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High Content Screening for Drug Repurposing: A New Resource

December 14, 2018
Genedata

Bringing a new therapy to market is incredibly costly. Drug repurposing can help reduce these costs. In this article, we discuss a recent resource that scientists at Calibr have developed to enable many types of organizations to perform drug repurposing screens.

Repurposing to Reduce Costs

Bringing therapies to market is a time-consuming and expensive process, creating a major hurdle for any company or organization interested in making a new drug. Companies have recognized that repurposing or repositioning drugs already approved for clinical use can dramatically reduce the time and resources required to develop new drugs, since the mechanism and patient safety has already been shown. It’s also been proposed that drug repurposing could provide an important boost to those who want to address rare diseases or diseases more prevalent in the developing world. As the decision to pursue a costly development cycle must be weighed against its commercial potential, drugs targeting such illnesses are oftentimes neglected. Workflows, however, that encourage drug repurposing are not only cost effective, but could prove to be life-saving for patients suffering from these diseases.

There are many approaches to drug repurposing, including purely data-driven methods.1 However, experimental approaches such as high-throughput and high-content screening can also contribute to repurposing initiatives.

Screening for Infectious Disease Therapeutics

To help enable non-profit and academic organizations that don’t have troves of preclinically-vetted compounds to perform repurposing screens, scientists at the California Institute for Biomedical Research (Calibr) at the Scripps Research Institute in San Diego built a library of ~12,000 commercially available compounds. These compounds are all coupled to rich existing chemical structural and preclinical safety data drawn from Citeline, Clarivate, and GOSTAR. Building this library was challenging, according to Arnab Chatterjee, vice president of Medicinal Chemistry at Calibr and co-lead author on the paper. “We had to determine which drugs have been safely dosed, what the chemical structures of some compounds were from patent literature, and synthesize almost half the collection ourselves."

To demonstrate the usefulness of ReFRAME, the scientists purchased or synthesized every compound in their collection and performed a high-content screen for drugs against a parasite called Cryptosporidium. This parasite spreads through water and food, and infection results in cryptosporidiosis, leading to life-threatening diarrhea especially in children. The disease is most prevalent in the developing world but also found in developed countries. At present, only one treatment for this disease exists, but it has limited efficacy.

The Calibr group’s high-content screening process involved a 384- and 1,536-well plate formats and employed robotic systems such as the HighRes Biosolutions® NanoCellTM and the Thermo ScientificTM CX5 CellInsightTM HCS Platform for imaging. For analyses, the authors could import the image data into Genedata Screener for High Content Screening to generate dose-response curves and select these hits. “All the Screener features proved useful for this project," said Chatterjee.

The researchers identified ~70 hits and went on to confirm two promising candidates in an animal model of cryptosporidiosis. Importantly, the safety of both candidates identified by the authors has already been tested in clinical trials for other disorders. If these candidates are pursued further, this may potentially accelerate drug development and delivery to patients.

The ReFRAME Database

The scientists dubbed their library ReFRAME (Repurposing, Focused Rescue, and Accelerated Medchem). Openly accessible at reframedb.org, you can search ReFRAME by typing a disease or a specific compound name, or by entering a chemical structure (which you can visually edit), and immediately view annotation data available for your compound of interest, as well for similar compounds. 

The site includes an assay description catalog that contains screens performed using the ReFRAME database. From this catalog, you can download data on the results of each screen, and see details about the methods and protocols. The site contains over 20 screens that have employed the database, including not only the cryptosporidiosis screen, but other screens for compounds to target zika virus and the bacteria responsible for tuberculosis.

Conclusion

This project illustrates how high-content screening is important for drug repurposing. "Alongside computational and data-driven approaches, high-content and phenotypic screening will absolutely remain an important approach for drug repurposing," said Chatterjee. Furthermore, such screening efforts are not limited to big pharmaceutical projects, but are within reach for research for nonprofit and academic organizations as well. ReFRAME may be especially useful for those who want to address unmet medical needs. Hopefully, ReFRAME’s database of assays will grow, and more resources like this will be made available to drug developers.

References

1. Pushpakom et al. “Drug repurposing: progress, challenges and recommendations.” Nature Reviews Drug Discovery doi.org/10.1038/nrd.2018.168 (2018)

2. Centers for Disease Control. “Crytosporidium.” www.cdc.gov/parasites/crypto/gen_info/infect.html (2018)

3. Janes et al. “The ReFRAME library as a comprehensive drug repurposing library and its application to the treatment of cryptosporidiosis.” Proceedings of the National Academy of Sciences of the USA 115:42 10750-10755 (2018)

4. Love et al. “A high-throughput phenotypic screen identifies clofazimine as a potential treatment for cryptosporidiosis.” PLOS Neglected Tropical Diseases 11:e0005373 (2017)