Selective polypharmacology, where a
drug acts on multiple rather than a single molecular target involved in a disease, emerges to develop a structure-based system biology approach to design drugs selectively targeting a disease-active
protein network. We focus on the bioaminergic receptors that belong to the group of
G-protein-coupled receptors (GPCRs) and represent targets for therapeutic agents against
schizophrenia and depression. Among them, it has been shown that the
serotonin (5-HT(2A) and 5-HT₆) and
dopamine (D₂ and D₃) receptors induce a cognition-enhancing effect (group 1), while the
histamine (H₁) and
serotonin (5-HT(2C)) receptors lead to metabolic side effects and the 5-HT(2B)
serotonin receptor causes
pulmonary hypertension (group 2). Thus, the problem arises to develop an approach that allows identifying drugs targeting only the disease-active receptors, i.e. group 1. The recent release of several crystal structures of the bioaminergic receptors, involving the D₃ and H₁ receptors, provides the possibility to model the structures of all receptors and initiate a study of the structural and dynamic context of selective polypharmacology. In this work, we use molecular dynamics simulations to generate a conformational space of the receptors and subsequently characterize its binding properties applying
molecular probe mapping. All-against-all comparison of the generated probe maps of the selected diverse conformations of all receptors with the Tanimoto similarity coefficient (Tc) enable the separation of the receptors of group 1 from group 2. The pharmacophore built based on the Tc-selected receptor conformations, using the multiple probe maps discovers structural features that can be used to design molecules selective toward the receptors of group 1. The importance of several predicted residues to
ligand selectivity is supported by the available mutagenesis and
ligand structure-activity relationship studies. In addition, the Tc-selected conformations of the receptors for group 1 show good performance in isolation of known
ligands from a random decoy. Our computational structure-based protocol to tackle selective polypharmacology of
antipsychotic drugs could be applied for other diseases involving multiple
drug targets, such as oncologic and infectious disorders.