Identification and characterization of approved drugs and drug-like compounds as covalent Escherichia coli ClpP inhibitors

Elisa Sassetti, Cristina Durante Cruz, Päivi Tammela, Mathias Winterhalter, Koen Augustyns, Philip Gribbon, Björn Windshügel

Research output: Contribution to journalArticleScientificpeer-review


The serine protease Caseinolytic protease subunit P (ClpP) plays an important role for protein homeostasis in bacteria and contributes to various developmental processes, as well as virulence. Therefore, ClpP is considered as a potential drug target in Gram-positive and Gram-negative bacteria. In this study, we utilized a biochemical assay to screen several small molecule libraries of approved and investigational drugs for Escherichia coli ClpP inhibitors. The approved drugs bortezomib, cefmetazole, cisplatin, as well as the investigational drug cDPCP, and the protease inhibitor 3,4-dichloroisocoumarin (3,4-DIC) emerged as ClpP inhibitors with IC50 values ranging between 0.04 and 31 mu M. Compound profiling of the inhibitors revealed cefmetazole and cisplatin not to inhibit the serine protease bovine -chymotrypsin, and for cefmetazole no cytotoxicity against three human cell lines was detected. Surface plasmon resonance studies demonstrated all novel ClpP inhibitors to bind covalently to ClpP. Investigation of the potential binding mode for cefmetazole using molecular docking suggested a dual covalent binding to Ser97 and Thr168. While only the antibiotic cefmetazole demonstrated an intrinsic antibacterial effect, cDPCP clearly delayed the bacterial growth recovery time upon chemically induced nitric oxide stress in a ClpP-dependent manner.

Original languageEnglish
Article number2686
JournalInternational Journal of Molecular Sciences
Issue number11
Number of pages13
Publication statusPublished - 1 Jun 2019
MoE publication typeA1 Journal article-refereed

Fields of Science

  • ACID
  • ClpP
  • Escherichia coli
  • covalent binding
  • high-throughput screening
  • inhibitor
  • nitric oxide stress
  • surface plasmon resonance
  • 317 Pharmacy
  • 1182 Biochemistry, cell and molecular biology
  • 116 Chemical sciences


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