1
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Petersen BM, Kirby MB, Chrispens KM, Irvin OM, Strawn IK, Haas CM, Walker AM, Baumer ZT, Ulmer SA, Ayala E, Rhodes ER, Guthmiller JJ, Steiner PJ, Whitehead TA. An integrated technology for quantitative wide mutational scanning of human antibody Fab libraries. Nat Commun 2024; 15:3974. [PMID: 38730230 PMCID: PMC11087541 DOI: 10.1038/s41467-024-48072-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 04/19/2024] [Indexed: 05/12/2024] Open
Abstract
Antibodies are engineerable quantities in medicine. Learning antibody molecular recognition would enable the in silico design of high affinity binders against nearly any proteinaceous surface. Yet, publicly available experiment antibody sequence-binding datasets may not contain the mutagenic, antigenic, or antibody sequence diversity necessary for deep learning approaches to capture molecular recognition. In part, this is because limited experimental platforms exist for assessing quantitative and simultaneous sequence-function relationships for multiple antibodies. Here we present MAGMA-seq, an integrated technology that combines multiple antigens and multiple antibodies and determines quantitative biophysical parameters using deep sequencing. We demonstrate MAGMA-seq on two pooled libraries comprising mutants of nine different human antibodies spanning light chain gene usage, CDR H3 length, and antigenic targets. We demonstrate the comprehensive mapping of potential antibody development pathways, sequence-binding relationships for multiple antibodies simultaneously, and identification of paratope sequence determinants for binding recognition for broadly neutralizing antibodies (bnAbs). MAGMA-seq enables rapid and scalable antibody engineering of multiple lead candidates because it can measure binding for mutants of many given parental antibodies in a single experiment.
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Affiliation(s)
- Brian M Petersen
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
| | - Monica B Kirby
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
| | - Karson M Chrispens
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
| | - Olivia M Irvin
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
| | - Isabell K Strawn
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
| | - Cyrus M Haas
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
| | - Alexis M Walker
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
| | - Zachary T Baumer
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
| | - Sophia A Ulmer
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
| | - Edgardo Ayala
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Emily R Rhodes
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
| | - Jenna J Guthmiller
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Paul J Steiner
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
| | - Timothy A Whitehead
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA.
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2
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Yang EC, Divine R, Miranda MC, Borst AJ, Sheffler W, Zhang JZ, Decarreau J, Saragovi A, Abedi M, Goldbach N, Ahlrichs M, Dobbins C, Hand A, Cheng S, Lamb M, Levine PM, Chan S, Skotheim R, Fallas J, Ueda G, Lubner J, Somiya M, Khmelinskaia A, King NP, Baker D. Computational design of non-porous pH-responsive antibody nanoparticles. Nat Struct Mol Biol 2024:10.1038/s41594-024-01288-5. [PMID: 38724718 DOI: 10.1038/s41594-024-01288-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 03/22/2024] [Indexed: 05/21/2024]
Abstract
Programming protein nanomaterials to respond to changes in environmental conditions is a current challenge for protein design and is important for targeted delivery of biologics. Here we describe the design of octahedral non-porous nanoparticles with a targeting antibody on the two-fold symmetry axis, a designed trimer programmed to disassemble below a tunable pH transition point on the three-fold axis, and a designed tetramer on the four-fold symmetry axis. Designed non-covalent interfaces guide cooperative nanoparticle assembly from independently purified components, and a cryo-EM density map closely matches the computational design model. The designed nanoparticles can package protein and nucleic acid payloads, are endocytosed following antibody-mediated targeting of cell surface receptors, and undergo tunable pH-dependent disassembly at pH values ranging between 5.9 and 6.7. The ability to incorporate almost any antibody into a non-porous pH-dependent nanoparticle opens up new routes to antibody-directed targeted delivery.
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Affiliation(s)
- Erin C Yang
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Graduate Program in Biological Physics, Structure & Design, University of Washington, Seattle, WA, USA
| | - Robby Divine
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Graduate Program in Biochemistry, University of Washington, Seattle, WA, USA
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Marcos C Miranda
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Medicine Solna, Division of Immunology and Allergy, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Andrew J Borst
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Will Sheffler
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Jason Z Zhang
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Justin Decarreau
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Amijai Saragovi
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Mohamad Abedi
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Nicolas Goldbach
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Technical University of Munich, Munich, Germany
| | - Maggie Ahlrichs
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Craig Dobbins
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Alexis Hand
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Suna Cheng
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Mila Lamb
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Paul M Levine
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Sidney Chan
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Rebecca Skotheim
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Jorge Fallas
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - George Ueda
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Joshua Lubner
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Masaharu Somiya
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- SANKEN, Osaka University, Osaka, Japan
| | - Alena Khmelinskaia
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Transdisciplinary Research Area 'Building Blocks of Matter and Fundamental Interactions (TRA Matter)', University of Bonn, Bonn, Germany
- Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Neil P King
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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3
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Yi Y, An HW, Wang H. Intelligent Biomaterialomics: Molecular Design, Manufacturing, and Biomedical Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2305099. [PMID: 37490938 DOI: 10.1002/adma.202305099] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/14/2023] [Indexed: 07/27/2023]
Abstract
Materialomics integrates experiment, theory, and computation in a high-throughput manner, and has changed the paradigm for the research and development of new functional materials. Recently, with the rapid development of high-throughput characterization and machine-learning technologies, the establishment of biomaterialomics that tackles complex physiological behaviors has become accessible. Breakthroughs in the clinical translation of nanoparticle-based therapeutics and vaccines have been observed. Herein, recent advances in biomaterials, including polymers, lipid-like materials, and peptides/proteins, discovered through high-throughput screening or machine learning-assisted methods, are summarized. The molecular design of structure-diversified libraries; high-throughput characterization, screening, and preparation; and, their applications in drug delivery and clinical translation are discussed in detail. Furthermore, the prospects and main challenges in future biomaterialomics and high-throughput screening development are highlighted.
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Affiliation(s)
- Yu Yi
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Haidian District, Beijing, 100190, China
| | - Hong-Wei An
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Haidian District, Beijing, 100190, China
| | - Hao Wang
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Haidian District, Beijing, 100190, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
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4
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Biewenga L, Vermathen R, Rosier BJ, Merkx M. A Generic Antibody-Blocking Protein That Enables pH-Switchable Activation of Antibody Activity. ACS Chem Biol 2024; 19:48-57. [PMID: 38110237 PMCID: PMC10804362 DOI: 10.1021/acschembio.3c00449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 12/20/2023]
Abstract
Molecular strategies that allow for reversible control of antibody activity have drawn considerable interest for both therapeutic and diagnostic applications. Protein M is a generic antibody-binding protein that binds to the Fv domain of IgGs and, in doing so, blocks antigen binding. However, the dissociation of protein M is essentially irreversible, which has precluded its use as an antibody affinity reagent and molecular mask to control antibody activity. Here, we show that introduction of 8 histidine residues on the Fv binding interface of protein M results in a variant that shows pH-switchable IgG binding. This protein M-8his variant provides an attractive and universal affinity resin for the purification of IgGs, antibody fragments (Fab and single-chain variable fragments (scFv)), and antibody conjugates. Moreover, protein M-8his enables the pH-dependent blocking of therapeutic antibodies, allowing the selective targeting of cells at pH 6.0.
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Affiliation(s)
- Lieuwe Biewenga
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Robin Vermathen
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Bas J.H.M. Rosier
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Maarten Merkx
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
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5
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Petersen BM, Kirby MB, Chrispens KM, Irvin OM, Strawn IK, Haas CM, Walker AM, Baumer ZT, Ulmer SA, Ayala E, Rhodes ER, Guthmiller JJ, Steiner PJ, Whitehead TA. An integrated technology for quantitative wide mutational scanning of human antibody Fab libraries. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.16.575852. [PMID: 38293170 PMCID: PMC10827193 DOI: 10.1101/2024.01.16.575852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Antibodies are engineerable quantities in medicine. Learning antibody molecular recognition would enable the in silico design of high affinity binders against nearly any proteinaceous surface. Yet, publicly available experiment antibody sequence-binding datasets may not contain the mutagenic, antigenic, or antibody sequence diversity necessary for deep learning approaches to capture molecular recognition. In part, this is because limited experimental platforms exist for assessing quantitative and simultaneous sequence-function relationships for multiple antibodies. Here we present MAGMA-seq, an integrated technology that combines multiple antigens and multiple antibodies and determines quantitative biophysical parameters using deep sequencing. We demonstrate MAGMA-seq on two pooled libraries comprising mutants of ten different human antibodies spanning light chain gene usage, CDR H3 length, and antigenic targets. We demonstrate the comprehensive mapping of potential antibody development pathways, sequence-binding relationships for multiple antibodies simultaneously, and identification of paratope sequence determinants for binding recognition for broadly neutralizing antibodies (bnAbs). MAGMA-seq enables rapid and scalable antibody engineering of multiple lead candidates because it can measure binding for mutants of many given parental antibodies in a single experiment.
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Affiliation(s)
- Brian M. Petersen
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80305, USA
| | - Monica B. Kirby
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80305, USA
| | - Karson M. Chrispens
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80305, USA
| | - Olivia M. Irvin
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80305, USA
| | - Isabell K. Strawn
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80305, USA
| | - Cyrus M. Haas
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80305, USA
| | - Alexis M. Walker
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80305, USA
| | - Zachary T. Baumer
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80305, USA
| | - Sophia A. Ulmer
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80305, USA
| | - Edgardo Ayala
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Emily R. Rhodes
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80305, USA
| | - Jenna J. Guthmiller
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Paul J. Steiner
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80305, USA
| | - Timothy A. Whitehead
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80305, USA
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6
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Tulika T, Pedersen RW, Rimbault C, Ahmadi S, Rivera‐de‐Torre E, Fernández‐Quintero ML, Loeffler JR, Bohn M, Ljungars A, Ledsgaard L, Voldborg BG, Ruso‐Julve F, Andersen JT, Laustsen AH. Phage display assisted discovery of a pH-dependent anti-α-cobratoxin antibody from a natural variable domain library. Protein Sci 2023; 32:e4821. [PMID: 37897425 PMCID: PMC10659949 DOI: 10.1002/pro.4821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 09/28/2023] [Accepted: 10/24/2023] [Indexed: 10/30/2023]
Abstract
Recycling IgG antibodies bind to their target antigen at physiological pH in the blood stream and release them upon endocytosis when pH levels drop, allowing the IgG antibodies to be recycled into circulation via FcRn-mediated cellular pathways, while the antigens undergo lysosomal degradation. This enables recycling antibodies to achieve comparable therapeutic effect at lower doses than their non-recycling counterparts. The development of such antibodies is typically achieved by histidine doping of their variable regions or by performing in vitro antibody selection campaigns utilizing histidine doped libraries. Both are strategies that may introduce sequence liabilities. Here, we present a methodology that employs a naïve antibody phage display library, consisting of natural variable domains, to discover antibodies that bind α-cobratoxin from the venom of Naja kaouthia in a pH-dependent manner. As a result, an antibody was discovered that exhibits a 7-fold higher off-rate at pH 5.5 than pH 7.4 in bio-layer interferometry experiments. Interestingly, no histidine residues were found in its variable domains, and in addition, the antibody showed pH-dependent binding to a histidine-devoid antigen mutant. As such, the results demonstrate that pH-dependent antigen-antibody binding may not always be driven by histidine residues. By employing molecular dynamics simulations, different protonation states of titratable residues were found, which potentially could be responsible for the observed pH-dependent antigen binding properties of the antibody. Finally, given the typically high diversity of naïve antibody libraries, the methodology presented here can likely be applied to discover recycling antibodies against different targets ab initio without the need for histidine doping.
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Affiliation(s)
- Tulika Tulika
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | - Rasmus W. Pedersen
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | - Charlotte Rimbault
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | - Shirin Ahmadi
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | | | - Monica L. Fernández‐Quintero
- Center for Molecular Biosciences Innsbruck, Department of GeneralInorganic and Theoretical Chemistry, University of InnsbruckInnsbruckAustria
| | - Johannes R. Loeffler
- Center for Molecular Biosciences Innsbruck, Department of GeneralInorganic and Theoretical Chemistry, University of InnsbruckInnsbruckAustria
| | - Markus‐Frederik Bohn
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | - Anne Ljungars
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | - Line Ledsgaard
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | - Bjørn G. Voldborg
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | - Fulgencio Ruso‐Julve
- Department of PharmacologyUniversity of OsloOsloNorway
- Department of ImmunologyOslo University Hospital RikshospitaletOsloNorway
- Precision Immunotherapy AllianceUniversity of OsloOsloNorway
| | - Jan Terje Andersen
- Department of PharmacologyUniversity of OsloOsloNorway
- Department of ImmunologyOslo University Hospital RikshospitaletOsloNorway
- Precision Immunotherapy AllianceUniversity of OsloOsloNorway
| | - Andreas H. Laustsen
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
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7
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Rohskopf Z, Kwon T, Ko SH, Bozinovski D, Jeon H, Mohan N, Springs SL, Han J. Continuous Online Titer Monitoring in CHO Cell Culture Supernatant Using a Herringbone Nanofluidic Filter Array. Anal Chem 2023; 95:14608-14615. [PMID: 37733929 DOI: 10.1021/acs.analchem.3c02104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
Abstract
Online monitoring of monoclonal antibody product titers throughout biologics process development and production enables rapid bioprocess decision-making and process optimization. Conventional analytical methods, including high-performance liquid chromatography and turbidimetry, typically require interfacing with an automated sampling system capable of online sampling and fractionation, which suffers from increased cost, a higher risk of failure, and a higher mechanical complexity of the system. In this study, a novel nanofluidic system for continuous direct (no sample preparation) IgG titer measurements was investigated. Tumor necrosis factor α (TNF-α), conjugated with fluorophores, was utilized as a selective binder for adalimumab in the unprocessed cell culture supernatant. The nanofluidic device can separate the bound complex from unbound TNF-α and selectively concentrate the bound complex for high-sensitivity detection. Based on the fluorescence intensity from the concentrated bound complex, a fluorescence intensity versus titer curve can be generated, which was used to determine the titer of samples from filtered, unpurified Chinese hamster ovary cell cultures continuously. The system performed direct monitoring of IgG titers with nanomolar resolution and showed a good correlation with the biolayer interferometry assays. Furthermore, by variation of the concentration of the indicator (TNF-α), the dynamic range of the system can be tuned and further expanded.
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Affiliation(s)
- Zhumei Rohskopf
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Taehong Kwon
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge,Massachusetts 02139, United States
| | - Sung Hee Ko
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge,Massachusetts 02139, United States
| | - Dragana Bozinovski
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Hyungkook Jeon
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Naresh Mohan
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Stacy L Springs
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Critical Analytics for Manufacturing Personalized-Medicine (CAMP) IRG, Singapore-MIT Alliance for Research and Technology (SMART) Centre, Singapore117583,Singapore
| | - Jongyoon Han
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge,Massachusetts 02139, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Critical Analytics for Manufacturing Personalized-Medicine (CAMP) IRG, Singapore-MIT Alliance for Research and Technology (SMART) Centre, Singapore117583,Singapore
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8
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Zhao Y, Jiang H, Yu J, Wang L, Du J. Engineered Histidine-Rich Peptides Enhance Endosomal Escape for Antibody-Targeted Intracellular Delivery of Functional Proteins. Angew Chem Int Ed Engl 2023; 62:e202304692. [PMID: 37283024 DOI: 10.1002/anie.202304692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/04/2023] [Accepted: 06/05/2023] [Indexed: 06/08/2023]
Abstract
Currently, the clinical application of protein/peptide therapeutics is mainly limited to the modulation of diseases in extracellular spaces. Intracellular targets are hardly accessed, owing largely to the endosomal entrapment of internalized proteins/peptides. Here, we report a strategy to design and construct peptides that enable endosome-to-cytosol delivery based on an extension of the "histidine switch" principle. By substituting the Arg/Lys residues in cationic cell-penetrating peptides (CPPs) with histidine, we obtained peptides with pH-dependent membrane-perturbation activity. These peptides do not randomly penetrate cells like CPPs, but imitate the endosomal escape of CPPs following cellular uptake. Working with one such 16-residue peptide (hsLMWP) with high endosomal escape capacity, we engineered modular fusion proteins and achieved antibody-targeted delivery of diverse protein cargoes-including the pro-apoptotic protein BID (BH3-interacting domain death agonist) and Cre recombinase-into the cytosol of multiple cancer cell types. After extensive in vitro testing, an in vivo analysis with xenograft mice ultimately demonstrated that a trastuzumab-hsLMWP-BID fusion conferred strong anti-tumor efficacy without apparent side effects. Notably, our fusion protein features a modular design, allowing flexible applications for any antibody/cargo combination of choice. Therefore, the potential applications extend throughout life science and biomedicine, including gene editing, cancer treatment, and immunotherapy.
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Affiliation(s)
- Yan Zhao
- School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
- Peking University-Tsinghua University-National Institute Biological Sciences (PTN) Joint Graduate Program, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Haolin Jiang
- School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
- Academy for Advanced Interdisciplinary Studies (AAIS), Peking University-Tsinghua University-National Institute Biological Sciences (PTN) Joint Graduate Program, Peking University, Beijing, 100871, China
| | - Jiazhen Yu
- School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Luyao Wang
- School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Juanjuan Du
- School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
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9
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Wei W, Hogues H, Sulea T. Comparative Performance of High-Throughput Methods for Protein p Ka Predictions. J Chem Inf Model 2023; 63:5169-5181. [PMID: 37549424 PMCID: PMC10466379 DOI: 10.1021/acs.jcim.3c00165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Indexed: 08/09/2023]
Abstract
The medically relevant field of protein-based therapeutics has triggered a demand for protein engineering in different pH environments of biological relevance. In silico engineering workflows typically employ high-throughput screening campaigns that require evaluating large sets of protein residues and point mutations by fast yet accurate computational algorithms. While several high-throughput pKa prediction methods exist, their accuracies are unclear due to the lack of a current comprehensive benchmarking. Here, seven fast, efficient, and accessible approaches including PROPKA3, DeepKa, PKAI, PKAI+, DelPhiPKa, MCCE2, and H++ were systematically tested on a nonredundant subset of 408 measured protein residue pKa shifts from the pKa database (PKAD). While no method outperformed the null hypotheses with confidence, as illustrated by statistical bootstrapping, DeepKa, PKAI+, PROPKA3, and H++ had utility. More specifically, DeepKa consistently performed well in tests across multiple and individual amino acid residue types, as reflected by lower errors, higher correlations, and improved classifications. Arithmetic averaging of the best empirical predictors into simple consensuses improved overall transferability and accuracy up to a root-mean-square error of 0.76 pKa units and a correlation coefficient (R2) of 0.45 to experimental pKa shifts. This analysis should provide a basis for further methodological developments and guide future applications, which require embedding of computationally inexpensive pKa prediction methods, such as the optimization of antibodies for pH-dependent antigen binding.
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Affiliation(s)
- Wanlei Wei
- Human Health Therapeutics
Research Centre, National Research Council
Canada, 6100 Royalmount Avenue, Montreal, Quebec H4P 2R2, Canada
| | - Hervé Hogues
- Human Health Therapeutics
Research Centre, National Research Council
Canada, 6100 Royalmount Avenue, Montreal, Quebec H4P 2R2, Canada
| | - Traian Sulea
- Human Health Therapeutics
Research Centre, National Research Council
Canada, 6100 Royalmount Avenue, Montreal, Quebec H4P 2R2, Canada
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10
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Esparza TJ, Su S, Francescutti CM, Rodionova E, Kim JH, Brody DL. Enhanced in vivo blood brain barrier transcytosis of macromolecular cargo using an engineered pH-sensitive mouse transferrin receptor binding nanobody. Fluids Barriers CNS 2023; 20:64. [PMID: 37620930 PMCID: PMC10463325 DOI: 10.1186/s12987-023-00462-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 08/10/2023] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND The blood brain barrier limits entry of macromolecular diagnostic and therapeutic cargos. Blood brain barrier transcytosis via receptor mediated transport systems, such as the transferrin receptor, can be used to carry macromolecular cargos with variable efficiency. Transcytosis involves trafficking through acidified intracellular vesicles, but it is not known whether pH-dependent unbinding of transport shuttles can be used to improve blood brain barrier transport efficiency. METHODS A mouse transferrin receptor binding nanobody, NIH-mTfR-M1, was engineered to confer greater unbinding at pH 5.5 vs 7.4 by introducing multiple histidine mutations. The histidine mutant nanobodies were coupled to neurotensin for in vivo functional blood brain barrier transcytosis testing via central neurotensin-mediated hypothermia in wild-type mice. Multi-nanobody constructs including the mutant M1R56H, P96H, Y102H and two copies of the P2X7 receptor-binding 13A7 nanobody were produced to test proof-of-concept macromolecular cargo transport in vivo using quantitatively verified capillary depleted brain lysates and in situ histology. RESULTS The most effective histidine mutant, M1R56H, P96H, Y102H-neurotensin, caused > 8 °C hypothermia after 25 nmol/kg intravenous injection. Levels of the heterotrimeric construct M1R56H, P96H, Y102H-13A7-13A7 in capillary depleted brain lysates peaked at 1 h and were 60% retained at 8 h. A control construct with no brain targets was only 15% retained at 8 h. Addition of the albumin-binding Nb80 nanobody to make M1R56H, P96H, Y102H-13A7-13A7-Nb80 extended blood half-life from 21 min to 2.6 h. At 30-60 min, biotinylated M1R56H, P96H, Y102H-13A7-13A7-Nb80 was visualized in capillaries using in situ histochemistry, whereas at 2-16 h it was detected in diffuse hippocampal and cortical cellular structures. Levels of M1R56H, P96H, Y102H-13A7-13A7-Nb80 reached more than 3.5 percent injected dose/gram of brain tissue after 30 nmol/kg intravenous injection. However, higher injected concentrations did not result in higher brain levels, compatible with saturation and an apparent substrate inhibitory effect. CONCLUSION The pH-sensitive mouse transferrin receptor binding nanobody M1R56H, P96H, Y102H may be a useful tool for rapid and efficient modular transport of diagnostic and therapeutic macromolecular cargos across the blood brain barrier in mouse models. Additional development will be required to determine whether this nanobody-based shuttle system will be useful for imaging and fast-acting therapeutic applications.
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Affiliation(s)
- Thomas J Esparza
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Shiran Su
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | | | - Elvira Rodionova
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Joong Hee Kim
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - David L Brody
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA.
- Center for Neuroscience and Regenerative Medicine, Bethesda, MD, USA.
- Department of Neurology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
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Sivelle C, Sierocki R, Lesparre Y, Lomet A, Quintilio W, Dubois S, Correia E, Moro AM, Maillère B, Nozach H. Combining deep mutational scanning to heatmap of HLA class II binding of immunogenic sequences to preserve functionality and mitigate predicted immunogenicity. Front Immunol 2023; 14:1197919. [PMID: 37575221 PMCID: PMC10416631 DOI: 10.3389/fimmu.2023.1197919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/10/2023] [Indexed: 08/15/2023] Open
Abstract
Removal of CD4 T cell epitopes from therapeutic antibody sequences is expected to mitigate their potential immunogenicity, but its application is complicated by the location of their T cell epitopes, which mainly overlap with complementarity-determining regions. We therefore evaluated the flexibility of antibody sequences to reduce the predicted affinity of corresponding peptides for HLA II molecules and to maintain antibody binding to its target in order to guide antibody engineering for mitigation of predicted immunogenicity. Permissive substitutions to reduce affinity of peptides for HLA II molecules were identified by establishing a heatmap of HLA class II binding using T-cell epitope prediction tools, while permissive substitutions preserving binding to the target were identified by means of deep mutational scanning and yeast surface display. Combinatorial libraries were then designed to identify active clones. Applied to adalimumab, an anti-TNFα human antibody, this approach identified 200 mutants with a lower HLA binding score than adalimumab. Three mutants were produced as full-length antibodies and showed a higher affinity for TNFα and neutralization ability than adalimumab. This study also sheds light on the permissiveness of antibody sequences with regard to functionality and predicted T cell epitope content.
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Affiliation(s)
- Coline Sivelle
- Université de Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, SIMoS, Gif-sur-Yvette, France
| | - Raphael Sierocki
- Université de Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, SIMoS, Gif-sur-Yvette, France
- Deeptope SAS, Orsay, France
| | | | - Aurore Lomet
- CEA List, Université Paris-Saclay, Palaiseau, France
| | - Wagner Quintilio
- Biopharmaceuticals Laboratory, Butantan Institute, Sao Paulo, Brazil
| | - Steven Dubois
- Université de Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, SIMoS, Gif-sur-Yvette, France
| | - Evelyne Correia
- Université de Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, SIMoS, Gif-sur-Yvette, France
| | - Ana Maria Moro
- Biopharmaceuticals Laboratory, Butantan Institute, Sao Paulo, Brazil
| | - Bernard Maillère
- Université de Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, SIMoS, Gif-sur-Yvette, France
| | - Hervé Nozach
- Université de Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, SIMoS, Gif-sur-Yvette, France
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12
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Esparza TJ, Su S, Francescutti CM, Rodionova E, Kim JH, Brody DL. Enhanced in Vivo Blood Brain Barrier Transcytosis of Macromolecular Cargo Using an Engineered pH-sensitive Mouse Transferrin Receptor Binding Nanobody. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.26.538462. [PMID: 37333358 PMCID: PMC10274906 DOI: 10.1101/2023.04.26.538462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Background The blood brain barrier limits entry of macromolecular diagnostic and therapeutic cargos. Blood brain barrier transcytosis via receptor mediated transport systems, such as the transferrin receptor, can be used to carry macromolecular cargos with variable efficiency. Transcytosis involves trafficking through acidified intracellular vesicles, but it is not known whether pH-dependent unbinding of transport shuttles can be used to improve blood brain barrier transport efficiency. Methods A mouse transferrin receptor binding nanobody, NIH-mTfR-M1, was engineered to confer greater unbinding at pH 5.5 vs 7.4 by introducing multiple histidine mutations. The histidine mutant nanobodies were coupled to neurotensin for in vivo functional blood brain barrier transcytosis testing via central neurotensin-mediated hypothermia in wild-type mice. Multi-nanobody constructs including the mutant M1 R56H, P96H, Y102H and two copies of the P2X7 receptor-binding 13A7 nanobody were produced to test proof-of-concept macromolecular cargo transport in vivo using quantitatively verified capillary depleted brain lysates and in situ histology. Results The most effective histidine mutant, M1 R56H, P96H, Y102H -neurotensin, caused >8°C hypothermia after 25 nmol/kg intravenous injection. Levels of the heterotrimeric construct M1 56,96,102His -13A7-13A7 in capillary depleted brain lysates peaked at 1 hour and were 60% retained at 8 hours. A control construct with no brain targets was only 15% retained at 8 hours. Addition of the albumin-binding Nb80 nanobody to make M1 R56H, P96H, Y102H -13A7-13A7-Nb80 extended blood half-life from 21 minutes to 2.6 hours. At 30-60 minutes, biotinylated M1 R56H, P96H, Y102H -13A7-13A7-Nb80 was visualized in capillaries using in situ histochemistry, whereas at 2-16 hours it was detected in diffuse hippocampal and cortical cellular structures. Levels of M1 R56H, P96H, Y102H -13A7-13A7-Nb80 reached more than 3.5 percent injected dose/gram of brain tissue after 30 nmol/kg intravenous injection. However, higher injected concentrations did not result in higher brain levels, compatible with saturation and an apparent substrate inhibitory effect. Conclusion The pH-sensitive mouse transferrin receptor binding nanobody M1 R56H, P96H, Y102H may be a useful tool for rapid and efficient modular transport of diagnostic and therapeutic macromolecular cargos across the blood brain barrier in mouse models. Additional development will be required to determine whether this nanobody-based shuttle system will be useful for imaging and fast-acting therapeutic applications.
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Affiliation(s)
- Thomas J. Esparza
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, United States of America
| | - Shiran Su
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, United States of America
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, United States of America
| | | | - Elvira Rodionova
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, United States of America
| | - Joong Hee Kim
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, United States of America
| | - David L. Brody
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, United States of America
- Center for Neuroscience and Regenerative Medicine, Bethesda, MD, United States of America
- Department of Neurology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States of America
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Selection of single domain anti-transferrin receptor antibodies for blood-brain barrier transcytosis using a neurotensin based assay and histological assessment of target engagement in a mouse model of Alzheimer's related amyloid-beta pathology. PLoS One 2022; 17:e0276107. [PMID: 36256604 PMCID: PMC9578589 DOI: 10.1371/journal.pone.0276107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 09/29/2022] [Indexed: 11/05/2022] Open
Abstract
The blood-brain barrier (BBB) presents a major obstacle in developing specific diagnostic imaging agents for many neurological disorders. In this study we aimed to generate single domain anti-mouse transferrin receptor antibodies (anti-mTfR VHHs) to mediate BBB transcytosis as components of novel MRI molecular contrast imaging agents. Anti-mTfR VHHs were produced by immunizing a llama with mTfR, generation of a VHH phage display library, immunopanning, and in vitro characterization of candidates. Site directed mutagenesis was used to generate additional variants. VHH fusions with neurotensin (NT) allowed rapid, hypothermia-based screening for VHH-mediated BBB transcytosis in wild-type mice. One anti-mTfR VHH variant was fused with an anti-amyloid-beta (Aβ) VHH dimer and labeled with fluorescent dye for direct assessment of in vivo target engagement in a mouse model of AD-related Aβ plaque pathology. An anti-mTfR VHH called M1 and variants had binding affinities to mTfR of <1nM to 1.52nM. The affinity of the VHH binding to mTfR correlated with the efficiency of the VHH-NT induced hypothermia effects after intravenous injection of 600 nmol/kg body weight, ranging from undetectable for nonbinding mutants to -6°C for the best mutants. The anti-mTfR VHH variant M1P96H with the strongest hypothermia effect was fused to the anti-Aβ VHH dimer and labeled with Alexa647; the dye-labeled VHH fusion construct still bound both mTfR and Aβ plaques at concentrations as low as 0.22 nM. However, after intravenous injection at 600 nmol/kg body weight into APP/PS1 transgenic mice, there was no detectible labeling of plaques above control levels. Thus, NT-induced hypothermia did not correlate with direct target engagement in cortex, likely because the concentration required for NT-induced hypothermia was lower than the concentration required to produce in situ labeling. These findings reveal an important dissociation between NT-induced hypothermia, presumably mediated by hypothalamus, and direct engagement with Aβ-plaques in cortex. Additional methods to assess anti-mTfR VHH BBB transcytosis will need to be developed for anti-mTfR VHH screening and the development of novel MRI molecular contrast agents.
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14
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Watkins JM, Watkins JD. An Engineered Monovalent Anti-TNF-α Antibody with pH-Sensitive Binding Abrogates Immunogenicity in Mice following a Single Intravenous Dose. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:829-839. [PMID: 35896334 PMCID: PMC10580234 DOI: 10.4049/jimmunol.2101180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 06/07/2022] [Indexed: 10/19/2023]
Abstract
Therapeutic Abs directed toward TNF-α display significant immunogenicity in humans, frequently leading to lower serum concentrations of the Ab that are associated with lower treatment efficacy. The enhanced incidence of immunogenicity observed with this class of therapeutics may be mediated by the expression of TNF-α as a homotrimer, both as a soluble serum protein and as a membrane-associated protein (mTNF-α) on the surface of dendritic cells. The TNF-α homotrimer enables the formation of polyvalent Ab-TNF-α immune complexes (ICs) that enhance binding to FcR and neonatal FcR. Polyvalent ICs and Ab bound to mTNF-α on the surface of dendritic cells can internalize, traffic to the lysosomes, and be processed for presentation by MHC molecules. To diminish immunogenicity caused by trafficking of ICs and mTNF-α to the lysosomes, we engineered a monovalent format of adalimumab with pH-sensitive binding to TNF-α. The engineered variant, termed AF-M2637, did not cross-link TNF-α trimers and consequently formed small, nonprecipitating ICs only. AF-M2637 bound TNF-α with high affinity at pH 7.4 (EC50 = 1.1 nM) and displayed a significantly faster dissociation rate than adalimumab at pH 6.0. No immune response to AF-M2637 was detected in mice following a single i.v. dose. In contrast, rapid immunization was detected following the injection of a single i.v. dose of adalimumab, monovalent adalimumab, or the bivalent form of the pH-sensitive variant. These data suggest that ICs and mTNF-α both contribute to the immunogenicity of adalimumab in mice and provide a general strategy for engineering less immunogenic therapeutic TNF-α Abs.
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15
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SpySwitch enables pH- or heat-responsive capture and release for plug-and-display nanoassembly. Nat Commun 2022; 13:3714. [PMID: 35764623 PMCID: PMC9240080 DOI: 10.1038/s41467-022-31193-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 06/07/2022] [Indexed: 11/23/2022] Open
Abstract
Proteins can be empowered via SpyTag for anchoring and nanoassembly, through covalent bonding to SpyCatcher partners. Here we generate a switchable version of SpyCatcher, allowing gentle purification of SpyTagged proteins. We introduce numerous histidines adjacent to SpyTag’s binding site, giving moderate pH-dependent release. After phage-based selection, our final SpySwitch allows purification of SpyTag- and SpyTag003-fusions from bacterial or mammalian culture by capture at neutral pH and release at pH 5, with purity far beyond His-tag methods. SpySwitch is also thermosensitive, capturing at 4 °C and releasing at 37 °C. With flexible choice of eluent, SpySwitch-purified proteins can directly assemble onto multimeric scaffolds. 60-mer multimerization enhances immunogenicity and we use SpySwitch to purify receptor-binding domains from SARS-CoV-2 and 11 other sarbecoviruses. For these receptor-binding domains we determine thermal resilience (for mosaic vaccine development) and cross-recognition by antibodies. Antibody EY6A reacts across all tested sarbecoviruses, towards potential application against new coronavirus pandemic threats. The SpyCatcher-SpyTag system allows protein anchoring and nanoassembly. Here, the authors engineer SpySwitch, a dually switchable Catcher which allows gentle purification of SpyTagged proteins prior to downstream applications such as the assembly of virus-like particles.
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16
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Ledsgaard L, Ljungars A, Rimbault C, Sørensen CV, Tulika T, Wade J, Wouters Y, McCafferty J, Laustsen AH. Advances in antibody phage display technology. Drug Discov Today 2022; 27:2151-2169. [PMID: 35550436 DOI: 10.1016/j.drudis.2022.05.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/24/2022] [Accepted: 05/04/2022] [Indexed: 01/06/2023]
Abstract
Phage display technology can be used for the discovery of antibodies for research, diagnostic, and therapeutic purposes. In this review, we present and discuss key parameters that can be optimized when performing phage display selection campaigns, including the use of different antibody formats and advanced strategies for antigen presentation, such as immobilization, liposomes, nanodiscs, virus-like particles, and whole cells. Furthermore, we provide insights into selection strategies that can be used for the discovery of antibodies with complex binding requirements, such as targeting a specific epitope, cross-reactivity, or pH-dependent binding. Lastly, we provide a description of specialized phage display libraries for the discovery of bispecific antibodies and pH-sensitive antibodies. Together, these methods can be used to improve antibody discovery campaigns against all types of antigen. Teaser: This review provides an overview of the different strategies that can be exploited to improve the success rate of antibody phage display discovery campaigns, addressing key parameters, such as antigen presentation, selection methodologies, and specialized libraries.
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Affiliation(s)
- Line Ledsgaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark.
| | - Anne Ljungars
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Charlotte Rimbault
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Christoffer V Sørensen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Tulika Tulika
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Jack Wade
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Yessica Wouters
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - John McCafferty
- Department of Medicine, Addenbrookes Hospital, Box 157, Hills Road, Cambridge, CB2 0QQ, UK; Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK
| | - Andreas H Laustsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark.
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Lee PS, MacDonald KG, Massi E, Chew PV, Bee C, Perkins P, Chau B, Thudium K, Lohre J, Nandi P, Deyanova EG, Barman I, Gudmundsson O, Dollinger G, Sproul T, Engelhardt JJ, Strop P, Rajpal A. Improved therapeutic index of an acidic pH-selective antibody. MAbs 2022; 14:2024642. [PMID: 35192429 PMCID: PMC8865267 DOI: 10.1080/19420862.2021.2024642] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Although therapeutically efficacious, ipilimumab can exhibit dose-limiting toxicity that prevents maximal efficacious clinical outcomes and can lead to discontinuation of treatment. We hypothesized that an acidic pH-selective ipilimumab (pH Ipi), which preferentially and reversibly targets the acidic tumor microenvironment over the neutral periphery, may have a more favorable therapeutic index. While ipilimumab has pH-independent CTLA-4 affinity, pH Ipi variants have been engineered to have up to 50-fold enhanced affinity to CTLA-4 at pH 6.0 compared to pH 7.4. In hCTLA-4 knock-in mice, these variants have maintained anti-tumor activity and reduced peripheral activation, a surrogate marker for toxicity. pH-sensitive therapeutic antibodies may be a differentiating paradigm and a novel modality for enhanced tumor targeting and improved safety profiles.
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Affiliation(s)
- Peter S Lee
- Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, CA, USA
| | | | - Evan Massi
- Immuno-Oncology Research, Bristol Myers Squibb, Redwood City, CA, USA
| | - Pamela V Chew
- Oncology Biology, Gilead Sciences, Foster City, CA, USA
| | - Christine Bee
- Discovery Biology, Frontier Medicines, South San Francisco, CA, USA
| | - Padma Perkins
- Immuno-Oncology Research, Bristol Myers Squibb, Redwood City, CA, USA
| | - Bryant Chau
- Kyverna, Synthetic Biology, Emeryville, CA, USA
| | - Kent Thudium
- Immuno-Oncology Research, Bristol Myers Squibb, Redwood City, CA, USA
| | - Jack Lohre
- In Vivo Pharmacology, Bristol Myers Squibb, Redwood City, CA, USA
| | - Pradyot Nandi
- Pharmaceutical Candidate Optimization, Bristol Myers Squibb, Lawrenceville, NJ, USA
| | - Ekaterina G Deyanova
- Pharmaceutical Candidate Optimization, Bristol Myers Squibb, Lawrenceville, NJ, USA
| | - Ishita Barman
- Therapeutic Discovery, 3T Biosciences, South San Francisco, CA, USA
| | - Olafur Gudmundsson
- Pharmaceutical Candidate Optimization, Bristol Myers Squibb, Lawrenceville, NJ, USA
| | - Gavin Dollinger
- Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, CA, USA
| | - Tim Sproul
- In Vivo Pharmacology, UNITY Biotechnology, South San Francisco, CA, USA
| | | | - Pavel Strop
- Biologics Discovery, Tallac Therapeutics, Burlingame, CA, USA
| | - Arvind Rajpal
- Large Molecule Drug Discovery, Genentech Research and Early Development, South San Francisco, CA, USA
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Abstract
pH-dependent antigen binding has proven useful in engineering next-generation therapeutics specifically via antibody recycling technology. This technology allows for half-life extension, thereby lowering the amount and frequency of dosing of therapeutics. Cell sorting, coupled with display techniques, has been used extensively for the selection of high-affinity binders. Herein, we describe a cell sorting methodology utilizing yeast surface display for selection of binding proteins with strong binding at physiological pH and weak to no binding at acidic pH. This methodology can be readily applied to engineer proteins and/or antibodies that do not have pH-dependent binding or for selection of de novo pH-dependent binders using library-based methods.
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Affiliation(s)
- Jenna N Meanor
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Albert J Keung
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Balaji M Rao
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
- Golden LEAF Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, NC, USA
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19
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Hori Y, Ohmine K, Katada H, Noguchi Y, Sato K, Nambu T, Adeline LR, Wan GS, Haraya K, Ozeki K, Nanami M, Tachibana T, Sampei Z, Kuramochi T, Nezu J, Hattori K, Igawa T. Elimination of plasma soluble antigen in cynomolgus monkeys by combining pH-dependent antigen binding and novel Fc engineering. MAbs 2022; 14:2068213. [PMID: 35482905 PMCID: PMC9067469 DOI: 10.1080/19420862.2022.2068213] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
A conventional antibody targeting a soluble antigen in circulation typically requires a huge dosage and frequent intravenous administration to neutralize the antigen. This is because antigen degradation is reduced by the formation of antigen–antibody immune complexes, which escape from lysosomal degradation using neonatal Fc receptor (FcRn)-mediated recycling. To address this, we developed an antigen-sweeping antibody that combines pH-dependent antigen binding and Fc engineering to enhance Fc receptor binding. The sweeping antibody actively eliminates the plasma antigens by increasing the cellular uptake of the immune complex and dissociating the antigens in the acidic endosome for degradation. Strong antigen sweeping can reduce the dosage, potentially achieve higher efficacy, and expand the scope of antigen space available for targeting by antibodies. In this study, to further improve the sweeping efficacy, we developed a novel antibody Fc variant by enhancing Fcγ receptor IIb (FcγRIIb) binding and modulating charge characteristics for increased cellular uptake of the immune complex, together with enhancing FcRn binding for efficient salvage of the antigen-free antibodies. Our Fc variant achieved strong antigen sweeping in cynomolgus monkeys with antibody pharmacokinetics comparable to a wild-type human IgG1 antibody. The positive-charge substitutions enhanced uptake of the immune complex by FcγRIIb-expressing cells in vitro, which was completely inhibited by an anti-FcγRIIb antibody. This suggests that the strong in vivo sweeping efficacy improved by the charge engineering is more likely achieved by FcγRIIb-dependent uptake of the immune complex rather than nonspecific uptake. We expect this novel Fc engineering can maximize the antigen sweeping efficacy even in humans and create novel therapeutic antibodies that meet unmet medical needs for patients.
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Affiliation(s)
- Yuji Hori
- Research Division, Chugai Pharmaceutical Co, Ltd, Gotemba, Japan
| | - Ken Ohmine
- Research Division, Chugai Pharmaceutical Co, Ltd, Gotemba, Japan
| | | | - Yuki Noguchi
- Research Division, Chugai Pharmaceutical Co, Ltd, Gotemba, Japan
| | - Kazuki Sato
- Research Division, Chugai Pharmaceutical Co, Ltd, Gotemba, Japan
| | | | | | | | - Kenta Haraya
- Research Division, Chugai Pharmaceutical Co, Ltd, Gotemba, Japan
| | - Kazuhisa Ozeki
- Research Division, Chugai Pharmaceutical Co, Ltd, Gotemba, Japan
| | - Masahiko Nanami
- Research Division, Chugai Pharmaceutical Co, Ltd, Gotemba, Japan
| | | | - Zenjiro Sampei
- Research Division, Chugai Pharmaceutical Co, Ltd, Gotemba, Japan
| | - Taichi Kuramochi
- Research Division, Chugai Pharmaceutical Co, Ltd, Gotemba, Japan
| | - Junichi Nezu
- Research Division, Chugai Pharmaceutical Co, Ltd, Chuo-ku, Tokyo, Japan
| | - Kunihiro Hattori
- Research Division, Chugai Pharmaceutical Co, Ltd, Kamakura, Japan
| | - Tomoyuki Igawa
- Research Division, Chugai Pharmaceutical Co, Ltd, Chuo-ku, Tokyo, Japan
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20
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Lucchi R, Bentanachs J, Oller-Salvia B. The Masking Game: Design of Activatable Antibodies and Mimetics for Selective Therapeutics and Cell Control. ACS CENTRAL SCIENCE 2021; 7:724-738. [PMID: 34079893 PMCID: PMC8161478 DOI: 10.1021/acscentsci.0c01448] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Indexed: 05/04/2023]
Abstract
The high selectivity and affinity of antibody binding have made antibodies all-pervasive tools in therapy, diagnosis, and basic science. A plethora of chemogenetic approaches has been devised to make antibodies responsive to stimuli ranging from light to enzymatic activity, temperature, pH, ions, and effector molecules. Within a single decade, the field of activatable antibodies has yielded marketed therapeutics capable of engaging antigens that could not be targeted with traditional antibodies, as well as new tools to control intracellular protein location and investigate biological processes. Many opportunities remain untapped, waiting for more efficient and generally applicable masking strategies to be developed at the interface between chemistry and biotechnology.
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Affiliation(s)
- Roberta Lucchi
- Grup d’Enginyeria
de Materials, Institut Químic de
Sarrià (IQS), Universitat Ramon Llull, 08017 Barcelona, Spain
| | - Jordi Bentanachs
- Grup d’Enginyeria
de Materials, Institut Químic de
Sarrià (IQS), Universitat Ramon Llull, 08017 Barcelona, Spain
| | - Benjamí Oller-Salvia
- Grup d’Enginyeria
de Materials, Institut Químic de
Sarrià (IQS), Universitat Ramon Llull, 08017 Barcelona, Spain
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21
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Valldorf B, Hinz SC, Russo G, Pekar L, Mohr L, Klemm J, Doerner A, Krah S, Hust M, Zielonka S. Antibody display technologies: selecting the cream of the crop. Biol Chem 2021; 403:455-477. [PMID: 33759431 DOI: 10.1515/hsz-2020-0377] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 03/05/2021] [Indexed: 02/07/2023]
Abstract
Antibody display technologies enable the successful isolation of antigen-specific antibodies with therapeutic potential. The key feature that facilitates the selection of an antibody with prescribed properties is the coupling of the protein variant to its genetic information and is referred to as genotype phenotype coupling. There are several different platform technologies based on prokaryotic organisms as well as strategies employing higher eukaryotes. Among those, phage display is the most established system with more than a dozen of therapeutic antibodies approved for therapy that have been discovered or engineered using this approach. In recent years several other technologies gained a certain level of maturity, most strikingly mammalian display. In this review, we delineate the most important selection systems with respect to antibody generation with an emphasis on recent developments.
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Affiliation(s)
- Bernhard Valldorf
- Chemical and Pharmaceutical Development, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
| | - Steffen C Hinz
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, D-64287Darmstadt, Germany
| | - Giulio Russo
- Abcalis GmbH, Inhoffenstrasse 7, D-38124Braunschweig, Germany.,Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106Braunschweig, Germany
| | - Lukas Pekar
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
| | - Laura Mohr
- Institute of Cell Biology and Neuroscience and Buchmann Institute for Molecular Life Sciences, University of Frankfurt, Max-von-Laue-Strasse 13, D-60438Frankfurt am Main, Germany
| | - Janina Klemm
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, D-64287Darmstadt, Germany
| | - Achim Doerner
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
| | - Simon Krah
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
| | - Michael Hust
- Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106Braunschweig, Germany
| | - Stefan Zielonka
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
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22
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Pedersen ME, Haegebaert RMS, Østergaard J, Jensen H. Size-based characterization of adalimumab and TNF-α interactions using flow induced dispersion analysis: assessment of avidity-stabilized multiple bound species. Sci Rep 2021; 11:4754. [PMID: 33637878 PMCID: PMC7910425 DOI: 10.1038/s41598-021-84113-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 02/10/2021] [Indexed: 12/16/2022] Open
Abstract
The understanding and characterization of protein interactions is crucial for elucidation of complicated biomolecular processes as well as for the development of new biopharmaceutical therapies. Often, protein interactions involve multiple binding, avidity, oligomerization, and are dependent on the local environment. Current analytical methodologies are unable to provide a detailed mechanistic characterization considering all these parameters, since they often rely on surface immobilization, cannot measure under biorelevant conditions, or do not feature a structurally-related readout for indicating formation of multiple bound species. In this work, we report the use of flow induced dispersion analysis (FIDA) for in-solution characterization of complex protein interactions under in vivo like conditions. FIDA is an immobilization-free ligand binding methodology employing Taylor dispersion analysis for measuring the hydrodynamic radius (size) of biomolecular complexes. Here, the FIDA technology is utilized for a size-based characterization of the interaction between TNF-α and adalimumab. We report concentration-dependent complex sizes, binding affinities (Kd), kinetics, and higher order stoichiometries, thus providing essential information on the TNF-α–adalimumab binding mechanism. Furthermore, it is shown that the avidity stabilized complexes involving formation of multiple non-covalent bonds are formed on a longer timescale than the primary complexes formed in a simple 1 to 1 binding event.
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Affiliation(s)
- Morten E Pedersen
- Fida Biosystems ApS, Fruebjergvej 3, 2100, Copenhagen O, Denmark.,Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen O, Denmark
| | - Ragna M S Haegebaert
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen O, Denmark
| | - Jesper Østergaard
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen O, Denmark
| | - Henrik Jensen
- Fida Biosystems ApS, Fruebjergvej 3, 2100, Copenhagen O, Denmark. .,Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen O, Denmark.
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23
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Hong ST, Su YC, Wang YJ, Cheng TL, Wang YT. Anti-TNF Alpha Antibody Humira with pH-dependent Binding Characteristics: A constant-pH Molecular Dynamics, Gaussian Accelerated Molecular Dynamics, and In Vitro Study. Biomolecules 2021; 11:334. [PMID: 33672169 PMCID: PMC7926962 DOI: 10.3390/biom11020334] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/18/2021] [Accepted: 02/20/2021] [Indexed: 12/17/2022] Open
Abstract
Humira is a monoclonal antibody that binds to TNF alpha, inactivates TNF alpha receptors, and inhibits inflammation. Neonatal Fc receptors can mediate the transcytosis of Humira-TNF alpha complex structures and process them toward degradation pathways, which reduces the therapeutic effect of Humira. Allowing the Humira-TNF alpha complex structures to dissociate to Humira and soluble TNF alpha in the early endosome to enable Humira recycling is crucial. We used the cytoplasmic pH (7.4), the early endosomal pH (6.0), and pKa of histidine side chains (6.0-6.4) to mutate the residues of complementarity-determining regions with histidine. Our engineered Humira (W1-Humira) can bind to TNF alpha in plasma at neutral pH and dissociate from the TNF alpha in the endosome at acidic pH. We used the constant-pH molecular dynamics, Gaussian accelerated molecular dynamics, two-dimensional potential mean force profiles, and in vitro methods to investigate the characteristics of W1-Humira. Our results revealed that the proposed Humira can bind TNF alpha with pH-dependent affinity in vitro. The W1-Humira was weaker than wild-type Humira at neutral pH in vitro, and our prediction results were close to the in vitro results. Furthermore, our approach displayed a high accuracy in antibody pH-dependent binding characteristics prediction, which may facilitate antibody drug design. Advancements in computational methods and computing power may further aid in addressing the challenges in antibody drug design.
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Affiliation(s)
- Shih-Ting Hong
- Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan;
| | - Yu-Cheng Su
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsin-Chu 300, Taiwan;
| | - Yu-Jen Wang
- Department of Mechanical and Electromechanical Engineering, National Sun Yat-sen University, Kaohsiung 80424, Taiwan;
| | - Tian-Lu Cheng
- Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan;
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Yeng-Tseng Wang
- Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan;
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- School of Post-Baccalaureate Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 80708, Taiwan
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24
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Sulea T, Rohani N, Baardsnes J, Corbeil CR, Deprez C, Cepero-Donates Y, Robert A, Schrag JD, Parat M, Duchesne M, Jaramillo ML, Purisima EO, Zwaagstra JC. Structure-based engineering of pH-dependent antibody binding for selective targeting of solid-tumor microenvironment. MAbs 2021; 12:1682866. [PMID: 31777319 PMCID: PMC6927761 DOI: 10.1080/19420862.2019.1682866] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Recent development of monoclonal antibodies as mainstream anticancer agents demands further optimization of their safety for use in humans. Potent targeting and/or effector activities on normal tissues is an obvious toxicity concern. Optimization of specific tumor targeting could be achieved by taking advantage of the extracellular acidity of solid tumors relative to normal tissues. Here, we applied a structure-based computational approach to engineer anti-human epidermal growth factor receptor 2 (Her2) antibodies with selective binding in the acidic tumor microenvironment. We used an affinity maturation platform in which dual-pH histidine-scanning mutagenesis was implemented for pH selectivity optimization. Testing of a small set of designs for binding to the recombinant Her2 ectodomain led to the identification of antigen-binding fragment (Fab) variants with the desired pH-dependent binding behavior. Binding selectivity toward acidic pH was improved by as much as 25-fold relative to the parental bH1-Fab. In vitro experiments on cells expressing intact Her2 confirmed that designed variants formatted as IgG1/k full-size antibodies have high affinity and inhibit the growth of tumor spheroids at a level comparable to that of the benchmark anti-Her2 antibody trastuzumab (Herceptin®) at acidic pH, whereas these effects were significantly reduced at physiological pH. In contrast, both Herceptin and the parental bH1 antibody exhibited strong cell binding and growth inhibition irrespective of pH. This work demonstrates the feasibility of computational optimization of antibodies for selective targeting of the acidic environment such as that found in many solid tumors.
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Affiliation(s)
- Traian Sulea
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Nazanin Rohani
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Jason Baardsnes
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Christopher R Corbeil
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Christophe Deprez
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Yuneivy Cepero-Donates
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Alma Robert
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Joseph D Schrag
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Marie Parat
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Mélanie Duchesne
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Maria L Jaramillo
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Enrico O Purisima
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - John C Zwaagstra
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
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25
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van Faassen H, Ryan S, Henry KA, Raphael S, Yang Q, Rossotti MA, Brunette E, Jiang S, Haqqani AS, Sulea T, MacKenzie CR, Tanha J, Hussack G. Serum albumin‐binding V
H
Hs with variable pH sensitivities enable tailored half‐life extension of biologics. FASEB J 2020; 34:8155-8171. [DOI: 10.1096/fj.201903231r] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 02/14/2020] [Accepted: 04/02/2020] [Indexed: 12/22/2022]
Affiliation(s)
- Henk van Faassen
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
| | - Shannon Ryan
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
| | - Kevin A. Henry
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
- Department of Biochemistry, Microbiology & Immunology University of Ottawa Ottawa ON Canada
| | - Shalini Raphael
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
| | - Qingling Yang
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
| | - Martin A. Rossotti
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
| | - Eric Brunette
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
| | - Susan Jiang
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
| | - Arsalan S. Haqqani
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
| | - Traian Sulea
- Human Health Therapeutics Research Centre National Research Council Canada Montréal QC Canada
| | - C. Roger MacKenzie
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
| | - Jamshid Tanha
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
- Department of Biochemistry, Microbiology & Immunology University of Ottawa Ottawa ON Canada
| | - Greg Hussack
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
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26
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Kocikowski M, Dziubek K, Parys M. Hyperprogression Under Immune Checkpoint-Based Immunotherapy-Current Understanding, The Role of PD-1/PD-L1 Tumour-Intrinsic Signalling, Future Directions and a Potential Large Animal Model. Cancers (Basel) 2020; 12:E804. [PMID: 32230745 PMCID: PMC7226013 DOI: 10.3390/cancers12040804] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/22/2020] [Accepted: 03/23/2020] [Indexed: 02/07/2023] Open
Abstract
Immune evasion is a major challenge for the development of successful cancer treatments. One of the known mechanisms is the expression of immune checkpoints (ICs)-proteins regulating the immune cells activation. The advent of immunotherapy using monoclonal antibodies (mAbs) to block the immune checkpoint receptor-ligand interaction brought about a landslide improvement in the treatment responses, leading to a prompt approval of such therapeutics. In recent years, it was discovered that a subset of patients receiving IC blockade treatment experienced a previously unknown pattern of treatment response called hyperprogression (HP), characterised by rapid deterioration on initialisation of the therapy. HP represents an urgent issue for clinicians and drug developers, while posing questions about the adequacy of the current clinical trial process. Here, we briefly summarise the state of knowledge and propose new directions for research into HP mechanisms, focusing on tumour-intrinsic signalling of IC proteins malignantly expressed by cancer. We also discuss the potential role of spontaneously occurring canine cancer in the assessment of immunotherapeutics, which can provide the missing link between murine and human studies.
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Affiliation(s)
- Mikolaj Kocikowski
- International Centre for Cancer Vaccine Science, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (M.K.); (K.D.)
- The Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Katarzyna Dziubek
- International Centre for Cancer Vaccine Science, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (M.K.); (K.D.)
| | - Maciej Parys
- The Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
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27
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Engelen W, Zhu K, Subedi N, Idili A, Ricci F, Tel J, Merkx M. Programmable Bivalent Peptide-DNA Locks for pH-Based Control of Antibody Activity. ACS CENTRAL SCIENCE 2020; 6:22-31. [PMID: 31989023 PMCID: PMC6978833 DOI: 10.1021/acscentsci.9b00964] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Indexed: 05/11/2023]
Abstract
The ability to control antibody activity by pH has important applications in diagnostics, therapeutic antibody targeting, and antibody-guided imaging. Here, we report the rational design of bivalent peptide-DNA ligands that allow pH-dependent control of antibody activity. Our strategy uses a pH-responsive DNA triple helix to control switching from a tight-binding bivalent peptide-DNA lock into a weaker-binding monovalent ligand. Different designs are introduced that allow antibody activation at both basic and acidic pHs, either autonomously or in the presence of an additional oligonucleotide trigger. The pH of antibody activation could be precisely tuned by changing the DNA triple helix sequence. The peptide-DNA locks allowed pH-dependent antibody targeting of tumor cells both in bulk and for single cells confined in water-in-oil microdroplets. The latter approach enables high-throughput antibody-mediated detection of single tumor cells based on their distinctive metabolic activity.
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Affiliation(s)
- Wouter Engelen
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven 5600 MB, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, Eindhoven 5600 MB, The Netherlands
| | - Kwankwan Zhu
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven 5600 MB, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, Eindhoven 5600 MB, The Netherlands
| | - Nikita Subedi
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, Eindhoven 5600 MB, The Netherlands
- Laboratory
of Immunoengineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven 5600 MB, The Netherlands
| | - Andrea Idili
- Dipartimento
di Scienze e Tecnologie Chimiche, University
of Rome, Tor Vergata, Rome 00133, Italy
| | - Francesco Ricci
- Dipartimento
di Scienze e Tecnologie Chimiche, University
of Rome, Tor Vergata, Rome 00133, Italy
| | - Jurjen Tel
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, Eindhoven 5600 MB, The Netherlands
- Laboratory
of Immunoengineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven 5600 MB, The Netherlands
| | - Maarten Merkx
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven 5600 MB, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, Eindhoven 5600 MB, The Netherlands
- E-mail:
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28
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Watanabe H, Yoshida C, Ooishi A, Nakai Y, Ueda M, Isobe Y, Honda S. Histidine-Mediated Intramolecular Electrostatic Repulsion for Controlling pH-Dependent Protein-Protein Interaction. ACS Chem Biol 2019; 14:2729-2736. [PMID: 31596562 DOI: 10.1021/acschembio.9b00652] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein-protein interactions that can be controlled by environmental triggers have immense potential in various biological and industrial applications. In the current study, we aimed to engineer a pH-dependent protein-protein interaction that employs intramolecular electrostatic repulsion through a structure-guided histidine substitution approach. We implemented this strategy on Streptococcal protein G, an affinity ligand for immunoglobulin G, and showed that even a single point mutation effectively improved the pH sensitivity of the binding interactions without adversely affecting its structural stability or its innate binding function. Depending on the pH of the environment, the protein-protein interaction was disrupted by the electrostatic repulsion between the substituted histidine and its neighboring positively charged residues. Structurally, the substituted histidine residue was located adjacent to a lysine residue that could form hydrogen bonds with immunoglobulin G. Thermodynamically, the introduced electrostatic repulsion was reflected in the significant loss of the exothermic heat of the binding under acidic conditions, whereas accompanying enthalpy-entropy compensation partly suppressed the improvement of the pH sensitivity. Thus, the engineered pH-sensitive protein G could enable antibody purification under mildly acidic conditions. This intramolecular design can be combined with conventional protein-protein interface design. Moreover, the method proposed here provides us with additional design criteria for optimization of pH-dependent molecular interactions.
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Affiliation(s)
- Hideki Watanabe
- The National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba 305-8566, Japan
| | - Chuya Yoshida
- The National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba 305-8566, Japan
| | - Ayako Ooishi
- The National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba 305-8566, Japan
| | - Yasuto Nakai
- Daicel Corporation, Innovation Park, 1239, Shinzaike, Aboshi, Himeji, Hyogo 671-1283, Japan
| | - Momoko Ueda
- Daicel Corporation, Innovation Park, 1239, Shinzaike, Aboshi, Himeji, Hyogo 671-1283, Japan
| | - Yutaka Isobe
- Daicel Corporation, Innovation Park, 1239, Shinzaike, Aboshi, Himeji, Hyogo 671-1283, Japan
| | - Shinya Honda
- The National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba 305-8566, Japan
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29
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Jorgolli M, Nevill T, Winters A, Chen I, Chong S, Lin F, Mock M, Chen C, Le K, Tan C, Jess P, Xu H, Hamburger A, Stevens J, Munro T, Wu M, Tagari P, Miranda LP. Nanoscale integration of single cell biologics discovery processes using optofluidic manipulation and monitoring. Biotechnol Bioeng 2019; 116:2393-2411. [PMID: 31112285 PMCID: PMC6771990 DOI: 10.1002/bit.27024] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 05/16/2019] [Accepted: 05/16/2019] [Indexed: 12/12/2022]
Abstract
The new and rapid advancement in the complexity of biologics drug discovery has been driven by a deeper understanding of biological systems combined with innovative new therapeutic modalities, paving the way to breakthrough therapies for previously intractable diseases. These exciting times in biomedical innovation require the development of novel technologies to facilitate the sophisticated, multifaceted, high-paced workflows necessary to support modern large molecule drug discovery. A high-level aspiration is a true integration of "lab-on-a-chip" methods that vastly miniaturize cellulmical experiments could transform the speed, cost, and success of multiple workstreams in biologics development. Several microscale bioprocess technologies have been established that incrementally address these needs, yet each is inflexibly designed for a very specific process thus limiting an integrated holistic application. A more fully integrated nanoscale approach that incorporates manipulation, culture, analytics, and traceable digital record keeping of thousands of single cells in a relevant nanoenvironment would be a transformative technology capable of keeping pace with today's rapid and complex drug discovery demands. The recent advent of optical manipulation of cells using light-induced electrokinetics with micro- and nanoscale cell culture is poised to revolutionize both fundamental and applied biological research. In this review, we summarize the current state of the art for optical manipulation techniques and discuss emerging biological applications of this technology. In particular, we focus on promising prospects for drug discovery workflows, including antibody discovery, bioassay development, antibody engineering, and cell line development, which are enabled by the automation and industrialization of an integrated optoelectronic single-cell manipulation and culture platform. Continued development of such platforms will be well positioned to overcome many of the challenges currently associated with fragmented, low-throughput bioprocess workflows in biopharma and life science research.
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Affiliation(s)
| | - Tanner Nevill
- Product ApplicationsBerkeley Lights, IncEmeryvilleCalifornia
| | - Aaron Winters
- Amgen ResearchOne Amgen Center DriveThousand OaksCalifornia
| | - Irwin Chen
- Amgen ResearchOne Amgen Center DriveThousand OaksCalifornia
| | - Su Chong
- Amgen ResearchOne Amgen Center DriveThousand OaksCalifornia
| | - Fen‐Fen Lin
- Amgen ResearchOne Amgen Center DriveThousand OaksCalifornia
| | - Marissa Mock
- Amgen ResearchOne Amgen Center DriveThousand OaksCalifornia
| | - Ching Chen
- Amgen ResearchOne Amgen Center DriveThousand OaksCalifornia
| | - Kim Le
- Drug Substance Technologies, One Amgen Center DriveThousand OaksCalifornia
| | - Christopher Tan
- Drug Substance Technologies, One Amgen Center DriveThousand OaksCalifornia
| | - Philip Jess
- Product ApplicationsBerkeley Lights, IncEmeryvilleCalifornia
| | - Han Xu
- Drug DiscoveryA2 BiotherapeuticsWestlake VillageCalifornia
| | - Agi Hamburger
- Drug DiscoveryA2 BiotherapeuticsWestlake VillageCalifornia
| | - Jennitte Stevens
- Drug Substance Technologies, One Amgen Center DriveThousand OaksCalifornia
| | - Trent Munro
- Drug Substance Technologies, One Amgen Center DriveThousand OaksCalifornia
| | - Ming Wu
- Department of Electrical Engineering and Computer SciencesUniversity of California at BerkeleyBerkeleyCalifornia
| | - Philip Tagari
- Amgen ResearchOne Amgen Center DriveThousand OaksCalifornia
| | - Les P. Miranda
- Amgen ResearchOne Amgen Center DriveThousand OaksCalifornia
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30
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Bogen JP, Hinz SC, Grzeschik J, Ebenig A, Krah S, Zielonka S, Kolmar H. Dual Function pH Responsive Bispecific Antibodies for Tumor Targeting and Antigen Depletion in Plasma. Front Immunol 2019; 10:1892. [PMID: 31447859 PMCID: PMC6697062 DOI: 10.3389/fimmu.2019.01892] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 07/26/2019] [Indexed: 01/08/2023] Open
Abstract
Shedding of membrane-bound cell surface proteins, where the extracellular domain is released and found in the circulation is a common phenomenon. A prominent example is CEACAM5 (CEA, CD66e), where the shed domain plays a pivotal role in tumor progression and metastasis. For treatment of solid tumors, the presence of the tumor-specific antigen in the plasma can be problematic since tumor-specific antibodies might be intercepted by the soluble antigen before invading their desired tumor target area. To overcome this problem, we developed a generic procedure to generate bispecific antibodies, where one arm binds the antigen in a pH-dependent manner thereby enhancing antigen clearance upon endosomal uptake, while the other arm is able to target tumor cells pH-independently. This was achieved by incorporating pH-sensitive binding modalities in the common light chain IGKV3-15*01 of a CEACAM5 binding heavy chain only antibody. Screening of a histidine-doped light chain library using yeast surface display enabled the isolation of pH-dependent binders. When such a light chain was utilized as a common light chain in a bispecific antibody format, only the respective heavy/light chain combination, identified during selections, displayed pH-responsive binding. In addition, we found that the altered common light chain does not negatively impact the affinity of other heavy chain only binders toward their respective antigen. Our strategy may open new avenues for the generation of bispecifics, where one arm efficiently removes a shed antigen from the circulation while the other arm targets a tumor marker in a pH-independent manner.
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Affiliation(s)
- Jan P Bogen
- Department of Applied Biochemistry, Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Steffen C Hinz
- Department of Applied Biochemistry, Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Julius Grzeschik
- Department of Applied Biochemistry, Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Aileen Ebenig
- Department of Applied Biochemistry, Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Simon Krah
- Protein Engineering and Antibody Technologies, Merck KGaA, Darmstadt, Germany
| | - Stefan Zielonka
- Protein Engineering and Antibody Technologies, Merck KGaA, Darmstadt, Germany
| | - Harald Kolmar
- Department of Applied Biochemistry, Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
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31
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Application of interpretable artificial neural networks to early monoclonal antibodies development. Eur J Pharm Biopharm 2019; 141:81-89. [DOI: 10.1016/j.ejpb.2019.05.017] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/17/2019] [Accepted: 05/17/2019] [Indexed: 11/20/2022]
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32
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Computer-assembled cross-species/cross-modalities two-pore physiologically based pharmacokinetic model for biologics in mice and rats. J Pharmacokinet Pharmacodyn 2019; 46:339-359. [PMID: 31079322 DOI: 10.1007/s10928-019-09640-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 05/05/2019] [Indexed: 12/11/2022]
Abstract
Two-pore physiologically-based pharmacokinetic (PBPK) models can be expected to describe the tissue distribution and elimination kinetics of soluble proteins, endogenous or dosed, as function of their size. In this work, we amalgamated our previous two-pore PBPK model for an inert domain antibody (dAb) in mice with the cross-species platform PBPK model for monoclonal antibodies described in literature into a unified two-pore platform that describes protein modalities of different sizes and includes neonatal Fc receptor (FcRn) mediated recycling. This unified PBPK model was parametrized for organ-specific lymph flow rates and the endosomal recycling rate constant using an extended tissue distribution time-course dataset that included an inert dAb, albumin and IgG in rats and mice. The model was evaluated by comparing the ab initio predictions for the tissue distribution and elimination properties of albumin-binding dAbs (AlbudAbsTM) in mice and rats with the experimental observations. Due to the large number of molecular species and reactions involved in large-scale PBPK models, we have also developed and deployed a MatlabTM script for automating the assembly of SimBiologyTM-based two-pore biologics PBPK models which drastically cuts the time and effort required for model building.
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Sampei Z, Haraya K, Tachibana T, Fukuzawa T, Shida-Kawazoe M, Gan SW, Shimizu Y, Ruike Y, Feng S, Kuramochi T, Muraoka M, Kitazawa T, Kawabe Y, Igawa T, Hattori K, Nezu J. Antibody engineering to generate SKY59, a long-acting anti-C5 recycling antibody. PLoS One 2018; 13:e0209509. [PMID: 30592762 PMCID: PMC6310256 DOI: 10.1371/journal.pone.0209509] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 12/06/2018] [Indexed: 01/08/2023] Open
Abstract
Modulating the complement system is a promising strategy in drug discovery for disorders with uncontrolled complement activation. Although some of these disorders can be effectively treated with an antibody that inhibits complement C5, the high plasma concentration of C5 requires a huge dosage and frequent intravenous administration. Moreover, a conventional anti-C5 antibody can cause C5 to accumulate in plasma by reducing C5 clearance when C5 forms an immune complex (IC) with the antibody, which can be salvaged from endosomal vesicles by neonatal Fc receptor (FcRn)-mediated recycling. In order to neutralize the increased C5, an even higher dosage of the antibody would be required. This antigen accumulation can be suppressed by giving the antibody a pH-dependent C5-binding property so that C5 is released from the antibody in the acidic endosome and then trafficked to the lysosome for degradation, while the C5-free antibody returns back to plasma. We recently demonstrated that a pH-dependent C5-binding antibody, SKY59, exhibited long-lasting neutralization of C5 in cynomolgus monkeys, showing potential for subcutaneous delivery or less frequent administration. Here we report the details of the antibody engineering involved in generating SKY59, from humanizing a rabbit antibody to improving the C5-binding property. Moreover, because the pH-dependent C5-binding antibodies that we first generated still accumulated C5, we hypothesized that the surface charges of the ICs partially contributed to a slow uptake rate of the C5–antibody ICs. This idea motivated us to engineer the surface charges of the antibody. Our surface-charge engineered antibody consequently exhibited a high capacity to sweep C5 and suppressed the C5 accumulation in vivo by accelerating the cycle of sweeping: uptake of ICs into cells, release of C5 from the antibody in endosomes, and salvage of the antigen-free antibody. Thus, our engineered anti-C5 antibody, SKY59, is expected to provide significant benefits for patients with complement-mediated disorders.
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Affiliation(s)
- Zenjiro Sampei
- Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
- * E-mail:
| | - Kenta Haraya
- Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Tatsuhiko Tachibana
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa, Japan
| | - Taku Fukuzawa
- Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Meiri Shida-Kawazoe
- Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Siok Wan Gan
- Chugai Pharmabody Research Pte. Ltd., Singapore, Singapore
| | | | - Yoshinao Ruike
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa, Japan
| | - Shu Feng
- Chugai Pharmabody Research Pte. Ltd., Singapore, Singapore
| | | | - Masaru Muraoka
- Chugai Pharmabody Research Pte. Ltd., Singapore, Singapore
| | - Takehisa Kitazawa
- Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Yoshiki Kawabe
- Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Tomoyuki Igawa
- Chugai Pharmabody Research Pte. Ltd., Singapore, Singapore
| | - Kunihiro Hattori
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa, Japan
| | - Junichi Nezu
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa, Japan
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Xu Y, Wang D, Mason B, Rossomando T, Li N, Liu D, Cheung JK, Xu W, Raghava S, Katiyar A, Nowak C, Xiang T, Dong DD, Sun J, Beck A, Liu H. Structure, heterogeneity and developability assessment of therapeutic antibodies. MAbs 2018; 11:239-264. [PMID: 30543482 DOI: 10.1080/19420862.2018.1553476] [Citation(s) in RCA: 155] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Increasing attention has been paid to developability assessment with the understanding that thorough evaluation of monoclonal antibody lead candidates at an early stage can avoid delays during late-stage development. The concept of developability is based on the knowledge gained from the successful development of approximately 80 marketed antibody and Fc-fusion protein drug products and from the lessons learned from many failed development programs over the last three decades. Here, we reviewed antibody quality attributes that are critical to development and traditional and state-of-the-art analytical methods to monitor those attributes. Based on our collective experiences, a practical workflow is proposed as a best practice for developability assessment including in silico evaluation, extended characterization and forced degradation using appropriate analytical methods that allow characterization with limited material consumption and fast turnaround time.
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Affiliation(s)
- Yingda Xu
- a Protein Analytics , Adimab , Lebanon , NH , USA
| | - Dongdong Wang
- b Analytical Department , Bioanalytix, Inc ., Cambridge , MA , USA
| | - Bruce Mason
- c Product Characterization , Alexion Pharmaceuticals, Inc ., New Haven , CT , USA
| | - Tony Rossomando
- c Product Characterization , Alexion Pharmaceuticals, Inc ., New Haven , CT , USA
| | - Ning Li
- d Analytical Chemistry , Regeneron Pharmaceuticals, Inc ., Tarrytown , NY , USA
| | - Dingjiang Liu
- e Formulation Development , Regeneron Pharmaceuticals, Inc ., Tarrytown , NY , USA
| | - Jason K Cheung
- f Pharmaceutical Sciences , MRL, Merck & Co., Inc ., Kenilworth , NJ , USA
| | - Wei Xu
- g Analytical Method Development , MRL, Merck & Co., Inc ., Kenilworth , NJ , USA
| | - Smita Raghava
- h Sterile Formulation Sciences , MRL, Merck & Co., Inc ., Kenilworth , NJ , USA
| | - Amit Katiyar
- i Analytical Development , Bristol-Myers Squibb , Pennington , NJ , USA
| | - Christine Nowak
- c Product Characterization , Alexion Pharmaceuticals, Inc ., New Haven , CT , USA
| | - Tao Xiang
- j Manufacturing Sciences , Abbvie Bioresearch Center , Worcester , MA , USA
| | - Diane D Dong
- j Manufacturing Sciences , Abbvie Bioresearch Center , Worcester , MA , USA
| | - Joanne Sun
- k Product development , Innovent Biologics , Suzhou Industrial Park , China
| | - Alain Beck
- l Analytical chemistry , NBEs, Center d'immunologie Pierre Fabre , St Julien-en-Genevois Cedex , France
| | - Hongcheng Liu
- c Product Characterization , Alexion Pharmaceuticals, Inc ., New Haven , CT , USA
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35
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Kroetsch A, Qiao C, Heavey M, Guo L, Shah DK, Park S. Engineered pH-dependent recycling antibodies enhance elimination of Staphylococcal enterotoxin B superantigen in mice. MAbs 2018; 11:411-421. [PMID: 30526311 DOI: 10.1080/19420862.2018.1545510] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
A new modality in antibody engineering has emerged in which the antigen affinity is designed to be pH dependent (PHD). In particular, combining high affinity binding at neutral pH with low affinity binding at acidic pH leads to a novel antibody that can more effectively neutralize the target antigen while avoiding antibody-mediated antigen accumulation. Here, we studied how the in vivo pharmacokinetics of the superantigen, Staphylococcal enterotoxin B (SEB), is affected by an engineered antibody with pH-dependent binding. PHD anti-SEB antibodies were engineered by introducing mutations into a high affinity anti-SEB antibody, 3E2, by rational design and directed evolution. Three antibody mutants engineered in the study have an affinity at pH 6.0 that is up to 68-fold weaker than the control antibody. The pH dependency of each mutant, measured as the pH-dependent affinity ratio (PAR - ratio of affinity at pH 7.4 and pH 6.0), ranged from 6.7-11.5 compared to 1.5 for the control antibody. The antibodies were characterized in mice by measuring their effects on the pharmacodynamics and pharmacokinetics (PK) of SEB after co-administration. All antibodies were effective in neutralizing the toxin and reducing the toxin-induced cytokine production. However, engineered PHD antibodies led to significantly faster elimination of the toxin from the circulation than wild type 3E2. The area under the curve computed from the SEB PK profile correlated well with the PAR value of antibody, indicating the importance of fine tuning the pH dependency of binding. These results suggest that a PHD recycling antibody may be useful to treat intoxication from a bacterial toxin by accelerating its clearance.
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Affiliation(s)
- Andrew Kroetsch
- a Department of Chemical and Biological Engineering , University at Buffalo , Buffalo , New York , USA
| | - Chunxia Qiao
- b Department of Pharmaceutical Sciences , University at Buffalo , Buffalo , New York , USA
| | - Mairead Heavey
- b Department of Pharmaceutical Sciences , University at Buffalo , Buffalo , New York , USA
| | - Leiming Guo
- b Department of Pharmaceutical Sciences , University at Buffalo , Buffalo , New York , USA
| | - Dhaval K Shah
- b Department of Pharmaceutical Sciences , University at Buffalo , Buffalo , New York , USA
| | - Sheldon Park
- a Department of Chemical and Biological Engineering , University at Buffalo , Buffalo , New York , USA
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36
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Roth L, Grzeschik J, Hinz SC, Becker S, Toleikis L, Busch M, Kolmar H, Krah S, Zielonka S. Facile generation of antibody heavy and light chain diversities for yeast surface display by Golden Gate Cloning. Biol Chem 2018; 400:383-393. [DOI: 10.1515/hsz-2018-0347] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 11/11/2018] [Indexed: 01/03/2023]
Abstract
Abstract
Antibodies can be successfully engineered and isolated by yeast or phage display of combinatorial libraries. Still, generation of libraries comprising heavy chain as well as light chain diversities is a cumbersome process involving multiple steps. Within this study, we set out to compare the output of yeast display screening of antibody Fab libraries from immunized rodents that were generated by Golden Gate Cloning (GGC) with the conventional three-step method of individual heavy- and light-chain sub-library construction followed by chain combination via yeast mating (YM). We demonstrate that the GGC-based one-step process delivers libraries and antibodies from heavy- and light-chain diversities with similar quality to the traditional method while being significantly less complex and faster. Additionally, we show that this method can also be used to successfully screen and isolate chimeric chicken/human antibodies following avian immunization.
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Affiliation(s)
- Lukas Roth
- Institute for Organic Chemistry and Biochemistry , Technische Universität Darmstadt , Alarich-Weiss-Strasse 4 , D-64287 Darmstadt , Germany
| | - Julius Grzeschik
- Institute for Organic Chemistry and Biochemistry , Technische Universität Darmstadt , Alarich-Weiss-Strasse 4 , D-64287 Darmstadt , Germany
| | - Steffen C. Hinz
- Institute for Organic Chemistry and Biochemistry , Technische Universität Darmstadt , Alarich-Weiss-Strasse 4 , D-64287 Darmstadt , Germany
| | - Stefan Becker
- Protein Engineering and Antibody Technologies, Merck KGaA , Frankfurter Strasse 250 , D-64293 Darmstadt , Germany
| | - Lars Toleikis
- Protein Engineering and Antibody Technologies, Merck KGaA , Frankfurter Strasse 250 , D-64293 Darmstadt , Germany
| | - Michael Busch
- Discovery Pharmacology, Merck KGaA , Frankfurter Strasse 250 , D-64293 Darmstadt , Germany
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry , Technische Universität Darmstadt , Alarich-Weiss-Strasse 4 , D-64287 Darmstadt , Germany
| | - Simon Krah
- Protein Engineering and Antibody Technologies, Merck KGaA , Frankfurter Strasse 250 , D-64293 Darmstadt , Germany
| | - Stefan Zielonka
- Protein Engineering and Antibody Technologies, Merck KGaA , Frankfurter Strasse 250 , D-64293 Darmstadt , Germany
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37
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Schröter C, Beck J, Krah S, Zielonka S, Doerner A, Rhiel L, Günther R, Toleikis L, Kolmar H, Hock B, Becker S. Selection of Antibodies with Tailored Properties by Application of High-Throughput Multiparameter Fluorescence-Activated Cell Sorting of Yeast-Displayed Immune Libraries. Mol Biotechnol 2018; 60:727-735. [PMID: 30076531 PMCID: PMC6132741 DOI: 10.1007/s12033-018-0109-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
In this study, we present a multiparameter screening procedure for the identification of target-specific antibodies with prescribed properties. Based on B cell receptor gene repertoires from transgenic rats, yeast surface display libraries were generated, and high-affinity human antibodies were readily isolated. We demonstrate that specific desirable features, i.e., species' cross-reactivity and a broad epitope coverage can be integrated into the screening procedure using high-throughput fluorescence-activated cell sorting. We show that the applied screening stringencies translate directly into binding properties of isolated human antibody variants.
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Affiliation(s)
- Christian Schröter
- Antibody Drug Conjugates and Targeted NBE Therapeutics, Merck KGaA, Frankfurter Strasse 250, 64293, Darmstadt, Germany
| | - Jan Beck
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, 64287, Darmstadt, Germany.,Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, 64293, Darmstadt, Germany
| | - Simon Krah
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, 64293, Darmstadt, Germany
| | - Stefan Zielonka
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, 64293, Darmstadt, Germany
| | - Achim Doerner
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, 64293, Darmstadt, Germany
| | - Laura Rhiel
- Antibody Drug Conjugates and Targeted NBE Therapeutics, Merck KGaA, Frankfurter Strasse 250, 64293, Darmstadt, Germany
| | - Ralf Günther
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, 64293, Darmstadt, Germany
| | - Lars Toleikis
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, 64293, Darmstadt, Germany
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, 64287, Darmstadt, Germany
| | - Björn Hock
- Antibody Drug Conjugates and Targeted NBE Therapeutics, Merck KGaA, Frankfurter Strasse 250, 64293, Darmstadt, Germany
| | - Stefan Becker
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, 64293, Darmstadt, Germany.
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38
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Improvement of pharmacokinetic properties of therapeutic antibodies by antibody engineering. Drug Metab Pharmacokinet 2018; 34:25-41. [PMID: 30472066 DOI: 10.1016/j.dmpk.2018.10.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 09/13/2018] [Accepted: 10/23/2018] [Indexed: 01/17/2023]
Abstract
Monoclonal antibodies (mAbs) have become an important therapeutic option for several diseases. Since several mAbs have shown promising efficacy in clinic, the competition to develop mAbs has become severe. In efforts to gain a competitive advantage over other mAbs and provide significant benefits to patients, innovations in antibody engineering have aimed at improving the pharmacokinetic properties of mAbs. Because engineering can provide therapeutics that are more convenient, safer, and more efficacious for patients in several disease areas, it is an attractive approach to provide significant benefits to patients. Further advances in engineering mAbs to modulate their pharmacokinetics were driven by the increase of total soluble target antigen concentration that is often observed after injecting a mAb, which then requires a high dosage to antagonize. To decrease the required dosage, several antibody engineering techniques have been invented that reduce the total concentration of soluble target antigen. Here, we review the various ways that antibody engineering can improve the pharmacokinetic properties of mAbs.
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39
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Next-generation flexible formats of VNAR domains expand the drug platform's utility and developability. Biochem Soc Trans 2018; 46:1559-1565. [PMID: 30381336 DOI: 10.1042/bst20180177] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 08/22/2018] [Accepted: 09/10/2018] [Indexed: 02/06/2023]
Abstract
Therapeutic mAbs have delivered several blockbuster drugs in oncology and autoimmune inflammatory disease. Revenue for mAbs continues to rise, even in the face of competition from a growing portfolio of biosimilars. Despite this success, there are still limitations associated with the use of mAbs as therapeutic molecules. With a molecular mass of 150 kDa, a two-chain structure and complex glycosylation these challenges include a high cost of goods, limited delivery options, and poor solid tumour penetration. There remains an urgency to create alternatives to antibody scaffolds in a bid to circumvent these limitations, while maintaining or improving the therapeutic success of conventional mAb formats. Smaller, less complex binders, with increased domain valency, multi-specific/paratopic targeting, tuneable serum half-life and low inherent immunogenicity are a few of the characteristics being explored by the next generation of biologic molecules. One novel 'antibody-like' binder that has naturally evolved over 450 million years is the variable new antigen receptor (VNAR) identified as a key component of the adaptive immune system of sharks. At only 11 kDa, these single-domain structures are the smallest IgG-like proteins in the animal kingdom and provide an excellent platform for molecular engineering and biologics drug discovery. VNAR attributes include high affinity for target, ease of expression, stability, solubility, multi-specificity, and increased potential for solid tissue penetration. This review article documents the recent drug developmental milestones achieved for therapeutic VNARs and highlights the first reported evidence of the efficacy of these domains in clinically relevant models of disease.
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40
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Isolation of pH-Sensitive Antibody Fragments by Fluorescence-Activated Cell Sorting and Yeast Surface Display. Methods Mol Biol 2018; 1685:311-331. [PMID: 29086318 DOI: 10.1007/978-1-4939-7366-8_19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Fluorescence-activated cell sorting (FACS) in combination with yeast surface display (YSD) has proven to be a valuable tool for the engineering of antibodies. It enables the fast and robust identification and isolation of candidates with prescribed characteristics from combinatorial libraries. A novel application for FACS and YSD that has recently evolved addresses the engineering of antibodies toward pH-switchable antigen binding, aiming at reduced binding at acidic pH, compared to neutral pH. Therefore, we give guidance for the incorporation of such pH switches into antibody variable domains using combinatorial histidine scanning libraries. The protocol describes a flow cytometric sorting technique for the enrichment of antigen-specific molecules. Moreover, we provide information on how to screen the obtained antibody pools from initial sorting to isolate and characterize pH-sensitive variants.
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41
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Sivelle C, Sierocki R, Ferreira-Pinto K, Simon S, Maillere B, Nozach H. Fab is the most efficient format to express functional antibodies by yeast surface display. MAbs 2018; 10:720-729. [PMID: 29708852 DOI: 10.1080/19420862.2018.1468952] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Multiple formats are available for engineering of monoclonal antibodies (mAbs) by yeast surface display, but they do not all lead to efficient expression of functional molecules. We therefore expressed four anti-tumor necrosis factor and two anti-IpaD mAbs as single-chain variable fragment (scFv), antigen-binding fragment (Fab) or single-chain Fabs and compared their expression levels and antigen-binding efficiency. Although the scFv and scFab formats are widely used in the literature, 2 of 6 antibodies were either not or weakly expressed. In contrast, all 6 antibodies expressed as Fab revealed strong binding and high affinity, comparable to that of the soluble form. We also demonstrated that the variations in expression did not affect Fab functionality and were due to variations in light chain display and not to misfolded dimers. Our results suggest that Fab is the most versatile format for the engineering of mAbs.
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Affiliation(s)
- Coline Sivelle
- a Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), CEA, Université Paris-Saclay , Gif/Yvette , France
| | - Raphaël Sierocki
- a Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), CEA, Université Paris-Saclay , Gif/Yvette , France
| | - Kelly Ferreira-Pinto
- a Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), CEA, Université Paris-Saclay , Gif/Yvette , France
| | - Stéphanie Simon
- b Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, Laboratoire d'Etudes et de Recherches en Immunoanalyse, Université Paris-Saclay , Gif/Yvette , France
| | - Bernard Maillere
- a Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), CEA, Université Paris-Saclay , Gif/Yvette , France
| | - Hervé Nozach
- a Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), CEA, Université Paris-Saclay , Gif/Yvette , France
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42
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Ngambenjawong C, Sylvestre M, Gustafson HH, Pineda JMB, Pun SH. Reversibly Switchable, pH-Dependent Peptide Ligand Binding via 3,5-Diiodotyrosine Substitutions. ACS Chem Biol 2018; 13:995-1002. [PMID: 29481044 DOI: 10.1021/acschembio.8b00171] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cell type-specific targeting ligands utilized in drug delivery applications typically recognize receptors that are overexpressed on the cells of interest. Nonetheless, these receptors may also be expressed, to varying extents, on off-target cells, contributing to unintended side effects. For the selectivity profile of targeting ligands in cancer therapy to be improved, stimuli-responsive masking of these ligands with acid-, redox-, or enzyme-cleavable molecules has been reported, whereby the targeting ligands are exposed in specific environments, e.g., acidic tumor hypoxia. One possible drawback of these systems lies in their one-time, permanent trigger, which enables the "demasked" ligands to bind off-target cells if released back into the systemic circulation. A promising strategy to address the aforementioned problem is to design ligands that show selective binding based on ionization state, which may be microenvironment-dependent. In this study, we report a systematic strategy to engineer low pH-selective targeting peptides using an M2 macrophage-targeting peptide (M2pep) as an example. 3,5-Diiodotyrosine mutagenesis into native tyrosine residues of M2pep confers pH-dependent binding behavior specific to acidic environment (pH 6) when the amino acid is protonated into the native tyrosine-like state. At physiological pH of 7.4, the hydroxyl group of 3,5-diiodotyrosine on the peptide is deprotonated leading to interruption of the peptide native binding property. Our engineered pH-responsive M2pep (Ac-Y-Î-Î) binds target M2 macrophages more selectively at pH 6 than at pH 7.4. In addition, 3,5-diiodotyrosine substitutions also improve serum stability of the peptide. Finally, we demonstrate pH-dependent reversibility in target binding via a postbinding peptide elution study. The strategy presented here should be applicable for engineering pH-dependent functionality of other targeting peptides with potential applications in physiology-dependent in vivo targeting applications (e.g., targeting hypoxic tumor/inflammation) or in in vitro receptor identification.
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Affiliation(s)
- Chayanon Ngambenjawong
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington 98195, United States
| | - Meilyn Sylvestre
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington 98195, United States
| | - Heather H. Gustafson
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington 98195, United States
| | - Julio Marco B. Pineda
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington 98195, United States
| | - Suzie H. Pun
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington 98195, United States
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43
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Könning D, Kolmar H. Beyond antibody engineering: directed evolution of alternative binding scaffolds and enzymes using yeast surface display. Microb Cell Fact 2018; 17:32. [PMID: 29482656 PMCID: PMC6389260 DOI: 10.1186/s12934-018-0881-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 02/22/2018] [Indexed: 01/08/2023] Open
Abstract
Pioneered exactly 20 years ago, yeast surface display (YSD) continues to take a major role in protein engineering among the high-throughput display methodologies that have been developed to date. The classical yeast display technology relies on tethering an engineered protein to the cell wall by genetic fusion to one subunit of a dimeric yeast-mating agglutination receptor complex. This method enables an efficient genotype–phenotype linkage while exploiting the benefits of a eukaryotic expression machinery. Over the past two decades, a plethora of protein engineering efforts encompassing conventional antibody Fab and scFv fragments have been reported. In this review, we will focus on the versatility of YSD beyond conventional antibody engineering and, instead, place the focus on alternative scaffold proteins and enzymes which have successfully been tailored for purpose with regard to improving binding, activity or specificity.
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Affiliation(s)
- Doreen Könning
- Antibody-Drug Conjugates and Targeted NBE Therapeutics, Merck KGaA, Frankfurter Strasse 250, 64293, Darmstadt, Germany.,Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, 64287, Darmstadt, Germany
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, 64287, Darmstadt, Germany.
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44
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Rosowski S, Becker S, Toleikis L, Valldorf B, Grzeschik J, Demir D, Willenbücher I, Gaa R, Kolmar H, Zielonka S, Krah S. A novel one-step approach for the construction of yeast surface display Fab antibody libraries. Microb Cell Fact 2018; 17:3. [PMID: 29316915 PMCID: PMC5759264 DOI: 10.1186/s12934-017-0853-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 12/20/2017] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Yeast surface display (YSD) has proven to be a versatile platform technology for antibody discovery. However, the construction of antibody Fab libraries typically is a tedious three-step process that involves the generation of heavy chain as well as light chain display plasmids in different haploid yeast strains followed by yeast mating. RESULTS Within this study, we aimed at implementing a focused Golden Gate Cloning approach for the generation of YSD libraries. For this, antibodies heavy and light chains were encoded on one single plasmid. Fab display on yeast cells was either mediated by a two-directional promoter system (2dir) or by ribosomal skipping (bicis). The general applicability of this methodology was proven by the functional display of a therapeutic antibody. Subsequently, we constructed large antibody libraries with heavy chain diversities derived from CEACAM5 immunized animals in combination with a common light chain. Target-specific antibodies from both display systems were readily obtained after three rounds of fluorescence activated cell sorting. Isolated variants exhibited high affinities in the nanomolar and subnanomolar range as well as appropriate biophysical properties. CONCLUSION We demonstrated that Golden Gate Cloning appears to be a valid tool for the generation of large yeast surface display antibody Fab libraries. This procedure simplifies the hit discovery process of antibodies from immune repertoires.
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Affiliation(s)
- Simon Rosowski
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, 64287 Darmstadt, Germany
| | - Stefan Becker
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany
| | - Lars Toleikis
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany
| | - Bernhard Valldorf
- Chemical and Pharmaceutical Development, Merck KGaA, Frankfurter Straße 250, 64293 Darmstadt, Germany
| | - Julius Grzeschik
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, 64287 Darmstadt, Germany
| | - Deniz Demir
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany
| | - Iris Willenbücher
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany
| | - Ramona Gaa
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, 64287 Darmstadt, Germany
| | - Stefan Zielonka
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany
| | - Simon Krah
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany
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45
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Könning D, Hinz S, Grzeschik J, Schröter C, Krah S, Zielonka S, Kolmar H. Construction of Histidine-Enriched Shark IgNAR Variable Domain Antibody Libraries for the Isolation of pH-Sensitive vNAR Fragments. Methods Mol Biol 2018; 1827:109-127. [PMID: 30196494 DOI: 10.1007/978-1-4939-8648-4_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The adaptive immune system of sharks comprises a heavy chain-only antibody isotype, referred to as immunoglobulin new antigen receptor (IgNAR). Antigen binding in case of IgNAR antibodies is mediated by a single variable domain (vNAR). Due to their inherent beneficial biophysical properties, such as small size and high thermal stability combined with a high specificity and affinity to their target antigens, vNAR domains emerged as promising tools for biotechnological and biomedical applications. Herein, we present detailed protocols for the engineering of pH-sensitivity into IgNAR V domains by constructing histidine-enriched and CDR3-diversified semisynthetic antibody libraries which can then be screened upon using yeast surface display. Protonation or deprotonation of incorporated histidine residues at different pH values results in structural transitions caused by altered electrostatic interactions. These interactions account for an altered binding behavior toward the target antigen. In the following protocol, we describe the generation of a semisynthetic vNAR master library that comprises two histidine residues on average in the 12-residue CDR3 loop. Moreover, once a pH-dependent vNAR population toward the target antigen is identified, this population can further be optimized in terms of affinity and pH sensitivity upon conducting a CDR1-mediated affinity maturation.
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Affiliation(s)
- Doreen Könning
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
- Antibody-Drug Conjugates and Targeted NBE Therapeutics, Merck KGaA, Darmstadt, Germany
| | - Steffen Hinz
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Julius Grzeschik
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Christian Schröter
- Antibody-Drug Conjugates and Targeted NBE Therapeutics, Merck KGaA, Darmstadt, Germany
| | - Simon Krah
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
- Protein Engineering and Antibody Technologies, Merck KGaA, Darmstadt, Germany
| | - Stefan Zielonka
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
- Protein Engineering and Antibody Technologies, Merck KGaA, Darmstadt, Germany
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany.
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46
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Krah S, Grzeschik J, Rosowski S, Gaa R, Willenbuecher I, Demir D, Toleikis L, Kolmar H, Becker S, Zielonka S. A Streamlined Approach for the Construction of Large Yeast Surface Display Fab Antibody Libraries. Methods Mol Biol 2018; 1827:145-161. [PMID: 30196496 DOI: 10.1007/978-1-4939-8648-4_8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Yeast surface display is a versatile platform technology for antibody discovery. Nevertheless, the construction of antibody Fab libraries typically is a tedious multistep process that involves the generation of heavy chain as well as light chain display plasmids in different haploid yeast strains followed by yeast mating. Here, we present a focused one-step Golden Gate cloning approach for the generation of yeast surface display Fab libraries that allows for simultaneous introduction of heavy-chain and light-chain variable regions into one single display vector. Thereby, the overall time as well as the materials needed for library generation can be reduced significantly.
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Affiliation(s)
- Simon Krah
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany.,Protein Engineering and Antibody Technologies, Merck KGaA, Darmstadt, Germany
| | - Julius Grzeschik
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Simon Rosowski
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Ramona Gaa
- Protein Engineering and Antibody Technologies, Merck KGaA, Darmstadt, Germany
| | - Iris Willenbuecher
- Protein Engineering and Antibody Technologies, Merck KGaA, Darmstadt, Germany
| | - Deniz Demir
- Protein Engineering and Antibody Technologies, Merck KGaA, Darmstadt, Germany
| | - Lars Toleikis
- Protein Engineering and Antibody Technologies, Merck KGaA, Darmstadt, Germany
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Stefan Becker
- Protein Engineering and Antibody Technologies, Merck KGaA, Darmstadt, Germany
| | - Stefan Zielonka
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany. .,Protein Engineering and Antibody Technologies, Merck KGaA, Darmstadt, Germany.
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47
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Structural basis of a novel PD-L1 nanobody for immune checkpoint blockade. Cell Discov 2017; 3:17004. [PMID: 28280600 PMCID: PMC5341541 DOI: 10.1038/celldisc.2017.4] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 01/05/2017] [Indexed: 12/12/2022] Open
Abstract
The use of antibodies to target immune checkpoints, particularly PD-1/PD-L1, has made a profound impact in the field of cancer immunotherapy. Here, we identified KN035, an anti-PD-L1 nanobody that can strongly induce T-cell responses and inhibit tumor growth. The crystal structures of KN035 complexed with PD-L1 and free PD-L1, solved here at 1.7 and 2.7 Å resolution, respectively, show that KN035 competes with PD-1 (programmed death protein 1) for the same flat surface on PD-L1, mainly through a single surface loop of 21 amino acids. This loop forms two short helices and develops key hydrophobic and ionic interactions with PD-L1 residues, such as Ile54, Tyr56 and Arg113, which are also involved in PD-1 binding. The detailed mutagenesis study identified the hotspot residues of the PD-L1 surface and provides an explanation for the stronger (~1 000-fold) binding of KN035 to PD-L1 than PD-1 and its lack of binding to PD-L2. Overall, this study reveals how a single immunoglobulin-variable scaffold of KN035 or PD-1 can bind to a flat protein surface through either a single surface loop or beta-sheet strands; and provides a basis for designing new immune checkpoint blockers and generating bi-specific antibodies for combination therapy.
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48
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Krayukhina E, Noda M, Ishii K, Maruno T, Wakabayashi H, Tada M, Suzuki T, Ishii-Watabe A, Kato M, Uchiyama S. Analytical ultracentrifugation with fluorescence detection system reveals differences in complex formation between recombinant human TNF and different biological TNF antagonists in various environments. MAbs 2017; 9:664-679. [PMID: 28387583 PMCID: PMC5419078 DOI: 10.1080/19420862.2017.1297909] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
A number of studies have attempted to elucidate the binding mechanism between tumor necrosis factor (TNF) and clinically relevant antagonists. None of these studies, however, have been conducted as close as possible to physiologic conditions, and so the relationship between the size distribution of TNF-antagonist complexes and the antagonists' biological activity or adverse effects remains elusive. Here, we characterized the binding stoichiometry and sizes of soluble TNF-antagonist complexes for adalimumab, infliximab, and etanercept that were formed in human serum and in phosphate-buffered saline (PBS). Fluorescence-detected sedimentation velocity analytical ultracentrifugation analyses revealed that adalimumab and infliximab formed a range of complexes with TNF, with the major complexes consisting of 3 molcules of the respective antagonist and one or 2 molcules of TNF. Considerably greater amounts of high-molecular-weight complexes were detected for infliximab in human serum. The emergence of peaks with higher sedimentation coefficients than the adalimumab monomer as a function of added human serum albumin (HSA) concentration in PBS suggested weak reversible interactions between HSA and immunoglobulins. Etanerept exclusively formed 1:1 complexes with TNF in PBS, and a small amount of complexes with higher stoichiometry was detected in human serum. Consistent with these biophysical characterizations, a reporter assay showed that adalimumab and infliximab, but not etanercept, exerted FcγRIIa- and FcγRIIIa-mediated cell signaling in the presence of TNF and that infliximab exhibited higher potency than adalimumab. This study shows that assessing distribution profiles in serum will contribute to a more comprehensive understanding of the in vivo behavior of therapeutic proteins.
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Affiliation(s)
- Elena Krayukhina
- a Graduate School of Engineering, Osaka University , Yamadaoka, Suita , Osaka , Japan.,b U-Medico Inc. , Yamadaoka, Suita , Osaka , Japan
| | - Masanori Noda
- a Graduate School of Engineering, Osaka University , Yamadaoka, Suita , Osaka , Japan.,b U-Medico Inc. , Yamadaoka, Suita , Osaka , Japan
| | - Kentaro Ishii
- c Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences , Higashiyama, Myodaiji, Okazaki , Aichi , Japan
| | - Takahiro Maruno
- a Graduate School of Engineering, Osaka University , Yamadaoka, Suita , Osaka , Japan.,b U-Medico Inc. , Yamadaoka, Suita , Osaka , Japan
| | - Hirotsugu Wakabayashi
- a Graduate School of Engineering, Osaka University , Yamadaoka, Suita , Osaka , Japan
| | - Minoru Tada
- d Division of Biological Chemistry and Biologicals , National Institute of Health Sciences , Kamiyoga, Setagaya-ku , Tokyo , Japan
| | - Takuo Suzuki
- d Division of Biological Chemistry and Biologicals , National Institute of Health Sciences , Kamiyoga, Setagaya-ku , Tokyo , Japan
| | - Akiko Ishii-Watabe
- d Division of Biological Chemistry and Biologicals , National Institute of Health Sciences , Kamiyoga, Setagaya-ku , Tokyo , Japan
| | - Masahiko Kato
- e Sysmex Corporation , Murotani, Nishi-ku, Kobe-shi , Hyogo , Japan
| | - Susumu Uchiyama
- a Graduate School of Engineering, Osaka University , Yamadaoka, Suita , Osaka , Japan.,b U-Medico Inc. , Yamadaoka, Suita , Osaka , Japan.,c Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences , Higashiyama, Myodaiji, Okazaki , Aichi , Japan
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49
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DeVay RM, Delaria K, Zhu G, Holz C, Foletti D, Sutton J, Bolton G, Dushin R, Bee C, Pons J, Rajpal A, Liang H, Shelton D, Liu SH, Strop P. Improved Lysosomal Trafficking Can Modulate the Potency of Antibody Drug Conjugates. Bioconjug Chem 2017; 28:1102-1114. [DOI: 10.1021/acs.bioconjchem.7b00013] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Rachel M. DeVay
- Rinat
Laboratories, Pfizer Inc., 230 East Grand Avenue, South
San Francisco, California 94080, United States
| | - Kathy Delaria
- Rinat
Laboratories, Pfizer Inc., 230 East Grand Avenue, South
San Francisco, California 94080, United States
| | - Guoyun Zhu
- Rinat
Laboratories, Pfizer Inc., 230 East Grand Avenue, South
San Francisco, California 94080, United States
| | - Charles Holz
- Rinat
Laboratories, Pfizer Inc., 230 East Grand Avenue, South
San Francisco, California 94080, United States
| | - Davide Foletti
- Rinat
Laboratories, Pfizer Inc., 230 East Grand Avenue, South
San Francisco, California 94080, United States
| | - Janette Sutton
- Rinat
Laboratories, Pfizer Inc., 230 East Grand Avenue, South
San Francisco, California 94080, United States
| | - Gary Bolton
- Rinat
Laboratories, Pfizer Inc., 230 East Grand Avenue, South
San Francisco, California 94080, United States
| | - Russell Dushin
- Worldwide
Medicinal Chemistry, Pfizer Inc., 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Christine Bee
- Rinat
Laboratories, Pfizer Inc., 230 East Grand Avenue, South
San Francisco, California 94080, United States
| | - Jaume Pons
- Rinat
Laboratories, Pfizer Inc., 230 East Grand Avenue, South
San Francisco, California 94080, United States
| | - Arvind Rajpal
- Rinat
Laboratories, Pfizer Inc., 230 East Grand Avenue, South
San Francisco, California 94080, United States
| | - Hong Liang
- Rinat
Laboratories, Pfizer Inc., 230 East Grand Avenue, South
San Francisco, California 94080, United States
| | - David Shelton
- Rinat
Laboratories, Pfizer Inc., 230 East Grand Avenue, South
San Francisco, California 94080, United States
| | - Shu-Hui Liu
- Rinat
Laboratories, Pfizer Inc., 230 East Grand Avenue, South
San Francisco, California 94080, United States
| | - Pavel Strop
- Rinat
Laboratories, Pfizer Inc., 230 East Grand Avenue, South
San Francisco, California 94080, United States
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50
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Könning D, Zielonka S, Sellmann C, Schröter C, Grzeschik J, Becker S, Kolmar H. Isolation of a pH-Sensitive IgNAR Variable Domain from a Yeast-Displayed, Histidine-Doped Master Library. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2016; 18:161-167. [PMID: 26838965 DOI: 10.1007/s10126-016-9690-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 12/08/2015] [Indexed: 06/05/2023]
Abstract
In recent years, engineering of pH-sensitivity into antibodies as well as antibody-derived fragments has become more and more attractive for biomedical and biotechnological applications. Herein, we report the isolation of the first pH-sensitive IgNAR variable domain (vNAR), which was isolated from a yeast-displayed, semi-synthetic master library. This strategy enables the direct identification of pH-dependent binders from a histidine-enriched CDR3 library. Displayed vNAR variants contained two histidine substitutions on average at random positions in their 12-residue CDR3 loop. Upon screening of seven rounds against the proof-of-concept target EpCAM (selection for binding at pH 7.4 and decreased binding at pH 6.0), a single clone was obtained that showed specific and pH-dependent binding as characterized by yeast surface display and biolayer interferometry. Potential applications for such pH-dependent vNAR domains include their employment in tailored affinity chromatography, enabling mild elution protocols. Moreover, utilizing a master library for the isolation of pH-sensitive vNAR variants may be a generic strategy to obtain binding entities with prescribed characteristics for applications in biotechnology, diagnostics, and therapy.
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Affiliation(s)
- Doreen Könning
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, D-64287, Darmstadt, Germany
| | - Stefan Zielonka
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, D-64287, Darmstadt, Germany
| | - Carolin Sellmann
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, D-64287, Darmstadt, Germany
| | - Christian Schröter
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, D-64287, Darmstadt, Germany
| | - Julius Grzeschik
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, D-64287, Darmstadt, Germany
| | - Stefan Becker
- Protein Engineering and Antibody Technologies, Merck-Serono, Merck KGaA, Frankfurter Straße 250, D-64293, Darmstadt, Germany
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, D-64287, Darmstadt, Germany.
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