The AAPS Journal

, Volume 17, Issue 3, pp 737–753 | Cite as

Allosteric Binding Site and Activation Mechanism of Class C G-Protein Coupled Receptors: Metabotropic Glutamate Receptor Family

  • Zhiwei Feng
  • Shifan Ma
  • Guanxing Hu
  • Xiang-Qun Xie
Research Article

Abstract

Metabotropic glutamate receptors (mGluR) are mainly expressed in the central nervous system (CNS) and contain eight receptor subtypes, named mGluR1 to mGluR8. The crystal structures of mGluR1 and mGluR5 that are bound with the negative allosteric modulator (NAM) were reported recently. These structures provide a basic model for all class C of G-protein coupled receptors (GPCRs) and may aid in the design of new allosteric modulators for the treatment of CNS disorders. However, these structures are only combined with NAMs in the previous reports. The conformations that are bound with positive allosteric modulator (PAM) or agonist of mGluR1/5 remain unknown. Moreover, the structural information of the other six mGluRs and the comparisons of the mGluRs family have not been explored in terms of their binding pockets, the binding modes of different compounds, and important binding residues. With these crystal structures as the starting point, we built 3D structural models for six mGluRs by using homology modeling and molecular dynamics (MD) simulations. We systematically compared their allosteric binding sites/pockets, the important residues, and the selective residues by using a series of comparable dockings with both the NAM and the PAM. Our results show that several residues played important roles for the receptors’ selectivity. The observations of detailed interactions between compounds and their correspondent receptors are congruent with the specificity and potency of derivatives or compounds bioassayed in vitro. We then carried out 100 ns MD simulations of mGluR5 (residue 26-832, formed by Venus Flytrap domain, a so-called cysteine-rich domain, and 7 trans-membrane domains) bound with antagonist/NAM and with agonist/PAM. Our results show that both the NAM and the PAM seemed stable in class C GPCRs during the MD. However, the movements of “ionic lock,” of trans-membrane domains, and of some activation-related residues in 7 trans-membrane domains of mGluR5 were congruent with the findings in class A GPCRs. Finally, we selected nine representative bound structures to perform 30 ns MD simulations for validating the stabilities of interactions, respectively. All these bound structures kept stable during the MD simulations, indicating that the binding poses in this present work are reasonable. We provided new insight into better understanding of the structural and functional roles of the mGluRs family and facilitated the future structure-based design of novel ligands of mGluRs family with therapeutic potential.

KEY WORDS

allosteric class C of G protein-coupled receptors homology model metabotropic glutamate receptor family molecular dynamics simulation 

Supplementary material

12248_2015_9742_MOESM1_ESM.docx (13.3 mb)
ESM 1Figure S1 shows the sequence alignments among mGluRs family. Figure S2 shows the comparisons of the crystal structure between mGluR1 and mGluR5. Figure S3 shows the Ramachandran plots of other six mGluRs, including mGluR2, mGluR3, mGluR4, mGluR6, mGluR7, and mGluR8. Figure S4 shows the common 3D structure of mGluRs family. Figure S5 shows the comparisons of the NAM between mGluR1 and mGluR5. Figure S6 shows the superposition and comparison of mGluR5 (class C) with D3R (class A), CRF1R (class B), and SMO receptor (class F). Figure S7 shows the structural information of compounds discussed in the present work. Figure S8 shows the comparisons of binding mode of MTEP and MPEP in mGluR5. Figure S9 shows the comparisons of mGluR5 bound with different compounds during 100 ns MD simulation. Figure S10 shows conformational changes (view from extracellular side) of 7TMD bound with different compounds after 100 ns MD simulation. Figure S11 shows the alignments of other nine complexes between before-MD and after-MD. Table S1 shows sequence identities of six subtypes with two group I mGluRs (mGluR1 and mGluR5). This material is available free of charge via the Internet at http://www.aaps.org. (DOCX 13644 kb)

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Copyright information

© American Association of Pharmaceutical Scientists 2015

Authors and Affiliations

  • Zhiwei Feng
    • 1
    • 2
    • 3
  • Shifan Ma
    • 1
    • 2
    • 3
  • Guanxing Hu
    • 1
    • 2
    • 3
  • Xiang-Qun Xie
    • 1
    • 2
    • 3
    • 4
  1. 1.Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of PharmacyUniversity of PittsburghPittsburghUSA
  2. 2.NIDA National Center of Excellence for Computational Drug Abuse ResearchUniversity of PittsburghPittsburghUSA
  3. 3.Drug Discovery InstituteUniversity of PittsburghPittsburghUSA
  4. 4.Departments of Computational Biology and of Structural BiologyUniversity of PittsburghPittsburghUSA

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