Phase II year
2018
(last award dollars: 2020)
Phase II Amount
$1,966,609
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. FBDD allows a more effective exploration of chemical space with a higher hit rate compared to high-throughput screening, and this can have significant effects in early drug discovery and in the case of challenging or non-druggable targets. FBDD has led to around 30 new drugs entering clinical trials and 2 that have entered the market. FBDD can also be used to discover and develop novel molecules for well-validated and important drug targets that already have marketed drugs against them, both for increasing efficacy with lower toxicity as well as creation of new intellectual property for off-patent drugs. 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. PX can also detect a wider range of binding affinities compared to other biophysical methods for fragment and compound screening and is independent of protein size. However, crystallography is expensive and inefficient for screening a large fragment library due to significant bottlenecks in mass production of crystals for co-crystallization, crystal soaking with fragments, crystal harvesting, X-ray data collection, structure determination and analysis. Complementary biophysical 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 a first-to-market, 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. In Phase I we evaluated a high-density crystallization grid that dramatically increased the efficiency of target-fragment co-crystallization, crystal soaking with fragments and synchrotron- based data collection, leading to a hit rate of ~5% in a single step while simultaneously producing 3D details of protein-fragment interactions. After successfully completing our Phase I aims, we are now moving ahead with our Phase II plan to integrate this experimental technology with a distributed computational crystallography pipeline and data management/informatics backbone that will allow us to efficiently process a large fragment library screen. We will use several druggable and non-druggable oncology targets implicated in various cancers, from our industry and academic customers, as proof-of-concept systems to demonstrate the utility of our overall platform. Our plans are well-aligned with all of NCATS Drug Discovery and Development SBIR topics of interest: Tools and technologies to enable assaying of compound activity on currently non- druggable targets; Co-crystallization high-throughput screening techniques; Tools and technologies that increase the predictivity or efficiency of medicinal chemistry, biologic or other intervention optimization; and Development of high-throughput imaging technologies that focus on making translational research more efficient.
Public Health Relevance Statement: Project Narrative Fragment-based drug discovery (FBDD) is widely used in the pharmaceutical industry to provide novel leads for developing new therapeutics. In FBDD, small compounds (<300 Da molecular weight), which bind with low millimolar affinity, serve as building blocks that can be elaborated into novel lead compounds. FBDD allows a more efficient scanning of chemical space with a higher hit rate compared to high-throughput screening, and this has important outcomes in early drug discovery and is especially relevant for challenging non-druggable targets. FBDD has resulted in 30 new drugs entering clinical trials with 2 that have entered the market. FBDD can also be an effective route to discovering and developing novel chemical entities or drugs for well-validated and important drug targets that already have marketed drugs against them, both for increasing efficacy and lowering toxicity as well as creation of new intellectual property for off-patent drugs. 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. Thus, 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 will 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 our first-to-market high-throughput platform for crystallography-based fragment screening, leveraging on a novel high- density crystallization grid, which will require a very small volume of purified protein sample (<1 mg for 1000 fragments) and will enable in situ fragment soaking and X-ray diffraction data collection. In our Phase I proposal, we tested the grid for all experimental steps including crystallization, fragment soaking and X-ray diffraction data collection. We optimized the design of the grid-based tools and demonstrated that they eliminated many of the key bottlenecks encountered in conventional crystallography. In this Phase II proposal, we will further optimize our experimental workflows and couple it with a distributed computational pipeline for structure determination, identification of weakly bound fragments and efficient crystallographic structure refinement. We will also develop the informatics necessary to manage the experimental platform and the large quantities of data produced by it. This informatics backbone will be essential for operating the platform and will be used to drive process improvements as we push ahead with commercialization.
NIH Spending Category: Biotechnology
Project Terms: Academia; Adopted; Affinity; base; Binding; Biological Assay; biophysical techniques; Biophysics; Chemicals; Clinical Trials; commercial application; commercialization; computerized data processing; cost; cost effective; Crystallization; Crystallography; Custom; Data; Data Analyses; Data Collection; data management; Data Set; data structure; Databases; density; design; Development; drug candidate; drug development; drug discovery; Drug Industry; drug market; Drug Targeting; experimental study; Failure; Goals; Gold; Harvest; high throughput screening; imaging system; Imaging technology; improved; In Situ; Industrialization; Industry; Informatics; Intellectual Property; interest; Intervention; Joints; Lead; Legal patent; Libraries; Liquid substance; Location; Malignant Neoplasms; Manuals; Marketing; Measures; Methods; Molecular; Molecular Weight; Monitor; National Institute of General Medical Sciences; new therapeutic target; novel; novel lead compound; novel therapeutics; Nuclear Magnetic Resonance; oncology; One-Step dentin bonding system; Outcome; Pharmaceutical Chemistry; Pharmaceutical Preparations; Phase; Positioning Attribute; Preclinical Testing; Preparation; Process; Production; programs; Protein Fragment; Protein Structure Initiative; Proteins; Resources; Roentgen Rays; Route; Sampling; Scanning; screening; Services; Small Business Innovation Research Grant; software development; Software Tools; structural biology; structural genomics; Structure; success; Surface Plasmon Resonance; Synchrotrons; System; Techniques; Technology; Testing; three dimensional structure; Time; tool; Toxic effect; Translational Research; Vertebral column; X ray diffraction analysis; X-Ray Crystallography
