Analysis of in Vitro Activity of the Clinically-Active ABL/FLT3 Inhibitor Ponatinib (AP24534) Against AC220-Resistant FLT3-ITD Mutants

Activating mutations in FLT3 are detected in approximately 30 percent of adult acute myeloid leukemia (AML) cases, most commonly in-tandem duplication (ITD) events. Ponatinib (AP24534) is a potent inhibitor of ABL and FLT3 that has shown clinical activity in CML as well as in a limited experience with FLT3-ITD-positive acute myeloid leukemia (AML) with 2/7 kinase inhibitor-naïve AML patients achieving CRi in a phase I study (Talpaz et al, ASCO 2011, abstract #6518). We recently reported that the FLT3 inhibitor AC220, which has achieved an interim composite CR rate of 43% in a phase II study in relapsed/refractory AML (Cortes, et al, EHA 2011, abstract #1019) is vulnerable to a limited number of resistance-conferring kinase domain mutations in vitro (Smith et al, AACR 2011, abstract #4737). Mutations at 2 of these residues, F691 and D835, have been identified in 9/9 FLT3-ITD+ patients who relapsed after achieving clearance of bone marrow blasts on AC220 (Smith et al, ASH 2011, submitted). Notably, AC220-resistant mutations were found to confer cross-resistance to sorafenib. Given that ponatinib retains activity against a wide range of TKI-resistant BCR-ABL mutants, we sought to test its activity against AC220-resistant mutants.

We assessed the activity of ponatinib against highly AC220-resistant FLT3-ITD mutations F691I/L, D835V/Y and Y842C/H. Ponatinib potently suppressed the growth of Ba/F3 cells transformed with native FLT3-ITD with an inhibitory concentration 50 (IC50) of 2 nM. Ba/F3 cells transformed with the “gatekeeper” F691I mutation retained sensitivity to ponatinib at a similar concentration (5 nM). This substitution is analogous to the BCR-ABL T315I mutation, which is clinically sensitive to ponatinib. The remaining AC220-resistant FLT3-ITD mutants, including the gatekeeper F691L substitution, conferred a substantial degree of relative cross-resistance to ponatinib. Mutations at the activation loop residue D835 confer the highest degree of resistance. In an effort to identify other substitutions in FLT3-ITD that are capable of conferring ponatinib resistance in vitro, we employed an in vitro mutagenesis strategy (Azam et al, Cell, 2003) of FLT3-ITD in varying concentrations of ponatinib. In a preliminary analysis, we have identified resistance-causing substitutions at D835, as well as other residues in the FLT3 activation loop including D839 and N841. Interestingly, one of these substitutions, D835N, confers resistance to ponatinib but not to AC220.

A molecular analysis of the ponatinib/FLT3 complex based on the crystal structure of ABL/ponatinib was performed and revealed that isoleucine substitution at the FLT3 “gatekeeper” residue (F691I), as with the T315I mutation in Abl, does not creates substantial steric clash with ponatinib. In contrast, the leucine substitution, (F691L), is more bulky than isoleucine and may cause more steric hindrance. In addition, as leucine is more rigid than isoleucine, more energy would be required for the F691L mutation to adopt a conformation compatible with ponatinib binding. As ponatinib binds to the “DFG-out” inactive conformation of FLT3, activation loop mutations such as D835V/Y and Y842C/H likely destabilize the activation loop conformation of FLT3 required for ponatinib binding.

Our studies demonstrate that gatekeeper and, in particular, activation loop substitutions in FLT3-ITD, confer a high degree of cross-resistance to the clinically-active FLT3 TKIs described to date. Ponatinib retains in vitro activity against the gatekeeper mutation FLT3-ITD/F691I, which confers a high degree of in vitro resistance to AC220, but leucine substitution at this residue notably confers a higher degree of resistance to ponatinib. Activation loop mutations confer substantial degrees of in vitro cross-resistance to ponatinib and are predicted to confer clinical resistance. Select substitutions at D835 appear to confer selective resistance to ponatinib. Categorization of the spectrum of resistance-conferring mutations may facilitate a more personalized approach toward patients with FLT3-ITD+ AML treated with clinically-active TKI therapy.

Off Label Use: Investigational agent ponatinib will be discussed. Zhu:Ariad Pharmaceuticals: Employment. Shah:Ariad: Consultancy, Research Funding; Novartis: Consultancy; Bristol-Myers Squibb: Consultancy, Research Funding.