Screening macrocyclic peptide libraries by yeast display allows control of selection process and affinity ranking
Abstract Macrocyclic peptides represent an attractive drug modality due to their favourable properties and amenability to in vitro evolution techniques such as phage or mRNA display. Although very powerful, these technologies are not without limitations. In this work, we address some of their drawba...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-06-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-60907-x |
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| author | Sara Linciano Ylenia Mazzocato Zhanna Romanyuk Filippo Vascon Lluc Farrera-Soler Edward Will Yuyu Xing Shiyu Chen Yoichi Kumada Marta Simeoni Alessandro Scarso Laura Cendron Christian Heinis Alessandro Angelini |
| author_facet | Sara Linciano Ylenia Mazzocato Zhanna Romanyuk Filippo Vascon Lluc Farrera-Soler Edward Will Yuyu Xing Shiyu Chen Yoichi Kumada Marta Simeoni Alessandro Scarso Laura Cendron Christian Heinis Alessandro Angelini |
| author_sort | Sara Linciano |
| collection | DOAJ |
| description | Abstract Macrocyclic peptides represent an attractive drug modality due to their favourable properties and amenability to in vitro evolution techniques such as phage or mRNA display. Although very powerful, these technologies are not without limitations. In this work, we address some of their drawbacks by developing a yeast display-based strategy to generate, screen and characterise structurally diverse disulfide-cyclised peptides. The use of quantitative flow cytometry enables real-time monitoring of the screening of millions of individual macrocyclic peptides, leading to the identification of ligands with good binding properties to five different protein targets. X-ray analysis of a selected ligand in complex with its target reveals optimal shape complementarity and extensive surface interaction, explaining its exquisite affinity and selectivity. The yeast display-based approach described here offers a facile, quantitative and cost-effective alternative to rapidly and efficiently discover and characterise genetically encoded macrocyclic peptide ligands with sufficiently good binding properties against therapeutically relevant targets. |
| format | Article |
| id | doaj-art-dce65fdb34f84de18b1d485d70413c8e |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-dce65fdb34f84de18b1d485d70413c8e2025-08-20T04:03:03ZengNature PortfolioNature Communications2041-17232025-06-0116112310.1038/s41467-025-60907-xScreening macrocyclic peptide libraries by yeast display allows control of selection process and affinity rankingSara Linciano0Ylenia Mazzocato1Zhanna Romanyuk2Filippo Vascon3Lluc Farrera-Soler4Edward Will5Yuyu Xing6Shiyu Chen7Yoichi Kumada8Marta Simeoni9Alessandro Scarso10Laura Cendron11Christian Heinis12Alessandro Angelini13Department of Molecular Sciences and Nanosystems, Ca’ Foscari University of VeniceDepartment of Molecular Sciences and Nanosystems, Ca’ Foscari University of VeniceDepartment of Molecular Sciences and Nanosystems, Ca’ Foscari University of VeniceDepartment of Biology, University of PaduaInstitute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL)Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL)Biotech Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of SciencesBiotech Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of SciencesDepartment of Functional Chemistry and Engineering, Kyoto Institute of Technology, 1 Matsugasaki-Hashikami-Cho, Sakyo-kuDepartment of Environmental Sciences, Informatics and Statistics, Ca’ Foscari University of VeniceDepartment of Molecular Sciences and Nanosystems, Ca’ Foscari University of VeniceDepartment of Biology, University of PaduaInstitute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL)Department of Molecular Sciences and Nanosystems, Ca’ Foscari University of VeniceAbstract Macrocyclic peptides represent an attractive drug modality due to their favourable properties and amenability to in vitro evolution techniques such as phage or mRNA display. Although very powerful, these technologies are not without limitations. In this work, we address some of their drawbacks by developing a yeast display-based strategy to generate, screen and characterise structurally diverse disulfide-cyclised peptides. The use of quantitative flow cytometry enables real-time monitoring of the screening of millions of individual macrocyclic peptides, leading to the identification of ligands with good binding properties to five different protein targets. X-ray analysis of a selected ligand in complex with its target reveals optimal shape complementarity and extensive surface interaction, explaining its exquisite affinity and selectivity. The yeast display-based approach described here offers a facile, quantitative and cost-effective alternative to rapidly and efficiently discover and characterise genetically encoded macrocyclic peptide ligands with sufficiently good binding properties against therapeutically relevant targets.https://doi.org/10.1038/s41467-025-60907-x |
| spellingShingle | Sara Linciano Ylenia Mazzocato Zhanna Romanyuk Filippo Vascon Lluc Farrera-Soler Edward Will Yuyu Xing Shiyu Chen Yoichi Kumada Marta Simeoni Alessandro Scarso Laura Cendron Christian Heinis Alessandro Angelini Screening macrocyclic peptide libraries by yeast display allows control of selection process and affinity ranking Nature Communications |
| title | Screening macrocyclic peptide libraries by yeast display allows control of selection process and affinity ranking |
| title_full | Screening macrocyclic peptide libraries by yeast display allows control of selection process and affinity ranking |
| title_fullStr | Screening macrocyclic peptide libraries by yeast display allows control of selection process and affinity ranking |
| title_full_unstemmed | Screening macrocyclic peptide libraries by yeast display allows control of selection process and affinity ranking |
| title_short | Screening macrocyclic peptide libraries by yeast display allows control of selection process and affinity ranking |
| title_sort | screening macrocyclic peptide libraries by yeast display allows control of selection process and affinity ranking |
| url | https://doi.org/10.1038/s41467-025-60907-x |
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