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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 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2012

Structure-Based Design of Potent Bcl-2/Bcl-xL Inhibitors with Strong in Vivo Antitumor Activity

Bcl-2 and Bcl-xL are key apoptosis regulators and attractive cancer therapeutic targets. We have designed and optimized a class of small-molecule inhibitors of Bcl-2 and Bcl-xL containing a 4,5-diphenyl-1H-pyrrole-3-carboxylic acid core structure. A 1.4 {angstrom} resolution crystal structure of a lead compound, 12, complexed with Bcl-xL has provided a basis for our optimization. The most potent compounds, 14 and 15, bind to Bcl-2 and Bcl-xL with subnanomolar K{sub i} values and are potent antagonists of Bcl-2 and Bcl-xL in functional assays. Compounds 14 and 15 inhibit cell growth with low nanomolar IC{sub 50} values in multiple small-cell lung cancer cell lines and induce robust apoptosis in cancer cells at concentrations as low as 10 nM. Compound 14 also achieves strong antitumor activity in an animal model of human cancer.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

N-Aryl-benzimidazolones as novel small molecule HSP90 inhibitors

We describe the development of a novel series of N-aryl-benzimidazolone HSP90 inhibitors (9) targeting the N-terminal ATP-ase site. SAR development was influenced by structure-based design based around X-ray structures of ligand bound HSP90 complexes. Lead compounds exhibited high binding affinities, ATP-ase inhibition and cellular client protein degradation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Pandemic drugs at pandemic speed: infrastructure for accelerating COVID-19 drug discovery with hybrid machine learning- and physics-based simulations on high-performance computers

The race to meet the challenges of the global pandemic has served as a reminder that the existing drug discovery process is expensive, inefficient and slow. There is a major bottleneck screening the vast number of potential small molecules to shortlist lead compounds for antiviral drug development. New opportunities to accelerate drug discovery lie at the interface between machine learning methods, in this case, developed for linear accelerators, and physics-based methods. The two in silico methods, each have their own advantages and limitations which, interestingly, complement each other. Here, we present an innovative infrastructural development that combines both approaches to accelerate drug discovery. The scale of the potential resulting workflow is such that it is dependent on supercomputing to achieve extremely high throughput. We have demonstrated the viability of this workflow for the study of inhibitors for four COVID-19 target proteins and our ability to perform the required large-scale calculations to identify lead antiviral compounds through repurposing on a variety of supercomputers.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2015

Diffused phase transitions in Pb(Zr{sub 0.65}Ti{sub 0.35})O{sub 3}-Pb(Fe{sub 2/3}W{sub 1/3})O{sub 3} multiferroics

The solid solutions of (1−x)Pb(Zr{sub 0.65}Ti{sub 0.35})O{sub 3}-xPb(Fe{sub 2/3}W{sub 1/3})O{sub 3} in different ratios were fabricated by a high-temperature solid-state reaction method using high-purity oxides for possible multi-ferroic applications. Structural analysis using x-ray diffraction powder patterns of the system by Rietveld refinement method exhibits the formation of rhombohedral phase with R3c space group. Detailed studies of dielectric permittivity as a function of temperature of the systems show that the frequency independent dielectric maximum temperature shifts toward room temperature on increasing x. In addition to this, the degree of diffuseness of the permittivity anomaly is more pronounced for higher content of Pb(Fe{sub 2/3}W{sub 1/3})O{sub 3}, implying the existence of a composition-induced diffuse phase transition for the limited range of compositional ratios. Detailed impedance spectroscopy analysis shows the contributions of grain, grain boundary, and interfacial polarizations in the resistive characteristics and conduction mechanism of the materials. The weak ferromagnetic and saturated ferroelectric loops indicate that system with x = 0.1, 0.2 have good multiferroic characteristics, and may be useful for future spintronic devices.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2012

Molecular Mechanism of Selectivity among G Protein-Coupled Receptor Kinase 2 Inhibitors

G protein-coupled receptors (GPCRs) are key regulators of cell physiology and control processes ranging from glucose homeostasis to contractility of the heart. A major mechanism for the desensitization of activated GPCRs is their phosphorylation by GPCR kinases (GRKs). Overexpression of GRK2 is strongly linked to heart failure, and GRK2 has long been considered a pharmaceutical target for the treatment of cardiovascular disease. Several lead compounds developed by Takeda Pharmaceuticals show high selectivity for GRK2 and therapeutic potential for the treatment of heart failure. To understand how these drugs achieve their selectivity, we determined crystal structures of the bovine GRK2-G{beta}{gamma} complex in the presence of two of these inhibitors. Comparison with the apoGRK2-G{beta}{gamma} structure demonstrates that the compounds bind in the kinase active site in a manner similar to that of the AGC kinase inhibitor balanol. Both balanol and the Takeda compounds induce a slight closure of the kinase domain, the degree of which correlates with the potencies of the inhibitors. Based on our crystal structures and homology modeling, we identified five amino acids surrounding the inhibitor binding site that we hypothesized could contribute to inhibitor selectivity. However, our results indicate that these residues are not major determinants of selectivity among GRK subfamilies. Rather, selectivity is achieved by the stabilization of a unique inactive conformation of the GRK2 kinase domain.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Structure-Based Development of Small Molecule PFKFB3 Inhibitors: A Framework for Potential Cancer Therapeutic Agents Targeting the Warburg Effect

Cancer cells adopt glycolysis as the major source of metabolic energy production for fast cell growth. The HIF-1-induced PFKFB3 plays a key role in this adaptation by elevating the concentration of Fru-2,6-BP, the most potent glycolysis stimulator. As this metabolic conversion has been suggested to be a hallmark of cancer, PFKFB3 has emerged as a novel target for cancer chemotherapy. Here, we report that a small molecular inhibitor, N4A, was identified as an initial lead compound for PFKFB3 inhibitor with therapeutic potential. In an attempt to improve its potency, we determined the crystal structure of the PFKFB3 {sm_bullet} N4A complex to 2.4 {angstrom} resolution and, exploiting the resulting molecular information, attained the more potent YN1. When tested on cultured cancer cells, both N4A and YN1 inhibited PFKFB3, suppressing the Fru-2,6-BP level, which in turn suppressed glycolysis and, ultimately, led to cell death. This study validates PFKFB3 as a target for new cancer therapies and provides a framework for future development efforts.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2013

Three Pb{sup II} coordination polymers based on 2-(pyridin-2-yl)-1H-imidazole-4,5-dicarboxylic acid: Syntheses, crystal structures, and fluorescent properties

Three lead coordination polymers, [PbCl(C{sub 10}H{sub 6}N{sub 3}O{sub 4})(H{sub 2}O)·H{sub 2}O]{sub n} (1), [Pb(C{sub 10}H{sub 6}N{sub 3}O{sub 4}){sub 2}(H{sub 2}O)]{sub n} (2) and [Pb{sub 3}(C{sub 10}H{sub 5}N{sub 3}O{sub 4}){sub 3}]{sub n} (3) (C{sub 10}H{sub 7}N{sub 3}O{sub 4}=2-(pyridin-2-yl)-1H-imidazole-4,5-dicarboxylic acid), have been hydrothermally synthesized and structurally characterized by single-crystal X-ray diffraction. In 1, Cl anions connected neighboring wave-like 2D layers, which are constructed with left- and right-handed helical chains, into a 3D network structure with a (6{sup 3})(6{sup 5}·8) topology. In 2, Pb cations are linked into a 3D 6{sup 6} network with left- and right-handed helixes by μ{sub 2}-bridging C{sub 10}H{sub 6}N{sub 3}O{sub 4}{sup −} ligands. In 3, C{sub 10}H{sub 5}N{sub 3}O{sub 4}{sup 2−} ligands link Pb{sub 6}O{sub 12} clusters into a 3D (4{sup 12}·6{sup 3}) network. Their fluorescent properties were also investigated. - Graphical abstract: Three 3D lead compounds based on 2-(pyridin-2-yl)-1H-imidazole-4,5-dicarboxylic acid have been hydrothermally synthesized. Four new coordination modes of the organic ligand are first reported. Display Omitted - Highlights: • Three new Pb(II) complexes have been synthesized and characterized. • Left- and right-handed helical chains can be found in the 3D networks of 1 and 2. • Pb{sub 6}O{sub 12} clusters are connected into (4{sup 12}·6{sup 3}) network in 3.

36 MATERIALS SCIENCE↗
DOE OSTI2013

Structural Characterization of Inhibitors with Selectivity against Members of a Homologous Enzyme Family

The aspartate biosynthetic pathway provides essential metabolites for many important biological functions, including the production of four essential amino acids. As this critical pathway is only present in plants and microbes, any disruptions will be fatal to these organisms. An early pathway enzyme, L-aspartate-{beta}-semialdehyde dehydrogenase, produces a key intermediate at the first branch point of this pathway. Developing potent and selective inhibitors against several orthologs in the L-aspartate-{beta}-semialdehyde dehydrogenase family can serve as lead compounds for antibiotic development. Kinetic studies of two small molecule fragment libraries have identified inhibitors that show good selectivity against L-aspartate-{beta}-semialdehyde dehydrogenases from two different bacterial species, Streptococcus pneumoniae and Vibrio cholerae, despite the presence of an identical constellation of active site amino acids in this homologous enzyme family. Structural characterization of enzyme-inhibitor complexes have elucidated different modes of binding between these structurally related enzymes. This information provides the basis for a structure-guided approach to the development of more potent and more selective inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Structure-activity relationships of novel dithiocarbamates containing α,β-unsaturated ketone fragment as potent anticancer agents

Based on the structure of novel lead compound 8 discovered by our group, systematic structural modification was carried out. A series of compound 8’s derivatives were synthesized and evaluated for their activities against human non-small cell lung cancer cell line H460. Among them, twelve compounds showed significant proliferation inhibition activities with IC{sub 50} values <1 μM and compound 12r was the most potent one. Further study on compound 12r revealed that it has significant inhibitory effect on the growth of eight kinds of cancer cell lines with IC{sub 50} values <1 μM. Especially for cell lines A375 and HCT116, the IC{sub 50} values of 12r achieved 63 nM and 66 nM, respectively. Meanwhile, our research results also revealed the following structure-activity relationships: (a) different substitutions on the benzene ring or heteroaromatic rings greatly effect on the activity; (b) the presence of α,β-unsaturated ketone fragment is favorable for the activity; (c) the receptor cavity binding with amine moiety might be a relatively small hydrophobic cavity. These results will be valuable for the further development of this novel kind of dithiocarbamates.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2011

Synthesis Activity and Structural Analysis of Novel alpha-Hydroxytropolone Inhibitors of Human Immunodeficiency Virus Reverse Transcriptase-Associated Ribonuclease H

The {alpha}-hydroxytroplone, manicol (5,7-dihydroxy-2-isopropenyl-9-methyl-1,2,3,4-tetrahydro-benzocyclohepten-6-one), potently and specifically inhibits ribonuclease H (RNase H) activity of human immunodeficiency virus reverse transcriptase (HIV RT) in vitro. However, manicol was ineffective in reducing virus replication in culture. Ongoing efforts to improve the potency and specificity over the lead compound led us to synthesize 14 manicol derivatives that retain the divalent metal-chelating {alpha}-hydroxytropolone pharmacophore. These efforts were augmented by a high resolution structure of p66/p51 HIV-1 RT containing the nonnucleoside reverse transcriptase inhibitor (NNRTI), TMC278 and manicol in the DNA polymerase and RNase H active sites, respectively. We demonstrate here that several modified {alpha}-hydroxytropolones exhibit antiviral activity at noncytotoxic concentrations. Inclusion of RNase H active site mutants indicated that manicol analogues can occupy an additional site in or around the DNA polymerase catalytic center. Collectively, our studies will promote future structure-based design of improved {alpha}-hydroxytropolones to complement the NRTI and NNRTI currently in clinical use.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2011

Rational Mutagenesis to Support Structure-based Drug Design: MAPKAP Kinase 2 as a Case Study

Structure-based drug design (SBDD) can provide valuable guidance to drug discovery programs. Robust construct design and expression, protein purification and characterization, protein crystallization, and high-resolution diffraction are all needed for rapid, iterative inhibitor design. We describe here robust methods to support SBDD on an oral anti-cytokine drug target, human MAPKAP kinase 2 (MK2). Our goal was to obtain useful diffraction data with a large number of chemically diverse lead compounds. Although MK2 structures and structural methods have been reported previously, reproducibility was low and improved methods were needed. Our construct design strategy had four tactics: N- and C-terminal variations; entropy-reducing surface mutations; activation loop deletions; and pseudoactivation mutations. Generic, high-throughput methods for cloning and expression were coupled with automated liquid dispensing for the rapid testing of crystallization conditions with minimal sample requirements. Initial results led to development of a novel, customized robotic crystallization screen that yielded MK2/inhibitor complex crystals under many conditions in seven crystal forms. In all, 44 MK2 constructs were generated, {approx}500 crystals were tested for diffraction, and {approx}30 structures were determined, delivering high-impact structural data to support our MK2 drug design effort. Key lessons included setting reasonable criteria for construct performance and prioritization, a willingness to design and use customized crystallization screens, and, crucially, initiation of high-throughput construct exploration very early in the drug discovery process.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Origin of resistivity anomaly in p-type leads chalcogenide multiphase compounds

The electrical resistivity curves for binary phase compounds of p-type lead chalcogenide (PbTe){sub (0.9−x)}(PbSe){sub 0.1}(PbS){sub x,} (x = 0.15, 0.2, 0.25), which contain PbS-rich secondary phases, show different behaviour on heating and cooling between 500-700 K. This is contrast to single phase compounds which exhibit similar behaviour on heating and cooling. We correlate these anomalies in the electrical resistivities of multiphase compounds to the variation in phase composition at high temperatures. The inhomogeneous distribution of dopants between the matrix and secondary phase is found to be crucial in the electronic transport properties of the multiphase compounds. These results can lead to further advances in designing composite Pb-chalcogenides with high thermoelectric performance.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Inhibition of Acinetobacter -Derived Cephalosporinase: Exploring the Carboxylate Recognition Site Using Novel β-Lactamase Inhibitors

Boronic acids are attracting a lot of attention as β-lactamase inhibitors, and in particular, compound S02030 (K i = 44 nM) proved to be a good lead compound against ADC-7 (Acinetobacter-derived cephalosporinase), one of the most significant resistance determinants in A. baumannii. The atomic structure of the ADC-7/S02030 complex highlighted the importance of critical structural determinants for recognition of the boronic acids. Herein, to elucidate the role in recognition of the R2-carboxylate, which mimics the C 3 /C 4 found in β-lactams, we designed, synthesized, and characterized six derivatives of S02030 (3a). Out of the six compounds, the best inhibitors proved to be those with an explicit negative charge (compounds 3a–c, 3h, and 3j, K i = 44–115 nM), which is in contrast to the derivatives where the negative charge is omitted, such as the amide derivative 3d (K i = 224 nM) and the hydroxyamide derivative 3e (K i = 155 nM). To develop a structural characterization of inhibitor binding in the active site, the X-ray crystal structures of ADC-7 in a complex with compounds 3c, SM23, and EC04 were determined. All three compounds share the same structural features as in S02030 but only differ in the carboxy-R2 side chain, thereby providing the opportunity of exploring the distinct binding mode of the negatively charged R2 side chain. This cephalosporinase demonstrates a high degree of versatility in recognition, employing different residues to directly interact with the carboxylate, thus suggesting the existence of a “carboxylate binding region” rather than a binding site in ADC enzymes. As a result, this class of compounds was tested against resistant clinical strains of A. baumannii and are effective at inhibiting bacterial growth in conjunction with a β-lactam antibiotic.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Design of Bcl-2 and Bcl-xL Inhibitors with Subnanomolar Binding Affinities Based upon a New Scaffold

Employing a structure-based strategy, we have designed a new class of potent small-molecule inhibitors of the anti-apoptotic proteins Bcl-2 and Bcl-xL. An initial lead compound with a new scaffold was designed based upon the crystal structure of Bcl-xL and U.S. Food and Drug Administration (FDA) approved drugs and was found to have an affinity of 100 {micro}M for both Bcl-2 and Bcl-xL. Linking this weak lead to another weak-affinity fragment derived from Abbott's ABT-737 led to an improvement of the binding affinity by a factor of >10,000. Further optimization ultimately yielded compounds with subnanomolar binding affinities for both Bcl-2 and Bcl-xL and potent cellular activity. The best compound (21) binds to Bcl-xL and Bcl-2 with K{sub i} < 1 nM, inhibits cell growth in the H146 and H1417 small-cell lung cancer cell lines with IC{sub 50} values of 60-90 nM, and induces robust cell death in the H146 cancer cell line at 30-100 nM.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Identification of Selective Dual ROCK1 and ROCK2 Inhibitors Using Structure-Based Drug Design

A HTS campaign identified compound 1, an excellent hit-like molecule to initiate medicinal chemistry efforts to optimize a dual ROCK1 and ROCK2 inhibitor. Substitution (2-Cl, 2-NH 2 , 2-F, 3-F) of the pyridine hinge binding motif or replacement with pyrimidine afforded compounds with a clean CYP inhibition profile. Cocrystal structures of an early lead compound were obtained in PKA, ROCK1, and ROCK2. This provided critical structural information for medicinal chemistry to drive compound design. The structural data indicated the preferred configuration at the central benzylic carbon would be $(R)$, and application of this information to compound design resulted in compound 16. This compound was shown to be a potent and selective dual ROCK inhibitor in both enzyme and cell assays and efficacious in the retinal nerve fiber layer model after oral dosing. This tool compound has been made available through the AbbVie Compound Toolbox. Finally, the cocrystal structures also identified that aspartic acid residues 176 and 218 in ROCK2, which are glutamic acids in PKA, could be targeted as residues to drive both potency and kinome selectivity. Introduction of a piperidin-3-ylmethanamine group to the compound series resulted in compound 58, a potent and selective dual ROCK inhibitor with excellent predicted drug-like properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Lysyl-tRNA synthetase as a drug target in malaria and cryptosporidiosis

Malaria and cryptosporidiosis, caused by apicomplexan parasites, remain major drivers of global child mortality. New drugs for the treatment of malaria and cryptosporidiosis, in particular, are of high priority; however, there are few chemically validated targets. The natural product cladosporin is active against blood- and liver-stage Plasmodium falciparum and Cryptosporidium parvum in cell-culture studies. Target deconvolution in P. falciparum has shown that cladosporin inhibits lysyl-tRNA synthetase (PfKRS1). Here, we report the identification of a series of selective inhibitors of apicomplexan KRSs. Following a biochemical screen, a small-molecule hit was identified and then optimized by using a structure-based approach, supported by structures of both PfKRS1 and C. parvum KRS (CpKRS). In vivo proof of concept was established in an SCID mouse model of malaria, after oral administration (ED 90 = 1.5 mg/kg, once a day for 4 d). Furthermore, we successfully identified an opportunity for pathogen hopping based on the structural homology between PfKRS1 and CpKRS. This series of compounds inhibit CpKRS and C. parvum and Cryptosporidium hominis in culture, and our lead compound shows oral efficacy in two cryptosporidiosis mouse models. X-ray crystallography and molecular dynamics simulations have provided a model to rationalize the selectivity of our compounds for PfKRS1 and CpKRS vs. (human) HsKRS. Our work validates apicomplexan KRSs as promising targets for the development of drugs for malaria and cryptosporidiosis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Structure-Guided In Vitro to In Vivo Pharmacokinetic Optimization of Propargyl-Linked Antifolates

Pharmacokinetic/pharmacodynamic properties are strongly correlated with the in vivo efficacy of antibiotics. Propargyl-linked antifolates, a novel class of antibiotics, demonstrate potent antibacterial activity against both Gram-positive and Gram-negative pathogenic bacteria, including multidrug-resistant Staphylococcus aureus. Here, we report our efforts to optimize the pharmacokinetic profile of this class to best match the established pharmacodynamic properties. High-resolution crystal structures were used in combination with in vitro pharmacokinetic models to design compounds that not only are metabolically stable in vivo but also retain potent antibacterial activity. The initial lead compound was prone to both N-oxidation and demethylation, which resulted in an abbreviated in vivo half-life (~20 minutes) in mice. Stability of leads toward mouse liver microsomes was primarily used to guide medicinal chemistry efforts so robust efficacy could be demonstrated in a mouse disease model. Structure-based drug design guided mitigation of N-oxide formation through substitutions of sterically demanding groups adjacent to the pyridyl nitrogen. Additionally, deuterium and fluorine substitutions were evaluated for their effect on the rate of oxidative demethylation. The resulting compound was characterized and demonstrated to have a low projected clearance in humans with limited potential for drug-drug interactions as predicted by cytochrome P450 inhibition as well as an in vivo exposure profile that optimizes the potential for bactericidal activity, highlighting how structural data, merged with substitutions to introduce metabolic stability, are a powerful approach to drug design.

59 BASIC BIOLOGICAL SCIENCES↗