Cyclin A/B RxL Macrocyclic Inhibitors to Treat Cancers with High E2F Activity

  • bioRxiv. 2024 Aug 1:2024.08.01.605889. doi: 10.1101/2024.08.01.605889.
Shilpa Singh ,  Catherine E Gleason ,  Min Fang ,  Yasmin N Laimon ,  Vishal Khivansara ,  Shanhai Xie ,  Yavuz T Durmaz ,  Aniruddha Sarkar ,  Kenneth Ngo ,  Varunika Savla ,  Yixiang Li ,  Muhannad Abu-Remaileh ,  Xinyue Li ,  Bishma Tuladhar ,  Ranya Odeh ,  Frances Hamkins-Indik ,  Daphne He ,  Miles W Membreno ,  Meisam Nosrati ,  Nathan N Gushwa ,  Siegfried S F Leung ,  Breena Fraga-Walton ,  Luis Hernandez ,  Miguel P Baldomero ,  Bryan M Lent ,  David Spellmeyer ,  Joshua F Luna ,  Dalena Hoang ,  Yuliana Gritsenko ,  Manesh Chand ,  Megan K DeMart ,  Sammy Metobo ,  Chinmay Bhatt ,  Justin A Shapiro ,  Kai Yang ,  Nathan J Dupper ,  Andrew T Bockus ,  John G Doench ,  James B Aggen ,  Li-Fen Liu ,  Bernard Levin ,  Evelyn W Wang ,  Iolanda Vendrell ,  Roman Fischer ,  Benedikt Kessler ,  Prafulla C Gokhale ,  Sabina Signoretti ,  Alexander Spektor ,  Constantine Kreatsoulas ,  Rajinder Singh ,  David J Earp ,  Pablo D Garcia ,  Deepak Nijhawan ,  Matthew G Oser
PMID: 39211113 DOI: 10.1101/2024.08.01.605889
Abstract

Cancer cell proliferation requires precise control of E2F1 activity; excess activity promotes Apoptosis. Here, we developed cell-permeable and bioavailable macrocycles that selectively kill Small Cell Lung Cancer (SCLC) cells with inherent high E2F1 activity by blocking RxL-mediated interactions of cyclin A and cyclin B with select substrates. Genome-wide CRISPR/Cas9 knockout and random mutagenesis screens found that cyclin A/B RxL macrocyclic inhibitors (cyclin A/Bi) induced Apoptosis paradoxically by cyclin B- and Cdk2-dependent spindle assembly checkpoint activation (SAC). Mechanistically, cyclin A/Bi hyperactivate E2F1 and cyclin B by blocking their RxL-interactions with cyclin A and Myt1, respectively, ultimately leading to SAC activation and mitotic cell death. Base editor screens identified cyclin B variants that confer cyclin A/Bi resistance including several variants that disrupted cyclin B:Cdk interactions. Unexpectedly but consistent with our base editor and knockout screens, cyclin A/Bi induced the formation of neo-morphic Cdk2-cyclin B complexes that promote SAC activation and Apoptosis. Finally, orally-bioavailable cyclin A/Bi robustly inhibited tumor growth in chemotherapy-resistant patient-derived xenograft models of SCLC. This work uncovers gain-of-function mechanisms by which cyclin A/Bi induce Apoptosis in cancers with high E2F activity, and suggests cyclin A/Bi as a therapeutic strategy for SCLC and other cancers driven by high E2F activity.

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