{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,9]],"date-time":"2024-09-09T17:53:28Z","timestamp":1725904408561},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"24","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,12,15]]},"abstract":"Abstract<\/jats:title>\n Motivation: Off-target interactions of a popular immunosuppressant Cyclosporine A (CSA) with several proteins besides its molecular target, cyclophilin A, are implicated in the activation of signaling pathways that lead to numerous side effects of this drug.<\/jats:p>\n Results: Using structural human proteome and a novel algorithm for inverse ligand binding prediction, ILbind, we determined a comprehensive set of 100+ putative partners of CSA. We empirically show that predictive quality of ILbind is better compared with other available predictors for this compound. We linked the putative target proteins, which include many new partners of CSA, with cellular functions, canonical pathways and toxicities that are typical for patients who take this drug. We used complementary approaches (molecular docking, molecular dynamics, surface plasmon resonance binding analysis and enzymatic assays) to validate and characterize three novel CSA targets: calpain 2, caspase 3 and p38 MAP kinase 14. The three targets are involved in the apoptotic pathways, are interconnected and are implicated in nephrotoxicity.<\/jats:p>\n Contact: \u00a0lkurgan@ece.ualberta.ca<\/jats:p>\n Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu581","type":"journal-article","created":{"date-parts":[[2014,8,30]],"date-time":"2014-08-30T00:28:26Z","timestamp":1409358506000},"page":"3561-3566","source":"Crossref","is-referenced-by-count":34,"title":["Human structural proteome-wide characterization of Cyclosporine A targets"],"prefix":"10.1093","volume":"30","author":[{"given":"Gang","family":"Hu","sequence":"first","affiliation":[{"name":"1 School of Mathematical Sciences and LPMC, Nankai University, Tianjin, 300071, PR China, 2 Department of Biochemistry, 3 Faculty of Pharmacy and Pharmaceutical Sciences, 4 Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, T6G 2R3, Canada and 5 State Key Laboratory for Medicinal Chemical Biology, Nankai University, Tianjin, 300071, PR China"}]},{"given":"Kui","family":"Wang","sequence":"additional","affiliation":[{"name":"1 School of Mathematical Sciences and LPMC, Nankai University, Tianjin, 300071, PR China, 2 Department of Biochemistry, 3 Faculty of Pharmacy and Pharmaceutical Sciences, 4 Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, T6G 2R3, Canada and 5 State Key Laboratory for Medicinal Chemical Biology, Nankai University, Tianjin, 300071, PR China"}]},{"given":"Jody","family":"Groenendyk","sequence":"additional","affiliation":[{"name":"1 School of Mathematical Sciences and LPMC, Nankai University, Tianjin, 300071, PR China, 2 Department of Biochemistry, 3 Faculty of Pharmacy and Pharmaceutical Sciences, 4 Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, T6G 2R3, Canada and 5 State Key Laboratory for Medicinal Chemical Biology, Nankai University, Tianjin, 300071, PR China"}]},{"given":"Khaled","family":"Barakat","sequence":"additional","affiliation":[{"name":"1 School of Mathematical Sciences and LPMC, Nankai University, Tianjin, 300071, PR China, 2 Department of Biochemistry, 3 Faculty of Pharmacy and Pharmaceutical Sciences, 4 Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, T6G 2R3, Canada and 5 State Key Laboratory for Medicinal Chemical Biology, Nankai University, Tianjin, 300071, PR China"}]},{"given":"Marcin J.","family":"Mizianty","sequence":"additional","affiliation":[{"name":"1 School of Mathematical Sciences and LPMC, Nankai University, Tianjin, 300071, PR China, 2 Department of Biochemistry, 3 Faculty of Pharmacy and Pharmaceutical Sciences, 4 Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, T6G 2R3, Canada and 5 State Key Laboratory for Medicinal Chemical Biology, Nankai University, Tianjin, 300071, PR China"}]},{"given":"Jishou","family":"Ruan","sequence":"additional","affiliation":[{"name":"1 School of Mathematical Sciences and LPMC, Nankai University, Tianjin, 300071, PR China, 2 Department of Biochemistry, 3 Faculty of Pharmacy and Pharmaceutical Sciences, 4 Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, T6G 2R3, Canada and 5 State Key Laboratory for Medicinal Chemical Biology, Nankai University, Tianjin, 300071, PR China"},{"name":"1 School of Mathematical Sciences and LPMC, Nankai University, Tianjin, 300071, PR China, 2 Department of Biochemistry, 3 Faculty of Pharmacy and Pharmaceutical Sciences, 4 Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, T6G 2R3, Canada and 5 State Key Laboratory for Medicinal Chemical Biology, Nankai University, Tianjin, 300071, PR China"}]},{"given":"Marek","family":"Michalak","sequence":"additional","affiliation":[{"name":"1 School of Mathematical Sciences and LPMC, Nankai University, Tianjin, 300071, PR China, 2 Department of Biochemistry, 3 Faculty of Pharmacy and Pharmaceutical Sciences, 4 Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, T6G 2R3, Canada and 5 State Key Laboratory for Medicinal Chemical Biology, Nankai University, Tianjin, 300071, PR China"}]},{"given":"Lukasz","family":"Kurgan","sequence":"additional","affiliation":[{"name":"1 School of Mathematical Sciences and LPMC, Nankai University, Tianjin, 300071, PR China, 2 Department of Biochemistry, 3 Faculty of Pharmacy and Pharmaceutical Sciences, 4 Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, T6G 2R3, Canada and 5 State Key Laboratory for Medicinal Chemical Biology, Nankai University, Tianjin, 300071, PR 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