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Avalle B, Padiolleau-Lefevre S, Friboulet A. Structural and Functional Mise en Abyme. Front Mol Biosci 2019; 6:131. [PMID: 31850365 PMCID: PMC6892749 DOI: 10.3389/fmolb.2019.00131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 11/08/2019] [Indexed: 11/13/2022] Open
Affiliation(s)
- Bérangère Avalle
- CNRS UMR 7025, Génie Enzymatique et Cellulaire. Centre de Recherche de Royallieu, Compiègne, France.,Sorbonne Universités, Université de Technologie de Compiègne, Génie Enzymatique et Cellulaire. Centre de Recherche de Royallieu, Compiègne, France
| | - Séverine Padiolleau-Lefevre
- CNRS UMR 7025, Génie Enzymatique et Cellulaire. Centre de Recherche de Royallieu, Compiègne, France.,Sorbonne Universités, Université de Technologie de Compiègne, Génie Enzymatique et Cellulaire. Centre de Recherche de Royallieu, Compiègne, France
| | - Alain Friboulet
- CNRS UMR 7025, Génie Enzymatique et Cellulaire. Centre de Recherche de Royallieu, Compiègne, France.,Sorbonne Universités, Université de Technologie de Compiègne, Génie Enzymatique et Cellulaire. Centre de Recherche de Royallieu, Compiègne, France
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2
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Shahsavarian MA, Chaaya N, Costa N, Boquet D, Atkinson A, Offmann B, Kaveri SV, Lacroix-Desmazes S, Friboulet A, Avalle B, Padiolleau-Lefèvre S. Multitarget selection of catalytic antibodies with β-lactamase activity using phage display. FEBS J 2017; 284:634-653. [PMID: 28075071 DOI: 10.1111/febs.14012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 10/29/2016] [Accepted: 01/09/2017] [Indexed: 01/24/2023]
Abstract
β-lactamase enzymes responsible for bacterial resistance to antibiotics are among the most important health threats to the human population today. Understanding the increasingly vast structural motifs responsible for the catalytic mechanism of β-lactamases will help improve the future design of new generation antibiotics and mechanism-based inhibitors of these enzymes. Here we report the construction of a large murine single chain fragment variable (scFv) phage display library of size 2.7 × 109 with extended diversity by combining different mouse models. We have used two molecularly different inhibitors of the R-TEM β-lactamase as targets for selection of catalytic antibodies with β-lactamase activity. This novel methodology has led to the isolation of five antibody fragments, which are all capable of hydrolyzing the β-lactam ring. Structural modeling of the selected scFv has revealed the presence of different motifs in each of the antibody fragments potentially responsible for their catalytic activity. Our results confirm (a) the validity of using our two target inhibitors for the in vitro selection of catalytic antibodies endowed with β-lactamase activity, and (b) the plasticity of the β-lactamase active site responsible for the wide resistance of these enzymes to clinically available inhibitors and antibiotics.
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Affiliation(s)
- Melody A Shahsavarian
- Génie Enzymatique et Cellulaire (GEC), FRE 3580 CNRS, Université de Technologie de Compiègne, France.,UMR S 1138, Sorbonne Universités, Université Pierre et Marie Curie - Paris VI, France
| | - Nancy Chaaya
- Génie Enzymatique et Cellulaire (GEC), FRE 3580 CNRS, Université de Technologie de Compiègne, France.,UMR S 1138, Sorbonne Universités, Université Pierre et Marie Curie - Paris VI, France
| | - Narciso Costa
- Service de Pharmacologie et d'Immuno-analyse (SPI), IBITECS, CEA, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Didier Boquet
- Service de Pharmacologie et d'Immuno-analyse (SPI), IBITECS, CEA, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Alexandre Atkinson
- Unité Fonctionnalité et Ingénierie des Protéines (UFIP), UMR CNRS 6286, Université de Nantes, France
| | - Bernard Offmann
- Unité Fonctionnalité et Ingénierie des Protéines (UFIP), UMR CNRS 6286, Université de Nantes, France
| | - Srini V Kaveri
- UMR S 1138, Sorbonne Universités, Université Pierre et Marie Curie - Paris VI, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U 1138, Paris, France.,Equipe Immunopathology and Therapeutic Immunointervention, Centre de Recherche des Cordeliers, Paris, France.,International Associated Laboratory IMPACT, Institut National de la Santé et de la Recherche Médicale-France and Indian Council of Medical Research-India, National Institute of Immunohaemotology, Mumbai, India
| | - Sébastien Lacroix-Desmazes
- UMR S 1138, Sorbonne Universités, Université Pierre et Marie Curie - Paris VI, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U 1138, Paris, France.,Equipe Immunopathology and Therapeutic Immunointervention, Centre de Recherche des Cordeliers, Paris, France.,International Associated Laboratory IMPACT, Institut National de la Santé et de la Recherche Médicale-France and Indian Council of Medical Research-India, National Institute of Immunohaemotology, Mumbai, India
| | - Alain Friboulet
- Génie Enzymatique et Cellulaire (GEC), FRE 3580 CNRS, Université de Technologie de Compiègne, France.,UMR S 1138, Sorbonne Universités, Université Pierre et Marie Curie - Paris VI, France
| | - Bérangère Avalle
- Génie Enzymatique et Cellulaire (GEC), FRE 3580 CNRS, Université de Technologie de Compiègne, France.,UMR S 1138, Sorbonne Universités, Université Pierre et Marie Curie - Paris VI, France
| | - Séverine Padiolleau-Lefèvre
- Génie Enzymatique et Cellulaire (GEC), FRE 3580 CNRS, Université de Technologie de Compiègne, France.,UMR S 1138, Sorbonne Universités, Université Pierre et Marie Curie - Paris VI, France
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3
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Identification of peptide inhibitors of penicillinase using a phage display library. Anal Biochem 2016; 494:4-9. [DOI: 10.1016/j.ab.2015.10.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 10/18/2015] [Accepted: 10/21/2015] [Indexed: 12/20/2022]
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4
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Alaybeyoglu B, Akbulut BS, Ozkirimli E. A novel chimeric peptide with antimicrobial activity. J Pept Sci 2015; 21:294-301. [PMID: 25597294 DOI: 10.1002/psc.2739] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Revised: 12/05/2014] [Accepted: 12/12/2014] [Indexed: 11/09/2022]
Abstract
Beta-lactamase-mediated bacterial drug resistance exacerbates the prognosis of infectious diseases, which are sometimes treated with co-administration of beta-lactam type antibiotics and beta-lactamase inhibitors. Antimicrobial peptides are promising broad-spectrum alternatives to conventional antibiotics in this era of evolving bacterial resistance. Peptides based on the Ala46-Tyr51 beta-hairpin loop of beta-lactamase inhibitory protein (BLIP) have been previously shown to inhibit beta-lactamase. Here, our goal was to modify this peptide for improved beta-lactamase inhibition and cellular uptake. Motivated by the cell-penetrating pVEC sequence, which includes a hydrophobic stretch at its N-terminus, our approach involved the addition of LLIIL residues to the inhibitory peptide N-terminus to facilitate uptake. Activity measurements of the peptide based on the 45-53 loop of BLIP for enhanced inhibition verified that the peptide was a competitive beta-lactamase inhibitor with a K(i) value of 58 μM. Incubation of beta-lactam-resistant cells with peptide decreased the number of viable cells, while it had no effect on beta-lactamase-free cells, indicating that this peptide had antimicrobial activity via beta-lactamase inhibition. To elucidate the molecular mechanism by which this peptide moves across the membrane, steered molecular dynamics simulations were carried out. We propose that addition of hydrophobic residues to the N-terminus of the peptide affords a promising strategy in the design of novel antimicrobial peptides not only against beta-lactamase but also for other intracellular targets.
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Affiliation(s)
- Begum Alaybeyoglu
- Chemical Engineering Department, Bogazici University, Bebek, 34342, Istanbul, Turkey
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5
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Ponomarenko N, Chatziefthimiou SD, Kurkova I, Mokrushina Y, Mokrushina Y, Stepanova A, Smirnov I, Avakyan M, Bobik T, Mamedov A, Mitkevich V, Belogurov A, Fedorova OS, Dubina M, Golovin A, Lamzin V, Friboulet A, Makarov AA, Wilmanns M, Gabibov A. Role of κ→λ light-chain constant-domain switch in the structure and functionality of A17 reactibody. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:708-19. [PMID: 24598740 PMCID: PMC3949517 DOI: 10.1107/s1399004713032446] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 11/27/2013] [Indexed: 11/10/2022]
Abstract
The engineering of catalytic function in antibodies requires precise information on their structure. Here, results are presented that show how the antibody domain structure affects its functionality. The previously designed organophosphate-metabolizing reactibody A17 has been re-engineered by replacing its constant κ light chain by the λ chain (A17λ), and the X-ray structure of A17λ has been determined at 1.95 Å resolution. It was found that compared with A17κ the active centre of A17λ is displaced, stabilized and made more rigid owing to interdomain interactions involving the CDR loops from the VL and VH domains. These VL/VH domains also have lower mobility, as deduced from the atomic displacement parameters of the crystal structure. The antibody elbow angle is decreased to 126° compared with 138° in A17κ. These structural differences account for the subtle changes in catalytic efficiency and thermodynamic parameters determined with two organophosphate ligands, as well as in the affinity for peptide substrates selected from a combinatorial cyclic peptide library, between the A17κ and A17λ variants. The data presented will be of interest and relevance to researchers dealing with the design of antibodies with tailor-made functions.
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Affiliation(s)
- Natalia Ponomarenko
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117871, Russian Federation
| | - Spyros D. Chatziefthimiou
- European Molecular Biology Laboratory, Hamburg Unit, c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
| | - Inna Kurkova
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117871, Russian Federation
| | - Yuliana Mokrushina
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117871, Russian Federation
| | - Yuliana Mokrushina
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117871, Russian Federation
| | - Anastasiya Stepanova
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117871, Russian Federation
| | - Ivan Smirnov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117871, Russian Federation
| | - Marat Avakyan
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117871, Russian Federation
| | - Tatyana Bobik
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117871, Russian Federation
| | - Azad Mamedov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117871, Russian Federation
| | - Vladimir Mitkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russian Federation
| | - Alexey Belogurov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117871, Russian Federation
- Institute of Gene Biology, Moscow 117334, Russian Federation
| | - Olga S. Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, Russian Federation
| | - Michael Dubina
- St Petersburg Academic University, St Petersburg 194021, Russian Federation
| | - Andrey Golovin
- Lomonosov Moscow State University, Moscow 119991, Russian Federation
| | - Victor Lamzin
- European Molecular Biology Laboratory, Hamburg Unit, c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
| | - Alain Friboulet
- Université de Technologie de Compiègne, Unité Mixte de Recherche 6022, Centre National de la Recherche Scientifique, 60205 Compiègne, France
| | - Alexander A. Makarov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russian Federation
| | - Matthias Wilmanns
- European Molecular Biology Laboratory, Hamburg Unit, c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
| | - Alexander Gabibov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117871, Russian Federation
- Institute of Gene Biology, Moscow 117334, Russian Federation
- Lomonosov Moscow State University, Moscow 119991, Russian Federation
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6
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Screening of peptide ligands for pyrroloquinoline quinone glucose dehydrogenase using antagonistic template-based biopanning. Int J Mol Sci 2013; 14:23244-56. [PMID: 24287902 PMCID: PMC3876041 DOI: 10.3390/ijms141223244] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 10/31/2013] [Accepted: 11/11/2013] [Indexed: 01/05/2023] Open
Abstract
We have developed a novel method, antagonistic template-based biopanning, for screening peptide ligands specifically recognizing local tertiary protein structures. We chose water-soluble pyrroloquinoline quinone (PQQ) glucose dehydrogenase (GDH-B) as a model enzyme for this screening. Two GDH-B mutants were constructed as antagonistic templates; these have some point mutations to induce disruption of local tertiary structures within the loop regions that are located at near glucose-binding pocket. Using phage display, we selected 12-mer peptides that specifically bound to wild-type GDH-B but not to the antagonistic templates. Consequently, a peptide ligand showing inhibitory activity against GDH-B was obtained. These results demonstrate that the antagonistic template-based biopanning is useful for screening peptide ligands recognizing the specific local tertiary structure of proteins.
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7
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Efficient refolding of a recombinant abzyme : structural and catalytic characterizations. Appl Microbiol Biotechnol 2012; 97:7721-31. [PMID: 23250220 DOI: 10.1007/s00253-012-4600-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 11/12/2012] [Accepted: 11/15/2012] [Indexed: 10/27/2022]
Abstract
Catalytic antibodies are currently being investigated in order to understand their role under physio-pathological situations. To this end, the knowledge of structure-function relationships is of great interest. Recombinant scFv fragments are smaller and easier to genetically manipulate than whole antibodies, making them well suited for this kind of study. Nevertheless they are often described as proteins being laborious to produce. This paper describes a highly efficient method to produce large quantities of refolded soluble catalytic scFv. For the first time, the functionality of a refolded catalytic scFv displaying a β-lactamase activity has been validated by three approaches: (1) use of circular dichroism to ensure that the refolded had secondary structure consistent with a native scFv fold, (2) development of enzyme-linked immunosorbant assay and surface plasmon resonance (SPR) approaches for testing that the binding characteristics of an inhibitory peptide have been retained, and (3) proof of the subtle catalytic properties conservation through the development of a new sensitive catalytic assay using a fluorogenic substrate.
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8
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Phichith D, Bun S, Padiolleau-Lefevre S, Guellier A, Banh S, Galleni M, Frere JM, Thomas D, Friboulet A, Avalle B. Novel peptide inhibiting both TEM-1 β-lactamase and penicillin-binding proteins. FEBS J 2010; 277:4965-72. [DOI: 10.1111/j.1742-4658.2010.07906.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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9
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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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10
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Wootla B, Dasgupta S, Mallet V, Kazatchkine MD, Nagaraja V, Friboulet A, Kaveri SV, Lacroix-Desmazes S. Physiopathology of catalytic antibodies: the case for factor VIII-hydrolyzing immunoglobulin G. Blood Coagul Fibrinolysis 2007; 17:229-34. [PMID: 16651863 DOI: 10.1097/01.mbc.0000224840.40839.5a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Antibodies that are able to catalyze the antigen for which they are specific are produced spontaneously by the immune system. Catalytic immunoglobulins (Igs) both of the IgM and IgG isotypes have been detected in the serum of healthy donors, where they have been proposed to participate in the removal of metabolic waste and in the defense of the organism against invading pathogens. Conversely, antigen-specific hydrolytic IgG have been reported in a number of inflammatory, autoimmune and neoplastic disorders: their pathogenic effects have been demonstrated occasionally. The pathophysiological relevance of catalytic antibodies thus remains an elusive issue. Through the description of the pro-coagulation factor VIII as a model target antigen for catalytic antibodies, we propose that catalytic antibodies have either a beneficial or a deleterious role depending on the physiopathological context. Physiology thus relies on a delicate equilibrium between the levels of soluble target antigen and that of antigen-specific hydrolyzing immunoglobulins. Indeed, in patients with hemophilia A, in whom endogenous factor VIII is deficient or missing and exogenous factor VIII needs to be administered to treat hemorrhagic events, the development of factor VIII-hydrolyzing IgG that inactivate the therapeutically administered factor VIII, may reveal deleterious. In contrast, in a situation in which excess factor VIII may be detrimental and lead to excessive coagulation, disseminated thrombosis and organ ischemia, as seen in severe sepsis, our recent data suggest that the presence of factor VIII-hydrolyzing IgG may be beneficial to the patient.
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Affiliation(s)
- Bharath Wootla
- INSERM UMRS 681, Universite Pierre & Marie Curie, UPMC-Paris 6/Institut des cordeliers, France
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Abstract
In the year 2003 there was a 17% increase in the number of publications citing work performed using optical biosensor technology compared with the previous year. We collated the 962 total papers for 2003, identified the geographical regions where the work was performed, highlighted the instrument types on which it was carried out, and segregated the papers by biological system. In this overview, we spotlight 13 papers that should be on everyone's 'must read' list for 2003 and provide examples of how to identify and interpret high-quality biosensor data. Although we still find that the literature is replete with poorly performed experiments, over-interpreted results and a general lack of understanding of data analysis, we are optimistic that these shortcomings will be addressed as biosensor technology continues to mature.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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