Binding Ensembles of p53-MDM2 Peptide Inhibitors by Combining Bayesian Inference and Atomistic Simulations

Designing peptide inhibitors of the p53-MDM2 interaction against cancer is of wide interest. Computational modeling and virtual screening are a well established step in the rational design of small molecules. But they face challenges for binding flexible peptide molecules that fold upon binding. We look at the ability of five different peptides, three of which are intrinsically disordered, to bind to MDM2 with a new Bayesian inference approach (MELD × MD). The method is able to capture the folding upon binding mechanism and differentiate binding preferences between the five peptides. Processing the ensembles with statistical mechanics tools depicts the most likely bound conformations and hints at differences in the binding mechanism. Finally, the study shows the importance of capturing two driving forces to binding in this system: the ability of peptides to adopt bound conformations (ΔGconformation) and the interaction between interface residues (ΔGinteraction).     

Additive telluromolybdates. Structure and catalysis in oxidation

Additive telluromolybdates, MoO₃·2TeO₂ and M^IIO·TeO₂·MoO₃ (M^IITeMoO₆; M^II = Co, Mn, Zn), converted ethyl lactate selectively to pyruvate in a vaporphase fixedbed flow system at 250–300 °C. A synergy in activity was observed for binary TeO₂–MoO₃, and crystalline Te₂MoO₇ was suggested as the active species. The Rietveld analysis of powder XRD patterns of ternary CoTeMoO₆ revealed the layer structure quite different from that of the reference Te₂MoO₇, but tellurium was again located adjacent to molybdenum linked through lattice oxygen.     

Ab initio structure determination of new compound Ba3(BO3)(PO4)

The crystal structure of new compound Ba₃BPO₇ was determined by ab initio method from high-resolution conventional X-ray powder diffraction data. The Rietveld refinement converged to R_p=5.92%, R_wp=8.87%, R_exp=5.00% with the following details: Hexagonal, space group P6₃mc, a=5.4898 (1) Å, c=14.7551(1) Å, Z=2. The basic unit of the structure is the [BaO₁₀]-[BO₃]-[PO₄] polar polyhedra-chain composed of Ba1-B-P-O cluster. These chains, running along c-axis, stack in a HCP mode to build the whole structure with triangular prism channels. The channels are parallel to c-axis too, in which Ba2 and Ba3 are located.     

A Minor New Flavone from Scutellaria baicalensis Georgi

A new flavone,6,2′-dihydroxy-5,7,8,6′-tetramethoxyflavone,was isolated from the roots of Scutellaria baicalensis. Its structure was established on the basis of spectral evidences.     

Reaction paths of some open-shell reactive intermediates

The intermolecular interaction energy for reacting systems in singlet, triplet and doublet states was partitioned by the perturbation expansion method into the chemically meaningful five interaction terms: the Coulomb, exchange-repulsion, induction, dispersion, and charge-transfer energies. In the local ZDO approximation, these energy terms were evaluated for the dimerization of methylenes (^1,3CH₂), the additions of carbenes (^1,3CH₂ and^1,3CF₂) as well as amino radicals (²NH₂ and²NF₂) toward ethylene, and the hydrogen abstractions by methylenes (^1,3CH₂), nitrene (³NH), and hydroxyl radical (²OH) from methane. It has been found that the reaction path is much influenced by the spinmultiplicity, and that the charge-transfer and exchange-repulsion terms play a dominant role in determining the course of reactions.     

1H and 13C assignments of two new triterpenes from Cladocolea grahami

The structure elucidation and 1H and 13C assignments of the new triterpenes 3beta-palmitoxy-7beta-hydroxyolean-12-ene (1) and its hydrolysis product 3beta,7beta-dihydroxyolean-12-ene (2) and 3beta-sn-glyceroyl-(1'-palmitoxy)urs-12-ene (3), isolated from the aerial parts of Cladocolea grahami (Loranthaceae), are reported.     

Synthesis and Insulin—sensitizing Activity of a Series of 2—Benzyl—1,3—dicarbonyl Derivatives

A series of 2-benzyl-1,3-dicabonyl derivatives was synthesized.Their insulin-sensitizing activity was evaluated in 3T3-L1 preadipocyte cells.Compounds3,26 and 27 were found to possess strong insulin-sensitizing activity in vitro and were selected for further hypoglycemic evaluation in vivo.     

Preparation of Y2Ba4Cu7O15-δ Superconductor without High Oxygen Pressure

The synthesis of bulk Y₂Ba₄Cu₇O_15-δ superconductor at atmospheric oxygen pressure via solid state sintering is reported. Temperature ranging from 860 to 890 °C as well as time interval over 2 to 15 days were used to investigate the formation of the Y₂Ba₄Cu₇O_15-δ phase. A time-temperature profile characterizing the conditions for the preparation of Y₂Ba₄Cu₇O_15-δ phase suggests the optimal condition to be sintering at 890 °C for over 10 days. Detailed results of X-ray diffraction, electrical resistivity, iodometric titration and magnetization measurements are described.     

COMPOSITION OF THE ESSENTIAL OIL OF Haplophyllum myrtifolium

The chemical composition of the essential oil ofHaplophyllum myrtifoliumBoiss., endemic to Turkey, was examined by GC/MS. Ninety-seven compounds were characterized with linalool (12.8%), -caryophyllene (10.3 %), and methyleugenol (5.9 %) as the main constituents.     

Molecular orbital studies on the conformation of GABA (γ-aminobutyric acid)

In distinction to Extended Hückel Theory which predicts as the most stable conformation of free zwitterionic GABA a totally extended form, PCILO and SCF ab initio studies show that the intrinsically preferred conformation of the isolated molecule is a highly folded one, resulting from strong interactions between the two charged ends. Computations are also carried out for hydrated GABA in the supermolecule approach allowing moreover for the flexibility of binding of some of the water molecules of the first hydration shell. They predict the coexistence in solution of a large number of conformations showing different degrees of folding (or extension), a result confirmed by recent NMR studies. This and a number of similar results show that we have to adapt our thinking on the role of conformations in pharmacological activity to this situation, which was frequently obscured by the more abundant results of X-ray crystallography yielding a single conformation.