Evolution of the Selection Methods of DNA-Encoded Chemical Libraries.
Evolution of the Selection Methods of DNA-Encoded Chemical Libraries.
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DOI：
10.1021/acs.accounts.1c00375
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发表时间：
2021-08
影响因子：
18.3
通讯作者：
Yinan Song;Xiaoyu Li
中科院分区：
文献类型：
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作者：
Yinan Song;Xiaoyu Li
概述在过去的二十年中，DNA编码的化学库（DEL或DECL）已经出现，并已成为药物发现以及化学生物学研究中配体发现的主要技术平台。尽管DEL基于一个简单的概念，即在组合化学库中用独特的DNA标签对每种化合物进行编码，但它已被证明是一种强大的工具，可以通过访问巨大的化学空间来询问生物靶标，而成本只是传统高通量筛选（HTS）的一小部分。此外，最近的技术进步和DEL兼容反应的快速发展极大地增强了DEL的化学多样性。如今，DEL 已被几乎所有主要制药公司采用，并且在学术界也得到了发展。然而，该领域严重偏向于文库编码和合成，并且 DEL 研究的一个尚未充分探索的方面是选择方法。一般来说，DEL 选择被认为是对固定化蛋白质进行的大规模结合测定，以使用典型的结合-洗涤-洗脱程序来鉴定物理结合剂。近年来，我们和其他研究小组开发了可以在溶液阶段进行 DEL 选择的新方法，这使得能够针对纯化蛋白质之外的复杂生物靶标进行选择。一方面，这些方法显着拓宽了 DEL 的目标范围；另一方面，他们使 DEL 的功能和潜在表型分析超越了简单的结合。本帐户提供了这些方法的概述。我们的实验室一直使用 DNA 编程亲和标记 (DPAL) 作为开发新的 DEL 选择方法的主要策略。 DPAL 基于 DNA 模板合成；通过使用已知的配体引导靶标结合，DPAL能够特异性地在靶蛋白和配体之间建立稳定的连接。靶标-配体缀合物的 DNA 标签可用作蛋白质表征或 DEL 选择情况下命中化合物解码的可编程句柄。 DPAL 还利用光交联的快速反应动力学来实现高标记特异性和保真度，特别是在选择 DNA 编码动态文库 (DEDL) 时。 DPAL 不仅可以在缓冲液和细胞裂解物中进行 DEL 选择，还可以在复杂的生物系统中进行 DEL 选择，例如大型蛋白质复合物和活细胞。此外，该策略还被用于其他生物学应用，例如位点特异性蛋白质标记、蛋白质检测、蛋白质分析和目标识别。在这篇文章中，我们描述了这些方法，强调了它们的基本原理，并以 DEL 技术发展的观点作为总结。
ConspectusIn the past two decades, a DNA-encoded chemical library (DEL or DECL) has emerged and has become a major technology platform for ligand discovery in drug discovery as well as in chemical biology research. Although based on a simple concept, i.e., encoding each compound with a unique DNA tag in a combinatorial chemical library, DEL has been proven to be a powerful tool for interrogating biological targets by accessing vast chemical space at a fraction of the cost of traditional high-throughput screening (HTS). Moreover, the recent technological advances and rapid developments of DEL-compatible reactions have greatly enhanced the chemical diversity of DELs. Today, DELs have been adopted by nearly all major pharmaceutical companies and are also gaining momentum in academia. However, this field is heavily biased toward library encoding and synthesis, and an underexplored aspect of DEL research is the selection methods. Generally, DEL selection is considered to be a massive binding assay conducted over an immobilized protein to identify the physical binders using the typical bind-wash-elute procedure. In recent years, we and other research groups have developed new approaches that can perform DEL selections in the solution phase, which has enabled the selection against complex biological targets beyond purified proteins. On the one hand, these methods have significantly widened the target scope of DELs; on the other hand, they have enabled the functional and potentially phenotypic assays of DELs beyond simple binding. An overview of these methods is provided in this Account.Our laboratory has been using DNA-programmed affinity labeling (DPAL) as the main strategy to develop new DEL selection methods. DPAL is based on DNA-templated synthesis; by using a known ligand to guide the target binding, DPAL is able to specifically establish a stable linkage between the target protein and the ligand. The DNA tag of the target-ligand conjugates serves as a programmable handle for protein characterization or hit compound decoding in the case of DEL selections. DPAL also takes advantage of the fast reaction kinetics of photo-cross-linking to achieve high labeling specificity and fidelity, especially in the selection of DNA-encoded dynamic libraries (DEDLs). DPAL has enabled DEL selections not only in buffer and cell lysates but also with complex biological systems, such as large protein complexes and live cells. Moreover, this strategy has also been employed in other biological applications, such as site-specific protein labeling, protein detection, protein profiling, and target identification. In the Account, we describe these methods, highlight their underlying principles, and conclude with perspectives of the development of the DEL technology.