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Clofarabine, a deoxyadenosine analog, was a potent hit in our in vitro high-throughput screening against murine ependymoma neurospheres. To prioritize clofarabine for further preclinical efficacy studies, we evaluated the plasma pharmacokinetic (PK) disposition and central nervous system penetration in a murine model of ependymoma. A plasma PK study of clofarabine (45 mg/kg IP) was performed using CD1 nude mice bearing ependymoma cortical allographs (Ink4a/Arf-null + RTBDN) to obtain initial plasma PK parameters. These estimates were used to derive D-optimal plasma sampling time-points (e.g., 0.25, 2.5, and 5 hr) for cerebral microdialysis studies. Comparison of the clofarabine systemic exposure obtained from the plasma PK study and that simulated from pediatric patients using a published population PK model (Bonate, Cancer Chemotherap Pharmacol, 2011) suggested a dosage of 30 mg/kg in mice would be equivalent to a pediatric dosage of 180 mg/m2 given as a 2 hr infusion. Cerebral microdialysis was applied in CD1 nude mice bearing ependymoma cortical allographs (Ink4a/Arf-null + RTBDN), which permitted repeated in situ sampling of clofarabine tumor extracellular fluid (tECF). A microdialysis probe (BASi; 1 mm membrane) was introduced into the tumor through a cannula inserted during tumor cell implantation. After microdialysis probe equilibration, 7 mice were dosed with 30 mg/kg of clofarabine IP. In each mouse, serial plasma samples were collected at 0.25, 2.5, and 5 h post-dose, and tECF dialysate fractions were collected over 60 min intervals for up to 5 h post-dose. To measure clofarabine in both plasma and tECF, a robust, sensitive LC-MS/MS method was developed and validated. Both within-day and between-day precision (%CV) were ≤ 5.1% and accuracy ranged from 86% to 109%. A two-compartment model with absorption and tumor compartments linked to a central compartment was fitted to plasma and tECF concentration-time data using a nonlinear mixed effects modeling approach (NONMEM 7.2.0). For modeling purposes, the volume of the tECF compartment was fixed to published values. Unbound fraction of clofarabine in murine plasma was 0.82 ± 0.14. The model derived area under unbound concentration-time curve (AUCu,0-8) values for 30 and 45 mg/kg dosages were 5185 ± 550 µg/L*hr and 7677 ± 699 µg/L*hr, respectively. Clofarabine was absorbed rapidly from the peritoneal cavity with Tmax (time to reach maximum concentration) value of 0.33 ± 0.17 hr. Tumor to plasma partition coefficient (Kpt,uu: ratio of tumor to plasma AUCu,0-inf) of clofarabine was 0.12 ± 0.05. The model predicted mean tECF clofarabine concentrations were below the in vitro 1-hr IC50 (1.34 µM) for ependymoma neurospheres. In summary, we have shown the tECF clofarabine concentrations were below that required for antitumor effect in our in vitro washout studies, thus we have not pursued clofarabine for detailed efficacy studies in our preclinical pipeline. Citation Format: Yogesh T. Patel, Megan O. Jacus, Abigail D. Davis, Pradeep Vuppala, Jason D. Dapper, Burgess B. Freeman, Nidal Boulos, Stacy L. Throm, Richard J. Gilbertson, Clinton F. Stewart. Clofarabine, a potent anticancer compound with limited penetration in an orthotopic murine model of ependymoma. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4645. doi:10.1158/1538-7445.AM2014-4645