# Structural Determination and Design of Drug Interactions with Ribonucleotide Reductase

> **NIH NIH F32** · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · 2021 · $65,994

## Abstract

PROJECT SUMMARY/ABSTRACT
The equilibrium of deoxyribonucleoside triphosphates (dNTPs), the building blocks of DNA, is critical for
maintaining human health. Known as the regulator of dNTP biosynthesis, ribonucleotide reductases (RNRs)
are essential enzymes found in all organisms that catalyze the reduction of ribonucleotides to
deoxyribonucleotides, an essential reaction for DNA replication and repair. Failure of cells to maintain
appropriate dNTP concentrations can lead to increased mutagenesis and uncontrolled proliferation,
characteristics that promote cancer development. RNR inhibition has been implicated in several types of
cancers and is a target for drug design. Although current drugs in clinical use are effective, our understanding
of the inhibition mechanism is incomplete. Specifically, nucleoside analogs are used as α-inhibitors and have
been shown to cause a distinct conformational change upon addition to the RNR α-subunit. Upon addition of
nucleoside analogs, α-hexamer rings are formed. α-hexamerization has been observed with three
triphosphorylated nucleoside analogs, clofarabine, cladribine and fludarabine; however, there are no near-
atomic resolution structures available. The work described in this proposal aims to obtain high resolution
structures of each α-inhibitor with Human RNR and to design and evaluate new RNR α-inhibitors. Cryo-
electron microscopy will be used to examine the structures of α-hexamers after addition of triphosphorylated
cladribine, clofarabine, and fludarabine to determine α-inhibitor binding locations, possible conformational
changes and noncovalent interactions that could explain α-hexamer stability, and how α-hexamerization
prevents RNR activity. Furthermore, new nucleoside analogs will be designed with the goal of increasing
binding affinity of the nucleoside analogs to study the effects of electronic properties on the stability of α-
hexamers. Together, this work aims to deepen our understanding of the mechanism of RNR inhibition by
understanding the formation of α-hexamers and utilize structure-based drug design to expand the library of
nucleoside analogs that can induce α-hexamerization.

## Key facts

- **NIH application ID:** 10313726
- **Project number:** 1F32GM143840-01
- **Recipient organization:** MASSACHUSETTS INSTITUTE OF TECHNOLOGY
- **Principal Investigator:** KELSEY Rose MILLER
- **Activity code:** F32 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $65,994
- **Award type:** 1
- **Project period:** 2021-09-01 → 2024-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10313726

## Citation

> US National Institutes of Health, RePORTER application 10313726, Structural Determination and Design of Drug Interactions with Ribonucleotide Reductase (1F32GM143840-01). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10313726. Licensed CC0.

---

*[NIH grants dataset](/datasets/nih-grants) · CC0 1.0*