Development of mirror-image monobodies targeting the oncogenic BCR::ABL1 kinase
Abstract Mirror-image proteins, composed of d-amino acids, are an attractive therapeutic modality, as they exhibit high metabolic stability and lack immunogenicity. Development of mirror-image binding proteins is achieved through chemical synthesis of d-target proteins, phage display library selecti...
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Nature Portfolio
2024-12-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-024-54901-y |
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| author | Nina Schmidt Amit Kumar Lukas Korf Adrian Valentin Dinh-Fricke Frank Abendroth Akiko Koide Uwe Linne Magdalena Rakwalska-Bange Shohei Koide Lars-Oliver Essen Olalla Vázquez Oliver Hantschel |
| author_facet | Nina Schmidt Amit Kumar Lukas Korf Adrian Valentin Dinh-Fricke Frank Abendroth Akiko Koide Uwe Linne Magdalena Rakwalska-Bange Shohei Koide Lars-Oliver Essen Olalla Vázquez Oliver Hantschel |
| author_sort | Nina Schmidt |
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| description | Abstract Mirror-image proteins, composed of d-amino acids, are an attractive therapeutic modality, as they exhibit high metabolic stability and lack immunogenicity. Development of mirror-image binding proteins is achieved through chemical synthesis of d-target proteins, phage display library selection of l-binders and chemical synthesis of (mirror-image) d-binders that consequently bind the physiological l-targets. Monobodies are well-established synthetic (l-)binding proteins and their small size (~90 residues) and lack of endogenous cysteine residues make them particularly accessible to chemical synthesis. Here, we develop monobodies with nanomolar binding affinities against the d-SH2 domain of the leukemic tyrosine kinase BCR::ABL1. Two crystal structures of heterochiral monobody-SH2 complexes reveal targeting of the pY binding pocket by an unconventional binding mode. We then prepare potent d-monobodies by either ligating two chemically synthesized d-peptides or by self-assembly without ligation. Their proper folding and stability are determined and high-affinity binding to the l-target is shown. d-monobodies are protease-resistant, show long-term plasma stability, inhibit BCR::ABL1 kinase activity and bind BCR::ABL1 in cell lysates and permeabilized cells. Hence, we demonstrate that functional d-monobodies can be developed readily. Our work represents an important step towards possible future therapeutic use of d-monobodies when combined with emerging methods to enable cytoplasmic delivery of monobodies. |
| format | Article |
| id | doaj-art-a94e9c2c9c8d495c80cae1346c9eb306 |
| institution | DOAJ |
| issn | 2041-1723 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-a94e9c2c9c8d495c80cae1346c9eb3062025-08-20T02:43:33ZengNature PortfolioNature Communications2041-17232024-12-0115111910.1038/s41467-024-54901-yDevelopment of mirror-image monobodies targeting the oncogenic BCR::ABL1 kinaseNina Schmidt0Amit Kumar1Lukas Korf2Adrian Valentin Dinh-Fricke3Frank Abendroth4Akiko Koide5Uwe Linne6Magdalena Rakwalska-Bange7Shohei Koide8Lars-Oliver Essen9Olalla Vázquez10Oliver Hantschel11Institute of Physiological Chemistry, Faculty of Medicine, Philipps University of MarburgInstitute of Physiological Chemistry, Faculty of Medicine, Philipps University of MarburgFaculty of Chemistry and Unit for Structural Biology, Philipps University of MarburgInstitute of Physiological Chemistry, Faculty of Medicine, Philipps University of MarburgFaculty of Chemistry and Unit for Chemical Biology, Philipps University of MarburgDepartment of Medicine, New York University School of MedicineFaculty of Chemistry and Unit for Mass Spectrometry, Philipps University of MarburgInstitute of Physiological Chemistry, Faculty of Medicine, Philipps University of MarburgLaura and Isaac Perlmutter Cancer Center, New York University Langone HealthFaculty of Chemistry and Unit for Structural Biology, Philipps University of MarburgFaculty of Chemistry and Unit for Chemical Biology, Philipps University of MarburgInstitute of Physiological Chemistry, Faculty of Medicine, Philipps University of MarburgAbstract Mirror-image proteins, composed of d-amino acids, are an attractive therapeutic modality, as they exhibit high metabolic stability and lack immunogenicity. Development of mirror-image binding proteins is achieved through chemical synthesis of d-target proteins, phage display library selection of l-binders and chemical synthesis of (mirror-image) d-binders that consequently bind the physiological l-targets. Monobodies are well-established synthetic (l-)binding proteins and their small size (~90 residues) and lack of endogenous cysteine residues make them particularly accessible to chemical synthesis. Here, we develop monobodies with nanomolar binding affinities against the d-SH2 domain of the leukemic tyrosine kinase BCR::ABL1. Two crystal structures of heterochiral monobody-SH2 complexes reveal targeting of the pY binding pocket by an unconventional binding mode. We then prepare potent d-monobodies by either ligating two chemically synthesized d-peptides or by self-assembly without ligation. Their proper folding and stability are determined and high-affinity binding to the l-target is shown. d-monobodies are protease-resistant, show long-term plasma stability, inhibit BCR::ABL1 kinase activity and bind BCR::ABL1 in cell lysates and permeabilized cells. Hence, we demonstrate that functional d-monobodies can be developed readily. Our work represents an important step towards possible future therapeutic use of d-monobodies when combined with emerging methods to enable cytoplasmic delivery of monobodies.https://doi.org/10.1038/s41467-024-54901-y |
| spellingShingle | Nina Schmidt Amit Kumar Lukas Korf Adrian Valentin Dinh-Fricke Frank Abendroth Akiko Koide Uwe Linne Magdalena Rakwalska-Bange Shohei Koide Lars-Oliver Essen Olalla Vázquez Oliver Hantschel Development of mirror-image monobodies targeting the oncogenic BCR::ABL1 kinase Nature Communications |
| title | Development of mirror-image monobodies targeting the oncogenic BCR::ABL1 kinase |
| title_full | Development of mirror-image monobodies targeting the oncogenic BCR::ABL1 kinase |
| title_fullStr | Development of mirror-image monobodies targeting the oncogenic BCR::ABL1 kinase |
| title_full_unstemmed | Development of mirror-image monobodies targeting the oncogenic BCR::ABL1 kinase |
| title_short | Development of mirror-image monobodies targeting the oncogenic BCR::ABL1 kinase |
| title_sort | development of mirror image monobodies targeting the oncogenic bcr abl1 kinase |
| url | https://doi.org/10.1038/s41467-024-54901-y |
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