1
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Gomes LGR, Dutra JCF, Profeta R, Dias MV, García GJY, Rodrigues DLN, Goés Neto A, Aburjaile FF, Tiwari S, Soares SC, Azevedo V, Jaiswal AK. Systematic review of reverse vaccinology and immunoinformatics data for non-viral sexually transmitted infections. AN ACAD BRAS CIENC 2023; 95:e20230617. [PMID: 38055447 DOI: 10.1590/0001-3765202320230617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 08/27/2023] [Indexed: 12/08/2023] Open
Abstract
Sexually Transmitted Infections (STIs) are a public health burden rising in developed and developing nations. The World Health Organization estimates nearly 374 million new cases of curable STIs yearly. Global efforts to control their spread have been insufficient in fulfilling their objective. As there is no vaccine for many of these infections, these efforts are focused on education and condom distribution. The development of vaccines for STIs is vital for successfully halting their spread. The field of immunoinformatics is a powerful new tool for vaccine development, allowing for the identification of vaccine candidates within a bacterium's genome and allowing for the design of new genome-based vaccine peptides. The goal of this review was to evaluate the usage of immunoinformatics in research focused on non-viral STIs, identifying fields where research efforts are concentrated. Here we describe gaps in applying these techniques, as in the case of Treponema pallidum and Trichomonas vaginalis.
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Affiliation(s)
- Lucas Gabriel R Gomes
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Laboratório de Genética Celular e Molecular (LGCM), Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Joyce C F Dutra
- Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Microbiologia, Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Rodrigo Profeta
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Laboratório de Genética Celular e Molecular (LGCM), Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Mariana V Dias
- Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Glen J Y García
- Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Bioinformática, Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Diego Lucas N Rodrigues
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Laboratório de Genética Celular e Molecular (LGCM), Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
- Universidade Federal de Minas Gerais (UFMG), Escola de Veterinária, Departamento de Medicina Veterinária, Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Aristóteles Goés Neto
- Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Microbiologia, Laboratório de Biologia Molecular e Computacional de Fungos, Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Flávia F Aburjaile
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Laboratório de Genética Celular e Molecular (LGCM), Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
- Universidade Federal de Minas Gerais (UFMG), Escola de Veterinária, Departamento de Medicina Veterinária, Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Sandeep Tiwari
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Laboratório de Genética Celular e Molecular (LGCM), Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
- Universidade Federal da Bahia, Instituto de Biologia, Rua Barão de Jeremoabo, s/n, Ondina, 40170-115 Salvador, BA, Brazil
- Universidade Federal da Bahia, Instituto de Ciências da Saúde, Av. Reitor Miguel Calmon, s/n, Vale do Canela, 40110-902 Salvador, BA, Brazil
| | - Siomar C Soares
- Universidade Federal do Triângulo Mineiro (UFTM), Instituto de Ciências Biológicas e Naturais, Departamento de Microbiologia, Imunologia, e Parasitologia, Rua Vigário Carlos, 100, Abadia, 38025-180 Uberaba, MG, Brazil
| | - Vasco Azevedo
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Laboratório de Genética Celular e Molecular (LGCM), Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Arun K Jaiswal
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Laboratório de Genética Celular e Molecular (LGCM), Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
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2
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Capelli R, Serapian SA, Colombo G. Computational Epitope Prediction and Design for Antibody Development and Detection. Methods Mol Biol 2023; 2552:255-266. [PMID: 36346596 DOI: 10.1007/978-1-0716-2609-2_13] [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] [Indexed: 06/16/2023]
Abstract
The design of optimized protein antigens is a fundamental step in the development of new vaccine candidates and in the detection of therapeutic antibodies. A fundamental prerequisite is the identification of antigenic regions that are most prone to interact with antibodies, namely, B-cell epitopes. Here, we describe an efficient structure-based computational method for epitope prediction, called MLCE. In this approach, all that is required is the 3D structure of the antigen of interest. MLCE can be applied to glycosylated proteins, facilitating the identification of immunoreactive versus immune-shielding carbohydrates.
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Affiliation(s)
- Riccardo Capelli
- SCITEC-CNR, Milan, Italy
- Politecnico di Torino, Department of Applied Science and Technology, Torino, Italy
| | | | - Giorgio Colombo
- SCITEC-CNR, Milan, Italy.
- Università di Pavia, Dipartimento di Chimica, Pavia, Italy.
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3
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Triveri A, Serapian SA, Marchetti F, Doria F, Pavoni S, Cinquini F, Moroni E, Rasola A, Frigerio F, Colombo G. SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: A Computational Model of Epitope Loss in Variants of Concern. J Chem Inf Model 2021; 61:4687-4700. [PMID: 34468141 PMCID: PMC8479857 DOI: 10.1021/acs.jcim.1c00857] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Indexed: 12/30/2022]
Abstract
The SARS-CoV-2 spike (S) protein is exposed on the viral surface and is the first point of contact between the virus and the host. For these reasons it represents the prime target for Covid-19 vaccines. In recent months, variants of this protein have started to emerge. Their ability to reduce or evade recognition by S-targeting antibodies poses a threat to immunological treatments and raises concerns for their consequences on vaccine efficacy. To develop a model able to predict the potential impact of S-protein mutations on antibody binding sites, we performed unbiased multi-microsecond molecular dynamics of several glycosylated S-protein variants and applied a straightforward structure-dynamics-energy based strategy to predict potential changes in immunogenic regions on each variant. We recover known epitopes on the reference D614G sequence. By comparing our results, obtained on isolated S-proteins in solution, to recently published data on antibody binding and reactivity in new S variants, we directly show that modifications in the S-protein consistently translate into the loss of potentially immunoreactive regions. Our findings can thus be qualitatively reconnected to the experimentally characterized decreased ability of some of the Abs elicited against the dominant S-sequence to recognize variants. While based on the study of SARS-CoV-2 spike variants, our computational epitope-prediction strategy is portable and could be applied to study immunoreactivity in mutants of proteins of interest whose structures have been characterized, helping the development/selection of vaccines and antibodies able to control emerging variants.
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Affiliation(s)
- Alice Triveri
- Department
of Chemistry, University of Pavia, Via Taramelli 12, Pavia 27100, Italy
| | - Stefano A. Serapian
- Department
of Chemistry, University of Pavia, Via Taramelli 12, Pavia 27100, Italy
| | - Filippo Marchetti
- Department
of Chemistry, University of Pavia, Via Taramelli 12, Pavia 27100, Italy
| | - Filippo Doria
- Department
of Chemistry, University of Pavia, Via Taramelli 12, Pavia 27100, Italy
| | - Silvia Pavoni
- Department
of Physical Chemistry, R&D Eni SpA, Via Maritano 27, San Donato Milanese, Milan 20097, Italy
| | - Fabrizio Cinquini
- Upstream
& Technical Services—TECS/STES—Eni Spa, Via Emilia 1, San
Donato Milanese, Milan 20097, Italy
| | - Elisabetta Moroni
- Istituto
di Scienze e Tecnologie Chimiche “Giulio Natta”—SCITEC, CNR Via Mario Bianco 9, Milano 20131, Italy
| | - Andrea Rasola
- Department
of Biomedical Sciences, University of Padua, Viale G. Colombo 3, Padova 35131, Italy
| | - Francesco Frigerio
- Department
of Physical Chemistry, R&D Eni SpA, Via Maritano 27, San Donato Milanese, Milan 20097, Italy
| | - Giorgio Colombo
- Department
of Chemistry, University of Pavia, Via Taramelli 12, Pavia 27100, Italy
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4
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Serapian S, Marchetti F, Triveri A, Morra G, Meli M, Moroni E, Sautto GA, Rasola A, Colombo G. The Answer Lies in the Energy: How Simple Atomistic Molecular Dynamics Simulations May Hold the Key to Epitope Prediction on the Fully Glycosylated SARS-CoV-2 Spike Protein. J Phys Chem Lett 2020; 11:8084-8093. [PMID: 32885971 PMCID: PMC7491317 DOI: 10.1021/acs.jpclett.0c02341] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/04/2020] [Indexed: 05/05/2023]
Abstract
SARS-CoV-2 is a health threat with dire socioeconomical consequences. As the crucial mediator of infection, the viral glycosylated spike protein (S) has attracted the most attention and is at the center of efforts to develop therapeutics and diagnostics. Herein, we use an original decomposition approach to identify energetically uncoupled substructures as antibody binding sites on the fully glycosylated S. Crucially, all that is required are unbiased MD simulations; no prior knowledge of binding properties or ad hoc parameter combinations is needed. Our results are validated by experimentally confirmed structures of S in complex with anti- or nanobodies. We identify poorly coupled subdomains that are poised to host (several) epitopes and potentially involved in large functional conformational transitions. Moreover, we detect two distinct behaviors for glycans: those with stronger energetic coupling are structurally relevant and protect underlying peptidic epitopes, and those with weaker coupling could themselves be prone to antibody recognition.
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Affiliation(s)
- Stefano
A. Serapian
- Department
of Chemistry, University of Pavia, viale Taramelli 12, 27100 Pavia, Italy
| | - Filippo Marchetti
- Department
of Chemistry, University of Pavia, viale Taramelli 12, 27100 Pavia, Italy
- Department
of Chemistry, University of Milan, via Venezian 21, 20133 Milano, Italy
| | - Alice Triveri
- Department
of Chemistry, University of Pavia, viale Taramelli 12, 27100 Pavia, Italy
| | - Giulia Morra
- SCITEC−CNR, via Mario Bianco 9, 20131 Milano, Italy
| | | | | | - Giuseppe A. Sautto
- Center
for Vaccines and Immunology, Department of Infectious Diseases, University of Georgia, 501 D. W. Brooks Drive, Athens, Georgia 30602, United States
| | - Andrea Rasola
- Dipartimento
di Scienze Biomediche, Università
di Padova, viale G. Colombo
3, 35131 Padova, Italy
| | - Giorgio Colombo
- Department
of Chemistry, University of Pavia, viale Taramelli 12, 27100 Pavia, Italy
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5
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Cretich M, Gori A, D'Annessa I, Chiari M, Colombo G. Peptides for Infectious Diseases: From Probe Design to Diagnostic Microarrays. Antibodies (Basel) 2019; 8:E23. [PMID: 31544829 PMCID: PMC6640701 DOI: 10.3390/antib8010023] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 02/28/2019] [Accepted: 03/04/2019] [Indexed: 01/03/2023] Open
Abstract
Peptides and peptidomimetics have attracted revived interest regarding their applications in chemical biology over the last few years. Their chemical versatility, synthetic accessibility and the ease of storage and management compared to full proteins have made peptides particularly interesting in diagnostic applications, where they proved to efficiently recapitulate the molecular recognition properties of larger protein antigens, and were proven to be able to capture antibodies circulating in the plasma and serum of patients previously exposed to bacterial or viral infections. Here, we describe the development, integration and application of strategies for computational prediction and design, advanced chemical synthesis, and diagnostic deployment in multiplexed assays of peptide-based materials which are able to bind antibodies of diagnostic as well as therapeutic interest. By presenting successful applications of such an integrated strategy, we argue that they will have an ever-increasing role in both basic and clinical realms of research, where important advances can be expected in the next few years.
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Affiliation(s)
- Marina Cretich
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco 9, 20131 Milano, Italy.
| | - Alessandro Gori
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco 9, 20131 Milano, Italy.
| | - Ilda D'Annessa
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco 9, 20131 Milano, Italy.
| | - Marcella Chiari
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco 9, 20131 Milano, Italy.
| | - Giorgio Colombo
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco 9, 20131 Milano, Italy.
- Dipartimento di Chimica, Università di Pavia, V.le Taramelli 12, 27100 Pavia, Italy.
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6
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Deka RK, Liu WZ, Tso SC, Norgard MV, Brautigam CA. Biophysical insights into a highly selective l-arginine-binding lipoprotein of a pathogenic treponeme. Protein Sci 2018; 27:2037-2050. [PMID: 30242931 DOI: 10.1002/pro.3510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 09/10/2018] [Accepted: 09/11/2018] [Indexed: 11/11/2022]
Abstract
Biophysical and biochemical studies on the lipoproteins and other periplasmic proteins from the spirochetal species Treponema pallidum have yielded numerous insights into the functioning of the organism's peculiar membrane organization, its nutritional requirements, and intermediary metabolism. However, not all T. pallidum proteins have proven to be amenable to biophysical studies. One such recalcitrant protein is Tp0309, a putative polar-amino-acid-binding protein of an ABC transporter system. To gain further information on its possible function, a homolog of the protein from the related species T. vincentii was used as a surrogate. This protein, Tv2483, was crystallized, resulting in the determination of its crystal structure at a resolution of 1.75 Å. The protein has a typical fold for a ligand-binding protein, and a single molecule of l-arginine was bound between its two lobes. Differential scanning fluorimetry and isothermal titration calorimetry experiments confirmed that l-arginine bound to the protein with unusually high selectivity. However, further comparison to Tp0309 showed differences in key amino-acid-binding residues may impart an alternate specificity for the T. pallidum protein.
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Affiliation(s)
- Ranjit K Deka
- Departments of Microbiology, 5323 Harry Hines Blvd., Dallas, Texas, 75390
| | - Wei Z Liu
- Departments of Microbiology, 5323 Harry Hines Blvd., Dallas, Texas, 75390
| | - Shih-Chia Tso
- Departments of Biophysics, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas, 75390
| | - Michael V Norgard
- Departments of Microbiology, 5323 Harry Hines Blvd., Dallas, Texas, 75390
| | - Chad A Brautigam
- Departments of Microbiology, 5323 Harry Hines Blvd., Dallas, Texas, 75390.,Departments of Biophysics, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas, 75390
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7
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Ferraro M, Colombo G. Targeting Difficult Protein-Protein Interactions with Plain and General Computational Approaches. Molecules 2018; 23:molecules23092256. [PMID: 30181519 PMCID: PMC6225287 DOI: 10.3390/molecules23092256] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 08/27/2018] [Accepted: 08/31/2018] [Indexed: 11/21/2022] Open
Abstract
Investigating protein-protein interactions (PPIs) holds great potential for therapeutic applications, since they mediate intricate cell signaling networks in physiological and disease states. However, their complex and multifaceted nature poses a major challenge for biochemistry and medicinal chemistry, thereby limiting the druggability of biological partners participating in PPIs. Molecular Dynamics (MD) provides a solid framework to study the reciprocal shaping of proteins’ interacting surfaces. Here, we review successful applications of MD-based methods developed in our group to predict interfacial areas involved in PPIs of pharmaceutical interest. We report two interesting examples of how structural, dynamic and energetic information can be combined into efficient strategies which, complemented by experiments, can lead to the design of new small molecules with promising activities against cancer and infections. Our advances in targeting key PPIs in angiogenic pathways and antigen-antibody recognition events will be discussed for their role in drug discovery and chemical biology.
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Affiliation(s)
- Mariarosaria Ferraro
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy.
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy.
- Dipartimento di Chimica, Università di Pavia, V.le Taramelli 10, 27100 Pavia, Italy.
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8
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Yeh HY, Kojima K, Mobley JA. Epitope mapping of Salmonella flagellar hook-associated protein, FlgK, with mass spectrometry-based immuno-capture proteomics using chicken (Gallus gallus domesticus) sera. Vet Immunol Immunopathol 2018; 201:20-25. [DOI: 10.1016/j.vetimm.2018.05.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 03/19/2018] [Accepted: 05/13/2018] [Indexed: 12/13/2022]
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9
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Sola L, Gagni P, D’Annessa I, Capelli R, Bertino C, Romanato A, Damin F, Bergamaschi G, Marchisio E, Cuzzocrea A, Bombaci M, Grifantini R, Chiari M, Colombo G, Gori A, Cretich M. Enhancing Antibody Serodiagnosis Using a Controlled Peptide Coimmobilization Strategy. ACS Infect Dis 2018; 4:998-1006. [PMID: 29570266 DOI: 10.1021/acsinfecdis.8b00014] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Antigen immunoreactivity is often determined by surface regions defined by the 3D juxtapositions of amino acids stretches that are not continuous in the linear sequence. As such, mimicking an antigen immunoreactivity by means of putative linear peptide epitopes for diagnostic purposes is not trivial. Here we present a straightforward and robust method to extend the reach of immune-diagnostic probes design by copresenting peptides belonging to the same antigenic surface. In this case study focused on a computationally predicted Zika virus NS1 protein putative antigenic region, we reached a diagnostic confidence by the oriented and spatially controlled coimmobilization of peptide sequences found adjacent within the protein fold, that cooperatively interacted to provide enhanced immunoreactivity with respect to single linear epitopes. Through our method, we were able to differentiate Zika infected individuals from healthy controls. Remarkably, our strategy fits well with the requirements to build high-throughput screening platforms of linear and mixed peptide libraries, and it could possibly facilitate the rapid identification of conformational immunoreactive regions.
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Affiliation(s)
- Laura Sola
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
| | - Paola Gagni
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
| | - Ilda D’Annessa
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
| | - Riccardo Capelli
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
| | - Camilla Bertino
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
| | - Alessandro Romanato
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
| | - Francesco Damin
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
| | - Greta Bergamaschi
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
| | - Edoardo Marchisio
- Diagnostic Bioprobes s.r.l. (DiaPro), via G. Carducci 27, 20090 Sesto San Giovanni, Italy
| | - Angela Cuzzocrea
- Diagnostic Bioprobes s.r.l. (DiaPro), via G. Carducci 27, 20090 Sesto San Giovanni, Italy
| | - Mauro Bombaci
- Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi” (INGM), Via Francesco Sforza. 35, 20122 Milano, Italy
| | - Renata Grifantini
- Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi” (INGM), Via Francesco Sforza. 35, 20122 Milano, Italy
| | - Marcella Chiari
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
| | - Giorgio Colombo
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
- Dipartimento di Chimica, Università di Pavia, V.le Taramelli 12, 27100 Pavia, Italy
| | - Alessandro Gori
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
| | - Marina Cretich
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
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10
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Heterogeneous expression of Chlamydia pneumoniae antigen candidates and high-level soluble expression of its inclusion membrane proteins in Escherichia coli. Mol Cell Toxicol 2017. [DOI: 10.1007/s13273-017-0043-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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11
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Candreva ÁM, Ferrer-Navarro M, Bronsoms S, Quiroga A, Curciarello R, Cauerhff A, Petruccelli S, Docena GH, Trejo SA. Identification of cross-reactive B-cell epitopes between Bos d 9.0101(Bos Taurus) and Gly m 5.0101 (Glycine max) by epitope mapping MALDI-TOF MS. Proteomics 2017; 17:1700069. [PMID: 28643898 DOI: 10.1002/pmic.201700069] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 05/23/2017] [Accepted: 06/02/2017] [Indexed: 11/08/2022]
Abstract
Exposure to cow's milk constitutes one of the most common causes of food allergy. In addition, exposure to soy proteins has become relevant in a restricted proportion of milk allergic pediatric patients treated with soy formulae as a dairy substitute, because of the cross-allergenicity described between soy and milk proteins. We have previously identified several cross-reactive allergens between milk and soy that may explain this intolerance. The purpose of the present work was to identify epitopes in the purified αS1-casein and the recombinant soy allergen Gly m 5.0101 (Gly m 5) using an α-casein-specific monoclonal antibody (1D5 mAb) through two different approaches for epitope mapping, to understand cross-reactivity between milk and soy. The 1D5 mAb was immobilized onto magnetic beads, incubated with the peptide mixture previously obtained by enzymatic digestion of the allergens, and the captured peptides were identified by MALDI-TOF MS analysis. On a second approach, the peptide mixture was resolved by RP-HPLC and immunodominant peptides were identified by dot blot with the mAb. Finally, recognized peptides were sequenced by MALDI-TOF MS. This novel MS based approach led us to identify and characterize four peptides on α-casein and three peptides on Gly m 5 with a common core motif. Information obtained from these cross-reactive epitopes allows us to gain valuable insight into the molecular mechanisms of cross-reactivity, to further develop new and more effective vaccines for food allergy.
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Affiliation(s)
- Ángela María Candreva
- Centro de Investigación y Desarrollo en Criotecnología de Alimentos (CIDCA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata (UNLP), La Plata, Argentina
- Instituto de Estudios Inmunológicos y Fisiopatológicos (IIFP), CONICET, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata (UNLP), La Plata, Argentina
| | - Mario Ferrer-Navarro
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Silvia Bronsoms
- Servei de Proteomica i Biologia Estructural (SePBioEs), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Alejandra Quiroga
- Centro de Investigación y Desarrollo en Criotecnología de Alimentos (CIDCA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata (UNLP), La Plata, Argentina
| | - Renata Curciarello
- Instituto de Estudios Inmunológicos y Fisiopatológicos (IIFP), CONICET, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata (UNLP), La Plata, Argentina
| | - Ana Cauerhff
- Laboratorio de Biología Molecular y Celular, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (UBA), CONICET, Buenos Aires, Argentina
| | - Silvana Petruccelli
- Centro de Investigación y Desarrollo en Criotecnología de Alimentos (CIDCA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata (UNLP), La Plata, Argentina
| | - Guillermo Horacio Docena
- Instituto de Estudios Inmunológicos y Fisiopatológicos (IIFP), CONICET, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata (UNLP), La Plata, Argentina
| | - Sebastián Alejandro Trejo
- Servei de Proteomica i Biologia Estructural (SePBioEs), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- Instituto Multidisciplinario de Biología Celular (IMBICE), CONICET, Comisión de Investigaciones Científicas de la Pcia. de Buenos Aires (CIC), Universidad Nacional de La Plata (UNLP), La Plata, Argentina
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12
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Gourlay L, Peri C, Bolognesi M, Colombo G. Structure and Computation in Immunoreagent Design: From Diagnostics to Vaccines. Trends Biotechnol 2017; 35:1208-1220. [PMID: 28739221 DOI: 10.1016/j.tibtech.2017.06.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 06/28/2017] [Accepted: 06/30/2017] [Indexed: 11/26/2022]
Abstract
Novel immunological tools for efficient diagnosis and treatment of emerging infections are urgently required. Advances in the diagnostic and vaccine development fields are continuously progressing, with reverse vaccinology and structural vaccinology (SV) methods for antigen identification and structure-based antigen (re)design playing increasingly relevant roles. SV, in particular, is predicted to be the front-runner in the future development of diagnostics and vaccines targeting challenging diseases such as AIDS and cancer. We review state-of-the-art methodologies for structure-based epitope identification and antigen design, with specific applicative examples. We highlight the implications of such methods for the engineering of biomolecules with improved immunological properties, potential diagnostic and/or therapeutic uses, and discuss the perspectives of structure-based rational design for the production of advanced immunoreagents.
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Affiliation(s)
- Louise Gourlay
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Claudio Peri
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Via Mario Bianco, 9, 20131, Milan, Italy
| | - Martino Bolognesi
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, 20133, Milan, Italy; Centro di Ricerca Pediatrica Romeo ed Enrica Invernizzi, Università di Milano, Milan, Italy.
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Via Mario Bianco, 9, 20131, Milan, Italy.
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13
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Gori A, Bolognesi M, Colombo G, Gourlay LJ. Structural Vaccinology for Melioidosis Vaccine Design and Immunodiagnostics. CURRENT TROPICAL MEDICINE REPORTS 2017. [DOI: 10.1007/s40475-017-0117-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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14
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Capelli R, Marchetti F, Tiana G, Colombo G. SAGE: A Fast Computational Tool for Linear Epitope Grafting onto a Foreign Protein Scaffold. J Chem Inf Model 2017; 57:6-10. [PMID: 27992203 DOI: 10.1021/acs.jcim.6b00584] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Computational design is becoming a driving force of structural vaccinology, whereby protein antigens are engineered to generate new biomolecules with optimized immunological properties. In particular, the design of new proteins that contain multiple, different epitopes can potentially provide novel highly efficient vaccine candidates. In this context, epitope grafting, which entails the transplantation of an antibody recognition motif from one protein onto a different protein scaffold (possibly containing other immunoreactive sequences) holds great promise for the realization of superantigens. Herein, we present SAGE (strategy for alignment and grafting of epitopes), an automated computational tool for the implantation of immunogenic epitopes onto a given scaffold. It is based on the comparison between the expected secondary structures of the candidates to be grafted with all the secondary structures in the target scaffold. Evaluating the differences both in sequence and in structure between the epitope and the scaffold returns a ranking of most probable molecules containing the new antigenic sequence. We validate this approach identifying the grafting positions obtained in previous works by experimental and computational methods, proving an efficient, flexible, and fast tool to perform the initial scanning for epitope grafting. This approach is fully general and may be applied to any target antigen and candidate epitopes with known 3D structures.
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Affiliation(s)
- Riccardo Capelli
- Center for Complexity & Biosystems and Dipartimento di Fisica, Università degli Studi di Milano and INFN , via Celoria 16, 20133 Milan, Italy.,Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche , via Mario Bianco 9, 20131 Milan, Italy
| | - Filippo Marchetti
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche , via Mario Bianco 9, 20131 Milan, Italy
| | - Guido Tiana
- Center for Complexity & Biosystems and Dipartimento di Fisica, Università degli Studi di Milano and INFN , via Celoria 16, 20133 Milan, Italy
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche , via Mario Bianco 9, 20131 Milan, Italy
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15
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Peri C, Gori A, Gagni P, Sola L, Girelli D, Sottotetti S, Cariani L, Chiari M, Cretich M, Colombo G. Evolving serodiagnostics by rationally designed peptide arrays: the Burkholderia paradigm in Cystic Fibrosis. Sci Rep 2016; 6:32873. [PMID: 27615705 PMCID: PMC5018727 DOI: 10.1038/srep32873] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 08/16/2016] [Indexed: 01/05/2023] Open
Abstract
Efficient diagnosis of emerging and novel bacterial infections is fundamental to guide decisions on therapeutic treatments. Here, we engineered a novel rational strategy to design peptide microarray platforms, which combines structural and genomic analyses to predict the binding interfaces between diverse protein antigens and antibodies against Burkholderia cepacia complex infections present in the sera of Cystic Fibrosis (CF) patients. The predicted binding interfaces on the antigens are synthesized in the form of isolated peptides and chemically optimized for controlled orientation on the surface. Our platform displays multiple Burkholderia-related epitopes and is shown to diagnose infected individuals even in presence of superinfections caused by other prevalent CF pathogens, with limited cost and time requirements. Moreover, our data point out that the specific patterns determined by combined probe responses might provide a characterization of Burkholderia infections even at the subtype level (genomovars). The method is general and immediately applicable to other bacteria.
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Affiliation(s)
- Claudio Peri
- Istituto di Chimica del Riconoscimento Molecolare, ICRM, CNR. Via Mario Bianco 9, 20131, Milano (Italy)
| | - Alessandro Gori
- Istituto di Chimica del Riconoscimento Molecolare, ICRM, CNR. Via Mario Bianco 9, 20131, Milano (Italy)
| | - Paola Gagni
- Istituto di Chimica del Riconoscimento Molecolare, ICRM, CNR. Via Mario Bianco 9, 20131, Milano (Italy)
| | - Laura Sola
- Istituto di Chimica del Riconoscimento Molecolare, ICRM, CNR. Via Mario Bianco 9, 20131, Milano (Italy)
| | - Daniela Girelli
- Cystic Fibrosis Microbiology Laboratory, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, via San Barnaba 8, 20122, Milano (Italy)
| | - Samantha Sottotetti
- Cystic Fibrosis Microbiology Laboratory, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, via San Barnaba 8, 20122, Milano (Italy)
| | - Lisa Cariani
- Cystic Fibrosis Microbiology Laboratory, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, via San Barnaba 8, 20122, Milano (Italy)
| | - Marcella Chiari
- Istituto di Chimica del Riconoscimento Molecolare, ICRM, CNR. Via Mario Bianco 9, 20131, Milano (Italy)
| | - Marina Cretich
- Istituto di Chimica del Riconoscimento Molecolare, ICRM, CNR. Via Mario Bianco 9, 20131, Milano (Italy)
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, ICRM, CNR. Via Mario Bianco 9, 20131, Milano (Italy)
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16
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Rey-Ladino J, Ross AGP, Cripps AW. Immunity, immunopathology, and human vaccine development against sexually transmitted Chlamydia trachomatis. Hum Vaccin Immunother 2016; 10:2664-73. [PMID: 25483666 PMCID: PMC4977452 DOI: 10.4161/hv.29683] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
This review examines the immunity, immunopathology, and contemporary problems of vaccine development against sexually transmitted Chlamydia trachomatis. Despite improved surveillance and treatment initiatives, the incidence of C. trachomatis infection has increased dramatically over the past 30 years in both the developed and developing world. Studies in animal models have shown that protective immunity to C. trachomatis is largely mediated by Th1 T cells producing IFN-γ which is needed to prevent dissemination of infection. Similar protection appears to develop in humans but in contrast to mice, immunity in humans may take years to develop. Animal studies and evidence from human infection indicate that immunity to C. trachomatis is accompanied by significant pathology in the upper genital tract. Although no credible evidence is currently available to indicate that autoimmunity plays a role, nevertheless, this underscores the necessity to design vaccines strictly based on chlamydial-specific antigens and to avoid those displaying even minimal sequence homologies with host molecules. Current advances in C. trachomatis vaccine development as well as alternatives for designing new vaccines for this disease are discussed. A novel approach for chlamydia vaccine development, based on targeting endogenous dendritic cells, is described.
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Affiliation(s)
- Jose Rey-Ladino
- a Department of Microbiology and Immunology; School of Medicine ; Alfaisal University ; Riyadh , Saudi Arabia
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17
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Hung MC, Humbert MV, Laver JR, Phillips R, Heckels JE, Christodoulides M. A putative amino acid ABC transporter substrate-binding protein, NMB1612, from Neisseria meningitidis, induces murine bactericidal antibodies against meningococci expressing heterologous NMB1612 proteins. Vaccine 2015. [PMID: 26207592 DOI: 10.1016/j.vaccine.2015.07.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The nmb1612 (NEIS1533) gene encoding the ~27-kDa putative amino acid ATP-binding cassette (ABC) transporter, periplasmic substrate-binding protein from Neisseria meningitidis serogroup B (MenB) strain MC58 was cloned and expressed in Escherichia coli, and the purified recombinant (r)NMB1612 was used for animal immunization studies. Immunization of mice with rNMB1612 adsorbed to Al(OH)3 and in liposomes with and without MPLA, induced antiserum with bactericidal activity in an assay using baby rabbit complement, against the homologous strain MC58 (encoding protein representative of Allele 62) and killed heterologous strains encoding proteins of three other alleles (representative of Alleles 1, 64 and 68), with similar SBA titres. However, strain MC58 was not killed (titre <4) in a human serum bactericidal assay (hSBA) using anti-rNMB1612 sera, although another strain (MC168) expressing the same protein was killed (median titres of 16-64 in the hSBA). Analysis of the NMB1612 amino acid sequences from 4351 meningococcal strains in the pubmlst.org/Neisseria database and a collection of 13 isolates from colonized individuals and from patients, showed that antibodies raised against rNMB1612 could potentially kill at least 72% of the MenB strains in the complete sequence database. For MenB disease occurring specifically in the UK from 2013 to 2015, >91% of the isolates causing disease in this recent period expressed NMB1612 protein encoded by Allele 1 and could be potentially killed by sera raised to the recombinant antigen in the current study. The NMB1612 protein was surface-accessible and expressed by different meningococcal strains. In summary, the properties of (i) NMB1612 protein conservation and expression, (ii) limited amino acid sequence variation between proteins encoded by different alleles, and (iii) the ability of a recombinant protein to induce cross-strain bactericidal antibodies, would all suggest a promising antigen for consideration for inclusion in new meningococcal vaccines.
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Affiliation(s)
- Miao-Chiu Hung
- Neisseria Research, Molecular Microbiology, Division of Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, University of Southampton Medical School, Southampton SO166YD, United Kingdom
| | - María Victoria Humbert
- Neisseria Research, Molecular Microbiology, Division of Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, University of Southampton Medical School, Southampton SO166YD, United Kingdom
| | - Jay R Laver
- Neisseria Research, Molecular Microbiology, Division of Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, University of Southampton Medical School, Southampton SO166YD, United Kingdom
| | - Renee Phillips
- Neisseria Research, Molecular Microbiology, Division of Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, University of Southampton Medical School, Southampton SO166YD, United Kingdom
| | - John E Heckels
- Neisseria Research, Molecular Microbiology, Division of Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, University of Southampton Medical School, Southampton SO166YD, United Kingdom
| | - Myron Christodoulides
- Neisseria Research, Molecular Microbiology, Division of Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, University of Southampton Medical School, Southampton SO166YD, United Kingdom.
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18
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Gaudesi D, Peri C, Quilici G, Gori A, Ferrer-Navarro M, Conchillo-Solé O, Thomas R, Nithichanon A, Lertmemongkolchai G, Titball R, Daura X, Colombo G, Musco G. Structure-based design of a B cell antigen from B. pseudomallei. ACS Chem Biol 2015; 10:803-12. [PMID: 25495888 DOI: 10.1021/cb500831y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Burkholderia pseudomallei is the etiological agent of melioidosis, a severe endemic disease in South-East Asia, causing septicemia and organ failure with high mortality rates. Current treatments and diagnostic approaches are largely ineffective. The development of new diagnostic tools and vaccines toward effective therapeutic opportunities against B. pseudomallei is therefore an urgent priority. In the framework of a multidisciplinary project tackling melioidosis through reverse and structural vaccinology, BPSL1050 was identified as a candidate for immunodiagnostic and vaccine development based on its reactivity against the sera of melioidosis patients. We determined its NMR solution structure and dynamics, and by novel computational methods we predicted immunogenic epitopes that once synthesized were able to elicit the production of antibodies inducing the agglutination of the bacterium and recognizing both BPSL1050 and B. pseudomallei crude extracts. Overall, these results hold promise for novel chemical biology approaches in the discovery of new diagnostic and prophylactic tools against melioidosis.
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Affiliation(s)
- Davide Gaudesi
- Biomolecular
NMR Laboratory, Division of Genetics and Cell Biology, S. Raffaele Scientific Institute, Milan, Italy
| | - Claudio Peri
- Department
of Computational Biology, Institute for Molecular Recognition Chemistry, Italian National Research Council, Milan, Italy
| | - Giacomo Quilici
- Biomolecular
NMR Laboratory, Division of Genetics and Cell Biology, S. Raffaele Scientific Institute, Milan, Italy
| | - Alessandro Gori
- Department
of Computational Biology, Institute for Molecular Recognition Chemistry, Italian National Research Council, Milan, Italy
| | - Mario Ferrer-Navarro
- Institute
of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Oscar Conchillo-Solé
- Institute
of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Rachael Thomas
- College
of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Arnone Nithichanon
- Center
for Research and Development of Medical Diagnostic Laboratories (CMDL),
Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Ganjana Lertmemongkolchai
- Center
for Research and Development of Medical Diagnostic Laboratories (CMDL),
Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Richard Titball
- College
of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Xavier Daura
- Institute
of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Giorgio Colombo
- Department
of Computational Biology, Institute for Molecular Recognition Chemistry, Italian National Research Council, Milan, Italy
| | - Giovanna Musco
- Biomolecular
NMR Laboratory, Division of Genetics and Cell Biology, S. Raffaele Scientific Institute, Milan, Italy
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19
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Gourlay LJ, Thomas RJ, Peri C, Conchillo-Solé O, Ferrer-Navarro M, Nithichanon A, Vila J, Daura X, Lertmemongkolchai G, Titball R, Colombo G, Bolognesi M. From crystal structure to in silico epitope discovery in the Burkholderia pseudomallei flagellar hook-associated protein FlgK. FEBS J 2015; 282:1319-33. [PMID: 25645451 DOI: 10.1111/febs.13223] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 01/29/2015] [Accepted: 01/30/2015] [Indexed: 11/28/2022]
Abstract
Melioidosis, caused by the Gram-negative bacterium Burkholderia pseudomallei, is a potentially fatal infection that is endemic in Southeast Asia and Northern Australia that is poorly controlled by antibiotics. Research efforts to identify antigenic components for a melioidosis vaccine have led to the identification of several proteins, including subunits forming the flagella that mediate bacterial motility, host colonization, and virulence. This study focuses on the B. pseudomallei flagellar hook-associated protein (FlgK(Bp)), and provides the first insights into the 3D structure of FlgK proteins as targets for structure-based antigen engineering. The FlgK(Bp) crystal structure (presented here at 1.8-Å resolution) reveals a multidomain fold, comprising two small β-domains protruding from a large elongated α-helical bundle core. The evident structural similarity to flagellin, the flagellar filament subunit protein, suggests that, depending on the bacterial species, flagellar hook-associated proteins are likely to show a conserved, elongated α-helical bundle scaffold coupled to a variable number of smaller domains. Furthermore, we present immune serum recognition data confirming, in agreement with previous findings, that recovered melioidosis patients produce elevated levels of antibodies against FlgK(Bp), in comparison with seronegative and seropositive healthy subjects. Moreover, we show that FlgK(Bp) has cytotoxic effects on cultured murine macrophages, suggesting an important role in bacterial pathogenesis. Finally, computational epitope prediction methods applied to the FlgK(Bp) crystal structure, coupled with in vitro mapping, allowed us to predict three antigenic regions that locate to discrete protein domains. Taken together, our results point to FlgK(Bp) as a candidate for the design and production of epitope-containing subunits/domains as potential vaccine components.
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20
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Donnarumma D, Golfieri G, Brier S, Castagnini M, Veggi D, Bottomley MJ, Delany I, Norais N. Neisseria meningitis GNA1030 is a ubiquinone-8 binding protein. FASEB J 2015; 29:2260-7. [PMID: 25713028 DOI: 10.1096/fj.14-263954] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 01/20/2015] [Indexed: 11/11/2022]
Abstract
Bexsero, a new vaccine against Neisseria meningitidis serogroup B (MenB), is composed of 3 main recombinant proteins and an outer membrane vesicle component. One of the main bactericidal antigens, neisseria heparin binding antigen (NHBA), is present as a fusion protein with the accessory protein genome-derived neisserial antigen (GNA) 1030 to further increase its immunogenicity. The gene encoding for GNA1030 is present and highly conserved in all Neisseria strains, and although orthologs are present in numerous species, its biologic function is unknown. Native mass spectrometry was used to demonstrate that GNA1030 forms a homodimer associated with 2 molecules of ubiquinone-8 (Ub8), a cofactor mainly involved in the electron transport chain and with antioxidant properties. Disc diffusion assays on the wild-type and knockout mutant of GNA1030, in the presence of various compounds, suggested that GNA1030 is not involved in oxidative stress or electron chain transport per se, although it contributes to constitutive refilling of the inner membrane with Ub8. These studies shed light on an accessory protein present in Bexsero and reveal functional insights into the family of related proteins. On the basis of our findings, we propose to name the protein neisseria ubiquinone binding protein (NUbp).
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21
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Horn AHC. A consistent force field parameter set for zwitterionic amino acid residues. J Mol Model 2014; 20:2478. [PMID: 25338816 DOI: 10.1007/s00894-014-2478-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Accepted: 09/21/2014] [Indexed: 12/20/2022]
Abstract
Isolated amino acids play an important role in biochemistry and are therefore an interesting object of study. Atomistic molecular dynamics (MD) simulations can provide a high-resolution picture of the dynamic features of these species, especially in their biological environment. Unfortunately, most standard force field packages lack libraries for isolated amino acids in their zwitterionic form. Although several studies have used ad-hoc parameterizations for single amino acids, a consistent force-field parameter set for these molecules is still missing. Here, we present such a parameter library derived from the widely used parm99SB set from the AMBER program package. The parameter derivation for all 20 proteinogenic amino acids transparently followed established procedures with histidine treated in three different protonation states. All amino acids were subjected to MD simulations in four different forms for comparison: zwitterionic, N-teminally capped with acetyl, C-terminally capped with N-methyl, and capped at both termini. Simulation results show similarities between the different forms. Five zwitterionic amino acids-arginine, glutamate, glycine, phenylalanine, leucine-were simulated in a protein environment. Proteins and ligands generally retained their initial structure. The new parameter set will thus facilitate future atomistic simulations of these species.
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Affiliation(s)
- Anselm H C Horn
- Bioinformatik, Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Fahrstr. 17, 91054, Erlangen, Germany,
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22
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Hanski L, Vuorela PM. Recent advances in technologies for developing drugs againstChlamydia pneumoniae. Expert Opin Drug Discov 2014; 9:791-802. [DOI: 10.1517/17460441.2014.915309] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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23
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Thomas S, Luxon BA. Vaccines based on structure-based design provide protection against infectious diseases. Expert Rev Vaccines 2014; 12:1301-11. [DOI: 10.1586/14760584.2013.840092] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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24
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Fiorucci S, Zacharias M. Computational antigenic epitope prediction by calculating electrostatic desolvation penalties of protein surfaces. Methods Mol Biol 2014; 1184:365-374. [PMID: 25048135 DOI: 10.1007/978-1-4939-1115-8_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The prediction of antigenic epitopes on the surface of proteins is of great importance for vaccine development and to specifically design recombinant antibodies. Computational methods based on the three-dimensional structure of the protein allow for the detection of noncontinuous epitopes in contrast to methods based on the primary amino-acid sequence only. A method recently developed to predict protein-protein binding sites is presented, and the application to predict putative antigenic epitopes is described in detail. The prediction approach is based on the local perturbation of the electrostatic field at the surface of a protein due to a neutral probe of low dielectric constant that represents an approaching binding partner. The calculated change in electrostatic energy corresponds to an energy penalty of desolvating a protein surface region, and antigenic epitope surface regions tend to be associated with a lower penalty compared to the average protein surface. The protocol to perform the calculations is described and illustrated on an example antigen, the outer surface protein A of Borrelia burgdorferi, a pathogenic organism causing lyme disease.
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Affiliation(s)
- Sébastien Fiorucci
- Faculté des Sciences, UMR-CNRS 7272, Institut de Chimie de Nice, Université de Nice-Sophia Antipolis, Nice Cedex 2, 06108, France,
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25
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Urosev D, Ferrer-Navarro M, Pastorello I, Cartocci E, Costenaro L, Zhulenkovs D, Maréchal JD, Leonchiks A, Reverter D, Serino L, Soriani M, Daura X. Crystal structure of c5321: a protective antigen present in uropathogenic Escherichia coli strains displaying an SLR fold. BMC STRUCTURAL BIOLOGY 2013; 13:19. [PMID: 24099525 PMCID: PMC3851747 DOI: 10.1186/1472-6807-13-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Accepted: 10/03/2013] [Indexed: 01/06/2023]
Abstract
Background Increasing rates of antimicrobial resistance among uropathogens led, among other efforts, to the application of subtractive reverse vaccinology for the identification of antigens present in extraintestinal pathogenic E. coli (ExPEC) strains but absent or variable in non-pathogenic strains, in a quest for a broadly protective Escherichia coli vaccine. The protein coded by locus c5321 from CFT073 E. coli was identified as one of nine potential vaccine candidates against ExPEC and was able to confer protection with an efficacy of 33% in a mouse model of sepsis. c5321 (known also as EsiB) lacks functional annotation and structurally belongs to the Sel1-like repeat (SLR) family. Herein, as part of the general characterization of this potential antigen, we have focused on its structural properties. Results We report the 1.74 Å-resolution crystal structure of c5321 from CFT073 E. coli determined by Se-Met SAD phasing. The structure is composed of 11 SLR units in a topological organisation that highly resembles that found in HcpC from Helicobacter pylori, with the main difference residing in how the super-helical fold is stabilised. The stabilising effect of disulfide bridges in HcpC is replaced in c5321 by a strengthening of the inter-repeat hydrophobic core. A metal-ion binding site, uncharacteristic of SLR proteins, is detected between SLR units 3 and 4 in the region of the inter-repeat hydrophobic core. Crystal contacts are observed between the C-terminal tail of one molecule and the C-terminal amphipathic groove of a neighbouring one, resembling interactions between ligand and proteins containing tetratricopeptide-like repeats. Conclusions The structure of antigen c5321 presents a mode of stabilization of the SLR fold different from that observed in close homologs of known structure. The location of the metal-ion binding site and the observed crystal contacts suggest a potential role in regulation of conformational flexibility and interaction with yet unidentified target proteins, respectively. These findings open new perspectives in both antigen design and for the identification of a functional role for this protective antigen.
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Affiliation(s)
- Dunja Urosev
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.
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Exploiting the Burkholderia pseudomallei acute phase antigen BPSL2765 for structure-based epitope discovery/design in structural vaccinology. ACTA ACUST UNITED AC 2013; 20:1147-56. [PMID: 23993463 DOI: 10.1016/j.chembiol.2013.07.010] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 06/14/2013] [Accepted: 07/23/2013] [Indexed: 11/20/2022]
Abstract
We solved the crystal structure of Burkholderia pseudomallei acute phase antigen BPSL2765 in the context of a structural vaccinology study, in the area of melioidosis vaccine development. Based on the structure, we applied a recently developed method for epitope design that combines computational epitope predictions with in vitro mapping experiments and successfully identified a consensus sequence within the antigen that, when engineered as a synthetic peptide, was selectively immunorecognized to the same extent as the recombinant protein in sera from melioidosis-affected subjects. Antibodies raised against the consensus peptide were successfully tested in opsonization bacterial killing experiments and antibody-dependent agglutination tests of B. pseudomallei. Our strategy represents a step in the development of immunodiagnostics, in the production of specific antibodies and in the optimization of antigens for vaccine development, starting from structural and physicochemical principles.
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EsiB, a novel pathogenic Escherichia coli secretory immunoglobulin A-binding protein impairing neutrophil activation. mBio 2013; 4:mBio.00206-13. [PMID: 23882011 PMCID: PMC3735183 DOI: 10.1128/mbio.00206-13] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
UNLABELLED In this study, we have characterized the functional properties of a novel Escherichia coli antigen named EsiB (E. coli secretory immunoglobulin A-binding protein), recently reported to protect mice from sepsis. Gene distribution analysis of a panel of 267 strains representative of different E. coli pathotypes revealed that esiB is preferentially associated with extraintestinal strains, while the gene is rarely found in either intestinal or nonpathogenic strains. These findings were supported by the presence of anti-EsiB antibodies in the sera of patients affected by urinary tract infections (UTIs). By solving its crystal structure, we observed that EsiB adopts a superhelical fold composed of Sel1-like repeats (SLRs), a feature often associated with bacterial proteins possessing immunomodulatory functions. Indeed, we found that EsiB interacts with secretory immunoglobulin A (SIgA) through a specific motif identified by an immunocapturing approach. Functional assays showed that EsiB binding to SIgA is likely to interfere with productive FcαRI signaling, by inhibiting both SIgA-induced neutrophil chemotaxis and respiratory burst. Indeed, EsiB hampers SIgA-mediated signaling events by reducing the phosphorylation status of key signal-transducer cytosolic proteins, including mitogen-activated kinases. We propose that the interference with such immune events could contribute to the capacity of the bacterium to avoid clearance by neutrophils, as well as reducing the recruitment of immune cells to the infection site. IMPORTANCE Pathogenic Escherichia coli infections have recently been exacerbated by increasing antibiotic resistance and the number of recurrent contagions. Attempts to develop preventive strategies against E. coli have not been successful, mainly due to the large antigenic and genetic variability of virulence factors, but also due to the complexity of the mechanisms used by the pathogen to evade the immune system. In this work, we elucidated the function of a recently discovered protective antigen, named EsiB, and described its capacity to interact with secretory immunoglobulin A (SIgA) and impair effector functions. This work unravels a novel strategy used by E. coli to subvert the host immune response and avoid neutrophil-dependent clearance.
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Understanding the molecular determinants driving the immunological specificity of the protective pilus 2a backbone protein of group B streptococcus. PLoS Comput Biol 2013; 9:e1003115. [PMID: 23825940 PMCID: PMC3694817 DOI: 10.1371/journal.pcbi.1003115] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 05/10/2013] [Indexed: 11/19/2022] Open
Abstract
The pilus 2a backbone protein (BP-2a) is one of the most structurally and functionally characterized components of a potential vaccine formulation against Group B Streptococcus. It is characterized by six main immunologically distinct allelic variants, each inducing variant-specific protection. To investigate the molecular determinants driving the variant immunogenic specificity of BP-2a, in terms of single residue contributions, we generated six monoclonal antibodies against a specific protein variant based on their capability to recognize the polymerized pili structure on the bacterial surface. Three mAbs were also able to induce complement-dependent opsonophagocytosis killing of live GBS and target the same linear epitope present in the structurally defined and immunodominant domain D3 of the protein. Molecular docking between the modelled scFv antibody sequences and the BP-2a crystal structure revealed the potential role at the binding interface of some non-conserved antigen residues. Mutagenesis analysis confirmed the necessity of a perfect balance between charges, size and polarity at the binding interface to obtain specific binding of mAbs to the protein antigen for a neutralizing response. Group B Streptococcus (GBS) is the leading cause of neonatal invasive diseases and pili, as long filamentous fibers protruding from the bacterial surface, have been discovered as important virulence factors and potential vaccine candidates. The bacterial surface is the main interface between host and pathogen, and the ability of the host to identify molecular determinants that are unique to pathogens has a crucial role for microbial clearance. Here, we describe a strategy to investigate the immunological and structural proprieties of a protective pilus protein, by elucidating the molecular mechanisms, in terms of single residue contributions, by which functional epitopes guide bacterial clearance. We generated neutralizing monoclonal antibodies raised against the protein and identified the epitope region in the antigen. Then, we performed computational docking analysis of the antibodies in complex with the target antigen and identified specific residues on the target protein that mediate hydrophobic interactions at the binding interface. Our results suggest that a perfect balance of shape and charges at the binding interface in antibody/antigen interactions is crucial for the antibody/antigen complex in driving a successful neutralizing response. Knowing the native molecular architecture of protective determinants might be useful to selectively engineer the antigens for effective vaccine formulations.
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Kulp DW, Schief WR. Advances in structure-based vaccine design. Curr Opin Virol 2013; 3:322-31. [PMID: 23806515 DOI: 10.1016/j.coviro.2013.05.010] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 05/13/2013] [Accepted: 05/13/2013] [Indexed: 01/02/2023]
Abstract
Despite the tremendous successes of current vaccines, infectious diseases still take a heavy toll on the global population, and that provides strong rationale for broadening our vaccine development repertoire. Structural vaccinology, in which protein structure information is utilized to design immunogens, has promise to provide new vaccines against traditionally difficult targets. Crystal structures of antigens containing one or more protection epitopes, especially when in complex with a protective antibody, are the launching point for immunogen design. Integrating structure and sequence information for families of broadly neutralizing antibodies (bNAbs) has recently enabled the creation of germline-targeting immunogens that bind and activate germline B-cells in order to initiate the elicitation of such antibodies. The contacts between antigen and neutralizing antibody define a structural epitope, and methods have been developed to transplant epitopes to scaffold proteins for structural stabilization, and to design minimized antigens that retain one or more key epitopes while eliminating other potentially distracting or unnecessary features. To develop vaccines that protect against antigenically variable pathogens, pioneering structure-based work demonstrated that multiple strain-specific epitopes could be engineered onto a single immunogen. We review these recent structural vaccinology efforts to engineer germline-targeting, epitope-specific, and/or broad coverage immunogens.
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Affiliation(s)
- Daniel W Kulp
- IAVI Neutralizing Antibody Center and Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
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Peri C, Gagni P, Combi F, Gori A, Chiari M, Longhi R, Cretich M, Colombo G. Rational epitope design for protein targeting. ACS Chem Biol 2013; 8:397-404. [PMID: 23138758 DOI: 10.1021/cb300487u] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We present a new multidisciplinary strategy integrating computational biology with high-throughput microarray analysis aimed to translate molecular understanding of protein-antibody recognition into the design of efficient and selective protein-based analytical and diagnostic tools. The structures of two proteins with different folds and secondary structure contents, namely, the beta-barrel FABP and the α-helical S100B, were used as the basis for the prediction and design of potential antibody-binding epitopes using the recently developed MLCE computational method. Starting from the idea that the structure, dynamics, and stability of a protein-antigen play a key role in the interaction with antibodies, MLCE integrates the analysis of the dynamical and energetic properties of proteins to identify nonoptimized, low-intensity energetic interaction-networks on the surface of the isolated antigens, which correspond to substructures that can aptly be recognized by a binding partner. The identified epitopes were next synthesized as free peptides and used to elicit specific antibodies in rabbits. Importantly, the resulting antibodies were proven to specifically and selectively recognize the original, full-length proteins in microarray-based tests. Competition experiments further demonstrated the specificity of the molecular recognition between the target immobilized proteins and the generated antibodies. Our integrated computational and microarray-based results demonstrate the possibility to rationally discover and design synthetic epitopes able to elicit antibodies specific for full-length proteins starting only from three-dimensional structural information on the target. We discuss implications for diagnosis and vaccine development purposes.
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Affiliation(s)
- Claudio Peri
- Isituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
| | - Paola Gagni
- Isituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
| | - Fabio Combi
- Isituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
| | - Alessandro Gori
- Isituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
| | - Marcella Chiari
- Isituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
| | - Renato Longhi
- Isituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
| | - Marina Cretich
- Isituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
| | - Giorgio Colombo
- Isituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
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Lu C, Peng B, Li Z, Lei L, Li Z, Chen L, He Q, Zhong G, Wu Y. Induction of protective immunity against Chlamydia muridarum intravaginal infection with the chlamydial immunodominant antigen macrophage infectivity potentiator. Microbes Infect 2013; 15:329-38. [PMID: 23416214 DOI: 10.1016/j.micinf.2013.02.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 01/28/2013] [Accepted: 02/03/2013] [Indexed: 12/21/2022]
Abstract
We previously reported that 5 Chlamydia muridarum antigens reacted with antisera from >90% mice urogenitally infected with C. muridarum and they are TC0660 (ABC transporter or ArtJ), TC0727 (outer membrane complex protein B or OmcB), TC0828 (macrophage infectivity potentiator or MIP), TC0726 (inclusion membrane protein or Inc) & TC0268 (hypothetical protein or HP). The orthologs of these antigens in Chlamydia trachomatis were also highly reactive with antisera from women urogenitally infected with C. trachomatis. In the current study, we evaluated these C. muridarum antigens for their ability to induce protection against a C. muridarum intravaginal challenge infection in mice. We found that only MIP induced the most pronounced protection against C. muridarum infection. The protection correlated well with robust C. muridarum MIP-specific antibody and Th1-dominant T cell responses. The MIP-immunized mice displayed significantly reduced live organism shedding from the lower genital tract and highly attenuated inflammatory pathologies in the upper genital tissues. These results demonstrate that MIP, an immunodominant antigen identified by both human and mouse antisera, may be considered a component of a multi-subunit chlamydial vaccine for inducing protective immunity.
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Affiliation(s)
- Chunxue Lu
- Department of Microbiology and Immunology, University of South China, 28 West Changsheng Rd., Hengyang, Hunan 421001, China
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Lassaux P, Peri C, Ferrer-Navarro M, Gourlay LJ, Gori A, Conchillo-Solé O, Rinchai D, Lertmemongkolchai G, Longhi R, Daura X, Colombo G, Bolognesi M. A structure-based strategy for epitope discovery in Burkholderia pseudomallei OppA antigen. Structure 2012; 21:167-175. [PMID: 23159127 DOI: 10.1016/j.str.2012.10.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 09/10/2012] [Accepted: 10/04/2012] [Indexed: 10/27/2022]
Abstract
We present an approach integrating structural and computational biology with immunological tests to identify epitopes in the OppA antigen from the Gram-negative pathogen Burkholderia pseudomallei, the etiological agent of melioidosis. The crystal structure of OppA(Bp), reported here at 2.1 Å resolution, was the basis for a computational analysis that identified three potential epitopes. In parallel, antigen proteolysis and immunocapturing allowed us to identify three additional peptides. All six potential epitopes were synthesized as free peptides and tested for their immunoreactivity against sera from healthy seronegative, healthy seropositive, and recovered melioidosis patients. Three synthetic peptides allowed the different patient groups to be distinguished, underlining the potential of this approach. Extension of the computational analysis, including energy-based decomposition methods, allowed rationalizing results of the predictive analyses and the immunocapture epitope mapping. Our results illustrate a structure-based epitope discovery process, whose application may expand our perspectives in the diagnostic and vaccine design fields.
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Affiliation(s)
- Patricia Lassaux
- Department of Biosciences, University of Milan, Milan 20133, Italy
| | - Claudio Peri
- Consiglio Nazionale delle Ricerche, Institute for Chemistry of Molecular Recognition, Department of Computational Biology, Milan 20131, Italy
| | - Mario Ferrer-Navarro
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Louise J Gourlay
- Department of Biosciences, University of Milan, Milan 20133, Italy
| | - Alessandro Gori
- Consiglio Nazionale delle Ricerche, Institute for Chemistry of Molecular Recognition, Department of Computational Biology, Milan 20131, Italy
| | - Oscar Conchillo-Solé
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Darawan Rinchai
- Center for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Ganjana Lertmemongkolchai
- Center for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Renato Longhi
- Consiglio Nazionale delle Ricerche, Institute for Chemistry of Molecular Recognition, Department of Computational Biology, Milan 20131, Italy
| | - Xavier Daura
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain; Catalan Institution for Research and Advanced Studies, Barcelona 08010, Spain
| | - Giorgio Colombo
- Consiglio Nazionale delle Ricerche, Institute for Chemistry of Molecular Recognition, Department of Computational Biology, Milan 20131, Italy.
| | - Martino Bolognesi
- Department of Biosciences, University of Milan, Milan 20133, Italy; Consiglio Nazionale delle Ricerche, Institute of Biophysics, University of Milan, Milan 20133, Italy.
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Bowen DM, Lewis JA, Lu W, Schein CH. Simplifying complex sequence information: a PCP-consensus protein binds antibodies against all four Dengue serotypes. Vaccine 2012; 30:6081-7. [PMID: 22863657 DOI: 10.1016/j.vaccine.2012.07.042] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Revised: 07/13/2012] [Accepted: 07/18/2012] [Indexed: 12/15/2022]
Abstract
Designing proteins that reflect the natural variability of a pathogen is essential for developing novel vaccines and drugs. Flaviviruses, including Dengue (DENV) and West Nile (WNV), evolve rapidly and can "escape" neutralizing monoclonal antibodies by mutation. Designing antigens that represent many distinct strains is important for DENV, where infection with a strain from one of the four serotypes may lead to severe hemorrhagic disease on subsequent infection with a strain from another serotype. Here, a DENV physicochemical property (PCP)-consensus sequence was derived from 671 unique sequences from the Flavitrack database. PCP-consensus proteins for domain 3 of the envelope protein (EdomIII) were expressed from synthetic genes in Escherichia coli. The ability of the purified consensus proteins to bind polyclonal antibodies generated in response to infection with strains from each of the four DENV serotypes was determined. The initial consensus protein bound antibodies from DENV-1-3 in ELISA and Western blot assays. This sequence was altered in 3 steps to incorporate regions of maximum variability, identified as significant changes in the PCPs, characteristic of DENV-4 strains. The final protein was recognized by antibodies against all four serotypes. Two amino acids essential for efficient binding to all DENV antibodies are part of a discontinuous epitope previously defined for a neutralizing monoclonal antibody. The PCP-consensus method can significantly reduce the number of experiments required to define a multivalent antigen, which is particularly important when dealing with pathogens that must be tested at higher biosafety levels.
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Affiliation(s)
- David M Bowen
- Computational Biology, Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555-0857, United States
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An automated image-based method for rapid analysis of Chlamydia infection as a tool for screening antichlamydial agents. Antimicrob Agents Chemother 2012; 56:4184-8. [PMID: 22615279 DOI: 10.1128/aac.00427-12] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A major limitation in the identification of novel antichlamydial compounds is the paucity of effective methods for large-scale compound screening. The immunofluorescence assay is the preferred approach for accurate quantification of the intracellular growth of Chlamydia. In this study, an immunofluorescence image-based method (termed image-based automated chlamydial identification and enumeration [iBAChIE]) was customized for fully automated quantification of Chlamydia infection using the freely available open-source image analysis software program CellProfiler and the complementary data exploration software program CellProfiler Analyst. The method yielded enumeration of different species and strains of Chlamydia highly comparably to the conventional manual methods while drastically reducing the analysis time. The inhibitory capability of established antichlamydial activity was also evaluated. Overall, these data support that iBAChIE is a highly effective tool for automated quantification of Chlamydia infection and assessment of antichlamydial activities of molecules. Furthermore, iBAChIE is expected to be amenable to high-throughput screening studies for inhibitory compounds and fluorescently labeled molecules to study host-pathogen interactions.
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Park SH, Chang JE, Hawkes HJK, Kang YH, Hwang KY. Structural analysis and serological test of arginine periplasmic binding protein 2 from Chlamydophila pneumoniae. Biochem Biophys Res Commun 2012; 418:518-24. [PMID: 22285188 DOI: 10.1016/j.bbrc.2012.01.058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Accepted: 01/11/2012] [Indexed: 10/14/2022]
Abstract
The 'art' genes encode specific arginine uptake proteins, and are repressed by the repressible promoters of ArgR, affecting transcription of artJ. Cpb0502, the arginine-binding periplasmic protein 2 precursor from Chlamydophila pneumoniae TW-183 strains, is responsible for arginine transport. As C. pneumoniae is difficult to isolate and culture, there have been many studies of better ways to detect it. A microimmunofluorescence assay (MIF) is still considered to be the 'gold standard' for detecting C. pneumoniae. Although MIF has its own limitations, a number of immunogenic antigens have been shown to be C. pneumoniae specific by this test. Here, we report Cpb0502 as a specific immunogenic antigen against C. pneumoniae as it was detected only in human infection sera of C. pneumoniae but not in Legionella pneumophila and Mycoplasma pneumoniae infection sera, showing high specificity and sensitivity by MIF, western blot and ELISA analysis. And also the crystal structure of Cpb0502 was determined to be a dimer at 2.07Å, revealing a similar backbone structure to a histidine kinase receptor, HK29S. Therefore we may suggest that Cpb0502 is a candidate immunogenic antigen for better diagnosis of C. pneumoniae.
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Affiliation(s)
- Sung-Ha Park
- Graduate School of Biotechnology, Korea University, Seoul, Republic of Korea
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Abstract
PURPOSE OF REVIEW The aim is to review recent findings on immunity and vaccine development to Chlamydia trachomatis. RECENT FINDINGS There is increasing knowledge on the interactions between C. trachomatis and infected host cells. During genital infection the organism avoids generating protective immunity but immune responses to a number of chlamydial proteins have been associated with reproductive tract pathology. Various vaccine and adjuvant preparations have been tried experimentally. Information generated by proteomics and complex studies of serological and T-lymphocyte immune responses points to novel vaccine candidates. SUMMARY C. trachomatis, an obligate intracellular bacterium, is the commonest sexually transmitted infection worldwide and is associated with reproductive pathology. To develop rational vaccines it is necessary to understand the complex lifecycle of the organism, the host immune response to infection and how these relate to disease. Infection does not prevent re-infection and antibiotic treatment prevents antibody production at a population level. It remains unclear what type of immune response would be sufficient to prevent infection and/or re-infection. Although the prevalence and demographics of infection and the severity of disease associations suggest that it would be desirable, there is no vaccine currently available. A number of studies have identified novel vaccine candidates.
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Koehler C, Carlier L, Veggi D, Balducci E, Di Marcello F, Ferrer-Navarro M, Pizza M, Daura X, Soriani M, Boelens R, Bonvin AMJJ. Structural and biochemical characterization of NarE, an iron-containing ADP-ribosyltransferase from Neisseria meningitidis. J Biol Chem 2011; 286:14842-51. [PMID: 21367854 PMCID: PMC3083161 DOI: 10.1074/jbc.m110.193623] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2010] [Revised: 02/15/2011] [Indexed: 11/06/2022] Open
Abstract
NarE is a 16 kDa protein identified from Neisseria meningitidis, one of the bacterial pathogens responsible for meningitis. NarE belongs to the family of ADP-ribosyltransferases (ADPRT) and catalyzes the transfer of ADP-ribose moieties to arginine residues in target protein acceptors. Many pathogenic bacteria utilize ADP-ribosylating toxins to modify and alter essential functions of eukaryotic cells. NarE is further the first ADPRT which could be shown to bind iron through a Fe-S center, which is crucial for the catalytic activity. Here we present the NMR solution structure of NarE, which shows structural homology to other ADPRTs. Using NMR titration experiments we could identify from Chemical Shift Perturbation data both the NAD binding site, which is in perfect agreement with a consensus sequence analysis between different ADPRTs, as well as the iron coordination site, which consists of 2 cysteines and 2 histidines. This atypical iron coordination is also capable to bind zinc. These results could be fortified by site-directed mutagenesis of the catalytic region, which identified two functionally crucial residues. We could further identify a main interaction region of NarE with antibodies using two complementary methods based on antibody immobilization, proteolytic digestion, and mass spectrometry. This study combines structural and functional features of NarE providing for the first time a characterization of an iron-dependent ADPRT.
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Affiliation(s)
- Christian Koehler
- From the Bijvoet Center for Biomolecular Research, Science Faculty, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Ludovic Carlier
- From the Bijvoet Center for Biomolecular Research, Science Faculty, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Daniele Veggi
- Novartis Vaccines and Diagnostics, 53100 Siena, Italy
| | - Enrico Balducci
- the School of Biosciences and Biotechnologies, University of Camerino, via Gentile III da Varano, 62032 Camerino, Italy
| | | | - Mario Ferrer-Navarro
- the Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain
| | | | - Xavier Daura
- the Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain
- the Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain, and
| | - Marco Soriani
- Novartis Vaccines and Diagnostics, 53100 Siena, Italy
| | - Rolf Boelens
- From the Bijvoet Center for Biomolecular Research, Science Faculty, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Alexandre M. J. J. Bonvin
- From the Bijvoet Center for Biomolecular Research, Science Faculty, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
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