AWS Collaborates with Chugai Pharmaceutical Co. on Quantum-Inspired and Constraint Programming Methods for Cyclic Peptide-Protein Docking

AWS and Chugai Pharmaceutical Co. collaborated on a quantum computing approach to solve cyclic peptide-protein docking challenges in drug discovery, exploring two computational methods:

• QUBO (Quantum Unconstrained Binary Optimization) approach
• Constraint Programming (CP) approach
• Goal: Determine optimal drug molecule orientation for protein binding
• Used tetrahedral lattice to discretize peptide structure

Key findings:

• QUBO successful for smaller problems (up to 6 peptide residues)
• CP approach more scalable, solving problems with up to 11 peptide residues
• CP method demonstrated better performance when protein was present
• Both methods showed comparable accuracy in matching real protein structures

The research suggests that hybrid classical-quantum approaches may be most promising for complex biomolecular modeling in the future.