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At least 127 records · Page 7

All sources NASA NTRS DOE OSTI

DOE OSTI2022

Hepatitis C virus NS3/4A inhibitors and other drug-like compounds as covalent binders of SARS-CoV-2 main protease

Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), threatens global public health. The world needs rapid development of new antivirals and vaccines to control the current pandemic and to control the spread of the variants. Among the proteins synthesized by the SARS-CoV-2 genome, main protease (M pro also known as 3CL pro ) is a primary drug target, due to its essential role in maturation of the viral polyproteins. In this study, we provide crystallographic evidence, along with some binding assay data, that three clinically approved anti hepatitis C virus drugs and two other drug-like compounds covalently bind to the M pro Cys145 catalytic residue in the active site. Also, molecular docking studies can provide additional insight for the design of new antiviral inhibitors for SARS-CoV-2 using these drugs as lead compounds. One might consider derivatives of these lead compounds with higher affinity to the M pro as potential COVID-19 therapeutics for further testing and possibly clinical trials.

36 MATERIALS SCIENCE↗

DOE OSTI2023

American Heart Association Protein Atlas Portal for Accelerated Drug Discovery

The American Heart Association's Protein Atlas Data Portal is a cutting-edge, open-source atlas of the structural determinants of the binding of drugs to (all of) their target proteins as an unbiased means to accelerate drug discovery. The portal will provide researchers with access to comprehensive data that can help increase the selection of effective drugs and cut the time-to-market of new drugs by half.

drug targets↗

DOE OSTI2023

Electrospun PVA Fibers for Drug Delivery: A Review

Innovation in biomedical science is always a field of interest for researchers. Drug delivery, being one of the key areas of biomedical science, has gained considerable significance. The utilization of simple yet effective techniques such as electrospinning has undergone significant development in the field of drug delivery. Various polymers such as PEG (polyethylene glycol), PLGA (Poly(lactic-co-glycolic acid)), PLA(Polylactic acid), and PCA (poly(methacrylate citric acid)) have been utilized to prepare electrospinning-based drug delivery systems (DDSs). Polyvinyl alcohol (PVA) has recently gained attention because of its biocompatibility, biodegradability, non-toxicity, and ideal mechanical properties as these are the key factors in developing DDSs. Moreover, it has shown promising results in developing DDSs individually and when combined with natural and synthetic polymers such as chitosan and polycaprolactone (PCL). Considering the outstanding properties of PVA, the aim of this review paper was therefore to summarize these recent advances by highlighting the potential of electrospun PVA for drug delivery systems.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2002

Monoclonal antibody to a cancer-specific and drug-responsive hydroquinone (NADH) oxidase from the sera of cancer patients

Monoclonal antibodies were generated in mice to a 34-kDa circulating form of a drug-responsive hydroquinone (NADH) oxidase with a protein disulfide-thiol interchange activity specific to the surface of cancer cells and the sera of cancer patients. Screening used Western blots with purified 34-kDa tNOX from HeLa cells and the sera of cancer patients. Epitopes were sought that inhibited the drug-responsive oxidation of NADH with the sera of cancer patients, but which had no effect on NADH oxidation with the sera of healthy volunteers. Two such antisera were generated. One, designated monoclonal antibody (mAb) 12.1, was characterized extensively. The NADH oxidase activity inhibited by mAb 12.1 also was inhibited by the quinone site inhibitor capsaicin (8-methyl- N-vanillyl-6-noneamide). The inhibition was competitive for the drug-responsive protein disulfide-thiol interchange activity assayed either by restoration of activity to scrambled RNase or by cleavage of a dithiodipyridine substrate, and was uncompetitive for NADH oxidation. Both the mAb 12.1 and the postimmune antisera immunoprecipitated drug-responsive NOX activity and identified the same 34-kDa tNOX protein in the sera of cancer patients that was absent from sera of healthy volunteers, and was utilized as immunogen. Preimmune sera from the same mouse as the postimmune antisera was without effect. Both mouse ascites containing mAb 12.1 and postimmune sera (but not preimmune sera) slowed the growth of human cancer cell lines in culture, but did not affect the growth of non-cancerous cell lines. Immunocytochemical and histochemical findings showed that mAb 12.1 reacted with the surface membranes of human carcinoma cells and tissues.

NASA Discipline Cell Biology↗

NASA NTRS2002

Baroreflex buffering and susceptibility to vasoactive drugs

BACKGROUND: The overall effect of vasoactive drugs on blood pressure is determined by a combination of the direct effect on vascular tone and an indirect baroreflex-mediated effect, a baroreflex buffering of blood pressure. Differences in baroreflex function affect the responsiveness to vasoactive medications, particularly baroreflex buffering of blood pressure; however, the magnitude is not known. METHODS AND RESULTS: We characterized baroreflex function and responses to vasoactive drugs in patients with idiopathic orthostatic intolerance, patients with essential hypertension, patients with monogenic hypertension and brachydactyly, patients with multiple system atrophy, and control subjects. We used phenylephrine sensitivity during ganglionic blockade as a measure of baroreflex buffering. Phenylephrine (25 microg) increased systolic blood pressure 6+/-1.6 mm Hg in control subjects, 6+/-1.1 mm Hg in orthostatic intolerance patients, 18+/-3.9 mm Hg in patients with essential hypertension, 31+/-3.4 mm Hg in patients with monogenic hypertension, and 25+/-3.4 mm Hg in patients with multiple system atrophy. Similar differences in sensitivities between groups were observed with nitroprusside. The sensitivity to vasoactive drugs was highly correlated with baroreflex buffering function and to a lesser degree with baroreflex control of heart rate. In control subjects, sensitivities to nitroprusside and phenylephrine infusions were correlated with baroreflex heart rate control and sympathetic nerve traffic. CONCLUSIONS: Our findings are consistent with an important effect of baroreflex blood pressure buffering on the sensitivity to vasoactive drugs. They suggest that even moderate changes in baroreflex function may have a substantial effect on the sensitivity to vasoactive medications.

NASA Discipline Regulatory Physiology↗

DOE OSTI2021

Integrated laser ablation-dropletProbe-mass spectrometry for absolute drug quantitation, metabolite detection, and distribution in tissue

Rationale: Spatially resolved and accurate quantitation of drug-related compounds in tissue is a much-needed capability in drug discovery research. In this work, application of an integrated laser ablation-dropletProbe-mass spectrometry surface sampling system (LADP-MS) is reported, which achieved absolute quantitation of propranolol measured from <500 × 500 μm thin tissue samples. Methods: Mouse liver and kidney thin tissue sections were coated with parylene C and analyzed for propranolol by a laser ablation/liquid extraction workflow. Non-coated adjacent sections were microdissected for validation and processed using standard bulk tissue extraction protocols. High-performance liquid chromatography with positive ion mode electrospray ionization tandem mass spectrometry was applied to detect the drug and its metabolites. Results: Absolute propranolol concentration in ~500 × 500 μm tissue regions measured by the two methods agreed within ±8% and had a relative standard deviation within ±17%. Quantitation down to ~400 × 400 μm tissue regions was shown, and this resolution was also used for automated mapping of propranolol and phase II hydroxypropranolol glucuronide metabolites in kidney tissue. Conclusions: This study exemplifies the capabilities of integrated laser ablation-dropletProbe-mass spectrometry (LADP-MS) for high resolution absolute drug quantitation analysis of thin tissue sections. This capability will be valuable for applications needing to quantitatively understand the spatial distribution of small molecules in tissue.

47 OTHER INSTRUMENTATION↗

DOE OSTI2025

A deep generative model for deciphering cellular dynamics and in silico drug discovery in complex diseases

Human diseases are characterized by intricate cellular dynamics. Single-cell transcriptomics provides critical insights, yet a persistent gap remains in computational tools for detailed disease progression analysis and targeted in silico drug interventions. Here we introduce UNAGI, a deep generative neural network tailored to analyse time-series single-cell transcriptomic data. This tool captures the complex cellular dynamics underlying disease progression, enhancing drug perturbation modelling and screening. When applied to a dataset from patients with idiopathic pulmonary fibrosis, UNAGI learns disease-informed cell embeddings that sharpen our understanding of disease progression, leading to the identification of potential therapeutic drug candidates. Validation using proteomics reveals the accuracy of UNAGI’s cellular dynamics analysis, and the use of the fibrotic cocktail-treated human precision-cut lung slices confirms UNAGI’s predictions that nifedipine, an antihypertensive drug, may have anti-fibrotic effects on human tissues. UNAGI’s versatility extends to other diseases, including COVID, demonstrating adaptability and confirming its broader applicability in decoding complex cellular dynamics beyond idiopathic pulmonary fibrosis, amplifying its use in the quest for therapeutic solutions across diverse pathological landscapes.

Neural Network↗

DOE OSTI2020

Non-Contact Vapor Detection of Illicit Drugs via Atmospheric Flow Tube-Mass Spectrometry

Real-time, non-contact detection of illicit drugs is a desirable goal for the interdiction of these controlled substances, but the relatively low vapor pressures of such species present a challenge for trace vapor detection technologies. The introduction of atmospheric flow tube-mass spectrometry (AFT-MS), which has previously been demonstrated to detect gas-phase analytes at low parts-per-quadrillion levels for explosives and organophosphorus compounds, also enables the potential for non-contact drug detection. With AFT-MS, direct vapor detection of cocaine and methamphetamine from ~5 µg residues at room temperature is demonstrated herein. Furthermore, thermal desorption of low- to sub-picogram levels of cocaine, methamphetamine, fentanyl, and heroin is observed via AFT-MS using a carrier flow rate of several L/min of air. These low levels can permit non-contact sampling through collection of vapor, effectively preconcentrating the analyte before desorption and analysis. Quantitative evaluation of the thermal desorption approach has yielded limits of detection (LODs) on order of 10 fg for cocaine and fentanyl, 100 fg for methamphetamine, and 1.6 pg for heroin. The LOD for heroin was lowered to 200 fg by using tributyl phosphate as a dopant to form a proton-bound heterodimer with heroin. When used with AFT-MS, the intentional formation of specific drug-dopant adducts has the potential to enhance detection limits and selectivity of additional drug species. Species that are prone to form adducts present a challenge to analysis, but that difficulty can be overcome by the intentional addition of a dopant. Molecules unlikely to form adducts will remain essentially unimpacted, but the adduct-forming species will interact with the dopant to compress the analyte signal into a single peak. This approach would be valuable in the application of non-contact screening for illicit substances via vapor collection followed by thermal desorption for analysis.

methamphetamine, cocaine, heroin, fentanyl, atmosp↗

DOE OSTI2025

Data imbalance in drug response prediction: multi-objective optimization approach in deep learning setting

Abstract Drug response prediction (DRP) methods tackle the complex task of associating the effectiveness of small molecules with the specific genetic makeup of the patient. Anti-cancer DRP is a particularly challenging task requiring costly experiments as underlying pathogenic mechanisms are broad and associated with multiple genomic pathways. The scientific community has exerted significant efforts to generate public drug screening datasets, giving a path to various machine learning models that attempt to reason over complex data space of small compounds and biological characteristics of tumors. However, the data depth is still lacking compared to application domains like computer vision or natural language processing domains, limiting current learning capabilities. To combat this issue and improves the generalizability of the DRP models, we are exploring strategies that explicitly address the imbalance in the DRP datasets. We reframe the problem as a multi-objective optimization across multiple drugs to maximize deep learning model performance. We implement this approach by constructing Multi-Objective Optimization Regularized by Loss Entropy loss function and plugging it into a Deep Learning model. We demonstrate the utility of proposed drug discovery methods and make suggestions for further potential application of the work to achieve desirable outcomes in the healthcare field.

Biochemistry & Molecular Biology↗

DOE OSTI2020

GPU-Accelerated Drug Discovery with Docking on the Summit Supercomputer: Porting, Optimization, and Application to COVID-19 Research

Protein-ligand docking is an in silico tool used to screen potential drug compounds for their ability to bind to a given protein receptor within a drug-discovery campaign. Experimental drug screening is expensive and time consuming, and it is desirable to carry out large scale docking calculations in a high-throughput manner to narrow the experimental search space. Few of the existing computational docking tools were designed with high performance computing in mind. Therefore, optimizations to maximize use of high-performance computational resources available at leadership-class computing facilities enables these facilities to be leveraged for drug discovery. Here we present the porting, optimization, and validation of the AutoDock-GPU program for the Summit supercomputer, and its application to initial compound screening efforts to target proteins of the SARS-CoV-2 virus responsible for the current COVID-19 pandemic.

LeGrand, Scott↗

DOE OSTI2020

Predicting potential adverse events using safety data from marketed drugs

Abstract Background While clinical trials are considered the gold standard for detecting adverse events, often these trials are not sufficiently powered to detect difficult to observe adverse events. We developed a preliminary approach to predict 135 adverse events using post-market safety data from marketed drugs. Adverse event information available from FDA product labels and scientific literature for drugs that have the same activity at one or more of the same targets, structural and target similarities, and the duration of post market experience were used as features for a classifier algorithm. The proposed method was studied using 54 drugs and a probabilistic approach of performance evaluation using bootstrapping with 10,000 iterations. Results Out of 135 adverse events, 53 had high probability of having high positive predictive value. Cross validation showed that 32% of the model-predicted safety label changes occurred within four to nine years of approval (median: six years). Conclusions This approach predicts 53 serious adverse events with high positive predictive values where well-characterized target-event relationships exist. Adverse events with well-defined target-event associations were better predicted compared to adverse events that may be idiosyncratic or related to secondary target effects that were poorly captured. Further enhancement of this model with additional features, such as target prediction and drug binding data, may increase accuracy.

Daluwatte, Chathuri↗

DOE OSTI2021

Targeting Drugs Against Fibroblast Growth Factor(s)-Induced Cell Signaling

Background:: The fibroblast growth factor (FGF) family is comprised of 23 highly regulatedmonomeric proteins that regulate a plethora of developmental and pathophysiological processes,including tissue repair, wound healing, angiogenesis, and embryonic development. Binding ofFGF to fibroblast growth factor receptor (FGFR), a tyrosine kinase receptor, is facilitated by a glycosaminoglycan,heparin. Activated FGFRs phosphorylate the tyrosine kinase residues that mediateinduction of downstream signaling pathways, such as RAS-MAPK, PI3K-AKT, PLCγ, andSTAT. Dysregulation of the FGF/FGFR signaling occurs frequently in cancer due to gene amplification,FGF activating mutations, chromosomal rearrangements, integration, and oncogenic fusions.Aberrant FGFR signaling also affects organogenesis, embryonic development, tissue homeostasis,and has been associated with cell proliferation, angiogenesis, cancer, and other pathophysiologicalchanges. Objective:: This comprehensive review will discuss the biology, chemistry, and functions of FGFs,and its current applications toward wound healing, diabetes, repair and regeneration of tissues, andfatty liver diseases. In addition, specific aberrations in FGFR signaling and drugs that target FGFRand aid in mitigating various disorders, such as cancer, are also discussed in detail. Conclusion:: Inhibitors of FGFR signaling are promising drugs in the treatment of several types ofcancers. The clinical benefits of FGF/FGFR targeting therapies are impeded due to the activationof other RTK signaling mechanisms or due to the mutations that abolish the drug inhibitory activityon FGFR. Thus, the development of drugs with a different mechanism of action for FGF/FGFRtargeting therapies is the recent focus of several preclinical and clinical studies.

Pharmacology & Pharmacy↗

DOE OSTI2025

Gestational exposure to HIV drugs alters intestinal mucosa-associated microbial diversity in adult rat offspring

The antiretroviral (ARV) drug combination of abacavir sulfate, dolutegravir, and lamivudine [ABC/DTG/3TC; Tri combination Anti-retroviral therapy (TC-ART)] has revolutionized HIV treatment by effectively targeting different stages of viral replication. Despite its therapeutic efficiency for maintaining low viremia in the mother during pregnancy, there are concerns for long-term liabilities in offspring that are indirectly exposed during vulnerable periods of development. The commensal microbiota plays a crucial role in maintaining overall gut health, and disruption of the microbiome is often linked to various extraintestinal effects such as immune dysregulation and inflammation. We recently reported the effects of this drug combination in altering fecal microbiome composition of aged rats perinatally exposed to ABC/DTG/3TC-ART. The fecal microbiome can provide only a snapshot of the composition of microbial community at the end of the digestive tract, which may not reflect the microbial population interacting with ileal mucosa. Thus, the current work reports the effects of this drug combination in the gut mucosa-associated microbiome of the same animals, which showed significant microbial diversity and species richness in high dose exposed female adult offspring, along with dose-dependent changes in Firmicutes/Bacteroidetes ratio. The high dose exposure also showed an increase in opportunistic bacterial species in male animals. Overall, we found that, similar to the fecal microbiome, perinatal exposure to TC-ART led to sex- and dose-dependent alterations in the gut mucosa-associated microbial population in aged rats, suggesting that early life exposure to these drugs may influence gut mucosa-associated immune responses and intestinal permeability.

Research & Experimental Medicine↗

DOE OSTI2021

The Promise of Mutation Resistant Drugs for SARS-CoV-2 That Interdict in the Folding of the Spike Protein Receptor Binding Domain

In recent work, we proposed that effective therapeutic drugs aimed at treating the SARS-CoV-2 infection could be developed based on interdicting in the early steps of the folding pathway of key viral proteins, including the receptor binding domain (RBD) of the spike protein. In order to provide for a drug target on the protein, the earliest contact-formation event along the dominant folding pathway of the RBD spike protein was predicted employing the Sequential Collapse Model (SCM). The segments involved in the predicted earliest contact were suggested to provide optimal folding interdiction target regions (FITRs) for potential therapeutic drugs, with a focus on folding interdicting peptides (FIPs). In this paper, we extend our analysis to include 13 known single mutations of the RBD spike protein as well as the triple mutation B1.351 and the recent double mutation B1.617.2. The results show that the location of the FITR does not change in any of the 15 studied mutations, providing for a mutation-resistant drug design strategy for the RBD-spike protein.

Bergasa-Caceres, Fernando↗

NASA NTRS1992

Effects of methiothepin on changes in brain serotonin release induced by repeated administration of high doses of anorectic serotoninergic drugs

We previously observed, using in vivo microdialysis, that the potassium-evoked release of frontocortical serotonin (5-HT) is suppressed after rats receive high doses (30 mg/kg, i.p., daily for 3 days) of fluoxetine, a selective blocker of 5-HT reuptake. We now describe similar impairments in 5-HT release after repeated administration of two other 5-HT uptake blockers, zimelidine and sertraline (both at 20 mg/kg, i.p. for 3 days) as well as after dexfenfluramine (7.5 mg/kg, i.p. daily for 3 days), a drug which both releases 5-HT and blocks its reuptake. Doses of these indirect serotonin agonists were about 4-6 times the drug's ED50 in producing anorexia, a serotonin-related behavior. In addition, methiothepin (20 microM), a non-selective receptor antagonist, locally perfused through the dialysis probe 24 h after the last drug injection, enhanced K(+)-evoked release of 5-HT at serotoninergic nerve terminals markedly in control rats and slightly in rats treated with high doses of dexfenfluramine or fluoxetine. On the other hand, pretreatment with methiothepin (10 mg/kg, i.p.) one hour before each of the daily doses of fluoxetine or dexfenfluramine given for 3 days, totally prevented the decrease in basal and K(+)-evoked release of 5-HT. Finally, when methiothepin was injected systemically the day before the first of 3 daily injections of dexfenfluramine, it partially attenuated the long-term depletion of brain 5-HT and 5-HIAA levels induced by repeated administration of high doses of dexfenfluramine. These data suggest that drugs which bring about the prolonged blockade of 5-HT reuptake - such as dexfenfluramine and fluoxetine - can, by causing prolonged increases in intrasynaptic 5-HT levels as measured by in vivo microdialysis, produce receptor-mediated long-term changes in the processes controlling serotonin levels and dynamics.

NASA Discipline Regulatory Physiology↗

DOE OSTI2021

Early Drug Discovery and Development of Novel Cancer Therapeutics Targeting DNA Polymerase Eta (POLH)

Polymerase eta (or Pol η or POLH) is a specialized DNA polymerase that is able to bypass certain blocking lesions, such as those generated by ultraviolet radiation (UVR) or cisplatin, and is deployed to replication foci for translesion synthesis as part of the DNA damage response (DDR). Inherited defects in the gene encoding POLH (a.k.a., XPV) are associated with the rare, sun-sensitive, cancer-prone disorder, xeroderma pigmentosum, owing to the enzyme’s ability to accurately bypass UVR-induced thymine dimers. In standard-of-care cancer therapies involving platinum-based clinical agents, e.g., cisplatin or oxaliplatin, POLH can bypass platinum-DNA adducts, negating benefits of the treatment and enabling drug resistance. POLH inhibition can sensitize cells to platinum-based chemotherapies, and the polymerase has also been implicated in resistance to nucleoside analogs, such as gemcitabine. POLH overexpression has been linked to the development of chemoresistance in several cancers, including lung, ovarian, and bladder. Co-inhibition of POLH and the ATR serine/threonine kinase, another DDR protein, causes synthetic lethality in a range of cancers, reinforcing that POLH is an emerging target for the development of novel oncology therapeutics. Using a fragment-based drug discovery approach in combination with an optimized crystallization screen, we have solved the first X-ray crystal structures of small novel drug-like compounds, i.e., fragments, bound to POLH, as starting points for the design of POLH inhibitors. The intrinsic molecular resolution afforded by the method can be quickly exploited in fragment growth and elaboration as well as analog scoping and scaffold hopping using medicinal and computational chemistry to advance hits to lead. An initial small round of medicinal chemistry has resulted in inhibitors with a range of functional activity in an in vitro biochemical assay, leading to the rapid identification of an inhibitor to advance to subsequent rounds of chemistry to generate a lead compound. Importantly, our chemical matter is different from the traditional nucleoside analog-based approaches for targeting DNA polymerases.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Endothelial surface translocation of mitochondrial PDCE2 involves the non-canonical secretory autophagy pathway: Putative molecular target for radiation-guided drug delivery

Highlights: • Radiation induces ectopic endothelial surface exposure of mitochondrial PDCE2. • PDCE2 translocation is associated with late-stage inhibition of autophagic flux. • Radiation damage overloads the degradative lysosomal pathway of autophagy. • PDCE2 trafficking occurs via autophagosomes and non-canonical secretory autophagy. • Surface PDCE2 provides a novel target for radiation-guided vascular drug delivery. Radiation has been proposed as a priming agent to induce discriminatory luminal biomarkers for vascular targeting and drug delivery in disorders such as brain arteriovenous malformations and cancers. We previously observed ectopic expression of intracellular proteins such as mitochondrial PDCE2 on irradiated endothelium in animal models. In this study we examined the mechanism of PDCE2 trafficking in human endothelial cells to better understand its suitability as a vascular target. Ionizing radiation induced PDCE2 surface localization in association with accumulation of autophagosome markers (L3CB and p62) indicative of late-stage inhibition of autophagic flux. This effect was abolished in the presence of Rapamycin, an autophagy-inducer, but replicated in the presence of Bafilomycin A, an autophagy blocker. PDCE2 co-localized with lysosomal markers of the canonical degradative autophagy pathway in response to radiation but also with recycling endosomes and SNARE proteins responsible for autophagosome-plasma membrane fusion. These findings demonstrate that radiation-induced blockade of autophagic flux stimulates redirection of intracellular molecules such as PDCE2 to the cell surface via a non-canonical secretory autophagy pathway. Intracellular membrane proteins trafficked in this way could provide a unique pool of radiation biomarkers for therapeutic drug delivery.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Membrane fusion and drug delivery with carbon nanotube porins

Significance The plasma membrane protects cell content from the outer environment. Overcoming this obstacle and delivering drugs efficiently into cells still remain a major hurdle for modern pharmacology and medicine. We developed and demonstrated a simple nanomaterial platform—a dimer of small-diameter carbon nanotube porins (CNTPs)—which functions as a potent membrane fusogen. Molecular simulations revealed a distinct fusion mechanism. CNTP-studded vesicles loaded with a chemotherapeutic agent, doxorubicin, delivered the drug to cancer cells, killing a majority of them. Our work provides new opportunities for understanding membrane fusion mechanisms, designing synthetic fusogens, and developing simple and efficient drug carriers for delivery of therapeutics and vaccines.

60 APPLIED LIFE SCIENCES↗