In collaboration with the Cambridge Crystallographic Data Centre (CCDC), we updated the prominent ReCore index to feature a colossal number of over 49 million possible 3D fragments for users to search in. ReCore is a part of the SeeSAR’s Inspirator Mode that can be used to screen libraries for geometric replacement of a molecular scaffold within a ligand. With this, users can perform scaffold hopping and all common fragment-based drug discovery methods including fragment merging and linking, as well as growing.
The respective file was created for the benefit of Cambridge Structural Database (CSD) subscribers and their drug discovery projects. The CSD is a certified and trusted collection of fully curated and enhanced organic and metal-organic structures, used by researchers across the globe for drug discovery projects. The CSD data undergoes extensive validation and cross-checking through automated workflows and manual curation resulting in accurate, consistent and high-quality information that enhances the likelihood of success.
By applying the genuine crystallographic data of compounds, users can replace undesired molecular structures (toxophores, structures protected by patent, etc.) and discover potential compatibles with improved physicochemical properties. Important interactions with the target can be maintained via pharmacophore constraints to ensure that the results share a similar profile to the query compound. With this data it is possible to discover the perfect linker two fragments or to screen for alternatives for a particular PROTAC linker substructure. Replacement of smaller molecule parts can propose structures that occupy unsatisfied binding pockets for fragment growing. Furthermore, the user can define what part of the molecule’s structure are kept, meaning that more than two replacement vectors can be selected.
Download our drug discovery dashboard SeeSAR and experience for yourself how easy and fun it can be to explore the Chemical Space around a ligand’s core motif.
Insights on how to apply ReCore can be found here.