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Aguilar-Pineda JA, González-Melchor M. Influence of the Water Model on the Structure and Interactions of the GPR40 Protein with the Lipid Membrane and the Solvent: Rigid versus Flexible Water Models. J Chem Theory Comput 2024. [PMID: 38991114 DOI: 10.1021/acs.jctc.4c00571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
G protein-coupled receptors (GPCR) are responsible for modulating various physiological functions and are thus related to the pathophysiology of different diseases. Being potential therapeutic targets, multiple computational methodologies have been developed to analyze their behavior and interactions with other species. The solvent, on the other hand, has received much less attention. In this work, we analyzed the effect of four explicit water models on the structure and interactions of the GPR40 receptor in its apo form. We employed the rigid SPC/E and TIP4P models, and their flexible versions, the FBA/ϵ and TIP4P/ϵflex. We explored the structural changes and their correlation with some bulk dynamic properties of water. Our results showed an adverse effect on the conservation of the secondary structure of the receptor with all the models due to the breaking of the intramolecular hydrogen bond network, being more evident for the TIP4P models. Notably, all four models brought the receptor to states similar to the active one, modifying the intracellular part of the TM5 and TM6 domains in a "hinge" type movement, allowing the opening of the structure. Regarding the dynamic properties, the rigid models showed results comparable to those obtained in other studies on membrane systems. However, flexible models exhibit disparities in the molecular representation of systems. Surprisingly, the FBA/ϵ model improves the molecular picture of several properties, even though their agreement with bulk diffusion is poorer. These findings reinforce our idea that exploring other water models or improving the current ones, to better represent the membrane interface, can lead to a positive impact on the description of the signal transduction mechanisms and the search of new drugs by targeting these receptors.
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Affiliation(s)
- Jorge Alberto Aguilar-Pineda
- Instituto de Física "Luis Rivera Terrazas", Benemérita Universidad Autónoma de Puebla, Av San Claudio, Cd Universitaria, Apdo. Postal J-48, Puebla 72570, México
| | - Minerva González-Melchor
- Instituto de Física "Luis Rivera Terrazas", Benemérita Universidad Autónoma de Puebla, Av San Claudio, Cd Universitaria, Apdo. Postal J-48, Puebla 72570, México
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Ding T, Karlov DS, Pino-Angeles A, Tikhonova IG. Intermolecular Interactions in G Protein-Coupled Receptor Allosteric Sites at the Membrane Interface from Molecular Dynamics Simulations and Quantum Chemical Calculations. J Chem Inf Model 2022; 62:4736-4747. [PMID: 36178787 PMCID: PMC9554917 DOI: 10.1021/acs.jcim.2c00788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Allosteric modulators are called promising candidates in G protein-coupled receptor (GPCR) drug development by displaying subtype selectivity and more specific receptor modulation. Among the allosteric sites known to date, cavities at the receptor-lipid interface represent an uncharacteristic binding location that raises many questions about the ligand interactions and stability, the binding site structure, and how all of these are affected by lipid molecules. In this work, we analyze interactions in the allosteric sites of the PAR2, C5aR1, and GCGR receptors in three lipid compositions using molecular dynamics simulations. In addition, we performed quantum chemical calculations involving the symmetry-adapted perturbation theory (SAPT) and the natural population analysis to quantify the strength of intermolecular interactions. We show that besides classical hydrogen bonds, weak polar interactions such as O-HC, O-Br, and long-range electrostatics with the backbone amides contribute to the stability of allosteric modulators at the receptor-lipid interface. The allosteric cavities are detectable in various membrane compositions. The availability of polar atoms for interactions in such cavities can be assessed by water molecules from simulations. Although ligand-lipid interactions are weak, lipid tails play a role in ligand binding pose stability and the size of allosteric cavities. We discuss physicochemical aspects of ligand binding at the receptor-lipid interface and suggest a compound library enriched by weak donor groups for ligand search in such sites.
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Affiliation(s)
- Tianyi Ding
- School of Pharmacy, Medical Biology Centre, Queen's University Belfast, Belfast, Northern IrelandBT9 7BL, U.K
| | - Dmitry S Karlov
- School of Pharmacy, Medical Biology Centre, Queen's University Belfast, Belfast, Northern IrelandBT9 7BL, U.K
| | - Almudena Pino-Angeles
- School of Pharmacy, Medical Biology Centre, Queen's University Belfast, Belfast, Northern IrelandBT9 7BL, U.K
| | - Irina G Tikhonova
- School of Pharmacy, Medical Biology Centre, Queen's University Belfast, Belfast, Northern IrelandBT9 7BL, U.K
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Deganutti G, Atanasio S, Rujan RM, Sexton PM, Wootten D, Reynolds CA. Exploring Ligand Binding to Calcitonin Gene-Related Peptide Receptors. Front Mol Biosci 2021; 8:720561. [PMID: 34513925 PMCID: PMC8427520 DOI: 10.3389/fmolb.2021.720561] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/13/2021] [Indexed: 01/31/2023] Open
Abstract
Class B1 G protein-coupled receptors (GPCRs) are important targets for many diseases, including cancer, diabetes, and heart disease. All the approved drugs for this receptor family are peptides that mimic the endogenous activating hormones. An understanding of how agonists bind and activate class B1 GPCRs is fundamental for the development of therapeutic small molecules. We combined supervised molecular dynamics (SuMD) and classic molecular dynamics (cMD) simulations to study the binding of the calcitonin gene-related peptide (CGRP) to the CGRP receptor (CGRPR). We also evaluated the association and dissociation of the antagonist telcagepant from the extracellular domain (ECD) of CGRPR and the water network perturbation upon binding. This study, which represents the first example of dynamic docking of a class B1 GPCR peptide, delivers insights on several aspects of ligand binding to CGRPR, expanding understanding of the role of the ECD and the receptor-activity modifying protein 1 (RAMP1) on agonist selectivity.
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Affiliation(s)
- Giuseppe Deganutti
- Centre for Sport, Exercise and Life Sciences, Coventry University, Coventry, United Kingdom
| | - Silvia Atanasio
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Roxana-Maria Rujan
- Centre for Sport, Exercise and Life Sciences, Coventry University, Coventry, United Kingdom
| | - Patrick M. Sexton
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
- ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Denise Wootten
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
- ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
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Deganutti G, Barkan K, Preti B, Leuenberger M, Wall M, Frenguelli BG, Lochner M, Ladds G, Reynolds CA. Deciphering the Agonist Binding Mechanism to the Adenosine A1 Receptor. ACS Pharmacol Transl Sci 2021; 4:314-326. [PMID: 33615181 PMCID: PMC7887845 DOI: 10.1021/acsptsci.0c00195] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Indexed: 12/21/2022]
Abstract
Despite being among the most characterized G protein-coupled receptors (GPCRs), adenosine receptors (ARs) have always been a difficult target in drug design. To date, no agonist other than the natural effector and the diagnostic regadenoson has been approved for human use. Recently, the structure of the adenosine A1 receptor (A1R) was determined in the active, Gi protein complexed state; this has important repercussions for structure-based drug design. Here, we employed supervised molecular dynamics simulations and mutagenesis experiments to extend the structural knowledge of the binding of selective agonists to A1R. Our results identify new residues involved in the association and dissociation pathway, they suggest the binding mode of N6-cyclopentyladenosine (CPA) related ligands, and they highlight the dramatic effect that chemical modifications can have on the overall binding mechanism, paving the way for the rational development of a structure-kinetics relationship of A1R agonists.
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Affiliation(s)
- Giuseppe Deganutti
- Centre
for Sport, Exercise and Life Sciences, Faculty of Health and Life
Sciences, Coventry University, Alison Gingell Building, Coventry CV1 5FB, U.K.
| | - Kerry Barkan
- Department
of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, U.K.
| | - Barbara Preti
- Institute
of Biochemistry and Molecular Medicine, University of Bern, 3012 Bern, Switzerland
| | - Michele Leuenberger
- Institute
of Biochemistry and Molecular Medicine, University of Bern, 3012 Bern, Switzerland
| | - Mark Wall
- School
of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K.
| | - Bruno G. Frenguelli
- School
of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K.
| | - Martin Lochner
- Institute
of Biochemistry and Molecular Medicine, University of Bern, 3012 Bern, Switzerland
| | - Graham Ladds
- Department
of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, U.K.
| | - Christopher A. Reynolds
- Centre
for Sport, Exercise and Life Sciences, Faculty of Health and Life
Sciences, Coventry University, Alison Gingell Building, Coventry CV1 5FB, U.K.
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Supervised molecular dynamics for exploring the druggability of the SARS-CoV-2 spike protein. J Comput Aided Mol Des 2020; 35:195-207. [PMID: 33103220 PMCID: PMC7585834 DOI: 10.1007/s10822-020-00356-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 10/15/2020] [Indexed: 12/17/2022]
Abstract
The recent outbreak of the respiratory syndrome-related coronavirus (SARS-CoV-2) is stimulating an unprecedented scientific campaign to alleviate the burden of the coronavirus disease (COVID-19). One line of research has focused on targeting SARS-CoV-2 proteins fundamental for its replication by repurposing drugs approved for other diseases. The first interaction between the virus and the host cell is mediated by the spike protein on the virus surface and the human angiotensin-converting enzyme (ACE2). Small molecules able to bind the receptor-binding domain (RBD) of the spike protein and disrupt the binding to ACE2 would offer an important tool for slowing, or even preventing, the infection. Here, we screened 2421 approved small molecules in silico and validated the docking outcomes through extensive molecular dynamics simulations. Out of six drugs characterized as putative RBD binders, the cephalosporin antibiotic cefsulodin was further assessed for its effect on the binding between the RBD and ACE2, suggesting that it is important to consider the dynamic formation of the heterodimer between RBD and ACE2 when judging any potential candidate.
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