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Research Interests:
Research Interests:
Restoring functional beta-cell mass is an important therapeutic goal for both type 1 and type 2 diabetes (1). While proliferation of existing beta cells is the primary means of beta-cell replacement in rodents (2), it is unclear whether a... more
Restoring functional beta-cell mass is an important therapeutic goal for both type 1 and type 2 diabetes (1). While proliferation of existing beta cells is the primary means of beta-cell replacement in rodents (2), it is unclear whether a similar principle applies to humans as human beta cells are remarkably resistant to stimulation of division (3, 4). Here, we show that 5-iodotubercidin (5-IT), an annotated adenosine kinase inhibitor previously reported to increase proliferation in rodent and porcine islets (5), strongly and selectively increases human beta-cell proliferation in vitro and in vivo. Remarkably, 5-IT also increased glucose-dependent insulin secretion after prolonged treatment. Kinome profiling revealed 5-IT to be a potent and selective inhibitor of the dual-specificity tyrosine phosphorylation-regulated kinase (DYRK) and cell division cycle (CDC)-like (CLK) kinase families. Induction of beta-cell proliferation by either 5-IT or harmine, another natural-product DYRK1A ...
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Research Interests:
High cancer death rates indicate the need for new anticancer therapeutic agents. Approaches to discovering new cancer drugs include target-based drug discovery and phenotypic screening. Here, we identified phosphodiesterase 3A modulators... more
High cancer death rates indicate the need for new anticancer therapeutic agents. Approaches to discovering new cancer drugs include target-based drug discovery and phenotypic screening. Here, we identified phosphodiesterase 3A modulators as cell-selective cancer cytotoxic compounds through phenotypic compound library screening and target deconvolution by predictive chemogenomics. We found that sensitivity to 6-(4-(diethylamino)-3-nitrophenyl)-5-methyl-4,5-dihydropyridazin-3(2H)-one, or DNMDP, across 766 cancer cell lines correlates with expression of the gene PDE3A, encoding phosphodiesterase 3A. Like DNMDP, a subset of known PDE3A inhibitors kill selected cancer cells, whereas others do not. Furthermore, PDE3A depletion leads to DNMDP resistance. We demonstrated that DNMDP binding to PDE3A promotes an interaction between PDE3A and Schlafen 12 (SLFN12), suggestive of a neomorphic activity. Coexpression of SLFN12 with PDE3A correlates with DNMDP sensitivity, whereas depletion of SLFN...
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Changes in cellular gene expression in response to small-molecule or genetic perturbations have yielded signatures that can connect unknown mechanisms of action (MoA) to ones previously established. We hypothesized that differential basal... more
Changes in cellular gene expression in response to small-molecule or genetic perturbations have yielded signatures that can connect unknown mechanisms of action (MoA) to ones previously established. We hypothesized that differential basal gene expression could be correlated with patterns of small-molecule sensitivity across many cell lines to illuminate the actions of compounds whose MoA are unknown. To test this idea, we correlated the sensitivity patterns of 481 compounds with ∼19,000 basal transcript levels across 823 different human cancer cell lines and identified selective outlier transcripts. This process yielded many novel mechanistic insights, including the identification of activation mechanisms, cellular transporters and direct protein targets. We found that ML239, originally identified in a phenotypic screen for selective cytotoxicity in breast cancer stem-like cells, most likely acts through activation of fatty acid desaturase 2 (FADS2). These data and analytical tools ...
Research Interests: Computational Biology, Principal Component Analysis, Biology, Medicine, Gene expression, and 11 moreWestern blotting, Humans, Computer Simulation, Female, Drug Delivery Systems, Gene, Aflatoxins, Biochemistry and cell biology, Molecular Structure, Breast Neoplasms, and real time polymerase chain reaction
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The histone methyltransferase G9a is overexpressed in a variety of cancer types, including pancreatic adenocarcinoma, and promotes tumor invasiveness and metastasis. We recently reported the discovery of BRD4770, a small-molecule... more
The histone methyltransferase G9a is overexpressed in a variety of cancer types, including pancreatic adenocarcinoma, and promotes tumor invasiveness and metastasis. We recently reported the discovery of BRD4770, a small-molecule inhibitor of G9a that induces senescence in PANC-1 cells. We observed that the cytotoxic effects of BRD4770 were dependent on genetic background, with cell lines lacking functional p53 being relatively resistant to compound treatment. To understand the mechanism of genetic selectivity, we used two complementary screening approaches to identify enhancers of BRD4770. The natural product and putative BH3 mimetic gossypol enhanced the cytotoxicity of BRD4770 in a synergistic manner in p53-mutant PANC-1 cells but not in immortalized non-tumorigenic pancreatic cells. The combination of gossypol and BRD4770 increased LC3-II levels and the autophagosome number in PANC-1 cells, and the compound combination appears to act in a BNIP3 (B-cell lymphoma 2 19-kDa interact...
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Pancreatic beta-cell regeneration, for example, by inducing proliferation, remains an important goal in developing effective treatments for diabetes. However, beta cells have mainly been considered quiescent. This “static” view has... more
Pancreatic beta-cell regeneration, for example, by inducing proliferation, remains an important goal in developing effective treatments for diabetes. However, beta cells have mainly been considered quiescent. This “static” view has recently been challenged by observations of relevant physiological conditions in which metabolic stress is compensated by an increase in beta-cell mass. Understanding the molecular mechanisms underlining these process could open the possibility of developing novel small molecules to increase beta-cell mass. Several cellular cell-cycle and signaling proteins provide attractive targets for high throughput screening, and recent advances in cell culture have enabled phenotypic screening for small molecule-induced beta-cell proliferation. We present here an overview of the current trends involving small-molecule approaches to induce beta-cell regeneration by proliferation.
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Research Interests: Physiology, Molecular Biology, Biology, Cytokines, Cell Biology, and 15 moreMedicine, Humans, Glucose, Insulin, Fatty acids, Luciferase, Beta Cell, Enzyme Linked Immunosorbent Assay, Secretion, Biochemistry and cell biology, cell metabolism, thapsigargin, Reporter gene, Medical biochemistry and metabolomics, and proinsulin
High-content screening for small-molecule inducers of insulin expression identified the compound BRD7389, which caused α-cells to adopt several morphological and gene expression features of a β-cell state. Assay-performance profile... more
High-content screening for small-molecule inducers of insulin expression identified the compound BRD7389, which caused α-cells to adopt several morphological and gene expression features of a β-cell state. Assay-performance profile analysis suggests kinase inhibition as a mechanism of action, and we show that biochemical and cellular inhibition of the RSK kinase family by BRD7389 is likely related to its ability induce a β-cell-like state. BRD7389 also increases the endocrine cell content and function of donor human pancreatic islets in culture.
Research Interests: Molecular Biology, Biology, Medicine, Gene expression, Multidisciplinary, and 13 moreBiological Sciences, RNA interference, Cell line, Cell Differentiation, Humans, Insulin, Mice, Animals, Quinolones, Protein Kinase Inhibitors, islets of Langerhans, Molecular Structure, and Tissue culture techniques
The transcriptional coactivator PGC-1α is a potent regulator of several metabolic pathways, including, in particular, the activation of oxidative phosphorylation and mitochondrial biogenesis. Recent evidence suggests that increasing... more
The transcriptional coactivator PGC-1α is a potent regulator of several metabolic pathways, including, in particular, the activation of oxidative phosphorylation and mitochondrial biogenesis. Recent evidence suggests that increasing PGC-1α activity may have beneficial effects in various conditions, including muscular dystrophy, diabetes, and neurodegenerative diseases. We describe here a high-throughput screen to identify small molecules that induce PGC-1α expression in skeletal muscle cells. A number of drug classes are identified, including glucocorticoids, microtubule inhibitors, and protein synthesis inhibitors. These drugs induce PGC-1α mRNA, and the expression of a number of genes known to be regulated by PGC-1α. No induction of these target genes is seen in PGC-1α −/− cells, demonstrating that the drugs act through PGC-1α. These data demonstrate the feasibility of high-throughput screening for inducers of PGC-1α. Moreover, the data identify microtubule inhibitors and protein ...
Research Interests: Biology, Medicine, Gene expression, Multidisciplinary, Mice, and 15 moreHigh throughput screening, Muscular Dystrophy, Animals, Phosphorylation, Microtubules, MITOCHONDRIAL BIOGENESIS, Oxidative phosphorylation, Neurodegenerative Disease, Metabolic pathway, Glucocorticoids, Protein Biosynthesis, Gene Expression Regulation, Gene expression profiling, Muscle cells, and Drug synergism
Using a diverse collection of small molecules generated from a variety of sources, we measured protein-binding activities of each individual compound against each of 100 diverse (sequence-unrelated) proteins using small-molecule... more
Using a diverse collection of small molecules generated from a variety of sources, we measured protein-binding activities of each individual compound against each of 100 diverse (sequence-unrelated) proteins using small-molecule microarrays. We also analyzed structural features, including complexity, of the small molecules. We found that compounds from different sources (commercial, academic, natural) have different protein-binding behaviors and that these behaviors correlate with general trends in stereochemical and shape descriptors for these compound collections. Increasing the content of sp 3 -hybridized and stereogenic atoms relative to compounds from commercial sources, which comprise the majority of current screening collections, improved binding selectivity and frequency. The results suggest structural features that synthetic chemists can target when synthesizing screening collections for biological discovery. Because binding proteins selectively can be a key feature of high...
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Research Interests: Biology, Mitochondria, Medicine, Gene expression, Multidisciplinary, and 15 moreNature, Cell line, Mitochondrial DNA, Mice, Animals, Microtubules, Genome, Cell nucleus, Oxidative phosphorylation, Large Scale, Molecular Structure, Gene Expression Regulation, Gene expression profiling, Pharmaceutical preparations, and Mitochondrion
ABSTRACT Chemical genomics is concerned with the effects of both genetic variation and chemical perturbation on the cellular effects of small molecules. Chemical genomics relies on selecting biological networks for study, such as those... more
ABSTRACT Chemical genomics is concerned with the effects of both genetic variation and chemical perturbation on the cellular effects of small molecules. Chemical genomics relies on selecting biological networks for study, such as those represented by different cell types or disease models, in order to build the desired specificity into the experimental design. The most relevant network property for such experiments is the global connectivity of all cellular proteins comprising the functional ensemble, as illustrated by case studies of the evolution of cyclooxygenase inhibitors and heat-shock protein modulators. Recent examples of chemical genomic profiling, particularly of different cell types, highlight the power of carefully planned experimental approaches in chemical genomics. These new approaches demonstrate the use of the genome to find new targets or new modes of biological interaction.
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Understanding the structure–activity relationships (SARs) of small molecules is important for developing probes and novel therapeutic agents in chemical biology and drug discovery. Increasingly, multiplexed small-molecule profiling assays... more
Understanding the structure–activity relationships (SARs) of small molecules is important for developing probes and novel therapeutic agents in chemical biology and drug discovery. Increasingly, multiplexed small-molecule profiling assays allow simultaneous measurement of many biological response parameters for the same compound (e.g., expression levels for many genes or binding constants against many proteins). Although such methods promise to capture SARs with high granularity, few computational methods are available to support SAR analyses of high-dimensional compound activity profiles. Many of these methods are not generally applicable or reduce the activity space to scalar summary statistics before establishing SARs. In this article, we present a versatile computational method that automatically extracts interpretable SAR rules from high-dimensional profiling data. The rules connect chemical structural features of compounds to patterns in their biological activity profiles. We ...
Research Interests: Computer Science, Data Mining, Computational Biology, Biology, Drug Discovery, and 13 morePharmaceutical Chemistry, Medicine, Software, Humans, Automation, Cluster Analysis, Chemical space, Small Molecule, Structure activity Relationship, Biochemistry and cell biology, Gene Expression Regulation, Gene expression profiling, and Histone deacetylase inhibitors
A small-molecule inducer of beta-cell proliferation in human islets represents a potential regeneration strategy for treating type 1 diabetes. However, the lack of suitable human beta cell lines makes such a discovery a challenge. Here,... more
A small-molecule inducer of beta-cell proliferation in human islets represents a potential regeneration strategy for treating type 1 diabetes. However, the lack of suitable human beta cell lines makes such a discovery a challenge. Here, we adapted an islet cell culture system to high-throughput screening to identify such small molecules. We prepared microtiter plates containing extracellular matrix from a human bladder carcinoma cell line. Dissociated human islets were seeded onto these plates, cultured for up to 7 days, and assessed for proliferation by simultaneous Ki67 and C-peptide immunofluorescence. Importantly, this environment preserved beta-cell physiological function, as measured by glucose-stimulated insulin secretion. Adenoviral overexpression of cdk-6 and cyclin D1, known inducers of human beta cell proliferation, was used as a positive control in our assay. This induction was inhibited by cotreatment with rapamycin, an immunosuppressant often used in islet transplantat...
Research Interests: Biology, Cell Biology, Extracellular Matrix, Cell Culture, Cell line, and 15 moreHumans, Glucose, Insulin, High throughput screening, Islet Transplantation, Very high throughput, Reproducibility of Results, Primary Cell Culture, Beta Cell, Cell Proliferation, Islet, Biochemistry and cell biology, islets of Langerhans, Cell Growth, and positive control
High-throughput screening allows rapid identification of new candidate compounds for biological probe or drug development. Here, we describe a principled method to generate “assay performance profiles” for individual compounds that can... more
High-throughput screening allows rapid identification of new candidate compounds for biological probe or drug development. Here, we describe a principled method to generate “assay performance profiles” for individual compounds that can serve as a basis for similarity searches and cluster analyses. Our method overcomes three challenges associated with generating robust assay performance profiles: (1) we transform data, allowing us to build profiles from assays having diverse dynamic ranges and variability; (2) we apply appropriate mathematical principles to handle missing data; and (3) we mitigate the fact that loss-of-signal assay measurements may not distinguish between multiple mechanisms that can lead to certain phenotypes (e.g., cell death). Our method connected compounds with similar mechanisms of action, enabling prediction of new targets and mechanisms both for known bioactives and for compounds emerging from new screens. Furthermore, we used Bayesian modeling of promiscuous ...
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Research Interests: Genetics, Organic Chemistry, Biology, DNA replication, Medicine, and 15 moreCell line, Humans, Peptides, Gas Chromatography, High Performance Liquid Chromatography, Ammonium Nitrate, Liquid Chromatography, Biological Process, Structural Complexity, Mass Spectroscopy, Microspheres, Chemistry Biology, Biochemistry and cell biology, Chemical Genetics, and Hydrogen fluoride
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Research Interests:
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Research Interests: Computational Biology, Mass Spectrometry, Biology, Drug Discovery, Medicine, and 15 moreNature, Saccharomyces cerevisiae, RNA interference, Humans, Animals, Reverse genetics, Phenotype, Small Molecule, Mechanism of action, Mechanism in Biology, Molecular Targeted Therapy, Isotope Labeling, Biochemistry and cell biology, Chemical Genetics, and Validation Studies as Topic
Hydrogen sulphide (H2S) is an endogenous gasotransmitter, involved in the regulation of several biological functions. Conversely, impaired biosynthesis of H2S is associated with important diseases. This paves the way to exciting... more
Hydrogen sulphide (H2S) is an endogenous gasotransmitter, involved in the regulation of several biological functions. Conversely, impaired biosynthesis of H2S is associated with important diseases. This paves the way to exciting pharmacological perspectives for drugs acting on the "H2S system". Areas covered: This paper attempts to overview the most representative compounds acting as sources of exogenous H2S and are promising drugs for a number of serious disorders: hypertension, heart diseases, asthma, neurodegenerations, etc. Fewest H2S-releasing drugs have been evaluated in models of human diseases, with truly exciting results. Natural H2S-donors are also present in edible plants and the release of H2S accounts for the beneficial effects on the human health. A limited number of other compounds showing heterogeneous H2S-releasing moieties have been reported, but poorly characterized by pharmacological point of view. Expert opinion: The rate of H2S generation, the physico...