Structure-affinity relationships of stereoisomers of norbenzomorphan-derived σ2R/TMEM97 modulators

The sigma 2 receptor (σ2R), which is identical to transmembrane protein 97 (TMEM97), is attracting increasing interest as a possible therapeutic target for various indications in neuroscience. In continuation of a program to identify novel compounds that bind with high affinity and selectivity to σ2R/TMEM97, we performed structure-affinity-relationship (SAfiR) studies of several sets of σ2R/TMEM97 ligands having a B-norbenzomorphan ring core. Binding data for σ2R/TMEM97 and σ1R of several enantiomeric pairs of piperazine-substituted norbenzomorphans show the (1S,5R)-enantiomers have affinities (Ki = 9-75 nM) for σ2R/TMEM97 that are 2-3-fold higher than their enantiomorphic (1R,5S)-analogs; however, there is no clear trend for selectivity for σ2R/TMEM97 vs σ1R. A series of N-alkyl piperazino (1S,5R)-norbenzomorphans was then evaluated, and with the exception of compounds having N-alkyl groups substituted with oxygen or amino groups at C (2) of an ethylene chain, Ki values for σ2R/TMEM97 are less than 25 nM, and several compounds have good selectivities (ca 7-16-fold) for σ2R/TMEM97 vs σ1R. Mono-substituted carbobenzyloxy analogs have Ki values for σ2R/TMEM97 comparable to the unsubstituted parent (Ki = ca 7-27 nM), but replacing the N-acyloxy group with N-acyl or N-arylsulfonyl groups provides analogs having lower affinity and selectivity. Some congeners with bioisosteric replacements of the piperazine group on the (1S,5R)-norbenzomorphan core have high affinity (Ki = <30 nM) for σ2R/TMEM97, but selectivities are modest. Computational docking studies for racemic pairs of piperazino norbenzomorphans show that individual (1S,5R)- and (1R,5S)-enantiomers adopt distinct poses upon binding to σ2R/TMEM97, whereas ligands belongingto the same enantiomeric series adopt closely similar binding poses. The protonated amino group in each of the enantiomorphic ligands engages in highly conserved salt bridges with Asp29 and cation-π interactions with Tyr150 that are the primary determinants of binding affinity. There is no correlation between any of the computational parameter outputs and Ki values, but this is unsurprising given the small energetic differences involved. Modeling also suggest sthat some compounds can extend deeper into σ2R/TMEM97 binding pocket forming salt bridges with Glu73.