Theoretical investigations based principally on Monte Carlo calculations were conducted to interpret the hindered mobility of protons which was experimentally observed in a hybrid biological/artificial nanopore constituted of the ion bio-channel gramicidin A confined inside an artificial solid-state nanopore. We show that this experimental outcome may result from the high concentration of gramicidin A that progressively diminishes the transfer of proton from one side to the other of the nanopore. More, using molecular dynamic simulations data we demonstrate that the water molecules are repelled from the gramicidin structure outside the nanopore, leading to a strong decrease of the proton transfer.