Abstract
The design of beta2 adrenoceptor (β2AR) agonists is attractive because of their wide-ranging applications in medicine, and the details of agonist interactions with β2AR are interesting because it is considered a prototype for G-protein coupled receptors. Preclinical studies for agonist development have involved biological assays with guinea pigs due to a similar physiology to humans. Boron-containing Albuterol derivatives (BCADs) designed as bronchodilators have improved potency and efficacy compared with their boron-free precursor on guinea pig β2ARs (gpβ2ARs), and two of the BCADs (BR-AEA and boronterol) conserve these features on cells expressing human β2ARs (hβ2ARs). The aim of this study was to test the BCAD Politerol on gpβ2ARs and hβ2ARs in vitro and in silico. Politerol displayed higher potency and efficacy on gpβ2AR than on hβ2AR in experimental assays, possible explanations are provided based on molecular modeling, and molecular dynamics simulations of about 0.25 µs were performed for the free and bound states adding up to 2 µs in total. There were slight differences, particularly in the role of the boron atom, in the interactions of Politerol with gpβ2ARs and hβ2ARs, affecting movements of transmembrane domains 5–7, known to be pivotal in receptor activation. These findings could be instrumental in the design of compounds selective for hβ2ARs.
Similar content being viewed by others
References
Amezcua-Gutiérrez MA, Ciprés-Flores FJ, Trujillo-Ferrara JG, Soriano-Ursúa MA (2012) Clinical implications of recent insights into the structural biology of beta2 adrenoceptors. Curr Drug Targets 13:1336–1346. https://doi.org/10.2174/138945012802429741
Bai Q, Shao Y, Pan D, Zhang Y, Liu H, Yao X (2014) Search for β2 adrenergic receptor ligands by virtual screening via grid computing and investigation of binding modes by docking and molecular dynamics simulations. PLoS One 9(9):e107837. https://doi.org/10.1371/journal.pone.0107837
Bello M, Campos-Rodriguez R, Rojas-Hernandez S, Contis-Montes de Oca A, Correa-Basurto J (2015) Predicting peptide vaccine candidates against H1N1 influenza virus through theoretical approaches. Immunol Res 62(1):3–15. https://doi.org/10.1007/s12026-015-8629-1
Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81:3684–3690. https://doi.org/10.1063/1.448118
Berendsen HJC, van der Spoel D, van Drunen R (1995) GROMACS. A message-passing parallel molecular dynamics implementation. Comput Phys Commun 91:43–56
Canning BJ, Chou Y (2008) Using guinea pigs in studies relevant to asthma and COPD. Pulm Pharmacol Ther 21:702–720. https://doi.org/10.1016/j.pupt.2008.01.004
Canning BJ, Wright JL (2008) Animal models of asthma and chronic obstructive pulmonary disease. Pulm Pharmacol Ther 21:695. https://doi.org/10.1016/j.pupt.2008.04.007
Case DA, Cheatham TE, Darden T, Gohlke H, Luo R, Merz KM, Onufriev A, Simmerling C, Wang B, Woods RJ (2005) The Amber biomolecular simulation programs. J Comput Chem 26:1668–1688. https://doi.org/10.1002/jcc.20290
Cazzola M, Matera MG (2014) Bronchodilators: current and future. Clin Chest Med 35:191–201. https://doi.org/10.1016/j.ccm.2013.10.005
Chan HC, Filipek S, Yuan S (2016) The principles of ligand specificity on beta-2-adrenergic receptor. Sci Rep 6:34736. https://doi.org/10.1038/srep34736
Chen VB, Arendall WB III, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D 66:12–21. https://doi.org/10.1107/S0907444909042073
Darden T, York D, Pedersen L (1993) Particle Mesh Ewald-an N.Log(N) method for Ewald sums in large systems. J Chem Phys 98:10089–10092. https://doi.org/10.1063/1.464397
DeLano WL (2002) The PyMOL molecular graphics system. DeLano Scientific, San Carlos, CA. http://www.pymol.org
DeVree BT, Mahoney JP, Vélez-Ruiz GA, Rasmussen SG, Kuszak AJ, Edwald E, Fung JJ, Manglik A, Masureel M, Du Y, Matt RA, Pardon E, Steyaert J, Kobilka BK, Sunahara RK (2016) Allosteric coupling from G protein to the agonist-binding pocket in GPCRs. Nature 535(7610):182–186. https://doi.org/10.1038/nature18324
Dickson CJ, Hornak V, Velez-Vega C, McKay DJ, Reilly J, Sandham DA, Shaw D, Fairhurst RA, Charlton SJ, Sykes DA, Pearlstein RA, Duca JS (2016) Uncoupling the structure-activity relationships of β2Adrenergic receptor ligands from membrane binding. J Med Chem 59(12):5780–5789. https://doi.org/10.1021/acs.jmedchem.6b00358
Frisch MJ, Trucks GW, Schlegel HB et al (2003) Gaussian03, Revision C.02. Gaussian Inc., Pittsburgh, PA
Fritze O, Filipek S, Kuksa V, Palczewski K, Hofmann KP, Ernst OP (2003) Role of the conserved NPxxY(x)5,6F motif in the rhodopsin ground state and during activation. Proc Natl Acad Sci USA 100(5):2290–2295. https://doi.org/10.1073/pnas.0435715100
Goetz AW, Williamson MJ, Xu D, Poole D, Le Grand S, Walker RC (2012) Routine microsecond molecular dynamics simulations with AMBER-Part I: generalized born. J Chem Theory Comput 8:1542–1555. https://doi.org/10.1021/ct200909j
Gohlke H, Case DA (2004) Converging free energy estimates: mMPB(GB)SA studies on the protein-protein complex Ras-Raf. J Comput Chem 25:238–250. https://doi.org/10.1002/jcc.10379
Goodford PJ (1985) A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J Med Chem 28:849–857. https://doi.org/10.1021/jm00145a002
Gregorio GG, Masureel M, Hilger D, Terry DS, Juette M, Zhao H et al (2017) Single-molecule of ligand efficacy in β2AR-G protein activation. Nature 547:68–73. https://doi.org/10.1038/nature22354
Hawkins GD, Cramer CJ, Truhlar DG (1996) Parametrized models of aqueous free energies of solvation based on pairwise descreening of solute atomic charges from a dielectric medium. J Phys Chem 100:19824–19839. https://doi.org/10.1021/jp961710n
Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph Model 14:33. https://doi.org/10.1016/0263-7855(96)00018-5
Jo S, Kim T, Im W (2007) Automated builder and database of protein/membrane complexes for molecular dynamics simulations. PLoS One 2:e880. https://doi.org/10.1371/journal.pone.0000880
Jo S, Lim JB, Klauda JB, Im W (2009) CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes. Biophys J 97(1):50–58. https://doi.org/10.1016/j.bpj.2009.04.013
Kollman PA, Massova I, Reyes C et al (2000) Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res 33:889–897. https://doi.org/10.1021/ar000033j
Lamichhane R, Liu JJ, Pljevaljcic G, White KL, van der Schans E, Katritch V, Stevens RC, Wüthrich K, Millar DP (2015) Single-molecule view of basal activity and activation mechanisms of the G protein-coupled receptor β2AR. Proc Natl Acad Sci USA. 112(46):14254–14259. https://doi.org/10.1073/pnas.1519626112
Laurie ATR, Jackson RM (2005) Q-SiteFinder: an energy-based method for the prediction of protein–ligand binding sites. Bioinformatics 21(9):1908–1916. https://doi.org/10.1093/bioinformatics/bti315
Lindahl E, Hess B, van der Spoel D (2001) GROMACS 3.0: a package for molecular simulation and trajectory analysis. J Mol Model 7:306–317. https://doi.org/10.1007/s008940100045
Lomize MA, Lomize AL, Pogozheva ID, Mosberg HI (2006) OPM: orientations of Proteins in Membranes database. Bioinformatics 22:623–625. https://doi.org/10.1093/bioinformatics/btk023
Miller BR, McGee TD, Swails JM, Homeyer N, Gohlke H, Roitberg AE (2012) MMPBSA.py: an efficient program for end-state free energy calculations. J Chem Theory Comput 8:3314–3321. https://doi.org/10.1021/ct300418h
Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson JA (2009) AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comp Chem 30:2785–2791. https://doi.org/10.1002/jcc.21256
Nygaard R, Zou Y, Dror RO, Mildorf TJ, Arlow DH, Manglik A, Pan AC, Liu CW, Fung JJ, Bokoch MP, Thian FS, Kobilka TS, Shaw DE, Mueller L, Prosser RS, Kobilka BK (2013) The dynamic process of β(2) adrenergic receptor activation. Cell 152(3):532–542. https://doi.org/10.1016/j.cell.2013.01.008
Plazinska A, Plazinski W (2017) Stereoselective binding of agonists to the β2-adrenergic receptor: insights into molecular details and thermodynamics from molecular dynamics simulations. Mol BioSyst 13:910–920. https://doi.org/10.1039/c6mb00814c
Pon CK, Lane JR, Sloan EK, Halls ML (2016) The β2-adrenoceptor activates a positive cAMP-calcium feedforward loop to drive breast cancer cell invasion. FASEB J 30(3):1144–1154. https://doi.org/10.1096/fj.15-277798
Rovati GE, Capra V, Neubig RR (2007) The highly conserved DRY motif of class A G protein-coupled receptors: beyond the ground state. Mol Pharmacol 71(4):959–964. https://doi.org/10.1124/mol.106.029470
Sali A, Blundell TL (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234(3):779–815. https://doi.org/10.1006/jmbi.1993.1626
Salomon-Ferrer R, Goetz AW, Poole D, Le Grand S, Walker RC (2013) Routine microsecond molecular dynamics simulations with AMBER-Part II: particle Mesh Ewald. J Chem Theory Comput 9:3878–3888. https://doi.org/10.1021/ct400314y
Sanner MF (1999) Python: a programming language for software integration and development. J Mol Graph Model 17:57–61
Sivamani RK, Lam ST, Isseroff RR (2007) Beta adrenergic receptors in keratinocytes. Dermatol Clin 25(4):643–653. https://doi.org/10.1016/j.det.2007.06.012
Skjevik ÅA, Madej BD, Walker RC, Teigen K (2012) LIPID11: a modular framework for lipid simulations using amber. J Phys Chem B 116(36):11124–11136. https://doi.org/10.1021/jp3059992
Soriano-Ursúa MA, Valencia-Hernández I, Arellano-Mendoza MG, Correa-Basurto J, Trujillo-Ferrara JG (2009a) Synthesis, pharmacological and in silico evaluation of 1-(4-di-hydroxy-3,5-dioxa-4-borabicyclo[4.4.0]deca-7,9,11-trien-9-yl)-2-(tert-butylamino) ethanol, a compound designed to act as a beta2 adrenoceptor agonist. Eur J Med Chem 44:2840–2846. https://doi.org/10.1016/j.ejmech.2008.12.016
Soriano-Ursúa MA, Trujillo-Ferrara J, Correa-Basurto J (2009b) Homology modeling and flex-ligand docking studies on the guinea pig β2 adrenoceptor: structural and experimental similarities/differences with the human β2. J Mol Model 15:1203–1211. https://doi.org/10.1007/s00894-009-0480-7
Soriano-Ursúa MA, Correa-Basurto J, Valencia-Hernández I, Amezcua-Gutiérrez MA, Padilla-Martínez II, Trujillo-Ferrara JG (2010) Design, synthesis and in vitro evaluation of (R)-4-(2-(tert-butylamino)-1-hydroxyethyl)-2-(hydroxymethyl)phenyl hydrogen phenylboronate: a novel Albuterol derivative with high intrinsic efficacy on the β2 adrenoceptor. Bioorg Med Chem Lett 20:5623–5629. https://doi.org/10.1016/j.bmcl.2010.08.040
Soriano-Ursúa MA, McNaught-Flores DA, Nieto-Alamilla G, Segura-Cabrera A, Correa-Basurto J, Arias-Montaño JA, Trujillo-Ferrara JG (2012) Cell-based and in silico studies on the high intrinsic activity of two boron-containing salbutamol derivatives at the human β2-adrenoceptor. Bioorg Med Chem 20(2):933–941. https://doi.org/10.1016/j.bmc.2011.11.054
Soriano-Ursúa MA, Trujillo-Ferrara JG, Arias-Montaño JA, Villalobos-Molina R (2015a) Insights into a defined secondary binding region on β-adrenoceptors and putative roles in ligand binding and drug design. Med Chem Commun 6:991–1002. https://doi.org/10.1039/C5MD00011D
Soriano-Ursúa MA, Arias-Montaño JA, Correa-Basurto J, Hernández-Martínez CF, López-Cabrera Y, Castillo-Hernández MC, Padilla-Martínez II, Trujillo-Ferrara JG (2015b) Insights on the role of boron containing moieties in the design of new potent and efficient agonists targeting the β2 adrenoceptor. Bioorg Med Chem Lett 25(4):820–825. https://doi.org/10.1016/j.bmcl.2014.12.077
Tikhonova IG, Selvam B, Ivetac A, Wereszczynski J, McCammon JA (2013) Simulations of biased agonists in the β(2) adrenergic receptor with accelerated molecular dynamics. Biochemistry 52(33):5593–5603. https://doi.org/10.1021/bi400499n
Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendensen HJ (2005) GROMACS. Fast, flexible, and free. J Comput Chem 26:1701–1718. https://doi.org/10.1002/jcc.20291
Van Gunsteren WF, Berendsen HJC (1977) Algorithms for macromolecular dynamics and constraint dynamics. Mol Phys 34:1311–1327. https://doi.org/10.1080/00268977700102571
Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA (2004) Development and testing of a general amber force field. J Comput Chem 25:1157–1174. https://doi.org/10.1002/jcc.20035
Warne T, Moukhametzianov R, Baker JG, Nehmé R, Edwards PC, Leslie AG, Schertler GF, Tate CG (2011) The structural basis for agonist and partial agonist action on a β(1)-adrenergic receptor. Nature 469(7329):241–244. https://doi.org/10.1038/nature09746
Weichert D, Stanek M, Hübner H, Gmeiner P (2016) Structure-guided development of dual β2 adrenergic/dopamine D2 receptor agonists. Bioorg Med Chem 24(12):2641–2653. https://doi.org/10.1016/j.bmc.2016.04.028
Woolf TB, Roux B (1994) Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer. Proc Natl Acad Sci USA 91:11631–11635
Acknowledgements
We thank Bruce Allan Larsen for reviewing the use of English in the manuscript. The authors are grateful for financial support and scholarships from Comisión de Operación y Fomento de Actividades Académicas, Secretaría de Investigación y Posgrado of the IPN (SIP-M1930), and Consejo Nacional de Ciencia y Tecnología (CONACyT CB235785). JCB thanks to CONACYT CB-254600, APN-782 and Proyecto INSIGNIA-IPN-2015. Also, we thank to Escuela Nacional de Ciencias Biológicas for sharing facilities for our projects with boron-containing compounds.
Author information
Authors and Affiliations
Contributions
MASU, MB and JGTF conceived of the presented idea. MASU, MB, CFHM, JCB developed the theory and performed the computations. MASU, MB, JGTF and JAAM verified the analytical methods. JAAM encouraged IST and RGR to investigate Cell-based assays and supervised the findings of this work. All authors discussed the results and contributed to the final manuscript.
Corresponding authors
Ethics declarations
Conflict of interest
The authors declare that there is no conflict of interest.
Electronic supplementary material
Below is the link to the electronic supplementary material.
249_2018_1336_MOESM1_ESM.pdf
This information includes the structure of boron-containing Albuterol adducts tested in silico on guinea pig and human β2AR models (Suppl. Fig. 1), docking studies to validate the procedure (In Suppl. Fig. 2, results from radioligand binding assays on membranes from transfected CHO-K1 cells (Suppl. Fig. 3 and Suppl. Table 1); the estimated affinity values for tested ligands (Suppl. Fig. 4), the MD simulation box of the extracellular and transmembrane regions of hβ2AR and gpβ2AR systems (Suppl. Fig. 5) and detailed data from MD simulations (Suppl. Fig. 6, Suppl. Fig. 7, Suppl. Table 2-5). 1 (PDF 1008 kb)
Rights and permissions
About this article
Cite this article
Soriano-Ursúa, M.A., Bello, M., Hernández-Martínez, C.F. et al. Cell-based assays and molecular dynamics analysis of a boron-containing agonist with different profiles of binding to human and guinea pig beta2 adrenoceptors. Eur Biophys J 48, 83–97 (2019). https://doi.org/10.1007/s00249-018-1336-9
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00249-018-1336-9