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At least 55 records · Page 3

The microassay on a card: A rugged, portable immunoassay

The Microassay on a Card (MAC) is a portable, hand-held, non-instrumental immunoassay that can test for the presence of a wide variety of substances in the environment. The MAC is a simple device to use. A drop of test solution is placed on one side of the card and within five minutes a color is developed on the other side in proportion to the amount of substance in the test solution, with sensitivity approaching 10 ng/ml. The MAC is self-contained and self-timed; no reagents or timing is necessary. The MAC may be configured with multiple wells to provide simultaneous testing for multiple species. As envisioned, the MAC will be employed first as an on-site screen for drugs of abuse in urine or saliva. If the MAC can be used as a screen of saliva for drugs of abuse, it could be applied to driving while intoxicated, use of drugs on the job, or testing of the identity of seized materials. With appropriate modifications, the MAC also could be used to test for environmental toxins or pollutants.

Kidwell, David↗

Vapor detection and vapor pressure measurements of fentanyl and fentanyl hydrochloride salt at ambient temperatures

There is a need for non-contact, real-time vapor detection of drugs to combat illicit transportation and help curb the opioid epidemic. The low-volatility of drugs, like fentanyl, makes room temperature vapor detection of illicit drugs challenging, but feasible by atmospheric flow tube-mass spectrometry (AFT-MS). AFT-MS is a non-contact vapor detection approach capable of ultra-trace detection of drugs, including fentanyl and its analogs at low parts-per-quadrillion (ppqv) levels. The determination of vapor pressure values of fentanyl is necessary to understand potential vapor concentrations that may be available for detection. In this paper, vapor pressures of fentanyl free base and fentanyl hydrochloride salt (a common form of the illicit drug) were measured as a function of temperature at or near ambient conditions using the transpiration (gas saturation) method and AFT-MS. Based on our measurements, the vapor pressure of fentanyl at 25 °C is 9.0 × 10-14 atm (90 ppqv), and the vapor pressure of fentanyl hydrochloride at 25 °C is 1.8 x 10-17 atm (0.018 ppqv). We also demonstrate non-contact, real-time vapor detection of fentanyl. Preconcentration of vapors can further extend the detection capabilities. The collection, desorption, and detection of fentanyl vapors at ambient conditions was demonstrated for sampling times of seconds to an hour resulting in increased signal. AFT-MS is a viable detection method of fentanyl and other drugs for screening of packages and cargo.

atmospheric flow tube-mass spectrometry (AFT-MS), ↗

Zam Is a Redox-Regulated Member of the RNB-Family Required for Optimal Photosynthesis in Cyanobacteria

The zam gene mediating resistance to acetazolamide in cyanobacteria was discovered thirty years ago during a drug tolerance screen. We use phylogenetics to show that Zam proteins are distributed across cyanobacteria and that they form their own unique clade of the ribonuclease II/R (RNB) family. Despite being RNB family members, multiple sequence alignments reveal that Zam proteins lack conservation and exhibit extreme degeneracy in the canonical active site—raising questions about their cellular function(s). Several known phenotypes arise from the deletion of zam, including drug resistance, slower growth, and altered pigmentation. Using room-temperature and low-temperature fluorescence and absorption spectroscopy, we show that deletion of zam results in decreased phycocyanin synthesis rates, altered PSI:PSII ratios, and an increase in coupling between the phycobilisome and PSII. Conserved cysteines within Zam are identified and assayed for function using in vitro and in vivo methods. We show that these cysteines are essential for Zam function, with mutation of either residue to serine causing phenotypes identical to the deletion of Zam. Redox regulation of Zam activity based on the reversible oxidation-reduction of a disulfide bond involving these cysteine residues could provide a mechanism to integrate the ‘central dogma’ with photosynthesis in cyanobacteria.

59 BASIC BIOLOGICAL SCIENCES↗

A Telomerase-Activated Magnetic Resonance Imaging Probe for Consecutively Monitoring Tumor Growth Kinetics and In Situ Screening Inhibitors

Telomerase has long been considered as a biomarker for cancer diagnosis and a therapeutic target for drug discovery. Detecting telomerase activity in vivo could provide more direct information of tumor progression and response to drug treatment, which, however, is hampered by the lack of an effective probe that can generate an output signal without a tissue penetration depth limit. Here in this study, using the principle of distance-dependent magnetic resonance tuning, we constructed a telomerase-activated magnetic resonance imaging probe (TAMP) by connecting superparamagnetic ferroferric oxide nanoparticles (SPFONs) and paramagnetic Gd-DOTA (Gd(III) 1,4,7,10- tetraazacyclododecane-1,4,7,10-tetraazacyclododecane-1,4,7,10-tet-raacetic acid) complexes via telomerase-responsive DNA motifs. Upon telomerase-catalyzed extension of the primer in TAMP, Gd-DOTA-conjugated oligonucleotides can be liberated from the surface of SPFONs through a DNA strand displacement reaction, restoring the T 1 signal of the Gd-DOTA for a direct readout of the telomerase activity. Here we show that, by tracking telomerase activity, this probe provides consistent monitoring of tumor growth kinetics during progression and in response to drug treatment and enables in situ screening of telomerase inhibitors in whole-animal models. This study provides an alternative toolkit for cancer diagnosis, treatment response assessment, and anticancer drug screening.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Quantitation of amiodarone and N-desethylamiodarone in single HepG2 cells by single-cell printing-liquid vortex capture-mass spectrometry

Quantitative measure of a drug and its associated metabolite(s) with single-cell resolution is often limited by sampling throughput or other compromises that limit broad use. Here, we demonstrate the use of single-cell printing-liquid vortex capture-mass spectrometry (SCP-LVC-MS) to quantitatively measure the intracellular concentrations of amiodarone (AMIO) and its metabolite, N-desethylamiodarone (NDEA), from thousands of single cells across several AMIO incubation concentrations ranging from 0 to 10 μM. Concentrations obtained by SCP-LVC-MS were validated through comparison with average assays and traditional measurement of cells in bulk. Average of SCP-LVC-MS measurements and aggregate vial collection assay the concentrations differed by < 5%. Both AMIO and NDEA had clear log-normal distributions with similar standard deviation of concentrations in the cell population. The mean of both AMIO and NDEA intracellular concentrations were positively correlated with AMIO incubation concentration, increasing from 0.026 to 0.520 and 0.0055 to 0.048 mM for AMIO and NDEA, respectively. The standard deviation of AMIO and NDEA log-normal distribution fits were relatively similar in value across incubation concentrations, 0.15–0.19 log 10 (mM), and exhibited a linear trend with respect to each other. The single cell-resolved conversion ratio of AMIO to NDEA increased with decreasing incubation concentration, 7 ± 2%, 18 ± 3%, and 20 ± 7% for 10.0, 1.0, and 0.1 μM AMIO incubation concentrations, respectively. Finally, association with simultaneously measured lipids had several ions with statistically significant difference in intensity but no clear correlations with AMIO intracellular content was observed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Studying the Collective Functional Response of a Receptor in Alchemical Ligand Binding Free Energy Simulations with Accelerated Solvation Layer Dynamics

Ligand binding free energy simulations (LB-FES) that involve sampling of protein functional conformations have been longstanding challenges in research on molecular recognition. Particularly, modeling of the conformational transition pathway and design of the heuristic biasing mechanism are severe bottlenecks for the existing enhanced configurational sampling (ECS) methods. Inspired by the key role of hydration in regulating conformational dynamics of macromolecules, this report proposes a novel ECS approach that facilitates binding-associated structural dynamics by accelerated hydration transitions in combination with the lambda-exchange of free energy perturbation (FEP). Further, two challenging protein-ligand binding processes involving large configurational transitions of the receptor are studied, with hydration transitions at binding sites accelerated by Hamiltonian-simulated annealing of the hydration layer. Without the need for pathway analysis or ad hoc barrier flattening potential, LB-FES were performed with FEP/lambda-exchange molecular dynamics simulation at a minor overhead for annealing of the hydration layer. The LB-FES studies showed that the accelerated rehydration significantly enhances the collective conformational transitions of the receptor, and convergence of binding affinity calculations is obtained at a sweet-spot simulation time scale. Alchemical LB-FES with the proposed ECS strategy is free from the effort of trial and error for the setup and realizes efficient on-the-fly sampling for the collective functional response of the receptor and bound water and therefore presents a practical approach to high-throughput screening in drug discovery.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Functional and transcriptional characterization of complex neuronal co-cultures

Brain-on-a-chip systems are designed to simulate brain activity using traditional in vitro cell culture on an engineered platform. It is a noninvasive tool to screen new drugs, evaluate toxicants, and elucidate disease mechanisms. However, successful recapitulation of brain function on these systems is dependent on the complexity of the cell culture. In this study, we increased cellular complexity of traditional (simple) neuronal cultures by co-culturing with astrocytes and oligodendrocyte precursor cells (complex culture). We evaluated and compared neuronal activity (e.g., network formation and maturation), cellular composition in long-term culture, and the transcriptome of the two cultures. Compared to simple cultures, neurons from complex co-cultures exhibited earlier synapse and network development and maturation, which was supported by localized synaptophysin expression, up-regulation of genes involved in mature neuronal processes, and synchronized neural network activity. Also, mature oligodendrocytes and reactive astrocytes were only detected in complex cultures upon transcriptomic analysis of age-matched cultures. Functionally, the GABA antagonist bicuculline had a greater influence on bursting activity in complex versus simple cultures. Collectively, the cellular complexity of brain-on-a-chip systems intrinsically develops cell type-specific phenotypes relevant to the brain while accelerating the maturation of neuronal networks, important features underdeveloped in traditional cultures.

59 BASIC BIOLOGICAL SCIENCES↗

Neuromuscular Junction Model Optimized for Electrical Platforms

Neuromuscular junctions (NMJs), specialized synapses between motor neurons and muscle fibers, are essential for muscle activity. A simple and reproducible cell-based in vitro NMJ platform is needed to test the impact of chemicals on the neuron-muscle communication. Our platform utilizes genetically modified neurons and muscle cells, optimized culture conditions, and commercially available multielectrode array system for recording action potentials. Neuronal cells (NSC34) were optogenetically modified with channelrhodopsin chimera to allow for simultaneous, light-mediated, millisecond-precise activation of neuronal population. This signal is propagated through functional synapses to the muscle fibers. Muscle cells (C2C12) were modified by incorporating gap junction protein (Connexin-43) to improve intracellular communication without affecting muscle differentiation. This communication between muscle fibers resulted in better signal propagation and signal strength. Optimized culture medium facilitated the growth and differentiation of both cell types together. Our system was validated using vecuronium, a muscle relaxant, which abolished the muscle response. This in vitro model provides a unique tool for establishing a NMJ platform that is easy to record and analyze. Potential applications include nondestructive long-term screening of drugs affecting the NMJ.

59 BASIC BIOLOGICAL SCIENCES↗

Improved Charge-Transfer Fluorescent Dyes

Improved charge-transfer fluorescent dyes have been developed for use as molecular probes. These dyes are based on benzofuran nuclei with attached phenyl groups substituted with, variously, electron donors, electron acceptors, or combinations of donors and acceptors. Optionally, these dyes could be incorporated as parts of polymer backbones or as pendant groups or attached to certain surfaces via self-assembly-based methods. These dyes exhibit high fluorescence quantum yields -- ranging from 0.2 to 0.98, depending upon solvents and chemical structures. The wavelengths, quantum yields, intensities, and lifetimes of the fluorescence emitted by these dyes vary with (and, hence, can be used as indicators of) the polarities of solvents in which they are dissolved: In solvents of increasing polarity, fluorescence spectra shift to longer wavelengths, fluorescence quantum yields decrease, and fluorescence lifetimes increase. The wavelengths, quantum yields, intensities, and lifetimes are also expected to be sensitive to viscosities and/or glass-transition temperatures. Some chemical species -- especially amines, amino acids, and metal ions -- quench the fluorescence of these dyes, with consequent reductions in intensities, quantum yields, and lifetimes. As a result, the dyes can be used to detect these species. Another useful characteristic of these dyes is a capability for both two-photon and one-photon absorption. Typically, these dyes absorb single photons in the ultraviolet region of the spectrum (wavelengths < 400 nm) and emit photons in the long-wavelength ultraviolet, visible, and, when dissolved in some solvents, near-infrared regions. In addition, these dyes can be excited by two-photon absorption at near-infrared wavelengths (600 to 800 nm) to produce fluorescence spectra identical to those obtained in response to excitation by single photons at half the corresponding wavelengths (300 to 400 nm). While many prior fluorescent dyes exhibit high quantum yields, solvent-polarity- dependent fluorescence behavior, susceptibility to quenching by certain chemical species, and/or two-photon fluorescence, none of them has the combination of all of these attributes. Because the present dyes do have all of these attributes, they have potential utility as molecular probes in a variety of applications. Examples include (1) monitoring curing and deterioration of polymers; (2) monitoring protein expression; (3) high-throughput screening of drugs; (4) monitoring such chemical species as glucose, amines, amino acids, and metal ions; and (5) photodynamic therapy of cancers and other diseases.

Meador, Michael↗

Studying Host-Pathogen Interactions In 3-D: Organotypic Models For Infectious Disease And Drug Development

Representative, reproducible and high-throughput models of human cells and tissues are critical for a meaningful evaluation of host-pathogen interactions and are an essential component of the research developmental pipeline. The most informative infection models - animals, organ explants and human trials - are not suited for extensive evaluation of pathogenesis mechanisms and screening of candidate drugs. At the other extreme, more cost effective and accessible infection models such as conventional cell culture and static co-culture may not capture physiological and three-dimensional aspects of tissue biology that are important in assessing pathogenesis, and effectiveness and cytotoxicity of therapeutics. Our lab has used innovative bioengineering technology to establish biologically meaningful 3-D models of human tissues that recapitulate many aspects of the differentiated structure and function of the parental tissue in vivo, and we have applied these models to study infectious disease. We have established a variety of different 3-D models that are currently being used in infection studies - including small intestine, colon, lung, placenta, bladder, periodontal ligament, and neuronal models. Published work from our lab has shown that our 3-D models respond to infection with bacterial and viral pathogens in ways that reflect the infection process in vivo. By virtue of their physiological relevance, 3-D cell cultures may also hold significant potential as models to provide insight into the neuropathogenesis of HIV infection. Furthermore, the experimental flexibility, reproducibility, cost-efficiency, and high throughput platform afforded by these 3-D models may have important implications for the design and development of drugs with which to effectively treat neurological complications of HIV infection.

Nickerson, Cheryl A.↗

Portability for GPU-accelerated molecular docking applications for cloud and HPC: can portable compiler directives provide performance across all platforms?

High-throughput structure-based screening of drug-like molecules has become a common tool in biomedical research. Recently, acceleration with graphics processing units (GPUs) has provided a large performance boost for molecular docking programs. Both cloud and high-performance computing (HPC) resources have been used for large screens with molecular docking programs; while NVIDIA GPUs have dominated cloud and HPC resources, new vendors such as AMD and Intel are now entering the field, creating the problem of software portability across different GPUs. Ideally, software productivity could be maximized with portable programming models that are able to maintain high performance across architectures. While in many cases compiler directives have been used as an easy way to offload parallel regions of a CPU-based program to a GPU accelerator, they may also be an attractive programming model for providing portability across different GPU vendors, in which case the porting process may proceed in the reverse direction: from low-level, architecture-specific code to higher-level directive-based abstractions. MiniMDock is a new mini-application (miniapp) designed to capture the essential computational kernels found in molecular docking calculations, such as are used in phar-maceutical drug discovery efforts, in order to test different solutions for porting across GPU architectures. Here we extend MiniMDock to GPU offloading with OpenMP directives, and compare to performance of kernels using CUDA and HIP on NVIDIA and AMD GPUs, respectively, as well as across different compilers, exploring performance bottlenecks. We document this reverse-porting process, from highly optimized device code to a higher-level version using directives, compare code structure, and describe barriers that were overcome in this effort.

Thavappiragasam, Mathialakan↗

Screening of Therapeutic Agents for COVID-19 Using Machine Learning and Ensemble Docking Studies

The current pandemic demands a search for therapeutic agents against the novel coronavirus SARS-CoV-2. In this work, we present an efficient computational strategy that combines machine learning (ML)-based models and high-fidelity ensemble docking studies to enable rapid screening of possible therapeutic ligands. Targeting the binding affinity of molecules for either the isolated SARS-CoV-2 S-protein at its host receptor region or the S-protein:human ACE2 interface complex, we screen ligands from drug and biomolecule data sets that can potentially limit and/or disrupt the host-virus interactions. Top scoring one hundred eighty-seven ligands (with 75 approved by the Food and Drug Administration) are further validated by all atom docking studies. Important molecular descriptors ( 2 χ n , topological surface area, and ring count) and promising chemical fragments (oxolane, hydroxy, and imidazole) are identified to guide future experiments. Overall, this work expands our knowledge of small-molecule treatment against COVID-19 and provides a general screening pathway (combining quick ML models with expensive high-fidelity simulations) for targeting several chemical/biochemical problems.

60 APPLIED LIFE SCIENCES↗

Changes in Liver Metabolic Gene Expression from Radiation Exposure

Radiation exposure is one of the unique physiological challenges of human spaceflight that is not encountered on earth. While radiation exposure is known to impart physiological stresses and alter normal function, it is unclear how it specifically affects drug metabolism. A major concern is that the actions of medications used in spaceflight may deviate from the expectations formed from terrestrial use. This concern was investigated at the molecular level by analyzing how gamma radiation exposure affected gene expression in the livers of mice. Three different doses of radiation were administered and after various intervals of recovery time, gene expression was measured with RT-qPCR screening arrays for drug metabolism and DNA repair. After examining the results of 192 genes total from each of 72 mice, 65 genes were found to be significantly affected by at least one of the doses of radiation. In general, the genes affected are involved in the metabolism of drugs with lipid or steroid hormone-like structures, as well as the maintenance of redox homeostasis and repair of DNA damage.

Peters, C. P.↗

A microCT-based platform to quantify drug targeting

Abstract Background Heterotopic ossification (HO) is a frequent and debilitating complication of traumatic musculoskeletal injuries and orthopedic procedures. Prophylactic dosing of botulinum toxin type A (BTxA) holds potential as a novel treatment option if accurately distributed throughout soft-tissue volumes where protection is clinically desired. We developed a high-resolution, microcomputed tomography (microCT)-based imaging strategy to assess drug distribution and validated this platform by quantifying distribution achieved via a prototype delivery system versus a single-bolus injection. Methods We injected an iodine-containing contrast agent (iodixanol 320 mg I/mL) into dissected rabbit musculature followed by microCT imaging and analysis. To contrast the performance of distributed versus bolus injections, a three-dimensional (3D) 64-cm 3 -printed soft-tissue holder was developed. A centered 2-cm 3 volume of interest (VOI) was targeted with a single-bolus injection or an equal volume distributed injection delivered via a 3D-printed prototype. VOI drug coverage was quantified as a percentage of the VOI volume that was < 1.0 mm from the injected fluid. Results The microCT-based approach enabled high-resolution quantification of injection distribution within soft tissue. The distributed dosing prototype provided significantly greater tissue coverage of the targeted VOI (72 ± 3%, mean ± standard deviation) when compared to an equal volume bolus dose (43 ± 5%, p = 0.031) while also enhancing the precision of injection targeting. Conclusions A microCT-based imaging technique precisely quantifies drug distribution within a soft-tissue VOI, providing a path to overcome a barrier for clinical translation of prophylactic inhibition of HO by BTxA. Relevance statement This platform will facilitate rapid optimization of injection parameters for clinical devices used to effectively and safely inhibit the formation of heterotopic ossification. Key points • MicroCT provides high-resolution quantification of soft-tissue drug distribution. • Distributed dosing is required to maximize soft-tissue drug coverage. • Imaging platform will enable rapid screening of 3D-printed drug distribution prototypes. Graphical Abstract

Ausk, Brandon J. (ORCID:0000000335338303)↗

Combatting melioidosis with chemical synthetic lethality

Burkholderia thailandensishas emerged as a nonpathogenic surrogate forBurkholderia pseudomallei, the causative agent of melioidosis, and an important Gram-negative model bacterium for studying the biosynthesis and regulation of secondary metabolism. We recently reported that subinhibitory concentrations of trimethoprim induce vast changes in both the primary and secondary metabolome ofB. thailandensis. In the current work, we show that the folate biosynthetic enzyme FolE2 is permissive under standard growth conditions but essential forB. thailandensisin the presence of subinhibitory doses of trimethoprim. Reasoning that FolE2 may serve as an attractive drug target, we screened for and identified ten inhibitors, including dehydrocostus lactone (DHL), parthenolide, and β-lapachone, all of which are innocuous individually but form a chemical-synthetic lethal combination with subinhibitory doses of trimethoprim. We show that DHL is a mechanism-based inhibitor of FolE2 and capture the structure of the covalently inhibited enzyme using X-ray crystallography. In vitro, the combination of subinhibitory trimethoprim and DHL is more potent than Bactrim, the current standard of care against melioidosis. Moreover, unlike Bactrim, this combination does not affect the growth of most commensal and beneficial gut bacteria tested, thereby providing a degree of specificity againstB. pseudomallei. Our work provides a path for identifying antimicrobial drug targets and for utilizing binary combinations of molecules that form a toxic cocktail based on metabolic idiosyncrasies of specific pathogens.

Science & Technology - Other Topics↗

Phagosomal chloride dynamics in the alveolar macrophage

Acidification in intracellular organelles is tightly linked to the influx of Cl – counteracting proton translocation by the electrogenic V-ATPase. We quantified the dynamics of Cl – transfer accompanying cargo incorporation into single phagosomes in alveolar macrophages (AMs). Phagosomal Cl – concentration and acidification magnitude were followed in real time with maximal acidification achieved at levels of approximately 200 mM. Live cell confocal microscopy verified that phagosomal Cl – influx utilized predominantly the Cl – channel CFTR. Relative levels of elemental chlorine (Cl) in hard X-ray fluorescence microprobe (XFM) analysis within single phagosomes validated the increase in Cl – content. XFM revealed the complex interplay between elemental K content inside the phagosome and changes in Cl – during phagosomal particle uptake. Cl – -dependent changes in phagosomal membrane potential were obtained using second harmonic generation (SHG) microscopy. These studies provide a mechanistic insight for screening studies in drug development targeting pulmonary inflammatory disease.

59 BASIC BIOLOGICAL SCIENCES↗