title: Identification of a Selective G1-Phase Benzimidazolone Inhibitor by a Senescence-Targeted Virtual Screen Using Artificial Neural Networks.
abstract: Cellular senescence is a barrier to tumorigenesis in normal cells, and tumor cells undergo senescence responses to genotoxic stimuli, which is a potential target phenotype for cancer therapy. However, in this setting, mixed-mode responses are common with apoptosis the dominant effect. Hence, more selective senescence inducers are required. Here we report a machine learning-based in silico screen to identify potential senescence agonists. We built profiles of differentially affected biological process networks from expression data obtained under induced telomere dysfunction conditions in colorectal cancer cells and matched these to a panel of 17 protein targets with confirmatory screening data in PubChem. We trained a neural network using 3517 compounds identified as active or inactive against these targets. The resulting classification model was used to screen a virtual library of ~2M lead-like compounds. One hundred and forty-seven virtual hits were acquired for validation in growth inhibition and senescence-associated β-galactosidase assays. Among the found hits, a benzimidazolone compound, CB-20903630, had low micromolar IC50 for growth inhibition of HCT116 cells and selectively induced senescence-associated β-galactosidase activity in the entire treated cell population without cytotoxicity or apoptosis induction. Growth suppression was mediated by G1 blockade involving increased p21 expression and suppressed cyclin B1, CDK1, and CDC25C. In addition, the compound inhibited growth of multicellular spheroids and caused severe retardation of population kinetics in long-term treatments. Preliminary structure-activity and structure clustering analyses are reported, and expression analysis of CB-20903630 against other cell cycle suppressor compounds suggested a PI3K/AKT-inhibitor-like profile in normal cells, with different pathways affected in cancer cells.
authors.affiliation: Institute of Cancer Sciences, University of Glasgow, Wolfson Wohl Cancer Research Centre, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, UK.
authors.forename: Alan E
authors.initials: AE
authors.lastname: Bilsland
authors.affiliation: Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK.
authors.forename: Angelo
authors.initials: A
authors.lastname: Pugliese
authors.affiliation: Institute of Cancer Sciences, University of Glasgow, Wolfson Wohl Cancer Research Centre, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, UK.
authors.forename: Yu
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Institute of Cancer Sciences, University of Glasgow, Wolfson Wohl Cancer Research Centre, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, UK.
authors.forename: John
authors.initials: J
authors.lastname: Revie
authors.affiliation: Institute of Cancer Sciences, University of Glasgow, Wolfson Wohl Cancer Research Centre, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, UK.
authors.forename: Sharon
authors.initials: S
authors.lastname: Burns
authors.affiliation: Institute of Cancer Sciences, University of Glasgow, Wolfson Wohl Cancer Research Centre, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, UK.
authors.forename: Carol
authors.initials: C
authors.lastname: McCormick
authors.affiliation: Institute of Cancer Sciences, University of Glasgow, Wolfson Wohl Cancer Research Centre, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, UK.
authors.forename: Claire J
authors.initials: CJ
authors.lastname: Cairney
authors.affiliation: Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK.
authors.forename: Justin
authors.initials: J
authors.lastname: Bower
authors.affiliation: Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK.
authors.forename: Martin
authors.initials: M
authors.lastname: Drysdale
authors.affiliation: University of Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre Robinson Way, Cambridge, CB2 0RE, UK.
authors.forename: Masashi
authors.initials: M
authors.lastname: Narita
authors.affiliation: Kyoto University, Graduate School of Biostudies, Yoshidakonoe-cho, Sakyo-ku Kyoto 606-8501 Japan.
authors.forename: Mahito
authors.initials: M
authors.lastname: Sadaie
authors.affiliation: Institute of Cancer Sciences, University of Glasgow, Wolfson Wohl Cancer Research Centre, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, UK. Electronic address: nicol.keith@glasgow.ac.uk.
authors.forename: W Nicol
authors.initials: WN
authors.lastname: Keith
mesh_terms: D001562:Benzimidazoles / Q000008:administration & dosage* / Q000378:metabolism; D016922:Cellular Senescence / Q000187:drug effects* / Q000502:physiology; D004305:Dose-Response Relationship, Drug; D016193:G1 Phase / Q000187:drug effects* / Q000502:physiology; D053263:Gene Regulatory Networks / Q000187:drug effects* / Q000502:physiology; D045325:HCT116 Cells; D006801:Humans; D016571:Neural Networks, Computer; D014584:User-Computer Interface
chemical_list: D001562:Benzimidazoles; C014353:benzimidazolone