Loss-of-function BRCA1/2 mutations lead to defective homologous recombination (HR) activity, a
frontline DNA damage repair pathway that accurately addresses double-strand breaks. In the absence of
sufficient HR activity, BRCA1/2-deficient cancers are suggested to activate a non-canonical DNA maintenance
mechanism dependent on the oncoprotein cancerous inhibitor of protein phosphatase 2A (CIP2A). CIP2A
colocalizes with the genome stability factor TOPBP1 at sites of DNA damage during mitosis. This complex is
suggested to physically tether fragmented chromosomes and centromere-bearing counterparts to ensure proper
division and cancer cell survival. After mitosis, chromosome fragments can undergo chromothripsis, a large-
scale error-prone genomic rearrangement. Chromothriptic fragments also rely on CIP2A for proper division in
the next cell cycle to ultimately potentiate oncogenesis. CIP2A knockdown is lethal in BRCA1/2-deficient cancers
but does not harm HR-proficient cells, indicating CIP2A to be a unique therapeutic vulnerability. However, a
bonafide CIP2A inhibitor has not yet been produced via standard drug discovery efforts and may require
innovative strategies. Recent chemoproteomic analyses identified nucleophilic cysteine residues in CIP2A that
can be covalently labeled (“liganded”) with electrophiles. While lead fragments provide starting points for further
development, these scaffolds also non-selectively engage other proteins. Furthermore, the functional
consequences of labeling CIP2A are unknown. The proposal will therefore achieve chemical inhibition of CIP2A
using covalent degraders (e.g., PROTAC) and focuses on the following aims: (1) Identify potent and selective
covalent ligands for CIP2A. (2) Develop heterobifunctional probes and evaluate proximity-dependent
degradation of CIP2A. (3) Analyze chemical inhibition of CIP2A in BRCA1/2-deficient cells. Encouragingly,
preliminary data indicate the proposed ligands label CIP2A in both cellular and in vitro settings. Building on these
results, the first aim will synthesize a focused probe collection based on computational guidance and then assess
target engagement using a state-of-the-art chemoproteomic workflow. In the second aim, selective ligands will
be converted into heterobifunctional degraders and characterized for CIP2A degradation in BRCA1/2-deficient
cells. The third aim will then evaluate the cellular activity of covalent degraders by tracking phenotypes indicative
of CIP2A inhibition and defective mitosis. This proposal will provide valuable chemical tools to probe CIP2A
function and lay the foundation for therapeutics to treat BRCA1/2-deficient cancers. During this fellowship, I am
grateful to be mentored by multiple professors from the Rockefeller University: Tarun Kapoor, my advisor, a
master in chemical probe design and cell division biology; Jiankun Lyu, an expert in computational chemistry;
Ekaterina Vinogradova, a leader in chemoproteomics. Their mentorship will be supplemented with additional
training both within Rockefeller and in the broader academic community. This fellowship represents an essential
step towards my goal of performing independent research at the interface of chemical and cancer biology.
