Formulas and numerical table for the radial part of overlap integrals with the same screening parameters of Slater-type orbitals

 The numerical properties of the radial part of overlap integrals with the same screening parameters in the form of polynomials in p = ξR over Slater-type orbitals have been studied and obtained by using three different methods. For that purpose, the characteristics of auxiliary functions were used first, then Fourier transform convolution theorem, and recurrence relations for the basic coefficients of A ^s _{n l λ, n ′ l ′λ} were used. The calculations of the radial part of overlap integrals with the same screening parameters were made in the range 1 ≤ n ≤ 75, 1 ≤ n′ ≤ 75, and 10⁻⁶ ≤ p. Received: 18 January 2001 / Accepted: 5 April 2001 / Published online: 27 June 2001     

3β-Methoxyolean-18-ene (miliacin) from the marine fungus Chaetomium olivaceum

A pentacyclic tritepenoid, 3-methoxyolean-18-ene (miliacin), was isolated for the first time from the marine fungus Chaetomium olivaceum. Its structure was determined on the basis of 2D NMR spectroscopy and X-ray diffraction data.     

stk: A python toolkit for supramolecular assembly

A tool for the automated assembly, molecular optimization and property calculation of supramolecular materials is presented. stk is a modular, extensible and open‐source Python library that provides a simple Python API and integration with third party computational codes. stk currently supports the construction of linear polymers, small linear oligomers, organic cages in multiple topologies and covalent organic frameworks (COFs) in multiple framework topologies, but is designed to be easy to extend to new, unrelated, supramolecules or new topologies. Extension to metal–organic frameworks (MOFs), metallocycles or supramolecules, such as catenanes, would be straightforward. Through integration with third party codes, stk offers the user the opportunity to explore the potential energy landscape of the assembled supramolecule and then calculate the supramolecule's structural features and properties. stk provides support for high‐throughput screening of large batches of supramolecules at a time. The source code of the program can be found at https://github.com/supramolecular-toolkit/stk . © 2018 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.     

Adsorbed hollow fiber‐based biological fingerprinting for the discovery of platelet aggregation inhibitors from Danshen–Honghua decoction

For lead compound discovery from natural products, hollow fiber cell fishing with chromatographic analysis is a newly developed method. In this study, an adsorbed hollow fiber‐based biological fingerprinting method was firstly developed to discover potential platelet aggregation inhibitors from Danshen–Honghua decoction. Platelets were seeded on the fiber and their survival rate was tested. Results indicated that more than 92% platelets survived during the whole operation process. Ranitidine and tirofiban were used as positive and negative control respectively to verify the reliability of the presented approach. The main variables such as amount of extract and stirring time that affect the adsorbed hollow fiber‐based biological fingerprinting process were optimized, and the repeatability of this method was also investigated. Finally, 12 potential active compounds in Danshen–Honghua decoction were successfully detected using the established approach and structures for nine of them were tentatively identified by liquid chromatography with mass spectrometry analysis. In addition, the in vitro platelet aggregation inhibition test was carried out for five of the nine hit compounds, and three active components, namely, lithospermic acid, salvianolic acid A, and salvianolic acid B were confirmed. These results proved that the proposed method could be an effective approach for screening platelet inhibitors from plant extracts.     

A Mechanism‐Based Approach to Screening Metagenomic Libraries for Discovery of Unconventional Glycosidases

Functional metagenomics has opened new opportunities for enzyme discovery. To exploit the full potential of this new tool, the design of selective screens is essential, especially when searching for rare enzymes. To identify novel glycosidases that employ cleavage strategies other than the conventional Koshland mechanisms, a suitable screen was needed. Focusing on the unsaturated glucuronidases (UGLs), it was found that use of simple aryl glycoside substrates did not allow sufficient discrimination against β‐glucuronidases, which are widespread in bacteria. While conventional glycosidases cannot generally hydrolyze thioglycosides efficiently, UGLs follow a distinct mechanism that allows them to do so. Thus, fluorogenic thioglycoside substrates featuring thiol‐based self‐immolative linkers were synthesized and assessed as selective substrates. The generality of the approach was validated with another family of unconventional glycosidases, the GH4 enzymes. Finally, the utility of these substrates was tested by screening a small metagenomic library.     

Schrödinger药物虚拟筛选流程模块在大学生物和化学信息学教学中的应用

介绍了Schr?dinger药物虚拟筛选的基本原理和流程,结合大学生物和化学信息学课程的相关教学内容,分别描述了蛋白受体的预处理、类药性五原则、毒药物动力学(ADME)、泛筛选干扰化合物(PAINS)、高通量虚拟筛选、标准精度筛选、高精度筛选和MM/GBSA的打分排序原理和使用方法。该软件可以在大学生物和化学信息学的教学中演示,有助于提高学生对蛋白结构、分子构象、药物虚拟筛选和计算机辅助分子设计的理解,该软件有很好的图形界面,可以给学生直观的体验,大大丰富了大学课堂的教学内容。此外,该软件在药物设计领域里面也有很好的应用价值,大大节约了药物筛选的成本,提高了药物发现的效率。     

Orbitrap高分辨质谱法高通量筛查生化药品、中成药与保健品中非法添加的13种消化类化学药物

建立了生化药品、中成药和保健品中非法添加的13种消化类化学药的超高效液相色谱-Orbitrap高分辨质谱(UHPLC-HRMS)高通量筛查方法。供试品以甲醇-水(50∶50)为提取溶剂,经Hypersil Gold C18(2.1 mm×100 mm,3μm)色谱柱分离,以乙腈-0.1%甲酸水为流动相进行梯度洗脱,单次分析仅需10min。采用正离子检测,Full MS/dd-MS2扫描模式。通过比较供试品与对照品的色谱保留时间、高分辨一级和二级质谱,判断供试品中是否非法添加消化类药物,并对阳性样品进行定量分析。13种化合物的线性范围均为8.0~800μg/L,相关系数(r)均不低于0.998 5,回收率为94.6%~106.2%,相对标准偏差为1.2%~2.9%。该法快速简便、通量高、选择性好、灵敏度高,并已用于生化药品、中成药及保健品非法添加消化类化学药的高通量筛查和测定,在38批中成药中发现5批阳性样品,在43批保健品中发现3批阳性样品。     

Optimizing Antimicrobial Peptide Dendrimers in Chemical Space

We used nearest‐neighbor searches in chemical space to improve the activity of the antimicrobial peptide dendrimer (AMPD) G3KL and identified dendrimer T7 , which has an expanded activity range against Gram‐negative pathogenic bacteria including Klebsiellae pneumoniae, increased serum stability, and promising activity in an in vivo infection model against a multidrug‐resistant strain of Acinetobacter baumannii. Imaging, spectroscopic studies, and a structural model from molecular dynamics simulations suggest that T7 acts through membrane disruption. These experiments provide the first example of using virtual screening in the field of dendrimers and show that dendrimer size does not limit the activity of AMPDs.     

Engineering Chiral Catalysts through Asymmetric Activation and Super High Throughput Screening (SHTS)

A conceptually new strategy for asymmetric catalysis, namely asymmetric activation, in which a chiral activator selectively activates one enantiomer of a racemic chiral catalyst, and a highly efficient screening system for finding the most effective catalysts, namely super high throughput screening (SHTS), by which the reaction can be conducted in parallel and the ee% of the product is allowed to determine within minutes, are summarized in the present account. It is reasonable to believe that SHTS technique combined with asymmetric activation or deactivation principle will provide a very powerful methodology for finding the new catalysts and the best catalyst tuning for asymmetric reactions.     

液相色谱/四极杆-飞行时间质谱法筛查奶酪中29种禁用和限用合成色素

建立了奶酪样品中29种禁用和限用合成色素的液相色谱/四极杆-飞行时间质谱(LC/Q-TOF MS)筛查方法。样品经正己烷-水(3:1, v/v)振荡提取,得到正己烷层、水层和残渣3部分。正己烷层经旋转蒸发浓缩后,用乙酸乙酯-环己烷(1:1, v/v)溶解,经过凝胶渗透色谱(GPC)净化去除油脂。水层经乙腈振荡提取,得到乙腈-水提取液。残渣经氨水-甲醇(1:99, v/v)溶液振荡提取,得到氨水-甲醇提取液。乙腈-水提取液和氨水-甲醇提取液不需净化直接分析。结果表明: 29种不同极性范围的合成色素化合物分别得到了有效的提取,提取回收率为70%～95%。而Q-TOF MS提供的精确质量数定性功能可以将不同种类的合成色素化合物筛查出来,各化合物与精确质量质谱库中化合物的匹配度为59.66～99.47。通过Target MS/MS扫描方式进行定量,得到8种苏丹类化合物的方法检出限为0.4～2.5 μg/kg, 21种水溶性合成色素及染料化合物的检出限为20～80 μg/kg。该方法对禁用和限用合成色素的筛查范围广泛,对含有蛋白质、脂肪等基质的食品具有较好的适用性。