1
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Sun R, Qian MG, Zhang X. T and B cell epitope analysis for the immunogenicity evaluation and mitigation of antibody-based therapeutics. MAbs 2024; 16:2324836. [PMID: 38512798 PMCID: PMC10962608 DOI: 10.1080/19420862.2024.2324836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 02/26/2024] [Indexed: 03/23/2024] Open
Abstract
The surge in the clinical use of therapeutic antibodies has reshaped the landscape of pharmaceutical therapy for many diseases, including rare and challenging conditions. However, the administration of exogenous biologics could potentially trigger unwanted immune responses such as generation of anti-drug antibodies (ADAs). Real-world experiences have illuminated the clear correlation between the ADA occurrence and unsatisfactory therapeutic outcomes as well as immune-related adverse events. By retrospectively examining research involving immunogenicity analysis, we noticed the growing emphasis on elucidating the immunogenic epitope profiles of antibody-based therapeutics aiming for mechanistic understanding the immunogenicity generation and, ideally, mitigating the risks. As such, we have comprehensively summarized here the progress in both experimental and computational methodologies for the characterization of T and B cell epitopes of therapeutics. Furthermore, the successful practice of epitope-driven deimmunization of biotherapeutics is exceptionally highlighted in this article.
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Affiliation(s)
- Ruoxuan Sun
- Global Drug Metabolism, Pharmacokinetics & Modeling, Preclinical & Translational Sciences, Takeda Development Center Americas, Inc. (TDCA), Cambridge, MA, USA
| | - Mark G. Qian
- Global Drug Metabolism, Pharmacokinetics & Modeling, Preclinical & Translational Sciences, Takeda Development Center Americas, Inc. (TDCA), Cambridge, MA, USA
| | - Xiaobin Zhang
- Global Drug Metabolism, Pharmacokinetics & Modeling, Preclinical & Translational Sciences, Takeda Development Center Americas, Inc. (TDCA), Cambridge, MA, USA
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2
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Misson Mindrebo L, Liu H, Ozorowski G, Tran Q, Woehl J, Khalek I, Smith J, Barman S, Zhao F, Keating C, Limbo O, Verma M, Liu J, Stanfield R, Zhu X, Turner H, Sok D, Huang PS, Burton D, Ward A, Wilson I, Jardine J. Fully synthetic platform to rapidly generate tetravalent bispecific nanobody-based immunoglobulins. Proc Natl Acad Sci U S A 2023; 120:e2216612120. [PMID: 37276407 PMCID: PMC10268213 DOI: 10.1073/pnas.2216612120] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 04/28/2023] [Indexed: 06/07/2023] Open
Abstract
Nanobodies bind a target antigen with a kinetic profile similar to a conventional antibody, but exist as a single heavy chain domain that can be readily multimerized to engage antigen via multiple interactions. Presently, most nanobodies are produced by immunizing camelids; however, platforms for animal-free production are growing in popularity. Here, we describe the development of a fully synthetic nanobody library based on an engineered human VH3-23 variable gene and a multispecific antibody-like format designed for biparatopic target engagement. To validate our library, we selected nanobodies against the SARS-CoV-2 receptor-binding domain and employed an on-yeast epitope binning strategy to rapidly map the specificities of the selected nanobodies. We then generated antibody-like molecules by replacing the VH and VL domains of a conventional antibody with two different nanobodies, designed as a molecular clamp to engage the receptor-binding domain biparatopically. The resulting bispecific tetra-nanobody immunoglobulins neutralized diverse SARS-CoV-2 variants with potencies similar to antibodies isolated from convalescent donors. Subsequent biochemical analyses confirmed the accuracy of the on-yeast epitope binning and structures of both individual nanobodies, and a tetra-nanobody immunoglobulin revealed that the intended mode of interaction had been achieved. This overall workflow is applicable to nearly any protein target and provides a blueprint for a modular workflow for the development of multispecific molecules.
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Affiliation(s)
- Laetitia Misson Mindrebo
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA92037
- International AIDS Vaccine Initiative, New York, NY10004
| | - Hejun Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Gabriel Ozorowski
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA92037
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA92037
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA92037
| | - Quoc Tran
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA92037
- International AIDS Vaccine Initiative, New York, NY10004
| | - Jordan Woehl
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA92037
- International AIDS Vaccine Initiative, New York, NY10004
| | - Irene Khalek
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA92037
- International AIDS Vaccine Initiative, New York, NY10004
| | - Jessica M. Smith
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA92037
- International AIDS Vaccine Initiative, New York, NY10004
| | - Shawn Barman
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA92037
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA92037
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA92037
| | - Fangzhu Zhao
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA92037
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA92037
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA92037
| | - Celina Keating
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA92037
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA92037
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA92037
| | - Oliver Limbo
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA92037
- International AIDS Vaccine Initiative, New York, NY10004
| | - Megan Verma
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA92037
- International AIDS Vaccine Initiative, New York, NY10004
| | - Jingjia Liu
- Department of Bioengineering, Stanford University, Stanford, CA94305
| | - Robyn L. Stanfield
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Hannah L. Turner
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA92037
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA92037
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA92037
| | - Devin Sok
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA92037
- International AIDS Vaccine Initiative, New York, NY10004
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA92037
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA92037
| | - Po-Ssu Huang
- Department of Bioengineering, Stanford University, Stanford, CA94305
| | - Dennis R. Burton
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA92037
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA92037
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA92037
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA02139
| | - Andrew B. Ward
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA92037
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA92037
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA92037
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA92037
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Joseph G. Jardine
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA92037
- International AIDS Vaccine Initiative, New York, NY10004
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3
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Tay PKR, Lim PY, Ow DSW. A SH3_5 Cell Anchoring Domain for Non-recombinant Surface Display on Lactic Acid Bacteria. Front Bioeng Biotechnol 2021; 8:614498. [PMID: 33585415 PMCID: PMC7873443 DOI: 10.3389/fbioe.2020.614498] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 12/30/2020] [Indexed: 12/17/2022] Open
Abstract
Lactic acid bacteria (LAB) are a group of gut commensals increasingly recognized for their potential to deliver bioactive molecules in vivo. The delivery of therapeutic proteins, in particular, can be achieved by anchoring them to the bacterial surface, and various anchoring domains have been described for this application. Here, we investigated a new cell anchoring domain (CAD4a) isolated from a Lactobacillus protein, containing repeats of a SH3_5 motif that binds non-covalently to peptidoglycan in the LAB cell wall. Using a fluorescent reporter, we showed that C-terminal CAD4a bound Lactobacillus fermentum selectively out of a panel of LAB strains, and cell anchoring was uniform across the cell surface. Conditions affecting CAD4a anchoring were studied, including temperature, pH, salt concentration, and bacterial growth phase. Quantitative analysis showed that CAD4a allowed display of 105 molecules of monomeric protein per cell. We demonstrated the surface display of a functional protein with superoxide dismutase (SOD), an antioxidant enzyme potentially useful for treating gut inflammation. SOD displayed on cells could be protected from gastric digestion using a polymer matrix. Taken together, our results show the feasibility of using CAD4a as a novel cell anchor for protein surface display on LAB.
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Affiliation(s)
- Pei Kun Richie Tay
- Microbial Cells Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Pei Yu Lim
- Microbial Cells Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Dave Siak-Wei Ow
- Microbial Cells Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
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4
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Expression and Characterization of Human Vascular Endothelial Growth Factor Produced in SiHa Cells Transduced with Adenoviral Vector. Protein J 2019; 38:693-703. [DOI: 10.1007/s10930-019-09867-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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5
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Najar TA, Khare S, Varadarajan R. Rapid Mapping of Protein Binding Sites and Conformational Epitopes by Coupling Yeast Surface Display to Chemical Labeling and Deep Sequencing. Methods Mol Biol 2019; 1785:77-88. [PMID: 29714013 DOI: 10.1007/978-1-4939-7841-0_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Delineating the precise regions on an antigen that are targeted by antibodies is important for the development of vaccines and antibody therapeutics. X-ray crystallography and NMR are considered the gold standard for providing precise information about these binding sites at atomic resolution. However, these are labor-intensive and require purified protein at high concentration. We have recently described [1] a rapid and reliable method that overcomes these constraints, using a panel of single cysteine mutants of the protein of interest and now provide protocols to facilitate its adoption. Mutants are displayed on the yeast cell surface either individually or as a pool, and labeled covalently with a cysteine specific probe. Binding site residues are inferred by monitoring loss of ligand or antibody binding by flow cytometry coupled to deep sequencing of sorted populations, or Sanger sequencing of individual clones. Buried cysteine residues are not labeled and library sizes are small, facilitating rapid identification of binding-site residues. The methodology was used to identify epitopes on the bacterial toxin CcdB targeted by twenty-four different monoclonal antibodies as well as by polyclonal sera. The method does not require purified protein or protein structural information and can be applied to a variety of display formats.
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Affiliation(s)
- Tariq Ahmad Najar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Shruti Khare
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Raghavan Varadarajan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India. .,Jawaharlal Nehru Center for Advanced Scientific Research, Bangalore, India.
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6
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Yao Y, Ding Q, Ou L. Biosynthesis of (deoxy)guanosine-5'-triphosphate by GMP kinase and acetate kinase fixed on the surface of E. coli. Enzyme Microb Technol 2018; 122:82-89. [PMID: 30638512 DOI: 10.1016/j.enzmictec.2018.12.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 11/23/2018] [Accepted: 12/19/2018] [Indexed: 11/19/2022]
Abstract
(Deoxy)guanosine-5'-triphosphate (5'-(d)GTP), the precursor for synthesizing DNA or RNA in vivo, is an important raw material for various modern biotechnologies based on PCR. In this study, we investigated the application of whole-cell catalysts constructed by bacterial cell surface display in biosynthetic reactions of 5'-(d)GTP from (deoxy)guanosine-5'-monophosphate (5'-(d)GMP). By N-terminal or N- and C-terminal fusion of the ice nucleation protein, we successfully displayed the GMP kinase of Lactobacillus bulgaricus and the acetate kinase of E. coli on the surface of E. coli cells. A large amount of soluble target protein was obtained upon induction with 0.2 mM IPTG at 25 °C for 30 h. The conversion of dGMP was up to 91% when catalysed by the surface-displayed enzymes at 37 °C for 4 h. Up to 95% of the GMP was converted after 3 h of reaction. The stability of the whole-cell catalyst at 37 °C was very good. The enzyme activity was maintained above 50% after 9 rounds of recovery. Our research showed that only one-twentieth of the initial substrate concentration of added ATP was sufficient to meet the reaction requirements.
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Affiliation(s)
- Yefeng Yao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Qingbao Ding
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA.
| | - Ling Ou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
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7
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Hu FJ, Volk AL, Persson H, Säll A, Borrebaeck C, Uhlen M, Rockberg J. Combination of phage and Gram-positive bacterial display of human antibody repertoires enables isolation of functional high affinity binders. N Biotechnol 2018; 45:80-88. [DOI: 10.1016/j.nbt.2017.07.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 06/28/2017] [Accepted: 07/31/2017] [Indexed: 10/19/2022]
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8
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Surface Display of Small Affinity Proteins on Synechocystis sp. Strain PCC 6803 Mediated by Fusion to the Major Type IV Pilin PilA1. J Bacteriol 2018; 200:JB.00270-18. [PMID: 29844032 DOI: 10.1128/jb.00270-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 05/22/2018] [Indexed: 11/20/2022] Open
Abstract
Functional surface display of small affinity proteins, namely, affibodies (6.5 kDa), was evaluated for the model cyanobacterium Synechocystis sp. strain PCC 6803 through anchoring to native surface structures. These structures included confirmed or putative subunits of the type IV pili, the S-layer protein, and the heterologous Escherichia coli autotransporter antigen 43 system. The most stable display system was determined to be through C-terminal fusion to PilA1, the major type IV pilus subunit in Synechocystis, in a strain unable to retract these pili (ΔpilT1). Type IV pilus synthesis was upheld, albeit reduced, when fusion proteins were incorporated. However, pilus-mediated functions, such as motility and transformational competency, were negatively affected. Display of affibodies on Synechocystis and the complementary anti-idiotypic affibodies on E. coli or Staphylococcus carnosus was able to mediate interspecies cell-cell binding by affibody complex formation. The same strategy, however, was not able to drive cell-cell binding and aggregation of Synechocystis-only mixtures. Successful affibody tagging of the putative minor pilin PilA4 showed that it locates to the type IV pili in Synechocystis and that its extracellular availability depends on PilA1. In addition, affibody tagging of the S-layer protein indicated that the domains responsible for the anchoring and secretion of this protein are located at the N and C termini, respectively. This study can serve as a basis for future surface display of proteins on Synechocystis for biotechnological applications.IMPORTANCE Cyanobacteria are gaining interest for their potential as autotrophic cell factories. Development of efficient surface display strategies could improve their suitability for large-scale applications by providing options for designed microbial consortia, cell immobilization, and biomass harvesting. Here, surface display of small affinity proteins was realized by fusing them to the major subunit of the native type IV pili in Synechocystis sp. strain PCC 6803. The display of complementary affinity proteins allowed specific cell-cell binding between Synechocystis and Escherichia coli or Staphylococcus carnosus Additionally, successful tagging of the putative pilin PilA4 helped determine its localization to the type IV pili. Analogous tagging of the S-layer protein shed light on the regions involved in its secretion and surface anchoring.
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9
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Epitope Mapping of Antibodies Using Bacterial Cell Surface Display of Gene Fragment Libraries. Methods Mol Biol 2018. [PMID: 29714017 DOI: 10.1007/978-1-4939-7841-0_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The unique property of specific high affinity binding to more or less any target of interest has made antibodies tremendously useful in numerous applications. Hence, knowledge of the precise binding site (epitope) of antibodies on the target protein is one of the most important features for understanding its performance and determining its reliability in immunoassays. Here, we describe an updated protocol for high-resolution method for mapping epitopes of antibodies based on bacterial surface expression of antigen fragments followed by antibody-based flow cytometric analysis. Epitopes are determined by DNA sequencing of the sorted antibody-binding cells followed by sequence alignment back to the antigen sequence. The method described here has been useful for the mapping of both monoclonal and polyclonal antibodies with varying sizes of epitopes.
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10
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Ibsen KN, Daugherty PS. Prediction of antibody structural epitopes via random peptide library screening and next generation sequencing. J Immunol Methods 2017; 451:28-36. [PMID: 28827189 PMCID: PMC5698135 DOI: 10.1016/j.jim.2017.08.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/14/2017] [Accepted: 08/17/2017] [Indexed: 12/24/2022]
Abstract
Next generation sequencing (NGS) is widely applied in immunological research, but has yet to become common in antibody epitope mapping. A method utilizing a 12-mer random peptide library expressed in bacteria coupled with magnetic-based cell sorting and NGS correctly identified >75% of epitope residues on the antigens of two monoclonal antibodies (trastuzumab and bevacizumab). PepSurf, a web-based computational method designed for structural epitope mapping was utilized to compare peptides in libraries enriched for monoclonal antibody (mAb) binders to antigen surfaces (HER2 and VEGF-A). Compared to mimotopes recovered from Sanger sequencing of plated colonies from the same sorting protocol, motifs derived from sets of the NGS data improved epitope prediction as defined by sensitivity and precision, from 18% to 82% and 0.27 to 0.51 for trastuzumab and 47% to 76% and 0.19 to 0.27 for bevacizumab. Specificity was similar for Sanger and NGS, 99% and 97% for trastuzumab and 66% and 67% for bevacizumab. These results indicate that combining peptide library screening with NGS yields epitope motifs that can improve prediction of structural epitopes.
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MESH Headings
- Algorithms
- Amino Acid Motifs
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/metabolism
- Antibody Specificity
- Antineoplastic Agents, Immunological/immunology
- Antineoplastic Agents, Immunological/metabolism
- Bevacizumab/immunology
- Bevacizumab/metabolism
- Binding Sites, Antibody
- Computational Biology
- Databases, Genetic
- Epitope Mapping/methods
- Epitopes
- High-Throughput Nucleotide Sequencing
- Immunomagnetic Separation
- Models, Chemical
- Peptide Library
- Protein Binding
- Receptor, ErbB-2/chemistry
- Receptor, ErbB-2/genetics
- Receptor, ErbB-2/immunology
- Receptor, ErbB-2/metabolism
- Structure-Activity Relationship
- Trastuzumab/immunology
- Trastuzumab/metabolism
- Vascular Endothelial Growth Factor A/chemistry
- Vascular Endothelial Growth Factor A/genetics
- Vascular Endothelial Growth Factor A/immunology
- Vascular Endothelial Growth Factor A/metabolism
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Affiliation(s)
- Kelly N Ibsen
- Department of Chemical Engineering, University of California Santa Barbara, CA 93106, USA.
| | - Patrick S Daugherty
- Department of Chemical Engineering, University of California Santa Barbara, CA 93106, USA
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11
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Löfblom J, Rosenstein R, Nguyen MT, Ståhl S, Götz F. Staphylococcus carnosus: from starter culture to protein engineering platform. Appl Microbiol Biotechnol 2017; 101:8293-8307. [PMID: 28971248 PMCID: PMC5694512 DOI: 10.1007/s00253-017-8528-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 09/08/2017] [Accepted: 09/11/2017] [Indexed: 02/04/2023]
Abstract
Since the 1950s, Staphylococcus carnosus is used as a starter culture for sausage fermentation where it contributes to food safety, flavor, and a controlled fermentation process. The long experience with S. carnosus has shown that it is a harmless and "food grade" species. This was confirmed by the genome sequence of S. carnosus TM300 that lacks genes involved in pathogenicity. Since the development of a cloning system in TM300, numerous genes have been cloned, expressed, and characterized and in particular, virulence genes that could be functionally validated in this non-pathogenic strain. A secretion system was developed for production and secretion of industrially important proteins and later modified to also enable display of heterologous proteins on the surface. The display system has been employed for various purposes, such as development of live bacterial delivery vehicles as well as microbial biocatalysts or bioadsorbents for potential environmental or biosensor applications. Recently, this surface display system has been utilized for display of peptide and protein libraries for profiling of protease substrates and for generation of various affinity proteins, e.g., Affibody molecules and scFv antibodies. In addition, by display of fragmented antigen-encoding genes, the surface expression system has been successfully used for epitope mapping of antibodies. Reviews on specific applications of S. carnosus have been published earlier, but here we provide a more extensive overview, covering a broad range of areas from food fermentation to sophisticated methods for protein-based drug discovery, which are all based on S. carnosus.
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Affiliation(s)
- John Löfblom
- Division of Protein Technology, School of Biotechnology, KTH-Royal Institute of Technology, AlbaNova University Center, Roslagstullsbacken 21, 106 91, Stockholm, Sweden
| | - Ralf Rosenstein
- Microbial Genetics, Interfaculty Institute of Microbiology and Infection Medicine and Infection Medicine (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Minh-Thu Nguyen
- Microbial Genetics, Interfaculty Institute of Microbiology and Infection Medicine and Infection Medicine (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Stefan Ståhl
- Division of Protein Technology, School of Biotechnology, KTH-Royal Institute of Technology, AlbaNova University Center, Roslagstullsbacken 21, 106 91, Stockholm, Sweden.
| | - Friedrich Götz
- Microbial Genetics, Interfaculty Institute of Microbiology and Infection Medicine and Infection Medicine (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany.
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12
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Galán A, Comor L, Horvatić A, Kuleš J, Guillemin N, Mrljak V, Bhide M. Library-based display technologies: where do we stand? MOLECULAR BIOSYSTEMS 2017; 12:2342-58. [PMID: 27306919 DOI: 10.1039/c6mb00219f] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Over the past two decades, library-based display technologies have been staggeringly optimized since their appearance in order to mimic the process of natural molecular evolution. Display technologies are essential for the isolation of specific high-affinity binding molecules (proteins, polypeptides, nucleic acids and others) for diagnostic and therapeutic applications in cancer, infectious diseases, autoimmune, neurodegenerative, inflammatory pathologies etc. Applications extend to other fields such as antibody and enzyme engineering, cell-free protein synthesis and the discovery of protein-protein interactions. Phage display technology is the most established of these methods but more recent fully in vitro alternatives, such as ribosome display, mRNA display, cis-activity based (CIS) display and covalent antibody display (CAD), as well as aptamer display and in vitro compartmentalization, offer advantages over phage in library size, speed and the display of unnatural amino acids and nucleotides. Altogether, they have produced several molecules currently approved or in diverse stages of clinical or preclinical testing and have provided researchers with tools to address some of the disadvantages of peptides and nucleotides such as their low affinity, low stability, high immunogenicity and difficulty to cross membranes. In this review we assess the fundamental technological features and point out some recent advances and applications of display technologies.
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Affiliation(s)
- Asier Galán
- ERA Chair FP7, Internal diseases, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000 Zagreb, Croatia.
| | - Lubos Comor
- Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, Kosice, Slovakia
| | - Anita Horvatić
- ERA Chair FP7, Internal diseases, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000 Zagreb, Croatia.
| | - Josipa Kuleš
- ERA Chair FP7, Internal diseases, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000 Zagreb, Croatia.
| | - Nicolas Guillemin
- ERA Chair FP7, Internal diseases, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000 Zagreb, Croatia.
| | - Vladimir Mrljak
- ERA Chair FP7, Internal diseases, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000 Zagreb, Croatia.
| | - Mangesh Bhide
- ERA Chair FP7, Internal diseases, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000 Zagreb, Croatia. and Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, Kosice, Slovakia and Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
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13
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Saeed AFUH, Wang R, Ling S, Wang S. Antibody Engineering for Pursuing a Healthier Future. Front Microbiol 2017; 8:495. [PMID: 28400756 PMCID: PMC5368232 DOI: 10.3389/fmicb.2017.00495] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 03/09/2017] [Indexed: 12/21/2022] Open
Abstract
Since the development of antibody-production techniques, a number of immunoglobulins have been developed on a large scale using conventional methods. Hybridoma technology opened a new horizon in the production of antibodies against target antigens of infectious pathogens, malignant diseases including autoimmune disorders, and numerous potent toxins. However, these clinical humanized or chimeric murine antibodies have several limitations and complexities. Therefore, to overcome these difficulties, recent advances in genetic engineering techniques and phage display technique have allowed the production of highly specific recombinant antibodies. These engineered antibodies have been constructed in the hunt for novel therapeutic drugs equipped with enhanced immunoprotective abilities, such as engaging immune effector functions, effective development of fusion proteins, efficient tumor and tissue penetration, and high-affinity antibodies directed against conserved targets. Advanced antibody engineering techniques have extensive applications in the fields of immunology, biotechnology, diagnostics, and therapeutic medicines. However, there is limited knowledge regarding dynamic antibody development approaches. Therefore, this review extends beyond our understanding of conventional polyclonal and monoclonal antibodies. Furthermore, recent advances in antibody engineering techniques together with antibody fragments, display technologies, immunomodulation, and broad applications of antibodies are discussed to enhance innovative antibody production in pursuit of a healthier future for humans.
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Affiliation(s)
- Abdullah F U H Saeed
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University Fuzhou, China
| | - Rongzhi Wang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University Fuzhou, China
| | - Sumei Ling
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University Fuzhou, China
| | - Shihua Wang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University Fuzhou, China
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14
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Najar TA, Khare S, Pandey R, Gupta SK, Varadarajan R. Mapping Protein Binding Sites and Conformational Epitopes Using Cysteine Labeling and Yeast Surface Display. Structure 2017; 25:395-406. [PMID: 28132782 DOI: 10.1016/j.str.2016.12.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 12/10/2016] [Accepted: 12/28/2016] [Indexed: 11/16/2022]
Abstract
We describe a facile method for mapping protein:ligand binding sites and conformational epitopes. The method uses a combination of Cys scanning mutagenesis, chemical labeling, and yeast surface display. While Ala scanning is widely used for similar purposes, often mutation to Ala (or other amino acids) has little effect on binding, except at hotspot residues. Many residues in physical contact with a binding partner are insensitive to substitution with Ala. In contrast, we show that labeling of Cys residues in a binding site consistently abrogates binding. We couple this methodology to yeast surface display and deep sequencing to map conformational epitopes targeted by both monoclonal antibodies and polyclonal sera as well as a protein:ligand binding site. The method does not require purified protein, can distinguish buried and exposed residues, and can be extended to other display formats, including mammalian cells and viruses, emphasizing its wide applicability.
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Affiliation(s)
- Tariq Ahmad Najar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Shruti Khare
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Rajesh Pandey
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110 020, India
| | - Satish K Gupta
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Raghavan Varadarajan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India; Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur, Bangalore 560 064, India.
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15
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Domina M, Lanza Cariccio V, Benfatto S, Venza M, Venza I, Borgogni E, Castellino F, Midiri A, Galbo R, Romeo L, Biondo C, Masignani V, Teti G, Felici F, Beninati C. Functional characterization of a monoclonal antibody epitope using a lambda phage display-deep sequencing platform. Sci Rep 2016; 6:31458. [PMID: 27530334 PMCID: PMC4987625 DOI: 10.1038/srep31458] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 07/18/2016] [Indexed: 11/10/2022] Open
Abstract
We have recently described a method, named PROFILER, for the identification of antigenic regions preferentially targeted by polyclonal antibody responses after vaccination. To test the ability of the technique to provide insights into the functional properties of monoclonal antibody (mAb) epitopes, we used here a well-characterized epitope of meningococcal factor H binding protein (fHbp), which is recognized by mAb 12C1. An fHbp library, engineered on a lambda phage vector enabling surface expression of polypeptides of widely different length, was subjected to massive parallel sequencing of the phage inserts after affinity selection with the 12C1 mAb. We detected dozens of unique antibody-selected sequences, the most enriched of which (designated as FrC) could largely recapitulate the ability of fHbp to bind mAb 12C1. Computational analysis of the cumulative enrichment of single amino acids in the antibody-selected fragments identified two overrepresented stretches of residues (H248-K254 and S140-G154), whose presence was subsequently found to be required for binding of FrC to mAb 12C1. Collectively, these results suggest that the PROFILER technology can rapidly and reliably identify, in the context of complex conformational epitopes, discrete “hot spots” with a crucial role in antigen-antibody interactions, thereby providing useful clues for the functional characterization of the epitope.
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Affiliation(s)
| | | | | | - Mario Venza
- Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | - Isabella Venza
- Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | | | | | - Angelina Midiri
- Department of Human Pathology, University of Messina, Messina, Italy
| | - Roberta Galbo
- Department of Biological, Chemical and Environmental Sciences, University of Messina, Messina, Italy
| | - Letizia Romeo
- Department of Human Pathology, University of Messina, Messina, Italy
| | - Carmelo Biondo
- Department of Human Pathology, University of Messina, Messina, Italy
| | | | - Giuseppe Teti
- Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy.,Charybdis Vaccines Srl, Messina, Italy
| | - Franco Felici
- Department of Biosciences and Territory, University of Molise, Pesche, Isernia, Italy
| | - Concetta Beninati
- Scylla Biotech Srl, Messina, Italy.,Department of Human Pathology, University of Messina, Messina, Italy
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16
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Volk AL, Hu FJ, Berglund MM, Nordling E, Strömberg P, Uhlen M, Rockberg J. Stratification of responders towards eculizumab using a structural epitope mapping strategy. Sci Rep 2016; 6:31365. [PMID: 27509843 PMCID: PMC4980765 DOI: 10.1038/srep31365] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 07/18/2016] [Indexed: 11/24/2022] Open
Abstract
The complement component 5 (C5)-binding antibody eculizumab is used to treat patients with paroxysmal nocturnal hemoglobinuria (PNH) and atypical haemolytic uremic syndrome (aHUS). As recently reported there is a need for a precise classification of eculizumab responsive patients to allow for a safe and cost-effective treatment. To allow for such stratification, knowledge of the precise binding site of the drug on its target is crucial. Using a structural epitope mapping strategy based on bacterial surface display, flow cytometric sorting and validation via haemolytic activity testing, we identified six residues essential for binding of eculizumab to C5. This epitope co-localizes with the contact area recently identified by crystallography and includes positions in C5 mutated in non-responders. The identified epitope also includes residue W917, which is unique for human C5 and explains the observed lack of cross-reactivity for eculizumab with other primates. We could demonstrate that Ornithodorus moubata complement inhibitor (OmCI), in contrast to eculizumab, maintained anti-haemolytic function for mutations in any of the six epitope residues, thus representing a possible alternative treatment for patients non-responsive to eculizumab. The method for stratification of patients described here allows for precision medicine and should be applicable to several other diseases and therapeutics.
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Affiliation(s)
- Anna-Luisa Volk
- KTH - Royal Institute of Technology, School of Biotechnology, Department of Proteomics and Nanobiotechnology, 106 91 Stockholm, Sweden.,KTH Center for Applied Proteomics, School of Biotechnology, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Francis Jingxin Hu
- KTH - Royal Institute of Technology, School of Biotechnology, Department of Proteomics and Nanobiotechnology, 106 91 Stockholm, Sweden.,KTH Center for Applied Proteomics, School of Biotechnology, KTH - Royal Institute of Technology, Stockholm, Sweden
| | | | - Erik Nordling
- Swedish Orphan Biovitrum AB, 11276 Stockholm, Sweden
| | | | - Mathias Uhlen
- KTH - Royal Institute of Technology, School of Biotechnology, Department of Proteomics and Nanobiotechnology, 106 91 Stockholm, Sweden.,KTH Center for Applied Proteomics, School of Biotechnology, KTH - Royal Institute of Technology, Stockholm, Sweden.,KTH - Royal Institute of Technology, Science for Life Laboratory, 17165 Stockholm, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2970 Hørsholm, Denmark
| | - Johan Rockberg
- KTH - Royal Institute of Technology, School of Biotechnology, Department of Proteomics and Nanobiotechnology, 106 91 Stockholm, Sweden
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17
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Epitope Mapping of a Monoclonal Antibody Directed against Neisserial Heparin Binding Antigen Using Next Generation Sequencing of Antigen-Specific Libraries. PLoS One 2016; 11:e0160702. [PMID: 27508302 PMCID: PMC4980009 DOI: 10.1371/journal.pone.0160702] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 07/22/2016] [Indexed: 01/07/2023] Open
Abstract
We explore here the potential of a newly described technology, which is named PROFILER and is based on next generation sequencing of gene-specific lambda phage-displayed libraries, to rapidly and accurately map monoclonal antibody (mAb) epitopes. For this purpose, we used a novel mAb (designated 31E10/E7) directed against Neisserial Heparin-Binding Antigen (NHBA), a component of the anti-group B meningococcus Bexsero® vaccine. An NHBA phage-displayed library was affinity-selected with mAb 31E10/E7, followed by massive sequencing of the inserts present in antibody-selected phage pools. Insert analysis identified an amino acid stretch (D91-A128) in the N-terminal domain, which was shared by all of the mAb-enriched fragments. Moreover, a recombinant fragment encompassing this sequence could recapitulate the immunoreactivity of the entire NHBA molecule against mAb 31E10/E7. These results were confirmed using a panel of overlapping recombinant fragments derived from the NHBA vaccine variant and a set of chemically synthetized peptides covering the 10 most frequent antigenic variants. Furthermore, hydrogen-deuterium exchange mass-spectrometry analysis of the NHBA-mAb 31E10/E7 complex was also compatible with mapping of the epitope to the D91-A128 region. Collectively, these results indicate that the PROFILER technology can reliably identify epitope-containing antigenic fragments and requires considerably less work, time and reagents than other epitope mapping methods.
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18
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Bao S, Yu S, Guo X, Zhang F, Sun Y, Tan L, Duan Y, Lu F, Qiu X, Ding C. Construction of a cell-surface display system based on the N-terminal domain of ice nucleation protein and its application in identification of mycoplasma
adhesion proteins. J Appl Microbiol 2015; 119:236-44. [DOI: 10.1111/jam.12824] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 03/30/2015] [Accepted: 03/31/2015] [Indexed: 11/30/2022]
Affiliation(s)
- S. Bao
- Shanghai Veterinary Research Institute; Chinese Academy of Agricultural Sciences; Shanghai China
- College of Veterinary Medicine; Gansu Agricultural University; Lanzhou China
| | - S. Yu
- Shanghai Veterinary Research Institute; Chinese Academy of Agricultural Sciences; Shanghai China
| | - X. Guo
- College of Veterinary Medicine; Gansu Agricultural University; Lanzhou China
| | - F. Zhang
- Shanghai Veterinary Research Institute; Chinese Academy of Agricultural Sciences; Shanghai China
| | - Y. Sun
- Shanghai Veterinary Research Institute; Chinese Academy of Agricultural Sciences; Shanghai China
| | - L. Tan
- Shanghai Veterinary Research Institute; Chinese Academy of Agricultural Sciences; Shanghai China
| | - Y. Duan
- Shanghai Veterinary Research Institute; Chinese Academy of Agricultural Sciences; Shanghai China
| | - F. Lu
- College of Veterinary Medicine; Gansu Agricultural University; Lanzhou China
| | - X. Qiu
- Shanghai Veterinary Research Institute; Chinese Academy of Agricultural Sciences; Shanghai China
| | - C. Ding
- Shanghai Veterinary Research Institute; Chinese Academy of Agricultural Sciences; Shanghai China
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19
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Hu FJ, Uhlen M, Rockberg J. Generation of HER2 monoclonal antibodies using epitopes of a rabbit polyclonal antibody. N Biotechnol 2014; 31:35-43. [PMID: 24120493 DOI: 10.1016/j.nbt.2013.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 09/25/2013] [Accepted: 10/01/2013] [Indexed: 10/26/2022]
Abstract
One of the issues in using polyclonal antibodies is the limited amount of reagent available from an immunisation, leading to batch-to-batch variation and difficulties in obtaining the same antibody performance when the same antigen is re-immunised into several separate animals. This led to the development of hybridoma technology allowing, at least theoretically, for an unlimited production of a specific binder. Nevertheless, polyclonal antibodies are widely used in research and diagnostics and there exists a need for robust methods to convert a polyclonal antibody with good binding performance into a renewable monoclonal with identical or similar binding specificity. Here we have used precise information regarding the functional recognition sequence (epitope) of a rabbit polyclonal antibody with attractive binding characteristics as the basis for generation of a renewable mouse monoclonal antibody. First, the original protein fragment antigen was used for immunisation and generation of mouse hybridoma, without obtaining binders to the same epitope region. Instead a peptide designed using the functional epitope and structural information was synthesised and used for hybridoma production. Several of the monoclonal antibodies generated were found to have similar binding characteristics to those of the original polyclonal antibody. These monoclonal antibodies detected native HER2 on cell lines and were also able to stain HER2 in immunohistochemistry using xenografted mice, as well as human normal and cancer tissues.
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Affiliation(s)
- Francis Jingxin Hu
- School of Biotechnology, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
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20
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Volk AL, Hu FJ, Rockberg J. Epitope mapping of monoclonal and polyclonal antibodies using bacterial cell surface display. Methods Mol Biol 2014; 1131:485-500. [PMID: 24515484 DOI: 10.1007/978-1-62703-992-5_29] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The unique property of specific high-affinity binding to more or less any target of interest has made antibodies tremendously useful in numerous applications. Hence knowledge of the precise binding site (epitope) of antibodies on the target protein is one of the most important features for understanding its performance and determining its reliability in immunoassays. Here, we describe a high-resolution method for mapping epitopes of antibodies based on bacterial surface expression of antigen fragments followed by antibody-based flow cytometric sorting. Epitopes are determined by DNA sequencing of the sorted antibody-binding cells followed by sequence alignment back to the antigen sequence. The method described here has been useful for the mapping of both monoclonal and polyclonal antibodies with varying sizes of epitopes.
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Affiliation(s)
- Anna-Luisa Volk
- School of Biotechnology, AlbaNova University Center, KTH - Royal Institute of Technology, Stockholm, Sweden
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21
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Castelli M, Cappelletti F, Diotti RA, Sautto G, Criscuolo E, Dal Peraro M, Clementi N. Peptide-based vaccinology: experimental and computational approaches to target hypervariable viruses through the fine characterization of protective epitopes recognized by monoclonal antibodies and the identification of T-cell-activating peptides. Clin Dev Immunol 2013; 2013:521231. [PMID: 23878584 PMCID: PMC3710646 DOI: 10.1155/2013/521231] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 06/06/2013] [Indexed: 12/20/2022]
Abstract
Defining immunogenic domains of viral proteins capable of eliciting a protective immune response is crucial in the development of novel epitope-based prophylactic strategies. This is particularly important for the selective targeting of conserved regions shared among hypervariable viruses. Studying postinfection and postimmunization sera, as well as cloning and characterization of monoclonal antibodies (mAbs), still represents the best approach to identify protective epitopes. In particular, a protective mAb directed against conserved regions can play a key role in immunogen design and in human therapy as well. Experimental approaches aiming to characterize protective mAb epitopes or to identify T-cell-activating peptides are often burdened by technical limitations and can require long time to be correctly addressed. Thus, in the last decade many epitope predictive algorithms have been developed. These algorithms are continually evolving, and their use to address the empirical research is widely increasing. Here, we review several strategies based on experimental techniques alone or addressed by in silico analysis that are frequently used to predict immunogens to be included in novel epitope-based vaccine approaches. We will list the main strategies aiming to design a new vaccine preparation conferring the protection of a neutralizing mAb combined with an effective cell-mediated response.
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Affiliation(s)
- Matteo Castelli
- Microbiology and Virology Institute, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Francesca Cappelletti
- Microbiology and Virology Institute, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Roberta Antonia Diotti
- Microbiology and Virology Institute, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Giuseppe Sautto
- Microbiology and Virology Institute, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Elena Criscuolo
- Microbiology and Virology Institute, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Matteo Dal Peraro
- Laboratory for Biomolecular Modeling, Institute of Bioingeneering, School of Life Sciences, Ecole Polytechnique Fédérale, 1015 Lausanne, Switzerland
| | - Nicola Clementi
- Microbiology and Virology Institute, Vita-Salute San Raffaele University, 20132 Milan, Italy
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