Pharmacophore Mapping Combined with dbCICA Reveal New Structural Features for the Development of Novel Ligands Targeting α4β2 and α7 Nicotinic Acetylcholine Receptors

Abstract

The neuronal nicotinic acetylcholine receptors (nAChRs) belong to the ligand-gated ion channel (GLIC) group, presenting a crucial role in several biological processes and neuronal disorders. The α4β2 and α7 nAChRs are the most abundant in the central nervous system (CNS), being involved in challenging diseases such as epilepsy, Alzheimer’s disease, schizophrenia, and anxiety disorder, as well as alcohol and nicotine dependencies. In addition, in silico-based strategies may contribute to revealing new insights into drug design and virtual screening to find new drug candidates to treat CNS disorders. In this context, the pharmacophore maps were constructed and validated for the orthosteric sites of α4β2 and α7 nAChRs, through a docking-based Comparative Intermolecular Contacts Analysis (dbCICA). In this sense, bioactive ligands were retrieved from the literature for each receptor. A molecular docking protocol was developed for all ligands in both receptors by using GOLD software, considering GoldScore, ChemScore, ASP, and ChemPLP scoring functions. Output GOLD results were post-processed through dbCICA to identify critical contacts involved in protein-ligand interactions. Moreover, Crossminer software was used to construct a pharmacophoric map based on the most well-behaved ligands and negative contacts from the dbCICA model for each receptor. Both pharmacophore maps were validated by using a ROC curve. The results revealed important features for the ligands, such as the presence of hydrophobic regions, a planar ring, and hydrogen bond donor and acceptor atoms for α4β2. Parallelly, a non-planar ring region was identified for α7. These results can enable fragment-based drug design (FBDD) strategies, such as fragment growing, linking, and merging, allowing an increase in the activity of known fragments. Thus, our results can contribute to a further understanding of structural subunits presenting the potential for key ligand-receptor interactions, favoring the search in molecular databases and the design of novel ligands.

Recent Advances in Computer-Aided Structure-Based Drug Design on Ion Channels

“…Thus, interactions between the α4β2 and α7 nAChRs and Aβ oligomers may induce malfunction of the synaptic neuron transfer [156,157]. Batista et al [158] designed a docking-based pharmacophore model that could be used to search for new nAChR inhibitors. The authors started by performing docking of known nAChR ligands (~200 molecules) with available bioactivity data and extensively described critical contacts and binding modes to obtain a pharmacophore model.…”

Towards Novel Potential Molecular Targets for Antidepressant and Antipsychotic Pharmacotherapies

“…Over the last decade, there has been a rapid increase in CADD-based studies of depression, including docking studies of ligands for serotonin reuptake [171,172], MAO A and MAO B [173,174], dual action on MAO-B/AChE [175], glycogen synthase kinase [176], sodium hNaV1.2 or hNaV1.7 channels [177], serotonin receptors (5HT1A, 5-HT2A, 5-HT2C and 5-HT4) [171,[178][179][180][181], adenosine A1/A2A receptors [182], T-type calcium channels [183], tryptophan 2,3-dioxygenase [184] and sigma receptor [185]. Similarly, application of docking in psychoses involved ligands for serotonin 5HT2 and dopamine D2 receptors [186], α4β2 and α7 nicotinic acetylcholine receptors [187,188], phosphodiesterase 10A [189], MAO A and B [190], a syntaxin-binding protein (STXBP1) [191], NMDA type subunit 1 (GRIN1) [192], fatty acid binding protein 7 (FABP7) [193,194], metabotropic glutamate mGluR5 receptor [195], ionotropic GABA-A receptor [196], glycine transporter type 1 (GlyT1) [197] and kynurenine aminotransferase II (KATII) [198].…”