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Evers A, Krah S, Demir D, Gaa R, Elter D, Schroeter C, Zielonka S, Rasche N, Dotterweich J, Knuehl C, Doerner A. Engineering hydrophobicity and manufacturability for optimized biparatopic antibody-drug conjugates targeting c-MET. MAbs 2024; 16:2302386. [PMID: 38214660 DOI: 10.1080/19420862.2024.2302386] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 01/03/2024] [Indexed: 01/13/2024] Open
Abstract
Optimal combinations of paratopes assembled into a biparatopic antibody have the capacity to mediate high-grade target cross-linking on cell membranes, leading to degradation of the target, as well as antibody and payload delivery in the case of an antibody-drug conjugate (ADC). In the work presented here, molecular docking suggested a suitable paratope combination targeting c-MET, but hydrophobic patches in essential binding regions of one moiety necessitated engineering. In addition to rational design of HCDR2 and HCDR3 mutations, site-specific spiking libraries were generated and screened in yeast and mammalian surface display approaches. Comparative analyses revealed similar positions amendable for hydrophobicity reduction, with a broad combinatorial diversity obtained from library outputs. Optimized variants showed high stability, strongly reduced hydrophobicity, retained affinities supporting the desired functionality and enhanced producibility. The resulting biparatopic anti-c-MET ADCs were comparably active on c-MET expressing tumor cell lines as REGN5093 exatecan DAR6 ADC. Structural molecular modeling of paratope combinations for preferential inter-target binding combined with protein engineering for manufacturability yielded deep insights into the capabilities of rational and library approaches. The methodologies of in silico hydrophobicity identification and sequence optimization could serve as a blueprint for rapid development of optimal biparatopic ADCs targeting further tumor-associated antigens in the future.
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Affiliation(s)
- Andreas Evers
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Simon Krah
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Deniz Demir
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Ramona Gaa
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Desislava Elter
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | | | - Stefan Zielonka
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Nicolas Rasche
- ADC and Targeted Therapeutics, Merck Healthcare KGaA, Darmstadt, Germany
| | | | - Christine Knuehl
- Research Unit Oncology, Merck Healthcare KGaA, Darmstadt, Germany
| | - Achim Doerner
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
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2
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Teymennet-Ramírez KV, Martínez-Morales F, Trejo-Hernández MR. Yeast Surface Display System: Strategies for Improvement and Biotechnological Applications. Front Bioeng Biotechnol 2022; 9:794742. [PMID: 35083204 PMCID: PMC8784408 DOI: 10.3389/fbioe.2021.794742] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 12/20/2021] [Indexed: 12/26/2022] Open
Abstract
Yeast surface display (YSD) is a “whole-cell” platform used for the heterologous expression of proteins immobilized on the yeast’s cell surface. YSD combines the advantages eukaryotic systems offer such as post-translational modifications, correct folding and glycosylation of proteins, with ease of cell culturing and genetic manipulation, and allows of protein immobilization and recovery. Additionally, proteins displayed on the surface of yeast cells may show enhanced stability against changes in temperature, pH, organic solvents, and proteases. This platform has been used to study protein-protein interactions, antibody design and protein engineering. Other applications for YSD include library screening, whole-proteome studies, bioremediation, vaccine and antibiotics development, production of biosensors, ethanol production and biocatalysis. YSD is a promising technology that is not yet optimized for biotechnological applications. This mini review is focused on recent strategies to improve the efficiency and selection of displayed proteins. YSD is presented as a cutting-edge technology for the vectorial expression of proteins and peptides. Finally, recent biotechnological applications are summarized. The different approaches described herein could allow for a better strategy cascade for increasing protein/peptide interaction and production.
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Affiliation(s)
- Karla V Teymennet-Ramírez
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mėxico
| | - Fernando Martínez-Morales
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mėxico
| | - María R Trejo-Hernández
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mėxico
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3
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Hao J, Wang J, Pan H, Sang Y, Wang D, Wang Z, Ai J, Lin B, Chen L. pH-redox responsive polymer-doxorubicin prodrug micelles studied by molecular dynamics, dissipative particle dynamics simulations and experiments. J Drug Deliv Sci Technol 2022. [DOI: 10.1016/j.jddst.2022.103136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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4
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Day K, Schneible JD, Young AT, Pozdin VA, Van Den Driessche G, Gaffney LA, Prodromou R, Freytes DO, Fourches D, Daniele M, Menegatti S. Photoinduced reconfiguration to control the protein-binding affinity of azobenzene-cyclized peptides. J Mater Chem B 2021; 8:7413-7427. [PMID: 32661544 DOI: 10.1039/d0tb01189d] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The impact of next-generation biorecognition elements (ligands) will be determined by the ability to remotely control their binding activity for a target biomolecule in complex environments. Compared to conventional mechanisms for regulating binding affinity (pH, ionic strength, or chaotropic agents), light provides higher accuracy and rapidity, and is particularly suited for labile targets. In this study, we demonstrate a general method to develop azobenzene-cyclized peptide ligands with light-controlled affinity for target proteins. Light triggers a cis/trans isomerization of the azobenzene, which results in a major structural rearrangement of the cyclic peptide from a non-binding to a binding configuration. Critical to this goal are the ability to achieve efficient photo-isomerization under low light dosage and the temporal stability of both cis and trans isomers. We demonstrated our method by designing photo-switchable peptides targeting vascular cell adhesion marker 1 (VCAM1), a cell marker implicated in stem cell function. Starting from a known VCAM1-binding linear peptide, an ensemble of azobenzene-cyclized variants with selective light-controlled binding were identified by combining in silico design with experimental characterization via spectroscopy and surface plasmon resonance. Variant cycloAZOB[G-VHAKQHRN-K] featured rapid, light-controlled binding of VCAM1 (KD,trans/KD,cis ∼ 130). Biotin-cycloAZOB[G-VHAKQHRN-K] was utilized to label brain microvascular endothelial cells (BMECs), showing co-localization with anti-VCAM1 antibodies in cis configuration and negligible binding in trans configuration.
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Affiliation(s)
- Kevin Day
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, North Carolina, USA.
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5
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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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6
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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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7
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Li S, Qiao J, Lin S, Liu Y, Ma L. A Highly Efficient Indirect P. pastoris Surface Display Method Based on the CL7/Im7 Ultra-High-Affinity System. Molecules 2019; 24:molecules24081483. [PMID: 30991754 PMCID: PMC6514646 DOI: 10.3390/molecules24081483] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/03/2019] [Accepted: 04/10/2019] [Indexed: 02/04/2023] Open
Abstract
Cell surface display systems for immobilization of peptides and proteins on the surface of cells have various applications, such as vaccine generation, protein engineering, bio-conversion and bio-adsorption. Though plenty of methods have been established in terms of traditional yeast surface display systems, the development of a universal display method with high efficiency remains a challenge. Here we report an indirect yeast surface display method by anchoring Im7 proteins on the surface of P. pastoris, achieving highly efficient display of target proteins, including fluorescence proteins (sfGFP and mCherry) or enzymes (human Arginase I), with a CL7 fusion tag through the ultra-high-affinity interaction between Im7 and CL7. This indirect P. pastoris surface display approach is highly efficient and provides a robust platform for displaying biomolecules.
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Affiliation(s)
- Shuntang Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China.
- Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China.
| | - Jie Qiao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China.
- Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China.
| | - Siyu Lin
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China.
- Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China.
| | - Yi Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China.
- Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China.
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, School of Life Sciences, Hubei University, Wuhan 430062, China.
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China.
- Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China.
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, School of Life Sciences, Hubei University, Wuhan 430062, China.
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8
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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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