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3D-QSAR of histone deacetylase inhibitors as anticancer agents by genetic function approximation

Fri, 01 Dec 2006 00:00:00 GMT

Title: 3D-QSAR of histone deacetylase inhibitors as anticancer agents by genetic function approximation Authors: Wagh, Nilesh K; Deokar, Hemantkumar S; Juvale, Dhanshri C; Kadam, Shivajirao S; Kulkarni, Vithal M Abstract: Histone deacetylases (HDACs) playa critical role in gene transcription and are implicated in cancer therapy and other diseases. Inhibitors of HDACs induce cell differentiation and suppress cell proliferation in the tumor cells. Although many such inhibitors have been designed and synthesized, but selective inhibitors for HDAC isoforms are lacking. Various hydroxamic acid analogues have been reported as HDAC inhibitors. Here, we report a three-dimensional quantitative structure-activity relationship (3D-QSAR) study performed using genetic function approximation (GFA) for this class of molecules. QSAR models were generated using a training set of 39 molecules and the predictive ability of final model was assessed using a test set of 17 molecules. The internal consistency of the final QSAR model was 0.712 and showed good external predictivity of 0.585. The results of the present QSAR study indicated that molecular shape analysis (MSA), thermodynamic and structural descriptors are important for inhibition of HDACs. Page(s): 360-371

Purification and characterization of trehalose-6-phosphate synthase from Saccharomycopsis fibuligera A11

Sun, 01 Oct 2006 00:00:00 GMT

Title: Purification and characterization of trehalose-6-phosphate synthase from Saccharomycopsis fibuligera A11 Authors: Liang, Likun; Chi, Zhenming; Gao, Lingmei; Ma, Liyan Abstract: Mutant A11, a mutant of Saccharomycopsis fibuligera Sdu with low acid and neutral trehalase was found to accumulate over 18% (w/w) trehalose from starch in its cells. In this study, trehalose-6-phosphate synthase (Tps1) was purified to homogeneity from this mutant, with a 30-fold increase in the specific enzyme activity, as compared to the concentrated cell-free extract, from initial cells. The molecular mass of the purified enzyme as determined by SDS-PAGE was 66 kDa. The optimum pH and temperature of the purified enzyme were 6.6 and 37°C, respectively. The enzyme was activated by Ca²⁺, K⁺ and Mg²⁺, with K⁺ showing the highest activation at 35 mM. On the other hand, Mn²⁺, Cu²⁺, Fe³⁺, Hg²⁺ and Co²⁺ inhibited the enzyme. The enzyme was also strongly inhibited by protease inhibitors such as iodoacetic acid, EOTA and PMSF. Page(s): 289-294

Characterization of carotenoid hydroxylase gene promoter in Haematococcus pluvialis

Sun, 01 Oct 2006 00:00:00 GMT

Title: Characterization of carotenoid hydroxylase gene promoter in Haematococcus pluvialis Authors: Meng, C X; Wei, W; Su, Z-L; Qin, S Abstract: Astaxanthin, a high-value ketocarotenoid is mainly used in fish aquaculture. It also has potential in human health due to its higher antioxidant capacity than β-carotene and vitamin E, The unicellular green alga Haematococcus pluvialis is known to accumulate astaxanthin in response to environmental stresses, such as high light intensity and salt stress. Carotenoid hydroxylase plays a key role in astaxanthin biosynthesis in H. pluvialis. In this paper, we report the characterization of a promoter-like region (-378 to -22 bp) of carotenoid hydroxylase gene by cloning, sequence analysis and functional verification of its 919 bp 5'-flanking region in H. pluvialis. The 5’-flanking region was characterized using micro-particle bombardment method and transient expression of LacZ reporter gene. Results of sequence analysis showed that the 5’-flanking region might have putative cis-acting elements, such as ABA (abscisic acid)-responsive element (ABRE), Crepeat/ dehydration responsive element (C-repeat/DRE), ethylene-responsive element (ERE), heat-shock element (HSE), wound-responsive element (WUN-motif), gibberellin-responsive element (P-box), MYB-binding site (MBS) etc., except for typical TATA and CCAAT boxes. Results of 5' deletions construct and β-galactosidase assays revealed that a highest promoter-like region might exist from -378 to -22 bp and some negative regulatory elements might lie in the region from -919 to -378 bp. Results of site-directed mutagenesis of a putative C-repeat/DRE and an ABRE-like motif in the promoterlike region (-378 to -22 bp) indicated that the putative C-repeat/DRE and ABRE-like motif might be important for expression of carotenoid hydroxylase gene. Page(s): 284-288

Iterative ACORN as a high throughput tool in structural genomics

Tue, 01 Aug 2006 00:00:00 GMT

Title: Iterative ACORN as a high throughput tool in structural genomics Authors: Selvanayagam, S; Velmurugan, D; Yamane, T Abstract: High throughput macromolecular structure determination is very essential in structural genomics as the available number of sequence information far exceeds the number of available 3D structures. ACORN, a freely available resource in the CCP4 suite of programs is a comprehensive and efficient program for phasing in the determination of protein structures, when atomic resolution data are available. ACORN with the automatic model-building program ARP/wARP and refinement program REFMAC is a suitable combination for the high throughput structural genomics. ACORN can also be run with secondary structural elements like helices and sheets as inputs with high resolution data. In situations, where ACORN phasing is not sufficient for building the protein model, the fragments (incomplete model/dummy atoms) can again be used as a starting input. Iterative ACORN is proved to work efficiently in the subsequent model building stages in congerin (PDB-ID: lis3) and catalase (PDB-ID: 1gwe) for which models are available. Page(s): 211-216