Journal: Scientific Reports

Article Title: Novel small molecule 11 β -HSD1 inhibitor from the endophytic fungus Penicillium commune

doi: 10.1038/srep26418

Figure Lengend Snippet: ( A ) Compound 3 was observed to occupy the active site with significant scores of ICM docking score and IMC docking mfScore, and adopted a conformation similar to that of known inhibitors. ( B ) Compound 3 had the ability to form key hydrophobic interaction with residues Leu126, Tyr177, Tyr183, and Leu171.

Article Snippet: Using the Molsoft ICM method (ICM-Pro 3.8 molecular docking software), we optimized the geometry of compound 3 and determined the binding site with the lowest-energy and the most favorable orientation of the compound.

Techniques:

Journal:

Article Title: Histone deacetylase inhibitors stimulate mitochondrial HMG-CoA synthase gene expression via a promoter proximal Sp1 site

doi:

Figure Lengend Snippet: Mitochondrial HMG-CoA synthase, a target gene for HDAC inhibitors: TSA induces mitochondrial HMG-CoA synthase mRNA expression through mitochondrial HMG-CoA synthase promoter acetylation in the chromatin complex. (A) HT-29 and Caco-2 cells were treated with 0.3 µM TSA (+) or DMSO (–) for 24 h. The mitochondrial HMG-CoA synthase mRNA levels were analyzed by northern blot. Levels of 18S rRNA are also shown to correct for gel loading variation. (B) ChIPs were performed using chromatin isolated from HT-29 and CaCo-2 cells either treated with TSA (+) for 24 h or untreated (–). The chromatin preparations were immunoprecipitated with antibodies against acetylated histone H4 (α-AcH4) and analyzed by PCR to detect the HMG-CoA synthase promoter associated to acetylated histones. Aliquots of chromatin were also analyzed before immunoprecipitation (Input). Relative histone acetylation levels (Fold of acetylation) were determined by quantitation of PCR product using BIOPROFIL® image analysis software, BIO-1D (Vilber Lourmat) and by correction with the input data and represented as the ratio of relative acetylation in the presence versus the absence of TSA treatment. (C) ChIP assay of HDAC1 bound to endogenous mitochondrial HMG-CoA synthase promoter. CaCo-2 chromatin, isolated as described above, was immunoprecipitated with increasing amounts of anti-HDAC1 or preimmune serum (IgG). PCRs shown in (B) and (C) were performed with 5 µl of DNA and 30 cycles of amplification were used.

Article Snippet: Relative histone acetylation levels (Fold of acetylation) were determined by quantitation of PCR product using BIOPROFIL® image analysis software, BIO-1D (Vilber Lourmat) and by correction with the input data and represented as the ratio of relative acetylation in the presence versus the absence of TSA treatment. ( C ) ChIP assay of HDAC1 bound to endogenous mitochondrial HMG-CoA synthase promoter.

Techniques: Expressing, Northern Blot, Isolation, Immunoprecipitation, Quantitation Assay, Software, Amplification