# Inhibition and Catalytic Degradation of Promutagenic DNA Deaminases

> **NIH NIH R21** · UNIVERSITY OF PENNSYLVANIA · 2024 · $216,512

## Abstract

PROJECT SUMMARY
This proposal aims to develop the first potent and specific antagonists of the pro-mutagenic effects of APOBEC
DNA deaminase enzymes in cells. Access to whole genome sequences has helped reveal common mutational
signatures across various cancers. One such prominent mutational signature, termed SBS2, includes
hypermutated clusters containing a high density of C to T/G substitutions on the same strand, a phenomenon
known as kataegis. These features, in addition to the enrichment of the mutations in 5’-TC motifs, point to a
causative role for APOBEC3 (A3) family enzymes. While these enzymes normally mutate and restrict
retroviruses or retroelements, studies have confirmed that two family members, APOBEC3A (A3A) and
APOBEC3B (A3B), have a prominent role in pathological mutagenesis targeting the host genome. The relative
contributions of each enzyme remain a matter of vigorous debate, as genetic approaches specifically targeting
A3A or A3B are limited by their high homology to one another and juxtaposition on the genome. Furthermore,
no molecular tools currently exist that can disrupt A3 function. There is therefore a pressing need for molecular
probes that can either inhibit or deplete A3 enzymes from cells. This proposal builds on the hypothesis that
insights into the mechanism and substrate selectivity of A3 enzymes can be leveraged to design potent and
specific antagonists. Specifically, we have demonstrated that mechanism-based inhibitor moieties can be
presented in preferred secondary structures and engineered into exonuclease-resistant DNA molecules to yield
potent nanomolar inhibitors of A3A. These molecules present the opportunity for facile functionalization, which
can be utilized to convert classical inhibitors into molecules capable of inducing the catalytic degradation of the
target APOBEC enzymes in cells, via an unprecedented combination of nucleic acid inhibitors and proteasome
targeting (PROTAC) technology. Taken together, this proposal aims to fill a critical gap in the field by introducing
tools to perturb APOBEC function in cells in order to reveal their underlying biology and offer a roadmap for
potential therapeutics.

## Key facts

- **NIH application ID:** 10883650
- **Project number:** 5R21CA277463-02
- **Recipient organization:** UNIVERSITY OF PENNSYLVANIA
- **Principal Investigator:** Rahul Manu Kohli
- **Activity code:** R21 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $216,512
- **Award type:** 5
- **Project period:** 2023-07-06 → 2025-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10883650

## Citation

> US National Institutes of Health, RePORTER application 10883650, Inhibition and Catalytic Degradation of Promutagenic DNA Deaminases (5R21CA277463-02). Retrieved via AI Analytics 2026-05-28 from https://api.ai-analytics.org/grant/nih/10883650. Licensed CC0.

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