FBDD: Fragment-Based Drug Design

Fragments cover a broad chemical space, offering more opportunities to identify novel drug candidates. This makes the approach cost-effective as fewer resources to screen and optimize are required.

As FBDD can identify molecules that form high-quality interactions to bind to a target structure, hits represent perfect starting points for rational design of more potent candidates.

The BioSolveIT platforms SeeSAR and infiniSee facilitate fragment-based campaigns from the 3D and 2D world.

Whether it’s identifying binding sites, docking fragments, or assessing generated poses in 3D, our tools support every stage of fragment-based drug discovery. The ability to mine ultra-vast collections of commercially available compounds from Chemical Spaces, each containing your substructure of interest, enhances the scope and sophistication of your campaigns. From docking to post-screening analysis, our applications streamline and advance FBDD efforts with precision and ease.

Fragment-based drug discovery (FBDD) is a key method in identifying and optimizing lead compounds. SeeSAR facilitates this journey by offering three primary approaches to explore and refine fragments into fully drug-like molecules:

• Growing: Expand a fragment into adjacent, unoccupied binding pockets within the target protein. This method allows you to systematically grow the size of your molecule while maintaining interactions with the target, optimizing its binding affinity and drug-like properties.
• Linking: Combine two distinct fragments that bind in separate pockets of the target protein by linking them with a chemical bridge. This technique helps in the development of more potent compounds by merging different interactions into one unified structure.
• Merging: Fuse two fragments that interact within the same binding site into a single scaffold. By merging these molecules, you create a new compound that incorporates the best features of both fragments, improving overall binding efficiency and activity.

These approaches are supported by our extensive databases, offering tailored solutions for various challenges in drug discovery. With SeeSAR, you can seamlessly transition from initial fragment hits to optimized, drug-like candidates.

Chemical Spaces are ultra-vast compound collections, containing trillions of drug-like, commercially available entries. These collections represent some of the largest catalogs of molecular motifs and scaffolds, offering unprecedented opportunities for drug discovery.

By exploring multiple commercial Chemical Spaces, researchers can access millions of compounds containing substructures of interest that are not available elsewhere.

With tools like Motif Matcher, researchers can perform exact substructure searches, retrieving compounds containing specific molecular motifs or functional groups. For broader and faster substructure matching, SpaceMACS offers a powerful, scalable solution for screening large compound libraries efficiently, allowing the discovery of relevant compounds based on common substructures across different chemical spaces.