Predicting protein-ligand binding affinities using novel geometrical descriptors and machine-learning methods

Inspired by the concept of knowledge-based scoring functions, a new quantitative structure-activity relationship (QSAR) approach is introduced for scoring protein-ligand interactions. This approach considers that the strength of ligand binding is correlated with the nature of specific ligand/binding site atom pairs in a distance-dependent manner. In this technique, atom pair occurrence and distance-dependent atom pair features are used to generate an interaction score. Scoring and pattern recognition results obtained using Kernel PLS (partial least squares) modeling and a genetic algorithm-based feature selection method are discussed.     

Flash Pyrolysis of 4-Arylmethylidene-oxazolones and -isoxazolones. A Versatile Synthesis of Arylacetylenes. Preliminary communication

Flash pyrolysis of 4-benzylidene-2-phenyl-5(4H)-oxazolone ( 1 ) yields carbonmonoxide, benzene, biphenyl, diphenylacetonitrile, and 2,3-diphenylsuccinonitrile; N-benzoylphenylketenimine is implicated as the primary intermediate. The flash pyrolysis of 4-arylmethylidene-3-methyl-5(4H)-isoxazolones ( 3 ) yields carbon dioxide, acetonitrile, and phenylacetylenes substituted by alkoxy, chloro, dimethylamino, and hydroxy groups, in yields of 45–95%. Arylmethylidenecarbenes are implicated as intermediates.     

Iminopropadienones R–NCCCO and carbon suboxide, C3O2. Theoretical and experimental C NMR spectra

The ¹³C NMR data of five iminopropadienones R–NCCCO as well as carbon suboxide, C₃O₂, have been examined theoretically and experimentally. The best theoretical results were obtained using the GIAO/B3LYP/6-31+G**//MP2/6-31G* level of theory, which reproduces the chemical shifts of the iminopropadienone substituents extremely well while underestimating those of the cumulenic carbons by 5–10 ppm. The computationally faster GIAO/HF/6-31+G**//B3LYP/6-31G* level is also adequate.     

Chiral separation of amines with N-benzoxycarbonylglycyl-L-proline as selector in non-aqueous capillary electrophoresis using methanol and 1,2-dichloroethane in the background electrolyte

N-Benzoxycarbonylglycyl-L-proline (L-ZGP) has been introduced as a chiral selector for enantioseparation of amines in non-aqueous capillary electrophoresis. Methanol mixed with different proportions of dichloromethane, 1,2-dichloroethane or 2-propanol containing L-ZGP and ammonium acetate was used as the background electrolyte. Enantioseparation of different types of pharmacologically active amines was performed, e.g. the local anaesthetic bupivacaine and the beta-adrenoceptor blocking agent pindolol. Addition of the solvents (dichloromethane, 1,2-dichloroethane or 2-propanol) gave an improved chiral separation partly due to a distinct decrease in the electroosmotic flow. The use of 1,2-dichloroethane in the background electrolyte gave higher precision in migration time (RSD 2.2%) compared to the systems containing dichloromethane. An enantiomeric separation of mepivacaine was performed within 72 s by use of short-end injection with an effective capillary length of 8.5 cm.     

Was Biofilme zusammenhält: Proteine,Polysaccharide ..

Extracellular polymeric substances (EPS) are biopolymers of microbial origin and consist mainly of polysaccharides, proteins, lipids and nucleic acids. The EPS mediate adhesion to surfaces and form a hydrogel matrix for biofilms and other microbial aggregates. This matrix can be considered as “house” of the microorganisms which allows for the formation of stable communities (“microconsortia”) of synergistic strains and enables them to degrade recalcitrant substances. EPS retain water and prevent desiccation. Cohesion and adhesion are provided by a network of fluctuating adhesion points. External pressure can change the structure from a gel to a highly viscous liquid. Due to their sorptive properties, dissolved nutrients from the water phase are accumulated and increase the survival chances of biofilm organisms in oligotrophic environments. The matrix facilitates gene exchange and regulation processes via signalling molecules. It provides a template for extracellular enzymes and prevents that they are washed out. Thus, it is of great importance for the degradation of solids and particles. Remnants of lysed cells are retained and can be utilized as food source. Thus, biofilms can be considered as a natural example for sustainable use of nutrients. Some EPS are biotechnologically employed as additives for food, drilling fluids and as biosurfactants.