1
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Ishikawa F, Homma M, Tanabe G, Uchihashi T. Protein degradation by a component of the chaperonin-linked protease ClpP. Genes Cells 2024. [PMID: 38965067 DOI: 10.1111/gtc.13141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 06/03/2024] [Accepted: 06/19/2024] [Indexed: 07/06/2024]
Abstract
In cells, proteins are synthesized, function, and degraded (dead). Protein synthesis (spring) is important for the life of proteins. However, how proteins die is equally important for organisms. Proteases are secreted from cells and used as nutrients to break down external proteins. Proteases degrade unwanted and harmful cellular proteins. In eukaryotes, a large enzyme complex called the proteasome is primarily responsible for cellular protein degradation. Prokaryotes, such as bacteria, have similar protein degradation systems. In this review, we describe the structure and function of the ClpXP complex in the degradation system, which is an ATP-dependent protease in bacterial cells, with a particular focus on ClpP.
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Affiliation(s)
| | - Michio Homma
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Genzoh Tanabe
- Faculty of Pharmacy, Kindai University, Osaka, Japan
| | - Takayuki Uchihashi
- Division of Material Science, Graduate School of Science, Nagoya University, Nagoya, Japan
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2
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Ishikawa F, Homma M, Tanabe G, Uchihashi T. [Protein degradation in bacteria: focus on the ClpP protease]. Nihon Saikingaku Zasshi 2024; 79:1-13. [PMID: 38382970 DOI: 10.3412/jsb.79.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Proteins in the cells are born (synthesized), work, and die (decomposed). In the life of a protein, its birth is obviously important, but how it dies is equally important in living organisms. Proteases secreted into the outside of cells are used to decompose the external proteins and the degradation products are taken as the nutrients. On the other hand, there are also proteases that decompose unnecessary or harmful proteins which are generated in the cells. In eukaryotes, a large enzyme complex called the proteasome is primarily responsible for degradation of such proteins. Bacteria, which are prokaryotes, have a similar system as the proteasome. We would like to explain the bacterial degradation system of proteins or the death of proteins, which is performed by ATP-dependent protease Clp, with a particular focus on the ClpXP complex, and with an aspect as a target for antibiotics against bacteria.
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Affiliation(s)
| | - Michio Homma
- Division of Physics, Graduate School of Science, Nagoya University
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3
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Malarney KP, Chang PV. Chemoproteomic Approaches for Unraveling Prokaryotic Biology. Isr J Chem 2023; 63:e202200076. [PMID: 37842282 PMCID: PMC10575470 DOI: 10.1002/ijch.202200076] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Indexed: 03/07/2023]
Abstract
Bacteria are ubiquitous lifeforms with important roles in the environment, biotechnology, and human health. Many of the functions that bacteria perform are mediated by proteins and enzymes, which catalyze metabolic transformations of small molecules and modifications of proteins. To better understand these biological processes, chemical proteomic approaches, including activity-based protein profiling, have been developed to interrogate protein function and enzymatic activity in physiologically relevant contexts. Here, chemoproteomic strategies and technological advances for studying bacterial physiology, pathogenesis, and metabolism are discussed. The development of chemoproteomic approaches for characterizing protein function and enzymatic activity within bacteria remains an active area of research, and continued innovations are expected to provide breakthroughs in understanding bacterial biology.
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Affiliation(s)
- Kien P Malarney
- Department of Microbiology, Cornell University, Ithaca, NY 14853 (USA)
| | - Pamela V Chang
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853 (USA)
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853 (USA)
- Cornell Center for Immunology, Cornell University, Ithaca, NY 14853 (USA)
- Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY 14853 (USA)
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4
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Liu R, Ali S, Huang D, Zhang Y, Lü P, Chen Q. A Sensitive Nucleic Acid Detection Platform for Foodborne Pathogens Based on CRISPR-Cas13a System Combined with Polymerase Chain Reaction. FOOD ANAL METHOD 2022. [DOI: 10.1007/s12161-022-02419-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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5
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Pankova AS. Two-Step Construction of Thiophene-Oxazole Dyads with Fluorescent Properties by the Ring Expansion of Aziridines. J Org Chem 2022; 87:11121-11130. [PMID: 35905291 DOI: 10.1021/acs.joc.2c01365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A general approach toward 2-thiophenylsubstituted oxazoles using aziridination of a double bond of (acyl)alkenyl thiophenes with the subsequent expansion of the aziridine ring is developed. The isolation of intermediate aziridine is not necessary. This expedient protocol covers a broad scope of readily available 2-, 3-, and benzothiophene derivatives, is practical and reliable, requires short reaction times, and is simple to set up and work up reaction mixtures. Thiophenyloxazoles, obtained by this method, exhibit fluorescence with high quantum yields.
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Affiliation(s)
- Alena S Pankova
- Institute of Chemistry, Saint Petersburg State University, 198504 Saint Petersburg, Russia
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6
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Schwarz M, Hübner I, Sieber SA. Tailored phenyl esters inhibit ClpXP and attenuate Staphylococcus aureus α-hemolysin secretion. Chembiochem 2022; 23:e202200253. [PMID: 35713329 PMCID: PMC9544270 DOI: 10.1002/cbic.202200253] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/15/2022] [Indexed: 11/14/2022]
Abstract
Novel strategies against multidrug‐resistant bacteria are urgently needed in order to overcome the current silent pandemic. Manipulation of toxin production in pathogenic species serves as a promising approach to attenuate virulence and prevent infections. In many bacteria such as Staphylococcus aureus or Listeria monocyotgenes, serine protease ClpXP is a key contributor to virulence and thus represents a prime target for antimicrobial drug discovery. The limited stability of previous electrophilic warheads has prevented a sustained effect of virulence attenuation in bacterial culture. Here, we systematically tailor the stability and inhibitory potency of phenyl ester ClpXP inhibitors by steric shielding of the ester bond and fine‐tuning the phenol leaving group. Out of 17 derivatives, two (MAS‐19 and MAS‐30) inhibited S. aureus ClpP peptidase and ClpXP protease activities by >60 % at 1 μM. Furthermore, the novel inhibitors did not exhibit pronounced cytotoxicity against human and bacterial cells. Unlike the first generation phenylester AV170, these molecules attenuated S. aureus virulence markedly and displayed increased stability in aqueous buffer compared to the previous benchmark AV170.
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Affiliation(s)
- Markus Schwarz
- Technical University Munich: Technische Universitat Munchen, Chemistry, Ernst-Otto-Fischer-Straße 8, 85748, Garching bei München, GERMANY
| | - Ines Hübner
- Technical University of Munich: Technische Universitat Munchen, Chemistry, GERMANY
| | - Stephan Axel Sieber
- Technische Universitat Munchen, Department of Chemistry, Lichtenbergstr. 4, 85747, Garching, GERMANY
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7
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Darnowski MG, Lanosky TD, Labana P, Brazeau-Henrie JT, Calvert ND, Dornan MH, Natola C, Paquette AR, Shuhendler AJ, Boddy CN. Armeniaspirol analogues with more potent Gram-positive antibiotic activity show enhanced inhibition of the ATP-dependent proteases ClpXP and ClpYQ. RSC Med Chem 2022; 13:436-444. [PMID: 35647545 PMCID: PMC9020616 DOI: 10.1039/d1md00355k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 02/07/2022] [Indexed: 11/21/2022] Open
Abstract
Antibiotics with fundamentally new mechanisms of action such as the armeniaspirols, which target the ATP-dependent proteases ClpXP and ClpYQ, must be developed to combat antimicrobial resistance. While the mechanism of action of armeniaspirol against Gram-positive bacteria is understood, little is known about the structure-activity relationship for its antibiotic activity. Based on the preliminary data showing that modifications of armeniaspirol's N-methyl group increased antibiotic potency, we probed the structure-activity relationship of N-alkyl armeniaspirol derivatives. A series of focused derivatives were synthesized and evaluated for antibiotic activity against clinically relevant pathogens including methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus. Replacement of the N-methyl with N-hexyl, various N-benzyl, and N-phenethyl substituents led to substantial increases in antibiotic activity and potency for inhibition of both ClpYQ and ClpXP. Docking studies identified binding models for ClpXP and ClpYQ that were consistent with the inhibition data. This work confirms the role of ClpXP and ClpYQ in the mechanism of action of armeniaspirol and provides important lead compounds for further antibiotic development.
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Affiliation(s)
- Michael G. Darnowski
- Department of Chemistry and Biomolecular Sciences, University of OttawaOttawaONK1N 6N5 Canadacboddy!uottawa.ca
| | - Taylor D. Lanosky
- Department of Chemistry and Biomolecular Sciences, University of OttawaOttawaONK1N 6N5 Canadacboddy!uottawa.ca
| | - Puneet Labana
- Department of Chemistry and Biomolecular Sciences, University of OttawaOttawaONK1N 6N5 Canadacboddy!uottawa.ca
| | - Jordan T. Brazeau-Henrie
- Department of Chemistry and Biomolecular Sciences, University of OttawaOttawaONK1N 6N5 Canadacboddy!uottawa.ca
| | - Nicholas D. Calvert
- Department of Chemistry and Biomolecular Sciences, University of OttawaOttawaONK1N 6N5 Canadacboddy!uottawa.ca
| | - Mark H. Dornan
- Department of Chemistry and Biomolecular Sciences, University of OttawaOttawaONK1N 6N5 Canadacboddy!uottawa.ca
| | - Claudia Natola
- Department of Chemistry and Biomolecular Sciences, University of OttawaOttawaONK1N 6N5 Canadacboddy!uottawa.ca
| | - André R. Paquette
- Department of Chemistry and Biomolecular Sciences, University of OttawaOttawaONK1N 6N5 Canadacboddy!uottawa.ca
| | - Adam J. Shuhendler
- Department of Chemistry and Biomolecular Sciences, University of OttawaOttawaONK1N 6N5 Canadacboddy!uottawa.ca
| | - Christopher N. Boddy
- Department of Chemistry and Biomolecular Sciences, University of OttawaOttawaONK1N 6N5 Canadacboddy!uottawa.ca
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8
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Small molecule inhibitors of the mitochondrial ClpXP protease possess cytostatic potential and re-sensitize chemo-resistant cancers. Sci Rep 2021; 11:11185. [PMID: 34045646 PMCID: PMC8160014 DOI: 10.1038/s41598-021-90801-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 05/17/2021] [Indexed: 12/18/2022] Open
Abstract
The human mitochondrial ClpXP protease complex (HsClpXP) has recently attracted major attention as a target for novel anti-cancer therapies. Despite its important role in disease progression, the cellular role of HsClpXP is poorly characterized and only few small molecule inhibitors have been reported. Herein, we screened previously established S. aureus ClpXP inhibitors against the related human protease complex and identified potent small molecules against human ClpXP. The hit compounds showed anti-cancer activity in a panoply of leukemia, liver and breast cancer cell lines. We found that the bacterial ClpXP inhibitor 334 impairs the electron transport chain (ETC), enhances the production of mitochondrial reactive oxygen species (mtROS) and thereby promotes protein carbonylation, aberrant proteostasis and apoptosis. In addition, 334 induces cell death in re-isolated patient-derived xenograft (PDX) leukemia cells, potentiates the effect of DNA-damaging cytostatics and re-sensitizes resistant cancers to chemotherapy in non-apoptotic doses.
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9
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Ju Y, An Q, Zhang Y, Sun K, Bai L, Luo Y. Recent advances in Clp protease modulation to address virulence, resistance and persistence of MRSA infection. Drug Discov Today 2021; 26:2190-2197. [PMID: 34048895 DOI: 10.1016/j.drudis.2021.05.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 04/17/2021] [Accepted: 05/20/2021] [Indexed: 02/05/2023]
Abstract
The Clp protease is an AAA+ protease that executes abnormally folded or malfunctioning proteins, and has an important role in producing virulence factors, forming biofilms or persisters and developing methicillin-resistant Staphylococcus aureus (MRSA). Recent studies showed that Clp protease controls virulence via agr signaling and degrades antitoxins of the toxin-antitoxin system to modulate the formation of persisters and biofilms. In this review, we focus on recent developments concerning the virulence and persistence regulatory pathways and resistance-related mechanism of Clp protease in S. aureus, with an overview of the Clp modulators developed to treat MRSA infection.
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Affiliation(s)
- Yuan Ju
- Center of Infectious Diseases and State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China; Sichuan University Library, Sichuan University, Chengdu 610041, China
| | - Qi An
- Public Health Clinical Center of Chengdu, Chengdu 610041, China
| | - Yiwen Zhang
- Center of Infectious Diseases and State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Ke Sun
- Center of Infectious Diseases and State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Lang Bai
- Center of Infectious Diseases and State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China.
| | - Youfu Luo
- Center of Infectious Diseases and State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China.
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10
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Dighe SN, van Akker SR, Mathew M, Perera M, Collet TA. Discovery of a Novel Antimicrobial Agent by the Virtual Screening of a Library of Small Molecules. Mol Inform 2021; 40:e2100035. [PMID: 33891375 DOI: 10.1002/minf.202100035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 11/12/2022]
Abstract
A virtual screening approach based upon a combination of docking and pharmacophore methods was utilized on a library of 1.4 million molecules to identify novel antimicrobial agents, which may potentially act via inhibition of the caseinolytic protease. Using this method, compound 6 was found to be bactericidal against three staphylococcal species (minimum inhibitory concentration (MIC)=4-16 μg/mL). Further, subsequent structural optimization of 6 led to the identification of compound 24, which was shown to be the most potent analog within the series (MIC=4 μg/mL) and outperforming the antibiotic controls for two of the staphylococcal species. The newly discovered antimicrobial agent (24) demonstrated excellent in silico ADME properties and was non-toxic when tested on two human skin cell lines. As such, compound 24 has the potential for use as a lead molecule in the development of a novel class of antimicrobial agents.
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Affiliation(s)
- Satish N Dighe
- Queensland University of Technology, Institute of Health & Biomedical Innovation, 60 Musk Avenue, Kelvin Grove, Brisbane, QLD, Australia, 4059
| | - Suzannah R van Akker
- Queensland University of Technology, Institute of Health & Biomedical Innovation, 60 Musk Avenue, Kelvin Grove, Brisbane, QLD, Australia, 4059
| | - Marina Mathew
- Queensland University of Technology, Institute of Health & Biomedical Innovation, 60 Musk Avenue, Kelvin Grove, Brisbane, QLD, Australia, 4059
| | - Madusha Perera
- Queensland University of Technology, Institute of Health & Biomedical Innovation, 60 Musk Avenue, Kelvin Grove, Brisbane, QLD, Australia, 4059
| | - Trudi A Collet
- Queensland University of Technology, Institute of Health & Biomedical Innovation, 60 Musk Avenue, Kelvin Grove, Brisbane, QLD, Australia, 4059
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11
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Zheng D, Xu Y, Yuan G, Wu X, Li Q. Bacterial ClpP Protease Is a Potential Target for Methyl Gallate. Front Microbiol 2021; 11:598692. [PMID: 33613462 PMCID: PMC7890073 DOI: 10.3389/fmicb.2020.598692] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/28/2020] [Indexed: 11/29/2022] Open
Abstract
Methyl gallate (MG) is an effective microbicide with great potential application in the integrated management of plant diseases and an important potential drug for clinical application. However, its target remains unknown. This study conducted a transposon sequencing (Tn-seq) under MG treatment in plant pathogenic bacterium Ralstonia solanacearum. Tn-seq identified that the mutation of caseinolytic protease proteolytic subunit gene clpP significantly increased the resistance of R. solanacearum to MG, which was validated by the in-frame gene deletion. iTRAQ (isobaric tags for relative and absolute quantitation) proteomics analysis revealed that chemotaxis and flagella associated proteins were the major substrates degraded by ClpP under the tested condition. Moreover, sulfur metabolism-associated proteins were potential substrates of ClpP and were upregulated by MG treatment in wild-type R. solanacearum but not in clpP mutant. Furthermore, molecular docking confirmed the possible interaction between MG and ClpP. Collectively, this study revealed that MG might target bacterial ClpP, inhibit the activity of ClpP, and consequently disturb bacterial proteostasis, providing a theoretical basis for the application of MG.
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Affiliation(s)
- Dehong Zheng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Yanan Xu
- Pharmaceutical College, Guangxi Medical University, Nanning, China
| | - Gaoqing Yuan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Xiaogang Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Qiqin Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
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12
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Dighe SN, Tippana M, van Akker S, Collet TA. Structure-Based Scaffold Repurposing toward the Discovery of Novel Cholinesterase Inhibitors. ACS OMEGA 2020; 5:30971-30979. [PMID: 33324805 PMCID: PMC7726787 DOI: 10.1021/acsomega.0c03848] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/12/2020] [Indexed: 05/06/2023]
Abstract
Cholinesterases (ChE) are well-known drug targets for the treatment of Alzheimer's disease (AD). In continuation of work to develop novel cholinesterase inhibitors, we utilized a structure-based scaffold repurposing approach and discovered six novel ChE inhibitors from our recently developed DNA gyrase inhibitor library. Among the identified hits, two compounds (denoted 3 and 18) were found to be the most potent inhibitor of acetylcholinesterase (AChE, IC50 = 6.10 ± 1.01 μM) and butyrylcholinesterase (BuChE, IC50 = 5.50 ± 0.007 μM), respectively. Compound 3 was responsible for the formation of H-bond and π-π stacking interactions within the active site of AChE. In contrast, compound 18 was well fitted in the choline-binding pocket and catalytic site of BuChE. Results obtained from in vitro cytotoxicity assays and in silico derived physicochemical and absorption, distribution, metabolism, and excretion (ADME) properties indicate that repurposed scaffold 3 and 18 could be potential drug candidates for further development as novel ChE inhibitors.
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13
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Ju Y, He L, Zhou Y, Yang T, Sun K, Song R, Yang Y, Li C, Sang Z, Bao R, Luo Y. Discovery of Novel Peptidomimetic Boronate ClpP Inhibitors with Noncanonical Enzyme Mechanism as Potent Virulence Blockers in Vitro and in Vivo. J Med Chem 2020; 63:3104-3119. [PMID: 32031798 DOI: 10.1021/acs.jmedchem.9b01746] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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.
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Affiliation(s)
- Yuan Ju
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Lihui He
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yuanzheng Zhou
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Tao Yang
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.,Laboratory of Human Disease and Immunotherapies, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ke Sun
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Rao Song
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yang Yang
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Chengwei Li
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.,Suzhou Zelgen Biopharmaceuticals Co., Ltd., Kunshan, Jiangsu 215301, China
| | - Zitai Sang
- Institute of Life Science, Luoyang Normal University, Luoyang, Henan 471934, China
| | - Rui Bao
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Youfu Luo
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
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14
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Lu K, Hou W, Xu XF, Chen Q, Li Z, Lin J, Chen WM. Biological evaluation and chemoproteomics reveal potential antibacterial targets of a cajaninstilbene-acid analogue. Eur J Med Chem 2020; 188:112026. [DOI: 10.1016/j.ejmech.2019.112026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/29/2019] [Accepted: 12/29/2019] [Indexed: 12/17/2022]
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15
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Mabanglo MF, Leung E, Vahidi S, Seraphim TV, Eger BT, Bryson S, Bhandari V, Zhou JL, Mao YQ, Rizzolo K, Barghash MM, Goodreid JD, Phanse S, Babu M, Barbosa LRS, Ramos CHI, Batey RA, Kay LE, Pai EF, Houry WA. ClpP protease activation results from the reorganization of the electrostatic interaction networks at the entrance pores. Commun Biol 2019; 2:410. [PMID: 31754640 PMCID: PMC6853987 DOI: 10.1038/s42003-019-0656-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 10/17/2019] [Indexed: 01/07/2023] Open
Abstract
Bacterial ClpP is a highly conserved, cylindrical, self-compartmentalizing serine protease required for maintaining cellular proteostasis. Small molecule acyldepsipeptides (ADEPs) and activators of self-compartmentalized proteases 1 (ACP1s) cause dysregulation and activation of ClpP, leading to bacterial cell death, highlighting their potential use as novel antibiotics. Structural changes in Neisseria meningitidis and Escherichia coli ClpP upon binding to novel ACP1 and ADEP analogs were probed by X-ray crystallography, methyl-TROSY NMR, and small angle X-ray scattering. ACP1 and ADEP induce distinct conformational changes in the ClpP structure. However, reorganization of electrostatic interaction networks at the ClpP entrance pores is necessary and sufficient for activation. Further activation is achieved by formation of ordered N-terminal axial loops and reduction in the structural heterogeneity of the ClpP cylinder. Activating mutations recapitulate the structural effects of small molecule activator binding. Our data, together with previous findings, provide a structural basis for a unified mechanism of compound-based ClpP activation.
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Affiliation(s)
- Mark F. Mabanglo
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
| | - Elisa Leung
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
| | - Siavash Vahidi
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8 Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6 Canada
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, Ontario M5G 0A4 Canada
| | - Thiago V. Seraphim
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2 Canada
| | - Bryan T. Eger
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
| | - Steve Bryson
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
- Ontario Cancer Institute/Princess Margaret Hospital, Campbell Family Institute for Cancer Research, Toronto, Ontario M5G 1L7 Canada
| | - Vaibhav Bhandari
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
| | - Jin Lin Zhou
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6 Canada
| | - Yu-Qian Mao
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
| | - Kamran Rizzolo
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
| | - Marim M. Barghash
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
| | - Jordan D. Goodreid
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6 Canada
| | - Sadhna Phanse
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2 Canada
| | - Mohan Babu
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2 Canada
| | | | - Carlos H. I. Ramos
- Institute of Chemistry, University of Campinas UNICAMP, Campinas SP, 13083-970 Brazil
| | - Robert A. Batey
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6 Canada
| | - Lewis E. Kay
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8 Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6 Canada
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, Ontario M5G 0A4 Canada
| | - Emil F. Pai
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8 Canada
- Ontario Cancer Institute/Princess Margaret Hospital, Campbell Family Institute for Cancer Research, Toronto, Ontario M5G 1L7 Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5S 1A8 Canada
| | - Walid A. Houry
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6 Canada
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16
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Lakemeyer M, Bertosin E, Möller F, Balogh D, Strasser R, Dietz H, Sieber SA. Tailored Peptide Phenyl Esters Block ClpXP Proteolysis by an Unusual Breakdown into a Heptamer–Hexamer Assembly. Angew Chem Int Ed Engl 2019; 58:7127-7132. [DOI: 10.1002/anie.201901056] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Indexed: 11/10/2022]
Affiliation(s)
- Markus Lakemeyer
- Center for Integrated Protein Science (CIPSM) at theDepartment of ChemistryTechnische Universität München Lichtenbergstr. 4 85747 Garching Germany
| | - Eva Bertosin
- Physics Department and Institute for Advanced StudyTechnische Universität München Am Coulombwall 4a 85748 Garching Germany
| | | | - Dóra Balogh
- Center for Integrated Protein Science (CIPSM) at theDepartment of ChemistryTechnische Universität München Lichtenbergstr. 4 85747 Garching Germany
| | - Ralf Strasser
- Dynamic Biosensors GmbH Lochhamerstr. 15 82152 Planegg Germany
| | - Hendrik Dietz
- Physics Department and Institute for Advanced StudyTechnische Universität München Am Coulombwall 4a 85748 Garching Germany
| | - Stephan A. Sieber
- Center for Integrated Protein Science (CIPSM) at theDepartment of ChemistryTechnische Universität München Lichtenbergstr. 4 85747 Garching Germany
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17
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Lakemeyer M, Bertosin E, Möller F, Balogh D, Strasser R, Dietz H, Sieber SA. Blockade der ClpXP‐vermittelten Proteolyse mit maßgeschneiderten Peptid‐Phenylestern durch den ungewöhnlichen Zerfall in eine Heptamer‐Hexamer‐Anordnung. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Markus Lakemeyer
- Center for Integrated Protein Science (CIPSM) amDepartment ChemieTechnische Universität München Lichtenbergstraße 4 85747 Garching Deutschland
| | - Eva Bertosin
- Physik Department und Institute for Advanced StudyTechnische Universität München Am Coulombwall 4a 85748 Garching Deutschland
| | - Friederike Möller
- Dynamic Biosensors GmbH Lochhamerstraße 15 82152 Planegg Deutschland
| | - Dóra Balogh
- Center for Integrated Protein Science (CIPSM) amDepartment ChemieTechnische Universität München Lichtenbergstraße 4 85747 Garching Deutschland
| | - Ralf Strasser
- Dynamic Biosensors GmbH Lochhamerstraße 15 82152 Planegg Deutschland
| | - Hendrik Dietz
- Physik Department und Institute for Advanced StudyTechnische Universität München Am Coulombwall 4a 85748 Garching Deutschland
| | - Stephan A. Sieber
- Center for Integrated Protein Science (CIPSM) amDepartment ChemieTechnische Universität München Lichtenbergstraße 4 85747 Garching Deutschland
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18
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Moreno-Cinos C, Goossens K, Salado IG, Van Der Veken P, De Winter H, Augustyns K. ClpP Protease, a Promising Antimicrobial Target. Int J Mol Sci 2019; 20:ijms20092232. [PMID: 31067645 PMCID: PMC6540193 DOI: 10.3390/ijms20092232] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/18/2019] [Accepted: 04/29/2019] [Indexed: 01/25/2023] Open
Abstract
The caseinolytic protease proteolytic subunit (ClpP) is a serine protease playing an important role in proteostasis of eukaryotic organelles and prokaryotic cells. Alteration of ClpP function has been proved to affect the virulence and infectivity of a number of pathogens. Increased bacterial resistance to antibiotics has become a global problem and new classes of antibiotics with novel mechanisms of action are needed. In this regard, ClpP has emerged as an attractive and potentially viable option to tackle pathogen fitness without suffering cross-resistance to established antibiotic classes and, when not an essential target, without causing an evolutionary selection pressure. This opens a greater window of opportunity for the host immune system to clear the infection by itself or by co-administration with commonly prescribed antibiotics. A comprehensive overview of the function, regulation and structure of ClpP across the different organisms is given. Discussion about mechanism of action of this protease in bacterial pathogenesis and human diseases are outlined, focusing on the compounds developed in order to target the activation or inhibition of ClpP.
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Affiliation(s)
- Carlos Moreno-Cinos
- Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium.
| | - Kenneth Goossens
- Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium.
| | - Irene G Salado
- Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium.
| | - Pieter Van Der Veken
- Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium.
| | - Hans De Winter
- Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium.
| | - Koen Augustyns
- Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium.
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19
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Bongard J, Schmitz AL, Wolf A, Zischinsky G, Pieren M, Schellhorn B, Bravo-Rodriguez K, Schillinger J, Koch U, Nussbaumer P, Klebl B, Steinmann J, Buer J, Sanchez-Garcia E, Ehrmann M, Kaiser M. Chemical Validation of DegS As a Target for the Development of Antibiotics with a Novel Mode of Action. ChemMedChem 2019; 14:1074-1078. [PMID: 30945468 DOI: 10.1002/cmdc.201900193] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Indexed: 12/29/2022]
Abstract
Despite the availability of hundreds of antibiotic drugs, infectious diseases continue to remain one of the most notorious health issues. In addition, the disparity between the spread of multidrug-resistant pathogens and the development of novel classes of antibiotics exemplify an important unmet medical need that can only be addressed by identifying novel targets. Herein we demonstrate, by the development of the first in vivo active DegS inhibitors based on a pyrazolo[1,5-a]-1,3,5-triazine scaffold, that the serine protease DegS and the cell envelope stress-response pathway σE represent a target for generating antibiotics with a novel mode of action. Moreover, DegS inhibition is synergistic with well-established membrane-perturbing antibiotics, thereby opening promising avenues for rational antibiotic drug design.
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Affiliation(s)
- Jens Bongard
- Microbiology, Faculty of Biology, Center of Medical Biotechnology, University Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
| | - Anna Laura Schmitz
- Chemical Biology, Faculty of Biology, Center of Medical Biotechnology, University Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
| | - Alex Wolf
- Lead Discovery Center GmbH, Otto-Hahn-Str. 15, 44227, Dortmund, Germany
| | | | - Michel Pieren
- BioVersys AG, Hochbergerstrasse 60C, 4057, Basel, Switzerland
| | | | - Kenny Bravo-Rodriguez
- Microbiology, Faculty of Biology, Center of Medical Biotechnology, University Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany.,Computational Biochemistry, Faculty of Biology & Faculty of Chemistry, Center of Medical Biotechnology, University Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
| | - Jasmin Schillinger
- Microbiology, Faculty of Biology, Center of Medical Biotechnology, University Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
| | - Uwe Koch
- Lead Discovery Center GmbH, Otto-Hahn-Str. 15, 44227, Dortmund, Germany
| | - Peter Nussbaumer
- Lead Discovery Center GmbH, Otto-Hahn-Str. 15, 44227, Dortmund, Germany
| | - Bert Klebl
- Lead Discovery Center GmbH, Otto-Hahn-Str. 15, 44227, Dortmund, Germany
| | - Jörg Steinmann
- University Hospital Essen, University of Duisburg-Essen, Institute of Medical Microbiology, Hufelandstr. 55, 45122, Essen, Germany.,Institute of Clinical Hygiene, Medical Microbiology and Infectiology, Paracelsus Medical University, Prof.-Ernst-Nathan-Straße 1, 90419, Nürnberg, Germany
| | - Jan Buer
- University Hospital Essen, University of Duisburg-Essen, Institute of Medical Microbiology, Hufelandstr. 55, 45122, Essen, Germany
| | - Elsa Sanchez-Garcia
- Computational Biochemistry, Faculty of Biology & Faculty of Chemistry, Center of Medical Biotechnology, University Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
| | - Michael Ehrmann
- Microbiology, Faculty of Biology, Center of Medical Biotechnology, University Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
| | - Markus Kaiser
- Chemical Biology, Faculty of Biology, Center of Medical Biotechnology, University Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
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20
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Affiliation(s)
- Lin-Lin Zhou
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai 201203 China
- University of the Chinese Academy of Sciences; Beijing 100049 China
| | - Cai-Guang Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai 201203 China
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21
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Moreno-Cinos C, Sassetti E, Salado IG, Witt G, Benramdane S, Reinhardt L, Cruz CD, Joossens J, Van der Veken P, Brötz-Oesterhelt H, Tammela P, Winterhalter M, Gribbon P, Windshügel B, Augustyns K. α-Amino Diphenyl Phosphonates as Novel Inhibitors of Escherichia coli ClpP Protease. J Med Chem 2019; 62:774-797. [PMID: 30571121 DOI: 10.1021/acs.jmedchem.8b01466] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Increased Gram-negative bacteria resistance to antibiotics is becoming a global problem, and new classes of antibiotics with novel mechanisms of action are required. The caseinolytic protease subunit P (ClpP) is a serine protease conserved among bacteria that is considered as an interesting drug target. ClpP function is involved in protein turnover and homeostasis, stress response, and virulence among other processes. The focus of this study was to identify new inhibitors of Escherichia coli ClpP and to understand their mode of action. A focused library of serine protease inhibitors based on diaryl phosphonate warheads was tested for ClpP inhibition, and a chemical exploration around the hit compounds was conducted. Altogether, 14 new potent inhibitors of E. coli ClpP were identified. Compounds 85 and 92 emerged as most interesting compounds from this study due to their potency and, respectively, to its moderate but consistent antibacterial properties as well as the favorable cytotoxicity profile.
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Affiliation(s)
- Carlos Moreno-Cinos
- Laboratory of Medicinal Chemistry , University of Antwerp , Universiteitsplein 1 , B-2610 Antwerp , Belgium
| | - Elisa Sassetti
- Fraunhofer Institute for Molecular Biology and Applied Ecology, ScreeningPort , Schnackenburgallee 114 , 22525 Hamburg , Germany.,Department of Life Sciences and Chemistry , Jacobs University Bremen gGmbH , Campus Ring 1 , 28759 Bremen , Germany
| | - Irene G Salado
- Laboratory of Medicinal Chemistry , University of Antwerp , Universiteitsplein 1 , B-2610 Antwerp , Belgium
| | - Gesa Witt
- Fraunhofer Institute for Molecular Biology and Applied Ecology, ScreeningPort , Schnackenburgallee 114 , 22525 Hamburg , Germany
| | - Siham Benramdane
- Laboratory of Medicinal Chemistry , University of Antwerp , Universiteitsplein 1 , B-2610 Antwerp , Belgium
| | - Laura Reinhardt
- Interfaculty Institute for Microbiology and Infection Medicine , University of Tübingen , Auf der Morgenstelle 28 , 72076 Tübingen , Germany
| | - Cristina D Cruz
- Drug Research Program, Division of Pharmaceutical Biosciences , University of Helsinki , Viikinkaari 5E , FI-00014 Helsinki , Finland
| | - Jurgen Joossens
- Laboratory of Medicinal Chemistry , University of Antwerp , Universiteitsplein 1 , B-2610 Antwerp , Belgium
| | - Pieter Van der Veken
- Laboratory of Medicinal Chemistry , University of Antwerp , Universiteitsplein 1 , B-2610 Antwerp , Belgium
| | - Heike Brötz-Oesterhelt
- Interfaculty Institute for Microbiology and Infection Medicine , University of Tübingen , Auf der Morgenstelle 28 , 72076 Tübingen , Germany
| | - Päivi Tammela
- Drug Research Program, Division of Pharmaceutical Biosciences , University of Helsinki , Viikinkaari 5E , FI-00014 Helsinki , Finland
| | - Mathias Winterhalter
- Department of Life Sciences and Chemistry , Jacobs University Bremen gGmbH , Campus Ring 1 , 28759 Bremen , Germany
| | - Philip Gribbon
- Fraunhofer Institute for Molecular Biology and Applied Ecology, ScreeningPort , Schnackenburgallee 114 , 22525 Hamburg , Germany
| | - Björn Windshügel
- Fraunhofer Institute for Molecular Biology and Applied Ecology, ScreeningPort , Schnackenburgallee 114 , 22525 Hamburg , Germany
| | - Koen Augustyns
- Laboratory of Medicinal Chemistry , University of Antwerp , Universiteitsplein 1 , B-2610 Antwerp , Belgium
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22
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Fetzer C, Korotkov VS, Sieber SA. Hydantoin analogs inhibit the fully assembled ClpXP protease without affecting the individual peptidase and chaperone domains. Org Biomol Chem 2019; 17:7124-7127. [DOI: 10.1039/c9ob01339c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new class of non-covalent inhibitors attenuates ClpXP turnover, neither impairing chaperone nor peptidase activity.
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Affiliation(s)
- Christian Fetzer
- Technische Universität München
- Center for Integrated Protein Science Munich (CIPSM)
- 85748 Garching
- Germany
| | - Vadim S. Korotkov
- Technische Universität München
- Center for Integrated Protein Science Munich (CIPSM)
- 85748 Garching
- Germany
| | - Stephan A. Sieber
- Technische Universität München
- Center for Integrated Protein Science Munich (CIPSM)
- 85748 Garching
- Germany
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23
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Lakemeyer M, Zhao W, Mandl FA, Hammann P, Sieber SA. Thinking Outside the Box-Novel Antibacterials To Tackle the Resistance Crisis. Angew Chem Int Ed Engl 2018; 57:14440-14475. [PMID: 29939462 DOI: 10.1002/anie.201804971] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Indexed: 12/13/2022]
Abstract
The public view on antibiotics as reliable medicines changed when reports about "resistant superbugs" appeared in the news. While reasons for this resistance development are easily spotted, solutions for re-establishing effective antibiotics are still in their infancy. This Review encompasses several aspects of the antibiotic development pipeline from very early strategies to mature drugs. An interdisciplinary overview is given of methods suitable for mining novel antibiotics and strategies discussed to unravel their modes of action. Select examples of antibiotics recently identified by using these platforms not only illustrate the efficiency of these measures, but also highlight promising clinical candidates with therapeutic potential. Furthermore, the concept of molecules that disarm pathogens by addressing gatekeepers of virulence will be covered. The Review concludes with an evaluation of antibacterials currently in clinical development. Overall, this Review aims to connect select innovative antimicrobial approaches to stimulate interdisciplinary partnerships between chemists from academia and industry.
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Affiliation(s)
- Markus Lakemeyer
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Weining Zhao
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Franziska A Mandl
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Peter Hammann
- R&D Therapeutic Area Infectious Diseases, Sanofi-Aventis (Deutschland) GmbH, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - Stephan A Sieber
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
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24
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Lakemeyer M, Zhao W, Mandl FA, Hammann P, Sieber SA. Über bisherige Denkweisen hinaus - neue Wirkstoffe zur Überwindung der Antibiotika-Krise. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804971] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Markus Lakemeyer
- Fakultät für Chemie; Lehrstuhl für Organische Chemie II, Center for Integrated Protein Science (CIPSM); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Weining Zhao
- Fakultät für Chemie; Lehrstuhl für Organische Chemie II, Center for Integrated Protein Science (CIPSM); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Franziska A. Mandl
- Fakultät für Chemie; Lehrstuhl für Organische Chemie II, Center for Integrated Protein Science (CIPSM); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Peter Hammann
- R&D Therapeutic Area Infectious Diseases; Sanofi-Aventis (Deutschland) GmbH; Industriepark Höchst 65926 Frankfurt am Main Deutschland
| | - Stephan A. Sieber
- Fakultät für Chemie; Lehrstuhl für Organische Chemie II, Center for Integrated Protein Science (CIPSM); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
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25
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Gronauer TF, Mandl MM, Lakemeyer M, Hackl MW, Meßner M, Korotkov VS, Pachmayr J, Sieber SA. Design and synthesis of tailored human caseinolytic protease P inhibitors. Chem Commun (Camb) 2018; 54:9833-9836. [PMID: 30109319 DOI: 10.1039/c8cc05265d] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Human caseinolytic protease P (hClpP) is important for degradation of misfolded proteins in the mitochondrial unfolded protein response. We here introduce tailored hClpP inhibitors that utilize a steric discrimination in their core naphthofuran scaffold to selectively address the human enzyme. This novel inhibitor generation exhibited superior activity compared to previously introduced beta-lactones, optimized for bacterial ClpP. Further insights into the bioactivity and binding to cellular targets were obtained via chemical proteomics as well as proliferation- and migration studies in cancer cells.
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Affiliation(s)
- Thomas F Gronauer
- Center for Integrated Protein Science Munich, Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany.
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26
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Suppression of Staphylococcus aureus virulence by a small-molecule compound. Proc Natl Acad Sci U S A 2018; 115:8003-8008. [PMID: 30012613 DOI: 10.1073/pnas.1720520115] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Emerging antibiotic resistance among bacterial pathogens has necessitated the development of alternative approaches to combat drug-resistance-associated infection. The abolition of Staphylococcus aureus virulence by targeting multiple-virulence gene products represents a promising strategy for exploration. A multiplex promoter reporter platform using gfp-luxABCDE dual-reporter plasmids with selected promoters from S. aureus-virulence-associated genes was used to identify compounds that modulate the expression of virulence factors. One small-molecule compound, M21, was identified from a chemical library to reverse virulent S. aureus into its nonvirulent state. M21 is a noncompetitive inhibitor of ClpP and alters α-toxin expression in a ClpP-dependent manner. A mouse model of infection indicated that M21 could attenuate S. aureus virulence. This nonantibiotic compound has been shown to suppress the expression of multiple unrelated virulence factors in S. aureus, suggesting that targeting a master regulator of virulence is an effective way to control virulence. Our results illustrate the power of chemical genetics in the modulation of virulence gene expression in pathogenic bacteria.
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27
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Zhu D, Guo H, Chang Y, Ni Y, Li L, Zhang ZM, Hao P, Xu Y, Ding K, Li Z. Cell- and Tissue-Based Proteome Profiling and Dual Imaging of Apoptosis Markers with Probes Derived from Venetoclax and Idasanutlin. Angew Chem Int Ed Engl 2018; 57:9284-9289. [PMID: 29768700 DOI: 10.1002/anie.201802003] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Indexed: 01/17/2023]
Affiliation(s)
- Dongsheng Zhu
- Guangdong Provincial Key Laboratory of Biocomputing; Guangzhou Institutes of Biomedicine and Health; Chinese Academy of Sciences; 190 Kaiyuan Avenue, Science Park Guangzhou 510530 China
- University of Chinese Academy of Sciences; 19 Yuquan Road Beijing 100049 China
| | - Haijun Guo
- School of Pharmacy; Jinan University; Guangzhou City Key, Laboratory of Precision Chemical Drug Development; International Cooperative Laboratory of Traditional Chinese, Medicine Modernization and Innovative Drug Development; Ministry of Education (MOE) of People's Republic of China; 601 Huangpu Avenue West Guangzhou 510632 China
| | - Yu Chang
- School of Pharmacy; Jinan University; Guangzhou City Key, Laboratory of Precision Chemical Drug Development; International Cooperative Laboratory of Traditional Chinese, Medicine Modernization and Innovative Drug Development; Ministry of Education (MOE) of People's Republic of China; 601 Huangpu Avenue West Guangzhou 510632 China
| | - Yun Ni
- Institute of Advanced Materials (IAM); Nanjing Tech University; China
| | - Lin Li
- Institute of Advanced Materials (IAM); Nanjing Tech University; China
| | - Zhi-Min Zhang
- School of Pharmacy; Jinan University; Guangzhou City Key, Laboratory of Precision Chemical Drug Development; International Cooperative Laboratory of Traditional Chinese, Medicine Modernization and Innovative Drug Development; Ministry of Education (MOE) of People's Republic of China; 601 Huangpu Avenue West Guangzhou 510632 China
| | - Piliang Hao
- School of Life Science and Technology; ShanghaiTech University; China
| | - Yong Xu
- Guangdong Provincial Key Laboratory of Biocomputing; Guangzhou Institutes of Biomedicine and Health; Chinese Academy of Sciences; 190 Kaiyuan Avenue, Science Park Guangzhou 510530 China
- University of Chinese Academy of Sciences; 19 Yuquan Road Beijing 100049 China
| | - Ke Ding
- School of Pharmacy; Jinan University; Guangzhou City Key, Laboratory of Precision Chemical Drug Development; International Cooperative Laboratory of Traditional Chinese, Medicine Modernization and Innovative Drug Development; Ministry of Education (MOE) of People's Republic of China; 601 Huangpu Avenue West Guangzhou 510632 China
| | - Zhengqiu Li
- School of Pharmacy; Jinan University; Guangzhou City Key, Laboratory of Precision Chemical Drug Development; International Cooperative Laboratory of Traditional Chinese, Medicine Modernization and Innovative Drug Development; Ministry of Education (MOE) of People's Republic of China; 601 Huangpu Avenue West Guangzhou 510632 China
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28
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Zhu D, Guo H, Chang Y, Ni Y, Li L, Zhang ZM, Hao P, Xu Y, Ding K, Li Z. Cell- and Tissue-Based Proteome Profiling and Dual Imaging of Apoptosis Markers with Probes Derived from Venetoclax and Idasanutlin. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201802003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Dongsheng Zhu
- Guangdong Provincial Key Laboratory of Biocomputing; Guangzhou Institutes of Biomedicine and Health; Chinese Academy of Sciences; 190 Kaiyuan Avenue, Science Park Guangzhou 510530 China
- University of Chinese Academy of Sciences; 19 Yuquan Road Beijing 100049 China
| | - Haijun Guo
- School of Pharmacy; Jinan University; Guangzhou City Key, Laboratory of Precision Chemical Drug Development; International Cooperative Laboratory of Traditional Chinese, Medicine Modernization and Innovative Drug Development; Ministry of Education (MOE) of People's Republic of China; 601 Huangpu Avenue West Guangzhou 510632 China
| | - Yu Chang
- School of Pharmacy; Jinan University; Guangzhou City Key, Laboratory of Precision Chemical Drug Development; International Cooperative Laboratory of Traditional Chinese, Medicine Modernization and Innovative Drug Development; Ministry of Education (MOE) of People's Republic of China; 601 Huangpu Avenue West Guangzhou 510632 China
| | - Yun Ni
- Institute of Advanced Materials (IAM); Nanjing Tech University; China
| | - Lin Li
- Institute of Advanced Materials (IAM); Nanjing Tech University; China
| | - Zhi-Min Zhang
- School of Pharmacy; Jinan University; Guangzhou City Key, Laboratory of Precision Chemical Drug Development; International Cooperative Laboratory of Traditional Chinese, Medicine Modernization and Innovative Drug Development; Ministry of Education (MOE) of People's Republic of China; 601 Huangpu Avenue West Guangzhou 510632 China
| | - Piliang Hao
- School of Life Science and Technology; ShanghaiTech University; China
| | - Yong Xu
- Guangdong Provincial Key Laboratory of Biocomputing; Guangzhou Institutes of Biomedicine and Health; Chinese Academy of Sciences; 190 Kaiyuan Avenue, Science Park Guangzhou 510530 China
- University of Chinese Academy of Sciences; 19 Yuquan Road Beijing 100049 China
| | - Ke Ding
- School of Pharmacy; Jinan University; Guangzhou City Key, Laboratory of Precision Chemical Drug Development; International Cooperative Laboratory of Traditional Chinese, Medicine Modernization and Innovative Drug Development; Ministry of Education (MOE) of People's Republic of China; 601 Huangpu Avenue West Guangzhou 510632 China
| | - Zhengqiu Li
- School of Pharmacy; Jinan University; Guangzhou City Key, Laboratory of Precision Chemical Drug Development; International Cooperative Laboratory of Traditional Chinese, Medicine Modernization and Innovative Drug Development; Ministry of Education (MOE) of People's Republic of China; 601 Huangpu Avenue West Guangzhou 510632 China
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29
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Bhandari V, Wong KS, Zhou JL, Mabanglo MF, Batey RA, Houry WA. The Role of ClpP Protease in Bacterial Pathogenesis and Human Diseases. ACS Chem Biol 2018; 13:1413-1425. [PMID: 29775273 DOI: 10.1021/acschembio.8b00124] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In prokaryotic cells and eukaryotic organelles, the ClpP protease plays an important role in proteostasis. The disruption of the ClpP function has been shown to influence the infectivity and virulence of a number of bacterial pathogens. More recently, ClpP has been found to be involved in various forms of carcinomas and in Perrault syndrome, which is an inherited condition characterized by hearing loss in males and females and by ovarian abnormalities in females. Hence, targeting ClpP is a potentially viable, attractive option for the treatment of different ailments. Herein, the biochemical and cellular activities of ClpP are discussed along with the mechanisms by which ClpP affects bacterial pathogenesis and various human diseases. In addition, a comprehensive overview is given of the new classes of compounds in development that target ClpP. Many of these compounds are currently primarily aimed at treating bacterial infections. Some of these compounds inhibit ClpP activity, while others activate the protease and lead to its dysregulation. The ClpP activators are remarkable examples of small molecules that inhibit protein-protein interactions but also result in a gain of function.
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Affiliation(s)
- Vaibhav Bhandari
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada
| | - Keith S. Wong
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada
| | - Jin Lin Zhou
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Mark F. Mabanglo
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada
| | - Robert A. Batey
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Walid A. Houry
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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30
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Fetzer C, Korotkov VS, Thänert R, Lee KM, Neuenschwander M, von Kries JP, Medina E, Sieber SA. Verringerung der Virulenz von multiresistentem Staphylococcus aureus
mithilfe eines chemischen Disruptors des ClpX-Chaperon-Komplexes. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201708454] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Christian Fetzer
- Center for Integrated Protein Science am Department Chemie; Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Vadim S. Korotkov
- Center for Integrated Protein Science am Department Chemie; Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Robert Thänert
- Infektionsimmunologie, Helmholtz-Zentrum für Infektionsforschung; Inhoffenstraße 7 38124 Braunschweig Deutschland
| | - Kyu Myung Lee
- Center for Integrated Protein Science am Department Chemie; Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Martin Neuenschwander
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie; Robert-Roessle-Straße 10 13125 Berlin Deutschland
| | - Jens Peter von Kries
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie; Robert-Roessle-Straße 10 13125 Berlin Deutschland
| | - Eva Medina
- Infektionsimmunologie, Helmholtz-Zentrum für Infektionsforschung; Inhoffenstraße 7 38124 Braunschweig Deutschland
| | - Stephan A. Sieber
- Center for Integrated Protein Science am Department Chemie; Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
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31
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Fetzer C, Korotkov VS, Thänert R, Lee KM, Neuenschwander M, von Kries JP, Medina E, Sieber SA. A Chemical Disruptor of the ClpX Chaperone Complex Attenuates the Virulence of Multidrug-Resistant Staphylococcus aureus. Angew Chem Int Ed Engl 2017; 56:15746-15750. [DOI: 10.1002/anie.201708454] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 09/08/2017] [Indexed: 12/27/2022]
Affiliation(s)
- Christian Fetzer
- Center for Integrated Protein Science at the Department of Chemistry; Technische Universität München; Lichtenbergstrasse 4 85747 Garching Germany
| | - Vadim S. Korotkov
- Center for Integrated Protein Science at the Department of Chemistry; Technische Universität München; Lichtenbergstrasse 4 85747 Garching Germany
| | - Robert Thänert
- Infection Immunology Research Group; Helmholtz Centre for Infection Research; Inhoffenstrasse 7 38124 Braunschweig Germany
| | - Kyu Myung Lee
- Center for Integrated Protein Science at the Department of Chemistry; Technische Universität München; Lichtenbergstrasse 4 85747 Garching Germany
| | - Martin Neuenschwander
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie; Robert-Roessle-Strasse 10 13125 Berlin Germany
| | - Jens Peter von Kries
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie; Robert-Roessle-Strasse 10 13125 Berlin Germany
| | - Eva Medina
- Infection Immunology Research Group; Helmholtz Centre for Infection Research; Inhoffenstrasse 7 38124 Braunschweig Germany
| | - Stephan A. Sieber
- Center for Integrated Protein Science at the Department of Chemistry; Technische Universität München; Lichtenbergstrasse 4 85747 Garching Germany
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32
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An amino acid domino effect orchestrates ClpP's conformational states. Curr Opin Chem Biol 2017; 40:102-110. [PMID: 28910721 DOI: 10.1016/j.cbpa.2017.08.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 07/26/2017] [Accepted: 08/22/2017] [Indexed: 01/08/2023]
Abstract
Maintaining the cellular protein homeostasis means managing life on the brink of death. This balance is largely based on precise fine-tuning of enzyme activities. For instance, the ClpP protease possesses several conformational switches which are fundamental to regulating its activity. Efforts have focused on revealing the structural basis of ClpP's conformational control. In the last decade, several amino acid clusters have been identified and functionally linked to specific activation states. Researchers have now begun to couple these hotspots to one another, uncovering a global network of residues that switch in response to internal and external stimuli. For these studies, they used small molecules to mimic intermolecular interactions and point-mutational studies to shortcut regulating amino acid circuits.
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33
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Ye F, Li J, Yang CG. The development of small-molecule modulators for ClpP protease activity. MOLECULAR BIOSYSTEMS 2017; 13:23-31. [PMID: 27831584 DOI: 10.1039/c6mb00644b] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The global spread of antibiotic resistance among important human pathogens emphasizes the need to find new antibacterial drugs with a novel mode of action. The ClpP protease has been shown to demonstrate its pivotal importance to both the survival and the virulence of pathogenic bacteria during host infection. Deregulating ClpP activity either through overactivation or inhibition could lead to antibacterial activity, declaiming the dual molecular mechanism for small-molecule modulation. Recently, natural products acyldepsipeptides (ADEPs) have been identified as a new class of antibiotics that activate ClpP to a dysfunctional state in the absence of cognate ATPases. ADEPs in combination with rifampicin eradicate deep-seated mouse biofilm infections. In addition, several non-ADEP compounds have been identified as activators of the ClpP proteolytic core without the involvement of ATPases. These findings indicate a general principle for killing dormant cells, the activation and corruption of the ClpP protease, rather than through conventional inhibition. Deletion of the clpP gene reduced the virulence of Staphylococcus aureus, thus making it an ideal antivirulence target. Multiple inhibitors have been developed in order to attenuate the production of extracellular virulence factors of bacteria through covalent modifications on serine in the active site or disruption of oligomerization of ClpP. Interestingly, due to the unusual composition and activation mechanism of ClpP in Mycobacterium tuberculosis, mycobacteria are killed by ADEPs through inhibition of ClpP activity rather than overactivation. In this short review, we will summarize recent progress in the development of small molecules modulating ClpP protease activity for both antibiotics and antivirulence.
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Affiliation(s)
- Fei Ye
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China
| | - Jiahui Li
- Laboratory of Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
| | - Cai-Guang Yang
- Laboratory of Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
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34
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Köcher S, Rey J, Bongard J, Tiaden AN, Meltzer M, Richards PJ, Ehrmann M, Kaiser M. Maßgeschneiderte Ahp-Cyclodepsipeptide als potente, nicht-kovalente Serinprotease-Inhibitoren. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701771] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Steffen Köcher
- Chemische Biologie, ZMB, Fakultät für Biologie; Universität Duisburg-Essen; Universitätsstraße 2 45117 Essen Deutschland
| | - Juliana Rey
- Mikrobiologie, ZMB, Fakultät für Biologie; Universität Duisburg-Essen; Deutschland
| | - Jens Bongard
- Mikrobiologie, ZMB, Fakultät für Biologie; Universität Duisburg-Essen; Deutschland
| | - André N. Tiaden
- Bone and Stem Cell Research Group, CABMM; Universität Zürich; Schweiz
| | - Michael Meltzer
- Mikrobiologie, ZMB, Fakultät für Biologie; Universität Duisburg-Essen; Deutschland
| | - Peter J. Richards
- Bone and Stem Cell Research Group, CABMM; Universität Zürich; Schweiz
- Zurich Center for Integrative Human Physiology (ZIHP); Universität Zürich; Schweiz
| | - Michael Ehrmann
- Mikrobiologie, ZMB, Fakultät für Biologie; Universität Duisburg-Essen; Deutschland
- School of Biosciences; Cardiff University; Großbritannien
| | - Markus Kaiser
- Chemische Biologie, ZMB, Fakultät für Biologie; Universität Duisburg-Essen; Universitätsstraße 2 45117 Essen Deutschland
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35
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Köcher S, Rey J, Bongard J, Tiaden AN, Meltzer M, Richards PJ, Ehrmann M, Kaiser M. Tailored Ahp-cyclodepsipeptides as Potent Non-covalent Serine Protease Inhibitors. Angew Chem Int Ed Engl 2017; 56:8555-8558. [PMID: 28514117 DOI: 10.1002/anie.201701771] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Indexed: 11/08/2022]
Abstract
The S1 serine protease family is one of the largest and most biologically important protease families. Despite their biomedical significance, generic approaches to generate potent, class-specific, bioactive non-covalent inhibitors for these enzymes are still limited. In this work, we demonstrate that Ahp-cyclodepsipeptides represent a suitable scaffold for generating target-tailored inhibitors of serine proteases. For efficient synthetic access, we developed a practical mixed solid- and solution-phase synthesis that we validated through performing the first chemical synthesis of the two natural products Tasipeptin A and B. The suitability of the Ahp-cyclodepsipeptide scaffold for tailored inhibitor synthesis is showcased by the generation of the most potent human HTRA protease inhibitors to date. We anticipate that our approach may also be applied to other serine proteases, thus opening new avenues for a systematic discovery of serine protease inhibitors.
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Affiliation(s)
- Steffen Köcher
- Chemical Biology, ZMB, University of Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
| | - Juliana Rey
- Microbiology, ZMB, University of Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
| | - Jens Bongard
- Microbiology, ZMB, University of Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
| | - André N Tiaden
- Bone and Stem Cell Research Group, CABMM, University of Zurich, Winterthurerstr. 190, 8057, Zürich, Switzerland
| | - Michael Meltzer
- Microbiology, ZMB, University of Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
| | - Peter J Richards
- Bone and Stem Cell Research Group, CABMM, University of Zurich, Winterthurerstr. 190, 8057, Zürich, Switzerland.,Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, Winterthurerstr. 190, 8057, Zürich, Switzerland
| | - Michael Ehrmann
- Microbiology, ZMB, University of Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany.,School of Biosciences, Cardiff University, Cardiff, CF10 3US, UK
| | - Markus Kaiser
- Chemical Biology, ZMB, University of Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
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36
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Krysiak J, Stahl M, Vomacka J, Fetzer C, Lakemeyer M, Fux A, Sieber SA. Quantitative Map of β-Lactone-Induced Virulence Regulation. J Proteome Res 2017; 16:1180-1192. [DOI: 10.1021/acs.jproteome.6b00705] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Joanna Krysiak
- Department of Chemistry, Chair
of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany
| | - Matthias Stahl
- Department of Chemistry, Chair
of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany
| | - Jan Vomacka
- Department of Chemistry, Chair
of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany
| | - Christian Fetzer
- Department of Chemistry, Chair
of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany
| | - Markus Lakemeyer
- Department of Chemistry, Chair
of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany
| | - Anja Fux
- Department of Chemistry, Chair
of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany
| | - Stephan A. Sieber
- Department of Chemistry, Chair
of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany
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37
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Wang L, Ishida A, Hashidoko Y, Hashimoto M. Dehydrogenation of the NH−NH Bond Triggered by Potassium
tert
‐Butoxide in Liquid Ammonia. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201610371] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Lei Wang
- Division of Applied Bioscience Graduate School of Agriculture Hokkaido University Kita 9, Nishi 9, Kita-ku Sapporo 060-8589 Japan
| | - Akiko Ishida
- Division of Applied Bioscience Graduate School of Agriculture Hokkaido University Kita 9, Nishi 9, Kita-ku Sapporo 060-8589 Japan
| | - Yasuyuki Hashidoko
- Division of Applied Bioscience Graduate School of Agriculture Hokkaido University Kita 9, Nishi 9, Kita-ku Sapporo 060-8589 Japan
| | - Makoto Hashimoto
- Division of Applied Bioscience Graduate School of Agriculture Hokkaido University Kita 9, Nishi 9, Kita-ku Sapporo 060-8589 Japan
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38
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Wang L, Ishida A, Hashidoko Y, Hashimoto M. Dehydrogenation of the NH-NH Bond Triggered by Potassium tert-Butoxide in Liquid Ammonia. Angew Chem Int Ed Engl 2016; 56:870-873. [PMID: 27936299 DOI: 10.1002/anie.201610371] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Indexed: 12/24/2022]
Abstract
A novel strategy for the dehydrogenation of the NH-NH bond is disclosed using potassium tert-butoxide (tBuOK) in liquid ammonia (NH3 ) under air at room temperature. Its synthetic value is well demonstrated by the highly efficient synthesis of aromatic azo compounds (up to 100 % yield, 3 min), heterocyclic azo compounds, and dehydrazination of phenylhydrazine. The broad application of this strategy and its benefit to chemical biology is proved by a novel, convenient, one-pot synthesis of aliphatic diazirines, which are important photoreactive agents for photoaffinity labeling.
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Affiliation(s)
- Lei Wang
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo, 060-8589, Japan
| | - Akiko Ishida
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo, 060-8589, Japan
| | - Yasuyuki Hashidoko
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo, 060-8589, Japan
| | - Makoto Hashimoto
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo, 060-8589, Japan
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39
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Balogh D, Dahmen M, Stahl M, Poreba M, Gersch M, Drag M, Sieber SA. Insights into ClpXP proteolysis: heterooligomerization and partial deactivation enhance chaperone affinity and substrate turnover in Listeria monocytogenes. Chem Sci 2016; 8:1592-1600. [PMID: 28451288 PMCID: PMC5361862 DOI: 10.1039/c6sc03438a] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 10/26/2016] [Indexed: 01/04/2023] Open
Abstract
Caseinolytic proteases (ClpP) are important for recognition and controlled degradation of damaged proteins. While the majority of bacterial organisms utilize only a single ClpP, Listeria monocytogenes expresses two isoforms (LmClpP1 and LmClpP2). LmClpPs assemble into either a LmClpP2 homocomplex or a LmClpP1/2 heterooligomeric complex. The heterocomplex in association with the chaperone ClpX, exhibits a boost in proteolytic activity for unknown reasons. Here, we use a combined chemical and biochemical strategy to unravel two activation principles of LmClpPs. First, determination of apparent affinity constants revealed a 7-fold elevated binding affinity between the LmClpP1/2 heterocomplex and ClpX, compared to homooligomeric LmClpP2. This tighter interaction favors the formation of the proteolytically active complex between LmClpX and LmClpP1/2 and thereby accelerating the overall turnover. Second, screening a diverse library of fluorescent labeled peptides and proteins with various ClpP mutants allowed the individual analysis of substrate preferences for both isoforms within the heterocomplex. In addition to Leu and Met, LmClpP2 preferred a long aliphatic chain (2-Aoc) in the P1 position for cleavage. Strikingly, design and synthesis of a corresponding 2-Aoc chloromethyl ketone inhibitor resulted in stimulation of proteolysis by 160% when LmClpP2 was partially alkylated on 20% of the active sites. Determination of apparent affinity constants also revealed an elevated complex stability between partially modified LmClpP2 and the cognate chaperone LmClpX. Thus, the stimulation of proteolysis through enhanced binding to the chaperone seems to be a characteristic feature of LmClpPs.
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Affiliation(s)
- Dóra Balogh
- Center for Integrated Protein Science at the Department of Chemistry , Technische Universität München , Lichtenbergstraße 4 , Garching bei München , D-85747 , Germany .
| | - Maria Dahmen
- Center for Integrated Protein Science at the Department of Chemistry , Technische Universität München , Lichtenbergstraße 4 , Garching bei München , D-85747 , Germany .
| | - Matthias Stahl
- Center for Integrated Protein Science at the Department of Chemistry , Technische Universität München , Lichtenbergstraße 4 , Garching bei München , D-85747 , Germany .
| | - Marcin Poreba
- Department of Bioorganic Chemistry , Faculty of Chemistry , Wrocław University of Technology , Wybrzeże Wyspiańskiego 27 , 50-370 Wrocław , Poland
| | - Malte Gersch
- Center for Integrated Protein Science at the Department of Chemistry , Technische Universität München , Lichtenbergstraße 4 , Garching bei München , D-85747 , Germany .
| | - Marcin Drag
- Department of Bioorganic Chemistry , Faculty of Chemistry , Wrocław University of Technology , Wybrzeże Wyspiańskiego 27 , 50-370 Wrocław , Poland
| | - Stephan A Sieber
- Center for Integrated Protein Science at the Department of Chemistry , Technische Universität München , Lichtenbergstraße 4 , Garching bei München , D-85747 , Germany .
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