  Molecular docking plays a pivotal role in drug discovery and precision
medicine, enabling us to understand protein functions and advance novel
therapeutics. Here, we introduce a potential alternative solution to this
problem, the digitized-counterdiabatic quantum approximate optimization
algorithm (DC-QAOA), which utilizes counterdiabatic driving and QAOA on a
quantum computer. Our method was applied to analyze diverse biological systems,
including the SARS-CoV-2 Mpro complex with PM-2-020B, the DPP-4 complex with
piperidine fused imidazopyridine 34, and the HIV-1 gp120 complex with
JP-III-048. The DC-QAOA exhibits superior performance, providing more accurate
and biologically relevant docking results, especially for larger molecular
docking problems. Moreover, QAOA-based algorithms demonstrate enhanced hardware
compatibility in the noisy intermediate-scale quantum era, indicating their
potential for efficient implementation under practical docking scenarios. Our
findings underscore quantum computing's potential in drug discovery and offer
valuable insights for optimizing protein-ligand docking processes.
