Role of bridging water molecules in GSK3β-inhibitor complexes: insights from QM/MM, MD, and molecular docking studies

The role of water molecules is increasingly gaining interest in drug design, and several studies have highlighted their paramount contributions to the specificity and the affinity of ligand binding. In this study, we employ the two-layer ONIOM-based quantum mechanics/molecular mechanics (QM/MM) calculations, molecular dynamics (MD) simulations, and molecular docking studies to investigate the effect of bridging water molecules at the GSK3β-inhibitors interfaces. The results obtained from the ONIOM geometry optimization and AIM analysis corroborated the presence of bridging water molecules that form hydrogen bonds with protein side chain of Thr138 and/or backbone of Gln185, and mediate interactions with inhibitors in the 10 selected GSK3β-inhibitor complexes. Subsequently, MD simulations carried out on a representative system of 1R0E demonstrated that the bridging water molecule is stable at the GSK3β-inhibitor interface and appears to contribute to the stability of the protein-inhibitor interactions. Furthermore, molecular docking studies of GSK3β-inhibitor complexes indicated that the inhibitors can increase binding affinities and the better docked conformation of inhibitors can be obtained by inclusion of the bridging water molecules, especially for the flexible inhibitors, in docking experiments into individual protein conformations. Our results elucidate the importance of bridging water molecules at the GSK3β-inhibitor interfaces and suggest that they might prove useful in rational drug design.     

On the conformation of the propranolol molecule

The structure of the propranolol molecule has been optimized within the AM1 and PM3 semiempirical framework followed by ab initio HF/6-31G^* refinement. On each calculation level the conformational space was sampled to search for the lowest-energy conformer(s) from among a few hundreds of conformers at the semiempirical step and next from among a few dozens of conformers at the ab initio level. Finally, five stable conformers were found; each stabilized by one or two of the three possible hydrogen bonds. The geometrical and electronic parameters were established and found to differ only slightly in the structures with the hydrogen bond either present or not.     

Studies on Hydroiodination and Deconjugation of 5—Aryloxy—（thiophenyl）—3—pentyn—2—one

One-pot hydroiodination and deconjugation of 5-aryloxy(or thiophenyl)-3-pentyn-2-one with a reagent system of sodium iodide/trimethylsilyl chloride/water in acetonitrile at 25℃ have been described.The plasuible mechanism was discussed.The reaction provided a simple and useful method for the preparation of (Z)-β-substituted β，γ-enones and (Z)-β-substituted α，β-unsaturated ketones.     

A small molecule promotes mitochondrial fusion in Mammalian cells

Mitochondrial dynamics: An image-based screen identified a small molecule, M1, that specifically promotes the fusion of fragmented mitochondria and protects cells from mitochondrial-fragmentation-associated cell death. Mechanistic studies revealed that M1 shifts the mitochondrial dynamic balance towards fusion.     

Towards the understanding of molecular mechanisms in the early stages of heat-induced aggregation of beta-lactoglobulin AB

Heat-induced aggregation of bovine β-lactoglobulin AB (10 mg/ml) was studied at 68.5 °C at two different pH values (6.7, 4.9) using gel electrophoresis techniques and matrix-assisted laser desorption ionization mass spectrometry (MALDI–TOF MS). Sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS–PAGE) analysis under non-reducing and reducing conditions showed that in the early stages of the aggregation of β-lactoglobulin disulfide linked aggregates were formed on heating at pH 6.7, but not at pH 4.9. We related this result to the pH-dependent activity of the free thiol group at C121. Mass spectrometric analyses were conducted in two steps. The first involved the analysis of intact non-native monomers and dimers following their ultrasonic passive elution into a suitable solvent mixture in order to confirm the identity of the different gel bands. The second step comprises the analysis of in-gel digests for the determination of disulfide patterns in non-native monomers, covalent dimers and trimers. The results of in-gel digestions analyzed by mass spectrometry suggest that non-native dimers could result from the formation of inter-molecular disulfide bonds C121–C66, C160–C160, or C121–C160. Moreover, two inter-molecular bonds C121–C66 and C160–C160 between two and the same monomer units have been detected, which may play an important role in limiting the process of covalent β-lactoglobulin network formation. The combination of SDS–PAGE and MALDI–TOF MS enables us to understand the mechanism of β-lactoglobulin aggregation at the macromolecular level.     

Catalytic Hydrogenation of α,β-Epoxyketones to β-Hydroxyketones with Two Sulfinyl Analogues of Coenzyme NADH Models

An efficient method for the selective hydrogenation of a series of α,β-epoxyketones to β-hydroxyketones using catalytic amount of two sulfinyl analogues of NAD^＋ model compounds is reported. The lack of any diastereoselectivity for the formation of β-hydroxyketones with optically pure sulfinyl analogue of NAD^＋ model supports the radical mechanism proposed previously.     

Evaluation of the immobilized artificial membrane phosphatidylcholine: Drug discovery column for high-performance liquid chromatographic screening of drug–membrane interactions

Chromatographic retention factors (k′) of a series of eight β-adrenoceptor antagonist compounds (β-adrenolytic drugs) were determined employing an immobilized artificial membrane column (IAM.PC.DD). The influence of mobile phase pH, ionic strength, and organic modifier composition was studied in order to examine column performance. After the IAM.PC.DD columns were exposed to approximately 7000 column volumes of a 0.01 M PBS mobile phase, five out of six columns tested showed significant peak broadening and decreased k′ values indicative of premature column failure. The data suggested that the immobilized phospholipids stationary phase was removed by the 0.01 M PBS mobile phase. The β-adrenolytic drug's log k′_IAM values obtained with an IAM.PC.DD column were compared to an ^esterIAM.PC.MG column for predicting drug membrane interactions. For the linear regression analysis between log k′_IAM and the logarithm of the n-octanol–water partition coefficients (r_IAM.PC.DD=0.8710 vs. r_IAM.PC.MG=0.9538), the C₁₈ HPLC retention factors (r_IAM.PC.DD=0.8408 vs. r_IAM.PC.MG=0.9380), the liposome partition coefficients (r_IAM.PC.DD=0.8887 vs. r_IAM.PC.MG=0.9187), and various pharmacokinetic parameters, significantly better correlations were obtained with the ^esterIAM.PC.MG column than the IAM.PC.DD column.     

5-雄烯-3β, 7α, 17β-三醇和5-雄烯-3β, 7β, 17β-三醇的合成

以5-雄烯二醇为原料,用微生物转化的方法合成了两个重要的神经甾体5-雄烯-3β, 7α, 17β-三醇和5-雄烯-3β, 7β, 17β-三醇。所用菌种总枝毛霉为我们自己筛选,并首次应用于5-雄烯-3β, 7α, 17β-三醇和5-雄烯-3β, 7β, 17β-三醇的合成中。     

Learning from nature: beta-sheet-mimicking copolymers get organized

The solution structures formed by coil-coil copolymers arise from the selective solvation of one of the two blocks and have been well described. In most cases in such relatively simple synthetic structures there are no specific attractive forces that can aid the aggregation process. Nature, however, provides plenty of inspiring polymeric architectures that are shaped and ordered hierarchically by noncovalent forces. The high level of structural definition displayed by proteins, for example, is unmatched by synthetic polymers. An emerging area of interest in polymer science tries to combine the best of both worlds, the natural and the synthetic, by conjugating synthetic polymers and beta-sheet-forming peptides. Understanding the supramolecular organization of the block copolymers driven exclusively by the intermolecular attractive forces of the peptide sequence is of particular interest. Not only do these peptide-polymer hybrid structures present an interesting new class of materials, they can also provide important insights into self-organization processes prevalent in nature.     

SmI2－Mediated Addition Reaction of α－Halomethylsulfones to Carbonyl Compounds. A Convenient Synthesis of β－Hydroxysulfones

Due to the chemoselective dehalogenation by SmI2, the addition of a-halomethylsulfones to carbonyl compounds afforded ,β-hydroxysulfones. Those reactions with α-bromomethylsulfones gave the products in moderate to good yields. The SmI2-mediated addition of gem-dihalomethylsulfones to ketones also afforded α-halo-β-hydroxysulfones in moderate yields.