固相有机合成小分子化学库

本文综述了1, 4-苯并二氮杂　、哌嗪二酮、异喹啉酮、二氢和四氢异喹啉、1, 4-二氢吡啶、Biginelli 型二氢嘧啶、乙内酰脲、吡咯烷、噻唑烷-4-羧酸、4-噻唑烷酮及42间噻嗪酮衍生物、咪唑衍生物、β-内酰胺及氮杂环丁酮衍生物等杂环化合物库与β-折叠模拟物、天门冬氨酸蛋白酶抑制剂、C₂ 对称HIV-1 蛋白酶抑制剂、碳酸酐酶抑制剂、含锌蛋白酶抑制剂、酪氨酸激酶抑制剂、雌激素受体配体化合物等靶向组合库固相有机合成研究方面的最新进展。     

Parallel synthesis of unsymmetrically substituted tetraphenyl porphyrins on Wang resin

A method for synthesizing combinatorial libraries of unsymmetrically substituted tetra-meso-phenyl porphyrins on polystyrene based resin is described. Attachment of 5,15-dibromo-10-(4-hydroxyphenyl)-20-(4-nitrophenyl)porphyrin onto brominated Wang resin gave a convenient scaffold for the synthesis of photoactive porphyrin libraries with three points for generating diversity. An array of nine TPP derivatives was prepared by sequential Suzuki coupling/nitro-reduction and acylation protocols.     

New scaffolds for combinatorial synthesis. 1. 5-sulfamoylisatins and their reactions with 1,2-diamines

3,3-Dichloro-5-(4-methylpiperidinosulfonyl)-2-indolinone (3) and 5-sulfamoylisatins 4 have been synthesized from 5-chlorosulfonyl-3,3-dichloro-2-indolinone (1). Compounds 4 are promising scaffolds for the solid- and liquid-phase syntheses of new combinatorial libraries of various heterocycles. Thus, the reactions of 4 with 1,2-diamines, such as o-phenylenediamine (5) and aminoguanidine hydrochloride (6), 1,2-diaminoimidazoles (9), and thiosemicarbazide led, respectively, to new heterocycles 7 and 8 and new combinatorial libraries of triazinoindoles 10 and 15. Chemsets 4, 10, and 15 were isolated as crystalline solids that were purified by recrystallization from a suitable solvent and characterized by spectroscopic methods.     

Assessing the scaffold diversity of screening libraries

Medicinal chemists have traditionally realized assessments of chemical diversity and subsequent compound acquisition, although a recent study suggests that experts are usually inconsistent in reviewing large data sets. To analyze the scaffold diversity of commercially available screening collections, we have developed a general workflow aimed at (1) identifying druglike compounds, (2) clustering them by maximum common substructures (scaffolds), (3) measuring the scaffold diversity encoded by each screening collection independently of its size, and finally (4) merging all common substructures in a nonredundant scaffold library that can easily be browsed by structural and topological queries. Starting from 2.4 million compounds out of 12 commercial sources, four categories of libraries could be identified: large- and medium-sized combinatorial libraries (low scaffold diversity), diverse libraries (medium diversity, medium size), and highly diverse libraries (high diversity, low size). The chemical space covered by the scaffold library can be searched to prioritize scaffold-focused libraries.     

Dynamic combinatorial libraries of macrocycles derived from phthalic aldehydes and α,ω-diamines

Dynamic combinatorial chemistry methodology was used to obtain eleven new polyazamacrocycles derived from isophthalic and terephthalic aldehyde and α,ω-diamines. Simple templates, such as alkali metal salts, were found to amplify large macrocycles: 45-membered [3+3]hexaazacrown and 60-membered [4+4]octaazacrown. Parent imine libraries were converted into corresponding secondary libraries of amines using a fast reduction protocol. Methyl carbamate protection of amine group allowed convenient isolation of polyazamacrocycles in very good yields.     

Liquid‐phase synthesis of mixture‐based bicyclic β‐lactam libraries

Five sets of 27‐membered combinatorial libraries of alicyclic β‐lactams were prepared via liquid‐phase Ugi 4‐center 3‐component reactions (U‐4C‐3CR) utilizing 3 different cis β‐amino acids, 3 different isonitriles and 5×3 sets of aldehydes. Through combinations of the building blocks of one of these libraries, all of the possible sublibraries were also generated. A few azetidinone derivatives were synthesized individually by parallel synthesis.     

Evaluation of evaporative light-scattering detector for combinatorial library quantitation by reversed phase HPLC

A quantitation study using reversed phase HPLC with UV and evaporative light-scattering detector (ELSD) was conducted on 90 library standards selected from 15 small molecule combinatorial libraries (six standards from each library). This study assessed the quantitation errors using a single calibration curve for rapid purity analysis of combinatorial libraries. The average quantitation error of six standards from one library at 200 microM by UV was 13. 4%, 20.6%, and 60.3%, at 214, 220, and 254 nm, respectively. By ELSD, the average quantitation error of these six standards at 200 micro was only 7.7%. Applying this ELSD calibration curve to 84 standards from 14 structurally diverse libraries, an average quantitation error of 16.4% was obtained. The average quantitation error of all 90 standards from 15 libraries using 15 calibration curves was 18.5%.     

Enzymatic Synthesis of Sequence‐Defined Synthetic Nucleic Acid Polymers with Diverse Functional Groups

The development and in‐depth analysis of T4 DNA ligase‐catalyzed DNA templated oligonucleotide polymerization toward the generation of diversely functionalized nucleic acid polymers is described. The NNNNT codon set enables low codon bias, high fidelity, and high efficiency for the polymerization of ANNNN libraries comprising various functional groups. The robustness of the method was highlighted in the copolymerization of a 256‐membered ANNNN library comprising 16 sub‐libraries modified with different functional groups. This enabled the generation of diversely functionalized synthetic nucleic acid polymer libraries with 93.8 % fidelity. This process should find ready application in DNA nanotechnology, DNA computing, and in vitro evolution of functional nucleic acid polymers.     

Selection of DNA‐Encoded Dynamic Chemical Libraries for Direct Inhibitor Discovery

Dynamic combinatorial libraries (DCLs) is a powerful tool for ligand discovery in biomedical research; however, the application of DCLs has been hampered by their low diversity. Recently, the concept of DNA encoding has been employed in DCLs to create DNA‐encoded dynamic libraries (DEDLs); however, all current DEDLs are limited to fragment identification, and a challenging process of fragment linking is required after selection. We report an anchor‐directed DEDL approach that can identify full ligand structures from large‐scale DEDLs. This method is also able to convert unbiased libraries into focused ones targeting specific protein classes. We demonstrated this method by selecting DEDLs against five proteins, and novel inhibitors were identified for all targets. Notably, several selective BD1/BD2 inhibitors were identified from the selections against bromodomain 4 (BRD4), an important anti‐cancer drug target. This work may provide a broadly applicable method for inhibitor discovery.     

Synthesis of substituted thienopyrimidine-4-ones

The parallel solution-phase synthesis of more than 3000 substituted thienopyrimidin-4-ones has been accomplished. Key reactions include assembly of the 2-thioxopyrimidin-4-one ring by condensation of isomeric aminothiophenecarboxylates or their appropriate reactive derivatives (isothiocyanates or dithiocarbamates) with the corresponding isothiocyanates or amines. The libraries from libraries were then obtained in good yields and purities using solution-phase alkylation and acylation methodologies. Simple manual techniques for parallel reactions using special CombiSyn synthesizers were coupled with easy purification procedures (crystallization from the reaction mixtures) to give high-purity final products. The scope and limitations of the developed approach are discussed.     

Selection of DNA-Encoded Dynamic Chemical Libraries for Direct Inhibitor Discovery

Dynamic combinatorial libraries (DCLs) is a powerful tool for ligand discovery in biomedical research; however, the application of DCLs has been hampered by their low diversity. Recently, the concept of DNA encoding has been employed in DCLs to create DNA-encoded dynamic libraries (DEDLs); however, all current DEDLs are limited to fragment identification, and a challenging process of fragment linking is required after selection. We report an anchor-directed DEDL approach that can identify full ligand structures from large-scale DEDLs. This method is also able to convert unbiased libraries into focused ones targeting specific protein classes. We demonstrated this method by selecting DEDLs against five proteins, and novel inhibitors were identified for all targets. Notably, several selective BD1/BD2 inhibitors were identified from the selections against bromodomain 4 (BRD4), an important anti-cancer drug target. This work may provide a broadly applicable method for inhibitor discovery.     

An efficient solid phase synthesis of 5'-phosphodiester and phosphoramidate monoester nucleoside analogues

An easy and efficient strategy to obtain libraries of 5'-phosphodiester and 5'-phosphoramidate monoester nucleoside analogues in a highly pure form has been developed, starting from a new nucleoside based solid support. The nucleoside scaffold has been anchored through a 5'-phosphodiester linkage to Tentagel HL resin, functionalized with a 3-chloro-4-hydroxyphenylacetic linker. The solid phase synthesis of small libraries of 5'-phosphodiester and 5'-phosphoramidate monoester thymidine analogues is also reported.     

Synthesis of substituted 4-oxo-2-thioxo-1,2,3,4-tetrahydroquinazolines and 4-oxo-3,4-dihydroquinazoline-2-thioles

We have developed a liquid-phase synthesis of combinatorial libraries of new disubstituted 4-oxo-2-thioxo-1,2,3,4-tetrahydroquinazolines and trisubstituted 4-oxo-3,4-dihydroquinazoline-2-thioles. The former were prepared using two general procedures: (i) cyclization of substituted methyl anthranilates with isothiocyanates, or (ii) cyclization of substituted 2-(methylcarboxy)benzeneisothiocyanates with primary amines or hydrazines. 4-Oxo-3,4-dihydroquinazoline-2-thioles were prepared by S-alkylation of disubstituted 4-oxo-2-thioxo-1,2,3,4-tetrahydroquinazolines with alkyl or aryl halides. The hydrolysis of methyl benzimidazo[1,2-c]quinazoline-6(5H)-thione-3-carboxylate led to the corresponding acid. This acid was utilized in the synthesis of new benzimidazo[1,2-c]quinazoline-6(5H)-thione-3-carboxamide and S-substituted 6-mecaptobenzimidazo[1,2-c]quinazoline-3-carboxamide libraries.     

A versatile and inexpensive apparatus for rapid parallel synthesis on solid support: description and synthesis illustration

A new inexpensive and practical apparatus for solid-phase chemistry and parallel synthesis is described. This new apparatus fills an important void in the availability of portable tools for the synthesis of libraries of compounds in multi-milligram amounts. Individual reaction tube capacities range in size from 4 mL to 500 mL of operating liquid volume. Reaction blocks of 36 tubes x 4 mL or 24 tubes x 150 mL allow flexibility of operation. Insert tubes with frit ends function as filter sticks for resin wash and for maintenance of inert atmosphere. An electronic controller device connects to the reaction tubes for programmable entry of pulses of inert gas for resin mixing or vacuum for resin wash. The utility of this apparatus is illustrated by the synthesis of libraries based on 4-methaneamine imidazoles.     

1,4-bis(3-aminopropyl)piperazine libraries: from the discovery of classical chloroquine-like antimalarials to the identification of new targets

The purpose of this review is to provide an update on our work based on the 1,4-bis(3-aminopropyl)piperazine skeleton and how it allowed our group to validate a new target. After a brief introduction where we will relate the way this substructure was introduced in our 4-aminoquinolinyl derivatives, we will present first the different libraries synthesized around this moiety: (1) libraries of sulfonamides, amides and amines derived from 4-aminoquinolines and, (2) libraries where the 4-aminoquinoline nucleus is replaced. High throughput evaluation of biological activity and physicochemical parameters will be presented. The evaluation of the anti-malarial activity of the compounds will be discussed in the light of a chloroquine-like mechanism (accumulation in the acidic food vacuole and inhibition of beta-hematin formation). In a second part we will present active 1,4-bis(3-aminopropyl)piperazine as tools for identification and/or validation of new antimalarial targets. Fluorescence assays on some derivatives show that they are surprisingly localized outside the food vacuole, suggesting the existence of other target(s). Secondly, we will present a library of 1,4-bis(3-aminopropyl)piperazine as inhibitors of the cytosolic aminopeptidase Pfa-M1, a new potential target for antimalarials.     

Parallel synthesis and antimalarial screening of a 4-aminoquinoline library

Due to growing problems with drug resistance, there is an outstanding need for new, cost-effective drugs for the treatment of malaria. The 4-aminoquinolines have provided a number of useful antimalarials, and Plasmodium falciparum, the causative organism for the most deadly form of human malaria, is generally slow to develop resistance to these drugs. Therefore, diverse screening libraries of quinolines continue to be useful for antimalarial drug discovery. We report herein the development of an efficient method for producing libraries of 4-aminoquinolines variant in the side chain portion of the molecule. The effects of these substitutions were evaluated by screening this library for activity against P. falciparum, revealing four potent compounds active against drug-resistant strains.     

High‐Throughput Synthesis and Screening of Combinatorial Heterogeneous Catalyst Libraries

In less than one minute the catalytic activity and selectivity of a single catalyst was measured in combinatorial libraries of ternary Rh‐Pd‐Pt‐Cu alloys. Only slightly more than two hours were needed to complete a library with 136 elements. The elements of the libraries (ca. 2–4 μg of material) are contained in a two‐dimensional array synthesized by a thin‐film technique. The analysis was performed by a scanning mass spectrometer (see picture).     

Translation of DNA into a library of 13,000 synthetic small-molecule macrocycles suitable for in vitro selection

DNA-templated organic synthesis enables the translation, selection, and amplification of DNA sequences encoding synthetic small-molecule libraries. Previously we described the DNA-templated multistep synthesis and model in vitro selection of a pilot library of 65 macrocycles. In this work, we report several key developments that enable the DNA-templated synthesis of much larger (>10,000-membered) small-molecule libraries. We developed and validated a capping-based approach to DNA-templated library synthesis that increases final product yields, simplifies the structure and preparation of reagents, and reduces the number of required manipulations. To expand the size and structural diversity of the macrocycle library, we augmented the number of building blocks in each DNA-templated step from 4 to 12, selected 8 different starting scaffolds which result in 4 macrocycle ring sizes and 2 building-block orientations, and confirmed the ability of the 36 building blocks and 8 scaffolds to generate DNA-templated macrocycle products. We computationally generated and experimentally validated an expanded set of codons sufficient to support 1728 combinations of step 1, step 2, and step 3 building blocks. Finally, we developed new high-resolution LC/MS analysis methods to assess the quality of large DNA-templated small-molecule libraries. Integrating these four developments, we executed the translation of 13,824 DNA templates into their corresponding small-molecule macrocycles. Analysis of the resulting libraries is consistent with excellent (>90%) representation of desired macrocycle products and a stringent test of sequence specificity suggests a high degree of sequence fidelity during translation. The quality and structural diversity of this expanded DNA-templated library provides a rich starting point for the discovery of functional synthetic small-molecule macrocycles.     

{\rtf1\ansi\ansicpg1250\deff0\deflang1038\deflangfe1038\deftab708{\fonttbl{\f0\froman\fprq2\fcharset238{\*\fname Times New Roman;}Times New Roman CE;}} \viewkind4\uc1\pard\f0\fs24 Status of software for PGNAA bulk analysis by the Monte Carlo - Library Least-Squares (MCLLS) approach \par }

Summary {\rtf1\ansi\ansicpg1250\deff0\deflang1038\deflangfe1038\deftab708{\fonttbl{\f0\froman\fprq2\fcharset238{\*\fname Times New Roman;}Times New Roman CE;}} \viewkind4\uc1\pard\f0\fs24 The Center for Engineering Applications of Radioisotopes (CEAR) has been working for about ten years on the Monte Carlo - Library Least-Squares (MCLLS) approach for treating the nonlinear inverse analysis problem for PGNAA bulk analysis. This approach consists essentially of using Monte Carlo simulation to generate the libraries of all the elements to be analyzed plus any other required libraries. These libraries are then used in the linear Library Least-Squares (LLS) approach with unknown sample spectra to analyze for all elements in the sample. The other libraries include all sources of background which includes: (1) gamma-rays emitted by the neutron source, (2) prompt gamma-rays produced in the analyzer construction materials, (3) natural gamma-rays from K-40 and the uranium and thorium decay chains, and (4) prompt and decay gamma-rays produced in the NaI detector by neutron activation. A number of unforeseen problems have arisen in pursuing this approach including: (1) the neutron activation of the most common detector (NaI) used in bulk analysis PGNAA systems, (2) the nonlinearity of this detector, and (3) difficulties in obtaining detector response functions for this (and other) detectors. These problems have been addressed by CEAR recently and have either been solved or are almost solved at the present time. We have now finished the development of Monte Carlo simulation for all of the libraries except the prompt gamma-ray library from the activation of the NaI detector. We must first determine a treatment for the coincidence schemes for Na and particularly I to complete the Monte Carlo simulation of this last library. \par }     

Microwave-Assisted Soluble Polymer-supported Synthesis of Peptoids

Libraries of peptide-like compounds are attractive sources of binding agents for proteomics applications. The synthesis of oligomeric combinatorial libraries of peptidomimetics is usually more straightforward than the creation of large libraries of more "drug-like" molecules. Herein we report synthesis of peptoids on soluble high loading Noncross-linked polystyrene. The synthesis route consists of: (a) preparation "soluble wang resin" from non-crosslinked polystyrene and 4-hydroxybenzyl alcohol via ether linkage, (b) an esterification step performed by the addition of bromoacetyl bromide to "soluble wang resin" and (c) a nucleophilic displacement of bromide with a primary amine.