1
|
Hong J, Choi Y, Choi Y, Lee J, Hong HJ. Epitope-Paratope Interaction of a Neutralizing Human Anti-Hepatitis B Virus PreS1 Antibody That Recognizes the Receptor-Binding Motif. Vaccines (Basel) 2021; 9:vaccines9070754. [PMID: 34358170 PMCID: PMC8310169 DOI: 10.3390/vaccines9070754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 11/16/2022] Open
Abstract
Hepatitis B virus (HBV) is a global health burden that causes acute and chronic hepatitis. To develop an HBV-neutralizing antibody that effectively prevents HBV infection, we previously generated a human anti-preS1 monoclonal antibody (1A8) that binds to genotypes A–D and validated its HBV-neutralizing activity in vitro. In the present study, we aimed to determine the fine epitope and paratope of 1A8 to understand the mechanism of HBV neutralization. We performed alanine-scanning mutagenesis on the preS1 (aa 19–34, genotype C) and the heavy (HCDR) and light (LCDR) chain complementarity-determining regions. The 1A8 recognized the three residues (Leu22, Gly23, and Phe25) within the highly conserved receptor-binding motif (NPLGFFP) of the preS1, while four CDR residues of 1A8 were critical in antigen binding. Structural analysis of the epitope–paratope interaction by molecular modeling revealed that Leu100 in the HCDR3, Ala50 in the HCDR2, and Tyr96 in the LCDR3 closely interacted with Leu22, Gly23, and Phe25 of the preS1. Additionally, we found that 1A8 also binds to the receptor-binding motif (NPLGFLP) of infrequently occurring HBV. The results suggest that 1A8 may broadly and effectively block HBV entry and thus have potential as a promising candidate for the prevention and treatment of HBV infection.
Collapse
Affiliation(s)
- Jisu Hong
- Department of Systems Immunology, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Korea; (J.H.); (Y.C.); (J.L.)
| | - Youngjin Choi
- Department of Systems Immunology, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Korea; (J.H.); (Y.C.); (J.L.)
| | - Yoonjoo Choi
- Medical Research Center, Chonnam National University Medical School, Hwasun 58128, Korea;
| | - Jiwoo Lee
- Department of Systems Immunology, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Korea; (J.H.); (Y.C.); (J.L.)
| | - Hyo Jeong Hong
- Department of Systems Immunology, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Korea; (J.H.); (Y.C.); (J.L.)
- Correspondence: ; Tel.: +82-33-250-8381; Fax: +82-33-259-5643
| |
Collapse
|
2
|
Immune Gene Rearrangements: Unique Signatures for Tracing Physiological Lymphocytes and Leukemic Cells. Genes (Basel) 2021; 12:genes12070979. [PMID: 34198966 PMCID: PMC8329920 DOI: 10.3390/genes12070979] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 06/25/2021] [Indexed: 02/07/2023] Open
Abstract
The tremendous diversity of the human immune repertoire, fundamental for the defense against highly heterogeneous pathogens, is based on the ingenious mechanism of immune gene rearrangements. Rearranged immune genes encoding the immunoglobulins and T-cell receptors and thus determining each lymphocyte's antigen specificity are very valuable molecular markers for tracing malignant or physiological lymphocytes. One of their most significant applications is tracking residual leukemic cells in patients with lymphoid malignancies. This so called 'minimal residual disease' (MRD) has been shown to be the most important prognostic factor across various leukemia subtypes and has therefore been given enormous attention. Despite the current rapid development of the molecular methods, the classical real-time PCR based approach is still being regarded as the standard method for molecular MRD detection due to the cumbersome standardization of the novel approaches currently in progress within the EuroMRD and EuroClonality NGS Consortia. Each of the molecular methods, however, poses certain benefits and it is therefore expectable that none of the methods for MRD detection will clearly prevail over the others in the near future.
Collapse
|
3
|
Madan B, Zhang B, Xu K, Chao CW, O'Dell S, Wolfe JR, Chuang GY, Fahad AS, Geng H, Kong R, Louder MK, Nguyen TD, Rawi R, Schön A, Sheng Z, Nimrania R, Wang Y, Zhou T, Lin BC, Doria-Rose NA, Shapiro L, Kwong PD, DeKosky BJ. Mutational fitness landscapes reveal genetic and structural improvement pathways for a vaccine-elicited HIV-1 broadly neutralizing antibody. Proc Natl Acad Sci U S A 2021; 118:e2011653118. [PMID: 33649208 PMCID: PMC7958426 DOI: 10.1073/pnas.2011653118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Vaccine-based elicitation of broadly neutralizing antibodies holds great promise for preventing HIV-1 transmission. However, the key biophysical markers of improved antibody recognition remain uncertain in the diverse landscape of potential antibody mutation pathways, and a more complete understanding of anti-HIV-1 fusion peptide (FP) antibody development will accelerate rational vaccine designs. Here we survey the mutational landscape of the vaccine-elicited anti-FP antibody, vFP16.02, to determine the genetic, structural, and functional features associated with antibody improvement or fitness. Using site-saturation mutagenesis and yeast display functional screening, we found that 1% of possible single mutations improved HIV-1 envelope trimer (Env) affinity, but generally comprised rare somatic hypermutations that may not arise frequently in vivo. We observed that many single mutations in the vFP16.02 Fab could enhance affinity >1,000-fold against soluble FP, although affinity improvements against the HIV-1 trimer were more measured and rare. The most potent variants enhanced affinity to both soluble FP and Env, had mutations concentrated in antibody framework regions, and achieved up to 37% neutralization breadth compared to 28% neutralization of the template antibody. Altered heavy- and light-chain interface angles and conformational dynamics, as well as reduced Fab thermal stability, were associated with improved HIV-1 neutralization breadth and potency. We also observed parallel sets of mutations that enhanced viral neutralization through similar structural mechanisms. These data provide a quantitative understanding of the mutational landscape for vaccine-elicited FP-directed broadly neutralizing antibody and demonstrate that numerous antigen-distal framework mutations can improve antibody function by enhancing affinity simultaneously toward HIV-1 Env and FP.
Collapse
Affiliation(s)
- Bharat Madan
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66045
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892
| | - Kai Xu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892
| | - Cara W Chao
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892
| | - Sijy O'Dell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892
| | - Jacy R Wolfe
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66045
| | - Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892
| | - Ahmed S Fahad
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66045
| | - Hui Geng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892
| | - Rui Kong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892
| | - Mark K Louder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892
| | - Thuy Duong Nguyen
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66045
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892
| | - Arne Schön
- Department of Biology, John Hopkins University, Baltimore, MD 21218
| | - Zizhang Sheng
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10027
| | - Rajani Nimrania
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66045
| | - Yiran Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892
| | - Bob C Lin
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892
| | - Nicole A Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892
| | - Lawrence Shapiro
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10027
- Aaron Diamond AIDS Research Center, Columbia University Irving Medical Center, New York, NY 10032
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10027
| | - Brandon J DeKosky
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66045;
- Department of Chemical Engineering, The University of Kansas, Lawrence, KS 66045
| |
Collapse
|
4
|
Hu FJ, Lundqvist M, Uhlén M, Rockberg J. SAMURAI (Solid-phase Assisted Mutagenesis by Uracil Restriction for Accurate Integration) for antibody affinity maturation and paratope mapping. Nucleic Acids Res 2019; 47:e34. [PMID: 30715449 PMCID: PMC6451119 DOI: 10.1093/nar/gkz050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 01/08/2019] [Accepted: 01/24/2019] [Indexed: 12/31/2022] Open
Abstract
Mutagenesis libraries are essential for combinatorial protein engineering. Despite improvements in gene synthesis and directed mutagenesis, current methodologies still have limitations regarding the synthesis of complete antibody single-chain variable fragment (scFv) genes and simultaneous diversification of all six CDRs. Here, we describe the generation of mutagenesis libraries for antibody affinity maturation using a cell-free solid-phase technique for annealing of single-strand mutagenic oligonucleotides. The procedure consists of PCR-based incorporation of uracil into a wild-type template, bead-based capture, elution of single-strand DNA, and in vitro uracil excision enzyme based degradation of the template DNA. Our approach enabled rapid (8 hours) mutagenesis and automated cloning of 50 position-specific alanine mutants for mapping of a scFv antibody paratope. We further exemplify our method by generating affinity maturation libraries with diversity introduced in critical, nonessential, or all CDR positions randomly. Assessment with Illumina deep sequencing showed less than 1% wild-type in two libraries and the ability to diversify all CDR positions simultaneously. Selections of the libraries with bacterial display and deep sequencing evaluation of the selection output showed that diversity introduced in non-essential positions allowed for a more effective enrichment of improved binders compared to the other two diversification strategies.
Collapse
Affiliation(s)
- Francis Jingxin Hu
- KTH - Royal Institute of Technology, Department of Protein Science, 106 91 Stockholm, Sweden
| | - Magnus Lundqvist
- KTH - Royal Institute of Technology, Department of Protein Science, 106 91 Stockholm, Sweden
| | - Mathias Uhlén
- KTH - Royal Institute of Technology, Department of Protein Science, 106 91 Stockholm, Sweden.,KTH - Royal Institute of Technology, Science for Life Laboratory, Solna 171 65, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2970 Hørsholm, Denmark
| | - Johan Rockberg
- KTH - Royal Institute of Technology, Department of Protein Science, 106 91 Stockholm, Sweden
| |
Collapse
|
5
|
Jian JW, Chen HS, Chiu YK, Peng HP, Tung CP, Chen IC, Yu CM, Tsou YL, Kuo WY, Hsu HJ, Yang AS. Effective binding to protein antigens by antibodies from antibody libraries designed with enhanced protein recognition propensities. MAbs 2019; 11:373-387. [PMID: 30526270 PMCID: PMC6380391 DOI: 10.1080/19420862.2018.1550320] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Antibodies provide immune protection by recognizing antigens of diverse chemical properties, but elucidating the amino acid sequence-function relationships underlying the specificity and affinity of antibody-antigen interactions remains challenging. We designed and constructed phage-displayed synthetic antibody libraries with enriched protein antigen-recognition propensities calculated with machine learning predictors, which indicated that the designed single-chain variable fragment variants were encoded with enhanced distributions of complementarity-determining region (CDR) hot spot residues with high protein antigen recognition propensities in comparison with those in the human antibody germline sequences. Antibodies derived directly from the synthetic antibody libraries, without affinity maturation cycles comparable to those in in vivo immune systems, bound to the corresponding protein antigen through diverse conformational or linear epitopes with specificity and affinity comparable to those of the affinity-matured antibodies from in vivo immune systems. The results indicated that more densely populated CDR hot spot residues were sustainable by the antibody structural frameworks and could be accompanied by enhanced functionalities in recognizing protein antigens. Our study results suggest that synthetic antibody libraries, which are not limited by the sequences found in antibodies in nature, could be designed with the guidance of the computational machine learning algorithms that are programmed to predict interaction propensities to molecules of diverse chemical properties, leading to antibodies with optimal characteristics pertinent to their medical applications.
Collapse
Affiliation(s)
- Jhih-Wei Jian
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan.,b Institute of Biomedical Informatics, National Yang-Ming University , Taipei , Taiwan.,c Bioinformatics Program, Taiwan International Graduate Program , Institute of Information Science, Academia Sinica , Taipei , Taiwan
| | - Hong-Sen Chen
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - Yi-Kai Chiu
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - Hung-Pin Peng
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - Chao-Ping Tung
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - Ing-Chien Chen
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - Chung-Ming Yu
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - Yueh-Liang Tsou
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - Wei-Ying Kuo
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - Hung-Ju Hsu
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - An-Suei Yang
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| |
Collapse
|
6
|
Schroeder HW, Imboden JB, Torres RM. Antigen Receptor Genes, Gene Products, and Coreceptors. Clin Immunol 2019. [DOI: 10.1016/b978-0-7020-6896-6.00004-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
7
|
Ovchinnikov V, Louveau JE, Barton JP, Karplus M, Chakraborty AK. Role of framework mutations and antibody flexibility in the evolution of broadly neutralizing antibodies. eLife 2018; 7:33038. [PMID: 29442996 PMCID: PMC5828663 DOI: 10.7554/elife.33038] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 02/13/2018] [Indexed: 01/13/2023] Open
Abstract
Eliciting antibodies that are cross reactive with surface proteins of diverse strains of highly mutable pathogens (e.g., HIV, influenza) could be key for developing effective universal vaccines. Mutations in the framework regions of such broadly neutralizing antibodies (bnAbs) have been reported to play a role in determining their properties. We used molecular dynamics simulations and models of affinity maturation to study specific bnAbs against HIV. Our results suggest that there are different classes of evolutionary lineages for the bnAbs. If germline B cells that initiate affinity maturation have high affinity for the conserved residues of the targeted epitope, framework mutations increase antibody rigidity as affinity maturation progresses to evolve bnAbs. If the germline B cells exhibit weak/moderate affinity for conserved residues, an initial increase in flexibility via framework mutations may be required for the evolution of bnAbs. Subsequent mutations that increase rigidity result in highly potent bnAbs. Implications of our results for immunogen design are discussed.
Collapse
Affiliation(s)
- Victor Ovchinnikov
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
| | - Joy E Louveau
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, United States
| | - John P Barton
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, United States.,Department of Physics, Massachusetts Institute of Technology, Cambridge, United States.,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, United States.,Ragon Institute of MGH, MIT and Harvard, Cambridge, United States
| | - Martin Karplus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States.,Laboratoire de Chimie Biophysique, ISIS, Universite de Strasbourg, Strasbourg, France
| | - Arup K Chakraborty
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, United States.,Department of Physics, Massachusetts Institute of Technology, Cambridge, United States.,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, United States.,Ragon Institute of MGH, MIT and Harvard, Cambridge, United States.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
| |
Collapse
|
8
|
Mishra AK, Mariuzza RA. Insights into the Structural Basis of Antibody Affinity Maturation from Next-Generation Sequencing. Front Immunol 2018; 9:117. [PMID: 29449843 PMCID: PMC5799246 DOI: 10.3389/fimmu.2018.00117] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 01/15/2018] [Indexed: 12/26/2022] Open
Abstract
Affinity maturation is the process whereby the immune system generates antibodies of higher affinities during a response to antigen. It is unique in being the only evolutionary mechanism known to operate on a molecule in an organism's own body. Deciphering the structural mechanisms through which somatic mutations in antibody genes increase affinity is critical to understanding the evolution of immune repertoires. Next-generation sequencing (NGS) has allowed the reconstruction of antibody clonal lineages in response to viral pathogens, such as HIV-1, which was not possible in earlier studies of affinity maturation. Crystal structures of antibodies from these lineages bound to their target antigens have revealed, at the atomic level, how antibodies evolve to penetrate the glycan shield of envelope glycoproteins, and how viruses in turn evolve to escape neutralization. Collectively, structural studies of affinity maturation have shown that increased antibody affinity can arise from any one or any combination of multiple diverse mechanisms, including improved shape complementarity at the interface with antigen, increased buried surface area upon complex formation, additional interfacial polar or hydrophobic interactions, and preorganization or rigidification of the antigen-binding site.
Collapse
Affiliation(s)
- Arjun K Mishra
- W. M. Keck Laboratory for Structural Biology, Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Rockville, MD, United States.,Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, College Park, MD, United States
| | - Roy A Mariuzza
- W. M. Keck Laboratory for Structural Biology, Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Rockville, MD, United States.,Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, College Park, MD, United States
| |
Collapse
|
9
|
Almagro JC, Daniels-Wells TR, Perez-Tapia SM, Penichet ML. Progress and Challenges in the Design and Clinical Development of Antibodies for Cancer Therapy. Front Immunol 2018; 8:1751. [PMID: 29379493 PMCID: PMC5770808 DOI: 10.3389/fimmu.2017.01751] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 11/24/2017] [Indexed: 11/14/2022] Open
Abstract
The remarkable progress in engineering and clinical development of therapeutic antibodies in the last 40 years, after the seminal work by Köhler and Milstein, has led to the approval by the United States Food and Drug Administration (FDA) of 21 antibodies for cancer immunotherapy. We review here these approved antibodies, with emphasis on the methods used for their discovery, engineering, and optimization for therapeutic settings. These methods include antibody engineering via chimerization and humanization of non-human antibodies, as well as selection and further optimization of fully human antibodies isolated from human antibody phage-displayed libraries and immunization of transgenic mice capable of generating human antibodies. These technology platforms have progressively led to the development of therapeutic antibodies with higher human content and, thus, less immunogenicity. We also discuss the genetic engineering approaches that have allowed isotype switching and Fc modifications to modulate effector functions and bioavailability (half-life), which together with the technologies for engineering the Fv fragment, have been pivotal in generating more efficacious and better tolerated therapeutic antibodies to treat cancer.
Collapse
Affiliation(s)
| | - Tracy R Daniels-Wells
- Division of Surgical Oncology, Department of Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | | | - Manuel L Penichet
- Division of Surgical Oncology, Department of Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States.,Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States.,Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, United States.,The Molecular Biology Institute, University of California, Los Angeles, CA, United States.,UCLA AIDS Institute, Los Angeles, CA, United States
| |
Collapse
|
10
|
Abstract
The immune systems protect our bodies from foreign molecules or antigens, where antibodies play important roles. Antibodies evolve over time upon antigen encounter by somatically mutating their genome sequences. The end result is a series of antibodies that display higher affinities and specificities to specific antigens. This process is called affinity maturation. Recent improvements in computer hardware and modeling algorithms now enable the rational design of protein structures and functions, and several works on computer-aided antibody design have been published. In this chapter, we briefly describe computational methods for antibody affinity maturation, focusing on methods for sampling antibody conformations and for scoring designed antibody variants. We also discuss lessons learned from the successful computer-aided design of antibodies.
Collapse
Affiliation(s)
- Daisuke Kuroda
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
| |
Collapse
|
11
|
Kirik U, Persson H, Levander F, Greiff L, Ohlin M. Antibody Heavy Chain Variable Domains of Different Germline Gene Origins Diversify through Different Paths. Front Immunol 2017; 8:1433. [PMID: 29180996 PMCID: PMC5694033 DOI: 10.3389/fimmu.2017.01433] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 10/16/2017] [Indexed: 02/04/2023] Open
Abstract
B cells produce antibodies, key effector molecules in health and disease. They mature their properties, including their affinity for antigen, through hypermutation events; processes that involve, e.g., base substitution, codon insertion and deletion, often in association with an isotype switch. Investigations of antibody evolution define modes whereby particular antibody responses are able to form, and such studies provide insight important for instance for development of efficient vaccines. Antibody evolution is also used in vitro for the design of antibodies with improved properties. To better understand the basic concepts of antibody evolution, we analyzed the mutational paths, both in terms of amino acid substitution and insertions and deletions, taken by antibodies of the IgG isotype. The analysis focused on the evolution of the heavy chain variable domain of sets of antibodies, each with an origin in 1 of 11 different germline genes representing six human heavy chain germline gene subgroups. Investigated genes were isolated from cells of human bone marrow, a major site of antibody production, and characterized by next-generation sequencing and an in-house bioinformatics pipeline. Apart from substitutions within the complementarity determining regions, multiple framework residues including those in protein cores were targets of extensive diversification. Diversity, both in terms of substitutions, and insertions and deletions, in antibodies is focused to different positions in the sequence in a germline gene-unique manner. Altogether, our findings create a framework for understanding patterns of evolution of antibodies from defined germline genes.
Collapse
Affiliation(s)
- Ufuk Kirik
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Helena Persson
- Science for Life Laboratory, Drug Discovery and Development Platform, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Fredrik Levander
- Department of Immunotechnology, Lund University, Lund, Sweden.,National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Department of Immunotechnology, Lund University, Lund, Sweden
| | - Lennart Greiff
- Department of Clinical Sciences, Lund University, Lund, Sweden.,Department of Otorhinolaryngology, Head and Neck Surgery, Skåne University Hospital, Lund, Sweden
| | - Mats Ohlin
- Department of Immunotechnology, Lund University, Lund, Sweden.,Science for Life Laboratory, Drug Discovery and Development Platform, Human Antibody Therapeutics, Lund University, Lund, Sweden.,U-READ, Lund School of Technology, Lund University, Lund, Sweden
| |
Collapse
|
12
|
Kim S, Park I, Park SG, Cho S, Kim JH, Ipper NS, Choi SS, Lee ES, Hong HJ. Generation, Diversity Determination, and Application to Antibody Selection of a Human Naïve Fab Library. Mol Cells 2017; 40:655-666. [PMID: 28927259 PMCID: PMC5638773 DOI: 10.14348/molcells.2017.0106] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 08/04/2017] [Accepted: 08/06/2017] [Indexed: 12/29/2022] Open
Abstract
We constructed a large naïve human Fab library (3 × 1010 colonies) from the lymphocytes of 809 human donors, assessed available diversities of the heavy-chain variable (VH) and κ light-chain variable (VK) domain repertoires, and validated the library by selecting Fabs against 10 therapeutically relevant antigens by phage display. We obtained a database of unique 7,373 VH and 41,804 VK sequences by 454 pyrosequencing, and analyzed the repertoires. The distribution of VH and VK subfamilies and germline genes in our antibody repertoires slightly differed from those in earlier published natural antibody libraries. The frequency of somatic hypermutations (SHMs) in heavy-chain complementarity determining region (HCDR)1 and HCDR2 are higher compared with the natural IgM repertoire. Analysis of position-specific SHMs in CDRs indicates that asparagine, threonine, arginine, aspartate and phenylalanine are the most frequent non-germline residues on the antibody-antigen interface and are converted mostly from the germline residues, which are highly represented in germline SHM hotspots. The amino acid composition and length-dependent changes in amino acid frequencies of HCDR3 are similar to those in previous reports, except that frequencies of aspartate and phenylalanine are a little higher in our repertoire. Taken together, the results show that this antibody library shares common features of natural antibody repertoires and also has unique features. The antibody library will be useful in the generation of human antibodies against diverse antigens, and the information about the diversity of natural antibody repertoires will be valuable in the future design of synthetic human antibody libraries with high functional diversity.
Collapse
Affiliation(s)
- Sangkyu Kim
- Department of Systems Immunology, College of Biomedical Science, Kangwon National University, Chuncheon 24341,
Korea
| | - Insoo Park
- Therapeutic Antibody Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141,
Korea
| | - Seung Gu Park
- Department of Medical Biotechnology, College of Biomedical Science, Kangwon National University, Chuncheon 24341,
Korea
| | - Seulki Cho
- Therapeutic Antibody Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141,
Korea
| | - Jin Hong Kim
- Therapeutic Antibody Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141,
Korea
| | - Nagesh S. Ipper
- Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 24341,
Korea
| | - Sun Shim Choi
- Department of Medical Biotechnology, College of Biomedical Science, Kangwon National University, Chuncheon 24341,
Korea
| | - Eung Suk Lee
- Scripps Korea Antibody Institute, Chuncheon 24341,
Korea
| | - Hyo Jeong Hong
- Department of Systems Immunology, College of Biomedical Science, Kangwon National University, Chuncheon 24341,
Korea
- Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 24341,
Korea
| |
Collapse
|
13
|
Mutational landscape of antibody variable domains reveals a switch modulating the interdomain conformational dynamics and antigen binding. Proc Natl Acad Sci U S A 2017; 114:E486-E495. [PMID: 28057863 DOI: 10.1073/pnas.1613231114] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Somatic mutations within the antibody variable domains are critical to the immense capacity of the immune repertoire. Here, via a deep mutational scan, we dissect how mutations at all positions of the variable domains of a high-affinity anti-VEGF antibody G6.31 impact its antigen-binding function. The resulting mutational landscape demonstrates that large portions of antibody variable domain positions are open to mutation, and that beneficial mutations can be found throughout the variable domains. We determine the role of one antigen-distal light chain position 83, demonstrating that mutation at this site optimizes both antigen affinity and thermostability by modulating the interdomain conformational dynamics of the antigen-binding fragment. Furthermore, by analyzing a large number of human antibody sequences and structures, we demonstrate that somatic mutations occur frequently at position 83, with corresponding domain conformations observed for G6.31. Therefore, the modulation of interdomain dynamics represents an important mechanism during antibody maturation in vivo.
Collapse
|
14
|
Abstract
This review explores the incessant evolutionary interaction and co-development between immune system evolution and somatic evolution, to put it into context with the short, over 60-year, detailed human study of this extraordinary protective system. Over millions of years, the evolutionary development of the immune system in most species has been continuously shaped by environmental interactions between microbes, and aberrant somatic cells, including malignant cells. Not only has evolution occurred in somatic cells to adapt to environmental pressures for survival purposes, but the immune system and its function has been successively shaped by those same evolving somatic cells and microorganisms through continuous adaptive symbiotic processes of progressive simultaneous immunological and somatic change to provide what we observe today. Indeed, the immune system as an environmental influence has also shaped somatic and microbial evolution. Although the immune system is tuned to primarily controlling microbiological challenges for combatting infection, it can also remove damaged and aberrant cells, including cancer cells to induce long-term cures. Our knowledge of how this occurs is just emerging. Here we consider the connections between immunity, infection and cancer, by searching back in time hundreds of millions of years to when multi-cellular organisms first began. We are gradually appreciating that the immune system has evolved into a truly brilliant and efficient protective mechanism, the importance of which we are just beginning to now comprehend. Understanding these aspects will likely lead to more effective cancer and other therapies.
Collapse
Affiliation(s)
- Brendon J Coventry
- Discipline of Surgery, Royal Adelaide Hospital, University of Adelaide, Adelaide, South Australia, 5000, Australia
| | - Maciej Henneberg
- Biological Anthropology and Comparative Anatomy Unit, University of Adelaide, Adelaide, South Australia, 5005, Australia.,Institute of Evolutionary Medicine, The University of Zurich, 8057 Zurich, Switzerland
| |
Collapse
|
15
|
Abstract
This review explores the incessant evolutionary interaction and co-development between immune system evolution and somatic evolution, to put it into context with the short, over 60-year, detailed human study of this extraordinary protective system. Over millions of years, the evolutionary development of the immune system in most species has been continuously shaped by environmental interactions between microbes, and aberrant somatic cells, including malignant cells. Not only has evolution occurred in somatic cells to adapt to environmental pressures for survival purposes, but the immune system and its function has been successively shaped by those same evolving somatic cells and microorganisms through continuous adaptive symbiotic processes of progressive simultaneous immunological and somatic change to provide what we observe today. Indeed, the immune system as an environmental influence has also shaped somatic and microbial evolution. Although the immune system is tuned to primarily controlling microbiological challenges for combatting infection, it can also remove damaged and aberrant cells, including cancer cells to induce long-term cures. Our knowledge of how this occurs is just emerging. Here we consider the connections between immunity, infection and cancer, by searching back in time hundreds of millions of years to when multi-cellular organisms first began. We are gradually appreciating that the immune system has evolved into a truly brilliant and efficient protective mechanism, the importance of which we are just beginning to now comprehend. Understanding these aspects will likely lead to more effective cancer and other therapies.
Collapse
Affiliation(s)
- Brendon J Coventry
- Discipline of Surgery, Royal Adelaide Hospital, University of Adelaide, Adelaide, South Australia, 5000, Australia
| | - Maciej Henneberg
- Biological Anthropology and Comparative Anatomy Unit, University of Adelaide, Adelaide, South Australia, 5005, Australia.,Institute of Evolutionary Medicine, The University of Zurich, 8057 Zurich, Switzerland
| |
Collapse
|
16
|
Lapidoth GD, Baran D, Pszolla GM, Norn C, Alon A, Tyka MD, Fleishman SJ. AbDesign: An algorithm for combinatorial backbone design guided by natural conformations and sequences. Proteins 2015; 83:1385-406. [PMID: 25670500 PMCID: PMC4881815 DOI: 10.1002/prot.24779] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 01/13/2015] [Accepted: 01/26/2015] [Indexed: 12/20/2022]
Abstract
Computational design of protein function has made substantial progress, generating new enzymes, binders, inhibitors, and nanomaterials not previously seen in nature. However, the ability to design new protein backbones for function--essential to exert control over all polypeptide degrees of freedom--remains a critical challenge. Most previous attempts to design new backbones computed the mainchain from scratch. Here, instead, we describe a combinatorial backbone and sequence optimization algorithm called AbDesign, which leverages the large number of sequences and experimentally determined molecular structures of antibodies to construct new antibody models, dock them against target surfaces and optimize their sequence and backbone conformation for high stability and binding affinity. We used the algorithm to produce antibody designs that target the same molecular surfaces as nine natural, high-affinity antibodies; in five cases interface sequence identity is above 30%, and in four of those the backbone conformation at the core of the antibody binding surface is within 1 Å root-mean square deviation from the natural antibodies. Designs recapitulate polar interaction networks observed in natural complexes, and amino acid sidechain rigidity at the designed binding surface, which is likely important for affinity and specificity, is high compared to previous design studies. In designed anti-lysozyme antibodies, complementarity-determining regions (CDRs) at the periphery of the interface, such as L1 and H2, show greater backbone conformation diversity than the CDRs at the core of the interface, and increase the binding surface area compared to the natural antibody, potentially enhancing affinity and specificity.
Collapse
Affiliation(s)
- Gideon D. Lapidoth
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Dror Baran
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Gabriele M. Pszolla
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Christoffer Norn
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Assaf Alon
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Michael D. Tyka
- Google Inc., 1600 Amphitheatre Pkwy, Mountain View, CA 94043
| | - Sarel J. Fleishman
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| |
Collapse
|
17
|
Keller T, Kalt R, Raab I, Schachner H, Mayrhofer C, Kerjaschki D, Hantusch B. Selection of scFv Antibody Fragments Binding to Human Blood versus Lymphatic Endothelial Surface Antigens by Direct Cell Phage Display. PLoS One 2015; 10:e0127169. [PMID: 25993332 PMCID: PMC4439027 DOI: 10.1371/journal.pone.0127169] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 04/13/2015] [Indexed: 12/04/2022] Open
Abstract
The identification of marker molecules specific for blood and lymphatic endothelium may provide new diagnostic tools and identify new targets for therapy of immune, microvascular and cancerous diseases. Here, we used a phage display library expressing human randomized single-chain Fv (scFv) antibodies for direct panning against live cultures of blood (BECs) and lymphatic (LECs) endothelial cells in solution. After six panning rounds, out of 944 sequenced antibody clones, we retrieved 166 unique/diverse scFv fragments, as indicated by the V-region sequences. Specificities of these phage clone antibodies for respective compartments were individually tested by direct cell ELISA, indicating that mainly pan-endothelial cell (EC) binders had been selected, but also revealing a subset of BEC-specific scFv antibodies. The specific staining pattern was recapitulated by twelve phage-independently expressed scFv antibodies. Binding capacity to BECs and LECs and differential staining of BEC versus LEC by a subset of eight scFv antibodies was confirmed by immunofluorescence staining. As one antigen, CD146 was identified by immunoprecipitation with phage-independent scFv fragment. This antibody, B6-11, specifically bound to recombinant CD146, and to native CD146 expressed by BECs, melanoma cells and blood vessels. Further, binding capacity of B6-11 to CD146 was fully retained after fusion to a mouse Fc portion, which enabled eukaryotic cell expression. Beyond visualization and diagnosis, this antibody might be used as a functional tool. Overall, our approach provided a method to select antibodies specific for endothelial surface determinants in their native configuration. We successfully selected antibodies that bind to antigens expressed on the human endothelial cell surfaces in situ, showing that BECs and LECs share a majority of surface antigens, which is complemented by cell-type specific, unique markers.
Collapse
Affiliation(s)
- Thomas Keller
- Clinical Institute of Pathology, Medical University of Vienna, Vienna, Austria
| | - Romana Kalt
- Clinical Institute of Pathology, Medical University of Vienna, Vienna, Austria
| | - Ingrid Raab
- Clinical Institute of Pathology, Medical University of Vienna, Vienna, Austria
| | - Helga Schachner
- Clinical Institute of Pathology, Medical University of Vienna, Vienna, Austria
| | - Corina Mayrhofer
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, Austria
| | - Dontscho Kerjaschki
- Clinical Institute of Pathology, Medical University of Vienna, Vienna, Austria
| | - Brigitte Hantusch
- Clinical Institute of Pathology, Medical University of Vienna, Vienna, Austria
- * E-mail:
| |
Collapse
|
18
|
Ravenni N, Weber M, Neri D. A human monoclonal antibody specific to placental alkaline phosphatase, a marker of ovarian cancer. MAbs 2014; 6:86-94. [PMID: 24247025 DOI: 10.4161/mabs.27230] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Placental alkaline phosphatase (PLAP) is a promising ovarian cancer biomarker. Here, we describe the isolation, affinity-maturation and characterization of two fully human monoclonal antibodies (termed B10 and D9) able to bind to human PLAP with a dissociation constant (Kd) of 10 and 30 nM, respectively. The ability of B10 and D9 antibodies to recognize the native antigen was confirmed by Biacore analysis, FACS and immunofluorescence studies using ovarian cancer cell lines and freshly-frozen human tissues. A quantitative biodistribution study in nude mice revealed that the B10 antibody preferentially localizes to A431 tumors, following intravenous administration. Anti-PLAP antibodies may serve as a modular building blocks for the development of targeted therapeutic products, armed with cytotoxic drugs, radionuclides or cytokines as payloads.
Collapse
|
19
|
Weber M, Bujak E, Putelli A, Villa A, Matasci M, Gualandi L, Hemmerle T, Wulhfard S, Neri D. A highly functional synthetic phage display library containing over 40 billion human antibody clones. PLoS One 2014; 9:e100000. [PMID: 24950200 PMCID: PMC4065035 DOI: 10.1371/journal.pone.0100000] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 05/20/2014] [Indexed: 12/31/2022] Open
Abstract
Several synthetic antibody phage display libraries have been created and used for the isolation of human monoclonal antibodies. The performance of antibody libraries, which is usually measured in terms of their ability to yield high-affinity binding specificities against target proteins of interest, depends both on technical aspects (such as library size and quality of cloning) and on design features (which influence the percentage of functional clones in the library and their ability to be used for practical applications). Here, we describe the design, construction and characterization of a combinatorial phage display library, comprising over 40 billion human antibody clones in single-chain fragment variable (scFv) format. The library was designed with the aim to obtain highly stable antibody clones, which can be affinity-purified on protein A supports, even when used in scFv format. The library was found to be highly functional, as >90% of randomly selected clones expressed the corresponding antibody. When selected against more than 15 antigens from various sources, the library always yielded specific and potent binders, at a higher frequency compared to previous antibody libraries. To demonstrate library performance in practical biomedical research projects, we isolated the human antibody G5, which reacts both against human and murine forms of the alternatively spliced BCD segment of tenascin-C, an extracellular matrix component frequently over-expressed in cancer and in chronic inflammation. The new library represents a useful source of binding specificities, both for academic research and for the development of antibody-based therapeutics.
Collapse
Affiliation(s)
- Marcel Weber
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, Zürich, Switzerland
- Philochem AG, Otelfingen, Switzerland
| | - Emil Bujak
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, Zürich, Switzerland
- Philochem AG, Otelfingen, Switzerland
| | - Alessia Putelli
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, Zürich, Switzerland
- Philochem AG, Otelfingen, Switzerland
| | | | | | | | | | | | - Dario Neri
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, Zürich, Switzerland
- * E-mail:
| |
Collapse
|
20
|
Houimel M. The analysis of VH and VL genes repertoires of Fab library built from peripheral B cells of human rabies virus vaccinated donors. Hum Immunol 2014; 75:745-55. [PMID: 24862931 DOI: 10.1016/j.humimm.2014.05.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 05/13/2014] [Accepted: 05/13/2014] [Indexed: 02/04/2023]
Abstract
A human combinatorial Fab antibody library was generated from immune repertoire based on peripheral B cells of ten rabies virus vaccinated donors. The analysis of random Fab fragments from the unselected library presented some bias of V gene usage towards IGHV-genes and IGLV-gen families. The screening of the Fab library on rabies virus allowed specific human Fab antibody fragments characterized for their gene encoding sequences, binding and specificities to RV. Genetic analysis of selected Fabs indicated that the IGHV and IGLV differ from the germ-line sequence. At the level of nucleotide sequences, the IGHV and IGLV domains were found to share 74-92% and 90-96% homology with sequences encoded by the corresponding human germ-line genes respectively. IGHV domains are characterized most frequently by IGHV3 genes, and large proportions of the anti-RV heavy chain IGHV domains are obtained following a VDJ recombination process that uses IGHD3, IGHD2, IGHD1 and IGHD6 genes. IGHJ3 and IGHJ4 genes are predominantly used in RV-Fab. The IGLV domains are dominated by IGKV1, IGLV1 and IGLV3 genes. Numerous somatic hypermutations in the RV-specific IGHV are detected, but only limited amino acid replacement in most of the RV-specific IGLV particularly in those encoded by J proximal IGLV or IGKV genes are found. Furthermore, IGHV3-IGKV1, IGHV3-IGVL1, and IGHV3-IGLV3 germ-line family pairings are preferentially enriched after the screening on rabies virus.
Collapse
Affiliation(s)
- Mehdi Houimel
- Laboratoire d'Epidémiologie et de Microbiologie Vétérinaire, Institut Pasteur de Tunis, Tunisia; Université Tunis El Manar, Tunis, Tunisia.
| |
Collapse
|
21
|
Burkovitz A, Sela-Culang I, Ofran Y. Large-scale analysis of somatic hypermutations in antibodies reveals which structural regions, positions and amino acids are modified to improve affinity. FEBS J 2013; 281:306-19. [PMID: 24279419 DOI: 10.1111/febs.12597] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2013] [Revised: 10/13/2013] [Accepted: 10/29/2013] [Indexed: 01/16/2023]
Abstract
The principles of affinity maturation of antibodies (Abs), which underlies B cell-mediated immunity, are still under debate. It is unclear whether the antigen (Ag) binding site is a preferred target for mutations, and what the role of activation-induced deaminase (AID) hotspots is in this process. Here we report a structural analysis of 3495 residues that have been replaced through somatic hypermutations (SHMs) in 196 Abs. We show that there is no correlation between the propensity of an amino acid to be in AID hotspot and the probability that it is replaced during the SHM process. Although AID hotspots may be necessary to enable SHMs, they are not a major driving force in determining which residues are mutated. We identified Ab positions that are highly mutated and significantly affect binding. The effect of mutation on binding energy is a major factor in determining which structural regions of the Ab are mutated. There is a clear preference for mutations at the Ag-binding site. However, positions outside this region that also affect binding are often preferred targets for SHMs. As for amino acid preferences, a general trend during SHM is to make Ab-Ag interfaces more similar to protein-protein interfaces in general. In different regions of the Ab, there are different sets of preferences for amino acid substitution. This mapping improves our understanding of Ab affinity maturation and may assist in Ab engineering.
Collapse
Affiliation(s)
- Anat Burkovitz
- The Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan, Israel
| | | | | |
Collapse
|
22
|
|
23
|
Phage display antibodies for diagnostic applications. Biologicals 2013; 41:209-16. [DOI: 10.1016/j.biologicals.2013.04.001] [Citation(s) in RCA: 218] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Revised: 03/29/2013] [Accepted: 04/02/2013] [Indexed: 11/23/2022] Open
|
24
|
Development of Norwalk virus-specific monoclonal antibodies with therapeutic potential for the treatment of Norwalk virus gastroenteritis. J Virol 2013; 87:9547-57. [PMID: 23785216 DOI: 10.1128/jvi.01376-13] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Passive immunoprophylaxis or immunotherapy with norovirus-neutralizing monoclonal antibodies (MAbs) could be a useful treatment for high-risk populations, including infants and young children, the elderly, and certain patients who are debilitated or immunocompromised. In order to obtain antinorovirus MAbs with therapeutic potential, we stimulated a strong adaptive immune response in chimpanzees to the prototype norovirus strain Norwalk virus (NV) (genogroup I.1). A combinatorial phage Fab display library derived from mRNA of the chimpanzees' bone marrow was prepared, and four distinct Fabs reactive with Norwalk recombinant virus-like particles (rVLPs) were recovered, with estimated binding affinities in the subnanomolar range. Mapping studies showed that the four Fabs recognized three different conformational epitopes in the protruding (P) domain of NV VP1, the major capsid protein. The epitope of one of the Fabs, G4, was further mapped to a specific site involving a key amino acid residue, Gly365. One additional specific Fab (F11) was recovered months later from immortalized memory B cells and partially characterized. The anti-NV Fabs were converted into full-length IgG (MAbs) with human γ1 heavy chain constant regions. The anti-NV MAbs were tested in the two available surrogate assays for Norwalk virus neutralization, which showed that the MAbs could block carbohydrate binding and inhibit hemagglutination by NV rVLP. By mixing a single MAb with live Norwalk virus prior to challenge, MAbs D8 and B7 neutralized the virus and prevented infection in a chimpanzee. Because chimpanzee immunoglobulins are virtually identical to human immunoglobulins, these chimpanzee anticapsid MAbs may have a clinical application.
Collapse
|
25
|
Pantazes RJ, Maranas CD. MAPs: a database of modular antibody parts for predicting tertiary structures and designing affinity matured antibodies. BMC Bioinformatics 2013; 14:168. [PMID: 23718826 PMCID: PMC3687570 DOI: 10.1186/1471-2105-14-168] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 05/24/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The de novo design of a novel protein with a particular function remains a formidable challenge with only isolated and hard-to-repeat successes to date. Due to their many structurally conserved features, antibodies are a family of proteins amenable to predictable rational design. Design algorithms must consider the structural diversity of possible naturally occurring antibodies. The human immune system samples this design space (2 1012) by randomly combining variable, diversity, and joining genes in a process known as V-(D)-J recombination. DESCRIPTION By analyzing structural features found in affinity matured antibodies, a database of Modular Antibody Parts (MAPs) analogous to the variable, diversity, and joining genes has been constructed for the prediction of antibody tertiary structures. The database contains 929 parts constructed from an analysis of 1168 human, humanized, chimeric, and mouse antibody structures and encompasses all currently observed structural diversity of antibodies. CONCLUSIONS The generation of 260 antibody structures shows that the MAPs database can be used to reliably predict antibody tertiary structures with an average all-atom RMSD of 1.9 Å. Using the broadly neutralizing anti-influenza antibody CH65 and anti-HIV antibody 4E10 as examples, promising starting antibodies for affinity maturation are identified and amino acid changes are traced as antibody affinity maturation occurs.
Collapse
|
26
|
Schroeder HW, Imboden JB, Torres RM. Antigen receptor genes, gene products, and co-receptors. Clin Immunol 2013. [DOI: 10.1016/b978-0-7234-3691-1.00028-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
27
|
Finlay WJJ, Almagro JC. Natural and man-made V-gene repertoires for antibody discovery. Front Immunol 2012; 3:342. [PMID: 23162556 PMCID: PMC3498902 DOI: 10.3389/fimmu.2012.00342] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2012] [Accepted: 10/27/2012] [Indexed: 01/15/2023] Open
Abstract
Antibodies are the fastest-growing segment of the biologics market. The success of antibody-based drugs resides in their exquisite specificity, high potency, stability, solubility, safety, and relatively inexpensive manufacturing process in comparison with other biologics. We outline here the structural studies and fundamental principles that define how antibodies interact with diverse targets. We also describe the antibody repertoires and affinity maturation mechanisms of humans, mice, and chickens, plus the use of novel single-domain antibodies in camelids and sharks. These species all utilize diverse evolutionary solutions to generate specific and high affinity antibodies and illustrate the plasticity of natural antibody repertoires. In addition, we discuss the multiple variations of man-made antibody repertoires designed and validated in the last two decades, which have served as tools to explore how the size, diversity, and composition of a repertoire impact the antibody discovery process.
Collapse
|
28
|
General strategy for the generation of human antibody variable domains with increased aggregation resistance. Proc Natl Acad Sci U S A 2012; 109:10879-84. [PMID: 22745168 DOI: 10.1073/pnas.1202866109] [Citation(s) in RCA: 156] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The availability of stable human antibody reagents would be of considerable advantage for research, diagnostic, and therapeutic applications. Unfortunately, antibody variable heavy and light domains (V(H) and V(L)) that mediate the interaction with antigen have the propensity to aggregate. Increasing their aggregation resistance in a general manner has proven to be a difficult and persistent problem, due to the high level of sequence diversity observed in human variable domains and the requirement to maintain antigen binding. Here we outline such an approach. By using phage display we identified specific positions that clustered in the antigen binding site (28, 30-33, 35 in V(H) and 24, 49-53, 56 in V(L)). Introduction of aspartate or glutamate at these positions endowed superior biophysical properties (non-aggregating, well-expressed, and heat-refoldable) onto domains derived from common human germline families (V(H)3 and V(κ)1). The effects of the mutations were highly positional and independent of sequence diversity at other positions. Moreover, crystal structures of mutant V(H) and V(L) domains revealed a surprising degree of structural conservation, indicating compatibility with V(H)/V(L) pairing and antigen binding. This allowed the retrofitting of existing binders, as highlighted by the development of robust high affinity antibody fragments derived from the breast cancer therapeutic Herceptin. Our results provide a general strategy for the generation of human antibody variable domains with increased aggregation resistance.
Collapse
|
29
|
Influence of variable domain glycosylation on anti-neutrophil cytoplasmic autoantibodies and anti-glomerular basement membrane autoantibodies. BMC Immunol 2012; 13:10. [PMID: 22404873 PMCID: PMC3324382 DOI: 10.1186/1471-2172-13-10] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Accepted: 03/09/2012] [Indexed: 02/05/2023] Open
Abstract
Background The pathophysiological significance of variable region glycosylation of autoantibodies is still unclear. In the current study, the influence of the variable region N-linked oligosaccharides on the reactivity of three autoantibody specificities was investigated with Sambucus nigra agglutinin (SNA), which mainly binds to oligosaccharides with terminal α2, 6-linked sialic acid on the variable region of IgG. Methods Twenty-seven patients with serum positive anti-neutrophil cytoplasmic autoantibodies (ANCA) against myeploperoxidase (MPO) or proteinase 3 (PR3), or autoantibodies against glomerular basement membrane (GBM) were included. Total IgG was isolated and separated into non-SNA-binding and SNA-binding fractions with SNA affinity chromatography. Antigen-specific IgG was purified by immunoaffinity chromatography. Results At the same concentration of IgG, the antigen binding level of non-SNA-binding IgG was significantly lower than that of SNA-binding IgG for MPO-ANCA (absorbance value at 405 nm, 0.572 ± 0.590 vs. 0.962 ± 0.670, P < 0.001) and for PR3-ANCA (0.362 ± 0.530 vs. 0.560 ± 0.531, P = 0.003). The antigen binding level of non-SNA-binding IgG was significantly higher than that of SNA-binding IgG for anti-GBM antibodies (1.301 ± 0.594 vs. 1.172 ± 0.583, P = 0.044). The level of variable region glycosylation of total IgG was significantly lower than that of affinity-purified MPO-ANCA (1.021 ± 0.201 vs. 1.434 ± 0.134, P = 0.004). The level of variable region glycosylation of total IgG was significantly higher than that of affinity-purified anti-GBM antibodies (1.034 ± 0.340 vs. 0.734 ± 0.333, P = 0.007). The SNA-binding fraction of MPO-ANCA-containing IgG and PR3-ANCA-containing IgG induced higher levels of neutrophil oxygen radical production than the corresponding non-SNA-binding fractions (P < 0.001 and P = 0.043, respectively). The level of variable region glycosylation of affinity-purified MPO-ANCA was higher in active AAV than the same patients in remission (P = 0.001). Conclusion Characteristics of variable region glycosylation of ANCA and anti-GBM antibodies were different from that of total IgG, which might influence the antigen-binding ability of these antibodies. Variable region glycosylation of ANCA might influence the effect of ANCA-induced neutrophils respiratory burst.
Collapse
|
30
|
Weiser AA, Wittenbrink N, Zhang L, Schmelzer AI, Valai A, Or-Guil M. Affinity maturation of B cells involves not only a few but a whole spectrum of relevant mutations. Int Immunol 2012; 23:345-56. [PMID: 21521882 DOI: 10.1093/intimm/dxr018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Affinity maturation of B lymphocytes within germinal centers involves both diversification of their B-cell receptors (BCRs) by somatic hypermutation (SHM) and a crucial receptor-mediated selection step. However, in contrast to recent advances in revealing the molecular mechanism of SHM, the fundamentals of the selection process are still poorly understood, i.e. it is often not clear how and how many mutations contribute to improving a BCR during the response against a given antigen. A general drawback in assessing the mutations relevant to the selection process is the difficult task of rating the relative contributions of selection and intrinsic biases to the experimentally observed mutation patterns of BCRs. The approach proposed here is premised on statistical comparison of the frequency distributions of nucleotide substitutions as observed in datasets of hypermutated BCRs against their frequency distribution expected under the null hypothesis of no selection. Thereby, we show that the spectrum of mutations relevant to maturation of canonical anti-(4-hydroxy-3-nitrophenyl)acetyl BCRs is much broader than previously acknowledged, going beyond the scope of single key mutations. Moreover, our results suggest that maturation not only involves selection by means of affinity but likewise expression and stabilization of BCRs.
Collapse
Affiliation(s)
- Armin A Weiser
- Systems Immunology Lab, Department of Biology, Institute for Theoretical Biology, Humboldt University, Invalidenstrasse 43, 10115 Berlin, Germany
| | | | | | | | | | | |
Collapse
|
31
|
Abstract
Rational engineering methods can be applied with success to optimize physicochemical characteristics of antibodies. Application of in silico analysis and prediction methods to antibody Fv regions can help to find residues affecting antibody-antigen affinity when high-resolution antibody structures or antibody-antigen complex structures are known. In these cases, the identification of residues affecting affinity can facilitate the selection of candidates for guided maturation by PCR using degenerate oligonucleotides. Here, we describe the utilization of a semi-rational approach to enhance the affinity of antibodies by combining in silico and traditional wet lab-based methods.
Collapse
|
32
|
Creation of the large and highly functional synthetic repertoire of human VH and Vκ domain antibodies. Methods Mol Biol 2012; 911:39-63. [PMID: 22886245 DOI: 10.1007/978-1-61779-968-6_4] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
This protocol describes a method for creation of a highly diverse and functional synthetic phage-displayed repertoire of fully human domain antibodies (dAbs). The repertoire is based on two human frameworks (one VH and one Vκ) that express well in bacteria and are frequently used in human antibodies. To achieve this, we first build dAb libraries, containing full synthetic diversity at key positions in the complementarity-determining regions (CDRs). We then use an antigen-independent preselection of this primary dAb repertoire on generic ligands of the VH and the Vκ scaffolds (namely, the bacterial superantigens, protein A and L) to enrich for folded dAbs. Finally, the CDRs of these preselected dAbs are randomly recombined to further expand genetic diversity. The resulting phage repertoire is in excess of 10(10) clones and is largely populated by correctly folded (over 50%) functional dAbs.
Collapse
|
33
|
Vincke C, Muyldermans S. Introduction to heavy chain antibodies and derived Nanobodies. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2012; 911:15-26. [PMID: 22886243 DOI: 10.1007/978-1-61779-968-6_2] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The immune response of infected or immunized dromedaries contains a diverse repertoire of conventional and heavy chain-only antibodies, both functional in antigen binding. By definition, a heavy chain antibody is devoid of a light chain and in the case of the heavy chain antibodies in camelids the CH1 domain is also missing. Consequently a camelid heavy chain antibody associates with its cognate antigen via a single domain, the variable heavy chain domain of a heavy chain antibody or VHH. An antigen-specific VHH, also known as Nanobody, with excellent biochemical properties can be obtained in various ways. Their recombinant expression provides access to user-friendly tools for a wide variety of applications.
Collapse
Affiliation(s)
- Cécile Vincke
- Department of Molecular and Cellular Interactions, VIB, Brussels, Belgium
| | | |
Collapse
|
34
|
Altshuler EP, Serebryanaya DV, Katrukha AG. Generation of recombinant antibodies and means for increasing their affinity. BIOCHEMISTRY (MOSCOW) 2011; 75:1584-605. [PMID: 21417996 DOI: 10.1134/s0006297910130067] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Highly specific interaction with foreign molecules is a unique feature of antibodies. Since 1975, when Keller and Milstein proposed the method of hybridoma technology and prepared mouse monoclonal antibodies, many antibodies specific to various antigens have been obtained. Recent development of methods for preparation of recombinant DNA libraries and in silico bioinformatics approaches for protein structure analysis makes possible antibody preparation using gene engineering approaches. The development of gene engineering methods allowed creating recombinant antibodies and improving characteristics of existing antibodies; this significantly extends the applicability of antibodies. By modifying biochemical and immunochemical properties of antibodies by changing their amino acid sequences it is possible to create antibodies with properties optimal for certain tasks. For example, application of recombinant technologies resulted in antibody preparation of high affinity significantly exceeding the initial affinity of natural antibodies. In this review we summarize information about the structure, modes of preparation, and application of recombinant antibodies and their fragments and also consider the main approaches used to increase antibody affinity.
Collapse
Affiliation(s)
- E P Altshuler
- Department of Biochemistry, Faculty of Biology, Lomonosov Moscow State University, Russia
| | | | | |
Collapse
|
35
|
Schelonka RL, Ivanov II, Vale AM, Dimmitt RA, Khaled M, Schroeder HW. Absence of N addition facilitates B cell development, but impairs immune responses. Immunogenetics 2011; 63:599-609. [PMID: 21660592 PMCID: PMC3181008 DOI: 10.1007/s00251-011-0543-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 05/24/2011] [Indexed: 12/02/2022]
Abstract
The programmed, stepwise acquisition of immunocompetence that marks the development of the fetal immune response proceeds during a period when both T cell receptor and immunoglobulin (Ig) repertoires exhibit reduced junctional diversity due to physiologic terminal deoxynucleotidyl transferase (TdT) insufficiency. To test the effect of N addition on humoral responses, we transplanted bone marrow from TdT-deficient (TdT(-/-)) and wild-type (TdT(+/+)) BALB/c mice into recombination activation gene 1-deficient BALB/c hosts. Mice transplanted with TdT(-/-) cells exhibited diminished humoral responses to the T-independent antigens α-1-dextran and (2,4,6-trinitrophenyl) hapten conjugated to AminoEthylCarboxymethyl-FICOLL, to the T-dependent antigens NP(19)CGG and hen egg lysozyme, and to Enterobacter cloacae, a commensal bacteria that can become an opportunistic pathogen in immature and immunocompromised hosts. An exception to this pattern of reduction was the T-independent anti-phosphorylcholine response to Streptococcus pneumoniae, which is normally dominated by the N-deficient T15 idiotype. Most of the humoral immune responses in the recipients of TdT(-/-) bone marrow were impaired, yet population of the blood with B and T cells occurred more rapidly. To further test the effect of N-deficiency on B cell and T cell population growth, transplanted TdT-sufficient and -deficient BALB/c IgM(a) and congenic TdT-sufficient CB17 IgM(b) bone marrow were placed in competition. TdT(-/-) cells demonstrated an advantage in populating the bone marrow, the spleen, and the peritoneal cavity. TdT deficiency, which characterizes fetal lymphocytes, thus appears to facilitate filling both central and peripheral lymphoid compartments, but at the cost of altered responses to a broad set of antigens.
Collapse
Affiliation(s)
- Robert L. Schelonka
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL 35294 USA
- Present Address: Oregon Health and Science University, Portland, OR 97239 USA
| | - Ivaylo I. Ivanov
- Department of Microbiology, University of Alabama at Birmingham, Shelby Building 401, 1530 3rd Avenue South, Birmingham, AL 35294-2182 USA
- Present Address: Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032 USA
| | - Andre M. Vale
- Department of Medicine, University of Alabama at Birmingham, Shelby Building 401, 1530 3rd Avenue South, Birmingham, AL 35294-2182 USA
| | - Reed A. Dimmitt
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL 35294 USA
| | - Mahnaz Khaled
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL 35294 USA
| | - Harry W. Schroeder
- Department of Microbiology, University of Alabama at Birmingham, Shelby Building 401, 1530 3rd Avenue South, Birmingham, AL 35294-2182 USA
- Department of Medicine, University of Alabama at Birmingham, Shelby Building 401, 1530 3rd Avenue South, Birmingham, AL 35294-2182 USA
- Department of Genetics, University of Alabama at Birmingham, Shelby Building 401, 1530 3rd Avenue South, Birmingham, AL 35294-2182 USA
| |
Collapse
|
36
|
Integrated mimicry of B cell antibody mutagenesis using yeast homologous recombination. Mol Biotechnol 2011; 47:57-69. [PMID: 20645027 DOI: 10.1007/s12033-010-9312-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Antibody affinity maturation proceeds in vivo via a combination of point mutations, insertions, deletions, and combinatorial shuffling of light chains or portions of the heavy chain, thereby reducing the probability of trapping in local affinity optima in sequence space. In vivo homologous recombination in yeast can be exploited to mimic the broad spectrum of mutational types deployed by B cells, incorporating both receptor revision and receptor editing together with polymerase-directed point mutagenesis. This method was used to effect a 10,000-fold affinity improvement in an anti-peptide single-chain antibody in three rounds of mutagenesis and screening, and a 1,000-fold affinity improvement in an anti-protein single-chain antibody in a single round. When recombinational mutagenesis (CDR or chain shuffling) was directly compared to error-prone PCR, the recombinational approach yielded greater affinity improvement with substantially reduced divergence from germline sequences, demonstrating an advantage of simultaneously testing a broad range of mutational strategies.
Collapse
|
37
|
Lerner RA. Rare antibodies from combinatorial libraries suggests an S.O.S. component of the human immunological repertoire. MOLECULAR BIOSYSTEMS 2011; 7:1004-12. [PMID: 21298133 DOI: 10.1039/c0mb00310g] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Convergence of observations from different sources is the norm in science. However, when convergence occurs in man for antibodies it is remarkable because the repertoire of possible immunoglobulin products is very large and diverse. Thus, one would not expect to see the same antibody twice from divergent populations unless there is special significance as to why the immune response is constrained. Now, broadly neutralizing antibodies isolated from combinatorial libraries from three separate populations have been shown to all use the same (V(H) 1-69) germ line gene and interact with the influenza virus in very similar ways. Here we discuss the reasons for this convergence in terms of how the immunological repertoire responds to emergency situations where time is short as occurs, for example, in potentially lethal infections. It is suggested that there is a first responder or S.O.S. component of the antibody repertoire that evolved to initiate rapid defense against infectious agents. The discovery of the homologies between these commonly produced antibodies may have significance for the design of novel vaccines. Finally, these convergent results may give much insight into why antibodies encoded by the V(H) 1-69 germ line gene are highly over represented in B-cell lymphomas.
Collapse
Affiliation(s)
- Richard A Lerner
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
| |
Collapse
|
38
|
Thomson CA, Little KQ, Reason DC, Schrader JW. Somatic diversity in CDR3 loops allows single V-genes to encode innate immunological memories for multiple pathogens. THE JOURNAL OF IMMUNOLOGY 2011; 186:2291-8. [PMID: 21228346 DOI: 10.4049/jimmunol.0904092] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The human Ab response to many common pathogens is oligoclonal, with restricted usage of Ig V-genes. Intriguingly, the IGVK3-11 and IGVH3-30 V-genes are repeatedly paired in protective Abs against the 23F polysaccharide of Streptococcus pneumoniae, as well as against the gB envelope protein of human CMV, where germline-encoded amino acids make key contacts with the gB protein. We constructed IgGs encoded by the germline IGVK3-11 and IGVH3-30 V-genes together with DNA encoding the respective CDR3 regions of the L chain and H chain found in a hypermutated anti-23F Ab. These IgGs encoded by germline V-genes bound specifically to 23F pneumococcal capsular polysaccharides with no reactivity to other serotypes of pneumococcal capsular polysaccharides or arrayed glycans and recognized L-rhamnose, a component of the 23F repeating subunit. IgGs encoded by this pair of germline V-genes mediated complement-dependent phagocytosis of encapsulated 23F S. pneumoniae by human neutrophils. Mutations in CDRL3 and CDRH3 had significant effects on binding. Thus, IGKV3-11 and IGHV3-30, depending on with which distinct DNA sequences encoding CDR3 they are recombined, can encode binding sites for protective Abs against chemically distinct Ags and thus, may encode innate immunological memory against human CMV and S. pneumoniae.
Collapse
Affiliation(s)
- Christy A Thomson
- The Biomedical Research Centre, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | | | | | | |
Collapse
|
39
|
Cizeau J, Torres MGP, Cowling SG, Stibbard S, Premsukh A, Entwistle J, MacDonald GC. Fusogenics: a recombinant immunotoxin-based screening platform to select internalizing tumor-specific antibody fragments. JOURNAL OF BIOMOLECULAR SCREENING 2011; 16:90-100. [PMID: 21131595 DOI: 10.1177/1087057110387425] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
Antibody-based therapeutics play a vital role in the treatment of certain cancers; however, despite commercial success, various strategies are being pursued to increase their potency and hence improve patient outcomes. The use of antibodies to deliver a cytotoxic payload offers a promising alternative for more efficacious therapies. Immunotoxins are composed of an internalizing antibody fragment linked to a bacterial or plant toxin. Once internalized, the payload, such as Pseudomonas exotoxin A (PE), blocks protein synthesis and induces apoptosis. Typically, immunotoxins are developed by first isolating a tumor-specific antibody, which is then either chemically linked to a toxin or reengineered as a fusion protein. Here, the authors describe the development of Fusogenics, an immunotoxin-based screening method that selects internalizing tumor-specific antibodies using a functional assay. Selected immune library clones were characterized and shown to be selective against normal tissues and specific to tumor tissues. In summary, the Fusogenics immunotoxin platform represents a unique, single-step selection approach combining specificity and functionality to isolate novel internalizing tumor-specific antibody fragments with potential for direct clinical application in the treatment of cancer.
Collapse
|
40
|
Li B, Zhao L, Wang C, Guo H, Wu L, Zhang X, Qian W, Wang H, Guo Y. The protein-protein interface evolution acts in a similar way to antibody affinity maturation. J Biol Chem 2010; 285:3865-3871. [PMID: 20007707 PMCID: PMC2823529 DOI: 10.1074/jbc.m109.076547] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2009] [Indexed: 12/22/2022] Open
Abstract
Understanding the evolutionary mechanism that acts at the interfaces of protein-protein complexes is a fundamental issue with high interest for delineating the macromolecular complexes and networks responsible for regulation and complexity in biological systems. To investigate whether the evolution of protein-protein interface acts in a similar way as antibody affinity maturation, we incorporated evolutionary information derived from antibody affinity maturation with common simulation techniques to evaluate prediction success rates of the computational method in affinity improvement in four different systems: antibody-receptor, antibody-peptide, receptor-membrane ligand, and receptor-soluble ligand. It was interesting to find that the same evolutionary information could improve the prediction success rates in all the four protein-protein complexes with an exceptional high accuracy (>57%). One of the most striking findings in our present study is that not only in the antibody-combining site but in other protein-protein interfaces almost all of the affinity-enhancing mutations are located at the germline hotspot sequences (RGYW or WA), indicating that DNA hot spot mechanisms may be widely used in the evolution of protein-protein interfaces. Our data suggest that the evolution of distinct protein-protein interfaces may use the same basic strategy under selection pressure to maintain interactions. Additionally, our data indicate that classical simulation techniques incorporating the evolutionary information derived from in vivo antibody affinity maturation can be utilized as a powerful tool to improve the binding affinity of protein-protein complex with a high accuracy.
Collapse
MESH Headings
- Amino Acid Sequence
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/genetics
- Antibodies, Monoclonal/metabolism
- Antibodies, Monoclonal, Murine-Derived
- Antibody Affinity/genetics
- Antibody Affinity/immunology
- Antigens, CD/chemistry
- Antigens, CD/genetics
- Antigens, CD/metabolism
- Base Sequence
- Binding Sites/genetics
- CTLA-4 Antigen
- Computer Simulation
- Crystallography, X-Ray
- Evolution, Molecular
- Interleukin-2 Receptor alpha Subunit/chemistry
- Interleukin-2 Receptor alpha Subunit/genetics
- Interleukin-2 Receptor alpha Subunit/metabolism
- Models, Molecular
- Molecular Sequence Data
- Mutation
- Protein Binding
- Protein Interaction Mapping/methods
- Protein Structure, Tertiary
- Proteins/chemistry
- Proteins/genetics
- Proteins/metabolism
- Rituximab
- Sequence Homology, Amino Acid
Collapse
Affiliation(s)
- Bohua Li
- From the International Joint Cancer Institute and 301 General Hospital Cancer Center, Second Military Medical University, Shanghai 200433; the National Engineering Research Center for Antibody Medicine and Shanghai Key Laboratory of Cell Engineering & Antibody, Shanghai 201203, and
| | - Lei Zhao
- From the International Joint Cancer Institute and 301 General Hospital Cancer Center, Second Military Medical University, Shanghai 200433
| | - Chong Wang
- the School of Medicine and School of Pharmacy, The Center for Antibody Medicine of Ministry of Education, Shanghai Jiao Tong University, 227 South Chongqing Road, Shanghai 200025, China
| | - Huaizu Guo
- the School of Medicine and School of Pharmacy, The Center for Antibody Medicine of Ministry of Education, Shanghai Jiao Tong University, 227 South Chongqing Road, Shanghai 200025, China
| | - Lan Wu
- From the International Joint Cancer Institute and 301 General Hospital Cancer Center, Second Military Medical University, Shanghai 200433
| | - Xunming Zhang
- From the International Joint Cancer Institute and 301 General Hospital Cancer Center, Second Military Medical University, Shanghai 200433
| | - Weizhu Qian
- From the International Joint Cancer Institute and 301 General Hospital Cancer Center, Second Military Medical University, Shanghai 200433; the National Engineering Research Center for Antibody Medicine and Shanghai Key Laboratory of Cell Engineering & Antibody, Shanghai 201203, and
| | - Hao Wang
- From the International Joint Cancer Institute and 301 General Hospital Cancer Center, Second Military Medical University, Shanghai 200433; the National Engineering Research Center for Antibody Medicine and Shanghai Key Laboratory of Cell Engineering & Antibody, Shanghai 201203, and
| | - Yajun Guo
- From the International Joint Cancer Institute and 301 General Hospital Cancer Center, Second Military Medical University, Shanghai 200433; the National Engineering Research Center for Antibody Medicine and Shanghai Key Laboratory of Cell Engineering & Antibody, Shanghai 201203, and; the School of Medicine and School of Pharmacy, The Center for Antibody Medicine of Ministry of Education, Shanghai Jiao Tong University, 227 South Chongqing Road, Shanghai 200025, China.
| |
Collapse
|
41
|
Wang M, Rada C, Neuberger MS. Altering the spectrum of immunoglobulin V gene somatic hypermutation by modifying the active site of AID. ACTA ACUST UNITED AC 2010; 207:141-53. [PMID: 20048284 PMCID: PMC2812546 DOI: 10.1084/jem.20092238] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
High-affinity antibodies are generated by somatic hypermutation with nucleotide substitutions introduced into the IgV in a semirandom fashion, but with intrinsic mutational hotspots strategically located to optimize antibody affinity maturation. The process is dependent on activation-induced deaminase (AID), an enzyme that can deaminate deoxycytidine in DNA in vitro, where its activity is sensitive to the identity of the 5'-flanking nucleotide. As a critical test of whether such DNA deamination activity underpins antibody diversification and to gain insight into the extent to which the antibody mutation spectrum is dependent on the intrinsic substrate specificity of AID, we investigated whether it is possible to change the IgV mutation spectrum by altering AID's active site such that it prefers a pyrimidine (rather than a purine) flanking the targeted deoxycytidine. Consistent with the DNA deamination mechanism, B cells expressing the modified AID proteins yield altered IgV mutation spectra (exhibiting a purine-->pyrimidine shift in flanking nucleotide preference) and altered hotspots. However, AID-catalyzed deamination of IgV targets in vitro does not yield the same degree of hotspot dominance to that observed in vivo, indicating the importance of features beyond AID's active site and DNA local sequence environment in determining in vivo hotspot dominance.
Collapse
Affiliation(s)
- Meng Wang
- Laboratory of Molecular Biology, Medical Research Council, Cambridge CB2 0QH, England, UK
| | | | | |
Collapse
|
42
|
von Schantz L, Gullfot F, Scheer S, Filonova L, Cicortas Gunnarsson L, Flint JE, Daniel G, Nordberg-Karlsson E, Brumer H, Ohlin M. Affinity maturation generates greatly improved xyloglucan-specific carbohydrate binding modules. BMC Biotechnol 2009; 9:92. [PMID: 19878581 PMCID: PMC2783032 DOI: 10.1186/1472-6750-9-92] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2009] [Accepted: 10/31/2009] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Molecular evolution of carbohydrate binding modules (CBM) is a new approach for the generation of glycan-specific molecular probes. To date, the possibility of performing affinity maturation on CBM has not been investigated. In this study we show that binding characteristics such as affinity can be improved for CBM generated from the CBM4-2 scaffold by using random mutagenesis in combination with phage display technology. RESULTS Two modified proteins with greatly improved affinity for xyloglucan, a key polysaccharide abundant in the plant kingdom crucial for providing plant support, were generated. Both improved modules differ from other existing xyloglucan probes by binding to galactose-decorated subunits of xyloglucan. The usefulness of the evolved binders was verified by staining of plant sections, where they performed better than the xyloglucan-binding module from which they had been derived. They discriminated non-fucosylated from fucosylated xyloglucan as shown by their ability to stain only the endosperm, rich in non-fucosylated xyloglucan, but not the integument rich in fucosylated xyloglucan, on tamarind seed sections. CONCLUSION We conclude that affinity maturation of CBM selected from molecular libraries based on the CBM4-2 scaffold is possible and has the potential to generate new analytical tools for detection of plant carbohydrates.
Collapse
|
43
|
Bostrom J, Yu SF, Kan D, Appleton BA, Lee CV, Billeci K, Man W, Peale F, Ross S, Wiesmann C, Fuh G. Variants of the Antibody Herceptin That Interact with HER2 and VEGF at the Antigen Binding Site. Science 2009; 323:1610-4. [DOI: 10.1126/science.1165480] [Citation(s) in RCA: 290] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
44
|
Finlay WJ, Cunningham O, Lambert MA, Darmanin-Sheehan A, Liu X, Fennell BJ, Mahon CM, Cummins E, Wade JM, O'Sullivan CM, Tan XY, Piche N, Pittman DD, Paulsen J, Tchistiakova L, Kodangattil S, Gill D, Hufton SE. Affinity maturation of a humanized rat antibody for anti-RAGE therapy: comprehensive mutagenesis reveals a high level of mutational plasticity both inside and outside the complementarity-determining regions. J Mol Biol 2009; 388:541-58. [PMID: 19285987 DOI: 10.1016/j.jmb.2009.03.019] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2009] [Revised: 03/06/2009] [Accepted: 03/07/2009] [Indexed: 12/16/2022]
Abstract
Antibodies that neutralize RAGE (receptor for advanced glycation end products)-ligand interactions have potential therapeutic applications in both acute and chronic diseases. We generated XT-M4, a rat anti-RAGE monoclonal antibody that has in vivo efficacy in an acute sepsis model. This antibody was subsequently humanized. To improve the affinity of this antibody for the treatment of chronic indications, we used random and targeted mutagenesis strategies in combination with ribosome and phage-display technologies, respectively, to generate libraries of XT-M4 variants. We identified a panel of single-chain Fv antibody fragments (scFv's) that was improved up to 110-fold in a homogeneous time-resolved fluorescence competition assay against parental XT-M4 immunoglobulin G (IgG). After reformatting to bivalent scFv-Fc fusions and IgGs, we observed similar gains in potency in the same assay. Further analysis of binding kinetics as IgG revealed multiple variants with subnanomolar apparent affinity that was dictated primarily by improvements in the off-rate. All variants also had improved binding to cell surface-expressed human RAGE, and all retained, or had improved, apparent affinity for mouse RAGE. F100bL in V(H) (variable region of the heavy chain) complementarity-determining region 3 (CDR3) was one of a number of key mutations that correlated with affinity improvements and was independently identified by both mutagenesis strategies. Random mutagenesis coupled with ribosome display and high-throughput screening revealed an unexpectedly high level of mutational plasticity across the whole length of the humanized scFv, suggesting greater scope for structural optimization outside of the primary antigen-combining site defined by V(H) CDR3 and V(kappa) CDR3. In summary, our comprehensive mutagenesis approach not only achieved the desired affinity maturation of XT-M4 but also defined multiple mutational hotspots across the antibody sequence, provided an insight into the specificity-determining residues of the antibody paratope, and identified additional sites within the CDR loops where human germ-line amino acids may be introduced without affecting function.
Collapse
Affiliation(s)
- William J Finlay
- Wyeth Research Ireland, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Abstract
Antibody molecules can be regarded as products of a protein engineering system for the generation of a virtually unlimited repertoire of complementary molecular surfaces. This extreme structural heterogeneity is required for recognition of the nearly infinite array of antigenic determinants. This chapter discusses the structures of antibodies and their specific recognition of antigens, the binding energetics of these interactions, the cross-reactivity and specificity of antibody-antigen interactions, the role of conformational flexibility in antigen recognition, and the structural basis of the antibody affinity maturation process.
Collapse
Affiliation(s)
- Eric J Sundberg
- Boston Biomedical Research Institute, 64 Grove Street, Watertown, MA 02472, USA
| |
Collapse
|
46
|
Germline V-genes sculpt the binding site of a family of antibodies neutralizing human cytomegalovirus. EMBO J 2008; 27:2592-602. [PMID: 18772881 DOI: 10.1038/emboj.2008.179] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2008] [Accepted: 08/13/2008] [Indexed: 12/31/2022] Open
Abstract
Immunoglobulin genes are generated somatically through specialized mechanisms resulting in a vast repertoire of antigen-binding sites. Despite the stochastic nature of these processes, the V-genes that encode most of the antigen-combining site are under positive evolutionary selection, raising the possibility that V-genes have been selected to encode key structural features of binding sites of protective antibodies against certain pathogens. Human, neutralizing antibodies to human cytomegalovirus that bind the AD-2S1 epitope on its gB envelope protein repeatedly use a pair of well-conserved, germline V-genes IGHV3-30 and IGKV3-11. Here, we present crystallographic, kinetic and thermodynamic analyses of the binding site of such an antibody and that of its primary immunoglobulin ancestor. These show that these germline V-genes encode key side chain contacts with the viral antigen and thereby dictate key structural features of the hypermutated, high-affinity neutralizing antibody. V-genes may thus encode an innate, protective immunological memory that targets vulnerable, invariant sites on multiple pathogens.
Collapse
|
47
|
Barderas R, Desmet J, Timmerman P, Meloen R, Casal JI. Affinity maturation of antibodies assisted by in silico modeling. Proc Natl Acad Sci U S A 2008; 105:9029-34. [PMID: 18574150 PMCID: PMC2449359 DOI: 10.1073/pnas.0801221105] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2008] [Indexed: 01/10/2023] Open
Abstract
Rational engineering methods can be applied with reasonable success to optimize physicochemical characteristics of proteins, in particular, antibodies. Here, we describe a combined CDR3 walking randomization and rational design-based approach to enhance the affinity of the human anti-gastrin TA4 scFv. The application of this methodology to TA4 scFv, displaying only a weak overall affinity for gastrin17 (K(D) = 6 microM), resulted in a set of nine affinity-matured scFv variants with near-nanomolar affinity (K(D) = 13.2 nM for scFv TA4.112). First, CDR-H3 and CDR-L3 randomization resulted in three scFvs with an overall affinity improvement of 15- to 35-fold over the parental. Then, the modeling of two scFv constructs selected from the previous step (TA4.11 and TA4.13) was followed by a combination of manual and molecular dynamics-based docking of gastrin17 into the respective binding sites, analysis of apparent packing defects, and selection of residues for mutagenesis through phage display. Nine scFv mutants were obtained from the second maturation step. A final 454-fold improvement in affinity compared with TA4 was obtained. These scFvs showed an enhanced potency to inhibit gastrin-induced proliferation in Colo 320 WT and BxPc3 tumoral cells. In conclusion, we propose a structure-based rational method to accelerate the development of affinity-matured antibody constructs with enhanced potential for therapeutic use.
Collapse
Affiliation(s)
- Rodrigo Barderas
- *Protein Technology Unit, Biotechnology Programme, Spanish National Cancer Center CNIO, 28029 Madrid, Spain
| | | | - Peter Timmerman
- Pepscan Therapeutics BV, 8219 PK Lelystad, The Netherlands
- Van 't Hoff Institute for Molecular Sciences, Faculty of Science, University of Amsterdam, 1018 WV, Amsterdam, The Netherlands; and
| | - Rob Meloen
- Pepscan Therapeutics BV, 8219 PK Lelystad, The Netherlands
- Academic Biomedical Center, University of Utrecht, 3508 TC, Utrecht, The Netherlands
| | - J. Ignacio Casal
- *Protein Technology Unit, Biotechnology Programme, Spanish National Cancer Center CNIO, 28029 Madrid, Spain
| |
Collapse
|
48
|
Galanis M, Irving RA, Hudson PJ. Bacteriophage library construction and selection of recombinant antibodies. ACTA ACUST UNITED AC 2008; Chapter 17:17.1.1-17.1.48. [PMID: 18432742 DOI: 10.1002/0471142735.im1701s34] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
This unit describes the use of E. coli and bacteriophages to display a diverse library of antibody fragments equivalent in complexity to the mammalian immune repertoire, and subsequent screening of the library for antibody fragments with specific binding affinities. The methods are also used for affinity enhancement (maturation), through the display and selection of improved affinity mutants derived from a single parent antibody. This unit discusses the following key components needed in library construction technology: a repertoire of antibody genes, typically amplified by polymerase chain reaction (PCR) technology; construction of scFv genes by PCR assembly; a method for producing a stable library, using bacteriophage that can both display individual antibodies on the viral surface and carry the gene encoding the antibody; a method of growing phage for selection; a method of selecting the highest-affinity antibody from the phage library; a method for monitoring progress of phage selection; an affinity-enhancement strategy for improving and manipulating the selected antibody; and expression of affinity-enhanced antibodies.
Collapse
Affiliation(s)
- M Galanis
- Cooperative Research Center for Diagnostic Technologies at CSIRO Molecular Science, Parkville, Victoria, Australia
| | | | | |
Collapse
|
49
|
Persson H, Wallmark H, Ljungars A, Hallborn J, Ohlin M. In vitro evolution of an antibody fragment population to find high-affinity hapten binders. Protein Eng Des Sel 2008; 21:485-93. [PMID: 18480091 DOI: 10.1093/protein/gzn024] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Recently, we constructed a focused antibody library tailored to interact with haptens. High functionality of this library was demonstrated, as specific binders could be retrieved to a range of different haptens. In the current study we have developed a mutagenesis and selection strategy in order to further fine-tune the hapten binding properties of these antibody fragments. Testosterone was chosen as model antigen for the investigation. A population, rather than a single clone, originating from this focused library and enriched for testosterone binders, was subjected to random mutagenesis and different phage display selection strategies of various stringencies. These included consecutively lowering the antigen concentration and having, or not having, soluble hapten present during the phage capture and elution steps. The different selection procedures resulted in a considerable increase in apparent affinities for several of the selected populations, from which the highest affinity antibody isolated had a K(D) of 2 nM, corresponding to an approximately 200-fold affinity improvement compared with the best clone of the starting population. Importantly, the polyclonal nature of the starting material allowed for the identification of novel unrelated variants that differed in fine-specificity, demonstrating that this approach is valuable for exploring different parts of structure space.
Collapse
Affiliation(s)
- Helena Persson
- Department of Immunotechnology, Lund University, BMC D13 SE-221 84, Lund
| | | | | | | | | |
Collapse
|
50
|
|