Histone Deacetylase Inhibitors: Structure-Based Modeling and Isoform-Selectivity Prediction

An enhanced version of comparative binding energy (COMBINE) analysis, named COMBINEr, based on both ligand-based and structure-based alignments has been used to build several 3-D QSAR models for the eleven human zinc-based histone deacetylases (HDACs). When faced with an abundance of data from diverse structure–activity sources, choosing the best paradigm for an integrative analysis is difficult. A common example from studies on enzyme–inhibitors is the abundance of crystal structures characterized by diverse ligands complexed with different enzyme isoforms. A novel comprehensive tool for data mining on such inhomogeneous set of structure–activity data was developed based on the original approach of Ortiz, Gago, and Wade, and applied to predict HDAC inhibitors’ isoform selectivity. The COMBINEr approach (apart from the AMBER programs) has been developed to use only software freely available to academics

Histone Deacetylase Inhibitors: Structure-Based Modeling and Isoform-Selectivity Prediction

An enhanced version of comparative binding energy (COMBINE) analysis, named COMBINEr, based on both ligand-based and structure-based alignments has been used to build several 3-D QSAR models for the eleven human zinc-based histone deacetylases (HDACs). When faced with an abundance of data from diverse structure–activity sources, choosing the best paradigm for an integrative analysis is difficult. A common example from studies on enzyme–inhibitors is the abundance of crystal structures characterized by diverse ligands complexed with different enzyme isoforms. A novel comprehensive tool for data mining on such inhomogeneous set of structure–activity data was developed based on the original approach of Ortiz, Gago, and Wade, and applied to predict HDAC inhibitors’ isoform selectivity. The COMBINEr approach (apart from the AMBER programs) has been developed to use only software freely available to academics

Histone Deacetylase Inhibitors: Structure-Based Modeling and Isoform-Selectivity Prediction

An enhanced version of comparative binding energy (COMBINE) analysis, named COMBINEr, based on both ligand-based and structure-based alignments has been used to build several 3-D QSAR models for the eleven human zinc-based histone deacetylases (HDACs). When faced with an abundance of data from diverse structure–activity sources, choosing the best paradigm for an integrative analysis is difficult. A common example from studies on enzyme–inhibitors is the abundance of crystal structures characterized by diverse ligands complexed with different enzyme isoforms. A novel comprehensive tool for data mining on such inhomogeneous set of structure–activity data was developed based on the original approach of Ortiz, Gago, and Wade, and applied to predict HDAC inhibitors’ isoform selectivity. The COMBINEr approach (apart from the AMBER programs) has been developed to use only software freely available to academics

<i>Bmp6</i> Expression in Murine Liver Non Parenchymal Cells: A Mechanism to Control their High Iron Exporter Activity and Protect Hepatocytes from Iron Overload?

<div><p><i>Bmp6</i> is the main activator of hepcidin, the liver hormone that negatively regulates plasma iron influx by degrading the sole iron exporter ferroportin in enterocytes and macrophages. <i>Bmp6</i> expression is modulated by iron but the molecular mechanisms are unknown. Although hepcidin is expressed almost exclusively by hepatocytes (HCs), <i>Bmp6</i> is produced also by non-parenchymal cells (NPCs), mainly sinusoidal endothelial cells (LSECs). To investigate the regulation of <i>Bmp6</i> in HCs and NPCs, liver cells were isolated from adult wild type mice whose diet was modified in iron content in acute or chronic manner and in disease models of iron deficiency (<i>Tmprss6</i> KO mouse) and overload (<i>Hjv</i> KO mouse). With manipulation of dietary iron in wild-type mice, <i>Bmp6</i> and <i>Tfr1</i> expression in both HCs and NPCs was inversely related, as expected. When hepcidin expression is abnormal in murine models of iron overload (<i>Hjv</i> KO mice) and deficiency (<i>Tmprss6</i> KO mice), <i>Bmp6</i> expression in NPCs was not related to <i>Tfr1</i>. Despite the low <i>Bmp6</i> in NPCs from <i>Tmprss6</i> KO mice, <i>Tfr1</i> mRNA was also low. Conversely, despite body iron overload and high expression of <i>Bmp6</i> in NPCs from <i>Hjv</i> KO mice, <i>Tfr1</i> mRNA and protein were increased. However, in the same cells ferritin L was only slightly increased, but the iron content was not, suggesting that <i>Bmp6</i> in these cells reflects the high intracellular iron import and export. We propose that NPCs, sensing the iron flux, not only increase hepcidin through <i>Bmp6</i> with a paracrine mechanism to control systemic iron homeostasis but, controlling hepcidin, they regulate their own ferroportin, inducing iron retention or release and further modulating <i>Bmp6</i> production in an autocrine manner. This mechanism, that contributes to protect HC from iron loading or deficiency, is lost in disease models of hepcidin production.</p></div

Total iron quantification in liver cells from wild type and <i>Hjv</i> KO mice.

<p>HCs: hepatocytes. KCs: kupffer cells. LSECs: liver sinusoidal endothelial cells.</p><p>*: <i>Hjv</i> KO vs wild type <i>P</i> = 0.036.</p><p>^ns: <i>Hjv</i> KO vs wild type non significant.</p><p>Total iron quantification in liver cells from wild type and <i>Hjv</i> KO mice.</p

<i>Bmp6</i> and <i>Tfr1</i> expression levels in acute dietary iron changes.

<p><i>Bmp6</i> (<b>A, C, E</b>) and <i>Tfr1</i> (<b>B, D, F</b>) mRNA expression was evaluated by qRT-PCR in HCs (<b>A, B</b>), KCs (<b>C, D</b>) and LSECs (<b>E, F)</b> isolated from 4–7 mice/group. <i>Hprt1</i> was used as housekeeping gene. mRNA expression ratio was normalized to control (ID-1 day) mean value set to 1. Error bars indicate SE. *: P<. 05; **: P<. 01; ***: P<. 001; ns: not significant.</p

<i>Bmp6</i> and <i>Tfr1</i> expression in chronic dietary iron changes.

<p><i>Bmp6</i> (<b>A, C, E</b>) and <i>Tfr1</i> (<b>B, D, F</b>) mRNA expression was evaluated by qRT-PCR in isolated HCs (<b>A, B</b>), KCs (<b>C, D</b>) and LSECs (<b>E, F</b>) from 4–12 mice/group. mRNA expression ratio was normGalized relative to housekeeping <i>Hprt1</i>. Mean control value of IB-treated mice was set to 1. Error bars indicate SE. *: P<. 05; **: P<. 01; ***: P<. 001; ns: not significant.</p

<i>Bmp6</i> and <i>Tfr1</i> expression in <i>Hjv</i> KO mice.

<p><i>Bmp6</i> (<b>A, C, E</b>) and <i>Tfr1</i> (<b>B, D, F</b>) mRNA expression was evaluated in liver cells isolated from 6–10 mice by qRT-PCR, using <i>Hprt1</i> as the referred housekeeping gene. mRNA expression ratio was normalized to control wild type (wt) mean value set to 1. Error bars indicate SE. **: P<. 01; ***: P<. 001; ****: P<. 0001.</p