Boronated thymidine analogues for boron neutron capture therapy

Concise synthetic methods for synthesizing 3-carboranyl thymidine analogues (3CTAs) modified with cyclic and acyclic alcohols have been developed. The synthesis of these potential boron neutron capture therapy (BNCT) agents and their preliminary biological evaluation is described.     

Boronated Thymidine Analogues for Boron Neutron Capture Therapy

Concise synthetic methods for synthesizing 3-carboranyl thymidine analogues (3CTAs) modified with cyclic and acyclic alcohols have been developed. The synthesis of these potential boron neutron capture therapy (BNCT) agents and their preliminary biological evaluation is described.     

Current strategies for characterization of mucin-domain glycoproteins

Glycosylation, and especially O-linked glycosylation, remains a critical blind spot in the understanding of post-translational modifications. Due to their nature as proteins defined by a large density and abundance of O-glycosylation, mucins present extra challenges in the analysis of their structure and function. However, recent breakthroughs in multiple areas of research have rendered mucin-domain glycoproteins more accessible to current characterization techniques. In particular, the adaptation of mucinases to glycoproteomic workflows, the manipulation of cellular glycosylation pathways, and the advances in synthetic methods to more closely mimic mucin domains have introduced new and exciting avenues to study mucin glycoproteins. Here, we summarize recent developments in understanding the structure and biological function of mucin domains and their associated glycans, from glycoproteomic tools and visualization methods to synthetic glycopeptide mimetics.     

Catalytic RNA,ribozyme, and its applications in synthetic biology

Ribozymes are functional RNA molecules that can catalyze biochemical reactions. Since the discovery of the first catalytic RNA, various functional ribozymes (e.g., self-cleaving ribozymes, splicing ribozymes, RNase P, etc.) have been uncovered, and their structures and mechanisms have been identified. Ribozymes have the advantage of possessing features of “RNA” molecules; hence, they are highly applicable for manipulating various biological systems. To fully employ ribozymes in a broad range of biological applications in synthetic biology, a variety of ribozymes have been developed and engineered. Here, we summarize the main features of ribozymes and the methods used for engineering their functions. We also describe the past and recent efforts towards exploiting ribozymes for effective and novel applications in synthetic biology. Based on studies on their significance in biological applications till date, ribozymes are expected to advance technologies in artificial biological systems.     

Can synthetic pesticides be replaced with biologically-based alternatives?—an industry perspective

Agricultural chemical companies have invested in the discovery and development of biological pesticides to complement synthetic pesticides for the control of insects, diseases, and weeds on agronomic and horticultural crops. For plant disease control, companies envisage biological fungicides entering markets where they have the best chance of performing and which are most receptive to using biological control methods. Fewer regulatory requirements can mean faster registration for a biological than a synthetic pesticide. However, industry’s requirements for competitive performance, effective formulations, and economic production can mean significant investments in time and money for a biological pesticide, although total investment may be less than for a synthetic pesticide. One biocontrol project in which industry has invested is baculoviruses for insect control. Insect baculoviruses, genetically modified to kill insects faster than wild-type viruses, are attractive biocontrol agents because their selectivity to insect pests and safety to beneficial insects and mammals enable them to compete with synthetic insecticides. Industry is looking for similar biocontrol opportunities in disease control. Biocontrol agents for seedling disease, root rot, and postharvest disease control have been registered by the EPA and are trying to compete with synthetic fungicides for market share. To date, effective biocontrol agents have not been identified for the control of serious foliar diseases, such as grape downy mildew, potato late blight, wheat powdery mildew, and apple scab. Farmers must rely on synthetic fungicides and agronomic methods to control these diseases for the foreseeable future. Received 06 February 1997/ Accepted in revised form 01 June 1997     

基因组工程在医学合成生物学中的应用

合成生物学旨在建立一套完整的工程理论和方法,通过设计和组装基本生物学元件,更为有效地实现复杂生物系统的设计,并使其完成可编程的生物学功能。近年来随着可编程基因组元件的出现,特别是CRISPR和CRISPRi技术平台的建立和完善,使得合成生物学进入了一个全新发展的时期。本文重点综述CRISPR等基因组编辑和调控技术,其在构建可编程生物学元件和复杂基因线路的应用以及合成生物学在医学中(称为医学合成生物学)的发展前景。     

Synthetic approaches to polycyclic semiochemicals and their derivatives: combinatorial methods towards phytochemicals

Semiochemicals are natural products occurring in plants, bacteria or animals which function as carriers of a special message. Depending on the mode of function of the semiochemicals, they are divided into pheromones that trigger a response in members of the same species and allelochemicals (kairomones, allomones) that act between individuals of different species. Semiochemicals are very important compounds that influence the behavior of plants and animals and their adaption to a changing environment. As their importance for plants, animals and the ecological system itself is huge, the synthetic access to these chemicals, their precursors and derivatives is of high interest. Beyond novel strategies for the construction of semiochemical skeletons, combinatorial methods have been implemented to synthesize medium-sized and large-sized libraries that enable diverse modifications of the active compounds. These combinatorial approaches allow the screening for more active compounds and they elucidate the mode of action of the semiochemical or of the biological target. This review summarizes the state of the art procedures for the synthesis of important skeletons appearing in semiochemicals and gives special synthetic procedures for selected examples if the procedure is suitable for a general transfer to the synthesis of derivatives. The synthetic examples are given in the context of known active phytochemicals and their function that allows an evaluation of the given procedures with respect to the fulfillment of the common structural requirements (the structural diversity and flexibility) and the importance for the regulation of biological systems. Parts of this review were given in a lecture at the BioCom 12 in Cadiz, 2012.     

Recent advances in the synthetic and medicinal perspective of quinolones: A review

In the modern scenario, the quinolone scaffold has emerged as a very potent motif considering its clinical significance. Quinolones possess wide range of pharmacological activities such as anticancer, antibacterial, antifungal, antiprotozoal, antiviral, anti-inflammatory, carbonic anhydrase inhibitory and diuretic activity etc. The versatile synthetic approaches have been successfully applied and several of the resulted synthesized compounds exhibit fascinating biological activities in numerous fields. This has prompted to discover quinolone-based analogues among the researchers due to its great diversity in biological activities. In the past few years, various new, efficient and convenient synthetic approaches (including green chemistry and microwave-assisted synthesis) have been designed and developed to synthesize diverse quinolone-based scaffolds which represent a growing area of interest in academic and industry as well as to explore their biological activities. In this review, an attempt has been made by the authors to summarize (1) One of the most comprehensive listings of quinolone-based drugs or agents in the market or under various stages of clinical development; (2) Recent advances in the synthetic strategies for quinolone derivatives as well as their biological implications including insight of mechanistic studies. (3) Further, the biological data is correlated with structure-activity relationship studies to provide an insight into the rational design of more active agents.     

生物元件的挖掘、改造与标准化

生物元件是合成生物学中的三大基本要素之一,是合成生物学的基石。现阶段,生物元件的挖掘、鉴定和改造仍然是合成生物学领域的重要研究方向之一。合成生物学与基因工程和代谢工程最显著的差别在于能够将大量的生物元件进行快速、随意的组装,而实现这一目标的前提是将生物元件标准化。目前,已经有大量基因组被解析,通过这些基因组数据库的注释与功能验证,并借助于各种生物信息学软件预测启动子、终止子、操纵了、转录因子和转录因子结合位点、核糖体结合位点以及蛋白质编码区等部件,为合成生物学提供丰富的生物元件信息资源。随着元基因组技术的兴起,大量未培养微生物中的基因和基因簇信息被解析,使得我们可以从占自然界中实际存在微生物总数99％的未知微生物中挖掘更多的生物元件。另外,生物元件可以从自然界分离出来,也可以对天然生物元件进行修饰、重组和改造后得到新的元件。酵母是异源蛋白表达的通用宿主和生物基产品生产的细胞工厂,但其本身可用的启动子非常有限,近年来各国学者在酵母启动子改造和文库构建方面做了很多工作,该文也将概述酵母启动子改造和在合成生物生物学研究领域中的应用方面的研究进展。     

Engineering chromatin states: Chemical and synthetic biology approaches to investigate histone modification function

Patterns of histone post-translational modifications (PTMs) and DNA modifications establish a landscape of chromatin states with regulatory impact on gene expression, cell differentiation and development. These diverse modifications are read out by effector protein complexes, which ultimately determine their functional outcome by modulating the activity state of underlying genes. From genome-wide studies employing high-throughput ChIP-Seq methods as well as proteomic mass spectrometry studies, a large number of PTMs are known and their coexistence patterns and associations with genomic regions have been mapped in a large number of different cell types. Conversely, the molecular interplay between chromatin effector proteins and modified chromatin regions as well as their resulting biological output is less well understood on a molecular level. Within the last decade a host of chemical approaches has been developed with the goal to produce synthetic chromatin with a defined arrangement of PTMs. These methods now permit systematic functional studies of individual histone and DNA modifications, and additionally provide a discovery platform to identify further interacting nuclear proteins. Complementary chemical- and synthetic-biology methods have emerged to directly observe and modulate the modification landscape in living cells and to readily probe the effect of altered PTM patterns on biological processes. Herein, we review current methodologies allowing chemical and synthetic biological engineering of distinct chromatin states in vitro and in vivo with the aim of obtaining a molecular understanding of histone and DNA modification function. This article is part of a Special Issue entitled: Molecular mechanisms of histone modification function.     

An overview of synthetic methods and applications of photoluminescence properties of carbon quantum dots

Carbon quantum dots (CQDs) are promising carbonaceous nanomaterials fortuitously discovered in 2004. CQDs are the rising stars in the nanotechnology ensemble because of their unique properties and widespread applications in sensing, imaging, medicine, catalysis, and optoelectronics. CQDs are notable for their excellent solubility and effective luminescence and, as a result, they are also known as carbon nanolights. Many strategies are used for the efficient and economical preparation of CQDs; however, CQDs prepared from waste or green sustainable methods have greater requirements due to their safety and ease of synthesis. Sustainable chemical strategies for CQDs have been developed, emphasizing green synthetic methodologies based on ‘top-down’ and ‘bottom-up’ approaches. This review summarizes many such studies relevant to the development of sustainable methods for photoluminescent CQDs. Furthermore, we have emphasized recent advances in CQDs' photoluminescence applications in chemical and biological fields. Finally, a brief overview of synthetic processes using the green source and their associated applications are tabulated, providing a clear understanding of the new optoelectronic materials.     

Bioflavoring and beer refermentation

Various techniques are used to adjust the flavors of foods and beverages to new market demands. Although synthetic flavoring chemicals are still widely used, flavors produced by biological methods (bioflavors) are now more and more requested by consumers, increasingly concerned with health and environmental problems caused by synthetic chemicals. Bioflavors can be extracted from plants or produced with plant cell cultures, microorganisms or isolated enzymes. This Mini-Review paper gives an overview of different systems for the microbial production of natural flavors, either de novo, or starting with selected flavor precursor molecules. Emphasis is put on the bioflavoring of beer and the possibilities offered by beer refermentation processes. The use of flavor precursors in combination with non-conventional or genetically modified yeasts for the production of new products is discussed.     

TinkerCell: modular CAD tool for synthetic biology

Background

Synthetic biology brings together concepts and techniques from engineering and biology. In this field, computer-aided design (CAD) is necessary in order to bridge the gap between computational modeling and biological data. Using a CAD application, it would be possible to construct models using available biological "parts" and directly generate the DNA sequence that represents the model, thus increasing the efficiency of design and construction of synthetic networks.

Results

An application named TinkerCell has been developed in order to serve as a CAD tool for synthetic biology. TinkerCell is a visual modeling tool that supports a hierarchy of biological parts. Each part in this hierarchy consists of a set of attributes that define the part, such as sequence or rate constants. Models that are constructed using these parts can be analyzed using various third-party C and Python programs that are hosted by TinkerCell via an extensive C and Python application programming interface (API). TinkerCell supports the notion of a module, which are networks with interfaces. Such modules can be connected to each other, forming larger modular networks. TinkerCell is a free and open-source project under the Berkeley Software Distribution license. Downloads, documentation, and tutorials are available at http://www.tinkercell.com.

Conclusion

An ideal CAD application for engineering biological systems would provide features such as: building and simulating networks, analyzing robustness of networks, and searching databases for components that meet the design criteria. At the current state of synthetic biology, there are no established methods for measuring robustness or identifying components that fit a design. The same is true for databases of biological parts. TinkerCell's flexible modeling framework allows it to cope with changes in the field. Such changes may involve the way parts are characterized or the way synthetic networks are modeled and analyzed computationally. TinkerCell can readily accept third-party algorithms, allowing it to serve as a platform for testing different methods relevant to synthetic biology.     

Synthetic cannabinoids: Analysis and metabolites

Cannabimimetics (commonly referred to as synthetic cannabinoids), a group of compounds encompassing a wide range of chemical structures, have been developed by scientists with the hope of achieving selectivity toward one or the other of the cannabinoid receptors CB1 and CB2. The goal was to have compounds that could possess high therapeutic activity without many side effects. However, underground laboratories have used the information generated by the scientific community to develop these compounds for illicit use as marijuana substitutes. This chapter reviews the different classes of these “synthetic cannabinoids” with particular emphasis on the methods used for their identification in the herbal products with which they are mixed and identification of their metabolites in biological specimens.     

聚苹果酸及其衍生物的制备与应用研究进展

摘要：天然和合成聚合物因优良的特性引起了越来越多研究者的兴趣,并已被广泛用于人类的日常生活中。聚苹果酸（Polymalic acid,PMLA）一种天然的高分子聚酯材料,具有良好的生物相容性和完全生物降解性,其衍生物同样具有优异的生物学性能,被广泛应用于众多领域中。本文就聚苹果酸及其衍生物的结构、性质和合成方法进行了概述,并全面总结了其在制药和其他领域的应用研究现状,最后对未来发展方向进行了展望。     

Uses and production of chiral 3-hydroxy-γ-butyrolactones and structurally related chemicals

Enantiopure (S)-3-hydroxy-γ-butyrolactone (HGB) and its structurally related C3–C4 chemicals are an important target for chiral building blocks in synthetic organic chemistry. For the production of these compounds, more economical and practical synthetic routes are required. To date, chiral HGBs have been produced from petrochemicals and biomass, especially malic acids and carbohydrates. This report provides a short review on the production and application of enantiopure HGBs and their related compounds. Emphasis is focused mainly on synthetic routes using biocatalysis (microbial and chemoenzymatic) and application of these compounds. Biological methods have concentrated on devising different kinds of enzymes for the synthesis of the same compound as shown in the case of hydroxynitrile, a key intermediate of synthetic statins, and integrating unit processes for the optically active HGBs and 4-chloro-3-hydroxybutyrate with recombinant microorganisms expressing multiple enzymes. Chemical methods involve selective hydrogenation of carbohydrate-based starting materials. Both types of pathways will require further improvement to serve as a basis for a scalable route to HGBs and related compounds. Several of their synthetic applications are also introduced.     

lambda-conotoxins, a new family of conotoxins with unique disulfide pattern and protein folding. Isolation and characterization from the venom of Conus marmoreus

Conotoxins are multiple disulfide-bonded peptides isolated from marine cone snail venom. These toxins have been classified into several families based on their disulfide pattern and biological properties. Here, we report a new family of Conus peptides, which have a novel cysteine motif. Three peptides of this family (CMrVIA, CMrVIB, and CMrX) have been purified from Conus marmoreus venom, and their structures have been determined. Their amino acid sequences are VCCGYK-LCHOC (CMrVIA), NGVCCGYKLCHOC (CMrVIB), and GICCGVSFCYOC (CMrX), where O represents 4-trans-hydroxyproline. Two of these peptides (CMrVIA and CMrX) have been chemically synthesized. Using a selective protection and deprotection strategy during disulfide bond formation, peptides with both feasible cysteine-pairing combinations were generated. The disulfide pattern (C(1)-C(4), C(2)-C(3)) in native toxins was identified by their co-elution with the synthetic disulfide-isomeric peptides on reverse-phase high pressure liquid chromatography. Although cysteine residues were found in comparable positions with those of alpha-conotoxins, these toxins exhibited a distinctly different disulfide bonding pattern; we have named this new family "lambda -conotoxins." CMrVIA and CMrX induced different biological effects when injected intra-cerebroventricularly in mice; CMrVIA induces seizures, whereas CMrX induces flaccid paralysis. The synthetic peptide with lambda-conotoxin folding is about 1150-fold more potent in inducing seizures than the mispaired isomer with alpha-conotoxin folding. Thus it appears that the unique disulfide pattern, and hence the "ribbon" conformation, in lambda-conotoxins is important for their biological activity.     

Facile synthesis of 2′,5′-dideoxy-, 2′,3′-dideoxy- and 3′-deoxy-1,N 6-ethenoadenosine nucleosides

Facile synthetic methods of 2′,5′-dideoxy-, 2′,3′-dideoxy- and 3′-deoxy-1,N ⁶-ethenoadenosine nucleosides by either an enzymatic dideoxyribosyl transfer reaction or a simple chemical reaction were proposed. The synthetic products were isolated and purified by preparative HPLC and their structures were confirmed by¹H NMR (500 MHz) and FAB-MS including high resolution mass measurement. These modified nucleoside analogs have not been reported yet. Therefore, these modified nucleoside analogs are of potential value to be studied further for biological activity such as anticancer or antiviral.     

Multicomponent Synthesis Strategies,Catalytic Activities,and Potential Therapeutic Applications of Pyranocoumarins: A Comprehensive Review

Fused coumarins, because of their remarkable biological and therapeutic properties, particularly pyranocoumarins, have caught the interest of synthetic organic chemists, leading to the development of more efficient and environmentally friendly protocols for synthesizing pyranocoumarin derivatives. These compounds are the most promising heterocycles discovered in both natural and synthetic sources, with anti-inflammatory, anti-HIV, antitubercular, antihyperglycemic, and antibacterial properties. This review employed the leading scientific databases Scopus, Web of Science, Google Scholar, and PubMed up to the end of 2022, as well as the combining terms pyranocoumarins, synthesis, isolation, structural elucidation, and biological activity. Among the catalysts employed, acidic magnetic nanocatalysts, transition metal catalysts, and carbon-based catalysts have all demonstrated improved reaction yields and facilitated reactions under milder conditions. Herein, the present review discusses the various multicomponent synthetic strategies for pyranocoumarins catalyzed by transition metal-based catalysts, transition metal-based nanocatalysts, transition metal-free catalysts, carbon-based nanocatalysts, and their potential pharmacological activities.     

Synthesis of polyhydroxy 7- and N-alkyl-azepanes as potent glycosidase inhibitors

An effective synthetic method for polyhydroxylated azepanes that contain an alkyl group (Me or Bu) at either the 7- or N-positions is developed. The synthetic routes are accomplished in eight to ten steps from d-(−)-quinic acid. Among the compounds synthesized, the polyhydroxy 7-butyl azepane (compound 3), which possessed the R-configuration at C-7 position, is shown to give potent inhibition against β-galactosidase (IC₅₀ = 3 μM). Preliminary biological data indicate that the length of alkyl groups along with the proper stereochemistry at the C-7 position is essential for acquiring extra binding affinity. Using similar synthetic routes, the polyhydroxy N-methyl and N-butyl azepanes are synthesized for the comparison of their biological activities.