# Discovery of inhibitors that target the Mtb ClpP1P2 protease

> **NIH NIH U19** · GLOBAL ALLIANCE FOR TB DRUG DEVELOPMENT · 2020 · $522,353

## Abstract

Project Summary
 As part of the program “Modulation of Protein Production and Degradation as an Integrated Approach to
Rapid Sterilization of Drug Sensitive and Resistant Mycobacterium tuberculosis (Mtb)”, Project 2 will focus on
“Discovery of inhibitors that target the Mtb ClpP1P2 protease”. Genetic studies suggest that the Clp system
represents a uniquely attractive drug target. It is essential under all conditions, both growing and non-growing.
And it is tightly regulated – even small changes in activity result in cell death. Upon depletion of Clp proteins,
cells rapidly die, both in vitro and in a mouse model of tuberculosis. In fact, the death is much more rapid than is
seen with depletion of traditional drug targets. Thus, an antibiotic that targeted Clp could provide a path to a
sought-after treatment-shortening regimen.
 Several compounds have been found that target the Clp complex. The vast majority of those compounds
target one of the ATPase components, ClpC1, and these compounds will be optimized as part of Project 1.
Project 2 will instead focus on modulators of the ClpP1P2 protease, the core function of Clp. In other bacteria,
activators of Clp proteolytic activity are lethal. Genetic studies have shown that inhibition of Clp protease in
mycobacteria also results in cell death. Moreover, a series of modified peptides inhibit Clp-mediated proteolysis
in vitro and kill Mtb in a Clp-dependent manner. Thus, the goal of Project 2 is to work together with all the
Scientific Cores to develop these promising compounds to improve their activity and pharmacology, towards the
program’s ultimate goal of developing new antituberculous agents. In particular, the project will work with Cores
A and C to help design and synthesize new inhibitors, and rely on Cores B and D for testing and product
development. Specifically, Project 2 will:
 1. Identify the sequence determinants of Clp-inhibitory peptides. Mapping of the sequence
specificity of the Clp protease has been used to design first generation inhibitors. This project will use purified
ClpP1P2 complexes in vitro to further define peptide characteristics to enable design of improved inhibitors.
 2. Develop optimized mechanism-based peptide inhibitors. The project will use information from
substrate identification to produce modified peptides that act as inhibitors. These will initially be tested for their
ability to inhibit the enzyme and then their ability to kill Mtb. For those that are optimal, pharmacologic and
toxicologic parameters will be determined as an initial step toward drug development.
 3. Identify non-peptidic analogues that act as Clp inhibitors. Peptides often have pharmacologic
issues that could make them non-optimal. Non-peptidic inhibitors will be designed using optimized substrates
and co-crystals. These will be tested with both purified enzymes and in whole cell assays.

## Key facts

- **NIH application ID:** 9904482
- **Project number:** 5U19AI142735-02
- **Recipient organization:** GLOBAL ALLIANCE FOR TB DRUG DEVELOPMENT
- **Principal Investigator:** Eric J. Rubin
- **Activity code:** U19 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $522,353
- **Award type:** 5
- **Project period:** — → —

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9904482

## Citation

> US National Institutes of Health, RePORTER application 9904482, Discovery of inhibitors that target the Mtb ClpP1P2 protease (5U19AI142735-02). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/9904482. Licensed CC0.

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