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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 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Viral Fate and Transport for COVID-19

The NVBL Viral Fate and Transport Team includes researchers from eleven DOE national laboratories and is utilizing unique experimental facilities combined with physics-based and data-driven modeling and simulation to study the transmission, transport, and fate of SARSCoV-2. The team was focused on understanding and ultimately predicting SARS-CoV-2 viability in varied environments with the goal of rapidly informing strategies that guide the nation’s resumption of normal activities. The primary goals of this project include prioritizing administrative and engineering controls that reduce the risk of SARS-CoV-2 transmission within an enclosed environment; identifying the chemical and physical properties that influence binding of SARS-CoV-2 to common surfaces; and understanding the contribution of environmental reservoirs and conditions on transmission and resurgence of SARS-CoV-2.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2006

Biomimetic/Optical Sensors for Detecting Bacterial Species

Biomimetic/optical sensors have been proposed as means of real-time detection of bacteria in liquid samples through real-time detection of compounds secreted by the bacteria. Bacterial species of interest would be identified through detection of signaling compounds unique to those species. The best-characterized examples of quorum-signaling compounds are acyl-homoserine lactones and peptides. Each compound, secreted by each bacterium of an affected species, serves as a signal to other bacteria of the same species to engage in a collective behavior when the population density of that species reaches a threshold level analogous to a quorum. A sensor according to the proposal would include a specially formulated biomimetic film, made of a molecularly imprinted polymer (MIP), that would respond optically to the signaling compound of interest. The MIP film would be integrated directly onto an opticalwaveguide- based ring resonator for optical readout. Optically, the sensor would resemble the one described in Chemical Sensors Based on Optical Ring Resonators (NPO-40601), NASA Tech Briefs, Vol. 29, No. 10 (October 2005), page 32. MIPs have been used before as molecular- recognition compounds, though not in the manner of the present proposal. Molecular imprinting is an approach to making molecularly selective cavities in a polymer matrix. These cavities function much as enzyme receptor sites: the chemical functionality and shape of a cavity in the polymer matrix cause the cavity to bind to specific molecules. An MIP matrix is made by polymerizing monomers in the presence of the compound of interest (template molecule). The polymer forms around the template. After the polymer solidifies, the template molecules are removed from the polymer matrix by decomplexing them from their binding sites and then dissolving them, leaving cavities that are matched to the template molecules in size, shape, and chemical functionality. The cavities thus become molecular-recognition sites that bind only to molecules matched to the sites; other molecules are excluded. In a sensor according to the proposal, the MIP would feature molecular recognition sites that would bind the specific signaling molecules selectively according to their size, shape, and chemical functionality (see figure). As the film took up the signaling molecules in the molecular recognition sites, the index of refraction and thickness of the film would change, causing a wavelength shift of the peak of the resonance spectrum. It has been estimated that by measuring this wavelength shift, it should be possible to detect as little as 10 picomoles of a peptide signaling compound.

Homer, Margie↗
NASA NTRS1993

Theoretical research program to study chemical reactions in AOTV bow shock tubes

The main focus was the development, implementation, and calibration of methods for performing molecular electronic structure calculations to high accuracy. These various methods were then applied to a number of chemical reactions and species of interest to NASA, notably in the area of combustion chemistry. Among the development work undertaken was a collaborative effort to develop a program to efficiently predict molecular structures and vibrational frequencies using energy derivatives. Another major development effort involved the design of new atomic basis sets for use in chemical studies: these sets were considerably more accurate than those previously in use. Much effort was also devoted to calibrating methods for computing accurate molecular wave functions, including the first reliable calibrations for realistic molecules using full CI results. A wide variety of application calculations were undertaken. One area of interest was the spectroscopy and thermochemistry of small molecules, including establishing small molecule binding energies to an accuracy rivaling, or even on occasion surpassing, the experiment. Such binding energies are essential input to modeling chemical reaction processes, such as combustion. Studies of large molecules and processes important in both hydrogen and hydrocarbon combustion chemistry were also carried out. Finally, some effort was devoted to the structure and spectroscopy of small metal clusters, with applications to materials science problems.

Taylor, Peter R.↗
DOE OSTI2021

Visualizing defects and pore connectivity within metal–organic frameworks by X-ray transmission tomography

Metal–Organic Frameworks (MOFs) have the potential to change the landscape of molecular separations in chemical processes owing to their ability of selectively binding molecules. Their molecular sorting properties generally rely on the micro- and meso-pore structure, as well as on the presence of coordinatively unsaturated sites that interact with the different chemical species present in the feed. In this work, we show a first-of-its-kind tomographic imaging of the crystal morphology of a metal– organic framework by means of transmission X-ray microscopy (TXM), including a detailed data reconstruction and processing approach. Corroboration with Focused Ion Beam-Scanning Electron Microscopy (FIB-SEM) images shows the potential of this strategy for further (non-destructively) assessing the inner architecture of MOF crystals. By doing this, we have unraveled the presence of large voids in the internal structure of a MIL-47(V) crystal, which are typically thought of as rather homogeneous lattices. This challenges the established opinion that hydrothermal syntheses yield relatively defect-free material and sheds further light on the internal morphology of crystals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Comparing GGA, GGA+ U , and meta-GGA functionals for redox-dependent binding at open metal sites in metal–organic frameworks

Metal–organic frameworks (MOFs) with open metal sites have been widely investigated for the selective adsorption of small molecules via redox mechanisms where charge transfer can take place between the binding site and the adsorbate of interest. Quantum-chemical screening methods based on density functional theory have emerged as a promising route to accelerate the discovery of MOFs with enhanced binding affinities toward various adsorbates. However, the success of this approach is linked to the accuracy of the underlying density functional approximations (DFAs). In this work, we compare commonly used generalized gradient approximation (GGA), GGA+U, and meta-GGA exchange-correlation functionals in modeling redox-dependent binding at open metal sites in MOFs using O 2 and N 2 as representative small molecules. We find that the self-interaction error inherent to the widely used Perdew, Burke, and Ernzerhof (PBE) GGA predicts metal sites that are artificially redox-active, as evidenced by their strong binding affinities, short metal–adsorbate bond distances, and large degree of charge transfer. The incorporation of metal-specific, empirical Hubbard U corrections based on the transition metal oxide literature systematically reduces the redox activity of the open metal sites, often improving agreement with experiment. Additionally, the binding behavior shifts from strong chemisorption to weaker physisorption as a function of U. The M06-L meta-GGA typically predicts binding energies between those of PBE-D3(BJ) and PBE-D3(BJ)+U when using empirically derived U values from the transition metal oxide literature. Despite the strong sensitivity of the binding affinities toward a given DFA, the GGA, GGA+U, and meta-GGA approaches often yield the same qualitative trends and structure–property relationships.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1979

Electron Spectroscopy for Chemical Analysis (ESCA) study of atmospheric particles

The results of analyses by ESCA (Electron Spectroscopy for Chemical Analysis) on several Nuclepore filters which were exposed during air pollution studies are presented along with correlative measurements by Neutron Activation Analysis and Scanning Electron Microscopy. Samples were exposed during air pollution studies at Norfolk, Virginia and the NASA Kennedy Space Center (KSC). It was demonstrated that with the ESCA technique it was possible to identify the chemical (bonding) state of elements contained in the atmospheric particulate matter collected on Nuclepore filters. Sulfur, nitrogen, mercury, chlorine, alkali, and alkaline earth metal species were identified in the Norfolk samples. ESCA binding energy data for aluminum indicated that three chemically different types of aluminum are present in the launch and background samples from NASA-KSC.

Dillard, J. G.↗
DOE OSTI2020

Bidentate Lewis bases are preferred for passivation of MAPbI 3 surfaces: A time-domain ab initio analysis

We report chemical passivation is a predominant approach to inhibit intrinsic defects responsible for electron–hole recombination in perovskite solar cells. Using time-domain density functional theory combined with nonadiabatic molecular dynamics, we demonstrate defect passivation by separation of electrons and holes in metal halide perovskites (MHPs), and show that bidentate ligands exhibit the best performance. Defects in traditional semiconductors create deep midgap states, and passivation eliminates these states. In contrast, common defects produce no deep midgap states in MHPs. Instead, defects localize electrons and holes around defect sites, enhancing electron–hole interaction. Defect passivation in MHPs acts to separate charges, decreasing electron–hole and charge–phonon interactions, and increasing charge lifetimes. Bidentate ligands work best, because they can passivate both unsaturated chemical bonds created due to vacancy defects. Bidentate ligands with spatially separated binding sites are preferred, since they provide better match to the sparse inorganic lattice of MHPs. Similar to the Lewis base ligands, water also acts as a ligand and extends charge lifetimes, with the oxygen atom donating its lone electron pair to the defect site. However, water accelerates chemical degradation of MHPs. The binding energy of most ligands is larger than that of water, and therefore, the ligands displace water, increase MHP stability and prolong carrier lifetimes. The established physical mechanism of defect passivation, and the specific principles guiding the choice of passivating molecules advance our understanding of the exceptional properties of MHPs and suggest routes for further improvement of MHP performance in solar energy and optoelectronic applications.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Observation of site-selective chemical bond changes via ultrafast chemical shifts

The concomitant motion of electrons and nuclei on the femtosecond time scale marks the fate of chemical and biological processes. Here we demonstrate the ability to initiate and track the ultrafast electron rearrangement and chemical bond breaking site-specifically in real time for the carbon monoxide diatomic molecule. We employ a local resonant x-ray pump at the oxygen atom and probe the chemical shifts of the carbon core-electron binding energy. We observe charge redistribution accompanying core-excitation followed by Auger decay, eventually leading to dissociation and hole trapping at one site of the molecule. The presented technique is general in nature with sensitivity to chemical environment changes including transient electronic excited state dynamics. This work provides a route to investigate energy and charge transport processes in more complex systems by tracking selective chemical bond changes on their natural timescale.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Hydrogen in Nanocatalysis

Hydrogen is ubiquitous in catalysis. It is involved in many important reactions such as water splitting, N 2 reduction, CO 2 reduction, and alkane activation. In this Perspective, we focus on the hydrogen atom and follow its electron as it interacts with a catalyst or behaves as part of a catalyst from a computational point of view. In this work, we present recent examples in both nanocluster and solid catalysts to elucidate the parameters governing the strength of the hydrogen–surface interactions based on site geometry and electronic structure. We further show the interesting behavior of hydride in nanometal and oxides for catalysis. Overall, the key take-home messages are: (1) the in-the-middle electronegativity and small size of hydrogen give it great versatility in interacting with active sites on nanoparticles and solid surfaces; (2) the strength of hydrogen binding to an active site on a surface is an important descriptor of the chemical and catalytic properties of the surface; (3) the energetics of the hydrogen binding is closely related to the electronic structure of the catalyst; (4) hydrides in nanoclusters and oxides and on surfaces offer unique reactivity for reduction reactions.

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

Self-adhesive ionomers for durable low-temperature anion exchange membrane electrolysis

Low-temperature water electrolysis using an anion conductive polymer electrolyte has several potential advantages over other technologies, however, the fabrication of durable alkaline electrodes remains a challenge. Detachment of catalysts results in the loss of electrochemical surface area. Simple mixtures of ionomer and catalyst can suffer from poor catalyst adhesion because only physical adhesion is used to bind the components together. A family of chemically bonded, self-adherent, hydroxide conducting ionomers were synthesized and tested under alkaline electrolysis conditions with nickel ferrite anode electrocatalysts and platinum-nickel cathode catalyst. The ionomers are based on hydroxide conducting poly(norbornene) polymers used as the solid polymer electrolyte in alkaline fuel cells and electrolyzers. The synthesized terpolymer ionomers have been functionalized to provide pendant sites for covalent chemical bonding of bis(phenyl)-A-diglycidyl ether to the ionomer, catalyst, and porous transport layer. The electrodes show excellent adhesion between the catalyst particles, porous transport layer and ionomer, as determined by adhesion measurements and electrolysis performance. As a result, the AEM electrolyzer had stable voltage performance under high current density (1 A/ cm 2 at 1.83 V (67% voltage efficiency)) for extended time periods (>600 h) without degradation.

08 HYDROGEN↗
DOE OSTI2023

Mycobacterium tuberculosis CitA activity is modulated by cysteine oxidation and pyruvate binding

As an adaptation for survival during infection, Mycobacterium tuberculosis becomes dormant, reducing its metabolism and growth. Two types of citrate synthases have been identified in Mycobacterium tuberculosis, GltA2 and CitA. Previous work shows that overexpression of CitA, the secondary citrate synthase, stimulates the growth of Mycobacterium tuberculosis under hypoxic conditions without showing accumulation of triacylglycerols and makes mycobacteria more sensitive to antibiotics, suggesting that CitA may play a role as a metabolic switch during infection and may be an interesting TB drug target. To assess the druggability and possible mechanisms of targeting CitA with small-molecule compounds, the CitA crystal structure was solved to 2.1 Å by X-ray crystallography. The solved structure shows that CitA lacks an NADH binding site that would afford allosteric regulation, which is atypical of most citrate synthases. However, a pyruvate molecule is observed within the analogous domain, suggesting pyruvate may instead be the allosteric regulator for CitA. Further, the R149 and R153 residues forming the charged portion of the pyruvate binding pocket were mutated to glutamate and methionine, respectively, to assess the effect of mutations on activity. Protein thermal shift assay shows thermal stabilization of CitA in the presence of pyruvate compared to the two CitA variants designed to decrease pyruvate affinity. Solved crystal structures of both variants show no significant structural changes. However, the catalytic efficiency of the R153M variant increases by 2.6-fold. Additionally, we show that covalent modification of C143 of CitA by Ebselen completely arrests enzyme activity. Similar inhibition is observed using two spirocyclic Michael acceptor containing compounds, which inhibit CitA with IC app 50 values of 6.6 and 10.9 μM. A crystal structure of CitA modified by Ebselen was solved, but significant structural changes were lacking. Considering that covalent modification of C143 inactivates CitA and the proximity of C143 to the pyruvate binding site, this suggests that structural and/or chemical changes in this sub-domain are responsible for regulating CitA enzymatic activity.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Resonant double-core excitations with ultrafast, intense X-ray pulses

Intense few-to-sub-femtosecond soft X-ray pulses can produce neutral, two-site excited double-core-hole states by promoting two core electrons to the same unoccupied molecular orbital. We theoretically investigate double nitrogen K-edge excitations of nitrous oxide (N$_2$O) with multiconfigurational electronic structure calculations. We show that the second core-excitation energy is reduced with respect to its ground state value. A site-selective double core-excitation mechanism using intense few-femtosecond x-rays is investigated using time-dependent Schrodinger equation (TDSE) simulations. The subsequent two-step Auger-Meitner and two-electrons-one-electron decay spectra of the double core-excited states are analysed using a Mulliken population analysis of the multiconfirational wavefunctions. The change in the electron emission lineshape between the absorption of 1 or 2 photons in the resonant core-excitation is predicted by combining this approach with the TDSE simulations. Furthermore, we examine the possibility of resolving the double core-excited states with X-ray pump-probe techniques by calculating the chemical shifts of the core-electron binding energy of the core-excited states and decay products.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Development of Anti- Yersinia pestis Human Antibodies with Features Required for Diagnostic and Therapeutic Applications

Yersinia pestis is a category A infective agent that causes bubonic, septicemic, and pneumonic plague. Notably, the acquisition of antimicrobial or multidrug resistance through natural or purposed means qualifies Y. pestis as a potential biothreat agent. Therefore, high-quality antibodies designed for accurate and sensitive Y. pestis diagnostics, and therapeutics potentiating or replacing traditional antibiotics are of utmost need for national security and public health preparedness. Here, we describe a set of human monoclonal immunoglobulins (IgG1s) targeting Y. pestis fraction 1 (F1) antigen, previously derived from in vitro evolution of a phage-display library of single-chain antibodies (scFv). We extensively characterized these antibodies and their effect on bacterial and mammalian cells via: ELISA, flow cytometry, mass spectrometry, spectroscopy, and various metabolic assays. Two of our anti-F1 IgG (αF1Ig 2 and αF1Ig 8) stood out for high production yield, specificity, and stability. These two antibodies were additionally attractive in that they displayed picomolar affinity, did not compete when binding Y. pestis, and retained immunoreactivity upon chemical derivatization. Most importantly, these antibodies detected < 1,000 Y. pestis cells in sandwich ELISA, did not harm respiratory epithelial cells, induced Y. pestis agglutination at low concentration (350 nM), and caused apparent reduction in cell growth when radiolabeled at a nonagglutinating concentration (34 nM). These antibodies are amenable to the development of accurate and sensitive diagnostics and immuno/radioimmunotherapeutics.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

First Examination of Irradiated Fuel with Pulsed Neutrons at LANSCE (Preliminary Results)

We present preliminary results on the characterization of an irradiated U-lOZr-lPd fuel sample that was prepared from the irradiated AFC-3A-R5A sample. U-lOZr metallic fuels are researched as host materials for potential transmutation fuels and the addition of palladium strives to bind lanthanides, thus preventing fuel-cladding chemical interactions (FCCI). These interactions limit the lifetime of metallic fuels and are caused by migration of lanthanide fission products to the periphery of the fuel slug, where they start to interact with the D9 or HT9 steel cladding, ultimately leading to failure of the mechanical integrity of the cladding. Neutrons offer bulk characterization of irradiated materials for which X-ray tomography methods are not suitable due to the immense gamma background emitted from the samples. In particular pulsed neutrons provide information from the ability to resolve the neutron energy using their time-of-flight and thus the potential to utilize neutron absorption resonance to characterize the spatial distribution of isotopes. This, in turn, may allow to characterize the distribution of fission and neutron capture products non-destructively and may ultimately be applied to the bulk of an irradiation capsule prior to destructive post-irradiation examination to identify regions of interest. To allow the characterization of entire irradiation capsules, a cask is under development in the advanced post-irradiation work package at LANL and progress on this development was reported elsewhere. In parallel, an irradiated U-lOZr-lPd sample cut from the AFC-3AR5A irradiation was shipped to LANL and will be fully characterized with an NSUF funded rapid turnaround experiment (RTE) in the 2020 LANSCE run cycle. The sample emits at a dose rate of ~3R/hr on contact and is therefore manageable with remote handling, without requiring a cask. The disk-shaped material is larger than samples prepared for analysis using electron or X-ray methods and is therefore an intermediate step towards characterization of bulk samples at LANSCE. However, since it covers the full diameter of the irradiated fuel slug, some insight on redistribution of elements, spatially resolved information on microstructure, e.g. phase composition and texture, will be possible using the pulsed neutron-based methods developed for fuel characterization at LANSCE. This report describes the development of procedures to handle the sample at LANSCE as well as preliminary data and results from tests conducted in December 2019 on the energy-resolved neutron imaging (ERNI) beam line at flight path 5 and the high pressure-preferred orientation diffractometer (HIPPO) at LANSCE. This effort is a collaboration between LANL, INL, and ORNL. To compare our capabilities with prior work, we present an overview of previously reported bulk characterization of irradiated or spent fuels. The overview addresses neutron diffraction and neutron absorption resonance spectroscopy, both of which have only few reported applications on irradiated or spent nuclear fuel, as well as neutron radiography. This literature review was already described in a previous report but is repeated here to put our current efforts in context of previous work.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2025

Development of a TSR-based method for understanding structural relationships of cofactors and local environments in photosystem I

All chemical forms of energy and oxygen on Earth are generated via photosynthesis where light energy is converted into redox energy by two photosystems (PS I and PS II). There is an increasing number of PS I 3D structures deposited in the Protein Data Bank (PDB). The Triangular Spatial Relationship (TSR)-based algorithm converts 3D structures into integers (TSR keys). A comprehensive study was conducted, by taking advantage of the PS I 3D structures and the TSR-based algorithm, to answer three questions: (i) Are electron cofactors including P700, A -1 and A 0 , which are chemically identical chlorophylls, structurally different? (ii) There are two electron transfer chains (A and B branches) in PS I. Are the cofactors on both branches structurally different? (iii) Are the amino acids in cofactor binding sites structurally different from those not in cofactor binding sites? The key contributions and important findings include: (i) a novel TSR-based method for representing 3D structures of pigments as well as for quantifying pigment structures was developed; (ii) the results revealed that the redox cofactor, P700, are structurally conserved and different from other redox factors. Similar situations were also observed for both A -1 and A 0 ; (iii) the results demonstrated structural differences between A and B branches for the redox cofactors P700, A -1 , A 0 and A 1 as well as their cofactor binding sites; (iv) the tryptophan residues close to A 0 and A 1 are structurally conserved; (v) The TSR-based method outperforms the Root Mean Square Deviation (RMSD) and the Ultrafast Shape Recognition (USR) methods. The structural analyses of redox cofactors and their binding sites provide a foundation for understanding the unique chemical and physical properties of each redox cofactor in PS I, which are essential for modulating the rate and direction of energy and electron transfers.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1990

On the bonding of La(+) and La(2+) to C2H2, C2H4, and C3H6

The interaction of La(+) and La(2+) with C2H2, C2H4, and C3H6 is studied using electronic structure calculations that include correlation. The calculations show that the bonding in the dication is electrostatic in origin, and the computed binding energies are in good agreement with experiment. The La(+) forms two chemical bonds with the hydrocarbons. Since the pi bond is weaker for C2H2 than C2H4, the La(+)-C2H2 binding energy is larger than for La(+)-C2H4, LaC3H6(+) rearranges to yield a stronger bond than in LaC2H4(+) even though both hydrocarbons have a double bond.

Rosi, Marzio↗
DOE OSTI2020

Molecular Dynamics Simulation of Atomic Interactions in the Vancomycin Binding Site

Vancomycin is a glycopeptide antibiotic produced by Amycolaptopsis orientalis used to treat serious infections by Grampositive pathogens including methicillin-resistant Staphylococcus aureus. Vancomycin inhibits cell wall biosynthesis by targeting lipid II, which is the membrane-bound peptidoglycan precursor. The heptapeptide aglycon structure of vancomycin binds to the D-Ala-D-Ala of the pentapeptide stem structure in lipid II. The third residue of vancomycin aglycon is asparagine, which is not directly involved in the dipeptide binding. Nonetheless, asparagine plays a crucial role in substrate recognition, as the vancomycin analogue with asparagine substituted by aspartic acid (V D ) shows a reduction in antibacterial activities. To characterize the function of asparagine, binding of vancomycin and its aspartic-acid-substituted analogue V D to L-Lys-D-Ala-D-Ala and L-Lys-D-Ala-D-Lac was investigated using molecular dynamic simulations. Binding interactions were analyzed using root-mean-square deviation (RMSD), two-dimensional (2D) contour plots, hydrogen bond analysis, and free energy calculations of the complexes. The analysis shows that the aspartate substitution introduced a negative charge to the binding cleft of V D , which altered the aglycon conformation that minimized the repulsive lone pair interaction in the binding of a depsipeptide. Our findings provide new insight for the development of novel glycopeptide antibiotics against the emerging vancomycin-resistant pathogens by chemical modification at the third residue in vancomycin to improve its binding affinity to the D-Ala-D-Lac-terminated peptidoglycan in lipid II found in vancomycin-resistant enterococci and vancomycinresistant S. aureus.

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

Developing a SARS-CoV-2 main protease binding prediction random forest model for drug repurposing for COVID-19 treatment

The coronavirus disease 2019 (COVID-19) global pandemic resulted in millions of people becoming infected with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus and close to seven million deaths worldwide. It is essential to further explore and design effective COVID-19 treatment drugs that target the main protease of SARS-CoV-2, a major target for COVID-19 drugs. In this study, machine learning was applied for predicting the SARS-CoV-2 main protease binding of Food and Drug Administration (FDA)-approved drugs to assist in the identification of potential repurposing candidates for COVID-19 treatment. Ligands bound to the SARS-CoV-2 main protease in the Protein Data Bank and compounds experimentally tested in SARS-CoV-2 main protease binding assays in the literature were curated. These chemicals were divided into training (516 chemicals) and testing (360 chemicals) data sets. To identify SARS-CoV-2 main protease binders as potential candidates for repurposing to treat COVID-19, 1188 FDA-approved drugs from the Liver Toxicity Knowledge Base were obtained. A random forest algorithm was used for constructing predictive models based on molecular descriptors calculated using Mold2 software. Model performance was evaluated using 100 iterations of fivefold cross-validations which resulted in 78.8% balanced accuracy. The random forest model that was constructed from the whole training dataset was used to predict SARS-CoV-2 main protease binding on the testing set and the FDA-approved drugs. Model applicability domain and prediction confidence on drugs predicted as the main protease binders discovered 10 FDA-approved drugs as potential candidates for repurposing to treat COVID-19. Our results demonstrate that machine learning is an efficient method for drug repurposing and, thus, may accelerate drug development targeting SARS-CoV-2.

Research & Experimental Medicine↗