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Fernández‐Quintero ML, Guarnera E, Musil D, Pekar L, Sellmann C, Freire F, Sousa RL, Santos SP, Freitas MC, Bandeiras TM, Silva MMS, Loeffler JR, Ward AB, Harwardt J, Zielonka S, Evers A. On the humanization of VHHs: Prospective case studies, experimental and computational characterization of structural determinants for functionality. Protein Sci 2024; 33:e5176. [PMID: 39422475 PMCID: PMC11487682 DOI: 10.1002/pro.5176] [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: 07/04/2024] [Revised: 08/28/2024] [Accepted: 08/30/2024] [Indexed: 10/19/2024]
Abstract
The humanization of camelid-derived variable domain heavy chain antibodies (VHHs) poses challenges including immunogenicity, stability, and potential reduction of affinity. Critical to this process are complementarity-determining regions (CDRs), Vernier and Hallmark residues, shaping the three-dimensional fold and influencing VHH structure and function. Additionally, the presence of non-canonical disulfide bonds further contributes to conformational stability and antigen binding. In this study, we systematically humanized two camelid-derived VHHs targeting the natural cytotoxicity receptor NKp30. Key structural positions in Vernier and Hallmark regions were exchanged with residues from the most similar human germline sequences. The resulting variants were characterized for binding affinities, yield, and purity. Structural binding modes were elucidated through crystal structure determination and AlphaFold2 predictions, providing insights into differences in binding affinity. Comparative structural and molecular dynamics characterizations of selected variants were performed to rationalize their functional properties and elucidate the role of specific sequence motifs in antigen binding. Furthermore, systematic analyses of next-generation sequencing (NGS) and Protein Data Bank (PDB) data was conducted, shedding light on the functional significance of Hallmark motifs and non-canonical disulfide bonds in VHHs in general. Overall, this study provides valuable insights into the structural determinants governing the functional properties of VHHs, offering a roadmap for their rational design, humanization, and optimization for therapeutic applications.
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Affiliation(s)
- Monica L. Fernández‐Quintero
- Department of Integrative Structural and Computational BiologyThe Scripps Research InstituteLa JollaCaliforniaUSA
| | - Enrico Guarnera
- Antibody Discovery and Protein EngineeringMerck Healthcare KGaADarmstadtGermany
| | - Djordje Musil
- Structural Biology and BiophysicsMerck Healthcare KGaADarmstadtGermany
| | - Lukas Pekar
- Antibody Discovery and Protein EngineeringMerck Healthcare KGaADarmstadtGermany
| | - Carolin Sellmann
- Antibody Discovery and Protein EngineeringMerck Healthcare KGaADarmstadtGermany
| | - Filipe Freire
- iBET, Instituto de Biologia Experimental e TecnológicaOeirasPortugal
| | - Raquel L. Sousa
- iBET, Instituto de Biologia Experimental e TecnológicaOeirasPortugal
| | - Sandra P. Santos
- iBET, Instituto de Biologia Experimental e TecnológicaOeirasPortugal
| | - Micael C. Freitas
- iBET, Instituto de Biologia Experimental e TecnológicaOeirasPortugal
| | | | | | - Johannes R. Loeffler
- Department of Integrative Structural and Computational BiologyThe Scripps Research InstituteLa JollaCaliforniaUSA
| | - Andrew B. Ward
- Department of Integrative Structural and Computational BiologyThe Scripps Research InstituteLa JollaCaliforniaUSA
| | - Julia Harwardt
- Antibody Discovery and Protein EngineeringMerck Healthcare KGaADarmstadtGermany
| | - Stefan Zielonka
- Antibody Discovery and Protein EngineeringMerck Healthcare KGaADarmstadtGermany
- Institute for Organic Chemistry and BiochemistryTechnical University of DarmstadtDarmstadtGermany
| | - Andreas Evers
- Antibody Discovery and Protein EngineeringMerck Healthcare KGaADarmstadtGermany
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2
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Page A, Chuvin N, Valladeau-Guilemond J, Depil S. Development of NK cell-based cancer immunotherapies through receptor engineering. Cell Mol Immunol 2024; 21:315-331. [PMID: 38443448 PMCID: PMC10978891 DOI: 10.1038/s41423-024-01145-x] [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: 11/07/2023] [Accepted: 02/09/2024] [Indexed: 03/07/2024] Open
Abstract
Natural killer (NK) cell-based immunotherapies are attracting increasing interest in the field of cancer treatment. Early clinical trials have shown promising outcomes, alongside satisfactory product efficacy and safety. Recent developments have greatly increased the therapeutic potential of NK cells by endowing them with enhanced recognition and cytotoxic capacities. This review focuses on surface receptor engineering in NK cell therapy and discusses its impact, challenges, and future directions.Most approaches are based on engineering with chimeric antigen receptors to allow NK cells to target specific tumor antigens independent of human leukocyte antigen restriction. This approach has increased the precision and potency of NK-mediated recognition and elimination of cancer cells. In addition, engineering NK cells with T-cell receptors also mediates the recognition of intracellular epitopes, which broadens the range of target peptides. Indirect tumor peptide recognition by NK cells has also been improved by optimizing immunoglobulin constant fragment receptor expression and signaling. Indeed, engineered NK cells have an improved ability to recognize and destroy target cells coated with specific antibodies, thereby increasing their antibody-dependent cellular cytotoxicity. The ability of NK cell receptor engineering to promote the expansion, persistence, and infiltration of transferred cells in the tumor microenvironment has also been explored. Receptor-based strategies for sustained NK cell functionality within the tumor environment have also been discussed, and these strategies providing perspectives to counteract tumor-induced immunosuppression.Overall, receptor engineering has led to significant advances in NK cell-based cancer immunotherapies. As technical challenges are addressed, these innovative treatments will likely reshape cancer immunotherapy.
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Affiliation(s)
- Audrey Page
- Centre de Recherche en Cancérologie de Lyon, UMR INSERM U1052 CNRS 5286, Centre Léon Bérard, Lyon, France.
| | | | - Jenny Valladeau-Guilemond
- Centre de Recherche en Cancérologie de Lyon, UMR INSERM U1052 CNRS 5286, Centre Léon Bérard, Lyon, France
| | - Stéphane Depil
- Centre de Recherche en Cancérologie de Lyon, UMR INSERM U1052 CNRS 5286, Centre Léon Bérard, Lyon, France.
- ErVimmune, Lyon, France.
- Centre Léon Bérard, Lyon, France.
- Université Claude Bernard Lyon 1, Lyon, France.
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3
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Zhang H, Wang Q, Yalavarthi S, Pekar L, Shamnoski S, Hu L, Helming L, Zielonka S, Xu C. Development of a c-MET x CD137 bispecific antibody for targeted immune agonism in cancer immunotherapy. Cancer Treat Res Commun 2024; 39:100805. [PMID: 38492435 DOI: 10.1016/j.ctarc.2024.100805] [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: 01/05/2024] [Revised: 02/29/2024] [Accepted: 03/02/2024] [Indexed: 03/18/2024]
Abstract
BACKGROUND Targeting the costimulatory receptor CD137 has shown promise as a therapeutic approach for cancer immunotherapy, resulting in anti-tumor efficacy demonstrated in clinical trials. However, the initial CD137 agonistic antibodies, urelumab and utomilumab, faced challenges in clinical trials due to the liver toxicity or lack of efficacy, respectively. Concurrently, c-MET has been identified as a highly expressed tumor-associated antigen (TAA) in various solid and soft tumors. METHODS In this study, we aimed to develop a bispecific antibody (BsAb) that targets both c-MET and CD137, optimizing the BsAb format and CD137 binder for efficient delivery of the CD137 agonist to the tumor microenvironment (TME). We employed a monovalent c-MET motif and a trimeric CD137 Variable Heavy domain of Heavy chain (VHH) for the BsAb design. RESULTS Our results demonstrate that the c-MET x CD137 BsAb provides co-stimulation to T cells through cross-linking by c-MET-expressing tumor cells. Functional immune assays confirmed the enhanced efficacy and potency of the c-MET x CD137 BsAb, as indicated by activation of CD137 signaling, target cell killing, and cytokine release in various tumor cell lines. Furthermore, the combination of c-MET x CD137 BsAb with Pembrolizumab showed a dose-dependent enhancement of target-induced T cell cytokine release. CONCLUSION Overall, the c-MET x CD137 BsAb exhibits a promising developability profile as a tumor-targeted immune agonist by minimizing off-target effects while effectively delivering immune agonism. It has the potential to overcome resistance to anti-PD-(L)1 therapies.
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Affiliation(s)
- Hong Zhang
- Research Unit Oncology, EMD Serono Research Center, 45 Middlesex Turnpike, Billerica, MA 01821, USA
| | - Qun Wang
- Research Unit Oncology, EMD Serono Research Center, 45 Middlesex Turnpike, Billerica, MA 01821, USA
| | - Sireesha Yalavarthi
- Research Unit Oncology, EMD Serono Research Center, 45 Middlesex Turnpike, Billerica, MA 01821, USA
| | - Lukas Pekar
- Antibody Discovery & Protein Engineering, Merck Healthcare KGaA, Frankfurter Str. 250, 64293 Darmstadt, Germany
| | - Steven Shamnoski
- Research Unit Oncology, EMD Serono Research Center, 45 Middlesex Turnpike, Billerica, MA 01821, USA
| | - Liufang Hu
- Research Unit Oncology, EMD Serono Research Center, 45 Middlesex Turnpike, Billerica, MA 01821, USA
| | - Laura Helming
- Research Unit Oncology, EMD Serono Research Center, 45 Middlesex Turnpike, Billerica, MA 01821, USA
| | - Stefan Zielonka
- Antibody Discovery & Protein Engineering, Merck Healthcare KGaA, Frankfurter Str. 250, 64293 Darmstadt, Germany
| | - Chunxiao Xu
- Research Unit Oncology, EMD Serono Research Center, 45 Middlesex Turnpike, Billerica, MA 01821, USA.
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4
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Lee RB, Maddineni S, Landry M, Diaz C, Tashfeen A, Yamada-Hunter SA, Mackall CL, Beinat C, Sunwoo JB, Cochran JR. An engineered NKp46 antibody for construction of multi-specific NK cell engagers. Protein Eng Des Sel 2024; 37:gzae013. [PMID: 39163262 PMCID: PMC11359164 DOI: 10.1093/protein/gzae013] [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: 04/10/2024] [Revised: 08/04/2024] [Indexed: 08/22/2024] Open
Abstract
Recent developments in cancer immunotherapy have highlighted the potential of harnessing natural killer (NK) cells in the treatment of neoplastic malignancies. Of these, bispecific antibodies, and NK cell engager (NKCE) protein therapeutics in particular, have been of interest. Here, we used phage display and yeast surface display to engineer RLN131, a unique cross-reactive antibody that binds to human, mouse, and cynomolgus NKp46, an activating receptor found on NK cells. RLN131 induced proliferation and activation of primary NK cells, and was used to create bispecific NKCE constructs of varying configurations and valency. All NKCEs were able to promote greater NK cell cytotoxicity against tumor cells than an unmodified anti-CD20 monoclonal antibody, and activity was observed irrespective of whether the constructs contained a functional Fc domain. Competition binding and fine epitope mapping studies were used to demonstrate that RLN131 binds to a conserved epitope on NKp46, underlying its species cross-reactivity.
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Affiliation(s)
- Robert B Lee
- Department of Chemical Engineering, Stanford University, 443 Via Ortega, Stanford, CA, 94305, United States
- Department of Bioengineering, Stanford University, 443 Via Ortega, Stanford, CA, 94305, United States
| | - Sainiteesh Maddineni
- Department of Otolaryngology, Head and Neck Surgery, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA, 94305, United States
| | - Madeleine Landry
- Department of Radiology, Molecular Imaging Program at Stanford, Stanford University, 1701 Page Mill Road, Palo Alto, CA, 94304, United States
| | - Celeste Diaz
- Cancer Biology Program, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA, 94305, United States
| | - Aanya Tashfeen
- Department of Electrical Engineering, Stanford University, 350 Jane Stanford Way, Stanford, CA, 94305, United States
| | - Sean A Yamada-Hunter
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA, 94305, United States
| | - Crystal L Mackall
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA, 94305, United States
| | - Corinne Beinat
- Department of Radiology, Molecular Imaging Program at Stanford, Stanford University, 1701 Page Mill Road, Palo Alto, CA, 94304, United States
| | - John B Sunwoo
- Department of Otolaryngology, Head and Neck Surgery, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA, 94305, United States
| | - Jennifer R Cochran
- Department of Bioengineering, Stanford University, 443 Via Ortega, Stanford, CA, 94305, United States
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5
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Boje AS, Pekar L, Koep K, Lipinski B, Rabinovich B, Evers A, Gehlert CL, Krohn S, Xiao Y, Krah S, Zaynagetdinov R, Toleikis L, Poetzsch S, Peipp M, Zielonka S, Klausz K. Impact of antibody architecture and paratope valency on effector functions of bispecific NKp30 x EGFR natural killer cell engagers. MAbs 2024; 16:2315640. [PMID: 38372053 PMCID: PMC10877975 DOI: 10.1080/19420862.2024.2315640] [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: 06/09/2023] [Accepted: 02/02/2024] [Indexed: 02/20/2024] Open
Abstract
Natural killer (NK) cells emerged as a promising effector population that can be harnessed for anti-tumor therapy. In this work, we constructed NK cell engagers (NKCEs) based on NKp30-targeting single domain antibodies (sdAbs) that redirect the cytotoxic potential of NK cells toward epidermal growth factor receptor (EGFR)-expressing tumor cells. We investigated the impact of crucial parameters such as sdAb location, binding valencies, the targeted epitope on NKp30, and the overall antibody architecture on the redirection capacity. Our study exploited two NKp30-specific sdAbs, one of which binds a similar epitope on NKp30 as its natural ligand B7-H6, while the other sdAb addresses a non-competing epitope. For EGFR-positive tumor targeting, humanized antigen-binding domains of therapeutic antibody cetuximab were used. We demonstrate that NKCEs bivalently targeting EGFR and bivalently engaging NKp30 are superior to monovalent NKCEs in promoting NK cell-mediated tumor cell lysis and that the architecture of the NKCE can substantially influence killing capacities depending on the NKp30-targeting sdAb utilized. While having a pronounced impact on NK cell killing efficacy, the capabilities of triggering antibody-dependent cellular phagocytosis or complement-dependent cytotoxicity were not significantly affected comparing the bivalent IgG-like NKCEs with cetuximab. However, the fusion of sdAbs can have a slight impact on the NK cell release of immunomodulatory cytokines, as well as on the pharmacokinetic profile of the NKCE due to unfavorable spatial orientation within the molecule architecture. Ultimately, our findings reveal novel insights for the engineering of potent NKCEs triggering the NKp30 axis.
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Affiliation(s)
- Ammelie Svea Boje
- Division of Antibody-Based Immunotherapy, Department of Internal Medicine II, University Medical Center Schleswig-Holstein and University of Kiel, Kiel, Germany
| | - Lukas Pekar
- Antibody Discovery & Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Katharina Koep
- Drug Metabolism and Pharmacokinetics, Merck Healthcare KGaA, Darmstadt, Germany
| | - Britta Lipinski
- Antibody Discovery & Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Brian Rabinovich
- Department of Oncology and Immuno-Oncology, EMD Serono Research & Development Institute Inc, 45A Middlesex Turnpike, Billerica, MA, USA
| | - Andreas Evers
- Antibody Discovery & Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Carina Lynn Gehlert
- Division of Antibody-Based Immunotherapy, Department of Internal Medicine II, University Medical Center Schleswig-Holstein and University of Kiel, Kiel, Germany
| | - Steffen Krohn
- Division of Antibody-Based Immunotherapy, Department of Internal Medicine II, University Medical Center Schleswig-Holstein and University of Kiel, Kiel, Germany
| | - Yanping Xiao
- Department of Oncology and Immuno-Oncology, EMD Serono Research & Development Institute Inc, 45A Middlesex Turnpike, Billerica, MA, USA
| | - Simon Krah
- Antibody Discovery & Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Rinat Zaynagetdinov
- Department of Oncology and Immuno-Oncology, EMD Serono Research & Development Institute Inc, 45A Middlesex Turnpike, Billerica, MA, USA
| | - Lars Toleikis
- Early Protein Supply & Characterization, Merck Healthcare KGaA, Darmstadt, Germany
| | - Sven Poetzsch
- Strategic Innovation, Merck Healthcare KGaA, Darmstadt, Germany
| | - Matthias Peipp
- Division of Antibody-Based Immunotherapy, Department of Internal Medicine II, University Medical Center Schleswig-Holstein and University of Kiel, Kiel, Germany
| | - Stefan Zielonka
- Antibody Discovery & Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany
| | - Katja Klausz
- Division of Antibody-Based Immunotherapy, Department of Internal Medicine II, University Medical Center Schleswig-Holstein and University of Kiel, Kiel, Germany
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6
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Yanakieva D, Vollmer L, Evers A, Siegmund V, Arras P, Pekar L, Doerner A, Valldorf B, Kolmar H, Zielonka S, Krah S. Cattle-derived knob paratopes grafted onto peripheral loops of the IgG1 Fc region enable the generation of a novel symmetric bispecific antibody format. Front Immunol 2023; 14:1238313. [PMID: 37942319 PMCID: PMC10628450 DOI: 10.3389/fimmu.2023.1238313] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 10/09/2023] [Indexed: 11/10/2023] Open
Abstract
In this work we present a novel symmetric bispecific antibody format based on engraftments of cattle-derived knob paratopes onto peripheral loops of the IgG1 Fc region. For this, knob architectures obtained from bovine ultralong CDR-H3 antibodies were inserted into the AB loop or EF loop of the CH3 domain, enabling the introduction of an artificial binding specificity into an IgG molecule. We demonstrate that inserted knob domains largely retain their binding affinities, resulting into bispecific antibody derivatives versatile for effector cell redirection. Essentially, generated bispecifics demonstrated adequate biophysical properties and were not compromised in their Fc mediated functionalities such as FcRn or FcγRIIIa binding.
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Affiliation(s)
- Desislava Yanakieva
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Lena Vollmer
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Andreas Evers
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Vanessa Siegmund
- Early Protein Supply and Characterization, Merck Healthcare KGaA, Darmstadt, Germany
| | - Paul Arras
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Lukas Pekar
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Achim Doerner
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | | | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Stefan Zielonka
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Simon Krah
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
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7
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Arras P, Yoo HB, Pekar L, Clarke T, Friedrich L, Schröter C, Schanz J, Tonillo J, Siegmund V, Doerner A, Krah S, Guarnera E, Zielonka S, Evers A. AI/ML combined with next-generation sequencing of VHH immune repertoires enables the rapid identification of de novo humanized and sequence-optimized single domain antibodies: a prospective case study. Front Mol Biosci 2023; 10:1249247. [PMID: 37842638 PMCID: PMC10575757 DOI: 10.3389/fmolb.2023.1249247] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 08/31/2023] [Indexed: 10/17/2023] Open
Abstract
Introduction: In this study, we demonstrate the feasibility of yeast surface display (YSD) and nextgeneration sequencing (NGS) in combination with artificial intelligence and machine learning methods (AI/ML) for the identification of de novo humanized single domain antibodies (sdAbs) with favorable early developability profiles. Methods: The display library was derived from a novel approach, in which VHH-based CDR3 regions obtained from a llama (Lama glama), immunized against NKp46, were grafted onto a humanized VHH backbone library that was diversified in CDR1 and CDR2. Following NGS analysis of sequence pools from two rounds of fluorescence-activated cell sorting we focused on four sequence clusters based on NGS frequency and enrichment analysis as well as in silico developability assessment. For each cluster, long short-term memory (LSTM) based deep generative models were trained and used for the in silico sampling of new sequences. Sequences were subjected to sequence- and structure-based in silico developability assessment to select a set of less than 10 sequences per cluster for production. Results: As demonstrated by binding kinetics and early developability assessment, this procedure represents a general strategy for the rapid and efficient design of potent and automatically humanized sdAb hits from screening selections with favorable early developability profiles.
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Affiliation(s)
- Paul Arras
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany
| | - Han Byul Yoo
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Lukas Pekar
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Thomas Clarke
- Bioinformatics, EMD Serono, Billerica, MA, United States
| | - Lukas Friedrich
- Computational Chemistry and Biologics, Merck Healthcare KGaA, Darmstadt, Germany
| | | | - Jennifer Schanz
- ADCs & Targeted NBE Therapeutics, Merck KGaA, Darmstadt, Germany
| | - Jason Tonillo
- ADCs & Targeted NBE Therapeutics, Merck KGaA, Darmstadt, Germany
| | - Vanessa Siegmund
- Early Protein Supply and Characterization, Merck Healthcare KGaA, Darmstadt, Germany
| | - Achim Doerner
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Simon Krah
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Enrico Guarnera
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Stefan Zielonka
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany
| | - Andreas Evers
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
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8
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Arras P, Yoo HB, Pekar L, Schröter C, Clarke T, Krah S, Klewinghaus D, Siegmund V, Evers A, Zielonka S. A library approach for the de novo high-throughput isolation of humanized VHH domains with favorable developability properties following camelid immunization. MAbs 2023; 15:2261149. [PMID: 37766540 PMCID: PMC10540653 DOI: 10.1080/19420862.2023.2261149] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
In this study, we generated a novel library approach for high throughput de novo identification of humanized single-domain antibodies following camelid immunization. To achieve this, VHH-derived complementarity-determining regions-3 (CDR3s) obtained from an immunized llama (Lama glama) were grafted onto humanized VHH backbones comprising moderately sequence-diversified CDR1 and CDR2 regions similar to natural immunized and naïve antibody repertoires. Importantly, these CDRs were tailored toward favorable in silico developability properties, by considering human-likeness as well as excluding potential sequence liabilities and predicted immunogenic motifs. Target-specific humanized single-domain antibodies (sdAbs) were readily obtained by yeast surface display. We demonstrate that, by exploiting this approach, high affinity sdAbs with an optimized in silico developability profile can be generated. These sdAbs display favorable biophysical, biochemical, and functional attributes and do not require any further sequence optimization. This approach is generally applicable to any antigen upon camelid immunization and has the potential to significantly accelerate candidate selection and reduce risks and attrition rates in sdAb development.
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Affiliation(s)
- Paul Arras
- Antibody Discovery & Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany
| | - Han Byul Yoo
- Antibody Discovery & Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
- Early Protein Supply & Characterization, Merck Healthcare KGaA, Darmstadt, Germany
| | - Lukas Pekar
- Antibody Discovery & Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | | | | | - Simon Krah
- Antibody Discovery & Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Daniel Klewinghaus
- Early Protein Supply & Characterization, Merck Healthcare KGaA, Darmstadt, Germany
| | - Vanessa Siegmund
- Early Protein Supply & Characterization, Merck Healthcare KGaA, Darmstadt, Germany
| | - Andreas Evers
- Antibody Discovery & Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Stefan Zielonka
- Antibody Discovery & Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany
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9
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Kolmar H, Grzeschik J, Könning D, Krah S, Zielonka S. Construction of Semisynthetic Shark vNAR Yeast Surface Display Antibody Libraries. Methods Mol Biol 2023; 2702:227-243. [PMID: 37679622 DOI: 10.1007/978-1-0716-3381-6_11] [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] [Indexed: 09/09/2023]
Abstract
The adaptive immune system of sharks comprises a unique heavy chain-only antibody isotype, termed immunoglobulin new antigen receptor (IgNAR), in which antigen binding is mediated by a single variable domain, referred to as vNAR. In recent years, efforts were made to harness these domains for biomedical and biotechnological applications particularly due to their high affinity and specificity combined with a small size and high stability. Herein, we describe protocols for the construction of semisynthetic, CDR3-randomized vNAR libraries for the isolation of target-specific paratopes by yeast surface display. Additionally, we provide guidance for affinity maturation of a panel of antigen-enriched vNAR domains through CDR1 diversification of the FACS-selected, antigen-enriched population and sublibrary establishment.
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Affiliation(s)
- Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany.
| | - Julius Grzeschik
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Doreen Könning
- Antibody-Drug Conjugates and Targeted NBE Therapeutics, Merck KGaA, Darmstadt, Germany
| | - Simon Krah
- Antibody Discovery & Protein Engineering, Merck KGaA, Darmstadt, Germany
| | - Stefan Zielonka
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany.
- Antibody Discovery & Protein Engineering, Merck KGaA, Darmstadt, Germany.
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