Structure-Based Design of Xanthine-Imidazopyridines and -Imidazothiazoles as Highly Potent and In Vivo Efficacious Tryptophan Hydroxylase Inhibitors.

Tryptophan hydroxylases catalyze the first and rate-limiting step in the biosynthesis of serotonin, a well-known neurotransmitter that plays an important role in multiple physiological functions. A reduction of serotonin levels, especially in the brain, can cause dysregulation leading to depression or insomnia. In contrast, overproduction of peripheral serotonin is associated with symptoms like carcinoid syndrome and pulmonary arterial hypertension. Recently, we developed a class of TPH inhibitors based on xanthine-benzimidazoles, characterized by a tripartite-binding mode spanning the binding sites of the cosubstrate pterin and the substrate tryptophan and by chelation of the catalytic iron ion. Herein, we describe the structure-based development of a second generation of xanthine-imidiazopyridines and -imidazothiazoles designed to inhibit TPH1 in the periphery while preventing the interaction with TPH2 in the brain. Lead compound 32 (TPT-004) shows superior pharmacokinetic and pharmacodynamic properties as well as efficacy in preclinical models of peripheral serotonin attenuation and colorectal tumor growth.

Structure-Based Design of Xanthine-Benzimidazole Derivatives as Novel and Potent Tryptophan Hydroxylase Inhibitors.

Tryptophan hydroxylases catalyze the first and rate-limiting step in the synthesis of serotonin. Serotonin is a key neurotransmitter in the central nervous system and, in the periphery, functions as a local hormone with multiple physiological functions. Studies in genetically altered mouse models have shown that dysregulation of peripheral serotonin levels leads to metabolic, inflammatory, and fibrotic diseases. Overproduction of serotonin by tumor cells causes severe symptoms typical for the carcinoid syndrome, and tryptophan hydroxylase inhibitors are already in clinical use for patients suffering from this disease. Here, we describe a novel class of potent tryptophan hydroxylase inhibitors, characterized by spanning all active binding sites important for catalysis, specifically those of the cosubstrate pterin, the substrate tryptophan as well as directly chelating the catalytic iron ion. The inhibitors were designed to efficiently reduce serotonin in the periphery while not passing the blood-brain barrier, thus preserving serotonin levels in the brain.

Myeloid transformation by MLL-ENL depends strictly on C/EBP.

Chromosomal rearrangements of the mixed-lineage leukemia gene MLL1 are the hallmark of infant acute leukemia. The granulocyte-macrophage progenitor state forms the epigenetic basis for myelomonocytic leukemia stemness and transformation by MLL-type oncoproteins. Previously, it was shown that the establishment of murine myelomonocytic MLL-ENL transformation, but not its maintenance, depends on the transcription factor C/EBPα, suggesting an epigenetic hit-and-run mechanism of MLL-driven oncogenesis. Here, we demonstrate that compound deletion of Cebpa/Cebpb almost entirely abrogated the growth and survival of MLL-ENL-transformed cells. Rare, slow-growing, and apoptosis-prone MLL-ENL-transformed escapees were recovered from compound Cebpa/Cebpb deletions. The escapees were uniformly characterized by high expression of the resident Cebpe gene, suggesting inferior functional compensation of C/EBPα/C/EBPß deficiency by C/EBPε. Complementation was augmented by ectopic C/EBPß expression and downstream activation of IGF1 that enhanced growth. Cebpe gene inactivation was accomplished only in the presence of complementing C/EBPß, but not in its absence, confirming the Cebpe dependency of the Cebpa/Cebpb double knockouts. Our data show that MLL-transformed myeloid cells are dependent on C/EBPs during the initiation and maintenance of transformation.

PRISMA: Protein Interaction Screen on Peptide Matrix Reveals Interaction Footprints and Modifications- Dependent Interactome of Intrinsically Disordered C/EBPß.

CCAAT enhancer-binding protein beta (C/EBPß) is a pioneer transcription factor that specifies cell differentiation. C/EBPß is intrinsically unstructured, a molecular feature common to many proteins involved in signal processing and epigenetics. The structure of C/EBPß differs depending on alternative translation initiation and multiple post-translational modifications (PTM). Mutation of distinct PTM sites in C/EBPß alters protein interactions and cell differentiation, suggesting that a C/EBPß PTM indexing code determines epigenetic outcomes. Herein, we systematically explored the interactome of C/EBPß using an array technique based on spot-synthesized C/EBPß-derived linear tiling peptides with and without PTM, combined with mass spectrometric proteomic analysis of protein interactions. We identified interaction footprints of ∼1,300 proteins in nuclear extracts, many with chromatin modifying, chromatin remodeling, and RNA processing functions. The results suggest that C/EBPß acts as a multi-tasking molecular switchboard, integrating signal-dependent modifications and structural plasticity to orchestrate interactions with numerous protein complexes directing cell fate and function.

Water Nanodroplet on a Hydrocarbon "Carpet"-The Mechanism of Water Contact Angle Stabilization by Airborne Contaminations on Graphene, Au, and PTFE Surfaces.

Wetting is very common phenomenon, and it is well documented that the wettability of a solid depends on the surface density of adsorbed airborne hydrocarbons. This "hydrocarbon hypothesis" has been experimentally confirmed for different surfaces, for example, graphene, TiO2, and SiO2; however, there are no scientific reports describing the influence of airborne contaminants on the water contact angle (WCA) value measured on the polytetrafluoroethylene (PTFE) surface. Using experimental data showing the influence of airborne hydrocarbons on the wettability of graphene, gold and PTFE by water, together with Molecular Dynamics simulation results we prove that the relation between the WCA and the surface concentration of hydrocarbons ( n-decane, n-tridecane, and n-tetracosane) is more complex than has been assumed up until now. We show, in contrast to commonly approved opinion, that adsorbed hydrocarbons can increase (graphene, Au) or decrease (PTFE) the WCA of a nanodroplet sitting on a surface. Using classical thermodynamics, a simple theoretical approach is developed. It is based on two adsorbed hydrocarbon states, namely, "carpet" and "dimple". In the "carpet" state a uniform layer of alkane molecules covers the entire substrate. In contrast, in the "dimple" state, the preadsorbed layer of alkane molecules covers only the open surface. Simple thermodynamic balance between the two states explains observed experimental and simulation results, forming a good starting point for future studies.

Water nanodroplet on a graphene surface-a new old system.

The major subject of our study is the accuracy of contact angle calculations. Reporting new simulation data for graphene-water systems, we show that the majority of previously reported data should be treated with caution, since the proper contact angle can be recorded only after a sufficiently long simulation time. It has been proven that-if one wants to gain accuracy greater than 0.1°-long calculations (exceeding 50 ns) are required. Finally, we also show, using both a Groningen Machine for Chemical Simulations (GROMACS) package and our new molecular dynamics (MD) code, that the changes in the contact angle, caused by graphene bottom layer rotation, are within the range of calculation error. We also propose a novel definition of the bottom of the droplet as the height where the density is half the density of liquid water. This new definition is applied in the method of the contact angle calculation from the MD simulation data.

Dynamics of effusive and diffusive gas separation on pillared graphene.

Pillared graphene structures, from a practical viewpoint, are very interesting novel carbon materials. Combining the properties of graphene and nanotubes, such as durability, chemical purity and a controlled structure, they were proven to be effective membranes for noble gas separation processes. Here, we examine their possible use for other, more commercially useful gas mixture separation, i.e. air and coal gas. The mechanism of air gas transport through the pillar channels is studied, and the prospective application of 2-D pillared membranes in effusion-like processes provided. The separative abilities of hybrid systems consisting of membranes with different channel diameters in relation to coal gas are proven to be promising.

A screen for transcription factor targets of glycogen synthase kinase-3 highlights an inverse correlation of NFκB and androgen receptor signaling in prostate cancer.

Expression of Glycogen Synthase Kinase-3 (GSK-3) is elevated in prostate cancer and its inhibition reduces prostate cancer cell proliferation, in part by reducing androgen receptor (AR) signaling. However, GSK-3 inhibition can also activate signals that promote cell proliferation and survival, which may preclude the use of GSK-3 inhibitors in the clinic. To identify such signals in prostate cancer, we screened for changes in transcription factor target DNA binding activity in GSK-3-silenced cells. Among the alterations was a reduction in AR DNA target binding, as predicted from previous studies, and an increase in NFκB DNA target binding. Consistent with the latter, gene silencing of GSK-3 or inhibition using the GSK-3 inhibitor CHIR99021 increased basal NFκB transcriptional activity. Activation of NFκB was accompanied by an increase in the level of the NFκB family member RelB. Conversely, silencing RelB reduced activation of NFκB by CHIR99021. Furthermore, the reduction of prostate cancer cell proliferation by CHIR99021 was potentiated by inhibition of NFκB signaling using the IKK inhibitor PS1145. Finally, stratification of human prostate tumor gene expression data for GSK3 revealed an inverse correlation between NFκB-dependent and androgen-dependent gene expression, consistent with the results from the transcription factor target DNA binding screen. In addition, there was a correlation between expression of androgen-repressed NFκB target genes and reduced survival of patients with metastatic prostate cancer. These findings highlight an association between GSK-3/AR and NFκB signaling and its potential clinical importance in metastatic prostate cancer.

Transcriptional repression of Hox genes by C. elegans HP1/HPL and H1/HIS-24.

Elucidation of the biological role of linker histone (H1) and heterochromatin protein 1 (HP1) in mammals has been difficult owing to the existence of a least 11 distinct H1 and three HP1 subtypes in mice. Caenorhabditis elegans possesses two HP1 homologues (HPL-1 and HPL-2) and eight H1 variants. Remarkably, one of eight H1 variants, HIS-24, is important for C. elegans development. Therefore we decided to analyse in parallel the transcriptional profiles of HIS-24, HPL-1/-2 deficient animals, and their phenotype, since hpl-1, hpl-2, and his-24 deficient nematodes are viable. Global transcriptional analysis of the double and triple mutants revealed that HPL proteins and HIS-24 play gene-specific roles, rather than a general repressive function. We showed that HIS-24 acts synergistically with HPL to allow normal reproduction, somatic gonad development, and vulval cell fate decision. Furthermore, the hpl-2; his-24 double mutant animals displayed abnormal development of the male tail and ectopic expression of C. elegans HOM-C/Hox genes (egl-5 and mab-5), which are involved in the developmental patterning of male mating structures. We found that HPL-2 and the methylated form of HIS-24 specifically interact with the histone H3 K27 region in the trimethylated state, and HIS-24 associates with the egl-5 and mab-5 genes. Our results establish the interplay between HPL-1/-2 and HIS-24 proteins in the regulation of positional identity in C. elegans males.

Pillared graphene as a gas separation membrane.

Graphene and carbon nanotubes are considered as future materials in various fields, including adsorption, accumulation and separation processes, and so are hybrid materials combining their properties. This paper reports our study on separative abilities of 3-D network structures consisting of graphene planes pillared with nanotube fragments. Results of molecular dynamics simulations confirm that such materials can be successfully applied as membranes in relation to noble gas mixtures. A simple explanation of the mechanism underlying the process is proposed.

Phenol adsorption on closed carbon nanotubes.

We present the results of systematic studies of phenol adsorption on closed commercially available, unmodified carbon nanotubes. Phenol adsorption is determined by the value of tube-specific surface area, the presence of small amount of surface groups influence adsorption only in very small amount. Phenol can be applied as a probe molecule for comparative analysis of tube surface areas. Tube curvature influences adsorption from solution, i.e., we observe increasing adsorption energy (and slower desorption process) with the decrease in tube curvature. This is in full accordance with molecular simulation results.

Molecular dynamics of zigzag single walled carbon nanotube immersion in water.

The results of enthalpy of immersion in water for finite single-walled carbon nanotubes are reported. Using molecular dynamics simulation, we discuss the relation between the value of this enthalpy and tube diameters showing that the obtained plot can be divided into three regions. The structure of water inside tubes in all three regions is discussed and it is shown that the existence of the strong maximum of enthalpy observed for tube diameter ca. 1.17 nm is due to freezing of water under confinement. The calculations of hydrogen bond statistics and water density profiles inside tubes are additionally reported to confirm the obtained results. Next, we show the results of calculation for the same tubes but containing surface carbonyl oxygen groups at pore entrances. A remarkable rise in the value of enthalpy of immersion in comparison to the initial tubes is observed. We also discuss the influence of charge distribution between oxygen and carbon atom forming surface carbonyls on the structure of confined water. It is concluded for the first time that the presence of surface oxygen atoms at the pore entrances remarkably influences the structure and stability of ice created inside nanotubes, and surface carbonyls appear to be chaotropic (i.e. structure breaking) for confined water. This effect is explained by the pore blocking leading to a decrease (compared to initial structure) in the number of confined water molecules after introduction of surface oxygen groups at pore entrances.

Activated carbon immersed in water-the origin of linear correlation between enthalpy of immersion and oxygen content studied by molecular dynamics simulation.

First Molecular Dynamics simulation results of activated carbon immersion in water are reported. Using a Virtual Porous Carbon Model of "soft" carbon the influence of surface oxygen content, distribution of groups and micropore diameter on the enthalpy of immersion is studied. The empirical relation between enthalpy and concentration of surface groups (as well as polar surface area) is reproduced by molecular simulation results. It is shown that for strongly hydrophobic carbons immersed in water, the water-vapour interface inside pores appears. This interface vanishes with the rise in content of surface oxygen. We discuss some nuances of the interfacial region using proximal distribution functions and hydrogen bonds statistics. Finally we conclude that the mechanism of immersion process is in accordance with Pratt-Chandler theory of hydrophobic interactions.

Molecular dynamics simulation insight into the mechanism of phenol adsorption at low coverages from aqueous solutions on microporous carbons.

MD simulation studies showing the influence of porosity and carbon surface oxidation on phenol adsorption from aqueous solutions on carbons are reported. Based on a realistic model of activated carbon, three carbon structures with gradually changed microporosity were created. Next, a different number of surface oxygen groups was introduced. The pores with diameters around 0.6 nm are optimal for phenol adsorption and after the introduction of surface oxygen functionalities, adsorption of phenol decreases (in accordance with experimental data) for all studied models. This decrease is caused by a pore blocking effect due to the saturation of surface oxygen groups by highly hydrogen-bounded water molecules.

Adsorption from aqueous solutions on opened carbon nanotubes--organic compounds speed up delivery of water from inside.

We report the results of first systematic studies of organic adsorption from aqueous solutions onto relatively long single walled carbon nanotubes (four tubes, in initial and oxidised forms). Using molecular dynamics simulations (GROMACS package) we discuss the behaviour of tube-water as well as tube-adsorbate systems, for three different adsorbates (benzene, phenol and paracetamol).

Ar, CCl(4) and C(6)H(6) adsorption outside and inside of the bundles of multi-walled carbon nanotubes-simulation study.

This is the first paper reporting the results of systematic study of the adsorption of Ar, C(6)H(6) and CCl(4) on the bundles of closed and opened multi-walled carbon nanotubes. Using grand canonical Monte Carlo (GCMC) and molecular dynamics (MD) simulations, we also study the effect of the introducing defects in the external and internal walls of osculating and separated nanotubes on Ar diffusion and on adsorption of all three adsorbates. The Ar diffusion coefficients obtained are very sensitive to the presence of defects. Simulated isotherms are discussed to show the relation between the shapes of the high resolution alpha(s)-plots and the mechanisms of adsorption. From obtained data, as well as from geometric considerations, from the VEGA ZZ package, and from simulations (ASA), the values of surface areas of all nanotubes are calculated and compared with those obtained using the most popular adsorption methods (BET, alpha(s) and the A,B,C-points). We show that the adsorption value for the C-point of the isotherm should be taken for the calculation of the specific surface area of carbon nanotubes to obtain a value which approaches the absolute geometric surface area. A fully packed monolayer is not created at the A-, B- or C-points of the isotherm; however, the number of molecules adsorbed at the latter point is closest to the number of molecules in the monolayer as calculated via the ASA method, the VEGA ZZ package or from geometric considerations.

Heterogeneous Do-Do model of water adsorption on carbons.

The model of water adsorption on carbons proposed five years ago by Do and Do is analyzed and improved. Following the experimental evidence that for activated carbons surface active groups differ in the value of the energy of interaction with water molecules, we propose to extend the original model to take this fundamental feature into account. For the original DD model, as well as proposed new heterogeneous one (HDDM), we develop also the corresponding isosteric enthalpy of adsorption formulas. The features of the HDDM are studied via simulations. It is shown that the new model predicts the shapes of adsorption isotherm as well as corresponding enthalpy observed for real experimental systems. Finally, the HDDM is successfully applied to description of arbitrarily chosen adsorption and enthalpy of adsorption data. Up to our knowledge, HDDM is the first model describing satisfactorily water adsorption isotherms and corresponding enthalpy data measured on different microporous activated carbons in the whole relative pressure range.