Analysis of Imatinib and Sorafenib Binding to p38α Compared with c-Abl and b-Raf Provides Structural Insights for Understanding the Selectivity of Inhibitors Targeting the DFG-Out Form of Protein Kinases

Abstract

Protein kinases c-Abl, b-Raf, and p38alpha are recognized as important targets for therapeutic intervention. c-Abl and b-Raf are major targets of marketed oncology drugs Imatinib (Gleevec) and Sorafenib (Nexavar), respectively, and BIRB-796 is a p38alpha inhibitor that reached Phase II clinical trials. A shared feature of these drugs is the fact that they bind to the DFG-out forms of their kinase targets. Although the discovery of this class of kinase inhibitors has increased the level of emphasis on the design of DFG-out inhibitors, the structural determinants for their binding and stabilization of the DFG-out conformation remain unclear. To improve our understanding of these determinants, we determined cocrystal structures of Imatinib and Sorafenib with p38alpha. We also conducted a detailed analysis of Imatinib and Sorafenib binding to p38alpha in comparison with BIRB-796, including binding kinetics, binding interactions, the solvent accessible surface area (SASA) of the ligands, and stabilization of key structural elements of the protein upon ligand binding. Our results yield an improved understanding of the structural requirements for stabilizing the DFG-out form and a rationale for understanding the genesis of ligand selectivity among DFG-out inhibitors of protein kinases.

Sorafenib Overcomes Irinotecan Resistance in Colorectal Cancer by Inhibiting the ABCG2 Drug-Efflux Pump

“…We have recently published that p38 MAPK is induced by SN-38 and is responsible for the development of resistance to and that the use of p38 inhibitor can enhance the cytotoxic activity of SN-38 (9). Interestingly, we have found that sorafenib can inhibit the p38 activation mediated by irinotecan in vivo, confirming its inhibitory effect shown by Namboodiri and Grossi, respectively, in vitro and in cellulo (39,40). Therefore, sorafenib, by inhibiting the MAPK p38 pathway make the cells more sensitive to irinotecan.…”

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

“…The total standard binding free energies of Gleevec, ΔG (°) , accounting for the thermodynamic contributions associated with the conformational change of the DFG-flip in apo kinase (ΔG in→out ) and the ligand-binding free energy to the DFG-out conformation, are −9.4 kcal/mol and −1.4 kcal/mol for Abl and c-Src, respectively. The measured inhibitory potency of the drug for unphosphorylated Abl and c-Src is 0.013 μM and 31.1 μM, respectively, corresponding to a standard binding affinity of −10.8 kcal/mol and −6.2 kcal/mol, respectively (7,20). The poorer agreement for c-Src may be due to the fact that 13 residues from the A-loop, unresolved in the X-ray structure, were modeled from the inactive conformation.…”

Sorafenib inhibits p38α activity in colorectal cancer cells and synergizes with the DFG-in inhibitor SB202190 to increase apoptotic response

“…It has also been shown to target the DFG-out conformational state of p38α and to affect p38α kinase activity in vitro. 13,14 Sorafenib induces apoptosis by downregulating Mcl-1 in several cell lines and xenografted tumors, including HT-29 and HCT-116 CRC cells. 13,15,16 It has been approved for clinical use by the FDA in hepatocellular carcinoma (HCC) and renal cell carcinoma (RCC), but failed to prove efficacy in CRC Figure 1.…”

“…1) of BRAF and p38α. 13,14 Notwithstanding, clinical trials failed to demonstrate a beneficial effect for sorafenib in CRC patients.…”