Understanding the Allosteric Modulation of PTH1R by a Negative Allosteric Modulator

Abstract

The parathyroid hormone type 1 receptor (PTH1R) acts as a canonical class B G protein-coupled receptor, regulating crucial functions including calcium homeostasis and bone formation. The identification and development of PTH1R non-peptide allosteric modulators have obtained widespread attention. It has been found that a negative allosteric modulator (NAM) could inhibit the activation of PTH1R, but the implied mechanism remains unclear. Herein, extensive molecular dynamics simulations together with multiple analytical approaches are utilized to unravel the mechanism of PTH1R allosteric inhibition. The results suggest that the binding of NAM destabilizes the structure of the PTH1R–PTH–spep/qpep (the C terminus of Gs/Gq proteins) complexes. Moreover, the presence of NAM weakens the binding of PTH/peps (spep and qpep) and PTH1R. The intra- and inter-molecular couplings are also weakened in PTH1R upon NAM binding. Interestingly, compared with our previous study of the positive allosteric effects induced by extracellular Ca2+, the enhanced correlation between the PTH and G-protein binding sites is significantly reduced by the replacement of this negative allosteric regulator. Our findings might contribute to the development of new therapeutic agents for diseases caused by the abnormal activation of PTH1R.

Allosteric inhibition of myosin by phenamacril: a synergistic mechanism revealed by computational and experimental approaches

“…For example, GPCRs, involved in numerous cellular signal transduction, are intrinsically allosteric proteins, activated by a diverse range of extracellular ligands and transmitting external environmental signals from one part of the protein to another (from extracellular to cytoplasmic). [53][54][55][56][57][58] Besides orthosteric sites recognized by endogenous agonists, many additional sites are spatially distinct but functionally linked to the orthosteric ones either positively or negatively, further increasing the complexity of GPCR function, and both ions and small molecules can act as GPCR allosteric modulators. 59,60 In addition, the binding of the allosteric effector might induce conformational or dynamics rearrangement of the PPI interface, and thereby interrupt or disrupt the recognition and interaction between PPI partners.…”

Unraveling the Interplay of Extracellular Domain Conformational Changes and Parathyroid Hormone Type 1 Receptor Activation in Class B1 G Protein-Coupled Receptors: Integrating Enhanced Sampling Molecular Dynamics Simulations and Markov State Models

“…In addition, the druggability score of P8 in the S1 microstate is also high, indicating that the allosteric site exists in both the active and intermediate states. Previous experiments have revealed the presence of both NAMs and PAMs in the extracellular region. − Moreover, the druggability score of P7 in the S1 microstate is also high, and P7 occupies a position similar to a specific binding site discovered in the critical intermediate state of AT1R . Thus, predicting implicit allosteric binding sites in intermediate states may aid in the design of the PTH1R allosteric modulators.…”

“…Furthermore, as shown in Figure , the outer region of transmembrane helices primarily includes three binding regions: (1) TM1/2/3 extracellular region, which is present in various states and contains binding sites for LSN3160440 [positive allosteric modulators (PAM)] and TT-OAD2 (PAM) and previously studied small-molecule Pitt12 (NAM); , (2) the middle region of TM6, which includes analytically regulated NAMs of class B1 GPCRs (such as PF06372222, NNC0640, MK0893, and CP376395); ,,− (3) the cytoplasmic region of TM6, predicted only in the active state, with a reported binding site for compound 2 (PAM) . Moreover, CavityPlus and DoGSiteScorer also focused on predicting potential binding sites in proteins and providing information about their features, shape, and location.…”

“…The ECD exhibits considerable dynamics in both the presence and absence of ligands compared to the TMD and G protein, suggesting that the ECD has enhanced flexibility or conformational kinetic properties relative to the core region of the TMD. The high flexibility of both peptide-bound and ligand-free forms of the ECD is supported by molecular dynamics (MD) simulations. − Moreover, the crystal structure of the GLP-1R without a peptide ligand reveals a unique closed conformation of the ECD, and significant conformational dynamics of the ECD are necessary for peptide ligand binding . Consequently, it is conceivable that PTH1R may also undergo a completely closed inhibitory state of the ECD.…”