Structure-Affinity relationships of novel σ2R/TMEM97 ligands.

The sigma 2 receptor (σ2R), which was recently identified as the transmembrane protein 97 (TMEM97), is increasingly attracting interest as a possible therapeutic target for indications in neuroscience. Toward identifying novel modulators of σ2R/TMEM97, we prepared a collection of benzoxazocine, benzomorphan, and methanobenzazepine ligands related to the known bioactive norbenzomorphans DKR-1677, FEM-1689, and EES-1686 and determined their Ki values for σ2R/TMEM97 and the sigma 1 receptor (σ1R). The σ2R/TMEM97 binding affinities and selectivities relative to σ1R of these new benzoxazocine, benzomorphan, and methanobenzazepine analogs are lower, often significantly lower, than their respective norbenzomorphan counterparts, suggesting the spatial orientation of pharmacophoric substituents is critical for binding to the two proteins. The benzoxazocine, benzomorphan, and methanobenzazepine congeners of DKR-1677 and FEM-1689 tend to be weakly selective for σ2R/TMEM97 versus σ1R, whereas EES-1686 derivatives exhibit the greatest selectivity, suggesting the size and/or nature of the substituent on the nitrogen atom of the scaffold may be important for selectivity. Computational docking studies were performed for the 1S,5R-and 1R,5S-enantiomers of DKR-1677, FEM-1689, and EES-1686 and their benzoxazocine, benzomorphan, and methanobenzazepine counterparts. These computations predict that the protonated amino group of each ligand forms a highly conserved salt bridge and a H-bonding interaction with Asp29 as well as a cation-π interaction with Tyr150 of σ2R/TMEM97. These electrostatic interactions are major driving forces for binding to σ2R/TMEM97 and are similar, though not identical, for each ligand. Other interactions within the well-defined binding pocket also tend to be comparable, but there are some major differences in how the hydrophobic aryl groups of various ligands interact with the protein surface external to the binding pocket. Overall, these studies show that the orientations of aryl and N-substituents on the norbenzomorphan and related scaffolds are important determinants of binding affinity of σ2R/TMEM97 ligands, and small changes can have significant effects upon binding profiles.

Improved Triplex-Forming Isoorotamide PNA Nucleobases for A-U Recognition of RNA Duplexes.

Four new isoorotamide (Io)-containing PNA nucleobases have been designed for A-U recognition of double helical RNA. New PNA monomers were prepared efficiently and incorporated into PNA nonamers for binding A-U in a PNA:RNA2 triplex. Isothermal titration calorimetry and UV thermal melting experiments revealed slightly improved binding affinity for singly modified PNA compared to known A-binding nucleobases. Molecular dynamics simulations provided further insights into binding of Io bases in the triple helix. Together, the data revealed interesting insights into binding modes including the notion that three Hoogsteen hydrogen bonds are unnecessary for strong selective binding of an extended nucleobase. Cationic monomer Io8 additionally gave the highest affinity observed for an A-binding nucleobase to date. These results will help inform future nucleobase design toward the goal of recognizing any sequence of double helical RNA.

Preparation of novel analogs of 2-arylpiperidines and evaluation of their sigma receptor binding affinities.

A number of substituted norbenzomorphans have been previously identified as high affinity ligands for the two known sigma receptors σ1R and σ2R/TMEM97, and some norbenzomorphans that are selective for σ2R/TMEM97 exhibit promise in animal models of several neurological disorders. Toward further assessing the effects of simplifying the norbenzomorphan scaffold, sets of 6-membered heterocycles were designed and prepared, and their binding affinities for σ1R and σ2R/TMEM97 were determined. Consistent with our design strategy, N-acyl-2-arylpiperidines show high affinity for σ2R/TMEM97, whereas those derived from morpholine and N-methylpiperazine have lower affinities. However, most of these 6-membered heterocycles unexpectedly exhibit even higher affinity for σ1R and are thus σ1R-selective. Computational docking studies show that representative 6-membered heterocycles bind and interact with σ2R/TMEM97 in a manner similar to that of a docked structure of their norbenzomorphan parent. Collectively, these binding and computational studies support our design strategy for developing simplified analogs of norbenzomorphans as σ2R/TMEM97 ligands, but they also underscore the challenges associated with developing selective modulators of σ2R/TMEM97.