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While enzyme-targeted inhibitors like IMT1B block POLRMT, their organelle specificity remains unclear. Here, we report a distinct strategy using mitochondria-accumulating nonplanar perylene diimides (PDIs). We demonstrate that the fluorescent lead compound PDIC-BL selectively accumulates within mitochondria. Single-molecule stretching assays showed that PDIC-BL interacts with mtDNA-derived double-stranded DNA templates in vitro with an affinity comparable to ethidium (Kd = 32 \u03bcM). In cells, this mitochondrial accumulation and DNA-binding capability enable PDIC-BL to suppress mitochondrially encoded gene expression, thereby contributing to mitochondrial dysfunction, oxidative stress, and apoptosis-associated cell death. Consequently, PDIC-BL exhibits potent antitumor activity in breast cancer cell lines (MCF-7, MDA-MB-231) and significantly suppresses tumor growth in vivo, with preliminary tolerability in a cancer xenograft model in nude mice. This work offers a generalizable strategy for developing mitochondria-biased DNA-binding therapeutics.<\/jats:p>","DOI":"10.1021\/acs.jmedchem.6c02119","type":"journal-article","created":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T17:01:55Z","timestamp":1791306115000},"page":"24601-24618","source":"Crossref","is-referenced-by-count":0,"title":["Mitochondria-Accumulating Nonplanar Perylene Diimides Suppress Mitochondrial DNA Transcription for Antitumor Therapy"],"prefix":"10.1021","volume":"69","author":[{"given":"Junfeng","family":"Huo","sequence":"first","affiliation":[{"name":"Huazhong University of Science and Technology , , ,","place":["Wuhan, China, 430030"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xin","family":"Jin","sequence":"additional","affiliation":[{"name":"Huazhong University of Science and Technology , , ,","place":["Wuhan, China, 430030"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meng","family":"Yin","sequence":"additional","affiliation":[{"name":"Huazhong University of Science and Technology , , ,","place":["Wuhan, China, 430030"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Na","family":"Hu","sequence":"additional","affiliation":[{"name":"Huazhong University of Science and Technology , , ,","place":["Wuhan, China, 430030"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tianyu","family":"Liu","sequence":"additional","affiliation":[{"name":"Huazhong University of Science and Technology , , ,","place":["Wuhan, China, 430030"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenwen","family":"Lu","sequence":"additional","affiliation":[{"name":"Key Laboratory of Organ Development and Regeneration of Zhejiang Province, College of Life and Environmental Sciences, Hangzhou Normal Universit , ,","place":["Hangzhou, China, 311121"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5218-0152","authenticated-orcid":true,"given":"Zhongwen","family":"Chen","sequence":"additional","affiliation":[{"name":"Chinese Academy of Sciences , , ,","place":["Shanghai, China, 203201"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Feiyu","family":"Duan","sequence":"additional","affiliation":[{"name":"Huazhong University of Science and Technology , , ,","place":["Wuhan, China, 430030"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0191-1792","authenticated-orcid":true,"given":"Lili","family":"Lu","sequence":"additional","affiliation":[{"name":"Huazhong University of Science and Technology , , ,","place":["Wuhan, China, 430030"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qingyi","family":"Tong","sequence":"additional","affiliation":[{"name":"Huazhong University of Science and Technology , , ,","place":["Wuhan, China, 430030"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9272-3390","authenticated-orcid":true,"given":"Jirong","family":"Huang","sequence":"additional","affiliation":[{"name":"Huazhong University of Science and Technology , , ,","place":["Wuhan, China, 430030"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5371-9666","authenticated-orcid":true,"given":"Huijuan","family":"You","sequence":"additional","affiliation":[{"name":"Huazhong University of Science and Technology , , ,","place":["Wuhan, China, 430030"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,10,6]]},"reference":[{"issue":"1","key":"2026102305065882300_cit1","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1038\/nchembio.1712","article-title":"Targeting mitochondria metabolism for cancer therapy","volume":"11","author":"Weinberg","year":"2015","journal-title":"Nat. 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