# Developing next-generation genomically recoded organisms to synthetically activate biomarkers for drug discovery

> **NIH NIH R01** · YALE UNIVERSITY · 2020 · $588,033

## Abstract

PROJECT SUMMARY
Healthy and diseased physiological states are governed by a complex web of interacting proteins that confer the
collective behavior observed in cells. The precise placement and chemical composition of post-translational
modifications (PTMs) decorated across proteins determines their structure, function, and impart specificity for
cellular signaling. Current progress toward the elucidation of PTM-mediated signaling and function is
hampered by the challenge of studying transient PTMs in cells and limited methods to produce proteins
containing specific combinations of modified amino acids. Recent advances in synthetic and chemical biology
have successfully demonstrated the ability to encode diverse nonstandard amino acids (nsAAs), including
physiologically relevant PTMs, into proteins. In particular, recent advances in the development of genomically
recoded organism (GROs) – recoded strains of E. coli with open coding channels – and engineered translation
systems that encode PTMs (e.g., phosphoserine) have allowed activation of human phosphoproteins. These
capabilities have precisely defined active protein states, map substrate networks, and implicate new function for
disease-relevant mutations. However, two important challenges have emerged that preclude a comprehensive
understanding of these protein networks and limit the translation of such insights into targeted clinical solutions.
First, the precise arrangement and contributions of distinct PTMs that lead to active protein states is often
unknown and hard to decipher. Second, the development of small molecules that target PTMs at molecular
precision to modulate protein activity is a defining challenge for the development of new drugs. Specific Aims:
In this proposal, we seek to leverage a strong foundation of genomic, biomolecular and proteomic technologies,
expertise in systems and synthetic biology, and preliminary data to construct a genomically recoded organism
(GRO) with three open codons in E. coli (Aim 1), engineer translational machinery that reassigns sense and stop
codons for site-specific incorporation of multiple nonstandard amino acids that encode post-translational
modifications into proteins (Aim 2), and utilize these technologies to develop a synthetic biology platform that
synthetically activates disease-relevant protein networks targeted for isolation of new drug candidates (Aim 3).
Significance: This work will be significant because it will enable the synthetic activation of physiologically
relevant protein networks at the molecular level in GROs. These activated protein systems can elucidate complex
biomolecular interactions that underlie disease and recapitulate human protein networks that are difficult to
study and manipulate in their native contexts. Challenging these activated protein networks to small molecule
libraries establishes a rapid and facile new approach to probe biomarkers at molecular specificity and sets the
stage for a new synthetic-biology ...

## Key facts

- **NIH application ID:** 10097168
- **Project number:** 1R01GM140481-01
- **Recipient organization:** YALE UNIVERSITY
- **Principal Investigator:** Farren J. Isaacs
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $588,033
- **Award type:** 1
- **Project period:** 2020-09-15 → 2024-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10097168

## Citation

> US National Institutes of Health, RePORTER application 10097168, Developing next-generation genomically recoded organisms to synthetically activate biomarkers for drug discovery (1R01GM140481-01). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10097168. Licensed CC0.

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