Proteome-Wide Ligand and Target Discovery by Using Covalent Probes and Natural Products

Due
to the lack of effective therapeutic targets for drug development,
many diseases remain difficult to treat. To address this issue, phenotypic
screening integrated with chemical proteomics has emerged as an efficient
strategy to expand the scope of druggable targets. In this study,
we constructed a covalent probe library based on diverse covalent
kinase inhibitors and natural products containing an α, β-unsaturated
ketone electrophilic warhead. Antiproliferation screening revealed
that these probes exhibit potent anticancer activity against triple-negative
breast cancer (TNBC) and human colon cancer. Subsequent proteomic
studies identified a series of novel covalently ligandable targets,
including ASNS, AKR1C1, DDX39B, and PRMT5. Functional validation demonstrated
that DDX39B may represent a new therapeutic target for TNBC. Moreover,
we identified a series of highly selective covalent probes targeting
ARK1C1, PDIA1, and ALDH1A1, which could serve as valuable tools for
detecting the expression and activity of these critical proteins.

由于药物研发领域缺乏有效的治疗靶点，诸多疾病至今仍难以获得临床有效治疗。为解决这一核心难题，整合化学蛋白质组学的表型筛选策略应运而生，成为拓展可药用靶点覆盖范围的高效研究手段。本研究基于一系列携带α,β-不饱和酮亲电弹头的多样化共价激酶抑制剂与天然产物，构建了共价探针库。抗增殖筛选实验显示，该系列探针对三阴性乳腺癌（TNBC）与人类结肠癌均展现出强效抗癌活性。后续蛋白质组学研究鉴定出一系列新型共价可配靶向靶点，涵盖ASNS、AKR1C1、DDX39B与PRMT5。功能验证实验证实，DDX39B或可成为三阴性乳腺癌的新型治疗靶点。此外，本研究还鉴定出一系列针对ARK1C1、PDIA1与ALDH1A1的高选择性共价探针，此类探针可作为检测上述关键蛋白表达与活性的实用研究工具。