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酵母展示化学扩展抗体文库的设计、构建与验证

Design, Construction, and Validation of a Yeast-Displayed Chemically Expanded Antibody Library.

作者信息

Rezhdo Arlinda, Hershman Rebecca L, Van Deventer James A

机构信息

Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, USA.

Biomedical Engineering Department, Tufts University, Medford, Massachusetts 02155, USA.

出版信息

bioRxiv. 2024 May 29:2024.05.29.596443. doi: 10.1101/2024.05.29.596443.

Abstract

display technologies, exemplified by phage and yeast display, have emerged as powerful platforms for antibody discovery and engineering. However, the identification of antibodies that disrupt target functions beyond binding remains a challenge. In particular, there are very few strategies that support identification and engineering of either protein-based irreversible binders or inhibitory enzyme binders. Expanding the range of chemistries in antibody libraries has the potential to lead to efficient discovery of function-disrupting antibodies. In this work, we describe a yeast display-based platform for the discovery of chemically diversified antibodies. We constructed a billion-member antibody library that supports the presentation of a range of chemistries within antibody variable domains via noncanonical amino acid (ncAA) incorporation and subsequent bioorthogonal click chemistry conjugations. Use of a polyspecific orthogonal translation system enables introduction of chemical groups with various properties, including photo-reactive, proximity-reactive, and click chemistry-enabled functional groups for library screening. We established conjugation conditions that facilitate modification of the full library, demonstrating the feasibility of sorting the full billion-member library in "protein-small molecule hybrid" format in future work. Here, we conducted initial library screens after introducing -(2-bromoethyl)tyrosine (OBeY), a weakly electrophilic ncAA capable of undergoing proximity-induced crosslinking to a target. Enrichments against donkey IgG and protein tyrosine phosphatase 1B (PTP1B) each led to the identification of several OBeY-substituted clones that bind to the targets of interest. Flow cytometry analysis on the yeast surface confirmed higher retention of binding for OBeY-substituted clones compared to clones substituted with ncAAs lacking electrophilic side chains after denaturation. However, subsequent crosslinking experiments in solution with ncAA-substituted clones yielded inconclusive results, suggesting that weakly reactive OBeY side chain is not sufficient to drive robust crosslinking in the clones isolated here. Nonetheless, this work establishes a multi-modal, chemically expanded antibody library and demonstrates the feasibility of conducting discovery campaigns in chemically expanded format. This versatile platform offers new opportunities for identifying and characterizing antibodies with properties beyond what is accessible with the canonical amino acids, potentially enabling discovery of new classes of reagents, diagnostics, and even therapeutic leads.

摘要

以噬菌体展示和酵母展示为代表的展示技术,已成为抗体发现和工程改造的强大平台。然而,鉴定除结合之外还能破坏靶标功能的抗体仍然是一项挑战。特别是,支持鉴定和工程改造基于蛋白质的不可逆结合剂或抑制性酶结合剂的策略非常少。扩大抗体库中的化学种类范围有可能导致高效发现功能破坏型抗体。在这项工作中,我们描述了一个基于酵母展示的平台,用于发现化学多样化的抗体。我们构建了一个包含十亿个成员的抗体库,该库通过非天然氨基酸(ncAA)掺入以及随后的生物正交点击化学偶联,支持在抗体可变域内呈现一系列化学种类。使用多特异性正交翻译系统能够引入具有各种性质的化学基团,包括用于文库筛选的光反应性、邻近反应性和点击化学可用的官能团。我们建立了便于对整个文库进行修饰的偶联条件,证明了在未来工作中以“蛋白质 - 小分子杂交”形式对整个包含十亿个成员的文库进行分选的可行性。在这里,我们在引入 -(2 - 溴乙基)酪氨酸(OBeY)后进行了初始文库筛选,OBeY是一种弱亲电的非天然氨基酸,能够与靶标发生邻近诱导的交联。针对驴IgG和蛋白酪氨酸磷酸酶1B(PTP1B)的富集分别导致鉴定出几个与感兴趣靶标结合的OBeY取代克隆。酵母表面的流式细胞术分析证实,与变性后用缺乏亲电侧链的非天然氨基酸取代的克隆相比,OBeY取代克隆的结合保留率更高。然而,随后在溶液中用非天然氨基酸取代克隆进行的交联实验结果不明确,这表明弱反应性的OBeY侧链不足以驱动此处分离的克隆中的强大交联。尽管如此,这项工作建立了一个多模态、化学扩展的抗体库,并证明了以化学扩展形式开展发现活动的可行性。这个通用平台为鉴定和表征具有超越天然氨基酸所能获得性质的抗体提供了新机会,有可能实现发现新型试剂、诊断方法甚至治疗先导物。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/efc3/11160716/38816696c4d4/nihpp-2024.05.29.596443v1-f0002.jpg

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