5D-QSAR for spirocyclic σ1 receptor ligands by Quasar receptor surface modeling

Based on a contiguous and structurally as well as biologically diverse set of 87 σ1 ligands, a 5D-QSAR study was conducted in which a quasi-atomistic receptor surface modeling approach (program package Quasar) was applied. The superposition of the ligands was performed with the tool Pharmacophore Elucidation (MOE-package), which takes all conformations of the ligands into account. This procedure led to four pharmacophoric structural elements with aromatic, hydrophobic, cationic and H-bond acceptor properties. Using the aligned structures a 3D-model of the ligand binding site of the σ1 receptor was obtained, whose general features are in good agreement with previous assumptions on the receptor structure, but revealed some novel insights since it represents the receptor surface in more detail. Thus, e.g., our model indicates the presence of an H-bond acceptor moiety in the binding site as counterpart to the ligands’ cationic ammonium center, rather than a negatively charged carboxylate group. The presented QSAR model is statistically valid and represents the biological data of all tested compounds, including a test set of 21 ligands not used in the modeling process, with very good to excellent accuracy [q2 (training set, n = 66; leave 1/3 out) = 0.84, p2 (test set, n = 21) = 0.64]. Moreover, the binding affinities of 13 further spirocyclic σ1 ligands were predicted with reasonable accuracy (mean deviation in pKi ≈ 0.8). Thus, in addition to novel insights into the requirements for binding of spirocyclic piperidines to the σ1 receptor, the presented model can be used successfully in the rational design of new σ1 ligands.

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