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1.
Yuqing Deng Jianzhao Peng Dr. Feng Xiong Yinan Song Dr. Yu Zhou Jianfu Zhang Fong Sang Lam Chao Xie Wenyin Shen Yiran Huang Ling Meng Prof. Xiaoyu Li 《Angewandte Chemie (Weinheim an der Bergstrasse, Germany)》2020,132(35):15075-15082
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. 相似文献
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Francesco V. Reddavide Weilin Lin Sarah Lehnert Dr. Yixin Zhang 《Angewandte Chemie (International ed. in English)》2015,54(27):7924-7928
Dynamic combinatorial chemistry (DCC) explores the thermodynamic equilibrium of reversible reactions. Its application in the discovery of protein binders is largely limited by difficulties in the analysis of complex reaction mixtures. DNA‐encoded chemical library (DECL) technology allows the selection of binders from a mixture of up to billions of different compounds; however, experimental results often show low a signal‐to‐noise ratio and poor correlation between enrichment factor and binding affinity. Herein we describe the design and application of DNA‐encoded dynamic combinatorial chemical libraries (EDCCLs). Our experiments have shown that the EDCCL approach can be used not only to convert monovalent binders into high‐affinity bivalent binders, but also to cause remarkably enhanced enrichment of potent bivalent binders by driving their in situ synthesis. We also demonstrate the application of EDCCLs in DNA‐templated chemical reactions. 相似文献
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Markus Leimbacher Dr. Yixin Zhang Dr. Luca Mannocci Michael Stravs Dr. Tim Geppert Dr. Jörg Scheuermann Prof. Gisbert Schneider Prof. Dario Neri 《Chemistry (Weinheim an der Bergstrasse, Germany)》2012,18(25):7729-7737
Libraries of chemical compounds individually coupled to encoding DNA tags (DNA‐encoded chemical libraries) hold promise to facilitate exceptionally efficient ligand discovery. We constructed a high‐quality DNA‐encoded chemical library comprising 30 000 drug‐like compounds; this was screened in 170 different affinity capture experiments. High‐throughput sequencing allowed the evaluation of 120 million DNA codes for a systematic analysis of selection strategies and statistically robust identification of binding molecules. Selections performed against the tumor‐associated antigen carbonic anhydrase IX (CA IX) and the pro‐inflammatory cytokine interleukin‐2 (IL‐2) yielded potent inhibitors with exquisite target specificity. The binding mode of the revealed pharmacophore against IL‐2 was confirmed by molecular docking. Our findings suggest that DNA‐encoded chemical libraries allow the facile identification of drug‐like ligands principally to any protein of choice, including molecules capable of disrupting high‐affinity protein–protein interactions. 相似文献
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Cedric J. Stress Basilius Sauter Lukas A. Schneider Timothy Sharpe Dennis Gillingham 《Angewandte Chemie (International ed. in English)》2019,58(28):9570-9574
Here we show a seven‐step chemical synthesis of a DNA‐encoded macrocycle library (DEML) on DNA. Inspired by polyketide and mixed peptide‐polyketide natural products, the library was designed to incorporate rich backbone diversity. Achieving this diversity, however, comes at the cost of the custom synthesis of bifunctional building block libraries. This study outlines the importance of careful retrosynthetic design in DNA‐encoded libraries, while revealing areas where new DNA synthetic methods are needed. 相似文献
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Identification of Structure–Activity Relationships from Screening a Structurally Compact DNA‐Encoded Chemical Library 下载免费PDF全文
Dr. Raphael M. Franzini Dr. Torun Ekblad Dr. Nan Zhong Moreno Wichert Willy Decurtins Angela Nauer Mauro Zimmermann Dr. Florent Samain Dr. Jörg Scheuermann Dr. Peter J. Brown Prof. Dr. Jonathan Hall Dr. Susanne Gräslund Prof. Dr. Herwig Schüler Prof. Dr. Dario Neri 《Angewandte Chemie (International ed. in English)》2015,54(13):3927-3931
Methods for the rapid and inexpensive discovery of hit compounds are essential for pharmaceutical research and DNA‐encoded chemical libraries represent promising tools for this purpose. We here report on the design and synthesis of DAL‐100K, a DNA‐encoded chemical library containing 103 200 structurally compact compounds. Affinity screening experiments and DNA‐sequencing analysis provided ligands with nanomolar affinities to several proteins, including prostate‐specific membrane antigen and tankyrase 1. Correlations of sequence counts with binding affinities and potencies of enzyme inhibition were observed and enabled the identification of structural features critical for activity. These results indicate that libraries of this type represent a useful source of small‐molecule binders for target proteins of pharmaceutical interest and information on structural features important for binding. 相似文献
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Nikolaus Krall Dr. Jörg Scheuermann Prof. Dario Neri 《Angewandte Chemie (International ed. in English)》2013,52(5):1384-1402
The targeted delivery of potent cytotoxic agents has emerged as a promising strategy for the treatment of cancer and other serious conditions. Traditionally, antibodies against markers of disease have been used as drug‐delivery vehicles. More recently, lower molecular weight ligands have been proposed for the generation of a novel class of targeted cytotoxics with improved properties. Advances in this field crucially rely on efficient methods for the identification and optimization of organic molecules capable of high‐affinity binding and selective recognition of target proteins. The advent of DNA‐encoded chemical libraries allows the construction and screening of compound collections of unprecedented size. In this Review, we survey developments in the field of small ligand‐based targeted cytotoxics and show how innovative library technologies will help develop the drugs of the future. 相似文献
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Selection of DNA‐Encoded Small Molecule Libraries Against Unmodified and Non‐Immobilized Protein Targets 下载免费PDF全文
Peng Zhao Zitian Chen Yizhou Li Dawei Sun Yuan Gao Prof. Yanyi Huang Prof. Xiaoyu Li 《Angewandte Chemie (International ed. in English)》2014,53(38):10056-10059
The selection of DNA‐encoded libraries against biological targets has become an important discovery method in chemical biology and drug discovery, but the requirement of modified and immobilized targets remains a significant disadvantage. With a terminal protection strategy and ligand‐induced photo‐crosslinking, we show that iterated selections of DNA‐encoded libraries can be realized with unmodified and non‐immobilized protein targets. 相似文献
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Nicholas Favalli Gabriele Bassi Tania Zanetti Jrg Scheuermann Dario Neri 《Helvetica chimica acta》2019,102(4)
The construction of DNA‐encoded chemical libraries (DECLs) crucially relies on the availability of chemical reactions, which are DNA‐compatible and which exhibit high conversion rates for a large number of diverse substrates. In this work, we present our optimization and validation procedures for three copper and palladium‐catalyzed reactions (Suzuki cross‐coupling, Sonogashira cross‐coupling, and copper(I)‐catalyzed alkyne‐azide cycloaddition (CuAAC)), which have been successfully used by our group for the construction of large encoded libraries. 相似文献
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Hongtao Xu Yuang Gu Shuning Zhang Huan Xiong Fei Ma Fengping Lu Qun Ji Lili Liu Peixiang Ma Wei Hou Guang Yang Richard A. Lerner 《Angewandte Chemie (International ed. in English)》2020,59(32):13273-13280
Conventional direct C?H selenylation suffers from simple selenation with limited atom economy and complicated reaction system. In this work, we designed benzoselenazolone as a novel bifunctional selenide reagent for both off‐ and on‐DNA C?H selenylation under rhodium(III) catalysis. We show that using benzoselenazolone allowed production of a series of selenylation products containing an adjacent aminoacyl group in a fast and efficient way, with high atom economy. The synthetic application of this method was demonstrated by taking advantage of the amide functionality as a nucleophile, directing group, and amide coupling partner. This work shows great potential in facilitating rapid construction of selenium‐containing DNA‐encoded chemical libraries (SeDELs), and lays the foundation for the development of selenium‐containing drugs. 相似文献
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Cover Picture: Selection of DNA‐Encoded Small Molecule Libraries Against Unmodified and Non‐Immobilized Protein Targets (Angew. Chem. Int. Ed. 38/2014) 下载免费PDF全文
Peng Zhao Zitian Chen Yizhou Li Dawei Sun Yuan Gao Prof. Yanyi Huang Prof. Xiaoyu Li 《Angewandte Chemie (International ed. in English)》2014,53(38):9963-9963
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A Mechanism‐Based Approach to Screening Metagenomic Libraries for Discovery of Unconventional Glycosidases 下载免费PDF全文
Seyed Amirhossein Nasseri Dr. Leo Betschart Daria Opaleva Dr. Peter Rahfeld Prof. Stephen G. Withers 《Angewandte Chemie (International ed. in English)》2018,57(35):11359-11364
Functional metagenomics has opened new opportunities for enzyme discovery. To exploit the full potential of this new tool, the design of selective screens is essential, especially when searching for rare enzymes. To identify novel glycosidases that employ cleavage strategies other than the conventional Koshland mechanisms, a suitable screen was needed. Focusing on the unsaturated glucuronidases (UGLs), it was found that use of simple aryl glycoside substrates did not allow sufficient discrimination against β‐glucuronidases, which are widespread in bacteria. While conventional glycosidases cannot generally hydrolyze thioglycosides efficiently, UGLs follow a distinct mechanism that allows them to do so. Thus, fluorogenic thioglycoside substrates featuring thiol‐based self‐immolative linkers were synthesized and assessed as selective substrates. The generality of the approach was validated with another family of unconventional glycosidases, the GH4 enzymes. Finally, the utility of these substrates was tested by screening a small metagenomic library. 相似文献
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Mohua Das Dr. Tianming Yang Jinghua Dong Fransisca Prasetya Yiming Xie Kendra H. Q. Wong Adeline Cheong Prof. Esther C. Y. Woon 《化学:亚洲杂志》2018,13(19):2854-2867
Dynamic combinatorial chemistry (DCC) is a powerful supramolecular approach for discovering ligands for biomolecules. To date, most, if not all, biologically templated DCC systems employ only a single biomolecule to direct the self‐assembly process. To expand the scope of DCC, herein, a novel multiprotein DCC strategy has been developed that combines the discriminatory power of a zwitterionic “thermal tag” with the sensitivity of differential scanning fluorimetry. This strategy is highly sensitive and could differentiate the binding of ligands to structurally similar subfamily members. Through this strategy, it was possible to simultaneously identify subfamily‐selective probes against two clinically important epigenetic enzymes: FTO ( 7 ; IC50=2.6 μm ) and ALKBH3 ( 8 ; IC50=3.7 μm ). To date, this is the first report of a subfamily‐selective ALKBH3 inhibitor. The developed strategy could, in principle, be adapted to a broad range of proteins; thus it is of broad scientific interest. 相似文献
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Dr. Rachael R. Jetson Prof. Casey J. Krusemark 《Angewandte Chemie (International ed. in English)》2016,55(33):9562-9566
A sensing approach is applied to encode quantitative enzymatic activity information into DNA sequence populations. The method utilizes DNA‐linked peptide substrates as activity probes. Signal detection involves chemical manipulation of a probe population downstream of sample exposure and application of purifying, selective pressure for enzyme products. Selection‐induced changes in DNA abundance indicate sample activity. The detection of protein kinase, protease, and farnesyltransferase activities is demonstrated. The assays were employed to measure enzyme inhibition by small molecules and activity in cell lysates using parallel DNA sequencing or quantitative PCR. This strategy will allow the extensive infrastructure for genetic analysis to be applied to proteomic assays, which has a number of advantages in throughput, sensitivity, and sample multiplexing. 相似文献
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We demonstrate an effective method for generating libraries of encoded compounds for fabricating large compound microarrays on solid supports. This method is based on one-bead, one-compound synthesis and employs a novel trilayer bead-partition scheme that ensures sufficient quantity of synthesized compounds releasable from each bead for compound microarray fabrication in high-throughput protein–ligand discovery assays.
[Supplementary materials are available for this article. Go to the publisher's online edition of Synthetic Communications® for the following free supplemental resource(s): Full experimental and spectral details.] 相似文献
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Chia‐Wei Hsu Prof. Ognjen Š. Miljanić 《Angewandte Chemie (International ed. in English)》2015,54(7):2219-2222
Differences in adsorption among the components of complex mixtures play a role in separations, surface‐based sensing, and heterogeneous catalysis, and have been implicated in theories of the origin of life. Herein, we consider mixtures of imines and we show that if such complex mixtures are also dynamic—that is, if their components equilibrate among themselves—then they can dramatically simplify in composition during the course of column chromatography. As they travel down the column, imines continuously trade their aldehyde and amine constituents, favoring the formation of molecules with extremes of polarity at the expense of species with intermediate polarities. Iterative application of this principle leads to simplification of imine libraries containing up to 16 members into 4 major products. 相似文献