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Advanced Technology | DBDD reveals membrane protein dynamics: a molecular movie of GPCR

Introduction

G protein-coupled receptors (GPCRs) are the largest family of receptors in cell membranes, and GPCRs play key roles in a variety of signaling pathways inside and outside the cell. They trigger complex intracellular signaling cascades upon recognition of external molecules (e.g., hormones, neurotransmitters, drugs, etc.) that regulate physiological processes such as growth, development, and metabolism in the body.

GPCRs account for 4% (799/20,595) of human genes and mediate the actions of two-thirds (342/515) of hormones and neurotransmitters. In fact, GPCRs are one of the most commonly used targets in drug development, with 34% of commercially available drugs acting on GPCRs.Based on amino acid sequence similarity, GPCRs have been classified into six classes, but only classes A, B, C, and F are present in the human body, with the majority of GPCR drugs currently targeting class A GPCRs (Fig. 1).GPCRs have been implicated in a number of physiological and pathological diseases, including diabetes, obesity, cancer, and other diseases. These include diabetes, obesity, cancer, Alzheimer's disease, asthma, pain, cardiovascular disease and many others.

Figure 1: Comparison of marketed phase GPCR drug target types and indications (Source: https://gpcrdb.org/)

Among the currently marketed GPCR drugs targeting different receptor types (Fig. 2), small molecule drugs are the most developed drug type of drugs, with 1,026 small molecule drugs approved for marketing. In addition, hormones, synthetic peptides and biosimilars are also more common drug types, and peptide drugs and antibody drugs can specifically and efficiently intervene in GPCR, resulting in better drug efficacy and safety. Therefore, the study of the mechanism of GPCR in these diseases and the development of GPCR-related drugs are of great clinical significance for the treatment of GPCR-related diseases

Figure 2: Receptor types and drug molecule types of marketed GPCR drugs (Source: https://gpcrdb.org/)

IGPCR structure and function

In general, mammalian GPCRs are divided into five classes: Rhodopsin (class A), Secretin (class B1), Adhesion (class B2), Glutamate (class C) and Frizzled/TAS2 family (class F).The GPCR family has a common molecular structure consisting of seven transmembrane regions (TM1-TM7), an extracellular region (N-terminal and three extracellular loops), and an intracellular region (three intracellular loops, an external helix8, and C-terminal). However, each class of GPCR has its own unique structural features. The most notable difference lies in the structure of the extracellular N-terminus (Fig. 3). Variations in the N-terminus, extracellular loop, and TM helix result in significant differences in the size, shape, and physical properties of the ligand-binding pocket in different GPCR subfamilies. Understanding the structural basis of GPCRs is important for the study of GPCR functions, including ligand recognition, receptor activation, and signaling.

Figure 3: Five classes of GPCR structures

In the case of class A GPCRs, when a signaling molecule (ligand) binds to the extracellular region of the GPCR, it causes a conformational change in the receptor (Fig. 4). This change activates the G protein, a heterotrimeric protein complex consisting of three subunits, including the α, β, and γ subunits.The G protein associates with the intracellular side of the receptor. Activation of the G protein separates the α subunit from the β-γ subunit and prompts the α subunit to replace the GDP (guanosine diphosphate) with GTP (guanosine triphosphate). Both the α-subunit and the β-γ-subunit can then regulate various downstream signaling pathways, such as the activation of enzymes or the regulation of ion channels.

Figure 4: Signal regulation mechanism of GPCR

There have been 1042 GPCR-related structures reported (data from gpcrdb.org/). A total of 1027 of these structures bind to the ligand and the ligand binds to the receptor in different conformational states.

Figure 5: Classification of reported GPCR structures (Source: https://gpcrdb.org/)

In living organisms, the structures of membrane proteins are usually highly dynamic, with their conformations changing in response to changes in the environment or interactions with other biomolecules, and are in different conformational states to perform their biological functions. GPCR activation is usually triggered by agonist binding in a metastable manner. Although X-ray crystallography cryo-electron microscopy has made great progress in the structure of GPCRs, most of the structures obtained are in a substable state, and such structures may not reflect the true functional state of membrane proteins in their biological environment.

Figure 6: GPCR activated and inactivated state conformations

Molecular dynamics reveals the dynamic mechanism of GPCR

Molecular dynamics simulation is a powerful computational tool for modeling the motions and interactions of proteins, membrane proteins, and biomolecules. For membrane proteins such as GPCR, the complexity and dynamics of their structure and function make molecular dynamics simulation an important tool for studying GPCR.

Molecular dynamics simulations of GPCRs usually start with a known crystal structure or a computer model (unknown structural protein), embedding the GPCR in a simulated cell membrane environment and adding water molecules to simulate the intracellular environment. Through all-atom molecular dynamics simulations of GPCRs, we can reveal the binding and dissociation processes between agonists and GPCRs.

Figure 7: A2A receptor binding/dissociation simulation with adenosine for class A GPCRs

(Source: https://doi.org/10.1038/s41467-020-17437-5)

For fully activated GPCR signaling mechanisms, complex dynamic processes are involved, including interactions between agonists and GPCRs and between GPCRs and G proteins. Molecular dynamics simulations can provide insight into the details and dynamics of these intermolecular interactions and how the interaction between GPCR and G proteins evolves in time and space.

Figure 8: Binding simulation of GPCR and G protein complex(Source: Alessandro Nicoli, @JanaSelent Lab)

Summary

Divamics can simulate the activation process of GPCR in a shorter simulation time through AI+ multiscale molecular dynamics technology, which will provide an in-depth understanding of the interactions and signaling mechanisms between GPCR and agonists and G proteins. These techniques will provide you with GPCR-related new drug design and reveal the details and mechanisms of GPCR activation. In addition, the use of molecular dynamics simulations will also provide you with the ability to assess the effects of GPCR mutations on protein structure and function, thus helping to explain disease-related GPCR variants.

Conventional molecular dynamics simulations (MD) are usually limited to short time scales, typically in the nanosecond to microsecond range. However, the fully activated GPCR signaling process occurs on much longer time scales and may require several milliseconds of simulation time. In response to this time-scale challenge, various MD techniques with enhanced sampling are available to simulate the GPCR activation process on longer time scales:

1. Random Acceleration Molecular Dynamics (RAMD): By applying a random external force, the dissociation process between agonist and GPCR or GPCR and G protein is accelerated, so that the process on a long time scale can be observed in a short simulation time.

2. Stretched MD (Steered Molecular Dynamics (sMD)): by applying external constraints, the interaction between the agonist or GPCR and G protein is stretched, thus facilitating the dissociation process.

3. Metadynamics (MTD): adopting the method of potential energy surface reconstruction, the simulated system is guided to explore on the free energy surface, thus overcoming the energy barriers and simulating complex conformational transitions.

4. Accelerated Molecular Dynamics (aMD): Accelerates the simulation of long time scale processes by applying an additional potential energy function that allows the simulation system to sample faster in the energy barrier region.

Divamics is carrying out GPCR-related drug development projects with a number of scientific research institutions and pharmaceutical companies, and warmly welcomes the cooperation of relevant pharmaceutical companies/scientific research institutions, with the expectation of jointly promoting the development of innovative drugs.

References

[1] Albert J Kooistra and others, GPCRdb in 2021: integrating GPCR sequence, structure and function, Nucleic Acids Research, Volume 49, Issue D1, 8 January 2021, Pages D335–D343.

[2] Mafi, A.; Kim, S.K.; Goddard, W.A., 3rd. The mechanism for ligand activation of the GPCR-G protein complex. Proc. Natl. Acad. Sci. USA 2022, 119, e2110085119.

[3] A. Gusach, I. Maslov, A. Luginina, V. Borshchevskiy, A. Mishin, V. CherezovBeyond structure: emerging approaches to study GPCR dynamics. Curr. Opin. Struct. Biol., 63 (2020), pp. 18-25.

[4] Souza, P.C.T., Thallmair, S., Conflitti, P. et al. Protein–ligand binding with the coarse-grained Martini model. Nat Commun 11, 3714 (2020)

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