Structure of the drug target ClpC1 unfoldase in action provides insights on antibiotic mechanism of action.

The Journal of biological chemistry, Volume: 298, Issue: 11
November 6, 2022
Katharina Weinhäupl K, Marcos Gragera M, M Teresa Bueno-Carrasco MT, Rocío Arranz R, Olga Krandor O, Tatos Akopian T, Raquel Soares R, Eric Rubin E, Jan Felix J, Hugo Fraga H

The unfoldase ClpC1 is one of the most exciting drug targets against tuberculosis. This AAA+ unfoldase works in cooperation with the ClpP1P2 protease and is the target of at least four natural product antibiotics: cyclomarin, ecumicin, lassomycin, and rufomycin. Although these molecules are promising starting points for drug development, their mechanisms of action remain largely unknown. Taking advantage of a middle domain mutant, we determined the first structure of Mycobacterium tuberculosis ClpC1 in its apo, cyclomarin-, and ecumicin-bound states via cryo-EM. The obtained structure displays features observed in other members of the AAA+ family and provides a map for further drug development. While the apo and cyclomarin-bound structures are indistinguishable and have N-terminal domains that are invisible in their respective EM maps, around half of the ecumicin-bound ClpC1 particles display three of their six N-terminal domains in an extended conformation. Our structural observations suggest a mechanism where ecumicin functions by mimicking substrate binding, leading to ATPase activation and changes in protein degradation profile.