Fragment-based Drug Discovery - back to top
Over the past few years a novel method for designing new leads in drug discovery has been developed as a fragment-based drug discovery (FBDD) approach. It uses X-ray crystallography to screen fragment libraries for a target protein. A protein crystal is soaked in a solution containing about 10 compound fragments, which range in size from 100-300 Daltons, for 3 to 24 hours. If a compound can form specific interactions with the protein, it will be determined in the co-crystal structure.
FBDD is developed based on the advantage of recent innovations in computer technology, software, automation and synchrotron X-ray sources that have become generally available in the macromolecule crystallography field in recent years. The co-crystal structures can be determined in a high throughput manner. X-ray crystallography is fast becoming a screening tool.
FBDD has a number of attractive features compared to other high-throughput screenings. The approach will only locate compounds that bind specifically with the target protein. It is able to detect fragments with relatively low affinity, from 100 μM-10 mM, a range which may be difficult to identify using other methods. Both theoretical considerations and practical experience have demonstrated that the chemical space for ligand binding can be covered with ~1000 fragment compounds.
High-affinity compounds will be created by linking several low-affinity fragments together. Based on structure information, a suitable linker will be designed and it will maintain the binding interactions of the individual fragments. With the FBDD method, novel clinical candidates have been identified at several drug discovery companies in as little as 2-3 years. A growing number of pharmaceutical companies have employed FBDD in their drug discoveries. Many advanced leads and clinical drug candidates were developed by this approach.
Proprietary Methods to Achieve High-Hit Rate
At SBD, we have developed proprietary methods to get high-hit rates of fragments in crystallographic screen. The keys in achieving high-hit rates using the FBDD method are crystal resolution and stability of the target crystal in a soaking solution containing high concentration of fragments. Higher resolution structures not only helps locate more hits, but also in determining the specific compound that bound with the protein from the cocktail. At SBD, it is our imperative to grow the highest resolution crystals to service our clients.
To get more hits of compounds, we usually soak the protein crystal with a compound cocktail containing 10 mM of individual compounds. We have developed techniques to find a stable soaking condition for both compounds and crystals using our proprietary methods. The crystals can be moved from their original crystallization solution to a soaking solution where they are more stable with high concentrations of compounds. We have successfully screened several drug targets with this method, and in such projects, we obtained a range of 5-8 % hits with soaked fragment cocktail compounds for a drug target.
Another option we utilize to obtain more hits is employing different crystal forms to soak with compounds. Protein molecules can typically be crystallized into several space groups. A protein molecule in different crystal forms has various contact surfaces. Some contacts in an individual crystal form may block compounds from accessing the binding site of interest. Thus, we employ multiple crystal forms to allow the compound to reach all possible binding sites, especially for sites targeted for new drug discovery purposes.
Fragment-based Crystallographic Screening Service
At Structure Based Design, Inc., we have built a platform using our large-scale protein expression, purification, proprietary technologies for co-crystal generation and high-throughput X-ray structure determination to offer fragment-based X-ray crystallographic screening services. This platform has demonstrated its ability to achieve high hit-rate fragments in co-crystal structures. The prepared crystals can be soaked with a client’s fragment library or SBD’s fragment library. We can solve three to ten complex structures a day, which can screen 30 to 100 compounds.
Feel free to contact us for a consultation and proposal for your project.