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Jabeen A, Vijayram R, Ranganathan S. A two-stage computational approach to predict novel ligands for a chemosensory receptor. Curr Res Struct Biol 2021; 2:213-221. [PMID: 34235481 PMCID: PMC8244491 DOI: 10.1016/j.crstbi.2020.10.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 09/29/2020] [Accepted: 10/03/2020] [Indexed: 11/01/2022] Open
Abstract
Olfactory receptor (OR) 1A2 is the member of largest superfamily of G protein-coupled receptors (GPCRs). OR1A2 is an ectopically expressed receptor with only 13 known ligands, implicated in reducing hepatocellular carcinoma progression, with enormous therapeutic potential. We have developed a two-stage screening approach to identify novel putative ligands of OR1A2. We first used a pharmacophore model based on atomic property field (APF) to virtually screen a library of 5942 human metabolites. We then carried out structure-based virtual screening (SBVS) for predicting the potential agonists, based on a 3D homology model of OR1A2. This model was developed using a biophysical approach for template selection, based on multiple parameters including hydrophobicity correspondence, applied to the complete set of available GPCR structures to pick the most appropriate template. Finally, the membrane-embedded 3D model was refined by molecular dynamics (MD) simulations in both the apo and holo forms. The refined model in the apo form was selected for SBVS. Four novel small molecules were identified as strong binders to this olfactory receptor on the basis of computed binding energies.
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Key Words
- APF, Atomic property field
- Amber, Assisted model Building with Energy Refinement
- Atomic property field
- Binding free energy calculation
- CSF, Cerebrospinal fluid
- ECL, Extracellular loop
- GPCR, G protein coupled receptor
- HCMV, Human cytomegalovirus
- HMDB, Human metabolome database
- Hydrophobicity correspondence
- LBVS, Ligand based virtual screening
- LC, Lung carcinoids
- MD, Molecular dynamics
- MMGBSA, Molecular mechanics generalized born surface area
- MMPBSA, Molecular mechanics Poisson–Boltzmann surface area
- Molecular dynamics
- NAFLD, Non-alcoholic fatty liver disease
- NASH, Nonalcoholic steatohepatitis
- OR, olfactory receptor
- OR1A2
- Olfactory receptor
- PMEMD, Particle-Mesh Ewald Molecular Dynamics
- POPC, 1-palmitoyl-2-oleoyl-sn-glycero- 3-phosphatidylcholine
- RMSD, Root mean square deviation
- RMSF, Root mean square fluctuation
- SBVS, Structure based virtual screening
- SSD, Sum of squared difference
- TM, Transmembrane
- Virtual ligand screening
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Affiliation(s)
- Amara Jabeen
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Ramya Vijayram
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, Tamilnadu, India
| | - Shoba Ranganathan
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
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2
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Jabeen A, Vijayram R, Ranganathan S. BIO-GATS: A Tool for Automated GPCR Template Selection Through a Biophysical Approach for Homology Modeling. Front Mol Biosci 2021; 8:617176. [PMID: 33898512 PMCID: PMC8059640 DOI: 10.3389/fmolb.2021.617176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 02/24/2021] [Indexed: 11/13/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are the largest family of membrane proteins with more than 800 members. GPCRs are involved in numerous physiological functions within the human body and are the target of more than 30% of the United States Food and Drug Administration (FDA) approved drugs. At present, over 400 experimental GPCR structures are available in the Protein Data Bank (PDB) representing 76 unique receptors. The absence of an experimental structure for the majority of GPCRs demand homology models for structure-based drug discovery workflows. The generation of good homology models requires appropriate templates. The commonly used methods for template selection are based on sequence identity. However, there exists low sequence identity among the GPCRs. Sequences with similar patterns of hydrophobic residues are often structural homologs, even with low sequence identity. Extending this, we propose a biophysical approach for template selection based principally on hydrophobicity correspondence between the target and the template. Our approach takes into consideration other relevant parameters, including resolution, similarity within the orthosteric binding pocket of GPCRs, and structure completeness, for template selection. The proposed method was implemented in the form of a free tool called Bio-GATS, to provide the user with easy selection of the appropriate template for a query GPCR sequence. Bio-GATS was successfully validated with recent published benchmarking datasets. An application to an olfactory receptor to select an appropriate template has also been provided as a case study.
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Affiliation(s)
- Amara Jabeen
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Ramya Vijayram
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - Shoba Ranganathan
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
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3
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Saqib U, Savai R, Liu D, Banerjee S, Baig MS. Drug repositioning as an effective therapy for protease-activated receptor 2 inhibition. J Cell Biochem 2019; 120:1522-1526. [PMID: 30370939 DOI: 10.1002/jcb.27334] [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: 03/20/2018] [Accepted: 06/28/2018] [Indexed: 01/24/2023]
Abstract
Proteinase-activated receptor 2 (PAR-2) is a G protein-coupled receptor activated by both trypsin and a specific agonist peptide, SLIGKV-NH2. It has been linked to various pathologies, including pain and inflammation. Several peptide and peptidomimetic agonizts for PAR-2 have been developed exhibiting high potency and efficacy. However, the number of PAR-2 antagonists is smaller. We screened the Food and Drug Administration library of approved compounds to retrieve novel antagonists for repositioning in the PAR-2 structure. The most efficacious compound bicalutamide bound to the PAR-2 binding groove near the extracellular domain as observed in the in silico studies. Further, it showed reduced Ca2+ release in trypsin activated cells in a dose-dependent manner. Hence, bicalutamide is a novel and potent PAR-2 antagonist which could be therapeutically useful in blocking multiple pathways diverging from PAR-2 signaling. Further, the novel scaffold of bicalutamide represents a new molecular structure for PAR-2 antagonism and can serve as a basis for further drug development.
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Affiliation(s)
- Uzma Saqib
- Discipline of Chemistry, Indian Institute of Technology Indore (IITI), Indore, India
| | - Rajkumar Savai
- Department of Lung Development and Remodeling, Member of the German Center for Lung Research (DZL), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - DongFang Liu
- Center for Inflammation & Epigenetics, Houston Methodist Research Institute, Houston, Texas.,Department of Microbiology and Immunology, Weill Cornell Medical College, Cornell University, New York
| | - Sreeparna Banerjee
- Department of Biological Sciences, Orta Doğu Teknik Üniversitesi (ODTU/METU), Ankara, Turkey
| | - Mirza S Baig
- Discipline of Biosciences and Biomedical Engineering (BSBE), Indian Institute of Technology Indore (IITI), Indore, India
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4
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Kennedy AJ, Ballante F, Johansson JR, Milligan G, Sundström L, Nordqvist A, Carlsson J. Structural Characterization of Agonist Binding to Protease-Activated Receptor 2 through Mutagenesis and Computational Modeling. ACS Pharmacol Transl Sci 2018; 1:119-133. [PMID: 32219208 DOI: 10.1021/acsptsci.8b00019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Indexed: 12/26/2022]
Abstract
Protease-activated receptor 2 (PAR2) is a G-protein-coupled receptor that is activated by proteolytic cleavage of its N-terminus. The unmasked N-terminal peptide then binds to the transmembrane bundle, leading to activation of intracellular signaling pathways associated with inflammation and cancer. Recently determined crystal structures have revealed binding sites of PAR2 antagonists, but the binding mode of the peptide agonist remains unknown. In order to generate a model of PAR2 in complex with peptide SLIGKV, corresponding to the trypsin-exposed tethered ligand, the orthosteric binding site was probed by iterative combinations of receptor mutagenesis, agonist ligand modifications, and data-driven structural modeling. Flexible-receptor docking identified a conserved binding mode for agonists related to the endogenous ligand that was consistent with the experimental data and allowed synthesis of a novel peptide (1-benzyl-1H[1,2,3]triazole-4-yl-LIGKV) with functional potency higher than that of SLIGKV. The final model may be used to understand the structural basis of PAR2 activation and in virtual screens to identify novel agonists and competitive antagonists. The combined experimental and computational approach to characterize agonist binding to PAR2 can be extended to study the many other G protein-coupled receptors that recognize peptides or proteins.
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Affiliation(s)
- Amanda J Kennedy
- Discovery Sciences and Cardiovascular Renal and Metabolism, IMED Biotech Unit, AstraZeneca, Gothenburg, SE-431 83 Mölndal, Sweden
| | - Flavio Ballante
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, SE-751 24 Uppsala, Sweden
| | - Johan R Johansson
- Discovery Sciences and Cardiovascular Renal and Metabolism, IMED Biotech Unit, AstraZeneca, Gothenburg, SE-431 83 Mölndal, Sweden
| | - Graeme Milligan
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Linda Sundström
- Discovery Sciences and Cardiovascular Renal and Metabolism, IMED Biotech Unit, AstraZeneca, Gothenburg, SE-431 83 Mölndal, Sweden
| | - Anneli Nordqvist
- Discovery Sciences and Cardiovascular Renal and Metabolism, IMED Biotech Unit, AstraZeneca, Gothenburg, SE-431 83 Mölndal, Sweden
| | - Jens Carlsson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, SE-751 24 Uppsala, Sweden
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5
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Lim VJY, Du W, Chen YZ, Fan H. A benchmarking study on virtual ligand screening against homology models of human GPCRs. Proteins 2018; 86:978-989. [DOI: 10.1002/prot.25533] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 05/20/2018] [Accepted: 06/04/2018] [Indexed: 12/28/2022]
Affiliation(s)
- Victor Jun Yu Lim
- Bioinformatics Institute (BII), Agency for Science; Technology and Research (A*STAR); Singapore 138671
- Saw Swee Hock School of Public Health; National University of Singapore; Singapore 117549
| | - Weina Du
- Bioinformatics Institute (BII), Agency for Science; Technology and Research (A*STAR); Singapore 138671
| | - Yu Zong Chen
- Department of Pharmacy; National University of Singapore; Singapore 117543
| | - Hao Fan
- Bioinformatics Institute (BII), Agency for Science; Technology and Research (A*STAR); Singapore 138671
- Department of Biological Sciences; National University of Singapore; Singapore 117558
- Center for Computational Biology; Duke-NUS Medical School; Singapore 169857
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6
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Readmond C, Wu C. Investigating detailed interactions between novel PAR1 antagonist F16357 and the receptor using docking and molecular dynamic simulations. J Mol Graph Model 2017; 77:205-217. [DOI: 10.1016/j.jmgm.2017.08.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/18/2017] [Accepted: 08/21/2017] [Indexed: 01/08/2023]
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7
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Suen J, Adams M, Lim J, Madala P, Xu W, Cotterell A, He Y, Yau M, Hooper J, Fairlie D. Mapping transmembrane residues of proteinase activated receptor 2 (PAR 2 ) that influence ligand-modulated calcium signaling. Pharmacol Res 2017; 117:328-342. [DOI: 10.1016/j.phrs.2016.12.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 12/07/2016] [Accepted: 12/07/2016] [Indexed: 12/22/2022]
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8
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Yau MK, Liu L, Suen JY, Lim J, Lohman RJ, Jiang Y, Cotterell AJ, Barry GD, Mak JYW, Vesey DA, Reid RC, Fairlie DP. PAR2 Modulators Derived from GB88. ACS Med Chem Lett 2016; 7:1179-1184. [PMID: 27994760 DOI: 10.1021/acsmedchemlett.6b00306] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 10/10/2016] [Indexed: 11/29/2022] Open
Abstract
PAR2 antagonists have potential for treating inflammatory, respiratory, gastrointestinal, neurological, and metabolic disorders, but few antagonists are known. Derivatives of GB88 (3) suggest that all four of its components bind at distinct PAR2 sites with the isoxazole, cyclohexylalanine, and isoleucine determining affinity and selectivity, while the C-terminal substituent determines agonist/antagonist function. Here we report structurally similar PAR2 ligands with opposing functions (agonist vs antagonist) upon binding to PAR2. A biased ligand AY117 (65) was found to antagonize calcium release induced by PAR2 agonists trypsin and hexapeptide 2f-LIGRLO-NH2 (IC50 2.2 and 0.7 μM, HT29 cells), but it was a selective PAR2 agonist in inhibiting cAMP stimulation and activating ERK1/2 phosphorylation. It showed anti-inflammatory properties both in vitro and in vivo.
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Affiliation(s)
- Mei-Kwan Yau
- Division
of Chemistry and Structural Biology, Centre for Inflammation and Disease
Research and ARC Centre of Excellence in Advanced Molecular Imaging,
Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Ligong Liu
- Division
of Chemistry and Structural Biology, Centre for Inflammation and Disease
Research and ARC Centre of Excellence in Advanced Molecular Imaging,
Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jacky Y. Suen
- Division
of Chemistry and Structural Biology, Centre for Inflammation and Disease
Research and ARC Centre of Excellence in Advanced Molecular Imaging,
Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Junxian Lim
- Division
of Chemistry and Structural Biology, Centre for Inflammation and Disease
Research and ARC Centre of Excellence in Advanced Molecular Imaging,
Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Rink-Jan Lohman
- Division
of Chemistry and Structural Biology, Centre for Inflammation and Disease
Research and ARC Centre of Excellence in Advanced Molecular Imaging,
Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Yuhong Jiang
- Division
of Chemistry and Structural Biology, Centre for Inflammation and Disease
Research and ARC Centre of Excellence in Advanced Molecular Imaging,
Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Adam J. Cotterell
- Division
of Chemistry and Structural Biology, Centre for Inflammation and Disease
Research and ARC Centre of Excellence in Advanced Molecular Imaging,
Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Grant D. Barry
- Division
of Chemistry and Structural Biology, Centre for Inflammation and Disease
Research and ARC Centre of Excellence in Advanced Molecular Imaging,
Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jeffrey Y. W. Mak
- Division
of Chemistry and Structural Biology, Centre for Inflammation and Disease
Research and ARC Centre of Excellence in Advanced Molecular Imaging,
Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David A. Vesey
- Centre
for Kidney Research, Department of Medicine, The University of Queensland, Princess Alexandra Hospital, Brisbane, Queensland 4102, Australia
| | - Robert C. Reid
- Division
of Chemistry and Structural Biology, Centre for Inflammation and Disease
Research and ARC Centre of Excellence in Advanced Molecular Imaging,
Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David P. Fairlie
- Division
of Chemistry and Structural Biology, Centre for Inflammation and Disease
Research and ARC Centre of Excellence in Advanced Molecular Imaging,
Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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9
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Cho NC, Seo SH, Kim D, Shin JS, Ju J, Seong J, Seo SH, Lee I, Lee KT, Kim YK, No KT, Pae AN. Pharmacophore-based virtual screening, biological evaluation and binding mode analysis of a novel protease-activated receptor 2 antagonist. J Comput Aided Mol Des 2016; 30:625-37. [DOI: 10.1007/s10822-016-9937-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 08/11/2016] [Indexed: 10/21/2022]
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10
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Benzylamide antagonists of protease activated receptor 2 with anti-inflammatory activity. Bioorg Med Chem Lett 2016; 26:986-991. [DOI: 10.1016/j.bmcl.2015.12.048] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 12/15/2015] [Indexed: 11/21/2022]
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11
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Emerging Approaches to GPCR Ligand Screening for Drug Discovery. Trends Mol Med 2015; 21:687-701. [DOI: 10.1016/j.molmed.2015.09.002] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 09/02/2015] [Accepted: 09/04/2015] [Indexed: 01/07/2023]
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12
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Xu W, Lim J, Goh CY, Suen JY, Jiang Y, Yau MK, Wu KC, Liu L, Fairlie DP. Repurposing Registered Drugs as Antagonists for Protease-Activated Receptor 2. J Chem Inf Model 2015; 55:2079-84. [DOI: 10.1021/acs.jcim.5b00500] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Weijun Xu
- Division
of Chemistry and
Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Junxian Lim
- Division
of Chemistry and
Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Chai-Yeen Goh
- Division
of Chemistry and
Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jacky Y. Suen
- Division
of Chemistry and
Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Yuhong Jiang
- Division
of Chemistry and
Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Mei-Kwan Yau
- Division
of Chemistry and
Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Kai-Chen Wu
- Division
of Chemistry and
Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Ligong Liu
- Division
of Chemistry and
Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David P. Fairlie
- Division
of Chemistry and
Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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