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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 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Synthesis, molecular docking, and apoptogenic efficacy of novel N-heterocycle analogs to target B-cell lymphoma 2/X-linked inhibitors of apoptosis proteins to regress melanoma

The novel series of piperidine conjugated benzophenone analogs with amide link 11a–l were synthesized in a multistep process. The structures of these compounds were confirmed by IR, {sup 1}H, {sup 13}C, NMR, and mass spectra and also by elemental analyses. The newly synthesized molecules were screened for selectivity against cancers of different origin through cell based assay system using B16F10, A375, A549, HepG2, ACHN, and MCF7 cells. The results postulated that compound 11f with two bromo groups at the para position in rings A and E and two methyl groups at ortho position in rings B and D evokes target specific action against melanoma highlighting the importance of substituted groups. Down the line studies further inferred compound 11f evokes the apoptotic cellular event leading to cell death. Investigation of eventual mechanism revealed that compound 11f turned out to be a dual inhibitor of B-cell lymphoma-2 and X-linked inhibitors of apoptosis causing the up regulation of Bax and Bad. Further, the antiproliferative effects were mimicked in murine melanoma with similar mechanisms. Molecular docking experiments further confirmed that compound 11f possessed a superior affinity for of B-cell lymphoma-2 and X-linked inhibitors of apoptosis through strong hydrogen bonds. The study implies the identification of compound 11f with selective target against melanoma by inducing apoptogenic effect, which could be the future hope for the treatment of skin cancer.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Synthesis, in vitro assays, molecular docking, theoretical ADMET prediction, and evaluation of 4-methoxy-phenylthiazole-2-amine derivatives as acetylcholinesterase inhibitors

Based on the cholinergic hypothesis of the reported compound, N-(4-(4-methoxy-phenyl)thiazol-2-yl)-3-(pyrrolidin-1-yl)propionamide, which had a good inhibitory activity to acetylcholinesterase (AChE), the new 4-methoxy-phenylthiazole-2-amine derivatives as AChE inhibitors (AChEIs) have been designed and synthesized in this study. Their chemical structures were confirmed by proton nuclear magnetic resonance, carbon-13 nuclear magnetic resonance, mass spectrometry, and infrared. Furthermore, their inhibitory activities against AChE in vitro were also tested by Ellman spectrophotometry, and the inhibitory activity test results showed that most of the compounds of 4-methoxy-phenylthiazole-2-amine derivatives had a certain AChE inhibitory activity in vitro, and the IC{sub 50} (half-maximal inhibitory concentration) value of compound 5g was 5.84 μmol/L, which was higher than that of the reference compound, rivastigmine. Moreover, it had almost no inhibitory effect on butyrylcholinesterase. In addition, compound 5g was subjected to enzyme inhibition kinetics experiments, and the result of Lineweaver–Burk’s V{sup −1}–[S]{sup −1} double-reciprocal plot showed that the acting type of compound 5g was mixed inhibition type. Furthermore, the AChE inhibitory activity mechanism of compound 5g was explored by the conformational analysis and molecular docking, which was based on the principle of the four-point pharmacophore model necessary for AChE inhibition. Finally, in silico molecular property and ADMET (absorption, distribution, metabolism, excretion, and toxicity) of the synthesized compounds were predicted by using Molinspiration and PreADMET online servers, respectively. It can be concluded that the lead AChEI compound 5g presented satisfactory drug-like characteristics and ADME properties.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Green synthesis, molecular docking, anti-oxidant and anti-inflammatory activities of α-aminophosphonates

The naturally viable α-amino acid surrogates have been synthesised via Kabachnik–Fields reaction by the condensation of 2-aminothiazole with various aldehydes and dialkyl phosphites in the presence of Caffeine hydrogen sulfate (CHS) as eco-friendly and reusable catalyst under microwave irradiation and solvent-free conditions. The title compounds were characterised by IR, {sup 1}H, {sup 13}C, {sup 31}P NMR and mass spectral data. All the synthesised (4a–j) compounds were screened for their insilico and in vitro studies. The results revealed that, out of all the titled compounds 4a, 4e, 4h and 4i have exhibited significant activity in terms of antioxidant and anti-inflammatory activity. In addition, molecular docking studies were also carried out against Cox-2 with celocoxib as the standard. .

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Antiaging activity, molecular docking, and prediction of percutaneous absorption parameters of quinoline–hydrazone hybrids

The application of antiaging agents can contribute to the prevention and control of skin photoaging. In the current research, nine quinoline–hydrazone hybrids were synthesized to obtain biologically active compounds as possible antiaging agents. The compounds were tested through a comprehensive in vitro evaluation of antielastase, anticollagenase, and antihyaluronidase activities along with the determination of their potential to quench reactive oxygen species (ROS) by the ORAC method. The selected hybrids were subsequently tested on human dermal fibroblasts (HDF) to reveal possible UVB photoprotective activity. The most potent antiaging protection of all the prepared compounds was shown by the trihydroxylated quinoline–hydrazones 5 and 9, which showed the best collagenase inhibition (IC{sub 50} = 39.4 and 45.6 µM, respectively). Compound 5 also showed activity against elastase and hyaluronidase (IC{sub 50} = 164.2 and 318.8 µM, respectively). The molecular docking results suggest that the difference of inhibition between 5 and 9 is principally attributed to the hydrogen bonds interactions in the residues His218 and His228, and Zn atom in collagenase, Val216 in elastase and Tyr75 in hyaluronidase. In addition, compounds 5 and 9 were able to significantly protect human skin cells from UVB radiation in vitro. These compounds significantly decreased UVB-induced MMP-1 and ROS production and inhibited the suppression of type I procollagen synthesis in cultured HDF. The in silico dermatopharmacokinetic parameters showed promising results. Therefore, our study presented promising results for antiaging drug discovery, focusing on quinoline–hydrazone hybrids as dual inhibitors of skin aging-related enzymes, antioxidants, and inhibitors of the biological effects of UVB irradiation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Discovery of the Biginelli hybrids as novel caspase-9 activators in apoptotic machines: Lipophilicity, molecular docking study, influence on angiogenesis gene and miR-21 expression levels

In order to investigate potential therapeutically agents, novel products of Biginelli reaction (4a-l) were synthesized and exposed to cytotoxic and caspase activities, angiogenesis, cell cycle distribution, gene and microRNA expression levels, lipophilicity assessment and docking study. Among the twelve novel compounds (4a-l) evaluated for the cytotoxic activity, five of them (4c, 4d, 4f, 4k and 4l) that showed excellent activity on the tested cell lines (HeLa, LS174 and A549) were selected for further evaluation. Interestingly, compound 4f has up to three times higher selectivity index (SI) towards cancer cells than cisplatin (on HeLa, LS174 and A549 SI = 18.2, 13.5 and 11.2, respectively). The obtained results from cell cycle distribution and caspase activity indicate that tested compounds (4c, 4d, 4f, 4k and 4l) promoted caspase-9 activation, implicated in the intrinsic pathway of apoptosis. Lipophilicity of 4a-l was determinate by using reversed-phase high-performance liquid chromatography. © 2019 Elsevier Inc.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Synthesis, characterization, anticancer evaluation and mechanisms of cytotoxic activity of novel 3-hydroxy-3-pyrrolin-2-ones bearing thenoyl fragment: DNA, BSA interactions and molecular docking study

In order to make a progress in discovering a new agents for chemotherapy with improved properties and bearing in mind the fact that substituted 3-hydroxy-3-pyrrolin-2-ones belong to a class of biologically active compounds, series of novel 1,5-diaryl-4-(2-thienylcarbonyl)-3-hydroxy-3-pyrrolin-2-ones were synthesized and characterized by spectral (UV–Vis, IR, NMR, ESI-MS), X-ray and elemental analysis. All compounds were examined for their cytotoxic effect on human cancer cell lines HeLa and MDA-MB 231 and normal fibroblasts (MRC-5). Four compounds, 3-hydroxy-1-(p-tolyl)-4-(2-thienylcarbonyl)-5-(4-chlorophenyl)-2,5-dihydro-1H-pyrrol-2-one (D10), 3-hydroxy-1-(3-nitrophenyl)-4-(2-thienylcarbonyl)-5-(4-(benzyloxy)phenyl)-2,5-dihydro-1H-pyrrol-2-one (D13), 3-hydroxy-1-(4-nitrophenyl)-4-(2-thienylcarbonyl)-5-(4-(benzyloxy)phenyl)-2,5-dihydro-1H-pyrrol-2-one (D14), and 3-hydroxy-1-(4-chlorophenyl)-4-(2-thienylcarbonyl)-5-(4-(benzyloxy)phenyl)-2,5-dihydro-1H-pyrrol-2-one (D15), that showed the highest cytotoxicity against malignant cells and the best selectivity towards normal cells were selected for further experiments. Results obtained by investigating mechanisms of cytotoxic activity suggest that selected 3-hydroxy-3-pyrrolin-2-one derivatives in HeLa cells induce apoptosis that is associated with S phase arrest (D13, D15, and D10) or unrelated to cell cycle distribution (D14). Additionally, to better understand their suitability for potential use as anticancer medicaments we studied the interactions between biomacromolecules (DNA or BSA) and D13 and D15. The results indicated that D13 and D15 have great affinity to displace EB from the EB-DNA complex through intercalation [K sv = (3.7 ± 0.1) and (3.4 ± 0.1) × 10 3 M -1 , respectively], an intercalative mode also confirmed through viscosity measurements. K a values, obtained as result of fluorescence titration of BSA with D13 and D15 [K a = (4.2 ± 0.2) and (2.6 ± 0.2) × 10 5 M, respectively], support the fact that a significant amount of the tested compounds could be transported and distributed through the cells. In addition, by DNA and BSA molecular docking study for D13, D14 and D15 is determined and predicted the binding mode and the interaction region. © 2019 Elsevier Inc.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

tinyIFD: A High-Throughput Binding Pose Refinement Workflow Through Induced-Fit Ligand Docking

A critical step in structure-based drug discovery is predicting whether and how a candidate molecule binds to a model of a therapeutic target. However, substantial protein side chain movements prevent current screening methods, such as docking, from accurately predicting the ligand conformations and require expensive refinements to produce viable candidates. Here, we present the development of a high-throughput and flexible ligand pose refinement workflow, called “tinyIFD”. The main features of the workflow include the use of specialized high-throughput, small-system MD simulation code mdgx.cuda and an actively learning model zoo approach. We show the application of this workflow on a large test set of diverse protein targets, achieving 66% and 76% success rates for finding a crystal-like pose within the top-2 and top-5 poses, respectively. We also applied this workflow to the SARS-CoV-2 main protease (M pro ) inhibitors, where we demonstrate the benefit of the active learning aspect in this workflow.

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

Formation of Linear Plasmonic Heterotrimers Using Nanoparticle Docking to DNA Origami Cages

The fabrication of complex assemblies with interesting collective properties from plasmonic nanoparticles (NPs) is often challenging. While DNA-directed self-assembly has emerged as one of the most promising approaches to forming such complex assemblies, the resulting structures tend to have large variability in gap sizes and shapes, as the DNA strands used to organize these particles are flexible, and the polydispersity of the NPs leads to variability in these critical structural features. Here, we use a new strategy termed docking to DNA origami cages (D-DOC) to organize spherical NPs into a linear heterotrimer with a precisely defined geometrical arrangement. Instead of binding NPs to the exterior of the DNA templates, D-DOC binds the NPs to either the interior or the opening of a 3D cage, which significantly reduces the variability of critical structural features by incorporating multiple diametrically arranged capture strands to tether NPs. Additionally, such a spatial arrangement of the capture strand can work synergistically with shape complementarity to achieve tighter confinement. To assemble NPs via D-DOC, we developed a multistep assembly process that first encapsulates an NP inside a cage and then binds two other NPs to the openings. Microscopic characterization shows low variability in the bond angles and gap sizes. Both UV–vis absorption and surface-enhanced Raman scattering (SERS) measurements showed strong plasmonic coupling that aligned with predictions by electrodynamic simulations, further confirming the precision of the assembly. These results suggest D-DOC could open new opportunities in biomolecular sensing, SERS and fluorescence spectroscopies, and energy harvesting through the self-assembly of NPs into more complex 3D assemblies.

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

Fe protein docking transduces conformational changes to MoFe nitrogenase active site in a nucleotide-dependent manner

The reduction of dinitrogen to ammonia catalyzed by nitrogenase involves a complex series of events, including ATP hydrolysis, electron transfer, and activation of metal clusters for N 2 reduction. Early evidence shows that an essential part of the mechanism involves transducing information between the nitrogenase component proteins through conformational dynamics. Here, millisecond time-resolved hydrogen-deuterium exchange mass spectrometry was used to unravel peptide-level protein motion on the time scale of catalysis of Mo-dependent nitrogenase from Azotobacter vinelandii. Normal mode analysis calculations complemented this data, providing insights into the specific signal transduction pathways that relay information across protein interfaces at distances spanning 100 Å. Together, these results show that conformational changes induced by protein docking are rapidly transduced to the active site, suggesting a specific mechanism for activating the metal cofactor in the enzyme active site.

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

Performance Portability of Molecular Docking Miniapp On Leadership Computing Platforms

Rapidly changing computer architectures, such as those found at high-performance computing (HPC) facilities, present the need for mini-applications (miniapps) that capture essential algorithms used in large applications to test program performance and portability, aiding transitions to new systems. The COVID-19 pandemic has fueled a flurry of activity in computational drug discovery, including the use of supercomputers and GPU acceleration for massive virtual screens for therapeutics. Recent work targeting COVID-19 at the Oak Ridge Leadership Computing Facility (OLCF) used the GPU-accelerated program AutoDock-GPU to screen billions of compounds on the Summit supercomputer. In this paper we present the development of a new miniapp, miniAutoDock-GPU, that can be used to evaluate the performance and portability of GPU-accelerated protein-ligand docking programs on different computer architectures. These tests are especially relevant as facilities transition from petascale systems and prepare for upcoming exascale systems that will use a variety of GPU vendors. The key calculations, namely, the Lamarckian genetic algorithm combined with a local search using a Solis-Wets based random optimization algorithm, are implemented. We developed versions of the miniapp using several different programming models for GPU acceleration, including a version using the CUDA runtime API for NVIDIA GPUs, and the Kokkos middle-ware API which is facilitated by C++ template libraries. A third version, currently in progress, uses the HIP programming model. These efforts will help facilitate the transition to exascale systems for this important emerging HPC application, as well as its use on a wide range of heterogeneous platforms.

Thavappiragasam, Mathialakan↗
DOE OSTI2022

Resveratrol Ameliorates Lipopolysaccharide-Induced Sudden Sensorineural Hearing Loss in In Vitro Model through Multitarget Antiapoptotic Mechanism Based on Network Pharmacology and Molecular Docking

Objective. To explore the effects of resveratrol (RSV) on hair cell apoptosis caused by sudden sensorineural hearing loss (SSNHL) and its effect on lipopolysaccharide-induced apoptosis of HEI-OC1 cells. Methods. We used the network pharmacology method to screen molecules related to RSV for the treatment of SSNHL and analyzed these molecules and their enriched biological processes and signaling pathways through Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analysis. We selected hub genes related to apoptosis using protein-protein interaction (PPI) analysis for in vitro and molecular docking verification. Results. Eighty overlapping genes were identified as potential targets for RSV treatment of SSNHL. Further GO analysis showed that the biological processes were mainly related to toxicity, cell proliferation, and lipopolysaccharide reactions. KEGG analysis showed that the AGE-RAGE signaling pathway in diabetic complications, Kaposi’s sarcoma-associated herpesvirus infection, FoxO signaling pathway, PI3K-Akt signaling pathway, and other inflammatory signaling pathways were concentrated. AKT1, STAT3, JUN, TNF, TP53, MAPK3, CASP3, and VEGFA were screened as HUB genes using PPI analysis. The apoptosis-related proteins TNF, CASP3, AKT1, and TP53 were selected for in vitro experiments, which showed that mRNA was significantly different before and after RSV intervention, confirming that the corresponding protein receptors could bind well with RSV. Conclusion. RSV mainly affects the prognosis of SSNHL through anti-inflammatory effects and may improve hair cell apoptosis caused by inflammatory factors through multitargeted interventions involving TNF, CASP3, AKT1, and TP53.

Ye, Shiming↗
DOE OSTI2018

Transmittal of Draft Consultation Letter to the New Mexico State Historic Preservation Officer Regarding the Proposed Loading Dock to Conference Room Conversion Building 303 at Technical Area 16

The U.S. Department of Energy (DOE), National Nuclear Security Administration (NNSA), Los Alamos Field Office (NA-LA) proposes to enclose the existing loading dock to create a conference room at building 303, located within Technical Area (TA) 16, Los Alamos National Laboratory (LANL). TA-16-303 has been determined eligible for listing in the National Register of Historic Places in correspondence with the New Mexico State Historic Preservation Division dated June 22, 2003. Eligibility status is based on its historical significance during the Cold War at Los Alamos and its representative architectural style, which is associated with high explosives research and development in support of the nation’s nuclear weapons program. As shown in the enclosed photograph, key architectural elements include a flat roof with overhangs, unpainted reinforced-concrete construction, green painted doors and trim.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2019

Improved Modeling of Peptide-Protein Binding Through Global Docking and Accelerated Molecular Dynamics Simulations

We find that peptides mediate up to 40% of known protein-protein interactions in higher eukaryotes and play a key role in cellular signaling, protein trafficking, immunology, and oncology. However, it is challenging to predict peptide-protein binding with conventional computational modeling approaches, due to slow dynamics and high peptide flexibility. Here, we present a prototype of the approach which combines global peptide docking using ClusPro PeptiDock and all-atom enhanced simulations using Gaussian accelerated molecular dynamics (GaMD). For three distinct model peptides, the lowest backbone root-mean-square deviations (RMSDs) of their bound conformations relative to X-ray structures obtained from PeptiDock were 3.3–4.8 Å, being medium quality predictions according to the Critical Assessment of PRediction of Interactions (CAPRI) criteria. GaMD simulations refined the peptide-protein complex structures with significantly reduced peptide backbone RMSDs of 0.6–2.7 Å, yielding two high quality (sub-angstrom) and one medium quality models. Furthermore, the GaMD simulations identified important low-energy conformational states and revealed the mechanism of peptide binding to the target proteins. Therefore, PeptiDock+GaMD is a promising approach for exploring peptide-protein interactions.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1963

RENDEZVOUS AND DOCKING TECHNIQUES

Various guidance phases are considered in spacecraft rendezvous and docking techniques, using specific earth orbital mission profile as an example

RENDEZVOUS GUIDANCE SYSTEM↗