Project goal

Develop a single small molecule capable of selectively inhibiting both mTOR (serine-threonine kinase) and EGFR (tyrosine kinase) by identifying a shared structural motif that engages distinct active-site interactions, achieving a dual-target effect.

Description of Activities (Stages)

• 1.

  Identification of Shared Structural Fragment: Screened structural databases and literature to hypothesize a core fragment potentially able to bind both mTOR and EGFR active sites via different interactions.

• 2.

  Generative Fragment Proposal: Applied a generative algorithm fed by a structural database of ~200,000 kinase inhibitors to propose fragment derivatives incorporating the shared core motif, ensuring compatibility with both target families.

• 3.

  Structure Preparation: Used Rosetta to prepare and refine three-dimensional structures of mTOR and EGFR kinase domains, optimizing protonation states and active-site conformations.

• 4.

  Candidate Library Construction: Assembled a library of candidate molecules embedding the identified fragment in various contexts, ensuring correct geometry for each active site.

• 5.

  Computational Binding Free Energy Estimation: Calculated binding free energies for candidates against mTOR and EGFR using ML-based prediction models. Benchmarking against reference inhibitors.

• 6.

  Data Management and Workflow Automation: Developed Python scripts to automate Rosetta workflows, format conversions, and database updates tracking candidate designs and computational results.

In Vitro Confirmation

Planned: biochemical kinase assays to measure IC50 values for mTOR and EGFR inhibition, cell-based assays to verify downstream pathway inhibition and assess efficacy in relevant cell models.