An effort to discover the preferred conformation of the potent AMG3 cannabinoid analog when reaching the active sites of the cannabinoid receptors

Most of current 3D-QSAR algorithms use alignments of compounds at the training set based on reference active ligands in the first step of the construction of the pharamacophore modeling. This first step mostly defines the success of constructed pharmacophore models. In this step, it is essential to find the bioactive conformation for solid and reliable 3D-QSAR models. Therefore, we have proceeded through different approaches for revealing the preferred conformations of Δ(8)-THC derivative AMG-3 at CB1 and CB2 receptors. In the first approach, we have applied conformational search methods in gas and in solvent phases for the ligand. The derived low energy conformers using these methodologies have been modeled through 3D-QSAR studies (first generation model). In the second approach, the low energy conformers derived from molecular docking studies have been used as input for 3D-QSAR studies (second generation model). In the current study, a new approach using MD calculations in a simulated biological environment, thus the CB receptors surrounded by a lipid bilayer environment has been used (third generation). The obtained results for different environments were compared and the approach deriving the highest statistic results was used for the generation of the novel AMG3 analogs for optimal and selective binding affinities at CB1 and CB2 receptors by the de novo drug design modeling

Inferring player experiences using facial expressions analysis

© 2014 ACM. Understanding player experiences is central to game design. Video captures of players is a common practice for obtaining rich reviewable data for analysing these experiences. However, not enough has been done in investigating ways of preprocessing the video for a more efficient analysis process. This paper consolidates and extends prior work on validating the feasibility of using automated facial expressions analysis as a natural quantitative method for evaluating player experiences. A study was performed on participants playing a first-person puzzle shooter game (Portal 2) and a social drawing trivia game (Draw My Thing), and results were shown to exhibit rich details for inferring player experiences from facial expressions. Significant correlations were also observed between facial expression intensities and self reports from the Game Experience Questionnaire. In particular, the challenge dimension consistently showed positive correlations with anger and joy. This paper eventually presents a case for increasing the application of computer vision in video analyses of gameplay

Interactions of the potent synthetic AT1 antagonist analog BV6 with membrane bilayers and mesoporous silicate matrices

The present work describes the drug:membrane interactions and a drug delivery system of the novel potent AT1 blocker BV6. This designed analog has most of the pharmacological segments of losartan and an additional biphenyltetrazole moiety resulting in increased lipophilicity. We found that BV6:membrane interactions lead to compact bilayers that may in part explain its higher in vitro activity compared to losartan since such environment may facilitate its approach to AT1 receptor. Its high docking score to AT1 receptor stems from more hydrophobic interactions compared to losartan. X-ray powder diffraction (XRPD) and thermogravimetric analysis (TGA) have shown that BV6 has a crystalline form that is not decomposed completely up to 600 °C. These properties are desirable for a drug molecule. BV6 can also be incorporated into a mesoporous silicate drug-delivery matrix SBA-15. The properties of the obtained drug-delivery system have been inspected by XRD, 13C CP/MAS, TGA and nitrogen sorption experiments

Losartan’s affinity to fluid bilayers modulates lipid–cholesterol interactions

Losartan is an angiotensin II receptor antagonist mainly used for the regulation of high blood pressure. Since it was anticipated that losartan reaches the receptor site via membrane diffusion, the impact of losartan on model membranes has been investigated by small angle X-ray scattering. For this purpose 2–20 mol% losartan was incorporated into dimyristoylphosphatidylcholine (DMPC) and palmitoyl-oleoyl-phosphatidylcholine (POPC) bilayers and into their binary mixtures with cholesterol in the concentration range of 0 to 40 mol%. Effects of losartan on single component bilayers are alike. Partitioning of losartan into the membranes confers a negative charge to the lipid bilayers that causes the formation of unilamellar vesicles and a reduction of the bilayer thickness by 3–4%. Analysis of the structural data resulted in an estimate for the partial area of losartan, ALos E 40 A˚ 2 . In the presence of cholesterol, differences between the effects of losartan on POPC and DMPC are striking. Membrane condensation by cholesterol is retarded by losartan in POPC. This contrasts with DMPC, where an increase of the cholesterol content shifts the partitioning equilibrium of losartan towards the aqueous phase, such that losartan gets depleted from the bilayers from 20 mol% cholesterol onwards. This indicates (i) a chain-saturation dependent competition of losartan with lipid–cholesterol interactions, and (ii) the insolubility of losartan in the liquid ordered phase of PCs. Consequently, losartan’s action is more likely to take place in fluid plasma membrane patches rather than in domains rich in cholesterol and saturated lipid species such as in membrane raft

Small angle X-ray diffraction studies on the topography of cannabinoids in synaptic plasma membranes

In a previous publication, we have described in detail how we used small angle x-ray diffraction to determine the topography of (-)-Δ8-tetrahydrocannabinol (Δ8-THC) in dimyristoylphophatidylcholine (DMPC) bilayers, and to deduce the conformation of the THC side chain by using the iodo-analog (5′-I-Δ8-THC) in the model membrane. We have now extended our studies to synaptic plasma membrane systems where the cannabinoids are believed to exert part of their pharmacological effects. Synaptic plasma membranes (SPM) were isolated from fresh bovine brains and Δ8-THC was incorporated into the membranes. By comparing the electron density profiles of drug free and drug-containing SPM preparations, we observed an electron density increase due to the presence of Δ8-THC in a region centered at 9.2 Å from the terminal methyl groups of the membrane bilayer. In an attempt to dissect the effects of different membrane components on the topography of Δ8-THC, we carried out parallel experiments using membrane preparations from the synaptosomal membrane total lipid extract (TLX) as well as from bovine brain phosphatidyl choline extract (PCX) containing 30 mole percent cholesterol (Chol). Our results regarding the topography of Δ8-THC and 5′-I-Δ8-THC in these lipid membranes show that the TLX bilayer simulates the natural membrane environment very closely whereas in the PCX/Chol bilayer Δ8-THC resides at a location approximately 4 Å closer to the membrane interface, similar to that found in our previous study using DMPC model membrane. These x-ray diffraction results provide insights regarding the location of the binding sites on the cannabinoid receptor and indicate that preparations of the total lipid extract from synaptosomal membranes duplicate very well the properties of the intact membrane preparation

Molecular requirements involving the human platelet protease-activated receptor-4 mechanism of activation by peptide analogues of its tetheredligand

Thrombin is the most potent agonist of human platelets and its effects are primarily mediated through the protease-activated receptors (PARs)-1 and -4. Although PAR-1 has higher affinity for thrombin than PAR-4, both receptors contribute to thrombin-mediated actions on platelets. Recently, a potent and selective PAR-1 antagonist (vorapaxar) was approved for clinical use in selected patients. In contrast, despite the fact that several PAR-4 antagonists have been developed, few of them have been tested in clinical trials. The aim of the present study was to elucidate the molecular requirements involving the PAR-4 mechanism of activation by peptide analogues of its tethered-ligand. Eight synthetic PAR-4 tethered-ligand peptide analogues were synthesized and studied for their agonistic/antagonistic potency and selectivity toward human washed platelet aggregation, using light transmittance aggregometry. In addition, in silico studies were conducted to describe the receptor–peptide interactions that are developed following PAR-4 exposure to the above analogues. To provide a first structure-activity relationship rationale on the bioactivity profiles recorded for the studied analogues, molecular docking was applied in a homology model of PAR-4, derived using the crystal structure of PAR-1. The following peptide analogues were synthesized: AYPGKF-NH2 (1), GYPGKF-NH2 (2), AcAYPGKF-NH2 (3), trans-cinnamoyl-AYPGKF-NH2 (4), YPGKF-NH2 (5), Ac-YPGKF-NH2 (6), transcinnamoyl-YPGKF-NH2 (7), and caffeoyl-YPGKF-NH2 (8). Peptide (1) is a selective PAR-4 agonist inducing platelet aggregation with an IC50 value of 26.2 μM. Substitution of Ala-1 with Gly-1 resulted in peptide (2), which significantly reduces the agonistic potency of peptide (1) by 25- fold. Importantly, substitution of Ala-1 with trans-cinnamoyl-1 resulted in peptide (7), which completely abolishes the agonistic activity of peptide (1) and renders it with a potent antagonistic activity toward peptide (1)-induced platelet aggregation. All other peptides tested were inactive. Tyr-2, residue, along with its neighboring environment was a key determinant in the PAR-4 recognition mode. When the neighboring residues to Tyr-2 provided an optimum spatial ability for the ligand to enter into the binding site of the transmembrane receptor, a biological response was propagated. These results were compared with the predicted binding poses of small molecule antagonists of PAR-4, denoted as YD-3, ML-354, and BMS-986120. π–π stacking interaction with Tyr-183 appears to be critical and common for both small molecules antagonists and the peptide trans-cinnamoyl-YPGKFNH2. Conclusively, the lipophilicity, size, and aromatic nature of the residue preceding Tyr-2 are determining factors on whether a human platelet PAR-4 tethered-ligand peptide analogue will exert an agonistic or antagonistic activit

Bilayer structure and physical dynamics of the cytochrome b5 dimyristoylphosphatidylcholine interaction

Cytochrome b5 is a microsomal membrane protein which provides reducing potential to delta 5-, delta 6-, and delta 9-fatty acid desaturases through its interaction with cytochrome b5 reductase. Low angle x-ray diffraction has been used to determine the structure of an asymmetrically reconstituted cytochrome b5:DMPC model membrane system. Differential scanning calorimetry and fluorescence anisotropy studies were performed to examine the bilayer physical dynamics of this reconstituted system. These latter studies allow us to constrain structural models to those which are consistent with physical dynamics data. Additionally, because the nonpolar peptide secondary structure remains unclear, we tested the sensitivity of our model to different nonpolar peptide domain configurations. In this modeling approach, the nonpolar peptide moiety was arranged in the membrane to meet such chemically determined criteria as protease susceptibility of carboxyl- and amino-termini, tyrosine availability for pH titration and tryptophan 109 location, et cetera. In these studies, we have obtained a reconstituted cytochrome b5:DMPC bilayer structure at approximately 6.3 A resolution and conclude that the nonpolar peptide does not penetrate beyond the bilayer midplane. Structural correlations with calorimetry, fluorescence anisotropy and acyl chain packing data suggest that asymmetric cytochrome b5 incorporation into the bilayer increases acyl chain order. Additionally, we suggest that the heme peptide:bilayer interaction facilitates a discreet heme peptide orientation which would be dependent upon phospholipid headgroup composition

Blink To Win: Blink Patterns of Video Game Players Are Connected to Expertise

In this study, we analyzed the blinking behavior of players in a video game tournament. Our aim was to test whether spontaneous blink patterns differ across levels of expertise. We used blink rate, blink duration, blink frequency, and eyelid movements represented by the Eye Aspect Ratio (EAR) to train a machine learning classifier to discriminate between different levels of expertise. Classifier performance was highly influenced by features such as the mean, standard deviation and median EAR. Moreover, further analysis suggests that blinking rate and blink duration are likely to increase along with the level of expertise. We speculate this may be indicative of a reduction in cognitive load and lowered stress of expert players. In general, our results suggest that EAR and blink patterns can be used to identify different levels of expertise of video game players

Discovery of a new generation of angiotensin receptor blocking drugs:Receptor mechanisms and in silico binding to enzymes relevant to SARS-CoV-2

The discovery and facile synthesis of a new class of sartan-like arterial antihypertensive drugs (angiotensin receptor blockers [ARBs]), subsequently referred to as “bisartans” is reported. In vivo results and complementary molecular modelling presented in this communication indicate bisartans may be beneficial for the treatment of not only heart disease, diabetes, renal dysfunction, and related illnesses, but possibly COVID-19. Bisartans are novel bis-alkylated imidazole sartan derivatives bearing dual symmetric anionic biphenyl tetrazole moieties. In silico docking and molecular dynamics studies revealed bisartans exhibited higher binding affinities for the ACE2/spike protein complex (PDB 6LZG) compared to all other known sartans. They also underwent stable docking to the Zn2+ domain of the ACE2 catalytic site as well as the critical interfacial region between ACE2 and the SARS-CoV-2 receptor binding domain. Additionally, semi-stable docking of bisartans at the arginine-rich furin-cleavage site of the SARS-CoV-2 spike protein (residues 681–686) required for virus entry into host cells, suggest bisartans may inhibit furin action thereby retarding viral entry into host cells. Bisartan tetrazole groups surpass nitrile, the pharmacophoric “warhead” of PF-07321332, in its ability to disrupt the cysteine charge relay system of 3CLpro. However, despite the apparent targeting of multifunctional sites, bisartans do not inhibit SARS-CoV-2 infection in bioassays as effectively as PF-07321332 (Paxlovid)