化学基元组学与药物创新

化学基元组学(chemomics)是与化学信息学、生物信息学、合成化学等学科相关的交叉学科.生物系统从内源性小分子(天然砌块)出发,通过酶催化的化学反应序列制造天然产物.生物系统通过化学反应和天然砌块向目标天然产物"砌入"一组原子,这样的一组原子称为化学基元(chemoyl).化学基元组(chemome)是生物组织中所含有的化学基元的全体.化学基元组学研究各种化学基元的结构、组装与演化的基本规律.在生存压力和繁衍需求的驱动下,生物系统已经进化出有效手段来合成天然产物以应付环境的变化,并产生了丰富多彩的生物和化学多样性.近年来,人们意识到药物创新的瓶颈之一是药物筛选资源的日益枯竭.化学基元组学可以解决这个瓶颈问题,它通过揭示生物系统制备化学多样性的规律,发展仿生合成方法制备类天然化合物库(quasi natural product libraries)以供药物筛选.本文综述了化学基元组学的主要研究内容及其在药物创新各领域中的潜在应用.     

点击化学及其应用

点击化学反应选用易得原料，通过可靠、高效化学反应快速合成大量新化合物，且反应条件温和、产物收率高和不需要专门的分离提纯。本文介绍了点击化学（click chemistry）的一些基本概念，综述了点击化学作为一种新的合成方法在药物中的先导化合物库、糖类化合物、天然化合物、生物大分子和高分子中聚合物上的应用，并对其发展前景进行了展望。     

多样性导向的“类天然产物”化合物库合成

天然产物是药物发现中先导化合物的重要来源.高通量筛选技术的发展和近年来化学生物学研究的深入,对拓展天然产物与活性相关的＂化学空间＂提出了新要求.用多样性导向合成方法建立骨架多样、构造复杂、立体化学多样性的＂类天然产物＂化合物库进行生物学相关研究,并以此为基础发现药物先导化合物正在成为一种趋势.在此过程中,发展具有立体选择性和区域选择性,能够广泛应用于多种底物的有机化学反应起着关键作用.     

活性天然产物和结构多样性类天然产物的合成

天然产物骨架的复杂性和丰富的官能团化赋予了天然产物类化合物独有的生物学活性,因此天然产物作为药物研究的先导化合物有其无法替代的独特性质,比如紫杉醇、红霉素和利福霉素帮助科学家们理解重要的生物过程。以往化学家对天然产物独有情钟,但仅仅以合成天然产物本身为最终目的。今天,化学家们开始利用传统的合成方法来制备结构多样性的类天然产物化合物。这种利用合成手段制备的小分子化合物在生物学的基础研究和药物研究中将起到关键的作用。     

酶-金属单原子复合催化剂在一锅法生物-化学反应的应用（英文）

酶催化与金属单原子催化结合,理论上可开发众多新的绿色化学合成反应,是催化科学的一个重要研究前沿方向.酶-金属单原子复合催化剂兼具酶和金属单原子催化剂的高效、高立体选择性等优点.目前已成功构建的单原子分散金属催化剂的载体一般为刚性的无机载体,利用柔性蛋白分子作为载体制备单原子分散金属催化剂的技术瓶颈问题在于蛋白分子具有柔性、构象易变的特点,并且氨基酸残基与金属原子之间的相互作用力较弱,蛋白分子表面的氨基酸残基难以与金属单原子稳定结合.针对这样一个关键技术瓶颈问题,我们建立了酶-金属单原子复合催化剂的光化学合成方法.本文研究酶-金属单原子复合催化剂在生物-化学一锅级联反应合成联苯类手性醇中的催化性能.联苯类手性醇是手性药物的重要中间体,通常通过多步化学法或生物-化学级联法制备.相比于多步化学法,利用生物-化学级联反应制备联苯类手性化合物具有反应条件温和、选择性高、环境友好等优点.采用光化学法合成脂肪酶-钯单原子复合催化剂(Pd₁/CALB-Pluronic),通过球差矫正扫描透射电镜和扩展X射线吸收精细结构表征复合催化剂的形貌.首先研究了Pd₁/...     

有机化学进展(2011~2012)

本文综述了中国大陆地区有机化学研究人员2011至2012年两年内在合成方法学、有机合成化学、元素有机化学以及天然产物化学等领域获得的重要成果。文章中共引用参考文献355篇,其中110多篇手性金属配合物和有机小分子催化的不对称反应、金属催化的碳氢键活化等合成方法学论文和30余篇氟有机化学论文基本来源于德国《应用化学》(国际版)和《美国化学杂志》。本文汇集了中国有机化学家两年中合成的150多个具有生物活性和化学结构多样性的天然产物,其中不乏具有高度挑战性的复杂天然分子。在近两年中中国有机化学家从陆地和海洋的生物体内发现各种不同类型新天然产物90多个。     

用组合化学建立天然产物类似物库

天然产物是药物先导化合物的重要来源.组合化学技术在天然产物的研究中起着越来越重要的作用.目前已构建并合成了许多以天然产物为模板的化合物库,为基于天然产物的药物研究开辟了广阔的空间.     

高通量天然产物化学和毛细管核磁共振探头技术的应用

介绍了近几年为高通量药物筛选构建大型天然产物样品库的高通量天然产物化学,即多通道平行高效液相制备和平行液质联用分析技术;详细介绍了核磁共振新技术即体积小和质量灵敏度高的毛细管核磁共振探头技术,该探头技术的成功应用使得天然产物样品库中活性化合物的结构鉴定所需样品量降低到前所未有的微克级水平;展望了源于中药的天然产物作为小分子探针开展脑功能方面的化学基因组学研究。     

海藻酸钠和壳聚糖聚电解质微胶囊及其生物医学应用

本文综述了天然多糖聚电解质海藻酸钠和壳聚糖的结构与化学性能（包括凝胶性能、生物相容性、生物可降解性及温和反应性）;微胶囊制备技术及其强度性能和膜渗透性评价方法;微胶囊作为细胞载体在体内分泌治疗性物质（如：胰岛素、多巴胺）或分解代谢毒性物质（如：尿素）,作为三维药物筛选系统、干细胞增殖分化研究工具,以及药物释放载体等生物医学领域的研究进展;最后讨论了天然多糖微胶囊研究与应用中需要解决的问题。     

凝聚态化学视角下的生物矿化

凝聚态化学是研究凝聚态材料的合成、组分、结构、性能、相互作用及相关化学反应等多个领域的一门学科。近年来对生物矿物这种特殊的天然凝聚态材料不断深入的探索,极大扩展了凝聚态化学原有的研究视野。这些生物矿物常通过非经典的方式,在温和而复杂的体内甚至体外环境中形成;它们具有长期进化筛选出的跨尺度多级组织结构,充分利用了材料微观形态和不同凝聚态材料间的表、界面相互作用,因此具有非常优异的性能。本文通过分析生物矿物形成和转化过程中涉及的几种特殊机制,阐明真实环境条件下凝聚态材料合成和凝聚态化学反应的一些新特征。同时,还将介绍由生物矿物相关研究推动的凝聚态化学的实际应用。最后,对该领域未来需要解决的问题和重要发展方向做出展望。     

Chemomics and drug innovation

Chemomics is an interdisciplinary study using approaches from chemoinformatics,bioinformatics,synthetic chemistry,and other related disciplines.Biological systems make natural products from endogenous small molecules (natural product building blocks) through a sequence of enzyme catalytic reactions.For each reaction,the natural product building blocks may contribute a group of atoms to the target natural product.We describe this group of atoms as a chemoyl.A chemome is the complete set of chemoyls in an organism.Chemomics studies chemomes and the principles of natural product syntheses and evolutions.Driven by survival and reproductive demands,biological systems have developed effective protocols to synthesize natural products in order to respond to environmental changes;this results in biological and chemical diversity.In recent years,it has been realized that one of the bottlenecks in drug discovery is the lack of chemical resources for drug screening.Chemomics may solve this problem by revealing the rules governing the creation of chemical diversity in biological systems,and by developing biomimetic synthesis approaches to make quasi natural product libraries for drug screening.This treatise introduces chemomics and outlines its contents and potential applications in the fields of drug innovation.     

High-throughput screening for bioactive components from traditional Chinese medicine

Throughout the centuries, traditional Chinese medicine has been a rich resource in the development of new drugs. Modern drug discovery, which relies increasingly on automated high throughput screening and quick hit-to-lead development, however, is confronted with the challenges of the chemical complexity associated with natural products. New technologies for biological screening as well as library building are in great demand in order to meet the requirements. Here we review the developments in these techniques under the perspective of their applicability in natural product drug discovery. Methods in library building, component characterizing, biological evaluation, and other screening methods including NMR and X-ray diffraction are discussed.     

Synthesis and Applications of Hajos–Parrish Ketone Isomers

Numerous natural products possess ring systems and functionality for which Hajos–Parrish ketone isomers with a transposed methyl group (termed “iso‐Hajos–Parrish ketones”) would be of value. However, such building blocks have not been exploited to the same degree as the more typical Hajos–Parrish hydrindane. An efficient three‐step synthesis of such materials was fueled by a simple method for the rapid preparation of highly functionalized cyclopentenones, several of which are new chemical entities that would be challenging to access through other approaches. Furthermore, one iso‐Hajos–Parrish ketone was converted into two distinct natural product analogues and one natural product. As one indication of the value of these new building blocks, that latter target was obtained in 10 steps, having previously been accessed in 18 steps using the Hajos–Parrish ketone.     

A concise route to virginiamycin M2

Modular, fully synthetic routes to structurally complex natural products provide useful avenues to access chemical diversity. Herein we report a concise route to virginiamycin M2, a member of the group A streptogramin class of natural products that inhibits bacterial protein synthesis. Our approach features a longest linear sequence of six steps from 7 simple building blocks, and is the shortest and highest yielding synthesis of any member of the streptogramin class reported to date. We believe this route will enable access to unexplored structural diversity and may serve as a useful tool to improve the therapeutic potential of the streptogramin class of antibiotics.     

Current progress in natural product-like libraries for discovery screening

Natural product-like libraries represent an effort to combine the attractive features of natural products and combinatorial libraries for high-throughput screening. Three approaches to natural product-like library design are discussed: (1) Libraries based on core scaffolds from individual natural products, (2) libraries of diverse structures with general structural characteristics of natural products, and (3) libraries of diverse structures based on specific structural motifs from classes of natural products. Examples of successful applications in discovery screening are described for each category. These studies highlight the exciting potential of natural product-like libraries in both chemical biology and drug discovery.     

Recent development in preparation reactivity and biological activity of enaminoketones and enaminothiones and their utilization to prepare heterocyclic compounds

Enaminoketones and esters are gaining increased interest, particularly cyclic‐β‐enaminoesters, which are known as important intermediates for the synthesis of heterocycles and natural products, because the enantioselective preparation of highly functionalized compounds is of central importance in synthetic chemistry. Enaminones are versatile synthetic intermediates that combine the ambident nucleophilicity of enamines with the ambident eletrophilicity of enones. Enaminoketones and enaminonitriles have proven to be versatile building blocks for the synthesis of various heterocycles such as pyridine, pyrimidine and pyrrole deriva tives. Enaminones systems have “enone” character, and may act as acceptors in both 1,2 and 1,4‐additions. In this way the enaminone serves as a scaffold for annulation, and can gain access to systems such as pyrroles indolizidines, quinolizidines and perhydroindoles, all of which are common motifs in alkaloid structures. Enaminones are frequently employed as building blocks for the preparation of a variety of bicyclic compounds of biological interest and have been recently recognized as potential anticonvulsant compounds. Since a large number of developments in the use of enaminones in heterocyclic synthesis have occurred, a review of the recent developments in the synthetic approaches, covering the literature since 1995 until 2004, to these interesting molecules and their useful chemical transformations and biological activity can be considered of considerable value.     

Wirkstoffe auf Basis biologisch aktiver Naturstoffe

The potential of natural products as sources for new drugs and lead structures is still largely unexplored and due to their unmatched structural diversity, secondary natural products continue to play a highly significant role in drug discovery. This article gives an overview on different strategies, chemical and biological methods as well as limiting problems for the search, screening, isolation and characterization of bioactive natural products from different sources. Ecological aspects and the importance of biodiversity and sustainable sourcing are also discussed.     

Electrophilic natural products and their biological targets

The study of biologically active natural products has resulted in seminal contributions to our understanding of living systems. In the case of electrophilic natural products, the covalent nature of their interaction has largely facilitated the identification of their biological binding partners. In this review, we provide a comprehensive compilation of electrophilic natural products from all major chemical classes together with their biological targets. Covering Michael acceptor systems, ring-strained compounds and other electrophiles, such as esters or carbamates, we highlight representative and instructive examples for over 20 electrophilic moieties. The fruitful cooperation of natural product chemistry, medicinal chemistry and chemical biology has produced a collection of well-studied examples for how electrophilic natural products exert their biological functions that range from antibiotic to antitumor effects. Special emphasis is put on the elucidation of their respective biological targets via activity-based protein profiling, which together with the recent advancements in mass spectrometry has been crucial to the success of the field. The wealth of naturally occurring electrophilic moieties and their chemical complexity enables binding of a large variety of biological targets, such as enzymes of all classes, nonenzymatic proteins, DNA and other cellular compounds. With approximately 30,000 genes in the human genome but only 266 confirmed protein drug targets, the study of biologically active, electrophilic natural products has the potential to provide insights into fundamental biological processes and to greatly aid the discovery of new drug targets.     

Natural product-likeness score and its application for prioritization of compound libraries

Natural products (NPs) have been optimized in a very long natural selection process for optimal interactions with biological macromolecules. NPs are therefore an excellent source of validated substructures for the design of novel bioactive molecules. Various cheminformatics techniques can provide useful help in analyzing NPs, and the results of such studies may be used with advantage in the drug discovery process. In the present study we describe a method to calculate the natural product-likeness score--a Bayesian measure which allows for the determination of how molecules are similar to the structural space covered by natural products. This score is shown to efficiently separate NPs from synthetic molecules in a cross-validation experiment. Possible applications of the NP-likeness score are discussed and illustrated on several examples including virtual screening, prioritization of compound libraries toward NP-likeness, and design of building blocks for the synthesis of NP-like libraries.     

Quality, not quantity: the role of natural products and chemical proteomics in modern drug discovery

Chemical genetics and reverse chemical genetics parallel classical genetics but target genes at the protein level and have proven useful in recent years for screening combinatorial libraries for compounds of biological interest. However, the performance of combinatorial chemistry in filling pharmaceutical pipelines has been lower than anticipated and the tide may be turning back to Nature in the search for new drug candidates. Even though diversity oriented synthesis is now producing molecules that are natural product-like in terms of size and complexity, these molecules have not evolved to interact with biomolecules. Natural products, on the other hand, have evolved to interact with biomolecules, which is why so many can be found in pharmacopoeias. However, the cellular targets and modes of action of these fascinating compounds are seldom known, hindering the drug development process. This review focuses on the emergence of chemical proteomics and reverse chemical proteomics as tools for the discovery of cellular receptors for natural products, thereby generating protein/ligand pairs that will prove useful in identifying new drug targets and new biologically active small molecule scaffolds. Such a system-wide approach to identifying new drugable targets and their small molecule ligands will help unblock the pharmaceutical product pipelines by speeding the process of target and lead identification.