Homology modeling, molecular dynamics and docking simulations of rat A2A receptor: a three-dimensional model validation under QSAR studies

Understanding the three-dimensional structure (3-D) of GPCRs (G protein coupled receptors) can aid in the design of applicable compounds for the treatment of several human disorders. To this end, several 3-D models have been obtained in recent years. In this work, we have built the rat adenosine receptor model (rA2AR) by employing computational tools. First, the 3-D rA2AR model was built by homology modeling using the human adenosine receptor (hA2AR) structure (PDB codes: 3EML) as a template. Then, the rA2AR model was refined by molecular dynamics simulations, in which the initial and refined 3-D structures were used for molecular docking simulations and Quantitative structure-activity relationship (QSAR) studies using a set of known experimentally tested ligands to validate this rA2AR model. The results showed that the hindrance effect caused by ribose attached to agonists play an important role in activating the receptor via formation of several hydrogen bonds. In contrast, the lack of this moiety allows blocking of the receptor. The theoretical affinity estimation shows good correlation with reported experimental data. Therefore, this work represents a good example for getting reliable GPCR models under computational procedures.We are grateful for the scholarships and financial support from CONACYT, México (132353), ICyTDF (PIRIVI09-9), COFAA and SIP-IPN (20110786), PAPIIT-DGAPA UNAM-215708 and Posgrado en Ciencias Biológicas UNAM. The authors thank the Centro Nacional de Supercomputo, México, for providing access to the “Argentum” cluster

KRas4BG12C/D/PDE6δ Heterodimeric Molecular Complex: A Target Molecular Multicomplex for the Identification and Evaluation of Nontoxic Pharmacological Compounds for the Treatment of Pancreatic Cancer

The search for new targeted therapies to improve the quality of life of patients with pancreatic cancer has taken about 30 years. Compounds that can inhibit the K-Ras4B oncoprotein signaling pathway have been sought. Taking into account that the interaction of KRas4B with PDE6δ is essential for its transport and subsequent activation in the plasma membrane, our working group identified and evaluated in vitro and in vivo small organic molecules that could act as molecular staples to stabilize the KRas4B/PDE6δ heterodimeric complex. From this group of molecules, 38 compounds with high interaction energies on the structure of the crystallized molecular complex were selected, indicating that they efficiently stabilized the molecular complex. In vitro evaluation of compounds called D14, C22, and C19 showed significant specific effects on the cell viability of pancreatic cancer cells (and not on normal cells), thus inducing death by apoptosis and significantly inhibiting the activation of the pathways, signaling AKT and ERK. In addition to these experimental findings, we were also able to detect that compounds D14 and C22 showed significant tumor growth inhibitory activity in pancreatic cancer cell-induced subcutaneous xenograft models

Molecular dynamics simulations to provide insights into epitopes coupled to the soluble and membrane-bound MHC-II complexes.

Epitope recognition by major histocompatibility complex II (MHC-II) is essential for the activation of immunological responses to infectious diseases. Several studies have demonstrated that this molecular event takes place in the MHC-II peptide-binding groove constituted by the α and β light chains of the heterodimer. This MHC-II peptide-binding groove has several pockets (P1-P11) involved in peptide recognition and complex stabilization that have been probed through crystallographic experiments and in silico calculations. However, most of these theoretical calculations have been performed without taking into consideration the heavy chains, which could generate misleading information about conformational mobility both in water and in the membrane environment. Therefore, in absence of structural information about the difference in the conformational changes between the peptide-free and peptide-bound states (pMHC-II) when the system is soluble in an aqueous environment or non-covalently bound to a cell membrane, as the physiological environment for MHC-II is. In this study, we explored the mechanistic basis of these MHC-II components using molecular dynamics (MD) simulations in which MHC-II was previously co-crystallized with a small epitope (P7) or coupled by docking procedures to a large (P22) epitope. These MD simulations were performed at 310 K over 100 ns for the water-soluble (MHC-IIw, MHC-II-P(7w), and MHC-II-P(22w)) and 150 ns for the membrane-bound species (MHC-IIm, MHC-II-P(7m), and MHC-II-P(22m)). Our results reveal that despite the different epitope sizes and MD simulation environments, both peptides are stabilized primarily by residues lining P1, P4, and P6-7, and similar noncovalent intermolecular energies were observed for the soluble and membrane-bound complexes. However, there were remarkably differences in the conformational mobility and intramolecular energies upon complex formation, causing some differences with respect to how the two peptides are stabilized in the peptide-binding groove

Schematic MHC-II-P₇ representation.

<p>A) Map of the interactions that stabilize the soluble MHC-II-P_7w complex. B) Map of the interactions that stabilize the membrane-bound MHC-II-P_7m. The residues of P₇ are represented by a single circle. Only the side chains of P₇ involved in hydrogen bonds or hydrophobic contacts are shown explicitly. MHC-II residues participating in hydrogen bonds (green dotted lines) are represented by a single box, and hydrophobic contacts are represented by red half circles.</p

pMHC-II interactions between peptide residues and pockets (Ps).

<p>Residues reported to be important for stabilizing MHC-II-peptide complexes <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0072575#pone.0072575-Sato1" target="_blank">[13]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0072575#pone.0072575-Painter1" target="_blank">[59]</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0072575#pone.0072575-Murthy1" target="_blank">[61]</a> are highlighted in bold.</p

Average structures of the pMHC-II complexes.

<p>A) MHC-II-P_22w, B) MHC-II-P_22m, C) MHC-II-P_7w and D) MHC-II-P_7m.</p

Geometrical properties of the peptide-free MHC-II and pMHC-II states in aqueous solution and pMHC-II anchored to a membrane.

*<p>Time at which the system had converged and the geometrical parameters were evaluated.</p

RMSF analysis of the soluble and membrane-bound MHC-II-P₂₂ complex.

<p>A-B) The soluble peptide-free (MHC-II_w, black line) and peptide-bound (MHC-II-P_22w, red line) complexes. C-D) The membrane-bound peptide-free (MHC-II_m, black line) and peptide-bound (MHC-II-P_22m, red line) complexes.</p

RMSF analysis of the water-soluble and membrane-bound MHC-II-P₇ complex.

<p>A-B) The soluble peptide-free (MHC-II_w, black line) and peptide-bound (MHC-II-P_7w, red line) species. C-D) The membrane-bound peptide-free (MHC-II_m, black line) and peptide-bound (MHC-II-P_7m, red line) complexes.</p