# A Next-Generation Scalable Platform to Discover Antimicrobials of Ribosomal Origin

> **NIH NIH R01** · UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN · 2024 · $743,463

## Abstract

PROJECT SUMMARY/ABSTRACT
Natural products are indisputably the most productive source of chemical matter for antibiotic development.
Unfortunately, the pharmacological deployment of new natural products has been outpaced by the waning utility
of approved antibiotics, especially those active against Gram-negative bacterial pathogens, Genomic
technologies and synthetic biology are uniquely positioned to address this shortfall, and towards that critical goal,
the previous project period developed a fully 6utomated, §,calable, and high-Ihroughput (FAST) pipeline for the
discovery of Ribosomally synthesized and Post-translationally modified Peptides (RiPPs), RiPPs are a class of
natural product covering nearly 50 known structural families. Despite their impressive structural and functional
diversity, RiPPs are united by a common biosynthetic strategy. A gene-encoded precursor peptide is comprised
of an N-terminal leader region, providing a binding site for the modification enzymes, and a C-terminal core
region, which receives all of the post-translational modifications.
This renewal project builds on our previous success in unlocking the potential of RiPPs as a source of new
antibacterials. For this project, we propose three interrelated but independently achievable specific aims. Aim 1
addresses pitfalls of the FAST-RiPPs procedure uncovered during the previous project period. Here, we will
enhance our ability to achieve high titers of any desired RiPP structural class. Among others, solutions to the
challenge of obtaining mature products involving radical S-adenosylmethionine-dependent enzymes are
proposed. Aim 2 develops the ways and means to prioritize RiPPs with a high probability of displaying
antibacterial activity. Lastly, Aim 3 addresses the grand challenge of predicting ring patterns directly from primary
sequence for multicyclic RiPPs. With several RiPP classes associated with multimacrocyclic scaffolds and often
encoding numerous macrocycle donor and acceptor residues in the core region, determining the structural
outcome of the enzymatic pathways has been impossible. However, with advances in bioinformatics, artificial
intelligence (Al), and new ring patterns discovered as a consequence of a functional FAST-RiPPs pipeline, a
solution to this problem becomes feasible. Given their proven success rates from the previous project period,
including the discovery of a potent anti-Klebsiella compound, lanthipeptides serve as our testbed for Al
algorithmic development.
This project blends cutting-edge Al, synthetic biology, biofoundry, and analytical chemistry techniques with
innovative solutions to heterologous expression deficiencies. We further will engineer broad host range plasmid
compatibility to overcome the need to reclone pathways when a heterologous host is deemed insufficient.
Success on this project will have a profound impact on the synthetic biology community and pharmaceutical
industry.

## Key facts

- **NIH application ID:** 10980213
- **Project number:** 2R01AI144967-06
- **Recipient organization:** UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN
- **Principal Investigator:** Douglas Alan Mitchell
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $743,463
- **Award type:** 2
- **Project period:** 2019-03-25 → 2029-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10980213

## Citation

> US National Institutes of Health, RePORTER application 10980213, A Next-Generation Scalable Platform to Discover Antimicrobials of Ribosomal Origin (2R01AI144967-06). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/10980213. Licensed CC0.

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