Drug Repurposing Screening for Rare and Neglected Diseases

National Center For Advancing Translational Sciences

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Abstract

In collaboration with NIH and external academic researchers, we have carried out assay development and performed drug repurposing screens for multiple projects across a range of therapeutic areas, including rare genetic disorders and drug resistant rare cancer. ASSAY TECHNOLOGY AND iPS CELL LINES FOR DISEASE MODELING: Disease modeling using patient cells is an effective approach that enables establishments of new disease models alternative to animal disease models. Human induced pluripotent stem cells (iPS) cells are generated from patient samples that can be further differentiated to various cell types such as neuronal cells, cardiomyocytes, and hepatocytes for disease modeling. These cell-based disease models are particularly useful for drug discovery and development for rare genetic diseases because the animal models are usually not available in the rare diseases. The patient derived iPS cells share the same genetic background with patients and have the same disease phenotypes that are suitable for screening of compounds. We have generated several patient derived iPS cell lines for Fibrodysplasia ossificans progressiva (FOP, Huang X. et al. Stem Cell Res 54, 102424.), Mucopolysaccharidosis type IIIB (MPS IIIB, Huang W. et al. Exp Cell Res 407, 112785), Mucopolysaccharidosis type II (MPS II, Hong J. et al. Exp Cell Res 412, 113007), and Alagille syndrome (ALGS, Brooks BM. Et al. Stem Cell Res 54, 102447). The iPS cells have been characterized and stably passaged over 10 passages. We also have applied the CRISPR gene editing technology and generated a NGLY1 mutation corrected iPS cell line that can be used as a control line for further studies (Pavlinov I. et al. Stem Cell Res 56, 102554). These iPS cells were differentiated to support generation of brain organoids that we subsequently profiled using RNAseq analysis and proteomics to identify disease phenotype and biomarkers (a manuscript is currently under preparation). These patient derived iPS cell lines are good research tools that have been deposited to the Coriell Cell Repository for access by other researchers. The patient iPS cell lines can be further differentiated into different cell types and organoids for disease modeling. DRUG RESISTANT CANCER: Cancer drug resistance is a severe clinical problem that often results in patient death. We performed drug repurposing screens for drug-resistant cell lines of liver cancer, and ovarian cancer refractory to multiple standard care chemotherapies. Several approved drugs have been identified that either suppress the drug-resistant cancer cells directly or re-sensitize the resistant cells to the anticancer activities of the standard drugs. We also found that diverse mechanisms are involved in ovarian cancer drug resistance such as the And-1 and SENP1/JAK2/STAT signaling pathways, indicating a personalized treatment strategy that can be obtained from personalized drug screens using patient-derived cancer samples. The results have been published recently (Li J. et al. Clin Transl Med. 11: e627, and Zhang Y. et al. Clin Transl Med 11, e649). LA CROSSE VIRUS INFECTION: La Crosse virus (LACV), a mosquito-borne orthobunyavirus, causes a rare, life-threatening neurological disease that results in 60 to 80 hospitalized pediatric encephalitis cases in the United States yearly. Currently, there is neither a vaccine nor an antiviral therapy approved by the Food and Drug Administration (FDA) to prevent or treat LACV. We have collaborated with researchers at NIAID for a drug repurposing screen of the approved and bioactive compound collections. A set of compounds were found that inhibited LACV virus-induced cell death in neuronal cell lines. The top hit, Rottlerin, reduced virus production in human inducible pluripotent stem cell-derived cerebral organoids that also confirmed in mice infected with LACV. The results were published in the journal of Nature Microbiology (Durbadal O. et al. Nat Microbiol 6, 1398-09). ZIKA AND DENGUE VIRUS INFECTIONS: Dengue virus (DENV) and Zika virus (ZIKV) are two closely related pathogens of the Flaviviridae family. They exhibit similar replicative processes but have distinct clinical outcomes. DENV was only isolated in 1943 and is still one of the most widespread global mosquito-borne viruses that contributes to symptoms in 96 million people and results in over 20,000 deaths each year. ZIKV was first discovered as a mild, obscure human pathogen in 1947, but has emerged as a major public health concern in the past few years largely due to its neuronal complications such as congenital microcephaly and GuillainBarre syndrome. Currently, there are no effective antiviral therapeutics for these two viral infections. We have collaborated with researchers at the Johns Hopkins University, Florida State University, and the University of Pennsylvania and performed a comprehensive protein network study on ZIKV and DENV. We have applied multiple screening technologies including a large human protein library screening, RNAi screening, and drug repurposing screening to analyze the interactions of interactions of ZIKV/DENV viral proteins with 20,240 human proteins. Multiple conserved cellular pathways and protein complexes including proteasome complexes were identified. This study provides a valuable multi-omics dataset resource for the ZIKV and DENV research community that also revealed new insights for understanding the molecular mechanisms of virushost interactions and pathogenesis (Guang S. et al. Genomics Proteomics Bioinformatics 38, 116119). DRUG COMBINATION THERAPY: Drug repurposing can be a very effective tool in rapidly identifying therapeutics for diseases lacking appropriate drug treatment. However, finding suitable drug candidates from repurposing screens can be challenging. First, drug repurposing screens may fail to identify any clinically useful compounds due to lack of activity and limited size of compound collections. Further, the identified hits may exhibit weak potency with effective concentration for 50% of the maximum response (IC50) values higher than the safely achievable plasma concentrations in humans indicating that they are not clinically useful for patient treatment. We performed drug combination screens in drug resistant ovarian cancer cells (as described in the above section) and identified several compounds that have synergy with cisplatin and overcome the existing resistance to cisplatin alone. We also have worked on drug combination screens using heparin binding compounds and autophagy regulating compounds (both identified in drug repurposing screens) against SARS-CoV-2 infection that are still in progress. We have reviewed the successful cases and reports for drug combination therapy (Shyr ZA. et al. Drug Combinations. A book chapter In: Kenakin, T. (Ed.), Comprehensive Pharmacology. vol. 2, pp. 789812; and Shyr ZA et al. Drug Discov Today 26:2367-76) that suggests that the drug combination therapy is an effective approach to enhance the success of drug repurposing and to effectively treat certain severe diseases. For example, treatments for chronic viral infections with single drugs have not been successful, as exemplified by human immunodeficiency virus (HIV) and hepatitis C virus (HCV) infections. Combination therapy for these diseases has led to improved clinical outcomes with dramatic reductions in viral load, morbidity, and mortality. Drug combinations can enhance therapeutic efficacy through additive, and ideally synergistic. This study will benefit our future research work on the drug repurposing and drug development.