# Innovative technologies to transform antibiotic discovery.  Project 1 Genomic applications to transform Gram-negative Antibiotic discovery

> **NIH NIH U19** · BROAD INSTITUTE, INC. · 2021 · $1,870,233

## Abstract

Since Alexander Fleming's discovery of penicillin, antibiotics have been arguably the single medical
intervention that has saved more lives than any other. However, this life saving intervention is now being
threatened by the problem of antibiotic resistance that is outpacing the discovery of new antibiotics, resulting in
the WHO and CDC declaring antibiotic resistance as one of the greatest threats to human health. Projections
include the possibility of 10 million deaths per year by 2050 with tremendous impact on the global economy in
the absence of a significant shift in the current antibiotic landscape
 We have developed novel strategies to interface genomics and high-throughput chemical screening
technologies to transform antibiotic discovery, with a focus here on the major Gram-negative pathogen
Pseudomonas aeruginosa (PsA), specifically targeting its essential outer membrane proteins (OMPs) and outer
membrane associated proteins (OMAPs) in order to circumvent the need for xenobiotic cytoplasmic
accumulation. We have performed chemical screening in a multiplexed fashion against a pool of bar-coded,
genetically engineered target-specific strains in which each of the essential OMP/OMAP target genes has been
knocked-down by promoter replacement. Next generation sequencing is used to enumerate amplified barcodes
to measure the census of each mutant strain in the pool in response to a small molecule. Controlled low
expression of the protein of interest in each of these strains hypersensitizes them to inhibitors of the
corresponding target. Importantly, this strategy has allowed us (1) to expand the numbers of small molecule
candidates by identifying small molecules that would have eluded discovery if screening simply against wild-type
PsA, (2) to couple whole cell screening with target-based discovery, and (3) to target essential proteins of
unknown function or lack a high-throughput assay. Using this approach to target 9 essential OMP/OMAP targets
in a single screen, we have identified candidates targeting the outer membrane proteins LptD and OprL, proteins
required for LPS transport and cell membrane integrity, respectively. Because these targets lack robust
functional assays, we have developed a high-throughput transcriptomics-driven pipeline coupled with machine
learning to identify and prioritize molecules with a high likelihood of specifically inhibiting these targets. We now
propose to develop the hits with completely novel mechanisms of action to lead optimization and demonstrate
in vivo proof of concept.

## Key facts

- **NIH application ID:** 10242002
- **Project number:** 5U19AI142780-03
- **Recipient organization:** BROAD INSTITUTE, INC.
- **Principal Investigator:** DEBORAH T HUNG
- **Activity code:** U19 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $1,870,233
- **Award type:** 5
- **Project period:** 2019-08-07 → 2024-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10242002

## Citation

> US National Institutes of Health, RePORTER application 10242002, Innovative technologies to transform antibiotic discovery.  Project 1 Genomic applications to transform Gram-negative Antibiotic discovery (5U19AI142780-03). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10242002. Licensed CC0.

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