Drug Repurposing Screening for Rare and Neglected Diseases

National Center For Advancing Translational Sciences

Investigators

Linked publications & trials

Abstract

In collaboration with NIH and external academic and industry researchers, we have carried out assay development and performed drug repurposing screens for multiple projects across a range of therapeutic areas, including COVID-19, rare genetic disorders and rare drug resistant cancers. DISEASE MODELING USING PATIENT IPSC-DERIVED CELLS: Disease modeling using patient cells is an effective approach to enable establishment of new alternative / non-animal disease models. Human induced pluripotent stem cells (iPSCs) 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 models are particularly useful for drug discovery and development for rare genetic diseases, as animal models are not always available. The patient derived iPSCs share the same genetic background with patients and have the same cellular disease phenotypes that are suitable for assay development to screen compounds. We have generated over 100 patient-derived iPSC lines for rare genetic diseases. In this period, we generated several iPSC lines from samples of Alagille Syndrome and healthy donors (Owusu-Ansah K et al., 2023. Stem Cell Res 71, 103135. PMID: 37393720). The iPSCs have been characterized and stably passaged over 10 passages. These iPSCs were differentiated to support generation of hepatocytes and liver organoids for ALGS disease modeling and assay development for repurposing screens. We have also deposited 6 patient iPSC lines previously generated, including for Mucopolysarcharidosis type I (MPS I) and Hunters syndrome (MPS II), to the Coriell Cell Repository as public resources to other researchers. 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 cells to the anticancer activities of the standard drugs. We found that terfenadine re-sensitized doxorubicin activity in drug-resistant ovarian cancer cells via inhibition of CaMKII/CREB1-mediated ABCB1 expression (Huang W et al., 2022. Front Oncology 12, 1068443. PMID: 36439493). We also found that PD1938306, a MEK inhibitor, enhances the efficacy of sorafenib (a standard therapeutic for liver cancer) in hepatocellular carcinoma cells through a repurposing screen (Hong J eta al. 2023. Comb Chem High Throughput Screen. 26: 1364-74. PMID: 36043792). These results are useful for further studies of the mechanisms of drug resistance and cancer target identification for new drug development. SARS-CoV-2 and COVID-19: We have developed a SARS-CoV-2 pseudotyped particle entry assay for use in BSL-2 laboratories to screen compound libraries and evaluate compound efficacy as SARS-CoV-2 entry inhibitors (Xu M et al. 2022. SLAS Discovery. 27:86-94. PMID: 35086793). We have also developed a homogenous compound screening assay that detects the nucleocapsid protein of SARS-CoV-2 in the viral replication process for high throughput screening in our collaborators BSL-3 lab (Gorshkov K et al. 2022. ACS Pharmacol Transl Sci 5, 8-19. PMID: 35036857). We performed repurposing screens using the pseudotyped particle assay and another assay to target the fusion process of SARS-CoV-2 infection (Park SB et al. 2022. mBio. e0323821. PMID: 35012356). Additionally, we collaborated with other NIH researchers on COVID-19 screens related to a nanobody against the SARS-CoV-2 spike protein, TMPRSS2 inhibitors, heparan-spike interaction, and estrogen receptor-spike interaction (Fu Y et al. 2022. PLoS One. 17: e0272364. PMID: 35947606; Shrimp JH. Et al. 2022. ACS Infect Dis. 8:1191-03. PMID: 35648838; Zhang Q. et al. 2022. Sci Rep. 12:6294. PMID: 35440680; Solis O et al. 2022. Sci Adv 8, eadd4150. PMID: 36449624). FOXG1 SYNDROME: FOXG1 Syndrome is a rare and debilitating neurodevelopmental disorder causing severe cognitive impairment. The disease is caused by heterozygous mutations in the transcription factor Forkhead Box G1 (FOXG1). Currently, there is no approved therapy for FOXG1 Syndrome. BELIEVE IN A CURE is a non-profit organization focused on developing treatments for FOXG1 syndrome. NCATS collaborated with the foundation to perform a drug repurposing screen in a FOXG1 reporter assay to identify up-regulators of the FOXG1 gene. Hits from the primary screen were further tested in a Western blot assay in patient iPSC-derived neural stem cells. NGLY1 DEFICIENCY: This is a low incidence genetic disease that primarily affects the neuronal system, resulting in neuromotor impairment, intellectual disability, and neuropathy. We have generated brain organoids using the NGLY1 patient iPSCs for disease modeling. We found that the patient midbrain organoids show altered neuronal development and reduced dopaminergic neurons compared to wild type organoids (Abbott J. et al. 2023. Front Cell Dev Biol. 11: 1039182. PMID: 36875753). We also worked on a neuromuscular junction platform using the patient iPSC-derived motor neurons to study the pathogenesis of disease. We observed reduced axon length, increased and shortened axon branches, motor neuron action potential bursting, and decreased action potential firing rate and amplitude in this system (Sasserath T. et al. 2022. Adv Ther 5:2200009, PMID: 36589922). The NGLY1 brain organoids and motor neurons are useful models for the study of disease mechanisms and evaluation of therapeutic candidates. LEBER CONGENITAL AMAUROSIS (LCA): LCA is an inherited disease of the eye that causes loss of sight in early childhood and lacks effective treatment. We performed a drug repurposing screen using retinal organoids differentiated from the iPSCs from a model of Leber congenital amaurosis. Reserpine, a drug used for the treatment of hypertension, was identified among a few other compounds that maintains photoreceptor survival in retinal ciliopathy (Chen HY. Et al. 2023. Elife, 12:e83205. PMID: 36975211). Currently, further study of the mechanism of action and potential preclinical development are in process. AI-BASED MODELING AND VIRTUAL SCREENING: Recent advancements in artificial intelligence (AI)- based modeling have enabled virtual compound screening for lead compound identification. The advantages of this approach for drug discovery are (1) a reduction in physical compound screening experiments that significantly decreases project costs; and (2) a significantly increased screening capacity, as virtual screens can cover in-house compound collections as well as large commercial collections (i.e., millions of compounds), both of which save time during the lead identification process. We have developed and optimized several AI-based compound screening tools that have been applied to several projects. The experimental screening data from a small compound collection (such as the collection of 2800 approved drugs available at NCATS) is typically used to establish, train, and optimize a computer model for a given project that is then employed in a virtual compound screen of larger compound collections (up to millions of compounds) to identify hits. After computerized hit selection and confirmation, the top list compounds (typically 50 to 200) are selected and ordered for a laboratory experiment to evaluate their activities. We have published the method of AI-based modeling and virtual screening using the SARS-CoV-2 entry inhibitor project as an example (Gao P et al., 2023. J Chem Inf Model. 62: 1988-97. PMID: 35404596) with several other manuscripts under preparation.