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At least 343 records · Page 19
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Bacterial Efflux Pumps and Their Inhibitors

Bacterial multidrug efflux transporters have distinct molecular features and mechanisms that enable their impressive substrate polyspecificity. These transporters are involved in all physiological processes where nonspecific but active transport across membranes is critical for survival and proliferation. Importantly, efflux pumps contribute to bacterial virulence and pathogenesis, as well as the spread of antibiotic resistance in clinics. Transporters belonging to several protein superfamilies have been selected for polyspecificity by evolution and augmented with accessory proteins that extend and couple transport reactions across the inner and outer membranes of the bacterium. As a result, bacteria are equipped with diverse efflux machines that protect cells from a broad variety of toxic compounds including antibiotics and other small molecule therapeutics. The inhibition of such polyspecific biomolecular machines is a challenging task, which still awaits an efficient solution. Here, we review the molecular mechanisms of efflux pumps from Gram-negative bacteria and recent advances and challenges associated with the discovery of effective inhibitors of these pumps.

Zgurskaya, Helen↗
DOE OSTI2020

Designing electrolytes with polymerlike glass-forming properties and fast ion transport at low temperatures

Significance Liquid electrolytes with thermophysical properties analogous to solid polymers, but with exceptional liquidlike ionic conductivities, are formed spontaneously when moderate amounts (≤1 M) of inorganic salts coordinate strongly with small molecules in a conventional aprotic solvent. Specifically, we report that electrolytes composed of the cyclic liquid ether, dioxolane (DOL), and containing the simple salt LiNO 3 are able to completely bypass the liquid → crystalline solid thermal transition, and to exhibit abnormally high bulk and interfacial ionic conductivities down to temperatures as low as −50 °C. Through physical, spectroscopic, and ion-transport measurements it is shown that strong interactions between LiNO 3 and DOL distort bonds in DOL, couple motions of individual solvent molecules, and lower the thermodynamic activity of the electrolyte.

36 MATERIALS SCIENCE↗
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 OSTI2025

Kinetic and structural evidence for specific DMSO interference with reversible binding of uncharged bis-oximes to hAChE and their reactivation kinetics of OP-hAChE

The structural basis of inhibitory effect of organic solvent dimethyl sulfoxide (DMSO) on human acetylcholinesterase (EC 3.1.1.7; hAChE) was inferred from the effect of DMSO on kinetics of reversible inhibition of uncharged, heterocyclic bis-oximes to hAChE, from DMSO effect on rates of reactivation of inactive organophosphate (OP)-hAChE conjugates by bis-oximes and by X-ray structures of bis-oxime and DMSO binding to hAChE. Here, the reversible inhibition constant of DMSO for hAChE in 0.1 M phosphate buffer pH 7.4 at 22 °C, was K i = (0.32 ± 0.04) % (or 45 ± 5 mM). The K i of the bis-oxime LG-703 for hAChE was 3.2-fold larger in 1 % DMSO, consistent with direct competition between LG-703 and DMSO. The X-ray structure of the LG-703∗hAChE complex (PDB ID: 6U3P) shows DMSO and LG-703 bound to individual hAChE monomers, LG-703 in the chain A and DMSO in the chain B. In the co-crystallization both small molecules were present at a similar excess over their corresponding K i values for hAChE (7.8-fold for DMSO and 6.5-fold for LG-703) and formation of two different complexes (DMSO∗hAChE and LG-703∗hAChE), in the same crystal, appears consistent with inhibition kinetics. Furthermore, rates of reactivation of paraoxon-inhibited hAChE (POX-hAChE) and of VX-hAChE by LG-703 and by a novel heterocyclic bis-oxime LG-1922 were reduced 2 – 3-fold in DMSO, consistent with observation of the active-center-bound DMSO molecules in the newly solved structure of the LG-1922∗POX-hAChE complex presented here and in our POX-hAChE structure (PDB ID: 8DT2) showing obstruction of the reactivator access to the conjugated P atom.

Acetylcholinesterase inhibition↗
DOE OSTI2026

Engineering Escherichia coli to produce medium chain oleochemicals from C 2 substrates

Many strategies to create a circular bioeconomy have been proposed. To be successful, CO 2 must be reduced with renewable energy into chemical building blocks, from which the chemical industry can be supported. Circular strategies include leveraging photosynthesis to produce sugar and lipid intermediates or renewable electricity to produce hydrogen or other electron carriers to support CO 2 reduction. Acetogens can anaerobically reduce CO 2 with H 2 to produce mixtures of small organic molecules in gas fermentations. We previously demonstrated that acetate, a common product of gas fermentation, can be converted to the model oleochemical dodecanol in engineered Escherichia coli. Here, we explored the conversion of ethanol and mixtures of ethanol and acetate to the same model oleochemicals. Co-feeding ethanol can supply both carbon and additional reducing power relative to acetate alone. In this work, we engineered E. coli to catabolize ethanol and expressed two distinct ethanol metabolism pathways in different operons and combined them with improved engineered acetate activation. We evaluated the performance of these operons in dodecanol-producing strains when fed ethanol or acetate and found ethanol to be a better carbon source when judged by product titers. The engineered strains fed ethanol produced about two-fold more dodecanol than the strains fed acetate. This increase was in part, due to change in product distribution. Cells fed ethanol produced predominantly dodecanol, whereas cells fed acetate generated a mixture of dodecanol and dodecanoic acid. Dodecanol titers were further improved by employing feeding strategies in controlled bioreactors.

Escherichia coli↗
DOE OSTI2025

SuFEx-enabled high-throughput medicinal chemistry for developing potent tamoxifen analogs as Ebola virus entry inhibitors

Ebola virus (EBOV) causes severe hemorrhagic fever with a high mortality rate in humans. In acute infection, an abnormal immune response results in excessive inflammatory cytokines and uncontrolled systemic inflammation that can result in organ damage and multi-organ failure. While vaccines and monoclonal antibody therapies are available, there is an urgent need for effective small-molecule antivirals against EBOV. Here, we report on the optimization of tamoxifen, an EBOV-glycoprotein (GP) binder that inhibits viral entry, using our Sulfur-Fluoride Exchange (SuFEx) click chemistry-based high-throughput medicinal chemistry (HTMC) strategy. Using a “Direct-to-Biology” approach, we generated a focused library of 2,496 tamoxifen analogs overnight and screened them in a cell-based pseudo-EBOV infection assay. The HTMC workflow enabled the development of a potent EBOV entry inhibitor with submicromolar EC 50 cellular antiviral activity and more than 50-fold improvement in binding affinity against EBOV-GP compared to the parent compound. Our findings underscore the use of SuFEx-enabled HTMC for rapidly generating and assessing potential therapeutic candidates against viral and immune-mediated diseases in a cell-based assay.

Immunology↗
DOE OSTI2021

Crowded electrolytes containing redoxmers in different states of charge: Solution structure, properties, and fundamental limits on energy density

Nonaqueous redox flow batteries use liquid electrolytes containing redox-active organic molecules (redoxmers) as their energy storage medium. To maximize energy density, the redoxmer concentration needs to be maximized while maintaining low viscosity and high ionic conductivity. During charge, a redoxmer molecule pairs with an ion in the electrolyte while another ion migrates across the membrane to maintain electric neutrality. In a crowded electrolyte, this reconstitution changes physical and chemical properties of the solution. To explore these behaviors, a phenothiazine redoxmer fully miscible with acetonitrile was used, and electrochemical charge was mimicked by chemical oxidation. The solutions were examined using small-angle X-ray scattering, nuclear magnetic resonance, and conductometry and modeled using classical molecular dynamics. Overall, our study indicates that physical and structural properties of redoxmer solutions in both states of charge make it exceedingly difficult to increase the redoxmer concentrations over 2 M at any temperature without compromising dynamic properties of such solutions. The cause for this limitation is proximity to a gel-like regime in which fluidity, diffusivity, and ionic conductivity exponentially decrease with increasing concentration. This tendency is compounded by non-Arrhenius behavior of the electrolyte: a small increase in the concentration outruns gains in fluidity and conductivity at a higher temperature. Thus the properties of crowded electrolytes generally make it impossible to operate when gel-like behavior sets in. Pushing the redoxmer concentration to 2.5-3 M might be possible for small redoxmer molecules, but it would require the use of ionic liquid electrolytes at 340-360 K. (C) 2021 Elsevier B.V. All rights reserved.

25 ENERGY STORAGE↗
DOE OSTI2024

Development and crystal structures of a potent second-generation dual degrader of BCL-2 and BCL-xL

Overexpression of BCL-xL and BCL-2 play key roles in tumorigenesis and cancer drug resistance. Advances in PROTAC technology facilitated recent development of the first BCL-xL/BCL-2 dual degrader, 753b, a VHL-based degrader with improved potency and reduced toxicity compared to previous small molecule inhibitors. Here, we determine crystal structures of VHL/753b/BCL-xL and VHL/753b/BCL-2 ternary complexes. The two ternary complexes exhibit markedly different architectures that are accompanied by distinct networks of interactions at the VHL/753b-linker/target interfaces. The importance of these interfacial contacts is validated via functional analysis and informed subsequent rational and structure-guided design focused on the 753b linker and BCL-2/BCL-xL warhead. This results in the design of a degrader, WH244, with enhanced potency to degrade BCL-xL/BCL-2 in cells. Using biophysical assays followed by in cell activities, we are able to explain the enhanced target degradation of BCL-xL/BCL-2 in cells. Most PROTACs are empirically designed and lack structural studies, making it challenging to understand their modes of action and specificity. Our work presents a streamlined approach that combines rational design and structure-based insights backed with cell-based studies to develop effective PROTAC-based cancer therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A 3D nonfullerene electron acceptor with a 9,9'-bicarbazole backbone for high-efficiency organic solar cells

One-dimensional ladder-type nonfullerene electron acceptors (NFAs) with large fused ring cores have been typically used in highly efficient organic solar cells (OSCs). Prior studies have demonstrated that small molecule acceptors with three-dimensional (3D) structures may exhibit low energy loss, and hence can lead to improved OSC performance. In this study, a new 3D NFA ( 99CZ-8F ) with a 9,9'-bicarbazole backbone was designed, synthesized, and characterized, where two linear A-D-A architectures were linked by a single N–N bond. 99CZ-8F showed strong absorption in the range of 500–800 nm in the solid state, which is complementary to the absorption of the donor material PM6 . After regulating the morphology of the active layer via binary solvent mixture, the optimized device exhibited a maximum power conversion efficiency (PCE) of 6.6 ± 0.1%, which is among the best reported values for 3D nonfullerene electron acceptor based OSCs

14 SOLAR ENERGY↗
DOE OSTI2024

Defining the Mechanism of Proton Pumping in Heme-Copper Oxidases

During this award, progress was made in two distinct areas of science, one was within the context of bioinorganic chemistry and another in the context of biomimetic, small molecule chemistry. The overarching goals of this work was to understand the fundamental mechanistic drivers for biological reactions specifically, proton transfer reactions. In the biochemical sphere, this goal was investigated through investigation of the bacterial proton pump, ubiquinol oxidase (UbO). Further work in the bioinorganic space was completed in collaboration with the Bandarian group on a novel natural peptide product. While in the biomimetic space, this work was explored through a computational collaborative study with the Riordan group relating to proton coupled electron transfers in iron complexes as relating to the heme active site in proton pumping enzymes.

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

Molecular interactions that drive morphological and mechanical stabilities in organic solar cells

Morphological and mechanical stabilities of organic solar cells (OSCs) are of paramount importance to ensure long-lived devices. However, the fundamental drivers of these stability metrics and their competing relationship have yet to be well defined. Here, in this work, several high-performance polymers and small molecule acceptors (SMAs) are considered to assist in the development of a comprehensive view of the molecular drivers of, and interrelationships between, morphological and mechanical stabilities. We find that the SMAs drive much of the embrittlement and diffusion characteristics in the blend films. However, the heterointeraction of the SMA and polymer, probed through dynamic mechanical analysis, is a key contributing factor to the film toughness. The heterointeraction energy is ideally maximally negative (i.e., repulsive), deviating from the geometric mean of the homointeraction energy. These findings assist in introducing a framework to understand the active layer stability and highlight material properties that lead to morphologically stable and physically robust OSCs.

14 SOLAR ENERGY↗
DOE OSTI2020

Role of Undercoordinated Sites for the Catalysis in Confined Spaces Formed by Two-Dimensional Material Overlayers

Adding a two-dimensional (2D) overlayer on a metal surface is a promising route for activating reactants confined in the interfacial space. However, an atomistic understanding of the role played by undercoordinated sites of the 2D overlayer in the activation of molecules in this nanoscaled confined space is yet to be developed. In this paper, we study CO dissociation as a prototypical reaction to investigate CO activation in the confined space enclosed by Rh(111) and a monolayer of hexagonal boron nitride (h-BN). The effect of the space size (i.e., the distance between h-BN and the metal surface), the type of undercoordinated sites, and the size of the defect are explicitly studied by density functional theory with dispersion correction. The following temperature-programmed X-ray photoelectron spectroscopy measurement suggests that a small portion of the CO dissociated during the desorption, leaving the residual atomic oxygen incorporated into the h-BN lattice, which validates the theoretical prediction. Finally, the combination of theory and experiment calls for further attention to be paid to the role of undercoordinated sites in the 2D overlayers in confined systems forming potential new catalytic environments.

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

Cross-kingdom expression of synthetic genetic elements promotes discovery of metabolites in the human microbiome

Small molecules encoded by biosynthetic pathways mediate cross-species interactions and harbor untapped potential, which has provided valuable compounds for medicine and biotechnology. Since studying biosynthetic gene clusters in their native context is often difficult, alternative efforts rely on heterologous expression, which is limited by host-specific metabolic capacity and regulation. Here, in this work, we describe a computational-experimental technology to redesign genes and their regulatory regions with hybrid elements for cross-species expression in Gram-negative and -positive bacteria and eukaryotes, decoupling biosynthetic capacity from host-range constraints to activate silenced pathways. These synthetic genetic elements enabled the discovery of a class of microbiome-derived nucleotide metabolites—tyrocitabines—from Lactobacillus iners. Tyrocitabines feature a remarkable orthoester-phosphate, inhibit translational activity, and invoke unexpected biosynthetic machinery, including a class of “Amadori synthases” and “abortive” tRNA synthetases. Our approach establishes a general strategy for the redesign, expression, mobilization, and characterization of genetic elements in diverse organisms and communities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Expanding the Domain of Applicability of Machine Learning Models with Limited Data for Drug Property Prediction

Accurate machine learning models for predicting small molecule interactions with biological targets are essential for therapeutic discovery, biothreat response, and computational drug design, but their performance is often limited for understudied targets with sparse experimental data. To address this challenge, we developed and evaluated methods to improve molecular property prediction under low-data conditions, using the NimA-related kinase (NEK) family as a proof-of-concept. This work focused on two complementary goals within the ATOM Modeling PipeLine (AMPL) and the Generative Molecular Design (GMD) loop: expanding model applicability through transfer learning, representation learning, feature scaling, sampling strategies, and active-learning-inspired compound selection; and enabling efficient virtual screening to prioritize compounds that balance predicted activity, design objectives, and synthetic accessibility.

organic↗
DOE OSTI2020

Inhibition of USP7 activity selectively eliminates senescent cells in part via restoration of p53 activity

The accumulation of senescent cells (SnCs) is a causal factor of various age-related diseases as well as some of the side effects of chemotherapy. Pharmacological elimination of SnCs (senolysis) has the potential to be developed into novel therapeutic strategies to treat these diseases and pathological conditions. Here we show that ubiquitin-specific peptidase 7 (USP7) is a novel target for senolysis because inhibition of USP7 with an inhibitor or genetic depletion of USP7 by RNA interference induces apoptosis selectively in SnCs. The senolytic activity of USP7 inhibitors is likely attributable in part to the promotion of the human homolog of mouse double minute 2 (MDM2) ubiquitination and degradation by the ubiquitin–proteasome system. This degradation increases the levels of p53, which in turn induces the pro-apoptotic proteins PUMA, NOXA, and FAS and inhibits the interaction of BCL-XL and BAK to selectively induce apoptosis in SnCs. Further, we show that treatment with a USP7 inhibitor can effectively eliminate SnCs and suppress the senescence-associated secretory phenotype (SASP) induced by doxorubicin in mice. These findings suggest that small molecule USP7 inhibitors are novel senolytics that can be exploited to reduce chemotherapy-induced toxicities and treat age-related diseases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Thermal stability and protective properties of phenylphosphonic acid on Cu(111)

Phenylphosphonic acid (PPA) adsorbed on Cu(111) has been studied by synchrotron radiation-based techniques in combination with density functional theory calculations. Here, the dehydrogenated phenylphosphonic acid molecule (PP) strongly bound in a tridentate geometry through oxygen atoms to Cu(111) is shown to be the dominant surface species in the temperature range 150–300 °C. The stable PP adlayer substantially protects the Cu(111) surface from oxidation during exposure to ambient conditions. Thermal treatment of the PPA adlayer at 375 °C initiates molecular decomposition through several channels: P–O bond scission forming C 6 H 5 PO 2 ; C–P bond scission forming phenyl and PO 3 ; and C–H bond scission forming C 6 H 4 PO 3 . All three reaction steps have activation barriers of 1.7–1.8 eV. Small products such as O, H, and phenyl can immediately react further and desorb, while the remaining phosphonate species undergo condensation. After annealing at a higher temperature, the phosphonate group is further reduced from oxygen-rich to phosphorus-rich species, which form the majority of remaining adsorbates after 500 °C treatment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Near-physiological-temperature serial crystallography reveals conformations of SARS-CoV-2 main protease active site for improved drug repurposing

The COVID-19 pandemic has resulted in 198 million reported infections and more than 4 million deaths as of July 2021 (covid19.who.int). Research to identify effective therapies for COVID-19 includes: (1) designing a vaccine as future protection; (2) de novo drug discovery; and (3) identifying existing drugs to repurpose them as effective and immediate treatments. To assist in drug repurposing and design, we determine two apo structures of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease at ambient temperature by serial femtosecond X-ray crystallography. We employ detailed molecular simulations of selected known main protease inhibitors with the structures and compare binding modes and energies. The combined structural and molecular modeling studies not only reveal the dynamics of small molecules targeting the main protease but also provide invaluable opportunities for drug repurposing and structure-based drug design strategies against SARS-CoV-2.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Crystal Structure of CYP3A4 Complexed with Fluorol Identifies the Substrate Access Channel as a High-Affinity Ligand Binding Site

Cytochrome P450 3A4 (CYP3A4) is a major human drug-metabolizing enzyme, notoriously known for its extreme substrate promiscuity, allosteric behavior, and implications in drug–drug interactions. Despite extensive investigations, the mechanism of ligand binding to CYP3A4 is not fully understood. We determined the crystal structure of CYP3A4 complexed with fluorol, a small fluorescent dye that can undergo hydroxylation. In the structure, fluorol associates to the substrate channel, well suited for the binding of planar polyaromatic molecules bearing polar groups, through which stabilizing H-bonds with the polar channel residues, such as Thr224 and Arg372, can be established. Mutagenesis, spectral, kinetic, and functional data confirmed the involvement but not strict requirement of Thr224 for the association of fluorol. Collectively, our data identify the substrate channel as a high-affinity ligand binding site and support the notion that hydrophobic ligands first dock to the nearby peripheral surface, before migrating to the channel and, subsequently, into the active site.

59 BASIC BIOLOGICAL SCIENCES↗