High-volume cellular screening for anticancer agents with combinatorial chemical libraries: A new methodology

Summary A single-step cancer cell cytotoxic assay system for anticancer drug discovery has been developed which facilitates rapid screening of large combinatorial chemical libraries synthesized using the one-bead-one-compound (OBOC) methodology. Each OBOC library bead incorporates two orthogonally cleavable linkers that release the bead-bound compound at a different pH. The assay utilizes high concentrations of tumor cells mixed directly with OBOC beads and plated in soft agarose containing tissue culture medium. One of the orthogonal linkers is cleaved at neutral pH in tissue culture releasing an aliquot of compound to diffuse at a relatively high local concentration into the soft agarose immediately surrounding the bead. Active compounds are identified visually from a clear ring of tumor cell lysis which forms within 48 h around just the rare bead releasing a cytotoxic compound. The bead releasing a cytotoxin is then plucked from the agar and the remaining compound still linked to the bead can be released for structural analysis, followed by compound resynthesis and confirmatory testing. This assay system has been successfully applied to identification of lead cytotoxic compounds from model peptidic and non-peptidic combinatorial chemical libraries. Use of this methodology may facilitate anticancer drug discovery.     

Statistical molecular design of peptoid libraries

Statistical experimental design provides an efficient approach for selecting the building blocks to span the structural space and increase the information content in a combinatorial library. A set of renin-inhibitors, hexapeptoids, is used to illustrate the approach. Multivariate quantitative structure-activity relationships (MQSARs) were developed relating renin inhibition to the peptoid sequences variation, parametrized by the z-scales. By using the information from the models, the number of building block sets could be reduced from six to three. Using a statistical molecular design (SMD) reduces the number of compounds from more than 100 000 down to 90. A second SMD was used for comparison, based on less prior knowledge. This gave a reduction from over 2 billion to 120 compounds.     

Sequence-selective nonmacrocyclic two-armed receptors for peptides

Summary Tweezer-like receptor molecules have proven their potential for molecular recognition on several occasions. We decided to make twofold use of this receptor design: firstly to learn whether simple molecular forceps consisting of two peptide chains linked by a spacer are able to selectively bind to small peptides, and secondly to investigate the importance of structural preorganization for the characteristics of the receptors. We prepared two encoded combinatorial libraries based on this design, featuring two combinatorial tripeptide chains held by different scaffolds: the use of chenodeoxycholic acid as spacer provided a rigid scaffold for the forceps, whereas linking the peptide chains by a pentamethylene chain yielded a very flexible forceps structure. Molecules from the cholic acid library recognize and discriminate various enkephalins with micromolar affinities. Molecules from the flexible library show distinct interactions with the enkephalins as well, but the specificity and affinity are clearly diminished. Thus, although the interactions of molecular forceps with peptides are not crucially dependent on structural preorganization, receptors with a rigid design are clearly superior to flexible molecular forceps. Supplementary Material comprising procedures for the preparation and spectroscopical data of compounds5 through8, as well as a listing of the 104 decoded sequences from the assay of the flexible library with⁵Leu-enkephalin/Disperse Red, can be obtained from the author on request.     

Solid phase organic synthesis (SPOS): A novel route to diketopiperazines and diketomorpholines

Summary The solid phase synthesis of libraries containing a 1,3,4,6-tetrasubstituted-2,5-diketo-1,4-piperazine scaffold (DKP) or a 3,4,6-trisubstituted-2,5-diketo-1,4-morpholme scaffold (DKM) from -bromocarboxylic acids and amines is described. Using a design strategy which we refer to as divergent library design, both templates were prepared from a common intermediate. The general utility of this synthetic route in creating novel, non-peptidyl chemical libraries is discussed.     

Synthesis of deuterium-enriched and fluorine-substituted plinabulin derivatives and evaluation of their antitumor activities

Deuterium-enriched and fluorine-substituted compounds have been widely applied in drug discovery due to their advantages in the studies of clinical pharmacokinetics and metabolic profiles. Herein we synthesized a library of deuterated and fluorine-substituted plinabulin derivatives, and all 15 D- or F-compounds were characterized by MS, \(^{1}\hbox {H}\) NMR and \(^{ 13}\hbox {C}\,\hbox {NMR}\). Their antitumor activities were evaluated against human Jurkat T lymphocyte cells.     

Combinatorial synthesis of deuterium-enriched atorvastatin

It becomes more and more difficult to discover a new drug by existing models. The concept of deuteration has gained attention due to its advantages in the study of clinical pharmacokinetics and metabolic profiles. Herein we built a library of deuterated atorvastatins using combinatorial chemistry, and all 16 D-compounds were characterized by \(^{1}\hbox {H}\) NMR, \(^{13}\hbox {C}\) NMR, MS, and elemental analysis.     

便携式拉曼光谱仪用于合成大麻素类物质快速定性分析探究

我国于2021年7月将合成大麻素类物质整类列入管制,在一线查缉现场对疑似合成大麻素样品进行快速定性分析是办案民警的迫切需求。研究系统考察了拉曼光谱对合成大麻素的整体区分能力,比较了四款手持式拉曼光谱仪分析实际缴获样品时的结果差异,探讨了制约拉曼光谱在一线查缉现场广泛应用的原因。ProTT-EZRaman-A7便携式拉曼光谱仪的整体性能介于台式拉曼和手持式拉曼之间,选用该仪器采集了90种合成大麻素对照品的拉曼光谱,并利用兼容性强的KnowItAll软件建立了90种合成大麻素通用拉曼光谱库。分析90种合成大麻素的拉曼光谱,结果表明,当不存在荧光干扰时,拉曼光谱可以区分所有合成大麻素物质,但对部分结构相差一个甲基、卤素原子等的结构类似物区分度欠佳。不同款拉曼光谱仪的性能差异大,为考察其原因,本研究选用了四款手持式拉曼光谱仪分别对120份实际缴获合成大麻素样品进行了测定,随后使用KnowItAll软件并选用包含90种合成大麻素的通用拉曼光谱库对每张光谱图进行谱库检索。四款手持式拉曼光谱仪的正确匹配率分别为71.7%, 68.3%, 46.7%和24.2%。抗荧光干扰能力和分辨率的不同是造成不同...     

Toward automated biochemotype annotation for large compound libraries

Summary Combinatorial chemistry allows scientists to probe large synthetically accessible chemical space. However, identifying the sub-space which is selectively associated with an interested biological target, is crucial to drug discovery and life sciences. This paper describes a process to automatically annotate biochemotypes of compounds in a library and thus to identify bioactivity related chemotypes (biochemotypes) from a large library of compounds. The process consists of two steps: (1) predicting all possible bioactivities for each compound in a library, and (2) deriving possible biochemotypes based on predictions. The Prediction of Activity Spectra for Substances program (PASS) was used in the first step. In second step, structural similarity and scaffold-hopping technologies are employed. These technologies are used to derive biochemotypes from bioactivity predictions and the corresponding annotated biochemotypes from MDL Drug Data Report (MDDR) database. About a one million (982,889) commercially available compound library (CACL) has been tested using this process. This paper demonstrates the feasibility of automatically annotating biochemotypes for large libraries of compounds. Nevertheless, some issues need to be considered in order to improve the process. First, the prediction accuracy of PASS program has no significant correlation with the number of compounds in a training set. Larger training sets do not necessarily increase the maximal error of prediction (MEP), nor do they increase the hit structural diversity. Smaller training sets do not necessarily decrease MEP, nor do they decrease the hit structural diversity. Second, the success of systematic bioactivity prediction relies on modeling, training data, and the definition of bioactivities (biochemotype ontology). Unfortunately, the biochemotype ontology was not well developed in the PASS program. Consequently, “ill-defined” bioactivities can reduce the quality of predictions. This paper suggests the ways in which the systematic bioactivities prediction program should be improved.     

What can a chemist learn from nature’s macrocycles? – A brief, conceptual view

Macrocyclic natural products often display remarkable biological activities, and many of these compounds (or their derivatives) are used as drugs. The chemical diversity of these compounds is immense and may provide inspiration for innovative drug design. Therefore, a database of naturally occurring macrocycles was analyzed for ring size, molecular weight distribution, and the frequency of some common substructural motifs. The underlying principles of the chemical diversity are reviewed in terms of biosynthetic origin and natures strategies for diversity and complexity generation in relation to the structural diversity and similarities found in the macrocycle database. Finally, it is suggested that synthetic chemists should use not only natures molecules, but also natures strategies as a source of inspiration. To illustrate this, the biosynthesis of macrocycles by non-ribosomal peptide synthetases and terpene and polyketide cyclases, as well as recent advances of these strategies in an integrated synthesis/biotechnology approach are briefly reviewed.     

Synthesis and Studies of Fluorescein Based Derivatives for their Optical Properties,Urease Inhibition and Molecular Docking

Herein, we design and synthesized new fluorescein based derivatives by insitu formation of fluorescein ester and further treated with corresponding hydrazide and amine to yield respective compounds i.e. FB1, FB2, FB3 and FB4. The spectral purity and characterization was done by using IR, NMR and Mass spectroscopies. The synthesized derivatives were examined for their photophysical properties by using variety of organic solvents and results were discussed in details. The structural diversity of synthesized compounds motivate us to evaluate these compounds for urease inhibition. The compound FB3 (IC₅₀?=?0.0456 μM) shows 100 fold more active against Jack bean urease than standard drug thiourea (IC₅₀?=?4.7455 μM). Other synthesized compounds showed potent activity. Free radical percentage scavenging assay further supported the capacity of compounds to urease inhibition. While, molecular docking simulations helps to examine the molecular interactions of active compounds FB1, FB2, FB3 and FB4 within the binding site of urease enzyme.     

Discovery of enzyme inhibitors through combinatorial chemistry

Summary This review serves to highlight the recent examples of combinatoric methodology as applied to the discovery and optimization of enzyme inhibitors. Early research efforts focused on the identification of polypeptides from libraries as inhibitors of proteases. As solution- and solid-phase chemistries gain in sophistication, libraries containing less peptidic structural motifs have been created. A recurring design stratagem relies on the synthesis of libraries incorporating pharmacophores with known affinity for the target enzyme. Screening of these structure-based libraries has led to the discovery of small-molecule inhibitors of both proteolytic and non-proteolytic enzymes alike. Two tables are provided listing the enzyme targeted libraries through 1996. A name, generic structure and size is given for each library citation, accompanied by the enzyme screen and the structure and potency of the most active library member.     

Bifunctional scaffolds as templates for synthetic combinatorial libraries

Summary A small-molecule synthetic combinatorial library was designed and synthesized that features potential pharmacophores attached to a variety of small cyclic scaffolds. The synthesis of the library involved randomization of three types of building blocks: 20 amino acids, 10 aromatic hydroxy acids and 21 alcohols, totaling a library complexity of 4200 compounds. Mitsunobu polymer-supported etherification was used in the last randomization. The library compounds were attached to beads via an ester-bond linkage enabling both on-bead as well as in-solution screening. When the library was tested against a model target, streptavidin, specific binders were found. The structures of the most active compounds were determined from the fragmentation pattern in MS/MS experiments.Abbreviations DCM dichloromethane - DEAD diethyl azodicarboxylate - DIAD diisopropyl azodicarboxylate - DIC diisopropyl carbodiimide - DMF dimethylformamide - Fmoc fluorenylmethyloxycarbonyl - HOBt N-hydroxybenzotriazole - MeOH methanol - PPh₃ triphenylphosphine - t-Bu tert-butyl - TFA trifluoroacetic acid - TG TentaGel-S-OH 130-m resin - THF tetrahydrofuran     

基于片段的先导化合物发现中的核磁应用

基于片段的药物筛选与设计在过去10年开始出现并获得了重要的应用,数十种基于片段的药物已经进入临床测试期. 源于靶标蛋白和小分子片段本质上的弱相互作用,现代核磁技术在其中发挥着无可替代的作用. 该文简略介绍了核磁片段筛选的基本流程和重要概念,包括靶标蛋白的选择、片段库的设计、质量控制和重要的核磁筛选技术. 在后续的基于片段的先导化合物发现阶段,阐述了核磁新技术的基本理论框架,包括化学位移扰动、分子间NOE、残留偶极耦合和顺磁标记等方法,以及这些新技术在靶标/配基复合体结构研究中的实际应用,穿插演示了片段组装的基本思路和成功案例.     

Identification of potential glutaminyl cyclase inhibitors from lead-like libraries by in silico and in vitro fragment-based screening

A glutaminyl cyclase (QC) fragment library was in silico selected by disconnection of the structure of known QC inhibitors and by lead-like 2D virtual screening of the same set. The resulting fragment library (204 compounds) was acquired from commercial suppliers and pre-screened by differential scanning fluorimetry followed by functional in vitro assays. In this way, 10 fragment hits were identified (\(\sim \)5 % hit rate, best inhibitory activity: 16 \(\upmu \hbox {M}\)). The in vitro hits were then docked to the active site of QC, and the best scoring compounds were analyzed for binding interactions. Two fragments bound to different regions in a complementary manner, and thus, linking those fragments offered a rational strategy to generate novel QC inhibitors. Based on the structure of the virtual linked fragment, a 77-membered QC target focused library was selected from vendor databases and docked to the active site of QC. A PubChem search confirmed that the best scoring analogues are novel, potential QC inhibitors.     

面向课堂教学的大学物理属性素材库设计

借助于计算机编程语言的面向对象属性概念提出了一种面向课堂教学的大学物理知识点属性素材库设计.利用这种素材库能够克服当前素材库使用中表现出的某些不足,使任课教师在保留自己原有上课风格的基础上能够灵活使用各类素材,使课堂更加生动,进一步提高教学效果.     

Straightforward synthesis of thiazoline-incorporated chalconoids from phenacyl halides

A series of thiazoline-incorporated chalconoids, designed based on natural product scaffold, were efficiently synthesized via the reaction of 3-methyl-4-arylthiazole-2(3 $H$ )-thiones and appropriate phenacyl halides, and subsequent desulfurization. The starting 3-methyl-4- arylthiazole-2(3 $H$ )-thiones were also prepared from phenacyl halides. The structural aspects and ( $Z$ )-geometry of compounds were confirmed by IR and $^{1}$ H NMR spectral data. This chemistry provides a new library of compounds basically originated from phenacyl halides as building blocks, with potential activity for biomedical screening.     

Pharmacophore-based screening and drug repurposing exemplified on glycogen synthase kinase-3 inhibitors

The current study was conducted to elaborate a novel pharmacophore model to accurately map selective glycogen synthase kinase-3 (GSK-3) inhibitors, and perform virtual screening and drug repurposing. Pharmacophore modeling was developed using PHASE on a data set of 203 maleimides. Two benchmarking validation data sets with focus on selectivity were assembled using ChEMBL and PubChem GSK-3 confirmatory assays. A drug repurposing experiment linking pharmacophore matching with drug information originating from multiple data sources was performed. A five-point pharmacophore model was built consisting of a hydrogen bond acceptor (A), hydrogen bond donor (D), hydrophobic (H), and two rings (RR). An atom-based 3D quantitative structure–activity relationship (QSAR) model showed good correlative and satisfactory predictive abilities (training set \({R}^{2}= 0.904\); test set: \({Q}^{2}= 0.676\); whole data set: stability \(s = 0.803\)). Virtual screening experiments revealed that selective GSK-3 inhibitors are ranked preferentially by Hypo-1, but fail to retrieve nonselective compounds. The pharmacophore and 3D QSAR models can provide assistance to design novel, potential GSK-3 inhibitors with high potency and selectivity pattern, with potential application for the treatment of GSK-3-driven diseases. A class of purine nucleoside antileukemic drugs was identified as potential inhibitor of GSK-3, suggesting the reassessment of the target range of these drugs.     

Structurally homogeneous and heterogeneous synthetic combinatorial libraries

Summary We have designed and synthesized structurally homogeneous and heterogeneous nonpeptide libraries. Structurally homogeneous libraries are characterized by the presence of one common structural unit, a scaffold, in all library compounds (e.g. cyclopentane, cyclohexane, diketopiperazine, thiazolidine). In structurally heterogeneous libraries different organic reactions (acylation, etherification, reductive amination, nucleophilic displacement) were applied to connect bifunctional building blocks unrelated in structure (aromatic hydroxy acids, aromatic hydroxy aldehydes, amino alcohols, diamines, and amino acids). The focus of this communication is to document the use of bifunctional building blocks for the design and synthesis of structurally heterogeneous libraries ofN-(alkoxy acyl)amino acids, N,N-bis-(alkoxy acyl)diamino acids,N-acylamino ethers,N-(alkoxy acyl)amino alcohols,N-alkylamino ethers, andN-(alkoxy aryl)diamines.Abbreviations AcOH acetic acid - DCE dichloroethane - DCM dichloromethane - DEAD diethyl azodicarboxylate - DIAD diisopropyl azodicarboxylate - DIC diisopropyl carbodiimide - DIEA diisopropylethylamine - DMAP dimethylaminopyridine - DMF dimethylformamide - Fmoc fluorenylmethyloxycarbonyl - HOBt N-hydroxybenzotriazole - MeCN acetonitrile - MeOH methanol - NaOH sodium hydroxide - PEG/PS polyethylene-grafted copolystyrene - PPh₃ triphenylphosphine - t-Bu tert- butyl - TFA trifluoroacetic acid - TG TentaGel - THE tetrahydrofuran