Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “compound screening”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Pharmacological Profiling of a Brugia malayi Muscarinic Acetylcholine Receptor as a Putative Antiparasitic Target

The diversification of anthelmintic targets and mechanisms of action will help ensure the sustainable control of nematode infections in response to the growing threat of drug resistance. G protein-coupled receptors (GPCRs) are established drug targets in human medicine but remain unexploited as anthelmintic substrates despite their important roles in nematode neuromuscular and physiological processes. Bottlenecks in exploring the druggability of parasitic nematode GPCRs include a limited helminth genetic toolkit and difficulties establishing functional heterologous expression. In an effort to address some of these challenges, we profile the function and pharmacology of muscarinic acetylcholine receptors in the human parasite Brugia malayi, an etiological agent of human lymphatic filariasis. While acetylcholine-gated ion channels are intensely studied as targets of existing anthelmintics, comparatively little is known about metabotropic receptor contributions to parasite cholinergic signaling. Using multivariate phenotypic assays in microfilariae and adults, we show that nicotinic and muscarinic compounds disparately affect parasite fitness traits. We identify a putative G protein-linked acetylcholine receptor of B. malayi (Bma-GAR-3) that is highly expressed across intramammalian life stages and adapt spatial RNA in situ hybridization to map receptor transcripts to critical parasite tissues. Tissue-specific expression of Bma-gar-3 in Caenorhabditis elegans (body wall muscle, sensory neurons, and pharynx) enabled receptor deorphanization and pharmacological profiling in a nematode physiological context. Finally, we developed an image-based feeding assay as a reporter of pharyngeal activity to facilitate GPCR screening in parasitized strains. We expect that these receptor characterization approaches and improved knowledge of GARs as putative drug targets will further advance the study of GPCR biology across medically important nematodes.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Robust highly durable solid oxide fuel cell cathodes – Improved materials compatibility & self-regulating surface chemistry

Solid oxide fuel cells (SOFCs) are electrochemical conversion devices that directly transform hydrogen or hydrocarbon fuels to electricity, with energy efficiencies as high as 90%, coupled with reduced emissions. Several factors, however, remain to be addressed when considering scale-up of SOFC technology, including the need to overcome decreased performance due to sluggish rates of the oxygen reduction reaction (ORR) at the cathode under reduced temperatures and susceptibility to degradation in performance from surface poisoning e.g. from chromia, while limiting the use of critical raw materials (lanthanides and transition metals) present in high performing mixed ionic electronic conducting electrodes like (La,Sr)CoO 3 (LSC). In this project we explored the key descriptors for determining ORR activity in SOFC electrodes and tried to recover performance degradation by applying them to SOFC electrodes. In order to do this, we first selected a model mixed ionic electronic conducting (MIEC) oxide, Pr-doped CeO 2 (Pr 0.1 Ce 0.9 O 2-δ , PCO), which is a chemically stable fluorite and free of inherent poison sources (e.g. Sr segregation in LSC) that potentially react with external impurities such as Cr-species vaporized from the interconnect. The three approaches originally planned in this project are as follows: 1) evaluation of scavenger exsolution characteristics, 2) study of scavengers gettering efficacy following Cr and Si poisoning and 3) integration of new compositions into porous electrodes. Among them, exceptional progress has been made in 2) and 3), especially understanding the role of surface infiltrants in impacting electrode performance and degradation of PCO materials. We found that the Smith acidity scale for binary oxides serves as a powerful descriptor for tuning and predicting the oxygen exchange kinetics on MIEC PCO surfaces. As a result, with infiltration with binary oxides, ranging from strongly basic (Li 2 O) to strongly acidic (SiO 2 ) onto the surface of porous PCO, it was possible to systematically vary the chemical surface exchange coefficient (k chem ) by 6 orders of magnitude! L i2 O increased k chem by nearly 1,000 times over that of pristine PCO, while SiO 2 decreased k chem by nearly the same factor. Strikingly, although the pre-exponential of k chem scales linearly with the acidity of the infiltrated binary oxide, there is nearly no change in the activation energy. With this insight, we attributed the origin of these dramatic changes in k chem values to the systematic increase and decrease in the surface electron density induced by infiltrated binary oxides. More interestingly, although both Cr 2 O 3 and SiO 2 were determined to be acidic by Smith, suggesting that this feature could likely be the primary reason that these compounds serve to poison the ORR on SOFC cathodes, the effect of poisoning could be subsequently tuned by adding multiple infiltrants and controlling their relative surface acidities. We also systematically examined the effect of serial infiltration of basic and acidic oxides. It turned out that serial infiltration of Li not only recovers approximately 20-fold degraded k chem of PCO by acidic Cr 2 O 3 but its k chem is enhanced even beyond that of the non-infiltrated PCO by more than three orders of magnitude. This was further verified with a screen-printing PCO symmetric cell in terms of the electrode performance (area-specific resistance, ASR) related to approach 3). These observations point to acidity as a key descriptor not only in tuning and predicting the ORR activity of SOFC cathodes that largely determines the overall performance of SOFC, but in mitigating and reactivating poisoned electrode performance. This work provides novel guidelines for making the electrode performance much more active and robust in SOFCs, which can further be applied to all applications requiring oxygen exchange reaction, such as electrolyzers, permeation membranes and gas sensors.

30 DIRECT ENERGY CONVERSION↗
DOE OSTI2024

Accelerating the Discovery of New, Single Phase High Entropy Ceramics via Active Learning

High-entropy ceramics have garnered interest due to their remarkable hardness, compressive strength, thermal stability, and fracture toughness; yet the discovery of new high-entropy ceramics (out of a tremendous number of possible elemental permutations) still largely requires costly, inefficient, trial-and-error experimental and computational approaches. The entropy forming ability (EFA) factor was recently proposed as a computational descriptor that positively correlates with the likelihood that a 5-metal high-entropy carbide (HECs) will form the desired single phase, homogeneous solid solution; however, discovery of new compositions is computationally expensive. If you consider 8 candidate metals, the HEC EFA approach uses 49 optimizations for each of the 56 unique 5-metal carbides, requiring a total of 2744 costly density functional theory calculations. Here, we describe an orders-of-magnitude more efficient active learning (AL) approach for identifying novel HECs. To begin, we compared numerous methods for generating composition-based feature vectors (e.g., magpie and mat2vec), deployed an ensemble of machine learning (ML) models to generate an average and distribution of predictions, and then utilized the distribution as an uncertainty. Here we then deployed an AL approach to extract new training data points where the ensemble of ML models predicted a high EFA value or was uncertain of the prediction. Our approach has the combined benefit of decreasing the amount of training data required to reach acceptable prediction qualities and biases the predictions toward identifying HECs with the desired high EFA values, which are tentatively correlated with the formation of single phase HECs. Using this approach, we increased the number of 5-metal carbides screened from 56 to 15,504, revealing 4 compositions with record-high EFA values that were previously unreported in the literature. Our AL framework is also generalizable and could be modified to rationally predict optimized candidate materials/combinations with a wide range of desired properties (e.g., mechanical stability, thermal conductivity).

36 MATERIALS SCIENCE↗
DOE OSTI2021

Computationally Accelerated Discovery and Experimental Demonstration of Gd0.5La0.5Co0.5Fe0.5O3 for Solar Thermochemical Hydrogen Production

Solar thermochemical hydrogen (STCH) production is a promising method to generate carbon neutral fuels by splitting water utilizing metal oxide materials and concentrated solar energy. The discovery of materials with enhanced water-splitting performance is critical for STCH to play a major role in the emerging renewable energy portfolio. While perovskite materials have been the focus of many recent efforts, materials screening can be time consuming due to the myriad chemical compositions possible. This can be greatly accelerated through computationally screening materials parameters including oxygen vacancy formation energy, phase stability, and electron effective mass. In this work, the perovskite Gd 0.5 La 0.5 Co 0.5 Fe 0.5 O 3 (GLCF), was computationally determined to be a potential water splitter, and its activity was experimentally demonstrated. During water splitting tests with a thermal reduction temperature of 1,350°C, hydrogen yields of 101 μmol/g and 141 μmol/g were obtained at re-oxidation temperatures of 850 and 1,000°C, respectively, with increasing production observed during subsequent cycles. This is a significant improvement from similar compounds studied before (La 0.6 Sr 0.4 Co 0.2 Fe 0.8 O 3 and LaFe 0.75 Co 0.25 O 3 ) that suffer from performance degradation with subsequent cycles. Confirmed with high temperature x-ray diffraction (HT-XRD) patterns under inert and oxidizing atmosphere, the GLCF mainly maintained its phase while some decomposition to Gd 2-x La x O 3 was observed.

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

Tnseq to identify catabolism of b-5 linked aromatics by Novosphingobium aromaticivorans

This study investigates the catabolism of the b-5 linked aromatic dimer dehydrodiconiferyl alcohol (DC-A) by the bacterium Novosphingobium aromaticivorans. We used genome wide screens to identify candidate genes involved in DC-A catabolism. Subsequent in vivo and in vitro analyses of these candidates elucidated a catabolic pathway composed of four required gene products and several partially redundant dehydrogenases that convert DC-A to aromatic monomers that can be funneled into the central aromatic metabolic pathway of N. aromaticivorans.

aromatic compounds↗
DOE OSTI2023

Real-space Green's function approach for intrinsic losses in x-ray spectra

Intrinsic inelastic losses in x-ray spectra originate from excitations in an interacting electron system due to a suddenly created core-hole. These losses characterize the features observed in x-ray photoemission spectra (XPS), as well as many-body effects such as satellites and edge-singularities in x-ray absorption spectra (XAS). However, they are usually neglected in practical calculations. As shown by Langreth these losses can be treated within linear response in terms of a cumulant Green's function in momentum space. Here we present a complementary ab initio real-space Green's function generalization of the Langreth cumulant in terms of the dynamically screened core-hole interaction W c (ω) and the independent particle response function. Here we find that the cumulant kernel β⁡(ω) is analogous to XAS, but with the transition operator replaced by the core-hole potential with monopole selection rules. The behavior reflects the analytic structure of the loss function, with peaks near the zeros of the dielectric function, consistent with delocalized quasiboson excitations. The approach simplifies when W c (ω) is localized and spherically symmetric. In conclusion, illustrative results and comparisons are presented for the electron gas, sodium, and some early transition metal compounds.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Establishing a versatile toolkit of flux enhanced strains and cell extracts for pathway prototyping

Building and optimizing biosynthetic pathways in engineered cells holds promise to address societal needs in energy, materials, and medicine, but it is often time-consuming. Cell-free synthetic biology has emerged as a powerful tool to accelerate design-build-test-learn cycles for pathway engineering with increased tolerance to toxic compounds. However, most cell-free pathway prototyping to date has been performed in extracts from wildtype cells which often do not have sufficient flux towards the pathways of interest, which can be enhanced by engineering. Here, in this study, to address this gap, we create a set of engineered Escherichia coli and Saccharomyces cerevisiae strains rewired via CRISPR-dCas9 to achieve high-flux toward key metabolic precursors; namely, acetyl-CoA, shikimate, triose-phosphate, oxaloacetate, α-ketoglutarate, and glucose-6-phosphate. Cell-free extracts generated from these strains are used for targeted enzyme screening in vitro. As model systems, we assess in vivo and in vitro production of triacetic acid lactone from acetyl-CoA and muconic acid from the shikimate pathway. The need for these platforms is exemplified by the fact that muconic acid cannot be detected in wildtype extracts provided with the same biosynthetic enzymes. We also perform metabolomic comparison to understand biochemical differences between the cellular and cell-free muconic acid synthesis systems (E. coli and S. cerevisiae cells and cell extracts with and without metabolic rewiring). While any given pathway has different interfaces with metabolism, we anticipate that this set of pre-optimized, flux enhanced cell extracts will enable prototyping efforts for new biosynthetic pathways and the discovery of biochemical functions of enzymes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Coping with Starvation: Contrasting Lipidomic Dynamics in the Cells of Two Sacoglossan Sea Slugs Incorporating Stolen Plastids from the Same Macroalga

Abstract Several species of sacoglossan sea slugs are able to sequester chloroplasts from algae and incorporate them into their cells. However, the ability to maintain functional “stolen” plastids (kleptoplasts) can vary significantly within the Sacoglossa, giving species different capacities to withstand periods of food shortage. The present study provides an insight on the comparative shifts experienced by the lipidome of two sacoglossan sea slug species, Elysia viridis (long-term retention of functional chloroplasts) and Placida dendritica (retention of non-functional chloroplasts). A hydrophilic interaction liquid chromatography–mass spectrometry approach was employed to screen the lipidome of specimens from both species feeding on the macroalga Codium tomentosum and after 1-week of starvation. The lipidome of E. viridis was generally unaffected by the absence of food, while that of P. dendritica varied significantly. The retention of functional chloroplasts by E. viridis cells allows this species to endure periods of food shortage, while in P. dendritica a significant reduction in the amount of main lipids was the consequence of the consumption of its own mass to endure starvation. The large proportion of ether phospholipids (plasmalogens) in both sea slug species suggests that these compounds may play a key role in chloroplast incorporation in sea slug cells and/or be involved in the reduction of the oxidative stress resulting from the presence of kleptoplasts.

Rey, Felisa↗
DOE OSTI2024

Novel Microbial Routes to Synthesize Industrially Significant Precursor Compounds

Ethylene is the most widely employed organic precursor compound in industry. The potential to impact ethylene formation via recently discovered microbial processes is tenable using plentiful CO2 feedstocks. The overall long-term objective of this project was to develop an industrially compatible microbial process to synthesize ethylene in high yields. The key objective of this project was to fully define and initially characterized a recently discovered and genetically regulated anaerobic pathway to produce high levels of ethylene called the Dihydroxyacetone Phosphate - Ethylene Pathway in phototrophic bacteria. This was addressed through the following specific aims: 1. Fully probe the catalytic potential of all enzymes of the DHAP ethylene pathway and determine the regulatory mechanism of DHAP-ethylene pathway gene expression. 2. Discover effective and active ethylene enzymes encoded in cultured and uncultured organisms from anoxic environments. 3.Model the thermodynamics and kinetics of ethylene synthetic pathways to guide engineering efforts in integrating best performing DHAP-ethylene pathway enzymes into model bacteria chassis for enhance ethylene yields. Through this project we discovered the initially missing genetic and enzyme component of the DHAP-ethylene pathway that directly synthesized ethylene and other important industrial compounds like methane and ethane from specific substrates. We uncovered and partially characterized a nitrogenase-like reductase that functions in DHAP-ethylene pathway specifically and in methionine synthesis in general. This nitrogenase-like system is called the Methylthio-Alkane Reductase (MAR) for its ability to cleave volatile organic sulfur compounds into methanethiol (CH3-SH) for methionine synthesis and a hydrocarbon byproduct. Key to the DHAP-ethylene pathway, MAR is the essential enzyme that cleaves 2-methylthioethanol (CH3-S-CH2-CH2-OH) into ethylene. Coordinately, we uncovered that the MAR genes and genes associated with conversion of methanethiol (CH3-SH) to methionine are under genetic control of a LysR Type Transcriptional Regulator called SalR, whose activity is dependent upon the amount of sulfate available to the cell. When sulfate as the preferred sulfur source for cell growth drops below 200 micromolar, SalR become active for expressing the MAR and methionine biosynthesis genes to enable the cell to grow from volatile organic sulfur compounds and make ethylene. Metabolic thermos-kinetic modeling revealed that these MAR reactions for ethylene and other hydrocarbon production are highly thermodynamically favorable and are one of the largest driving forces for ethylene production by the DHAP-ethylene pathway for high ethylene yields. Modeling also indicated that a key aldolase and to a lesser extent an isomerase of the DHAP-ethylene pathway for production of the ethylene precursor, 2-methylthioethanol, also would increase ethylene yields. Through metagenomic mining and gene synthesis by the JGI DNA synthesis program, over 500 aldolase and isomerase homologs were synthesized and screened. From this, variants were uncovered with substantially higher activity that increased ethylene yields 5-fold via the aldolase reaction and 1.5-fold via the isomerase reaction. Each of these elements that increase ethylene production were integrated together via plasmid under appropriate gene promoter elements in the phototrophic bacterium, Rhodospirillum rubrum, resulting in at least 3 orders of magnitude increase in ethylene yield from carbon dioxide feedstock.

10 SYNTHETIC FUELS↗
DOE OSTI2022

High-throughput screening of tribological properties of monolayer films using molecular dynamics and machine learning

Monolayer films have shown promise as a lubricating layer to reduce friction and wear of mechanical devices with separations on the nanoscale. These films have a vast design space with many tunable properties that can affect their tribological effectiveness. For example, terminal group chemistry, film composition, and backbone chemistry can all lead to films with significantly different tribological properties. This design space, however, is very difficult to explore without a combinatorial approach and an automatable, reproducible, and extensible workflow to screen for promising candidate films. Here, using the Molecular Simulation Design Framework (MoSDeF), a combinatorial screening study was performed to explore 9747 unique monolayer films (116 964 total simulations) and a machine learning (ML) model using a random forest regressor, an ensemble learning technique, to explore the role of terminal group chemistry and its effect on tribological effectiveness. The most promising films were found to contain small terminal groups such as cyano and ethylene. The ML model was subsequently applied to screen terminal group candidates identified from the ChEMBL small molecule library. Approximately 193 131 unique film candidates were screened with approximately a five order of magnitude speed-up in analysis compared to simulation alone. The ML model was thus able to be used as a predictive tool to greatly speed up the initial screening of promising candidate films for future simulation studies, suggesting that computational screening in combination with ML can greatly increase the throughput in combinatorial approaches to generate in silico data and then train ML models in a controlled, self-consistent fashion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Origin of replication discovery for environmentally isolated Pantoea strain enables expression of heterologous proteins, pathways and products

Leveraging predicted origin sequences from a previously characterized groundwater plasmidome, we constructed a barcoded plasmid library to screen for previously unknown origins. Testing this library against a panel of representative bacterial strains led to the identification of 3 previously unknown origins that replicate in gram-negative bacteria not previously associated with these origin sequences. Experimental validation confirmed that a plasmid bearing origin 6911 as the sole origin could replicate with a copy number of 9 (±2) in Pantoea sp. MT58, a fast growing and metal tolerant, environmentally important bacterium. Plasmids based on this new origin were used to express the reporter protein GFP, and non-native metabolite pathways for the natural product indigoidine and the terpenoid compound isoprenol. Functional previously unknown origins of replication in such non-model organisms can expand the toolkit for genetic manipulations of both model and less-studied bacteria.

molecular biology↗
DOE OSTI2020

Programmable Synthesis of Multimetallic Phosphide Nanorods Mediated by Core/Shell Structure Formation and Conversion

Generalized synthetic strategies for nanostructures with well-defined physical dimensions and broad-range chemical compositions are at the frontier of advanced nanomaterials design, functionalization, and application. In this paper, we report a composition-programmable synthesis of multimetallic phosphide CoMP x nanorods (NRs) wherein M can be controlled to be Fe, Ni, Mn, Cu, and their binary combinations. Forming Co 2 P/MP x core/shell NRs and subsequently converting them into CoMP x solid-solution NRs through thermal post-treatment are essential to overcome the obstacle of morphology/structure inconsistency faced in conventional synthesis of CoMP x with the different M compositions. The resultant CoMP x with uniform one-dimensional (1-D) structure provides us a platform to unambiguously screen the M synergistic effects in improving the electrocatalytic activity, as exemplified by the oxygen evolution reaction. This new approach mediated by core/shell nanostructure formation and conversion can be extended to other multicomponent nanocrystal systems (metal alloy, mixed oxide, and chalcogenide, etc.) for diverse applications.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Global compilation of soil methane uptake measurements from 1984 to 2018

This data package contains a global compilation of soil methane uptake measurements collected from published field studies between 1989 and 2022. The dataset was developed to support machine learning (ML) estimation of the global terrestrial methane soil sink and includes monthly methane uptake rates, measurement dates, site coordinates, and associated ecosystem information from different ecosystems. Data were compiled from 164 peer-reviewed publications across approximately 260 study sites, resulting in ~12,000 monthly observations after quality control screening and removal of manipulated experimental treatments. The database was further processed to generate site-averaged methane uptake estimates for comparison between process-based (PB) and ML models.

earth science↗
DOE OSTI2021

Prediction of solubility parameters of lignin and ionic liquids using multi-resolution simulation approaches

The solubility parameter (SP) of a molecular species is a vital feature that indicates polarity and quantifies the ‘like-seeks-like’ principle, which is used in chemistry to screen solvents for dissolution. Recent studies have demonstrated that ionic liquids (ILs) and deep eutectic solvents (DESs) efficiently solubilize lignocellulosic biomass and promote enzymatic saccharification into sugars used for the production of biofuels and value-added chemicals. Understanding the solubility of plant biopolymers, particularly lignin, in ILs and DESs is critical for selecting candidate ILs and DESs for biomass pretreatment; however, experimentally measuring SPs is challenging. Thus, the present study investigates lignin dissolution mechanisms in IL/DES and prediction of the solubility parameters (Hildebrand and Hansen) of lignin, ILs, and DESs using multi-resolution simulation approaches. Here, solubility parameters of the studied compounds were predicted using molecular dynamics (MD) simulations, and the SP of lignin was determined to be 23–27 MPa 1/2 , which was close to the polymeric lignin solubility parameter (24.3–25.5 MPa 1/2 ). The SPs of ILs namely [Ch][Lys], [Ch][Oct], and [Emim][Lys] were predicted to be ~26 MPa 1/2 , which is close to lignin's SPs and resulted in increased biomass delignification. The MD simulated SPs were validated by both the COSMO-RS model and experimental investigations, with the results showing a close agreement between the predicted and experimentally obtained SPs. In addition, the enthalpy of vaporization (ΔH vap ) of ILs/DESs was predicted based on the potential energy of the system, and the ΔH vap of ILs/DESs was around 40–65 kcal mol –1 , which is 5–8 times higher than that of traditional organic solvents.

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

Screening two-dimensional materials with topological flat bands

The topological flat band (TFB) has been proposed theoretically in various lattice models, to exhibit a rich spectrum of intriguing physical behaviors. However, the experimental demonstration of flat band (FB) properties has been severely hindered by the lack of materials realization. In this study, by screening materials from a first-principles materials database, we identify a group of two-dimensional materials with TFBs near the Fermi level, covering some simple line-graph and generalized line-graph FB lattice models. These include the kagome sublattice of O in Ti O 2 yielding a spin-unpolarized TFB, and that of V in ferromagnetic V 3 F 8 yielding a spin-polarized TFB. The monolayer Nb 3 Te Cl 7 and its counterparts from element substitution are found to be breathing-kagome-lattice crystals. The family of monolayer II I 2 V I 3 compounds exhibit a TFB representing the coloring-triangle lattice model. Re F 3 , Mn F 3 , and Mn Br 3 are all predicted to be diatomic-kagome-lattice crystals, with TFB transitions induced by atomic substitution. Finally, Hg F 2 , Cd F 2 , and Zn F 2 are discovered to host dual TFBs in the diamond-octagon lattice. Our findings pave the way to further experimental exploration of eluding FB materials and properties.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Chronic Cardiotoxicity Assays Using Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes (hiPSC-CMs)

Cardiomyocytes (CMs) differentiated from human induced pluripotent stem cells (hiPSCs) are increasingly used in cardiac safety assessment, disease modeling and regenerative medicine. A vast majority of cardiotoxicity studies in the past have tested acute effects of compounds and drugs; however, these studies lack information on the morphological or physiological responses that may occur after prolonged exposure to a cardiotoxic compound. In this review, we focus on recent advances in chronic cardiotoxicity assays using hiPSC-CMs. We summarize recently published literature on hiPSC-CMs assays applied to chronic cardiotoxicity induced by anticancer agents, as well as non-cancer classes of drugs, including antibiotics, anti-hepatitis C virus (HCV) and antidiabetic drugs. We then review publications on the implementation of hiPSC-CMs-based assays to investigate the effects of non-pharmaceutical cardiotoxicants, such as environmental chemicals or chronic alcohol consumption. We also highlight studies demonstrating the chronic effects of smoking and implementation of hiPSC-CMs to perform genomic screens and metabolomics-based biomarker assay development. The acceptance and wide implementation of hiPSC-CMs-based assays for chronic cardiotoxicity assessment will require multi-site standardization of assay protocols, chronic cardiac maturity marker reproducibility, time points optimization, minimal cellular variation (commercial vs. lab reprogrammed), stringent and matched controls and close clinical setting resemblance. A comprehensive investigation of long-term repeated exposure-induced effects on both the structure and function of cardiomyocytes can provide mechanistic insights and recapitulate drug and environmental cardiotoxicity.

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

Ligand-Based Compound Activity Prediction via Few-Shot Learning

Predicting the activities of new compounds against biophysical or phenotypic assays based on the known activities of one or a few existing compounds is a common goal in early stage drug discovery. This problem can be cast as a “few-shot learning” challenge, and prior studies have developed few-shot learning methods to classify compounds as active versus inactive. However, the ability to go beyond classification and rank compounds by expected affinity is more valuable. We describe Few-Shot Compound Activity Prediction (FS-CAP), a novel neural architecture trained on a large bioactivity data set to predict compound activities against an assay outside the training set, based on only the activities of a few known compounds against the same assay. Our model aggregates encodings generated from the known compounds and their activities to capture assay information and uses a separate encoder for the new compound whose activity is to be predicted. The new method provides encouraging results relative to traditional chemical-similarity-based techniques as well as other state-of-the-art few-shot learning methods in tests on a variety of ligand-based drug discovery settings and data sets.

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

Toward Machine Learning-Driven Mass Spectrometric Identification of Trichothecenes in the Absence of Standard Reference Materials

While a significant body of work exists on the detection of commonly known trichothecene toxins, biological, environmental, and other transformational processes can generate many under-characterized and unknown modified trichothecenes. Lacking both analytical reference standards and associated mass spectral databases, identification of these modified compounds reflects both a challenge and a critical gap from forensic and public health perspectives. Here we report here the application of machine learning (ML) techniques toward identification of discriminative fragment ions from mass spectrometric data that can be exploited to detect evidence of type A and B trichothecenes. The goal of this work is to establish a new method for the identification of unknown, though structurally similar trichothecenes, by leveraging objective ML techniques. Discriminative fragments derived from a series of gradient-boosted machine learners are then used to develop ML-driven precursor ion scan (PIS) methods on a triple quadrupole mass spectrometer (QQQ) for screening of “unknown unknown” trichothecenes. Specifically, we apply the PIS method to a laboratory-synthesized trichothecene, a first step in demonstrating the power of alternative, machine learning-driven mass spectrometric methods.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗