Ye Xiyun, Lee Yen-Chun, Gates Zachary P, Ling Yingjie, Mortensen Jennifer C, Yang Fan-Shen, Lin Yu-Shan, Pentelute Bradley L
Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA.
Department of Chemistry, National Cheng Kung University, No.1, University Road, Tainan City, 701, Taiwan.
Commun Chem. 2022 Oct 14;5(1):128. doi: 10.1038/s42004-022-00737-w.
Establishing structure-activity relationships is crucial to understand and optimize the activity of peptide-based inhibitors of protein-protein interactions. Single alanine substitutions provide limited information on the residues that tolerate simultaneous modifications with retention of biological activity. To guide optimization of peptide binders, we use combinatorial peptide libraries of over 4,000 variants-in which each position is varied with either the wild-type residue or alanine-with a label-free affinity selection platform to study protein-ligand interactions. Applying this platform to a peptide binder to the oncogenic protein MDM2, several multi-alanine-substituted analogs with picomolar binding affinity were discovered. We reveal a non-additive substitution pattern in the selected sequences. The alanine substitution tolerances for peptide ligands of the 12ca5 antibody and 14-3-3 regulatory protein are also characterized, demonstrating the general applicability of this new platform. We envision that binary combinatorial alanine scanning will be a powerful tool for investigating structure-activity relationships.
建立构效关系对于理解和优化基于肽的蛋白质-蛋白质相互作用抑制剂的活性至关重要。单丙氨酸取代提供的关于能够耐受同时修饰并保留生物活性的残基的信息有限。为了指导肽结合剂的优化，我们使用了包含超过4000个变体的组合肽库（其中每个位置用野生型残基或丙氨酸进行变化），并结合无标记亲和选择平台来研究蛋白质-配体相互作用。将该平台应用于致癌蛋白MDM2的肽结合剂，发现了几种具有皮摩尔结合亲和力的多丙氨酸取代类似物。我们揭示了所选序列中的非加性取代模式。还对12ca5抗体和14-3-3调节蛋白的肽配体的丙氨酸取代耐受性进行了表征，证明了这个新平台的普遍适用性。我们设想二元组合丙氨酸扫描将成为研究构效关系的有力工具。
