The development of point-of-care detection methodologies for biologically relevant analytes that can facilitate rapid and appropriate treatment is at the forefront of current research efforts and interests. Among the various approaches, those exploiting host–guest chemistries where the optoelectronic signals of the chemical sensor can be modulated upon interaction with the target analyte are of particular interest. In aiding their rational development, judicious selection of peripheral functional groups anchored to core motifs with desired properties is critical. Herein, we report an in-depth investigation of the binding of three psychoactive substances, MDAI, mexedrone, and phenibut, to receptors of the monoamine transporters for dopamine, norepinephrine, and serotonin, particularly focusing on the role of individual amino acid residues. We first evaluated the conformational flexibility of the ligands by comparing their experimentally determined crystal structure geometries to those optimized by means of quantum as well as molecular mechanics, observing significant changes in the case of phenibut. Molecular docking studies were employed to identify preferential binding sites by means of calculated docking scores. In all cases, irrespective of the monoamine transporter, psychoactive substances exhibited preferred interaction with the S1 or central site of the proteins, in line with previous studies. However, we observed that experimental trends for their relative potency on the three transporters were only reproduced in the case of mexedrone. Subsequently, to further understand these findings and to pave the way for the rational development of superior chemical sensors for these substances, we computed the individual contributions of each nearest neighbor amino acid residue to the binding to the target analytes. Interestingly, these results are now in agreement with those experimental potency trends. In addition, these observations were in all cases associated with key intermolecular interactions with neighboring residues, such as tyrosine and aspartic acid, in the binding of the ligands to the monoamine transporter for dopamine. As a result, we believe this work will be of interest to those engaged in the rational development of chemical sensors for small molecule analytes as well as to those interested in the use of computational approaches to further understand protein–ligand interactions.