Understanding principles of molecular recognition is a challenging problem in contemporary molecular biology and theoretical biochemistry that could be approached with molecular modeling. Peptidyl-prolyl cis-trans isomerase FKBP1A (known as FKBP12) is a member of the immunophilin protein family, which plays a role in immunoregulation and basic cellular processes involving protein folding and trafficking and that binds the immunosuppressants rapamycin (sirolimus), everolimus and temsirolimus. An overexpression of this protein had been detected in several types of cancers. Therefore it is important to understand the interaction of immunosuppressants above with FKBP12. The aim of this work is to identify the interactions of three mentioned immunosuppressants with the FKBP12 intramolecular receptor by in silico evaluation. Molecular docking simulations were employed in order to corroborate the moieties in the immunosuppressants that play an active role in the interactions with FKBP12. Quantum chemistry calculations based on Density Functional Theory of these molecules followed with a characterization of them based on the dual and Fukui’s descriptors, a charge population analysis and a mapping of the electrostatic potential surface were performed. The molecular docking results demonstrated that predominant interactions of the immunosuppressants with FKBP12 are between the pyridine moieties of the drugs with the hydrophobic residues of the protein´s active site. The quantum characterization of molecular properties allowed the proposal of new radiolabelled candidates targeting the studied receptor. A synthesis strategy with the click chemistry approach was also proposed. These results should be confirmed with thermodynamic calculations, molecular dynamics simulations and further experimental results.