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Computational investigation of functional water molecules in GPCRs bound to G protein or arrestin

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Abstract

G protein-coupled receptors (GPCRs) are membrane proteins constituting the largest family of drug targets. The activated GPCR binds either the heterotrimeric G proteins or arrestin through its activation cycle. Water molecules have been reported to play a role in GPCR activation. Nevertheless, reported studies are focused on the hydrophobic helical bundle region. How water molecules function in GPCR bound either G protein or arrestin is rarely studied. To address this issue, we carried out computational studies on water molecules in both GPCR/G protein complexes and GPCR/arrestin complexes. Using inhomogeneous fluid theory (IFT), we locate all possible hydration sites in GPCRs binding either to G protein or arrestin. We observe that the number of water molecules on the interaction surface between GPCRs and signal proteins are correlated with the insertion depths of the α5-helix from G-protein or “finger loop” from arrestin in GPCRs. In three out of the four simulation pairs, the interfaces of Rhodopsin, M2R and NTSR1 in the G protein-associated systems show more water-mediated hydrogen-bond networks when compared to these in arrestin-associated systems. This reflects that more functionally relevant water molecules may probably be attracted in G protein-associated structures than that in arrestin-associated structures. Moreover, we find the water-mediated interaction networks throughout the NPxxY region and the orthosteric pocket, which may be a key for GPCR activation. Reported studies show that non-biased agonist, which can trigger both GPCR-G protein and GPCR-arrestin activation signal, can result in pharmacologically toxicities. Our comprehensive studies of the hydration sites in GPCR/G protein complexes and GPCR/arrestin complexes may provide important insights in the design of G-protein biased agonists.

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Data availability

Data are freely available upon request of the corresponding author.

Abbreviations

GPCR:

G-protein coupled receptor

IFT:

Inhomogeneous fluid theory

β1AR:

β1-Adrenergic receptor

NTSR1:

Neurotensin receptor-1

Wb:

Water in β1-adrenergic receptor

Wr:

Water in Rhodopsin

MD:

Molecular dynamics

POPC:

1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine

M2R:

Muscarinic acetylcholine-2-receptor

Wn:

Water in neurotensin receptor-1

Wm:

Water in muscarinic acetylcholine-2-receptor

TIP3P:

Transferable interatomic potential with three points

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Acknowledgements

We thank Yuan Zhao, Abbisko Therapeutics Co., Ltd.,for providing the protein preparation module of schrödinger.

Funding

All the simulations were performed on our own high-performance computing cluster in Jiangxi Science & Technology Normal University. This work was supported by the National Natural Science Foundation of China (Grant 22063004), the Youth project of Jiangxi Provincial Department of Education (Grant GJJ170696), the University Doctoral Fund (Grant 2017BSQD016), the Open Fund of Provincial Research Platform (Grant KFGJ19014), the College Students' innovation project (Grant S202011318063), and the horizontal research funding (Grant H20210713181758000003).

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Authors and Affiliations

  1. Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang, China

    Jiaqi Hu & Jianxin Cheng

  2. AutoDrug Biotech Co. Ltd, No. 58 XiangKe Rd., Pudong New Area, Shanghai, China

    Xianqiang Sun & Zhengzhong Kang

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  1. Jiaqi Hu
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Contributions

JH carried out the molecular dynamics simulations. JH and XS designed the study and analyzed the data. ZK and JC were responsible for the project. JH, XS, ZK and JC contributed to writing and commenting on the manuscript.

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Correspondence to Zhengzhong Kang or Jianxin Cheng.

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Hu, J., Sun, X., Kang, Z. et al. Computational investigation of functional water molecules in GPCRs bound to G protein or arrestin. J Comput Aided Mol Des 37, 91–105 (2023). https://doi.org/10.1007/s10822-022-00492-z

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