1
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Walther R, Westermann LM, Carmali S, Jackson SE, Brötz-Oesterhelt H, Spring DR. Identification of macrocyclic peptides which activate bacterial cylindrical proteases. RSC Med Chem 2023; 14:1186-1191. [PMID: 37360394 PMCID: PMC10285738 DOI: 10.1039/d3md00136a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 05/15/2023] [Indexed: 06/28/2023] Open
Abstract
The caseinolytic protease complex ClpXP is an important house-keeping enzyme in prokaryotes charged with the removal and degradation of misfolded and aggregated proteins and performing regulatory proteolysis. Dysregulation of its function, particularly by inhibition or allosteric activation of the proteolytic core ClpP, has proven to be a promising strategy to reduce virulence and eradicate persistent bacterial infections. Here, we report a rational drug-design approach to identify macrocyclic peptides which increase proteolysis by ClpP. This work expands the understanding of ClpP dynamics and sheds light on the conformational control exerted by its binding partner, the chaperone ClpX, by means of a chemical approach. The identified macrocyclic peptide ligands may, in the future, serve as a starting point for the development of ClpP activators for antibacterial applications.
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Affiliation(s)
- Raoul Walther
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road CB2 1EW Cambridge UK
| | - Linda M Westermann
- Interfaculty Institute of Microbiology and Infection Medicine, Dept. of Bioactive Compounds, University of Tübingen Auf der Morgenstelle 28 72076 Tübingen Germany
| | - Sheiliza Carmali
- School of Pharmacy, Queen's University Belfast BT9 7BL Belfast UK
| | - Sophie E Jackson
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road CB2 1EW Cambridge UK
| | - Heike Brötz-Oesterhelt
- Interfaculty Institute of Microbiology and Infection Medicine, Dept. of Bioactive Compounds, University of Tübingen Auf der Morgenstelle 28 72076 Tübingen Germany
- Cluster of Excellence Controlling Microbes to Fight Infections Germany
| | - David R Spring
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road CB2 1EW Cambridge UK
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2
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Schmitz KR, Handy EL, Compton CL, Gupta S, Bishai WR, Sauer RT, Sello JK. Acyldepsipeptide Antibiotics and a Bioactive Fragment Thereof Differentially Perturb Mycobacterium tuberculosis ClpXP1P2 Activity in Vitro. ACS Chem Biol 2023; 18:724-733. [PMID: 32083462 PMCID: PMC7842861 DOI: 10.1021/acschembio.9b00454] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Proteolytic complexes in Mycobacterium tuberculosis (Mtb), the deadliest bacterial pathogen, are major foci in tuberculosis drug development programs. The Clp proteases, which are essential for Mtb viability, are high-priority targets. These proteases function through the collaboration of ClpP1P2, a barrel-shaped heteromeric peptidase, with associated ATP-dependent chaperones like ClpX and ClpC1 that recognize and unfold specific substrates in an ATP-dependent fashion. The critical interaction of the peptidase and its unfoldase partners is blocked by the competitive binding of acyldepsipeptide antibiotics (ADEPs) to the interfaces of the ClpP2 subunits. The resulting inhibition of Clp protease activity is lethal to Mtb. Here, we report the surprising discovery that a fragment of the ADEPs retains anti-Mtb activity yet stimulates rather than inhibits the ClpXP1P2-catalyzed degradation of proteins. Our data further suggest that the fragment stabilizes the ClpXP1P2 complex and binds ClpP1P2 in a fashion distinct from that of the intact ADEPs. A structure-activity relationship study of the bioactive fragment defines the pharmacophore and points the way toward the development of new drug leads for the treatment of tuberculosis.
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Affiliation(s)
- Karl R. Schmitz
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA
- Department of Biological Sciences, University of Delaware, Newark, DE
| | - Emma L. Handy
- Department of Chemistry, Brown University, Providence, RI
| | | | - Shashank Gupta
- Department of Chemistry, Brown University, Providence, RI
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University, Baltimore, MD
| | - William R. Bishai
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University, Baltimore, MD
| | - Robert T. Sauer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA
| | - Jason K. Sello
- Department of Chemistry, Brown University, Providence, RI
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA
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3
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Acyldepsipeptide Analogues: A Future Generation Antibiotics for Tuberculosis Treatment. Pharmaceutics 2022; 14:pharmaceutics14091956. [PMID: 36145704 PMCID: PMC9502522 DOI: 10.3390/pharmaceutics14091956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/09/2022] [Accepted: 09/12/2022] [Indexed: 11/25/2022] Open
Abstract
Acyldepsipeptides (ADEPs) are a new class of emerging antimicrobial peptides (AMPs), which are currently explored for treatment of pathogenic infections, including tuberculosis (TB). These cyclic hydrophobic peptides have a unique bacterial target to the conventional anti-TB drugs, and present a therapeutic window to overcome Mycobacterium Tuberculosis (M. tb) drug resistance. ADEPs exerts their antibacterial activity on M. tb strains through activation of the protein homeostatic regulatory protease, the caseinolytic protease (ClpP1P2). ClpP1P2 is normally regulated and activated by the ClpP-ATPases to degrade misfolded and toxic peptides and/or short proteins. ADEPs bind and dysregulate all the homeostatic capabilities of ClpP1P2 while inducing non-selective proteolysis. The uncontrolled proteolysis leads to M. tb cell death within the host. ADEPs analogues that have been tested possess cytotoxicity and poor pharmacokinetic and pharmacodynamic properties. However, these can be improved by drug design techniques. Moreover, the use of nanomaterial in conjunction with ADEPs would yield effective synergistic effect. This new mode of action has potential to combat and eradicate the extensive multi-drug resistance (MDR) problem that is currently faced by the public health pertaining bacterial infections, especially TB.
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4
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Generation of Lasso Peptide-Based ClpP Binders. Int J Mol Sci 2021; 23:ijms23010465. [PMID: 35008890 PMCID: PMC8745299 DOI: 10.3390/ijms23010465] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/28/2021] [Accepted: 12/30/2021] [Indexed: 11/17/2022] Open
Abstract
The Clp protease system fulfills a plethora of important functions in bacteria. It consists of a tetradecameric ClpP barrel holding the proteolytic centers and two hexameric Clp-ATPase rings, which recognize, unfold, and then feed substrate proteins into the ClpP barrel for proteolytic degradation. Flexible loops carrying conserved tripeptide motifs protrude from the Clp-ATPases and bind into hydrophobic pockets (H-pockets) on ClpP. Here, we set out to engineer microcin J25 (MccJ25), a ribosomally synthesized and post-translationally modified peptide (RiPP) of the lasso peptide subfamily, by introducing the conserved tripeptide motifs into the lasso peptide loop region to mimic the Clp-ATPase loops. We studied the capacity of the resulting lasso peptide variants to bind to ClpP and affect its activity. From the nine variants generated, one in particular (12IGF) was able to activate ClpP from Staphylococcus aureus and Bacillus subtilis. While 12IGF conferred stability to ClpP tetradecamers and stimulated peptide degradation, it did not trigger unregulated protein degradation, in contrast to the H-pocket-binding acyldepsipeptide antibiotics (ADEPs). Interestingly, synergistic interactions between 12IGF and ADEP were observed.
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5
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Brötz-Oesterhelt H, Vorbach A. Reprogramming of the Caseinolytic Protease by ADEP Antibiotics: Molecular Mechanism, Cellular Consequences, Therapeutic Potential. Front Mol Biosci 2021; 8:690902. [PMID: 34109219 PMCID: PMC8182300 DOI: 10.3389/fmolb.2021.690902] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 04/28/2021] [Indexed: 12/14/2022] Open
Abstract
Rising antibiotic resistance urgently calls for the discovery and evaluation of novel antibiotic classes and unique antibiotic targets. The caseinolytic protease Clp emerged as an unprecedented target for antibiotic therapy 15 years ago when it was observed that natural product-derived acyldepsipeptide antibiotics (ADEP) dysregulated its proteolytic core ClpP towards destructive proteolysis in bacterial cells. A substantial database has accumulated since on the interaction of ADEP with ClpP, which is comprehensively compiled in this review. On the molecular level, we describe the conformational control that ADEP exerts over ClpP, the nature of the protein substrates degraded, and the emerging structure-activity-relationship of the ADEP compound class. On the physiological level, we review the multi-faceted antibacterial mechanism, species-dependent killing modes, the activity against carcinogenic cells, and the therapeutic potential of the compound class.
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Affiliation(s)
- Heike Brötz-Oesterhelt
- Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tübingen, Germany.,Cluster of Excellence: Controlling Microbes to Fight Infection, Tübingen, Germany
| | - Andreas Vorbach
- Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tübingen, Germany
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6
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Acyldepsipeptide activated ClpP1P2 macromolecule of Leptospira, an ideal Achilles' heel to hamper the cell survival and deregulate ClpP proteolytic activity. Res Microbiol 2021; 172:103797. [PMID: 33460738 DOI: 10.1016/j.resmic.2021.103797] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 12/30/2020] [Accepted: 01/07/2021] [Indexed: 11/22/2022]
Abstract
Antibiotic acyldepsipeptide (ADEP) targets the bacterial ClpP serine protease and can inhibit the growth of numerous bacterial species by activating/dysregulating the protease activity within the cell. The spirochete Leptospira interrogans harbors two ClpP isoforms (LepClpP1 and LepClpP2). Supplementation of ADEP in the Leptospira growth medium resulted in the inhibition of bacterial growth. The ADEP mediated activation of the LepClpP mixture was dependent on the time allowed for the self-assembly of LepClpP1 and LepClpP2. The dynamic light scattering of the LepClpP mixture in the presence of the ADEP indicated a conformational transformation of the LepClpP machinery. Serine 98, a catalytic triad residue of the LepClpP1 in the LepClpP1P2 heterocomplex, was critical for the ADEP mediated activation. The computational prototype of the LepClpP1P2 structure suggested that the hydrophobic pockets wherein the ADEPs or the physiological chaperone ClpX predominantly dock are exclusively present in the LepClpP2 heptamer. Using the ADEP as a tool, this investigation provides an insight into the molecular function of the LepClpP1P2 in a coalition with its ATPase chaperone LepClpX. The shreds of the evidence illustrated in this investigation verify that ADEP1 possesses the ability to control the LepClpP system in an unconventional approach than the other organisms.
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7
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Malik IT, Pereira R, Vielberg M, Mayer C, Straetener J, Thomy D, Famulla K, Castro H, Sass P, Groll M, Brötz‐Oesterhelt H. Functional Characterisation of ClpP Mutations Conferring Resistance to Acyldepsipeptide Antibiotics in Firmicutes. Chembiochem 2020; 21:1997-2012. [PMID: 32181548 PMCID: PMC7496096 DOI: 10.1002/cbic.201900787] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Indexed: 12/18/2022]
Abstract
Acyldepsipeptide (ADEP) is an exploratory antibiotic with a novel mechanism of action. ClpP, the proteolytic core of the caseinolytic protease, is deregulated towards unrestrained proteolysis. Here, we report on the mechanism of ADEP resistance in Firmicutes. This bacterial phylum contains important pathogens that are relevant for potential ADEP therapy. For Staphylococcus aureus, Bacillus subtilis, enterococci and streptococci, spontaneous ADEP-resistant mutants were selected in vitro at a rate of 10-6 . All isolates carried mutations in clpP. All mutated S. aureus ClpP proteins characterised in this study were functionally impaired; this increased our understanding of the mode of operation of ClpP. For molecular insights, crystal structures of S. aureus ClpP bound to ADEP4 were determined. Well-resolved N-terminal domains in the apo structure allow the pore-gating mechanism to be followed. The compilation of mutations presented here indicates residues relevant for ClpP function and suggests that ADEP resistance will occur at a lower rate during the infection process.
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Affiliation(s)
- Imran T. Malik
- Interfaculty Institute of Microbiology and Infection MedicineDept. of Microbial Bioactive CompoundsUniversity of TübingenAuf der Morgenstelle 2872076TuebingenGermany
| | - Rebeca Pereira
- Interfaculty Institute of Microbiology and Infection MedicineDept. of Microbial Bioactive CompoundsUniversity of TübingenAuf der Morgenstelle 2872076TuebingenGermany
- Laboratory of AntibioticsBiochemistryEducation and Molecular modelingDepartment of Molecular and Cell BiologyFederal Fluminense UniversityOuteiro São João Batista, CentroNiterói24210130Rio de JaneiroBrazil
| | - Marie‐Theres Vielberg
- Center for Integrated Protein Science at the Department of ChemistryTechnical University MunichLichtenbergstrasse 485748GarchingGermany
| | - Christian Mayer
- Interfaculty Institute of Microbiology and Infection MedicineDept. of Microbial Bioactive CompoundsUniversity of TübingenAuf der Morgenstelle 2872076TuebingenGermany
| | - Jan Straetener
- Interfaculty Institute of Microbiology and Infection MedicineDept. of Microbial Bioactive CompoundsUniversity of TübingenAuf der Morgenstelle 2872076TuebingenGermany
| | - Dhana Thomy
- Interfaculty Institute of Microbiology and Infection MedicineDept. of Microbial Bioactive CompoundsUniversity of TübingenAuf der Morgenstelle 2872076TuebingenGermany
| | - Kirsten Famulla
- Institute for Pharmaceutical Biology and BiotechnologyUniversity of DüsseldorfUniversitätsstrasse 1, Building 26.23.40225DüsseldorfGermany
| | - Helena Castro
- Laboratory of AntibioticsBiochemistryEducation and Molecular modelingDepartment of Molecular and Cell BiologyFederal Fluminense UniversityOuteiro São João Batista, CentroNiterói24210130Rio de JaneiroBrazil
| | - Peter Sass
- Interfaculty Institute of Microbiology and Infection MedicineDept. of Microbial Bioactive CompoundsUniversity of TübingenAuf der Morgenstelle 2872076TuebingenGermany
| | - Michael Groll
- Center for Integrated Protein Science at the Department of ChemistryTechnical University MunichLichtenbergstrasse 485748GarchingGermany
| | - Heike Brötz‐Oesterhelt
- Interfaculty Institute of Microbiology and Infection MedicineDept. of Microbial Bioactive CompoundsUniversity of TübingenAuf der Morgenstelle 2872076TuebingenGermany
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8
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Kong X, Wei B, Yu C, Guan X, Ma W, Liu G, Yang C, Nan F. Design, Synthesis and Biological Evaluation of Bengamide Analogues as
ClpP
Activators. CHINESE J CHEM 2020. [DOI: 10.1002/cjoc.202000133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Xue‐Qing Kong
- Chinese National Center for Drug Screening, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 555 Zuchongzhi Road Shanghai 201203 China
- University of Chinese Academy of Sciences No. 19A Yuquan Road Beijing 100049 China
| | - Bing‐Yan Wei
- Chinese National Center for Drug Screening, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 555 Zuchongzhi Road Shanghai 201203 China
- University of Chinese Academy of Sciences No. 19A Yuquan Road Beijing 100049 China
| | - Chen‐Xi Yu
- Chinese National Center for Drug Screening, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 555 Zuchongzhi Road Shanghai 201203 China
- University of Chinese Academy of Sciences No. 19A Yuquan Road Beijing 100049 China
| | - Xiang‐Na Guan
- Chinese National Center for Drug Screening, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 555 Zuchongzhi Road Shanghai 201203 China
- University of Chinese Academy of Sciences No. 19A Yuquan Road Beijing 100049 China
| | - Wei‐Ping Ma
- Chinese National Center for Drug Screening, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 555 Zuchongzhi Road Shanghai 201203 China
| | - Gang Liu
- Chinese National Center for Drug Screening, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 555 Zuchongzhi Road Shanghai 201203 China
| | - Cai‐Guang Yang
- Chinese National Center for Drug Screening, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 555 Zuchongzhi Road Shanghai 201203 China
| | - Fa‐Jun Nan
- Chinese National Center for Drug Screening, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 555 Zuchongzhi Road Shanghai 201203 China
- Yantai Key Laboratory of Nanomedicine & Advanced Preparations, Yantai Institute of Materia Medica, No. 39, Science and Technology Avenue, High‐tech Industrial Development Zone Yantai Shandong 264000 China
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9
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Imipridone Anticancer Compounds Ectopically Activate the ClpP Protease and Represent a New Scaffold for Antibiotic Development. Genetics 2020; 214:1103-1120. [PMID: 32094149 PMCID: PMC7153937 DOI: 10.1534/genetics.119.302851] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 02/06/2020] [Indexed: 11/18/2022] Open
Abstract
The imipridones ONC201 and ONC212 selectively kill cancer cells and have been ascribed multiple mechanisms-of-action. Genome-wide CRISPR knockout screens revealed that loss of the mitochondrial proteases CLPP and MIPEP confer strong resistance to both compounds... Systematic genetic interaction profiles can reveal the mechanisms-of-action of bioactive compounds. The imipridone ONC201, which is currently in cancer clinical trials, has been ascribed a variety of different targets. To investigate the genetic dependencies of imipridone action, we screened a genome-wide clustered regularly interspaced short palindromic repeats (CRISPR) knockout library in the presence of either ONC201 or its more potent analog ONC212. Loss of the mitochondrial matrix protease CLPP or the mitochondrial intermediate peptidase MIPEP conferred strong resistance to both compounds. Biochemical and surrogate genetic assays showed that impridones directly activate CLPP and that MIPEP is necessary for proteolytic maturation of CLPP into a catalytically competent form. Quantitative proteomic analysis of cells treated with ONC212 revealed degradation of many mitochondrial as well as nonmitochondrial proteins. Prompted by the conservation of ClpP from bacteria to humans, we found that the imipridones also activate ClpP from Escherichia coli, Bacillus subtilis, and Staphylococcus aureus in biochemical and genetic assays. ONC212 and acyldepsipeptide-4 (ADEP4), a known activator of bacterial ClpP, caused similar proteome-wide degradation profiles in S. aureus. ONC212 suppressed the proliferation of a number of Gram-positive (S. aureus, B. subtilis, and Enterococcus faecium) and Gram-negative species (E. coli and Neisseria gonorrhoeae). Moreover, ONC212 enhanced the ability of rifampin to eradicate antibiotic-tolerant S. aureus persister cells. These results reveal the genetic dependencies of imipridone action in human cells and identify the imipridone scaffold as a new entry point for antibiotic development.
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10
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Eyermann B, Meixner M, Brötz-Oesterhelt H, Antes I, Sieber SA. Acyldepsipeptide Probes Facilitate Specific Detection of Caseinolytic Protease P Independent of Its Oligomeric and Activity State. Chembiochem 2020; 21:235-240. [PMID: 31487112 PMCID: PMC7003903 DOI: 10.1002/cbic.201900477] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Indexed: 12/21/2022]
Abstract
Caseinolytic protease P (ClpP) is a tetradecameric peptidase that assembles with chaperones such as ClpX to gain proteolytic activity. Acyldepsipeptides (ADEPs) are small-molecule mimics of ClpX that bind into hydrophobic pockets on the apical site of the complex, thereby activating ClpP. Detection of ClpP has so far been facilitated with active-site-directed probes which depend on the activity and oligomeric state of the complex. To expand the scope of ClpP labeling, we took a stepwise synthetic approach toward customized ADEP photoprobes. Structure-activity relationship studies with small fragments and ADEP derivatives paired with modeling studies revealed the design principles for suitable probe molecules. The derivatives were tested for activation of ClpP and subsequently applied in labeling studies of the wild-type peptidase as well as enzymes bearing mutations at the active site and an oligomerization sensor. Satisfyingly, the ADEP photoprobes provided a labeling readout of ClpP independent of its activity and oligomeric state.
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Affiliation(s)
- Barbara Eyermann
- Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Maximilian Meixner
- Department für Biowissenschaften, Technische Universität München, Emil-Erlenmeyer-Forum 8, 85354, Freising, Germany
| | - Heike Brötz-Oesterhelt
- Interfaculty Institute of Microbiology and Infection Medicine, Microbial Bioactive Compounds, University of Tübingen, Auf der Morgenstelle 28, E-Bau, Ebene 8, 72076, Tübingen, Germany
| | - Iris Antes
- Department für Biowissenschaften, Technische Universität München, Emil-Erlenmeyer-Forum 8, 85354, Freising, Germany
| | - Stephan A Sieber
- Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85748, Garching, Germany
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11
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Wong KS, Houry WA. Recent Advances in Targeting Human Mitochondrial AAA+ Proteases to Develop Novel Cancer Therapeutics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1158:119-142. [PMID: 31452139 DOI: 10.1007/978-981-13-8367-0_8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The mitochondrion is a vital organelle that performs diverse cellular functions. In this regard, the cell has evolved various mechanisms dedicated to the maintenance of the mitochondrial proteome. Among them, AAA+ ATPase-associated proteases (AAA+ proteases) such as the Lon protease (LonP1), ClpXP complex, and the membrane-bound i-AAA, m-AAA and paraplegin facilitate the clearance of misfolded mitochondrial proteins to prevent the accumulation of cytotoxic protein aggregates. Furthermore, these proteases have additional regulatory functions in multiple biological processes that include amino acid metabolism, mitochondria DNA transcription, metabolite and cofactor biosynthesis, maturation and turnover of specific respiratory and metabolic proteins, and modulation of apoptosis, among others. In cancer cells, the increase in intracellular ROS levels promotes tumorigenic phenotypes and increases the frequency of protein oxidation and misfolding, which is compensated by the increased expression of specific AAA+ proteases as part of the adaptation mechanism. The targeting of AAA+ proteases has led to the discovery and development of novel anti-cancer compounds. Here, we provide an overview of the molecular characteristics and functions of the major mitochondrial AAA+ proteases and summarize recent research efforts in the development of compounds that target these proteases.
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Affiliation(s)
- Keith S Wong
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Walid A Houry
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada. .,Department of Chemistry, University of Toronto, Toronto, ON, Canada.
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12
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Stahl M, Korotkov VS, Balogh D, Kick LM, Gersch M, Pahl A, Kielkowski P, Richter K, Schneider S, Sieber SA. Selektive Aktivierung der humanen caseinolytischen Protease P (ClpP). Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201808189] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Matthias Stahl
- Fakultät für Chemie; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
- Department of Oncology-Pathology; Science for Life Laboratory; Karolinska Institutet; Tomtebodavägen 23A 171 65 Solna Schweden
| | - Vadim S. Korotkov
- Fakultät für Chemie; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Dóra Balogh
- Fakultät für Chemie; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Leonhard M. Kick
- Fakultät für Chemie; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Malte Gersch
- Fakultät für Chemie; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
- Medical Research Council Laboratory of, Molecular Biology; Francis Crick Avenue CB2 0QH Cambridge Großbritannien
| | - Axel Pahl
- Fakultät für Chemie; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
- Max-Planck-Institut für Molekulare Physiologie; Compound Management and Screening Center (COMAS); Otto-Hahn-Straße 11 44227 Dortmund Deutschland
| | - Pavel Kielkowski
- Fakultät für Chemie; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Klaus Richter
- Fakultät für Chemie; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Sabine Schneider
- Fakultät für Chemie; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Stephan A. Sieber
- Fakultät für Chemie; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
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13
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Stahl M, Korotkov VS, Balogh D, Kick LM, Gersch M, Pahl A, Kielkowski P, Richter K, Schneider S, Sieber SA. Selective Activation of Human Caseinolytic Protease P (ClpP). Angew Chem Int Ed Engl 2018; 57:14602-14607. [DOI: 10.1002/anie.201808189] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 08/15/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Matthias Stahl
- Department of Chemistry; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Germany
- Present address: Department of Oncology-Pathology; Science for Life Laboratory; Karolinska Institutet; Tomtebodavägen 23A 171 65 Solna Sweden
| | - Vadim S. Korotkov
- Department of Chemistry; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Germany
| | - Dóra Balogh
- Department of Chemistry; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Germany
| | - Leonhard M. Kick
- Department of Chemistry; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Germany
| | - Malte Gersch
- Department of Chemistry; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Germany
- Present address; Medical Research Council Laboratory of Molecular Biology; Francis Crick Avenue CB2 0QH Cambridge UK
| | - Axel Pahl
- Department of Chemistry; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Germany
- Present address: Max-Planck-Institut für Molekulare Physiologie; Compound Management and Screening Center (COMAS); Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - Pavel Kielkowski
- Department of Chemistry; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Germany
| | - Klaus Richter
- Department of Chemistry; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Germany
| | - Sabine Schneider
- Department of Chemistry; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Germany
| | - Stephan A. Sieber
- Department of Chemistry; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Germany
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14
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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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15
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Li Y, Lavey NP, Coker JA, Knobbe JE, Truong DC, Yu H, Lin YS, Nimmo SL, Duerfeldt AS. Consequences of Depsipeptide Substitution on the ClpP Activation Activity of Antibacterial Acyldepsipeptides. ACS Med Chem Lett 2017; 8:1171-1176. [PMID: 29152050 DOI: 10.1021/acsmedchemlett.7b00320] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 10/19/2017] [Indexed: 11/30/2022] Open
Abstract
The acyldepsipeptide (ADEP) antibiotics operate through a clinically unexploited mechanism of action and thus have attracted attention from several antibacterial development groups. The ADEP scaffold is synthetically tractable, and deep-seated modifications have produced extremely potent antibacterial leads against Gram-positive pathogens. Although newly identified ADEP analogs demonstrate remarkable antibacterial activity against bacterial isolates and in mouse models of bacterial infections, stability issues pertaining to the depsipeptide core remain. To date, no study has been reported on the natural ADEP scaffold that evaluates the sole importance of the macrocyclic linkage on target engagement, molecular conformation, and bioactivity. To address this gap in ADEP structure-activity relationships, we synthesized three ADEP analogs that only differ in the linkage motif (i.e., ester, amide, and N-methyl amide) and provide a side-by-side comparison of conformational behavior and biological activity. We demonstrate that while replacement of the naturally occurring ester linkage with a secondary amide maintains in vitro biochemical activity, this simple substitution results in a significant drop in whole-cell activity. This study provides direct evidence that ester to amide linkage substitution is unlikely to provide a reasonable solution for ADEP instability.
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Affiliation(s)
| | | | | | | | | | - Hongtao Yu
- Department
of Chemistry, Tufts University, 62 Talbot Avenue, Medford, Massachusetts 02155, United States
| | - Yu-Shan Lin
- Department
of Chemistry, Tufts University, 62 Talbot Avenue, Medford, Massachusetts 02155, United States
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16
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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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17
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Malik IT, Brötz-Oesterhelt H. Conformational control of the bacterial Clp protease by natural product antibiotics. Nat Prod Rep 2017; 34:815-831. [DOI: 10.1039/c6np00125d] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Natural products targeting the bacterial Clp protease unravel key interfaces for protein–protein–interaction and long-distance conformational control.
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Affiliation(s)
- I. T. Malik
- Department of Microbial Bioactive Compounds
- Interfaculty Institute of Microbiology and Infection Medicine
- University of Tuebingen
- Germany
| | - H. Brötz-Oesterhelt
- Department of Microbial Bioactive Compounds
- Interfaculty Institute of Microbiology and Infection Medicine
- University of Tuebingen
- Germany
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18
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Culp E, Wright GD. Bacterial proteases, untapped antimicrobial drug targets. J Antibiot (Tokyo) 2016; 70:366-377. [PMID: 27899793 DOI: 10.1038/ja.2016.138] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 09/29/2016] [Accepted: 10/06/2016] [Indexed: 01/05/2023]
Abstract
Bacterial proteases are an extensive collection of enzymes that have vital roles in cell viability, stress response and pathogenicity. Although their perturbation clearly offers the potential for antimicrobial drug development, both as traditional antibiotics and anti-virulence drugs, they are not yet the target of any clinically used therapeutics. Here we describe the potential for and recent progress in the development of compounds targeting bacterial proteases with a focus on AAA+ family proteolytic complexes and signal peptidases (SPs). Caseinolytic protease (ClpP) belongs to the AAA+ family of proteases, a group of multimeric barrel-shaped complexes whose activity is tightly regulated by associated AAA+ ATPases. The opportunity for chemical perturbation of these complexes is demonstrated by compounds targeting ClpP for inhibition, activation or perturbation of its associated ATPase. Meanwhile, SPs are also a proven antibiotic target. Responsible for the cleavage of targeting peptides during protein secretion, both type I and type II SPs have been successfully targeted by chemical inhibitors. As the threat of pan-antibiotic resistance continues to grow, these and other bacterial proteases offer an arsenal of novel antibiotic targets ripe for development.
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Affiliation(s)
- Elizabeth Culp
- Michael G. DeGroote Institute for Infectious Disease Research and the Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Gerard D Wright
- Michael G. DeGroote Institute for Infectious Disease Research and the Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
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19
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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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20
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Ni T, Ye F, Liu X, Zhang J, Liu H, Li J, Zhang Y, Sun Y, Wang M, Luo C, Jiang H, Lan L, Gan J, Zhang A, Zhou H, Yang CG. Characterization of Gain-of-Function Mutant Provides New Insights into ClpP Structure. ACS Chem Biol 2016; 11:1964-72. [PMID: 27171654 DOI: 10.1021/acschembio.6b00390] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
ATP-dependent Clp protease (ClpP), a highly conserved serine protease in vast bacteria, could be converted into a noncontrollable enzyme capable of degrading mature proteins in the presence of acyldepsipeptides (ADEPs). Here, we design such a gain-of-function mutant of Staphylococcus aureus ClpP (SaClpP) capable of triggering the same level of dysfunctional activity that occurs upon ADEPs treatment. The SaClpPY63A mutant degrades FtsZ in vivo and inhibits staphylococcal growth. The crystal structure of SaClpPY63A indicates that Asn42 would be an important domino to fall for further activation of ClpP. Indeed, the SaClpPN42AY63A mutant demonstrates promoted self-activated proteolysis, which is a result of an enlarged entrance pore as observed in cryo-electron microscopy images. In addition, the expression of the engineered clpP allele phenocopies treatment with ADEPs; inhibition of cell division occurs as does showing sterilizing with rifampicin antibiotics. Collectively, we show that the gain-of-function SaClpPN42AY63A mutant becomes a fairly nonspecific protease and kills persisters by degrading over 500 proteins, thus providing new insights into the structure of the ClpP protease.
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Affiliation(s)
- Tengfeng Ni
- Laboratory
of Chemical Biology, State Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fei Ye
- College
of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China
- Drug
Design and Discovery Center, State Key Laboratory of Drug Research,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xing Liu
- CAS
Key Laboratory of Receptor Research, Shanghai Institute of Materia
Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jie Zhang
- Laboratory
of Chemical Biology, State Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hongchuan Liu
- Laboratory
of Chemical Biology, State Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, 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
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yingyi Zhang
- National
Center for Protein Science Shanghai, Institute of Biochemistry and
Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 201210, China
| | - Yinqiang Sun
- Experiment
Center for Science and Technology, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Meining Wang
- CAS
Key Laboratory of Receptor Research, Shanghai Institute of Materia
Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Cheng Luo
- Drug
Design and Discovery Center, State Key Laboratory of Drug Research,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hualiang Jiang
- University of Chinese Academy of Sciences, Beijing 100049, China
- Drug
Design and Discovery Center, State Key Laboratory of Drug Research,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Lefu Lan
- Laboratory
of Chemical Biology, State Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianhua Gan
- School
of Life Sciences, Fudan University, Shanghai 200433, China
| | - Ao Zhang
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS
Key Laboratory of Receptor Research, Shanghai Institute of Materia
Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hu Zhou
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS
Key Laboratory of Receptor 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
- University of Chinese Academy of Sciences, Beijing 100049, China
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21
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Lavey NP, Coker JA, Ruben EA, Duerfeldt AS. Sclerotiamide: The First Non-Peptide-Based Natural Product Activator of Bacterial Caseinolytic Protease P. JOURNAL OF NATURAL PRODUCTS 2016; 79:1193-1197. [PMID: 26967980 PMCID: PMC4841720 DOI: 10.1021/acs.jnatprod.5b01091] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Caseinolytic protease P (ClpP) maintains essential roles in bacterial homeostasis. As such, both the inhibition and activation of this enzyme result in bactericidal activity, making ClpP a promising target for antibacterial drug development. Herein, we report the results of a fluorescence-based screen of ∼450 structurally diverse fungal and bacterial secondary metabolites. Sclerotiamide (1), a paraherquamide-related indolinone, was identified as the first non-peptide-based natural product activator of ClpP. Structure-activity relationships arising from the initial screen, preliminary biochemical evaluation of 1, and rationale for the exploitation of this chemotype to develop novel ClpP activators are presented.
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Affiliation(s)
- Nathan P. Lavey
- Institute for Natural Products Applications and Research Technologies, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
- Department of Chemistry & Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Jesse A. Coker
- Institute for Natural Products Applications and Research Technologies, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
- Department of Chemistry & Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Eliza A. Ruben
- Department of Chemistry & Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
- Protein Production Core, University of Oklahoma COBRE in Structural Biology, Norman, Oklahoma 73019, United States
| | - Adam S. Duerfeldt
- Institute for Natural Products Applications and Research Technologies, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
- Department of Chemistry & Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
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22
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Goodreid JD, Janetzko J, Santa Maria JP, Wong KS, Leung E, Eger BT, Bryson S, Pai EF, Gray-Owen SD, Walker S, Houry WA, Batey RA. Development and Characterization of Potent Cyclic Acyldepsipeptide Analogues with Increased Antimicrobial Activity. J Med Chem 2016; 59:624-46. [PMID: 26818454 DOI: 10.1021/acs.jmedchem.5b01451] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The problem of antibiotic resistance has prompted the search for new antibiotics with novel mechanisms of action. Analogues of the A54556 cyclic acyldepsipeptides (ADEPs) represent an attractive class of antimicrobial agents that act through dysregulation of caseinolytic protease (ClpP). Previous studies have shown that ADEPs are active against Gram-positive bacteria (e.g., MRSA, VRE, PRSP (penicillin-resistant Streptococcus pneumoniae)); however, there are currently few studies examining Gram-negative bacteria. In this study, the synthesis and biological evaluation of 14 novel ADEPs against a variety of pathogenic Gram-negative and Gram-positive organisms is outlined. Optimization of the macrocyclic core residues and N-acyl side chain culminated in the development of 26, which shows potent activity against the Gram-negative species Neisseria meningitidis and Neisseria gonorrheae and improved activity against the Gram-positive organisms Staphylococcus aureus and Enterococcus faecalis in comparison with known analogues. In addition, the co-crystal structure of an ADEP-ClpP complex derived from N. meningitidis was solved.
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Affiliation(s)
- Jordan D Goodreid
- Davenport Research Laboratories, Department of Chemistry, University of Toronto , 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - John Janetzko
- Department of Microbiology and Immunobiology, Harvard Medical School , Boston, Massachusetts 02115, United States
- Department of Chemistry and Chemical Biology, Harvard University , Cambridge, Massachusetts 02138, United States
| | - John P Santa Maria
- Department of Microbiology and Immunobiology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Keith S Wong
- Department of Biochemistry, University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Elisa Leung
- Department of Biochemistry, University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Bryan T Eger
- Department of Biochemistry, University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Steve Bryson
- Department of Biochemistry, University of Toronto , Toronto, Ontario M5S 1A8, Canada
- The Campbell Family Institute for Cancer Research, University Health Network , Toronto, Ontario M5G 1L7, Canada
| | - Emil F Pai
- Department of Biochemistry, University of Toronto , Toronto, Ontario M5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto , Toronto, Ontario M5S 1A8, Canada
- Department of Medical Biophysics, University of Toronto , Toronto, Ontario M5S 1A8, Canada
- The Campbell Family Institute for Cancer Research, University Health Network , Toronto, Ontario M5G 1L7, Canada
| | - Scott D Gray-Owen
- Department of Molecular Genetics, University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Suzanne Walker
- Department of Microbiology and Immunobiology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Walid A Houry
- Department of Biochemistry, University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Robert A Batey
- Davenport Research Laboratories, Department of Chemistry, University of Toronto , 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
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23
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Pahl A, Lakemeyer M, Vielberg M, Hackl MW, Vomacka J, Korotkov VS, Stein ML, Fetzer C, Lorenz‐Baath K, Richter K, Waldmann H, Groll M, Sieber SA. Reversible Inhibitors Arrest ClpP in a Defined Conformational State that Can Be Revoked by ClpX Association. Angew Chem Int Ed Engl 2015; 54:15892-6. [DOI: 10.1002/anie.201507266] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 09/15/2015] [Indexed: 01/29/2023]
Affiliation(s)
- Axel Pahl
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching (Germany)
| | - Markus Lakemeyer
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching (Germany)
| | - Marie‐Theres Vielberg
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching (Germany)
| | - Mathias W. Hackl
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching (Germany)
| | - Jan Vomacka
- 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)
| | - Martin L. Stein
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching (Germany)
| | - Christian Fetzer
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching (Germany)
| | - Katrin Lorenz‐Baath
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching (Germany)
| | - Klaus Richter
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching (Germany)
| | - Herbert Waldmann
- Department of Chemistry and Chemical Biology, Technische Universität Dortmund, Otto‐Hahn‐Strasse 6, 44221 Dortmund (Germany)
| | - Michael Groll
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching (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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24
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Pahl A, Lakemeyer M, Vielberg M, Hackl MW, Vomacka J, Korotkov VS, Stein ML, Fetzer C, Lorenz‐Baath K, Richter K, Waldmann H, Groll M, Sieber SA. Reversible Inhibitoren arretieren ClpP in einer definierten Konformation, die durch Bindung von ClpX aufgehoben wird. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507266] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Axel Pahl
- Center for Integrated Protein Science am Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching (Deutschland)
| | - Markus Lakemeyer
- Center for Integrated Protein Science am Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching (Deutschland)
| | - Marie‐Theres Vielberg
- Center for Integrated Protein Science am Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching (Deutschland)
| | - Mathias W. Hackl
- Center for Integrated Protein Science am Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching (Deutschland)
| | - Jan Vomacka
- 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)
| | - Martin L. Stein
- Center for Integrated Protein Science am Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching (Deutschland)
| | - Christian Fetzer
- Center for Integrated Protein Science am Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching (Deutschland)
| | - Katrin Lorenz‐Baath
- Center for Integrated Protein Science am Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching (Deutschland)
| | - Klaus Richter
- Center for Integrated Protein Science am Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching (Deutschland)
| | - Herbert Waldmann
- Department für Chemie und Chemische Biologie, Technische Universität Dortmund, Otto‐Hahn‐Straße 6, 44221 Dortmund (Deutschland)
| | - Michael Groll
- Center for Integrated Protein Science am Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching (Deutschland)
| | - Stephan A. Sieber
- Center for Integrated Protein Science am Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching (Deutschland)
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25
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Carney DW, Schmitz KR, Scruse AC, Sauer RT, Sello JK. Examination of a Structural Model of Peptidomimicry by Cyclic Acyldepsipeptide Antibiotics in Their Interaction with the ClpP Peptidase. Chembiochem 2015; 16:1875-1879. [PMID: 26147653 PMCID: PMC4992462 DOI: 10.1002/cbic.201500234] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Indexed: 11/11/2022]
Abstract
The cyclic acyldepsipeptide (ADEP) antibiotics act by binding the ClpP peptidase and dysregulating its activity. Their exocyclic N-acylphenylalanine is thought to structurally mimic the ClpP-binding, (I/L)GF tripeptide loop of the peptidase's accessory ATPases. We found that ADEP analogues with exocyclic N-acyl tripeptides or dipeptides resembling the (I/L)GF motif were weak ClpP activators and had no bioactivity. In contrast, ADEP analogues possessing difluorophenylalanine N-capped with methyl-branched acyl groups-like the side chains of residues in the (I/L)GF motifs-were superior to the parent ADEP with respect to both ClpP activation and bioactivity. We contend that the ADEP's N-acylphenylalanine moiety is not simply a stand-in for the ATPases' (I/L)GF motif; it likely has physicochemical properties that are better suited for ClpP binding. Further, our finding that the methyl-branching on the acyl group of the ADEPs improves activity opens new avenues for optimization.
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Affiliation(s)
- Daniel W Carney
- Department of Chemistry, Brown University, 324 Brook Street, Providence, RI 02912 (USA)
| | - Karl R Schmitz
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 (USA)
| | - Anthony C Scruse
- Department of Chemistry, Brown University, 324 Brook Street, Providence, RI 02912 (USA)
- Department of Chemistry, Morehouse College, 830 Westview Drive SW, Atlanta, GA 30312 (USA)
| | - Robert T Sauer
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 (USA)
| | - Jason K Sello
- Department of Chemistry, Brown University, 324 Brook Street, Providence, RI 02912 (USA)
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26
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Compton CL, Carney DW, Groomes PV, Sello JK. Fragment-Based Strategy for Investigating and Suppressing the Efflux of Bioactive Small Molecules. ACS Infect Dis 2015; 1:53-8. [PMID: 27620145 DOI: 10.1021/id500009f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Membrane protein-mediated drug efflux is a phenomenon that compromises our ability to treat both infectious diseases and cancer. Accordingly, there is much interest in the development of strategies for suppression of the mechanisms by which therapeutic agents are effluxed. Here, using resistance to the cyclic acyldepsipeptide (ADEP) antibacterial agents as a model, we demonstrate a new counter-efflux strategy wherein a fragment of an actively exported bioactive compound competitively interferes with its efflux and potentiates its activity. A fragment comprising the N-heptenoyldifluorophenylalanine side chain of the pharmacologically optimized ADEPs potentiates the antibacterial activity of the ADEPs against actinobacteria to a greater extent than reserpine, a well-known efflux inhibitor. Beyond their validation of a new approach to studying molecular recognition by drug efflux pumps, our findings have important implications for killing Mycobacterium tuberculosis with ADEPs and reclaiming the efficacies of therapeutic agents whose activity has been compromised by efflux pumps.
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Affiliation(s)
- Corey L. Compton
- Department of Chemistry, Brown University, 324 Brook
Street, Providence, Rhode
Island 02912, United States
| | - Daniel W. Carney
- Department of Chemistry, Brown University, 324 Brook
Street, Providence, Rhode
Island 02912, United States
| | - Patrice V. Groomes
- Department of Chemistry, Brown University, 324 Brook
Street, Providence, Rhode
Island 02912, United States
| | - Jason K. Sello
- Department of Chemistry, Brown University, 324 Brook
Street, Providence, Rhode
Island 02912, United States
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Schmitz KR, Carney DW, Sello JK, Sauer RT. Crystal structure of Mycobacterium tuberculosis ClpP1P2 suggests a model for peptidase activation by AAA+ partner binding and substrate delivery. Proc Natl Acad Sci U S A 2014; 111:E4587-95. [PMID: 25267638 PMCID: PMC4217457 DOI: 10.1073/pnas.1417120111] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Caseinolytic peptidase P (ClpP), a double-ring peptidase with 14 subunits, collaborates with ATPases associated with diverse activities (AAA+) partners to execute ATP-dependent protein degradation. Although many ClpP enzymes self-assemble into catalytically active homo-tetradecamers able to cleave small peptides, the Mycobacterium tuberculosis enzyme consists of discrete ClpP1 and ClpP2 heptamers that require a AAA+ partner and protein-substrate delivery or a peptide agonist to stabilize assembly of the active tetradecamer. Here, we show that cyclic acyldepsipeptides (ADEPs) and agonist peptides synergistically activate ClpP1P2 by mimicking AAA+ partners and substrates, respectively, and determine the structure of the activated complex. Our studies establish the basis of heteromeric ClpP1P2 assembly and function, reveal tight coupling between the conformations of each ring, show that ADEPs bind only to one ring but appear to open the axial pores of both rings, provide a foundation for rational drug development, and suggest strategies for studying the roles of individual ClpP1 and ClpP2 rings in Clp-family proteolysis.
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Affiliation(s)
- Karl R Schmitz
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139; and
| | - Daniel W Carney
- Department of Chemistry, Brown University, Providence, RI 02912
| | - Jason K Sello
- Department of Chemistry, Brown University, Providence, RI 02912
| | - Robert T Sauer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139; and
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