Hassan Muhammad Murtaza, Li Yen-Der, Ma Michelle W, Teng Mingxing, Byun Woong Sub, Puvar Kedar, Lumpkin Ryan, Sandoval Brittany, Rutter Justine C, Jin Cyrus Y, Wang Michelle Y, Xu Shawn, Schmoker Anna M, Cheong Hakyung, Groendyke Brian J, Qi Jun, Fischer Eric S, Ebert Benjamin L, Gray Nathanael S
Department of Chemical and Systems Biology, ChEM-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA.
Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA.
bioRxiv. 2023 Oct 10:2023.10.07.561308. doi: 10.1101/2023.10.07.561308.
Small molecules that can induce protein degradation by inducing proximity between a desired target and an E3 ligase have the potential to greatly expand the number of proteins that can be manipulated pharmacologically. Current strategies for targeted protein degradation are mostly limited in their target scope to proteins with preexisting ligands. Alternate modalities such as molecular glues, as exemplified by the glutarimide class of ligands for the CUL4 ligase, have been mostly discovered serendipitously. We recently reported a -labelling covalent glue mechanism which we named 'Template-assisted covalent modification', where an electrophile decorated small molecule binder of BRD4 was effectively delivered to a cysteine residue on an E3 ligase DCAF16 as a consequence of a BRD4-DCAF16 protein-protein interaction. Herein, we report our medicinal chemistry efforts to evaluate how various electrophilic modifications to the BRD4 binder, JQ1, affect DCAF16 -labeling and subsequent BRD4 degradation efficiency. We discovered a decent correlation between the ability of the electrophilic small molecule to induce ternary complex formation between BRD4 and DCAF16 with its ability to induce BRD4 degradation. Moreover, we show that a more solvent-exposed warhead presentation is optimal for DCAF16 recruitment and subsequent BRD4 degradation. Unlike the sensitivity of CUL4 glue degraders to chemical modifications, the diversity of covalent attachments in this class of BRD4 glue degraders suggests a high tolerance and tunability for the BRD4-DCAF16 interaction. This offers a potential new avenue for a rational design of covalent glue degraders by introducing covalent warheads to known binders.
能够通过诱导目标蛋白与E3连接酶靠近来诱导蛋白质降解的小分子，有潜力极大地扩展可通过药理学手段操控的蛋白质数量。目前的靶向蛋白质降解策略大多在其靶标范围上局限于具有预先存在配体的蛋白质。诸如分子胶这类替代模式，以CUL4连接酶的戊二酰亚胺类配体为例，大多是偶然发现的。我们最近报道了一种α-标记共价胶机制，我们将其命名为“模板辅助共价修饰”，其中由于BRD4与DCAF16的蛋白质-蛋白质相互作用，带有亲电试剂的BRD4小分子结合剂被有效地递送至E3连接酶DCAF16上的一个半胱氨酸残基。在此，我们报告我们的药物化学研究工作，以评估对BRD4结合剂JQ1进行的各种亲电修饰如何影响DCAF16的标记以及随后的BRD4降解效率。我们发现亲电小分子诱导BRD4与DCAF16之间形成三元复合物的能力与其诱导BRD4降解的能力之间存在良好的相关性。此外，我们表明更暴露于溶剂的弹头呈现方式对于DCAF16的募集以及随后的BRD4降解是最佳的。与CUL4胶降解剂对化学修饰的敏感性不同，这类BRD4胶降解剂中共价连接的多样性表明对BRD4-DCAF16相互作用具有高耐受性和可调节性。这通过将共价弹头引入已知结合剂为共价胶降解剂的合理设计提供了一条潜在的新途径。
