title: Computational study of EGFR inhibition: molecular dynamics studies on the active and inactive protein conformations.
abstract: The structural diversity observed across protein kinases, resulting in subtly different active site cavities, is highly desirable in the pursuit of selective inhibitors, yet it can also be a hindrance from a structure-based design perspective. An important challenge in structure-based design is to better understand the dynamic nature of protein kinases and the underlying reasons for specific conformational preferences in the presence of different inhibitors. To investigate this issue, we performed molecular dynamics simulation on both the active and inactive wild type epidermal growth factor receptor (EGFR) protein with both type-I and type-II inhibitors. Our goal is to better understand the origin of the two distinct EGFR protein conformations, their dynamic differences, and their relative preference for Type-I inhibitors such as gefitinib and Type-II inhibitors such as lapatinib. We discuss the implications of protein dynamics from a structure-based design perspective.
authors.affiliation: Department of Biochemistry, Faculty of Science, Kasetsart University, 50 Phaholyothin Rd, Chatuchak, Bangkok, 10900, Thailand.
authors.forename: Napat
authors.initials: N
authors.lastname: Songtawee
authors.forename: M Paul
authors.initials: MP
authors.lastname: Gleeson
authors.forename: Kiattawee
authors.initials: K
authors.lastname: Choowongkomon
mesh_terms: D000255:Adenosine Triphosphate / Q000737:chemistry; D001665:Binding Sites; D015195:Drug Design; D066246:ErbB Receptors / Q000737:chemistry*; D000077156:Gefitinib; D006801:Humans; D057927:Hydrophobic and Hydrophilic Interactions; D007700:Kinetics; D000077341:Lapatinib; D056004:Molecular Dynamics Simulation; D047428:Protein Kinase Inhibitors / Q000737:chemistry*; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011799:Quinazolines / Q000737:chemistry*; D055672:Static Electricity; D013329:Structure-Activity Relationship; D013816:Thermodynamics
chemical_list: D047428:Protein Kinase Inhibitors; D011799:Quinazolines; D000077341:Lapatinib; D000255:Adenosine Triphosphate; C512478:EGFR protein, human; D066246:ErbB Receptors; D000077156:Gefitinib