For the development of nature-inspired chiral nanostructures, controlling the chirality communication along the assembling pathways in aqueous media is a crucial task. Herein, we designed and synthesized pyrazine-based derivative Pyra-Met with an L-methionine group as a chiral handle. Due to the presence of flexible side chains in the Pyra-Met building block, its interactions with the solvent molecules in the assembled state are restricted, which leads to the generation of nanospheres in aqueous media. The Pyra-Met nanospheres selectively interact with Au3+ ions to generate dynamic helical fibers of the Pyra-Met:Au3+ ensemble with 'hidden' chirality. Finally, superhelices with the desired helical sense are achieved in the presence of L/D-methionine via a co-assembly process. This work presents a feasible strategy to achieve the desired handedness of supramolecular assemblies for better understanding of chirality translation in supramolecular chemistry and it highlights the importance of fine tailoring of building block to control the morphology of the assembled architecture.