Kamel Emadeldin M, Ali Mohamed A M, Allam Ahmed A, Ahmed Noha A, Abalkhail Adil, Aba Alkhayl Faris F, Lamsabhi Al Mokhtar
Chemistry Department, Faculty of Science, Beni-Suef University, Beni-Suef, 62514, Egypt.
Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, 11623, Saudi Arabia.
Funct Integr Genomics. 2025 Sep 17;25(1):194. doi: 10.1007/s10142-025-01708-9.
Maintenance DNA methylation relies on a coordinated partnership between DNMT1 and its chromatin cofactor UHRF1. UHRF1's SRA domain flips 5-methylcytosine out of hemimethylated DNA, and UHRF1-installed ubiquitin marks on histone H3 (H3K18/K23Ub; H3Ub₂) and PAF15 (PAF15Ub₂) are recognized by the DNMT1 RFTS domain to relieve autoinhibition and license copying of parental methylation during S phase. Tumors often upregulate this axis to enforce promoter hypermethylation programs, whereas approved azanucleosides act via DNMT1 trapping and are associated with DNA-damage-linked toxicities. Over ~ 15 years of structural work-from the 2008 SRA-DNA complexes to a 2022 cryo-EM structure of DNMT1 engaged with hemimethylated DNA and H3Ub₂-has mapped two tractable sites: the UHRF1-SRA aromatic cage and the ubiquitin-binding surface on DNMT1's RFTS. These insights catalyzed small-molecule discovery. The anthraquinone UM63 validated SRA-pocket engagement but intercalates into DNA; newer non-intercalating SRA-directed inhibitors AMSA-2 (hydroxyanthracene/anthrarobin) and MPB-7 (imidazoquinoline) retain low-micromolar potency. In cells, AMSA-2 and MPB-7 disrupt UHRF1/DNMT1 colocalization at replication foci and induce replication-coupled global hypomethylation, with preferential cytotoxicity in UHRF1-high cancer lines relative to non-transformed cells. Beyond SRA antagonism, DNMT1 can be down-regulated pharmacologically: the non-nucleoside inhibitor GSK-3,484,862 triggers proteasome-dependent DNMT1 degradation alongside hypomethylation, and the first DNMT1-targeting PROTAC (KW0113) achieves selective DNMT1 degradation and growth inhibition in AML models. Remaining hurdles include potency ceilings, nuclear exposure/pharmacokinetics, and adaptive chromatin rewiring upon DNMT1 inhibition; nonetheless, structure-guided optimization and degrader strategies outline a credible path to precision epigenetic therapeutics that directly disrupt the DNMT1-UHRF1 maintenance machinery.
维持性DNA甲基化依赖于DNA甲基转移酶1（DNMT1）与其染色质辅因子泛素样含PHD和RING结构域的蛋白1（UHRF1）之间的协同作用。UHRF1的SRA结构域将5-甲基胞嘧啶从半甲基化DNA中翻转出来，UHRF1在组蛋白H3（H3K18/K23Ub；H3Ub₂）和PAF15（PAF15Ub₂）上安装的泛素标记被DNMT1的RFTS结构域识别，以解除自身抑制并允许在S期复制亲本甲基化。肿瘤通常会上调这一轴以强化启动子高甲基化程序，而获批的氮杂核苷通过捕获DNMT1起作用，并与DNA损伤相关的毒性有关。在大约15年的结构研究中——从2008年的SRA-DNA复合物到2022年DNMT1与半甲基化DNA和H3Ub₂结合的冷冻电镜结构——已经确定了两个易于处理的位点：UHRF1-SRA芳香笼和DNMT1的RFTS上的泛素结合表面。这些见解推动了小分子的发现。蒽醌类化合物UM63验证了与SRA口袋的结合，但会嵌入DNA；更新的非嵌入性SRA导向抑制剂AMSA-2（羟基蒽/蒽罗宾）和MPB-7（咪唑并喹啉）保持低微摩尔效力。在细胞中，AMSA-2和MPB-7破坏UHRF1/DNMT1在复制灶的共定位，并诱导复制偶联的全基因组低甲基化，相对于未转化细胞，在UHRF1高表达的癌细胞系中具有优先的细胞毒性。除了SRA拮抗作用外，DNMT1还可以通过药理学方法下调：非核苷抑制剂GSK-3,484,862在诱导低甲基化的同时触发蛋白酶体依赖性的DNMT1降解，首个靶向DNMT1的PROTAC（KW0113）在急性髓系白血病（AML）模型中实现了选择性DNMT1降解和生长抑制。剩下的障碍包括效力上限、核暴露/药代动力学以及DNMT1抑制后的适应性染色质重塑；尽管如此，基于结构的优化和降解策略为直接破坏DNMT1-UHRF1维持机制的精准表观遗传治疗勾勒出了一条可靠的途径。
