Fragment-based drug discovery (FBDD) is a widely used method in the pharmaceutical industry for the de novo design of molecules that target new drug candidates. Protein x-ray crystallography (PX) is the gold standard for determining the exact 3D location and orientation of a given fragment bound to a drug target. However, crystallography is expensive and inefficient for screening a large fragment library due to significant bottlenecks in crystallization, crystal soaking with fragments, crystal harvesting, X-ray data collection, structure determination and analysis. Complementary techniques are often used to prescreen for fragments that bind and PX is then used in a second step to determine the exact binding pose of each fragment. Accelero Biostructures is developing an efficient one-step PX-based fragment library-screening platform that can revolutionize the field by dramatically increasing the efficiency and reducing the cost of developing novel lead molecules for preclinical testing. Our Phase I plan is to evaluate a high-density crystallization grid, which will dramatically increase efficiency of target-fragment co-crystallization, crystal soaking with fragments and synchrotron-based data collection. Our Phase II plan will include a complete integration of this technology into our overall platform. Throughout we will use a previously ?non-druggable? target implicated in various cancers as proof-of-concept. Our plans align well with NCATS SBIR's topics of interest ?Tools and technologies to enable assaying of compound activity on currently ?non-druggable? targets? and ?Co-crystallization high- throughput screening techniques?.
Fragment-based drug discovery (FBDD) is widely used in the pharmaceutical industry to provide novel leads for developing new therapeutics. It is based on the principle that small compounds (<300 Da molecular weight), which bind with low millimolar affinity, can serve as useful building blocks for the development of novel lead compounds. X-ray crystallography is the gold standard for determining the exact binding orientation of a fragment, as an essential step in this process. However, conventional crystallography is inefficient for screening a large fragment library due to expense and effort. Due to this, complementary techniques, such as Surface Plasmon Resonance (SPR), Thermal Shift Assay (TSA) or Nuclear Magnetic Resonance (NMR), are often used to prescreen for fragments that bind, while protein crystallography is used in a second step to determine the exact binding pose of each fragment. An efficient, cost-effective crystallography-based fragment screen can accelerate the development of lead compounds by directly providing 3D structures of fragments bound to a target of interest. The goal of this proposal is to develop of a high-throughput platform for crystallography-based fragment screening leveraging a novel high-density sample crystallization grid, which will require a very small volume of purified protein sample (<1 mg). In this proposal we will evaluate the novel grid, which will eliminate key bottlenecks associated with crystallization (produce apo-crystals for fragments/ligands soaks or co-crystallization with fragments/ligands), crystal mounting, and rapid synchrotron data collection. In Phase I, we will test the grid for all experimental steps including crystallization, fragment soaking and data collection. In Phase II, we will optimize the grid design for FBDD applications. In addition, we will integrate this technology into the Accelero Biostructures ABSTM platform, by further developing informatics and data analysis to efficiently handle large fragment library screens and rapidly provide 3D fragment-bound structures.
