Explaining why Gleevec is a specific and potent inhibitor of Abl kinase

Abstract

Tyrosine kinases present attractive drug targets for specific types of cancers. Gleevec, a well-known therapeutic agent against chronic myelogenous leukemia, is an effective inhibitor of Abl tyrosine kinase. However, Gleevec fails to inhibit closely homologous tyrosine kinases, such as c-Src. Because many structural features of the binding site are conserved, the molecular determinants responsible for binding specificity are not immediately apparent. Some have attributed the difference in binding specificity of Gleevec to subtle variations in ligand-protein interactions (binding affinity control), whereas others have proposed that it is the conformation of the DFG motif, in which ligand binding is only accessible to Abl and not to c-Src (conformational selection control). To address this issue, the absolute binding free energy was computed using all-atom molecular dynamics simulations with explicit solvent. The results of the free energy simulations are in good agreement with experiments, thereby enabling a meaningful decomposition of the binding free energy to elucidate the factors controlling Gleevec's binding specificity. The latter is shown to be controlled by a conformational selection mechanism and also by differences in key van der Waals interactions responsible for the stabilization of Gleevec in the binding pocket of Abl.

Fig. 1.

Structural comparison of Abl and c-Src in the Gleevec-bound kinase domain.

Fig. 2.

One-dimensional PMF of DFG-flip in Abl (red line) and c-Src (blue line) as a function of χ ≡ Ala380C β-Ala380C α-Asp381C α-Asp381C γ (Abl numbering).

Fig. 3.

PMFs of rmsd of Gleevec in bulk solution (black line) and in the binding sites of Abl (red line) and c-Src (blue line).

Fig. 4.

(Top) Difference in the average interaction energies of the DFG-flip ΔΔE between Abl and c-Src as a function of residue index. ΔΔE is defined as [E(DFG-out, c-Abl) − E(DFG-in, c-Abl)] − [E(DFG-out, c-Src) − E(DFG-in, c-Src),] where E represents the average interaction energy of a conformation in a kinase (calculated over 500 structures). Residues with a ||ΔΔE|| greater than 0.5 kcal/mol are marked explicitly, and their corresponding indices in the sequence are also shown. In the text boxes displaying residue indices, Abl residues are on the top and c-Src residues are at the bottom. The ΔΔE values of residues ranging from index 320–350 or larger than 402 were negligible (not shown). The ΔΔE of water, which is 9.36 kcal/mol, is truncated to fit within the plot. (Middle) rmsd between Abl and c-Src X-ray structures (truncated at 15 Å). (Bottom) Difference in the average interaction kinase–ligand interaction energies ΔE between Abl and c-Src as a function of residue index. ΔE is defined as [E(Abl) − E(Src)], where E represents the average interaction energy of Gleevec with a given kinase (calculated over 550 structures). The ΔE values of Ile360, His361, and water (−8.22, 7.14, and −7.32 kcal/mol, respectively) were truncated at 4 kcal/mol to fit within the plot.