Analysis and modeling of mycolyl-transferases in the CMN group

Mycolyl-transferases are a family of proteins that are specifically present in the CMN (Corynebacterium, Mycobacterium and Nocardia) genera and are responsible for the synthesis of cell wall components. We modeled the three-dimensional structures of mycolyl-transfersases from Corynebacterium and Nocardia using homology modeling methods based on the crystal structures of mycolyl-transferases from M. tuberculosis. Comparison of the models revealed significant differences in their substrate binding site. Some mycolyl-transferases identified by the following Gene Ids: Nfa25110, Nfa45560, Nfa7210, Nfa38260, Nfa32420, Nfa23770, Nfa43800, Nfa30260, Dip0365, Ncgl0987, Ce1488, Ncgl0885, Ce0984, Ncgl2101, Ncgl0336, Ce0356 are associated with a relatively larger substrate binding site and amino acid residue mutations (D40N, R43D/G, S236N/A) are likely to affect binding to trehalose.     

Inhibitory effect of β-diketones and their metal complexes on TNF-α induced expression of ICAM-1 on human endothelial cells

Recent reports show that the natural β-diketone curcumin displays important biological properties regarding the intercellular adhesion molecule-1 (ICAM-1), which plays a critical role in the immune responses and inflammation. In this study the ICAM-1 inhibitory activity of β-diketone compounds, which are curcumin models lacking aromatic peripheral hydroxyl and methoxy groups, along with some metal derivatives is investigated. β-Diketones are systematically more active than metal complexes and the best obtained inhibition is 75% for both groups. The best inhibitors are 4-benzoyl-3-methyl-1-phenyl-pyrazol-5-one (HQ^Ph) among the ligands, and sodium benzoylacetonato among metal derivatives. These results appear in line with the reported antitumor activity of related species. Since 4-acyl-5-pyrazolones posses four tautomeric forms, those corresponding to HQ^Ph were investigated using density functional theory. Docking of all HQ^Ph tautomers on ICAM-1 protein was performed suggesting one keto-enol form favored to act in biological environment.     

Development and characterization of lysine based tripeptide analogues as inhibitors of Sir2 activity

Sirtuins are NAD⁺ dependent deacetylases that modulate various essential cellular functions. Development of peptide based inhibitors of Sir2s would prove useful both as pharmaceutical agents and as effectors by which downstream cellular alterations can be monitored. Click chemistry that utilizes Huisgen’s 1,3-dipolar cycloaddition permits attachment of novel modifications onto the side chain of lysine. Herein, we report the synthesis of peptide analogues prepared using click reactions on Nε-propargyloxycarbonyl protected lysine residues and their characterization as inhibitors of Plasmodium falciparum Sir2 activity. The peptide based inhibitors exhibited parabolic competitive inhibition with respect to acetylated-peptide substrate and parabolic non-competitive inhibition with NAD⁺ supporting the formation of EI₂ and E·NAD⁺·I₂ complexes. Cross-competition inhibition analysis with the non-competitive inhibitor nicotinamide (NAM) ruled out the possibility of the NAM-binding site being the second inhibitor binding site, suggesting the presence of a unique alternate pocket accommodating the inhibitor. One of these compounds was also found to be a potent inhibitor of the intraerythrocytic growth of P. falciparum with 50% inhibitory concentration in the micromolar range.     

H2SO4-silica-promoted 'on-column' removal of benzylidene, isopropylidene, trityl and tert-butyldimethylsilyl groups

H₂SO₄-silica-promoted removal of benzylidene, isopropylidene, trityl and tert-butyldimethylsilyl groups from sugar derivatives was accomplished by following an ‘on-column’ protocol in a virtually waste-free condition.     

Molecular basis of anticlastogenic potential of vanadium in vivo during the early stages of diethylnitrosamine-induced hepatocarcinogenesis in rats

Carcinogen-induced DNA base modification and subsequent DNA lesions are the critical events for the expression of premalignant phenotype of the cell. We have therefore investigated the chemopreventive efficacy of a vanadium salt against diethylnitrosamine (DEN)-induced early DNA and chromosomal damages in rat liver. Hepatocarcinogenesis was induced in male Sprague-Dawley rats with a single, necrogenic, intraperitoneal injection of DEN (200mg/kg body weight). 8-Hydroxy-2'-deoxyguanosines (8-OHdGs), strand-breaks and DNA-protein crosslinks (DPCs) were measured by HPLC, comet assay and spectrofluorimetry, respectively. There was a significant and steady elevation of modified bases 8-OHdGs along with substantial increments of the extent of single-strand-breaks (SSBs), DPCs and chromosomal aberrations (CAs) following DEN exposure. Supplementation of vanadium as ammonium metavanadate (NH(4)VO(3), +V oxidation state) at a dose of 0.5ppm in terms of the salt weight throughout the experiment abated the formations of 8-OHdGs (P<0.0001; 79.54%), tailed DNA (P<0.05; 31.55%) and length:width of DNA mass (P<0.02; 61.25%) in preneoplastic rat liver. Vanadium treatment also inhibited DPCs (P<0.0001; 58.47%) and CAs (P<0.001; 45.17%) studied at various time points. The results indicate that the anticlastogenic potential of vanadium in vivo might be due to the observed reductions in liver-specific 8-OHdGs, SSBs and/or DPCs by this trace metal. We conclude that, vanadium plays a significant role in limiting DEN-induced genotoxicity and clastogenicity during the early stages of hepatocarcinogenesis in rats.     

Further delineation of hydrophobic binding sites in dopamine D2/D3 receptors for N-4 substituents on the piperazine ring of the hybrid template 5/7-{[2-(4-aryl-piperazin-1-yl)-ethyl]-propyl-amino}-5,6,7,8-tetrahydro-naphthalen-2-ol

Here we report a structure–activity relationship (SAR) study of analogues of 5/7-{[2-(4-aryl-piperazin-1-yl)-ethyl]-propyl-amino}-5,6,7,8-tetrahydro-naphthalen-2-ol. Our SAR is focused on introduction of various substitutions in the piperazine ring of the hybrid template. The goal behind this study is to delineate the nature of the binding pocket for N-aryl substitution in the piperazine ring by observing the effect of various hydrophobic and other heteroaromatic substitutions on binding affinity (K_i), as measured with tritiated spiperone and HEK-293 cells expressing either D₂ or D₃ receptors. Functional activity of selected compounds was assessed with the GTPγS binding assay. Compound 8d was the most selective for the D₃ receptor in the spiperone binding assay. An interesting similarity in binding affinity was observed between isoquinoline derivative D-301 and the 2-substituted pyridine derivative 8d, suggesting the importance of relative spatial relationships between the N-atom of the ligand and the molecular determinants of the binding pocket in D₂/D₃ receptors. Functional activity assays demonstrated high potency and selectivity of (+)-8a and (?)-28b (D₂/D₃ (ratio of EC₅₀): 105 and 202, respectively) for the D₃ receptor and both compounds were more selective compared to the reference drug ropinirole (D₂/D₃ (ratio of EC₅₀): 29.5).     

Unusual fluorescence of W168 in Plasmodium falciparum triosephosphate isomerase, probed by single-tryptophan mutants.

Plasmodium falciparum triosephosphate isomerase (PfTIM) contains two tryptophan residues, W11 and W168. One is positioned in the interior of the protein, and the other is located on the active-site loop 6. Two single-tryptophan mutants, W11F and W168F, were constructed to evaluate the contributions of each chromophore to the fluorescence of the wild-type (wt) protein and to probe the utility of the residues as spectroscopic reporters. A comparative analysis of the fluorescence spectra of PfTIMwt and the two mutant proteins revealed that W168 possesses an unusual, blue-shifted emission (321 nm) and exhibits significant red-edge excitation shift of fluorescence. In contrast, W11 emits at 332 nm, displays no excitation dependence of fluorescence, and behaves like a normal buried chromophore. W168 has a much shorter mean lifetime (2.7 ns) than W11 (4.6 ns). The anomalous fluorescence properties of W168 are abolished on unfolding of the protein in guanidinium chloride (GdmCl) or at low pH. Analysis of the tryptophan environment using a 1.1-A crystal structure established that W168 is rigidly held by a complex network of polar interactions including a strong hydrogen bond from Y164 to the indole NH group. The environment is almost completely polar, suggesting that electrostatic effects determine the unusually low emission wavelength of W168. To our knowledge this is a unique observation of a blue-shifted emission from a tryptophan in a polar environment in the protein. The wild-type and mutant proteins show similar levels of enzymatic activity and secondary and tertiary structure. However, the W11F mutation appreciably destabilizes the protein to unfolding by urea and GdmCl. The fluorescence of W168 is shown to be extremely sensitive to binding of the inhibitor, 2-phosphoglycolic acid.     

Aromatic interactions in tryptophan-containing peptides: crystal structures of model tryptophan peptides and phenylalanine analogs.

The crystal structures of the peptides, Boc-Leu-Trp-Val-OMe (1), Ac-Leu-Trp-Val-OMe (2a and 2b), Boc-Leu-Phe-Val-OMe (3), Ac-Leu-Phe-Val-OMe (4), and Boc-Ala-Aib-Leu-Trp-Val-OMe (5) have been determined by X-ray diffraction in order to explore the nature of interactions between aromatic rings, specifically the indole side chain of Trp residues. Peptide 1 adopts a type I beta-turn conformation stabilized by an intramolecular 4-->1 hydrogen bond. Molecules of 1 pack into helical columns stabilized by two intermolecular hydrogen bonds, Leu(1)NH...O(2)Trp(2) and IndoleNH...O(1)Leu(1). The superhelical columns further pack into the tetragonal space group P4(3) by means of a continuous network of indole-indole interactions. Peptide 2 crystallizes in two polymorphic forms, P2(1) (2a) and P2(1)2(1)2(1) (2b). In both forms, the peptide backbone is extended, with antiparallel beta-sheet association being observed in crystals. Extended strand conformations and antiparallel beta-sheet formation are also observed in the Phe-containing analogs, Boc-Leu-Phe-Val-OMe (3) and Ac-Leu-Phe-Val-OMe (4). Peptide 5 forms a short stretch of 3(10)-helix. Analysis of aromatic-aromatic and aromatic-amide interactions in the structures of peptides, 1, 2a, 2b are reported along with the examples of 14 Trp-containing peptides from the Cambridge Crystallographic Database. The results suggest that there is no dramatic preference for a preferred orientation of two proximal indole rings. In Trp-containing peptides specific orientations of the indole ring, with respect to the preceding and succeeding peptide units, appear to be preferred in beta-turns and extended structures.