1
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Rappazzo CG, Fernández-Quintero ML, Mayer A, Wu NC, Greiff V, Guthmiller JJ. Defining and Studying B Cell Receptor and TCR Interactions. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:311-322. [PMID: 37459189 PMCID: PMC10495106 DOI: 10.4049/jimmunol.2300136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 04/15/2023] [Indexed: 07/20/2023]
Abstract
BCRs (Abs) and TCRs (or adaptive immune receptors [AIRs]) are the means by which the adaptive immune system recognizes foreign and self-antigens, playing an integral part in host defense, as well as the emergence of autoimmunity. Importantly, the interaction between AIRs and their cognate Ags defies a simple key-in-lock paradigm and is instead a complex many-to-many mapping between an individual's massively diverse AIR repertoire, and a similarly diverse antigenic space. Understanding how adaptive immunity balances specificity with epitopic coverage is a key challenge for the field, and terms such as broad specificity, cross-reactivity, and polyreactivity remain ill-defined and are used inconsistently. In this Immunology Notes and Resources article, a group of experimental, structural, and computational immunologists define commonly used terms associated with AIR binding, describe methodologies to study these binding modes, as well as highlight the implications of these different binding modes for therapeutic design.
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Affiliation(s)
| | | | - Andreas Mayer
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Nicholas C. Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Victor Greiff
- Department of Immunology, University of Oslo and Oslo University Hospital, 0372 Oslo, Norway
| | - Jenna J. Guthmiller
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
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2
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Arslan M, Uluçay T, Kale S, Kalyoncu S. Engineering of conserved residues near antibody heavy chain complementary determining region 3 (HCDR3) improves both affinity and stability. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140915. [PMID: 37059314 DOI: 10.1016/j.bbapap.2023.140915] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 04/11/2023] [Accepted: 04/11/2023] [Indexed: 04/16/2023]
Abstract
Affinity and stability are crucial parameters in antibody development and engineering approaches. Although improvement in both metrics is desirable, trade-offs are almost unavoidable. Heavy chain complementarity determining region 3 (HCDR3) is the best-known region for antibody affinity but its impact on stability is often neglected. Here, we present a mutagenesis study of conserved residues near HCDR3 to elicit the role of this region in the affinity-stability trade-off. These key residues are positioned around the conserved salt bridge between VH-K94 and VH-D101 which is crucial for HCDR3 integrity. We show that the additional salt bridge at the stem of HCDR3 (VH-K94:VH-D101:VH-D102) has an extensive impact on this loop's conformation, therefore simultaneous improvement in both affinity and stability. We find that the disruption of π-π stacking near HCDR3 (VH-Y100E:VL-Y49) at the VH-VL interface cause an irrecoverable loss in stability even if it improves the affinity. Molecular simulations of putative rescue mutants exhibit complex and often non-additive effects. We confirm that our experimental measurements agree with the molecular dynamic simulations providing detailed insights for the spatial orientation of HCDR3. VH-V102 right next to HCDR3 salt bridge might be an ideal candidate to overcome affinity-stability trade-off.
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Affiliation(s)
- Merve Arslan
- Izmir Biomedicine and Genome Center, Balçova, 35340 Izmir, Turkey; Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balçova, 35340 Izmir, Turkey
| | - Tuğçe Uluçay
- Izmir Biomedicine and Genome Center, Balçova, 35340 Izmir, Turkey
| | - Seyit Kale
- Izmir Biomedicine and Genome Center, Balçova, 35340 Izmir, Turkey
| | - Sibel Kalyoncu
- Izmir Biomedicine and Genome Center, Balçova, 35340 Izmir, Turkey.
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3
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An effective strategy for the humanization of antibody fragments under an accelerated timeline. Int J Biol Macromol 2022; 216:465-474. [PMID: 35803408 DOI: 10.1016/j.ijbiomac.2022.06.195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 11/22/2022]
Abstract
The use of monoclonal antibodies (mAbs) in therapy is gradually advancing and discussions entail its safety, rentability and effectiveness. To this date, around a hundred mAbs have been approved by the FDA for the treatment of various diseases. Aiming for their large-scale production, recombinant DNA technology is mainly employed, and antibodies can be expressed in various eukaryotic and prokaryotic systems. Moreover, considering their heterologous origin and potential immunogenicity, various strategies have been developed for mAb humanization, considering that around 50 % of commercial mAbs are humanized. Hence, we introduce LimAb7, a mouse mAb capable of binding and neutralizing brown spider's Loxosceles intermedia dermonecrotic toxins in vivo/in vitro. This antibody has been produced in mouse and humanized scFv and diabody formats, however results indicated losses in antigen-binding affinity, stability, and neutralizing ability. Intending to develop evolved, stable, and neutralizing antibody fragments, we report for the first time the design of humanized antibody V-domains produced as Fab fragments, against spider venom toxins. Improvements in constructs were observed regarding their physicochemical stability, target binding and binding pattern maintenance. As their neutralizing features remain to be characterized, we believe this data sheds new light on antibody humanization by producing a parental molecule in different recombinant formats.
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4
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Sang Z, Xiang Y, Bahar I, Shi Y. Llamanade: An open-source computational pipeline for robust nanobody humanization. Structure 2022; 30:418-429.e3. [PMID: 34895471 DOI: 10.1016/j.str.2021.11.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/21/2021] [Accepted: 11/17/2021] [Indexed: 12/15/2022]
Abstract
Nanobodies (Nbs) have emerged as a promising class of biologics. Despite having marked physicochemical properties, Nbs are derived from camelids and may require humanization to improve translational potentials. By systematically analyzing the sequence and structural properties of Nbs, we found substantial framework diversities and revealed the key differences between Nbs and human immunoglobulin G antibodies. We identified conserved residues that may contribute to enhanced solubility, structural stability, and antigen binding, providing insights into Nb humanization. Based on big data analysis, we developed "Llamanade," an open-source software to facilitate rational humanization of Nbs. Using sequence as input, Llamanade can rapidly extract sequence features, model structures, and optimize solutions to humanize Nbs. Finally, we used Llamanade to successfully humanize a cohort of structurally diverse and potent SARS-CoV-2 neutralizing Nbs. Llamanade is freely available and will be easily accessible on a server to support the development of therapeutic Nbs into safe and effective trials.
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Affiliation(s)
- Zhe Sang
- Department of Cell Biology, Pittsburgh, PA, USA; Department Computational and Systems Biology, Pittsburgh, PA, USA; University of Pittsburgh-Carnegie Mellon University Program in Computational Biology, Pittsburgh, PA, USA
| | - Yufei Xiang
- Department of Cell Biology, Pittsburgh, PA, USA
| | - Ivet Bahar
- Department Computational and Systems Biology, Pittsburgh, PA, USA; University of Pittsburgh-Carnegie Mellon University Program in Computational Biology, Pittsburgh, PA, USA
| | - Yi Shi
- Department of Cell Biology, Pittsburgh, PA, USA; University of Pittsburgh-Carnegie Mellon University Program in Computational Biology, Pittsburgh, PA, USA.
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5
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Sheng Z, Bimela JS, Katsamba PS, Patel SD, Guo Y, Zhao H, Guo Y, Kwong PD, Shapiro L. Structural Basis of Antibody Conformation and Stability Modulation by Framework Somatic Hypermutation. Front Immunol 2022; 12:811632. [PMID: 35046963 PMCID: PMC8761896 DOI: 10.3389/fimmu.2021.811632] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 12/07/2021] [Indexed: 11/25/2022] Open
Abstract
Accumulation of somatic hypermutation (SHM) is the primary mechanism to enhance the binding affinity of antibodies to antigens in vivo. However, the structural basis of the effects of many SHMs remains elusive. Here, we integrated atomistic molecular dynamics (MD) simulation and data mining to build a high-throughput structural bioinformatics pipeline to study the effects of individual and combination SHMs on antibody conformation, flexibility, stability, and affinity. By applying this pipeline, we characterized a common mechanism of modulation of heavy-light pairing orientation by frequent SHMs at framework positions 39H, 91H, 38L, and 87L through disruption of a conserved hydrogen-bond network. Q39LH alone and in combination with light chain framework 4 (FWR4L) insertions further modulated the elbow angle between variable and constant domains of many antibodies, resulting in improved binding affinity for a subset of anti-HIV-1 antibodies. Q39LH also alleviated aggregation induced by FWR4L insertion, suggesting remote epistasis between these SHMs. Altogether, this study provides tools and insights for understanding antibody affinity maturation and for engineering functionally improved antibodies.
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Affiliation(s)
- Zizhang Sheng
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States.,Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, United States
| | - Jude S Bimela
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States
| | - Phinikoula S Katsamba
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States
| | - Saurabh D Patel
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States
| | - Yicheng Guo
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States.,Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, United States
| | - Haiqing Zhao
- Department of Systems Biology, Columbia University, New York, NY, United States
| | - Youzhong Guo
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA, United States.,Institute for Structural Biology, Drug Discovery, and Development, Virginia Commonwealth University, Richmond, VA, United States
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, United States
| | - Lawrence Shapiro
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States.,Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, United States.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, United States
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6
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Sang Z, Xiang Y, Bahar I, Shi Y. Llamanade : an open-source computational pipeline for robust nanobody humanization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.08.03.455003. [PMID: 34373858 PMCID: PMC8351782 DOI: 10.1101/2021.08.03.455003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Nanobodies (Nbs) have recently emerged as a promising class of antibody fragments for biomedical and therapeutic applications. Despite having marked physicochemical properties, Nbs are derived from camelids and may require "humanization" to improve translational potentials for clinical trials. Here we have systematically analyzed the sequence and structural properties of Nbs based on NGS (next-generation sequencing) databases and high-resolution structures. Our analysis reveals substantial framework diversities and underscores the key differences between Nbs and human Immunoglobulin G (IgG) antibodies. We identified conserved residues that may contribute to enhanced solubility, structural stability, and antigen-binding, providing insights into Nb humanization. Based on big data analysis, we developed " Llamanade '', a user-friendly, open-source to facilitate rational humanization of Nbs. Using Nb sequence as input, Llamanade provides information on the sequence features, model structures, and optimizes solutions to humanize Nbs. The full analysis for a given Nb takes less than a minute on a local computer. To demonstrate the robustness of this tool, we applied it to successfully humanize a cohort of structurally diverse and highly potent SARS-CoV-2 neutralizing Nbs. Llamanade is freely available and will be easily accessible on a web server to support the development of a rapidly expanding repertoire of therapeutic Nbs into safe and effective trials. AUTHOR SUMMARY Camelid Nbs are characterized by small size, excellent pharmacological properties and high flexibility in bioengineering for therapeutic development. However, Nbs are "xeno" antibodies, which require "humanization" to improve their translational potential. Currently, there is a lack of systematic investigation of Nbs to rationally guide humanization. No dedicated software has been developed for this purpose. Here, we report the development of Llamanade , an open-source computational pipeline and the first dedicated software to facilitate rational humanization of Nbs. To subjectively evaluate Llamanade , we used it to humanize a cohort of structurally diverse and ultrapotent antiviral Nbs against SARS-CoV-2. Robust humanization by Llamanade significantly improved the humanness level of Nbs to closely resemble fully human IgGs. Importantly, these highly humanized antiviral Nbs remained excellent solubility and comparably high bioactivities to the non-humanized Nb precursors. We envision that Llamanade will help advance Nb research into therapeutic development.
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Affiliation(s)
- Zhe Sang
- Department of Cell Biology, Pittsburgh, PA, USA
- Department Computational and Systems Biology, Pittsburgh, PA, USA
- University of Pittsburgh-Carnegie Mellon University Program in Computational Biology, Pittsburgh, PA, USA
| | - Yufei Xiang
- Department of Cell Biology, Pittsburgh, PA, USA
| | - Ivet Bahar
- Department Computational and Systems Biology, Pittsburgh, PA, USA
- University of Pittsburgh-Carnegie Mellon University Program in Computational Biology, Pittsburgh, PA, USA
| | - Yi Shi
- Department of Cell Biology, Pittsburgh, PA, USA
- University of Pittsburgh-Carnegie Mellon University Program in Computational Biology, Pittsburgh, PA, USA
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7
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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.
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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
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8
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Huang S, van Duijnhoven SMJ, Sijts AJAM, van Elsas A. Bispecific antibodies targeting dual tumor-associated antigens in cancer therapy. J Cancer Res Clin Oncol 2020; 146:3111-3122. [PMID: 32989604 PMCID: PMC7679314 DOI: 10.1007/s00432-020-03404-6] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 09/21/2020] [Indexed: 02/07/2023]
Abstract
PURPOSE Bispecific antibodies (BsAbs) have emerged as a leading drug class for cancer therapy and are becoming increasingly of interest for therapeutic applications. As of April 2020, over 123 BsAbs are under clinical evaluation for use in oncology (including the two marketed BsAbs Blinatumomab and Catumaxomab). The majority (82 of 123) of BsAbs under clinical evaluation can be categorized as bispecific immune cell engager whereas a second less well-discussed subclass of BsAbs targets two tumor-associated antigens (TAAs). In this review, we summarize the clinical development of dual TAAs targeting BsAbs and provide an overview of critical considerations when designing dual TAA targeting BsAbs. METHODS Herein the relevant literature and clinical trials published in English until April 1st 2020 were searched using PubMed and ClinicalTrials.gov database. BsAbs were considered to be active in clinic if their clinical trials were not terminated, withdrawn or completed before 2018 without reporting results. Data missed by searching ClinicalTrials.gov was manually curated. RESULTS Dual TAAs targeting BsAbs offer several advantages including increased tumor selectivity, potential to concurrently modulate two functional pathways in the tumor cell and may yield improved payload delivery. CONCLUSIONS Dual TAAs targeting BsAbs represent a valuable class of biologics and early stage clinical studies have demonstrated promising anti-tumor efficacy in both hematologic malignancies and solid tumors.
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Affiliation(s)
- Shuyu Huang
- Aduro Biotech Europe, Oss, The Netherlands.,Faculty of Veterinary Medicine, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
| | | | - Alice J A M Sijts
- Faculty of Veterinary Medicine, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
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9
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A novel efficient bispecific antibody format, combining a conventional antigen-binding fragment with a single domain antibody, avoids potential heavy-light chain mis-pairing. J Immunol Methods 2020; 483:112811. [PMID: 32569598 DOI: 10.1016/j.jim.2020.112811] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/21/2020] [Accepted: 06/15/2020] [Indexed: 01/04/2023]
Abstract
Due to the technical innovations in generating bispecific antibodies (BsAbs) in recent years, BsAbs have become important reagents for diagnostic and therapeutic applications. However, the difficulty of producing a heterodimer consisting of two different arms with high yield and purity constituted a major limitation for their application in academic and clinical settings. Here, we describe a novel Fc-containing BsAb format (Fab × sdAb-Fc) composed of a conventional antigen-binding fragment (Fab), and a single domain antibody (sdAb), which avoids heavy-light chain mis-pairing during antibody assembly. In this study, the Fab x sdAb-Fc BsAbs were efficiently produced by three widely used heavy-heavy chain heterodimerization methods: Knobs-into-holes (KIH), Charge-pairs (CP) and controlled Fab-arm exchange (cFAE), respectively. The novel Fab x sdAb-Fc format provided a rapid and efficient strategy to generate BsAb with high purity and a unique possibility to further purify desired BsAbs from undesired antibodies based on molecular weight (MW). Compared to conventional BsAb formats, the advantages of Fab x sdAb-Fc format may thus provide a straightforward opportunity to apply bispecific antibody principles to research and development of novel targets and pathways in diseases such as cancer and autoimmunity.
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10
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Ling WL, Lua WH, Gan SKE. Sagacity in antibody humanization for therapeutics, diagnostics and research purposes: considerations of antibody elements and their roles. Antib Ther 2020; 3:71-79. [PMID: 33928226 PMCID: PMC7990220 DOI: 10.1093/abt/tbaa005] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/27/2020] [Accepted: 04/07/2020] [Indexed: 12/15/2022] Open
Abstract
The humanization of antibodies for therapeutics is a critical process that can determine the success of antibody drug development. However, the science underpinning this process remains elusive with different laboratories having very different methods. Well-funded laboratories can afford automated high-throughput screening methods to derive their best binder utilizing a very expensive initial set of equipment affordable only to a few. Often within these high-throughput processes, only standard key parameters, such as production, binding and aggregation are analyzed. Given the lack of suitable animal models, it is only at clinical trials that immunogenicity and allergy adverse effects are detected through anti-human antibodies as per FDA guidelines. While some occurrences that slip through can be mitigated by additional desensitization protocols, such adverse reactions to grafted humanized antibodies can be prevented at the humanization step. Considerations such as better antibody localization, avoidance of unspecific interactions to superantigens and the tailoring of antibody dependent triggering of immune responses, the antibody persistence on cells, can all be preemptively considered through a holistic sagacious approach, allowing for better outcomes in therapy and for research and diagnostic purposes.
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Affiliation(s)
- Wei-Li Ling
- Antibody & Product Development Lab, Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Wai-Heng Lua
- Antibody & Product Development Lab, Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Samuel Ken-En Gan
- Antibody & Product Development Lab, Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
- p53 Laboratory, ASTAR, 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore 138648
- Experimental Drug Development Center, ASTAR, 10 Biopolis Road, #05-01, Chromos, Singapore 138670
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11
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Khowsathit J, Bazzoli A, Cheng H, Karanicolas J. Computational Design of an Allosteric Antibody Switch by Deletion and Rescue of a Complex Structural Constellation. ACS CENTRAL SCIENCE 2020; 6:390-403. [PMID: 32232139 PMCID: PMC7099597 DOI: 10.1021/acscentsci.9b01065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Indexed: 05/08/2023]
Abstract
Therapeutic monoclonal antibodies have transformed medicine, especially with regards to treating cancers and disorders of the immune system. More than 50 antibody-derived drugs have already reached the clinic, the majority of which target cytokines or cell-surface receptors. Unfortunately, many of these targets have pleiotropic functions: they serve multiple different roles, and often not all of these roles are disease-related. This can be problematic because antibodies act throughout the body, and systemic neutralization of such targets can lead to safety concerns. To address this, we have developed a strategy whereby an antibody's ability to recognize its antigen is modulated by a second layer of control, relying on addition of an exogenous small molecule. In previous studies, we began to explore this idea by introducing a deactivating tryptophan-to-glycine mutation in the domain-domain interface of a single-chain variable fragment (scFv), and then restoring activity by adding back indole to fit the designed cavity. Here, we now describe a novel computational strategy for enumerating larger cavities that can be formed by simultaneously introducing multiple adjacent large-to-small mutations; we then carry out a complementary virtual screen to identify druglike compounds to match each candidate cavity. We first demonstrate the utility of this strategy in a fluorescein-binding single-chain variable fragment (scFv) and experimentally characterize a triple mutant with reduced antigen-binding (Rip-3) that can be rescued using a complementary ligand (Stitch-3). Because our design is built upon conserved residues in the antibody framework, we then show that the same mutation/ligand pair can also be used to modulate antigen-binding in an scFv build from a completely unrelated framework. This set of residues is present in many therapeutic antibodies as well, suggesting that this mutation/ligand pair may serve as a general starting point for introducing ligand-dependence into many clinically relevant antibodies.
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Affiliation(s)
- Jittasak Khowsathit
- Program
in Molecular Therapeutics, Fox Chase Cancer
Center, Philadelphia, Pennsylvania 19111, United States
- Department of Molecular
Biosciences and Center for Computational Biology, University
of Kansas, Lawrence, Kansas 66045, United
States
| | - Andrea Bazzoli
- Department of Molecular
Biosciences and Center for Computational Biology, University
of Kansas, Lawrence, Kansas 66045, United
States
| | - Hong Cheng
- Program
in Molecular Therapeutics, Fox Chase Cancer
Center, Philadelphia, Pennsylvania 19111, United States
| | - John Karanicolas
- Program
in Molecular Therapeutics, Fox Chase Cancer
Center, Philadelphia, Pennsylvania 19111, United States
- Department of Molecular
Biosciences and Center for Computational Biology, University
of Kansas, Lawrence, Kansas 66045, United
States
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12
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Dietrich S, Gross AW, Becker S, Hock B, Stadlmayr G, Rüker F, Wozniak-Knopp G. Constant domain-exchanged Fab enables specific light chain pairing in heterodimeric bispecific SEED-antibodies. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1868:140250. [PMID: 31295556 DOI: 10.1016/j.bbapap.2019.07.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/13/2019] [Accepted: 07/03/2019] [Indexed: 10/26/2022]
Abstract
BACKGROUND Bispecific antibodies promise to broadly expand the clinical utility of monoclonal antibody technology. Several approaches for heterodimerization of heavy chains have been established to produce antibodies with two different Fab arms, but promiscuous pairing of heavy and light chains remains a challenge for their manufacturing. METHODS We have designed a solution in which the CH1 and CL domain pair in one of the Fab fragments is replaced with a CH3-domain pair and heterodimerized to facilitate correct modified Fab-chain pairing in bispecific heterodimeric antibodies based on a strand-exchange engineered domain (SEED) scaffold with specificity for epithelial growth factor receptor and either CD3 or CD16 (FcγRIII). RESULTS Bispecific antibodies retained binding to their target antigens and redirected primary T cells or NK cells to induce potent killing of target cells. All antibodies were expressed at a high yield in Expi293F cells, were detected as single sharp symmetrical peaks in size exclusion chromatography and retained high thermostability. Mass spectrometric analysis revealed specific heavy-to-light chain pairing for the bispecific SEED antibodies as well as for one-armed SEED antibodies co-expressed with two different competing light chains. CONCLUSION Incorporation of a constant domain-exchanged Fab fragment into a SEED antibody yields functional molecules with favorable biophysical properties. GENERAL SIGNIFICANCE Our results show that the novel engineered bispecific SEED antibody scaffold with an incorporated Fab fragment with CH3-exchanged constant domains is a promising tool for the generation of complete heterodimeric bispecific antibodies with correct light chain pairing.
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Affiliation(s)
- Sylvia Dietrich
- Christian Doppler Laboratory for Antibody Engineering, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Alec W Gross
- Protein Engineering and Antibody Technologies, EMD Serono Research and Development Institute, Inc., 45A Middlesex Turnpike, Billerica, MA 01821, USA
| | - Stefan Becker
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany
| | - Björn Hock
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany
| | - Gerhard Stadlmayr
- Christian Doppler Laboratory for Innovative Immunotherapeutics, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Florian Rüker
- Christian Doppler Laboratory for Innovative Immunotherapeutics, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Gordana Wozniak-Knopp
- Christian Doppler Laboratory for Innovative Immunotherapeutics, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria.
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Benschop RJ, Chow CK, Tian Y, Nelson J, Barmettler B, Atwell S, Clawson D, Chai Q, Jones B, Fitchett J, Torgerson S, Ji Y, Bina H, Hu N, Ghanem M, Manetta J, Wroblewski VJ, Lu J, Allan BW. Development of tibulizumab, a tetravalent bispecific antibody targeting BAFF and IL-17A for the treatment of autoimmune disease. MAbs 2019; 11:1175-1190. [PMID: 31181988 PMCID: PMC6748573 DOI: 10.1080/19420862.2019.1624463] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 04/26/2019] [Accepted: 05/22/2019] [Indexed: 12/23/2022] Open
Abstract
We describe a bispecific dual-antagonist antibody against human B cell activating factor (BAFF) and interleukin 17A (IL-17). An anti-IL-17 single-chain variable fragment (scFv) derived from ixekizumab (Taltz®) was fused via a glycine-rich linker to anti-BAFF tabalumab. The IgG-scFv bound both BAFF and IL-17 simultaneously with identical stoichiometry as the parental mAbs. Stability studies of the initial IgG-scFv revealed chemical degradation and aggregation not observed in either parental antibody. The anti-IL-17 scFv showed a high melting temperature (Tm) by differential scanning calorimetry (73.1°C), but also concentration-dependent, initially reversible, protein self-association. To engineer scFv stability, three parallel approaches were taken: labile complementary-determining region (CDR) residues were replaced by stable, affinity-neutral amino acids, CDR charge distribution was balanced, and a H44-L100 interface disulfide bond was introduced. The Tm of the disulfide-stabilized scFv was largely unperturbed, yet it remained monodispersed at high protein concentration. Fluorescent dye binding titrations indicated reduced solvent exposure of hydrophobic residues and decreased proteolytic susceptibility was observed, both indicative of enhanced conformational stability. Superimposition of the H44-L100 scFv (PDB id: 6NOU) and ixekizumab antigen-binding fragment (PDB id: 6NOV) crystal structures revealed nearly identical orientation of the frameworks and CDR loops. The stabilized bispecific molecule LY3090106 (tibulizumab) potently antagonized both BAFF and IL-17 in cell-based and in vivo mouse models. In cynomolgus monkey, it suppressed B cell development and survival and remained functionally intact in circulation, with a prolonged half-life. In summary, we engineered a potent bispecific antibody targeting two key cytokines involved in human autoimmunity amenable to clinical development.
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Affiliation(s)
- Robert J. Benschop
- Biotechnology Discovery Research, Lilly Research Laboratories, Eli Lilly and Company Corporate Center, Indianapolis, IN, USA
| | - Chi-Kin Chow
- Biotechnology Discovery Research, Lilly Research Laboratories, Eli Lilly and Company Corporate Center, Indianapolis, IN, USA
| | - Yu Tian
- Biotechnology Discovery Research, Lilly Research Laboratories, Eli Lilly and Company Corporate Center, Indianapolis, IN, USA
| | - James Nelson
- Biotechnology Discovery Research, Applied Molecular Evolution, Eli Lilly and Company, San Diego, CA, USA
| | - Barbra Barmettler
- Biotechnology Discovery Research, Applied Molecular Evolution, Eli Lilly and Company, San Diego, CA, USA
| | - Shane Atwell
- Biotechnology Discovery Research, Applied Molecular Evolution, Eli Lilly and Company, San Diego, CA, USA
| | - David Clawson
- Discovery Chemistry Research and Technologies, Eli Lilly and Company Corporate Center, Indianapolis, IN, USA
| | - Qing Chai
- Biotechnology Discovery Research, Applied Molecular Evolution, Eli Lilly and Company, San Diego, CA, USA
| | - Bryan Jones
- Biotechnology Discovery Research, Applied Molecular Evolution, Eli Lilly and Company, San Diego, CA, USA
| | - Jon Fitchett
- Biotechnology Discovery Research, Applied Molecular Evolution, Eli Lilly and Company, San Diego, CA, USA
| | - Stacy Torgerson
- Department of Drug Disposition Development/Commercialization; Lilly Research Laboratories, Eli Lilly and Company Corporate Center, Indianapolis, IN, USA
| | | | - Holly Bina
- Biotechnology Discovery Research, Lilly Research Laboratories, Eli Lilly and Company Corporate Center, Indianapolis, IN, USA
| | - Ningjie Hu
- Biotechnology Discovery Research, Lilly Research Laboratories, Eli Lilly and Company Corporate Center, Indianapolis, IN, USA
| | | | - Joseph Manetta
- Biotechnology Discovery Research, Lilly Research Laboratories, Eli Lilly and Company Corporate Center, Indianapolis, IN, USA
| | - Victor J. Wroblewski
- Department of Drug Disposition Development/Commercialization; Lilly Research Laboratories, Eli Lilly and Company Corporate Center, Indianapolis, IN, USA
| | - Jirong Lu
- Biotechnology Discovery Research, Lilly Research Laboratories, Eli Lilly and Company Corporate Center, Indianapolis, IN, USA
| | - Barrett W. Allan
- Biotechnology Discovery Research, Applied Molecular Evolution, Eli Lilly and Company, San Diego, CA, USA
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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: 56] [Impact Index Per Article: 8.0] [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.
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15
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Zhang YF, Ho M. Humanization of high-affinity antibodies targeting glypican-3 in hepatocellular carcinoma. Sci Rep 2016; 6:33878. [PMID: 27667400 PMCID: PMC5036187 DOI: 10.1038/srep33878] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 09/05/2016] [Indexed: 01/03/2023] Open
Abstract
Glypican-3 (GPC3) is a cell-surface heparan sulfate proteoglycan highly expressed in hepatocellular carcinoma (HCC). We have generated a group of high-affinity mouse monoclonal antibodies targeting GPC3. Here, we report the humanization and testing of these antibodies for clinical development. We compared the affinity and cytotoxicity of recombinant immunotoxins containing mouse single-chain variable regions fused with a Pseudomonas toxin. To humanize the mouse Fvs, we grafted the combined KABAT/IMGT complementarity determining regions (CDR) into a human IgG germline framework. Interestingly, we found that the proline at position 41, a non-CDR residue in heavy chain variable regions (VH), is important for humanization of mouse antibodies. We also showed that two humanized anti-GPC3 antibodies (hYP7 and hYP9.1b) in the IgG format induced antibody-dependent cell-mediated cytotoxicity and complement-dependent-cytotoxicity in GPC3-positive cancer cells. The hYP7 antibody was tested and showed inhibition of HCC xenograft tumor growth in nude mice. This study successfully humanizes and validates high affinity anti-GPC3 antibodies and sets a foundation for future development of these antibodies in various clinical formats in the treatment of liver cancer.
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Affiliation(s)
- Yi-Fan Zhang
- Antibody Therapy Section, Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Mitchell Ho
- Antibody Therapy Section, Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
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Steinmetz A, Vallée F, Beil C, Lange C, Baurin N, Beninga J, Capdevila C, Corvey C, Dupuy A, Ferrari P, Rak A, Wonerow P, Kruip J, Mikol V, Rao E. CODV-Ig, a universal bispecific tetravalent and multifunctional immunoglobulin format for medical applications. MAbs 2016; 8:867-78. [PMID: 26984268 DOI: 10.1080/19420862.2016.1162932] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Bispecific immunoglobulins (Igs) typically contain at least two distinct variable domains (Fv) that bind to two different target proteins. They are conceived to facilitate clinical development of biotherapeutic agents for diseases where improved clinical outcome is obtained or expected by combination therapy compared to treatment by single agents. Almost all existing formats are linear in their concept and differ widely in drug-like and manufacture-related properties. To overcome their major limitations, we designed cross-over dual variable Ig-like proteins (CODV-Ig). Their design is akin to the design of circularly closed repeat architectures. Indeed, initial results showed that the traditional approach of utilizing (G4S)x linkers for biotherapeutics design does not identify functional CODV-Igs. Therefore, we applied an unprecedented molecular modeling strategy for linker design that consistently results in CODV-Igs with excellent biochemical and biophysical properties. CODV architecture results in a circular self-contained structure functioning as a self-supporting truss that maintains the parental antibody affinities for both antigens without positional effects. The format is universally suitable for therapeutic applications targeting both circulating and membrane-localized proteins. Due to the full functionality of the Fc domains, serum half-life extension as well as antibody- or complement-dependent cytotoxicity may support biological efficiency of CODV-Igs. We show that judicious choice in combination of epitopes and paratope orientations of bispecific biotherapeutics is anticipated to be critical for clinical outcome. Uniting the major advantages of alternative bispecific biotherapeutics, CODV-Igs are applicable in a wide range of disease areas for fast-track multi-parametric drug optimization.
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Affiliation(s)
- Anke Steinmetz
- c Sanofi R&D, LGCR, Center de Recherche Vitry-sur-Seine , Vitry-sur-Seine Cedex , France
| | - François Vallée
- c Sanofi R&D, LGCR, Center de Recherche Vitry-sur-Seine , Vitry-sur-Seine Cedex , France
| | - Christian Beil
- a Sanofi-Aventis Deutschland GmbH, R&D, Global Biotherapeutics, Industriepark Hoechst , Frankfurt am Main , Germany
| | - Christian Lange
- a Sanofi-Aventis Deutschland GmbH, R&D, Global Biotherapeutics, Industriepark Hoechst , Frankfurt am Main , Germany
| | - Nicolas Baurin
- c Sanofi R&D, LGCR, Center de Recherche Vitry-sur-Seine , Vitry-sur-Seine Cedex , France
| | - Jochen Beninga
- a Sanofi-Aventis Deutschland GmbH, R&D, Global Biotherapeutics, Industriepark Hoechst , Frankfurt am Main , Germany
| | - Cécile Capdevila
- b Sanofi R&D, Global Biotherapeutics, Center de Recherche Vitry-sur-Seine , Vitry-sur-Seine Cedex , France
| | - Carsten Corvey
- a Sanofi-Aventis Deutschland GmbH, R&D, Global Biotherapeutics, Industriepark Hoechst , Frankfurt am Main , Germany
| | - Alain Dupuy
- c Sanofi R&D, LGCR, Center de Recherche Vitry-sur-Seine , Vitry-sur-Seine Cedex , France
| | - Paul Ferrari
- b Sanofi R&D, Global Biotherapeutics, Center de Recherche Vitry-sur-Seine , Vitry-sur-Seine Cedex , France
| | - Alexey Rak
- c Sanofi R&D, LGCR, Center de Recherche Vitry-sur-Seine , Vitry-sur-Seine Cedex , France
| | - Peter Wonerow
- a Sanofi-Aventis Deutschland GmbH, R&D, Global Biotherapeutics, Industriepark Hoechst , Frankfurt am Main , Germany
| | - Jochen Kruip
- a Sanofi-Aventis Deutschland GmbH, R&D, Global Biotherapeutics, Industriepark Hoechst , Frankfurt am Main , Germany
| | - Vincent Mikol
- c Sanofi R&D, LGCR, Center de Recherche Vitry-sur-Seine , Vitry-sur-Seine Cedex , France
| | - Ercole Rao
- a Sanofi-Aventis Deutschland GmbH, R&D, Global Biotherapeutics, Industriepark Hoechst , Frankfurt am Main , Germany
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17
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Uzasci L, Bianchet MA, Cotter RJ, Nath A. Identification of nitrated immunoglobulin variable regions in the HIV-infected human brain: implications in HIV infection and immune response. J Proteome Res 2014; 13:1614-23. [PMID: 24479669 PMCID: PMC4088966 DOI: 10.1021/pr401117m] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
HIV can infiltrate the brain and lead to HIV-associated neurocognitive
disorders (HAND). The pathophysiology of HAND is poorly understood,
and there are no diagnostic biomarkers for it. Previously, an increase
in inducible nitric oxide synthase levels and protein tyrosine nitration
in the brain were found to correlate with the severity of HAND.1,2 In this study, we analyzed human brains from individuals who had
HIV infection without encephalitis and with encephalitis/HAND and
compared them to the brains of healthy individuals. We identified
the nitrated proteins and determined the sites of modification using
affinity enrichment followed by high-resolution and high-mass-accuracy
nanoLC–MS/MS. We found that nitrated proteins were predominantly
present in the HIV-infected individuals with encephalitis, and, interestingly,
the modifications were predominantly located on immunoglobulin variable
regions. Our molecular model indicated potential interactions with
HIV envelope proteins and changes on the heavy and light chain interface
upon the nitration and nitrohydroxylation of these residues. Therefore,
our findings suggest a role for these modifications in the immune
response, which may have implications in disease pathogenesis.
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Affiliation(s)
- Lerna Uzasci
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine , Baltimore, Maryland 21205, United States
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18
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Sela-Culang I, Kunik V, Ofran Y. The structural basis of antibody-antigen recognition. Front Immunol 2013; 4:302. [PMID: 24115948 PMCID: PMC3792396 DOI: 10.3389/fimmu.2013.00302] [Citation(s) in RCA: 293] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2013] [Accepted: 09/12/2013] [Indexed: 11/18/2022] Open
Abstract
The function of antibodies (Abs) involves specific binding to antigens (Ags) and activation of other components of the immune system to fight pathogens. The six hypervariable loops within the variable domains of Abs, commonly termed complementarity determining regions (CDRs), are widely assumed to be responsible for Ag recognition, while the constant domains are believed to mediate effector activation. Recent studies and analyses of the growing number of available Ab structures, indicate that this clear functional separation between the two regions may be an oversimplification. Some positions within the CDRs have been shown to never participate in Ag binding and some off-CDRs residues often contribute critically to the interaction with the Ag. Moreover, there is now growing evidence for non-local and even allosteric effects in Ab-Ag interaction in which Ag binding affects the constant region and vice versa. This review summarizes and discusses the structural basis of Ag recognition, elaborating on the contribution of different structural determinants of the Ab to Ag binding and recognition. We discuss the CDRs, the different approaches for their identification and their relationship to the Ag interface. We also review what is currently known about the contribution of non-CDRs regions to Ag recognition, namely the framework regions (FRs) and the constant domains. The suggested mechanisms by which these regions contribute to Ag binding are discussed. On the Ag side of the interaction, we discuss attempts to predict B-cell epitopes and the suggested idea to incorporate Ab information into B-cell epitope prediction schemes. Beyond improving the understanding of immunity, characterization of the functional role of different parts of the Ab molecule may help in Ab engineering, design of CDR-derived peptides, and epitope prediction.
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Affiliation(s)
- Inbal Sela-Culang
- The Goodman Faculty of Life Sciences, Bar Ilan University , Ramat Gan , Israel
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19
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Rodríguez-Rodríguez ER, Ledezma-Candanoza LM, Contreras-Ferrat LG, Olamendi-Portugal T, Possani LD, Becerril B, Riaño-Umbarila L. A Single Mutation in Framework 2 of the Heavy Variable Domain Improves the Properties of a Diabody and a Related Single-Chain Antibody. J Mol Biol 2012; 423:337-50. [DOI: 10.1016/j.jmb.2012.07.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Revised: 07/02/2012] [Accepted: 07/06/2012] [Indexed: 10/28/2022]
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20
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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.
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Affiliation(s)
- E P Altshuler
- Department of Biochemistry, Faculty of Biology, Lomonosov Moscow State University, Russia
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21
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Ihara M, Suzuki T, Kobayashi N, Goto J, Ueda H. Open-sandwich enzyme immunoassay for one-step noncompetitive detection of corticosteroid 11-deoxycortisol. Anal Chem 2010; 81:8298-304. [PMID: 19778030 DOI: 10.1021/ac900700a] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A noncompetitive immunoassay has the potential for improved sensitivity and working range compared with corresponding competitive assays. However, monovalent antigens with less than 1000 in molecular weight are not susceptible to sandwich assays due to their small size. As a noncompetitive immunoassay that can be performed with a clone of an antibody, an open-sandwich immunoassay (OS-IA) based on the antigen-dependent stabilization of the antibody variable region (V(H) + V(L)) was applied to the quantification of 11-deoxycortisol (11-DC; M(r) 346.5), a corticosteroid serving as a diagnostic index for pituitary-adrenal function, as a model target hapten. By one step OS-IA detection of enzyme-labeled V(H) fragment bound to immobilized V(L) in the presence of sample in microplate wells, 11-DC was measured with a femtomolar detection limit and the working range was wider than that with corresponding competitive assay. In addition, the selectivity against analogues was found almost identical to that of conventional assays. The effect of the mutagenesis of a V(H) residue at the V(H)/V(L) interface to reduce background signal was also shown, implying the wider application of OS-IA in small molecule analyses.
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Affiliation(s)
- Masaki Ihara
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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22
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Clark KR, Walsh STR. Crystal structure of a 3B3 variant--a broadly neutralizing HIV-1 scFv antibody. Protein Sci 2009; 18:2429-41. [PMID: 19785005 PMCID: PMC2821263 DOI: 10.1002/pro.255] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We present the crystal structure determination of an anti-HIV-1 gp120 single-chain variable fragment antibody variant, 3B3, at 2.5 A resolution. This 3B3 variant was derived from the b12 antibody, using phage display and site-directed mutagenesis of the variable heavy chain (V(H)) complementary-determining regions (CDRs). 3B3 exhibits enhanced binding affinity and neutralization activity against several cross-clade primary isolates of HIV-1 by interaction with the recessed CD4-binding site on the gp120 envelope protein. Comparison with the structures of the unbound and bound forms of b12, the 3B3 structure closely resembles these structures with minimal differences with two notable exceptions. First, there is a reorientation of the CDR-H3 of the V(H) domain where the primary sequences evolved from b12 to 3B3. The structural changes in CDR-H3 of 3B3, in light of the b12-gp120 complex structure, allow for positioning an additional Trp side chain in the binding interface with gp120. Finally, the second region of structural change involves two peptide bond flips in CDR-L3 of the variable light (V(L)) domain triggered by a point mutation in CDR-H3 of Q100eY resulting in changes in the intramolecular hydrogen bonding patterning between the V(L) and V(H) domains. Thus, the enhanced binding affinities and neutralization capabilities of 3B3 relative to b12 probably result from higher hydrophobic driving potential by burying more aromatic residues at the 3B3-gp120 interface and by indirect stabilization of intramolecular contacts of the core framework residues between the V(L) and V(H) domains possibly through more favorable entropic effect through the expulsion of water.
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Affiliation(s)
- K Reed Clark
- Center for Gene Therapy, Nationwide Children's HospitalColumbus, Ohio 43205,Department of Pediatrics, College of Medicine, The Ohio State UniversityColumbus, Ohio 43210
| | - Scott T R Walsh
- W. M. Keck Laboratory for Structural Biology, Center for Advanced Research in Biotechnology, University of Maryland Biotechnology InstituteRockville, Maryland 20850,*Correspondence to: Scott T. R. Walsh, Laboratory for Structural Biology, Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, Rockville, MD 20850. E-mail:
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23
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Gion K, Sakurai Y, Watari A, Inui H. Designed Recombinant Transcription Factor with Antibody-Variable Regions. Anal Chem 2009; 81:10162-6. [DOI: 10.1021/ac902054z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Keiko Gion
- Research Center for Environmental Genomics, and Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Yuki Sakurai
- Research Center for Environmental Genomics, and Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Akito Watari
- Research Center for Environmental Genomics, and Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Hideyuki Inui
- Research Center for Environmental Genomics, and Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, Hyogo 657-8501, Japan
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Robert R, Dolezal O, Waddington L, Hattarki MK, Cappai R, Masters CL, Hudson PJ, Wark KL. Engineered antibody intervention strategies for Alzheimer's disease and related dementias by targeting amyloid and toxic oligomers. Protein Eng Des Sel 2008; 22:199-208. [PMID: 18927231 DOI: 10.1093/protein/gzn052] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Most neurodegenerative disorders, such as Alzheimer's (AD), Parkinson's, Huntington's and Creutzfeldt-Jakob disease, are characterised by the accumulation of insoluble filamentous aggregates known as amyloid. These pathologies share common pathways involving protein aggregation which can lead to fibril formation and amyloid plaques. The 4 kDa Abeta peptide (39-43 amino acids) derived from the proteolysis of the amyloid precursor protein is currently a validated target for therapy in AD. Both active and passive immunisation studies against Abeta are being trialled as potential AD therapeutic approaches. In this study, we have characterised engineered antibody fragments derived from the monoclonal antibody, WO-2 which recognises an epitope in the N-terminal region of Abeta (amino acids 2-8 of Abeta). A chimeric recombinant Fab (rFab) and single chain fragments (scFvs) of WO-2 were constructed and expressed in Escherichia coli. Rationally designed mutants to improve the stability of antibody fragments were also constructed. All antibody formats retained high affinity (K(D) approximately 8 x 10(-9) M) for the Abeta peptide, comparable with the intact parental IgG as measured by surface plasmon resonance. Likewise, all engineered fragments were able to: (i) prevent amyloid fibrillisation, (ii) disaggregate preformed Abeta(1-42) fibrils and (iii) inhibit Abeta(1-42) oligomer-mediated neurotoxicity in vitro as efficiently as the whole IgG molecule. These data indicate that the WO-2 antibody and its fragments have immunotherapeutic potential. The perceived advantages of using small Fab and scFv engineered antibody formats which lack the effector function include more efficient passage across the blood-brain barrier and minimising the risk of triggering inflammatory side reactions. Hence, these recombinant antibody fragments represent attractive candidates and safer formulations of passive immunotherapy for AD.
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Affiliation(s)
- Remy Robert
- CSIRO Molecular and Health Technologies, University of Melbourne, Australia.
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Nakanishi T, Tsumoto K, Yokota A, Kondo H, Kumagai I. Critical contribution of VH-VL interaction to reshaping of an antibody: the case of humanization of anti-lysozyme antibody, HyHEL-10. Protein Sci 2008; 17:261-70. [PMID: 18227432 DOI: 10.1110/ps.073156708] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
To clarify the effects of humanizing a murine antibody on its specificity and affinity for its target, we examined the interaction between hen egg white lysozyme (HEL) and its antibody, HyHEL-10 variable domain fragment (Fv). We selected a human antibody framework sequence with high homology, grafted sequences of six complementarity-determining regions of murine HyHEL-10 onto the framework, and investigated the interactions between the mutant Fvs and HEL. Isothermal titration calorimetry indicated that the humanization led to 10-fold reduced affinity of the antibody for its target, due to an unfavorable entropy change. Two mutations together into the interface of the variable domains, however, led to complete recovery of antibody affinity and specificity for the target, due to reduction of the unfavorable entropy change. X-ray crystallography of the complex of humanized antibodies, including two mutants, with HEL demonstrated that the complexes had almost identical structures and also paratope and epitope residues were almost conserved, except for complementary association of variable domains. We conclude that adjustment of the interfacial structures of variable domains can contribute to the reversal of losses of affinity or specificity caused by humanization of murine antibodies, suggesting that appropriate association of variable domains is critical for humanization of murine antibodies without loss of function.
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Affiliation(s)
- Takeshi Nakanishi
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan
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Yoshitake K, Waki S, Ueda H. Dimerization-based homogeneous fluorosensor proteins for the detection of specific dsDNA. Biosens Bioelectron 2007; 23:1266-71. [PMID: 18178076 DOI: 10.1016/j.bios.2007.11.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2007] [Revised: 10/26/2007] [Accepted: 11/21/2007] [Indexed: 11/27/2022]
Abstract
While there are many hybridization-based DNA sensors, none of them can detect native double-stranded DNA (dsDNA), which is most commonly found in physiological conditions. Here we made novel fluorosensor proteins comprised of a pair of two zinc fingers with an N-terminal dimerization motif and a C-terminal GFP variant to detect specific dsDNA sequence in a homogeneous solution. When a pair of purified zinc finger-GFP color variant proteins (Zif12-eCFP, Zif12-eYFP) were mixed and added with specific dsDNA with 12 bp inverted repeat (IR), fluorescence spectra of the solution showed significant concentration-dependent enhancement of fluorescence resonance energy transfer (FRET), with the detection limit of approximately 10nM. No significant change in FRET was observed if nonspecific DNA was added, indicating dsDNA-dependent dimerization of the two proteins. This dimerization-based dsDNA sensors will have a range of applications where conventional hybridization-based assay is difficult.
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Affiliation(s)
- Kazutoshi Yoshitake
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
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Acierno JP, Braden BC, Klinke S, Goldbaum FA, Cauerhff A. Affinity Maturation Increases the Stability and Plasticity of the Fv Domain of Anti-protein Antibodies. J Mol Biol 2007; 374:130-46. [DOI: 10.1016/j.jmb.2007.09.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2007] [Revised: 08/13/2007] [Accepted: 09/05/2007] [Indexed: 11/26/2022]
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Daly KA, Digby M, Lefèvre C, Mailer S, Thomson P, Nicholas K, Williamson P. Analysis of the expression of immunoglobulins throughout lactation suggests two periods of immune transfer in the tammar wallaby (Macropus eugenii). Vet Immunol Immunopathol 2007; 120:187-200. [PMID: 17727962 DOI: 10.1016/j.vetimm.2007.07.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2007] [Revised: 07/09/2007] [Accepted: 07/17/2007] [Indexed: 12/28/2022]
Abstract
Marsupial young are born in an under-developed state without mature immune responses. Prior to the maturation of an immune system, marsupial young are heavily reliant upon immune factors secreted in the milk to defend them against potential microbial pathogens in the environment. In this study, we identified and characterized the immunoglobulin heavy chain constant regions, light chains, polymeric Ig receptor (pIgR), J chain, neonatal Fc receptor (alpha chain) (FcRn) and the chemokine CCL28 from the model marsupial species, the tammar wallaby (Macropus eugenii). Low levels of conservation were seen in motifs in C alpha and C gamma associated with receptor binding and or transcytosis, and this may have potential implications for functionality. We evaluated the expression of immunoglobulin genes in the tammar mammary gland throughout lactation and found that two periods of increased expression of immunoglobulin genes occur. These two periods coincide with the birth of the young, and with its first emergence from the pouch. This increased expression may represent a strategy for maternal immunological protection of the pouch young.
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Affiliation(s)
- Kerry A Daly
- Centre for Advanced Technologies in Animal Genetics and Reproduction, Faculty of Veterinary Science, University of Sydney, NSW 2006, Australia; Cooperative Research Centre for Innovative Dairy Products, Australia
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Rich RL, Myszka DG. Survey of the year 2006 commercial optical biosensor literature. J Mol Recognit 2007; 20:300-66. [DOI: 10.1002/jmr.862] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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