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Li H, Sun X, Cui W, Xu M, Dong J, Ekundayo BE, Ni D, Rao Z, Guo L, Stahlberg H, Yuan S, Vogel H. Computational drug development for membrane protein targets. Nat Biotechnol 2024; 42:229-242. [PMID: 38361054 DOI: 10.1038/s41587-023-01987-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 09/13/2023] [Indexed: 02/17/2024]
Abstract
The application of computational biology in drug development for membrane protein targets has experienced a boost from recent developments in deep learning-driven structure prediction, increased speed and resolution of structure elucidation, machine learning structure-based design and the evaluation of big data. Recent protein structure predictions based on machine learning tools have delivered surprisingly reliable results for water-soluble and membrane proteins but have limitations for development of drugs that target membrane proteins. Structural transitions of membrane proteins have a central role during transmembrane signaling and are often influenced by therapeutic compounds. Resolving the structural and functional basis of dynamic transmembrane signaling networks, especially within the native membrane or cellular environment, remains a central challenge for drug development. Tackling this challenge will require an interplay between experimental and computational tools, such as super-resolution optical microscopy for quantification of the molecular interactions of cellular signaling networks and their modulation by potential drugs, cryo-electron microscopy for determination of the structural transitions of proteins in native cell membranes and entire cells, and computational tools for data analysis and prediction of the structure and function of cellular signaling networks, as well as generation of promising drug candidates.
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Affiliation(s)
- Haijian Li
- Center for Computer-Aided Drug Discovery, Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology/Chinese Academy of Sciences (SIAT/CAS), Shenzhen, China
| | - Xiaolin Sun
- Center for Computer-Aided Drug Discovery, Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology/Chinese Academy of Sciences (SIAT/CAS), Shenzhen, China
| | - Wenqiang Cui
- Center for Computer-Aided Drug Discovery, Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology/Chinese Academy of Sciences (SIAT/CAS), Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Marc Xu
- Center for Computer-Aided Drug Discovery, Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology/Chinese Academy of Sciences (SIAT/CAS), Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Junlin Dong
- Center for Computer-Aided Drug Discovery, Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology/Chinese Academy of Sciences (SIAT/CAS), Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Babatunde Edukpe Ekundayo
- Laboratory of Biological Electron Microscopy, IPHYS, SB, EPFL and Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Dongchun Ni
- Laboratory of Biological Electron Microscopy, IPHYS, SB, EPFL and Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Zhili Rao
- Center for Computer-Aided Drug Discovery, Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology/Chinese Academy of Sciences (SIAT/CAS), Shenzhen, China
| | - Liwei Guo
- Center for Computer-Aided Drug Discovery, Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology/Chinese Academy of Sciences (SIAT/CAS), Shenzhen, China
| | - Henning Stahlberg
- Laboratory of Biological Electron Microscopy, IPHYS, SB, EPFL and Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.
| | - Shuguang Yuan
- Center for Computer-Aided Drug Discovery, Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology/Chinese Academy of Sciences (SIAT/CAS), Shenzhen, China.
| | - Horst Vogel
- Center for Computer-Aided Drug Discovery, Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology/Chinese Academy of Sciences (SIAT/CAS), Shenzhen, China.
- Institut des Sciences et Ingénierie Chimiques (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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Luo HM, Ye JR, Pu FQ, Luo HL, Zhang WJ. Role and therapeutic target of P2X2/3 receptors in visceral pain. Neuropeptides 2023; 101:102355. [PMID: 37390743 DOI: 10.1016/j.npep.2023.102355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/02/2023]
Abstract
Visceral pain (VP) is caused by internal organ disease. VP is involved in nerve conduction and related signaling molecules, but its specific pathogenesis has not yet been fully elucidated. Currently, there are no effective methods for treating VP. The role of P2X2/3 in VP has progressed. After visceral organs are subjected to noxious stimulation, cells release ATP, activate P2X2/3, enhance the sensitivity of peripheral receptors and the plasticity of neurons, enhance sensory information transmission, sensitize the central nervous system, and play an important role in the development of VP. However, antagonists possess the pharmacological effect of relieving pain. Therefore, in this review, we summarize the biological functions of P2X2/3 and discuss the intrinsic link between P2X2/3 and VP. Moreover, we focus on the pharmacological effects of P2X2/3 antagonists on VP therapy and provide a theoretical basis for its targeted therapy.
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Affiliation(s)
- Hong-Mei Luo
- Department of Rheumatology, The Affiliated Hospital of Jiangxi University of Chinese Medicine, Nanchang City, Jiangxi province 343000, China
| | - Jia-Rong Ye
- Department of Gastrointestinal surgery, The Second Affiliated Hospital, Nanchang University, Nanchang City, Jiangxi province 343000, China
| | - Fan-Qin Pu
- Department of Rheumatology, The Affiliated Hospital of Jiangxi University of Chinese Medicine, Nanchang City, Jiangxi province 343000, China
| | - Hong-Liang Luo
- Department of Rehabilitation Medicine, The Second Affiliated Hospital, Nanchang University, Nanchang City, Jiangxi province 343000, China
| | - Wen-Jun Zhang
- Department of Rehabilitation Medicine, The Second Affiliated Hospital, Nanchang University, Nanchang City, Jiangxi province 343000, China.
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Allert MJ, Kumar S, Wang Y, Beese LS, Hellinga HW. Chromophore carbonyl twisting in fluorescent biosensors encodes direct readout of protein conformations with multicolor switching. Commun Chem 2023; 6:168. [PMID: 37598249 PMCID: PMC10439942 DOI: 10.1038/s42004-023-00982-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/11/2023] [Indexed: 08/21/2023] Open
Abstract
Fluorescent labeling of proteins is a powerful tool for probing structure-function relationships with many biosensing applications. Structure-based rules for systematically designing fluorescent biosensors require understanding ligand-mediated fluorescent response mechanisms which can be challenging to establish. We installed thiol-reactive derivatives of the naphthalene-based fluorophore Prodan into bacterial periplasmic glucose-binding proteins. Glucose binding elicited paired color exchanges in the excited and ground states of these conjugates. X-ray structures and mutagenesis studies established that glucose-mediated color switching arises from steric interactions that couple protein conformational changes to twisting of the Prodan carbonyl relative to its naphthalene plane. Mutations of residues contacting the carbonyl can optimize color switching by altering fluorophore conformational equilibria in the apo and glucose-bound proteins. A commonly accepted view is that Prodan derivatives report on protein conformations via solvatochromic effects due to changes in the dielectric of their local environment. Here we show that instead Prodan carbonyl twisting controls color switching. These insights enable structure-based biosensor design by coupling ligand-mediated protein conformational changes to internal chromophore twists through specific steric interactions between fluorophore and protein.
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Affiliation(s)
- Malin J Allert
- Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710, USA
| | - Shivesh Kumar
- Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710, USA
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - You Wang
- Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710, USA
| | - Lorena S Beese
- Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710, USA
| | - Homme W Hellinga
- Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710, USA.
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Durner A, Durner E, Nicke A. Improved ANAP incorporation and VCF analysis reveal details of P2X7 current facilitation and a limited conformational interplay between ATP binding and the intracellular ballast domain. eLife 2023; 12:82479. [PMID: 36598131 PMCID: PMC9859053 DOI: 10.7554/elife.82479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 01/03/2023] [Indexed: 01/05/2023] Open
Abstract
The large intracellular C-terminus of the pro-inflammatory P2X7 ion channel receptor (P2X7R) is associated with diverse P2X7R-specific functions. Cryo-EM structures of the closed and ATP-bound open full-length P2X7R recently identified a membrane-associated anchoring domain, an open-state stabilizing "cap" domain, and a globular "ballast domain" containing GTP/GDP and dinuclear Zn2+-binding sites with unknown functions. To investigate protein dynamics during channel activation, we improved incorporation of the environment-sensitive fluorescent unnatural amino acid L-3-(6-acetylnaphthalen-2-ylamino)-2-aminopropanoic acid (ANAP) into Xenopus laevis oocyte-expressed P2X7Rs and performed voltage clamp fluorometry. While we confirmed predicted conformational changes within the extracellular and the transmembrane domains, only 3 out of 41 mutants containing ANAP in the C-terminal domain resulted in ATP-induced fluorescence changes. We conclude that the ballast domain functions rather independently from the extracellular ATP binding domain and might require activation by additional ligands and/or protein interactions. Novel tools to study these are presented.
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Affiliation(s)
- Anna Durner
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of Medicine, LMU MunichMunichGermany
| | - Ellis Durner
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, LMU MunichMunichGermany
| | - Annette Nicke
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of Medicine, LMU MunichMunichGermany
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Sattler C, Benndorf K. Enlightening activation gating in P2X receptors. Purinergic Signal 2022; 18:177-191. [PMID: 35188598 PMCID: PMC9123132 DOI: 10.1007/s11302-022-09850-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/04/2022] [Indexed: 12/20/2022] Open
Abstract
P2X receptors are trimeric nonselective cation channels gated by ATP. They assemble from seven distinct subunit isoforms as either homo- or heteromeric complexes and contain three extracellularly located binding sites for ATP. P2X receptors are expressed in nearly all tissues and are there involved in physiological processes like synaptic transmission, pain, and inflammation. Thus, they are a challenging pharmacological target. The determination of crystal and cryo-EM structures of several isoforms in the last decade in closed, open, and desensitized states has provided a firm basis for interpreting the huge amount of functional and biochemical data. Electrophysiological characterization in conjugation with optical approaches has generated significant insights into structure–function relationships of P2X receptors. This review focuses on novel optical and related approaches to better understand the conformational changes underlying the activation of these receptors.
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Affiliation(s)
- Christian Sattler
- Institut Für Physiologie II, Universitätsklinikum Jena, Friedrich-Schiller-Universität Jena, 07740, Jena, Germany.
| | - Klaus Benndorf
- Institut Für Physiologie II, Universitätsklinikum Jena, Friedrich-Schiller-Universität Jena, 07740, Jena, Germany.
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