Computational Study of C-X-C Chemokine Receptor (CXCR)3 Binding with Its Natural Agonists Chemokine (C-X-C Motif) Ligand (CXCL)9, 10 and 11 and with Synthetic Antagonists: Insights of Receptor Activation towards Drug Design for Vitiligo

Abstract

Vitiligo is a hypopigmentary skin pathology resulting from the death of melanocytes due to the activity of CD8+ cytotoxic lymphocytes and overexpression of chemokines. These include CXCL9, CXCL10, and CXCL11 and its receptor CXCR3, both in peripheral cells of the immune system and in the skin of patients diagnosed with vitiligo. The three-dimensional structure of CXCR3 and CXCL9 has not been reported experimentally; thus, homology modeling and molecular dynamics could be useful for the study of this chemotaxis-promoter axis. In this work, a homology model of CXCR3 and CXCL9 and the structure of the CXCR3/Gαi/0βγ complex with post-translational modifications of CXCR3 are reported for the study of the interaction of chemokines with CXCR3 through all-atom (AA-MD) and coarse-grained molecular dynamics (CG-MD) simulations. AA-MD and CG-MD simulations showed the first activation step of the CXCR3 receptor with all chemokines and the second activation step in the CXCR3-CXCL10 complex through a decrease in the distance between the chemokine and the transmembrane region of CXCR3 and the separation of the βγ complex from the α subunit in the G-protein. Additionally, a general protein–ligand interaction model was calculated, based on known antagonists binding to CXCR3. These results contribute to understanding the activation mechanism of CXCR3 and the design of new molecules that inhibit chemokine binding or antagonize the receptor, provoking a decrease of chemotaxis caused by the CXCR3/chemokines axis.

Behavior of Chemokine Receptor 6 (CXCR6) in Complex with CXCL16 Soluble form Chemokine by Molecular Dynamic Simulations: General Protein‒Ligand Interaction Model and 3D-QSAR Studies of Synthetic Antagonists

“…Based on previous works by our research group [ 20 , 43 ], the methodology was modified accordingly, as stated in the following subsections.…”

“…Then, molecular docking was performed with AutoDock 4.2.6(cripps Institute, La Jolla, CA, USA) optimized for GPU, using a total of 50 runs and 25,000,000 evaluations with a Lamarckian genetic algorithm and a Solis–Wets local search [ 70 ]. Using the binding site of the molecule with the best IC50, a new grid was calculated, of 80 × 80 × 80 Å with a spacing of 0.375 Å, and a second molecular docking was performed using AutoDock 4.2.6 optimized for GPU, using a total of 50 runs and 25,000,000 evaluations with a Lamarckian genetic algorithm and a Solis–Wets local search [ 20 ].…”

“…Pharmer (2015, Pittsburgh, PA, USA) [ 71 ] was used to identify the pharmacophoric elements such as hydrogen bond acceptors (HAc), hydrogen bond donors (HDn), aromatic rings (Arm), hydrophobic groups (Hph), positive-charged groups (PIn), and negative-charged groups (NIn) of the docked ligands in their most frequent binding conformation, which were obtained by clustering the results from the second docking of each ligand with a root mean standard deviation (RMSD) cutoff of 2 Å on their protein–ligand complexes [ 20 , 43 ]. These characteristics were clustered according to their nature, position, and size using the partitioning around medoids statistical method [ 72 ], implemented in the cluster package [ 73 ] available in the statistical software R (3.5.2, R Foundation for Statistical Computing, Vienna, Austria) [ 67 ] to build a general protein‒ligand interaction model [ 20 ].…”

“…The proposed activation of the chemokine receptors has two steps: first, the interaction of a chemokine with the amino terminal (NH 2 -T) promotes its movement into the transmembrane region; and then a change in the H-bonds between transmembrane segments (TMs) activates the receptor. Other authors have proposed the separation of the βγ complex from the α subunit in G-protein as the second activation step ( Figure 1 ) [ 17 , 18 , 19 , 20 ]. Furthermore, the rotation and polar interactions of TMs are related to GPCR activation [ 21 , 22 ].…”

“…In silico methodologies such as homology modeling, molecular docking, and molecular dynamics simulations are helpful when the tridimensional structure of a protein has not been resolved experimentally. Among these computational methodologies, protein homology modeling allows for an approximation of a protein to a three-dimensional structure based on the principle that “similar primary sequences will have a similar three-dimensional conformation” [ 20 , 37 ]. Additionally, molecular docking is used to model the interaction between two chemical entities, which can be small ligands, proteins, or nucleic acids, and molecular dynamics simulations, in order to study the vibration, torsion, and behavior of bonds, as well as non-bonding interactions such as electrostatic interactions and van der Waals forces, and to observe the evolution of a system in the presence of a ligand (small molecule, peptide, or protein) under constant conditions of pressure, temperature, volume, and energy [ 38 , 39 , 40 ].…”