Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502 Leiden, The Netherlands.
Chemical Biology and Drug Discovery Group, Utrecht University, P.O. Box 80082 Utrecht, The Netherlands.
Molecules. 2020 Oct 26;25(21):4951. doi: 10.3390/molecules25214951.
Targeting of proteins in the histone modification machinery has emerged as a promising new direction to fight disease. The search for compounds that inhibit proteins that readout histone modification has led to several new epigenetic drugs, mostly for proteins involved in recognition of acetylated lysines. However, this approach proved to be a challenging task for methyllysine readers, which typically feature shallow binding pockets. Moreover, reader proteins of trimethyllysine K36 on the histone H3 (H3K36me3) not only bind the methyllysine but also the nucleosomal DNA. Here, we sought to find peptide-based binders of H3K36me3 reader PSIP1, which relies on DNA interactions to tightly bind H3K36me3 modified nucleosomes. We designed several peptides that mimic the nucleosomal context of H3K36me3 recognition by including negatively charged Glu-rich regions. Using a detailed NMR analysis, we find that addition of negative charges boosts binding affinity up to 50-fold while decreasing binding to the trimethyllysine binding pocket. Since screening and selection of compounds for reader domains is typically based solely on affinity measurements due to their lack of enzymatic activity, our case highlights the need to carefully control for the binding mode, in particular for the challenging case of H3K36me3 readers.
靶向组蛋白修饰机制中的蛋白质已成为治疗疾病的一种很有前途的新方法。寻找能够抑制读取组蛋白修饰蛋白的化合物已经导致了几种新的表观遗传药物，这些药物主要针对参与识别乙酰化赖氨酸的蛋白质。然而，这种方法对于甲基赖氨酸读取器来说是一项具有挑战性的任务，因为它们通常具有浅的结合口袋。此外，组蛋白 H3 上的三甲基赖氨酸 K36 的读取器 PSIP1 不仅结合甲基赖氨酸，还结合核小体 DNA。在这里，我们试图寻找基于肽的 H3K36me3 读取器 PSIP1 的结合物，该蛋白依赖于 DNA 相互作用来紧密结合 H3K36me3 修饰的核小体。我们设计了几个肽，通过包含带负电荷的富含 Glu 区域来模拟 H3K36me3 识别的核小体环境。通过详细的 NMR 分析，我们发现添加负电荷可将结合亲和力提高多达 50 倍，同时降低对三甲基赖氨酸结合口袋的结合。由于缺乏酶活性，读者结构域化合物的筛选和选择通常仅基于亲和力测量，因此我们的案例强调了需要仔细控制结合模式，特别是对于具有挑战性的 H3K36me3 读取器的情况。
