Generic placeholder image

Current Pharmaceutical Design

Editor-in-Chief

ISSN (Print): 1381-6128
ISSN (Online): 1873-4286

Review Article

Recent Advances in the In-silico Structure-based and Ligand-based Approaches for the Design and Discovery of Agonists and Antagonists of A2A Adenosine Receptor

Author(s): Nikhil Agrawal*, Balakumar Chandrasekaran and Amal Al-Aboudi

Volume 25, Issue 7, 2019

Page: [774 - 782] Pages: 9

DOI: 10.2174/1381612825666190306162006

Price: $65

Abstract

A2A receptor belongs to the family of GPCRs, which are the most abundant membrane protein family. Studies in the last few decades have shown the therapeutic applications of A2A receptor in various diseases. In the present mini-review, we have discussed the recent progress in the in-silico studies of the A2A receptor. Herein, we described the different structures of A2A receptor, the discovery of new agonists and antagonists using virtualscreening/ docking, pharmacophore modeling, and QSAR based pharmacophore modeling. We have also discussed various molecular dynamics (MD) simulations studies of A2A receptor in complex with ligands.

Keywords: A2A receptor, GPCR, virtual screening, pharmacophore modeling, MD simulations, in-silico.

[1]
Sheth S, Brito R, Mukherjea D, Rybak LP, Ramkumar V. Adenosine receptors: expression, function and regulation. Int J Mol Sci 2014; 15(2): 2024-52.
[2]
Dal Ben D, Lambertucci C, Vittori S, Volpini R, Cristalli G. GPCRs as therapeutic targets: a view on adenosine receptors structure and functions, and molecular modeling support. J Iran Chem Soc 2005; 2: 176-88.
[3]
Fredholm BB, IJzerman AP, Jacobson KA, Klotz K-N, Linden J. International Union of Pharmacology. XXV. Nomenclature and classification of adenosine receptors. Pharmacol Rev 2001; 53: 527-52.
[4]
Valls MD, Cronstein BN, Montesinos MC. Adenosine receptor agonists for promotion of dermal wound healing. Biochem Pharmacol 2009; 77: 1117-24.
[5]
Morelli M, Carta AR, Jenner P. Adenosine A 2A receptors and Parkinson’s disease.In: ed. Adenosine receptors in health and disease. Springer 2009; pp. 589-615
[6]
Gessi S, Bencivenni S, Battistello E, et al. Inhibition of A2A Adenosine Receptor Signaling in Cancer Cells Proliferation by the Novel Antagonist TP455. Front Pharmacol 2017; 8: 888.
[7]
Field JJ, Nathan DG, Linden J. The role of adenosine signaling in sickle cell therapeutics. Hematol Oncol Clin North Am 2014; 28: 287-99.
[8]
Haskó G, Pacher P. A2A receptors in inflammation and injury: lessons learned from transgenic animals. J Leukoc Biol 2008; 83: 447-55.
[9]
de Lera Ruiz M, Lim Y-H, Zheng J. Adenosine A2A receptor as a drug discovery target. J Med Chem 2013; 57: 3623-50.
[10]
Kishore DP, Balakumar C, Rao AR, Roy PP, Roy K. QSAR of adenosine receptor antagonists: exploring physicochemical requirements for binding of pyrazolo [4, 3-e]-1, 2, 4-triazolo [1, 5-c] pyrimidine derivatives with human adenosine A 3 receptor subtype. Bioorg Med Chem Lett 2011; 21: 818-23.
[11]
Balakumar C, Kishore DP, Rao KV, et al. Design, microwave-assisted synthesis and in silico docking studies of new 4H-pyrimido [2, 1-b] benzothiazole-2-arylamino-3-cyano-4-ones as possible adenosine A2B receptor antagonists. Indian J Chem Sect B 2012; 51B(48): 1105-13.
[12]
Banda V, Chandrasekaran B, Köse M, et al. Synthesis of Novel Pyrido [3, 2‐e][1, 2, 4] triazolo [1, 5‐c] pyrimidine Derivatives: Potent and Selective Adenosine A3 Receptor Antagonists. Arch Pharm 2013; 346: 699-707.
[13]
Lebon G, Warne T, Edwards PC, et al. Agonist-bound adenosine A 2A receptor structures reveal common features of GPCR activation. Nature 2011; 474: 521.
[14]
Xu F, Wu H, Katritch V, et al. Structure of an agonist-bound human A2A adenosine receptor. Science 2011; 332: 322-7.
[15]
Doré AS, Robertson N, Errey JC, et al. Structure of the adenosine A2A receptor in complex with ZM241385 and the xanthines XAC and caffeine. Structure 2011; 19: 1283-93.
[16]
Lebon G, Edwards PC, Leslie AG, Tate CG. Molecular determinants of CGS21680 binding to the human adenosine A2A receptor. Mol Pharmacol 2015; 87(6): 907-15.
[17]
Jaakola V-P, Griffith MT, Hanson MA, et al. The 2.6 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonist. Science 2008; 322: 1211-7.
[18]
Sun B, Bachhawat P, Chu ML-H, et al. Crystal structure of the adenosine A2A receptor bound to an antagonist reveals a potential allosteric pocket. Proc Natl Acad Sci USA 2017; 114(8): 2066-71.
[19]
Piirainen H, Ashok Y, Nanekar RT, Jaakola V-P. Structural features of adenosine receptors: from crystal to function. Biochim Biophys Acta Biomembr 2011; 1808: 1233-44.
[20]
Thal DM, Vuckovic Z, Draper-Joyce CJ, et al. Recent advances in the determination of G protein-coupled receptor structures. Curr Opin Struct Biol 2018; 51: 28-34.
[21]
Bill RM, Henderson PJ, Iwata S, et al. Overcoming barriers to membrane protein structure determination. Nat Biotechnol 2011; 29: 335.
[22]
Rucktooa P, Cheng RK, Segala E, et al. Towards high throughput GPCR crystallography: in meso soaking of adenosine A 2A Receptor crystals. Sci Rep 2018; 8: 41.
[23]
Weinert T, Olieric N, Cheng R, et al. Serial millisecond crystallography for routine room-temperature structure determination at synchrotrons. Nat Commun 2017; 8: 542.
[24]
Carpenter B, Nehmé R, Warne T, Leslie AG, Tate CG. Structure of the adenosine A 2A receptor bound to an engineered G protein. Nature 2016; 536: 104.
[25]
Hino T, Arakawa T, Iwanari H, et al. G-protein-coupled receptor inactivation by an allosteric inverse-agonist antibody. Nature 2012; 482: 237.
[26]
García-Nafría J, Lee Y, Bai X, Carpenter B, Tate CG. Cryo-EM structure of the adenosine A2A receptor coupled to an engineered heterotrimeric G protein. eLife 2018; 7e35946
[27]
Eddy MT, Lee M-Y, Gao Z-G, et al. Allosteric coupling of drug binding and intracellular signaling in the A2A adenosine receptor. Cell 2018; 172: 68-80.e12.
[28]
Batyuk A, Galli L, Ishchenko A, et al. Native phasing of x-ray free-electron laser data for a G protein–coupled receptor. Sci Adv 2016; 2e1600292
[29]
Cheng RK, Segala E, Robertson N, et al. Structures of human A1 and A2A adenosine receptors with xanthines reveal determinants of selectivity. Structure 2017; 25: 1275-85.e4.
[30]
White KL, Eddy MT, Gao Z-G, et al. Structural Connection between Activation Microswitch and Allosteric Sodium Site in GPCR Signaling. Structure 2018; 26: 259-69.e5.
[31]
Jacobson KA, Gao Z-G. Adenosine receptors as therapeutic targets. Nat Rev Drug Discov 2006; 5: 247.
[32]
Chandrasekaran B, Agrawal N, Kaushik S. Pharmacophore Development.In: Ranganathan S, Gribskov M, Nakai K, Schönbach C, ed.Encyclopedia of Bioinformatics and Computational Biology. Academic Press Oxford 2019; pp. 677-87.
[33]
Kalva S, Vinod D, Saleena LM. Combined structure-and ligand-based pharmacophore modeling and molecular dynamics simulation studies to identify selective inhibitors of MMP-8. J Mol Model 2014; 20: 2191.
[34]
Kalva S, Vadivelan S, Sanam R, Jagarlapudi SA, Saleena LM. Lead identification and optimization of novel collagenase inhibitors; pharmacophore and structure based studies. Bioinformation 2012; 8: 301.
[35]
Kalva S, Saranyah K, Suganya PR, Nisha M, Saleena LM. Potent inhibitors precise to S1′ loop of MMP-13, a crucial target for osteoarthritis. J Mol Graph Model 2013; 44: 297-310.
[36]
Xu Z, Cheng F, Da C, Liu G, Tang Y. Pharmacophore modeling of human adenosine receptor A 2A antagonists. J Mol Model 2010; 16: 1867-76.
[37]
Wei J, Wang S, Gao S, Dai X, Gao Q. 3D-pharmacophore models for selective A2A and A2B adenosine receptor antagonists. J Chem Inf Model 2007; 47: 613-25.
[38]
Khanfar MA, Al-Qtaishat S, Habash M, Taha MO. Discovery of potent adenosine A2a antagonists as potential anti-Parkinson disease agents. Non-linear QSAR analyses integrated with pharmacophore modeling. Chem Biol Interact 2016; 254: 93-101.
[39]
Bacilieri M, Ciancetta A, Paoletta S, et al. Revisiting a receptor-based pharmacophore hypothesis for human A2a adenosine receptor antagonists. J Chem Inf Model 2013; 53: 1620-37.
[40]
Mantri M, de Graaf O, van Veldhoven J, et al. 2-Amino-6-furan-2-yl-4-substituted nicotinonitriles as A2A adenosine receptor antagonists. J Med Chem 2008; 51: 4449-55.
[41]
Chen JB, Liu EM, Chern TR, et al. Design and Synthesis of Novel Dual‐Action Compounds Targeting the Adenosine A2A Receptor and Adenosine Transporter for Neuroprotection. ChemMedChem 2011; 6: 1390-400.
[42]
Shoichet BK. Virtual screening of chemical libraries. Nature 2004; 432: 862.
[43]
Lionta E, Spyrou GK, Vassilatis D, Cournia Z. Structure-based virtual screening for drug discovery: principles, applications and recent advances. Curr Top Med Chem 2014; 14: 1923-38.
[44]
Taddese B, Simpson LM, Wall ID, Blaney FE, Reynolds CA. Modeling active GPCR conformations. In: ed. Methods in enzymology. Elsevier, 2013; pp. 21-35.
[45]
Shaik K, Deb PK, Mailavaram RP, et al. 7-Amino-2-aryl/heteroaryl-5-oxo-5,8-dihydro [1,2,4]triazolo [1,5-a]pyridine-6-carbonitriles: Synthesis and Adenosine Receptor Binding Studies. Chem Biol Drug Des 2019.
[http://dx.doi.org/10.1111/cbdd.13528]
[46]
Langmead CJ, Andrews SP, Congreve M, et al. Identification of novel adenosine A2A receptor antagonists by virtual screening. J Med Chem 2012; 55: 1904-9.
[47]
Congreve M, Andrews SP, Doré AS, et al. Discovery of 1, 2, 4-triazine derivatives as adenosine A2A antagonists using structure based drug design. J Med Chem 2012; 55: 1898-903.
[48]
Wei J, Qu W, Ye Y, Gao Q. 3D pharmacophore based virtual screening of A2A adenosine receptor antagonists. Protein Pept Lett 2010; 17: 332-9.
[49]
Katritch V, Jaakola V-P, Lane JR, et al. Structure-based discovery of novel chemotypes for adenosine A2A receptor antagonists. J Med Chem 2010; 53: 1799-809.
[50]
Lagarias P, Vrontaki E, Lambrinidis G, et al. Discovery of Novel Adenosine Receptor Antagonists through a Combined Structure-and Ligand-Based Approach Followed by Molecular Dynamics Investigation of Ligand Binding Mode. J Chem Inf Model 2018; 58: 794-815.
[51]
Carlsson J, Yoo L, Gao Z-G, Irwin JJ, Shoichet BK, Jacobson KA. Structure-based discovery of A2A adenosine receptor ligands. J Med Chem 2010; 53: 3748-55.
[52]
Chen D, Ranganathan A, IJzerman AP, Siegal G, Carlsson J. Complementarity between in silico and biophysical screening approaches in fragment-based lead discovery against the A2A adenosine receptor. J Chem Inf Model 2013; 53: 2701-14.
[53]
Rodríguez D, Gao Z-G, 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.
[54]
Deb PK, Mailavaram R, Chandrasekaran B, et al. Synthesis, adenosine receptor binding and molecular modelling studies of novel thieno [2, 3‐d] pyrimidine derivatives. Chem Biol Drug Des 2018; 91: 962-9.
[55]
Agrawal N, Skelton AA. 12-crown-4 ether disrupts the patient brain-derived amyloid-β-fibril trimer: Insight from all-atom molecular dynamics simulations. ACS Chem Neurosci 2016; 7: 1433-41.
[56]
Agrawal N, Skelton AA. Binding of 12-crown-4 with Alzheimer’s Aβ40 and Aβ42 monomers and its effect on their conformation: insight from molecular dynamics simulations. Mol Pharm 2017; 15: 289-99.
[57]
Tewatia P, Agrawal N, Gaur M, Sahi S. Insights into the conformational perturbations of novel agonists with β3-adrenergic receptor using molecular dynamics simulations. Biochimie 2014; 101: 168-82.
[58]
Kalva S, Agrawal N, Skelton AA, Saleena LM. Identification of novel selective MMP-9 inhibitors as potential anti-metastatic lead using structure-based hierarchical virtual screening and molecular dynamics simulation. Mol Biosyst 2016; 12: 2519-31.
[59]
Al-Qattan MN, Deb PK, Tekade RK. Molecular dynamics simulation strategies for designing carbon-nanotube-based targeted drug delivery. Drug Discov Today 2018; 23: 235-50.
[60]
Omolo CA, Kalhapure RS, Agrawal N, Rambharose S, Mocktar C, Govender T. Formulation and Molecular Dynamics Simulations of a Fusidic Acid Nanosuspension for Simultaneously Enhancing Solubility and Antibacterial Activity. Mol Pharm 2018; 15: 3512-26.
[61]
Omolo CA, Kalhapure RS, Agrawal N, et al. A hybrid of mPEG-b-PCL and G1-PEA dendrimer for enhancing delivery of antibiotics. J Control Release 2018; 290: 112-28.
[62]
Ng HW, Laughton CA, Doughty SW. Molecular dynamics simulations of the adenosine A2a receptor: structural stability, sampling, and convergence. J Chem Inf Model 2013; 53: 1168-78.
[63]
Pang X, Yang M, Han K. Antagonist binding and induced conformational dynamics of GPCR A2A adenosine receptor. Proteins 2013; 81: 1399-410.
[64]
Guo D, Pan AC, Dror RO, et al. Molecular basis of ligand dissociation from the adenosine A2A receptor. Mol Pharmacol 2016; 89(5): 485-91.
[65]
Cao R, Giorgetti A, Bauer A, Neumaier B, Rossetti G, Carloni P. Role of Extracellular Loops and Membrane Lipids for Ligand Recognition in the Neuronal Adenosine Receptor Type 2A: An Enhanced Sampling Simulation Study. Molecules 2018; 23: 2616.
[66]
Cao R, Rossetti G, Bauer A. CarIoni P. Binding of the Antagonist Caffeine to the Human Adenosine Receptor hA2AR in Nearly Physiological Conditions. PLoS One 2015; 10e0126833
[67]
Liu Y, Burger SK, Ayers PW, Vöhringer-Martinez E. Computational study of the binding modes of caffeine to the adenosine A2A receptor. J Phys Chem B 2011; 115: 13880-90.
[68]
Lee JY, Lyman E. Agonist dynamics and conformational selection during microsecond simulations of the A2A adenosine receptor. Biophys J 2012; 102: 2114-20.
[69]
Sabbadin D, Ciancetta A, Deganutti G, Cuzzolin A, Moro S. Exploring the recognition pathway at the human A 2A adenosine receptor of the endogenous agonist adenosine using supervised molecular dynamics simulations. MedChemComm 2015; 6: 1081-5.
[70]
Guixà-González R, Albasanz JL, Rodriguez-Espigares I, et al. Membrane cholesterol access into a G-protein-coupled receptor. Nat Commun 2017; 8: 14505.
[71]
Rouviere E, Arnarez C, Yang L, Lyman E. Identification of Two New Cholesterol Interaction Sites on the A 2A Adenosine Receptor. Biophys J 2017; 113: 2415-24.
[72]
Lee JY, Lyman E. Predictions for cholesterol interaction sites on the A2A adenosine receptor. J Am Chem Soc 2012; 134: 16512-5.

Rights & Permissions Print Cite
© 2024 Bentham Science Publishers | Privacy Policy