title: Computational exploration of the binding mode of heme-dependent stimulators into the active catalytic domain of soluble guanylate cyclase.
abstract: Soluble guanylate cyclase (sGC), the main target of nitric oxide (NO), has been proven to have a significant role in coronary artery disease, pulmonary hypertension, erectile dysfunction, and myocardial infarction. One of its agonists, BAY 41-2272 (Riociguat), has been recently approved for treatment of pulmonary arterial hypertension (PHA), while some others are in clinical phases of development. However, the location of the binding sites for the two known types of agonists, heme-dependent stimulators and heme-independent activators, is a matter of debate, particularly for the first group where both a location on the regulatory (H-NOX) and on the catalytic domain have been suggested by different authors. Here, we address its potential location on the catalytic domain, the unique well characterized at the structural level, by an "in silico" approach. Homology models of the catalytic domain of sGC in "inactive" or "active" conformations were constructed using the structure of previously described crystals of the catalytic domains of "inactive" sGCs (2WZ1, 3ET6) and of "active" adenylate cyclase (1CJU). Each model was submitted to six independent molecular dynamics simulations of about 1 μs. Docking of YC-1, a classic heme-dependent stimulator, to all frames of representative trajectories of "inactive" and "active" conformations, followed by calculation of absolute binding free energies with the linear interaction energy (LIE) method, revealed a potential high-affinity binding site on the "active" structure. The site, located between the pseudo-symmetric and the catalytic site just over the loop β2 -β3 , does not overlap with the forskolin binding site on adenylate cyclases. Proteins 2016; 84:1534-1548. © 2016 Wiley Periodicals, Inc.
authors.affiliation: Department of Systems Biology, U Science Tech, University of Vic - Central University of Catalonia (UVIC-UCC), Vic, 08500, Spain. luis.agullo@uvic.cat.
authors.forename: Luis
authors.initials: L
authors.lastname: Agulló
authors.affiliation: Computational Biophysics Laboratory, Hospital Del Mar Medical Research Institute (IMIM), Barcelona, 08003, Spain.
authors.forename: Ignasi
authors.initials: I
authors.lastname: Buch
authors.affiliation: Department of Cell and Molecular Biology, Uppsala University, Uppsala Biomedicinska Centrum BMC, Uppsala, 75124, Sweden.
authors.forename: Hugo
authors.initials: H
authors.lastname: Gutiérrez-de-Terán
authors.affiliation: Cardiocirculatory Pathology Group, Vall D'Hebron Research Institute (VHIR), Barcelona, 08035, Spain.
authors.forename: David
authors.initials: D
authors.lastname: Garcia-Dorado
authors.affiliation: Department of Systems Biology, U Science Tech, University of Vic - Central University of Catalonia (UVIC-UCC), Vic, 08500, Spain.
authors.forename: Jordi
authors.initials: J
authors.lastname: Villà-Freixa
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D020134:Catalytic Domain; D016825:Chlamydomonas reinhardtii / Q000737:chemistry / Q000201:enzymology; D015870:Gene Expression; D006160:Guanosine Triphosphate / Q000737:chemistry* / Q000378:metabolism; D006418:Heme / Q000737:chemistry* / Q000378:metabolism; D006801:Humans; D008024:Ligands; D062105:Molecular Docking Simulation; D058977:Molecular Sequence Annotation; D011485:Protein Binding; D000072417:Protein Domains; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011720:Pyrazoles / Q000737:chemistry*; D011725:Pyridines / Q000737:chemistry*; D051381:Rats; D016415:Sequence Alignment; D000071756:Soluble Guanylyl Cyclase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D040681:Structural Homology, Protein; D013379:Substrate Specificity; D013816:Thermodynamics
chemical_list: C423582:3-(4-Amino-5-cyclopropylpyrimidine-2-yl)-1-(2-fluorobenzyl)-1H-pyrazolo(3,4-b)pyridine; D008024:Ligands; D011720:Pyrazoles; D011725:Pyridines; D006418:Heme; D006160:Guanosine Triphosphate; D000071756:Soluble Guanylyl Cyclase
keywords: YC-1 docking; homology modeling; linear interaction energy; molecular dynamics simulations