A shift of dynamic equilibrium between the KIT active and inactive states causes drug resistance

• Published in: Proteins, structure, function, and bioinformatics Vol. 88; no. 11; pp. 1434 - 1446
• Main Authors: Srikakulam, Sanjay K., Bastys, Tomas, Kalinina, Olga V.
• Format: Journal Article
• Language: English
• Published: Hoboken, USA John Wiley & Sons, Inc 01.11.2020; Wiley Subscription Services, Inc
• Subjects: Antineoplastic Agents - chemistry; Antineoplastic Agents - metabolism; Aspartic Acid - chemistry; Aspartic Acid - metabolism; Binding Sites; Biological activity; Cancer; Cell differentiation; Databases, Protein; Destabilization; Differentiation (biology); Drug resistance; Drug Resistance, Neoplasm - genetics; Drugs; Enzymes; Gastrointestinal cancer; Growth factors; Humans; Hydrogen Bonding; Inhibitors; Kinases; KIT tyrosine kinase; Leukemia; Ligands; Malignancy; Melanoma; Metastases; Molecular dynamics; Molecular Dynamics Simulation; molecular dynamics simulations; Mutants; Mutation; mutation Y823D; Phosphorylation; Protein Binding; Protein Conformation, alpha-Helical; Protein Conformation, beta-Strand; Protein Interaction Domains and Motifs; Protein Kinase Inhibitors - chemistry; Protein Kinase Inhibitors - metabolism; Protein Processing, Post-Translational; Protein Stability; Protein-tyrosine kinase; Proteins; Proto-Oncogene Proteins c-kit - antagonists & inhibitors; Proto-Oncogene Proteins c-kit - chemistry; Proto-Oncogene Proteins c-kit - genetics; Proto-Oncogene Proteins c-kit - metabolism; Regulatory sequences; secondary resistance; signal transduction; Stem cells; Substrate Specificity; Thermodynamics; Tumors; Tyrosine; Tyrosine - chemistry; Tyrosine - metabolism; molecular dynamics simulations; secondary resistance; cancer; KIT tyrosine kinase; signal transduction; mutation Y823D
• ISSN: 0887-3585; 1097-0134
• DOI: 10.1002/prot.25963

Tyrosine phosphorylation, a highly regulated post‐translational modification, is carried out by the enzyme tyrosine kinase (TK). TKs are important mediators in signaling cascades, facilitating diverse biological processes in response to stimuli. TKs may acquire mutations leading to malignancy and are viable targets for anti‐cancer drugs. Mast/stem cell growth factor receptor KIT is a TK involved in cell differentiation, whose dysregulation leads to various types of cancer, including gastrointestinal stromal tumors, leukemia, and melanoma. KIT can be targeted by a range of inhibitors that predominantly bind to the inactive state of the enzyme. A mutation Y823D in the activation loop of KIT is known to be responsible for the loss of sensitivity to some drugs in metastatic tumors. We used all‐atom molecular dynamics simulations to study the impact of Y823D on the KIT conformation and dynamics and compared it to the effect of phosphorylation of Y823. We simulated in total 6.4 μs of wild‐type, mutant and phosphorylated KIT in the active‐ and inactive‐state conformations. We found that Y823D affects the protein dynamics differently: in the active state, the mutation increases the protein stability, whereas in the inactive state it induces local destabilization, thus shifting the dynamic equilibrium towards the active state, altering the communication between distant regulatory regions. The observed dynamics of the Y823D mutant is similar to the dynamics of KIT phosphorylated at position Y823, thus we hypothesize that this mutation mimics a constitutively active kinase, which is not responsive to inhibitors that bind its inactive conformation.