Deep Learning Dynamic Allostery of G-Protein-Coupled Receptors

Abstract

G-protein-coupled receptors (GPCRs) are the largest superfamily of human membrane proteins and represent primary targets of ~ 1/3 of currently marketed drugs. Allosteric modulators have emerged as more selective drug candidates compared with orthosteric agonists and antagonists. However, many X-ray and cryo-EM structures of GPCRs resolved so far exhibit negligible differences upon binding of positive and negative allosteric modulators (PAMs and NAMs). Mechanism of dynamic allosteric modulation in GPCRs remains unclear. In this work, we have systematically mapped dynamic changes in free energy landscapes of GPCRs upon binding of allosteric modulators using the Gaussian accelerated molecular dynamics (GaMD), Deep Learning (DL) and free energy prOfiling Workflow (GLOW). A total of 18 available high-resolution experimental structures of allosteric modulator-bound class A and B GPCRs were collected for simulations. A number of 8 computational models were generated to examine selectivity of the modulators by changing their target receptors to different subtypes. All-atom GaMD simulations were performed for a total of 66 µs on 44 GPCR systems in the presence/absence of the modulator. DL and free energy calculations revealed significantly reduced conformational space of GPCRs upon modulator binding. While the modulator-free GPCRs often sampled multiple low-energy conformational states, the NAMs and PAMs confined the inactive and active agonist-G protein-bound GPCRs, respectively, to mostly only one specific conformation for signaling. Such cooperative effects were significantly reduced for binding of the selective modulators to “non-cognate” receptor subtypes in the computational models. Therefore, comprehensive DL of extensive GaMD simulations has revealed a general dynamic mechanism of GPCR allostery, which will greatly facilitate rational design of selective allosteric drugs of GPCRs.

Orthosteric and allosteric modulation of human HCAR2 signaling complex

“…The high-resolution structures revealed that compound 9n binds to a previously unidentified crevice between TM5-TM6-ECL2 on the extracellular side (Fig. 4c) 37,38 .Detailed analysis showed that compound 9n predominantly forms hydrophobic interactions with neighboring residues in this pocket (Fig. 4c).…”

“…Compared to orthosteric ligands, allosteric modulators bind to nonconserved sites and offer promising opportunities for the development of novel therapeutic approaches with improved receptor selectivity and reduced side-effects [34][35][36] . However, despite their potential, only a limited number of class A GPCR structures in complex with positive allosteric modulators (PAMs) have been reported 37,38 ; this highlights the necessity for further investigation into the binding and actions of PAMs. The existing structures reveal that PAMs bind to four broad regions within class A GPCRs (Fig.…”