Insights into the Ligand Binding to Bromodomain-Containing Protein 9 (BRD9): A Guide to the Selection of Potential Binders by Computational Methods

The estimation of the binding of a set of molecules against BRD9 protein was carried out through an in silico molecular dynamics-driven exhaustive analysis to guide the identification of potential novel ligands. Starting from eight crystal structures of this protein co-complexed with known binders and one apo form, we conducted an exhaustive molecular docking/molecular dynamics (MD) investigation. To balance accuracy and an affordable calculation time, the systems were simulated for 100 ns in explicit solvent. Moreover, one complex was simulated for 1 µs to assess the influence of simulation time on the results. A set of MD-derived parameters was computed and compared with molecular docking-derived and experimental data. MM-GBSA and the per-residue interaction energy emerged as the main indicators for the good interaction between the specific binder and the protein counterpart. To assess the performance of the proposed analysis workflow, we tested six molecules featuring different binding affinities for BRD9, obtaining promising outcomes. Further insights were reported to highlight the influence of the starting structure on the molecular dynamics simulations evolution. The data confirmed that a ranking of BRD9 binders using key parameters arising from molecular dynamics is advisable to discard poor ligands before moving on with the synthesis and the biological tests.     

Analyte response in laser ablation inductively coupled plasma mass spectrometry

The dependence of analyte sensitivity and vaporization efficiency on the operating parameters of an inductively coupled plasma mass spectrometer (ICPMS) was investigated for a wide range of elements in aerosols, produced by laser ablation of silicate glass. The ion signals were recorded for different carrier gas flow rates at different plasma power for two different laser ablation systems and carrier gases. Differences in atomization efficiency and analyte sensitivity are significant for the two gases and the particle size distribution of the aerosol. Vaporization of the aerosol is enhanced when helium is used, which is attributed to a better energy-transfer from the plasma to the central channel of the ICP and a higher diffusion rate of the vaporized material. This minimizes elemental fractionation caused by sequential evaporation and reduces diffusion losses in the ICP. The sensitivity change with carrier gas flow variation is dependent on m/z of the analyte ion and the chemical properties of the element. Elements with high vaporization temperatures reach a maximum at lower gas flow rates than easily vaporized elements. The sensitivity change is furthermore dependent on m/z of the analyte ion, due to the mass dependence of the ion kinetic energies. The mass response curve of the ICPMS is thus not only a result of space charge effects in the ion optics but is also affected by radial diffusion of analyte ions and the mismatch between their kinetic energy after expansion in the vacuum interface and the ion optic settings.     

Development and Validation of Analytical Methods for the Detection and Quantification of a Novel Dimeric Ceramide in Stratum Corneum and Other Layers of the Skin

Ceramides (CERs) are integral parts of the intercellular lipid lamellae of the stratum corneum (SC), which is responsible for the barrier function of the skin. Many skin diseases such as atopic dermatitis and psoriasis are associated with depletion or disturbance of the level of CERs in the SC. Administration of an exogenous novel dimeric ceramide (dCER) deep into the SC may help to stabilize the SC barrier substantially and to treat some skin disease conditions and with the help of the existing technology it might be possible to formulate various pharmaceutical dosage forms that can facilitate penetration of dCER into the SC. However, assessment of the rate and extent of permeability of the exogenous dCER involves appropriate analytical techniques which can discriminately quantify the exogenous dCER in the SC and in the other skin layers. Therefore, an attempt was made to develop an AMD-HPTLC and an HPLC/APCI-MS method for the detection and quantification of exogenous dCER in the SC as well as other skin layers. The method involved synthesis of the dCER and development of appropriate HPTLC and LC/ESI-MS methods for the separation and quantification of the dCER in the SC and deeper layers of the skin. The methods developed were optimized for quantification of a novel dCER. In comparison to the AMD-HPTLC method, the HPLC/MS method offers a higher sensitivity. Both methods could be used for the quantification of dCER in presence of a complex matrix (e.g., skin extract). The developed methods are complementary and could be used for the quantification of dCER in any further stage of substance research and industrial application. The methods developed are robust, linear and sensitive with a low limit of detection (LOD) and low limit of quantification (LOQ).

     

Functionalization of bolalipid nanofibers by silicification and subsequent one-dimensional fixation of gold nanoparticles

In the present work, we describe the successful stabilization of bolalipid nanofibers by sol-gel condensation (silicification) of tetraethoxysilane (TEOS) or 3-mercaptopropyltriethoxysilane (MP-TEOS), respectively, onto the nanofibers. The conditions for an effective and reproducible silicification reaction were determined, and the silicification process was pursued by transmission electron microscopy (TEM). The resulting bolalipid-silica composite nanofibers were characterized by means of differential scanning calorimetry (DSC), TEM, (13)C, and (31)P NMR spectroscopy. Finally, the novel silicified bolalipid nanofibers were used as templates for the fixation of 5 and 2 nm AuNPs, respectively, resulting in one of the rare examples of one-dimensional AuNP arrangements in aqueous suspension.     

Chirality and Symmetry Breaking in a Discrete Internal Space

In previous papers the permutation group S ₄ has been suggested as an ordering scheme for quarks and leptons, and the appearance of this finite symmetry group was taken as indication for the existence of a discrete inner symmetry space underlying elementary particle interactions. Here it is pointed out that a more suitable choice than the tetrahedral group S ₄ is the pyritohedral group A ₄×Z ₂ because its vibrational spectrum exhibits exactly the mass multiplet structure of the 3 fermion generations. Furthermore it is noted that the same structure can also be obtained from a primordial symmetry breaking S ₄→A ₄. Since A ₄ is a chiral group, while S ₄ is achiral, an argument can be given why the chirality of the inner pyritohedral symmetry leads to parity violation of the weak interactions.     

Monolayers of mono- and bipolar palmitic acid derivatives

Monopolar and bipolar derivatives of hexadecanoic acid (HA), 16-hydroxyhexadecanoic acid (HHA), methyl hexadecanoate (MH) and methyl 16-hydroxyhexadecanoate (MHH) have been investigated on pure water and NaCl solutions with different ion concentrations (1, 2 and 3 mol l⁻¹). Surface pressure area isotherms show that HA forms a fully condensed monolayer on pure water at 20 °C [E. Teer, C.M. Knobler, S. Siegel, D. Vollhardt, G. Brezesinski, J. Phys. Chem., B104, 43, 2000, pp. 10053–10058] whereas in the case of the corresponding bipolar HHA the hydroxy group as a second polar moiety leads to a destabilization of the monolayer. The presence of two relatively strong hydrophilic polar groups at opposite ends of the chain prevents the formation of condensed films. The esterification of the carboxyl group (MH) changes the phase sequence from L₂–Ov–LS for HA to L₂–LS. Inserting a hydroxy group at the end of the chain (MHH) shifts the liquid expanded/liquid condensed (LE/LC) phase transition to higher surface pressures but does not change the phase sequence, however it increases the chain tilt. The pressure of the first-order phase transition LE/LC is strongly temperature dependent for MH, while the transition pressure of MHH is almost temperature independent. The phase behavior of MHH and MH on pure water was further studied by surface potential, Brewster angle microscopy (BAM), fluorescence microscopy and grazing incidence X-ray diffraction (GIXD) measurements. The LC domains of MHH on pure water are so small that no inner texture can be observed by BAM in contrast to the LC domains of MH. 3M NaCl in the subphase does not change the MH textures, while it increases the size of the LC domains of MHH. The influence of the hydroxy group on the monolayer behavior is discussed in terms of the formation of hydrogen bonds. The presence of NaCl in the subphase expands the monolayers. The results obtained are explained by changes in monolayer–monolayer and monolayer–subphase interactions.     

Enzyme Aided Analysis of the Substituent Distribution along the Chain of Cellulose Acetates Regioselectively Modified by the Action of an Aspergillus niger Acetylesterase

Two cellulose acetates (CA) were regioselectively deacetylated by action of a pure Aspergillus niger acetylesterase from the carbohydrate esterase family 1. The action of acetyl esterase along the polymeric chain was monitored by a new enzyme-aided method. CA with and without esterase modification was hydrolysed with a pure endoglucanase. The fragments were deutero-acetylated and separated by preparative SEC in CHCl₃. The partial degree of substitution of the individual fragments was determined by ¹H-NMR spectroscopy. The investigation confirmed the uniform regioselective and regular deacetylation along the polysaccharide chain. The partial substitution in C₂ seemed to be of major importance for the enzyme's mode of action.