Ibrutinib targets mutant-EGFR kinase with a distinct binding conformation.
Ibrutinib, a clinically approved irreversible BTK kinase inhibitor for Mantle Cell Lymphoma (MCL) and Chronic Lymphocytic Leukemia (CLL) etc, has been reported to be potent against EGFR mutant kinase and currently being evaluated in clinic for Non Small Cell Lung Cancer (NSCLC). Through EGFR wt/mutant engineered isogenic BaF3 cell lines we confirmed the irreversible binding mode of Ibrutinib with EGFR wt/mutant kinase via Cys797. However, comparing to typical irreversible EGFR inhibitor, such as WZ4002, the washing-out experiments revealed a much less efficient covalent binding for Ibrutinib. The biochemical binding affinity examination in the EGFR L858R/T790M kinase revealed that, comparing to more efficient irreversible inhibitor WZ4002 (Kd: 0.074 μM), Ibrutinib exhibited less efficient binding (Kd: 0.18 μM). An X-ray crystal structure of EGFR (T790M) in complex with Ibrutinib exhibited a unique DFG-in/c-Helix-out inactive binding conformation, which partially explained the less efficiency of covalent binding and provided insight for further development of highly efficient irreversible binding inhibitor for the EGFR mutant kinase. These results also imply that, unlike the canonical irreversible inhibitor, sustained effective concentration might be required for Ibrutinib in order to achieve the maximal efficacy in the clinic application against EGFR driven NSCLC.
High Magnetic Field Laboratory, Chinese Academy of Sciences, Anhui, Hefei 230031, P. R. China.|University of Science and Technology of China, Anhui, Hefei 230036, P. R. China.
Aoli
A
Wang
Institute of Systems Biomedicine, Department of Biophysics, Beijing Key Laboratory of Tumor Systems Biology and Center for Molecular and Translational Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, P. R. China.
Xiao-E
XE
Yan
High Magnetic Field Laboratory, Chinese Academy of Sciences, Anhui, Hefei 230031, P. R. China.|University of Science and Technology of China, Anhui, Hefei 230036, P. R. China.
Hong
H
Wu
High Magnetic Field Laboratory, Chinese Academy of Sciences, Anhui, Hefei 230031, P. R. China.|Hefei Science Center, Chinese Academy of Sciences, Anhui, Hefei 230031, P. R. China.
Wenchao
W
Wang
High Magnetic Field Laboratory, Chinese Academy of Sciences, Anhui, Hefei 230031, P. R. China.|University of Science and Technology of China, Anhui, Hefei 230036, P. R. China.
Chen
C
Hu
High Magnetic Field Laboratory, Chinese Academy of Sciences, Anhui, Hefei 230031, P. R. China.|University of Science and Technology of China, Anhui, Hefei 230036, P. R. China.
Cheng
C
Chen
High Magnetic Field Laboratory, Chinese Academy of Sciences, Anhui, Hefei 230031, P. R. China.|Hefei Science Center, Chinese Academy of Sciences, Anhui, Hefei 230031, P. R. China.
Zheng
Z
Zhao
Institute of Systems Biomedicine, Department of Biophysics, Beijing Key Laboratory of Tumor Systems Biology and Center for Molecular and Translational Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, P. R. China.
Peng
P
Zhao
High Magnetic Field Laboratory, Chinese Academy of Sciences, Anhui, Hefei 230031, P. R. China.
Xixiang
X
Li
High Magnetic Field Laboratory, Chinese Academy of Sciences, Anhui, Hefei 230031, P. R. China.|University of Science and Technology of China, Anhui, Hefei 230036, P. R. China.
Li
L
Wang
High Magnetic Field Laboratory, Chinese Academy of Sciences, Anhui, Hefei 230031, P. R. China.|University of Science and Technology of China, Anhui, Hefei 230036, P. R. China.
Beilei
B
Wang
Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, P. R. China.
Zi
Z
Ye
Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.|Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
Jinhua
J
Wang
Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, P. R. China.
Chu
C
Wang
Collaborative Innovation Center of Cancer Medicine, National Institute of Biological Sciences, Beijing 102206, P. R. China.
Wei
W
Zhang
Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.|Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
Nathanael S
NS
Gray
Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.
Ellen L
EL
Weisberg
Collaborative Innovation Center of Cancer Medicine, National Institute of Biological Sciences, Beijing 102206, P. R. China.
Liang
L
Chen
High Magnetic Field Laboratory, Chinese Academy of Sciences, Anhui, Hefei 230031, P. R. China.|Hefei Science Center, Chinese Academy of Sciences, Anhui, Hefei 230031, P. R. China.
Jing
J
Liu
Institute of Systems Biomedicine, Department of Biophysics, Beijing Key Laboratory of Tumor Systems Biology and Center for Molecular and Translational Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, P. R. China.
Cai-Hong
CH
Yun
High Magnetic Field Laboratory, Chinese Academy of Sciences, Anhui, Hefei 230031, P. R. China.|University of Science and Technology of China, Anhui, Hefei 230036, P. R. China.|Hefei Science Center, Chinese Academy of Sciences, Anhui, Hefei 230031, P. R. China.
Qingsong
Q
Liu
D000178:Acrylamides / Q000494:pharmacology; D000225:Adenine / Q000031:analogs & derivatives; D002289:Carcinoma, Non-Small-Cell Lung / Q000188:drug therapy; D045744:Cell Line, Tumor; D066246:ErbB Receptors / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000235:genetics; D006801:Humans; D008175:Lung Neoplasms / Q000188:drug therapy; D008968:Molecular Conformation; D009154:Mutation; D010880:Piperidines; D047428:Protein Kinase Inhibitors / Q000494:pharmacology*; D011720:Pyrazoles / Q000737:chemistry / Q000378:metabolism / Q000494:pharmacology*; D011743:Pyrimidines / Q000737:chemistry / Q000378:metabolism / Q000494:pharmacology*
D000178:Acrylamides; D010880:Piperidines; D047428:Protein Kinase Inhibitors; D011720:Pyrazoles; D011743:Pyrimidines; C551803:ibrutinib; C571455:WZ4002; D066246:ErbB Receptors; D000225:Adenine
DFG-in/c-Helix-out; EGFR kinase; Ibrutinib; NSCLC; inactive conformation