The study of the binding and effects of polyaromatic hydrocarbons (PAH) to proteins remains one of the fundamental aspects of research in biophysics. Among other processes, ligand binding can regulate the function of proteins including inhibiting their action. Binding to small ligands remains a very important aspect in the study of the function of many proteins. We studied a new class of 3,9-substituted perylene derivatives designed to optimize electron donating properties that would optimize photoinduced electron transfer (PET) from the ligand to the protein and prompt charge-induced conformational changes.Our study focuses on the interaction of four 3,9-substituted perylenes with Human Serum Albumin (HSA), which is the prime protein model for the binding of PAH. We present docking simulation results for possible sites for the perylenes within HSA with the lowest free energy of binding and correlate the docking simulations with fluorescence result. Docking simulations reveal that all the peylen derivatives bind at the core of HSA and that the dimethoxy derivative has larger affinity than the other perylenes. Docking seems to be stabilized by aromatic interactions with Tyr and Trp groups.