Structural basis for σ₁ receptor ligand recognition

Abstract

The σ 1 receptor is a poorly understood integral membrane protein expressed in most cells and tissues in the human body. It has been shown to modulate the activity of other membrane proteins such as ion channels and G protein-coupled receptors 1-4 , and ligands targeting the σ 1 receptor are currently in clinical trials for treatment of Alzheimer's disease 5 , ischemic stroke 6 , and neuropathic pain 7 . Despite its importance, relatively little is known regarding σ 1 receptor function at the molecular level. Here, we present crystal structures of the human σ 1 receptor bound to the classical antagonists haloperidol and NE-100, as well as the agonist (+)-pentazocine, at crystallographic resolutions of 3.1 Å, 2.9 Å, and 3.1 Å respectively. These structures reveal a unique binding pose for the agonist. The structures and accompanying molecular dynamics (MD) simulations demonstrate that the agonist induces subtle structural rearrangements in the receptor. In addition, we show that ligand binding and dissociation from σ 1 is a multistep process, with extraordinarily slow kinetics limited by receptor conformational change. We use MD simulations to reconstruct a ligand binding pathway that requires two major conformational changes. Taken together, these data provide a framework for understanding the molecular basis for agonist action at σ 1 .Discovered in 1976 8 , the σ 1 receptor has attracted interest because it binds a host of structurally dissimilar pharmacologically active compounds with high affinity (Fig. 1a). These include benzomorphans, antipsychotics, psychosis-inducing drugs, the antifungal agent fenpropimorph, sterols such as progesterone, and numerous other compounds 9 . These molecules contain few shared features, although most include a basic nitrogen atom flanked on two sides by longer hydrophobic moieties (typically

Distinct Regulation of σ1 Receptor Multimerization by Its Agonists and Antagonists in Transfected Cells and Rat Liver Membranes

“…Such structural architecture differs from a dimer-tetramer model postulated by early work (Chu and Ruoho, 2016). Further, crystal structures of σ1R bound with agonist (+)-pentazocine or antagonist haloperidol showed similar homo-trimer organization, with limited conformational rearrangement (Schmidt et al, 2018), suggesting that trimers may be the lowest free energy state of σ1R during crystallization. It remains unclear whether ligand binding affects the native highorder organization of σ1R.…”

“…Comparison between σ1R structures bound with (+)-pentazocine and NE-100 revealed limited conformational rearrangement (Schmidt et al, 2018). These structures likely provided snapshots of σ1R in its lowest free energy state.…”

“…As most σ1R is located on intracellular membranes, during incubation drugs permeated through cell membranes to bind σ1R, and most likely they remained bound to σ1R during cell lysis, since (+)-pentazocine and haloperidol were shown to dissociate very slowly from σ1R (dissociation t1/2 > 3 h) using traditional radioligand off-rate method (Bowen et al, 1993) or scintillation proximity assay (Schmidt et al, 2018). Further, if lysates from drug-naïve cells were incubated with drugs overnight on ice, similar effects as those in preincubation were seen (Supplemental Fig.…”

“…Further, drug binding to σ1R may exhibit different cooperativity. Although (+)-pentazocine fully occupied the binding pocket of each σ1R protomer in crystal structures, binding kinetic analysis of Flag-tagged σ1R and molecular dynamics simulation supported a multi-step model of (+)pentazocine binding (Schmidt et al, 2018). Whether PRE-084 or NE-100 induces different conformational changes or binding cooperativity of σ1R from (+)-pentazocine will require more sophisticated techniques.…”

Association of sigma‐1 receptor with dopamine transporter attenuates the binding of methamphetamine via distinct helix–helix interactions

“…Moreover, σ1R has been implicated as a potential molecular target for the treatment of psychostimulant addiction (Nguyen et al., 2015). The structures of σ1R in complex with diverse ligands were crystallized as trimers, with each protomer containing a single transmembrane helical domain (α1) and a β‐barrel fold flanked by four α‐helices (α2–α5) (Schmidt et al., 2016, 2018). The function of σ1R can be activated by agonists or inhibited by antagonists.…”