox chemistry are also covered. In addition, synthetic protocols to prepare a wide range of low-valent compounds are presented.

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

MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration

Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Siloxane-functional small molecule acceptor for high-performance organic solar cells with 16.6% efficiency

As one of the simple but most effective molecular design strategies, side-chain engineering has been widely employed to modify the photoelectric properties of active layer materials for boosting the photovoltaic performance of organic solar cells (OSCs). In this work, a functionalized small molecule acceptor (SMA) named BTSi-4F with a bulky siloxane-terminated solubilizing group as side-chains, derived from a classical SMA of Y6, was designed and synthesized. The results demonstrate that the introduction of siloxane-functional terminated groups into SMA not only affects the optical absorption and molecular energy levels, but also regulates the miscibility between the polymer donor and SMA. Compared to the original Y6, BTSi-4F exhibits a better solubility, upshifted lowest unoccupied molecular orbital (LUMO) energy level, more ordered molecular packing, and higher electron-mobility. Matched with a wide bandgap polymer donor PM6, the chlorobenzene-processed OSCs based on PM6:BTSi-4F achieved a superior power conversion efficiency (PCE) of 16.6% with both high open-circuit voltage (V oc ) of 0.90 V and high fill factor (FF) of 0.77, while the devices based on PM6:Y6 obtained a much lower PCE of 13.0% with a V oc of 0.81 V and FF of 0.69 under the same conditions. This work offers a promising molecular design strategy of siloxane-terminated side chain engineering to develop high-performance SMAs for efficient OSCs.

14 SOLAR ENERGY↗
DOE OSTI2020

Methane Activation on Cu Containing Zeolite Catalysts (Final Report)

In order to increase the value of the light alkane ethane found in shale gas, we investigated the transformation of ethane into ethylene and aromatic hydrocarbons using zinc-containing microporous catalysts. We investigated the kinetics of the reaction, and identified various active sites for the ethane dehydrogenation and aromatization. In addition, we investigated iron-containing zeolites, as catalysts for the addition of methyl groups to small olefins containing 2, 3 and 4 carbon molecules. We determined the reaction mechanism, the identity of the active site, and details of the reaction kinetics. We concluded that the use of iron zeolites is very promising to upgrade small olefins (2-4 carbon species) into larger olefins (4-7 carbon species) that are more valuable as fuels and as petrochemical products.

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

Do Molecular Fingerprints Identify Diverse Active Drugs in Large-Scale Virtual Screening? (No)

Computational approaches for small-molecule drug discovery now regularly scale to the consideration of libraries containing billions of candidate small molecules. One promising approach to increased the speed of evaluating billion-molecule libraries is to develop succinct representations of each molecule that enable the rapid identification of molecules with similar properties. Molecular fingerprints are thought to provide a mechanism for producing such representations. Here, we explore the utility of commonly used fingerprints in the context of predicting similar molecular activity. We show that fingerprint similarity provides little discriminative power between active and inactive molecules for a target protein based on a known active—while they may sometimes provide some enrichment for active molecules in a drug screen, a screened data set will still be dominated by inactive molecules. We also demonstrate that high-similarity actives appear to share a scaffold with the query active, meaning that they could more easily be identified by structural enumeration. Furthermore, even when limited to only active molecules, fingerprint similarity values do not correlate with compound potency. In sum, these results highlight the need for a new wave of molecular representations that will improve the capacity to detect biologically active molecules based on their similarity to other such molecules.

59 BASIC BIOLOGICAL SCIENCES↗