Quantum algorithm for protein-ligand docking sites identification in the interaction space

Abstract

Over the past two decades, the development of novel drugs evolved into a high-demanding computational field. There is a constant and increasing need for advanced methods for determining protein-ligand binding in the drug design process. Even after the introduction and use of High-Performance Computers in drug design, fundamental problems and constraints have not been dealt with in a satisfactory manner. This is partially due to the fact that ligand docking in proteins is a quantum mechanical process. With the quantum computers available today, the question “Can quantum computers be used in drug design and how?” arises naturally. A novel quantum algorithm for protein-ligand docking site identification is presented here. In detail, the protein lattice model has been expanded to include protein-ligand interactions. Quantum state labelling for the interaction sites is introduced, and an extended and modified Grover quantum search algorithm is implemented to search for docking sites. This algorithm has been tested and executed on both a quantum simulator and a real quantum computer. The results show that the quantum algorithm can identify effectively docking sites. The quantum algorithm is highly scalable and well-suited for identifying docking sites within large proteins, poised to harness the potential of increased quantum bits in the future.