Generic method for systematic phase selection and method development of biochromatographic processes. Part I. Selection of a suitable cation-exchanger for the purification of a pharmaceutical protein

Even if the first protein therapeutics are now for more than 20 years on the market the selection of suitable adsorbents for the preparative downstream processing (DSP) of these biomolecules as well as the method development towards process conditions are still based mainly on 'trial and error'. Therefore, theses processes are not perfectly efficient, but indeed very time consuming and laborious. In this study a novel systematic method is introduced to find a suitable adsorbent (not necessarily the best one) with appropriate separation parameters for a specific separation with reduced effort. Following this strategy, the adsorbents must first be packed into columns under preparative conditions and then characterized completely with regard to, e.g. pressure drop, k'-values, plate heights (HETP curves), selectivity and capacity by using test substances, which are similar in their characteristics (molecular mass, size, charge distribution, hydrophobicity) to the target proteins. With the database once determined, a preselection of most suitable adsorbents including separation parameters is made regarding chromatographic and also economical properties. After this, preparative experiments must be conducted with a reduced number of adsorbents to figure out the individual influence of side components. This approach is demonstrated for the separation of an exemplary industrial protein mixture using cation-exchange chromatography (CEX). Characterization of different weak CEX-adsorbents is illustrated. After comparing these phases with each other, a first preselection and a prediction of suitable adsorbents is made. In the following preparative separation conditions (load, velocity, gradient) are determined for the preparative separations using the database and results of some additional experiments. The final comparison of separation performance in preparative scale confirms this selection and so the applicability of the new method.     

Competition STD NMR for the detection of high-affinity ligands and NMR-based screening

The reported competition STD NMR method combines saturation transfer difference (STD) NMR with competition binding experiments to allow the detection of high-affinity ligands that undergo slow chemical exchange on the NMR time-scale. With this technique, the presence of a competing high-affinity ligand in the compound mixture can be detected by the disappearance or reduction of the STD signals of a low-affinity indicator ligand. This is demonstrated on a BACE1 (beta-site amyloid precursor protein cleaving enzyme 1) protein-inhibitor system. This method can also be used to derive an approximate value, or a lower limit, for the dissociation constant of the potential ligand based on the reduction of the signal intensity of the STD indicator, which is illustrated on an HSA (human serum albumin) model system. This leads to important applications of the competition STD NMR method for lead discovery: it can be used (i) for compound library screening against a broad range of drug targets to identify both high- and low-affinity ligands and (ii) to rank order analogs rapidly and derive structure-activity relationships, which are used to optimize these NMR hits into viable drug leads.     

超高效液相色谱-四极杆/静电场轨道阱高分辨质谱快速筛查染发剂中32种染料成分

建立了超高效液相色谱-四极杆/静电场轨道阱高分辨质谱快速筛查和分析染发剂中32种禁限用染料的分析方法。样品经甲醇-2 g/L抗坏血酸水溶液溶解提取,正己烷净化,用ZORBAX Eclipse Plus C_(18)(3.0 mm×100 mm,1.8μm)色谱柱分离,以甲醇-5 mmol/L乙酸铵水溶液为流动相进行梯度洗脱,采用正、负离子切换同时测定了32种染料成分,显著提高了检测通量。以全扫描模式下提取的保留时间和一级母离子精确质量数以及同位素丰度比,实现对染发剂中多种染料成分的快速筛查;以自动触发采集的二级碎片离子精确质量数进行确证。32种染料在相应的质量浓度范围内线性关系良好,相关系数(r~2)均大于0.99;定量下限(LOQ)为0.2～40μg/g,回收率为81.0%～110%,相对标准偏差(RSD)为3.3%～9.9%。该方法简单、准确、快速,适用于染发剂中多种禁限用染料成分的高通量快速定性筛查和定量分析。     

Improving (Q)SAR predictions by examining bias in the selection of compounds for experimental testing

ABSTRACT

Existing data on structures and biological activities are limited and distributed unevenly across distinct molecular targets and chemical compounds. The question arises if these data represent an unbiased sample of the general population of chemical-biological interactions. To answer this question, we analyzed ChEMBL data for 87,583 molecules tested against 919 protein targets using supervised and unsupervised approaches. Hierarchical clustering of the Murcko frameworks generated using Chemistry Development Toolkit showed that the available data form a big diffuse cloud without apparent structure. In contrast hereto, PASS-based classifiers allowed prediction whether the compound had been tested against the particular molecular target, despite whether it was active or not. Thus, one may conclude that the selection of chemical compounds for testing against specific targets is biased, probably due to the influence of prior knowledge. We assessed the possibility to improve (Q)SAR predictions using this fact: PASS prediction of the interaction with the particular target for compounds predicted as tested against the target has significantly higher accuracy than for those predicted as untested (average ROC AUC are about 0.87 and 0.75, respectively). Thus, considering the existing bias in the data of the training set may increase the performance of virtual screening.     

SARS-CoV protease inhibitors design using virtual screening method from natural products libraries

Two natural products databases, the marine natural products database (MNPD) and the traditional Chinese medicines database (TCMD), were used to find novel structures of potent SARS-CoV protease inhibitors through virtual screening. Before the procedure, the databases were filtered by Lipinski's ROF and Xu's extension rules. The results were analyzed by statistic methods to eliminate the bias in target-based database screening toward higher molecular weight compounds for enhancing the hit rate. Eighteen lead compounds were recommended by the screening procedure. They were useful for experimental scientists in prioritizing drug candidates and studying the interaction mechanism. The binding mechanism was also analyzed between the best screening compound and the SARS protein.     

Preferential Uniplanar Orientation of Cellulose Microfibrils Reinvestigated by the FTIR Technique

A simple detection method to observe the uniplanar orientation behavior of native cellulose microfibrils to the cell wall surface by using Fourier transform infrared (FTIR) spectroscopy in the transmission mode is reported. Four bands at 1372, 1355, 1337, and 1317 cm⁻¹ (the latter two have been mentioned previously by Liang and Marchessault (1960, J. Polym. Sci. 43: 85–100)) were found to be sensitive to such orientation: the two middle bands at 1355 and 1337 cm⁻¹ increase remarkably when the 0.60–61 nm lattice planes lie parallel to the cell wall surfaces. The reverse was true when the 0.53–54 nm lattice planes oriented preferentially. Polarization of the two bands at 1372 and 1355 cm⁻¹ was parallel, while that of the other two bands at lower wavenumbers, i.e., at 1337 and 1317 cm⁻¹, was perpendicular to the molecular axis of cellulose. These bands were assigned to OH-related motion, probably to in-plane OH bending, as reported by Maréchal and Chanzy (2000, J. Mol. Spectrosc. 523: 183–196).     

基于近红外光谱的维生素C片无损鉴别分析

基于近红外光谱技术与化学计量学方法,建立了一种国内外不同品牌维生素C片的无损鉴别方法。采集了国内外8个品牌的维生素C片共计40个样本的近红外光谱数据,比较了完整样品以及粉末样品的近红外光谱,采用连续小波变换技术消除背景干扰和基线漂移,基于标准偏差与相对标准偏差的变量筛选方法筛选出具有代表性的波数点,结合主成分分析方法对国内外不同品牌维生素C片进行鉴别分析。结果表明:原始光谱存在着明显的背景干扰和基线漂移现象,且粉末样品的重现性要优于完整样品;单纯使用原始光谱无法辨别来自不同品牌的维生素C片;连续小波变换可以有效消除背景干扰,提高模型鉴别能力;完整样品的鉴别准确率优于粉末样品,说明国内外不同品牌维生素C片主要成分基本一致,可能是辅剂和工艺上存在细微差异。通过结合近红外光谱分析技术与化学计量学方法,可实现对国产以及进口不同品牌维生素C片的鉴别分析。     

Production and purification of CGTase of alkalophylicBacillus isolated from Brazilian soil

Alkalophylic bacilli that produce cyclodextringlycosyltransferase (CGTase) were isolated from Brazilian soil, with a scheme of two plating steps. In the first step, the bacterial isolate forms a halo in the cultivation medium that contains γ-cyclodextrin (CD) complexing dyes. The CGTase of an isolate was purified 157-fold by biospecific affinity chromatography, with β-CD showing a mol wt of 77,580 Daltons. It produces a γ- to β-CD ratio of 0.156 and a small amount of α-CD, using maltodextrin 10% as substrate, at 50°C, pH 8.0 and 22 h reaction time, reaching 21.4% conversion of the substrate to cyclodextrins. In the second screening step, the isolates chosen give larger halos with β-CD complexing dyes, and smaller halos with β-CD complexing dyes, leading to a 30% improvement in γ-CD selectivity, although at lower total yield for cyclodextrins (11.5%).     

Computer based screening of compound databases: 1. Preselection of benzamidine-based thrombin inhibitors

We present a computational protocol which uses the known three-dimensional structure of a target enzyme to identify possible ligands from databases of compounds with low molecular weight. This is accomplished by first mapping the essential interactions in the binding site with the program GRID. The resulting regions of favorable interaction between target and ligand are translated into a database query, and with UNITY a flexible 3D database search is performed. The feasibility of this approach is calibrated with thrombin as the target. Our results show that the resulting hit lists are enriched with thrombin inhibitors compared to the total database.     

Janoxepin and brevicompanine B: antiplasmodial metabolites from the fungus Aspergillus janus

Two compounds janoxepin (1) and brevicompanine B (2) were isolated from the fungus Aspergillus janus and the structures elucidated by one- and two-dimensional NMR spectroscopic methods and mass spectrometry. Janoxepin is a novel oxepin derivative with a rare d-leucine incorporated. Brevicompanine B has previously only been isolated from Penicillium brevicompactum. Both compounds were tested in antimicrobial assays and found to be active against the malaria parasite Plasmodium falciparum 3D7 (IC₅₀-values of 28 and 35 mg/ml, respectively). However, no activity was observed in antifungal or antibacterial assays.