Structure-activity relationships of fluorene compounds inhibiting HCV variants

Approximately 71 million people suffer from hepatitis C virus (HCV) infection worldwide. Persistent HCV infection causes liver diseases such as chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma, resulting in approximately 400,000 deaths annually. Effective direct-acting antiviral agents (DAAs) have been developed and are currently used for HCV treatment targeting the following three proteins: NS3/4A proteinase that cleaves the HCV polyprotein into various functional proteins, RNA-dependent RNA polymerase (designated as NS5B), and NS5A, which is required for the formation of double membrane vesicles serving as RNA replication organelles. At least one compound inhibiting NS5A is included in current HCV treatment regimens due to the high efficacy and low toxicity of drugs targeting NS5A. Here we report fluorene compounds showing strong inhibitory effects on GT 1b and 3a of HCV. Moreover, some compounds were effective against resistance-associated variants to DAAs. The structure-activity relationships of the compounds were analyzed. Furthermore, we investigated the molecular bases of the inhibitory activities of some compounds by the molecular docking method.11Ysciescopu

Structural Insights from Binding Poses of CCR2 and CCR5 with Clinically Important Antagonists: A Combined In Silico Study

Chemokine receptors are G protein-coupled receptors that contain seven transmembrane domains. In particular, CCR2 and CCR5 and their ligands have been implicated in the pathophysiology of a number of diseases, including rheumatoid arthritis and multiple sclerosis. Based on their roles in disease, they have been attractive targets for the pharmaceutical industry, and furthermore, targeting both CCR2 and CCR5 can be a useful strategy. Owing to the importance of these receptors, information regarding the binding site is of prime importance. Structural studies have been hampered due to the lack of X-ray crystal structures, and templates with close homologs for comparative modeling. Most of the previous models were based on the bovine rhodopsin and β2-adrenergic receptor. In this study, based on a closer homolog with higher resolution (CXCR4, PDB code: 3ODU 2.5 Å), we constructed three-dimensional models. The main aim of this study was to provide relevant information on binding sites of these receptors. Molecular dynamics simulation was done to refine the homology models and PROCHECK results indicated that the models were reasonable. Here, binding poses were checked with some established inhibitors of high pharmaceutical importance against the modeled receptors. Analysis of interaction modes gave an integrated interpretation with detailed structural information. The binding poses confirmed that the acidic residues Glu291 (CCR2) and Glu283 (CCR5) are important, and we also found some additional residues. Comparisons of binding sites of CCR2/CCR5 were done sequentially and also by docking a potent dual antagonist. Our results can be a starting point for further structure-based drug design

Computational modeling of human coreceptor CCR5 antagonist as a HIV-1 entry inhibitor: using an integrated homology modeling, docking, and membrane molecular dynamics simulation analysis approach

<div><p>Chemokine receptor 5 (CCR5) is an integral membrane protein that is utilized during human immunodeficiency virus type-1 entry into host cells. CCR5 is a G-protein coupled receptor that contains seven transmembrane (TM) helices. However, the crystal structure of CCR5 has not been reported. A homology model of CCR5 was developed based on the recently reported CXCR4 structure as template. Automated docking of the most potent (<b>14</b>), medium potent (<b>37</b>), and least potent (<b>25</b>) CCR5 antagonists was performed using the CCR5 model. To characterize the mechanism responsible for the interactions between ligands (<b>14</b>, <b>25</b>, and <b>37</b>) and CCR5, membrane molecular dynamic (MD) simulations were performed. The position and orientation of ligands (<b>14</b>, <b>25</b>, and <b>37</b>) were found to be changed after MD simulations, which demonstrated the ability of this technique to identify binding modes. Furthermore, at the end of simulation, it was found that residues identified by docking were changed and some new residues were introduced in the proximity of ligands. Our results are in line with the majority of previous mutational reports. These results show that hydrophobicity is the determining factor of CCR5 antagonism. In addition, salt bridging and hydrogen bond contacts between ligands (<b>14</b>, <b>25</b>, and <b>37</b>) and CCR5 are also crucial for inhibitory activity. The residues newly identified by MD simulation are Ser160, Phe166, Ser180, His181, and Trp190, and so far no site-directed mutagenesis studies have been reported. To determine the contributions made by these residues, additional mutational studies are suggested. We propose a general binding mode for these derivatives based on the MD simulation results of higher (<b>14</b>), medium (<b>37</b>), and lower (<b>25</b>) potent inhibitors. Interestingly, we found some trend for these inhibitors such as, salt bridge interaction between basic nitrogen of ligand and acidic Glu283 seemed necessary for inhibitory activity. Also, two aromatic pockets (pocket I – TM1-3 and pocket II – TM3-6) were linked by the central polar region in TM7, and the simulated inhibitors show important interactions with the Trp86, Tyr89, Tyr108, Phe112, Ile198, Tyr251, Leu255, and Gln280 and Glu283 residues. These results shed light on the usage of MD simulation to identify more stable, optimal binding modes of the inhibitors.</p> </div

Binding modes of CCR2 inhibitors.

<p>TM helices are shown in pale green color, whereas constructed binding pocket residues were shown in cyan sticks. All the TM's are labeled by blue color on the top of helices. Docked ligands were shown in magenta color. (a) Docking model of Teijin shows key salt bridge interaction between pyrrolidine nitrogen and Glu291 by magenta dotted lines. Hydrogen bonding interactions are also observed with Tyr120 and His121. (b) RS-50323 shows salt bridge interaction between the linker nitrogen of the ligand and Glu291 which is indicated by magenta dotted lines. (c) Pyridyl derivative show crucial interaction between the hydrogen atom of the nitrogen and Glu291 which is indicated by magenta dotted lines. Hydrogen bonding interaction is also observed with Thr287. (d) Docking model of cyclohexyl derivatives identified crucial interaction between the hydrogen atom of nitrogen and Glu291 (magenta dotted lines). In addition, the same atom also hydrogen bonded with Tyr120.</p

Validation results of CCR2/CCR5 homology model before and after MDS.

<p>Validation results of CCR2/CCR5 homology model before and after MDS.</p

Binding modes of CCR5 inhibitors.

<p>TM helices are shown in light brown color, whereas constructed binding pocket residues were shown in green sticks. All the TM's are labeled by blue color on the top of helices. Docked ligands were shown in yellow color. (a) Docked pose of Maraviroc in CCR5, the key salt bridge interaction with Glu283 is shown by magenta dotted line. Hydrogen bonds with Try37 and Tyr108 were shown in blue dotted lines. (b) Docking model of SCH-C show a key salt bridge interaction with Glu283 and represented by magenta dotted line. Hydrogen bond with Try37 is shown as blue dotted lines. Pyridine-N-Oxide ring of ligand interacts through strong aromatic π-stacking interaction with the Trp86 of CCR5. (c) TAK779 in CCR5 shows salt bridge interaction with Glu283 which is designated by magenta dotted line. Hydrogen bonds with Try37 and Thr167 are shown in blue dotted lines. Phenyl group of TAK779 docked deeply inside the cavity formed by Ile198, Tyr251, Asn252 and Leu255. (d) Docking model of Vicriviroc shows salt bridge interaction with Glu283 which is indicated by magenta dotted line. Pyrimidine ring of ligand interacts strongly via π-stacking interaction with Trp86. Tri-fluoro-phenyl of ligand is docked deeply into the cavity formed by Phe112, Ile198, Trp248, Tyr251, Asn252 and Leu255 residues.</p

Top views of putative binding pockets after MD simulation for docking analyses.

<p>(a) CCR2 transmembrane (TM) helices are shown in light green, whereas, constructed binding pocket residues were shown in smudge green sticks. All the TM regions are labeled by blue color on the top of helices. The binding pocket is also represented as transparent molecular surfaces. (b) CCR5 TM helices are shown in light brown color, whereas constructed binding pocket residues were shown in green sticks. Figure generated using Pymol program (<a href="http://www.pymol.org" target="_blank">http://www.pymol.org</a>).</p

Graphical representation of root mean square deviation (RMSD) plot.

<p>RMSD for (a) CCR2 and (b) CCR5 Cα from the initial structures throughout the simulation of 5 ns as function of time.</p

Chemical structures of studied compounds using molecular docking.

<p>CCR2 (Compound 2, 14, RS-504393 and Teijin), CCR5 (Maraviroc, SCH351125, TAK779 and Vicriviroc) and dual inhibitors (Compound 19).</p