ClpC1 Modulating Ohmyungsamycin A and Ecumicin Natural Product Analogues are Potent Antimycobacterials

Herein, we describe the design, synthesis, and evaluation of modified cyclic peptides based upon the privileged structure of the cyclic depsipeptide natural products, ohmyungsamycin and ecumicin, that target <i>Mycobacterium tuberculosis</i> (<i>Mtb</i>) caseinolytic-like protein 1 (ClpC1). Simplified analogues featuring substitution at three sites (l-Thr-3, <i>N</i>-Me-l-Trp-9, and/or the N-terminus) were designed and synthesized via a novel and robust strategy, employing an oxazolidine-protected C-terminal amino acid, to enable late-stage, epimerization-free, solution-phase macrolactamization. Lead analogues had nanomolar affinity for the ClpC1 N-terminal domain (NTD), possessed potent activity against <i>Mtb</i> in vitro and were shown to inhibit protein degradation by the mycobacterial ClpC1:ClpP1P2 protease with an associated enhancement of ClpC1 ATPase activity. The most promising analogue from the series exhibited prolonged bactericidal killing activity against <i>Mtb</i> without the emergence of resistance and retained activity in an in vivo zebrafish model of mycobacterial infection.