Synergy and Antagonism between Allosteric and Active‐Site Inhibitors of Abl Tyrosine Kinase

Abstract

Allosteric inhibitors of Abl kinase are being explored in the clinic, often in combination with ATP‐site inhibitors of Abl kinase. However, there are conflicting data on whether both ATP‐competitive inhibitors and myristoyl‐site allosteric inhibitors can simultaneously bind Abl kinase. Here, we determine whether there is synergy or antagonism between ATP‐competitive inhibitors and allosteric inhibitors of Abl. We observe that clinical ATP‐competitive inhibitors are not synergistic with allosteric ABL inhibitors, however, conformation‐selective ATP‐site inhibitors that modulate the global conformation of Abl can afford synergy. We demonstrate that kinase conformation is the key driver to simultaneously bind two compounds to Abl kinase. Finally, we explore the interaction of allosteric and conformation selective ATP‐competitive inhibitors in a series of biochemical and cellular assays.

Reply to Correspondence on “Synergy and Antagonism between Allosteric and Active‐Site Inhibitors of Abl Tyrosine Kinase”

“…This mismatch of conformation is the basis for the antagonism we observe between asciminib and clinical ATP‐competitive inhibitors. Consistent with the crystal structures of the ternary complex, we reported in our Communication that saturating concentrations of DAS‐DFGO‐II (an ATP‐competitive inhibitor that stabilizes the αC‐helix‐in, open kinase conformation [3, 4] )+asciminib leads to an αC‐helix‐in, open kinase (Figure 2B in our Communication) [2] …”

Correspondence on “Synergy and Antagonism between Allosteric and Active‐Site Inhibitors of Abl Tyrosine Kinase”**

“…Firstly, we employed NMR spectroscopy to investigate the simultaneous binding of asciminib and dasatinib to ABL1 kinase. According to the cellular combination experiments of Johnson et al., dasatinib is the most antagonistic ATP‐site binder in combination with asciminib [9] . However, our NMR data unambiguously show that even dasatinib can bind to a binary complex of ABL1 and asciminib to form a ternary complex (Figure 1; Supporting Information, Figures S1 and S2).…”

“…From their observation of weak antagonism between asciminib and ATP-site inhibitors in cellular experiments, Johnson et al conclude that "clinical ATP-competitive inhibitors cannot bind simultaneously to ABL with allosteric inhibitors". [9] While we appreciate the quality of the cellular combination experiments, we disagree with the conclusion that weak antagonism with combination indices between 1.24 and 1.44 means that both inhibitors cannot bind to ABL kinase at the same time. In our opinion, this would simply suggest that the binding affinity of the second drug is slightly weaker in the presence of the first drug, but both drugs can still bind simultaneously.…”

“…[8] Soellner and co-workers have published their findings from studies on combinations of ATP-competitive inhibitors and allosteric inhibitors that bind to the myristate pocket. [9] In experiments using mouse BaF3 cells engineered to be dependent upon the kinase activity of BCR-ABL1, they report weak antagonism of asciminib with ATP-competitive inhibitors, with combination indices (CI) ranging from 1.24 with nilotinib to 1.44 for dasatinib (the CI scale for antagonism is 1-∞, for synergy CI ranges between 1 and zero). [10] The authors then rationalise the observed weak antagonism by the fact that ATP-site inhibitors favour an open global conformation, while allosteric inhibitors bind to a closed global conformation.…”

Reply to Correspondence on “Synergy and Antagonism between Allosteric and Active‐Site Inhibitors of Abl Tyrosine Kinase”

“…While our main text listed only CI 75 values for the cellular synergy studies (which are solely considered in the Manley et al. Correspondence), the Supporting Information of our Communication lists all CI values we obtained [2] …”