A novel microtubule destabilizing entity from orthogonal synthesis of triazine library and zebrafish embryo screening

The first orthogonal combinatorial synthesis of a high-purity triazine library was demonstrated. Novel triazine-based microtubule inhibitors were discovered by an efficient zebrafish embryo screening and in vitro microtubule polymerization assay.     

Facilitated forward chemical genetics using a tagged triazine library and zebrafish embryo screening

An improved forward chemical genetics approach was successfully demonstrated using a tagged library concept. A small-molecule triazine library with linkers was used to screen for brain/eye developmental phenotypes in a zebrafish embryo system. This approach enabled the rapid isolation of the target proteins by facile affinity matrix preparation and elucidated the first small-molecule inhibitors for several ribosomal accessory proteins or their complex as the target.     

Anti-Obesity Natural Products Tested in Juvenile Zebrafish Obesogenic Tests and Mouse 3T3-L1 Adipogenesis Assays

(1) Background: The obesity epidemic has been drastically progressing in both children and adults worldwide. Pharmacotherapy is considered necessary for its treatment. However, many anti-obesity drugs have been withdrawn from the market due to their adverse effects. Instead, natural products (NPs) have been studied as a source for drug discovery for obesity, with the goal of limiting the adverse effects. Zebrafish are ideal model animals for in vivo testing of anti-obesity NPs, and disease models of several types of obesity have been developed. However, the evidence for zebrafish as an anti-obesity drug screening model are still limited. (2) Methods: We performed anti-adipogenic testing using the juvenile zebrafish obesogenic test (ZOT) and mouse 3T3-L1 preadipocytes using the focused NP library containing 38 NPs and compared their results. (3) Results: Seven and eleven NPs reduced lipid accumulation in zebrafish visceral fat tissues and mouse adipocytes, respectively. Of these, five NPs suppressed lipid accumulation in both zebrafish and 3T3-L1 adipocytes. We confirmed that these five NPs (globin-digested peptides, green tea extract, red pepper extract, nobiletin, and Moringa leaf powder) exerted anti-obesity effects in diet-induced obese adult zebrafish. (4) Conclusions: ZOT using juvenile fish can be a high-throughput alternative to ZOT using adult zebrafish and can be applied for in vivo screening to discover novel therapeutics for visceral obesity and potentially also other disorders.     

Gene-expression profiling in gill and liver of zebrafish exposed to produced water

The effects of produced water (a by-product of oil and gas extraction) on gene expression were studied in gills and liver tissues of zebrafish. Adult, non-breeding zebrafish were exposed to control (freshwater mixed with 5% seawater) or produced water (freshwater mixed with 5% of produced water from the Oceberg C Oil Platform in the North Sea). A zebrafish library was used to make a microarray that consisted of 15,806 unique genes. The results indicate that 27 genes in the gills and 55 genes in the liver show significantly altered expression (greater than two-fold change). More than 70% of these gene sequences have not been annotated in the Gene Ontology (GO) database, making it difficult to characterize the affected genes. CYP1A displayed the greatest upregulation in the gills (eightfold, verified with quantitative real-time PCR). This study illustrates the utility of microarray approaches in investigations of environmental effects of toxicants.     

Library Design Guided by In-house Developed Computer Tools

In recent years, combinatorial library synthesis for drug discovery begins to migrate from library synthesis solely dictated by chemistry availability to design and synthesis of libraries with more drug-like properties. Lipinski's rule of five has been used to evaluate drug-like properties of individual compound; recently LibProTM, a new computation program has been developed at Pharmacopeia to evaluate durg-like properties of libraries. By using LibPrpTM, chemists at Pharmacopeia are able to obtain information of molecular weight and ClogP distribution of a library, and percentage of library members that violate Lipinski's rule after input structures of synthons for each combinatorial step. Currently, a "virtual library design” approach that is to calculate properties of a library at conceptual phase of the library design has been used to predetermine the value of the library. Also a new computer program used to predict "Absorption” of compounds will also be discussed.     

A concise and diversity-oriented approach to the synthesis of SAG derivatives

An efficient and rapid solution-phase combinatorial synthesis of the SAG library was developed. The salient features for this library synthesis is the application of carbothioamide-derived palladacycle-catalyzed Suzuki coupling reactions for the parallel synthesis of a series of pyridine-based biaryl aldehydes under aerobic conditions and a direct N-alkylation of carbamates using NaH as base in DMF in the presence of catalytic amount of water. The resultant library has been submitted to biological screening to evaluate their potential role in the regulation of Hedgehog pathway.     

Multi-step polymer-assisted solution-phase (PASP) library synthesis of functionalized diaminobenzamides

A parallel solution-phase library synthesis of functionalized diaminobenzamides is described. The four-step library synthesis is accomplished using polymer-assisted solution-phase (PASP) synthesis techniques. This high-yielding, multi-step sequence utilizes sequestering resins for the removal of reactants, reactant by-products, and employs a resin capture/release strategy as a key library synthesis step. Step one of the sequence relies on the displacement of an activated fluoro-group from the aromatic ring of 1a, b with a variety of primary amines to introduce the first diversity position. Step two is hydrolysis of the benzoate ester to a benzoic acid which is subsequently captured on a polyamine resin, washed, and released to give 4a, b in pure form. Step three utilizes PASP resins to mediate the amide coupling of a benzoic acid with a variety of primary amines to give the aminonitrobenzamides 5a, b and introduces the second diversity position. Step four is the parallel reduction of the aminonitrobenzamides 5a, b to the functionalized diaminobenzamides 6a, b. This library synthesis proceeds with high overall purities which average 80 % over the 4-step sequence.     

Solid-phase synthesis of a thymidinyl dipeptide urea library

A thymidinyl dipeptide urea library with structural similarity to the nucleoside peptide class of antibiotics was designed and synthesized. To generate the library, a solid-phase synthesis was developed starting from 5'-azidothymidine attached to a polystyrene butyl diethylsilane (PS-DES) resin support. This study describes the prelibrary solid-phase synthesis development including maximum loading capacity optimization, selection of orthogonal functionalized side-chain protection strategies, synthesis of a 64-member test library, and optimization of the final cleavage step. Using the optimized procedures, we synthesized a 1000-member library in a 50 micromol quantity using IRORI-directed sorting technology in MiniKans, producing the target library in good yields and purity.     

海带碳点对斑马鱼胚胎发育的影响

以水产养殖常见的藻类海带为原料,通过水热法绿色、便捷、高效地合成了生物质碳点,全程实现了从原料选择到材料合成的绿色环保无污染。选择斑马鱼模式生物作为研究对象,研究不同浓度碳点在斑马鱼胚胎发育过程中的荧光成像以及代谢情况。并通过研究碳点对斑马鱼胚胎发育的影响,包括孵化率、心率和成鱼存活率等指标,评价了制备的海带碳点的生物安全性。     

Receptor-assisted combinatorial chemistry: thermodynamics and kinetics in drug discovery

Current drug discovery using combinatorial chemistry involves synthesis followed by screening, but emerging methods involve receptor-assistance to combine these steps. Adding stoichiometric amounts of receptor during library synthesis alters the kinetics or thermodynamics of the synthesis in a way that identifies the best-binding library members. Three main methods have emerged thus far in receptor-assisted combinatorial chemistry: dynamic combinatorial libraries, receptor-accelerated synthesis, and a new method, pseudo-dynamic libraries. Pseudo-dynamic libraries apply both thermodynamics and kinetics to amplify library members to easily observable levels, and attain selectivity heretofore unseen in receptor-assisted systems.     

海带碳点对斑马鱼胚胎发育的影响

以水产养殖常见的藻类海带为原料, 通过水热法绿色、便捷、高效地合成了生物质碳点, 全程实现了从原料选择到材料合成的绿色环保无污染。选择斑马鱼模式生物作为研究对象, 研究不同浓度碳点在斑马鱼胚胎发育过程中的荧光成像以及代谢情况。并通过研究碳点对斑马鱼胚胎发育的影响, 包括孵化率、心率和成鱼存活率等指标, 评价了制备的海带碳点的生物安全性。     

Copper (II)-mediated arylation with aryl boronic acids for the N-derivatization of pyrazole libraries

A N-derivatized 3-dimethylaminopropyloxypyrazole library was prepared using solution-phase parallel synthesis. The library was designed using physicochemical constraints designed to remove non-membrane-permeable molecules. Cupric acetate-mediated N-arylation with aryl boronic acids proceeded regioselectively to form the N-2-substituted derivatives. The presence of the 3-dimethylaminopropyloxy group was found to completely control the regioselectivity of the arylation. Presence of a dimethylaminoethyloxy or dimethylaminobutyloxy group gave a lesser degree of regioselectivity. The scope of the method as applied to library synthesis is discussed.     

Library design practices for success in lead generation with small molecule libraries

The generation of novel structures amenable to rapid and efficient lead optimization comprises an emerging strategy for success in modern drug discovery. Small molecule libraries of sufficient size and diversity to increase the chances of discovery of novel structures make the high throughput synthesis approach the method of choice for lead generation. Despite an industry trend for smaller, more focused libraries, the need to generate novel lead structures makes larger libraries a necessary strategy. For libraries of a several thousand or more members, solid phase synthesis approaches are the most suitable. While the technology and chemistry necessary for small molecule library synthesis continue to advance, success in lead generation requires rigorous consideration in the library design process to ensure the synthesis of molecules possessing the proper characteristics for subsequent lead optimization. Without proper selection of library templates and building blocks, solid phase synthesis methods often generate molecules which are too heavy, too lipophilic and too complex to be useful for lead optimization. The appropriate filtering of virtual library designs with multiple computational tools allows the generation of information-rich libraries within a drug-like molecular property space. An understanding of the hit-to-lead process provides a practical guide to molecular design characteristics. Examples of leads generated from library approaches also provide a benchmarking of successes as well as aspects for continued development of library design practices.     

Solid-phase convergent synthesis of a benzimidazolone library via the combination of two smaller arrays of carboxylic acids and secondary amines

The concept of convergent synthesis can be extended to combinatorial chemistry in order to obtain collections of products characterized by considerable chemical diversity and a certain molecular complexity. In this work, a library consisting of three carboxylic acids containing a benzimidazolonic functionality with variations at two positions was synthesized on solid phase. After cleavage, this library was combined with a second library consisting of 16 solid-supported amines containing two points of variation. IRORI technology was used for the split-and-mix synthesis of the final 48 members library.     

Solid-phase synthesis of macrolide analogues

The synthesis of a solid-phase macrolide library is described. The library introduces three sites of diversity to a suitable macrolide scaffold via reductive aminations.     

Small-molecule discovery from DNA-encoded chemical libraries

Researchers seeking to improve the efficiency and cost effectiveness of the bioactive small-molecule discovery process have recently embraced selection-based approaches, which in principle offer much higher throughput and simpler infrastructure requirements compared with traditional small-molecule screening methods. Since selection methods benefit greatly from an information-encoding molecule that can be readily amplified and decoded, several academic and industrial groups have turned to DNA as the basis for library encoding and, in some cases, library synthesis. The resulting DNA-encoded synthetic small-molecule libraries, integrated with the high sensitivity of PCR and the recent development of ultra high-throughput DNA sequencing technology, can be evaluated very rapidly for binding or bond formation with a target of interest while consuming minimal quantities of material and requiring only modest investments of time and equipment. In this tutorial review we describe the development of two classes of approaches for encoding chemical structures and reactivity with DNA: DNA-recorded library synthesis, in which encoding and library synthesis take place separately, and DNA-directed library synthesis, in which DNA both encodes and templates library synthesis. We also describe in vitro selection methods used to evaluate DNA-encoded libraries and summarize successful applications of these approaches to the discovery of bioactive small molecules and novel chemical reactivity.     

Soluble polymer-supported convergent parallel library synthesis

Soluble polymer-supported convergent synthesis has for the first time been successfully exploited for parallel library synthesis; sub-libraries of tripeptide iodoarenes and arylboronic acids reacted smoothly in a multipolymer PdII-catalyzed Suzuki coupling reaction to generate a library of bisaryl-linked hexapeptides.     

Efficient synthesis of a beta-peptide combinatorial library with microwave irradiation

The predictable relationship between beta-amino acid sequence and folding has inspired several biological applications of beta-peptides. For many such applications, it would be desirable to prepare and screen beta-peptide libraries. However, standard peptide synthesis protocols are not efficient enough to support a library approach for many types of beta-peptides. We recently optimized the solid-phase synthesis of beta-peptides using microwave irradiation, and we have now adapted this approach to synthesis on polystyrene macrobeads. We rapidly prepared a high-quality beta-peptide combinatorial library via a split-and-mix strategy. This library was screened in search of beta-peptide antagonists of the p53-MDM2 protein-protein interaction.     

Synthesis of an octahydroindolinone scaffold for a diversity-based chemical compound library

The synthesis of a chemical compound library using diversity-oriented synthesis (DOS) is discussed. The library is structurally inspired by the Amaryllidaceae alkaloids, a family of natural products which has been known to demonstrate potent antiviral and antineoplastic activity. Highlights of this work include the rapid, high-yielding construction of the octahydroindolinone core and the solid-phase diversification of the lactam using a neutral phosphazene base.     

Synthesis and Profiling of a Diverse Collection of Azetidine-Based Scaffolds for the Development of CNS-Focused Lead-like Libraries

The synthesis and diversification of a densely functionalized azetidine ring system to gain access to a wide variety of fused, bridged, and spirocyclic ring systems is described. The in vitro physicochemical and pharmacokinetic properties of representative library members are measured in order to evaluate the use of these scaffolds for the generation of lead-like molecules to be used in targeting the central nervous system. The solid-phase synthesis of a 1976-membered library of spirocyclic azetidines is also described.