1
|
Fan S, Guo C, Yang G, Hong L, Li H, Ma J, Zhou Y, Fan S, Xue Y, Zeng F. GPR160 regulates the self-renewal and pluripotency of mouse embryonic stem cells via JAK1/STAT3 signaling pathway. J Genet Genomics 2024; 51:1055-1065. [PMID: 38750952 DOI: 10.1016/j.jgg.2024.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 07/14/2024]
Abstract
G-protein-coupled receptors (GPCRs) are the largest family of transmembrane receptors and regulate various physiological and pathological processes. Despite extensive studies, the roles of GPCRs in mouse embryonic stem cells (mESCs) remain poorly understood. Here, we show that GPR160, a class A member of GPCRs, is dramatically downregulated concurrent with mESC differentiation into embryoid bodies in vitro. Knockdown of Gpr160 leads to downregulation of the expression of pluripotency-associated transcription factors and upregulation of the expression of lineage markers, accompanying with the arrest of the mESC cell-cycle in the G0/G1 phase. RNA-seq analysis shows that GPR160 participates in the JAK/STAT signaling pathway crucial for maintaining ESC stemness, and the knockdown of Gpr160 results in the downregulation of STAT3 phosphorylation level, which in turn is partially rescued by colivelin, a STAT3 activator. Consistent with these observations, GPR160 physically interacts with JAK1, and cooperates with leukemia inhibitory factor receptor (LIFR) and gp130 to activate the STAT3 pathway. In summary, our results suggest that GPR160 regulates mESC self-renewal and pluripotency by interacting with the JAK1-LIFR-gp130 complex to mediate the JAK1/STAT3 signaling pathway.
Collapse
Affiliation(s)
- Shasha Fan
- Department of Histo-Embryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai 200040, China; NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular Biology & Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai 200040, China
| | - Chuanliang Guo
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai 200040, China; NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular Biology & Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai 200040, China
| | - Guanheng Yang
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai 200040, China; NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular Biology & Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai 200040, China
| | - Lei Hong
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai 200040, China; NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular Biology & Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai 200040, China
| | - Hongyu Li
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai 200040, China; NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular Biology & Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai 200040, China
| | - Ji Ma
- Department of Histo-Embryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai 200040, China; NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular Biology & Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai 200040, China
| | - Yiye Zhou
- Department of Histo-Embryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai 200040, China; NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular Biology & Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai 200040, China
| | - Shuyue Fan
- Department of Histo-Embryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular Biology & Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai 200040, China
| | - Yan Xue
- Department of Histo-Embryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai 200040, China; NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular Biology & Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai 200040, China.
| | - Fanyi Zeng
- Department of Histo-Embryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai 200040, China; NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular Biology & Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai 200040, China; School of Pharmacy, Macau University of Science and Technology, Macau 999078, China.
| |
Collapse
|
2
|
Alhumaid NK, Tawfik EA. Reliability of AlphaFold2 Models in Virtual Drug Screening: A Focus on Selected Class A GPCRs. Int J Mol Sci 2024; 25:10139. [PMID: 39337622 PMCID: PMC11432040 DOI: 10.3390/ijms251810139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2024] [Revised: 09/19/2024] [Accepted: 09/19/2024] [Indexed: 09/30/2024] Open
Abstract
Protein three-dimensional (3D) structure prediction is one of the most challenging issues in the field of computational biochemistry, which has overwhelmed scientists for almost half a century. A significant breakthrough in structural biology has been established by developing the artificial intelligence (AI) system AlphaFold2 (AF2). The AF2 system provides a state-of-the-art prediction of protein structures from nearly all known protein sequences with high accuracy. This study examined the reliability of AF2 models compared to the experimental structures in drug discovery, focusing on one of the most common protein drug-targeted classes known as G protein-coupled receptors (GPCRs) class A. A total of 32 representative protein targets were selected, including experimental structures of X-ray crystallographic and Cryo-EM structures and their corresponding AF2 models. The quality of AF2 models was assessed using different structure validation tools, including the pLDDT score, RMSD value, MolProbity score, percentage of Ramachandran favored, QMEAN Z-score, and QMEANDisCo Global. The molecular docking was performed using the Genetic Optimization for Ligand Docking (GOLD) software. The AF2 models' reliability in virtual drug screening was determined by their ability to predict the ligand binding poses closest to the native binding pose by assessing the Root Mean Square Deviation (RMSD) metric and docking scoring function. The quality of the docking and scoring function was evaluated using the enrichment factor (EF). Furthermore, the capability of using AF2 models in molecular docking to identify hits with key protein-ligand interactions was analyzed. The posing power results showed that the AF2 models successfully predicted ligand binding poses (RMSD < 2 Å). However, they exhibited lower screening power, with average EF values of 2.24, 2.42, and 1.82 for X-ray, Cryo-EM, and AF2 structures, respectively. Moreover, our study revealed that molecular docking using AF2 models can identify competitive inhibitors. In conclusion, this study found that AF2 models provided docking results comparable to experimental structures, particularly for certain GPCR targets, and could potentially significantly impact drug discovery.
Collapse
Affiliation(s)
- Nada K Alhumaid
- Advanced Diagnostics and Therapeutics Institute, Health Sector, King Abdulaziz City for Science and Technology (KACST), Riyadh 11442, Saudi Arabia
| | - Essam A Tawfik
- Advanced Diagnostics and Therapeutics Institute, Health Sector, King Abdulaziz City for Science and Technology (KACST), Riyadh 11442, Saudi Arabia
| |
Collapse
|
3
|
Mezei M, Latif R, Das B, Davies TF. Implications of an Improved Model of the TSH Receptor Transmembrane Domain (TSHR-TMD-TRIO). Endocrinology 2021; 162:6161546. [PMID: 33693584 PMCID: PMC8183494 DOI: 10.1210/endocr/bqab051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Indexed: 11/19/2022]
Abstract
The thyroid-stimulating hormone receptor (TSHR) is a G-protein-coupled receptor group A family member with 7 transmembrane helices. We generated 3 new models of its entire transmembrane region using a 600 ns molecular simulation. The simulation started from our previously published model, which we have now revised by also modeling the intracellular loops and the C-terminal tail, adding internal waters and embedding it into a lipid bilayer with a water layer and with ions added to complete the system. We have named this model TSHR-TMD-TRIO since 3 representative dominant structures were then extracted from the simulation trajectory and compared with the original model. These structures each showed small but significant changes in the relative positions of the helices. The 3 models were also used as targets to dock a set of small molecules that are known active compounds including a new TSHR antagonist (BT362), which confirmed the appropriateness of the model with some small molecules showing significant preference for one or other of the structures.
Collapse
Affiliation(s)
- Mihaly Mezei
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Correspondence: Mihaly Mezei, PhD, Icahn School of Medicine at Mount Sinai, New York, NY, USA. E-mail:
| | - Rauf Latif
- Thyroid Research Unit, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- James J. Peters VA Medical Center, New York, NY, USA
| | - Bhaskar Das
- Arnold & Marie Schwartz College of Pharmacy & Health Sciences, Long Island University, New York, NY, USA
| | - Terry F Davies
- Thyroid Research Unit, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- James J. Peters VA Medical Center, New York, NY, USA
| |
Collapse
|
4
|
Frank T, Niemann I, Reichel A, Stamminger T. Emerging roles of cytomegalovirus-encoded G protein-coupled receptors during lytic and latent infection. Med Microbiol Immunol 2019; 208:447-456. [PMID: 30900091 DOI: 10.1007/s00430-019-00595-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 03/09/2019] [Indexed: 12/28/2022]
Abstract
Cytomegaloviruses (CMVs) have developed multiple diverse strategies to ensure their replicative success and to evade immune recognition. Given the fact that G protein-coupled receptors (GPCRs) are key regulators of numerous cellular processes and modify a variety of signaling pathways, it is not surprising that CMVs and other herpesviruses have hijacked mammalian GPCRs during their coevolution. Human cytomegalovirus (HCMV) encodes for four viral GPCR homologues (vGPCRs), termed US27, US28, UL33, and UL78. Although HCMV-encoded GPCRs were first described in 1990, the pivotal functions of these viral receptor proteins were detected only recently. Here, we summarize seminal knowledge on the functions of herpesviral vGPCRs with a focus on novel roles of cytomegalovirus-encoded vGPCRs for viral spread and the regulation of latency.
Collapse
Affiliation(s)
- Theresa Frank
- Institute of Clinical and Molecular Virology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Ina Niemann
- Institute of Clinical and Molecular Virology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Anna Reichel
- Institute for Virology, Ulm University Medical Center, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Thomas Stamminger
- Institute for Virology, Ulm University Medical Center, Albert-Einstein-Allee 11, 89081, Ulm, Germany.
| |
Collapse
|
5
|
Wouters E, Vasudevan L, Ciruela F, Saini DK, Stove C, Van Craenenbroeck K. Assessing GPCR Dimerization in Living Cells: Comparison of the NanoBiT Assay with Related Bioluminescence- and Fluorescence-Based Approaches. RECEPTOR-RECEPTOR INTERACTIONS IN THE CENTRAL NERVOUS SYSTEM 2018. [DOI: 10.1007/978-1-4939-8576-0_15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
|
6
|
He S, Stankowska DL, Ellis DZ, Krishnamoorthy RR, Yorio T. Targets of Neuroprotection in Glaucoma. J Ocul Pharmacol Ther 2017; 34:85-106. [PMID: 28820649 DOI: 10.1089/jop.2017.0041] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Progressive neurodegeneration of the optic nerve and the loss of retinal ganglion cells is a hallmark of glaucoma, the leading cause of irreversible blindness worldwide, with primary open-angle glaucoma (POAG) being the most frequent form of glaucoma in the Western world. While some genetic mutations have been identified for some glaucomas, those associated with POAG are limited and for most POAG patients, the etiology is still unclear. Unfortunately, treatment of this neurodegenerative disease and other retinal degenerative diseases is lacking. For POAG, most of the treatments focus on reducing aqueous humor formation, enhancing uveoscleral or conventional outflow, or lowering intraocular pressure through surgical means. These efforts, in some cases, do not always lead to a prevention of vision loss and therefore other strategies are needed to reduce or reverse the progressive neurodegeneration. In this review, we will highlight some of the ocular pharmacological approaches that are being tested to reduce neurodegeneration and provide some form of neuroprotection.
Collapse
Affiliation(s)
- Shaoqing He
- North Texas Eye Research Institute, University of North Texas Health Science Center , Fort Worth, Texas
| | - Dorota L Stankowska
- North Texas Eye Research Institute, University of North Texas Health Science Center , Fort Worth, Texas
| | - Dorette Z Ellis
- North Texas Eye Research Institute, University of North Texas Health Science Center , Fort Worth, Texas
| | - Raghu R Krishnamoorthy
- North Texas Eye Research Institute, University of North Texas Health Science Center , Fort Worth, Texas
| | - Thomas Yorio
- North Texas Eye Research Institute, University of North Texas Health Science Center , Fort Worth, Texas
| |
Collapse
|
7
|
Xu XX, Zhang LH, Xie X. Somatostatin receptor type 2 contributes to the self-renewal of murine embryonic stem cells. Acta Pharmacol Sin 2014; 35:1023-30. [PMID: 24998255 DOI: 10.1038/aps.2014.51] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 05/23/2014] [Indexed: 01/21/2023] Open
Abstract
AIM The roles of G-protein coupled receptors (GPCRs) in stem cell biology remain unclear. In this study, we aimed to identify GPCRs that might contribute to the self-renewal of mouse embryonic stem cells (mESCs). METHODS The expression levels of pluripotent genes and GPCR gene were detected in E14 mESCs using PCR array and RT-PCR. Immunofluorescent staining was used to examine the expression of pluripotent markers and the receptor translocation. Western blot analysis was used to detect phosphorylation of signal proteins. Knock-down of receptor was conducted to confirm its role in pluripotency maintenance. RESULTS In leukemia inhibitory factor (LIF)-free medium, mESCs lost the typical morphology of pluripotency, accompanied by markedly decreases in expression of somatostatin receptor type 2 (SSTR2), as well as the pluripotency biomarkers Oct4, Sox2, Rex1 and Nanog. Addition of the SSTR2 agonist octreotide or seglitide (0.1-30 μmol/L) in LIF-free medium dose-dependently promoted the self-renewal of mESCs, whereas the SSTR2 antagonist S4 (0.03-3 μmol/L) dose-dependently blocked octreotide-induced self-renewal. Knock-down of SSTR2 significantly decreased the self-renewal of mESCs even in the presence of LIF. Addition of LIF (1000 U/mL) or octreotide (1 μmol/L) in LIF-free medium significantly increased both phosphorylation and nuclear ocalization of STAT3. CONCLUSION The activation of SSTR2 contributes to the self-renewal of mESCs via activation of the STAT3 pathway.
Collapse
|
8
|
Rataj K, Witek J, Mordalski S, Kosciolek T, Bojarski AJ. Impact of template choice on homology model efficiency in virtual screening. J Chem Inf Model 2014; 54:1661-8. [PMID: 24813470 DOI: 10.1021/ci500001f] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Homology modeling is a reliable method of predicting the three-dimensional structures of proteins that lack NMR or X-ray crystallographic data. It employs the assumption that a structural resemblance exists between closely related proteins. Despite the availability of many crystal structures of possible templates, only the closest ones are chosen for homology modeling purposes. To validate the aforementioned approach, we performed homology modeling of four serotonin receptors (5-HT1AR, 5-HT2AR, 5-HT6R, 5-HT7R) for virtual screening purposes, using 10 available G-Protein Coupled Receptors (GPCR) templates with diverse evolutionary distances to the targets, with various approaches to alignment construction and model building. The resulting models were further validated in two steps by means of ligand docking and enrichment calculation, using Glide software. The final quality of the models was determined in virtual screening-like experiments by the AUROC score of the resulting ROC curves. The outcome of this research showed that no correlation between sequence identity and model quality was found, leading to the conclusion that the closest phylogenetic relative is not always the best template for homology modeling.
Collapse
Affiliation(s)
- Krzysztof Rataj
- Department of Medicinal Chemistry, Institute of Pharmacology, Polish Academy of Sciences , 12 Smętna Street, 31-343 Krakow, Poland
| | | | | | | | | |
Collapse
|