2-Oxoglutarate derivatives can selectively enhance or inhibit the activity of human oxygenases

Abstract2-Oxoglutarate (2OG) oxygenases are validated agrochemical and human drug targets. The potential for modulating their activity with 2OG derivatives has not been explored, possibly due to concerns regarding selectivity. We report proof-of-principle studies demonstrating selective enhancement or inhibition of 2OG oxygenase activity by 2-oxo acids. The human 2OG oxygenases studied, factor inhibiting hypoxia-inducible transcription factor HIF-α (FIH) and aspartate/asparagine-β-hydroxylase (AspH), catalyze C3 hydroxylations of Asp/Asn-residues. Of 35 tested 2OG derivatives, 10 enhance and 17 inhibit FIH activity. Comparison with results for AspH reveals that 2OG derivatives selectively enhance or inhibit FIH or AspH. Comparison of FIH structures complexed with 2OG derivatives to those for AspH provides insight into the basis of the observed selectivity. 2-Oxo acid derivatives have potential as drugs, for use in biomimetic catalysis, and in functional studies. The results suggest that the in vivo activity of 2OG oxygenases may be regulated by natural 2-oxo acids other than 2OG.

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Early block to erythromegakaryocytic development conferred by loss of transcription factor GATA-1

Blood ◽

10.1182/blood-2005-07-2740 ◽

2006 ◽

Vol 107 (1) ◽

pp. 87-97 ◽

Cited By ~ 76

Author(s):

David L. Stachura ◽

Stella T. Chou ◽

Mitchell J. Weiss

Keyword(s):

Transcription Factor ◽

Early Stage ◽

Embryonic Stem ◽

Erythroid Progenitors ◽

Acute Megakaryoblastic Leukemia ◽

Megakaryoblastic Leukemia ◽

Murine Embryonic Stem Cell ◽

Naturally Occurring ◽

Insight Into

Abstract Transcription factor GATA-1 is essential at multiple stages of hematopoiesis. Murine gene targeting and analysis of naturally occurring human mutations demonstrate that GATA-1 drives the maturation of committed erythroid precursors and megakaryocytes. Prior studies also suggest additional, poorly defined, roles for GATA-1 at earlier stages of erythromegakaryocytic differentiation. To investigate these functions further, we stimulated Gata1- murine embryonic stem-cell-derived hematopoietic cultures with thrombopoietin, a multistage cytokine. Initially, the cultures generated a wave of mutant megakaryocytes. However, these were rapidly overgrown by a unique population of thrombopoietin-dependent blasts that express immature markers and proliferate indefinitely. Importantly, on restoration of GATA-1 function, these cells differentiated into both erythroid and megakaryocytic lineages, suggesting that they represent bipotential progenitors. Identical cells are also present in vivo, as indicated by flow cytometry and culture analysis of fetal livers from Gata1- chimeric mice. Our findings indicate that loss of GATA-1 impairs the maturation of megakaryocyte-erythroid progenitors. This defines a new role for GATA-1 at a relatively early stage of hematopoiesis and provides potential insight into recent discoveries that human GATA1 mutations promote acute megakaryoblastic leukemia, a clonal malignancy with features of both erythroid and megakaryocyte maturation.

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A systematic genome-wide account of binding sites for the model transcription factor Gcn4

Genome Research ◽

10.1101/gr.276080.121 ◽

2021 ◽

pp. gr.276080.121

Author(s):

Christopher T Coey ◽

David J. Clark

Keyword(s):

Gene Regulation ◽

Transcription Factor ◽

Binding Sites ◽

Yeast Genome ◽

High Affinity ◽

First Approximation ◽

Genome Wide ◽

Insight Into

Sequence-specific DNA-binding transcription factors are central to gene regulation. They are often associated with consensus binding sites that predict far more genomic sites than are bound in vivo. One explanation is that most sites are blocked by nucleosomes, such that only sites in nucleosome-depleted regulatory regions are bound. We compared the binding of the yeast transcription factor Gcn4 in vivo using published ChIP-seq data (546 sites) and in vitro, using a modified SELEX method ("G-SELEX"), which utilizes short genomic DNA fragments to quantify binding at all sites. We confirm that Gcn4 binds strongly to an AP-1-like sequence (TGACTCA) and weakly to half-sites. However, Gcn4 binds only some of the 1078 exact matches to this sequence, even in vitro. We show that there are only 166 copies of the high-affinity RTGACTCAY site (exact match) in the yeast genome, all occupied in vivo, largely independently of whether they are located in nucleosome-depleted or nucleosomal regions. Generally, RTGACTCAR/YTGACTCAY sites are bound much more weakly and YTGACTCAR sites are unbound, with biological implications for determining induction levels. We conclude that, to a first approximation, Gcn4 binding can be predicted using the high-affinity site, without reference to chromatin structure. We propose that transcription factor binding sites should be defined more precisely using quantitative data, allowing more accurate genome-wide prediction of binding sites and greater insight into gene regulation.

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Molecular Docking of Phytochemicals against Streptococcus mutans Virulence Targets: A Proteomic Insight into Drug Planning

10.5772/intechopen.101506 ◽

2022 ◽

Author(s):

Diego Romário da Silva ◽

Tahyná Duda Deps ◽

Otavio Akira Souza Sakaguchi ◽

Edja Maria Melo de Brito Costa ◽

Carlus Alberto Oliveira dos Santos ◽

...

Keyword(s):

Streptococcus Mutans ◽

Drug Targets ◽

Bioactive Molecules ◽

Target Proteins ◽

In Silico Study ◽

Target Action ◽

Atp Binding Protein ◽

Insight Into

Streptococcus mutans (S. mutans) is the most prevalent and most associated with dental caries. Here we aim to identify, through an in silico study, potential bioactive molecules against S. mutans. Twenty-four bioactive molecules with proven action against S. mutans were selected: 1-methoxyficifolinol; 5,7,2′,4′-tetrahydroxy-8-lavandulylflavanone (sophoraflavanone G); 6,8-diprenylgenistein; apigenin; artocarpesin; artocarpin; darbergioidin; dihydrobiochanin A; dihydrocajanin (5,2′,4′-trihydroxy-7-methoxyisoflavanone); erycristagallin; Erystagallin; ferreirin; fisetin; kaempferol; licoricidin; licorisoflavan A; licorisoflavan C; licorisoflavan E; luteolin (3′,4′,5,7-tetrahydroxyflavone); malvidin-3,5-diglucoside; myricetin; orientanol B; quercetin; and quercitrin. Moreover, we selected nine important target proteins for the virulence of this microorganism to perform as drug targets: antigen I/II (region V) (PDB: 1JMM); Antigen I/II (carbox-terminal region) (PDB: 3QE5); Spap (PDB: 3OPU); UA159sp signaling peptide (PDB: 2I2J); TCP3 signaling peptide (PDB: 2I2H); ATP-binding protein ComA (PDB: 3VX4); glucanosucrase (PDB: 3AIC); dextranase (PDB: 3VMO), and Hemolysin (PDB: 2RK5). Five molecules were revealed to be the best ligands for at least three target proteins, highlighting the following compounds: 11 (erystagallin), 10 (erycristagallin), 1 (methoxyficifonilol), 20 (malvidin-3,5-diglucoside), and 2 (sophoraflavanone G), which indicates a possible multi-target action of these compounds. Therefore, based on these findings, in vitro and in vivo tests should be performed to validate the effectiveness of these compounds in inhibiting S. mutans virulence factors. Furthermore, the promising results of these assays will allow the incorporation of these phytoconstituents in products for oral use for the control of tooth decay.

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Conserved Region 2.1 of Escherichia coli Heat Shock Transcription Factor σ32 Is Required for Modulating both Metabolic Stability and Transcriptional Activity

Journal of Bacteriology ◽

10.1128/jb.186.22.7474-7480.2004 ◽

2004 ◽

Vol 186 (22) ◽

pp. 7474-7480 ◽

Cited By ~ 21

Author(s):

Mina Horikoshi ◽

Takashi Yura ◽

Sachie Tsuchimoto ◽

Yoshihiro Fukumori ◽

Masaaki Kanemori

Keyword(s):

Escherichia Coli ◽

Transcription Factor ◽

Heat Shock ◽

Transcriptional Activity ◽

Heat Shock Transcription Factor ◽

Metabolic Stability ◽

Wild Type ◽

Shock Proteins ◽

Insight Into

ABSTRACT Escherichia coli heat shock transcription factor σ32 is rapidly degraded in vivo, with a half-life of about 1 min. A set of proteins that includes the DnaK chaperone team (DnaK, DnaJ, GrpE) and ATP-dependent proteases (FtsH, HslUV, etc.) are involved in degradation of σ32. To gain further insight into the regulation of σ32 stability, we isolated σ32 mutants that were markedly stabilized. Many of the mutants had amino acid substitutions in the N-terminal half (residues 47 to 55) of region 2.1, a region highly conserved among bacterial σ factors. The half-lives ranged from about 2-fold to more than 10-fold longer than that of the wild-type protein. Besides greater stability, the levels of heat shock proteins, such as DnaK and GroEL, increased in cells producing stable σ32. Detailed analysis showed that some stable σ32 mutants have higher transcriptional activity than the wild type. These results indicate that the N-terminal half of region 2.1 is required for modulating both metabolic stability and the activity of σ32. The evidence suggests that σ32 stabilization does not result from an elevated affinity for core RNA polymerase. Region 2.1 may, therefore, be involved in interactions with the proteolytic machinery, including molecular chaperones.

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Loss of AML1/Runx1 accelerates the development of MLL-ENL leukemia through down-regulation of p19ARF

Blood ◽

10.1182/blood-2010-10-315440 ◽

2011 ◽

Vol 118 (9) ◽

pp. 2541-2550 ◽

Cited By ~ 24

Author(s):

Nahoko Nishimoto ◽

Shunya Arai ◽

Motoshi Ichikawa ◽

Masahiro Nakagawa ◽

Susumu Goyama ◽

...

Keyword(s):

Bone Marrow ◽

Transcription Factor ◽

Bone Marrow Cells ◽

Leukemic Cells ◽

Down Regulation ◽

Intact Cells ◽

Mechanistic Basis ◽

Insight Into ◽

Major Target

Abstract Dysfunction of AML1/Runx1, a transcription factor, plays a crucial role in the development of many types of leukemia. Additional events are often required for AML1 dysfunction to induce full-blown leukemia; however, a mechanistic basis of their cooperation is still elusive. Here, we investigated the effect of AML1 deficiency on the development of MLL-ENL leukemia in mice. Aml1 excised bone marrow cells lead to MLL-ENL leukemia with shorter duration than Aml1 intact cells in vivo. Although the number of MLL-ENL leukemia-initiating cells is not affected by loss of AML1, the proliferation of leukemic cells is enhanced in Aml1-excised MLL-ENL leukemic mice. We found that the enhanced proliferation is the result of repression of p19ARF that is directly regulated by AML1 in MLL-ENL leukemic cells. We also found that down-regulation of p19ARF induces the accelerated onset of MLL-ENL leukemia, suggesting that p19ARF is a major target of AML1 in MLL-ENL leukemia. These results provide a new insight into a role for AML1 in the progression of leukemia.

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Opportunities and Challenges in Functional Genomics Research in Osteoporosis: Report From a Workshop Held by the Causes Working Group of the Osteoporosis and Bone Research Academy of the Royal Osteoporosis Society on October 5th 2020

Frontiers in Endocrinology ◽

10.3389/fendo.2020.630875 ◽

2021 ◽

Vol 11 ◽

Author(s):

Jonathan H. Tobias ◽

Emma L. Duncan ◽

Erika Kague ◽

Chrissy L. Hammond ◽

Celia L. Gregson ◽

...

Keyword(s):

Bone Mass ◽

Functional Genomics ◽

Drug Targets ◽

Large Scale ◽

Functional Evaluation ◽

Genetic Associations ◽

Functional Studies ◽

Causal Pathways ◽

Genomics Research

The discovery that sclerostin is the defective protein underlying the rare heritable bone mass disorder, sclerosteosis, ultimately led to development of anti-sclerostin antibodies as a new treatment for osteoporosis. In the era of large scale GWAS, many additional genetic signals associated with bone mass and related traits have since been reported. However, how best to interrogate these signals in order to identify the underlying gene responsible for these genetic associations, a prerequisite for identifying drug targets for further treatments, remains a challenge. The resources available for supporting functional genomics research continues to expand, exemplified by “multi-omics” database resources, with improved availability of datasets derived from bone tissues. These databases provide information about potential molecular mediators such as mRNA expression, protein expression, and DNA methylation levels, which can be interrogated to map genetic signals to specific genes based on identification of causal pathways between the genetic signal and the phenotype being studied. Functional evaluation of potential causative genes has been facilitated by characterization of the “osteocyte signature”, by broad phenotyping of knockout mice with deletions of over 7,000 genes, in which more detailed skeletal phenotyping is currently being undertaken, and by development of zebrafish as a highly efficient additional in vivo model for functional studies of the skeleton. Looking to the future, this expanding repertoire of tools offers the hope of accurately defining the major genetic signals which contribute to osteoporosis. This may in turn lead to the identification of additional therapeutic targets, and ultimately new treatments for osteoporosis.

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Plasminogen Activation In Vivo upon Intravenous Infusion of DDAVP

Thrombosis and Haemostasis ◽

10.1055/s-0038-1648390 ◽

1992 ◽

Vol 67 (01) ◽

pp. 111-116 ◽

Cited By ~ 64

Author(s):

Marcel Levi ◽

Jan Paul de Boer ◽

Dorina Roem ◽

Jan Wouter ten Cate ◽

C Erik Hack

Keyword(s):

Monoclonal Antibodies ◽

Plasminogen Activator ◽

Plasma Levels ◽

Fold Increase ◽

Fibrinolytic System ◽

Plasminogen Activation ◽

Plasminogen Activator Activity ◽

Insight Into

SummaryInfusion of desamino-d-arginine vasopressin (DDAVP) results in an increase in plasma plasminogen activator activity. Whether this increase results in the generation of plasmin in vivo has never been established.A novel sensitive radioimmunoassay (RIA) for the measurement of the complex between plasmin and its main inhibitor α2 antiplasmin (PAP complex) was developed using monoclonal antibodies preferentially reacting with complexed and inactivated α2-antiplasmin and monoclonal antibodies against plasmin. The assay was validated in healthy volunteers and in patients with an activated fibrinolytic system.Infusion of DDAVP in a randomized placebo controlled crossover study resulted in all volunteers in a 6.6-fold increase in PAP complex, which was maximal between 15 and 30 min after the start of the infusion. Hereafter, plasma levels of PAP complex decreased with an apparent half-life of disappearance of about 120 min. Infusion of DDAVP did not induce generation of thrombin, as measured by plasma levels of prothrombin fragment F1+2 and thrombin-antithrombin III (TAT) complex.We conclude that the increase in plasminogen activator activity upon the infusion of DDAVP results in the in vivo generation of plasmin, in the absence of coagulation activation. Studying the DDAVP induced increase in PAP complex of patients with thromboembolic disease and a defective plasminogen activator response upon DDAVP may provide more insight into the role of the fibrinolytic system in the pathogenesis of thrombosis.

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