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Wang Z, Li D, Chen Y, Sun Y, Jin C, Hu C, Feng Y, Su J, Ren L, Hao Y, Wang S, Zhu M, Liu Y, Qi J, Zhu B, Shao Y. Characterization of RBD-specific cross-neutralizing antibodies responses against SARS-CoV-2 variants from COVID-19 convalescents. Front Immunol 2023; 14:1160283. [PMID: 37234155 PMCID: PMC10207940 DOI: 10.3389/fimmu.2023.1160283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 04/25/2023] [Indexed: 05/27/2023] Open
Abstract
Introduction The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been posing a severe threat to global public health. Although broadly neutralizing antibodies have been used to prevent or treat corona virus disease 2019 (COVID-19), new emerging variants have been proven resistant to these antibodies. Methods In this study, we isolated receptor binding domain (RBD)-specific memory B cells using single-cell sorting method from two COVID-19 convalescents and expressed the antibody to test their neutralizing activity against diverse SARS-CoV-2 variants. Then, we resolved antibody-RBD complex structures of potent RBD-specific neutralizing antibodies by X-ray diffraction method. Finally, we analyzed the whole antibody repertoires of the two donors and studied the evolutionary pathway of potent neutralizing antibodies. Results and discussion We identified three potent RBD-specific neutralizing antibodies (1D7, 3G10 and 3C11) from two COVID-19 convalescents that neutralized authentic SARS-CoV-2 WH-1 and Delta variant, and one of them, 1D7, presented broadly neutralizing activity against WH-1, Beta, Gamma, Delta and Omicron authentic viruses. The resolved antibody-RBD complex structures of two antibodies, 3G10 and 3C11, indicate that both of them interact with the external subdomain of the RBD and that they belong to the RBD-1 and RBD-4 communities, respectively. From the antibody repertoire analysis, we found that the CDR3 frequencies of the light chain, which shared high degrees of amino acid identity with these three antibodies, were higher than those of the heavy chain. This research will contribute to the development of RBD-specific antibody-based drugs and immunogens against multiple variants.
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Affiliation(s)
- Zheng Wang
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Dan Li
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yulu Chen
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yeping Sun
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Changzhong Jin
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Caiqin Hu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yi Feng
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Junwei Su
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Li Ren
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yanling Hao
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shuo Wang
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Meiling Zhu
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ying Liu
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Biao Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yiming Shao
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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Desta IT, Kotelnikov S, Jones G, Ghani U, Abyzov M, Kholodov Y, Standley DM, Sabitova M, Beglov D, Vajda S, Kozakov D. Mapping of antibody epitopes based on docking and homology modeling. Proteins 2023; 91:171-182. [PMID: 36088633 PMCID: PMC9822860 DOI: 10.1002/prot.26420] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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] [Received: 07/25/2022] [Revised: 08/25/2022] [Accepted: 09/06/2022] [Indexed: 01/11/2023]
Abstract
Antibodies are key proteins produced by the immune system to target pathogen proteins termed antigens via specific binding to surface regions called epitopes. Given an antigen and the sequence of an antibody the knowledge of the epitope is critical for the discovery and development of antibody based therapeutics. In this work, we present a computational protocol that uses template-based modeling and docking to predict epitope residues. This protocol is implemented in three major steps. First, a template-based modeling approach is used to build the antibody structures. We tested several options, including generation of models using AlphaFold2. Second, each antibody model is docked to the antigen using the fast Fourier transform (FFT) based docking program PIPER. Attention is given to optimally selecting the docking energy parameters depending on the input data. In particular, the van der Waals energy terms are reduced for modeled antibodies relative to x-ray structures. Finally, ranking of antigen surface residues is produced. The ranking relies on the docking results, that is, how often the residue appears in the docking poses' interface, and also on the energy favorability of the docking pose in question. The method, called PIPER-Map, has been tested on a widely used antibody-antigen docking benchmark. The results show that PIPER-Map improves upon the existing epitope prediction methods. An interesting observation is that epitope prediction accuracy starting from antibody sequence alone does not significantly differ from that of starting from unbound (i.e., separately crystallized) antibody structure.
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Affiliation(s)
- Israel T. Desta
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Sergei Kotelnikov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | - George Jones
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Usman Ghani
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | | | | | - Daron M. Standley
- Department of Genome Informatics, Osaka University, Osaka, 565-0871, Japan
- Center for Infectious Disease Education and Research, Osaka University, Osaka, 565-0871, Japan
| | - Maria Sabitova
- Department of Mathematics, CUNY Queens College, Flushing, NY 11367, USA
| | - Dmitri Beglov
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Sandor Vajda
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Dima Kozakov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
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Bondarenko P, Nichols AC, Xiao G, Shi RL, Chan PK, Dillon TM, Garces F, Semin DJ, Ricci MS. Identification of critical chemical modifications and paratope mapping by size exclusion chromatography of stressed antibody-target complexes. MAbs 2021; 13:1887629. [PMID: 33615991 PMCID: PMC7899697 DOI: 10.1080/19420862.2021.1887629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Therapeutic proteins including antibodies and Fc-fusion proteins undergo a large number of chemical modifications during cell culture, purification, storage and in human circulation. They are also exposed to harsh conditions during stress studies, including elevated temperature, extremes of pH, forced oxidation, physiological pH, UV light to assess the possible degradation pathways and suitability of methods for detecting them. Some of these modifications are located on residues in binding regions, leading to loss of binding and potency and classified as critical quality attributes. Currently, criticality of modifications is assessed by a laborious process of collecting antibody fractions from the soft chromatography techniques ion exchange and hydrophobic interaction chromatography and characterizing the fractions one-by-one for potency and chemical modifications. Here, we describe a method for large-scale, parallel identification of all critical chemical modifications in one experiment. In the first step, the antibody is stressed by one or several stress methods. It is then mixed with target protein and separated by size-exclusion chromatography (SEC) on bound antibody-target complex and unbound antibody. Peptide mapping of fractions and statistical analysis are performed to identify modifications on amino acid residues that affect binding. To identify the modifications leading to slight decreases in binding, competitive SEC of antibody and antigen mixtures was developed and described in a companion study by Shi et al, where target protein is provided at lower level, below the stoichiometry. The newly described method was successfully correlated to crystallography for assessing criticality of chemical modifications and paratope mapping. It is more sensitive to low-level modifications, better streamlined and platform ready.
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Affiliation(s)
- Pavel Bondarenko
- Attribute Sciences, Process Development, Amgen Inc , Thousand Oaks, CA, USA
| | - Andrew C Nichols
- Attribute Sciences, Process Development, Amgen Inc , Thousand Oaks, CA, USA
| | - Gang Xiao
- Attribute Sciences, Process Development, Amgen Inc , Thousand Oaks, CA, USA
| | - Rachel Liuqing Shi
- Attribute Sciences, Process Development, Amgen Inc , Thousand Oaks, CA, USA
| | - Pik Kay Chan
- Attribute Sciences, Process Development, Amgen Inc , Thousand Oaks, CA, USA
| | - Thomas M Dillon
- Attribute Sciences, Process Development, Amgen Inc , Thousand Oaks, CA, USA
| | - Fernando Garces
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc , Thousand Oaks, CA, USA
| | - David J Semin
- Attribute Sciences, Process Development, Amgen Inc , Thousand Oaks, CA, USA
| | - Margaret S Ricci
- Attribute Sciences, Process Development, Amgen Inc , Thousand Oaks, CA, USA
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Chukwu JE, Congdon EE, Sigurdsson EM, Kong XP. Structural characterization of monoclonal antibodies targeting C-terminal Ser 404 region of phosphorylated tau protein. MAbs 2019; 11:477-488. [PMID: 30794086 DOI: 10.1080/19420862.2019.1574530] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 10/27/2022] Open
Abstract
Targeting tau with immunotherapies is currently the most common approach taken in clinical trials of patients with Alzheimer's disease. The most prominent pathological feature of tau is its hyperphosphorylation, which may cause the protein to aggregate into toxic assemblies that collectively lead to neurodegeneration. Of the phospho-epitopes, the region around Ser396/Ser404 has received particular attention for therapeutic targeting because of its prominence and stability in diseased tissue. Herein, we present the antigen-binding fragment (Fab)/epitope complex structures of three different monoclonal antibodies (mAbs) that target the pSer404 tau epitope region. Most notably, these structures reveal an antigen conformation similar to a previously described pathogenic tau epitope, pSer422, which was shown to have a β-strand structure that may be linked to the seeding core in tau oligomers. In addition, we have previously reported on the similarly ordered conformation observed in a pSer396 epitope, which is in tandem with pSer404. Our data are the first Fab structures of mAbs bound to this epitope region of the tau protein and support the existence of proteopathic tau conformations stabilized by specific phosphorylation events that are viable targets for immune modulation.
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Affiliation(s)
- Jessica E Chukwu
- a Department of Biochemistry & Molecular Pharmacology , New York University School of Medicine , New York , NY , USA
| | - Erin E Congdon
- b Departments of Neuroscience & Physiology, & Psychiatry , New York University School of Medicine , New York , NY , USA
| | - Einar M Sigurdsson
- b Departments of Neuroscience & Physiology, & Psychiatry , New York University School of Medicine , New York , NY , USA
| | - Xiang-Peng Kong
- a Department of Biochemistry & Molecular Pharmacology , New York University School of Medicine , New York , NY , USA
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Mleczko J, Defort A, Kozioł JJ, Nguyen TT, Mirończyk A, Zapotoczny B, Nowak-Jary J, Gronczewska E, Marć M, Dudek MR. Limitation of tuning the antibody-antigen reaction by changing the value of pH and its consequence for hyperthermia. J Biochem 2015; 159:421-7. [PMID: 26634446 DOI: 10.1093/jb/mvv120] [Citation(s) in RCA: 5] [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: 07/30/2015] [Accepted: 10/17/2015] [Indexed: 01/31/2023] Open
Abstract
Distribution of the isoelectric point (pI) was calculated for the hypervariable regions of Fab fragments of the antibody molecules, which structure is annotated in the structural antibody database SabDab. The distribution is consistent with the universal for all organisms dividing the proteome into two sets of acidic and basic proteins. It shows the additional fine structure in a form of the narrow-sized peaks of pI values. This is an explanation why a small change of the environmental pH can have a strong effect on the antibody-antigen affinity. To show this, a typical enzyme-linked immunospecific assay experiment for testing the reaction of goat anti-human IgA antibodies with human IgA immunoglobulins of saliva as antigens was modified in such a way that Fe3O4magnetic nanoparticles were added to PBS buffer. The magnetic nanoparticles were remotely heated by the radio frequency magnetic field providing the local change of temperature and pH. It was observed that short times of the heating were significantly increasing the antibody-antigen binding strength while it was not the case for a longer time. The finding discussed in the study can be useful for biopharmaceuticals using antibodies, the immunoassay techniques as well as for control over the use of hyperthermia.
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Affiliation(s)
- J Mleczko
- Institute of Genetics and Microbiology, University of Wrocław, ul. Przybyszewskiego 63/77, 51-148 Wrocław, Poland
| | - A Defort
- Faculty of Biological Sciences, University of Zielona Góra, ul. Szafrana 1, 65-516 Zielona Góra, Poland; and
| | - J J Kozioł
- Faculty of Biological Sciences, University of Zielona Góra, ul. Szafrana 1, 65-516 Zielona Góra, Poland; and
| | - T T Nguyen
- Institute of Physics, University of Zielona Góra, ul. Szafrana 4a, 65-516 Zielona Góra, Poland
| | - A Mirończyk
- Faculty of Biological Sciences, University of Zielona Góra, ul. Szafrana 1, 65-516 Zielona Góra, Poland; and
| | - B Zapotoczny
- Institute of Physics, University of Zielona Góra, ul. Szafrana 4a, 65-516 Zielona Góra, Poland
| | - J Nowak-Jary
- Faculty of Biological Sciences, University of Zielona Góra, ul. Szafrana 1, 65-516 Zielona Góra, Poland; and
| | - E Gronczewska
- Faculty of Biological Sciences, University of Zielona Góra, ul. Szafrana 1, 65-516 Zielona Góra, Poland; and
| | - M Marć
- Institute of Physics, University of Zielona Góra, ul. Szafrana 4a, 65-516 Zielona Góra, Poland
| | - M R Dudek
- Institute of Physics, University of Zielona Góra, ul. Szafrana 4a, 65-516 Zielona Góra, Poland
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