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Lee KH, Shi L. Unraveling Activation-Related Rearrangements and Intrinsic Divergence from Ligand-Specific Conformational Changes of the Dopamine D3 and D2 Receptors. J Chem Inf Model 2024; 64:1778-1793. [PMID: 38454785 DOI: 10.1021/acs.jcim.3c01956] [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] [Indexed: 03/09/2024]
Abstract
Effective rational drug discovery hinges on understanding the functional states of the target protein and distinguishing it from homologues. However, for the G protein coupled receptors, both activation-related conformational changes (ACCs) and intrinsic divergence among receptors can be misled or obscured by ligand-specific conformational changes (LCCs). Here, we unraveled ACCs and intrinsic divergence from LCCs of the dopamine D3 and D2 receptors (D3R and D2R), by analyzing their experimentally determined structures and the molecular dynamics (MD) simulation results of the receptors bound with various ligands. In addition to the ACCs common to other aminergic receptors, we revealed unique ACCs for these two receptors, including the extracellular portion of TM5 (TM5e) and TM6e shifting away from TM2e and TM3e, with a subtle rotation of TM5e. In identifying intrinsic divergence, we found more outward tilting of TM6e in the D2R compared to the D3R in both the experimental structures and simulations bound with ligands in different scaffolds. However, this difference was drastically reduced in the simulations bound with nonselective agonist quinpirole, suggesting a misleading effect of LCCs. Further, in the quinpirole-bound simulations, TM1 showed a greater disparity between these receptors, indicating that LCCs may also obscure intrinsic divergence. Importantly, our MD simulations revealed divergence in the dynamics of these receptors. Specifically, the D2R exhibited heightened flexibility compared to the D3R in the extracellular loops and TMs 5e, 6e, and 7e, associated with its greater ligand binding site plasticity. Our results lay the groundwork for crafting ligands specifically targeting the D2R and D3R with more precise pharmacological profiles.
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Affiliation(s)
- Kuo Hao Lee
- Computational Chemistry and Molecular Biophysics Section, National Institute on Drug Abuse - Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, United States
| | - Lei Shi
- Computational Chemistry and Molecular Biophysics Section, National Institute on Drug Abuse - Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, United States
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Lee KH, Shi L. Unraveling activation-related rearrangements and intrinsic divergence from ligand-induced conformational changes of the dopamine D3 and D2 receptors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.11.566699. [PMID: 38014309 PMCID: PMC10680602 DOI: 10.1101/2023.11.11.566699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Effective rational drug discovery targeting a specific protein hinges on understanding their functional states and distinguishing it from homologs. However, for the G protein coupled receptors, both the activation-related conformational changes (ACCs) and the intrinsic divergence among receptors can be misled or obscured by ligand-induced conformational changes (LCCs). Here, we unraveled ACCs and intrinsic divergence from LCCs of the dopamine D3 and D2 receptors (D3R and D2R), by analyzing their experimentally determined structures and the molecular dynamics simulation results of the receptors bound with different ligands. In addition to the ACCs common to other aminergic receptors, we revealed unique ACCs for these two receptors including TM5e and TM6e shifting away from TM2e and TM3e, with a subtle rotation of TM5e. In identifying intrinsic divergence, we found pronounced outward tilting of TM6e in the D2R compared to the D3R in both experimental structures and simulations with ligands in different scaffolds. This tilting was drastically reduced in the simulations of the receptors bound with nonselective full agonist quinpirole, suggesting a misleading impact of LCCs. Further, in the quinpirole-bound simulations, TM1 showed a greater disparity between these receptors, indicating that LCCs may obscure intrinsic divergence. In addition, our analysis showed that the impact of the nonconserved TM1 propagated to conserved Trp7.40 and Glu2.65, both are ligand binding residues. We also found that the D2R exhibited heightened flexibility compared to the D3R in the extracellular portions of TMs 5, 6, and 7, potentially associated with its greater ligand binding site plasticity. Our results lay the groundwork for crafting ligands specifically targeting D2R or D3R with more precise pharmacological profiles.
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Affiliation(s)
- Kuo Hao Lee
- Computational Chemistry and Molecular Biophysics Section, National Institute on Drug Abuse – Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Lei Shi
- Computational Chemistry and Molecular Biophysics Section, National Institute on Drug Abuse – Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
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Zou R, Wang X, Li S, Chan HCS, Vogel H, Yuan S. The role of metal ions in G protein‐coupled receptor signalling and drug discovery. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1565] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Rongfeng Zou
- Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen China
- AlphaMol Science Ltd Shenzhen China
| | - Xueying Wang
- Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen China
| | - Shu Li
- Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen China
| | - H. C. Stephen Chan
- Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen China
| | - Horst Vogel
- Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen China
- AlphaMol Science Ltd Shenzhen China
- Ecole Polytechnique Fédérale de Lausanne (EPFL) Lausanne Switzerland
| | - Shuguang Yuan
- Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen China
- AlphaMol Science Ltd Shenzhen China
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Lane JR, Abramyan AM, Adhikari P, Keen AC, Lee KH, Sanchez J, Verma RK, Lim HD, Yano H, Javitch JA, Shi L. Distinct inactive conformations of the dopamine D2 and D3 receptors correspond to different extents of inverse agonism. eLife 2020; 9:e52189. [PMID: 31985399 PMCID: PMC7053997 DOI: 10.7554/elife.52189] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 01/24/2020] [Indexed: 01/07/2023] Open
Abstract
By analyzing and simulating inactive conformations of the highly homologous dopamine D2 and D3 receptors (D2R and D3R), we find that eticlopride binds D2R in a pose very similar to that in the D3R/eticlopride structure but incompatible with the D2R/risperidone structure. In addition, risperidone occupies a sub-pocket near the Na+ binding site, whereas eticlopride does not. Based on these findings and our experimental results, we propose that the divergent receptor conformations stabilized by Na+-sensitive eticlopride and Na+-insensitive risperidone correspond to different degrees of inverse agonism. Moreover, our simulations reveal that the extracellular loops are highly dynamic, with spontaneous transitions of extracellular loop 2 from the helical conformation in the D2R/risperidone structure to an extended conformation similar to that in the D3R/eticlopride structure. Our results reveal previously unappreciated diversity and dynamics in the inactive conformations of D2R. These findings are critical for rational drug discovery, as limiting a virtual screen to a single conformation will miss relevant ligands.
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Affiliation(s)
- J Robert Lane
- Division of Pharmacology, Physiology and Neuroscience, School of Life Sciences, Queen’s Medical Centre, University of NottinghamNottinghamUnited Kingdom
- Centre of Membrane Protein and Receptors, Universities of Birmingham and NottinghamNottinghamUnited Kingdom
| | - Ara M Abramyan
- Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse - Intramural Research Program, National Institutes of HealthBaltimoreUnited States
| | - Pramisha Adhikari
- Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse - Intramural Research Program, National Institutes of HealthBaltimoreUnited States
| | - Alastair C Keen
- Division of Pharmacology, Physiology and Neuroscience, School of Life Sciences, Queen’s Medical Centre, University of NottinghamNottinghamUnited Kingdom
- Centre of Membrane Protein and Receptors, Universities of Birmingham and NottinghamNottinghamUnited Kingdom
- Drug Discovery Biology, Department of Pharmacology and Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash UniversityParkvilleAustralia
| | - Kuo-Hao Lee
- Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse - Intramural Research Program, National Institutes of HealthBaltimoreUnited States
| | - Julie Sanchez
- Division of Pharmacology, Physiology and Neuroscience, School of Life Sciences, Queen’s Medical Centre, University of NottinghamNottinghamUnited Kingdom
- Centre of Membrane Protein and Receptors, Universities of Birmingham and NottinghamNottinghamUnited Kingdom
| | - Ravi Kumar Verma
- Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse - Intramural Research Program, National Institutes of HealthBaltimoreUnited States
| | - Herman D Lim
- Drug Discovery Biology, Department of Pharmacology and Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash UniversityParkvilleAustralia
| | - Hideaki Yano
- Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse - Intramural Research Program, National Institutes of HealthBaltimoreUnited States
| | - Jonathan A Javitch
- Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia UniversityNew YorkUnited States
- Division of Molecular Therapeutics, New York State Psychiatric InstituteNew YorkUnited States
- Department of PharmacologyVagelos College of Physicians and Surgeons, Columbia UniversityNew YorkUnited States
| | - Lei Shi
- Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse - Intramural Research Program, National Institutes of HealthBaltimoreUnited States
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Cao X, Zhang Y, Chen Y, Qiu Y, Yu M, Xu X, Liu X, Liu BF, Zhang L, Zhang G. Synthesis and Biological Evaluation of Fused Tricyclic Heterocycle Piperazine (Piperidine) Derivatives As Potential Multireceptor Atypical Antipsychotics. J Med Chem 2018; 61:10017-10039. [PMID: 30383372 DOI: 10.1021/acs.jmedchem.8b01096] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Herein, a novel series of multireceptor ligands was developed as polypharmacological antipsychotic agents using the designed multiple ligand approach between dopamine receptors and serotonin receptors. Among them, compound 47 possessed unique pharmacological features, exhibiting high affinities for D2, D3, 5-HT1A, 5-HT2A, and 5-HT6 receptors and low efficacy at the off-target receptors (5-HT2C, histamine H1, and adrenergic α1 receptor). Compound 47 showed dose-dependent inhibition of apomorphine- and MK-801-induced motor behavior, and the conditioned avoidance response with low cataleptic effect. Moreover, compound 47 resulted nonsignificantly serum prolactin levels and weight gain change compared with risperidone. Additionally, compound 47 possessed a favorable pharmacokinetic profile with oral bioavailability of 58.8% in rats. Furthermore, compound 47 displayed procognition properties in a novel object recognition task in rats. Taken together, compound 47 may constitute a novel class of atypical antipsychotic drugs for schizophrenia.
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Affiliation(s)
- Xudong Cao
- Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology , Huazhong University of Science and Technology , Wuhan 430074 , China
| | - Yifang Zhang
- Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology , Huazhong University of Science and Technology , Wuhan 430074 , China
| | - Yin Chen
- Jiangsu Nhwa Pharmaceutical Co., Ltd. 69 Democratic South Road , Xuzhou , Jiangsu 221116 , China
| | - Yinli Qiu
- Jiangsu Nhwa Pharmaceutical Co., Ltd. 69 Democratic South Road , Xuzhou , Jiangsu 221116 , China
| | - Minquan Yu
- Jiangsu Nhwa Pharmaceutical Co., Ltd. 69 Democratic South Road , Xuzhou , Jiangsu 221116 , China
| | - Xiangqing Xu
- Jiangsu Nhwa Pharmaceutical Co., Ltd. 69 Democratic South Road , Xuzhou , Jiangsu 221116 , China
| | - Xin Liu
- Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology , Huazhong University of Science and Technology , Wuhan 430074 , China
| | - Bi-Feng Liu
- Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology , Huazhong University of Science and Technology , Wuhan 430074 , China
| | - Liangren Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences , Peking University , Beijing 100191 , China
| | - Guisen Zhang
- Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology , Huazhong University of Science and Technology , Wuhan 430074 , China.,Jiangsu Nhwa Pharmaceutical Co., Ltd. 69 Democratic South Road , Xuzhou , Jiangsu 221116 , China
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