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Results for “small molecule activation”

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 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Development of a CNS-permeable reactivator for nerve agent exposure: an iterative, multi-disciplinary approach

Nerve agents have experienced a resurgence in recent times with their use against civilian targets during the attacks in Syria (2012), the poisoning of Sergei and Yulia Skripal in the United Kingdom (2018) and Alexei Navalny in Russia (2020), strongly renewing the importance of antidote development against these lethal substances. The current standard treatment against their effects relies on the use of small molecule-based oximes that can efficiently restore acetylcholinesterase (AChE) activity. Despite their efficacy in reactivating AChE, the action of drugs like 2-pralidoxime (2-PAM) is primarily limited to the peripheral nervous system (PNS) and, thus, provides no significant protection to the central nervous system (CNS). This lack of action in the CNS stems from their ionic nature that, on one end makes them very powerful reactivators and on the other renders them ineffective at crossing the Blood Brain Barrier (BBB) to reach the CNS. In this report, we describe the use of an iterative approach composed of parallel chemical and in silico syntheses, computational modeling, and a battery of detailed in vitro and in vivo assays that resulted in the identification of a promising, novel CNS-permeable oxime reactivator. Additional experiments to determine acute and chronic toxicity are ongoing.

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

Mechanochemically accelerated deconstruction of chemically recyclable plastics

Plastics redesign for circularity has primarily focused on monomer chemistries enabling faster deconstruction rates concomitant with high monomer yields. Yet, during deconstruction, polymer chains interact with their reaction medium, which remains underexplored in polymer reactivity. Here, we show that, when plastics are deconstructed in reaction media that promote swelling, initial rates are accelerated by over sixfold beyond those in small-molecule analogs. This unexpected acceleration is primarily tied to mechanochemical activation of strained polymer chains; however, changes in the activity of water under polymer confinement and bond activation in solvent-separated ion pairs are also important. Together, deconstruction times can be shortened by seven times by codesigning plastics and their deconstruction processes.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Designed and biologically active protein lattices

Versatile methods to organize proteins in space are required to enable complex biomaterials, engineered biomolecular scaffolds, cell-free biology, and hybrid nanoscale systems. Here, we demonstrate how the tailored encapsulation of proteins in DNA-based voxels can be combined with programmable assembly that directs these voxels into biologically functional protein arrays with prescribed and ordered two-dimensional (2D) and three-dimensional (3D) organizations. We apply the presented concept to ferritin, an iron storage protein, and its iron-free analog, apoferritin, in order to form single-layers, double-layers, as well as several types of 3D protein lattices. Our study demonstrates that internal voxel design and inter-voxel encoding can be effectively employed to create protein lattices with designed organization, as confirmed by in situ X-ray scattering and cryo-electron microscopy 3D imaging. The assembled protein arrays maintain structural stability and biological activity in environments relevant for protein functionality. The framework design of the arrays then allows small molecules to access the ferritins and their iron cores and convert them into apoferritin arrays through the release of iron ions. The presented study introduces a platform approach for creating bio-active protein-containing ordered nanomaterials with desired 2D and 3D organizations.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
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 OSTI2021

Predictive Rules of Efflux Inhibition and Avoidance in Pseudomonas aeruginosa

Antibiotic-resistant bacteria rapidly spread in clinical and natural environments and challenge our modern lifestyle. A major component of defense against antibiotics in Gram-negative bacteria is a drug permeation barrier created by active efflux across the outer membrane. We identified molecular determinants defining the propensity of small peptidomimetic molecules to avoid and inhibit efflux pumps in Pseudomonas aeruginosa, a human pathogen notorious for its antibiotic resistance. Combining experimental and computational protocols, we mapped the fate of the compounds from structure-activity relationships through their dynamic behavior in solution, permeation across both the inner and outer membranes, and interaction with MexB, the major efflux transporter of P. aeruginosa. We identified predictors of efflux avoidance and inhibition and demonstrated their power by using a library of traditional antibiotics and compound series and by generating new inhibitors of MexB. The identified predictors will enable the discovery and optimization of antibacterial agents suitable for treatment of P. aeruginosa infections.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Mapping the catalytic conformations of an assembly-line polyketide synthase module

Assembly-line polyketide synthases, such as the 6-deoxyerythronolide B synthase (DEBS), are large enzyme factories prized for their ability to produce specific and complex polyketide products. By channeling protein-tethered substrates across multiple active sites in a defined linear sequence, these enzymes facilitate programmed small-molecule syntheses that could theoretically be harnessed to access countless polyketide product structures. Additionally, using cryogenic electron microscopy to study DEBS module 1, we present a structural model describing this substrate-channeling phenomenon. Our 3.2- to 4.3-angstrom-resolution structures of the intact module reveal key domain-domain interfaces and highlight an unexpected module asymmetry. We also present the structure of a product-bound module that shines light on a recently described “turnstile” mechanism for transient gating of active sites along the assembly line.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Structure-Based Design of Small-Molecule Inhibitors of Human Interleukin-6

Human Interleukin-6 (hIL-6) is a pro inflammatory cytokine that binds to its receptor, IL-6Rα followed by binding to gp130 and subsequent dimerization to form a hexamer signaling complex. As a critical inflammation mediator, hIL-6 is associated with a diverse range of diseases and monoclonal antibodies in clinical use that either target IL-6Rα or hIL-6 to inhibit signaling. Here, we perform high-throughput structure-based computational screening using ensemble docking for small-molecule antagonists for which the target conformations were taken from 600 ns long molecular dynamics simulations of the apo protein. Prior knowledge of the contact sites from binary complex studies and experimental work was incorporated into the docking studies. The top 20 scoring ligands from the in silico studies after post analysis were subjected to in vitro functional assays. Among these compounds, the ligand with the second-highest calculated binding affinity experimentally showed an ~84% inhibitory effect on IL6-induced STAT3 reporter activity at 10 μM concentration. This finding may pave the way for designing small-molecule inhibitors of hIL-6 of therapeutic significance.

Human Interleukin-6↗
NASA NTRS1992

Destruction and survival of polycyclic aromatic hydrocarbons in active galaxies

Infrared spectra of dusty galactic environments often contain emission features attributed to polycyclic aromatic hydrocarbons or PAHs, which can be considered to be very small grains or very large molecules. Although IR spectra of starburst galaxies almost always show these emission features, similar spectra of active galaxies are usually featureless. Even in those active galaxies that do exhibit PAH emission, the PAHs still appear to be eradicated from the nuclear region. This dichotomy suggests that PAHs are destroyed by the intense hard radiation field from an AGN. Laboratory experiments show that certain PAHs are, in fact, so effectively destroyed by individual EUV and X-ray photons that they cannot survive even at kiloparsec distances from active nuclei. Regions within active galaxies that do show PAH emission must therefore be shielded from the central X-ray source by a substantial column density of X-ray absorbing gas.

Voit, G. M.↗
DOE OSTI2020

Charge generation mechanism tuned via film morphology in small molecule bulk-heterojunction photovoltaic materials

Small organic molecules have emerged as promising component materials for organic photovoltaic devices. Compared to most conjugated polymers for the same application, small molecules have unique morphologies that promote electronic processes relevant to organic solar cell (OSC) function that can be significantly different from those of conjugated polymeric materials. Here we investigate constituent loading-dependent effects on OSC morphology and function using the classical fullerene acceptor, PC 61 BM, in a heterojunction blend with the small molecule donor, NDT (thiophene-capped diketopyrrolopyrrole naphthodithiophene). The evolution of active layer morphology as well as exciton speciation and dynamics as a function of the PC 61 BM content are examined in combined structural studies using GIWAXS and spectroscopic studies using transient absorption spectroscopy. We observe evidence for three types of coexisting excitons and details of the interplay between them determines the yield of charge separated states that afford sustained device efficiency.

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

Materials for controlling the epitaxial growth of photoactive layers in photovoltaic devices

There is disclosed ultrathin film material templating layers that force the morphology of subsequently grown electrically active thin films have been found to increase the performance of small molecule organic photovoltaic (OPV) cells. There is disclosed electron-transporting material, such as hexaazatriphenylene-hexacarbonitrile (HAT-CN) can be used as a templating material that forces donor materials, such as copper phthalocyanine (CuPc) to assume a vertical-standing morphology when deposited onto its surface on an electrode, such as an indium tin oxide (ITO) electrode. It has been shown that for a device with HAT-CN as the templating buffer layer, the fill factor and short circuit current of CuPc:C60 OPVs were both improved compared with cells lacking the HAT-CN template. This is explained by the reduction of the series resistance due to the improved crystallinity of CuPc grown onto the ITO surface.

Forrest, Stephen R.↗
DOE OSTI2025

Discovery of an autoinhibited conformation in mesotrypsin reveals a strategy for selective serine protease inhibition

Selective inhibition of the more than 100 S1 family serine proteases is a long-standing challenge due to their active site similarity. Mesotrypsin, implicated in cancer progression, exemplifies these difficulties; no current inhibitors achieve selectivity over other human trypsins. We found an unexpected autoinhibited conformation of mesotrypsin via x-ray crystallography, revealing a cryptic pocket adjacent to the active site. Using high-throughput virtual screening targeting this cryptic pocket, we identified a conformationally selective small-molecule inhibitor that stabilizes the inactive state of mesotrypsin. This inhibitor demonstrates selectivity for mesotrypsin over other trypsins. Our findings challenge the accepted view of digestive trypsins as constitutively active enzymes lacking potential for allosteric regulation. Furthermore, analyses of other structures suggest that dynamic sampling of closed states with analogous allosteric cryptic pockets appears widespread among S1 serine proteases. These observations point to a potentially generalizable strategy to achieve selective inhibition, offering broad implications for drug development targeting serine proteases in cancer and other diseases.

Coban, Matt↗
DOE OSTI2022

Recent advances in cooperative activation of CO 2 and N 2 O by bimetallic coordination complexes or binuclear reaction pathways

The gaseous small molecules, CO 2 and N 2 O, play important roles in climate change and ozone layer depletion, and they hold promise as underutilized reagents and chemical feedstocks. Furthermore, productive transformations of these heteroallenes are difficult to achieve because of their inertness. In nature, these gases are cycled through ecological systems by metalloenzymes featuring multimetallic active sites that employ cooperative mechanisms. Thus, cooperative bimetallic chemistry is an important strategy for synthetic systems, as well. In this Perspective, recent advances (since 2010) in cooperative activation of CO 2 and N 2 O are reviewed, including examples involving s-block, p-block, d-block, and f-block metals and different combinations thereof.

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

C 1 Chemistry on Metal Carbide Nanoparticles: Boosting the Conversion of CO 2 and CH 4

The studies described in this Perspective show that transition metal carbide (TMC) nanoparticles can be very useful for the activation of three molecules located at the heart of C 1 chemistry: H 2 , CH 4 , and CO 2 . They also can play a major role in the trapping and conversion of two major greenhouse gases. A combination of experiment and theory has shed light on the physical and chemical properties of these systems, which can be very different from those of bulk carbides. Molecular clusters of these compounds, which can be inserted inside the cages of zeolites or carbon nanotubes, have unsaturated metal and carbon atoms that frequently work in a cooperative way when dealing with hard-to-activate molecules, such as CH 4 and CO 2 . These molecular clusters can evolve into nanoparticles of small to medium size (<15 nm) that have unique carbon/metal ratios and structures not seen in the bulk metal carbides. Even when their structures are cuts from bulk lattices, the TMC nanoparticles have corner or edge atoms that are active for the cleavage and conversion of C–H and C–O bonds. In this paper, we cover experimental and theoretical studies with well-defined metal carbide nanoparticles prepared by different methods, free and supported on diverse substrates. The Perspective ends with a discussion of current challenges and potential applications.

03 NATURAL GAS↗
DOE OSTI2021

Suppression of hepatitis B virus through therapeutic activation of RIG-I and IRF3 signaling in hepatocytes

Hepatitis B virus (HBV) mediates persistent infection, chronic hepatitis, and liver disease. HBV covalently closed circular (ccc)DNA is central to viral persistence such that its elimination is considered the cornerstone for HBV cure. Inefficient detection by pathogen recognition receptors (PRRs) in the infected hepatocyte facilitates HBV persistence via avoidance of innate immune activation and interferon regulatory factor (IRF)3 induction of antiviral gene expression. We evaluated a small molecule compound, F7, and 5'-triphosphate-poly-U/UC pathogen-associated-molecular-pattern (PAMP) RNA agonists of RIG-I, a PRR that signals innate immunity, for ability to suppress cccDNA. F7 and poly-U/UC PAMP treatment of HBV-infected cells induced RIG-I signaling of IRF3 activation to induce antiviral genes for suppression of cccDNA formation and accelerated decay of established cccDNA, and were additive to the actions of entecavir. Our study shows that activation of the RIG-I pathway and IRF3 to induce innate immune actions offers therapeutic benefit toward elimination of cccDNA.

60 APPLIED LIFE SCIENCES↗
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↗
DOE OSTI2020

Selective inhibition of human translation termination by a drug-like compound

Methods to directly inhibit gene expression using small molecules hold promise for the development of new therapeutics targeting proteins that have evaded previous attempts at drug discovery. Among these, small molecules including the drug-like compound PF-06446846 (PF846) selectively inhibit the synthesis of specific proteins, by stalling translation elongation. These molecules also inhibit translation termination by an unknown mechanism. Using cryo-electron microscopy (cryo-EM) and biochemical approaches, we show that PF846 inhibits translation termination by arresting the nascent chain (NC) in the ribosome exit tunnel. The arrested NC adopts a compact α-helical conformation that induces 28 S rRNA nucleotide rearrangements that suppress the peptidyl transferase center (PTC) catalytic activity stimulated by eukaryotic release factor 1 (eRF1). These data support a mechanism of action for a small molecule targeting translation that suppresses peptidyl-tRNA hydrolysis promoted by eRF1, revealing principles of eukaryotic translation termination and laying the foundation for new therapeutic strategies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Chromatin activity precipitation method and system

Methods and systems for identifying binding sites in macromolecules using small molecule mimics of naturally occurring molecules is disclosed. A reactive probe is provided that mimics small molecule cofactors. A target macromolecule is irreversibly bound to the probe in vivo to selectively pull down or precipitate probe-bound macromolecules. The macromolecules may be, but are not limited to, DNA, RNA, and proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Molecular understanding of heteronuclear active sites in heme–copper oxidases, nitric oxide reductases, and sulfite reductases through biomimetic modelling

Heme-copper oxidases (HCO), nitric oxide reductases (NOR), and sulfite reductases (SiR) catalyze the multi-electron and multi-proton reductions of O 2 , NO, and SO 3 2- , respectively. Each of these reactions is important to drive cellular energy production through respiratory metabolism and HCO, NOR, and SiR evolved to contain heteronuclear active sites containing heme/copper, heme/nonheme iron, and heme-[4Fe-4S] centers, respectively. The complexity of the structures and reactions of these native enzymes, along with their large sizes and/or membrane associations, make it challenging to fully understand the crucial structural features responsible for the catalytic properties of these active sites. Here, we summarize progress that has been made to better understand these heteronuclear metalloenzymes at the molecular level though study of the native enzymes along with insights gained from biomimetic models comprising either small molecules or proteins. Further understanding the reaction selectivity of these enzymes is discussed through comparisons of their similar heteronuclear active sites, and we offer outlook for further investigations and areas of ongoing study.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗