Covalent labeling of a chromatin reader domain using proximity-reactive cyclic peptides

Chemical probes for chromatin reader proteins are valuable tools for investigating epigenetic regulatory mechanisms and evaluating whether the target of interest holds therapeutic potential. Developing potent inhibitors for the plant homeodomain (PHD) family of methylation readers remains a difficult task due to the charged, shallow and extended nature of the histone binding site that precludes effective engagement of conventional small molecules. Herein, we describe the development of novel proximity-reactive cyclopeptide inhibitors for PHD3—a trimethyllysine reader domain of histone demethylase KDM5A. Guided by the PHD3–histone co-crystal structure, we designed a sidechain-to-sidechain linking strategy to improve peptide proteolytic stability whilst maintaining binding affinity. We have developed an operationally simple solid-phase macrocyclization pathway, capitalizing on the inherent reactivity of the dimethyllysine ε-amino group to generate scaffolds bearing charged tetraalkylammonium functionalities that effectively engage the shallow aromatic ‘groove’ of PHD3. Leveraging a surface-exposed lysine residue on PHD3 adjacent to the ligand binding site, cyclic peptides were rendered covalent through installation of an arylsulfonyl fluoride warhead. The resulting lysine-reactive cyclic peptides demonstrated rapid and efficient labeling of the PHD3 domain in HEK293T lysates, showcasing the feasibility of employing proximity-induced reactivity for covalent labeling of this challenging family of reader domains.

We describe the development of covalent cyclic peptide ligands which target a chromatin methylation reader domain using a proximity-reactive sulfonyl fluoride moiety.     

COHERENT OPTICAL PHONON EXCITATION BY FEMTOSECOND LASER PULSE IN YBa2Cu3O7-δ THIN FILMS

With a correlation of nonequilibrium carriers relaxation and coherent phonons displacive excitation, the coherent optical phonon oscillations in YBa₂Cu₃O_7-δ thin films excited by femtosecond laser pulse are simulated theoretically. It is revealed that as the oxygen concentration decreases, the coherent phonon oscillations become easier to be observed due to the decrease of the local coupling between the carriers and the lattice vibrations in the CuO₂ plane.     

Theoretical prediction of the damping of a railway wheel with sandwich-type dampers

This paper presents a procedure for predicting the damping added to a railway wheel when sandwich-type dampers are installed. Although there are different ways to reduce the noise generated by a railway wheel, most devices are based on the mechanism of increasing wheel damping. This is why modal damping ratios are a clear indicator of the efficiency of the damping device and essential when a vibro-acoustic study of a railway wheel is carried out. Based on a number of output variables extracted from the wheel and damper models, the strategy explained herein provides the final damping ratios of the damped wheel. Several different configurations are designed and experimentally tested. Theoretical and experimental results agree adequately, and it is demonstrated that this procedure is a good tool for qualitative comparison between different solutions in the design stages.     

Monitoring and Evolution of the Pollution by Volatile Organic Compounds (Vocs) in the Groundwaters of The Najerilla River Basin (Spain)

VOCs were detected and identified in the water of several wells in the area of Nájera (La Rioja). The past uncontrolled spills from an important painting and varnishing industry and from other smaller ones devoted to the manufacture of furniture and varnishing activities were the sources of the VOCs plume detected in this aquifer. This article shows the results obtained in the monitoring and assessment of the pollution at 18 sampling points for more than a year. It has allowed us to study the evolution of the different pollutants and the influence of a remediation process applied by the company in the main pollution source. The analytical method is based on headspace-solid-phase microextraction (SPME) using a 75-μm carboxen-polydimethylsiloxane fibre. Quantification was carried out by gas chromatography with flame ionization detection. This method has allowed us to determine the 13 VOCs identified in the polluted underground samples providing good sensitivity (LOD between 0.1 and 6.0 ng/mL) and reproducibility (r.s.d. less than 10%).     

Synthesis,structural characterization and in vitro cytotoxic activity of novel polymeric triorganotin(IV) complexes of urocanic acid

Two novel triorganotin carboxylate complexes of the biologically active urocanic acid have been synthesized and characterized. Elemental analysis, melting point, spectroscopic techniques – IR, ¹H, ¹³C and ¹¹⁹Sn NMR – mass spectrometry and X‐ray diffraction studies have been used for structural characterization. Crystal structures of the tin(IV) derivatives show that urocanic acid acts as a bridging bidentate ligand through its imidazole nitrogen atom and its carboxylic group, producing a polymeric one‐dimensional chain. The molecular structures of the complexes, catena‐poly‐tri(n‐butyl)tin(IV) 3‐(3H‐imidazol‐4‐yl)prop‐2‐enoate (1) and catena‐poly‐triphenyltin(IV) 3‐(3H‐imidazol‐4‐yl)prop‐2‐enoate (2), present a distorted trigonal–bipyramidal configuration. This is further confirmed by ¹¹⁹Sn NMR in the solid state. The tin(IV) derivatives form double‐stranded ribbons via N―H^…O―H bonds. Nevertheless, the compounds are essentially monomeric in solution, with a tetrahedral configuration as observed by ¹¹⁹Sn NMR in solution. The cytotoxic activity of the titled compounds has been tested against six human cell lines and the corresponding IC₅₀ values are reported. Both tin(IV) compounds have a high to very high in vitro cytotoxic activity against the tumor cell lines K562, HCT‐15 and MCF‐7. Compound 1 is 86 times more active than cisplatin in the HTC‐15 cell line. Copyright © 2012 John Wiley & Sons, Ltd.     

Tributyltin(IV) Schiff base complexes with amino acid derivatives: synthesis,characterization and biological activity

The synthesis in one‐pot reactions and structural characterization of six new tri‐n‐butyltin(IV) derivatives of Schiff bases are reported. The compounds are derived from a condensation reaction between l ‐alanine, l ‐valine, l ‐isoleucine, l ‐methionine, l ‐phenylalanine or l ‐tryptophan and 3,5‐di‐tert‐butyl‐2‐hydroxybenzaldehyde. Characterization was completed using elemental analysis, infrared spectroscopy, mass spectrometry, one‐ and two‐dimensional solution NMR (¹H, ¹³C and ¹¹⁹Sn) as well as solid‐state ¹¹⁹Sn NMR. In addition, the crystal structures of three of the compounds were confirmed using single‐crystal X‐ray diffraction. Although five‐coordinated and polymeric in the solid state, the tin compounds are four‐coordinated and monomeric in solution. The coordination environment around the triorganotin units comprises three carbon atoms and two oxygen atoms from two ligands in a trigonal bipyramidal geometry. The anti‐proliferative effect of these compounds on the cervical carcinoma cell lines HeLa, CaSki and ViBo was screened in vitro, the compounds showing cytotoxic activity against all three strains and null or low cytotoxic activity (necrotic) as well. Copyright © 2016 John Wiley & Sons, Ltd.     

TG/MS study of the thermal devolatization of Copoazú peels (Theobroma grandiflorum)

The Amazonian rain forest is the source of several numbers of species in the world, some of those vegetal species have been carried to different places due to their utility. One of those species is the Thehobroma grandiflorum, pulp and seeds of which have several usages in the food industry, but the shell has no extensive use. One of the possibilities due to the nature of the material is the pyrolysis process for obtaining valuable products. Thermal analysis was studied for the biomass thermochemical conversion process under TG/MS techniques. Three different heating rates were used for the thermochemical process. A variety of hydrocarbon and oxygenated products with industrial importance were obtained. The kinetics of the evolved species was studied under three different models. DAEM model fit the thermogravimetric data with good agreement. The parameters obtained for the model agreed with the studied intensities of the MS data. Those ones that did not fit were due to possible gas-phase reactions between the compounds obtained.