Discovery of Novel Peptidomimetic Boronate ClpP Inhibitors with Noncanonical Enzyme Mechanism as Potent Virulence Blockers in Vitro and in Vivo

Yuan Ju; Lihui He; Yuanzheng Zhou; Tao Yang; Ke Sun; Rao Song; Yang Yang; Chengwei Li; Zitai Sang; Rui Bao; Youfu Luo

doi:10.1021/acs.jmedchem.9b01746

Discovery of Novel Peptidomimetic Boronate ClpP Inhibitors with Noncanonical Enzyme Mechanism as Potent Virulence Blockers in Vitro and in Vivo

J Med Chem. 2020 Mar 26;63(6):3104-3119. doi: 10.1021/acs.jmedchem.9b01746. Epub 2020 Feb 20.

Authors

Yuan Ju¹, Lihui He¹, Yuanzheng Zhou¹, Tao Yang^{1

2}, Ke Sun¹, Rao Song¹, Yang Yang¹, Chengwei Li^{1

3}, Zitai Sang⁴, Rui Bao¹, Youfu Luo¹

Affiliations

¹ State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.
² Laboratory of Human Disease and Immunotherapies, West China Hospital, Sichuan University, Chengdu 610041, China.
³ Suzhou Zelgen Biopharmaceuticals Co., Ltd., Kunshan, Jiangsu 215301, China.
⁴ Institute of Life Science, Luoyang Normal University, Luoyang, Henan 471934, China.

PMID: 32031798
DOI: 10.1021/acs.jmedchem.9b01746

Abstract

Caseinolytic protease P (ClpP) is considered as a promising target for the treatment of Staphylococcus aureus infections. In an unbiased screen of 2632 molecules, a peptidomimetic boronate, MLN9708, was found to be a potent suppressor of SaClpP function. A time-saving and cost-efficient strategy integrating in silico position scanning, multistep miniaturized synthesis, and bioactivity testing was deployed for optimization of this hit compound and led to fast exploration of structure-activity relationships. Five of 150 compounds from the miniaturized synthesis exhibited improved inhibitory activity. Compound 43Hf was the most active inhibitor and showed reversible covalent binding to SaClpP while did not destabilize the tetradecameric structure of SaClpP. The crystal structure of 43Hf-SaClpP complex provided mechanistic insight into the covalent binding mode of peptidomimetic boronate and SaClpP. Furthermore, 43Hf could bind endogenous ClpP in S. aureus cells and exhibited significant efficacy in attenuating S. aureus virulence in vitro and in vivo.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Anti-Bacterial Agents / metabolism
Anti-Bacterial Agents / pharmacology
Anti-Bacterial Agents / therapeutic use*
Bacterial Proteins / antagonists & inhibitors
Bacterial Proteins / metabolism
Boron Compounds / pharmacology
Boronic Acids / metabolism
Boronic Acids / pharmacology
Boronic Acids / therapeutic use*
Endopeptidase Clp / antagonists & inhibitors*
Endopeptidase Clp / metabolism
Female
Glycine / analogs & derivatives
Glycine / pharmacology
Humans
Methicillin-Resistant Staphylococcus aureus / drug effects
Methicillin-Resistant Staphylococcus aureus / enzymology
Mice, Inbred BALB C
Molecular Docking Simulation
Molecular Structure
Peptidomimetics / metabolism
Peptidomimetics / pharmacology
Peptidomimetics / therapeutic use*
Protein Binding
Serine Proteinase Inhibitors / metabolism
Serine Proteinase Inhibitors / pharmacology
Serine Proteinase Inhibitors / therapeutic use*
Skin / pathology
Small Molecule Libraries / pharmacology
Staphylococcal Skin Infections / drug therapy*
Structure-Activity Relationship
Virulence / drug effects

Substances

Anti-Bacterial Agents
Bacterial Proteins
Boron Compounds
Boronic Acids
Peptidomimetics
Serine Proteinase Inhibitors
Small Molecule Libraries
ixazomib
Endopeptidase Clp
Glycine