1
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Medrano FJ, Hernando-Amado S, Martínez JL, Romero A. A new type of Class C β-lactamases defined by PIB-1. A metal-dependent carbapenem-hydrolyzing β-lactamase, from Pseudomonas aeruginosa: Structural and functional analysis. Int J Biol Macromol 2024; 277:134298. [PMID: 39097051 DOI: 10.1016/j.ijbiomac.2024.134298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 07/18/2024] [Accepted: 07/28/2024] [Indexed: 08/05/2024]
Abstract
Antibiotic resistance is one of most important health concerns nowadays, and β-lactamases are the most important resistance determinants. These enzymes, based on their structural and functional characteristics, are grouped in four categories (A, B, C and D). We have solved the structure of PIB-1, a Pseudomonas aeruginosa chromosomally-encoded β-lactamase, in its apo form and in complex with meropenem and zinc. These crystal structures show that it belongs to the Class C β-lactamase group, although it shows notable differences, especially in the Ω- and P2-loops, which are important for the enzymatic activity. Functional analysis showed that PIB-1 is able to degrade carbapenems but not cephalosporins, the typical substrate of Class C β-lactamases, and that its catalytic activity increases in the presence of metal ions, especially zinc. They do not bind to the active-site but they induce the formation of trimers that show an increased capacity for the degradation of the antibiotics, suggesting that this oligomer is more active than the other oligomeric species. While PIB-1 is structurally a Class C β-lactamase, the low sequence conservation, substrate profile and its metal-dependence, prompts us to position this enzyme as the founder of a new group inside the Class C β-lactamases. Consequently, its diversity might be wider than expected.
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Affiliation(s)
- Francisco Javier Medrano
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain.
| | - Sara Hernando-Amado
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Darwin 3, 28043 Madrid, Spain
| | - José Luis Martínez
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Darwin 3, 28043 Madrid, Spain
| | - Antonio Romero
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain.
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2
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Fram B, Su Y, Truebridge I, Riesselman AJ, Ingraham JB, Passera A, Napier E, Thadani NN, Lim S, Roberts K, Kaur G, Stiffler MA, Marks DS, Bahl CD, Khan AR, Sander C, Gauthier NP. Simultaneous enhancement of multiple functional properties using evolution-informed protein design. Nat Commun 2024; 15:5141. [PMID: 38902262 PMCID: PMC11190266 DOI: 10.1038/s41467-024-49119-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 05/24/2024] [Indexed: 06/22/2024] Open
Abstract
A major challenge in protein design is to augment existing functional proteins with multiple property enhancements. Altering several properties likely necessitates numerous primary sequence changes, and novel methods are needed to accurately predict combinations of mutations that maintain or enhance function. Models of sequence co-variation (e.g., EVcouplings), which leverage extensive information about various protein properties and activities from homologous protein sequences, have proven effective for many applications including structure determination and mutation effect prediction. We apply EVcouplings to computationally design variants of the model protein TEM-1 β-lactamase. Nearly all the 14 experimentally characterized designs were functional, including one with 84 mutations from the nearest natural homolog. The designs also had large increases in thermostability, increased activity on multiple substrates, and nearly identical structure to the wild type enzyme. This study highlights the efficacy of evolutionary models in guiding large sequence alterations to generate functional diversity for protein design applications.
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Affiliation(s)
- Benjamin Fram
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Yang Su
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Ian Truebridge
- Institute for Protein Innovation, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- AI Proteins, Boston, MA, USA
| | - Adam J Riesselman
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Program in Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - John B Ingraham
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Alessandro Passera
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030, Vienna, Austria
| | - Eve Napier
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
| | - Nicole N Thadani
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Apriori Bio, Cambridge, MA, USA
| | - Samuel Lim
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Kristen Roberts
- Selux Diagnostics Inc., 56 Roland Street, Charlestown, MA, USA
| | - Gurleen Kaur
- Selux Diagnostics Inc., 56 Roland Street, Charlestown, MA, USA
| | - Michael A Stiffler
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Dyno Therapeutics, 343 Arsenal Street, Watertown, MA, USA
| | - Debora S Marks
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christopher D Bahl
- Institute for Protein Innovation, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- AI Proteins, Boston, MA, USA
| | - Amir R Khan
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Chris Sander
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nicholas P Gauthier
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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3
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Yi HB, Lee S, Seo K, Kim H, Kim M, Lee HS. Cellular and Biophysical Applications of Genetic Code Expansion. Chem Rev 2024; 124:7465-7530. [PMID: 38753805 DOI: 10.1021/acs.chemrev.4c00112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Despite their diverse functions, proteins are inherently constructed from a limited set of building blocks. These compositional constraints pose significant challenges to protein research and its practical applications. Strategically manipulating the cellular protein synthesis system to incorporate novel building blocks has emerged as a critical approach for overcoming these constraints in protein research and application. In the past two decades, the field of genetic code expansion (GCE) has achieved significant advancements, enabling the integration of numerous novel functionalities into proteins across a variety of organisms. This technological evolution has paved the way for the extensive application of genetic code expansion across multiple domains, including protein imaging, the introduction of probes for protein research, analysis of protein-protein interactions, spatiotemporal control of protein function, exploration of proteome changes induced by external stimuli, and the synthesis of proteins endowed with novel functions. In this comprehensive Review, we aim to provide an overview of cellular and biophysical applications that have employed GCE technology over the past two decades.
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Affiliation(s)
- Han Bin Yi
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Seungeun Lee
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Kyungdeok Seo
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Hyeongjo Kim
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Minah Kim
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Hyun Soo Lee
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
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4
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Fram B, Truebridge I, Su Y, Riesselman AJ, Ingraham JB, Passera A, Napier E, Thadani NN, Lim S, Roberts K, Kaur G, Stiffler M, Marks DS, Bahl CD, Khan AR, Sander C, Gauthier NP. Simultaneous enhancement of multiple functional properties using evolution-informed protein design. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.09.539914. [PMID: 37214973 PMCID: PMC10197589 DOI: 10.1101/2023.05.09.539914] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Designing optimized proteins is important for a range of practical applications. Protein design is a rapidly developing field that would benefit from approaches that enable many changes in the amino acid primary sequence, rather than a small number of mutations, while maintaining structure and enhancing function. Homologous protein sequences contain extensive information about various protein properties and activities that have emerged over billions of years of evolution. Evolutionary models of sequence co-variation, derived from a set of homologous sequences, have proven effective in a range of applications including structure determination and mutation effect prediction. In this work we apply one of these models (EVcouplings) to computationally design highly divergent variants of the model protein TEM-1 β-lactamase, and characterize these designs experimentally using multiple biochemical and biophysical assays. Nearly all designed variants were functional, including one with 84 mutations from the nearest natural homolog. Surprisingly, all functional designs had large increases in thermostability and most had a broadening of available substrates. These property enhancements occurred while maintaining a nearly identical structure to the wild type enzyme. Collectively, this work demonstrates that evolutionary models of sequence co-variation (1) are able to capture complex epistatic interactions that successfully guide large sequence departures from natural contexts, and (2) can be applied to generate functional diversity useful for many applications in protein design.
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Affiliation(s)
- Benjamin Fram
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Ian Truebridge
- Institute for Protein Innovation, Boston, Massachusetts, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School; Boston, MA, USA
- current address: AI Proteins; Boston, MA, USA
| | - Yang Su
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Adam J. Riesselman
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Program in Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - John B. Ingraham
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Alessandro Passera
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- current address: Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Eve Napier
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
| | - Nicole N. Thadani
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Samuel Lim
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Kristen Roberts
- Selux Diagnostics, Inc., 56 Roland Street, Charlestown, MA, USA
| | - Gurleen Kaur
- Selux Diagnostics, Inc., 56 Roland Street, Charlestown, MA, USA
| | - Michael Stiffler
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Debora S. Marks
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Christopher D. Bahl
- Institute for Protein Innovation, Boston, Massachusetts, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School; Boston, MA, USA
- current address: AI Proteins; Boston, MA, USA
| | - Amir R. Khan
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
- Division of Newborn Medicine, Boston Children’s Hospital, Boston, MA, USA
| | - Chris Sander
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Nicholas P. Gauthier
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
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5
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Alkekhia D, LaRose C, Shukla A. β-Lactamase-Responsive Hydrogel Drug Delivery Platform for Bacteria-Triggered Cargo Release. ACS APPLIED MATERIALS & INTERFACES 2022; 14:27538-27550. [PMID: 35675049 DOI: 10.1021/acsami.2c02614] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Antibiotic resistance is a growing public health threat that complicates the treatment of infections. β-Lactamase enzymes, which hydrolyze the β-lactam ring present in many common antibiotics, are a major cause of this resistance and are produced by a broad range of bacterial pathogens. Here, we developed hydrogels that degrade specifically in the presence of β-lactamases and β-lactamase-producing bacteria as a platform for bacteria-triggered drug delivery. A maleimide-functionalized β-lactamase-cleavable cephalosporin was used as a crosslinker in the fabrication of hydrogels through end-crosslinked polymerization with multiarm thiol-terminated poly(ethylene glycol) macromers via Michael-type addition. We demonstrated that only hydrogels containing the responsive crosslinker were degraded by β-lactamases and β-lactamase-producing bacteria in vitro and in an ex vivo porcine skin infection model. Fluorescent polystyrene nanoparticles, encapsulated in the hydrogels as model cargo, were released at rates that closely tracked hydrogel wet mass loss, confirming β-lactamase-triggered controlled cargo release. Nonresponsive hydrogels, lacking the β-lactam crosslinker, remained stable in the presence of β-lactamases and β-lactamase-producing bacteria and exhibited no change in mass or nanoparticle release. Furthermore, the responsive hydrogels remained stable in non-β-lactamase enzymes, including collagenases and lipases. These hydrogels have the potential to be used as a bacteria-triggered drug delivery system to control unnecessary exposure to encapsulated antimicrobials, which can provide effective infection treatment without exacerbating resistance.
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Affiliation(s)
- Dahlia Alkekhia
- School of Engineering, Center for Biomedical Engineering, Brown University, Providence, Rhode Island 02912, United States
| | - Cassi LaRose
- School of Engineering, Center for Biomedical Engineering, Brown University, Providence, Rhode Island 02912, United States
| | - Anita Shukla
- School of Engineering, Center for Biomedical Engineering, Brown University, Providence, Rhode Island 02912, United States
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6
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Abstract
Class C β-lactamases or cephalosporinases can be classified into two functional groups (1, 1e) with considerable molecular variability (≤20% sequence identity). These enzymes are mostly encoded by chromosomal and inducible genes and are widespread among bacteria, including Proteobacteria in particular. Molecular identification is based principally on three catalytic motifs (64SXSK, 150YXN, 315KTG), but more than 70 conserved amino-acid residues (≥90%) have been identified, many close to these catalytic motifs. Nevertheless, the identification of a tiny, phylogenetically distant cluster (including enzymes from the genera Legionella, Bradyrhizobium, and Parachlamydia) has raised questions about the possible existence of a C2 subclass of β-lactamases, previously identified as serine hydrolases. In a context of the clinical emergence of extended-spectrum AmpC β-lactamases (ESACs), the genetic modifications observed in vivo and in vitro (point mutations, insertions, or deletions) during the evolution of these enzymes have mostly involved the Ω- and H-10/R2-loops, which vary considerably between genera, and, in some cases, the conserved triplet 150YXN. Furthermore, the conserved deletion of several amino-acid residues in opportunistic pathogenic species of Acinetobacter, such as A. baumannii, A. calcoaceticus, A. pittii and A. nosocomialis (deletion of residues 304-306), and in Hafnia alvei and H. paralvei (deletion of residues 289-290), provides support for the notion of natural ESACs. The emergence of higher levels of resistance to β-lactams, including carbapenems, and to inhibitors such as avibactam is a reality, as the enzymes responsible are subject to complex regulation encompassing several other genes (ampR, ampD, ampG, etc.). Combinations of resistance mechanisms may therefore be at work, including overproduction or change in permeability, with the loss of porins and/or activation of efflux systems.
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7
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Bahr G, González LJ, Vila AJ. Metallo-β-lactamases in the Age of Multidrug Resistance: From Structure and Mechanism to Evolution, Dissemination, and Inhibitor Design. Chem Rev 2021; 121:7957-8094. [PMID: 34129337 PMCID: PMC9062786 DOI: 10.1021/acs.chemrev.1c00138] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Antimicrobial resistance is one of the major problems in current practical medicine. The spread of genes coding for resistance determinants among bacteria challenges the use of approved antibiotics, narrowing the options for treatment. Resistance to carbapenems, last resort antibiotics, is a major concern. Metallo-β-lactamases (MBLs) hydrolyze carbapenems, penicillins, and cephalosporins, becoming central to this problem. These enzymes diverge with respect to serine-β-lactamases by exhibiting a different fold, active site, and catalytic features. Elucidating their catalytic mechanism has been a big challenge in the field that has limited the development of useful inhibitors. This review covers exhaustively the details of the active-site chemistries, the diversity of MBL alleles, the catalytic mechanism against different substrates, and how this information has helped developing inhibitors. We also discuss here different aspects critical to understand the success of MBLs in conferring resistance: the molecular determinants of their dissemination, their cell physiology, from the biogenesis to the processing involved in the transit to the periplasm, and the uptake of the Zn(II) ions upon metal starvation conditions, such as those encountered during an infection. In this regard, the chemical, biochemical and microbiological aspects provide an integrative view of the current knowledge of MBLs.
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Affiliation(s)
- Guillermo Bahr
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Lisandro J. González
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Alejandro J. Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
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8
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Crystal structure of AmpC BER and molecular docking lead to the discovery of broad inhibition activities of halisulfates against β-lactamases. Comput Struct Biotechnol J 2020; 19:145-152. [PMID: 33425247 PMCID: PMC7773887 DOI: 10.1016/j.csbj.2020.12.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 12/08/2020] [Accepted: 12/13/2020] [Indexed: 11/23/2022] Open
Abstract
AmpC BER is an extended-spectrum (ES) class C β-lactamase with a two-amino-acid insertion in the H10 helix region located at the boundary of the active site compared with its narrow spectrum progenitor. The crystal structure of the wild-type AmpC BER revealed that the insertion widens the active site by restructuring the flexible H10 helix region, which is the structural basis for its ES activity. Besides, two sulfates originated from the crystallization solution were observed in the active site. The presence of sulfate-binding subsites, together with the recognition of ring-structured chemical scaffolds by AmpC BER, led us to perform in silico molecular docking experiments with halisulfates, natural products isolated from marine sponge. Inspired by the snug fit of halisulfates within the active site, we demonstrated that halisulfate 3 and 5 significantly inhibit ES class C β-lactamases. Especially, halisulfate 5 is comparable to avibactam in terms of inhibition efficiency; it inhibits the nitrocefin-hydrolyzing activity of AmpC BER with a Ki value of 5.87 μM in a competitive manner. Furthermore, halisulfate 5 displayed moderate and weak inhibition activities against class A and class B/D enzymes, respectively. The treatment of β-lactamase inhibitors (BLIs) in combination with β-lactam antibiotics is a working strategy to cope with infections by pathogens producing ES β-lactamases. Considering the emergence and dissemination of enzymes insensitive to clinically-used BLIs, the broad inhibition spectrum and structural difference of halisulfates would be used to develop novel BLIs that can escape the bacterial resistance mechanism mediated by β-lactamases.
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9
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Structural Insights into Inhibition of the Acinetobacter-Derived Cephalosporinase ADC-7 by Ceftazidime and Its Boronic Acid Transition State Analog. Antimicrob Agents Chemother 2020; 64:AAC.01183-20. [PMID: 32988830 DOI: 10.1128/aac.01183-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 09/16/2020] [Indexed: 02/08/2023] Open
Abstract
Extended-spectrum class C β-lactamases have evolved to rapidly inactivate expanded-spectrum cephalosporins, a class of antibiotics designed to be resistant to hydrolysis by β-lactamase enzymes. To better understand the mechanism by which Acinetobacter-derived cephalosporinase-7 (ADC-7), a chromosomal AmpC enzyme, hydrolyzes these molecules, we determined the X-ray crystal structure of ADC-7 in an acyl-enzyme complex with the cephalosporin ceftazidime (2.40 Å) as well as in complex with a boronic acid transition state analog inhibitor that contains the R1 side chain of ceftazidime (1.67 Å). In the acyl-enzyme complex, the carbonyl oxygen is situated in the oxyanion hole where it makes key stabilizing interactions with the main chain nitrogens of Ser64 and Ser315. The boronic acid O1 hydroxyl group is similarly positioned in this area. Conserved residues Gln120 and Asn152 form hydrogen bonds with the amide group of the R1 side chain in both complexes. These complexes represent two steps in the hydrolysis of expanded-spectrum cephalosporins by ADC-7 and offer insight into the inhibition of ADC-7 by ceftazidime through displacement of the deacylating water molecule as well as blocking its trajectory to the acyl carbonyl carbon. In addition, the transition state analog inhibitor, LP06, was shown to bind with high affinity to ADC-7 (Ki , 50 nM) and was able to restore ceftazidime susceptibility, offering the potential for optimization efforts of this type of inhibitor.
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10
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Papp-Wallace KM, Mack AR, Taracila MA, Bonomo RA. Resistance to Novel β-Lactam-β-Lactamase Inhibitor Combinations: The "Price of Progress". Infect Dis Clin North Am 2020; 34:773-819. [PMID: 33011051 DOI: 10.1016/j.idc.2020.05.001] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Significant advances were made in antibiotic development during the past 5 years. Novel agents were added to the arsenal that target critical priority pathogens, including multidrug-resistant Pseudomonas aeruginosa and carbapenem-resistant Enterobacterales. Of these, 4 novel β-lactam-β-lactamase inhibitor combinations (ceftolozane-tazobactam, ceftazidime-avibactam, meropenem-vaborbactam, and imipenem-cilastatin-relebactam) reached clinical approval in the United States. With these additions comes a significant responsibility to reduce the possibility of emergence of resistance. Reports in the rise of resistance toward ceftolozane-tazobactam and ceftazidime-avibactam are alarming. Clinicians and scientists must make every attempt to reverse or halt these setbacks.
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Affiliation(s)
- Krisztina M Papp-Wallace
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs, 151W, 10701 East Boulevard, Cleveland, OH 44106, USA.
| | - Andrew R Mack
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs, 151W, 10701 East Boulevard, Cleveland, OH 44106, USA
| | - Magdalena A Taracila
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs, 151W, 10701 East Boulevard, Cleveland, OH 44106, USA
| | - Robert A Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs, 151W, 10701 East Boulevard, Cleveland, OH 44106, USA.
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11
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Xiao F, Dong S, Liu Y, Feng Y, Li H, Yun CH, Cui Q, Li W. Structural Basis of Specificity for Carboxyl-Terminated Acyl Donors in a Bacterial Acyltransferase. J Am Chem Soc 2020; 142:16031-16038. [PMID: 32803979 DOI: 10.1021/jacs.0c07331] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Macrolactins (MLNs) are a class of important antimacular degeneration and antitumor agents. Malonylated/succinylated MLNs are even more important due to their efficacy in overcoming multi-drug-resistant bacteria. However, which enzyme catalyzes this reaction remains enigmatic. Herein, we deciphered a β-lactamase homologue BmmI to be responsible for this step. BmmI could specifically attach C3-C5 alkyl acid thioesters onto 7-OH of MLN A and also exhibits substrate promiscuity toward acyl acceptors with different scaffolds. The crystal structure of BmmI covalently linked to the succinyl group and systematic mutagenesis highlighted the role of oxyanion holelike geometry in the recognition of carboxyl-terminated acyl donors. The engineering of this geometry expanded its substrate scope, with the R166A/G/Q variants recognizing up to C12 alkyl acid thioester. The structure of BmmI with acyl acceptor MLN A revealed the importance of Arg292 in the recognition of macrolide substrates. Moreover, the mechanism of the BmmI-catalyzed acyltransfer reaction was established, unmasking the deft role of Lys76 in governing acyl donors as well as catalysis. Our studies uncover the delicate mechanism underlying the substrate selectivity of acyltransferases, which would guide rational enzyme engineering for drug development.
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Affiliation(s)
- Fei Xiao
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 266003 Qingdao, China
| | | | - Yang Liu
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 266003 Qingdao, China
| | | | - Huayue Li
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 266003 Qingdao, China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, 266237 Qingdao, China
| | - Cai-Hong Yun
- Department of Biochemistry and Biophysics & Department of Integration of Chinese and Western Medicine, School of Basic Medical Sciences, Peking University, 38 Xueyuan Road, 100191 Beijing, China
| | | | - Wenli Li
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 266003 Qingdao, China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, 266237 Qingdao, China
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12
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Cheng Q, DeYonker NJ. Acylation and deacylation mechanism and kinetics of penicillin G reaction with Streptomyces R61 DD-peptidase. J Comput Chem 2020; 41:1685-1697. [PMID: 32323874 DOI: 10.1002/jcc.26210] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 02/26/2020] [Accepted: 04/05/2020] [Indexed: 12/20/2022]
Abstract
Two quantum mechanical (QM)-cluster models are built for studying the acylation and deacylation mechanism and kinetics of Streptomyces R61 DD-peptidase with the penicillin G at atomic level detail. DD-peptidases are bacterial enzymes involved in the cross-linking of peptidoglycan to form the cell wall, necessary for bacterial survival. The cross-linking can be inhibited by antibiotic beta-lactam derivatives through acylation, preventing the acyl-enzyme complex from undergoing further deacylation. The deacylation step was predicted to be rate-limiting. Transition state and intermediate structures are found using density functional theory in this study, and thermodynamic and kinetic properties of the proposed mechanism are evaluated. The acyl-enzyme complex is found lying in a deep thermodynamic sink, and deacylation is indeed the severely rate-limiting step, leading to suicide inhibition of the peptidoglycan cross-linking. The usage of QM-cluster models is a promising technique to understand, improve, and design antibiotics to disrupt function of the Streptomyces R61 DD-peptidase.
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Affiliation(s)
- Qianyi Cheng
- Department of Chemistry, University of Memphis, Memphis, Tennessee, USA
| | - Nathan J DeYonker
- Department of Chemistry, University of Memphis, Memphis, Tennessee, USA
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13
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A Standard Numbering Scheme for Class C β-Lactamases. Antimicrob Agents Chemother 2020; 64:AAC.01841-19. [PMID: 31712217 DOI: 10.1128/aac.01841-19] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 11/08/2019] [Indexed: 11/20/2022] Open
Abstract
Unlike for classes A and B, a standardized amino acid numbering scheme has not been proposed for the class C (AmpC) β-lactamases, which complicates communication in the field. Here, we propose a scheme developed through a collaborative approach that considers both sequence and structure, preserves traditional numbering of catalytically important residues (Ser64, Lys67, Tyr150, and Lys315), is adaptable to new variants or enzymes yet to be discovered and includes a variation for genetic and epidemiological applications.
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14
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Abstract
A standard numbering scheme has been proposed for class C β-lactamases. This will significantly enhance comparison of biochemical and biophysical studies performed on different members of this class of enzymes and facilitate communication in the field.
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15
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Tooke CL, Hinchliffe P, Bragginton EC, Colenso CK, Hirvonen VHA, Takebayashi Y, Spencer J. β-Lactamases and β-Lactamase Inhibitors in the 21st Century. J Mol Biol 2019; 431:3472-3500. [PMID: 30959050 PMCID: PMC6723624 DOI: 10.1016/j.jmb.2019.04.002] [Citation(s) in RCA: 440] [Impact Index Per Article: 88.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 03/27/2019] [Accepted: 04/01/2019] [Indexed: 12/31/2022]
Abstract
The β-lactams retain a central place in the antibacterial armamentarium. In Gram-negative bacteria, β-lactamase enzymes that hydrolyze the amide bond of the four-membered β-lactam ring are the primary resistance mechanism, with multiple enzymes disseminating on mobile genetic elements across opportunistic pathogens such as Enterobacteriaceae (e.g., Escherichia coli) and non-fermenting organisms (e.g., Pseudomonas aeruginosa). β-Lactamases divide into four classes; the active-site serine β-lactamases (classes A, C and D) and the zinc-dependent or metallo-β-lactamases (MBLs; class B). Here we review recent advances in mechanistic understanding of each class, focusing upon how growing numbers of crystal structures, in particular for β-lactam complexes, and methods such as neutron diffraction and molecular simulations, have improved understanding of the biochemistry of β-lactam breakdown. A second focus is β-lactamase interactions with carbapenems, as carbapenem-resistant bacteria are of grave clinical concern and carbapenem-hydrolyzing enzymes such as KPC (class A) NDM (class B) and OXA-48 (class D) are proliferating worldwide. An overview is provided of the changing landscape of β-lactamase inhibitors, exemplified by the introduction to the clinic of combinations of β-lactams with diazabicyclooctanone and cyclic boronate serine β-lactamase inhibitors, and of progress and strategies toward clinically useful MBL inhibitors. Despite the long history of β-lactamase research, we contend that issues including continuing unresolved questions around mechanism; opportunities afforded by new technologies such as serial femtosecond crystallography; the need for new inhibitors, particularly for MBLs; the likely impact of new β-lactam:inhibitor combinations and the continuing clinical importance of β-lactams mean that this remains a rewarding research area.
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Affiliation(s)
- Catherine L Tooke
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Philip Hinchliffe
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Eilis C Bragginton
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Charlotte K Colenso
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Viivi H A Hirvonen
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Yuiko Takebayashi
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom.
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16
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Dalal V, Kumar P, Rakhaminov G, Qamar A, Fan X, Hunter H, Tomar S, Golemi-Kotra D, Kumar P. Repurposing an Ancient Protein Core Structure: Structural Studies on FmtA, a Novel Esterase of Staphylococcus aureus. J Mol Biol 2019; 431:3107-3123. [DOI: 10.1016/j.jmb.2019.06.019] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 06/15/2019] [Accepted: 06/18/2019] [Indexed: 11/28/2022]
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17
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Wang F, Shen L, Zhou H, Wang S, Wang X, Tao P. Machine Learning Classification Model for Functional Binding Modes of TEM-1 β-Lactamase. Front Mol Biosci 2019; 6:47. [PMID: 31355207 PMCID: PMC6629954 DOI: 10.3389/fmolb.2019.00047] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 06/11/2019] [Indexed: 11/13/2022] Open
Abstract
TEM family of enzymes is one of the most commonly encountered β-lactamases groups with different catalytic capabilities against various antibiotics. Despite the studies investigating the catalytic mechanism of TEM β-lactamases, the binding modes of these enzymes against ligands in different functional catalytic states have been largely overlooked. But the binding modes may play a critical role in the function and even the evolution of these proteins. In this work, a newly developed machine learning analysis approach to the recognition of protein dynamics states was applied to compare the binding modes of TEM-1 β-lactamase with regard to penicillin in different catalytic states. While conventional analysis methods, including principal components analysis (PCA), could not differentiate TEM-1 in different binding modes, the application of a machine learning method led to excellent classification models differentiating these states. It was also revealed that both reactant/product states and apo/product states are more differentiable than the apo/reactant states. The feature importance generated by the training procedure of the machine learning model was utilized to evaluate the contribution from residues at active sites and in different secondary structures. Key active site residues, Ser70 and Ser130, play a critical role in differentiating reactant/product states, while other active site residues are more important for differentiating apo/product states. Overall, this study provides new insights into the different dynamical function states of TEM-1 and may open a new venue for β-lactamases functional and evolutional studies in general.
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Affiliation(s)
- Feng Wang
- Department of Chemistry, Center for Scientific Computation, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, TX, United States
| | - Li Shen
- Department of Chemistry, Center for Scientific Computation, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, TX, United States
| | - Hongyu Zhou
- Department of Chemistry, Center for Scientific Computation, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, TX, United States
| | - Shouyi Wang
- Department of Industrial, Manufacturing, and Systems Engineering, University of Texas at Arlington, Arlington, TX, United States
| | - Xinlei Wang
- Department of Statistical Science, Southern Methodist University, Dallas, TX, United States
| | - Peng Tao
- Department of Chemistry, Center for Scientific Computation, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, TX, United States
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18
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Characterization of Organic Solvent-Tolerant Lipolytic Enzyme from Marinobacter lipolyticus Isolated from the Antarctic Ocean. Appl Biochem Biotechnol 2018; 187:1046-1060. [PMID: 30151635 DOI: 10.1007/s12010-018-2865-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 08/17/2018] [Indexed: 01/12/2023]
Abstract
The Antarctic marine environment provides a good source of novel lipolytic enzymes that possess beneficial properties, i.e., resistance to extreme physical and chemical conditions. We found a lipolytic Escherichia coli colony that was transformed using genomic DNA from Marinobacter lipolyticus 27-A9 isolated from the Antarctic Ross Sea. DNA sequence analysis revealed an open reading frame of lipolytic enzyme gene. The gene translates a protein (LipA9) of 404 amino acids with molecular mass of 45,247 Da. Recombinant LipA9 was expressed in E. coli BL21 (DE3) cells and purified by anion exchange and gel filtration chromatography. The kcat/Km of LipA9 was 175 s-1 μM-1, and the optimum temperature and pH were 70 °C and pH 8.0, respectively. LipA9 had quite high organic solvent stability; it was stable toward several common organic solvents up to 50% concentration. Substrate specificity studies showed that LipA9 preferred a short acyl chain length of p-nitrophenyl ester and triglyceride. Sequence analysis showed that LipA9 contained catalytic Ser72 and Lys75 in S-x-x-K motif, like family VIII esterases. Homology modeling and site-directed mutagenesis studies revealed that Tyr141 and Tyr188 residues were located near the conserved motif and played an important role in catalytic activity.
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19
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Awasthi S, Gupta S, Tripathi R, Nair NN. Mechanism and Kinetics of Aztreonam Hydrolysis Catalyzed by Class-C β-Lactamase: A Temperature-Accelerated Sliced Sampling Study. J Phys Chem B 2018; 122:4299-4308. [DOI: 10.1021/acs.jpcb.8b01287] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Shalini Awasthi
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Shalini Gupta
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Ravi Tripathi
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Nisanth N. Nair
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
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20
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Das CK, Nair NN. Molecular insights into avibactam mediated class C β-lactamase inhibition: competition between reverse acylation and hydrolysis through desulfation. Phys Chem Chem Phys 2018; 20:14482-14490. [DOI: 10.1039/c8cp01670d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The spatial water probability density plots show that the axial –NHOSO3 group of avibactam impedes the deacylating water molecule(s) to enter the active site, while the –NHSO3 group in aztreonam is unable to prevent the water molecule(s) to diffuse into the active site.
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Affiliation(s)
- Chandan Kumar Das
- Department of Chemistry
- Indian Institute of Technology Kanpur
- Kanpur
- India
| | - Nisanth N. Nair
- Department of Chemistry
- Indian Institute of Technology Kanpur
- Kanpur
- India
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21
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Wang J, Zheng S, Liu Y, Zhang Z, Lin Z, Li J, Zhang G, Wang X, Li J, Chen PR. Palladium-Triggered Chemical Rescue of Intracellular Proteins via Genetically Encoded Allene-Caged Tyrosine. J Am Chem Soc 2016; 138:15118-15121. [PMID: 27797486 DOI: 10.1021/jacs.6b08933] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Chemical de-caging has emerged as an attractive strategy for gain-of-function study of proteins via small-molecule reagents. The previously reported chemical de-caging reactions have been largely centered on liberating the side chain of lysine on a given protein. Herein, we developed an allene-based caging moiety and the corresponding palladium de-caging reagents for chemical rescue of tyrosine (Tyr) activity on intracellular proteins. This bioorthogonal de-caging pair has been successfully applied to unmask enzymatic Tyr sites (e.g., Y671 on Taq polymerase and Y728 on Anthrax lethal factor) as well as the post-translational Tyr modification site (Y416 on Src kinase) in vitro and in living cells. Our strategy provides a general platform for chemical rescue of Tyr-dependent protein activity inside cells.
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Affiliation(s)
- Jie Wang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, China.,Academy for Advanced Interdisciplinary Studies, Peking University , Beijing 100871, China
| | - Siqi Zheng
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, China
| | - Yanjun Liu
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, China
| | - Zhaoyue Zhang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, China
| | - Zhi Lin
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, China
| | - Jiaofeng Li
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, China
| | - Gong Zhang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, China.,Academy for Advanced Interdisciplinary Studies, Peking University , Beijing 100871, China
| | - Xin Wang
- Academy for Advanced Interdisciplinary Studies, Peking University , Beijing 100871, China.,Peking-Tsinghua Center for Life Sciences, Peking University , Beijing 100871, China
| | - Jie Li
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, China
| | - Peng R Chen
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, China.,Peking-Tsinghua Center for Life Sciences, Peking University , Beijing 100871, China
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22
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Tripathi R, Nair NN. Deacylation Mechanism and Kinetics of Acyl-Enzyme Complex of Class C β-Lactamase and Cephalothin. J Phys Chem B 2016; 120:2681-90. [PMID: 26918257 DOI: 10.1021/acs.jpcb.5b11623] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Understanding the molecular details of antibiotic resistance by the bacterial enzymes β-lactamases is vital for the development of novel antibiotics and inhibitors. In this spirit, the detailed mechanism of deacylation of the acyl-enzyme complex formed by cephalothin and class C β-lactamase is investigated here using hybrid quantum-mechanical/molecular-mechanical molecular dynamics methods. The roles of various active-site residues and substrate in the deacylation reaction are elucidated. We identify the base that activates the hydrolyzing water molecule and the residue that protonates the catalytic serine (Ser64). Conformational changes in the active sites and proton transfers that potentiate the efficiency of the deacylation reaction are presented. We have also characterized the oxyanion holes and other H-bonding interactions that stabilize the reaction intermediates. Together with the kinetic and mechanistic details of the acylation reaction, we analyze the complete mechanism and the overall kinetics of the drug hydrolysis. Finally, the apparent rate-determining step in the drug hydrolysis is scrutinized.
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Affiliation(s)
- Ravi Tripathi
- Department of Chemistry, Indian Institute of Technology Kanpur , Kanpur 208016, India
| | - Nisanth N Nair
- Department of Chemistry, Indian Institute of Technology Kanpur , Kanpur 208016, India
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23
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Xu F, Chen S, Xu G, Wu J, Yang L. Discovery and expression of a Pseudomonas sp. esterase as a novel biocatalyst for the efficient biosynthesis of a chiral intermediate of pregabalin. BIOTECHNOL BIOPROC E 2015. [DOI: 10.1007/s12257-015-0069-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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24
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Brown JR, Livesay DR. Flexibility Correlation between Active Site Regions Is Conserved across Four AmpC β-Lactamase Enzymes. PLoS One 2015; 10:e0125832. [PMID: 26018804 PMCID: PMC4446314 DOI: 10.1371/journal.pone.0125832] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 03/26/2015] [Indexed: 11/24/2022] Open
Abstract
β-lactamases are bacterial enzymes that confer resistance to β-lactam antibiotics, such as penicillins and cephalosporins. There are four classes of β-lactamase enzymes, each with characteristic sequence and structure properties. Enzymes from class A are the most common and have been well characterized across the family; however, less is known about how physicochemical properties vary across the C and D families. In this report, we compare the dynamical properties of four AmpC (class C) β-lactamases using our distance constraint model (DCM). The DCM reliably predicts thermodynamic and mechanical properties in an integrated way. As a consequence, quantitative stability/flexibility relationships (QSFR) can be determined and compared across the whole family. The DCM calculates a large number of QSFR metrics. Perhaps the most useful is the flexibility index (FI), which quantifies flexibility along the enzyme backbone. As typically observed in other systems, FI is well conserved across the four AmpC enzymes. Cooperativity correlation (CC), which quantifies intramolecular couplings within structure, is rarely conserved across protein families; however, it is in AmpC. In particular, the bulk of each structure is composed of a large rigid cluster, punctuated by three flexibly correlated regions located at the active site. These regions include several catalytic residues and the Ω-loop. This evolutionary conservation combined with active their site location strongly suggests that these coupled dynamical modes are important for proper functioning of the enzyme.
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Affiliation(s)
- Jenna R. Brown
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28262, United States of America
| | - Dennis R. Livesay
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28262, United States of America
- * E-mail:
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25
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Mitchell JM, Clasman JR, June CM, Kaitany KCJ, LaFleur JR, Taracila MA, Klinger NV, Bonomo RA, Wymore T, Szarecka A, Powers RA, Leonard DA. Structural basis of activity against aztreonam and extended spectrum cephalosporins for two carbapenem-hydrolyzing class D β-lactamases from Acinetobacter baumannii. Biochemistry 2015; 54:1976-87. [PMID: 25710192 DOI: 10.1021/bi501547k] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The carbapenem-hydrolyzing class D β-lactamases OXA-23 and OXA-24/40 have emerged worldwide as causative agents for β-lactam antibiotic resistance in Acinetobacter species. Many variants of these enzymes have appeared clinically, including OXA-160 and OXA-225, which both contain a P → S substitution at homologous positions in the OXA-24/40 and OXA-23 backgrounds, respectively. We purified OXA-160 and OXA-225 and used steady-state kinetic analysis to compare the substrate profiles of these variants to their parental enzymes, OXA-24/40 and OXA-23. OXA-160 and OXA-225 possess greatly enhanced hydrolytic activities against aztreonam, ceftazidime, cefotaxime, and ceftriaxone when compared to OXA-24/40 and OXA-23. These enhanced activities are the result of much lower Km values, suggesting that the P → S substitution enhances the binding affinity of these drugs. We have determined the structures of the acylated forms of OXA-160 (with ceftazidime and aztreonam) and OXA-225 (ceftazidime). These structures show that the R1 oxyimino side-chain of these drugs occupies a space near the β5-β6 loop and the omega loop of the enzymes. The P → S substitution found in OXA-160 and OXA-225 results in a deviation of the β5-β6 loop, relieving the steric clash with the R1 side-chain carboxypropyl group of aztreonam and ceftazidime. These results reveal worrying trends in the enhancement of substrate spectrum of class D β-lactamases but may also provide a map for β-lactam improvement.
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Affiliation(s)
| | | | | | | | | | - Magdalena A Taracila
- ∥Departments of Medicine, Pharmacology, Biochemistry, and Molecular Biology and Microbiology, Case Western Reserve University and Research Service, and Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States
| | | | - Robert A Bonomo
- ∥Departments of Medicine, Pharmacology, Biochemistry, and Molecular Biology and Microbiology, Case Western Reserve University and Research Service, and Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States
| | - Troy Wymore
- ⊥UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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26
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Tsang MW, So PK, Liu SY, Tsang CW, Chan PH, Wong KY, Leung YC. Catalytically impaired fluorescent Class C β-lactamase enables rapid and sensitive cephalosporin detection by stabilizing fluorescence signals: Implications for biosensor design. Biotechnol J 2014; 10:126-35. [PMID: 25181520 DOI: 10.1002/biot.201400140] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 07/17/2014] [Accepted: 08/29/2014] [Indexed: 01/06/2023]
Affiliation(s)
- Man-Wah Tsang
- Department of Applied Biology and Chemical Technology, and State Key Laboratory of Chirosciences, The Hong Kong Polytechnic University, Hong Kong, China
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Avibactam and class C β-lactamases: mechanism of inhibition, conservation of the binding pocket, and implications for resistance. Antimicrob Agents Chemother 2014; 58:5704-13. [PMID: 25022578 DOI: 10.1128/aac.03057-14] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Avibactam is a novel non-β-lactam β-lactamase inhibitor that inhibits a wide range of β-lactamases. These include class A, class C, and some class D enzymes, which erode the activity of β-lactam drugs in multidrug-resistant pathogens like Pseudomonas aeruginosa and Enterobacteriaceae spp. Avibactam is currently in clinical development in combination with the β-lactam antibiotics ceftazidime, ceftaroline fosamil, and aztreonam. Avibactam has the potential to be the first β-lactamase inhibitor that might provide activity against class C-mediated resistance, which represents a growing concern in both hospital- and community-acquired infections. Avibactam has an unusual mechanism of action: it is a covalent inhibitor that acts via ring opening, but in contrast to other currently used β-lactamase inhibitors, this reaction is reversible. Here, we present a high-resolution structure of avibactam bound to a class C β-lactamase, AmpC, from P. aeruginosa that provided insight into the mechanism of both acylation and recyclization in this enzyme class and highlighted the differences observed between class A and class C inhibition. Furthermore, variants resistant to avibactam that identified the residues important for inhibition were isolated. Finally, the structural information was used to predict effective inhibition by sequence analysis and functional studies of class C β-lactamases from a large and diverse set of contemporary clinical isolates (P. aeruginosa and several Enterobacteriaceae spp.) obtained from recent infections to understand any preexisting variability in the binding pocket that might affect inhibition by avibactam.
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28
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Mirzaie S, Najafi K, Hakhamaneshi MS, Shahverdi AR, Fathi F. Investigation for antimicrobial resistance-modulating activity of diethyl malate and 1-methyl malate against beta-lactamase class A fromBacillus licheniformisby molecular dynamics,in vitroandin vivostudies. J Biomol Struct Dyn 2014; 33:1016-26. [PMID: 24836845 DOI: 10.1080/07391102.2014.924877] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Sako Mirzaie
- a Department of Biochemistry, Sanandaj Branch , Islamic Azad University , Sanandaj , Iran
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29
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Reclaiming the efficacy of β-lactam-β-lactamase inhibitor combinations: avibactam restores the susceptibility of CMY-2-producing Escherichia coli to ceftazidime. Antimicrob Agents Chemother 2014; 58:4290-7. [PMID: 24820081 DOI: 10.1128/aac.02625-14] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
CMY-2 is a plasmid-encoded Ambler class C cephalosporinase that is widely disseminated in Enterobacteriaceae and is responsible for expanded-spectrum cephalosporin resistance. As a result of resistance to both ceftazidime and β-lactamase inhibitors in strains carrying blaCMY, novel β-lactam-β-lactamase inhibitor combinations are sought to combat this significant threat to β-lactam therapy. Avibactam is a bridged diazabicyclo [3.2.1]octanone non-β-lactam β-lactamase inhibitor in clinical development that reversibly inactivates serine β-lactamases. To define the spectrum of activity of ceftazidime-avibactam, we tested the susceptibilities of Escherichia coli clinical isolates that carry bla(CMY-2) or bla(CMY-69) and investigated the inactivation kinetics of CMY-2. Our analysis showed that CMY-2-containing clinical isolates of E. coli were highly susceptible to ceftazidime-avibactam (MIC(90), ≤ 0.5 mg/liter); in comparison, ceftazidime had a MIC90 of >128 mg/liter. More importantly, avibactam was an extremely potent inhibitor of CMY-2 β-lactamase, as demonstrated by a second-order onset of acylation rate constant (k2/K) of (4.9 ± 0.5) × 10(4) M(-1) s(-1) and the off-rate constant (k(off)) of (3.7 ± 0.4) × 10(-4) s(-1). Analysis of the reaction of avibactam with CMY-2 using mass spectrometry to capture reaction intermediates revealed that the CMY-2-avibactam acyl-enzyme complex was stable for as long as 24 h. Molecular modeling studies raise the hypothesis that a series of successive hydrogen-bonding interactions occur as avibactam proceeds through the reaction coordinate with CMY-2 (e.g., T316, G317, S318, T319, S343, N346, and R349). Our findings support the microbiological and biochemical efficacy of ceftazidime-avibactam against E. coli containing plasmid-borne CMY-2 and CMY-69.
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Crystal structure analysis of EstA from Arthrobacter sp. Rue61a--an insight into catalytic promiscuity. FEBS Lett 2014; 588:1154-60. [PMID: 24613918 DOI: 10.1016/j.febslet.2014.02.045] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 02/11/2014] [Accepted: 02/15/2014] [Indexed: 12/22/2022]
Abstract
In this article we analyze the reasons for catalytic promiscuity of a type VIII esterase with β-lactamase fold and the ability to cleave β-lactams. We compared the structure of this enzyme to those of an esterase of the same type without any lactamase ability, an esterase with moderate lactamase ability, and a class C β-lactamase with similar fold. Our results show that for these enzymes, the difference in the substrate specificity is sterically driven.
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31
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Bhattacharya M, Toth M, Antunes NT, Smith CA, Vakulenko SB. Structure of the extended-spectrum class C β-lactamase ADC-1 from Acinetobacter baumannii. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:760-71. [PMID: 24598745 PMCID: PMC3949520 DOI: 10.1107/s1399004713033014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 12/05/2013] [Indexed: 11/10/2022]
Abstract
ADC-type class C β-lactamases comprise a large group of enzymes that are encoded by genes located on the chromosome of Acinetobacter baumannii, a causative agent of serious bacterial infections. Overexpression of these enzymes renders A. baumannii resistant to various β-lactam antibiotics and thus severely compromises the ability to treat infections caused by this deadly pathogen. Here, the high-resolution crystal structure of ADC-1, the first member of this clinically important family of antibiotic-resistant enzymes, is reported. Unlike the narrow-spectrum class C β-lactamases, ADC-1 is capable of producing resistance to the expanded-spectrum cephalosporins, rendering them inactive against A. baumannii. The extension of the substrate profile of the enzyme is likely to be the result of structural differences in the R2-loop, primarily the deletion of three residues and subsequent rearrangement of the A10a and A10b helices. These structural rearrangements result in the enlargement of the R2 pocket of ADC-1, allowing it to accommodate the bulky R2 substituents of the third-generation cephalosporins, thus enhancing the catalytic efficiency of the enzyme against these clinically important antibiotics.
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Affiliation(s)
- Monolekha Bhattacharya
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Marta Toth
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Nuno Tiago Antunes
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Clyde A. Smith
- Stanford Synchrotron Radiation Lightsource, Stanford University, Menlo Park, California USA
| | - Sergei B. Vakulenko
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
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32
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Tripathi R, Nair NN. Mechanism of acyl-enzyme complex formation from the Henry-Michaelis complex of class C β-lactamases with β-lactam antibiotics. J Am Chem Soc 2013; 135:14679-90. [PMID: 24010547 DOI: 10.1021/ja405319n] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Bacteria that cause most of the hospital-acquired infections make use of class C β-lactamase (CBL) among other enzymes to resist a wide spectrum of modern antibiotics and pose a major public health concern. Other than the general features, details of the defensive mechanism by CBL, leading to the hydrolysis of drug molecules, remain a matter of debate, in particular the identification of the general base and role of the active site residues and substrate. In an attempt to unravel the detailed molecular mechanism, we carried out extensive hybrid quantum mechanical/molecular mechanical Car-Parrinello molecular dynamics simulation of the reaction with the aid of the metadynamics technique. On this basis, we report here the mechanism of the formation of the acyl-enzyme complex from the Henry-Michaelis complex formed by β-lactam antibiotics and CBL. We considered two β-lactam antibiotics, namely, cephalothin and aztreonam, belonging to two different subfamilies. A general mechanism for the formation of a β-lactam antibiotic-CBL acyl-enzyme complex is elicited, and the individual roles of the active site residues and substrate are probed. The general base in the acylation step has been identified as Lys67, while Tyr150 aids the protonation of the β-lactam nitrogen through either the substrate carboxylate group or a water molecule.
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Affiliation(s)
- Ravi Tripathi
- Department of Chemistry, Indian Institute of Technology Kanpur , 208016 Kanpur, India
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Dahyot S, Broutin I, de Champs C, Guillon H, Mammeri H. Contribution of asparagine 346 residue to the carbapenemase activity of CMY-2 β-lactamase. FEMS Microbiol Lett 2013; 345:147-53. [PMID: 23763375 DOI: 10.1111/1574-6968.12199] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2013] [Revised: 06/06/2013] [Accepted: 06/11/2013] [Indexed: 11/30/2022] Open
Abstract
Only a few plasmid-borne AmpC (pAmpC) β-lactamases, such as CMY-2, can account for carbapenem resistance in Enterobacteriaceae in combination with outer membrane impermeability. The aim of this study was to elucidate the contribution of Asn-346, which is well conserved among carbapenem-hydrolyzing pAmpCs, to the hydrolysis spectrum of CMY-2. Site-directed mutagenesis experiments were carried out to replace Asn-346 with glycine, alanine, valine, glutamate, aspartate, serine, threonine, glutamine, tyrosine, isoleucine, lysine, and histidine. The recombinant plasmids were transferred into wild-type and porin-deficient Escherichia coli strains. Asn-346 replacement reduced significantly the MICs of all β-lactams, except the Asn-346-Ile substitution that increased the MICs of cephalosporins, whereas it decreased those of carbapenems. The biochemical characterization, along with a molecular modeling study, showed that the size and the polarity of the side chain at position 346 assisted substrate binding and turnover. This study shows for the first time that the amino acid at position 346 contributes to the β-lactamase activity of cephalosporinases. Asparagine and isoleucine residues, which are well conserved at position 346 among AmpC-type enzymes, modulate their hydrolysis spectrum in an opposing sense. Ile-346 confers higher level of cephalosporins resistance, whereas Asn-346 confers carbapenem resistance in combination with outer membrane impermeability.
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Affiliation(s)
- Sandrine Dahyot
- Service de Bactériologie, Centre Hospitalo-Universitaire d'Amiens, Amiens, France
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34
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Mokoena N, Mathiba K, Tsekoa T, Steenkamp P, Rashamuse K. Functional characterisation of a metagenome derived family VIII esterase with a deacetylation activity on β-lactam antibiotics. Biochem Biophys Res Commun 2013; 437:342-8. [PMID: 23827391 DOI: 10.1016/j.bbrc.2013.06.076] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 06/20/2013] [Indexed: 10/26/2022]
Abstract
Family VIII esterases represent a poorly characterised esterase family, with high sequence identity to class C β-lactamases, peptidases and penicillin binding proteins. This study reports on the metagenomic library screening and biochemical characterisation of a novel esterase (Est22) derived from an acidic Leachate environment. The enzyme is 423 amino acids in length and contained 22 aa signal peptide. The Est22 primary structure revealed the presence of N-terminus S-x-x-K sequence, which is also highly conserved in class C β-lactamases, peptidases as well as carboxylesterases belonging to family VIII. Phylogenetic analysis using the representative sequences from class C β-lactamases and family VIII esterases indicated that Est22 is a member of family VIII esterases. Substrate specificity profiling using p-nitrophenyl esters (C2-C16) indicated that Est22 preferred shorter chain p-nitrophenyl esters (C2-C5), a characteristic that is typical for true carboxylesterases. In addition of hydrolysing Nitrocefin, Est22 also hydrolysed first generation cephalosporin based derivatives. Detailed selectivity study using different cephalosporin based substrates indicated that Est22 selectively hydrolyse the ester bond of a cephalosporin derivatives leaving the amide bond of the β-lactam ring intact. The selective nature of Est22 makes this enzyme a potential candidate for the use in the synthesis and modification cephalosporin based molecules.
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Affiliation(s)
- Nobalanda Mokoena
- CSIR Biosciences, Scientia Campus, P.O. Box 395, Pretoria 0184, South Africa
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35
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Ruble JF, Lefurgy ST, Cornish VW, Powers RA. Structural analysis of the Asn152Gly mutant of P99 cephalosporinase. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1189-93. [PMID: 22948919 DOI: 10.1107/s0907444912024080] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 05/26/2012] [Indexed: 11/10/2022]
Abstract
P99 cephalosporinase is a class C β-lactamase that is responsible in part for the widespread bacterial resistance to β-lactam antibiotics. Mutations of the conserved active-site residue Asn152 of the enzyme have been shown to alter β-lactam substrate specificity in vivo. Mutation of Asn152 to a glycine is notable in that it exhibits in vivo substrate-selectivity switching. In order to better understand the structural basis for this observed switch, the X-ray crystal structure of the apo Asn152Gly mutant of P99 was determined to 1.95 Å resolution. Unexpectedly, the artificial C-terminal His(6) tag of a symmetrically-related molecule was observed bound in the active site. The His(6) tag makes several interactions with key active-site residues, as well as with several sulfate ions. Additionally, the overall C-terminus occupies the space left vacant upon the mutation of Asn152 to glycine.
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Affiliation(s)
- James F Ruble
- Department of Chemistry, Grand Valley State University, Allendale, MI 49401, USA
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36
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Identification of amino acids involved in the hydrolytic activity of lipase LipBL from Marinobacter lipolyticus. Microbiology (Reading) 2012; 158:2192-2203. [DOI: 10.1099/mic.0.058792-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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37
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Smoum R, Rubinstein A, Dembitsky VM, Srebnik M. Boron containing compounds as protease inhibitors. Chem Rev 2012; 112:4156-220. [PMID: 22519511 DOI: 10.1021/cr608202m] [Citation(s) in RCA: 303] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Reem Smoum
- The School of Pharmacy, Institute for Drug Research, The Hebrew University of Jerusalem, Faculty of Medicine, Jerusalem, Israel.
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38
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Tripathi R, Nair NN. Thermodynamic and Kinetic Stabilities of Active Site Protonation States of Class C β-Lactamase. J Phys Chem B 2012; 116:4741-53. [DOI: 10.1021/jp212186q] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Ravi Tripathi
- Department of Chemistry, Indian Institute of Technology, Kanpur, 208016 Kanpur,
India
| | - Nisanth N. Nair
- Department of Chemistry, Indian Institute of Technology, Kanpur, 208016 Kanpur,
India
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39
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Hydrolysis spectrum extension of CMY-2-like β-lactamases resulting from structural alteration in the Y-X-N loop. Antimicrob Agents Chemother 2012; 56:1151-6. [PMID: 22232281 DOI: 10.1128/aac.05630-11] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Citrobacter freundii isolate CHA, which was responsible for postoperative peritonitis after 10 days of cefepime therapy, displayed a phenotype of resistance consistent with extended-spectrum AmpC (ESAC) β-lactamase. The chromosome-borne bla(AmpC-CHA) gene was amplified and sequenced, revealing five amino acid substitutions, I125V, R148H, Q196H, V305A, and V348A, in the product compared to the sequence of native AmpC. A cloning experiment yielded the Escherichia coli TOP10(pAmpC-CHA) strain, which was resistant to all extended-spectrum cephalosporins (ESCs), including cefepime. To ascertain whether the R148H substitution accounted for the hydrolysis spectrum extension, it was reverted by site-directed mutagenesis. The resulting E. coli TOP10(pAmpC-CHA-H148R) strain was fully susceptible to cefepime, thus confirming that the Arg-148 replacement was mandatory for substrate profile enlargement. To further characterize the phenotypical and biochemical effects induced by the R148H change, it was introduced by site-directed mutagenesis into the CMY-2 β-lactamase, which is structurally related to the chromosome-borne cephalosporinase of C. freundii. The CMY-2-R148H variant conferred increased MICs of ESCs, whereas those of carbapenems were unchanged even in a porin-deficient E. coli strain. Moreover, it exhibited increased catalytic efficiency (k(cat)/K(m)) toward ceftazidime (100-fold) due to an enhanced hydrolysis rate (k(cat)), whereas the enzymatic parameters toward imipenem were unchanged. The structural analysis of the AmpC variant showed that the R148H replacement occurred in the loop containing the Y-X-N motif, which is the counterpart of the SDN loop in class A β-lactamases. This study shows that the Y-X-N loop is a novel hot spot for mutations accounting for hydrolysis spectrum extension in CMY-2-type enzymes.
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40
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The evolution of cefotaximase activity in the TEM β-lactamase. J Mol Biol 2011; 415:205-20. [PMID: 22075446 DOI: 10.1016/j.jmb.2011.10.041] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 10/18/2011] [Accepted: 10/25/2011] [Indexed: 11/21/2022]
Abstract
The development of a molecular-level understanding of drug resistance through β-lactamase is critical not only in designing newer-generation antibacterial agents but also in providing insight into the evolutionary mechanisms of enzymes in general. In the present study, we have evaluated the effect of four drug resistance mutations (A42G, E104K, G238S, and M182T) on the cefotaximase activity of the TEM-1 β-lactamase. Using computational methods, including docking and molecular mechanics calculations, we have been able to correctly identify the relative order of catalytic activities associated with these four single point mutants. Further analyses suggest that the changes in catalytic efficiency for mutant enzymes are correlated to structural changes within the binding site. Based on the energetic and structural analyses of the wild-type and mutant enzymes, structural rearrangement is suggested as a mechanism of evolution of drug resistance through TEM β-lactamase. The present study not only provides molecular-level insight into the effect of four drug resistance mutations on the structure and function of the TEM β-lactamase but also establishes a foundation for a future molecular-level analysis of complete evolutionary trajectory for this class of enzymes.
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41
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Chen L, Kong X, Liang Z, Ye F, Yu K, Dai W, Wu D, Luo C, Jiang H. Theoretical Study of the Mechanism of Proton Transfer in the Esterase Estb from Burkholderia Gladioli. J Phys Chem B 2011; 115:13019-25. [DOI: 10.1021/jp206297d] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Liang Chen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- The Key Laboratory of Biomedical Information Engineering of the Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
| | - Xiangqian Kong
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Zhongjie Liang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Fei Ye
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Kunqian Yu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Weiyi Dai
- The Key Laboratory of Biomedical Information Engineering of the Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
| | - Daocheng Wu
- The Key Laboratory of Biomedical Information Engineering of the Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
| | - Cheng Luo
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- Center for Systems Biology, Soochow University, Jiangsu 215006, China
| | - Hualiang Jiang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
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42
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Verma V, Testero SA, Amini K, Wei W, Liu J, Balachandran N, Monoharan T, Stynes S, Kotra LP, Golemi-Kotra D. Hydrolytic mechanism of OXA-58 enzyme, a carbapenem-hydrolyzing class D β-lactamase from Acinetobacter baumannii. J Biol Chem 2011; 286:37292-303. [PMID: 21880707 DOI: 10.1074/jbc.m111.280115] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Carbapenem-hydrolyzing class D β-lactamases (CHDLs) represent an emerging antibiotic resistance mechanism encountered among the most opportunistic Gram-negative bacterial pathogens. We report here the substrate kinetics and mechanistic characterization of a prominent CHDL, the OXA-58 enzyme, from Acinetobacter baumannii. OXA-58 uses a carbamylated lysine to activate the nucleophilic serine used for β-lactam hydrolysis. The deacylating water molecule approaches the acyl-enzyme species, anchored at this serine (Ser-83), from the α-face. Our data show that OXA-58 retains the catalytic machinery found in class D β-lactamases, of which OXA-10 is representative. Comparison of the homology model of OXA-58 and the recently solved crystal structures of OXA-24 and OXA-48 with the OXA-10 crystal structure suggests that these CHDLs have evolved the ability to hydrolyze imipenem, an important carbapenem in clinical use, by subtle structural changes in the active site. These changes may contribute to tighter binding of imipenem to the active site and removal of steric hindrances from the path of the deacylating water molecule.
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Affiliation(s)
- Vidhu Verma
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
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43
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Kotsakis SD, Tzouvelekis LS, Petinaki E, Tzelepi E, Miriagou V. Effects of the Val211Gly substitution on molecular dynamics of the CMY-2 cephalosporinase: implications on hydrolysis of expanded-spectrum cephalosporins. Proteins 2011; 79:3180-92. [PMID: 21989938 DOI: 10.1002/prot.23150] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Revised: 07/04/2011] [Accepted: 07/14/2011] [Indexed: 11/05/2022]
Abstract
CMY-30, a naturally occurring class C β-lactamase differing from the Citrobacter freundii-derived CMY-2 by a Val211Gly substitution in the Ω-loop, exhibits increased hydrolytic efficiency against ceftazidime and cefotaxime. Kinetic constants of CMY-2 and CMY-30 against the latter substrates suggested that the improved efficiency of the Gly211 variant was due to an increase in k(cat). The structural basis of the increased turn-over rates of oxyimino-cephalosporins caused by Val211Gly was studied using 5 ns molecular dynamics simulations of CMY-2 and CMY-30 in their free forms and in covalent complexes with ceftazidime (acyl-enzyme) as well as a boronic acid analogue of ceftazidime (deacylation transition state). Analysis of thermal factors indicated that Val211Gly increased the flexibility of the Ω-loop/H7-helix and the Q120-loop formed by amino acids 112-125, and also altered the vibrations of the H10-helix/R2-loop. Structural elements containing the catalytic residues remained relatively rigid except Tyr150 in acyl-enzyme species. Regions exhibiting altered flexibility due to the substitution appear to move in a concerted manner in both enzymes. This movement was more intense in CMY-30 and also at directions different to those observed for CMY-2. Additionally, it appeared that the Val211Gly increased the available space for the accommodation of the R1 side chain of ceftazidime. These findings are likely associated with the significantly increased vibrations of the bound compounds observed in CMY-30 complexes. Therefore, the extended spectrum properties of CMY-30 seem to arise through a complex process implicating changes in protein movement and in the mode of substrate accommodation.
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Affiliation(s)
- Stathis D Kotsakis
- Laboratory of Bacteriology, Hellenic Pasteur Institute, 11521 Athens, Greece
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44
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Li R, Liao JM, Gu CR, Wang YT, Chen CL. Theoretical investigation on reaction of sulbactam with wild-type SHV-1 β-lactamase: acylation, tautomerization, and deacylation. J Phys Chem B 2011; 115:10298-310. [PMID: 21797222 DOI: 10.1021/jp111572v] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular dynamics (MD) simulation and quantum mechanical (QM) calculations were used to investigate the reaction mechanism of sulbactam with class A wild-type SHV-1 β-lactamase including acylation, tautomerization, and deacylation. Five different sulbactam-enzyme configurations were investigated by MD simulations. In the acylation step, we found that Glu166 cannot activate Ser70 directly for attacking on the carbonyl carbon, and Lys73 would participate in the reaction acting as a relay. Additionally, we found that sulbactam carboxyl can also act as a general base. QM calculations were performed on the formation mechanism of linear intermediates. We suggest that both imine and trans-enamine intermediates can be obtained in the opening of a five-membered thiazolidine ring. By MD simulation, we found that imine intermediate can exist in two conformations, which can generate subsequent trans- and cis-enamine intermediates, respectively. The QM calculations revealed that trans-enamine intermediate is much more stable than other intermediates. The deacylation mechanism of three linear intermediates (imine, trans-enamine, cis-enamine) was investigated separately. It is remarkably noted that, in cis-enamine intermediate, Glu166 cannot activate water for attacking on the carbonyl carbon directly. This leads to a decreasing of the deacylation rate of cis-enamine. These findings will be potentially useful in the development of new inhibitors.
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Affiliation(s)
- Rui Li
- The Department of Chemistry, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan
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45
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Investigation of the acylation mechanism of class C beta-lactamase: pKa calculation, molecular dynamics simulation and quantum mechanical calculation. J Mol Model 2011; 18:481-92. [PMID: 21541744 DOI: 10.1007/s00894-011-1087-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Accepted: 04/07/2011] [Indexed: 01/22/2023]
Abstract
β-Lactamases are bacterial enzymes that act as a bacterial defense system against β-lactam antibiotics. β-Lactamase cleaves the β-lactam ring of the antibiotic by a two step mechanism involving acylation and deacylation steps. Although class C β-lactamases have been investigated extensively, the details of their mechanism of action are not well understood at the molecular level. In this study, we investigated the mechanism of the acylation step of class C β-lactamase using pKa calculations, molecular dynamics (MD) simulations and quantum mechanical (QM) calculations. Serine64 (Ser64) is an active site residue that attacks the β-lactam ring. In this study, we considered three possible scenarios for activation of the nucleophile Ser64, where the activation base is (1) Tyrosine150 (Tyr150), (2) Lysine67 (Lys67), or (3) substrate. From the pKa calculation, we found that Tyr150 and Lys67 are likely to remain in their protonated states in the pre-covalent complex between the enzyme and substrate, although their role as activator would require them to be in the deprotonated state. It was found that the carboxylate group of the substrate remained close to Ser64 for most of the simulation. The energy barrier for hydrogen abstraction from Ser64 by the substrate was calculated quantum mechanically using a large truncated model of the enzyme active site and found to be close to the experimental energy barrier, which suggests that the substrate can initiate the acylation mechanism in class C β-lactamase.
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46
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Drawz SM, Taracila M, Caselli E, Prati F, Bonomo RA. Exploring sequence requirements for C₃/C₄ carboxylate recognition in the Pseudomonas aeruginosa cephalosporinase: Insights into plasticity of the AmpC β-lactamase. Protein Sci 2011; 20:941-58. [PMID: 21404358 DOI: 10.1002/pro.612] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Revised: 02/11/2011] [Accepted: 02/14/2011] [Indexed: 11/06/2022]
Abstract
In Pseudomonas aeruginosa, the chromosomally encoded class C cephalosporinase (AmpC β-lactamase) is often responsible for high-level resistance to β-lactam antibiotics. Despite years of study of these important β-lactamases, knowledge regarding how amino acid sequence dictates function of the AmpC Pseudomonas-derived cephalosporinase (PDC) remains scarce. Insights into structure-function relationships are crucial to the design of both β-lactams and high-affinity inhibitors. In order to understand how PDC recognizes the C₃/C₄ carboxylate of β-lactams, we first examined a molecular model of a P. aeruginosa AmpC β-lactamase, PDC-3, in complex with a boronate inhibitor that possesses a side chain that mimics the thiazolidine/dihydrothiazine ring and the C₃/C₄ carboxylate characteristic of β-lactam substrates. We next tested the hypothesis generated by our model, i.e. that more than one amino acid residue is involved in recognition of the C₃/C₄ β-lactam carboxylate, and engineered alanine variants at three putative carboxylate binding amino acids. Antimicrobial susceptibility testing showed that the PDC-3 β-lactamase maintains a high level of activity despite the substitution of C₃/C₄ β-lactam carboxylate recognition residues. Enzyme kinetics were determined for a panel of nine penicillin and cephalosporin analog boronates synthesized as active site probes of the PDC-3 enzyme and the Arg349Ala variant. Our examination of the PDC-3 active site revealed that more than one residue could serve to interact with the C₃/C₄ carboxylate of the β-lactam. This functional versatility has implications for novel drug design, protein evolution, and resistance profile of this enzyme.
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Affiliation(s)
- Sarah M Drawz
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
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47
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Identification of the Catalytic Residues of Carboxylesterase from Arthrobacter globiformisby Diisopropyl Fluorophosphate-Labeling and Site-Directed Mutagenesis. Biosci Biotechnol Biochem 2011; 75:89-94. [DOI: 10.1271/bbb.100576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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48
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Pelto RB, Pratt RF. Serendipitous discovery of α-hydroxyalkyl esters as β-lactamase substrates. Biochemistry 2010; 49:10496-506. [PMID: 21087009 DOI: 10.1021/bi101071r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
O-(1-Carboxy-1-alkyloxycarbonyl) hydroxamates were found to spontaneously decarboxylate in aqueous neutral buffer to form O-(2-hydroxyalkylcarbonyl) hydroxamates. While the former molecules do not react rapidly with serine β-lactamases, the latter are quite good substrates of representative class A and C, but not D, enzymes, and particularly of a class C enzyme. The enzymes catalyze hydrolysis of these compounds to a mixture of the α-hydroxy acid and hydroxamate. Analogous compounds containing aryloxy leaving groups rather that hydroxamates are also substrates. Structure-activity experiments showed that the α-hydroxyl group was required for any substantial substrate activity. Although both d- and l-α-hydroxy acid derivatives were substrates, the former were preferred. The response of the class C activity to pH and to alternative nucleophiles (methanol and d-phenylalanine) suggested that the same active site functional groups participated in catalysis as for classical substrates. Molecular modeling was employed to explore how the α-hydroxy group might interact with the class C β-lactamase active site. Incorporation of the α-hydroxyalkyl moiety into novel inhibitors will be of considerable interest.
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Affiliation(s)
- Ryan B Pelto
- Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459, United States
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Delmas J, Leyssene D, Dubois D, Birck C, Vazeille E, Robin F, Bonnet R. Structural insights into substrate recognition and product expulsion in CTX-M enzymes. J Mol Biol 2010; 400:108-20. [PMID: 20452359 DOI: 10.1016/j.jmb.2010.04.062] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Revised: 04/28/2010] [Accepted: 04/29/2010] [Indexed: 11/25/2022]
Abstract
beta-Lactamase-mediated resistance to beta-lactam antibiotics poses a major threat to our antibiotic armamentarium. Among beta-lactamases, a significant threat comes from enzymes that hydrolyze extended-spectrum cephalosporins such as cefotaxime. Among the enzymes that exhibit this phenotype, the CTX-M family is found worldwide. These enzymes have a small active site, which makes it difficult to explain how they hydrolyze the bulky extended-spectrum cephalosporins into the binding site. We investigated noncovalent substrate recognition and product release in CTX-M enzymes using steered molecular dynamics simulation and X-ray diffraction. An arginine residue located far from the binding site favors the capture and tracking of substrates during entrance into the catalytic pocket. We show that the accommodation of extended-spectrum cephalosporins by CTX-M enzymes induced subtle changes in the active site and established a high density of electrostatic interactions. Interestingly, the product of the catalytic reaction initiates its own release because of steric hindrances and electrostatic repulsions. This suggests that there exists a general mechanism for product release for all members of the beta-lactamase family and probably for most carboxypeptidases.
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Affiliation(s)
- Julien Delmas
- CHU Clermont-Ferrand, Laboratoire de Bactériologie, Clermont-Ferrand F-63003, France
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Endimiani A, Doi Y, Bethel CR, Taracila M, Adams-Haduch JM, O'Keefe A, Hujer AM, Paterson DL, Skalweit MJ, Page MGP, Drawz SM, Bonomo RA. Enhancing resistance to cephalosporins in class C beta-lactamases: impact of Gly214Glu in CMY-2. Biochemistry 2010; 49:1014-23. [PMID: 19938877 DOI: 10.1021/bi9015549] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The biochemical properties of CMY-32, a class C enzyme possessing a single-amino acid substitution in the Omega loop (Gly214Glu), were compared to those of the parent enzyme, CMY-2, a widespread class C beta-lactamase. In parallel with our microbiological characterization, the Gly214Glu substitution in CMY-32 reduced catalytic efficiency (k(cat)/K(m)) by 50-70% against "good" substrates (i.e., cephalothin) while increasing k(cat)/K(m) against "poor" substrates (i.e., cefotaxime). Additionally, CMY-32 was more susceptible to inactivation by sulfone beta-lactamase inhibitors (i.e., sulbactam and tazobactam) than CMY-2. Timed electrospray ionization mass spectrometry (ESI-MS) analysis of the reaction of CMY-2 and CMY-32 with different substrates and inhibitors suggested that both beta-lactamases formed similar intermediates during catalysis and inactivation. We next showed that the carbapenems (imipenem, meropenem, and doripenem) form long-lived acyl-enzyme intermediates and present evidence that there is beta-lactamase-catalyzed elimination of the C(6) hydroxyethyl substituent. Furthermore, we discovered that the monobactam aztreonam and BAL29880, a new beta-lactamase inhibitor of the monobactam class, inactivate CMY-2 and CMY-32 by forming an acyl-enzyme intermediate that undergoes elimination of SO(3)(2-). Molecular modeling and dynamics simulations suggest that the Omega loop is more constrained in CMY-32 than CMY-2. Our model also proposes that Gln120 adopts a novel conformation in the active site while new interactions form between Glu214 and Tyr221, thus explaining the increased level of cefotaxime hydrolysis. When it is docked in the active site, we observe that BAL29880 exploits contacts with highly conserved residues Lys67 and Asn152 in CMY-2 and CMY-32. These findings highlight (i) the impact of single-amino acid substitutions on protein evolution in clinically important AmpC enzymes and (ii) the novel insights into the mechanisms by which carbapenems and monobactams interact with CMY-2 and CMY-32 beta-lactamases.
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Affiliation(s)
- Andrea Endimiani
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, USA
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