NTRK kinase domain mutations in cancer variably impact sensitivity to type I and type II inhibitors

Area of Science:

• Oncology
• Molecular Biology
• Drug Discovery

Background:

• Tyrosine kinase domains exist in type I (DFG-in) and type II (DFG-out) conformations.
• Data comparing type I and type II inhibitors for NTRK fusion-driven cancers is limited.
• Larotrectinib is a type I inhibitor, and resistance mutations are emerging.

Purpose of the Study:

• To investigate the efficacy of a type II inhibitor, altiratinib, against larotrectinib-resistant NTRK mutations.
• To explore the structural basis for differential inhibitor sensitivity in NTRK mutants.
• To identify potential new therapeutic strategies for NTRK fusion-driven cancers with resistance mutations.

Main Methods:

• Utilized altiratinib (a type II inhibitor) as a model compound.
• Assessed the inhibitory potential against specific larotrectinib-resistant NTRK1 mutations (V573M, F589L, G667C).
• Employed molecular modeling to understand inhibitor-target interactions.

Main Results:

• A subset of larotrectinib-resistant NTRK1 mutations (V573M, F589L, G667C) showed retained sensitivity to altiratinib.
• NTRK1^V573M and NTRK1^G667C (xDFG motif) mutations were highly sensitive to type II inhibitors (altiratinib, cabozantinib, foretinib).
• Molecular modeling indicated that sulfur substitutions (methionine, cysteine) in the binding pocket confer hypersensitivity to type II inhibitors.

Conclusions:

• Type II inhibitors can overcome certain resistance mechanisms to type I inhibitors in NTRK-driven cancers.
• Sulfur-containing mutations in NTRK kinases create specific vulnerabilities exploitable by type II inhibitors.
• Findings support the development of precision treatment strategies targeting specific NTRK kinase mutants.