1
|
Gutiérrez LJ, Tosso RD, Zarycz MNC, Enriz RD, Baldoni HA. Epitopes mapped onto SARS-CoV-2 receptor-binding motif by five distinct human neutralising antibodies. Molecular Simulation 2022. [DOI: 10.1080/08927022.2022.2111421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Lucas J. Gutiérrez
- Multidisciplinary Institute of Biological Research (IMIBIO-SL. CONICET), San Luis, Argentina
- Faculty of Chemistry, Biochemistry and Pharmacy, National University of San Luis, San Luis, Argentina
| | - Rodrigo D. Tosso
- Multidisciplinary Institute of Biological Research (IMIBIO-SL. CONICET), San Luis, Argentina
- Faculty of Chemistry, Biochemistry and Pharmacy, National University of San Luis, San Luis, Argentina
| | - M. Natalia C. Zarycz
- Multidisciplinary Institute of Biological Research (IMIBIO-SL. CONICET), San Luis, Argentina
| | - Ricardo D. Enriz
- Multidisciplinary Institute of Biological Research (IMIBIO-SL. CONICET), San Luis, Argentina
- Faculty of Chemistry, Biochemistry and Pharmacy, National University of San Luis, San Luis, Argentina
| | - Héctor A. Baldoni
- Faculty of Chemistry, Biochemistry and Pharmacy, National University of San Luis, San Luis, Argentina
- Institute of Applied Mathematics of San Luis (IMASL. CONICET), San Luis, Argentina
| |
Collapse
|
2
|
Mittal L, Srivastava M, Kumari A, Tonk RK, Awasthi A, Asthana S. Interplay among Structural Stability, Plasticity, and Energetics Determined by Conformational Attuning of Flexible Loops in PD-1. J Chem Inf Model 2021; 61:358-384. [PMID: 33433201 DOI: 10.1021/acs.jcim.0c01080] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The dynamics and plasticity of the PD-1/PD-L1 axis are the bottlenecks for the discovery of small-molecule antagonists to perturb this interaction interface significantly. Understanding the process of this protein-protein interaction (PPI) is of fundamental biological interest in structure-based drug designing. Food and Drug Administration (FDA)-approved anti-PD-1 monoclonal antibodies (mAbs) are the first-in-class with distinct binding modes to access this axis clinically; however, their mechanistic aspects remain elusive. Here, we have unveiled the interactive interfaces with PD-L1 and mAbs to investigate the native plasticity of PD-1 at global (structural and dynamical) and local (residue side-chain orientations) levels. We found that the structural stability and coordinated Cα movements are increased in the presence of PD-1's binding partners. The rigorous analysis of these PPIs using computational biophysical approaches revealed PD-1's intrinsic plasticity, its concerted loops' movement (BC, FG, and CC'), distal side-chain motions, and the thermodynamic landscape, which are perturbed remarkably from its unbound to bound states. Based on intra-/inter-residues' contact networks and energetics, the hot-spots have been identified that were found to be essential to arrest the dynamical motions of PD-1 significantly for the rational design of therapeutic agents by mimicking the mAbs mechanism.
Collapse
Affiliation(s)
- Lovika Mittal
- NCR Biotech Science Cluster, Translational Health Science and Technology Institute (THSTI), 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, Haryana 121001, India.,Delhi Pharmaceutical Sciences and Research University (DPSRU), Delhi 110017, India
| | - Mitul Srivastava
- NCR Biotech Science Cluster, Translational Health Science and Technology Institute (THSTI), 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, Haryana 121001, India
| | - Anita Kumari
- NCR Biotech Science Cluster, Translational Health Science and Technology Institute (THSTI), 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, Haryana 121001, India
| | - Rajiv K Tonk
- Delhi Pharmaceutical Sciences and Research University (DPSRU), Delhi 110017, India
| | - Amit Awasthi
- NCR Biotech Science Cluster, Translational Health Science and Technology Institute (THSTI), 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, Haryana 121001, India
| | - Shailendra Asthana
- NCR Biotech Science Cluster, Translational Health Science and Technology Institute (THSTI), 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, Haryana 121001, India
| |
Collapse
|
3
|
Abstract
The increase in the number of both patients and healthcare practitioners who grew up using the Internet and computers (so-called "digital natives") is likely to impact the practice of precision medicine, and requires novel platforms for data integration and mining, as well as contextualized information retrieval. The "Illuminating the Druggable Genome Knowledge Management Center" (IDG KMC) quantifies data availability from a wide range of chemical, biological, and clinical resources, and has developed platforms that can be used to navigate understudied proteins (the "dark genome"), and their potential contribution to specific pathologies. Using the "Target Importance and Novelty Explorer" (TIN-X) highlights the role of LRRC10 (a dark gene) in dilated cardiomyopathy. Combining mouse and human phenotype data leads to increased strength of evidence, which is discussed for four additional dark genes: SLX4IP and its role in glucose metabolism, the role of HSF2BP in coronary artery disease, the involvement of ELFN1 in attention-deficit hyperactivity disorder and the role of VPS13D in mouse neural tube development and its confirmed role in childhood onset movement disorders. The workflow and tools described here are aimed at guiding further experimental research, particularly within the context of precision medicine.
Collapse
Affiliation(s)
- Tudor I Oprea
- Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM, USA. .,UNM Comprehensive Cancer Center, Albuquerque, NM, USA. .,Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden. .,Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
4
|
Alzogaray V, Urrutia M, Berguer P, Rossi A, Zylberman V, Pardo R, Bonomi HR, Goldbaum FA. Characterization of folding-sensitive nanobodies as tools to study the expression and quality of protein particle immunogens. J Biotechnol 2019; 293:17-23. [PMID: 30690101 DOI: 10.1016/j.jbiotec.2019.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 12/04/2018] [Accepted: 01/07/2019] [Indexed: 01/05/2023]
Abstract
Vaccination is as one of the most beneficial biopharmaceutical interventions against pathogens due to its ability to induce adaptive immunity through targeted activation of the immune system. Each vaccine needs a tailor-made set of tests in order to monitor its quality throughout the development and manufacturing. The analysis of the conformational state of protein nanoparticles is one of the key steps in vaccine quality control. The enzyme lumazine synthase from Brucella spp. (BLS) acts as a potent oral and systemic immunogen. BLS has been used as a carrier of foreign peptides, protein domains and whole proteins, serving as a versatile platform for vaccine engineering purposes. Here, we show the generation and characterization of four families of nanobodies (Nbs) which only recognize BLS in its native conformational state and that bind to its active site. The present results support the use of conformation-sensitive Nbs as molecular probes during the development and production of vaccines based on the BLS platform. Finally, we propose Nbs as useful molecular tools targeting other protein scaffolds with potential applications in nano-and biotechnology.
Collapse
Affiliation(s)
- Vanina Alzogaray
- Fundación Instituto Leloir, IIBBA-CONICET, Avenida Patricias Argentinas 435 (C1405BWE), Ciudad de Buenos Aires, Argentina
| | - Mariela Urrutia
- Fundación Instituto Leloir, IIBBA-CONICET, Avenida Patricias Argentinas 435 (C1405BWE), Ciudad de Buenos Aires, Argentina
| | - Paula Berguer
- Fundación Instituto Leloir, IIBBA-CONICET, Avenida Patricias Argentinas 435 (C1405BWE), Ciudad de Buenos Aires, Argentina
| | - Andrés Rossi
- Fundación Instituto Leloir, IIBBA-CONICET, Avenida Patricias Argentinas 435 (C1405BWE), Ciudad de Buenos Aires, Argentina
| | - Vanesa Zylberman
- INMUNOVA, 25 de Mayo 1021 (B1650HMI), San Martin, Buenos Aires, Argentina
| | - Romina Pardo
- INMUNOVA, 25 de Mayo 1021 (B1650HMI), San Martin, Buenos Aires, Argentina
| | - Hernán R Bonomi
- Fundación Instituto Leloir, IIBBA-CONICET, Avenida Patricias Argentinas 435 (C1405BWE), Ciudad de Buenos Aires, Argentina
| | - Fernando A Goldbaum
- Fundación Instituto Leloir, IIBBA-CONICET, Avenida Patricias Argentinas 435 (C1405BWE), Ciudad de Buenos Aires, Argentina.
| |
Collapse
|
5
|
Li J, Chen G. The use of fast photochemical oxidation of proteins coupled with mass spectrometry in protein therapeutics discovery and development. Drug Discov Today 2019; 24:829-34. [DOI: 10.1016/j.drudis.2018.12.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 11/27/2018] [Accepted: 12/18/2018] [Indexed: 01/05/2023]
|
6
|
Opuni KFM, Al-Majdoub M, Yefremova Y, El-Kased RF, Koy C, Glocker MO. Mass spectrometric epitope mapping. Mass Spectrom Rev 2018; 37:229-241. [PMID: 27403762 DOI: 10.1002/mas.21516] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 06/23/2016] [Indexed: 06/06/2023]
Abstract
Mass spectrometric epitope mapping has become a versatile method to precisely determine a soluble antigen's partial structure that directly interacts with an antibody in solution. Typical lengths of investigated antigens have increased up to several 100 amino acids while experimentally determined epitope peptides have decreased in length to on average 10-15 amino acids. Since the early 1990s more and more sophisticated methods have been developed and have forwarded a bouquet of suitable approaches for epitope mapping with immobilized, temporarily immobilized, and free-floating antibodies. While up to now monoclonal antibodies have been mostly used in epitope mapping experiments, the applicability of polyclonal antibodies has been proven. The antibody's resistance towards enzymatic proteolysis has been of key importance for the two mostly applied methods: epitope excision and epitope extraction. Sample consumption has dropped to low pmol amounts on both, the antigen and the antibody. While adequate in-solution sample handling has been most important for successful epitope mapping, mass spectrometric analysis has been found the most suitable read-out method from early on. The rapidity by which mass spectrometric epitope mapping nowadays is executed outperforms all alternative methods. Thus, it can be asserted that mass spectrometric epitope mapping has reached a state of maturity, which allows it to be used in any mass spectrometry laboratory. After 25 years of constant and steady improvements, its application to clinical samples, for example, for patient characterization and stratification, is anticipated in the near future. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 37:229-241, 2018.
Collapse
Affiliation(s)
- Kwabena F M Opuni
- Proteome Center Rostock, University Medicine and Natural Science Faculty, University of Rostock, Rostock, Germany
| | - Mahmoud Al-Majdoub
- Proteome Center Rostock, University Medicine and Natural Science Faculty, University of Rostock, Rostock, Germany
| | - Yelena Yefremova
- Proteome Center Rostock, University Medicine and Natural Science Faculty, University of Rostock, Rostock, Germany
| | - Reham F El-Kased
- Microbiology and Immunology Faculty of Pharmacy, The British University in Egypt, Cairo, Egypt
| | - Cornelia Koy
- Proteome Center Rostock, University Medicine and Natural Science Faculty, University of Rostock, Rostock, Germany
| | - Michael O Glocker
- Proteome Center Rostock, University Medicine and Natural Science Faculty, University of Rostock, Rostock, Germany
| |
Collapse
|
7
|
Criscuolo E, Clementi N, Mancini N, Burioni R, Miduri M, Castelli M, Clementi M. Synergy evaluation of anti-Herpes Simplex Virus type 1 and 2 compounds acting on different steps of virus life cycle. Antiviral Res 2018; 151:71-77. [DOI: 10.1016/j.antiviral.2018.01.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 01/08/2018] [Accepted: 01/14/2018] [Indexed: 01/06/2023]
|
8
|
Clementi N, Cappelletti F, Criscuolo E, Castelli M, Mancini N, Burioni R, Clementi M. Role and potential therapeutic use of antibodies against herpetic infections. Clin Microbiol Infect 2017; 23:381-386. [DOI: 10.1016/j.cmi.2016.12.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 12/14/2016] [Accepted: 12/24/2016] [Indexed: 11/30/2022]
|
9
|
Xin L, Yu H, Hong Q, Bi X, Zhang X, Zhang Z, Kong Z, Zheng Q, Gu Y, Zhao Q, Zhang J, Li S, Xia N. Identification of Strategic Residues at the Interface of Antigen-Antibody Interactions by In Silico Mutagenesis. Interdiscip Sci 2017; 10:438-448. [PMID: 28560699 DOI: 10.1007/s12539-017-0242-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 04/17/2017] [Accepted: 05/22/2017] [Indexed: 11/24/2022]
Abstract
Structural information pertaining to antigen-antibody interactions is fundamental in immunology, and benefits structure-based vaccine design. Modeling of antigen-antibody immune complexes from co-crystal structures or molecular docking simulations provides an extensive profile of the epitope at the interface; however, the key amino acids involved in the interaction must be further clarified, often through the use of experimental mutagenesis and subsequent binding assays. Here, we describe an in silico mutagenesis method to identify key sites at antigen-antibody interfaces, using significant increase in pH-dependency energy among saturated point mutations. Through a comprehensive analysis of the crystal structures of three antigen-antibody immune complexes, we show that a cutoff value of 1 kcal/mol of increased interaction energy provides good congruency with the experimental non-binding mutations conducted in vitro. This in silico mutagenesis strategy, in association with energy calculations, may provide an efficient tool for antibody-antigen interface analyses, epitope optimization, and/or conformation prediction in structure-based vaccine design.
Collapse
Affiliation(s)
- Lu Xin
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, 361002, Fujian, People's Republic of China
| | - Hai Yu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, 361002, Fujian, People's Republic of China. .,School of Public Health, Xiamen University, Xiamen, 361005, Fujian, People's Republic of China.
| | - Qiyang Hong
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Sciences, Xiamen University, Xiamen, 361002, Fujian, People's Republic of China
| | - Xingjian Bi
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, 361002, Fujian, People's Republic of China
| | - Xiao Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, 361002, Fujian, People's Republic of China
| | - Zhiqing Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, 361002, Fujian, People's Republic of China
| | - Zhibo Kong
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, 361002, Fujian, People's Republic of China
| | - Qingbing Zheng
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, 361002, Fujian, People's Republic of China
| | - Ying Gu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, 361002, Fujian, People's Republic of China.,National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Sciences, Xiamen University, Xiamen, 361002, Fujian, People's Republic of China
| | - Qinjian Zhao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, 361002, Fujian, People's Republic of China
| | - Jun Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, 361002, Fujian, People's Republic of China
| | - Shaowei Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, 361002, Fujian, People's Republic of China.,National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Sciences, Xiamen University, Xiamen, 361002, Fujian, People's Republic of China
| | - Ningshao Xia
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, 361002, Fujian, People's Republic of China.,National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Sciences, Xiamen University, Xiamen, 361002, Fujian, People's Republic of China
| |
Collapse
|
10
|
Clementi N, Criscuolo E, Cappelletti F, Quaranta P, Pistello M, Diotti RA, Sautto GA, Tarr AW, Mailland F, Concas D, Burioni R, Clementi M, Mancini N. Entry inhibition of HSV-1 and -2 protects mice from viral lethal challenge. Antiviral Res 2017; 143:48-61. [PMID: 28396205 DOI: 10.1016/j.antiviral.2017.03.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 03/29/2017] [Accepted: 03/31/2017] [Indexed: 11/26/2022]
Abstract
The present study focused on inhibition of HSV-1 and -2 replication and pathogenesis in vitro and in vivo, through the selective targeting of the envelope glycoprotein D. Firstly, a human monoclonal antibody (Hu-mAb#33) was identified that could neutralise both HSV-1 and -2 at nM concentrations, including clinical isolates from patients affected by different clinical manifestations and featuring different susceptibility to acyclovir in vitro. Secondly, the potency of inhibition of both infection by cell-free viruses and cell-to-cell virus transmission was also assessed. Finally, mice receiving a single systemic injection of Hu-mAb#33 were protected from death and severe clinical manifestations following both ocular and vaginal HSV-1 and -2 lethal challenge. These results pave the way for further studies reassessing the importance of HSV entry as a novel target for therapeutic intervention and inhibition of cell-to-cell virus transmission.
Collapse
Affiliation(s)
- Nicola Clementi
- Microbiology and Virology Unit, 'Vita-Salute San Raffaele' University, Milan, Italy.
| | - Elena Criscuolo
- Microbiology and Virology Unit, 'Vita-Salute San Raffaele' University, Milan, Italy
| | | | - Paola Quaranta
- Department of Translational Research, University of Pisa, Pisa, Italy
| | - Mauro Pistello
- Department of Translational Research, University of Pisa, Pisa, Italy
| | - Roberta A Diotti
- Microbiology and Virology Unit, 'Vita-Salute San Raffaele' University, Milan, Italy
| | - Giuseppe A Sautto
- Microbiology and Virology Unit, 'Vita-Salute San Raffaele' University, Milan, Italy
| | - Alexander W Tarr
- School of Life Sciences & NIHR Biomedical Research Unit in Gastrointestinal & Liver Diseases, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, United Kingdom
| | | | - Daniela Concas
- Wezen Bio AG, Fondation pour Recherches Medicales, Geneva, Switzerland
| | - Roberto Burioni
- Microbiology and Virology Unit, 'Vita-Salute San Raffaele' University, Milan, Italy; Laboratory of Microbiology and Virology, San Raffaele Hospital, Milan, Italy
| | - Massimo Clementi
- Microbiology and Virology Unit, 'Vita-Salute San Raffaele' University, Milan, Italy; Laboratory of Microbiology and Virology, San Raffaele Hospital, Milan, Italy
| | - Nicasio Mancini
- Microbiology and Virology Unit, 'Vita-Salute San Raffaele' University, Milan, Italy; Laboratory of Microbiology and Virology, San Raffaele Hospital, Milan, Italy
| |
Collapse
|
11
|
Li J, Wei H, Krystek SR, Bond D, Brender TM, Cohen D, Feiner J, Hamacher N, Harshman J, Huang RYC, Julien SH, Lin Z, Moore K, Mueller L, Noriega C, Sejwal P, Sheppard P, Stevens B, Chen G, Tymiak AA, Gross ML, Schneeweis LA. Mapping the Energetic Epitope of an Antibody/Interleukin-23 Interaction with Hydrogen/Deuterium Exchange, Fast Photochemical Oxidation of Proteins Mass Spectrometry, and Alanine Shave Mutagenesis. Anal Chem 2017; 89:2250-2258. [PMID: 28193005 PMCID: PMC5347259 DOI: 10.1021/acs.analchem.6b03058] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Epitope mapping the specific residues of an antibody/antigen interaction can be used to support mechanistic interpretation, antibody optimization, and epitope novelty assessment. Thus, there is a strong need for mapping methods, particularly integrative ones. Here, we report the identification of an energetic epitope by determining the interfacial hot-spot that dominates the binding affinity for an anti-interleukin-23 (anti-IL-23) antibody by using the complementary approaches of hydrogen/deuterium exchange mass spectrometry (HDX-MS), fast photochemical oxidation of proteins (FPOP), alanine shave mutagenesis, and binding analytics. Five peptide regions on IL-23 with reduced backbone amide solvent accessibility upon antibody binding were identified by HDX-MS, and five different peptides over the same three regions were identified by FPOP. In addition, FPOP analysis at the residue level reveals potentially key interacting residues. Mutants with 3-5 residues changed to alanine have no measurable differences from wild-type IL-23 except for binding of and signaling blockade by the 7B7 anti-IL-23 antibody. The M5 IL-23 mutant differs from wild-type by five alanine substitutions and represents the dominant energetic epitope of 7B7. M5 shows a dramatic decrease in binding to BMS-986010 (which contains the 7B7 Fab, where Fab is fragment antigen-binding region of an antibody), yet it maintains functional activity, binding to p40 and p19 specific reagents, and maintains biophysical properties similar to wild-type IL-23 (monomeric state, thermal stability, and secondary structural features).
Collapse
Affiliation(s)
- Jing Li
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130-4889, USA
| | - Hui Wei
- Biologics Development, Bristol-Myers Squibb, 311 Pennington-Rocky Hill Road, Pennington, NJ 08534
| | - Stanley R. Krystek
- Molecular Structure & Design, Bristol-Myers Squibb, Rt. 206 & Province Line Rd, Princeton, NJ 08543
| | - Derek Bond
- Process Development, Bristol-Myers Squibb, 1201 Eastlake Ave E., Seattle WA 98102
| | - Ty M. Brender
- Discovery Biology, Bristol-Myers Squibb, 1201 Eastlake Ave E., Seattle WA 98102
| | - Daniel Cohen
- Protein Science, Bristol-Myers Squibb, Rt. 206 & Province Line Rd, Princeton, NJ 08543
| | - Jena Feiner
- Applied Genomics, Bristol-Myers Squibb, 311 Pennington-Rocky Hill Road, Pennington, NJ 08534
| | - Nels Hamacher
- Molecular Structure & Design, Bristol-Myers Squibb, Rt. 206 & Province Line Rd, Princeton, NJ 08543
| | - Johanna Harshman
- Molecular Structure & Design, Bristol-Myers Squibb, Rt. 206 & Province Line Rd, Princeton, NJ 08543
| | - Richard Y.-C. Huang
- Bioanalytical and Discovery Analytical Sciences, Research and Development, Bristol-Myers Squibb, Rt. 206 & Province Line Rd, Princeton, NJ 08543
| | - Susan H. Julien
- Protein Engineering, Bristol-Myers Squibb, 1201 Eastlake Ave E., Seattle WA 98102
| | - Zheng Lin
- Protein Science, Bristol-Myers Squibb, Rt. 206 & Province Line Rd, Princeton, NJ 08543
| | - Kristina Moore
- Protein Science, Bristol-Myers Squibb, Rt. 206 & Province Line Rd, Princeton, NJ 08543
| | - Luciano Mueller
- Bioanalytical and Discovery Analytical Sciences, Research and Development, Bristol-Myers Squibb, Rt. 206 & Province Line Rd, Princeton, NJ 08543
| | - Claire Noriega
- Protein Engineering, Bristol-Myers Squibb, 1201 Eastlake Ave E., Seattle WA 98102
| | - Preeti Sejwal
- Bioanalytical and Discovery Analytical Sciences, Research and Development, Bristol-Myers Squibb, Rt. 206 & Province Line Rd, Princeton, NJ 08543
| | - Paul Sheppard
- Protein Engineering, Bristol-Myers Squibb, 1201 Eastlake Ave E., Seattle WA 98102
| | - Brenda Stevens
- Protein Engineering, Bristol-Myers Squibb, 1201 Eastlake Ave E., Seattle WA 98102
| | - Guodong Chen
- Bioanalytical and Discovery Analytical Sciences, Research and Development, Bristol-Myers Squibb, Rt. 206 & Province Line Rd, Princeton, NJ 08543
| | - Adrienne A. Tymiak
- Bioanalytical and Discovery Analytical Sciences, Research and Development, Bristol-Myers Squibb, Rt. 206 & Province Line Rd, Princeton, NJ 08543
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130-4889, USA
| | - Lumelle A. Schneeweis
- Protein Science, Bristol-Myers Squibb, Rt. 206 & Province Line Rd, Princeton, NJ 08543
| |
Collapse
|
12
|
Deng B, Lento C, Wilson DJ. Hydrogen deuterium exchange mass spectrometry in biopharmaceutical discovery and development – A review. Anal Chim Acta 2016; 940:8-20. [DOI: 10.1016/j.aca.2016.08.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 07/25/2016] [Accepted: 08/07/2016] [Indexed: 01/14/2023]
|
13
|
Clementi N, Criscuolo E, Cappelletti F, Burioni R, Clementi M, Mancini N. Novel therapeutic investigational strategies to treat severe and disseminated HSV infections suggested by a deeper understanding of in vitro virus entry processes. Drug Discov Today 2016; 21:682-91. [PMID: 26976690 DOI: 10.1016/j.drudis.2016.03.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 02/11/2016] [Accepted: 03/04/2016] [Indexed: 01/28/2023]
Abstract
The global burden of herpes simplex virus (HSV) legitimates the critical need to develop new prevention strategies, such as drugs and vaccines that are able to fight either primary HSV infections or reactivations. Moreover, the ever-growing number of patients receiving transplants increases the number of severe HSV infections that are unresponsive to current therapies. Finally, the high global incidence of genital HSV-2 infection increases the risk of perinatal transmission to newborns, in which disseminated infection or central nervous system (CNS) involvement is frequent, with associated high morbidity and mortality rates. There are several key features shared by novel anti-HSV drugs, from currently available optimized drugs to small molecules able to interfere with various virus replication steps. However, several virological aspects of the disease and associated clinical needs highlight why an ideal anti-HSV drug has yet to be developed.
Collapse
Affiliation(s)
- Nicola Clementi
- Microbiology and Virology Unit, 'Vita-Salute San Raffaele' University, 20132 Milan, Italy.
| | - Elena Criscuolo
- Microbiology and Virology Unit, 'Vita-Salute San Raffaele' University, 20132 Milan, Italy
| | - Francesca Cappelletti
- Microbiology and Virology Unit, 'Vita-Salute San Raffaele' University, 20132 Milan, Italy
| | - Roberto Burioni
- Microbiology and Virology Unit, 'Vita-Salute San Raffaele' University, 20132 Milan, Italy
| | - Massimo Clementi
- Microbiology and Virology Unit, 'Vita-Salute San Raffaele' University, 20132 Milan, Italy
| | - Nicasio Mancini
- Microbiology and Virology Unit, 'Vita-Salute San Raffaele' University, 20132 Milan, Italy
| |
Collapse
|
14
|
Iacob RE, Krystek SR, Huang RYC, Wei H, Tao L, Lin Z, Morin PE, Doyle ML, Tymiak AA, Engen JR, Chen G. Hydrogen/deuterium exchange mass spectrometry applied to IL-23 interaction characteristics: potential impact for therapeutics. Expert Rev Proteomics 2015; 12:159-69. [PMID: 25711416 DOI: 10.1586/14789450.2015.1018897] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
IL-23 is an important therapeutic target for the treatment of inflammatory diseases. Adnectins are targeted protein therapeutics that are derived from domain III of human fibronectin and have a similar protein scaffold to antibodies. Adnectin 2 was found to bind to IL-23 and compete with the IL-23/IL-23R interaction, posing a potential protein therapeutic. Hydrogen/deuterium exchange mass spectrometry and computational methods were applied to probe the binding interactions between IL-23 and Adnectin 2 and to determine the correlation between the two orthogonal methods. This review summarizes the current structural knowledge about IL-23 and focuses on the applicability of hydrogen/deuterium exchange mass spectrometry to investigate the higher order structure of proteins, which plays an important role in the discovery of new and improved biotherapeutics.
Collapse
Affiliation(s)
- Roxana E Iacob
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Iacob RE, Chen G, Ahn J, Houel S, Wei H, Mo J, Tao L, Cohen D, Xie D, Lin Z, Morin PE, Doyle ML, Tymiak AA, Engen JR. The influence of adnectin binding on the extracellular domain of epidermal growth factor receptor. J Am Soc Mass Spectrom 2014; 25:2093-2102. [PMID: 25223306 PMCID: PMC4224629 DOI: 10.1007/s13361-014-0973-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 07/29/2014] [Accepted: 08/03/2014] [Indexed: 06/03/2023]
Abstract
The precise and unambiguous elucidation and characterization of interactions between a high affinity recognition entity and its cognate protein provides important insights for the design and development of drugs with optimized properties and efficacy. In oncology, one important target protein has been shown to be the epidermal growth factor receptor (EGFR) through the development of therapeutic anticancer antibodies that are selective inhibitors of EGFR activity. More recently, smaller protein derived from the 10th type III domain of human fibronectin termed an adnectin has also been shown to inhibit EGFR in clinical studies. The mechanism of EGFR inhibition by either an adnectin or an antibody results from specific binding of the high affinity protein to the extracellular portion of EGFR (exEGFR) in a manner that prevents phosphorylation of the intracellular kinase domain of the receptor and thereby blocks intracellular signaling. Here, the structural changes induced upon binding were studied by probing the solution conformations of full length exEGFR alone and bound to a cognate adnectin through hydrogen/deuterium exchange mass spectrometry (HDX MS). The effects of binding in solution were identified and compared with the structure of a bound complex determined by X-ray crystallography.ᅟ
Collapse
Affiliation(s)
- Roxana E. Iacob
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA USA
| | - Guodong Chen
- Bioanalytical and Discovery Analytical Sciences, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Joomi Ahn
- Waters Corporation, Milford, MA, USA
| | | | - Hui Wei
- Bioanalytical and Discovery Analytical Sciences, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Jingjie Mo
- Bioanalytical and Discovery Analytical Sciences, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Li Tao
- Biologics Manufacturing and Process Development, Global Manufacturing and Supply, Bristol-Myers Squibb Company, Hopewell, NJ, USA
| | - Daniel Cohen
- Protein Science, Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Dianlin Xie
- Protein Science, Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Zheng Lin
- Protein Science, Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Paul E. Morin
- Protein Science, Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Michael L. Doyle
- Protein Science, Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Adrienne A. Tymiak
- Bioanalytical and Discovery Analytical Sciences, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - John R. Engen
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA USA
| |
Collapse
|
16
|
Clementi N, Mancini N, Criscuolo E, Cappelletti F, Clementi M, Burioni R. Epitope mapping by epitope excision, hydrogen/deuterium exchange, and peptide-panning techniques combined with in silico analysis. Methods Mol Biol 2014; 1131:427-46. [PMID: 24515481 DOI: 10.1007/978-1-62703-992-5_26] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
The fine characterization of protective B cell epitopes plays a pivotal role in the development of novel vaccines. The development of epitope-based vaccines, in fact, cannot be possible without a clear definition of the antigenic regions involved in the binding between the protective antibody (Ab) and its molecular target. To achieve this result, different epitope-mapping approaches have been widely described (Clementi et al. Drug Discov Today 18(9-10):464-471, 2013). Nowadays, the best way to characterize an Ab bound region is still the resolution of Ab-antigen (Ag) co-crystal structure. Unfortunately, the crystallization approaches are not always feasible. However, different experimental strategies aimed to predict Ab-Ag interaction and followed by in silico analysis of the results may be good surrogate approaches to achieve this result. Here, we review few experimental techniques followed by the use of "basic" informatics tools for the analysis of the results.
Collapse
Affiliation(s)
- Nicola Clementi
- Microbiology and Virology Unit, "Vita-Salute" San Raffaele University, Milan, Italy
| | | | | | | | | | | |
Collapse
|
17
|
Abbott WM, Damschroder MM, Lowe DC. Current approaches to fine mapping of antigen-antibody interactions. Immunology 2014; 142:526-35. [PMID: 24635566 DOI: 10.1111/imm.12284] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 03/10/2014] [Accepted: 03/11/2014] [Indexed: 12/23/2022] Open
Abstract
A number of different methods are commonly used to map the fine details of the interaction between an antigen and an antibody. Undoubtedly the method that is now most commonly used to give details at the level of individual amino acids and atoms is X-ray crystallography. The feasibility of undertaking crystallographic studies has increased over recent years through the introduction of automation, miniaturization and high throughput processes. However, this still requires a high level of sophistication and expense and cannot be used when the antigen is not amenable to crystallization. Nuclear magnetic resonance spectroscopy offers a similar level of detail to crystallography but the technical hurdles are even higher such that it is rarely used in this context. Mutagenesis of either antigen or antibody offers the potential to give information at the amino acid level but suffers from the uncertainty of not knowing whether an effect is direct or indirect due to an effect on the folding of a protein. Other methods such as hydrogen deuterium exchange coupled to mass spectrometry and the use of short peptides coupled with ELISA-based approaches tend to give mapping information over a peptide region rather than at the level of individual amino acids. It is quite common to use more than one method because of the limitations and even with a crystal structure it can be useful to use mutagenesis to tease apart the contribution of individual amino acids to binding affinity.
Collapse
Affiliation(s)
- W Mark Abbott
- Discovery Sciences, AstraZeneca, Macclesfield, Cheshire, UK
| | | | | |
Collapse
|
18
|
Deng X, Zheng X, Yang H, Moreira JM, Brünner N, Christensen H. Comparative analysis of evolutionarily conserved motifs of epidermal growth factor receptor 2 (HER2) predicts novel potential therapeutic epitopes. PLoS One 2014; 9:e106448. [PMID: 25192037 DOI: 10.1371/journal.pone.0106448] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 07/29/2014] [Indexed: 01/01/2023] Open
Abstract
Overexpression of human epidermal growth factor receptor 2 (HER2) is associated with tumor aggressiveness and poor prognosis in breast cancer. With the availability of therapeutic antibodies against HER2, great strides have been made in the clinical management of HER2 overexpressing breast cancer. However, de novo and acquired resistance to these antibodies presents a serious limitation to successful HER2 targeting treatment. The identification of novel epitopes of HER2 that can be used for functional/region-specific blockade could represent a central step in the development of new clinically relevant anti-HER2 antibodies. In the present study, we present a novel computational approach as an auxiliary tool for identification of novel HER2 epitopes. We hypothesized that the structurally and linearly evolutionarily conserved motifs of the extracellular domain of HER2 (ECD HER2) contain potential druggable epitopes/targets. We employed the PROSITE Scan to detect structurally conserved motifs and PRINTS to search for linearly conserved motifs of ECD HER2. We found that the epitopes recognized by trastuzumab and pertuzumab are located in the predicted conserved motifs of ECD HER2, supporting our initial hypothesis. Considering that structurally and linearly conserved motifs can provide functional specific configurations, we propose that by comparing the two types of conserved motifs, additional druggable epitopes/targets in the ECD HER2 protein can be identified, which can be further modified for potential therapeutic application. Thus, this novel computational process for predicting or searching for potential epitopes or key target sites may contribute to epitope-based vaccine and function-selected drug design, especially when x-ray crystal structure protein data is not available.
Collapse
|
19
|
Castelli M, Clementi N, Sautto GA, Pfaff J, Kahle KM, Barnes T, Doranz BJ, Dal Peraro M, Clementi M, Burioni R, Mancini N. HCV E2 core structures and mAbs: something is still missing. Drug Discov Today 2014; 19:1964-70. [PMID: 25172800 DOI: 10.1016/j.drudis.2014.08.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 07/17/2014] [Accepted: 08/21/2014] [Indexed: 02/07/2023]
Abstract
The lack of structural information on hepatitis C virus (HCV) surface proteins has so far hampered the development of effective vaccines. Recently, two crystallographic structures have described the core portion (E2c) of E2 surface glycoprotein, the primary mediator of HCV entry. Despite the importance of these studies, the E2 overall structure is still unknown and, most importantly, several biochemical and functional studies are in disagreement with E2c structures. Here, the main literature will be discussed and an alternative disulfide bridge pattern will be proposed, based on unpublished human monoclonal antibody reactivity. A modeling strategy aiming at recapitulating the available structural and functional studies of E2 will also be proposed.
Collapse
|
20
|
Sowole MA, Konermann L. Effects of Protein–Ligand Interactions on Hydrogen/Deuterium Exchange Kinetics: Canonical and Noncanonical Scenarios. Anal Chem 2014; 86:6715-22. [DOI: 10.1021/ac501849n] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Modupeola A. Sowole
- Department
of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department
of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| |
Collapse
|
21
|
Konermann L, Rodriguez AD, Sowole MA. Type 1 and Type 2 scenarios in hydrogen exchange mass spectrometry studies on protein–ligand complexes. Analyst 2014; 139:6078-87. [DOI: 10.1039/c4an01307g] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Ligand binding to a protein can elicit a wide range of responses when studied by HDX mass spectrometry.
Collapse
Affiliation(s)
- Lars Konermann
- Department of Chemistry
- The University of Western Ontario
- London, Canada
| | | | | |
Collapse
|
22
|
Burioni R, Lang AB, Capra JD. Human monoclonal antibodies as a new class of antiinfective compounds. Clin Dev Immunol 2013; 2013:297120. [PMID: 24106516 DOI: 10.1155/2013/297120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 08/01/2013] [Indexed: 11/22/2022]
|
23
|
Wei H, Mo J, Tao L, Russell RJ, Tymiak AA, Chen G, Iacob RE, Engen JR. Hydrogen/deuterium exchange mass spectrometry for probing higher order structure of protein therapeutics: methodology and applications. Drug Discov Today 2013; 19:95-102. [PMID: 23928097 DOI: 10.1016/j.drudis.2013.07.019] [Citation(s) in RCA: 150] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Revised: 07/19/2013] [Accepted: 07/29/2013] [Indexed: 10/26/2022]
Abstract
The higher order structure of protein therapeutics can be interrogated with hydrogen/deuterium exchange mass spectrometry (HDX-MS). HDX-MS is now a widely used tool in the structural characterization of protein therapeutics. In this review, HDX-MS based workflows designed for protein therapeutic discovery and development processes are presented, focusing on the specific applications of epitope mapping for protein/drug interactions and biopharmaceutical comparability studies. Future trends in the application of HDX-MS in protein therapeutics characterization are also described.
Collapse
Affiliation(s)
- Hui Wei
- Bioanalytical and Discovery Analytical Sciences, Research and Development, Bristol-Myers Squibb, Princeton, NJ, USA
| | - Jingjie Mo
- Bioanalytical and Discovery Analytical Sciences, Research and Development, Bristol-Myers Squibb, Princeton, NJ, USA
| | - Li Tao
- Biologics Manufacturing and Process Development, Global Manufacturing and Supply, Bristol-Myers Squibb, Hopewell, NJ, USA
| | - Reb J Russell
- Biologics Manufacturing and Process Development, Global Manufacturing and Supply, Bristol-Myers Squibb, Bloomsbury, NJ, USA
| | - Adrienne A Tymiak
- Bioanalytical and Discovery Analytical Sciences, Research and Development, Bristol-Myers Squibb, Princeton, NJ, USA
| | - Guodong Chen
- Bioanalytical and Discovery Analytical Sciences, Research and Development, Bristol-Myers Squibb, Princeton, NJ, USA.
| | - Roxana E Iacob
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, USA
| | - John R Engen
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, USA.
| |
Collapse
|
24
|
Sautto G, Tarr AW, Mancini N, Clementi M. Structural and antigenic definition of hepatitis C virus E2 glycoprotein epitopes targeted by monoclonal antibodies. Clin Dev Immunol. 2013;2013:450963. [PMID: 23935648 PMCID: PMC3722892 DOI: 10.1155/2013/450963] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 06/10/2013] [Indexed: 12/24/2022]
Abstract
Hepatitis C virus (HCV) is the major cause of chronic liver disease as well as the major indication for liver transplantation worldwide. Current standard of care is not completely effective, not administrable in grafted patients, and burdened by several side effects. This incomplete effectiveness is mainly due to the high propensity of the virus to continually mutate under the selective pressure exerted by the host immune response as well as currently administered antiviral drugs. The E2 envelope surface glycoprotein of HCV (HCV/E2) is the main target of the host humoral immune response and for this reason one of the major variable viral proteins. However, broadly cross-neutralizing monoclonal antibodies (mAbs) directed against HCV/E2 represent a promising tool for the study of virus-host interplay as well as for the development of effective prophylactic and therapeutic approaches. In the last few years many anti-HCV/E2 mAbs have been evaluated in preclinical and clinical trials as possible candidate antivirals, particularly for administration in pre- and post-transplant settings. In this review we summarize the antigenic and structural characteristics of HCV/E2 determined through the use of anti-HCV/E2 mAbs, which, given the absence of a crystal structure of this glycoprotein, represent currently the best tool available.
Collapse
|
25
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|