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.     

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．     

有机合成在创新药物研发中的应用与进展

论述了现代有机合成化学在一些创新药物尤其是"重磅炸弹"新药,如索非布韦(Sofosbuvir)、利伐沙班(Rivaroxaban)、恩杂鲁胺(Enzalutamide)、卡格列净(Canagliflozin)和托法替尼(Tofacitinib),研发中的应用和进展,突出显示了催化过程、闭环复分解反应、钯催化的交叉偶联、绿色化学和叠缩工艺等合成方法.通过数十个新分子实体药物发明历程的回顾,诠释了现代有机合成在新药开发中的重要作用.     

金属配合物在天然药物研究及分析中的应用进展

评述了天然药物中有效成分的金属配合物在新药开发，天然药物中有效成分定量分析的应用进展，引用文献68篇。     

量子点在分析检测中的应用进展

量子点是一类粒径在纳米尺度的荧光材料,因其独特而优良的光学性质已在化学、生物和医学的研究及应用方面取得了很大进展。本文综述了近年来量子点在重金属离子和有机分子的定量分析、药物分析以及生命分析等领域的应用进展。     

酶在光学活性药物合成中的应用

作为天然的生物催化剂，酶催化化学反应具有催化效率和立体选择性高、反应条件温和的特点。酶不仅适于外消旋药物及其合成子的有效拆分，而且可用于光学活性药物手性中心的直接构建。本文介绍水解酶、氧化还原酶及其酶源在光学活性药物合成中的应用。参考文献２９篇     

人工智能发现活性分子背景下天然药物化学教学的转型与发展*

人工智能(AI)在活性分子发现及药物筛选方面的应用日趋深入,革新了传统发现天然药物的方式,重构了药物发现及设计的格局。这就要求天然药物化学人才熟练掌握天然药物化学基础知识、具备多学科交叉分析问题能力以及培养和树立与时俱进的逻辑思维。为顺应人工智能时代发展要求,天然药物化学教学需要构建AI参与天然药物发现教学体系、提供AI参与天然药物发现的直观教学、筛选优秀网络教学资源引导学生自主学习,同时培养学生在AI参与天然药物发现中的思考能力。     

肽自组装水凝胶的制备及在生物医学中的应用

短肽自组装水凝胶作为一种新型的生物材料,具有生物相容性高、免疫原性低、含水量高、降解产物可被机体重吸收利用、结构与天然细胞外基质类似等优点,使其在材料科学、生物医药及临床医学等领域具有广阔的应用前景。在这篇综述中,我们主要介绍了常用的几种制备稳定的肽自组装水凝胶方法,包括酶催化的水凝胶化、化学/物理交联的水凝胶化以及光催化的水凝胶化。进一步,我们介绍一些关于肽自组装水凝胶在药物递送和抗肿瘤治疗、抗菌和伤口愈合以及3D生物打印和组织工程中的应用。我们希望通过本文的论述能引起更多的人对肽自组装水凝胶的关注,以推进其在生物医学领域应用的发展。     

天然-合成高分子生物杂化材料在生物医学领域中的应用

综述了天然—合成高分子生物杂化材料在生物医学领域中的应用，并分析了它作为组织工程基质和药物载体的优点，指出生物杂化材料是生物医用材料的发展趋势。     

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。     

序列特异性DNA断裂蛋白质

序列特异性DNA断裂蛋白质是在序列特异性DNA结合蛋白质及小分子DNA断裂试剂基础上设计合成的。其基本原理是在含有DN A结合域的蛋白质上引入一个金属鳌合剂并鳌合一个适当的金属离子,其中序列特异性DNA结合蛋白质具有与DNA特定序列结合的能力,从而可以起导向物的作用,而引入的金属鳌合齐J与金属离子复合物具有断裂DNA的功能,两者协同作用可以达到序列特异性断裂DNA的目的。     

高通量筛选策略在细胞色素P450单加氧酶定向进化中的应用

细胞色素P450单加氧酶具有催化活性混杂性的特点,可以催化多种氧化反应,因而在生物催化领域受到了极大的关注。然而P450单加氧酶往往存在催化活性低、稳定性差、区域和立体选择性不理想等问题,从而限制了其在生物催化领域的广泛运用。蛋白质定向进化的发展与运用为改善P450单加氧酶的催化性能提供了有效的途径,而一种高效的高通量筛选策略是保证酶蛋白定向进化成功实施的关键。本文综述了P450单加氧酶定向进化过程中高通量筛选策略的最新进展。     

浅谈2018年诺贝尔化学奖:驾驭进化的力量

In living organisms, protein functions are constantly evolving over generations throughout the history. Through iterative rounds of genetic mutations and natural selection of fit phenotypes, protein functions have been gradually optimized. This process could be mimicked and even greatly accelerated in the laboratory, when the selection pressure is directly applied to biomolecules of interest, which forms the basis of a technique called directed evolution. The Nobel Prize in chemistry 2018 was awarded jointly to Frances Arnold, George Smith and Gregory P. Winter for their pioneering contributions to the development and applications of directed evolution. Here we briefly review the history of this technique and its impact on renewable energy and pharmaceutical industry.     

Surface-supported bilayers with transmembrane proteins: role of the polymer cushion revisited

Protein lateral mobility in surface-supported bilayers is often much lower than the mobility of the lipids. In the present study we explore whether the incorporation of a PEG cushion between the bilayer and the substrate increases the lateral mobility of transmembrane proteins in bilayers produced via directed assembly, a method based on Langmuir-Blodgett deposition techniques. In our experiments, the PEG cushions were incorporated by adding PEG lipids to the protein/lipid monolayer at the air/water interface, at the first step of bilayer assembly. The protein and lipid mobilities in 160 different bilayers, with various PEG molecular weights and PEG lipid concentrations, were measured and compared. We found that the measured diffusion coefficients do not depend on the PEG molecular weight or the PEG lipid concentration and are very similar to the values measured in the absence of PEG. Therefore, contrary to our expectations, we found that a PEG cushion does not necessarily increase protein mobility, suggesting that the low protein mobility is not a consequence of protein-substrate interactions. Furthermore, we showed that the low protein mobility is not due to protein aggregation. The major determinant of protein mobility in surface-supported bilayer systems appears to be the method of bilayer assembly. While proteins were always mobile if the bilayers were prepared using the directed assembly method, in the presence and absence of a PEG cushion, other bilayer assembly protocols resulted in complete lack of protein mobility.     

DNA tile based self-assembly: building complex nanoarchitectures.

DNA tile based self-assembly provides an attractive route to create nanoarchitectures of programmable patterns. It also offers excellent scaffolds for directed self-assembly of nanometer-scale materials, ranging from nanoparticles to proteins, with potential applications in constructing nanoelectronic/nanophotonic devices and protein/ligand nanoarrays. This Review first summarizes the currently available DNA tile toolboxes and further emphasizes recent developments toward self-assembling DNA nanostructures with increasing complexity. Exciting progress using DNA tiles for directed self-assembly of other nanometer scale components is also discussed.     

Lysine‐directed staining of proteins for MS‐based analyses

Visualization of proteins and MS‐based analyses are elemental tasks in modern biochemistry. Nevertheless, reports about covalent protein dyes and their suitability for subsequent MS experiments remain scarce. In a recent work, we demonstrated that covalent prestaining of proteins with Uniblue A drastically speeds up proteomic workflows. The present study introduces dabsyl chloride as another truly MS‐compatible protein stain. Remarkably, although Uniblue A and dabsyl chloride employ different nucleophilic reaction mechanisms, both are highly specific for lysine residues. The predictable peptide modifications allow easy integration into state‐of‐the‐art bioinformatic workflows. Further, lysine‐directed derivatizations with hydrophobic reagents such as dabsyl chloride complement the cysteine‐directed ALiPHAT strategy for increasing the sensitivity of peptide identifications.     

Controlling and switching the morphology of micellar nanoparticles with enzymes

Micelles were prepared from polymer-peptide block copolymer amphiphiles containing substrates for protein kinase A, protein phosphatase-1, and matrix metalloproteinases 2 and 9. We examine reversible switching of the morphology of these micelles through a phosphorylation-dephosphorylation cycle and study peptide-sequence directed changes in morphology in response to proteolysis. Furthermore, the exceptional uniformity of these polymer-peptide particles makes them amenable to cryo-TEM reconstruction techniques lending insight into their internal structure.     

Templated assembly of organic-inorganic materials using the core shell structure of the P22 bacteriophage

Biomimetic chemistry offers new approaches to supramolecular materials synthesis and assembly. We have demonstrated that an assembled viral protein cage, comprising an organic core-shell structure, can be used as a template for the size constrained synthesis of Fe(2)O(3). Particle nucleation is directed by the inner scaffold protein layer, while the size constraints are determined by the outer capsid layer.     

Fluorescence activated cell sorting for enzymatic activity

Directed evolution is a reliable method for protein engineering and as a tool for investigating structure/function relationships. A key for a successful directed evolution experiment is oftentimes the screen. Fluorescence activated cell sorting (FACS) is powerful high-throughput screening approach to isolate and identify mutants from large protein libraries. FACS has been successful in isolating proteins with improved or altered binding affinity. However, FACS screening for mutants with enhanced catalytic activity has been met with limited success. This review focuses on the FACS screening of protein libraries for enzymatic activity.     

Electrochemical Oxidation of Glucose Using Mutant Glucose Oxidase from Directed Protein Evolution for Biosensor and Biofuel Cell Applications

In this study, electrochemical characterisation of glucose oxidation has been carried out in solution and using enzyme polymer electrodes prepared by mutant glucose oxidase (B11-GOx) obtained from directed protein evolution and wild-type enzymes. Higher glucose oxidation currents were obtained from B11-GOx both in solution and polymer electrodes compared to wt-GOx. This demonstrates an improved electrocatalytic activity towards electrochemical oxidation of glucose from the mutant enzyme. The enzyme electrode with B11-GOx also showed a faster electron transfer indicating a better electronic interaction with the polymer mediator. These encouraging results have shown a promising application of enzymes developed by directed evolution tailored for the applications of biosensors and biofuel cells.