# Activity-Based DNA-Encoded Library Technology

> **NIH NIH R35** · UNIVERSITY OF CALIFORNIA-IRVINE · 2023 · $378,032

## Abstract

Project Summary
The vast majority of the human proteome is considered “undruggable.” Undruggable proteins may be difficult
to express, lack surface binding clefts, do not have corresponding activity assays, or some combination thereof.
This concept is symptomatic of a major liability of contemporary drug discovery, which requires significant
investment to generate and scale up protein expression or cell culture and engineering an activity assay for
every new target. It may be possible to bypass these bottlenecks by directly targeting translation intermediates,
or “ribosome nascent chains” (RNCs), with small molecules that selectively inhibit protein synthesis by
interacting with an RNC and stalling translation. RNCs represent a vast source of new drug targets that do not
follow the rules of druggability, but high-throughput screens for RNC-targeting “Selective Terminators of
Protein Synthesis” (SToPS) have been roundly unsuccessful due to the limited scope of structures in standard
compound screening decks. During the previously funded project, our instrumentation and systems
engineering laboratory developed solid-phase DNA-encoded library (DEL) synthesis methods and microfluidic
DEL screening technology that collectively enabled unprecedented activity-based screens on these large
collections of novel chemical matter. We demonstrated that this platform can efficiently search DELs of
drug-like small molecules to identify novel bioactive molecules for several clinically relevant drug targets. The
proposed MIRA program will leverage our activity-based DEL screening capabilities to establish a SToPS
discovery platform through two parallel technology development initiatives. The first is a synthetic
biology-driven microfluidic droplet-scale in vitro translation-based approach to identifying small molecule
SToPS of a specific target RNC. The second is a polymer/tissue culture engineering approach that will explore
cellular assays of translation stalling, the screening format that identified the original examples of SToPS
targeting the hypercholesterolemia-associated protein, PCSK9. Both approaches will benefit from DEL-based
chemical diversity, which can be designed to explore chemical space known to elicit ribosome binding and
selective translation stalling. Cellular DEL screening technology will ensure that screening hits are cell active,
and more broadly will deliver a long-sought screening modality to the field of drug discovery. Following
proof-of-concept SToPS screens, we will develop computational workflows that mine publicly available
ribosome profiling data sets to predict candidate stall sites for SToPS screening, tackling CCR5 (anti-HIV) and
the bacterial signal sequence as examples of undruggable targets. We envision a completely plug-and-play
chemical probe discovery strategy for translating human genome sequence directly into SToPS as chemical
probes, thereby fulfilling the original vision of the Human Genome Project and eliminating “undr...

## Key facts

- **NIH application ID:** 10553645
- **Project number:** 5R35GM140890-03
- **Recipient organization:** UNIVERSITY OF CALIFORNIA-IRVINE
- **Principal Investigator:** Brian M Paegel
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2023
- **Award amount:** $378,032
- **Award type:** 5
- **Project period:** 2021-04-01 → 2026-01-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10553645

## Citation

> US National Institutes of Health, RePORTER application 10553645, Activity-Based DNA-Encoded Library Technology (5R35GM140890-03). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10553645. Licensed CC0.

---

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