1
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Sha Z, Fishovitz J, Wang S, Chilakala S, Xu Y, Lee I. A Selective Fluorogenic Peptide Substrate for the Human Mitochondrial ATP-Dependent Protease Complex ClpXP. Chembiochem 2020; 21:2037-2048. [PMID: 32180333 DOI: 10.1002/cbic.202000030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/01/2020] [Indexed: 11/07/2022]
Abstract
The goal of this work is to identify differences in the substrate determinants of two human mitochondrial matrix ATP-dependent proteases, human ClpXP (hClpXP) and human Lon (hLon). This information allows the generation of protease-specific peptide substrates that can be used as chemical biology tools to investigate the physiological functions of hClpXP. These enzymes play a role in protein quality control, but currently the physiological functions of human ClpXP are not well defined. In this study, the degradation profile of casein, an alanine positional scanning decapeptide library, and a specific peptide sequence found in an endogenous substrate of bacterial ClpXP by hClpXP as well as hLon were examined. Based on our findings, we generated a specific fluorogenic peptide substrate, FR-Cleptide, for hClpXP with a kcat of 2.44±0.15 s-1 and Km =262±43 μM, respectively. The FR-Cleptide substrate was successfully used to identify a leucine methyl ketone as a potent lead inhibitor, and to detect endogenous hClpXP activity in HeLa cell lysate. We propose that the fluorogenic peptide substrate is a valuable tool for quantitatively monitoring the activity of hClpXP in cell lysate, as well as mechanistic characterization of hClpXP. The peptide-based chemical tools developed in this study will complement the substrates developed for human Lon in aiding the investigation of the physiological functions of the respective protease.
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Affiliation(s)
- Zhou Sha
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio, 44106, USA
| | - Jennifer Fishovitz
- Department of Chemistry and Physics, Saint Mary's College, Notre Dame, Indiana, 46556, USA
| | - Susan Wang
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio, 44106, USA
| | - Sujatha Chilakala
- Department of Chemistry, Cleveland State University, Cleveland, Ohio, 44115, USA.,Lawrence J. Ellison Institute for Transformative Medicine of USC, University of Southern California, Beverly Hills, CA, 90211, USA
| | - Yan Xu
- Department of Chemistry, Cleveland State University, Cleveland, Ohio, 44115, USA
| | - Irene Lee
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio, 44106, USA
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2
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Sha Z, Chilakala S, Crabill G, Cheng I, Xu Y, Fishovitz J, Lee I. A Proteolytic Site-Directed Affinity Label to Inhibit the Human ATP-Dependent Protease Caseinolytic Complex XP. Chembiochem 2020; 21:2049-2059. [PMID: 32180302 DOI: 10.1002/cbic.202000031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/01/2020] [Indexed: 11/10/2022]
Abstract
Human caseinolytic protease component X and P (hClpXP) is a heterooligomeric ATP-dependent protease. The hClpX subunit catalyzes ATP hydrolysis whereas the hClpP subunit catalyzes peptide bond cleavage. In this study, we generated a peptidyl chloromethyl ketone (dansyl-FAPAL-CMK) that inhibited the hClpP subunit through alkylation of the catalytic His122, which was detected by LC-MS. This inhibitor is composed of a peptide sequence derived from a hydrolyzed peptide product of a substrate cleaved by hClpXP. Binding of FAPAL positions the electrophilic chloromethyl ketone moiety near His122 where alkylation occurs. Dansyl FAPAL-CMK exhibits selectivity for hClpXP over other ATP-dependent proteases such as hLon and the 26S proteasome and abolishes hClpXP activity in HeLa cell lysate. Using the fluorogenic peptide substrate FR-Cleptide as reporter, we detected biphasic inhibition time courses; this supports a slow-binding, time-dependent, covalent inhibition mechanism that is often found in active-site directed affinity labels. Because this inhibitor reacts only with hClpXP but not hLon or the proteasome, it has the potential to serve as a chemical tool to help validate endogenous protein substrates of hClpXP in cell lysate, thereby benefiting investigation of the physiological functions of hClpXP in different cell types or tissue samples.
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Affiliation(s)
- Zhou Sha
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio, 44106, USA
| | - Sujatha Chilakala
- Department of Chemistry, Cleveland State University, Cleveland, Ohio, 44115, USA.,Present address: Lawrence J. Ellison Institute for Transformative Medicine of USC, University of Southern California, Beverly Hills, CA, 90211, USA
| | - George Crabill
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio, 44106, USA.,Present address: University of Maryland School of Medicine, Baltimore, MD, 21202, USA
| | - Iteen Cheng
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio, 44106, USA.,Present address: Agilent Technologies, Cleveland, OH, 44106, USA
| | - Yan Xu
- Department of Chemistry, Cleveland State University, Cleveland, Ohio, 44115, USA
| | - Jennifer Fishovitz
- Department of Chemistry and Physics, Saint Mary's College, Notre Dame, Indiana, 46556, USA
| | - Irene Lee
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio, 44106, USA
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3
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Speri E, Kim C, De Benedetti S, Qian Y, Lastochkin E, Fishovitz J, Fisher JF, Mobashery S. Cinnamonitrile Adjuvants Restore Susceptibility to β-Lactams against Methicillin-Resistant Staphylococcus aureus. ACS Med Chem Lett 2019; 10:1148-1153. [PMID: 31413798 DOI: 10.1021/acsmedchemlett.9b00169] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Accepted: 07/01/2019] [Indexed: 11/28/2022] Open
Abstract
β-Lactams are used routinely to treat Staphylococcus aureus infections. However, the emergence of methicillin-resistant S. aureus (MRSA) renders them clinically precarious. We describe a class of cinnamonitrile adjuvants that restore the activity of oxacillin (a penicillin member of the β-lactams) against MRSA. The lead adjuvants were tested against six important strains of MRSA, one vancomycin-intermediate S. aureus (VISA) strain, and one linezolid-resistant S. aureus strain. Five compounds out of 84 total compounds showed broad potentiation. At 8 μM (E)-3-(5-(3,4-dichlorobenzyl)-2-(trifluoromethoxy)phenyl)-2-(methylsulfonyl)acrylonitrile (26) potentiated oxacillin with a >4000-fold reduction of its MIC (from 256 to 0.06 mg·L-1). This class of adjuvants holds promise for reversal of the resistance phenotype of MRSA.
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Affiliation(s)
- Enrico Speri
- Department Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Choon Kim
- Department Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Stefania De Benedetti
- Department Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Yuanyuan Qian
- Department Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Elena Lastochkin
- Department Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Jennifer Fishovitz
- Department Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Jed F. Fisher
- Department Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Shahriar Mobashery
- Department Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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4
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Speri E, Fishovitz J, Mobashery S. Structure-activity relationship of the cinnamamide family of antibiotic potentiators for methicillin-resistant Staphylococcus aureus (MRSA). Medchemcomm 2018; 9:2008-2016. [PMID: 30746061 DOI: 10.1039/c8md00479j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 10/19/2018] [Indexed: 11/21/2022]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a global public health threat. MRSA has evolved a complex set of biochemical processes that mobilize the organism for inducible resistance on challenge by β-lactam antibiotics. Interfering pharmacologically with this machinery has the potential to reverse the β-lactam-resistance phenotype, whereby susceptibility to obsolete antibiotics would be restored. We describe herein our discovery of one class of such agents, the cinnamamide family of antibiotic potentiators. A hit compound of the class (compound 1) showed modest potentiation of the activity of oxacillin, a penicillin antibiotic, against an MRSA strain. A total of 50 analogues of compound 1 were prepared and screened. Seven of these compounds showed more dramatic potentiation of the antibacterial activity, which lowered the minimal-inhibitory concentrations (MICs) for the antibiotic by as much as 64- to 128-fold.
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Affiliation(s)
- Enrico Speri
- Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , IN 46556 , USA .
| | - Jennifer Fishovitz
- Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , IN 46556 , USA .
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , IN 46556 , USA .
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5
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Fishovitz J, Sha Z, Chilakala S, Cheng I, Xu Y, Lee I. Utilization of Mechanistic Enzymology to Evaluate the Significance of ADP Binding to Human Lon Protease. Front Mol Biosci 2017; 4:47. [PMID: 28744459 PMCID: PMC5504276 DOI: 10.3389/fmolb.2017.00047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 06/21/2017] [Indexed: 01/09/2023] Open
Abstract
Lon, also known as Protease La, is one of the simplest ATP-dependent proteases. It is a homooligomeric enzyme comprised of an ATPase domain and a proteolytic domain in each enzyme subunit. Despite sharing about 40% sequence identity, human and Escherichia coli Lon proteases utilize a highly conserved ATPase domain found in the AAA+ family to catalyze ATP hydrolysis, which is needed to activate protein degradation. In this study, we utilized mechanistic enzymology techniques to show that despite comparable kcat and Km parameters found in the ATPase activity, human and E. coli Lon exhibit significantly different susceptibility to ADP inhibition. Due to the low affinity of human Lon for ADP, the conformational changes in human Lon generated from the ATPase cycle are also different. The relatively low affinity of human Lon for ADP cannot be accounted for by reversibility in ATP hydrolysis, as a positional isotope exchange experiment demonstrated both E. coli Lon and human Lon catalyzed ATP hydrolysis irreversibly. A limited tryptic digestion study however indicated that human and E. coli Lon bind to ADP differently. Taken together, the findings reported in this research article suggest that human Lon is not regulated by a substrate-promoted ADP/ATP exchange mechanism as found in the bacterial enzyme homolog. The drastic difference in structural changes associated with ADP interaction with the two protease homologs offer potential for selective inhibitor design and development through targeting the ATPase sites. In addition to revealing unique mechanistic differences that distinguish human vs. bacterial Lon, this article underscores the benefit of mechanistic enzymology in deciphering the physiological mechanism of action of Lon proteases and perhaps other closely related ATP-dependent proteases in the future.
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Affiliation(s)
- Jennifer Fishovitz
- Department of Chemistry and Physics, Saint Mary's CollegeNotre Dame, IN, United States
| | - Zhou Sha
- Department of Chemistry, Case Western Reserve UniversityCleveland, OH, United States
| | - Sujatha Chilakala
- Department of Chemistry, Cleveland State UniversityCleveland, OH, United States
| | - Iteen Cheng
- Department of Chemistry, Case Western Reserve UniversityCleveland, OH, United States
| | - Yan Xu
- Department of Chemistry, Cleveland State UniversityCleveland, OH, United States
| | - Irene Lee
- Department of Chemistry, Case Western Reserve UniversityCleveland, OH, United States
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6
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Lee M, Hesek D, Dik DA, Fishovitz J, Lastochkin E, Boggess B, Fisher JF, Mobashery S. From Genome to Proteome to Elucidation of Reactions for All Eleven Known Lytic Transglycosylases from Pseudomonas aeruginosa. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611279] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Mijoon Lee
- Department of Chemistry and Biochemistry; University of Notre Dame; Notre Dame IN 46556 USA
| | - Dusan Hesek
- Department of Chemistry and Biochemistry; University of Notre Dame; Notre Dame IN 46556 USA
| | - David A. Dik
- Department of Chemistry and Biochemistry; University of Notre Dame; Notre Dame IN 46556 USA
| | - Jennifer Fishovitz
- Department of Chemistry and Biochemistry; University of Notre Dame; Notre Dame IN 46556 USA
| | - Elena Lastochkin
- Department of Chemistry and Biochemistry; University of Notre Dame; Notre Dame IN 46556 USA
| | - Bill Boggess
- Department of Chemistry and Biochemistry; University of Notre Dame; Notre Dame IN 46556 USA
| | - Jed F. Fisher
- Department of Chemistry and Biochemistry; University of Notre Dame; Notre Dame IN 46556 USA
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry; University of Notre Dame; Notre Dame IN 46556 USA
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7
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Lee M, Hesek D, Dik DA, Fishovitz J, Lastochkin E, Boggess B, Fisher JF, Mobashery S. From Genome to Proteome to Elucidation of Reactions for All Eleven Known Lytic Transglycosylases from Pseudomonas aeruginosa. Angew Chem Int Ed Engl 2017; 56:2735-2739. [PMID: 28128504 DOI: 10.1002/anie.201611279] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 12/09/2016] [Indexed: 11/07/2022]
Abstract
An enzyme superfamily, the lytic transglycosylases (LTs), occupies the space between the two membranes of Gram-negative bacteria. LTs catalyze the non-hydrolytic cleavage of the bacterial peptidoglycan cell-wall polymer. This reaction is central to the growth of the cell wall, for excavating the cell wall for protein insertion, and for monitoring the cell wall so as to initiate resistance responses to cell-wall-acting antibiotics. The nefarious Gram-negative pathogen Pseudomonas aeruginosa encodes eleven LTs. With few exceptions, their substrates and functions are unknown. Each P. aeruginosa LT was expressed as a soluble protein and evaluated with a panel of substrates (both simple and complex mimetics of their natural substrates). Thirty-one distinct products distinguish these LTs with respect to substrate recognition, catalytic activity, and relative exolytic or endolytic ability. These properties are foundational to an understanding of the LTs as catalysts and as antibiotic targets.
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Affiliation(s)
- Mijoon Lee
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Dusan Hesek
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - David A Dik
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Jennifer Fishovitz
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Elena Lastochkin
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Bill Boggess
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Jed F Fisher
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
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8
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Dik DA, Domínguez-Gil T, Lee M, Hesek D, Byun B, Fishovitz J, Boggess B, Hellman LM, Fisher JF, Hermoso JA, Mobashery S. Muropeptide Binding and the X-ray Structure of the Effector Domain of the Transcriptional Regulator AmpR of Pseudomonas aeruginosa. J Am Chem Soc 2017; 139:1448-1451. [PMID: 28079369 DOI: 10.1021/jacs.6b12819] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A complex link exists between cell-wall recycling/repair and the manifestation of resistance to β-lactam antibiotics in many Enterobacteriaceae and Pseudomonas aeruginosa. This process is mediated by specific cell-wall-derived muropeptide products. These muropeptides are internalized into the cytoplasm and bind to the transcriptional regulator AmpR, which controls the cytoplasmic events that lead to expression of β-lactamase, an antibiotic-resistance determinant. The effector-binding domain (EBD) of AmpR was purified to homogeneity. We document that the EBD exists exclusively as a dimer, even at a concentration as low as 1 μM. The EBD binds to the suppressor ligand UDP-N-acetyl-β-d-muramyl-l-Ala-γ-d-Glu-meso-DAP-d-Ala-d-Ala and binds to two activator muropeptides, N-acetyl-β-d-glucosamine-(1→4)-1,6-anhydro-N-acetyl-β-d-muramyl-l-Ala-γ-d-Glu-meso-DAP-d-Ala-d-Ala and 1,6-anhydro-N-acetyl-β-d-muramyl-l-Ala-γ-d-Glu-meso-DAP-d-Ala-d-Ala, as assessed by non-denaturing mass spectrometry. The EBD does not bind to 1,6-anhydro-N-acetyl-β-d-muramyl-l-Ala-γ-d-Glu-meso-DAP. This binding selectivity revises the dogma in the field. The crystal structure of the EBD dimer was solved to 2.2 Å resolution. The EBD crystallizes in a "closed" conformation, in contrast to the "open" structure required to bind the muropeptides. Structural issues of this ligand recognition are addressed by molecular dynamics simulations, which reveal significant differences among the complexes with the effector molecules.
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Affiliation(s)
- David A Dik
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Teresa Domínguez-Gil
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Rocasolano", Consejo Superior de Investigaciones Científicas , 28006 Madrid, Spain
| | - Mijoon Lee
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Dusan Hesek
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Byungjin Byun
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Jennifer Fishovitz
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Bill Boggess
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Lance M Hellman
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Jed F Fisher
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Rocasolano", Consejo Superior de Investigaciones Científicas , 28006 Madrid, Spain
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
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9
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Boudreau MA, Fishovitz J, Llarrull LI, Xiao Q, Mobashery S. Phosphorylation of BlaR1 in Manifestation of Antibiotic Resistance in Methicillin-Resistant Staphylococcus aureus and Its Abrogation by Small Molecules. ACS Infect Dis 2015; 1:454-9. [PMID: 27623311 DOI: 10.1021/acsinfecdis.5b00086] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA), an important human pathogen, has evolved an inducible mechanism for resistance to β-lactam antibiotics. We report herein that the integral membrane protein BlaR1, the β-lactam sensor/signal transducer protein, is phosphorylated on exposure to β-lactam antibiotics. This event is critical to the onset of the induction of antibiotic resistance. Furthermore, we document that BlaR1 phosphorylation and the antibiotic-resistance phenotype are both reversed in the presence of synthetic protein kinase inhibitors of our design, restoring susceptibility of the organism to a penicillin, resurrecting it from obsolescence in treatment of these intransigent bacteria.
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Affiliation(s)
- Marc A. Boudreau
- Department of Chemistry and
Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Jennifer Fishovitz
- Department of Chemistry and
Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Leticia I. Llarrull
- Department of Chemistry and
Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Qiaobin Xiao
- Department of Chemistry and
Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Shahriar Mobashery
- Department of Chemistry and
Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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10
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Fishovitz J, Taghizadeh N, Fisher JF, Chang M, Mobashery S. The Tipper-Strominger Hypothesis and Triggering of Allostery in Penicillin-Binding Protein 2a of Methicillin-Resistant Staphylococcus aureus (MRSA). J Am Chem Soc 2015; 137:6500-5. [PMID: 25964995 DOI: 10.1021/jacs.5b01374] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The transpeptidases involved in the synthesis of the bacterial cell wall (also known as penicillin-binding proteins, PBPs) have evolved to bind the acyl-D-Ala-D-Ala segment of the stem peptide of the nascent peptidoglycan for the physiologically important cross-linking of the cell wall. The Tipper-Strominger hypothesis stipulates that β-lactam antibiotics mimic the acyl-D-Ala-D-Ala moiety of the stem and, thus, are recognized by the PBPs with bactericidal consequences. We document that this mimicry exists also at the allosteric site of PBP2a of methicillin-resistant Staphylococcus aureus (MRSA). Interactions of different classes of β-lactam antibiotics, as mimics of the acyl-D-Ala-D-Ala moiety at the allosteric site, lead to a conformational change, across a distance of 60 Å to the active site. We directly visualize this change using an environmentally sensitive fluorescent probe affixed to the protein loops that frame the active site. This conformational mobility, documented in real time, allows antibiotic access to the active site of PBP2a. Furthermore, we document that this allosteric trigger enables synergy between two different β-lactam antibiotics, wherein occupancy at the allosteric site by one facilitates occupancy by a second at the transpeptidase catalytic site, thus lowering the minimal-inhibitory concentration. This synergy has important implications for the mitigation of facile emergence of resistance to these antibiotics by MRSA.
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Affiliation(s)
- Jennifer Fishovitz
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Negin Taghizadeh
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Jed F Fisher
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Mayland Chang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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11
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Fishovitz J, Rojas-Altuve A, Otero L, Dawley M, Carrasco-López C, Chang M, Hermoso JA, Mobashery S. Disruption of allosteric response as an unprecedented mechanism of resistance to antibiotics. J Am Chem Soc 2014; 136:9814-7. [PMID: 24955778 PMCID: PMC4210145 DOI: 10.1021/ja5030657] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Indexed: 02/07/2023]
Abstract
Ceftaroline, a recently approved β-lactam antibiotic for treatment of infections by methicillin-resistant Staphylococcus aureus (MRSA), is able to inhibit penicillin-binding protein 2a (PBP2a) by triggering an allosteric conformational change that leads to the opening of the active site. The opened active site is now vulnerable to inhibition by a second molecule of ceftaroline, an event that impairs cell-wall biosynthesis and leads to bacterial death. The triggering of the allosteric effect takes place by binding of the first antibiotic molecule 60 Å away from the active site of PBP2a within the core of the allosteric site. We document, by kinetic studies and by determination of three X-ray structures of the mutant variants of PBP2a that result in resistance to ceftaroline, that the effect of these clinical mutants is the disruption of the allosteric trigger in this important protein in MRSA. This is an unprecedented mechanism for antibiotic resistance.
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Affiliation(s)
- Jennifer Fishovitz
- Department
of Chemistry and Biochemistry, University
of Notre Dame, Nieuwland
Science Hall, Notre Dame, Indiana 46556, United
States
| | - Alzoray Rojas-Altuve
- Department
of Crystallography and Structural Biology, Instituto de Química-Física “Rocasolano”,
CSIC, Serrano 119, 28006 Madrid, Spain
| | - Lisandro
H. Otero
- Department
of Crystallography and Structural Biology, Instituto de Química-Física “Rocasolano”,
CSIC, Serrano 119, 28006 Madrid, Spain
| | - Matthew Dawley
- Department
of Chemistry and Biochemistry, University
of Notre Dame, Nieuwland
Science Hall, Notre Dame, Indiana 46556, United
States
| | - Cesar Carrasco-López
- Department
of Crystallography and Structural Biology, Instituto de Química-Física “Rocasolano”,
CSIC, Serrano 119, 28006 Madrid, Spain
| | - Mayland Chang
- Department
of Chemistry and Biochemistry, University
of Notre Dame, Nieuwland
Science Hall, Notre Dame, Indiana 46556, United
States
| | - Juan A. Hermoso
- Department
of Crystallography and Structural Biology, Instituto de Química-Física “Rocasolano”,
CSIC, Serrano 119, 28006 Madrid, Spain
| | - Shahriar Mobashery
- Department
of Chemistry and Biochemistry, University
of Notre Dame, Nieuwland
Science Hall, Notre Dame, Indiana 46556, United
States
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12
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Fishovitz J, Hermoso JA, Chang M, Mobashery S. Penicillin-binding protein 2a of methicillin-resistant Staphylococcus aureus. IUBMB Life 2014; 66:572-7. [PMID: 25044998 DOI: 10.1002/iub.1289] [Citation(s) in RCA: 147] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 06/01/2014] [Indexed: 01/31/2023]
Abstract
High-level resistance to β-lactam antibiotics in methicillin-resistant Staphylococcus aureus (MRSA) is due to expression of penicillin-binding protein 2a (PBP2a), a transpeptidase that catalyzes cell-wall crosslinking in the face of the challenge by β-lactam antibiotics. The activity of this protein is regulated by allostery at a site 60 Å distant from the active site, where crosslinking of cell wall takes place. This review discusses the state of knowledge on this important enzyme of cell-wall biosynthesis in MRSA.
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Affiliation(s)
- Jennifer Fishovitz
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
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Otero LH, Rojas-Altuve A, Llarrull LI, Carrasco-López C, Kumarasiri M, Lastochkin E, Fishovitz J, Dawley M, Hesek D, Lee M, Johnson JW, Fisher JF, Chang M, Mobashery S, Hermoso JA. How allosteric control of Staphylococcus aureus penicillin binding protein 2a enables methicillin resistance and physiological function. Proc Natl Acad Sci U S A 2013; 110:16808-13. [PMID: 24085846 PMCID: PMC3800995 DOI: 10.1073/pnas.1300118110] [Citation(s) in RCA: 180] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The expression of penicillin binding protein 2a (PBP2a) is the basis for the broad clinical resistance to the β-lactam antibiotics by methicillin-resistant Staphylococcus aureus (MRSA). The high-molecular mass penicillin binding proteins of bacteria catalyze in separate domains the transglycosylase and transpeptidase activities required for the biosynthesis of the peptidoglycan polymer that comprises the bacterial cell wall. In bacteria susceptible to β-lactam antibiotics, the transpeptidase activity of their penicillin binding proteins (PBPs) is lost as a result of irreversible acylation of an active site serine by the β-lactam antibiotics. In contrast, the PBP2a of MRSA is resistant to β-lactam acylation and successfully catalyzes the DD-transpeptidation reaction necessary to complete the cell wall. The inability to contain MRSA infection with β-lactam antibiotics is a continuing public health concern. We report herein the identification of an allosteric binding domain--a remarkable 60 Å distant from the DD-transpeptidase active site--discovered by crystallographic analysis of a soluble construct of PBP2a. When this allosteric site is occupied, a multiresidue conformational change culminates in the opening of the active site to permit substrate entry. This same crystallographic analysis also reveals the identity of three allosteric ligands: muramic acid (a saccharide component of the peptidoglycan), the cell wall peptidoglycan, and ceftaroline, a recently approved anti-MRSA β-lactam antibiotic. The ability of an anti-MRSA β-lactam antibiotic to stimulate allosteric opening of the active site, thus predisposing PBP2a to inactivation by a second β-lactam molecule, opens an unprecedented realm for β-lactam antibiotic structure-based design.
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Affiliation(s)
- Lisandro H. Otero
- Departamento de Cristalografía y Biología Estructural, Instituto de Química-Física “Rocasolano,” Consejo Superior de Investigaciones Cientificas, 28006 Madrid, Spain; and
| | - Alzoray Rojas-Altuve
- Departamento de Cristalografía y Biología Estructural, Instituto de Química-Física “Rocasolano,” Consejo Superior de Investigaciones Cientificas, 28006 Madrid, Spain; and
| | - Leticia I. Llarrull
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Cesar Carrasco-López
- Departamento de Cristalografía y Biología Estructural, Instituto de Química-Física “Rocasolano,” Consejo Superior de Investigaciones Cientificas, 28006 Madrid, Spain; and
| | - Malika Kumarasiri
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Elena Lastochkin
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Jennifer Fishovitz
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Matthew Dawley
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Dusan Hesek
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Mijoon Lee
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Jarrod W. Johnson
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Jed F. Fisher
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Mayland Chang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Juan A. Hermoso
- Departamento de Cristalografía y Biología Estructural, Instituto de Química-Física “Rocasolano,” Consejo Superior de Investigaciones Cientificas, 28006 Madrid, Spain; and
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Mikita N, Cheng I, Fishovitz J, Huang J, Lee I. Processive Degradation of Unstructured Protein by Escherichia coli Lon Occurs via the Slow, Sequential Delivery of Multiple Scissile Sites Followed by Rapid and Synchronized Peptide Bond Cleavage Events. Biochemistry 2013; 52:5629-44. [DOI: 10.1021/bi4008319] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Natalie Mikita
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Iteen Cheng
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Jennifer Fishovitz
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Jonathan Huang
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Irene Lee
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States
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Kumarasiri M, Llarrull LI, Borbulevych O, Fishovitz J, Lastochkin E, Baker BM, Mobashery S. An amino acid position at crossroads of evolution of protein function: antibiotic sensor domain of BlaR1 protein from Staphylococcus aureus versus clasS D β-lactamases. J Biol Chem 2012; 287:8232-41. [PMID: 22262858 DOI: 10.1074/jbc.m111.333179] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The integral membrane protein BlaR1 of Staphylococcus aureus senses the presence of β-lactam antibiotics in the milieu and transduces the information to its cytoplasmic side, where its activity unleashes the expression of a set of genes, including that for BlaR1 itself, which manifest the antibiotic-resistant phenotype. The x-ray structure of the sensor domain of this protein exhibits an uncanny similarity to those of the class D β-lactamases. The former is a membrane-bound receptor/sensor for the β-lactam antibiotics, devoid of catalytic competence for substrate turnover, whereas the latter are soluble periplasmic enzymes in gram-negative bacteria with avid ability for β-lactam turnover. The two are clearly related to each other from an evolutionary point of view. However, the high resolution x-ray structures for both by themselves do not reveal why one is a receptor and the other an enzyme. It is documented herein that a single amino acid change at position 439 of the BlaR1 protein is sufficient to endow the receptor/sensor protein with modest turnover ability for cephalosporins as substrates. The x-ray structure for this mutant protein and the dynamics simulations revealed how a hydrolytic water molecule may sequester itself in the antibiotic-binding site to enable hydrolysis of the acylated species. These studies document how the nature of the residue at position 439 is critical for the fate of the protein in imparting unique functions on the same molecular template, to result in one as a receptor and in another as a catalyst.
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Affiliation(s)
- Malika Kumarasiri
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
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16
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Fishovitz J, Li M, Frase H, Hudak J, Craig S, Ko K, Berdis AJ, Suzuki CK, Lee I. Active-site-directed chemical tools for profiling mitochondrial Lon protease. ACS Chem Biol 2011; 6:781-8. [PMID: 21520912 DOI: 10.1021/cb100408w] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Lon and ClpXP are the only soluble ATP-dependent proteases within the mammalian mitochondria matrix, which function in protein quality control by selectively degrading misfolded, misassembled, or damaged proteins. Chemical tools to study these proteases in biological samples have not been identified, thereby hindering a clear understanding of their respective functions in normal and disease states. In this study, we applied a proteolytic site-directed approach to identify a peptide reporter substrate and a peptide inhibitor that are selective for Lon but not ClpXP. These chemical tools permit quantitative measurements that distinguish Lon-mediated proteolysis from that of ClpXP in biochemical assays with purified proteases, as well as in intact mitochondria and mitochondrial lysates. This chemical biology approach provides needed tools to further our understanding of mitochondrial ATP-dependent proteolysis and contributes to the future development of diagnostic and pharmacological agents for treating diseases associated with defects in mitochondrial protein quality.
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Affiliation(s)
| | - Min Li
- Department of Biochemistry and Molecular Biology, University of Medicine and Dentistry of New Jersey, Newark, New Jersey 07101-1709, United States
| | | | | | | | | | | | - Carolyn K. Suzuki
- Department of Biochemistry and Molecular Biology, University of Medicine and Dentistry of New Jersey, Newark, New Jersey 07101-1709, United States
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Thomas J, Fishovitz J, Lee I. Utilization of positional isotope exchange experiments to evaluate reversibility of ATP hydrolysis catalyzed by Escherichia coli Lon proteaseThis paper is one of a selection of papers published in this special issue entitled 8th International Conference on AAA Proteins and has undergone the Journal's usual peer review process. Biochem Cell Biol 2010; 88:119-28. [DOI: 10.1139/o09-117] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Lon protease, also known as protease La, is an ATP-dependent serine protease. Despite the presence of a proteolytic Ser–Lys dyad, the enzyme only catalyzes protein degradation in the presence of ATP. Lon possesses an intrinsic ATPase activity that is stimulated by protein and certain peptide substrates. Through sequence alignment and analysis, it is concluded that Lon belongs to the AAA+ protein family. Previous kinetic characterization of the ATPase domain of Escherichia coli Lon protease implicates a half-site reactivity model in which only 50% of the ATP bound to Lon are hydrolyzed to yield ADP; the remaining ATPase sites remain bound with ATP and are considered non-catalytic. In this model, it is implied that ATP hydrolysis is irreversible. To further evaluate the proposed half-site reactivity model, the reversibility of the ATPase activity of E. coli Lon was evaluated by positional isotope exchange experiments. The ATPase reactions were conducted in the 18O-enriched buffer such that the extent of 18O incorporation into inorganic phosphate generated from ATP hydrolysis could be used to evaluate the extent of reversibility in ATP hydrolysis. Collectively, our experimental data reveal that the ATPase reaction catalyzed by E. coli Lon in the presence and absence of peptide substrate that stimulated the enzyme’s ATPase activity is irreversible. Therefore, the half-site ATPase reactivity of E. coli Lon is validated, and can be used to account for the kinetic mechanism of the ATP-dependent peptidase activity of the enzyme.
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Affiliation(s)
- Jennifer Thomas
- WIL Research Laboratories, LLC, Ashland, OH 44805, USA
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH 44106, USA
| | - Jennifer Fishovitz
- WIL Research Laboratories, LLC, Ashland, OH 44805, USA
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH 44106, USA
| | - Irene Lee
- WIL Research Laboratories, LLC, Ashland, OH 44805, USA
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH 44106, USA
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18
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Knott K, Fishovitz J, Thorpe SB, Lee I, Santos WL. N-Terminal peptidic boronic acids selectively inhibit human ClpXP. Org Biomol Chem 2010; 8:3451-6. [DOI: 10.1039/c004247a] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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