Unveiling New Binding Sites and Allosteric Regulation Mechanisms of LSD1 for Novel Therapeutics

Lysine-specific demethylase 1 (LSD1) regulates key cellular
processes
through both demethylase-dependent and -independent functions. Current
clinical LSD1 inhibitors target its demethylase functions, and issues
like the inability to fully modulate LSD1’s demethylase-independent
functions have limited their clinical efficacy. SP2509, an allosteric
LSD1 inhibitor, can affect both demethylase-dependent and -independent
functions of LSD1. Understanding the allosteric regulation mechanisms
of SP2509 may facilitate the development of new LSD1 inhibitors. Using
SP2509 as a probe, two new binding modes are identified in this work,
both of which can alter the conformation of substrate binding pocket,
effectively blocking H3 substrate binding and inhibiting the demethylase
activity. Interestingly, one binding mode induces significant allosteric
bending of Tower/CoREST domain, disrupting the nucleosome substrate
bindingan effect not previously reported. This unique binding
mode is also validated through in vitro biochemical
characterizations. These findings provide invaluable structural insights
for designing next-generation LSD1 inhibitors for novel therapeutics.

赖氨酸特异性去甲基化酶1（Lysine-specific demethylase 1, LSD1）通过依赖去甲基化酶活性与不依赖去甲基化酶活性的双重功能调控关键细胞进程。当前临床应用的LSD1抑制剂仅靶向其去甲基化酶活性功能，而无法完全调控LSD1非依赖去甲基化酶活性的功能这类问题，限制了这类药物的临床疗效。变构LSD1抑制剂SP2509可同时影响LSD1依赖去甲基化酶活性与不依赖去甲基化酶活性的双重功能。阐明SP2509的变构调控机制，有望推动新型LSD1抑制剂的开发。本研究以SP2509为探针，鉴定出两种全新的结合模式，二者均可改变底物结合口袋的构象，有效阻断H3底物结合并抑制其去甲基化酶活性。值得注意的是，其中一种结合模式可诱导Tower/CoREST结构域发生显著的变构弯曲，破坏核小体底物的结合——这一效应此前尚未见报道。该独特结合模式亦通过体外生化表征得到了验证。上述研究结果为开发用于新型治疗的下一代LSD1抑制剂提供了极具价值的结构生物学见解。