Nanoconfinement effects on hydrated excess protons in layered materials.

Thin water layers confined between surfaces are known for their surprising properties. Layered minerals, such as mackinawite, are naturally occurring systems where water is known to intercalate. Here we report, based on ab initio simulations, how excess protons can be hosted by the resulting nanostructured water film depending on the mackinawite interlayer distance. Even extreme nanoconfinement due to the mackinawite sheets is shown to not affect the dynamical nature of the topological defect, thus not localizing the excess protons but rather conserving the efficient structural (Grotthuss) diffusion process known in bulk water. Yet, depending on the width of the slit pore, the defect can bridge the bilayer water structure, thus forcing the excess proton into the water-depleted region between the bilayers.

Water confined between sheets of mackinawite FeS minerals.

Wet iron-sulfur minerals have been shown to be ideal environments to allow for simple chemical reactions to occur in nature, for instance, in the framework of prebiotic chemistry. Yet, not much is known about such water/mineral interfaces beyond those involving pyrite, FeS(2), which is, however, chemically rather inert. In contrast, mackinawite is chemically reactive and consists of a layered crystal structure comprising FeS sheets that can be easily cleaved. Here, the properties of water confined between such sheets in lamella-like setups is investigated in the spirit of surface science model systems. The properties of this intercalated water are found to depend significantly on the interlayer distance and change from "arrested water" (in the limit of small interlayer distances) to liquid-like behavior.

Antifungal activities of novel non-azole molecules against S. cerevisiae and C. albicans.

Because of the increasing number of immunocompromised patients and due to problems with antifungal treatment, especially with the most widely used antifungals, azoles, there is an urgent need for new, potent and safe antifungals with fewer cytochrome P450 (CYP)-mediated interactions with other drugs. In the present study, 54 novel non-azole molecules were selected with the help of molecular modelling and virtual molecule database screening to identify new fungistatic or fungicidic compounds with functional groups that would produce reactive intermediates killing the yeast cells. Database screening and selection of tested compounds were based on the construction of two pharmacophores and docking hits to the active site of the CYP51 homology model. Inhibition potency of the compounds was tested against Saccharomyces cerevisiae and/or Candida albicans. Two new structured compounds, 2-({4-[(2-cyanoethyl)(methyl) amino]benzylidene} amino)-5-(3,4-dimethoxyphenyl)-4-methylthiophene-3-carbonitrile and 2-[([1,1'-biphenyl]-4-ylmethylene)amino]-5-(3,4-dimethoxyphenyl)-4-methylthiophene-3-carbonitrile were discovered to have promising antifungal properties based on bioassays. Inhibition screen of human hepatic CYP enzymes revealed that these two compounds did not inhibit potently five human recombinant CYP enzymes. The results of this study indicate that the functional groups of the two compounds may produce reactive intermediates when located at the active site of CYP51.

Identification of novel CYP2A6 inhibitors by virtual screening.

The human CYP2A6 enzyme metabolises several xenobiotics including nicotine, the addictive component in tobacco. Reduced activity of CYP2A6, either for genetic reasons or by administering inhibitors of CYP2A6, reduces tobacco smoking. The aim was to design novel inhibitors of CYP2A6 using 3D-QSAR analysis combined with virtual screening. A 3D-QSAR model was utilised to identify the most important features of the inhibitors, and this knowledge was used to design inhibitors for CYP2A6. Chemical database screening yielded several potent inhibitor candidates such as alkylamine derivatives (compound no. 5, IC(50)=0.1 µM) and 1-benzothiophene-3-carbaldehyde that can be used as lead compounds in the development of drugs for smoking reduction therapy.

Peptide synthesis in aqueous environments: the role of extreme conditions and pyrite mineral surfaces on formation and hydrolysis of peptides.

A comprehensive study of free energy landscapes and mechanisms of COS-mediated polymerization of glycine via N-carboxy anhydrides (NCAs, "Leuchs anhydrides") and peptide hydrolysis at the water-pyrite interface at extreme thermodynamic conditions is presented. Particular emphasis is set on the catalytic effects of the mineral surface including the putative role of the ubiquitous sulfur vacancy defects. It is found that the mere presence of a surface is able to change the free energetics of the elementary reaction steps. This effect can be understood in terms of a reduction of entropic contributions to the reactant state by immobilizing the reactants and/or screening them from bulk water in a purely geometric ("steric") sense. Additionally, the pyrite directly participates chemically in some of the reaction steps, thus changing the reaction mechanism qualitatively compared to the situation in bulk water. First, the adsorption of reactants on the surface can preform a product-like structure due to immobilizing and scaffolding them appropriately. Second, pyrite can act as a proton acceptor, thus replacing water in this role. Third, sulfur vacancies are found to increase the reactivity of the surface. The finding that the presence of pyrite speeds up the rate-determining step in the formation of peptides with respect to the situation in bulk solvent while stabilizing the produced peptide against hydrolysis is of particular interest to the hypothesis of prebiotic peptide formation at hydrothermal aqueous conditions. Apart from these implications, the generality of the studied organic reactions are of immediate relevance to many fields such as (bio)geochemistry, biomineralization, and environmental chemistry.

Screening the partition behavior of a large number of chemicals with a quantum-chemical software.

For 8500 organic chemicals from the Canadian Domestic Substances List, air/water and octanol/water partition coefficients have been calculated with COSMOfrag a predictive a priori method based on quantum mechanics and statistical thermodynamics provided by COSMOlogic. The results were compared with predictions from the EPI Suite. On average a difference of 1.8 log units between both methods was observed for the predicted logK(aw) values. This has consequences for the classification in terms of atmospheric long range transport potential and bioaccumulation in the terrestrial food chain where 11% and 17% of all compounds were classified differently. Much better agreement was observed for the predicted logK(ow). Principal differences became obvious for compounds that occur as isomers or conformers. The modules of the EPI Suite are not designed to account for information on stereochemistry of molecules or E/Z isomers. Intramolecular H-bonds are only accounted for if specific correction factors exist from the calibration procedure. In contrast, COSMOfrag in combination with COSMOtherm can identify the existence of such isomers or H-bond conformers and account for these effects in the calculations.

Oxadiazole-carbonylaminothioureas as SIRT1 and SIRT2 inhibitors.

A new inhibitor for human sirtuin type proteins 1 and 2 (SIRT1 and SIRT2) was discovered through virtual database screening in search of new scaffolds. A series of compounds was synthesized based on the hit compound (3-[[3-(4-tert-butylphenyl)1,2,4-oxadiazole-5-carbonyl]amino]-1-[3-(trifluoromethyl)phenyl]thiourea). The most potent compound in the series was nearly as potent as the reference compound (6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1-carboxamide).

N,N'-Bisbenzylidenebenzene-1,4-diamines and N,N'-Bisbenzylidenenaphthalene-1,4-diamines as Sirtuin Type 2 (SIRT2) Inhibitors.

A series of N,N'-bisbenzylidenebenzene-1,4-diamine and N,N'-bisbenzylidenenaphthalene-1,4-diamine derivatives were synthesized as inhibitors for human sirtuin type 2 (SIRT2). The design of the new compounds was based on two earlier reported hits from molecular modeling and virtual screening. The most potent compound was N,N'-bis(2-hydroxybenzylidene)benzene-1,4-diamine, which was equipotent with the most potent hit compound and well-known SIRT2 inhibitor sirtinol.

Comparative and pharmacophore model for deacetylase SIRT1.

Sirtuins are NAD-dependent histone deacetylases, which cleave the acetyl-group from acetylated proteins, such as histones but also the acetyl groups from several transcription factors, and in this way can change their activities. Of all seven mammalian SirTs, the human sirtuin SirT1 has been the most extensively studied. However, there is no crystal structure or comparative model reported for SirT1. We have therefore built up a three-dimensional comparison model of the SirT1 protein catalytic core (domain area from residues 244 to 498 of the full length SirT1) in order to assist in the investigation of active site-ligand interactions and in the design of novel SirT1 inhibitors. In this study we also propose the binding-mode of recently reported set of indole-based inhibitors in SirT1. The site of interaction and the ligand conformation were predicted by the use of molecular docking techniques. To distinguish between active and inactive compounds, a post-docking filter based on H-bond network was constructed. Docking results were used to investigate the pharmacophore and to identify a filter for database mining.

Predictive three-dimensional quantitative structure-activity relationship of cytochrome P450 1A2 inhibitors.

The purpose of this study was to determine the cytochrome P450 1A2 (CYP1A2) inhibition potencies of structurally diverse compounds to create a comprehensive three-dimensional quantitative structure-activity relationship (3D-QSAR) model of CYP1A2 inhibitors and to use this model to predict the inhibition potencies of an external set of compounds. Fifty-two compounds including naphthalene, lactone and quinoline derivatives were assayed in a 96-well plate format for CYP1A2 inhibition activity using 7-ethoxyresorufin O-dealkylation as the probe reaction. The IC50 values of the tested compounds varied from 2.3 microM to over 40,000 microM. On the basis of this data set, a comparative molecular field analysis (CoMFA) and GRID/GOLPE models were created that yielded novel structural information about the interaction between inhibitory molecules and the CYP1A2 active site. The created CoMFA model was able to accurately predict inhibitory potencies of several structurally unrelated compounds, including selective inhibitors of other cytochrome P450 forms.

Quantitative structure-activity relationship analysis of inhibitors of the nicotine metabolizing CYP2A6 enzyme.

The purpose of this study was to develop screening and in silico modeling methods to obtain accurate information on the active center of CYP2A6, a nicotine oxidizing enzyme. The inhibitory potencies of 26 naphthalene and 16 non-naphthalene derivatives were determined for human CYP2A6 and mouse CYP2A5 enzymes. Several comparative molecular field analysis (CoMFA) models were developed to find out what types of steric and electrostatic properties are required for potent inhibitors. The IC(50) values of the tested compounds varied from 0.55 to 35 400 microM for CYP2A6 and from 1 to 1500 microM for CYP2A5. The generated CoMFA models were able to accurately predict the inhibition potencies of an external test set of chemicals. Potent and specific inhibitors of the CYP2A6 enzyme can be used in the future to increase nicotine bioavailability and thus make oral nicotine administration feasible in smoking cessation therapy.

Integrin specificity of the cyclic Arg-Gly-Asp motif and its role in integrin-targeted gene transfer.

Targeted gene transfer, addressing the alphavbeta3 integrin by coupling the appropriate ligand, cRGD (S(2)-bridged cyclic Arg-Gly-Asp containing peptide) motif, on to a DNA condensing sequence was described as early as 1995 by Hart, Harbottle, Cooper, Miller, Williamson and Coutelle [(1995) Gene Ther. 2, 552-554]. Their work was followed by a series of publications, introducing the cRGD motif in polycationic DNA carriers, such as peptides, proteins and liposomes. Polyethylenimine and even adenoviruses were additionally ligated using the cRGD motif. 'Integrin specificity' has been determined from the significantly improved transfection efficiency compared with the DNA carriers with control ligands, mainly the cRGE (S(2)-bridged cyclic-Arg-Gly-Glu-containing peptide) motif. However, by observing the physicochemical appearance of the resulting complexes and their controls such as the poly(L-lysine)-DNA complexes carrying the cRGD and the cRGE motifs, we doubted the integrin-mediated specificity of the increased transfection efficiency. To clarify this contradiction, we investigated the suitability of the cRGD motif for targeted gene transfer. We proved the specificity of the RGD motif and its controls using computational docking procedures and molecular modelling methods. Since we were confident of the motifs used, we improved our transfection method. Since aggregation of the RGD-ligated poly(L-lysine)-DNA complexes under physiological conditions caused an enormous amount of unspecific cell uptake and transfection, a method had to be designed to exclude aggregation processes of the motif-polycation-DNA complexes. Small complex sizes are necessary for receptor-specific uptake. The complexes were therefore recharged using poly(vinyl sulphate). Inhibited aggregation of the targeted DNA carriers under physiological conditions is a necessary prerequisite for successful in vivo gene transfer.