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Homology model and docking studies on porcine β2 adrenoceptor: description of two binding sites

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Abstract

The affinity of the classical β2 adrenoceptor-selective inverse agonist ICI118,551 is notoriously lower for porcine β2 adrenoceptors (p2βAR) than for human β2 adrenoceptors (hβ2AR) but molecular mechanisms for this difference are still unclear. Homology 3-D models of pβ2AR can be useful in predicting similarities and differences, which might in turn increase the comparative understanding of ligand interactions with the hβ2AR. In this work, the pβ2AR amino acid sequence was used to carry out homology modeling. The selected pβ2AR 3-D structure was structurally and energetically optimized and used as a model for further theoretical study. The homology model of pβ2AR has a 3-D structure very similar to the crystal structures of recently studied hβ2AR. This was also corroborated by sequence identity, RMSD, Ramachandran map, TM-score and docking results. Upon performing molecular docking simulations with the AutoDock4.0.1 program on pβ2AR, it was found that a set of well-known β2AR ligands reach two distinct binding sites on pβ2AR. Whereas one of these sites is similar to that reported on the hβ2AR crystal structure, the other can explain some important experimental observations. Additionally, the theoretical affinity estimated for ICI118,551 closely agrees with affinities estimated from experimental in vitro data. The experimental differences between the human/porcine β2ARs in relation to ligand affinity can in part be elucidated by observations in this molecular modeling study.

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Acknowledgments

We are grateful for the scholarships and financial support by the Consejo Nacional de Ciencia y Tecnología (Grant 62488), Comisión de Fomento de Actividades Académicas, y Secretaría de Investigación y Posgrado del Instituto Politécnico Nacional provided to MASU, JTF and JCB. Finally, we wish to thank Dr. Vsevolod Katritch for sharing the coordinates of his S-carazolol-hβ2AR model for this study with us, and Bruce Allan Larsen for his critical reading of the manuscript. The hardware used in this study was purchased with INNOVAPyME program support (110703 and 139391) provided to Instituto Politécnico Nacional and Laboratorio Médico Químico Biológico.

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Authors and Affiliations

  1. Departments of Physiology, Biochemistry and Molecular Modeling. Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, 11340, Mexico City, Mexico

    Marvin A. Soriano-Ursúa, José Correa-Basurto & José G. Trujillo-Ferrara

  2. Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Physiology Building, Cambridge, Cambridge, CB2 3EG, UK

    Alberto J. Kaumann

  3. Departamento de Fisiología y Farmacología, Escuela Superior de Medicina, Plan de San Luis y Díaz Mirón, Mexico City, D.F., 11340, Mexico

    Marvin A. Soriano-Ursúa

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  1. Marvin A. Soriano-Ursúa
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  2. José Correa-Basurto
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  3. José G. Trujillo-Ferrara
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Correspondence to Marvin A. Soriano-Ursúa.

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Table S1

The pβ2AR models. (DOC 37 kb)

Suppl. Fig. 1

Amino acids alignment of pβ2AR and hβ2AR (JPEG 402 kb)

High resolution image file (TIFF 111 kb)

Suppl. Fig. 2

(a) Ramachandran plot and (b) outlier amino acids depicted as blue beads on the refined pβ2AR (residues 30 to 230 and 267 to 345). Five amino acids included in the main binding site are shown as red spheres. (JPEG 248 kb)

High resolution image file (TIFF 198 kb)

Suppl. Fig. 3

The sites availability at pβ2AR or hβ2AR reported by Q-site finder server. Porcine β2AR (at the center) and comparison with the crystallized conformation of hβ2AR (on left) and after 600 ns of molecular dinamycs simulation (from reference 53). (JPEG 242 kb)

High resolution image file (TIFF 241 kb)

Suppl. Fig. 4

Amino acids with which S,S-ICI118551 interacts on both, pβ2AR and hβ2AR. The estimated pKd of each complex is in red numbers. (a) On rigid_pβ2AR-site 2, (b) on rigid_pβ2AR-site 1, (c) on flexibleTM5_pβ2AR (d) on rigid_our_hβ2AR, (e) on flexibleTM5_our_hβ2AR, (f) on rigid_byKatritch_hβ2AR (g) on flexibleTM5_ byKatritch_hβ2AR. (JPEG 1444 kb)

High resolution image file (TIFF 1371 kb)

Suppl. Fig. 5

Linear regression for experimental vs. theoretical pKd values showed in Fig. 2 (as filled rhombs and filled circles, respectively). Values for ICI118,551 and salbutamol were considered as outliers for building this chart. (JPEG 52 kb)

High resolution image file (TIFF 14 kb)

Suppl. Fig. 6

The impact of TM5-flexibility on the affinity prediction complexes ICI118551-β2AR. (JPEG 94 kb)

High resolution image file (TIFF 28 kb)

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Soriano-Ursúa, M.A., Correa-Basurto, J., Trujillo-Ferrara, J.G. et al. Homology model and docking studies on porcine β2 adrenoceptor: description of two binding sites. J Mol Model 17, 2525–2538 (2011). https://doi.org/10.1007/s00894-010-0915-1

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