Computational Investigation Identified Potential Chemical Scaffolds for Heparanase as Anticancer Therapeutics

Heparanase (Hpse) is an endo-β-D-glucuronidase capable of cleaving heparan sulfate side chains. Its upregulated expression is implicated in tumor growth, metastasis and angiogenesis, thus making it an attractive target in cancer therapeutics. Currently, a few small molecule inhibitors have been reported to inhibit Hpse, with promising oral administration and pharmacokinetic (PK) properties. In the present study, a ligand-based pharmacophore model was generated from a dataset of well-known active small molecule Hpse inhibitors which were observed to display favorable PK properties. The compounds from the InterBioScreen database of natural (69,034) and synthetic (195,469) molecules were first filtered for their drug-likeness and the pharmacophore model was used to screen the drug-like database. The compounds acquired from screening were subjected to molecular docking with Heparanase, where two molecules used in pharmacophore generation were used as reference. From the docking analysis, 33 compounds displayed higher docking scores than the reference and favorable interactions with the catalytic residues. Complex interactions were further evaluated by molecular dynamics simulations to assess their stability over a period of 50 ns. Furthermore, the binding free energies of the 33 compounds revealed 2 natural and 2 synthetic compounds, with better binding affinities than reference molecules, and were, therefore, deemed as hits. The hit compounds presented from this in silico investigation could act as potent Heparanase inhibitors and further serve as lead scaffolds to develop compounds targeting Heparanase upregulation in cancer.     

A Structure−Activity Relationship Study of Novel Hydroxamic Acid Inhibitors around the S1 Subsite of Human Aminopeptidase N

Aminopeptidase N (APN/CD13) is a zinc-dependent ubiquitous transmembrane ectoenzyme that is widely present in different types of cells. APN is one of the most extensively studied metalloaminopeptidases as an anti-cancer target due to its significant role in the regulation of metastasis and angiogenesis. Previously, we identified a potent and selective APN inhibitor, N-(2-(Hydroxyamino)-2-oxo-1-(3′,4′,5′-trifluoro-[1,1′-biphenyl]-4-yl)ethyl)-4-(methylsulfonamido)benzamide ( 3 ). Herein, we report the further modifications performed to explore SAR around the S1 subsite of APN and to improve the physicochemical properties. A series of hydroxamic acid analogues were synthesised, and the pharmacological activities were evaluated in vitro. N-(1-(3′-Fluoro-[1,1′-biphenyl]-4-yl)-2-(hydroxyamino)-2-oxoethyl)-4-(methylsulfonamido)benzamide ( 6 f ) was found to display an extremely potent inhibitory activity in the sub-nanomolar range.     

Two Methods,One Goal: Structural Differences between Cocrystallization and Crystal Soaking to Discover Ligand Binding Poses

In lead optimization, protein crystallography is an indispensable tool to analyze drug binding. Binding modes and non-covalent interaction inventories are essential to design follow-up synthesis candidates. Two protocols are commonly applied to produce protein–ligand complexes: cocrystallization and soaking. Because of its time and cost effectiveness, soaking is the more popular method. Taking eight ligand hinge binders of protein kinase A, we demonstrate that cocrystallization is superior. Particularly for flexible proteins, such as kinases, and larger ligands cocrystallization captures more reliable the correct binding pose and induced protein adaptations. The geometrical discrepancies between soaking and cocrystallization appear smaller for fragment-sized ligands. For larger flexible ligands that trigger conformational changes of the protein, soaking can be misleading and underestimates the number of possible polar interactions due to inadequate, highly impaired positions of protein amino-acid side and main chain atoms. Thus, if applicable cocrystallization should be the gold standard to study protein–ligand complexes.     

钨中空位及其团簇的能量学和动力学性质参数

在总结前人钨中空位及其团簇的能量学和动力学行为的研究成果基础上，采用第一性原理方法系统计算了钨中空位及其团簇的结合能和扩散能垒。研究发现，交换关联泛函PW91和PBE较PBEsol、AM05和LDA更适合用于计算钨空位的能量学性质。基于第一性原理计算结果对文献中单空位形成能、双空位作用性质等争议性问题进行了讨论，并对钨经验势进行了评估。研究结果表明，钨中孤立单空位间总是相互排斥，而空位团簇（V_n>3）对单空位具有很强的吸引作用，其结合能随着所含空位个数增多呈现波动性增大的趋势。空位团簇稳定结构可通过最小化Wigner-Seitz表面积来确定，其结合能与V_n与V_n-1之间的Wigner-Seitz面积之差呈正比。     

Topological Characterization of Book Graph and Stacked Book Graph

Degree based topological indices are being widely used in computer-aided modeling, structural activity relations, and drug designing to predict the underlying topological properties of networks and graphs. In this work, we compute the certain important degree based topological indices like Randic index, sum connectivity index, ABC index, ABC₄ index, GA index and GA₅ index of Book graph B_n and Stacked book graph B_m,n. The results are analyzed by using edge partition, and the general formulas are derived for the above-mentioned families of graphs.     

多肽螯合钙的研究进展

钙作为一种必需营养素,在人体中有着极为重要的作用。现如今,补钙制剂在市场上占有极大的份额,但以无机钙和有机钙为主的第一、第二代补钙制剂仍有较大缺陷,吸收率和生物利用率低,而多肽螯合钙作为第三代具有活性结构的生物钙补钙制剂稳定性好、抗干扰能力强、吸收效果好、生物利用度高,因此越来越受到关注。该文对多肽螯合钙的结合机制、制备方法、吸收途径、生物利用度等方面的研究进行综述,以期对补钙制剂的研究及开发提供新思路。     

Human Cellular Retinol Binding Protein II Forms a Domain-Swapped Trimer Representing a Novel Fold and a New Template for Protein Engineering

Domain-swapping is a mechanism for evolving new protein structure from extant scaffolds, and has been an efficient protein-engineering strategy for tailoring functional diversity. However, domain swapping can only be exploited if it can be controlled, especially in cases where various folds can coexist. Herein, we describe the structure of a domain-swapped trimer of the iLBP family member hCRBPII, and suggest a mechanism for domain-swapped trimerization. It is further shown that domain-swapped trimerization can be favored by strategic installation of a disulfide bond, thus demonstrating a strategy for fold control. We further show the domain-swapped trimer to be a useful protein design template by installing a high-affinity metal binding site through the introduction of a single mutation, taking advantage of its threefold symmetry. Together, these studies show how nature can promote oligomerization, stabilize a specific oligomer, and generate new function with minimal changes to the protein sequence.     

古籍装具用纸板的安全性分析

纸板是制作古籍装具的重要材料,其质量决定了装具的安全性。满足文物保护要求的纸板能够对古籍起到保护作用,延长藏品保存寿命。考察了14个纸板样品的安全性,结果表明:大部分纸板的p H值和碱储量可以达到国家标准的要求,而卡伯值是目前制约纸板质量的主要因素。