Evaluation of docking/scoring approaches: A comparative study based on MMP3 inhibitors

An increasing number of docking/scoring programs are available that use different sampling and scoring algorithms. A reliable scoring function is the crucial element of such approaches. Comparative studies are needed to evaluate their current capabilities. DOCK4 with force field and PMF scoring as well as FlexX were used to evaluate the predictive power of these docking/scoring approaches to identify the correct binding mode of 61 MMP-3 inhibitors in a crystal structure of stromelysin and also to rank them according to their different binding affinities. It was found that DOCK4/PMF scoring performs significantly better than FlexX and DOCK4/FF in both ranking ligands and predicting their binding modes. Most notably, DOCK4/PMF was the only scoring/docking approach that found a significant correlation between binding affinity and predicted score of the docked inhibitors. However, comparing only those cases where the correct binding mode was identified (scoring highest among sampled poses), FlexX showed the best `fine tuning' (lowest rmsd) in predicted binding modes. The results suggest that not so much the sampling procedure but rather the scoring function is the crucial element of a docking program.     

Dynamic identification of phosphopeptides using immobilized metal ion affinity chromatography enrichment, subsequent partial beta-elimination/chemical tagging and matrix-assisted laser desorption/ionization mass spectrometric analysis

The enrichment of phosphopeptides using immobilized metal ion affinity chromatography (IMAC) and subsequent mass spectrometric analysis is a powerful protocol for detecting phosphopeptides and analyzing their phosphorylation state. However, nonspecific binding peptides, such as acidic, nonphosphorylated peptides, often coelute and make analyses of mass spectra difficult. This study used a partial chemical tagging reaction of a phosphopeptide mixture, enriched by IMAC and contaminated with nonspecific binding peptides, following a modified beta-elimination/Michael addition method, and dynamic mass analysis of the resulting peptide pool. Mercaptoethanol was used as a chemical tag and nitrilotriacetic acid (NTA) immobilized on Sepharose beads was used for IMAC enrichment. The time-dependent dynamic mass analysis of the partially tagged reaction mixture detected intact phosphopeptides and their mercaptoethanol-tagged derivatives simultaneously by their mass difference (-20 Da for each phosphorylation site). The number of new peaks appearing with the mass shift gave the number of multiply phosphorylated sites in a phosphopeptide. Therefore, this partial chemical tagging/dynamic mass analysis method can be a powerful tool for rapid and efficient phosphopeptide identification and analysis of the phosphorylation state concurrently using only MS analysis data.     

Diversity‐Oriented Approach for Chemical Biology

Synthetic molecules that modulate and probe biological events are critical tools in chemical biology. Utilizing combinatorial and diversity‐oriented synthetic strategies, access to large numbers of small molecules is becoming more and more feasible, and research groups in this field can take advantage of the power of chemical diversity. Since the majority of early studies were focused on the discovery of compounds that perturb protein functions, diversity‐based approaches are often considered as therapeutic lead discovery tactics. However, the diversity‐oriented approach can also be applied to advance distinct aims, such as target protein identification, or the development of imaging probes and sensors. This review provides a personal perspective of the chemical‐diversity‐based approach and how this principle can be adapted to various chemical biology studies.     

ANALYSIS OF THE LOCALIZATION OF DAMAGE AND THE COMPLETE STRESS-STRAIN RELATION FOR MESOSCOPIC HETEROGENEOUS ROCK UNDER UNIAXIAL TENSILE LOADING

The mechanical behavior of rock under uniaxial tensile loading is different from that of rock under compressive loads. A micromechanics-based model was proposed for mesoscopic heterogeneous brittle rock undergoing irreversible changes of their microscopic structures due to microcrack growth. The complete stress-strain relation including linear elasticity, nonlinear hardening, rapid stress drop and strain softening was obtained. The influence of all microcracks with different sizes and orientations were introduced into the constitutive relation by using the probability density function describing the distribution of orientations and the probability density function describing the distribution of sizes. The influence of Weibull distribution describing the distribution of orientations and Rayleigh function describing the distribution of sizes on the constitutive relation were researched. Theoretical predictions have shown to be consistent with the experimental results.     

食品中7种常见的非食用色素检测研究进展

食用色素可以明显改善食品外观,激发食欲,在食品行业有着广泛的应用,但若向食品中添加非食用色素来代替食用色素,则会对人体存在致癌风险。食品中常见的非食用色素有以下7种:碱性嫩黄O、碱性橙Ⅱ、酸性橙Ⅱ、苏丹红、若丹明B、美术绿和孔雀石绿,而目前对这7种非食用色素检测的国家标准还未全部建立。本文综述了近3年来食品行业中针对这7种非食用色素的各种检验方法,以期为食品安全监督检测提供参考。     

A partition coefficient calculation method with the SFED model

The Solvation Free Energy Density (SFED) model, a solvation model proposed by No et al. was modified to give better solvation free energies of the molecules having high polarizable groups. The SFED at a point around the molecule was represented by a linear combination of four basis functions, the contribution from the cavitation free energy of a solvent, and a constant. As an application of the SFED model, the linear expansion coefficients of the Hydration Free Energy Density (HFED) and the 1-Octanol Free Energy Density (1-OFED) were determined. Both calculated hydration free energy and 1-octanol solvation free energy of selected 95 organic molecules agreed well with experimental values. The standard errors were 0.47 and 0.39 kcal/mol, respectively. 1-Octanol/water partition coefficients (P) of the molecules were calculated from the difference of the HFE and 1-OFE of the molecules. At the same time, the logP density (LPD) of a molecule was represented by the same basis functional form with the SFED model. The logP of a molecule can be obtained by the integration of the LPD of the molecule. The coefficients of the basis functions were determined by using experimental logP as constraints through an optimization procedure. Both logPs calculated from the free energy difference and from the LPD agreed well with the experimental data. The absolute mean errors were obtained as 0.34 and 0.32, respectively.     

Changes in Isoflavone Profile from Soybean Seeds during Cheonggukjang Fermentation Based on High-Resolution UPLC-DAD-QToF/MS: New Succinylated and Phosphorylated Conjugates

In this study, thirty-eight isoflavone derivatives were comprehensively identified and quantified from the raw, steamed and fermented seeds of four selected soybean cultivars based on UPLC-DAD-QToF/MS results with reference to the previously reported LC-MS library and flavonoid database, and summarized by acylated group including glucosides (Glu), malonyl-glucosides (Mal-Glu), acetyl-glucosides (Ac-Glu), succinyl-glucosides (Suc-Glu) and phosphorylated conjugates (Phos) in addition to aglycones. Among them, Suc-Glu and Phos derivatives were newly generated due to fermentation by B. subtilis AFY-2 (cheonggukjang). In particular, Phos were characterized for the first time in fermented soy products using Bacillus species. From a proposed roadmap on isoflavone-based biotransformation, predominant Mal-Glu (77.5–84.2%, raw) decreased rapidly by decarboxylation and deesterification into Ac-Glu and Glu (3.5–8.1% and 50.0–72.2%) during steaming, respectively. As fermentation continued, the increased Glu were mainly succinylated and phosphorylated as well as gradually hydrolyzed into their corresponding aglycones. Thus, Suc-Glu and Phos (17.3–22.4% and 1.5–5.4%, 36 h) determined depending on cultivar type and incubation time, and can be considered as important biomarkers generated during cheonggukjang fermentation. Additionally, the changes of isoflavone profile can be used as a fundamental report in applied microbial science as well as bioavailability research from fermented soy foods.     

Association of Paraoxonase 1 (PON1) polymorphisms with osteoporotic fracture risk in postmenopausal Korean women

There is increasing evidence of a biochemical link between lipid oxidation and bone metabolism. Paraoxonase 1 (PON1) prevents the oxidation of low-density lipoprotein (LDL) and metabolizes biologically active phospholipids in oxidized LDLs. Here, we performed association analyses of genetic variation in PON1 to ascertain its contribution to osteoporotic fractures (OFs) and bone mineral density (BMD). We directly sequenced the PON1 gene in 24 Korean individuals and identified 26 sequence variants. A large population of Korean postmenopausal women (n=1,329) was then genotyped for eight selected PON1 polymorphisms. BMD at the lumbar spine and femoral neck was measured using dual-energy X-ray absorptiometry. Lateral thoracolumbar (T4-L4) radiographs were obtained for vertebral fracture assessment, and the occurrence of non-vertebral fractures (i.e., wrist, hip, forearm, humerus, rib, and pelvis) was examined using self-reported data. Multivariate analyses showed that none of the polymorphisms was associated with BMD at either site. However, +5989A>G and +26080T>C polymorphisms were significantly associated with non-vertebral and vertebral fractures, respectively, after adjustment for covariates. Specifically, the minor allele of +5989A>G exerted a highly protective effect against non-vertebral fractures (OR=0.59, P=0.036), whereas the minor allele of +26080T>C was associated with increased susceptibility to vertebral fractures (OR=1.73, P=0.020). When the risk for any OFs (i.e., vertebral or non-vertebral) was considered, the statistical significance of both polymorphisms persisted (P=0.002-0.010). These results suggest that PON1 polymorphisms could be one of useful genetic markers for OF risk in postmenopausal women.     

Fabrication of hollow and mesoporous germania microspheres by templating against plasma-treated polystyrene microspheres

The surfaces of monodisperse polystyrene (PS) colloids have been modified with hydroxyl groups by means of plasma treatment technique. By templating against these surface-modified PS colloids, the germania coating PS composite microspheres were prepared via a sol–gel process. After removal of PS cores, the resulting composite microspheres converted into hollow germania microspheres with mesoporous structure. The shell thickness of these hollow spheres can be controlled by varying the concentration of germania precursor. BET results indicated that the hollow germania microspheres shell exhibits slightly broader pore size distribution than that of corresponding composite one owing to the swelling effects of the PS core during the etching process. In addition, the as-prepared germania exhibits amorphous phase which can be converted into crystalline phase by calcination treatment. It is worthy to noting that this fabrication protocol demonstrated a facile, low-cost and environment-benign way for fabricating hollow germania structures by templating method. Moreover, this protocol is not limit to germania; it also could be used to create the other hollow inorganic oxides spheres.     

Synthesis of urethane acrylates modified by linseed oil and study on EBC coatings

In this paper, five different structural urethane acrylates modified by linseed oil were synthesized and then properties of their electron beam cured (EBC) coatings, i.e., adhesion, gloss, flexibility, impact resistance, hardness, tensile strength and elongation were studied. It was shown that these synthesizing conditions of urethane acrylates modified by linseed oil were temperate. Effect of structure of urethane acrylates modified by linseed oil on these properties of their EBC coatings was obvious, except gloss. According to synthetical properties of EBC coatings, the optimum oligomer among these was No. A, whose main chains were formed by hexane diacid, average functionality was 2, and oil content was 25.5%. With increasing of absorbed doses, these properties of EBC coatings, except gloss, changed correspondingly. It was advisable that absorbed dose wasn’t greater than 180 kGy. At higher absorbed doses, cobaltous naphthenate had obvious effect on these properties of EBC coatings, whose oil content of linseed oil was rather high.