Discovery of Anti-Tuberculosis Lead Compounds from Actinomycetes

Drug-resistant TB has lent urgency to finding drug leads with novel modes of action. Screening of more than 65,000 actinomycete extracts for inhibition of Mycobacterium tuberculosis (Mtb), followed by orthogonal chromatography and comprehensive spectroscopy, led to the isolation and identification of ecumicin, a macrocyclic tridecapeptide. Ecumicin exerts potent, selective bactericidal activity against Mtb in vitro including drug-resistant strains as well as non-replicating cells and inhibits Mtb growth in mouse lungs. Genome sequencing identified several presumed ecumicin biosynthetic genes in Nonomuraea sp. MJM 5123. Genome mining of ecumicin-resistant Mtb identified as the likely target, the ClpC1 ATPase complex, which functions in protein breakdown with the ClpP1P2 protease complex. Ecumicin markedly enhanced the ATPase activity of WT ClpC1 but prevented activation of proteolysis by ClpC1. Less stimulation was observed with ClpC1 from ecumicin-resistant mutants. Thus ClpC1 is a valid drug target against Mtb, and ecumicin may serve as a lead compound for anti-TB drug development. The structures of ecumicin analogs were elucidated using a new method – NMR structure sequencing. This method mainly uses information from the most sensitive NMR experiment, the 1D 1H NMR, and treats each new peptide as a mixture of individual amino acid residues, for expedited structure elucidation.