Wang Min-Ran, He Jing-Yang, He Ji-Xiang, Liu Ke-Ke, Yang Jing
State Key Laboratory of Proteomics, National Center for Protein Sciences - Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics 38 Life Sci. Park Road, Changping District Beijing 102206 China
Chem Sci. 2021 Oct 15;12(43):14557-14563. doi: 10.1039/d1sc02230j. eCollection 2021 Nov 10.
Natural systems produce various γ-dicarbonyl-bearing compounds that can covalently modify lysine in protein targets the classic Paal-Knorr reaction. Among them is a unique class of lipid-derived electrophiles - isoketals that exhibit high chemical reactivity and critical biological functions. However, their target selectivity and profiles in complex proteomes remain unknown. Here we report a Paal-Knorr agent, 4-oxonon-8-ynal (herein termed ONAyne), for surveying the reactivity and selectivity of the γ-dicarbonyl warhead in biological systems. Using an unbiased open-search strategy, we demonstrated the lysine specificity of ONAyne on a proteome-wide scale and characterized six probe-derived modifications, including the initial pyrrole adduct and its oxidative products (, lactam and hydroxylactam adducts), an enlactam adduct from dehydration of hydroxylactam, and two chemotypes formed in the presence of endogenous formaldehyde (, fulvene and aldehyde adducts). Furthermore, combined with quantitative chemoproteomics in a competitive format, ONAyne permitted global, , and site-specific profiling of targeted lysine residues of two specific isomers of isoketals, levuglandin (LG) D2 and E2. The functional analyses reveal that LG-derived adduction drives inhibition of malate dehydrogenase MDH2 and exhibits a crosstalk with two epigenetic marks on histone H2B in macrophages. Our approach should be broadly useful for target profiling of bioactive γ-dicarbonyls in diverse biological contexts.
自然系统会产生各种含γ-二羰基的化合物，这些化合物可以与蛋白质靶标中的赖氨酸发生共价修饰，即经典的帕尔-克诺尔反应。其中有一类独特的脂质衍生亲电试剂——异酮缩醛，它们具有高化学反应活性和关键的生物学功能。然而，它们在复杂蛋白质组中的靶标选择性和分布情况仍然未知。在此，我们报道了一种用于研究生物系统中γ-二羰基弹头反应活性和选择性的帕尔-克诺尔试剂，4-氧代壬-8-炔醛（在此称为ONAyne）。通过一种无偏向的开放搜索策略，我们在全蛋白质组范围内证明了ONAyne对赖氨酸的特异性，并鉴定了六种探针衍生的修饰，包括初始的吡咯加合物及其氧化产物（内酰胺和羟基内酰胺加合物）、羟基内酰胺脱水形成的烯内酰胺加合物，以及在内源性甲醛存在下形成的两种化学类型（富烯和醛加合物）。此外，结合竞争性定量化学蛋白质组学，ONAyne能够对异酮缩醛的两种特定异构体——左型前列腺素（LG）D2和E2的靶向赖氨酸残基进行全局、相对和位点特异性分析。功能分析表明，LG衍生的加合物会抑制苹果酸脱氢酶MDH2，并在巨噬细胞中与组蛋白H2B上的两种表观遗传标记产生串扰。我们的方法对于在不同生物学背景下对生物活性γ-二羰基进行靶标分析应具有广泛的用途。
