Yang Maojun, Culhane Jeffrey C, Szewczuk Lawrence M, Jalili Pegah, Ball Haydn L, Machius Mischa, Cole Philip A, Yu Hongtao
Departments of Pharmacology, The University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, Texas 75390, USA.
Biochemistry. 2007 Jul 10;46(27):8058-65. doi: 10.1021/bi700664y. Epub 2007 Jun 15.
Histone modifications, such as acetylation and methylation, are important epigenetic marks that regulate diverse biological processes that use chromatin as the template, including transcription. Dysregulation of histone acetylation and methylation leads to the silencing of tumor suppressor genes and contributes to cancer progression. Inhibitors of enzymes that catalyze the addition and removal of these epigenetic marks thus have therapeutic potential for treating cancer. Lysine-specific demethylase 1 (LSD1) is the first discovered histone lysine demethylase and, with the help of its cofactor CoREST, specifically demethylates mono- and dimethylated histone H3 lysine 4 (H3-K4), thus repressing transcription. Because LSD1 belongs to the family of flavin adenine dinucleotide (FAD)-dependent amine oxidases, certain inhibitors of monoamine oxidases (MAOs), including the clinically used antidepressant trans-2-phenylcyclopropylamine (PCPA; tranylcypromine; Parnate), are also capable of inhibiting LSD1. In this study, we have further measured the kinetic parameters of the inhibition of LSD1 by PCPA and determined the crystal structure of LSD1-CoREST in the presence of PCPA. Our structural and mass spectrometry analyses are consistent with PCPA forming a covalent adduct with FAD in LSD1 that is distinct from the FAD-PCPA adduct of MAO B. The structure also reveals that the phenyl ring of the FAD-PCPA adduct in LSD1 does not form extensive interactions with active-site residues. This study thus provides the basis for designing more potent inhibitors of LSD1 that contain substitutions on the phenyl ring of PCPA to fully engage neighboring residues.
组蛋白修饰，如乙酰化和甲基化，是重要的表观遗传标记，可调节多种以染色质为模板的生物过程，包括转录。组蛋白乙酰化和甲基化失调会导致肿瘤抑制基因沉默，并促进癌症进展。因此，催化这些表观遗传标记添加和去除的酶的抑制剂具有治疗癌症的潜力。赖氨酸特异性去甲基化酶1（LSD1）是首个被发现的组蛋白赖氨酸去甲基化酶，在其辅因子CoREST的帮助下，特异性地使单甲基化和二甲基化的组蛋白H3赖氨酸4（H3-K4）去甲基化，从而抑制转录。由于LSD1属于黄素腺嘌呤二核苷酸（FAD）依赖性胺氧化酶家族，某些单胺氧化酶（MAO）抑制剂，包括临床使用的抗抑郁药反式-2-苯基环丙胺（PCPA；反苯环丙胺；Parnate），也能够抑制LSD1。在本研究中，我们进一步测定了PCPA抑制LSD1的动力学参数，并确定了在PCPA存在下LSD1-CoREST的晶体结构。我们的结构和质谱分析结果表明，PCPA与LSD1中的FAD形成了一种共价加合物，该加合物与MAO B的FAD-PCPA加合物不同。该结构还显示，LSD1中FAD-PCPA加合物的苯环与活性位点残基没有广泛的相互作用。因此，本研究为设计更有效的LSD1抑制剂提供了基础，这些抑制剂在PCPA的苯环上含有取代基，以充分结合相邻残基。
