{"doi":"10.1101/2020.10.23.352666","title":"Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19","abstract":"Abstract The novel SARS-CoV-2 virus emerged in December 2019 and has few effective treatments. We applied a computational drug repositioning pipeline to SARS-CoV-2 differential gene expression signatures derived from publicly available data. We utilized three independent published studies to acquire or generate lists of differentially expressed genes between control and SARS-CoV-2-infected samples. Using a rank-based pattern matching strategy based on the Kolmogorov-Smirnov Statistic, the signatures were queried against drug profiles from Connectivity Map (CMap). We validated sixteen of our top predicted hits in live SARS-CoV-2 antiviral assays in either Calu-3 or 293T-ACE2 cells. Validation experiments in human cell lines showed that 11 of the 16 compounds tested to date (including clofazimine, haloperidol and others) had measurable antiviral activity against SARS-CoV-2. These initial results are encouraging as we continue to work towards a further analysis of these predicted drugs as potential therapeutics for the treatment of COVID-19.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2020,"id":121339,"datarank":0.42623281619473546,"base_score":2.0794415416798357,"endowment":2.0794415416798357,"self_citation_contribution":0.31191623125197543,"citation_network_contribution":0.11431658494276004,"self_endowment_contribution":0.31191623125197543,"citer_contribution":0.11431658494276004,"corpus_percentile":null,"corpus_rank":null,"citation_count":7,"citer_count":6,"citers_with_citation_signal":5,"citers_with_endowment":5,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9341,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":56514,"name":"Gaia Andreoletti","orcid":"0000-0002-0452-0009","position":1,"is_corresponding":false},{"id":559243,"name":"Tomiko Oskotsky","orcid":"0000-0001-7393-5120","position":2,"is_corresponding":false},{"id":560691,"name":"Albert Vallejo-Gracia","orcid":"0000-0003-4815-5039","position":3,"is_corresponding":false},{"id":1477,"name":"Romel Rosales","orcid":"0000-0001-5326-4753","position":4,"is_corresponding":false},{"id":95641,"name":"Katharine Yu","orcid":"0000-0001-8310-8815","position":5,"is_corresponding":false},{"id":52431,"name":"Idit Kosti","orcid":"0000-0003-2212-5472","position":6,"is_corresponding":false},{"id":227698,"name":"Kristoffer E. Leon","orcid":"0000-0003-2424-0458","position":7,"is_corresponding":false},{"id":238106,"name":"Daniel Bunis","orcid":"0000-0002-0010-1616","position":8,"is_corresponding":false},{"id":560692,"name":"Christine Li","orcid":"0009-0007-7360-5958","position":9,"is_corresponding":false},{"id":107216,"name":"G. Renuka Kumar","orcid":"0000-0001-6090-3285","position":10,"is_corresponding":false},{"id":1481,"name":"Kris M. White","orcid":"0000-0003-0889-0506","position":11,"is_corresponding":false},{"id":1489,"name":"Adolfo Garcı́a-Sastre","orcid":"0000-0002-6551-1827","position":12,"is_corresponding":false},{"id":103701,"name":"Mélanie Ott","orcid":"0000-0002-5697-1274","position":13,"is_corresponding":false},{"id":2824,"name":"Marina Sirota","orcid":"0000-0002-7246-6083","position":14,"is_corresponding":false},{"id":482706,"name":"Brian L. Le","orcid":"0009-0000-4062-094X","position":0,"is_corresponding":true}],"reference_count":55,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-18T23:14:42.734024Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}