Computational Analyses of Human Kinome against EGFR-TKIs using Homology Modeling and Molecular Docking Approaches Orathai Sawatdichaikul Institute of Food Research and Product Development Adisak Ongsawas, Kiattawee Choowongkomon Department of Biochemistry, Faculty of Science

Human Kinome 2 G.Manning Science 2002

Human Kinome 3 G.Manning Science 2002

Protein Tyrosine Kinases 4 31 sub-families 91 tyrosine kinase proteins G.Manning Science 2002

5 Protein Tyrosine Kinases

6 Hanahan and Weinberg, Cell 2000 Protein Tyrosine Kinases

7 91 Human tyrosine kinase proteins PDB (available) Retrieve 3D- structure (PDB file) Retrieve primary sequence(s) Sequence alignment Homology modeling Protein preparation Molecular Docking NoYes

The Structures of PTKs in Protein Data Bank (PDB) 8 Only 51 PTKs exist, other 40 PTKs still unavailable

9 91 Human tyrosine kinase proteins PDB (available) Retrieve 3D- structure (PDB file) Protein preparation Molecular Docking NoYes Retrieve primary sequence(s) Sequence alignment Homology modeling

10

11 91 Human tyrosine kinase proteins PDB (available) Retrieve 3D- structure (PDB file) Protein preparation Molecular Docking NoYes Retrieve primary sequence(s) Sequence alignment Homology modeling ErbBs-TK inhibitors

EGFRs-TK inhibitors 12 Lapatinib 0 UN Hydrazone Gefitinib Oxime inhibitor AEE 788 Erlotinib Neratinib 03 Q TAK- 285 Approved drug for lung and breast cancers

EGFR-TKIs and ErbB2-TKIs 13 Gefitinib Erlotinib Lapatinib Neretinib 0 UN EGFR-TKIs Dual-TKIs (binding with EGFR and/or ErbB 2 )

EGFR-TKIs and ErbB2-TKIs 14 Hydrazone Oxime inhibitor 03 Q TAK- 285 AEE 788 Dual-TKIs (binding with EGFR and/or ErbB 2 )

15 Docked-score chart Hydrazone Oxime inhibitor Lapatinib

Conclusions 16  The post-docking analysis suggested that all ligands can bind tightly into ATP-binding pocket of ErbB members and can bind to some tyrosine kinase proteins (JAK2, KDR, PDGFRa, HCK, BLK, TYRO 3, EphA 2, EphA 3, EphA 5, EphA 10, EphB 4, IRR, INSR, ROS, RYK, ABL 2, ZAP 70, FGFR 1, FGFR 3, FGFR 4 and TYK 2 ~b).  However, they cannot form strong interaction with the binding site of TIE, FES, FAK and SuRTK106 families.

Conclusions 17  Because of their low specificity, pyrrolotriazine inhibitors can bind to the binding sites of many PTKs.  Interestingly, one of the EGFR-HER2 dual inhibitors, lapatinib, can bind to activation site of most SRC family members. Hydrazone Oxime inhibitor

Benefits 18  Be able to apply this protocol to predict the binding affinity of the other small molecules among human tyrosine kinases with rapid and efficient

Further plans 19  Implement inhibitors of the other tyrosine kinase families to observe the selectivity profile  Improve the protocol for applying with the set of in silico screened compounds targeted to EGFR-TK

Acknowledgements 20  Institute of Food Research and Product Development  Laboratory of Protein Engineering and Modeling, Department of Biochemistry, Faculty of Science, Kasetsart University  Assist. Prof. Kiattawee Choowongkomon  Mr. Adisak Ongsawas  Miss Wannarat Yim-Im

Acknowledgements: Computing Resources 21  Laboratory of Protein Engineering and Modeling, Department of Biochemistry, Faculty of Science, Kasetsart University  National Center of Excellence in Petroleum, Petrochemical Technology and Advanced Materials, Department of Chemistry, Faculty of Science, Kasetsart University  The National Nanotechnology Center (NANOTEC), the National Science and Technology Development Agency (NSTDA), Thailand

22 Thank you for Your Attention

Objective 23  To study the three dimensional ( 3 D) structure of 91 types of human tyrosine kinases in 31 the protein families  To construct the 3 D-structure of PTKs using homology modeling technique based on amino acid sequences of the protein(s)  To study binding Specificity of known EGFR/ErbB 2 -TKIs against all PTKs in human using molecular docking approach.

Structural Validation(s) 24

Protein Tyrosine Kinase 25  Abnormal regulatory of PTKs cause cancer development.  Therefore, these proteins are the target for the cancer therapy.

EGFR Family Inhibitors 26  EGFR family inhibitors classified into eight chemical categories :  N-phenylpyrimidin- 2 -amine  N-phenylquinazolin- 4 -amine  N-phenylquinolin- 4 -amine  N 4 -( 1 -methyl- 1 H-indazol- 5 -yl)pyrimidine- 4, 6 -diamine  N-ethyl- 7 H-pyrrolo[ 2, 3 -d]pyrimidin- 4 -amine  N-(pyridin- 3 -yl)- 7 H-pyrrolo[ 3, 2 -d]pyrimidin- 4 -amine  N-phenyl- 7 H-pyrrolo[ 3, 2 -d]pyrimidin- 4 -amine