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Phage Display-Derived Peptides and Antibodies for Bacterial Infectious Diseases Therapy and Diagnosis. Molecules 2023; 28:molecules28062621. [PMID: 36985593 PMCID: PMC10052323 DOI: 10.3390/molecules28062621] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/01/2023] [Accepted: 03/06/2023] [Indexed: 03/17/2023] Open
Abstract
The emergence of antibiotic-resistant-bacteria is a serious public health threat, which prompts us to speed up the discovery of novel antibacterial agents. Phage display technology has great potential to screen peptides or antibodies with high binding capacities for a wide range of targets. This property is significant in the rapid search for new antibacterial agents for the control of bacterial resistance. In this paper, we not only summarized the recent progress of phage display for the discovery of novel therapeutic agents, identification of action sites of bacterial target proteins, and rapid detection of different pathogens, but also discussed several problems of this technology that must be solved. Breakthrough in these problems may further promote the development and application of phage display technology in the biomedical field in the future.
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2
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Knies JL, Cai F, Weinreich DM. Enzyme Efficiency but Not Thermostability Drives Cefotaxime Resistance Evolution in TEM-1 β-Lactamase. Mol Biol Evol 2017; 34:1040-1054. [PMID: 28087769 PMCID: PMC5400381 DOI: 10.1093/molbev/msx053] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A leading intellectual challenge in evolutionary genetics is to identify the specific phenotypes that drive adaptation. Enzymes offer a particularly promising opportunity to pursue this question, because many enzymes' contributions to organismal fitness depend on a comparatively small number of experimentally accessible properties. Moreover, on first principles the demands of enzyme thermostability stand in opposition to the demands of catalytic activity. This observation, coupled with the fact that enzymes are only marginally thermostable, motivates the widely held hypothesis that mutations conferring functional improvement require compensatory mutations to restore thermostability. Here, we explicitly test this hypothesis for the first time, using four missense mutations in TEM-1 β-lactamase that jointly increase cefotaxime Minimum Inhibitory Concentration (MIC) ∼1500-fold. First, we report enzymatic efficiency (kcat/KM) and thermostability (Tm, and thence ΔG of folding) for all combinations of these mutations. Next, we fit a quantitative model that predicts MIC as a function of kcat/KM and ΔG. While kcat/KM explains ∼54% of the variance in cefotaxime MIC (∼92% after log transformation), ΔG does not improve explanatory power of the model. We also find that cefotaxime MIC rises more slowly in kcat/KM than predicted. Several explanations for these discrepancies are suggested. Finally, we demonstrate substantial sign epistasis in MIC and kcat/KM, and antagonistic pleiotropy between phenotypes, in spite of near numerical additivity in the system. Thus constraints on selectively accessible trajectories, as well as limitations in our ability to explain such constraints in terms of underlying mechanisms are observed in a comparatively "well-behaved" system.
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Affiliation(s)
- Jennifer L Knies
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI
| | - Fei Cai
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI
| | - Daniel M Weinreich
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI
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3
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Solution structures of the Bacillus cereus metallo-β-lactamase BcII and its complex with the broad spectrum inhibitor R-thiomandelic acid. Biochem J 2015; 456:397-407. [PMID: 24059435 PMCID: PMC3898119 DOI: 10.1042/bj20131003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Metallo-β-lactamases, enzymes which inactivate β-lactam antibiotics, are of increasing biological and clinical significance as a source of antibiotic resistance in pathogenic bacteria. In the present study we describe the high-resolution solution NMR structures of the Bacillus cereus metallo-β-lactamase BcII and of its complex with R-thiomandelic acid, a broad-spectrum inhibitor of metallo-β-lactamases. This is the first reported solution structure of any metallo-β-lactamase. There are differences between the solution structure of the free enzyme and previously reported crystal structures in the loops flanking the active site, which are important for substrate and inhibitor binding and catalysis. The binding of R-thiomandelic acid and the roles of active-site residues are defined in detail. Changes in the enzyme structure upon inhibitor binding clarify the role of the mobile β3–β4 loop. Comparisons with other metallo-β-lactamases highlight the roles of individual amino-acid residues in the active site and the β3–β4 loop in inhibitor binding and provide information on the basis of structure–activity relationships among metallo-β-lactamase inhibitors. Metallo-β-lactamases are important in antibiotic resistance in micro-organisms. We report the first solution structure of a metallo-β-lactamase and its complex with an inhibitor, allowing the key flexible loops flanking the active site and their role in inhibitor binding to be properly defined.
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4
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Karsisiotis AI, Damblon C, Roberts GCK. Complete ¹H, ¹⁵N, and ¹³C resonance assignments of Bacillus cereus metallo-β-lactamase and its complex with the inhibitor R-thiomandelic acid. BIOMOLECULAR NMR ASSIGNMENTS 2014; 8:313-318. [PMID: 23838816 PMCID: PMC4145196 DOI: 10.1007/s12104-013-9507-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 06/29/2013] [Indexed: 06/02/2023]
Abstract
β-Lactamases inactivate β-lactam antibiotics by hydrolysis of their endocyclic β-lactam bond and are a major cause of antibiotic resistance in pathogenic bacteria. The zinc dependent metallo-β-lactamase enzymes are of particular concern since they are located on highly transmissible plasmids and have a broad spectrum of activity against almost all β-lactam antibiotics. We present here essentially complete (>96%) backbone and sidechain sequence-specific NMR resonance assignments for the Bacillus cereus subclass B1 metallo-β-lactamase, BcII, and for its complex with R-thiomandelic acid, a broad spectrum inhibitor of metallo-β-lactamases. These assignments have been used as the basis for determination of the solution structures of the enzyme and its inhibitor complex and can also be used in a rapid screen for other metallo-β-lactamase inhibitors.
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Affiliation(s)
- Andreas Ioannis Karsisiotis
- The Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Lancaster Road, PO Box 138, Leicester, LE1 9HN UK
- The School of Pharmacy and Pharmaceutical Sciences, Biomedical Sciences Research Institute, University of Ulster, Coleraine, BT52 1SA Northern Ireland UK
| | - Christian Damblon
- The Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Lancaster Road, PO Box 138, Leicester, LE1 9HN UK
- Chimie Biologique Structurale, Institut de Chimie, Sart-Tilman (B6c), Université de Liège, 4000 Liège, Belgium
| | - Gordon C. K. Roberts
- The Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Lancaster Road, PO Box 138, Leicester, LE1 9HN UK
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5
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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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6
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Szarecka A, Lesnock KR, Ramirez-Mondragon CA, Nicholas HB, Wymore T. The Class D beta-lactamase family: residues governing the maintenance and diversity of function. Protein Eng Des Sel 2011; 24:801-9. [PMID: 21859796 PMCID: PMC3170078 DOI: 10.1093/protein/gzr041] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Revised: 07/14/2011] [Accepted: 07/26/2011] [Indexed: 12/29/2022] Open
Abstract
Class D β-lactamases, a major source of bacterial resistance to β-lactam antibiotic therapies, represent a distinct subset of the β-lactamase superfamily. They share a serine hydrolase mechanism with Classes A/C vs. Class B. Further understanding of their sequence-structure-function relationships would benefit efforts to design a new generation of antibiotics as well as to predict evolutionary mechanisms in response to such therapies. Here we describe analyses based on our high-resolution multiple sequence alignment and phylogenetic tree of ∼80 Class D β-lactamases that leverage several 3D structures of these enzymes. We observe several sequence clusters on the phylogenetic tree, some that are species specific while others include several species from α-, β- and γ-proteobacteria. Residues characteristic of a specific cluster were identified and shown to be located just outside the active site, possibly modulating the function of the catalytic residues to facilitate reactions with specific types of β-lactams. Most significant was the discovery of a likely disulfide bond in a large group composed of α-, β- and γ-proteobacteria that would contribute to enzyme stability and hence bacterial viability under antibiotic assault. A network of co-evolving residues was identified which suggested the importance of maintaining a surface for binding a highly conserved Phe69.
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Affiliation(s)
- Agnieszka Szarecka
- Department of Cell and Molecular Biology, Grand Valley State University, Henry Hall, 1 Campus Drive, Allendale, MI 49401, USA
| | - Kimberly R. Lesnock
- National Resource for Biomedical Supercomputing, Pittsburgh Supercomputing Center, 300 South Craig Street, Pittsburgh, PA 15215, USA
| | - Carlos A. Ramirez-Mondragon
- National Resource for Biomedical Supercomputing, Pittsburgh Supercomputing Center, 300 South Craig Street, Pittsburgh, PA 15215, USA
| | - Hugh B. Nicholas
- National Resource for Biomedical Supercomputing, Pittsburgh Supercomputing Center, 300 South Craig Street, Pittsburgh, PA 15215, USA
| | - Troy Wymore
- National Resource for Biomedical Supercomputing, Pittsburgh Supercomputing Center, 300 South Craig Street, Pittsburgh, PA 15215, USA
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7
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Bou G, Santillana E, Sheri A, Beceiro A, Sampson J, Kalp M, Bethel CR, Distler AM, Drawz SM, Pagadala SRR, van den Akker F, Bonomo RA, Romero A, Buynak JD. Design, synthesis, and crystal structures of 6-alkylidene-2'-substituted penicillanic acid sulfones as potent inhibitors of Acinetobacter baumannii OXA-24 carbapenemase. J Am Chem Soc 2010; 132:13320-31. [PMID: 20822105 PMCID: PMC3393087 DOI: 10.1021/ja104092z] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Class D β-lactamases represent a growing and diverse class of penicillin-inactivating enzymes that are usually resistant to commercial β-lactamase inhibitors. As many such enzymes are found in multi-drug resistant (MDR) Acinetobacter baumannii and Pseudomonas aeruginosa, novel β-lactamase inhibitors are urgently needed. Five unique 6-alkylidene-2'-substituted penicillanic acid sulfones (1-5) were synthesized and tested against OXA-24, a clinically important β-lactamase that inactivates carbapenems and is found in A. baumannii. Based upon the roles Tyr112 and Met223 play in the OXA-24 β-lactamase, we also engineered two variants (Tyr112Ala and Tyr112Ala,Met223Ala) to test the hypothesis that the hydrophobic tunnel formed by these residues influences inhibitor recognition. IC(50) values against OXA-24 and two OXA-24 β-lactamase variants ranged from 10 ± 1 (4 vs WT) to 338 ± 20 nM (5 vs Tyr112Ala, Met223Ala). Compound 4 possessed the lowest K(i) (500 ± 80 nM vs WT), and 1 possessed the highest inactivation efficiency (k(inact)/K(i) = 0.21 ± 0.02 μM(-1) s(-1)). Electrospray ionization mass spectrometry revealed a single covalent adduct, suggesting the formation of an acyl-enzyme intermediate. X-ray structures of OXA-24 complexed to four inhibitors (2.0-2.6 Å) reveal the formation of stable bicyclic aromatic intermediates with their carbonyl oxygen in the oxyanion hole. These data provide the first structural evidence that 6-alkylidene-2'-substituted penicillin sulfones are effective mechanism-based inactivators of class D β-lactamases. Their unique chemistry makes them developmental candidates. Mechanisms for class D hydrolysis and inhibition are discussed, and a pathway for the evolution of the BlaR1 sensor of Staphylococcus aureus to the class D β-lactamases is proposed.
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Affiliation(s)
| | | | | | | | - Jared Sampson
- Departments of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Matthew Kalp
- Departments of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH
| | | | - Anne M. Distler
- Department of Pharmacology, Case Western Reserve University School of Medicine
| | - Sarah M. Drawz
- Department of Pathology, Case Western Reserve University School of Medicine
| | | | - Focco van den Akker
- Departments of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Robert A. Bonomo
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH
- Department of Pharmacology, Case Western Reserve University School of Medicine
- Department of Molecular Biology and Microbiology, Case Western Reserve University
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8
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Phichith D, Bun S, Padiolleau-Lefèvre S, Banh S, Thomas D, Friboulet A, Avalle B. Mutational and inhibitory analysis of a catalytic antibody. Implication for drug discovery. Mol Immunol 2009; 47:348-56. [DOI: 10.1016/j.molimm.2009.09.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Accepted: 09/03/2009] [Indexed: 11/29/2022]
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9
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Kather I, Jakob RP, Dobbek H, Schmid FX. Increased folding stability of TEM-1 beta-lactamase by in vitro selection. J Mol Biol 2008; 383:238-51. [PMID: 18706424 DOI: 10.1016/j.jmb.2008.07.082] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2008] [Revised: 07/16/2008] [Accepted: 07/29/2008] [Indexed: 10/21/2022]
Abstract
In vitro selections of stabilized proteins lead to more robust enzymes and, at the same time, yield novel insights into the principles of protein stability. We employed Proside, a method of in vitro selection, to find stabilized variants of TEM-1 beta-lactamase from Escherichia coli. Proside links the increased protease resistance of stabilized proteins to the infectivity of a filamentous phage. Several libraries of TEM-1 beta-lactamase variants were generated by error-prone PCR, and variants with increased protease resistance were obtained by raising temperature or guanidinium chloride concentration during proteolytic selections. Despite the small size of phage libraries, several strongly stabilizing mutations could be obtained, and a manual combination of the best shifted the profiles for thermal unfolding and temperature-dependent inactivation of beta-lactamase by almost 20 degrees C to a higher temperature. The wild-type protein unfolds in two stages: from the native state via an intermediate of the molten-globule type to the unfolded form. In the course of the selections, the native protein was stabilized by 27 kJ mol(-1) relative to the intermediate and the cooperativity of unfolding was strongly increased. Three of our stabilizing replacements (M182T, A224V, and R275L) had been identified independently in naturally occurring beta-lactamase variants with extended substrate spectrum. In these variants, they acted as global suppressors of destabilizations caused by the mutations in the active site. The comparison between the crystal structure of our best variant and the crystal structure of the wild-type protein indicates that most of the selected mutations optimize helices and their packing. The stabilization by the E147G substitution is remarkable. It removes steric strain that originates from an overly tight packing of two helices in the wild-type protein. Such unfavorable van der Waals repulsions are not easily identified in crystal structures or by computational approaches, but they strongly reduce the conformational stability of a protein.
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Affiliation(s)
- Insa Kather
- Laboratorium für Biochemie und Bayreuther, Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, 95440 Bayreuth, Germany
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10
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Hu Z, Periyannan GR, Crowder MW. Folding strategy to prepare Co(II)-substituted metallo-beta-lactamase L1. Anal Biochem 2008; 378:177-83. [PMID: 18445468 PMCID: PMC2587373 DOI: 10.1016/j.ab.2008.04.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2008] [Revised: 04/01/2008] [Accepted: 04/03/2008] [Indexed: 11/24/2022]
Abstract
In an effort to overcome previous problems with the preparation of Co(II)-substituted metallo-beta-lactamase L1, two strategies were undertaken. Attempts to prepare Co(II)-substituted L1 using biological incorporation resulted in an enzyme that contained only 1 Eq of cobalt and exhibited no catalytic activity. Co(II)-substituted L1 could be prepared by refolding metal-free L1 in the presence of Co(II), and the resulting enzyme contained 1.8 Eq of cobalt, yielded a UV-Vis spectrum consistent with 5-coordinate Co(II), and exhibited a k(cat) of 63 s(-1) and K(m) of 20 microM when using nitrocefin as the substrate. Pre-steady-state fluorescence and UV-Vis studies demonstrated that refolded, Co(II)-substituted L1 uses the same kinetic mechanism as Zn(II)-containing L1, in which a reaction intermediate is formed when using nitrocefin as substrate. The described refolding strategy can be used to prepare other Co(II)-substituted Zn(II)-metalloenzymes, particularly those that contain a solvent-exposable disulfide, which often causes oxidation of Co(II) to Co(III).
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Affiliation(s)
- Zhenxin Hu
- Department of Chemistry and Biochemistry, 160 Hughes Hall, Miami University, Oxford, OH 45056
| | - Gopal R. Periyannan
- Department of Chemistry and Biochemistry, 160 Hughes Hall, Miami University, Oxford, OH 45056
| | - Michael W. Crowder
- Department of Chemistry and Biochemistry, 160 Hughes Hall, Miami University, Oxford, OH 45056
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11
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Biswas S, Raoult D, Rolain JM. A bioinformatic approach to understanding antibiotic resistance in intracellular bacteria through whole genome analysis. Int J Antimicrob Agents 2008; 32:207-20. [PMID: 18619818 DOI: 10.1016/j.ijantimicag.2008.03.017] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2008] [Accepted: 03/19/2008] [Indexed: 12/17/2022]
Abstract
Intracellular bacteria survive within eukaryotic host cells and are difficult to kill with certain antibiotics. As a result, antibiotic resistance in intracellular bacteria is becoming commonplace in healthcare institutions. Owing to the lack of methods available for transforming these bacteria, we evaluated the mechanisms of resistance using molecular methods and in silico genome analysis. The objective of this review was to understand the molecular mechanisms of antibiotic resistance through in silico comparisons of the genomes of obligate and facultative intracellular bacteria. The available data on in vitro mutants reported for intracellular bacteria were also reviewed. These genomic data were analysed to find natural mutations in known target genes involved in antibiotic resistance and to look for the presence or absence of different resistance determinants. Our analysis revealed the presence of tetracycline resistance protein (Tet) in Bartonella quintana, Francisella tularensis and Brucella ovis; moreover, most of the Francisella strains possessed the blaA gene, AmpG protein and metallo-beta-lactamase family protein. The presence or absence of folP (dihydropteroate synthase) and folA (dihydrofolate reductase) genes in the genome could explain natural resistance to co-trimoxazole. Finally, multiple genes encoding different efflux pumps were studied. This in silico approach was an effective method for understanding the mechanisms of antibiotic resistance in intracellular bacteria. The whole genome sequence analysis will help to predict several important phenotypic characteristics, in particular resistance to different antibiotics. In the future, stable mutants should be obtained through transformation methods in order to demonstrate experimentally the determinants of resistance in intracellular bacteria.
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Affiliation(s)
- Silpak Biswas
- URMITE UMR 6236, CNRS IRD, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, 27 Bd Jean Moulin, 13385 Marseille Cedex 05, France
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12
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Santillana E, Beceiro A, Bou G, Romero A. Crystal structure of the carbapenemase OXA-24 reveals insights into the mechanism of carbapenem hydrolysis. Proc Natl Acad Sci U S A 2007; 104:5354-9. [PMID: 17374723 PMCID: PMC1838445 DOI: 10.1073/pnas.0607557104] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Combating bacterial resistance to beta-lactams, the most widely used antibiotics, is an emergent and clinically important challenge. OXA-24 is a class D beta-lactamase isolated from a multiresistant epidemic clinical strain of Acinetobacter baumannii. We have investigated how OXA-24 specifically hydrolyzes the last resort carbapenem antibiotic, and we have determined the crystal structure of OXA-24 at a resolution of 2.5 A. The structure shows that the carbapenem's substrate specificity is determined by a hydrophobic barrier that is established through the specific arrangement of the Tyr-112 and Met-223 side chains, which define a tunnel-like entrance to the active site. The importance of these residues was further confirmed by mutagenesis studies. Biochemical and microbiological analyses of specific point mutants selected on the basis of structural criteria significantly reduced the catalytic efficiency (k(cat)/K(m)) against carbapenems, whereas the specificity for oxacillin was noticeably increased. This is the previously unrecognized crystal structure that has been obtained for a class D carbapenemase enzyme. Accordingly, this information may help to improve the development of effective new drugs to combat beta-lactam resistance. More specifically, it may help to overcome carbapenem resistance in A. baumannii, probably one of the most worrying infectious threats in hospitals worldwide.
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Affiliation(s)
- Elena Santillana
- *Departamento de Estructura y Función de Proteínas, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Cientificas, Ramiro de Maeztu 9, E-28040 Madrid, Spain; and
| | - Alejandro Beceiro
- Servicio de Microbiología-Unidad de Investigación, Complejo Hospitalario Universitario Juan Canalejo, As Xubias 84, E-15006 La Coruña, Spain
| | - Germán Bou
- Servicio de Microbiología-Unidad de Investigación, Complejo Hospitalario Universitario Juan Canalejo, As Xubias 84, E-15006 La Coruña, Spain
| | - Antonio Romero
- *Departamento de Estructura y Función de Proteínas, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Cientificas, Ramiro de Maeztu 9, E-28040 Madrid, Spain; and
- To whom correspondence should be addressed. E-mail:
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13
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Marrero A, Mallorquí-Fernández G, Guevara T, García-Castellanos R, Gomis-Rüth FX. Unbound and acylated structures of the MecR1 extracellular antibiotic-sensor domain provide insights into the signal-transduction system that triggers methicillin resistance. J Mol Biol 2006; 361:506-21. [PMID: 16846613 DOI: 10.1016/j.jmb.2006.06.046] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2006] [Revised: 06/15/2006] [Accepted: 06/16/2006] [Indexed: 11/25/2022]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) strains are responsible for most hospital-onset bacterial infections. Lately, they have become a major threat to the community through infections of skin, soft tissue and respiratory tract, and subsequent septicaemia or septic shock. MRSA strains are resistant to most beta-lactam antibiotics (BLAs) as a result of the biosynthesis of a penicillin-binding protein with low affinity for BLAs, called PBP2a, PBP2' or MecA. This response is regulated by the chromosomal mec-divergon, which encodes a signal-transduction system including a transcriptional repressor, MecI, and a sensor/transducer, MecR1, as well as the structural mecA gene. This system is similar to those encoded by bla divergons in S. aureus and Bacillus licheniformis. MecR1 comprises an integral-membrane latent metalloprotease domain facing the cytosol and an extracellular sensor domain. The latter binds BLAs and transmits a signal through the membrane that eventually triggers activation of the metalloprotease moiety, which in turn switches off MecI-induced repression of mecA transcription. The MecR1 sensor domain, MecR1-PBD, reveals a two-domain structure of alpha/beta-type fold reminiscent of penicillin-binding proteins and beta-lactamases, and a catalytic serine residue as the ultimate cause for BLA-binding. Covalent complexes with benzylpenicillin and oxacillin provide evidence that serine acylation does not entail significant structural changes, thus supporting the hypothesis that additional extracellular segments of MecR1 are involved in signal transmission. The chemical nature of the residues shaping the active-site cleft favours stabilisation of the acyl enzyme complexes in MecR1-PBD, in contrast to the closely related OXA beta-lactamases, where the cleft is more likely to promote subsequent hydrolysis. The present structural data provide insights into the mec-encoded BLA-response mechanism and an explanation for kinetic differences in signal transmission with the related bla-encoded systems.
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Affiliation(s)
- Aniebrys Marrero
- Institut de Biologia Molecular de Barcelona, C.I.D.-C.S.I.C. C/Jordi Girona, 18-26 08034 Barcelona, Spain
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14
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Meroueh SO, Fisher JF, Schlegel HB, Mobashery S. Ab Initio QM/MM Study of Class A β-Lactamase Acylation: Dual Participation of Glu166 and Lys73 in a Concerted Base Promotion of Ser70. J Am Chem Soc 2005; 127:15397-407. [PMID: 16262403 DOI: 10.1021/ja051592u] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Beta-lactamase acquisition is the most prevalent basis for Gram-negative bacteria resistance to the beta-lactam antibiotics. The mechanism used by the most common class A Gram-negative beta-lactamases is serine acylation followed by hydrolytic deacylation, destroying the beta-lactam. The ab initio quantum mechanical/molecular mechanical (QM/MM) calculations, augmented by extensive molecular dynamics simulations reported herein, describe the serine acylation mechanism for the class A TEM-1 beta-lactamase with penicillanic acid as substrate. Potential energy surfaces (based on approximately 350 MP2/6-31+G calculations) reveal the proton movements that govern Ser70 tetrahedral formation and then collapse to the acyl-enzyme. A remarkable duality of mechanism for tetrahedral formation is implicated. Following substrate binding, the pathway initiates by a low energy barrier (5 kcal mol(-1)) and an energetically favorable transfer of a proton from Lys73 to Glu166, through the catalytic water molecule and Ser70. This gives unprotonated Lys73 and protonated Glu166. Tetrahedral formation ensues in a concerted general base process, with Lys73 promoting Ser70 addition to the beta-lactam carbonyl. Moreover, the three-dimensional potential energy surface also shows that the previously proposed pathway, involving Glu166 as the general base promoting Ser70 through a conserved water molecule, exists in competition with the Lys73 process. The existence of two routes to the tetrahedral species is fully consistent with experimental data for mutant variants of the TEM beta-lactamase.
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Affiliation(s)
- Samy O Meroueh
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
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15
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Periyannan G, Shaw PJ, Sigdel T, Crowder MW. In vivo folding of recombinant metallo-beta-lactamase L1 requires the presence of Zn(II). Protein Sci 2004; 13:2236-43. [PMID: 15238636 PMCID: PMC2279831 DOI: 10.1110/ps.04742704] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Metallo-beta-lactamase L1, secreted by pathogenic Stenotrophomonas maltophilia, is a dinuclear Zn(II)-containing enzyme that hydrolyzes almost all known penicillins, cephalosporins, and carbapenems. The presence of Zn(II) ions in both metal binding sites is essential for full enzymatic activity; however, the mechanism of physiological metal incorporation is unknown. To probe metal incorporation, L1 was over-expressed in minimal media with (mmL1+Zn) and without (mmL1-Zn) Zn(II) added to the media, and the resulting proteins were purified and characterized. The mmL1+Zn sample was bound by a Q-Sepharose column, exhibited steady-state kinetic properties, bound Zn(II), existed as a tetramer, and yielded fluorescence emission and CD spectra similar to L1 overexpressed in rich media. On the other hand, the mmL1-Zn sample did not bind to a Q-Sepharose column, and gel filtration studies demonstrated that this protein was monomeric. The mmL1-Zn sample exhibited a lower kcat value, bound less Zn(II), and yielded fluorescence emission and CD spectra consistent with this enzyme being folded improperly. Taken together, these data demonstrate that the proper folding of L1 requires the presence of Zn(II) and suggest that in vitro, thermodynamic metal binding studies do not accurately reflect physiological metal incorporation into L1.
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Affiliation(s)
- Gopalraj Periyannan
- Miami University, Department of Chemistry and Biochemistry, Oxford, Ohio 45056, USA
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16
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Buynak JD, Chen H, Vogeti L, Gadhachanda VR, Buchanan CA, Palzkill T, Shaw RW, Spencer J, Walsh TR. Penicillin-derived inhibitors that simultaneously target both metallo- and serine-β-lactamases. Bioorg Med Chem Lett 2004; 14:1299-304. [PMID: 14980686 DOI: 10.1016/j.bmcl.2003.12.037] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2003] [Revised: 12/04/2003] [Accepted: 12/05/2003] [Indexed: 11/23/2022]
Abstract
The synthesis and beta-lactamase inhibitory activity of four 6-(mercaptomethyl)penicillinates and the four corresponding 6-(hydroxymethyl)penicillinates are described. These penicillins include both C6 stereoisomers as well as the sulfide and sulfone oxidation states of the penam thiazolidine sulfur. All compounds were evaluated as inhibitors of representative metallo- and serine-beta-lactamases enzymes. Selected (mercaptomethyl)penicillinates are shown to inactivate both metallo- and serine-beta-lactamases and to display synergism with piperacillin against beta-lactamase producing strains.
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Affiliation(s)
- John D Buynak
- Department of Chemistry, Southern Methodist University, Dallas, TX 75275-0314, USA.
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17
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Copar A, Prevec T, Anzic B, Mesar T, Selic L, Vilar M, Solmajer T. Design, synthesis and bioactivity evaluation of tribactam beta lactamase inhibitors. Bioorg Med Chem Lett 2002; 12:971-5. [PMID: 11959006 DOI: 10.1016/s0960-894x(02)00061-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Known carbapenem compounds with inhibitory effect towards beta-lactamase enzymes are formed from bicyclical beta lactam structural scaffolds. On the basis of results from theoretical computational methods and molecular modelling we have designed and developed a synthetic route towards novel, biologically active tricyclic derivatives of carbapenems.
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Affiliation(s)
- Anton Copar
- Lek d.d., Research and Development, Celovska 135, 1526, Ljubljana, Slovenia
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18
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Pernot L, Frénois F, Rybkine T, L'Hermite G, Petrella S, Delettré J, Jarlier V, Collatz E, Sougakoff W. Crystal structures of the class D beta-lactamase OXA-13 in the native form and in complex with meropenem. J Mol Biol 2001; 310:859-74. [PMID: 11453693 DOI: 10.1006/jmbi.2001.4805] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The therapeutic problems posed by class D beta-lactamases, a family of serine enzymes that hydrolyse beta-lactam antibiotics following an acylation-deacylation mechanism, are increased by the very low level of sensitivity of these enzymes to beta-lactamase inhibitors. To gain structural and mechanistic insights to aid the design of new inhibitors, we have determined the crystal structure of OXA-13 from Pseudomonas aeruginosa in the apo form and in complex with the carbapenem meropenem. The native form consisted of a dimer displaying an overall organisation similar to that found in the closely related enzyme OXA-10. In the acyl-enzyme complex, the positioning of the antibiotic appeared to be ensured mainly by (i) the covalent acyl bond and (ii) a strong salt-bridge involving the carboxylate moiety of the drug. Comparison of the structures of OXA-13 in the apo form and in complex with meropenem revealed an unsuspected flexibility in the region of the essential serine 115 residue, with possible consequences for the catalytic properties of the enzyme. In the apo form, the Ser115 side-chain is oriented outside the active site, whereas the general base Lys70 adopts a conformation that seems to be incompatible with the activation of the catalytic water molecule required for the deacylation step. In the OXA-13:meropenem complex, a 3.5 A movement of the backbone of the 114-116 loop towards the side-chain of Lys70 was observed, which seems to be driven by a displacement of the neighbouring 91-104 loop and which results in the repositioning of the side-chain hydroxyl group of Ser115 toward the catalytic centre. Concomitantly, the side-chain of Lys70 is forced to curve in the direction of the deacylating water molecule, which is then strongly bound and activated by this residue. However, a distance of ca 5 A separates the catalytic water molecule from the acyl carbonyl group of meropenem, a structural feature that accounts for the inhibition of OXA-13 by this drug. Finally, the low level of penicillinase activity revealed by the kinetic analysis of OXA-13 could be related to the specific presence in position 73 of a serine residue located close to the general base Lys70, which results in a decrease of the number of hydrogen-bonding interactions stabilising the catalytic water molecule.
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Affiliation(s)
- L Pernot
- Laboratoire de Recherche Moléculaire sur les Antibiotiques (LRMA), Facultés de Médecine Pitié-Salpêtrière and Broussais-Hôtel Dieu, Université Pierre et Marie Curie, 91 bd de l'Hôpital, Paris cedex 13, 75634, France
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19
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Rudgers GW, Palzkill T. Protein minimization by random fragmentation and selection. PROTEIN ENGINEERING 2001; 14:487-92. [PMID: 11522922 DOI: 10.1093/protein/14.7.487] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Protein-protein interactions are involved in most biological processes and are important targets for drug design. Over the past decade, there has been increased interest in the design of small molecules that mimic functional epitopes of protein inhibitors. BLIP is a 165 amino acid protein that is a potent inhibitor of TEM-1 beta-lactamase (K(i) = 0.1 nM). To aid in the development of new inhibitors of beta-lactamase, the gene encoding BLIP was randomly fragmented and DNA segments encoding peptides that retain the ability to bind TEM-1 beta-lactamase were isolated using phage display. The selected peptides revealed a common, overlapping region that includes BLIP residues C30-D49. Synthesis and binding analysis of the C30-D49 peptide indicate that this peptide inhibits TEM-1 beta-lactamase. Therefore, a peptide derivative of BLIP that has been reduced in size by 88% compared with wild-type BLIP retains the ability to bind and inhibit beta-lactamase.
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Affiliation(s)
- G W Rudgers
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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20
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Maveyraud L, Golemi D, Kotra LP, Tranier S, Vakulenko S, Mobashery S, Samama JP. Insights into class D beta-lactamases are revealed by the crystal structure of the OXA10 enzyme from Pseudomonas aeruginosa. Structure 2000; 8:1289-98. [PMID: 11188693 DOI: 10.1016/s0969-2126(00)00534-7] [Citation(s) in RCA: 105] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND beta-lactam antibiotic therapies are commonly challenged by the hydrolytic activities of beta-lactamases in bacteria. These enzymes have been grouped into four classes: A, B, C, and D. Class B beta-lactamases are zinc dependent, and enzymes of classes A, C, and D are transiently acylated on a serine residue in the course of the turnover chemistry. While class A and C beta-lactamases have been extensively characterized by biochemical and structural methods, class D enzymes remain the least studied despite their increasing importance in the clinic. RESULTS The crystal structure of the OXA10 class D beta-lactamase has been solved to 1.66 A resolution from a gold derivative and MAD phasing. This structure reveals that beta-lactamases from classes D and A, despite very poor sequence similarity, share a similar overall fold. An additional beta strand in OXA10 mediates the association into dimers characterized by analytical ultracentrifugation. Major differences are found when comparing the molecular details of the active site of this class D enzyme to the corresponding regions in class A and C beta-lactamases. In the native structure of the OXA10 enzyme solved to 1.8 A, Lys-70 is carbamylated. CONCLUSIONS Several features were revealed by this study: the dimeric structure of the OXA10 beta-lactamase, an extension of the substrate binding site which suggests that class D enzymes may bind other substrates beside beta-lactams, and carbamylation of the active site Lys-70 residue. The CO2-dependent activity of the OXA10 enzyme and the kinetic properties of the natural OXA17 mutant protein suggest possible relationships between carbamylation, inhibition of the enzyme by anions, and biphasic behavior of the enzyme.
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Affiliation(s)
- L Maveyraud
- Groupe de Cristallographie Biologique IPBS-CNRS, Toulouse, France
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