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Zhang H, Im W. Ligand Binding Affinity Prediction for Membrane Proteins with Alchemical Free Energy Calculation Methods. J Chem Inf Model 2024. [PMID: 38959405 DOI: 10.1021/acs.jcim.4c00764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
Alchemical relative binding free energy (ΔΔG) calculations have shown high accuracy in predicting ligand binding affinity and have been used as important tools in computer-aided drug discovery and design. However, there has been limited research on the application of ΔΔG methods to membrane proteins despite the fact that these proteins represent a significant proportion of drug targets, play crucial roles in biological processes, and are implicated in numerous diseases. In this study, to predict the binding affinity of ligands to G protein-coupled receptors (GPCRs), we employed two ΔΔG calculation methods: thermodynamic integration (TI) with AMBER and the alchemical transfer method (AToM) with OpenMM. We calculated ΔΔG values for 53 transformations involving four class A GPCRs and evaluated the performance of AMBER-TI and AToM-OpenMM. In addition, we conducted tests using different numbers of windows and varying simulation times to achieve reliable ΔΔG results and to optimize resource utilization. Overall, both AMBER-TI and AToM-OpenMM show good agreement with the experimental data. Our results validate the applicability of AMBER-TI and AToM-OpenMM for optimization of lead compounds targeting membrane proteins.
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Affiliation(s)
- Han Zhang
- Departments of Biological Sciences and Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Wonpil Im
- Departments of Biological Sciences and Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
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Yuan X, Zhao X, Wang W, Li C. Mechanosensing by Piezo1 and its implications in the kidney. Acta Physiol (Oxf) 2024; 240:e14152. [PMID: 38682304 DOI: 10.1111/apha.14152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 03/27/2024] [Accepted: 04/15/2024] [Indexed: 05/01/2024]
Abstract
Piezo1 is an essential mechanosensitive transduction ion channel in mammals. Its unique structure makes it capable of converting mechanical cues into electrical and biological signals, modulating biological and (patho)physiological processes in a wide variety of cells. There is increasing evidence demonstrating that the piezo1 channel plays a vital role in renal physiology and disease conditions. This review summarizes the current evidence on the structure and properties of Piezo1, gating modulation, and pharmacological characteristics, with special focus on the distribution and (patho)physiological significance of Piezo1 in the kidney, which may provide insights into potential treatment targets for renal diseases involving this ion channel.
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Affiliation(s)
- Xi Yuan
- Department of Physiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Institute of Hypertension, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xiaoduo Zhao
- Department of Pathology, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Weidong Wang
- Institute of Hypertension, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Pathophysiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Chunling Li
- Department of Physiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Institute of Hypertension, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
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Goon S, Shiu Chen Liu C, Ghosh Dastidar U, Paul B, Mukherjee S, Sarkar HS, Desai M, Jana R, Pal S, Sreedevi NV, Ganguly D, Talukdar A. Exploring the Structural Attributes of Yoda1 for the Development of New-Generation Piezo1 Agonist Yaddle1 as a Vaccine Adjuvant Targeting Optimal T Cell Activation. J Med Chem 2024; 67:8225-8246. [PMID: 38716967 DOI: 10.1021/acs.jmedchem.4c00322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2024]
Abstract
Piezo1, a mechano-activated ion channel, has wide-ranging physiological and therapeutic implications, with the ongoing development of specific agonists unveiling cellular responses to mechanical stimuli. In our study, we systematically analyzed the chemical subunits in Piezo1 protein agonist Yoda1 to comprehend the structure-activity relationship and push forward next-generation agonist development. Preliminary screening assays for Piezo1 agonism were performed using the Piezo1-mCherry-transfected HEK293A cell line, keeping Yoda1 as a positive control. We introduce a novel Piezo1 agonist Yaddle1 (34, 0.40 μM), featuring a trifluoromethyl group, with further exploration through in vitro studies and density functional theory calculations, emphasizing its tetrel interactions, to act as an ambidextrous wedge between the domains of Piezo1. In contrast to the poor solubility of the established agonist Yoda1, our results showed that the kinetic solubility of Yaddle1 (26.72 ± 1.8 μM at pH 7.4) is 10-fold better than that of Yoda1 (1.22 ± 0.11 μM at pH 7.4). Yaddle1 (34) induces Ca2+ influx in human CD4+ T cell, suggesting its potential as a vaccine adjuvant for enhanced T cell activation.
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Affiliation(s)
- Sunny Goon
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, WB, India
| | - Chinky Shiu Chen Liu
- IICB-Translational Research Unit of Excellence, Department of Cancer Biology and Inflammatory Disorders, CSIR-Indian Institute of Chemical Biology, CN6, Sector V, Salt Lake, Kolkata 700091, WB, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Uddipta Ghosh Dastidar
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, WB, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Barnali Paul
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, WB, India
| | - Suravi Mukherjee
- IICB-Translational Research Unit of Excellence, Department of Cancer Biology and Inflammatory Disorders, CSIR-Indian Institute of Chemical Biology, CN6, Sector V, Salt Lake, Kolkata 700091, WB, India
| | - Himadri Sekhar Sarkar
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, WB, India
| | - Milie Desai
- IICB-Translational Research Unit of Excellence, Department of Cancer Biology and Inflammatory Disorders, CSIR-Indian Institute of Chemical Biology, CN6, Sector V, Salt Lake, Kolkata 700091, WB, India
| | - Rituparna Jana
- IICB-Translational Research Unit of Excellence, Department of Cancer Biology and Inflammatory Disorders, CSIR-Indian Institute of Chemical Biology, CN6, Sector V, Salt Lake, Kolkata 700091, WB, India
| | - Sourav Pal
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, WB, India
| | - Namala Venkata Sreedevi
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, WB, India
| | - Dipyaman Ganguly
- IICB-Translational Research Unit of Excellence, Department of Cancer Biology and Inflammatory Disorders, CSIR-Indian Institute of Chemical Biology, CN6, Sector V, Salt Lake, Kolkata 700091, WB, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Arindam Talukdar
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, WB, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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Du Y, Xu B, Li Q, Peng C, Yang K. The role of mechanically sensitive ion channel Piezo1 in bone remodeling. Front Bioeng Biotechnol 2024; 12:1342149. [PMID: 38390363 PMCID: PMC10882629 DOI: 10.3389/fbioe.2024.1342149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/16/2024] [Indexed: 02/24/2024] Open
Abstract
Piezo1 (2010) was identified as a mechanically activated cation channel capable of sensing various physical forces, such as tension, osmotic pressure, and shear force. Piezo1 mediates mechanosensory transduction in different organs and tissues, including its role in maintaining bone homeostasis. This review aimed to summarize the function and possible mechanism of Piezo1 in the mechanical receptor cells in bone tissue. We found that it is a potential therapeutic target for the treatment of bone diseases.
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Affiliation(s)
- Yugui Du
- Department of Orthodontics, School of Stomatology, Capital Medical University, Beijing, China
| | - Bowen Xu
- Department of Orthodontics, School of Stomatology, Capital Medical University, Beijing, China
| | - Quiying Li
- Department of Orthodontics, School of Stomatology, Capital Medical University, Beijing, China
| | - Chuhan Peng
- Department of Orthodontics, School of Stomatology, Capital Medical University, Beijing, China
| | - Kai Yang
- Department of Orthodontics, School of Stomatology, Capital Medical University, Beijing, China
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