Hybrid approach to structure modeling of the histamine H3 receptor: Multi-level assessment as a tool for model verification

<div><p>The crucial role of G-protein coupled receptors and the significant achievements associated with a better understanding of the spatial structure of known receptors in this family encouraged us to undertake a study on the histamine H3 receptor, whose crystal structure is still unresolved. The latest literature data and availability of different software enabled us to build homology models of higher accuracy than previously published ones. The new models are expected to be closer to crystal structures; and therefore, they are much more helpful in the design of potential ligands. In this article, we describe the generation of homology models with the use of diverse tools and a hybrid assessment. Our study incorporates a hybrid assessment connecting knowledge-based scoring algorithms with a two-step ligand-based docking procedure. Knowledge-based scoring employs probability theory for global energy minimum determination based on information about native amino acid conformation from a dataset of experimentally determined protein structures. For a two-step docking procedure two programs were applied: GOLD was used in the first step and Glide in the second. Hybrid approaches offer advantages by combining various theoretical methods in one modeling algorithm. The biggest advantage of hybrid methods is their intrinsic ability to self-update and self-refine when additional structural data are acquired. Moreover, the diversity of computational methods and structural data used in hybrid approaches for structure prediction limit inaccuracies resulting from theoretical approximations or fuzziness of experimental data. The results of docking to the new H3 receptor model allowed us to analyze ligand—receptor interactions for reference compounds.</p></div

Structure of the histamine H3 receptor ligands used in the docking studies.

<p>pK_i values for ligand binding with the human H3 receptor [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0186108#pone.0186108.ref087" target="_blank">87</a>].</p

Binding mode of compound ABT 239 (blue) within the histamine H3 receptor.

<p>The amino acids involved in the non-polar interactions are highlighted in yellow. Amino acids involved in polar interactions (green line: cation– π, purple arrow: salt bridge) are marked in green.</p

Three main conformations of the E5.46 observed during docking.

<p>Green color represents the conformation preferred by the ligands in docking. Red represents conformation from models where docking poses reach high RMSD values.</p

Binding mode of compound A349821 (blue) within the histamine H3 receptor.

<p>The amino acids involved in the non-polar interactions are highlighted in yellow. Amino acids involved in polar interactions (red arrow: hydrogen bond, green line: cation– π, purple dash: salt bridge) are marked in green.</p

Binding mode of ciproxifan within the histamine H3 receptor.

<p>The amino acids involved in the non-polar interactions are highlighted in yellow. Amino acids involved in polar interactions (red arrow: hydrogen bond, green line: cation– π, purple dashes: salt bridge) are marked in green.</p

Results of ligand-based docking assessment for the best generated model.

<p>Docking with GOLD, presented as a ChemPLP score for the best pose of each ligand (A) with a cutoff score line, the percentage of ligand pose located in the active site of the H3 receptor after docking with GOLD (B). Average RMSD values across all poses of each ligand in each docking. Ligands compared to best scored pose (C). Absolute GlideScore values for the best ligand pose (D). Colors represent the individual ligands: A331440 –purple, A349821 –orange, ABT 239 –gray, Ciproxifan—yellow, Clobenpropit—red, JNJ520785 –green, Thioperamide—blue.</p

Binding mode of thioperamide within the histamine H3 receptor.

<p>The amino acids involved in the non-polar interactions are highlighted in yellow. Amino acids involved in polar interactions (purple dashes: salt bridge) are marked in green.</p

Binding mode of compound JNJ5207852 within the histamine H3 receptor.

<p>The amino acids involved in the non-polar interactions are highlighted in yellow. Amino acids involved in polar interactions (red arrow: hydrogen bond, green line: cation– π, purple dashes: salt bridge) are marked in green.</p

Position of W6.48 and ECL2 amino acids F45.54(F192) and F45.55(F193).

<p>Green color represents the conformation preferred by the ligands in docking with GOLD. Red represents the conformation from models where docking poses reach high RMSD values.</p