1
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Do HN, Wang J, Miao Y. Deep Learning Dynamic Allostery of G-Protein-Coupled Receptors. JACS AU 2023; 3:3165-3180. [PMID: 38034960 PMCID: PMC10685416 DOI: 10.1021/jacsau.3c00503] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 10/10/2023] [Accepted: 10/18/2023] [Indexed: 12/02/2023]
Abstract
G-protein-coupled receptors (GPCRs) make up the largest superfamily of human membrane proteins and represent primary targets of ∼1/3 of currently marketed drugs. Allosteric modulators have emerged as more selective drug candidates compared with orthosteric agonists and antagonists. However, many X-ray and cryo-EM structures of GPCRs resolved so far exhibit negligible differences upon the binding of positive and negative allosteric modulators (PAMs and NAMs). The mechanism of dynamic allosteric modulation in GPCRs remains unclear. In this work, we have systematically mapped dynamic changes in free energy landscapes of GPCRs upon binding of allosteric modulators using the Gaussian accelerated molecular dynamics (GaMD), deep learning (DL), and free energy prOfiling Workflow (GLOW). GaMD simulations were performed for a total of 66 μs on 44 GPCR systems in the presence and absence of the modulator. DL and free energy calculations revealed significantly reduced dynamic fluctuations and conformational space of GPCRs upon modulator binding. While the modulator-free GPCRs often sampled multiple low-energy conformational states, the NAMs and PAMs confined the inactive and active agonist-G-protein-bound GPCRs, respectively, to mostly only one specific conformation for signaling. Such cooperative effects were significantly reduced for binding of the selective modulators to "non-cognate" receptor subtypes. Therefore, GPCR allostery exhibits a dynamic "conformational selection" mechanism. In the absence of available modulator-bound structures as for most current GPCRs, it is critical to use a structural ensemble of representative GPCR conformations rather than a single structure for compound docking ("ensemble docking"), which will potentially improve structure-based design of novel allosteric drugs of GPCRs.
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Affiliation(s)
| | - Jinan Wang
- Computational Biology Program
and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, United States
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2
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Maria-Solano MA, Choi S. Dynamic allosteric networks drive adenosine A 1 receptor activation and G-protein coupling. eLife 2023; 12:RP90773. [PMID: 37656635 PMCID: PMC10473838 DOI: 10.7554/elife.90773] [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] [Indexed: 09/03/2023] Open
Abstract
G-protein coupled receptors (GPCRs) present specific activation pathways and signaling among receptor subtypes. Hence, an extensive knowledge of the structural dynamics of the receptor is critical for the development of therapeutics. Here, we target the adenosine A1 receptor (A1R), for which a negligible number of drugs have been approved. We combine molecular dynamics simulations, enhanced sampling techniques, network theory and pocket detection to decipher the activation pathway of A1R, decode the allosteric networks and identify transient pockets. The A1R activation pathway reveal hidden intermediate and pre-active states together with the inactive and fully-active states observed experimentally. The protein energy networks computed throughout these conformational states successfully unravel the extra and intracellular allosteric centers and the communication pathways that couples them. We observe that the allosteric networks are dynamic, being increased along activation and fine-tuned in presence of the trimeric G-proteins. Overlap of transient pockets and energy networks uncover how the allosteric coupling between pockets and distinct functional regions of the receptor is altered along activation. By an in-depth analysis of the bridge between activation pathway, energy networks and transient pockets, we provide a further understanding of A1R. This information can be useful to ease the design of allosteric modulators for A1R.
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Affiliation(s)
- Miguel A Maria-Solano
- Global AI Drug Discovery Center, College of Pharmacy and Graduate School of Pharmaceutical Science, Ewha Womans UniversitySeoulRepublic of Korea
| | - Sun Choi
- Global AI Drug Discovery Center, College of Pharmacy and Graduate School of Pharmaceutical Science, Ewha Womans UniversitySeoulRepublic of Korea
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3
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Matricon P, Nguyen AT, Vo DD, Baltos JA, Jaiteh M, Luttens A, Kampen S, Christopoulos A, Kihlberg J, May LT, Carlsson J. Structure-based virtual screening discovers potent and selective adenosine A 1 receptor antagonists. Eur J Med Chem 2023; 257:115419. [PMID: 37301076 DOI: 10.1016/j.ejmech.2023.115419] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 06/12/2023]
Abstract
Development of subtype-selective leads is essential in drug discovery campaigns targeting G protein-coupled receptors (GPCRs). Herein, a structure-based virtual screening approach to rationally design subtype-selective ligands was applied to the A1 and A2A adenosine receptors (A1R and A2AR). Crystal structures of these closely related subtypes revealed a non-conserved subpocket in the binding sites that could be exploited to identify A1R selective ligands. A library of 4.6 million compounds was screened computationally against both receptors using molecular docking and 20 A1R selective ligands were predicted. Of these, seven antagonized the A1R with micromolar activities and several compounds displayed slight selectivity for this subtype. Twenty-seven analogs of two discovered scaffolds were designed, resulting in antagonists with nanomolar potency and up to 76-fold A1R-selectivity. Our results show the potential of structure-based virtual screening to guide discovery and optimization of subtype-selective ligands, which could facilitate the development of safer drugs.
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Affiliation(s)
- Pierre Matricon
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, SE-751 24, Uppsala, Sweden
| | - Anh Tn Nguyen
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
| | - Duc Duy Vo
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, SE-751 24, Uppsala, Sweden
| | - Jo-Anne Baltos
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
| | - Mariama Jaiteh
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, SE-751 24, Uppsala, Sweden
| | - Andreas Luttens
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, SE-751 24, Uppsala, Sweden
| | - Stefanie Kampen
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, SE-751 24, Uppsala, Sweden
| | - Arthur Christopoulos
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University, SE-751 23, Uppsala, Sweden
| | - Lauren Therese May
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia.
| | - Jens Carlsson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, SE-751 24, Uppsala, Sweden.
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4
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Do H, Wang J, Miao Y. Deep Learning Dynamic Allostery of G-Protein-Coupled Receptors. RESEARCH SQUARE 2023:rs.3.rs-2543463. [PMID: 36865316 PMCID: PMC9980202 DOI: 10.21203/rs.3.rs-2543463/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
G-protein-coupled receptors (GPCRs) are the largest superfamily of human membrane proteins and represent primary targets of ~ 1/3 of currently marketed drugs. Allosteric modulators have emerged as more selective drug candidates compared with orthosteric agonists and antagonists. However, many X-ray and cryo-EM structures of GPCRs resolved so far exhibit negligible differences upon binding of positive and negative allosteric modulators (PAMs and NAMs). Mechanism of dynamic allosteric modulation in GPCRs remains unclear. In this work, we have systematically mapped dynamic changes in free energy landscapes of GPCRs upon binding of allosteric modulators using the Gaussian accelerated molecular dynamics (GaMD), Deep Learning (DL) and free energy prOfiling Workflow (GLOW). A total of 18 available high-resolution experimental structures of allosteric modulator-bound class A and B GPCRs were collected for simulations. A number of 8 computational models were generated to examine selectivity of the modulators by changing their target receptors to different subtypes. All-atom GaMD simulations were performed for a total of 66 μs on 44 GPCR systems in the presence/absence of the modulator. DL and free energy calculations revealed significantly reduced conformational space of GPCRs upon modulator binding. While the modulator-free GPCRs often sampled multiple low-energy conformational states, the NAMs and PAMs confined the inactive and active agonist-G protein-bound GPCRs, respectively, to mostly only one specific conformation for signaling. Such cooperative effects were significantly reduced for binding of the selective modulators to "non-cognate" receptor subtypes in the computational models. Therefore, comprehensive DL of extensive GaMD simulations has revealed a general dynamic mechanism of GPCR allostery, which will greatly facilitate rational design of selective allosteric drugs of GPCRs.
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5
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Do HN, Wang J, Miao Y. Deep Learning Dynamic Allostery of G-Protein-Coupled Receptors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.15.524128. [PMID: 36711515 PMCID: PMC9882226 DOI: 10.1101/2023.01.15.524128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
G-protein-coupled receptors (GPCRs) are the largest superfamily of human membrane proteins and represent primary targets of ~1/3 of currently marketed drugs. Allosteric modulators have emerged as more selective drug candidates compared with orthosteric agonists and antagonists. However, many X-ray and cryo-EM structures of GPCRs resolved so far exhibit negligible differences upon binding of positive and negative allosteric modulators (PAMs and NAMs). Mechanism of dynamic allosteric modulation in GPCRs remains unclear. In this work, we have systematically mapped dynamic changes in free energy landscapes of GPCRs upon binding of allosteric modulators using the Gaussian accelerated molecular dynamics (GaMD), Deep Learning (DL) and free energy prOfiling Workflow (GLOW). A total of 18 available high-resolution experimental structures of allosteric modulator-bound class A and B GPCRs were collected for simulations. A number of 8 computational models were generated to examine selectivity of the modulators by changing their target receptors to different subtypes. All-atom GaMD simulations were performed for a total of 66 μs on 44 GPCR systems in the presence/absence of the modulator. DL and free energy calculations revealed significantly reduced conformational space of GPCRs upon modulator binding. While the modulator-free GPCRs often sampled multiple low-energy conformational states, the NAMs and PAMs confined the inactive and active agonist-G protein-bound GPCRs, respectively, to mostly only one specific conformation for signaling. Such cooperative effects were significantly reduced for binding of the selective modulators to "non-cognate" receptor subtypes in the computational models. Therefore, comprehensive DL of extensive GaMD simulations has revealed a general dynamic mechanism of GPCR allostery, which will greatly facilitate rational design of selective allosteric drugs of GPCRs.
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Affiliation(s)
- Hung N. Do
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047
| | - Jinan Wang
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047
| | - Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047
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6
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The full activation mechanism of the adenosine A 1 receptor revealed by GaMD and Su-GaMD simulations. Proc Natl Acad Sci U S A 2022; 119:e2203702119. [PMID: 36215480 PMCID: PMC9586258 DOI: 10.1073/pnas.2203702119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The full activation process of G protein-coupled receptor (GPCR) plays an important role in cellular signal transduction. However, it remains challenging to simulate the whole process in which the GPCR is recognized and activated by a ligand and then couples to the G protein on a reasonable simulation timescale. Here, we developed a molecular dynamics (MD) approach named supervised (Su) Gaussian accelerated MD (GaMD) by incorporating a tabu-like supervision algorithm into a standard GaMD simulation. By using this Su-GaMD method, from the active and inactive structure of adenosine A1 receptor (A1R), we successfully revealed the full activation mechanism of A1R, including adenosine (Ado)-A1R recognition, preactivation of A1R, and A1R-G protein recognition, in hundreds of nanoseconds of simulations. The binding of Ado to the extracellular side of A1R initiates conformational changes and the preactivation of A1R. In turn, the binding of Gi2 to the intracellular side of A1R causes a decrease in the volume of the extracellular orthosteric site and stabilizes the binding of Ado to A1R. Su-GaMD could be a useful tool to reconstruct or even predict ligand-protein and protein-protein recognition pathways on a short timescale. The intermediate states revealed in this study could provide more detailed complementary structural characterizations to facilitate the drug design of A1R in the future.
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7
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Wang X, Jespers W, Wolff KAN, Buytelaar J, IJzerman AP, van Westen GJP, Heitman LH. Cancer-Related Somatic Mutations in Transmembrane Helices Alter Adenosine A1 Receptor Pharmacology. Molecules 2022; 27:3742. [PMID: 35744872 PMCID: PMC9229843 DOI: 10.3390/molecules27123742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/25/2022] [Accepted: 06/08/2022] [Indexed: 11/16/2022] Open
Abstract
Overexpression of the adenosine A1 receptor (A1AR) has been detected in various cancer cell lines. However, the role of A1AR in tumor development is still unclear. Thirteen A1AR mutations were identified in the Cancer Genome Atlas from cancer patient samples. We have investigated the pharmacology of the mutations located at the 7-transmembrane domain using a yeast system. Concentration-growth curves were obtained with the full agonist CPA and compared to the wild type hA1AR. H78L3.23 and S246T6.47 showed increased constitutive activity, while only the constitutive activity of S246T6.47 could be reduced to wild type levels by the inverse agonist DPCPX. Decreased constitutive activity was observed on five mutant receptors, among which A52V2.47 and W188C5.46 showed a diminished potency for CPA. Lastly, a complete loss of activation was observed in five mutant receptors. A selection of mutations was also investigated in a mammalian system, showing comparable effects on receptor activation as in the yeast system, except for residues pointing toward the membrane. Taken together, this study will enrich the view of the receptor structure and function of A1AR, enlightening the consequences of these mutations in cancer. Ultimately, this may provide an opportunity for precision medicine for cancer patients with pathological phenotypes involving these mutations.
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Affiliation(s)
- Xuesong Wang
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Einsteinweg 55, 2333 CC Leiden, The Netherlands; (X.W.); (W.J.); (K.A.N.W.); (J.B.); (A.P.I.)
| | - Willem Jespers
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Einsteinweg 55, 2333 CC Leiden, The Netherlands; (X.W.); (W.J.); (K.A.N.W.); (J.B.); (A.P.I.)
| | - Kim A. N. Wolff
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Einsteinweg 55, 2333 CC Leiden, The Netherlands; (X.W.); (W.J.); (K.A.N.W.); (J.B.); (A.P.I.)
| | - Jill Buytelaar
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Einsteinweg 55, 2333 CC Leiden, The Netherlands; (X.W.); (W.J.); (K.A.N.W.); (J.B.); (A.P.I.)
| | - Adriaan P. IJzerman
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Einsteinweg 55, 2333 CC Leiden, The Netherlands; (X.W.); (W.J.); (K.A.N.W.); (J.B.); (A.P.I.)
| | - Gerard J. P. van Westen
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Einsteinweg 55, 2333 CC Leiden, The Netherlands; (X.W.); (W.J.); (K.A.N.W.); (J.B.); (A.P.I.)
| | - Laura H. Heitman
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Einsteinweg 55, 2333 CC Leiden, The Netherlands; (X.W.); (W.J.); (K.A.N.W.); (J.B.); (A.P.I.)
- Oncode Institute, 2333 CC Leiden, The Netherlands
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8
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Wang X, Jespers W, de Waal JJ, Wolff KAN, van Uden L, IJzerman AP, van Westen GJP, Heitman LH. Cancer-related somatic mutations alter adenosine A 1 receptor pharmacology-A focus on mutations in the loops and C-terminus. FASEB J 2022; 36:e22358. [PMID: 35604751 DOI: 10.1096/fj.202200203rr] [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: 02/07/2022] [Revised: 05/03/2022] [Accepted: 05/07/2022] [Indexed: 11/11/2022]
Abstract
G protein-coupled receptors (GPCRs) are known to be involved in tumor progression and metastasis. The adenosine A1 receptor (A1 AR) has been detected to be over-expressed in various cancer cell lines. However, the role of A1 AR in tumor development is not yet well characterized. A series of A1 AR mutations were identified in the Cancer Genome Atlas from cancer patient samples. In this study, we have investigated the pharmacology of mutations located outside of the 7-transmembrane domain by using a "single-GPCR-one-G protein" yeast system. Concentration-growth curves were obtained with the full agonist CPA for 12 mutant receptors and compared to the wild-type hA1 AR. Most mutations located at the extracellular loops (EL) reduced the levels of constitutive activity of the receptor and agonist potency. For mutants at the intracellular loops (ILs) of the receptor, an increased constitutive activity was found for mutant receptor L211R5.69 , while a decreased constitutive activity and agonist response were found for mutant receptor L113F34.51 . Lastly, mutations identified on the C-terminus did not significantly influence the pharmacological function of the receptor. A selection of mutations was also investigated in a mammalian system. Overall, similar effects on receptor activation compared to the yeast system were found with mutations located at the EL, but some contradictory effects were observed for mutations located at the IL. Taken together, this study will enrich the insight of A1 AR structure and function, enlightening the consequences of these mutations in cancer. Ultimately, this may provide potential precision medicine in cancer treatment.
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Affiliation(s)
- Xuesong Wang
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden, the Netherlands
| | - Willem Jespers
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden, the Netherlands
| | - Just J de Waal
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden, the Netherlands
| | - Kim A N Wolff
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden, the Netherlands
| | - Liedeke van Uden
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden, the Netherlands
| | - Adriaan P IJzerman
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden, the Netherlands
| | - Gerard J P van Westen
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden, the Netherlands
| | - Laura H Heitman
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden, the Netherlands.,Oncode Institute, Leiden, the Netherlands
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9
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Do HN, Wang J, Bhattarai A, Miao Y. GLOW: A Workflow Integrating Gaussian-Accelerated Molecular Dynamics and Deep Learning for Free Energy Profiling. J Chem Theory Comput 2022; 18:1423-1436. [PMID: 35200019 PMCID: PMC9773012 DOI: 10.1021/acs.jctc.1c01055] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We introduce a Gaussian-accelerated molecular dynamics (GaMD), deep learning (DL), and free energy profiling workflow (GLOW) to predict molecular determinants and map free energy landscapes of biomolecules. All-atom GaMD-enhanced sampling simulations are first performed on biomolecules of interest. Structural contact maps are then calculated from GaMD simulation frames and transformed into images for building DL models using a convolutional neural network. Important structural contacts are further determined from DL models of attention maps of the structural contact gradients, which allow us to identify the system reaction coordinates. Finally, free energy profiles are calculated for the selected reaction coordinates through energetic reweighting of the GaMD simulations. We have also successfully demonstrated GLOW for the characterization of activation and allosteric modulation of a G protein-coupled receptor, using the adenosine A1 receptor (A1AR) as a model system. GLOW findings are highly consistent with previous experimental and computational studies of the A1AR, while also providing further mechanistic insights into the receptor function. In summary, GLOW provides a systematic approach to mapping free energy landscapes of biomolecules. The GLOW workflow and its user manual can be downloaded at http://miaolab.org/GLOW.
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Affiliation(s)
- Hung N. Do
- The Center for Computational Biology and Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas 66047
| | - Jinan Wang
- The Center for Computational Biology and Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas 66047
| | - Apurba Bhattarai
- The Center for Computational Biology and Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas 66047
| | - Yinglong Miao
- The Center for Computational Biology and Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas 66047,Corresponding author:
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10
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Draper-Joyce CJ, Bhola R, Wang J, Bhattarai A, Nguyen ATN, Cowie-Kent I, O'Sullivan K, Chia LY, Venugopal H, Valant C, Thal DM, Wootten D, Panel N, Carlsson J, Christie MJ, White PJ, Scammells P, May LT, Sexton PM, Danev R, Miao Y, Glukhova A, Imlach WL, Christopoulos A. Positive allosteric mechanisms of adenosine A 1 receptor-mediated analgesia. Nature 2021; 597:571-576. [PMID: 34497422 PMCID: PMC8711093 DOI: 10.1038/s41586-021-03897-2] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 08/11/2021] [Indexed: 02/08/2023]
Abstract
The adenosine A1 receptor (A1R) is a promising therapeutic target for non-opioid analgesic agents to treat neuropathic pain1,2. However, development of analgesic orthosteric A1R agonists has failed because of a lack of sufficient on-target selectivity as well as off-tissue adverse effects3. Here we show that [2-amino-4-(3,5-bis(trifluoromethyl)phenyl)thiophen-3-yl)(4-chlorophenyl)methanone] (MIPS521), a positive allosteric modulator of the A1R, exhibits analgesic efficacy in rats in vivo through modulation of the increased levels of endogenous adenosine that occur in the spinal cord of rats with neuropathic pain. We also report the structure of the A1R co-bound to adenosine, MIPS521 and a Gi2 heterotrimer, revealing an extrahelical lipid-detergent-facing allosteric binding pocket that involves transmembrane helixes 1, 6 and 7. Molecular dynamics simulations and ligand kinetic binding experiments support a mechanism whereby MIPS521 stabilizes the adenosine-receptor-G protein complex. This study provides proof of concept for structure-based allosteric drug design of non-opioid analgesic agents that are specific to disease contexts.
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Affiliation(s)
- Christopher J Draper-Joyce
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria, Australia
| | - Rebecca Bhola
- Department of Physiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jinan Wang
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
| | - Apurba Bhattarai
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
| | - Anh T N Nguyen
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - India Cowie-Kent
- Department of Physiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Kelly O'Sullivan
- Department of Physiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Ling Yeong Chia
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Hariprasad Venugopal
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Celine Valant
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - David M Thal
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Denise Wootten
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Nicolas Panel
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Jens Carlsson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Macdonald J Christie
- Discipline of Pharmacology, Faculty of Medicine and Health, University of Sydney, Camperdown, New South Wales, Australia
| | - Paul J White
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Peter Scammells
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Lauren T May
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Patrick M Sexton
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Radostin Danev
- Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
| | - Alisa Glukhova
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia.
- Structural Biology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, Victoria, Australia.
| | - Wendy L Imlach
- Department of Physiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
| | - Arthur Christopoulos
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia.
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia.
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11
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Deganutti G, Barkan K, Ladds G, Reynolds CA. Multisite Model of Allosterism for the Adenosine A1 Receptor. J Chem Inf Model 2021; 61:2001-2015. [PMID: 33779168 DOI: 10.1021/acs.jcim.0c01331] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Despite being a target for about one-third of approved drugs, G protein-coupled receptors (GPCRs) still represent a tremendous reservoir for therapeutic strategies against diseases. For example, several cardiovascular and central nervous system conditions could benefit from clinical agents that activate the adenosine 1 receptor (A1R); however, the pursuit of A1R agonists for clinical use is usually impeded by both on- and off-target side effects. One of the possible strategies to overcome this issue is the development of positive allosteric modulators (PAMs) capable of selectively enhancing the effect of a specific receptor subtype and triggering functional selectivity (a phenomenon also referred to as bias). Intriguingly, besides enforcing the effect of agonists upon binding to an allosteric site, most of the A1R PAMs display intrinsic partial agonism and orthosteric competition with antagonists. To rationalize this behavior, we simulated the binding of the prototypical PAMs PD81723 and VCP171, the full-agonist NECA, the antagonist 13B, and the bitopic agonist VCP746. We propose that a single PAM can bind several A1R sites rather than a unique allosteric pocket, reconciling the structure-activity relationship and the mutagenesis results.
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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
| | - 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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12
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Comeo E, Trinh P, Nguyen AT, Nowell CJ, Kindon ND, Soave M, Stoddart LA, White JM, Hill SJ, Kellam B, Halls ML, May LT, Scammells PJ. Development and Application of Subtype-Selective Fluorescent Antagonists for the Study of the Human Adenosine A 1 Receptor in Living Cells. J Med Chem 2021; 64:6670-6695. [PMID: 33724031 DOI: 10.1021/acs.jmedchem.0c02067] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The adenosine A1 receptor (A1AR) is a G-protein-coupled receptor (GPCR) that provides important therapeutic opportunities for a number of conditions including congestive heart failure, tachycardia, and neuropathic pain. The development of A1AR-selective fluorescent ligands will enhance our understanding of the subcellular mechanisms underlying A1AR pharmacology facilitating the development of more efficacious and selective therapies. Herein, we report the design, synthesis, and application of a novel series of A1AR-selective fluorescent probes based on 8-functionalized bicyclo[2.2.2]octylxanthine and 3-functionalized 8-(adamant-1-yl) xanthine scaffolds. These fluorescent conjugates allowed quantification of kinetic and equilibrium ligand binding parameters using NanoBRET and visualization of specific receptor distribution patterns in living cells by confocal imaging and total internal reflection fluorescence (TIRF) microscopy. As such, the novel A1AR-selective fluorescent antagonists described herein can be applied in conjunction with a series of fluorescence-based techniques to foster understanding of A1AR molecular pharmacology and signaling in living cells.
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Affiliation(s)
- Eleonora Comeo
- Medicinal Chemistry, Monash University, Parkville, Victoria 3052, Australia.,Division of Biomolecular Sciences and Medicinal Chemistry, School of Pharmacy, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, United Kingdom.,Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, B15 2TT and University of Nottingham, Birmingham NG7 2UH, United Kingdom
| | - Phuc Trinh
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Anh T Nguyen
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Cameron J Nowell
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Nicholas D Kindon
- Division of Biomolecular Sciences and Medicinal Chemistry, School of Pharmacy, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, United Kingdom.,Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, B15 2TT and University of Nottingham, Birmingham NG7 2UH, United Kingdom
| | - Mark Soave
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham NG7 2UH, United Kingdom.,Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, B15 2TT and University of Nottingham, Birmingham NG7 2UH, United Kingdom
| | - Leigh A Stoddart
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham NG7 2UH, United Kingdom.,Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, B15 2TT and University of Nottingham, Birmingham NG7 2UH, United Kingdom
| | - Jonathan M White
- School of Chemistry and the Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Stephen J Hill
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham NG7 2UH, United Kingdom.,Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, B15 2TT and University of Nottingham, Birmingham NG7 2UH, United Kingdom
| | - Barrie Kellam
- Division of Biomolecular Sciences and Medicinal Chemistry, School of Pharmacy, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, United Kingdom.,Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, B15 2TT and University of Nottingham, Birmingham NG7 2UH, United Kingdom
| | - Michelle L Halls
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Lauren T May
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Peter J Scammells
- Medicinal Chemistry, Monash University, Parkville, Victoria 3052, Australia
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13
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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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14
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Essential role of the C148–C227 disulphide bridge in the human 5-HT2A homodimeric receptor. Biochem Pharmacol 2020; 177:113985. [DOI: 10.1016/j.bcp.2020.113985] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/15/2020] [Indexed: 01/12/2023]
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15
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Salmaso V, Jacobson KA. In Silico Drug Design for Purinergic GPCRs: Overview on Molecular Dynamics Applied to Adenosine and P2Y Receptors. Biomolecules 2020; 10:E812. [PMID: 32466404 PMCID: PMC7356333 DOI: 10.3390/biom10060812] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/21/2020] [Accepted: 05/22/2020] [Indexed: 12/14/2022] Open
Abstract
Molecular modeling has contributed to drug discovery for purinergic GPCRs, including adenosine receptors (ARs) and P2Y receptors (P2YRs). Experimental structures and homology modeling have proven to be useful in understanding and predicting structure activity relationships (SAR) of agonists and antagonists. This review provides an excursus on molecular dynamics (MD) simulations applied to ARs and P2YRs. The binding modes of newly synthesized A1AR- and A3AR-selective nucleoside derivatives, potentially of use against depression and inflammation, respectively, have been predicted to recapitulate their SAR and the species dependence of A3AR affinity. P2Y12R and P2Y1R crystallographic structures, respectively, have provided a detailed understanding of the recognition of anti-inflammatory P2Y14R antagonists and a large group of allosteric and orthosteric antagonists of P2Y1R, an antithrombotic and neuroprotective target. MD of A2AAR (an anticancer and neuroprotective target), A3AR, and P2Y1R has identified microswitches that are putatively involved in receptor activation. The approach pathways of different ligands toward A2AAR and P2Y1R binding sites have also been explored. A1AR, A2AAR, and A3AR were utilizes to study allosteric phenomena, but locating the binding site of structurally diverse allosteric modulators, such as an A3AR enhancer LUF6000, is challenging. Ligand residence time, a predictor of in vivo efficacy, and the structural role of water were investigated through A2AAR MD simulations. Thus, new MD and other modeling algorithms have contributed to purinergic GPCR drug discovery.
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Affiliation(s)
| | - Kenneth A. Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA;
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16
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New Insights into Key Determinants for Adenosine 1 Receptor Antagonists Selectivity Using Supervised Molecular Dynamics Simulations. Biomolecules 2020; 10:biom10050732. [PMID: 32392873 PMCID: PMC7278174 DOI: 10.3390/biom10050732] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 12/13/2022] Open
Abstract
Adenosine receptors (ARs), like many otherGprotein-coupledreceptors (GPCRs), are targets of primary interest indrug design. However, one of the main limits for the development of drugs for this class of GPCRs is the complex selectivity profile usually displayed by ligands. Numerous efforts have been madefor clarifying the selectivity of ARs, leading to the development of many ligand-based models. The structure of the AR subtype A1 (A1AR) has been recently solved, providing important structural insights. In the present work, we rationalized the selectivity profile of two selective A1AR and A2AAR antagonists, investigating their recognition trajectories obtained by Supervised Molecular Dynamics from an unbound state and monitoring the role of the water molecules in the binding site.
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17
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Deb PK, Deka S, Borah P, Abed SN, Klotz KN. Medicinal Chemistry and Therapeutic Potential of Agonists, Antagonists and Allosteric Modulators of A1 Adenosine Receptor: Current Status and Perspectives. Curr Pharm Des 2020; 25:2697-2715. [PMID: 31333094 DOI: 10.2174/1381612825666190716100509] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 07/01/2019] [Indexed: 12/28/2022]
Abstract
Adenosine is a purine nucleoside, responsible for the regulation of a wide range of physiological and pathophysiological conditions by binding with four G-protein-coupled receptors (GPCRs), namely A1, A2A, A2B and A3 adenosine receptors (ARs). In particular, A1 AR is ubiquitously present, mediating a variety of physiological processes throughout the body, thus represents a promising drug target for the management of various pathological conditions. Agonists of A1 AR are found to be useful for the treatment of atrial arrhythmia, angina, type-2 diabetes, glaucoma, neuropathic pain, epilepsy, depression and Huntington's disease, whereas antagonists are being investigated for the treatment of diuresis, congestive heart failure, asthma, COPD, anxiety and dementia. However, treatment with full A1 AR agonists has been associated with numerous challenges like cardiovascular side effects, off-target activation as well as desensitization of A1 AR leading to tachyphylaxis. In this regard, partial agonists of A1 AR have been found to be beneficial in enhancing insulin sensitivity and subsequently reducing blood glucose level, while avoiding severe CVS side effects and tachyphylaxis. Allosteric enhancer of A1 AR is found to be potent for the treatment of neuropathic pain, culminating the side effects related to off-target tissue activation of A1 AR. This review provides an overview of the medicinal chemistry and therapeutic potential of various agonists/partial agonists, antagonists and allosteric modulators of A1 AR, with a particular emphasis on their current status and future perspectives in clinical settings.
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Affiliation(s)
- Pran Kishore Deb
- Faculty of Pharmacy, Philadelphia University, PO Box - 1, 19392, Amman, Jordan
| | - Satyendra Deka
- Pratiksha Institute of Pharmaceutical Sciences, Chandrapur Road, Panikhaiti, Guwahati-26, Assam, India
| | - Pobitra Borah
- Pratiksha Institute of Pharmaceutical Sciences, Chandrapur Road, Panikhaiti, Guwahati-26, Assam, India
| | - Sara N Abed
- Faculty of Pharmacy, Philadelphia University, PO Box - 1, 19392, Amman, Jordan
| | - Karl-Norbert Klotz
- University of Würzburg, Department of Pharmacology and Toxicology Versbacher Str. 9, D-97078 Würzburg, Germany
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18
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Bhattarai A, Wang J, Miao Y. Retrospective ensemble docking of allosteric modulators in an adenosine G-protein-coupled receptor. Biochim Biophys Acta Gen Subj 2020; 1864:129615. [PMID: 32298791 DOI: 10.1016/j.bbagen.2020.129615] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/26/2020] [Accepted: 04/08/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND Ensemble docking has proven useful in drug discovery and development. It increases the hit rate by incorporating receptor flexibility into molecular docking as demonstrated on important drug targets including G-protein-coupled receptors (GPCRs). Adenosine A1 receptor (A1AR) is a key GPCR that has been targeted for treating cardiac ischemia-reperfusion injuries, neuropathic pain and renal diseases. Development of allosteric modulators, compounds binding to distinct and less conserved GPCR target sites compared with agonists and antagonists, has attracted increasing interest for designing selective drugs of the A1AR. Despite significant advances, more effective approaches are needed to discover potent and selective allosteric modulators of the A1AR. METHODS Ensemble docking that integrates Gaussian accelerated molecular dynamic (GaMD) simulations and molecular docking using Autodock has been implemented for retrospective docking of known positive allosteric modulators (PAMs) in the A1AR. RESULTS Ensemble docking outperforms docking of the receptor cryo-EM structure. The calculated docking enrichment factors (EFs) and the area under the receiver operating characteristic curves (AUC) are significantly increased. CONCLUSIONS Receptor ensembles generated from GaMD simulations are able to increase the success rate of discovering PAMs of A1AR. It is important to account for receptor flexibility through GaMD simulations and flexible docking. GENERAL SIGNIFICANCE Ensemble docking is a promising approach for drug discovery targeting flexible receptors.
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Affiliation(s)
- Apurba Bhattarai
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66047, USA
| | - Jinan Wang
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66047, USA
| | - Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66047, USA.
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19
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Giusti F, Casiraghi M, Point E, Damian M, Rieger J, Bon CL, Pozza A, Moncoq K, Banères JL, Catoire LJ. Structure of the agonist 12-HHT in its BLT2 receptor-bound state. Sci Rep 2020; 10:2630. [PMID: 32060341 PMCID: PMC7021728 DOI: 10.1038/s41598-020-59571-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 01/28/2020] [Indexed: 12/25/2022] Open
Abstract
G Protein-Coupled receptors represent the main communicating pathway for signals from the outside to the inside of most of eukaryotic cells. They define the largest family of integral membrane receptors at the surface of the cells and constitute the main target of the current drugs on the market. The low affinity leukotriene receptor BLT2 is a receptor involved in pro- and anti-inflammatory pathways and can be activated by various unsaturated fatty acid compounds. We present here the NMR structure of the agonist 12-HHT in its BLT2-bound state and a model of interaction of the ligand with the receptor based on a conformational homology modeling associated with docking simulations. Put into perspective with the data obtained with leukotriene B4, our results illuminate the ligand selectivity of BLT2 and may help define new molecules to modulate the activity of this receptor.
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Affiliation(s)
- Fabrice Giusti
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS/Université de Paris, Institut de Biologie Physico-Chimique (FRC 550), 13 rue Pierre et Marie Curie, F-75005, Paris, France.,Institut de Chimie Séparative de Marcoule, ICSM UMR 5257, Site de Marcoule, Bâtiment 426, BP 17171, F-30207, Bagnols sur Cèze Cedex, France
| | - Marina Casiraghi
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS/Université de Paris, Institut de Biologie Physico-Chimique (FRC 550), 13 rue Pierre et Marie Curie, F-75005, Paris, France.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, 94305, Stanford California, USA
| | - Elodie Point
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS/Université de Paris, Institut de Biologie Physico-Chimique (FRC 550), 13 rue Pierre et Marie Curie, F-75005, Paris, France
| | - Marjorie Damian
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université Montpellier, ENSCM, , 15 av. Charles Flahault, 34093, Montpellier, France
| | - Jutta Rieger
- Institut Parisien de Chimie Moléculaire, Sorbonne Université, CNRS, UMR 8232, Equipe Chimie des Polymères, 4 place Jussieu, 75252, Paris Cedex, 05, France
| | - Christel Le Bon
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS/Université de Paris, Institut de Biologie Physico-Chimique (FRC 550), 13 rue Pierre et Marie Curie, F-75005, Paris, France
| | - Alexandre Pozza
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS/Université de Paris, Institut de Biologie Physico-Chimique (FRC 550), 13 rue Pierre et Marie Curie, F-75005, Paris, France
| | - Karine Moncoq
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS/Université de Paris, Institut de Biologie Physico-Chimique (FRC 550), 13 rue Pierre et Marie Curie, F-75005, Paris, France
| | - Jean-Louis Banères
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université Montpellier, ENSCM, , 15 av. Charles Flahault, 34093, Montpellier, France
| | - Laurent J Catoire
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS/Université de Paris, Institut de Biologie Physico-Chimique (FRC 550), 13 rue Pierre et Marie Curie, F-75005, Paris, France.
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20
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Allosteric Modulation of Cannabinoid Receptor 1-Current Challenges and Future Opportunities. Int J Mol Sci 2019; 20:ijms20235874. [PMID: 31771126 PMCID: PMC6928801 DOI: 10.3390/ijms20235874] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 02/07/2023] Open
Abstract
The cannabinoid receptor type 1 (CB1R), a G protein-coupled receptor (GPCR), plays an essential role in the control of many physiological processes such as hunger, memory loss, gastrointestinal activity, catalepsy, fear, depression, and chronic pain. Therefore, it is an attractive target for drug discovery to manage pain, neurodegenerative disorders, obesity, and substance abuse. However, the psychoactive adverse effects, generated by CB1R activation in the brain, limit the use of the orthosteric CB1R ligands as drugs. The discovery of CB1R allosteric modulators during the last decade provided new tools to target the CB1R. Moreover, application of the site-directed mutagenesis in combination with advanced physical methods, especially X-ray crystallography and computational modeling, has opened new horizons for understanding the complexity of the structure, function, and activity of cannabinoid receptors. In this paper, we present the latest advances in research on the CB1R, its allosteric modulation and allosteric ligands, and their translational potential. We focused on structural essentials of the cannabinoid 1 receptor- ligand (drug) interactions, as well as modes of CB1R signaling regulation.
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21
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Li Y, Wang M, Gao N, Li D, Lin J. The effect of dimerization on the activation and conformational dynamics of adenosine A 1 receptor. Phys Chem Chem Phys 2019; 21:22763-22773. [PMID: 31595279 DOI: 10.1039/c9cp04060a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The adenosine A1 receptor (A1R) is one of four adenosine receptors in humans, which are involved in the function of the cardiovascular, respiratory and central nervous systems. Experimental results indicate that A1R can form a homodimer and that the protomer-protomer interaction in the A1R dimer is related to certain pharmacological characteristics of A1R activation. In this work, we performed docking, metadynamics simulation, conventional molecular dynamics simulations, Gaussian-accelerated molecular dynamics simulations, potential of mean force calculations, dynamic cross-correlation motions analysis and community network analysis to study the binding mode of 5'-N-ethylcarboxamidoadenosine (NECA) to A1R and the effect of dimerization on the activation of A1R. Our results show that NECA binds to A1R in a similar mode to adenosine in the A1R crystal structure and NECA in the A2AR crystal structure. The A1R homodimer can be activated by one or two agonists with NECA occupying its orthosteric pockets in one (which we call the NECA-A1R system) or both protomers (which we call the dNECA-A1R system). In the NECA-A1R system, activation is predicated in the protomer without NECA bound. In the dNECA-A1R system, only one protomer achieves the active state. These findings suggest an asymmetrical activation mechanism of the homodimer and a negative cooperativity between the two protomers. We envision that our results may further facilitate the drug development of A1R.
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Affiliation(s)
- Yang Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People's Republic of China.
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22
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Pal S, Chattopadhyay A. Extramembranous Regions in G Protein-Coupled Receptors: Cinderella in Receptor Biology? J Membr Biol 2019; 252:483-497. [DOI: 10.1007/s00232-019-00092-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 08/20/2019] [Indexed: 12/22/2022]
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23
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Wang J, Miao Y. Mechanistic Insights into Specific G Protein Interactions with Adenosine Receptors. J Phys Chem B 2019; 123:6462-6473. [PMID: 31283874 DOI: 10.1021/acs.jpcb.9b04867] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Coupling between G-protein-coupled receptors (GPCRs) and the G proteins is a key step in cellular signaling. Despite extensive experimental and computational studies, the mechanism of specific GPCR-G protein coupling remains poorly understood. This has greatly hindered effective drug design of GPCRs that are primary targets of ∼1/3 of currently marketed drugs. Here, we have employed all-atom simulations using a robust Gaussian accelerated molecular dynamics (GaMD) method to decipher the mechanism of the GPCR-G protein interactions. Adenosine receptors (ARs) were used as model systems based on very recently determined cryo-EM structures of the A1AR and A2AAR coupled with the Gi and Gs proteins, respectively. Changing the Gi protein to the Gs led to increased fluctuations in the A1AR and agonist adenosine (ADO), while agonist 5'-N-ethylcarboxamidoadenosine (NECA) binding in the A2AAR could be still stabilized upon changing the Gs protein to the Gi. Free energy calculations identified one stable low-energy conformation for each of the A1AR-Gi and A2AAR-Gs complexes as in the cryo-EM structures, similarly for the A2AAR-Gi complex. In contrast, the ADO agonist and Gs protein sampled multiple conformations in the A1AR-Gs system. GaMD simulations thus indicated that the A1AR preferred to couple with the Gi protein to the Gs, while the A2AAR could couple with both the Gs and Gi proteins, being highly consistent with experimental findings of the ARs. More importantly, detailed analysis of the atomic simulations showed that the specific AR-G protein coupling resulted from remarkably complementary residue interactions at the protein interface, involving mainly the receptor transmembrane 6 helix and the Gα α5 helix and α4-β6 loop. In summary, the GaMD simulations have provided unprecedented insights into the dynamic mechanism of specific GPCR-G protein interactions at an atomistic level.
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Affiliation(s)
- Jinan Wang
- Center for Computational Biology and Department of Molecular Biosciences , University of Kansas , Lawrence , Kansas 66047 , United States
| | - Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences , University of Kansas , Lawrence , Kansas 66047 , United States
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24
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Al-Shar'i NA, Al-Balas QA. Molecular Dynamics Simulations of Adenosine Receptors: Advances, Applications and Trends. Curr Pharm Des 2019; 25:783-816. [DOI: 10.2174/1381612825666190304123414] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 02/26/2019] [Indexed: 01/09/2023]
Abstract
:
Adenosine receptors (ARs) are transmembrane proteins that belong to the G protein-coupled receptors
(GPCRs) superfamily and mediate the biological functions of adenosine. To date, four AR subtypes are known,
namely A1, A2A, A2B and A3 that exhibit different signaling pathways, tissue localization, and mechanisms of
activation. Moreover, the widespread ARs and their implication in numerous physiological and pathophysiological
conditions had made them pivotal therapeutic targets for developing clinically effective agents.
:
The crystallographic success in identifying the 3D crystal structures of A2A and A1 ARs has dramatically enriched
our understanding of their structural and functional properties such as ligand binding and signal transduction.
This, in turn, has provided a structural basis for a larger contribution of computational methods, particularly molecular
dynamics (MD) simulations, toward further investigation of their molecular properties and designing
bioactive ligands with therapeutic potential. MD simulation has been proved to be an invaluable tool in investigating
ARs and providing answers to some critical questions. For example, MD has been applied in studying ARs
in terms of ligand-receptor interactions, molecular recognition, allosteric modulations, dimerization, and mechanisms
of activation, collectively aiding in the design of subtype selective ligands.
:
In this review, we focused on the advances and different applications of MD simulations utilized to study the
structural and functional aspects of ARs that can foster the structure-based design of drug candidates. In addition,
relevant literature was briefly discussed which establishes a starting point for future advances in the field of drug
discovery to this pivotal group of drug targets.
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Affiliation(s)
- Nizar A. Al-Shar'i
- Department of Medicinal Chemistry and Pharmacognosy, Faculty of Pharmacy, Jordan University of Science and Technology, P.O. Box 3030, Irbid 22110, Jordan
| | - Qosay A. Al-Balas
- Department of Medicinal Chemistry and Pharmacognosy, Faculty of Pharmacy, Jordan University of Science and Technology, P.O. Box 3030, Irbid 22110, Jordan
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25
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Mahmod Al-Qattan MN, Mordi MN. Molecular Basis of Modulating Adenosine Receptors Activities. Curr Pharm Des 2019; 25:817-831. [DOI: 10.2174/1381612825666190304122624] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 02/26/2019] [Indexed: 01/04/2023]
Abstract
Modulating cellular processes through extracellular chemical stimuli is medicinally an attractive approach to control disease conditions. GPCRs are the most important group of transmembranal receptors that produce different patterns of activations using intracellular mediators (such as G-proteins and Beta-arrestins). Adenosine receptors (ARs) belong to GPCR class and are divided into A1AR, A2AAR, A2BAR and A3AR. ARs control different physiological activities thus considered valuable target to control neural, heart, inflammatory and other metabolic disorders. Targeting ARs using small molecules essentially works by binding orthosteric and/or allosteric sites of the receptors. Although targeting orthosteric site is considered typical to modulate receptor activity, allosteric sites provide better subtype selectivity, saturable modulation of activity and variable activation patterns. Each receptor exists in dynamical equilibrium between conformational ensembles. The equilibrium is affected by receptor interaction with other molecules. Changing the population of conformational ensembles of the receptor is the method by which orthosteric, allosteric and other cellular components control receptor signaling. Herein, the interactions of ARs with orthosteric, allosteric ligands as well as intracellular mediators are described. A quinary interaction model for the receptor is proposed and energy wells for major conformational ensembles are retrieved.
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Affiliation(s)
| | - Mohd Nizam Mordi
- Centre For Drug Research, Universiti Sains Malaysia, 11800 Gelugor, Penang, Malaysia
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26
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Cooper SL, Soave M, Jörg M, Scammells PJ, Woolard J, Hill SJ. Probe dependence of allosteric enhancers on the binding affinity of adenosine A 1 -receptor agonists at rat and human A 1 -receptors measured using NanoBRET. Br J Pharmacol 2019; 176:864-878. [PMID: 30644086 PMCID: PMC6433648 DOI: 10.1111/bph.14575] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 11/02/2018] [Accepted: 12/04/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND AND PURPOSE Adenosine is a local mediator that regulates a number of physiological and pathological processes via activation of adenosine A1 -receptors. The activity of adenosine can be regulated at the level of its target receptor via drugs that bind to an allosteric site on the A1 -receptor. Here, we have investigated the species and probe dependence of two allosteric modulators on the binding characteristics of fluorescent and nonfluorescent A1 -receptor agonists. EXPERIMENTAL APPROACH A Nano-luciferase (Nluc) BRET (NanoBRET) methodology was used. This used N-terminal Nluc-tagged A1 -receptors expressed in HEK293T cells in conjunction with both fluorescent A1 -receptor agonists (adenosine and NECA analogues) and a fluorescent antagonist CA200645. KEY RESULTS PD 81,723 and VCP171 elicited positive allosteric effects on the binding affinity of orthosteric agonists at both the rat and human A1 -receptors that showed clear probe dependence. Thus, the allosteric effect on the highly selective partial agonist capadenoson was much less marked than for the full agonists NECA, adenosine, and CCPA in both species. VCP171 and, to a lesser extent, PD 81,723, also increased the specific binding of three fluorescent A1 -receptor agonists in a species-dependent manner that involved increases in Bmax and pKD . CONCLUSIONS AND IMPLICATIONS These results demonstrate the power of the NanoBRET ligand-binding approach to study the effect of allosteric ligands on the binding of fluorescent agonists to the adenosine A1 -receptor in intact living cells. Furthermore, our studies suggest that VCP171 and PD 81,723 may switch a proportion of A1 -receptors to an active agonist conformation (R*).
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Affiliation(s)
- Samantha L Cooper
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK.,Centre of Membrane Proteins and Receptors, University of Birmingham and University of Nottingham, The Midlands, UK
| | - Mark Soave
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK.,Centre of Membrane Proteins and Receptors, University of Birmingham and University of Nottingham, The Midlands, UK
| | - Manuela Jörg
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Peter J Scammells
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Jeanette Woolard
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK.,Centre of Membrane Proteins and Receptors, University of Birmingham and University of Nottingham, The Midlands, UK
| | - Stephen J Hill
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK.,Centre of Membrane Proteins and Receptors, University of Birmingham and University of Nottingham, The Midlands, UK
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27
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Moo EV, Sexton PM, Christopoulos A, Valant C. Utility of an "Allosteric Site-Impaired" M 2 Muscarinic Acetylcholine Receptor as a Novel Construct for Validating Mechanisms of Action of Synthetic and Putative Endogenous Allosteric Modulators. Mol Pharmacol 2018; 94:1298-1309. [PMID: 30213802 DOI: 10.1124/mol.118.112490] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 09/10/2018] [Indexed: 11/22/2022] Open
Abstract
Muscarinic acetylcholine receptors (mAChRs) are exemplar models for understanding G protein-coupled receptor (GPCR) allostery, possessing a "common" allosteric site in an extracellular vestibule (ECV) for synthetic modulators including gallamine, strychnine, and brucine. In addition, there is intriguing evidence of endogenous peptides/proteins that may target this region at the M2 mAChR. A common feature of synthetic and endogenous M2 mAChR negative allosteric modulators (NAMs) is their cationic nature. Using a structure-based approach, we previously designed a mutant M2 mAChR (N410K+T423K) to specifically abrogate binding of ECV cationic modulators (Dror et al., 2013). Herein, we used this "allosteric site-impaired" receptor to investigate allosteric interactions of synthetic modulators as well as basic peptides (poly-l-arginine, endogenously produced protamine, and major basic protein). Using [3H]N-methylscopolamine equilibrium and kinetic binding and functional assays of guanosine 5'-O-[γ-thio]triphosphate [35S] binding and extracellular signal-regulated kinases 1 and 2 phosphorylation, we found modest effects of the mutations on potencies of orthosteric antagonists and an increase in the affinity of the cognate agonist, acetylcholine, likely reflecting the effect of the mutations on the access/egress of these ligands into the orthosteric pocket. More importantly, we noted a significant abrogation in affinity for all synthetic or peptidic modulators at the mutant mAChR, validating their allosteric nature. Collectively, these findings provide evidence for a hitherto-unappreciated role of endogenous cationic peptides interacting allosterically at the M2 mAChR and identify the allosteric site-impaired GPCR as a tool for validating NAM activity as well as a potential candidate for future chemogenetic strategies to understand the physiology of endogenous allosteric substances.
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Affiliation(s)
- Ee Von Moo
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Patrick M Sexton
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Arthur Christopoulos
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Celine Valant
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
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28
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Vecchio EA, Baltos JA, Nguyen ATN, Christopoulos A, White PJ, May LT. New paradigms in adenosine receptor pharmacology: allostery, oligomerization and biased agonism. Br J Pharmacol 2018; 175:4036-4046. [PMID: 29679502 DOI: 10.1111/bph.14337] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 03/29/2018] [Accepted: 04/04/2018] [Indexed: 12/17/2022] Open
Abstract
Adenosine receptors are a family of GPCRs containing four subtypes (A1 , A2A , A2B and A3 receptors), all of which bind the ubiquitous nucleoside adenosine. These receptors play an important role in physiology and pathophysiology and therefore represent attractive drug targets for a range of conditions. The theoretical framework surrounding drug action at adenosine receptors now extends beyond the notion of prototypical agonism and antagonism to encompass more complex pharmacological concepts. New paradigms include allostery, in which ligands bind a topographically distinct receptor site from that of the endogenous agonist, homomeric or heteromeric interactions across receptor oligomers and biased agonism, that is, ligand-dependent differential intracellular signalling. This review provides a concise overview of allostery, oligomerization and biased agonism at adenosine receptors and outlines how these paradigms may enhance future drug discovery endeavours focussed on the development of novel therapeutic agents acting at adenosine receptors. LINKED ARTICLES This article is part of a themed section on Molecular Pharmacology of GPCRs. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v175.21/issuetoc.
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Affiliation(s)
- Elizabeth A Vecchio
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC, Australia.,Department of Pharmacology, Monash University, Melbourne, VIC, Australia
| | - Jo-Anne Baltos
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC, Australia.,Department of Pharmacology, Monash University, Melbourne, VIC, Australia
| | - Anh T N Nguyen
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC, Australia.,Department of Pharmacology, Monash University, Melbourne, VIC, Australia
| | - Arthur Christopoulos
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC, Australia.,Department of Pharmacology, Monash University, Melbourne, VIC, Australia
| | - Paul J White
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC, Australia
| | - Lauren T May
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC, Australia.,Department of Pharmacology, Monash University, Melbourne, VIC, Australia
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29
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Structure of the adenosine-bound human adenosine A1 receptor–Gi complex. Nature 2018; 558:559-563. [DOI: 10.1038/s41586-018-0236-6] [Citation(s) in RCA: 224] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 05/16/2018] [Indexed: 12/19/2022]
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30
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Kang SW, Jayanthi S, Nagarajan G, Suresh Kumar TK, Kuenzel WJ. Identification of avian vasotocin receptor subtype-specific antagonists involved in the stress response of the chicken, Gallus gallus. J Biomol Struct Dyn 2018; 37:1685-1699. [PMID: 29658387 DOI: 10.1080/07391102.2018.1464957] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Vasotocin 1a and 1b receptors (V1aR and V1bR) have been shown to play important roles in the neuroendocrine regulation of stress responses via the anterior pituitary (AP) of birds. To identify effective subtype-specific antagonists for the chicken V1aR (cV1aR) and cV1bR, potential antagonists to the mammalian V1R were screened against the cV1aR and cV1bR 3D structural models by molecular docking analysis with determination of binding pocket/amino acid residues involved in the interaction. The antagonistic effects of the selected ligands were examined by measuring pro-opiomelanocortin (POMC) heteronuclear RNA (hnPOMC) levels following the in vitro stress administration to primary chicken AP cells. Results of in silico analysis showed that the Manning compound and several other antagonists were bound to cV1bR with higher affinity than the natural agonist, arginine vasotocin (AVT). Similarities and differences in the antagonist-receptor binding interface with receptors were characterized for each ligand. Non-peptide mammalian V1bR antagonists, SSR-149415 and L-368899, were shown to be effective and had an additive effect in blocking POMC hnRNA expression in pituitary cell culture studies. SR-49059 antagonized the effect(s) of AVT/CRH on the downregulation of the cV1aR and the upregulation of the cCRH-R2 expression but not the cV1bR and cCRH-R1. The Manning compound antagonized the downregulation of cV1aR, cV1bR and cCRH-R1 and the upregulation of cCRH-R2 expression. The specificity of antagonists apparently resulted from unique differences in the interacting residues and their binding affinities. Collectively, these results provide valuable leads for future development of novel compounds capable of blocking or attenuating the AP stress response of avian species and perhaps other non-mammalian vertebrates as well.
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Affiliation(s)
- Seong W Kang
- a Department of Poultry Sciences , University of Arkansas , Fayetteville , AR , USA
| | - Srinivas Jayanthi
- b Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , AR , USA
| | - Gurueswar Nagarajan
- a Department of Poultry Sciences , University of Arkansas , Fayetteville , AR , USA
| | | | - Wayne J Kuenzel
- a Department of Poultry Sciences , University of Arkansas , Fayetteville , AR , USA
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31
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Aurelio L, Baltos JA, Ford L, Nguyen ATN, Jörg M, Devine SM, Valant C, White PJ, Christopoulos A, May LT, Scammells PJ. A Structure–Activity Relationship Study of Bitopic N6-Substituted Adenosine Derivatives as Biased Adenosine A1 Receptor Agonists. J Med Chem 2018; 61:2087-2103. [DOI: 10.1021/acs.jmedchem.8b00047] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Luigi Aurelio
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Jo-Anne Baltos
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, Victoria 3052, Australia
| | - Leigh Ford
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Anh T. N. Nguyen
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, Victoria 3052, Australia
| | - Manuela Jörg
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Shane M. Devine
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Celine Valant
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, Victoria 3052, Australia
| | - Paul J. White
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, Victoria 3052, Australia
| | - Arthur Christopoulos
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, Victoria 3052, Australia
| | - Lauren T. May
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, Victoria 3052, Australia
| | - Peter J. Scammells
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
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32
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Structural Mapping of Adenosine Receptor Mutations: Ligand Binding and Signaling Mechanisms. Trends Pharmacol Sci 2018; 39:75-89. [DOI: 10.1016/j.tips.2017.11.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 11/06/2017] [Accepted: 11/06/2017] [Indexed: 12/16/2022]
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33
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Kalash L, Val C, Azuaje J, Loza MI, Svensson F, Zoufir A, Mervin L, Ladds G, Brea J, Glen R, Sotelo E, Bender A. Computer-aided design of multi-target ligands at A 1R, A 2AR and PDE10A, key proteins in neurodegenerative diseases. J Cheminform 2017; 9:67. [PMID: 29290010 PMCID: PMC5748027 DOI: 10.1186/s13321-017-0249-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 12/01/2017] [Indexed: 01/30/2023] Open
Abstract
Compounds designed to display polypharmacology may have utility in treating complex diseases, where activity at multiple targets is required to produce a clinical effect. In particular, suitable compounds may be useful in treating neurodegenerative diseases by promoting neuronal survival in a synergistic manner via their multi-target activity at the adenosine A1 and A2A receptors (A1R and A2AR) and phosphodiesterase 10A (PDE10A), which modulate intracellular cAMP levels. Hence, in this work we describe a computational method for the design of synthetically feasible ligands that bind to A1 and A2A receptors and inhibit phosphodiesterase 10A (PDE10A), involving a retrosynthetic approach employing in silico target prediction and docking, which may be generally applicable to multi-target compound design at several target classes. This approach has identified 2-aminopyridine-3-carbonitriles as the first multi-target ligands at A1R, A2AR and PDE10A, by showing agreement between the ligand and structure based predictions at these targets. The series were synthesized via an efficient one-pot scheme and validated pharmacologically as A1R/A2AR-PDE10A ligands, with IC50 values of 2.4-10.0 μM at PDE10A and Ki values of 34-294 nM at A1R and/or A2AR. Furthermore, selectivity profiling of the synthesized 2-amino-pyridin-3-carbonitriles against other subtypes of both protein families showed that the multi-target ligand 8 exhibited a minimum of twofold selectivity over all tested off-targets. In addition, both compounds 8 and 16 exhibited the desired multi-target profile, which could be considered for further functional efficacy assessment, analog modification for the improvement of selectivity towards A1R, A2AR and PDE10A collectively, and evaluation of their potential synergy in modulating cAMP levels.
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Affiliation(s)
- Leen Kalash
- Department of Chemistry, Centre for Molecular Informatics, University of Cambridge, Lensfield Road, Cambridge, CB21EW UK
| | - Cristina Val
- Center for Research in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
- Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Jhonny Azuaje
- Center for Research in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - María I. Loza
- Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Fredrik Svensson
- Department of Chemistry, Centre for Molecular Informatics, University of Cambridge, Lensfield Road, Cambridge, CB21EW UK
- IOTA Pharmaceuticals Ltd, St Johns Innovation Centre, Cowley Road, Cambridge, CB40WS UK
| | - Azedine Zoufir
- Department of Chemistry, Centre for Molecular Informatics, University of Cambridge, Lensfield Road, Cambridge, CB21EW UK
| | - Lewis Mervin
- Department of Chemistry, Centre for Molecular Informatics, University of Cambridge, Lensfield Road, Cambridge, CB21EW UK
- Discovery Sciences, AstraZeneca R&D, Cambridge Science Park, Cambridge, UK
| | - Graham Ladds
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB21QJ UK
| | - José Brea
- Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Robert Glen
- Department of Chemistry, Centre for Molecular Informatics, University of Cambridge, Lensfield Road, Cambridge, CB21EW UK
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Eddy Sotelo
- Center for Research in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Andreas Bender
- Department of Chemistry, Centre for Molecular Informatics, University of Cambridge, Lensfield Road, Cambridge, CB21EW UK
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34
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Synergistic Use of GPCR Modeling and SDM Experiments to Understand Ligand Binding. Methods Mol Biol 2017. [PMID: 29188570 DOI: 10.1007/978-1-4939-7465-8_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
There is a substantial amount of historical ligand binding data available from site-directed mutagenesis (SDM) studies of many different GPCR subtypes. This information was generated prior to the wave of GPCR crystal structure, in an effort to understand ligand binding with a view to drug discovery. Concerted efforts to determine the atomic structure of GPCRs have proven extremely successful and there are now more than 80 GPCR crystal structure in the PDB database, many of which have been obtained in the presence of receptor ligands and associated G proteins. These structural data enable the generation of computational model structures for all GPCRs, including those for which crystal structures do not yet exist. The power of these models in designing novel ligands, especially those with improved residence times, and for better understanding receptor function can be enhanced tremendously by combining them synergistically with historic SDM ligand binding data. Here, we describe a protocol by which historic SDM binding data and receptor models may be used together to identify novel key residues for mutagenesis studies.
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35
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Deganutti G, Zhukov A, Deflorian F, Federico S, Spalluto G, Cooke RM, Moro S, Mason JS, Bortolato A. Impact of protein-ligand solvation and desolvation on transition state thermodynamic properties of adenosine A 2A ligand binding kinetics. In Silico Pharmacol 2017; 5:16. [PMID: 29308352 PMCID: PMC5755719 DOI: 10.1007/s40203-017-0037-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 11/14/2017] [Indexed: 12/26/2022] Open
Abstract
Ligand-protein binding kinetic rates are growing in importance as parameters to consider in drug discovery and lead optimization. In this study we analysed using surface plasmon resonance (SPR) the transition state (TS) properties of a set of six adenosine A2A receptor inhibitors, belonging to both the xanthine and the triazolo-triazine scaffolds. SPR highlighted interesting differences among the ligands in the enthalpic and entropic components of the TS energy barriers for the binding and unbinding events. To better understand at a molecular level these differences, we developed suMetaD, a novel molecular dynamics (MD)-based approach combining supervised MD and metadynamics. This method allows simulation of the ligand unbinding and binding events. It also provides the system conformation corresponding to the highest energy barrier the ligand is required to overcome to reach the final state. For the six ligands evaluated in this study their TS thermodynamic properties were linked in particular to the role of water molecules in solvating/desolvating the pocket and the small molecules. suMetaD identified kinetic bottleneck conformations near the bound state position or in the vestibule area. In the first case the barrier is mainly enthalpic, requiring the breaking of strong interactions with the protein. In the vestibule TS location the kinetic bottleneck is instead mainly of entropic nature, linked to the solvent behaviour.
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Affiliation(s)
- Giuseppe Deganutti
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, Padua, Italy
| | - Andrei Zhukov
- Heptares Therapeutics Ltd., BioPark, Broadwater Road, Welwyn Garden City, Herts AL7 3AX UK
| | - Francesca Deflorian
- Heptares Therapeutics Ltd., BioPark, Broadwater Road, Welwyn Garden City, Herts AL7 3AX UK
| | - Stephanie Federico
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Piazzale Europa, 34127 Trieste, Italy
| | - Giampiero Spalluto
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Piazzale Europa, 34127 Trieste, Italy
| | - Robert M. Cooke
- Heptares Therapeutics Ltd., BioPark, Broadwater Road, Welwyn Garden City, Herts AL7 3AX UK
| | - Stefano Moro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, Padua, Italy
| | - Jonathan S. Mason
- Heptares Therapeutics Ltd., BioPark, Broadwater Road, Welwyn Garden City, Herts AL7 3AX UK
| | - Andrea Bortolato
- Heptares Therapeutics Ltd., BioPark, Broadwater Road, Welwyn Garden City, Herts AL7 3AX UK
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36
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Structure-Based Design of Potent and Selective Ligands at the Four Adenosine Receptors. Molecules 2017; 22:molecules22111945. [PMID: 29125553 PMCID: PMC6150288 DOI: 10.3390/molecules22111945] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 11/07/2017] [Accepted: 11/08/2017] [Indexed: 12/19/2022] Open
Abstract
The four receptors that signal for adenosine, A1, A2A, A2B and A3 ARs, belong to the superfamily of G protein-coupled receptors (GPCRs). They mediate a number of (patho)physiological functions and have attracted the interest of the biopharmaceutical sector for decades as potential drug targets. The many crystal structures of the A2A, and lately the A1 ARs, allow for the use of advanced computational, structure-based ligand design methodologies. Over the last decade, we have assessed the efficient synthesis of novel ligands specifically addressed to each of the four ARs. We herein review and update the results of this program with particular focus on molecular dynamics (MD) and free energy perturbation (FEP) protocols. The first in silico mutagenesis on the A1AR here reported allows understanding the specificity and high affinity of the xanthine-antagonist 8-Cyclopentyl-1,3-dipropylxanthine (DPCPX). On the A2AAR, we demonstrate how FEP simulations can distinguish the conformational selectivity of a recent series of partial agonists. These novel results are complemented with the revision of the first series of enantiospecific antagonists on the A2BAR, and the use of FEP as a tool for bioisosteric design on the A3AR.
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37
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Soave M, Cseke G, Hutchings CJ, Brown AJH, Woolard J, Hill SJ. A monoclonal antibody raised against a thermo-stabilised β 1-adrenoceptor interacts with extracellular loop 2 and acts as a negative allosteric modulator of a sub-set of β 1-adrenoceptors expressed in stable cell lines. Biochem Pharmacol 2017; 147:38-54. [PMID: 29102678 PMCID: PMC5770334 DOI: 10.1016/j.bcp.2017.10.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Accepted: 10/31/2017] [Indexed: 11/30/2022]
Abstract
Recent interest has focused on antibodies that can discriminate between different receptor conformations. Here we have characterised the effect of a monoclonal antibody (mAb3), raised against a purified thermo-stabilised turkey β1-adrenoceptor (β1AR-m23 StaR), on β1-ARs expressed in CHO-K1 or HEK 293 cells. Immunohistochemical and radioligand-binding studies demonstrated that mAb3 was able to bind to ECL2 of the tβ1-AR, but not its human homologue. Specific binding of mAb3 to tβ1-AR was inhibited by a peptide based on the turkey, but not the human, ECL2 sequence. Studies with [3H]-CGP 12177 demonstrated that mAb3 prevented the binding of orthosteric ligands to a subset (circa 40%) of turkey β1-receptors expressed in both CHO K1 and HEK 293 cells. MAb3 significantly reduced the maximum specific binding capacity of [3H]-CGP-12177 without influencing its binding affinity. Substitution of ECL2 of tβ1-AR with its human equivalent, or mutation of residues D186S, P187D, Q188E prevented the inhibition of [3H]-CGP 12177 binding by mAb3. MAb3 also elicited a negative allosteric effect on agonist-stimulated cAMP responses. The identity of the subset of turkey β1-adrenoceptors influenced by mAb3 remains to be established but mAb3 should become an important tool to investigate the nature of β1-AR conformational states and oligomeric complexes.
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Affiliation(s)
- Mark Soave
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK; Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
| | - Gabriella Cseke
- Heptares Therapeutics Ltd., Bio Park, Welwyn Garden City AL7 3AX, UK
| | | | | | - Jeanette Woolard
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK; Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK.
| | - Stephen J Hill
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK; Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK.
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Rafehi M, Neumann A, Baqi Y, Malik EM, Wiese M, Namasivayam V, Müller CE. Molecular Recognition of Agonists and Antagonists by the Nucleotide-Activated G Protein-Coupled P2Y 2 Receptor. J Med Chem 2017; 60:8425-8440. [PMID: 28938069 DOI: 10.1021/acs.jmedchem.7b00854] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A homology model of the nucleotide-activated P2Y2R was created based on the X-ray structures of the P2Y1 receptor. Docking studies were performed, and receptor mutants were created to probe the identified binding interactions. Mutation of residues predicted to interact with the ribose (Arg110) and the phosphates of the nucleotide agonists (Arg265, Arg292) or that contribute indirectly to binding (Tyr288) abolished activity. The Y114F, R194A, and F261A mutations led to inactivity of diadenosine tetraphosphate and to a reduced response of UTP. Significant reduction in agonist potency was observed for all other receptor mutants (Phe111, His184, Ser193, Phe261, Tyr268, Tyr269) predicted to be involved in agonist recognition. An ionic lock between Asp185 and Arg292 that is probably involved in receptor activation interacts with the phosphate groups. The antagonist AR-C118925 and anthraquinones likely bind to the orthosteric site. The updated homology models will be useful for virtual screening and drug design.
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Affiliation(s)
- Muhammad Rafehi
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical Chemistry I, University of Bonn , 53121 Bonn, Germany
| | - Alexander Neumann
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical Chemistry I, University of Bonn , 53121 Bonn, Germany
| | - Younis Baqi
- Department of Chemistry, Faculty of Science, Sultan Qaboos University , PO Box 36, Postal Code 123, Muscat, Oman
| | - Enas M Malik
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical Chemistry I, University of Bonn , 53121 Bonn, Germany
| | - Michael Wiese
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry II, University of Bonn , 53121 Bonn, Germany
| | - Vigneshwaran Namasivayam
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical Chemistry I, University of Bonn , 53121 Bonn, Germany.,PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry II, University of Bonn , 53121 Bonn, Germany
| | - Christa E Müller
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical Chemistry I, University of Bonn , 53121 Bonn, Germany
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Iglesias A, Cimadevila M, la Fuente RAD, Martí-Solano M, Cadavid MI, Castro M, Selent J, Loza MI, Brea J. Serotonin 2A receptor disulfide bridge integrity is crucial for ligand binding to different signalling states but not for its homodimerization. Eur J Pharmacol 2017; 815:138-146. [PMID: 28899696 DOI: 10.1016/j.ejphar.2017.09.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/28/2017] [Accepted: 09/08/2017] [Indexed: 02/06/2023]
Abstract
The serotonin 2A (5-HT2A) receptor is a G-protein coupled receptor (GPCR) with a conserved disulfide bridge formed by Cys148 (transmembrane helix 3, TM3) and Cys227 (extracellular loop 2, ECL-2). We hypothesized that disulfide bridges may determine serotonin 5-HT2A receptor functions such as receptor activation, functional selectivity and ligand recognition. We used the reducing agent dithiothreitol (DTT) to determine how the reduction of disulfide bridges affects radioligand binding, second messenger mobilization and receptor dimerization. A DTT-induced decrease in the number of binding sites (1190 ± 63.55 fmol/mg protein for control cells compared with 921.2 ± 60.84 fmol/mg protein for DTT-treated cells) as well as in the efficacy of both signalling pathways characterized was observed, although the affinity and potency were unchanged. Bioluminiscence resonance energy transfer (BRET) assays revealed the DTT treatment did not modify the homodimeric nature of serotonin 5-HT2A receptors. In molecular dynamic simulations, the ECL-2 of the receptor with a broken cysteine bond adopts a wider variety of conformations, some of which protrude deeper into the receptor orthosteric binding pocket leading to collapse of the pocket. A shrunken binding pocket would be incapable of accommodating lysergic acid diethylamide (LSD). Our findings suggest that the decrease of efficacy may be due to disruption of disulfide bridge between TM3 and ECL-2. This reveals the integrity of the ECL-2 epitope, which should be explored in the development of novel ligands acting as allosteric modulators of serotonin 5-HT2A receptors.
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Affiliation(s)
- Alba Iglesias
- BioFarma Research Group, Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Avenida de Barcelona 22, 15782 Santiago de Compostela, Spain
| | - Marta Cimadevila
- BioFarma Research Group, Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Avenida de Barcelona 22, 15782 Santiago de Compostela, Spain
| | - Rocío Ailim de la Fuente
- BioFarma Research Group, Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Avenida de Barcelona 22, 15782 Santiago de Compostela, Spain; Molecular Pharmacology of G Protein-coupled Receptors Laboratory, Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Avenida de Barcelona 22, 15782 Santiago de Compostela, Spain
| | - María Martí-Solano
- GPCR Drug Discovery Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM) - Department of Experimental and Health Sciences of Pompeu Fabra University (UPF), Barcelona, Spain
| | - María Isabel Cadavid
- BioFarma Research Group, Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Avenida de Barcelona 22, 15782 Santiago de Compostela, Spain
| | - Marián Castro
- BioFarma Research Group, Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Avenida de Barcelona 22, 15782 Santiago de Compostela, Spain; Molecular Pharmacology of G Protein-coupled Receptors Laboratory, Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Avenida de Barcelona 22, 15782 Santiago de Compostela, Spain
| | - Jana Selent
- GPCR Drug Discovery Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM) - Department of Experimental and Health Sciences of Pompeu Fabra University (UPF), Barcelona, Spain
| | - María Isabel Loza
- BioFarma Research Group, Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Avenida de Barcelona 22, 15782 Santiago de Compostela, Spain.
| | - José Brea
- BioFarma Research Group, Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Avenida de Barcelona 22, 15782 Santiago de Compostela, Spain.
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A kinetic view of GPCR allostery and biased agonism. Nat Chem Biol 2017; 13:929-937. [DOI: 10.1038/nchembio.2431] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 05/31/2017] [Indexed: 12/21/2022]
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Varani K, Vincenzi F, Merighi S, Gessi S, Borea PA. Biochemical and Pharmacological Role of A1 Adenosine Receptors and Their Modulation as Novel Therapeutic Strategy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1051:193-232. [DOI: 10.1007/5584_2017_61] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Priming GPCR signaling through the synergistic effect of two G proteins. Proc Natl Acad Sci U S A 2017; 114:3756-3761. [PMID: 28325873 DOI: 10.1073/pnas.1617232114] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Although individual G-protein-coupled receptors (GPCRs) are known to activate one or more G proteins, the GPCR-G-protein interaction is viewed as a bimolecular event involving the formation of a ternary ligand-GPCR-G-protein complex. Here, we present evidence that individual GPCR-G-protein interactions can reinforce each other to enhance signaling through canonical downstream second messengers, a phenomenon we term "GPCR priming." Specifically, we find that the presence of noncognate Gq protein enhances cAMP stimulated by two Gs-coupled receptors, β2-adrenergic receptor (β2-AR) and D1 dopamine receptor (D1-R). Reciprocally, Gs enhances IP1 through vasopressin receptor (V1A-R) but not α1 adrenergic receptor (α1-AR), suggesting that GPCR priming is a receptor-specific phenomenon. The C terminus of either the Gαs or Gαq subunit is sufficient to enhance Gα subunit activation and cAMP levels. Interaction of Gαs or Gαq C termini with the GPCR increases signaling potency, suggesting an altered GPCR conformation as the underlying basis for GPCR priming. We propose three parallel mechanisms involving (i) sequential G-protein interactions at the cognate site, (ii) G-protein interactions at distinct allosteric and cognate sites on the GPCR, and (iii) asymmetric GPCR dimers. GPCR priming suggests another layer of regulation in the classic GPCR ternary-complex model, with broad implications for the multiplicity inherent in signaling networks.
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Glukhova A, Thal DM, Nguyen AT, Vecchio EA, Jörg M, Scammells PJ, May LT, Sexton PM, Christopoulos A. Structure of the Adenosine A1 Receptor Reveals the Basis for Subtype Selectivity. Cell 2017; 168:867-877.e13. [DOI: 10.1016/j.cell.2017.01.042] [Citation(s) in RCA: 188] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 12/15/2016] [Accepted: 01/30/2017] [Indexed: 01/10/2023]
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Nguyen ATN, Vecchio EA, Thomas T, Nguyen TD, Aurelio L, Scammells PJ, White PJ, Sexton PM, Gregory KJ, May LT, Christopoulos A. Role of the Second Extracellular Loop of the Adenosine A1 Receptor on Allosteric Modulator Binding, Signaling, and Cooperativity. Mol Pharmacol 2016; 90:715-725. [PMID: 27683013 DOI: 10.1124/mol.116.105015] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 09/27/2016] [Indexed: 02/05/2023] Open
Abstract
Allosteric modulation of adenosine A1 receptors (A1ARs) offers a novel therapeutic approach for the treatment of numerous central and peripheral disorders; however, despite decades of research, there is a relative paucity of structural information regarding the A1AR allosteric site and mechanisms governing cooperativity with orthosteric ligands. We combined alanine-scanning mutagenesis of the A1AR second extracellular loop (ECL2) with radioligand binding and functional interaction assays to quantify effects on allosteric ligand affinity, cooperativity, and efficacy. Docking and molecular dynamics (MD) simulations were performed using an A1AR homology model based on an agonist-bound A2AAR structure. Substitution of E172ECL2 for alanine reduced the affinity of the allosteric modulators PD81723 and VCP171 for the unoccupied A1AR. Residues involved in cooperativity with the orthosteric agonist NECA were different in PD81723 and VCP171; positive cooperativity between PD81723 and NECA was reduced on alanine substitution of a number of ECL2 residues, including E170ECL2 and K173ECL2, whereas mutation of W146ECL2 and W156ECL2 decreased VCP171 cooperativity with NECA. Molecular modeling localized a likely allosteric pocket for both modulators to an extracellular vestibule that overlaps with a region used by orthosteric ligands as they transit into the canonical A1AR orthosteric site. MD simulations confirmed a key interaction between E172ECL2 and both modulators. Bound PD81723 is flanked by another residue, E170ECL2, which forms hydrogen bonds with adjacent K168ECL2 and K173ECL2. Collectively, our data suggest E172ECL2 is a key allosteric ligand-binding determinant, whereas hydrogen-bonding networks within the extracellular vestibule may facilitate the transmission of cooperativity between orthosteric and allosteric sites.
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Affiliation(s)
- Anh T N Nguyen
- Monash Institute of Pharmaceutical Sciences (A.T.N.N., E.A.V., T.T., L.A., P.J.S., P.J.W., P.M.S., K.J.G., L.T.M., A.C.), Monash e-Research Centre (T.D.N.), and Department of Pharmacology (A.T.N.N., E.A.V., P.M.S., K.J.G., L.T.M., A.C), Monash University, Victoria, Australia
| | - Elizabeth A Vecchio
- Monash Institute of Pharmaceutical Sciences (A.T.N.N., E.A.V., T.T., L.A., P.J.S., P.J.W., P.M.S., K.J.G., L.T.M., A.C.), Monash e-Research Centre (T.D.N.), and Department of Pharmacology (A.T.N.N., E.A.V., P.M.S., K.J.G., L.T.M., A.C), Monash University, Victoria, Australia
| | - Trayder Thomas
- Monash Institute of Pharmaceutical Sciences (A.T.N.N., E.A.V., T.T., L.A., P.J.S., P.J.W., P.M.S., K.J.G., L.T.M., A.C.), Monash e-Research Centre (T.D.N.), and Department of Pharmacology (A.T.N.N., E.A.V., P.M.S., K.J.G., L.T.M., A.C), Monash University, Victoria, Australia
| | - Toan D Nguyen
- Monash Institute of Pharmaceutical Sciences (A.T.N.N., E.A.V., T.T., L.A., P.J.S., P.J.W., P.M.S., K.J.G., L.T.M., A.C.), Monash e-Research Centre (T.D.N.), and Department of Pharmacology (A.T.N.N., E.A.V., P.M.S., K.J.G., L.T.M., A.C), Monash University, Victoria, Australia
| | - Luigi Aurelio
- Monash Institute of Pharmaceutical Sciences (A.T.N.N., E.A.V., T.T., L.A., P.J.S., P.J.W., P.M.S., K.J.G., L.T.M., A.C.), Monash e-Research Centre (T.D.N.), and Department of Pharmacology (A.T.N.N., E.A.V., P.M.S., K.J.G., L.T.M., A.C), Monash University, Victoria, Australia
| | - Peter J Scammells
- Monash Institute of Pharmaceutical Sciences (A.T.N.N., E.A.V., T.T., L.A., P.J.S., P.J.W., P.M.S., K.J.G., L.T.M., A.C.), Monash e-Research Centre (T.D.N.), and Department of Pharmacology (A.T.N.N., E.A.V., P.M.S., K.J.G., L.T.M., A.C), Monash University, Victoria, Australia
| | - Paul J White
- Monash Institute of Pharmaceutical Sciences (A.T.N.N., E.A.V., T.T., L.A., P.J.S., P.J.W., P.M.S., K.J.G., L.T.M., A.C.), Monash e-Research Centre (T.D.N.), and Department of Pharmacology (A.T.N.N., E.A.V., P.M.S., K.J.G., L.T.M., A.C), Monash University, Victoria, Australia
| | - Patrick M Sexton
- Monash Institute of Pharmaceutical Sciences (A.T.N.N., E.A.V., T.T., L.A., P.J.S., P.J.W., P.M.S., K.J.G., L.T.M., A.C.), Monash e-Research Centre (T.D.N.), and Department of Pharmacology (A.T.N.N., E.A.V., P.M.S., K.J.G., L.T.M., A.C), Monash University, Victoria, Australia
| | - Karen J Gregory
- Monash Institute of Pharmaceutical Sciences (A.T.N.N., E.A.V., T.T., L.A., P.J.S., P.J.W., P.M.S., K.J.G., L.T.M., A.C.), Monash e-Research Centre (T.D.N.), and Department of Pharmacology (A.T.N.N., E.A.V., P.M.S., K.J.G., L.T.M., A.C), Monash University, Victoria, Australia
| | - Lauren T May
- Monash Institute of Pharmaceutical Sciences (A.T.N.N., E.A.V., T.T., L.A., P.J.S., P.J.W., P.M.S., K.J.G., L.T.M., A.C.), Monash e-Research Centre (T.D.N.), and Department of Pharmacology (A.T.N.N., E.A.V., P.M.S., K.J.G., L.T.M., A.C), Monash University, Victoria, Australia
| | - Arthur Christopoulos
- Monash Institute of Pharmaceutical Sciences (A.T.N.N., E.A.V., T.T., L.A., P.J.S., P.J.W., P.M.S., K.J.G., L.T.M., A.C.), Monash e-Research Centre (T.D.N.), and Department of Pharmacology (A.T.N.N., E.A.V., P.M.S., K.J.G., L.T.M., A.C), Monash University, Victoria, Australia
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