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Cheng J, Chen M, Wang S, Liang T, Chen H, Chen CJ, Feng Z, Xie XQ. Binding Characterization of Agonists and Antagonists by MCCS: A Case Study from Adenosine A 2A Receptor. ACS Chem Neurosci 2021; 12:1606-1620. [PMID: 33856784 DOI: 10.1021/acschemneuro.1c00082] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Characterizing the structural basis of ligand recognition of adenosine A2A receptor (AA2AR) will facilitate its rational design and development of small molecules with high affinity and selectivity, as well as optimal therapeutic effects for pain, cancers, drug abuse disorders, etc. In the present work, we applied our reported algorithm, molecular complex characterizing system (MCCS), to characterize the binding features of AA2AR based on its reported 3D structures of protein-ligand complexes. First, we compared the binding score to the reported experimental binding affinities of each compound. Then, we calculated an output example of residue energy contribution using MCCS and compared the results with data obtained from MM/GBSA. The consistency in results indicated that MCCS is a powerful, fast, and accurate method. Sequentially, using a receptor-ligand data set of 57 crystallized structures of AA2ARs, we characterized the binding features of the binding pockets in AA2AR, summarized the key residues that distinguish antagonist from agonist, produced heatmaps of residue energy contribution for clustering various statuses of AA2ARs, explored the selectivity between AA2AR and AA1AR, etc. All the information provided new insights into the protein features of AA2AR and will facilitate its rational drug design.
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Affiliation(s)
- Jin Cheng
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, and National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States.,Department of Pharmacy, Jiangsu Vocational College of Medicine, Yancheng, Jiangsu 224005, China
| | - Maozi Chen
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, and National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Siyi Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, and National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Tianjian Liang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, and National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Hui Chen
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, and National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Chih-Jung Chen
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, and National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Zhiwei Feng
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, and National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, and National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
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Identification of Novel Chemical Entities for Adenosine Receptor Type 2A Using Molecular Modeling Approaches. Molecules 2020; 25:molecules25051245. [PMID: 32164183 PMCID: PMC7179438 DOI: 10.3390/molecules25051245] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/01/2020] [Accepted: 03/06/2020] [Indexed: 12/20/2022] Open
Abstract
Adenosine Receptor Type 2A (A2AAR) plays a role in important processes, such as anti-inflammatory ones. In this way, the present work aimed to search for compounds by pharmacophore-based virtual screening. The pharmacokinetic/toxicological profiles of the compounds, as well as a robust QSAR, predicted the binding modes via molecular docking. Finally, we used molecular dynamics to investigate the stability of interactions from ligand-A2AAR. For the search for A2AAR agonists, the UK-432097 and a set of 20 compounds available in the BindingDB database were studied. These compounds were used to generate pharmacophore models. Molecular properties were used for construction of the QSAR model by multiple linear regression for the prediction of biological activity. The best pharmacophore model was used by searching for commercial compounds in databases and the resulting compounds from the pharmacophore-based virtual screening were applied to the QSAR. Two compounds had promising activity due to their satisfactory pharmacokinetic/toxicological profiles and predictions via QSAR (Diverset 10002403 pEC50 = 7.54407; ZINC04257548 pEC50 = 7.38310). Moreover, they had satisfactory docking and molecular dynamics results compared to those obtained for Regadenoson (Lexiscan®), used as the positive control. These compounds can be used in biological assays (in vitro and in vivo) in order to confirm the potential activity agonist to A2AAR.
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Al-Attraqchi OH, Attimarad M, Venugopala KN, Nair A, Al-Attraqchi NH. Adenosine A2A Receptor as a Potential Drug Target - Current Status and Future Perspectives. Curr Pharm Des 2019; 25:2716-2740. [DOI: 10.2174/1381612825666190716113444] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 07/03/2019] [Indexed: 12/18/2022]
Abstract
Adenosine receptors (ARs) are a class of G-protein coupled receptors (GPCRs) that are activated by
the endogenous substance adenosine. ARs are classified into 4 subtype receptors, namely, the A1, A2A, A2B and A3
receptors. The wide distribution and expression of the ARs in various body tissues as well as the roles they have
in controlling different functions in the body make them potential drug targets for the treatment of various pathological
conditions, such as cardiac diseases, cancer, Parkinson’s disease, inflammation and glaucoma. Therefore,
in the past decades, there have been extensive investigations of ARs with a high number of agonists and antagonists
identified that can interact with these receptors. This review shall discuss the A2A receptor (A2AAR) subtype
of the ARs. The structure, properties and the recent advances in the therapeutic potential of the receptor are discussed
with an overview of the recent advances in the methods of studying the receptor. Also, molecular modeling
approaches utilized in the design of A2AAR ligands are highlighted with various recent examples.
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Affiliation(s)
- Omar H.A. Al-Attraqchi
- Faculty of Pharmacy, Philadelphia University-Jordan, P.O BOX (1), Philadelphia University-19392, Amman, Jordan
| | - Mahesh Attimarad
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Katharigatta N. Venugopala
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Anroop Nair
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia
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Lu Y, Qin S, Zhang B, Dai A, Cai X, Ma M, Gao ZG, Yang D, Stevens RC, Jacobson KA, Wang MW, Shui W. Accelerating the Throughput of Affinity Mass Spectrometry-Based Ligand Screening toward a G Protein-Coupled Receptor. Anal Chem 2019; 91:8162-8169. [PMID: 31094506 PMCID: PMC6669887 DOI: 10.1021/acs.analchem.9b00477] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Affinity mass spectrometry (MS) enables rapid screening of compound mixtures for ligands bound to a specific protein target, yet its current throughput is limited to individually assay pools of 400-2000 compounds. Typical affinity MS screens implemented in pharmaceutical industry laboratories identify putative ligands based on qualitative analysis of compound binding to the target whereas no quantitative information is acquired to discriminate high- and low-affinity ligands in the screening phase. Furthermore, these screens require purification of a stabilized form of the protein target, which poses a great challenge for membrane receptor targets. Here, we describe a new, potentially general affinity MS strategy that allows screening of 20,000 compounds in one pool for highly efficient ligand discovery toward a G protein-coupled receptor (GPCR) target. Quantitative measurement of compound binding to the receptor enables high-affinity ligand selection using both the purified receptor and receptor-embedded cell membranes. This high-throughput, label-free and quantitative affinity MS screen resulted in discovery of three new antagonists of the A2A adenosine receptor.
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Affiliation(s)
- Yan Lu
- iHuman Institute, ShanghaiTech University, 201210 Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, 201210 Shanghai, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Shanshan Qin
- iHuman Institute, ShanghaiTech University, 201210 Shanghai, China
| | - Bingjie Zhang
- iHuman Institute, ShanghaiTech University, 201210 Shanghai, China
| | - Antao Dai
- The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203 Shanghai, China
| | - Xiaoqing Cai
- The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203 Shanghai, China
| | - Mengna Ma
- iHuman Institute, ShanghaiTech University, 201210 Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, 201210 Shanghai, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Zhan-Guo Gao
- National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, Maryland 20892 United States
| | - Dehua Yang
- The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203 Shanghai, China
| | - Raymond C. Stevens
- iHuman Institute, ShanghaiTech University, 201210 Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, 201210 Shanghai, China
| | - Kenneth A. Jacobson
- National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, Maryland 20892 United States
| | - Ming-Wei Wang
- University of Chinese Academy of Sciences, 100049 Beijing, China
- The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203 Shanghai, China
- School of Pharmacy, Fudan University, 201203 Shanghai, China
| | - Wenqing Shui
- iHuman Institute, ShanghaiTech University, 201210 Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, 201210 Shanghai, China
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Acúrcio RC, Scomparin A, Satchi‐Fainaro R, Florindo HF, Guedes RC. Computer‐aided drug design in new druggable targets for the next generation of immune‐oncology therapies. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2019. [DOI: 10.1002/wcms.1397] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Rita C. Acúrcio
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy Universidade de Lisboa Lisbon Portugal
| | - Anna Scomparin
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine Tel Aviv University Tel Aviv Israel
| | - Ronit Satchi‐Fainaro
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine Tel Aviv University Tel Aviv Israel
| | - Helena F. Florindo
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy Universidade de Lisboa Lisbon Portugal
| | - Rita C. Guedes
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy Universidade de Lisboa Lisbon Portugal
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Jiang X, Yu J, Zhou Z, Kongsted J, Song Y, Pannecouque C, De Clercq E, Kang D, Poongavanam V, Liu X, Zhan P. Molecular design opportunities presented by solvent‐exposed regions of target proteins. Med Res Rev 2019; 39:2194-2238. [DOI: 10.1002/med.21581] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 03/09/2019] [Accepted: 03/16/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Xiangyi Jiang
- Department of Medicinal ChemistryKey Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University Jinan Shandong People's Republic of China
| | - Ji Yu
- Department of Medicinal ChemistryKey Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University Jinan Shandong People's Republic of China
| | - Zhongxia Zhou
- Department of Medicinal ChemistryKey Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University Jinan Shandong People's Republic of China
| | - Jacob Kongsted
- Department of Physics, Chemistry and PharmacyUniversity of Southern Denmark Odense Denmark
| | - Yuning Song
- Department of Clinical PharmacyQilu Hospital of Shandong University Jinan China
| | - Christophe Pannecouque
- Rega Institute for Medical ResearchLaboratory of Virology and Chemotherapy Leuven Belgium
| | - Erik De Clercq
- Rega Institute for Medical ResearchLaboratory of Virology and Chemotherapy Leuven Belgium
| | - Dongwei Kang
- Department of Medicinal ChemistryKey Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University Jinan Shandong People's Republic of China
| | | | - Xinyong Liu
- Department of Medicinal ChemistryKey Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University Jinan Shandong People's Republic of China
| | - Peng Zhan
- Department of Medicinal ChemistryKey Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University Jinan Shandong People's Republic of China
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7
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Congreve M, Brown GA, Borodovsky A, Lamb ML. Targeting adenosine A2A receptor antagonism for treatment of cancer. Expert Opin Drug Discov 2018; 13:997-1003. [DOI: 10.1080/17460441.2018.1534825] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Miles Congreve
- Heptares Therapeutics Limited, Steinmetz Building, Cambridge, Granta Park, UK
| | - Giles A. Brown
- Heptares Therapeutics Limited, Steinmetz Building, Cambridge, Granta Park, UK
| | | | - Michelle L. Lamb
- Medicinal Chemistry, Oncology, IMED Biotech Unit, AstraZeneca, Boston, MA, USA
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Breakthrough in GPCR Crystallography and Its Impact on Computer-Aided Drug Design. Methods Mol Biol 2018; 1705:45-72. [PMID: 29188558 DOI: 10.1007/978-1-4939-7465-8_3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Recent crystallographic structures of G protein-coupled receptors (GPCRs) have greatly advanced our understanding of the recognition of their diverse agonist and antagonist ligands. We illustrate here how this applies to A2A adenosine receptors (ARs) and to P2Y1 and P2Y12 receptors (P2YRs) for ADP. These X-ray structures have impacted the medicinal chemistry aimed at discovering new ligands for these two receptor families, including receptors that have not yet been crystallized but are closely related to the known structures. In this Chapter, we discuss recent structure-based drug design projects that led to the discovery of: (a) novel A3AR agonists based on a highly rigidified (N)-methanocarba scaffold for the treatment of chronic neuropathic pain and other conditions, (b) fluorescent probes of the ARs and P2Y14R, as chemical tools for structural probing of these GPCRs and for improving assay capabilities, and (c) new more drug-like antagonists of the inflammation-related P2Y14R. We also describe the computationally enabled molecular recognition of positive (for A3AR) and negative (P2Y1R) allosteric modulators that in some cases are shown to be consistent with structure-activity relationship (SAR) data. Thus, computational modeling has become an essential tool for the design of purine receptor ligands.
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9
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Hothersall JD, Guo D, Sarda S, Sheppard RJ, Chen H, Keur W, Waring MJ, IJzerman AP, Hill SJ, Dale IL, Rawlins PB. Structure-Activity Relationships of the Sustained Effects of Adenosine A2A Receptor Agonists Driven by Slow Dissociation Kinetics. Mol Pharmacol 2016; 91:25-38. [PMID: 27803241 PMCID: PMC5198511 DOI: 10.1124/mol.116.105551] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 10/28/2016] [Indexed: 12/02/2022] Open
Abstract
The duration of action of adenosine A2A receptor (A2A) agonists is critical for their clinical efficacy, and we sought to better understand how this can be optimized. The in vitro temporal response profiles of a panel of A2A agonists were studied using cAMP assays in recombinantly (CHO) and endogenously (SH-SY5Y) expressing cells. Some agonists (e.g., 3cd; UK-432,097) but not others (e.g., 3ac; CGS-21680) demonstrated sustained wash-resistant agonism, where residual receptor activation continued after washout. The ability of an antagonist to reverse pre-established agonist responses was used as a surrogate read-out for agonist dissociation kinetics, and together with radioligand binding studies suggested a role for slow off-rate in driving sustained effects. One compound, 3ch, showed particularly marked sustained effects, with a reversal t1/2 > 6 hours and close to maximal effects that remained for at least 5 hours after washing. Based on the structure-activity relationship of these compounds, we suggest that lipophilic N6 and bulky C2 substituents can promote stable and long-lived binding events leading to sustained agonist responses, although a high compound logD is not necessary. This provides new insight into the binding interactions of these ligands and we anticipate that this information could facilitate the rational design of novel long-acting A2A agonists with improved clinical efficacy.
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Affiliation(s)
- J Daniel Hothersall
- AstraZeneca, Discovery Sciences, Alderley Park, United Kingdom (J.D.H., S.S.); AstraZeneca, Oncology, Cambridge, United Kingdom (R.J.S.); AstraZeneca, Discovery Sciences, Mölndal, Sweden (H.C.); AstraZeneca, Discovery Sciences, Cambridge Science Park, United Kingdom (I.L.D., P.B.R.); AstraZeneca, Oncology, Alderley Park, United Kingdom (M.J.W.); Leiden Academic Centre for Drug Research, Division of Medicinal Chemistry, The Netherlands (D.G., W.K., A.P.I.J.); and University of Nottingham, School of Life Sciences, United Kingdom (S.J.H.)
| | - Dong Guo
- AstraZeneca, Discovery Sciences, Alderley Park, United Kingdom (J.D.H., S.S.); AstraZeneca, Oncology, Cambridge, United Kingdom (R.J.S.); AstraZeneca, Discovery Sciences, Mölndal, Sweden (H.C.); AstraZeneca, Discovery Sciences, Cambridge Science Park, United Kingdom (I.L.D., P.B.R.); AstraZeneca, Oncology, Alderley Park, United Kingdom (M.J.W.); Leiden Academic Centre for Drug Research, Division of Medicinal Chemistry, The Netherlands (D.G., W.K., A.P.I.J.); and University of Nottingham, School of Life Sciences, United Kingdom (S.J.H.)
| | - Sunil Sarda
- AstraZeneca, Discovery Sciences, Alderley Park, United Kingdom (J.D.H., S.S.); AstraZeneca, Oncology, Cambridge, United Kingdom (R.J.S.); AstraZeneca, Discovery Sciences, Mölndal, Sweden (H.C.); AstraZeneca, Discovery Sciences, Cambridge Science Park, United Kingdom (I.L.D., P.B.R.); AstraZeneca, Oncology, Alderley Park, United Kingdom (M.J.W.); Leiden Academic Centre for Drug Research, Division of Medicinal Chemistry, The Netherlands (D.G., W.K., A.P.I.J.); and University of Nottingham, School of Life Sciences, United Kingdom (S.J.H.)
| | - Robert J Sheppard
- AstraZeneca, Discovery Sciences, Alderley Park, United Kingdom (J.D.H., S.S.); AstraZeneca, Oncology, Cambridge, United Kingdom (R.J.S.); AstraZeneca, Discovery Sciences, Mölndal, Sweden (H.C.); AstraZeneca, Discovery Sciences, Cambridge Science Park, United Kingdom (I.L.D., P.B.R.); AstraZeneca, Oncology, Alderley Park, United Kingdom (M.J.W.); Leiden Academic Centre for Drug Research, Division of Medicinal Chemistry, The Netherlands (D.G., W.K., A.P.I.J.); and University of Nottingham, School of Life Sciences, United Kingdom (S.J.H.)
| | - Hongming Chen
- AstraZeneca, Discovery Sciences, Alderley Park, United Kingdom (J.D.H., S.S.); AstraZeneca, Oncology, Cambridge, United Kingdom (R.J.S.); AstraZeneca, Discovery Sciences, Mölndal, Sweden (H.C.); AstraZeneca, Discovery Sciences, Cambridge Science Park, United Kingdom (I.L.D., P.B.R.); AstraZeneca, Oncology, Alderley Park, United Kingdom (M.J.W.); Leiden Academic Centre for Drug Research, Division of Medicinal Chemistry, The Netherlands (D.G., W.K., A.P.I.J.); and University of Nottingham, School of Life Sciences, United Kingdom (S.J.H.)
| | - Wesley Keur
- AstraZeneca, Discovery Sciences, Alderley Park, United Kingdom (J.D.H., S.S.); AstraZeneca, Oncology, Cambridge, United Kingdom (R.J.S.); AstraZeneca, Discovery Sciences, Mölndal, Sweden (H.C.); AstraZeneca, Discovery Sciences, Cambridge Science Park, United Kingdom (I.L.D., P.B.R.); AstraZeneca, Oncology, Alderley Park, United Kingdom (M.J.W.); Leiden Academic Centre for Drug Research, Division of Medicinal Chemistry, The Netherlands (D.G., W.K., A.P.I.J.); and University of Nottingham, School of Life Sciences, United Kingdom (S.J.H.)
| | - Michael J Waring
- AstraZeneca, Discovery Sciences, Alderley Park, United Kingdom (J.D.H., S.S.); AstraZeneca, Oncology, Cambridge, United Kingdom (R.J.S.); AstraZeneca, Discovery Sciences, Mölndal, Sweden (H.C.); AstraZeneca, Discovery Sciences, Cambridge Science Park, United Kingdom (I.L.D., P.B.R.); AstraZeneca, Oncology, Alderley Park, United Kingdom (M.J.W.); Leiden Academic Centre for Drug Research, Division of Medicinal Chemistry, The Netherlands (D.G., W.K., A.P.I.J.); and University of Nottingham, School of Life Sciences, United Kingdom (S.J.H.)
| | - Adriaan P IJzerman
- AstraZeneca, Discovery Sciences, Alderley Park, United Kingdom (J.D.H., S.S.); AstraZeneca, Oncology, Cambridge, United Kingdom (R.J.S.); AstraZeneca, Discovery Sciences, Mölndal, Sweden (H.C.); AstraZeneca, Discovery Sciences, Cambridge Science Park, United Kingdom (I.L.D., P.B.R.); AstraZeneca, Oncology, Alderley Park, United Kingdom (M.J.W.); Leiden Academic Centre for Drug Research, Division of Medicinal Chemistry, The Netherlands (D.G., W.K., A.P.I.J.); and University of Nottingham, School of Life Sciences, United Kingdom (S.J.H.)
| | - Stephen J Hill
- AstraZeneca, Discovery Sciences, Alderley Park, United Kingdom (J.D.H., S.S.); AstraZeneca, Oncology, Cambridge, United Kingdom (R.J.S.); AstraZeneca, Discovery Sciences, Mölndal, Sweden (H.C.); AstraZeneca, Discovery Sciences, Cambridge Science Park, United Kingdom (I.L.D., P.B.R.); AstraZeneca, Oncology, Alderley Park, United Kingdom (M.J.W.); Leiden Academic Centre for Drug Research, Division of Medicinal Chemistry, The Netherlands (D.G., W.K., A.P.I.J.); and University of Nottingham, School of Life Sciences, United Kingdom (S.J.H.)
| | - Ian L Dale
- AstraZeneca, Discovery Sciences, Alderley Park, United Kingdom (J.D.H., S.S.); AstraZeneca, Oncology, Cambridge, United Kingdom (R.J.S.); AstraZeneca, Discovery Sciences, Mölndal, Sweden (H.C.); AstraZeneca, Discovery Sciences, Cambridge Science Park, United Kingdom (I.L.D., P.B.R.); AstraZeneca, Oncology, Alderley Park, United Kingdom (M.J.W.); Leiden Academic Centre for Drug Research, Division of Medicinal Chemistry, The Netherlands (D.G., W.K., A.P.I.J.); and University of Nottingham, School of Life Sciences, United Kingdom (S.J.H.)
| | - Philip B Rawlins
- AstraZeneca, Discovery Sciences, Alderley Park, United Kingdom (J.D.H., S.S.); AstraZeneca, Oncology, Cambridge, United Kingdom (R.J.S.); AstraZeneca, Discovery Sciences, Mölndal, Sweden (H.C.); AstraZeneca, Discovery Sciences, Cambridge Science Park, United Kingdom (I.L.D., P.B.R.); AstraZeneca, Oncology, Alderley Park, United Kingdom (M.J.W.); Leiden Academic Centre for Drug Research, Division of Medicinal Chemistry, The Netherlands (D.G., W.K., A.P.I.J.); and University of Nottingham, School of Life Sciences, United Kingdom (S.J.H.)
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10
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Jazayeri A, Andrews SP, Marshall FH. Structurally Enabled Discovery of Adenosine A 2A Receptor Antagonists. Chem Rev 2016; 117:21-37. [PMID: 27333206 DOI: 10.1021/acs.chemrev.6b00119] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Over the past decade there has been a revolution in the field of G protein-coupled receptor (GPCR) structural biology. Many years of innovative research from different areas have come together to fuel this significant change in the fortunes of this field, which for many years was characterized by the paucity of high-resolution structures. The determination to succeed has been in part due to the recognized importance of these proteins as drug targets, and although the pharmaceutical industry has been focusing on these receptors, it can be justifiably argued and demonstrated that many of the approved and commercially successful GPCR drugs can be significantly improved to increase efficacy and/or reduce undesired side effects. In addition, many validated targets in this class remain to be drugged. It is widely recognized that application of structure-based drug design approaches can help medicinal chemists a long way toward discovering better drugs. The achievement of structural biologists in providing high-resolution insight is beginning to transform drug discovery efforts, and there are a number of GPCR drugs that have been discovered by use of structural information that are in clinical development. This review aims to highlight the key developments that have brought success to GPCR structure resolution efforts and exemplify the practical application of structural information for the discovery of adenosine A2A receptor antagonists that have potential to treat multiple conditions.
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Affiliation(s)
- Ali Jazayeri
- Heptares Therapeutics Limited , BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, United Kingdom
| | - Stephen P Andrews
- Heptares Therapeutics Limited , BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, United Kingdom
| | - Fiona H Marshall
- Heptares Therapeutics Limited , BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, United Kingdom
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11
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Guo D, Heitman LH, IJzerman AP. Kinetic Aspects of the Interaction between Ligand and G Protein-Coupled Receptor: The Case of the Adenosine Receptors. Chem Rev 2016; 117:38-66. [DOI: 10.1021/acs.chemrev.6b00025] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Dong Guo
- Division of Medicinal Chemistry,
Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Laura H. Heitman
- Division of Medicinal Chemistry,
Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Adriaan P. IJzerman
- Division of Medicinal Chemistry,
Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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12
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Åstrand ABM, Lamm Bergström E, Zhang H, Börjesson L, Söderdahl T, Wingren C, Jansson AH, Smailagic A, Johansson C, Bladh H, Shamovsky I, Tunek A, Drmota T. The discovery of a selective and potent A2a agonist with extended lung retention. Pharmacol Res Perspect 2015; 3:e00134. [PMID: 26236482 PMCID: PMC4492750 DOI: 10.1002/prp2.134] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 02/19/2015] [Indexed: 11/07/2022] Open
Abstract
Although the anti-inflammatory role of the A2a receptor is well established, controversy remains with regard to the therapeutic value for A2a agonists in treatment of inflammatory lung diseases, also as a result of unwanted A2a-mediated cardiovascular effects. In this paper, we describe the discovery and characterization of a new, potent and selective A2a agonist (compound 2) with prolonged lung retention and limited systemic exposure following local administration. To support the lead optimization chemistry program with compound selection and profiling, multiple in vitro and in vivo assays were used, characterizing compound properties, pharmacodynamics (PD), and drug concentrations. Particularly, pharmacokinetic-PD modeling was applied to quantify the effects on the cardiovascular system, and an investigative toxicology study in rats was performed to explore potential myocardial toxicities. Compound 2, in comparison to a reference A2a agonist, UK-432,097, demonstrated higher solubility, lower lipophilicity, lower plasma protein binding, high rat lung retention (28% remaining after 24 h), and was efficacious in a lung inflammatory rat model following intratracheal dosing. Despite these properties, compound 2 did not provide a sufficient therapeutic index, that is, separation of local anti-inflammatory efficacy in the lung from systemic side effects in the cardiovascular system. The plasma concentration that resulted in induction of hypotension (half maximal effective concentration; EC50 0.5 nmol/L) correlated to the in vitro A2a potency (rIC50 0.6 nmol/L). Histopathological lesions in the heart were observed at a dose level which is threefold above the efficacious dose level in the inflammatory rat lung model. In conclusion, compound 2 is a highly potent and selective A2a agonist with significant lung retention after intratracheal administration. Despite its local anti-inflammatory efficacy in rat lung, small margins to the cardiovascular effects suggested limited therapeutic value of this compound for treatment of inflammatory lung disease by the inhaled route.
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Affiliation(s)
| | | | - Hui Zhang
- Drug Safety & Metabolism, AstraZeneca R&D MölndalSE-431 59, Mölndal, Sweden
| | - Lena Börjesson
- RIA iMed, AstraZeneca R&D MölndalSE-431 59, Mölndal, Sweden
| | - Therese Söderdahl
- Drug Safety & Metabolism, AstraZeneca R&D MölndalSE-431 59, Mölndal, Sweden
| | | | | | - Amir Smailagic
- RIA iMed, AstraZeneca R&D MölndalSE-431 59, Mölndal, Sweden
| | - Camilla Johansson
- Drug Safety & Metabolism, AstraZeneca R&D MölndalSE-431 59, Mölndal, Sweden
| | | | - Igor Shamovsky
- RIA iMed, AstraZeneca R&D MölndalSE-431 59, Mölndal, Sweden
| | - Anders Tunek
- RIA iMed, AstraZeneca R&D MölndalSE-431 59, Mölndal, Sweden
| | - Tomas Drmota
- RIA iMed, AstraZeneca R&D MölndalSE-431 59, Mölndal, Sweden
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13
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Preti D, Baraldi PG, Saponaro G, Romagnoli R, Aghazadeh Tabrizi M, Baraldi S, Cosconati S, Bruno A, Novellino E, Vincenzi F, Ravani A, Borea PA, Varani K. Design, synthesis, and biological evaluation of novel 2-((2-(4-(substituted)phenylpiperazin-1-yl)ethyl)amino)-5'-N-ethylcarboxamidoadenosines as potent and selective agonists of the A2A adenosine receptor. J Med Chem 2015; 58:3253-67. [PMID: 25780876 DOI: 10.1021/acs.jmedchem.5b00215] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Stimulation of A2A adenosine receptors (AR) promotes anti-inflammatory responses in animal models of allergic rhinitis, asthma, chronic obstructive pulmonary disease, and rheumatic diseases. Herein we describe the results of a research program aimed at identifying potent and selective agonists of the A2AAR as potential anti-inflammatory agents. The recent crystallographic analysis of A2AAR agonists and antagonists in complex with the receptor provided key information on the structural determinants leading to receptor activation or blocking. In light of this, we designed a new series of 2-((4-aryl(alkyl)piperazin-1-yl)alkylamino)-5'-N-ethylcarboxamidoadenosines with high A2AAR affinity, activation potency and selectivity obtained by merging distinctive structural elements of known agonists and antagonists of the investigated target. Docking-based SAR optimization allowed us to identify compound 42 as one of the most potent and selective A2A agonist discovered so far (Ki hA2AAR = 4.8 nM, EC50 hA2AAR = 4.9 nM, Ki hA1AR > 10 000 nM, Ki hA3AR = 1487 nM, EC50 hA2BAR > 10 000 nM).
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Affiliation(s)
- Delia Preti
- †Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Ferrara, Via Fossato di Mortara 17, 44121 Ferrara, Italy
| | - Pier Giovanni Baraldi
- †Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Ferrara, Via Fossato di Mortara 17, 44121 Ferrara, Italy
| | - Giulia Saponaro
- †Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Ferrara, Via Fossato di Mortara 17, 44121 Ferrara, Italy
| | - Romeo Romagnoli
- †Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Ferrara, Via Fossato di Mortara 17, 44121 Ferrara, Italy
| | - Mojgan Aghazadeh Tabrizi
- †Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Ferrara, Via Fossato di Mortara 17, 44121 Ferrara, Italy
| | - Stefania Baraldi
- †Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Ferrara, Via Fossato di Mortara 17, 44121 Ferrara, Italy
| | - Sandro Cosconati
- §DiSTABiF, Seconda Università di Napoli, Via Vivaldi 43, 81100 Caserta, Italy
| | - Agostino Bruno
- ∥Dipartimento di Farmacia, Università di Napoli "Federico II", Via D. Montesano 49, 80131 Napoli, Italy
| | - Ettore Novellino
- ∥Dipartimento di Farmacia, Università di Napoli "Federico II", Via D. Montesano 49, 80131 Napoli, Italy
| | - Fabrizio Vincenzi
- ‡Dipartimento di Scienze Mediche, Sezione di Farmacologia, Università degli Studi di Ferrara, Via Fossato di Mortara 17, 44121 Ferrara, Italy
| | - Annalisa Ravani
- ‡Dipartimento di Scienze Mediche, Sezione di Farmacologia, Università degli Studi di Ferrara, Via Fossato di Mortara 17, 44121 Ferrara, Italy
| | - Pier Andrea Borea
- ‡Dipartimento di Scienze Mediche, Sezione di Farmacologia, Università degli Studi di Ferrara, Via Fossato di Mortara 17, 44121 Ferrara, Italy
| | - Katia Varani
- ‡Dipartimento di Scienze Mediche, Sezione di Farmacologia, Università degli Studi di Ferrara, Via Fossato di Mortara 17, 44121 Ferrara, Italy
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14
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Rodríguez D, Gao ZG, Moss SM, Jacobson KA, Carlsson J. Molecular docking screening using agonist-bound GPCR structures: probing the A2A adenosine receptor. J Chem Inf Model 2015; 55:550-63. [PMID: 25625646 DOI: 10.1021/ci500639g] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Crystal structures of G protein-coupled receptors (GPCRs) have recently revealed the molecular basis of ligand binding and activation, which has provided exciting opportunities for structure-based drug design. The A2A adenosine receptor (A2AAR) is a promising therapeutic target for cardiovascular diseases, but progress in this area is limited by the lack of novel agonist scaffolds. We carried out docking screens of 6.7 million commercially available molecules against active-like conformations of the A2AAR to investigate whether these structures could guide the discovery of agonists. Nine out of the 20 predicted agonists were confirmed to be A2AAR ligands, but none of these activated the ARs. The difficulties in discovering AR agonists using structure-based methods originated from limited atomic-level understanding of the activation mechanism and a chemical bias toward antagonists in the screened library. In particular, the composition of the screened library was found to strongly reduce the likelihood of identifying AR agonists, which reflected the high ligand complexity required for receptor activation. Extension of this analysis to other pharmaceutically relevant GPCRs suggested that library screening may not be suitable for targets requiring a complex receptor-ligand interaction network. Our results provide specific directions for the future development of novel A2AAR agonists and general strategies for structure-based drug discovery.
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Affiliation(s)
- David Rodríguez
- †Science for Life Laboratory, Stockholm University, Box 1031, SE-171 21 Solna, Sweden.,‡Swedish e-Science Research Center (SeRC), SE-100 44 Stockholm, Sweden.,§Department of Biochemistry and Biophysics and Center for Biomembrane Research, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Zhang-Guo Gao
- ∥Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Steven M Moss
- ∥Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Kenneth A Jacobson
- ∥Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Jens Carlsson
- †Science for Life Laboratory, Stockholm University, Box 1031, SE-171 21 Solna, Sweden.,‡Swedish e-Science Research Center (SeRC), SE-100 44 Stockholm, Sweden.,§Department of Biochemistry and Biophysics and Center for Biomembrane Research, Stockholm University, SE-106 91 Stockholm, Sweden
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15
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Naranjo AN, Chevalier A, Cousins GD, Ayettey E, McCusker EC, Wenk C, Robinson AS. Conserved disulfide bond is not essential for the adenosine A2A receptor: Extracellular cysteines influence receptor distribution within the cell and ligand-binding recognition. BIOCHIMICA ET BIOPHYSICA ACTA 2015; 1848:603-14. [PMID: 25445670 PMCID: PMC4565196 DOI: 10.1016/j.bbamem.2014.11.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Revised: 10/22/2014] [Accepted: 11/10/2014] [Indexed: 11/16/2022]
Abstract
G protein-coupled receptors (GPCRs) are integral membrane proteins involved in cellular signaling and constitute major drug targets. Despite their importance, the relationship between structure and function of these receptors is not well understood. In this study, the role of extracellular disulfide bonds on the trafficking and ligand-binding activity of the human A2A adenosine receptor was examined. To this end, cysteine-to-alanine mutations were conducted to replace individual and both cysteines in three disulfide bonds present in the first two extracellular loops. Although none of the disulfide bonds were essential for the formation of plasma membrane-localized active GPCR, loss of the disulfide bonds led to changes in the distribution of the receptor within the cell and changes in the ligand-binding affinity. These results indicate that in contrast to many class A GPCRs, the extracellular disulfide bonds of the A2A receptor are not essential, but can modulate the ligand-binding activity, by either changing the conformation of the extracellular loops or perturbing the interactions of the transmembrane domains.
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Affiliation(s)
- Andrea N Naranjo
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, DE 19716, USA.
| | - Amy Chevalier
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, DE 19716, USA.
| | - Gregory D Cousins
- Department of Computer Science, Tulane University, 6823 St. Charles Ave, New Orleans, LA 70118, USA
| | - Esther Ayettey
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, DE 19716, USA
| | - Emily C McCusker
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, DE 19716, USA.
| | - Carola Wenk
- Department of Computer Science, Tulane University, 6823 St. Charles Ave, New Orleans, LA 70118, USA.
| | - Anne S Robinson
- Department of Chemical and Biomolecular Engineering, Tulane University, 300 Lindy Boggs Laboratory, 6823 St. Charles Ave, New Orleans, LA 70118, USA; Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, DE 19716, USA.
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16
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Rodríguez A, Guerrero A, Gutierrez-de-Terán H, Rodríguez D, Brea J, Loza MI, Rosell G, Pilar Bosch M. New selective A2A agonists and A3 antagonists for human adenosine receptors: synthesis, biological activity and molecular docking studies. MEDCHEMCOMM 2015. [DOI: 10.1039/c5md00086f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Synthesis and pharmacological characterization of a new series of adenosine derivatives on the four human adenosine receptors are reported.
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Affiliation(s)
- Anna Rodríguez
- Department of Biological Chemistry and Molecular Modelling
- IQAC (CSIC)
- 08034 Barcelona
- Spain
| | - Angel Guerrero
- Department of Biological Chemistry and Molecular Modelling
- IQAC (CSIC)
- 08034 Barcelona
- Spain
| | - Hugo Gutierrez-de-Terán
- Department of Cell and Molecular Biology
- Uppsala University
- Biomedical Center
- SE-751 24 Uppsala
- Sweden
| | - David Rodríguez
- Department of Biochemistry and Biophysics and Center for Biomembrane Research
- Stockholm University
- Sweden
| | - José Brea
- Biofarma Research Group, Center of Research in Molecular Medicine and Chronic Diseases (CIMUS)
- 15782 Santiago de Compostela
- Spain
| | - María I. Loza
- Biofarma Research Group, Center of Research in Molecular Medicine and Chronic Diseases (CIMUS)
- 15782 Santiago de Compostela
- Spain
| | - Gloria Rosell
- Department of Pharmacology and Medicinal Chemistry (Unit Associated to CSIC)
- Faculty of Pharmacy
- University of Barcelona
- 08028 Barcelona
- Spain
| | - M. Pilar Bosch
- Department of Biological Chemistry and Molecular Modelling
- IQAC (CSIC)
- 08034 Barcelona
- Spain
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17
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Yuan G, Gedeon NG, Jankins TC, Jones GB. Novel approaches for targeting the adenosine A2Areceptor. Expert Opin Drug Discov 2014; 10:63-80. [DOI: 10.1517/17460441.2015.971006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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18
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Keränen H, Gutiérrez-de-Terán H, Åqvist J. Structural and energetic effects of A2A adenosine receptor mutations on agonist and antagonist binding. PLoS One 2014; 9:e108492. [PMID: 25285959 PMCID: PMC4186821 DOI: 10.1371/journal.pone.0108492] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 09/01/2014] [Indexed: 11/18/2022] Open
Abstract
To predict structural and energetic effects of point mutations on ligand binding is of considerable interest in biochemistry and pharmacology. This is not only useful in connection with site-directed mutagenesis experiments, but could also allow interpretation and prediction of individual responses to drug treatment. For G-protein coupled receptors systematic mutagenesis has provided the major part of functional data as structural information until recently has been very limited. For the pharmacologically important A(2A) adenosine receptor, extensive site-directed mutagenesis data on agonist and antagonist binding is available and crystal structures of both types of complexes have been determined. Here, we employ a computational strategy, based on molecular dynamics free energy simulations, to rationalize and interpret available alanine-scanning experiments for both agonist and antagonist binding to this receptor. These computer simulations show excellent agreement with the experimental data and, most importantly, reveal the molecular details behind the observed effects which are often not immediately evident from the crystal structures. The work further provides a distinct validation of the computational strategy used to assess effects of point-mutations on ligand binding. It also highlights the importance of considering not only protein-ligand interactions but also those mediated by solvent water molecules, in ligand design projects.
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Affiliation(s)
- Henrik Keränen
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Uppsala, Sweden
| | - Hugo Gutiérrez-de-Terán
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Uppsala, Sweden
| | - Johan Åqvist
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Uppsala, Sweden
- * E-mail:
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19
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Moss SM, Jayasekara PS, Paoletta S, Gao ZG, Jacobson KA. Structure-Based Design of Reactive Nucleosides for Site-Specific Modification of the A2A Adenosine Receptor. ACS Med Chem Lett 2014; 5:1043-8. [PMID: 25221664 DOI: 10.1021/ml5002486] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 07/11/2014] [Indexed: 11/28/2022] Open
Abstract
Adenosine receptors (ARs) are members of the G protein-coupled receptor (GPCR) superfamily and have shown much promise as therapeutic targets. We have used an agonist-bound A2AAR X-ray crystallographic structure to design a chemically reactive agonist for site-specific chemical modification of the receptor. To further explore and chemically engineer its binding cavity, a 2-nitrophenyl active ester was attached through an elongated chain at adenine C2 position. This general structure was designed for irreversible transfer of a terminal acyl group to a nucleophilic amino group on the A2AAR. Preincubation with several O-acyl derivatives prevented radioligand binding that was not regenerated upon extensive washing. In silico receptor docking suggested two lysine residues (second extracellular loop) as potential target sites for an O-acetyl derivative (MRS5854, 3a), and site-directed mutagenesis indicated that K153 but not K150 is essential. Similarly, a butyl azide for click reaction was incorporated in the active ester moiety (3b). These promising results indicate a stable, covalent modification of the receptor by several reactive adenosine derivatives, which could be chemical tools for future imaging, structural probing, and drug discovery. Thus, structure-based ligand design has guided the site-specific modification of a GPCR.
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Affiliation(s)
- Steven M. Moss
- Molecular Recognition Section,
Laboratory of Bioorganic Chemistry, National Institute of Diabetes
and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0810, United States
| | - P. Suresh Jayasekara
- Molecular Recognition Section,
Laboratory of Bioorganic Chemistry, National Institute of Diabetes
and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0810, United States
| | - Silvia Paoletta
- Molecular Recognition Section,
Laboratory of Bioorganic Chemistry, National Institute of Diabetes
and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0810, United States
| | - Zhan-Guo Gao
- Molecular Recognition Section,
Laboratory of Bioorganic Chemistry, National Institute of Diabetes
and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0810, United States
| | - Kenneth A. Jacobson
- Molecular Recognition Section,
Laboratory of Bioorganic Chemistry, National Institute of Diabetes
and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0810, United States
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20
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Congreve M, Dias JM, Marshall FH. Structure-based drug design for G protein-coupled receptors. PROGRESS IN MEDICINAL CHEMISTRY 2014; 53:1-63. [PMID: 24418607 DOI: 10.1016/b978-0-444-63380-4.00001-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Our understanding of the structural biology of G protein-coupled receptors has undergone a transformation over the past 5 years. New protein-ligand complexes are described almost monthly in high profile journals. Appreciation of how small molecules and natural ligands bind to their receptors has the potential to impact enormously how medicinal chemists approach this major class of receptor targets. An outline of the key topics in this field and some recent examples of structure- and fragment-based drug design are described. A table is presented with example views of each G protein-coupled receptor for which there is a published X-ray structure, including interactions with small molecule antagonists, partial and full agonists. The possible implications of these new data for drug design are discussed.
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Affiliation(s)
- Miles Congreve
- Heptares Therapeutics Ltd, BioPark, Welwyn Garden City, Hertfordshire, United Kingdom
| | - João M Dias
- Heptares Therapeutics Ltd, BioPark, Welwyn Garden City, Hertfordshire, United Kingdom
| | - Fiona H Marshall
- Heptares Therapeutics Ltd, BioPark, Welwyn Garden City, Hertfordshire, United Kingdom
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21
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Leonis G, Avramopoulos A, Salmas RE, Durdagi S, Yurtsever M, Papadopoulos MG. Elucidation of Conformational States, Dynamics, and Mechanism of Binding in Human κ-Opioid Receptor Complexes. J Chem Inf Model 2014; 54:2294-308. [DOI: 10.1021/ci5002873] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Georgios Leonis
- Institute
of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens, Attiki 11635, Greece
| | - Aggelos Avramopoulos
- Institute
of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens, Attiki 11635, Greece
| | - Ramin Ekhteiari Salmas
- Department
of Chemistry, Istanbul Technical University, Istanbul, Istanbul 34469, Turkey
| | - Serdar Durdagi
- Department
of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Istanbul 34349, Turkey
| | - Mine Yurtsever
- Department
of Chemistry, Istanbul Technical University, Istanbul, Istanbul 34469, Turkey
| | - Manthos G. Papadopoulos
- Institute
of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens, Attiki 11635, Greece
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22
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Jacobson KA. Crystal structures of the A 2A adenosine receptor and their use in medicinal chemistry. In Silico Pharmacol 2013; 1:22. [PMID: 24660138 PMCID: PMC3956660 DOI: 10.1186/2193-9616-1-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
New insights into drug design are derived from the X-ray crystallographic structures of G protein-coupled receptors (GPCRs), and the adenosine receptors (ARs) are at the forefront of this effort. The 3D knowledge of receptor binding and activation promises to enable drug discovery for GPCRs in general, and specifically for the ARs. The predictability of modeling based on the X-ray structures of the A2AAR has been well demonstrated in the identification, design and modification of both known and novel AR agonists and antagonists. It is expected that structure-based design of drugs acting through ARs will provide new avenues to clinically useful agents.
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23
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Andrews SP, Brown GA, Christopher JA. Structure-Based and Fragment-Based GPCR Drug Discovery. ChemMedChem 2013; 9:256-75. [DOI: 10.1002/cmdc.201300382] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 11/15/2013] [Indexed: 01/05/2023]
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24
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Sheftel S, Muratore KE, Black M, Costanzi S. Graph analysis of β2 adrenergic receptor structures: a "social network" of GPCR residues. In Silico Pharmacol 2013; 1:16. [PMID: 25505660 PMCID: PMC4230308 DOI: 10.1186/2193-9616-1-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 11/25/2013] [Indexed: 02/07/2023] Open
Abstract
Purpose G protein-coupled receptors (GPCRs) are a superfamily of membrane proteins of vast pharmaceutical interest. Here, we describe a graph theory-based analysis of the structure of the β2 adrenergic receptor (β2 AR), a prototypical GPCR. In particular, we illustrate the network of direct and indirect interactions that link each amino acid residue to any other residue of the receptor. Methods Networks of interconnected amino acid residues in proteins are analogous to social networks of interconnected people. Hence, they can be studied through the same analysis tools typically employed to analyze social networks – or networks in general – to reveal patterns of connectivity, influential members, and dynamicity. We focused on the analysis of closeness-centrality, which is a measure of the overall connectivity distance of the member of a network to all other members. Results The residues endowed with the highest closeness-centrality are located in the middle of the seven transmembrane domains (TMs). In particular, they are mostly located in the middle of TM2, TM3, TM6 or TM7, while fewer of them are located in the middle of TM1, TM4 or TM5. At the cytosolic end of TM6, the centrality detected for the active structure is markedly lower than that detected for the corresponding residues in the inactive structures. Moreover, several residues acquire centrality when the structures are analyzed in the presence of ligands. Strikingly, there is little overlap between the residues that acquire centrality in the presence of the ligand in the blocker-bound structures and the agonist-bound structures. Conclusions Our results reflect the fact that the receptor resembles a bow tie, with a rather tight knot of closely interconnected residues and two ends that fan out in two opposite directions: one toward the extracellular space, which hosts the ligand binding cavity, and one toward the cytosol, which hosts the G protein binding cavity. Moreover, they underscore how interaction network is by the conformational rearrangements concomitant with the activation of the receptor and by the presence of agonists or blockers. Electronic supplementary material The online version of this article (doi:10.1186/2193-9616-1-16) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Samuel Sheftel
- Department of Chemistry, American University, 4400 Massachusetts Ave, Northwest, Washington, DC 20016 USA
| | - Kathryn E Muratore
- Department of Chemistry, American University, 4400 Massachusetts Ave, Northwest, Washington, DC 20016 USA
| | - Michael Black
- Department of Computer Science, American University, Northwest, Washington, DC 20016 USA
| | - Stefano Costanzi
- Department of Chemistry, American University, 4400 Massachusetts Ave, Northwest, Washington, DC 20016 USA ; Center for Behavioral Neuroscience, American University, Northwest, Washington, DC 20016 USA
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25
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Jacobson KA. Structure-based approaches to ligands for G-protein-coupled adenosine and P2Y receptors, from small molecules to nanoconjugates. J Med Chem 2013; 56:3749-67. [PMID: 23597047 PMCID: PMC3701956 DOI: 10.1021/jm400422s] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Adenosine receptor (ARs) and P2Y receptors (P2YRs) that respond to extracellular nucleosides/nucleotides are associated with new directions for therapeutics. The X-ray structures of the A2AAR complexes with agonists and antagonists are examined in relationship to the G-protein-coupled receptor (GPCR) superfamily and applied to drug discovery. Much of the data on AR ligand structure from early SAR studies now are explainable from the A2AAR X-ray crystallography. The ligand-receptor interactions in related GPCR complexes can be identified by means of modeling approaches, e.g., molecular docking. Thus, molecular recognition in binding and activation processes has been studied effectively using homology modeling and applied to ligand design. Virtual screening has yielded new nonnucleoside AR antagonists, and existing ligands have been improved with knowledge of the receptor interactions. New agonists are being explored for central nervous system and peripheral therapeutics based on in vivo activity, such as chronic neuropathic pain. Ligands for receptors more distantly related to the X-ray template, i.e., P2YRs, have been introduced and are mainly used as pharmacological tools for elucidating the physiological role of extracellular nucleotides. Other ligand tools for drug discovery include fluorescent probes, radioactive probes, multivalent probes, and functionalized nanoparticles.
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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, Maryland 20892, USA.
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26
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Weiss DR, Ahn S, Sassano MF, Kleist A, Zhu X, Strachan R, Roth BL, Lefkowitz RJ, Shoichet BK. Conformation guides molecular efficacy in docking screens of activated β-2 adrenergic G protein coupled receptor. ACS Chem Biol 2013; 8:1018-26. [PMID: 23485065 PMCID: PMC3658555 DOI: 10.1021/cb400103f] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
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A prospective,
large library virtual screen against an activated
β2-adrenergic receptor (β2AR) structure returned potent
agonists to the exclusion of inverse-agonists, providing the first
complement to the previous virtual screening campaigns against inverse-agonist-bound
G protein coupled receptor (GPCR) structures, which predicted only
inverse-agonists. In addition, two hits recapitulated the signaling
profile of the co-crystal ligand with respect to the G protein and
arrestin mediated signaling. This functional fidelity has important
implications in drug design, as the ability to predict ligands with
predefined signaling properties is highly desirable. However, the
agonist-bound state provides an uncertain template for modeling the
activated conformation of other GPCRs, as a dopamine D2 receptor (DRD2)
activated model templated on the activated β2AR structure returned
few hits of only marginal potency.
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Affiliation(s)
- Dahlia R. Weiss
- Department of Pharmaceutical
Chemistry, University of California San Francisco, San Francisco, California 94158-2550, United States
| | | | - Maria F. Sassano
- Department of Pharmacology
and
National Institute of Mental Health Psychoactive Drug Screening Program
School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | | | | | | | - Bryan L. Roth
- Department of Pharmacology
and
National Institute of Mental Health Psychoactive Drug Screening Program
School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | | | - Brian K. Shoichet
- Department of Pharmaceutical
Chemistry, University of California San Francisco, San Francisco, California 94158-2550, United States
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27
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Rosen H, Stevens RC, Hanson M, Roberts E, Oldstone MBA. Sphingosine-1-phosphate and its receptors: structure, signaling, and influence. Annu Rev Biochem 2013; 82:637-62. [PMID: 23527695 DOI: 10.1146/annurev-biochem-062411-130916] [Citation(s) in RCA: 167] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The sphingosine-1-phosphate (S1P) receptor signaling system has biological and medical importance and is the first lipid G protein-coupled receptor (GPCR) structure to be solved to 2.8-Å resolution. S1P binds to five high-affinity GPCRs generating multiple downstream signals that play essential roles in vascular development and endothelial integrity, control of cardiac rhythm, and routine oral treatment of multiple sclerosis. Genetics, chemistry, and now structural biology have advanced this integrated biochemical system. The S1P receptors have a novel N-terminal fold that occludes access to the binding pocket from the extracellular environment as well as orthosteric and bitopic ligands with very different physicochemical properties. S1P receptors and metabolizing enzymes have been deleted, inducibly deleted, and knocked in as tagged or altered receptors in mice. An array of genetic models allows analysis of integrated receptor function in vivo. We can now directly understand causal relationships among protein expression, signal, and control points in physiology and pathology.
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Affiliation(s)
- Hugh Rosen
- Department of Chemical Physiology and Immunology, The Scripps Research Institute, La Jolla, California 92037, USA.
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28
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Abstract
The adenosine receptors (ARs) provide an example of how to accurately predict ligand recognition, even prior to the availability of a crystallographic structure. Homology modeling has been used to gain structural insight, in conjunction with site-directed mutagenesis, and structure-activity relationships of small molecular ligands. Recent X-ray structures greatly improved the accuracy of knowledge of AR ligand recognition and furthermore characterized conformational changes induced by receptor activation. Now, homology modeling extends these structural insights to related GPCRs and suggests new ligand structures. This strategy is also being applied to the eight subtypes of P2Y receptors for extracellular nucleotides, which lack X-ray structures and are best modeled by homology to the CXCR4 (peptide) receptor. Neoceptors, as studied for three of the four AR subtypes, create a molecular complementarity between a mutant receptor and a chemically tailored agonist ligand to selectively enhance affinity, implying direct physical contact and thus validating docking hypotheses.
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Affiliation(s)
- Kenneth A Jacobson
- Laboratory of Biological Modeling, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA.
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29
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Andrews SP, Tehan B. Stabilised G protein-coupled receptors in structure-based drug design: a case study with adenosine A2A receptor. MEDCHEMCOMM 2013. [DOI: 10.1039/c2md20164j] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The first example of structure-based drug design with stabilised GPCRs has enabled the identification of a preclinical candidate for the treatment of Parkinson's disease.
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Affiliation(s)
| | - Benjamin Tehan
- Heptares Therapeutics Limited
- BioPark
- Welwyn Garden City
- UK
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30
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The GPCR Network: a large-scale collaboration to determine human GPCR structure and function. Nat Rev Drug Discov 2012; 12:25-34. [PMID: 23237917 DOI: 10.1038/nrd3859] [Citation(s) in RCA: 229] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
G protein-coupled receptors (GPCRs) are targeted by ∼30-40% of marketed drugs, and their key roles in normal physiology and in disease demonstrate that an understanding of their structure and function is valuable to researchers in both basic science and drug discovery. However, until recently, detailed structural information on this protein family was limited by challenges in X-ray crystallographic analysis of such membrane proteins. The GPCR Network was created in 2010 with the goal of structurally characterizing 15-25 representative human GPCRs within 5 years, based on an active outreach programme addressing an interdisciplinary community of scientists interested in GPCR structure, chemistry and biology. Here, we provide an overview of how this collaborative effort has enabled the structural determination and characterization of eight human GPCRs so far, and discuss some of the challenges that remain in gaining more detailed insights into structure-function relationships in this receptor superfamily.
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31
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Liu W, Chun E, Thompson AA, Chubukov P, Xu F, Katritch V, Han GW, Roth CB, Heitman LH, IJzerman AP, Cherezov V, Stevens RC. Structural basis for allosteric regulation of GPCRs by sodium ions. Science 2012; 337:232-6. [PMID: 22798613 DOI: 10.1126/science.1219218] [Citation(s) in RCA: 746] [Impact Index Per Article: 62.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Pharmacological responses of G protein-coupled receptors (GPCRs) can be fine-tuned by allosteric modulators. Structural studies of such effects have been limited due to the medium resolution of GPCR structures. We reengineered the human A(2A) adenosine receptor by replacing its third intracellular loop with apocytochrome b(562)RIL and solved the structure at 1.8 angstrom resolution. The high-resolution structure allowed us to identify 57 ordered water molecules inside the receptor comprising three major clusters. The central cluster harbors a putative sodium ion bound to the highly conserved aspartate residue Asp(2.50). Additionally, two cholesterols stabilize the conformation of helix VI, and one of 23 ordered lipids intercalates inside the ligand-binding pocket. These high-resolution details shed light on the potential role of structured water molecules, sodium ions, and lipids/cholesterol in GPCR stabilization and function.
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Affiliation(s)
- Wei Liu
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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32
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Jacobson KA, Costanzi S. New insights for drug design from the X-ray crystallographic structures of G-protein-coupled receptors. Mol Pharmacol 2012; 82:361-71. [PMID: 22695719 DOI: 10.1124/mol.112.079335] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Methodological advances in X-ray crystallography have made possible the recent solution of X-ray structures of pharmaceutically important G protein-coupled receptors (GPCRs), including receptors for biogenic amines, peptides, a nucleoside, and a sphingolipid. These high-resolution structures have greatly increased our understanding of ligand recognition and receptor activation. Conformational changes associated with activation common to several receptors entail outward movements of the intracellular side of transmembrane helix 6 (TM6) and movements of TM5 toward TM6. Movements associated with specific agonists or receptors have also been described [e.g., extracellular loop (EL) 3 in the A(2A) adenosine receptor]. The binding sites of different receptors partly overlap but differ significantly in ligand orientation, depth, and breadth of contact areas in TM regions and the involvement of the ELs. A current challenge is how to use this structural information for the rational design of novel potent and selective ligands. For example, new chemotypes were discovered as antagonists of various GPCRs by subjecting chemical libraries to in silico docking in the X-ray structures. The vast majority of GPCR structures and their ligand complexes are still unsolved, and no structures are known outside of family A GPCRs. Molecular modeling, informed by supporting information from site-directed mutagenesis and structure-activity relationships, has been validated as a useful tool to extend structural insights to related GPCRs and to analyze docking of other ligands in already crystallized GPCRs.
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Affiliation(s)
- Kenneth A Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0810, USA.
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33
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Tosh DK, Deflorian F, Phan K, Gao ZG, Wan TC, Gizewski E, Auchampach JA, Jacobson KA. Structure-guided design of A(3) adenosine receptor-selective nucleosides: combination of 2-arylethynyl and bicyclo[3.1.0]hexane substitutions. J Med Chem 2012; 55:4847-60. [PMID: 22559880 PMCID: PMC3371665 DOI: 10.1021/jm300396n] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
(N)-Methanocarba adenosine 5'-methyluronamides containing known A(3) AR (adenosine receptor)-enhancing modifications, i.e., 2-(arylethynyl)adenine and N(6)-methyl or N(6)-(3-substituted-benzyl), were nanomolar full agonists of human (h) A(3)AR and highly selective (K(i) ∼0.6 nM, N(6)-methyl 2-(halophenylethynyl) analogues 13 and 14). Combined 2-arylethynyl-N(6)-3-chlorobenzyl substitutions preserved A(3)AR affinity/selectivity in the (N)-methanocarba series (e.g., 3,4-difluoro full agonist MRS5698 31, K(i) 3 nM, human and mouse A(3)) better than that for ribosides. Polyaromatic 2-ethynyl N(6)-3-chlorobenzyl analogues, such as potent linearly extended 2-p-biphenylethynyl MRS5679 34 (K(i) hA(3) 3.1 nM; A(1), A(2A), inactive) and fluorescent 1-pyrene adduct MRS5704 35 (K(i) hA(3) 68.3 nM), were conformationally rigid; receptor docking identified a large, mainly hydrophobic binding region. The vicinity of receptor-bound C2 groups was probed by homology modeling based on recent X-ray structure of an agonist-bound A(2A)AR, with a predicted helical rearrangement requiring an agonist-specific outward displacement of TM2 resembling opsin. Thus, the X-ray structure of related A(2A)AR is useful in guiding the design of new A(3)AR agonists.
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Affiliation(s)
- Dilip K. Tosh
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - Francesca Deflorian
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - Khai Phan
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - Zhan-Guo Gao
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - Tina C. Wan
- Department of Pharmacology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226
| | - Elizabeth Gizewski
- Department of Pharmacology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226
| | - John A. Auchampach
- Department of Pharmacology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226
| | - Kenneth A. Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
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34
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Tosh DK, Phan K, Gao ZG, Gakh AA, Xu F, Deflorian F, Abagyan R, Stevens RC, Jacobson KA, Katritch V. Optimization of adenosine 5'-carboxamide derivatives as adenosine receptor agonists using structure-based ligand design and fragment screening. J Med Chem 2012; 55:4297-308. [PMID: 22486652 PMCID: PMC3479662 DOI: 10.1021/jm300095s] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Structures of G protein-coupled receptors (GPCRs) have a proven utility in the discovery of new antagonists and inverse agonists modulating signaling of this important family of clinical targets. Applicability of active-state GPCR structures to virtual screening and rational optimization of agonists, however, remains to be assessed. In this study of adenosine 5' derivatives, we evaluated the performance of an agonist-bound A(2A) adenosine receptor (AR) structure in retrieval of known agonists and then employed the structure to screen for new fragments optimally fitting the corresponding subpocket. Biochemical and functional assays demonstrate high affinity of new derivatives that include polar heterocycles. The binding models also explain modest selectivity gain for some substituents toward the closely related A(1)AR subtype and the modified agonist efficacy of some of these ligands. The study suggests further applicability of in silico fragment screening to rational lead optimization in GPCRs.
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Affiliation(s)
- Dilip K. Tosh
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Khai Phan
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Zhan-Guo Gao
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Andrei A. Gakh
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Fei Xu
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Francesca Deflorian
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Ruben Abagyan
- University of California, San Diego Skaggs School of Pharmacy and Pharmaceutical Sciences, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Raymond C. Stevens
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Kenneth A. Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Vsevolod Katritch
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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