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Maeta S, Nakakido M, Matsuura H, Sakai N, Hirata K, Kuroda D, Fukunaga A, Tsumoto K. Arginine cluster introduction on framework region in anti-lysozyme antibody improved association rate constant by changing conformational diversity of CDR loops. Protein Sci 2023; 32:e4745. [PMID: 37550885 PMCID: PMC10461459 DOI: 10.1002/pro.4745] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 05/30/2023] [Accepted: 08/01/2023] [Indexed: 08/09/2023]
Abstract
Antibodies are used for many therapeutic and biotechnological purposes. Because the affinity of an antibody to the antigen is critical for clinical efficacy of pharmaceuticals, many affinity maturation strategies have been developed. Although we previously reported an affinity maturation strategy in which the association rate of the antibody toward its antigen is improved by introducing a cluster of arginine residues into the framework region of the antibody, the detailed molecular mechanism responsible for this improvement has been unknown. In this study, we introduced five arginine residues into an anti-hen egg white lysozyme antibody (HyHEL10) Fab fragment to create the R5-mutant and comprehensively characterized the interaction between antibody and antigen using thermodynamic analysis, X-ray crystallography, and molecular dynamics (MD) simulations. Our results indicate that introduction of charged residues strongly enhanced the association rate, as previously reported, and the antibody-antigen complex structure was almost the same for the R5-mutant and wild-type Fabs. The MD simulations indicate that the mutation increased conformational diversity in complementarity-determining region loops and thereby enhanced the association rate. These observations provide the molecular basis of affinity maturation by R5 mutation.
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Affiliation(s)
- Shingo Maeta
- Bio‐Diagnostic Reagent Technology CenterSysmex CorporationKobeJapan
- Department of Bioengineering, School of EngineeringThe University of TokyoTokyoJapan
| | - Makoto Nakakido
- Department of Bioengineering, School of EngineeringThe University of TokyoTokyoJapan
- Department of Chemistry and Biotechnology, Graduate School of EngineeringThe University of TokyoTokyoJapan
| | - Hiroaki Matsuura
- Life Science Research Infrastructure Group, RIKEN SPring‐8 CenterSaitamaJapan
| | - Naoki Sakai
- Life Science Research Infrastructure Group, RIKEN SPring‐8 CenterSaitamaJapan
| | - Kunio Hirata
- Life Science Research Infrastructure Group, RIKEN SPring‐8 CenterSaitamaJapan
| | - Daisuke Kuroda
- Department of Bioengineering, School of EngineeringThe University of TokyoTokyoJapan
- Department of Chemistry and Biotechnology, Graduate School of EngineeringThe University of TokyoTokyoJapan
- Research Center for Drug and Vaccine DevelopmentNational Institute of Infectious DiseasesTokyoJapan
| | - Atsushi Fukunaga
- Bio‐Diagnostic Reagent Technology CenterSysmex CorporationKobeJapan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of EngineeringThe University of TokyoTokyoJapan
- Department of Chemistry and Biotechnology, Graduate School of EngineeringThe University of TokyoTokyoJapan
- Institute of Medical ScienceThe University of TokyoTokyoJapan
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2
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Communication pathways bridge local and global conformations in an IgG4 antibody. Sci Rep 2021; 11:23197. [PMID: 34853348 PMCID: PMC8636491 DOI: 10.1038/s41598-021-02323-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 11/15/2021] [Indexed: 12/15/2022] Open
Abstract
The affinity of an antibody for its antigen is primarily determined by the specific sequence and structural arrangement of the complementarity-determining regions (CDRs). Recent evidence, however, points toward a nontrivial relation between the CDR and distal sites: variations in the binding strengths have been observed upon mutating residues separated from the paratope by several nanometers, thus suggesting the existence of a communication network within antibodies, whose extension and relevance might be deeper than insofar expected. In this work, we test this hypothesis by means of molecular dynamics (MD) simulations of the IgG4 monoclonal antibody pembrolizumab, an approved drug that targets the programmed cell death protein 1 (PD-1). The molecule is simulated in both the apo and holo states, totalling 4 μs of MD trajectory. The analysis of these simulations shows that the bound antibody explores a restricted range of conformations with respect to the apo one, and that the global conformation of the molecule correlates with that of the CDR. These results support the hypothesis that pembrolizumab featues a multi-scale hierarchy of intertwined global and local conformational changes. The analysis pipeline developed in this work is general, and it can help shed further light on the mechanistic aspects of antibody function.
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3
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Führer S, Kamenik AS, Zeindl R, Nothegger B, Hofer F, Reider N, Liedl KR, Tollinger M. Inverse relation between structural flexibility and IgE reactivity of Cor a 1 hazelnut allergens. Sci Rep 2021; 11:4173. [PMID: 33603065 PMCID: PMC7892832 DOI: 10.1038/s41598-021-83705-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/05/2021] [Indexed: 11/09/2022] Open
Abstract
A major proportion of allergic reactions to hazelnuts (Corylus avellana) are caused by immunologic cross-reactivity of IgE antibodies to pathogenesis-related class 10 (PR-10) proteins. Intriguingly, the four known isoforms of the hazelnut PR-10 allergen Cor a 1, denoted as Cor a 1.0401-Cor a 1.0404, share sequence identities exceeding 97% but possess different immunologic properties. In this work we describe the NMR solution structures of these proteins and provide an in-depth study of their biophysical properties. Despite sharing highly similar three-dimensional structures, the four isoforms exhibit remarkable differences regarding structural flexibility, hydrogen bonding and thermal stability. Our experimental data reveal an inverse relation between structural flexibility and IgE-binding in ELISA experiments, with the most flexible isoform having the lowest IgE-binding potential, while the isoform with the most rigid backbone scaffold displays the highest immunologic reactivity. These results point towards a significant entropic contribution to the process of antibody binding.
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Affiliation(s)
- Sebastian Führer
- grid.5771.40000 0001 2151 8122Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Anna S. Kamenik
- grid.5771.40000 0001 2151 8122Institute of General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Ricarda Zeindl
- grid.5771.40000 0001 2151 8122Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Bettina Nothegger
- grid.5361.10000 0000 8853 2677Department of Dermatology, Venerology and Allergology, Medical University of Innsbruck, Anichstraße 35, 6020 Innsbruck, Austria
| | - Florian Hofer
- grid.5771.40000 0001 2151 8122Institute of General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Norbert Reider
- grid.5361.10000 0000 8853 2677Department of Dermatology, Venerology and Allergology, Medical University of Innsbruck, Anichstraße 35, 6020 Innsbruck, Austria
| | - Klaus R. Liedl
- grid.5771.40000 0001 2151 8122Institute of General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Martin Tollinger
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria.
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4
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Structure-based design and discovery of novel anti-tissue factor antibodies with cooperative double-point mutations, using interaction analysis. Sci Rep 2020; 10:17590. [PMID: 33067496 PMCID: PMC7567794 DOI: 10.1038/s41598-020-74545-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 10/05/2020] [Indexed: 01/21/2023] Open
Abstract
The generation of a wide range of candidate antibodies is important for the successful development of drugs that simultaneously satisfy multiple requirements. To find cooperative mutations and increase the diversity of mutants, an in silico double-point mutation approach, in which 3D models of all possible double-point mutant/antigen complexes are constructed and evaluated using interaction analysis, was developed. Starting from an antibody with very high affinity, four double-point mutants were designed in silico. Two of the double-point mutants exhibited improved affinity or affinity comparable to that of the starting antibody. The successful identification of two active double-point mutants showed that a cooperative mutation could be found by utilizing information regarding the interactions. The individual single-point mutants of the two active double-point mutants showed decreased affinity or no expression. These results suggested that the two active double-point mutants cannot be obtained through the usual approach i.e. a combination of improved single-point mutants. In addition, a triple-point mutant, which combines the distantly located active double-point mutation and an active single-point mutation collaterally obtained in the process of the double-point mutation strategy, was designed. The triple-point mutant showed improved affinity. This finding suggested that the effects of distantly located mutations are independent and additive. The double-point mutation approach using the interaction analysis of 3D structures expands the design repertoire for mutants, and hopefully paves a way for the identification of cooperative multiple-point mutations.
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5
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Tarasov SA, Gorbunov EA, Don ES, Emelyanova AG, Kovalchuk AL, Yanamala N, Schleker ASS, Klein-Seetharaman J, Groenestein R, Tafani JP, van der Meide P, Epstein OI. Insights into the Mechanism of Action of Highly Diluted Biologics. THE JOURNAL OF IMMUNOLOGY 2020; 205:1345-1354. [PMID: 32727888 DOI: 10.4049/jimmunol.2000098] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 07/04/2020] [Indexed: 12/12/2022]
Abstract
The therapeutic use of Abs in cancer, autoimmunity, transplantation, and other fields is among the major biopharmaceutical advances of the 20th century. Broader use of Ab-based drugs is constrained because of their high production costs and frequent side effects. One promising approach to overcome these limitations is the use of highly diluted Abs, which are produced by gradual reduction of an Ab concentration to an extremely low level. This technology was used to create a group of drugs for the treatment of various diseases, depending on the specificity of the used Abs. Highly diluted Abs to IFN-γ (hd-anti-IFN-γ) have been demonstrated to be efficacious against influenza and other respiratory infections in a variety of preclinical and clinical studies. In the current study, we provide evidence for a possible mechanism of action of hd-anti-IFN-γ. Using high-resolution solution nuclear magnetic resonance spectroscopy, we show that the drug induced conformational changes in the IFN-γ molecule. Chemical shift changes occurred in the amino acids located primarily at the dimer interface and at the C-terminal region of IFN-γ. These molecular changes could be crucial for the function of the protein, as evidenced by an observed hd-anti-IFN-γ-induced increase in the specific binding of IFN-γ to its receptor in U937 cells, enhanced induced production of IFN-γ in human PBMC culture, and increased survival of influenza A-infected mice.
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Affiliation(s)
- Sergey A Tarasov
- OOO "NPF "Materia Medica Holding," 127473 Moscow, Russian Federation.,The Institute of General Pathology and Pathophysiology, 125315 Moscow, Russian Federation
| | | | - Elena S Don
- OOO "NPF "Materia Medica Holding," 127473 Moscow, Russian Federation.,The Institute of General Pathology and Pathophysiology, 125315 Moscow, Russian Federation
| | - Alexandra G Emelyanova
- OOO "NPF "Materia Medica Holding," 127473 Moscow, Russian Federation.,The Institute of General Pathology and Pathophysiology, 125315 Moscow, Russian Federation
| | | | - Naveena Yanamala
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260
| | - A Sylvia S Schleker
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260
| | - Judith Klein-Seetharaman
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260
| | | | | | | | - Oleg I Epstein
- OOO "NPF "Materia Medica Holding," 127473 Moscow, Russian Federation.,The Institute of General Pathology and Pathophysiology, 125315 Moscow, Russian Federation
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6
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Yanaka S, Yogo R, Kato K. Biophysical characterization of dynamic structures of immunoglobulin G. Biophys Rev 2020; 12:637-645. [PMID: 32410186 PMCID: PMC7311591 DOI: 10.1007/s12551-020-00698-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 05/01/2020] [Indexed: 12/25/2022] Open
Abstract
Immunoglobulin G (IgG) is a major antibody and functions as a hub linking specific antigen binding and recruitment of effector molecules typified by Fcγ receptors (FcγRs). These activities are associated primarily with interactions involving its Fab and Fc sites, respectively. An IgG molecule is characterized by a multiple domain modular structure with conserved N-glycosylation in Fc. The molecule displays significant freedom in internal motion on various spatiotemporal scales. The consequent conformational flexibility and plasticity of IgG glycoproteins are functionally significant and potentially important factors for design and engineering of antibodies with enhanced functionality. In this article, experimental and computational approaches are outlined for characterizing the conformational dynamics of IgG molecules in solution. In particular, the importance of integration of these approaches is highlighted, as illustrated by dynamic intramolecular interactions between the pair of N-glycans and their proximal amino acid residues in Fc. These interactions can critically affect effector functions mediated by human IgG1 and FcγRIII. Further improvements in individual biophysical techniques and their integration will advance understanding of dynamic behaviors of antibodies in physiological and pathological conditions. Such understanding will provide opportunities for engineering antibodies through controlling allosteric networks in IgG molecules.
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Affiliation(s)
- Saeko Yanaka
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi, 467-8603, Japan
| | - Rina Yogo
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi, 467-8603, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan.
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi, 467-8603, Japan.
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7
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Chiu ML, Goulet DR, Teplyakov A, Gilliland GL. Antibody Structure and Function: The Basis for Engineering Therapeutics. Antibodies (Basel) 2019; 8:antib8040055. [PMID: 31816964 PMCID: PMC6963682 DOI: 10.3390/antib8040055] [Citation(s) in RCA: 218] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/25/2019] [Accepted: 11/28/2019] [Indexed: 12/11/2022] Open
Abstract
Antibodies and antibody-derived macromolecules have established themselves as the mainstay in protein-based therapeutic molecules (biologics). Our knowledge of the structure–function relationships of antibodies provides a platform for protein engineering that has been exploited to generate a wide range of biologics for a host of therapeutic indications. In this review, our basic understanding of the antibody structure is described along with how that knowledge has leveraged the engineering of antibody and antibody-related therapeutics having the appropriate antigen affinity, effector function, and biophysical properties. The platforms examined include the development of antibodies, antibody fragments, bispecific antibody, and antibody fusion products, whose efficacy and manufacturability can be improved via humanization, affinity modulation, and stability enhancement. We also review the design and selection of binding arms, and avidity modulation. Different strategies of preparing bispecific and multispecific molecules for an array of therapeutic applications are included.
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Affiliation(s)
- Mark L. Chiu
- Drug Product Development Science, Janssen Research & Development, LLC, Malvern, PA 19355, USA
- Correspondence:
| | - Dennis R. Goulet
- Department of Medicinal Chemistry, University of Washington, P.O. Box 357610, Seattle, WA 98195-7610, USA;
| | - Alexey Teplyakov
- Biologics Research, Janssen Research & Development, LLC, Spring House, PA 19477, USA; (A.T.); (G.L.G.)
| | - Gary L. Gilliland
- Biologics Research, Janssen Research & Development, LLC, Spring House, PA 19477, USA; (A.T.); (G.L.G.)
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8
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Balakrishnan N, Gurunathan B, Surapaneni KM. Application of proteometric approach for identification of functional mutant sites to improve the binding affinity of anticancer biologic trastuzumab with its antigen human epidermal growth factor receptor 2. J Mol Recognit 2019; 33:e2818. [DOI: 10.1002/jmr.2818] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 09/15/2019] [Accepted: 09/22/2019] [Indexed: 11/07/2022]
Affiliation(s)
- Nataraj Balakrishnan
- Biotechnology Division, R&D CentreOrchid Pharma Ltd. (Formerly known as Orchid Chemicals and Pharmaceuticals Ltd.) Chennai India
| | - Baskar Gurunathan
- Department of BiotechnologySt. Joseph's College of Engineering Chennai India
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9
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Structural and thermodynamic basis for the recognition of the substrate-binding cleft on hen egg lysozyme by a single-domain antibody. Sci Rep 2019; 9:15481. [PMID: 31664051 PMCID: PMC6820745 DOI: 10.1038/s41598-019-50722-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 09/10/2019] [Indexed: 01/06/2023] Open
Abstract
Single-domain antibodies (VHHs or nanobodies), developed from heavy chain-only antibodies of camelids, are gaining attention as next-generation therapeutic agents. Despite their small size, the high affinity and specificity displayed by VHHs for antigen molecules rival those of IgGs. How such small antibodies achieve that level of performance? Structural studies have revealed that VHHs tend to recognize concave surfaces of their antigens with high shape-complementarity. However, the energetic contribution of individual residues located at the binding interface has not been addressed in detail, obscuring the actual mechanism by which VHHs target the concave surfaces of proteins. Herein, we show that a VHH specific for hen egg lysozyme, D3-L11, not only displayed the characteristic binding of VHHs to a concave region of the surface of the antigen, but also exhibited a distribution of energetic hot-spots like those of IgGs and conventional protein-protein complexes. The highly preorganized and energetically compact interface of D3-L11 recognizes the concave epitope with high shape complementarity by the classical lock-and-key mechanism. Our results shed light on the fundamental basis by which a particular VHH accommodate to the concave surface of an antigens with high affinity in a specific manner, enriching the mechanistic landscape of VHHs.
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10
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Thermodynamic Analysis of Protein-Lipid Interactions by Isothermal Titration Calorimetry. Methods Mol Biol 2019; 2003:71-89. [PMID: 31218614 DOI: 10.1007/978-1-4939-9512-7_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Isothermal titration calorimetry is a highly sensitive and powerful technique for the study of molecular interactions. This method can be applied universally for studying the interaction between moleculeAbstracts, molecular assembles and ions as it measures the heat changes resulting from such interactions and does not need any probe molecule/moiety to be incorporated into the system under investigation. This method has been applied quite extensively to investigate the interaction of proteins with other biomolecules such as small ligands, other proteins, nucleic acids, lipid membranes as well as to study the interaction of antibodies, drugs, metal ions and nanoparticles with target proteins or antigens, nucleic acids, and membranes. In this chapter, we describe the application of ITC for the investigation of thermodynamics of protein-lipid interaction. A number of important parameters such as enthalpy of binding (ΔH), entropy of binding (ΔS), association constant (Ka), binding stoichiometry (n) and free energy of binding (ΔG) can be obtained from a single calorimetric titration, providing a complete thermodynamic characterization of the interaction. The method is described in detail taking the major protein of the bovine seminal plasma, PDC-109, which exhibits a high preference for interaction with choline-containing lipids, as an example. The method can be applied to investigate thermodynamic parameters associated with the interaction of other soluble proteins with lipid membranes.
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11
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Structure-guided design fine-tunes pharmacokinetics, tolerability, and antitumor profile of multispecific frizzled antibodies. Proc Natl Acad Sci U S A 2019; 116:6812-6817. [PMID: 30894493 DOI: 10.1073/pnas.1817246116] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Aberrant activation of Wnt/β-catenin signaling occurs frequently in cancer. However, therapeutic targeting of this pathway is complicated by the role of Wnt in stem cell maintenance and tissue homeostasis. Here, we evaluated antibodies blocking 6 of the 10 human Wnt/Frizzled (FZD) receptors as potential therapeutics. Crystal structures revealed a common binding site for these monoclonal antibodies (mAbs) on FZD, blocking the interaction with the Wnt palmitoleic acid moiety. However, these mAbs displayed gastrointestinal toxicity or poor plasma exposure in vivo. Structure-guided engineering was used to refine the binding of each mAb for FZD receptors, resulting in antibody variants with improved in vivo tolerability and developability. Importantly, the lead variant mAb significantly inhibited tumor growth in the HPAF-II pancreatic tumor xenograft model. Taken together, our data demonstrate that anti-FZD cancer therapeutic antibodies with broad specificity can be fine-tuned to navigate in vivo exposure and tolerability while driving therapeutic efficacy.
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12
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Moraes AH, Asam C, Almeida FCL, Wallner M, Ferreira F, Valente AP. Structural basis for cross-reactivity and conformation fluctuation of the major beech pollen allergen Fag s 1. Sci Rep 2018; 8:10512. [PMID: 30002383 PMCID: PMC6043577 DOI: 10.1038/s41598-018-28358-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 03/20/2018] [Indexed: 01/08/2023] Open
Abstract
Fag s 1 is a member of the Pathogen Related protein family 10 (PR-10) and can elicit cross-reaction with IgE antibodies produced against the birch pollen allergen Bet v 1. The Nuclear Magnetic Resonance (NMR) structure of Fag s 1 is presented along with its dynamic properties. It shares 66% identity with Bet v 1 and exhibits the expected three α-helices and seven β-sheets arranged as a semi-beta barrel and exposing the residues mapped as the Bet v 1 IgE epitope. The structural dynamics of Fag s 1 were monitored on the fast and intermediate timescales, using relaxation rates. The complex dynamics of Fag s 1 are closely related to the internal cavity, and they modulate IgE and ligand binding.
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Affiliation(s)
- Adolfo H Moraes
- Chemistry Department, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Claudia Asam
- Department of Molecular Biology, University of Salzburg, Salzburg, Austria
| | - Fabio C L Almeida
- National NMR Center, Department of Structural Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Michael Wallner
- Department of Molecular Biology, University of Salzburg, Salzburg, Austria
| | - Fatima Ferreira
- Department of Molecular Biology, University of Salzburg, Salzburg, Austria
| | - Ana Paula Valente
- National NMR Center, Department of Structural Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
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13
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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.
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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.
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