BacPROTAC-induced degradation of ClpC1 as a new strategy against drug-resistant mycobacteria

Abstract

Antimicrobial resistance (AMR) is a global public health threat that urgently requires development of new treatment concepts. In general, these treatments should not only be able to overcome existing resistance, but designed to slow down or prevent emergence of new resistance mechanisms. Targeted protein degradation (TPD), whereby a drug redirects cellular proteolytic machinery towards degrading a specific target, is an emerging concept in drug discovery. Here, we demonstrate that a TPD strategy represents an effective approach for addressing AMR in Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB) and one of the deadliest bacterial pathogens. We developed proteolysis targeting chimeras active in bacteria (BacPROTACs) that bind to ClpC1, a component of the mycobacterial protein degradation machinery. The anti-Mtb BacPROTACs were derived from cyclomarins, natural products known to bind to ClpC1. To create dual targeting modalities, cyclomarins were dimerized by click chemistry or olefin metathesis, resulting in compounds that recruit and degrade ClpC1. The resulting BacPROTACs reduced levels of endogenous ClpC1 in a model organism Mycobacterium smegmatis (Msm), as well as displayed minimum inhibitory concentrations in the low micro- to nanomolar range in Msm and Mtb strains, including multiple drug resistant isolates. Additionally, the compounds also killed Mtb resident in macrophages. Taken together, anti-Mtb BacPROTACs that degrade ClpC1, a core component of the mycobacterial protein degradation machinery, represent a fundamentally different strategy for targeting Mtb and overcoming drug resistance.

A Perspective on Newly Emerging Proteolysis-Targeting Strategies in Antimicrobial Drug Discovery

“…A simplified desoxycyclomarin derivative was used as the active compound for the development of BacPROTAC against the tuberculosis H37Rv strains residing on the THP-1 macrophages. Homo-BacPROTAC molecule was made by dimerizing the cyclomarin molecules, and it was known to show high degradation efficiency at the sub-nM level [ 65 ].…”

BacPROTACs targeting Clp protease: a promising strategy for anti-mycobacterial drug discovery

“…Phenotypic assays against Mycobacterium tuberculosis showed that CymA was active against several MDR-TB clinical isolates and hypoxic non replicating bacillus, without effects against Gram-negative and Gram-positive bacteria (Schimitt et al, 2011b). Using molecular modification approach, it was synthesized a cyclic peptide with a slightly simplified structure, named desoxycyclomarin C (dCym) (Junk et al, 2023). Chemical structure of BacPROTACs-1, -2 and -3.…”