Screening, Growing, and Validation by Catalog: Using Synthetic Intermediates from Natural Product Libraries to Discover Fragments for an Aspartic Protease Through Crystallography
Fragment screening directly on protein crystals has been applied using AnalytiCon’s collection of intermediates that have been utilized to generate libraries of larger synthetic natural product-like molecules. The fragments with well-balanced physicochemical properties show an impressively high hit...
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MDPI AG
2024-08-01
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| Series: | Crystals |
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| Online Access: | https://www.mdpi.com/2073-4352/14/9/755 |
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| author | Franziska U. Huschmann Janis Mueller Alexander Metz Moritz Ruf Johanna Senst Serghei Glinca Johannes Schiebel Andreas Heine Gerhard Klebe |
| author_facet | Franziska U. Huschmann Janis Mueller Alexander Metz Moritz Ruf Johanna Senst Serghei Glinca Johannes Schiebel Andreas Heine Gerhard Klebe |
| author_sort | Franziska U. Huschmann |
| collection | DOAJ |
| description | Fragment screening directly on protein crystals has been applied using AnalytiCon’s collection of intermediates that have been utilized to generate libraries of larger synthetic natural product-like molecules. The fragments with well-balanced physicochemical properties show an impressively high hit rate for a screen using the aspartic protease endothiapepsin. The subsequent validation and expansion of the discovered fragment hits benefits from AnalytiCon’s comprehensive library design. Since the screened fragments are intermediates that share a common core with larger and closely related analogs with modulated substitution patterns, they allow for the retrieval of off-the-shelf follow-up compounds, which enable the development of design strategies for fragment optimization. A promising bicyclic core scaffold found in several fragment hits could be validated by selecting a set of enlarged follow-up compounds. Due to unexpected changes in binding mode and no significant improvement in ligand efficiency, this series was quickly deemed unsuitable and therefore discontinued. The structures of follow-up compounds of two other fragments helped to evaluate a putative fusion of two overlapping fragment hits. A design concept on how to fuse the two fragments could be proposed and helps to plan a suitable substitution pattern and promising central bridging element. |
| format | Article |
| id | doaj-art-4e95b53a82e24820bf05c4f364b32dbd |
| institution | OA Journals |
| issn | 2073-4352 |
| language | English |
| publishDate | 2024-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Crystals |
| spelling | doaj-art-4e95b53a82e24820bf05c4f364b32dbd2025-08-20T01:55:22ZengMDPI AGCrystals2073-43522024-08-0114975510.3390/cryst14090755Screening, Growing, and Validation by Catalog: Using Synthetic Intermediates from Natural Product Libraries to Discover Fragments for an Aspartic Protease Through CrystallographyFranziska U. Huschmann0Janis Mueller1Alexander Metz2Moritz Ruf3Johanna Senst4Serghei Glinca5Johannes Schiebel6Andreas Heine7Gerhard Klebe8Helmholtz-Zentrum Berlin, Macromolecular Crystallography (HZB-MX), Albert-Einstein-Str. 15, D-12489 Berlin, GermanyCrystalsFirst GmbH, Marbacher Weg 6, D-35037 Marburg, GermanyInstitute of Pharmaceutical Chemistry, Philipps-Universität Marburg, Marbacher Weg 6, D-35032 Marburg, GermanyCrystalsFirst GmbH, Marbacher Weg 6, D-35037 Marburg, GermanyCrystalsFirst GmbH, Marbacher Weg 6, D-35037 Marburg, GermanyCrystalsFirst GmbH, Marbacher Weg 6, D-35037 Marburg, GermanyInstitute of Pharmaceutical Chemistry, Philipps-Universität Marburg, Marbacher Weg 6, D-35032 Marburg, GermanyInstitute of Pharmaceutical Chemistry, Philipps-Universität Marburg, Marbacher Weg 6, D-35032 Marburg, GermanyInstitute of Pharmaceutical Chemistry, Philipps-Universität Marburg, Marbacher Weg 6, D-35032 Marburg, GermanyFragment screening directly on protein crystals has been applied using AnalytiCon’s collection of intermediates that have been utilized to generate libraries of larger synthetic natural product-like molecules. The fragments with well-balanced physicochemical properties show an impressively high hit rate for a screen using the aspartic protease endothiapepsin. The subsequent validation and expansion of the discovered fragment hits benefits from AnalytiCon’s comprehensive library design. Since the screened fragments are intermediates that share a common core with larger and closely related analogs with modulated substitution patterns, they allow for the retrieval of off-the-shelf follow-up compounds, which enable the development of design strategies for fragment optimization. A promising bicyclic core scaffold found in several fragment hits could be validated by selecting a set of enlarged follow-up compounds. Due to unexpected changes in binding mode and no significant improvement in ligand efficiency, this series was quickly deemed unsuitable and therefore discontinued. The structures of follow-up compounds of two other fragments helped to evaluate a putative fusion of two overlapping fragment hits. A design concept on how to fuse the two fragments could be proposed and helps to plan a suitable substitution pattern and promising central bridging element.https://www.mdpi.com/2073-4352/14/9/755crystallographic fragment screeningaspartyl proteasesnatural product-like moleculesfragment validation with enlarged follow-up compoundsoff-the-shelf follow-up compounds |
| spellingShingle | Franziska U. Huschmann Janis Mueller Alexander Metz Moritz Ruf Johanna Senst Serghei Glinca Johannes Schiebel Andreas Heine Gerhard Klebe Screening, Growing, and Validation by Catalog: Using Synthetic Intermediates from Natural Product Libraries to Discover Fragments for an Aspartic Protease Through Crystallography Crystals crystallographic fragment screening aspartyl proteases natural product-like molecules fragment validation with enlarged follow-up compounds off-the-shelf follow-up compounds |
| title | Screening, Growing, and Validation by Catalog: Using Synthetic Intermediates from Natural Product Libraries to Discover Fragments for an Aspartic Protease Through Crystallography |
| title_full | Screening, Growing, and Validation by Catalog: Using Synthetic Intermediates from Natural Product Libraries to Discover Fragments for an Aspartic Protease Through Crystallography |
| title_fullStr | Screening, Growing, and Validation by Catalog: Using Synthetic Intermediates from Natural Product Libraries to Discover Fragments for an Aspartic Protease Through Crystallography |
| title_full_unstemmed | Screening, Growing, and Validation by Catalog: Using Synthetic Intermediates from Natural Product Libraries to Discover Fragments for an Aspartic Protease Through Crystallography |
| title_short | Screening, Growing, and Validation by Catalog: Using Synthetic Intermediates from Natural Product Libraries to Discover Fragments for an Aspartic Protease Through Crystallography |
| title_sort | screening growing and validation by catalog using synthetic intermediates from natural product libraries to discover fragments for an aspartic protease through crystallography |
| topic | crystallographic fragment screening aspartyl proteases natural product-like molecules fragment validation with enlarged follow-up compounds off-the-shelf follow-up compounds |
| url | https://www.mdpi.com/2073-4352/14/9/755 |
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