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

Autores da FMUP

• Raquel Ângela Silva Soares Lino

  Autor

Participantes de fora da FMUP

• Weinhaupl, K
• Gragera, M
• Bueno Carrasco, MT
• Arranz, R
• Krandor, O
• Akopian, T
• Rubin, E
• Felix, J
• Fraga, H

Unidades de investigação

• Biomedicina

Abstract

The unfoldase ClpC1 is one of the most exciting drug targets against tuberculosis. This AAA+ unfoldase works in coopera-tion 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 Myco-bacterium 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.

Keywords

• Anti-Bacterial Agents; Bacterial Proteins; Humans; Molecular Chaperones; Mycobacterium tuberculosis; Tuberculosis; Electron microscopes; Medical imaging; Proteins; antiinfective agent; bacterial protein; chaperone; Bound-states; Chaperon; Cryo-electron microscopy; Drug development; Drug targets; Mechanism of action; Mycobacterium tuberculosis; N-terminal domains; Natural products; Protein degradation; amino terminal sequence; anion exchange chromatography; antibiotic therapy; Article; Bacillus subtilis; binding site; circular dichroism; computer model; conformational transition; cryoelectron microscopy; crystal structure; crystallography; DNA sequencing; enzyme activity; Escherichia coli; fluorometry; minimum inhibitory concentration; mitochondrial respiration; molecular docking; molecular dynamics; Mycobacterium tuberculosis; nonhuman; protein aggregation; protein conformation; protein degradation; protein interaction; protein structure; sequence homology; site directed mutagenesis; S