LC-MS-MS Determination of Cyclo{(2S)-2-amino-8-[(aminocarbonyl)hydrazono] decanoyl-1-l-tryptophyl-l-isoleucyl-(2R)-2-piperidinecarbonyl} a Novel Histone Deacetylase Inhibitor in Rat Serum

A rapid and sensitive liquid chromatography-tandem mass spectrometry assay was developed for the determination of a novel histone deacetylase inhibitor, cyclo{(2S)-2-amino-8-[(aminocarbonyl)hydrazono]decanoyl-1-l-tryptophyl-l-isoleucyl-(2R)-2-piperidinecarbonyl} (SD-2007), in rat serum. The mobile phase consisted of acetonitrile and ammonium formate (10 mM) (85:15 v/v), and the flow rate was 0.25 mL min⁻¹. Chromatographic separations were achieved by isocratic elution on a C₁₈ column. Multiple reaction monitoring was based on the transition of m/z = 681.8 → 83.6 for SD-2007 and 372.1 → 176.1 for trazodone (internal standard). A linearity was observed over a concentration range from 2 to 1,000 ng mL⁻¹ (r ² > 0.999), with the lower limit of quantification at 2 ng mL⁻¹ with 100 μL of rat serum. The mean intra- and inter-day assay accuracy ranged from 98.5–109.7% to 95.2–102.7%, respectively, and the mean intra- and inter-day precision was between 4.3–11.3% and 2.9–13.3%. The developed assay was applied to a pharmacokinetic study of SD-2007 in rats after intravenous injection (dose 4 mg kg⁻¹).     

Development and validation of a LC‐MS assay for the quantification of ikh12 a novel anti‐tumor candidate in rat plasma and tissues and its application in a pharmacokinetic study

IKH12 is a novel histone deacetylase 6 selective inhibitor. A rapid and sensitive liquid chromatography tandem mass spectrometry method was developed and validated for the quantification of IKH12 in rat plasma and tissue with kendine 91 as internal standard (IS). The samples were prepared by liquid–liquid extraction with tert‐butyl methyl ether. The chromatographic separation was accomplished by using a Zorbax Extend C₁₈ 4.6 × 150 mm, 5 µm column, with a mobile phase consisting of methanol and 0.1% formic acid (75:25 v/v). Multiple reaction monitoring, using electrospray ionization in positive ion mode, was employed to quantitatively detect IKH12 and IS. The monitored transitions were set at m/z 418 → 252 and 444 → 169 for IKH12 and kendine 91, respectively. The calibration curve was linear over the concentration range 2–1000 ng mL^?1. The intra‐ and inter‐assay precision and accuracy of the quality controls and the limit of quantification were satisfactory in all cases (according to European Medicines Agency guidelines). Stability studies showed that plasma samples were stable in the chromatography rack for 24 h and at ?80 °C for 2 months and also after three freeze–thaw cycles. This method was successfully applied to a pharmacokinetic study of IKH12 in rat. Copyright © 2015 John Wiley & Sons, Ltd.     

Dynamics simulation on the flexibility and backbone motions of HP1 chromodomain bound to free and lysine 9‐methylated histone H3 tails

Histone methylation has emerged as a central epigenetic modification with both activating and repressive roles in eukaryotic chromatin. Drosophila HP1 (heterochromatin‐associated protein 1) is one of the chromodomain proteins that contain the essential aromatic residues as the recognition pocket for lysine methylated histone H3 tail. The aromatic cage indicates that the complex of chromodomain protein binding lysine methylated histone H3 tail can be seen as a typical host–guest system between protein and protein. About 10‐ns molecular dynamics simulations have been carried out in this study to examine how the presence of mono‐, trimethylated lysine 9 histone H3 tail (Me1K9, Me3K9 H3) influences the motions of HP1 protein receptor. The study shows that the conformation of HP1 protein free of H3 tail easily changes, whereas that of HP1 protein bound to methylated H3 tail does not. But the conformation of inserted Me1K9 H3 changes obviously as the Me1K recognition makes hydrogen‐bonded interactions associated with the aromatic cage even more unstable than those in free HP1 protein. The conformational change of Me1K9 H3 is correlated with the motions of HP1 protein. As the recognition factor going from Me1K to Me3K produces a more favorable interaction for aromatic ring, hydrogen‐bonded interactions associated with aromatic cage in Me3K9 H3‐HP1 complex were observed to be much more stable than those in Me1K9 H3‐HP1 complex and free HP1. Because of correlation, the flexibility of Me3K9 H3 decreases. The simulations indicate that both the MeK and the surrounding histone tail sequence are necessary features of recognition which significantly affect the flexibility and backbone motions of HP1 chromodomain. These findings confirm a regulatory mechanism of protein–protein interactions through a trimethylated post‐translational modification. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Profiling of Substrates for Zinc-dependent Lysine Deacylase Enzymes: HDAC3 Exhibits Decrotonylase Activity In Vitro

Systematic screening of the activities of the eleven human zinc-dependent lysine deacylases against a series of fluorogenic substrates as well as kinetic evaluation revealed substrates for screenings of histone deacetylases HDAC10 and HDAC11 at reasonably low enzyme concentrations. Furthermore, HDAC3 in complex with nuclear receptor corepressor?1 (HDAC3-NCoR1) was shown to harbor decrotonylase activity in?vitro.     

应用光学生物传感器测定DNA与组蛋白H1的结合常数

用一种新的基于共振镜技术(resonant mirror)的IAsys光生物传感器分别测定了小牛胸腺DNA(ctDNA),鲑鱼精DNA(hsDNA),pUC-18质粒DNA与组蛋白H1相互作用的结合和解离的动力学速率常数(ka,kd)和解离平衡常数(KD).结果表明ctDNA与H1的结合作用最强,其KD值为5.44×10-7mol.L-1,hsDNA,pUC-18质粒DNA与组蛋白H1的KD值分别为73.34×10-7,67.93×10-7mol.L-1.     

Histone deacetylase inhibitor induced the production of three novel prenylated tryptophan analogs in the entomopathogenic fungus, Torrubiella luteorostrata

Suberoyl bis-hydroxamic acid (SBHA), a histone deacetylase (HDAC) inhibitor, led to significant changes in the secondary metabolism of an entomopathogenic fungus, Torrubiella luteorostrata, and induced the production of three new prenylated tryptophan analogs, luteorides A-C (1-3). The structures are characterized by the presence of an (E)-oxime group, which is an unusual functional group in natural products, and a 3-methylbuta-1,3-dienyl unit as a common substituent. The method of culturing entomopathogenic fungi in the presence of HDAC inhibitors, such as SBHA, is convenient and attractive for obtaining novel secondary metabolites.     

Comprehensive Profiling for Histone H4of Human Liver Cells Using High Resolution LTQ-Orbitrap Mass Spectrometry

The post translational modifications of histone variants are playing an important role in the structure of chro‐ matin, the regulation of gene activities and the diagnosis of diseases, and conducting in‐depth researches and discovering new sites depend on new and rational analytical methods to some extent. In this work, the combinatorial method of high resolution LTQ‐Orbitrap mass spectrometry and multiple enzymes was employed to identify the post translational modifications (PTMs) of histone H4 of human liver cells. The novel methylation site, argnine 67 (R 67), was observed besides some sites reported previously such as lysine 31 (K 31), lysine 44 (K 44), argnine 55 (R 55) and lysine 59 (K 59) in the global domain. Meanwhile, various combinations of acetylation of lysine 5 (K 5), lysine 8 (K 8), lysine 12 (K 12), lysine 16 (K 16) and methylation of lysine 20 (K 20) in the NH₂‐terminal tails were also identified after the LC‐MS/MS analysis of trypsin, Arg‐C, Glu‐C and chymotrypsin digests.