Pharmacophore model of the quercetin binding site of the SIRT6 protein.

SIRT6 is a histone deacetylase that has been proposed as a potential therapeutic target for metabolic disorders and the prevention of age-associated diseases. We have previously reported on the identification of quercetin and vitexin as SIRT6 inhibitors, and studied structurally related flavonoids including luteolin, kaempferol, apigenin and naringenin. It was determined that the SIRT6 protein remained active after immobilization and that a single frontal displacement could correctly predict the functional activity of the immobilized enzyme. The previous study generated a preliminary pharmacophore for the quercetin binding site on SIRT6, containing 3 hydrogen bond donors and one hydrogen bond acceptor. In this study, we have generated a refined pharmacophore with an additional twelve quercetin analogs. The resulting model had a positive linear behavior between the experimental elution time verses the fit values obtained from the model with a correlation coefficient of 0.8456.

Searching for non-B DNA-forming motifs using nBMST (non-B DNA motif search tool).

This unit describes basic protocols on using the non-B DNA Motif Search Tool (nBMST) to search for sequence motifs predicted to form alternative DNA conformations that differ from the canonical right-handed Watson-Crick double-helix, collectively known as non-B DNA, and on using the associated PolyBrowse, a GBrowse-based genomic browser. The nBMST is a Web-based resource that allows users to submit one or more DNA sequences to search for inverted repeats (cruciform DNA), mirror repeats (triplex DNA), direct/tandem repeats (slipped/hairpin structures), G4 motifs (tetraplex, G-quadruplex DNA), alternating purine-pyrimidine tracts (left-handed Z-DNA), and A-phased repeats (static bending). The nBMST is versatile, simple to use, does not require bioinformatics skills, and can be applied to any type of DNA sequences, including viral and bacterial genomes, up to an aggregate of 20 megabasepairs (Mbp).

Allellic variants in regulatory regions of cyclooxygenase-2: association with advanced colorectal adenoma.

Cyclooxygenase 2 (Cox-2) is upregulated in colorectal adenomas and carcinomas. Polymorphisms in the Cox-2 gene may influence its function and/or its expression and may modify the protective effect of nonsteroidal anti-inflammatory drugs (NSAIDs), thereby impacting individuals' risk of developing colorectal cancer and response to prevention/intervention strategies. In a nested case-control study, four polymorphisms in the Cox-2 gene (two in the promoter, -663 insertion/deletion, GT/(GT) and -798 A/G; one in intron 5-5229, T/G; one in 3'untranslated region (UTR)-8494, T/C) were genotyped in 726 cases of colorectal adenomas and 729 age- and gender-matched controls in the prostate, lung, colorectal, and ovarian (PLCO) cancer screening trial. There was no significant association between the Cox-2 polymorphisms and adenoma development in the overall population. However, in males, the relatively rare heterozygous genotype GT/(GT) at -663 in the promoter and the variant homozygous genotype G/G at intron 5-5229 appeared to have inverse associations (odds ratio (OR)=0.59, confidence interval (CI): 0.34-1.02 and OR=0.48, CI: 0.24-0.99, respectively), whereas the heterozygous genotype T/C at 3'UTR-8494 had a positive association (OR=1.31, CI: 1.01-1.71) with adenoma development. Furthermore, the haplotype carrying the risk-conferring 3'UTR-8494 variant was associated with a 35% increase in the odds for adenoma incidence in males (OR=1.35, CI: 1.07-1.70), but the one with a risk allele at 3'UTR-8494 and a protective allele at intron 5-5229 had no effect on adenoma development (OR=0.85, CI: 0.66-1.09). Gender-related differences in adenoma risk were also noted with tobacco usage and protective effects of NSAIDs. Our analysis underscores the significance of the overall allelic architecture of Cox-2 as an important determinant for risk assessment.

Fuzzy structure-activity relationships.

While quantitative structure-activity relationships attempt to predict the numerical value of the activities, it is found that statistically good predictors do not always do a good job of qualitatively determining the activity. This study shows how Fuzzy classifiers can be used to generate Fuzzy structure-activity relationships which can more accurately determine whether or not a compound will be highly inactive, moderately inactive or active, or highly active. Four examples of these classifiers are presented and applied to a well-studied activity dataset.

Theoretical investigation of the role of clay edges in prebiotic peptide bond formation. II. Structures and thermodynamics of the activated complex species.

Amino acid activation by anhydride formation in model tetrahedral silicate and aluminate sites in clays and neutral phosphates have been studied by semi-empirical molecular orbital calculations. The results have been compared to previous ab initio studies on the reactant species and were found to be in good agreement. The geometries of all species were totally optimized and heats of formation obtained. Relative heats of formation of the anhydrides indicate the extent of anhydride formation to be A1 greater than Si greater than P which is the same order as the stability of hydrolysis. The relative efficacy of the anhydrides in promoting peptide bond formation has been evaluated using both thermodynamic and chemical reactivity criteria. Heats of reaction for model reactions were calculated from calculated enthalpies of formation of the products and reactants. The electrophilicity of the carbonyl carbon and the nucleophilicity of the oxygen were specifically used as indicators of chemical reactivity towards dipeptide formation by the activated amino acids. Our results indicate that if the reaction mechanism is dominated by the nucleophilic character of the oxygen, tetrahedral A1 sites should be more active than Si, and if the electrophilic character dominates, the order would be reversed.

A theoretical investigation of atmospheric sulfur chemistry. 1. The HSO/HOS energy separation and the heat of formation of HSO, HOS, and HS2.

The energy separation between the ground-state structures of HSO and HOS has been determined by using two independent ab initio methods. In the first method, the optimized geometry of all species was obtained at the HF/6-31G(d) level, as were harmonic vibrational frequencies for zero-point energy corrections. The energies were calculated by using fourth-order Moller-Plesset perturbation theory and a 6-31G(d,p) basis set. After corrections for extrapolation of the Moller-Plesset series to infinite order and extension of the basis set to include diffuse sp-, extra d-, and f-type Gaussian functions, the predicted energy separation, including zero-point vibrational effects, is 2.5 kcal/mol. HOS is the more stable isomer. The second method uses a double-zeta basis augmented with an extra set of p functions and two sets of d functions on the sulfur and oxygen atoms and a double-zeta + p basis on hydrogen. With this basis, equilibrium structures of HSO and HOS were obtained from MCSCF calculations; the energy separation between these structures was corrected by using large scale configuration interaction. In good agreement with the first method, HOS is the more stable isomer by 3.1 kcal/mol. Through calculation of the energy change in the reaction HO2 + XY --> O2 + HXY, the first method predicts the heats of formation of HXY = HSO, HOS, and HS2 to be -0.4, -2.9, and 26.7 kcal/mol, respectively.

Theoretical investigation of the role of clay edges in prebiotic peptide bond formation. I. Structures of acetic acid, glycine, H2SO4, H3PO4, Si(OH)4, Al(OH)4-.

Activation of amino acids appears to have played a crucial role in prebiotic peptide bond formation. As a model of this process in living systems, phosphates have been used as amino acid activators. The possible role of clay and other minerals has also been investigated. We are presently using ab initio methods to investigate the activation of amino acids by these agents, as an initial step in peptide bond formation. A model of this activation process is described by the reaction: ZCH2COOH + XO4Hn+1 --> ZCH2COOXO3Hn + H2O. The first step in such an investigation, reported here, was to determine the lowest energy structures of a suitable set of reactions. As initial models of amino acids, Z was chosen to be H and NH2, corresponding to acetic acid and glycine, respectively, XO4Hn+1 = H3PO4 represents a phosphate group, while Si(OH)4 describes an edge tetrahedral site of a clay mineral. Al(OH)4- was also included to represent tetrahedral edge site where the silicon is replaced by an aluminum. Finally, to complete the series XO4Hn+1, H2SO4 was added to the set of reactants. All species were optimized using the STO-3G and STO-3G* basis sets. For H3PO4 and Al(OH)4-, STO-3G* full optimizations were not possible. In these cases, certain torsional angles were optimized separately, then held at the optimized value, while the rest of the bond lengths and angles were optimized. All structures were compared to other calculations and to experimental geometries when available.