Synthesis and Preliminary Biological Study of Bisindolylmethanes Accessed by an Acid-Catalyzed Hydroarylation of Vinylindoles

An acid-catalyzed hydroarylation reaction of vinyl indoles is reported, which tolerates a wide range of heterocycles as the exogenous nucleophile such as indoles, pyrroles, and indolizines. The method rapidly accesses the biologically relevant bisindolylmethane scaffold in good to excellent yields. Evaluation of the biological activity of several synthesized analogues reveals cytotoxic activity against and selectivity for the MCF-7 breast cancer cell line.     

On the transferability of folding and threading potentials and sequence-independent filters for protein folding simulations

Significant progress has recently been made in de novo protein structure prediction. The Rosetta method by Baker and colleagues, which is based on the idea of assembling putative models from a library of k-mer fragments derived from known three-dimensional protein structures, proved to be particularly successful. Critical components of the Rosetta approach are various sequence-dependent as well as sequence-independent measures that are used to rank alternative models and to enhance sampling of native-like conformations. In the present work we revisit several sequence-independent filters that have been used to enhance the discrimination of native and native-like structures from misfolded structures, such as the overall compactness of the structure and its contact order. We also propose a novel sequence-independent filter, based on the shape of the mean inter-residue radial distribution function. Using the Rosetta, Park–Levitt and CASP4 sets of decoys it is shown that sequence-independent filters are in fact more successful in distinguishing native structures in Rosetta and CASP4 tests than commonly used knowledge-based pairwise potentials. The latter are typically designed to distinguish native structures in a population of well-folded alternatives, and they fail to discriminate between native-like and non-physically packed misfolded structures from Rosetta simulations. Moreover, a rigorous attempt to optimize pairwise potentials for recognition of homologous structures in threading by using a linear programming approach leads to further deterioration of performance in terms of recognition of native structures from the Rosetta set. These findings shed light onto the success of tailored scoring functions used in the Rosetta protocol and provide support for explicit inclusion of both sequence dependent and sequence independent measures in the design of scoring functions. A Web server that enables ranking of decoy structures according to sequence independent filters considered here is available at http://sift.chmcc.org.     

VUV photon induced fluorescence study of SF5CF3

The interaction of SF(5)CF(3) with vacuum-UV radiation has been investigated by photon induced fluorescence spectroscopy. Total fluorescence yield and dispersed fluorescence spectra of SF(5)CF(3) were recorded in the 200-1000 nm fluorescence window. In all cases, the fluorescence spectra resemble those of CF(3)X (X = H, F, Cl, and Br) molecules. At photon energies below 20 eV, the emission is attributed to the excited CF(3) and CF(2) fragments. The threshold for the CF(3) emission is 10.2 +/- 0.2 eV, giving an upper limit estimate for the SF(5)-CF(3) bond dissociation energy of 3.9 +/- 0.3 eV. The excitation functions of the CF(3) and CF(2) emissions were measured in the photon energy range 13.6-27.0 eV. The resonant structures observed in SF(5)CF(3) are attributed to electronic transitions from valence to Rydberg orbitals, following similar assignments in CF(3)X molecules. The photoabsorption spectrum of SF(5)CF(3) shows features at the same energies, indicating a strong contribution from Rydberg excitations.     

Viscoelastic properties of dendrimers in the melt from nonequlibrium molecular dynamics

The viscoelastic properties of dendrimers of generation 1-4 are studied using nonequilibrium molecular dynamics. Flow properties of dendrimer melts under shear are compared to systems composed of linear chain polymers of the same molecular weight, and the influence of molecular architecture is discussed. Rheological material properties, such as the shear viscosity and normal stress coefficients, are calculated and compared for both systems. We also calculate and compare the microscopic properties of both linear chain and dendrimer molecules, such as their molecular alignment, order parameters and rotational velocities. We find that the highly symmetric shape of dendrimers and their highly constrained geometry allows for substantial differences in their material properties compared to traditional linear polymers of equivalent molecular weight.     

Maximum feasibility guideline in the design and analysis of protein folding potentials

Protein folding potentials are expected to have the lowest energy for the native shape. The Linear Programming (LP) approach achieves exactly that goal for a training set, or indicates that this goal is impossible to obtain. If a solution cannot be found (i.e., the problem is infeasible) two possible routes are possible: (a) choosing a new functional form for the potential, (b) finding the best potential with a feasible subset of the data, and (or) detecting inconsistent subset of the data in the training set. Here, we explore option (b). A simple heuristic for finding an approximate solution to an infeasible set of linear inequalities is outlined. An approximately feasible solution is obtained iteratively, starting from a certain initial guess, by computing a series of analytic centers of the polyhedra defined by all the inequalities satisfied at the subsequent iterations. Standard interior point algorithms for Linear Programming can be used to compute efficiently the analytic center of a polyhedron. We demonstrate how this procedure can be used for the design of folding potentials that are linear in their parameters. The procedure shows an improvement in the quality of the potentials and sometimes points to flaws in the original data.     

Matrix-assisted laser desorption/ionization-mass spectrometry of cuticular lipid profiles can differentiate sex, age, and mating status of Anopheles gambiae mosquitoes

Malaria is a devastating mosquito-borne disease, which affects hundreds of millions of people each year. It is transmitted predominantly by Anopheles gambiae, whose females must be >10 days old to become infective. In this study, cuticular lipids from a laboratory strain of this mosquito species were analyzed using a mass spectrometry method to evaluate their utility for age, sex and mating status differentiation. Matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS), in conjunction with an acenaphthene/silver nitrate matrix preparation, was shown to be 100% effective in classifying A. gambiae females into 1, 7–10, and 14 days of age. MALDI-MS analysis, supported by multivariate statistical methods, was also effective in detecting cuticular lipid differences between the sexes and between virgin and mated females. The technique requires further testing, but the obtained results suggest that MALDI-MS cuticular lipid spectra could be used for age grading of A. gambiae females with precision greater than with other available methods.     

The effect of hydration on the photo-deactivation pathways of 4-aminopyrimidine

The influence of water on the photo-deactivation process of 4-aminopyrimidine has been investigated by means of microsolvation and continuum solvation models. Two- and four-water models were used for the former purpose. Vertical excitations, stationary points on the first excited singlet surface, conical intersections (minima on the crossing seam) and reaction paths have been investigated at the state-averaged complete active space self-consistent field (CASSCF) and multistate CAS perturbation theory to second order (MS-CASPT2) levels of theory. A destabilizing effect of 0.2–0.3 eV has been observed for nπ∗ states while the ππ∗ state is almost unaffected. The two-water model gives already a good representation of hydration effects, especially when combined with the continuum model. A small enhancement of energy barriers (∼0.1 eV) is observed leading to the conclusion that the photodynamics of 4-aminopyrimidine should be affected only little by these solvent effects.     

Theoretical contact angles on a nano-heterogeneous surface composed of parallel apolar and polar strips

Neumann-Good's parallel strip model (J. Colloid Interface Sci. 1972, 38, 341) was used to analyze the contact angle hysteresis for a liquid on a heterogeneous surface composed of alternatively aligned horizontal apolar (theta = 70 degrees ) and polar (theta = 0 degree ) strips. The critical size of the strip width, below which the contact angle hysteresis disappears, was determined on the basis of the analysis of the activation energy for wetting to be from 6 to 12 nm. This calculated value of the critical strip size is 1 order of magnitude smaller than that of 0.1 microm, which has been commonly considered as the limit of heterogeneity size causing the appearance of the contact angle hysteresis.     

Probability issues in molecular design: predictive and modeling ability in 3D-QSAR schemes

In the current work we investigated 3D-QSAR data by the use of the coupled leave-several-out (LSO) and leave-one-out (LOO) cross-validation (CV) procedures. We verified the above mentioned scheme using both simulated data and real 3D QSAR data describing a series of CoMFA steroids, heterocyclic azo dyes and styrylquinoline HIV integrase inhibitors. Unlike in standard analyses, this technique characterizes individual method not by a single performance metrics but screens a whole possible modeling space by sampling different molecules into the training and test sets, respectively. This allowed us for the discussion of the information included in the estimators validating cross-validation procedures, as well as the comparison of the efficiency of several 3D QSAR schemes, in particular, Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Surface Analysis (CoMSA). Moreover, it allows one to acquire some general knowledge about predictive and modeling ability in 3D QSAR method.     

Mass spectrometry of N-(Pyrimidin-2-yl)amino acids and their methyl esters

N(Pyrimidin-2-yl)-glycine, -alanine and -phenylalanine (1-3) and their methyl esters (4-6) were investigated using electron impact (EI) mass Spectrometry. The results showed that EI-induced decomposition occurs on the carboxylic group or involves the loss of R₂OH. In contrast to earlier investigations on N-(pyrimidin-4-yl)amino acids, elimination of water (in 1-3) or methanol (in 4-6) was found to be of EI-induced nature. The loss of 'COOH from M⁺ of ester 4 suggests the occurrence of a skeletal rearrangement leading to the isomeric N-methylamino acid.