New insights into the stereochemical requirements of the bradykinin B2 receptor antagonists binding

Abstract

Abstract:Bradykinin (BK) is a member of the kinin family, released in response to inflammation, trauma, burns, shock, allergy and some cardiovascular diseases, provoking vasodilatation and increased vascular permeability among other effects. Their actions are mediated through at least two G-protein coupled receptors, B1 a receptor upregulated during inflammation episodes or tissue trauma and B2 that is constitutively expressed in a variety of cell types. The goal of the present work is to carry out a structure-activity study of BK B2 antagonism, taking into account the stereochemical features of diverse non-peptide antagonists and the way these features translate into ligand anchoring points to complementary regions of the receptor, through the analysis of the respective ligand-receptor complex. For this purpose an atomistic model of the BK B2 receptor was built by homology modeling and subsequently refined embedded in a lipid bilayer by means of a 600 ns molecular dynamics trajectory. The average structure from the last hundred nanoseconds of the molecular dynamics trajectory was energy minimized and used as model of the receptor for docking studies. For this purpose, a set of compounds with antagonistic profile, covering maximal diversity were selected from the literature. Specifically, the set of compounds include Fasitibant, FR173657, Anatibant, WIN64338, Bradyzide, CHEMBL442294, and JSM10292. Molecules were docked into the BK B2 receptor model and the corresponding complexes analyzed to understand ligand-receptor interactions. The outcome of this study is summarized in a 3D pharmacophore that explains the observed structureactivity results and provides insight into the design of novel molecules with antagonistic profile. To prove the validity of the pharmacophore hypothesized a virtual screening process was also carried out. The pharmacophore was used as query to identify new hits using diverse databases of molecules. The results of this study revealed a set of new hits with structures not connected to the molecules used for pharmacophore development. A few of these structures were purchased and tested. The results of the binding studies show about a 33% success rate with a correlation between the number of pharmacophore points fulfilled and their antagonistic potency. Some of these Powered by Editorial Manager® and ProduXion Manager® from Aries Systems Corporationstructures are disclosed in the present work.Response to Reviewers: We sincerely appreciate the involvement of reviewer #1 and are deeply obliged. The reviewer was right in pointing the distortion of the ring and the amide in Figure 8 that has now been fixed in the revised version of Figure 8. We have also modified the viewpoint of Figure 9 to clearly show the protonation status of the terminal amine that was unfortunately hidden in the previous version of Figure 9 this study is summarized in a 3D pharmacophore that explains the observed structure-activity results and provides insight into the design of novel molecules with antagonistic profile. ...

Molecular Features of Non-Selective Small Molecule Antagonists of the Bradykinin Receptors

“…The 3D models of the B1 and B2 were constructed by homology modeling using the chemokine CXCR4 receptor as template (pdb entry code 3ODU) [47], following the procedure explained elsewhere [32,33]. Initial crude models of the receptors were constructed by threading the sequences of the B1 and B2 receptors onto the backbone of the template following the sequence alignment and subsequently validated using the Modeller 9 version 8 (9v8) software [48].…”

“…Next, models were refined using molecular dynamics simulations using a system consisting of each of the respective receptors embedded in a lipid bilayer of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipids and water molecules, using GROMACS 4.6 package [49] as described elsewhere [50]. B1 and B2 small molecule pharmacophores were defined after docking studies of diverse non-peptide selective ligands to each of the two receptors [32,33]. Docking studies were carried out using a set of unique conformations resulted from thorough conformational searches for the diverse ligands studied and rank ordered using the XP score function of GLIDE [51].…”

“…Due to the lack of crystallographic structures of the BK receptors, the construction of 3D models at atomic resolution by homology modeling of the B1 and B2 receptors was recently performed and reported [32,33]. Models were subsequently used to undertake a docking study that permitted the analysis of diverse ligand-receptor complexes of known selective small molecule compounds.…”

“…Virtual screening methods can be very valuable in drug repurposing, provided we count on specific structural knowledge of the therapeutic target of interest [31]. Specifically, for BK we recently reported the results of a modeling study addressed to analyze the stereochemical features required for non-peptide selective ligands to bind to the B1 and B2 receptors [32,33]. Furthermore, the results of the study also permitted to identify the stereochemical features associated with selective binding to each of them [34].…”

Bifunctional ligands of the bradykinin B 2 and B 1 receptors: An exercise in peptide hormone plasticity

“…Novel approaches promise to facilitate the design of original kinin receptor ligands in the future, such as the in silico definition of pharmacophores from the analysis of the docking of several non-peptide antagonists; this has been done for 3-dimensional models of both the B 1 R and B 2 R [90,91]. The pro-drug agonist peptides may be further optimized for additional peptidases that will provide targeted actions on a specific tissue of a selective physiological function.…”