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Protein-ligand binding affinity prediction is a key element of computer-aided drug discovery. Most of the existing deep learning methods for protein-ligand binding affinity prediction utilize single models and suffer from low accuracy and generalization capability. In this paper, we train 13 deep learning models from combinations of 5 input features. Then, we explore all possible ensembles of the trained models to find the best ensembles. Our deep learning models use cross-attention and self-attention layers to extract short and long-range interactions. Our method is named Ensemble Binding Affinity (EBA). EBA extracts information from various models using different combinations of input features, such as simple 1D sequential and structural features of the protein-ligand complexes rather than 3D complex features. EBA is implemented to accurately predict the binding affinity of a protein-ligand complex. One of our ensembles achieves the highest Pearson correlation coefficient (R) value of 0.914 and the lowest root mean square error (RMSE) value of 0.957 on the well-known benchmark test set CASF2016. Our ensembles show significant improvements of more than 15% in R-value and 19% in RMSE on both well-known benchmark CSAR-HiQ test sets over the second-best predictor named CAPLA. Furthermore, the superior performance of the ensembles across all metrics compared to existing state-of-the-art protein-ligand binding affinity prediction methods on all five benchmark test datasets demonstrates the effectiveness and robustness of our approach. Therefore, our approach to improving binding affinity prediction between proteins and ligands can contribute to improving the success rate of potential drugs and accelerate the drug development process. [ABSTRACT FROM AUTHOR]

Maintaining life (respiration), cell death (apoptosis), oxygen transport and immunity are main biological functions of heme containing proteins. These functions are controlled by the axial ligands and the redox status of the iron ion (oscillations between Fe2+ and Fe3+) in the heme group. This paper aims to evaluate the current state of knowledge on oxidation and oxygenation effects in heme proteins. We determined the redox status of the iron ion in whole blood (without and with anticoagulant), hemoglobin in erythrocytes, in isolated cytochrome c and cytochrome c in mitochondria of the human lung cancer cells using UV–VIS electronic absorption spectroscopy, Raman spectroscopy and Raman imaging. Here we discussed the mechanism responsible for the Q electronic absorption band spectral behavior, i.e., its splitting, and its change in extinction coefficient, as well as vibrational modifications upon oxygenation and oxidation. We compared the redox status of heme in hemoglobin of human erythrocytes and cytochrome c in mitochondria of human lung cancer cells. Presented results allow simultaneous identification of oxy- and deoxy-Hb, where 1547 and 1604 cm−1 vibrations correspond to deoxygenated hemoglobin, while 1585 and 1638 cm−1 correspond to oxyhemoglobin, respectively. Our results extend knowledge of oxidation and oxygenation effects in heme proteins. We demonstrated experimentally the mechanism of electronic-vibrational coupling for the Q band splitting. Presented results extend knowledge on oxidation and oxygenation effects in heme proteins and provide evidence that both processes are strongly coupled. We showed that retinoic acid affects the redox state of heme in cytochrome c in mitochondria. The change of the redox status of cytochrome c in mitochondria from the oxidized form to the reduced form has very serious consequences in dysfunction of mitochondria resulting in inhibition of respiration, apoptosis and cytokine induction. [ABSTRACT FROM AUTHOR]

An amendment to this paper has been published and can be accessed via a link at the top of the paper. [ABSTRACT FROM AUTHOR]

In this paper, we successfully fabricated color conversion layers (CCLs) for full-color-mico-LED display using a perovskite quantum dot (PQD)/siloxane composite by ligand exchanged PQD with silane composite followed by surface activation by an addition of halide-anion containing salt. Due to this surface activation, it was possible to construct the PQD surface with a silane ligand using a non-polar organic solvent that does not damage the PQD. As a result, the ligand-exchanged PQD with a silane compound exhibited high dispersibility in the siloxane matrix and excellent atmospheric stability due to sol–gel condensation. Based on highly ambient stable PQD/siloxane composite based CCLs, full-color micro-LED display has a 1 mm pixel pitch, about 25.4 pixels per inch (PPI) resolution was achieved. In addition, due to the thin thickness of the black matrix to prevent blue light interference, the possibility of a flexible display that can be operated without damage even with a bending radius of 5 mm was demonstrated. [ABSTRACT FROM AUTHOR]

Several biochemical and biophysical methods are available to determine ligand binding affinities between a biological target and its ligands, most of which require purification, labelling or surface immobilisation. These measurements, however, remain challenging in regards to membrane proteins, as purification processes require their extraction from their native lipid environment, which may in turn impact receptor conformation and functionality. In this study, we have developed a novel experimental procedure using microscale thermophoresis (MST) directly from cell membrane fragments, to determine different ligand binding affinities to a membrane protein, the dopamine D2 receptor (D2R). In order to achieve this, two main challenges had to be overcome: determining the concentration of dopamine D2R in the crude sample; finding ways to minimize or account for non-specific binding of the ligand to cell fragments. Using MST, we were able to determine the D2R concentration in cell membrane fragments to approximately 36.8 ± 2.6 pmol/mg. Next, the doses-responses curves allowed for the determination of KD, to approximately 5.3 ± 1.7 nM, which is very close to the reported value. Important details of the experimental procedure have been detailed in this paper to allow the application of this novel method to various membrane proteins. [ABSTRACT FROM AUTHOR]

An amendment to this paper has been published and can be accessed via a link at the top of the paper. [ABSTRACT FROM AUTHOR]

An amendment to this paper has been published and can be accessed via a link at the top of the paper. [ABSTRACT FROM AUTHOR]

An amendment to this paper has been published and can be accessed via a link at the top of the paper. [ABSTRACT FROM AUTHOR]

The current study describes the construction of various ligand-based machine learning models to be used for drug-repurposing against the family of G-Protein Coupled Receptors (GPCRs). In building these models, we collected > 500,000 data points, encompassing experimentally measured molecular association data of > 160,000 unique ligands against > 250 GPCRs. These data points were retrieved from the GPCR-Ligand Association (GLASS) database. We have used diverse molecular featurization methods to describe the input molecules. Multiple supervised ML algorithms were developed, tested and compared for their accuracy, F scores, as well as for their Matthews' correlation coefficient scores (MCC). Our data suggest that combined with molecular fingerprinting, ensemble decision trees and gradient boosted trees ML algorithms are on the accuracy border of the rather sophisticated deep neural nets (DNNs)-based algorithms. On a test dataset, these models displayed an excellent performance, reaching a ~ 90% classification accuracy. Additionally, we showcase a few examples where our models were able to identify interesting connections between known drugs from the Drug-Bank database and members of the GPCR family of receptors. Our findings are in excellent agreement with previously reported experimental observations in the literature. We hope the models presented in this paper synergize with the currently ongoing interest of applying machine learning modeling in the field of drug repurposing and computational drug discovery in general. [ABSTRACT FROM AUTHOR]

Hydrogen has the potential to play an important role in decarbonising our energy systems. Crucial to achieving this is the ability to produce clean sources of hydrogen using renewable energy sources. Currently platinum is commonly used as a hydrogen evolution catalyst, however, the scarcity and expense of platinum is driving the need to develop non-platinum-based catalysts. Here we report a protein-based hydrogen evolution catalyst based on a recombinant silk protein from honeybees and a metal macrocycle, cobalt protoporphyrin (CoPPIX). We enhanced the hydrogen evolution activity three fold compared to the unmodified silk protein by varying the coordinating ligands to the metal centre. Finally, to demonstrate the use of our biological catalyst, we built a proton exchange membrane (PEM) water electrolysis cell using CoPPIX-silk as the hydrogen evolution catalyst that is able to produce hydrogen with a 98% Faradaic efficiency. This represents an exciting advance towards allowing protein-based catalysts to be used in electrolysis cells. [ABSTRACT FROM AUTHOR]

Chiral chloro-indeno pybox has served as a new ligand for the Yb(OTf)3-catalyzed asymmetric Friedel–Crafts alkylation reaction of indoles with nitroalkenes. The tunable nature of pybox ligands enables the rational design of catalysts for optimal performance in terms of both activity and stereoselectivity in a Friedel–Crafts-type reaction. Good to excellent yields and enantioselectivities were obtained for a relatively wide range of substrates, including sterically hindered compounds, under optimized reaction conditions. [ABSTRACT FROM AUTHOR]

Two new supramolecular photocatalysts containing Ru(II) polypyridine units as light-harvesting photosensitizers and Re(I) polypyridine subunits as catalytic centers have been prepared. The new species, RuRe2A and Ru2ReA, contain catalytic Re(I) subunits coordinated by the preformed CO2TEOA adduct (known to be the effective catalytic subunits; TEOA is triethanolamine) and exhibit quite efficient and selective photoreduction of CO2 to CO, with outstanding TONs of 2368 and 2695 and a selectivity of 99.9% and 98.9%, respectively. Such photocatalytic properties are significantly improved with respect to those of previously studied RuRe2 and Ru2Re parent compounds, containing chloride ligands instead of the CO2TEOA adduct. Comparison between photocatalytic performance of the new species and their parent compounds allows to investigate the effect of the CO2TEOA insertion process as well as the eventual effect of the presence of chloride ions in solution on the photocatalytic processes. The improved photocatalytic properties of RuRe2A and Ru2ReA compared with their parent species are attributed to a combined effect of different distribution of the one-electron reduced form of the supramolecular photocatalysts on the Ru-subunit(s) (leading to decreased CO formation due to a poisoning ligand loss process) and on the Re-subunit(s) and to the presence of chloride ions in solution for RuRe2 and Ru2Re, which could interfere with the CO2TEOA adduct formation, a needed requisite for CO forming catalysis. These results strongly indicate the utility of preparing supramolecular photocatalysts containing preformed adducts. [ABSTRACT FROM AUTHOR]

The cyclic peptide hormone somatostatin regulates physiological processes involved in growth and metabolism, through its binding to G-protein coupled somatostatin receptors. The isoform 2 (SSTR2) is of particular relevance for the therapy of neuroendocrine tumours for which different analogues to somatostatin are currently in clinical use. We present an extensive and systematic computational study on the dynamics of SSTR2 in three different states: active agonist-bound, inactive antagonist-bound and apo inactive. We exploited the recent burst of SSTR2 experimental structures to perform μs-long multi-copy molecular dynamics simulations to sample conformational changes of the receptor and rationalize its binding to different ligands (the agonists somatostatin and octreotide, and the antagonist CYN154806). Our findings suggest that the apo form is more flexible compared to the holo ones, and confirm that the extracellular loop 2 closes upon the agonist octreotide but not upon the antagonist CYN154806. Based on interaction fingerprint analyses and free energy calculations, we found that all peptides similarly interact with residues buried into the binding pocket. Conversely, specific patterns of interactions are found with residues located in the external portion of the pocket, at the basis of the extracellular loops, particularly distinguishing the agonists from the antagonist. This study will help in the design of new somatostatin-based compounds for theranostics of neuroendocrine tumours. [ABSTRACT FROM AUTHOR]

Binding MOAD is a database of protein–ligand complexes and their affinities with many structured relationships across the dataset. The project has been in development for over 20 years, but now, the time has come to bring it to a close. Currently, the database contains 41,409 structures with affinity coverage for 15,223 (37%) complexes. The website BindingMOAD.org provides numerous tools for polypharmacology exploration. Current relationships include links for structures with sequence similarity, 2D ligand similarity, and binding-site similarity. In this last update, we have added 3D ligand similarity using ROCS to identify ligands which may not necessarily be similar in two dimensions but can occupy the same three-dimensional space. For the 20,387 different ligands present in the database, a total of 1,320,511 3D-shape matches between the ligands were added. Examples of the utility of 3D-shape matching in polypharmacology are presented. Finally, plans for future access to the project data are outlined. [ABSTRACT FROM AUTHOR]

MR1-restricted T (MR1T) cells recognize microbial small molecule metabolites presented on the MHC Class I-like molecule MR1 and have been implicated in early effector responses to microbial infection. As a result, there is considerable interest in identifying chemical properties of metabolite ligands that permit recognition by MR1T cells, for consideration in therapeutic or vaccine applications. Here, we made chemical modifications to known MR1 ligands to evaluate the effect on MR1T cell activation. Specifically, we modified 6,7-dimethyl-8-d-ribityllumazine (DMRL) to generate 6,7-dimethyl-8-d-ribityldeazalumazine (DZ), and then further derivatized DZ to determine the requirements for retaining MR1 surface stabilization and agonistic properties. Interestingly, the IFN-γ response toward DZ varied widely across a panel of T cell receptor (TCR)-diverse MR1T cell clones; while one clone was agnostic toward the modification, most displayed either an enhancement or depletion of IFN-γ production when compared with its response to DMRL. To gain insight into a putative mechanism behind this phenomenon, we used in silico molecular docking techniques for DMRL and its derivatives and performed molecular dynamics simulations of the complexes. In assessing the dynamics of each ligand in the MR1 pocket, we found that DMRL and DZ exhibit differential dynamics of both the ribityl moiety and the aromatic backbone, which may contribute to ligand recognition. Together, our results support an emerging hypothesis for flexibility in MR1:ligand-MR1T TCR interactions and enable further exploration of the relationship between MR1:ligand structures and MR1T cell recognition for downstream applications targeting MR1T cells. [ABSTRACT FROM AUTHOR]

Recently, academic and industrial scientific communities involved in kinetics-based drug development have become immensely interested in predicting the drug target residence time. Screening drug candidates in terms of their computationally predicted residence times, which is a measure of drug efficacy in vivo, and simultaneously assessing computational binding affinities are becoming inevitable. Non-equilibrium molecular simulation approaches are proven to be useful in this purpose. Here, we have implemented an optimized approach of combining the data derived from steered molecular dynamics simulations and the Bell-Evans model to predict the absolute residence times of the antagonist ZMA241385 and agonist NECA that target the A2A adenosine receptor of the G-protein-coupled receptor (GPCR) protein family. We have predicted the absolute ligand residence times on the timescale of seconds. However, our predictions were many folds shorter than those determined experimentally. Additionally, we calculated the thermodynamics of ligand binding in terms of ligand binding energies and the per-residue contribution of the receptor. Subsequently, binding pocket hotspot residues that would be important for further computational mutagenesis studies were identified. In the experiment, similar sets of residues were found to be in significant contact with both ligands under study. Our results build a strong foundation for further improvement of our approach by rationalizing the kinetics of ligand unbinding with the thermodynamics of ligand binding. [ABSTRACT FROM AUTHOR]

Citrate (Cit) and Deferoxamine B (DFOB) are two important organic ligands coexisting in soils with distinct different affinities for metal ions. It has been theorized that siderophores and weak organic ligands play a synergistic role during the transport of micronutrients in the rhizosphere, but the geochemical controls of this process remain unknown. Here we test the hypothesis that gradients in pH and ion strength regulate and enable the cooperation. To this end, first we use potentiometric titrations to identify the dominant Zn(II)–Cit and Zn(II)–DFOB complexes and to determine their ionic strength dependent stability constants between 0 and 1 mol dm−3. We parametrise the Extended Debye-Hückel (EDH) equation and determine accurate intrinsic association constants (logβ0) for the formation of the complexes present. The speciation model developed confirms the presence of [Zn(Cit)]−, [Zn(HCit)], [Zn2(Cit)2(OH)2]4−, and [Zn(Cit)2]4−, with [Zn(Cit)]− and [Zn2(Cit)2(OH)2]4− the dominant species in the pH range relevant to rhizosphere. We propose the existence of a new [Zn(Cit)(OH)3]4− complex above pH 10. We also verify the existence of two hexadentate Zn(II)–DFOB species, i.e., [Zn(DFOB)]− and [Zn(HDFOB)], and of one tetradentate species [Zn(H2DFOB)]+. Second, we identify the pH and ionic strength dependent ligand exchange points (LEP) of Zn with citrate and DFOB and the stability windows for Zn(II)–Cit and Zn(II)–DFOB complexes in NaCl and rice soil solutions. We find that the LEPs fall within the pH and ionic strength gradients expected in rhizospheres and that the stability windows for Zn(II)–citrate and Zn(II)–DFOB, i.e., low and high affinity ligands, can be distinctly set off. This suggests that pH and ion strength gradients allow for Zn(II) complexes with citrate and DFOB to dominate in different parts of the rhizosphere and this explains why mixtures of low and high affinity ligands increase leaching of micronutrients in soils. Speciation models of soil solutions using newly determined association constants demonstrate that the presence of dissolved organic matter and inorganic ligands (i.e., bicarbonate, phosphate, sulphate, or chlorides) do neither affect the position of the LEP nor the width of the stability windows significantly. In conclusion, we demonstrate that cooperative and synergistic ligand interaction between low and high affinity ligands is a valid mechanism for controlling zinc transport in the rhizosphere and possibly in other environmental reservoirs such as in the phycosphere. Multiple production of weak and strong ligands is therefore a valid strategy of plants and other soil organisms to improve access to micronutrients. [ABSTRACT FROM AUTHOR]

The concept of Molecular Crowding depicts the high density of diverse molecules present in the cellular interior. Here, we determine the impact of low molecular weight and larger molecules on binding capacity of single-stranded DNA (ssDNA) to the cold shock protein B (CspB). Whereas structural features of ssDNA-bound CspB are fully conserved in crowded environments as probed by high-resolution NMR spectroscopy, intrinsic fluorescence quenching experiments reveal subtle changes in equilibrium affinity. Kinetic stopped-flow data showed that DNA-to-protein association is significantly retarded independent of choice of the molecule that is added to the solution, but dissociation depends in a nontrivial way on its size and chemical characteristics. Thus, for this DNA–protein interaction, excluded volume effect does not play the dominant role but instead observed effects are dictated by the chemical properties of the crowder. We propose that surrounding molecules are capable of specific modification of the protein's hydration shell via soft interactions that, in turn, tune protein–ligand binding dynamics and affinity. [ABSTRACT FROM AUTHOR]

Odorant-binding proteins (OBPs), as they occur in insects, form a distinct class of proteins that apparently has no closely related representatives in other animals. However, ticks, mites, spiders and millipedes contain genes encoding proteins with sequence similarity to insect OBPs. In this work, we have explored the structure and function of such non-insect OBPs in the mite Varroa destructor, a major pest of honey bee. Varroa OBPs present six cysteines paired into three disulphide bridges, but with positions in the sequence and connections different from those of their insect counterparts. VdesOBP1 structure was determined in two closely related crystal forms and appears to be a monomer. Its structure assembles five α-helices linked by three disulphide bridges, one of them exhibiting a different connection as compared to their insect counterparts. Comparison with classical OBPs reveals that the second of the six α-helices is lacking in VdesOBP1. Ligand-binding experiments revealed molecules able to bind only specific OBPs with a moderate affinity, suggesting that either optimal ligands have still to be identified, or post-translational modifications present in the native proteins may be essential for modulating binding activity, or else these OBPs might represent a failed attempt in evolution and are not used by the mites. [ABSTRACT FROM AUTHOR]

Centrosomal P4.1-associated protein (CPAP) plays a critical role in restricting the centriole length in human cells. Here, we report a novel, positive regulatory influence for CPAP on endocytic vesicular transport (EVT) and lysosome targeting of internalized-cell surface receptor EGFR. We observed that higher CPAP levels cause an increase in the abundance of multi-vesicular body (MVB) and EGFR is detectable in CPAP-overexpression induced puncta. The surface and cellular levels of EGFR are higher under CPAP deficiency and lower under CPAP overexpression. While ligand-engagement induced internalization or routing of EGFR into early endosomes is not influenced by cellular levels of CPAP, we found that targeting of ligand-activated, internalized EGFR to lysosome is impacted by CPAP levels. Transport of ligand-bound EGFR from early endosome to late endosome/MVB and lysosome is diminished in CPAP-depleted cells. Moreover, CPAP depleted cells appear to show a diminished ability to form MVB structures upon EGFR activation. These observations suggest a positive regulatory effect of CPAP on EVT of ligand-bound EGFR-like cell surface receptors to MVB and lysosome. Overall, identification of a non-centriolar function of CPAP in endocytic trafficking provides new insights in understanding the non-canonical cellular functions of CPAP. [ABSTRACT FROM AUTHOR]

Kokumi taste is a well-accepted and characterised taste modality and is described as a sensation of enhancement of sweet, salty, and umami tastes. The Calcium Sensing Receptor (CaSR) has been designated as the putative kokumi taste receptor for humans, and a number of kokumi-active ligands of CaSR have been discovered recently with activity confirmed both in vivo and in vitro. Domestic cats (Felis catus) are obligate carnivores and accordingly, their diet is abundant in proteins, peptides, and amino acids. We hypothesised that CaSR is a key taste receptor for carnivores, due to its role in the detection of different peptides and amino acids in other species. Using in silico, in vitro and in vivo approaches, here we compare human CaSR to that of a model carnivore, the domestic cat. We found broad similarities in ligand specificity, but differences in taste sensitivity between the two species. Indeed our in vivo data shows that cats are sensitive to CaCl2 as a kokumi compound, but don't show this same activity with Glutathione, whereas for humans the reverse is true. Collectively, our data suggest that kokumi is an important taste modality for carnivores that drives the palatability of meat-derived compounds such as amino acids and peptides, and that there are differences in the perception of kokumi taste between carnivores and omnivores. [ABSTRACT FROM AUTHOR]

CX-5461 is a G-quadruplex (G4) ligand currently in trials with initial indications of clinical activity in cancers with defects in homologous recombination repair. To identify more genetic defects that could sensitize tumors to CX-5461, we tested synthetic lethality for 480 DNA repair and genome maintenance genes to CX-5461, pyridostatin (PDS), a structurally unrelated G4-specific stabilizer, and BMH-21, which binds GC-rich DNA but not G4 structures. We identified multiple members of HRD, Fanconi Anemia pathways, and POLQ, a polymerase with a helicase domain important for G4 structure resolution. Significant synthetic lethality was observed with UBE2N and RNF168, key members of the DNA damage response associated ubiquitin signaling pathway. Loss-of-function of RNF168 and UBE2N resulted in significantly lower cell survival in the presence of CX-5461 and PDS but not BMH-21. RNF168 recruitment and histone ubiquitination increased with CX-5461 treatment, and nuclear ubiquitination response frequently co-localized with G4 structures. Pharmacological inhibition of UBE2N acted synergistically with CX-5461. In conclusion, we have uncovered novel genetic vulnerabilities to CX-5461 with potential significance for patient selection in future clinical trials. [ABSTRACT FROM AUTHOR]

The interactions of derivatives of lumisterol (L3) and vitamin D3 (D3) with liver X receptors (LXRs) were investigated. Molecular docking using crystal structures of the ligand binding domains (LBDs) of LXRα and β revealed high docking scores for L3 and D3 hydroxymetabolites, similar to those of the natural ligands, predicting good binding to the receptor. RNA sequencing of murine dermal fibroblasts stimulated with D3-hydroxyderivatives revealed LXR as the second nuclear receptor pathway for several D3-hydroxyderivatives, including 1,25(OH)2D3. This was validated by their induction of genes downstream of LXR. L3 and D3-derivatives activated an LXR-response element (LXRE)-driven reporter in CHO cells and human keratinocytes, and by enhanced expression of LXR target genes. L3 and D3 derivatives showed high affinity binding to the LBD of the LXRα and β in LanthaScreen TR-FRET LXRα and β coactivator assays. The majority of metabolites functioned as LXRα/β agonists; however, 1,20,25(OH)3D3, 1,25(OH)2D3, 1,20(OH)2D3 and 25(OH)D3 acted as inverse agonists of LXRα, but as agonists of LXRβ. Molecular dynamics simulations for the selected compounds, including 1,25(OH)2D3, 1,20(OH)2D3, 25(OH)D3, 20(OH)D3, 20(OH)L3 and 20,22(OH)2L3, showed different but overlapping interactions with LXRs. Identification of D3 and L3 derivatives as ligands for LXRs suggests a new mechanism of action for these compounds. [ABSTRACT FROM AUTHOR]

Limited evidence has suggested that terpenes found in Cannabis sativa are analgesic, and could produce an "entourage effect" whereby they modulate cannabinoids to result in improved outcomes. However this hypothesis is controversial, with limited evidence. We thus investigated Cannabis sativa terpenes alone and with the cannabinoid agonist WIN55,212 using in vitro and in vivo approaches. We found that the terpenes α-humulene, geraniol, linalool, and β-pinene produced cannabinoid tetrad behaviors in mice, suggesting cannabimimetic activity. Some behaviors could be blocked by cannabinoid or adenosine receptor antagonists, suggesting a mixed mechanism of action. These behavioral effects were selectively additive with WIN55,212, suggesting terpenes can boost cannabinoid activity. In vitro experiments showed that all terpenes activated the CB1R, while some activated other targets. Our findings suggest that these Cannabis terpenes are multifunctional cannabimimetic ligands that provide conceptual support for the entourage effect hypothesis and could be used to enhance the therapeutic properties of cannabinoids. [ABSTRACT FROM AUTHOR]

We have performed multicanonical molecular dynamics (McMD) based dynamic docking simulations to study and compare the binding mechanism between two medium-sized inhibitors (ABT-737 and WEHI-539) that bind to the cryptic site of Bcl-xL, by exhaustively sampling the conformational and configurational space. Cryptic sites are binding pockets that are transiently formed in the apo state or are induced upon ligand binding. Bcl-xL, a pro-survival protein involved in cancer progression, is known to have a cryptic site, whereby the shape of the pocket depends on which ligand is bound to it. Starting from the apo-structure, we have performed two independent McMD-based dynamic docking simulations for each ligand, and were able to obtain near-native complex structures in both cases. In addition, we have also studied their interactions along their respective binding pathways by using path sampling simulations, which showed that the ligands form stable binding configurations via predominantly hydrophobic interactions. Although the protein started from the apo state, both ligands modulated the pocket in different ways, shifting the conformational preference of the sub-pockets of Bcl-xL. We demonstrate that McMD-based dynamic docking is a powerful tool that can be effectively used to study binding mechanisms involving a cryptic site, where ligand binding requires a large conformational change in the protein to occur. [ABSTRACT FROM AUTHOR]

The development of functionally selective or biased ligands is a promising approach towards drugs with less side effects. Biased ligands for G protein-coupled receptors can selectively induce G protein activation or β-arrestin recruitment. The consequences of this selective action on cellular functions, however, are not fully understood. Here, we investigated the impact of five biased and balanced dopamine D2 receptor agonists and antagonists on the global protein expression in HEK293T cells by untargeted nanoscale liquid chromatography–tandem mass spectrometry. The proteome analysis detected 5290 protein groups. Hierarchical clustering and principal component analysis based on the expression levels of 1462 differential proteins led to a separation of antagonists and balanced agonist from the control treatment, while the biased ligands demonstrated larger similarities to the control. Functional analysis of affected proteins revealed that the antagonists haloperidol and sulpiride regulated exocytosis and peroxisome function. The balanced agonist quinpirole, but not the functionally selective agonists induced a downregulation of proteins involved in synaptic signaling. The β-arrestin-preferring agonist BM138, however, regulated several proteins related to neuron function and the dopamine receptor-mediated signaling pathway itself. The G protein-selective partial agonist MS308 influenced rather broad functional terms such as DNA processing and mitochondrial translation. [ABSTRACT FROM AUTHOR]

Although redox reactions are recognized to fractionate iron (Fe) isotopes, the dominant mechanisms controlling the Fe isotope fractionation and notably the role of organic matter (OM) are still debated. Here, we demonstrate how binding to organic ligands governs Fe isotope fractionation beyond that arising from redox reactions. The reductive biodissolution of soil Fe(III) enriched the solution in light Fe isotopes, whereas, with the extended reduction, the preferential binding of heavy Fe isotopes to large biological organic ligands enriched the solution in heavy Fe isotopes. Under oxic conditions, the aggregation/sedimentation of Fe(III) nano-oxides with OM resulted in an initial enrichment of the solution in light Fe isotopes. However, heavy Fe isotopes progressively dominate the solution composition in response to their binding with large biologically-derived organic ligands. Confronted with field data, these results demonstrate that Fe isotope systematics in wetlands are controlled by the OM flux, masking Fe isotope fractionation arising from redox reactions. This work sheds light on an overseen aspect of Fe isotopic fractionation and calls for a reevaluation of the parameters controlling the Fe isotopes fractionation to clarify the interpretation of the Fe isotopic signature. [ABSTRACT FROM AUTHOR]

We developed a computational method named Molecule Optimization by Reinforcement Learning and Docking (MORLD) that automatically generates and optimizes lead compounds by combining reinforcement learning and docking to develop predicted novel inhibitors. This model requires only a target protein structure and directly modifies ligand structures to obtain higher predicted binding affinity for the target protein without any other training data. Using MORLD, we were able to generate potential novel inhibitors against discoidin domain receptor 1 kinase (DDR1) in less than 2 days on a moderate computer. We also demonstrated MORLD's ability to generate predicted novel agonists for the D4 dopamine receptor (D4DR) from scratch without virtual screening on an ultra large compound library. The free web server is available at http://morld.kaist.ac.kr. [ABSTRACT FROM AUTHOR]

Recently, the fundamental and nanoscale understanding of complex phenomena in materials research and the life sciences, witnessed considerable progress. However, elucidating the underlying mechanisms, governed by entangled degrees of freedom such as lattice, spin, orbit, and charge for solids or conformation, electric potentials, and ligands for proteins, has remained challenging. Techniques that allow for distinguishing between different contributions to these processes are hence urgently required. In this paper we demonstrate the application of scattering-type scanning near-field optical microscopy (s-SNOM) as a novel type of nano-probe for tracking transient states of matter. We introduce a sideband-demodulation technique that allows for probing exclusively the stimuli-induced change of near-field optical properties. We exemplify this development by inspecting the decay of an electron-hole plasma generated in SiGe thin films through near-infrared laser pulses. Our approach can universally be applied to optically track ultrafast/-slow processes over the whole spectral range from UV to THz frequencies. [ABSTRACT FROM AUTHOR]

The neurotrophin receptor p75NTR plays crucial roles in neuron development and regulates important neuronal processes like degeneration, apoptosis and cell survival. At the same time the detailed mechanism of signal transduction is unclear. One of the main hypotheses known as the snail-tong mechanism assumes that in the inactive state, the death domains interact with each other and in response to ligand binding there is a conformational change leading to their exposure. Here, we show that neither rat nor human p75NTR death domains homodimerize in solution. Moreover, there is no interaction between the death domains in a more native context: the dimerization of transmembrane domains in liposomes and the presence of activating mutation in extracellular juxtamembrane region do not lead to intracellular domain interaction. These findings suggest that the activation mechanism of p75NTR should be revised. Thus, we propose a novel model of p75NTR functioning based on interaction with "helper" protein. [ABSTRACT FROM AUTHOR]

Fluorescence/luminescence-based techniques play an increasingly important role in the development of test systems for the characterization of future drug candidates, especially in terms of receptor binding in the field of G protein-coupled receptors (GPCRs). In this article, we present the establishment of a homogeneous live cell-based BRET binding assay for the histamine H2 receptor with different fluorescently labeled squaramide-type compounds synthesized in the course of this study. Py-1-labeled ligand 8 (UR-KAT478) was found to be most suitable in BRET saturation binding experiments with respect to receptor affinity (pKd = 7.35) and signal intensity. Real-time kinetic experiments showed a full association of 8 within approximately 30 min and a slow dissociation of the ligand from the receptor. Investigation of reference compounds in BRET-based competition binding with 8 yielded pKi values in agreement with radioligand binding data. This study shows that the BRET binding assay is a versatile test system for the characterization of putative new ligands at the histamine H2 receptor and represents a valuable fluorescence-based alternative to canonical binding assays. [ABSTRACT FROM AUTHOR]

Although high affinity binding between streptavidin and biotin is widely exploited, the accompanying low rate of dissociation prevents its use in many applications where rapid ligand release is also required. To combine extremely tight and reversible binding, we have introduced disulfide bonds into opposite sides of a flexible loop critical for biotin binding, creating streptavidin muteins (M88 and M112) with novel disulfide-switchable binding properties. Crystal structures reveal how each disulfide exerts opposing effects on structure and function. Whereas the disulfide in M112 disrupts the closed conformation to increase koff, the disulfide in M88 stabilizes the closed conformation, decreasing koff 260-fold relative to streptavidin. The simple and efficient reduction of this disulfide increases koff 19,000-fold, thus creating a reversible redox-dependent switch with 70-fold faster dissociation kinetics than streptavidin. The facile control of disulfide formation in M88 will enable the development of many new applications requiring high affinity and reversible binding. [ABSTRACT FROM AUTHOR]

G-protein-coupled receptors (GPCRs)—the largest family of cell-surface membrane proteins—mediate the intracellular signal transduction of many external ligands. Thus, GPCRs have become important drug targets. X-ray crystal structures of GPCRs are very useful for structure-based drug design (SBDD). Herein, we produced a new antibody (SRP2070) targeting the thermostabilised apocytochrome b562 from Escherichia coli M7W/H102I/R106L (BRIL). We found that a fragment of this antibody (SRP2070Fab) facilitated the crystallisation of the BRIL-tagged, ligand bound GPCRs, 5HT1B and AT2R. Furthermore, the electron densities of the ligands were resolved, suggesting that SPR2070Fab is versatile and adaptable for GPCR SBDD. We anticipate that this new tool will significantly accelerate structure determination of other GPCRs and the design of small molecular drugs targeting them. [ABSTRACT FROM AUTHOR]

Toll-like receptor 9 (TLR9) agonists have gained traction in recent years as potential adjuvants for the induction of adaptive immune responses. It has nonetheless remained unclear to what extent such ligands can facilitate the priming events that generate antigen-specific effector and/or memory CD8+ T-cell populations. We used an established in vitro model to prime naive precursors from human peripheral blood mononuclear cells in the presence of various adjuvants, including CpG ODN 2006, a synthetic oligonucleotide TLR9 ligand (TLR9L). Unexpectedly, we found that TLR9L induced a suboptimal inflammatory milieu and promoted the antigen-driven expansion and functional maturation of naive CD8+ T cells ineffectively compared with either ssRNA40 or 2′3′-cGAMP, which activate other pattern recognition receptors (PRRs). TLR9L also inhibited the priming efficacy of 2′3′-cGAMP. Collectively, these results suggest that TLR9L is unlikely to be a good candidate for the optimal induction of de novo CD8+ T-cell responses, in contrast to adjuvants that operate via discrete PRRs. [ABSTRACT FROM AUTHOR]

The addition of chalcone and amine components into indirubin-3′-oxime resulted in 15 new derivatives with high yields. Structures of new derivatives were also elucidated through 1D, 2D-NMR and HR-MS(ESI) spectra and X-ray crystallography. All designed compounds were screened for cytotoxic activity against four human cancer cell lines (HepG2, LU-1, SW480 and HL-60) and one human normal kidney cell line (HEK-293). Compound 6f exhibited the most marked cytotoxicity meanwhile cytotoxicity of compounds 6e, 6h and 6l was more profound toward cancer cell lines than toward normal cell. These new derivatives were further analyzed via molecular docking studies on GSK-3β enzyme. Docking analysis shows that most of the derivatives exhibited potential inhibition activity against GSK-3β with characteristic interacting residues in the binding site. The fast pulling of ligand scheme was then employed to refine the binding affinity and mechanism between ligands and GSK-3β enzyme. The computational results are expected to contribute to predicting enzyme target of the trial inhibitors and their possible interaction, from which the design of new cytotoxic agents could be created in the future. [ABSTRACT FROM AUTHOR]

The biggest challenge in colorectal cancer therapy is to avoid intestinal drug absorption before reaching the colon, while focusing on tumor specific delivery with high local concentration and minimal toxicity. In our work, thymoquinone (TQ)-loaded polymeric nanocapsules were prepared using the nanoprecipitation technique using Eudragit S100 as polymeric shell. Conjugation of anisamide as a targeting ligand for sigma receptors overexpressed by colon cancer cells to Eudragit S100 was carried out via carbodiimide coupling reaction, and was confirmed by thin layer chromatography and 1H-NMR. TQ nanocapsules were characterized for particle size, surface morphology, zeta potential, entrapment efficiency % (EE%), in vitro drug release and physical stability. A cytotoxicity study on three colon cancer cell lines (HT-29, HCT-116, Caco-2) was performed. Results revealed that the polymeric nanocapsules were successfully prepared, and the in vitro characterization showed a suitable size, zeta potential, EE% and physical stability. TQ exhibited a delayed release pattern from the nanocapsules in vitro. Anisamide-targeted TQ nanocapsules showed higher cytotoxicity against HT-29 cells overexpressing sigma receptors compared to their non-targeted counterparts and free TQ after incubation for 48 h, hence delineating anisamide as a promising ligand for active colon cancer targeting. [ABSTRACT FROM AUTHOR]

Mononuclear molybdoenzymes of the dimethyl sulfoxide reductase (DMSOR) family catalyze a number of reactions essential to the carbon, nitrogen, sulfur, arsenic, and selenium biogeochemical cycles. These enzymes are also ancient, with many lineages likely predating the divergence of the last universal common ancestor into the Bacteria and Archaea domains. We have constructed rooted phylogenies for over 1,550 representatives of the DMSOR family using maximum likelihood methods to investigate the evolution of the arsenic biogeochemical cycle. The phylogenetic analysis provides compelling evidence that formylmethanofuran dehydrogenase B subunits, which catalyze the reduction of CO2 to formate during hydrogenotrophic methanogenesis, constitutes the most ancient lineage. Our analysis also provides robust support for selenocysteine as the ancestral ligand for the Mo/W atom. Finally, we demonstrate that anaerobic arsenite oxidase and respiratory arsenate reductase catalytic subunits represent a more ancient lineage of DMSORs compared to aerobic arsenite oxidase catalytic subunits, which evolved from the assimilatory nitrate reductase lineage. This provides substantial support for an active arsenic biogeochemical cycle on the anoxic Archean Earth. Our work emphasizes that the use of chalcophilic elements as substrates as well as the Mo/W ligand in DMSORs has indelibly shaped the diversification of these enzymes through deep time. [ABSTRACT FROM AUTHOR]

Anti-programmed cell death-1 (PD-1) antibodies has been approved to treat HCC. Some PD-1 ligands (PD–L1 and PD–L2) negative tumors respond to treatment of anti-PD-1 antibodies, and this fact may be caused by the expression of PD-1 ligands on non-tumor cells. PD–L1 was recently found to be expressed on CD14+ cells from cancer patients. We investigate PD-1 ligands expression on CD14+ cells of patients with HCC and the role of CD14+ cells in an antitumor response. In this study, 87 patients diagnosed with HCC were enrolled. CD14+ cells from patients with HCC expressed PD–L1 (4.5–95.5%) and PD–L2 (0.2–95.0%). According to cut-off values, we classified patients as those either with PD–L1+PD–L2+CD14+ cells or other types of CD14+ cells. The overall survival of patients with PD–L1+PD–L2+CD14+ cells was shorter than that of patients with other types of CD14+ cells (p = 0.0023). PD–L1+PD–L2+CD14+ cells produced IL-10 and CCL1, and showed little tumoricidal activity against HepG2 cells. The tumoricidal activity of CD8+ cells from patients with PD–L1+PD–L2+CD14+ cells were suppressed by co-cultivation with CD14+ cells from the syngeneic patient. Furthermore, anti-PD-1 antibody restored their tumoricidal activity of CD8+ cells. In conclusion, some patients with HCC have PD–L1+PD–L2+CD14+ cells that suppress their antitumor response. These inhibitory functions of CD14+ cells may be associated with a poor prognosis in these patients. [ABSTRACT FROM AUTHOR]

Plasmodium falciparum is the causative agent of the deadliest human malaria. New molecules are needed that can specifically bind to erythrocytes that are infected with P. falciparum for diagnostic purposes, to disrupt host-parasite interactions, or to deliver chemotherapeutics. Aptamer technology has the potential to revolutionize biological diagnostics and therapeutics; however, broad adoption is hindered by the high failure rate of the systematic evolution of ligands by exponential enrichment (SELEX). Here we performed parallel SELEX experiments to compare the impact of two different methods for single-strand recovery on the efficiency of aptamer enrichment. Our experimental results and analysis of SELEX publications spanning 13 years implicate the alkaline denaturation step as a significant cause for inefficient aptamer selection. Thus, we applied an exonuclease single-strand recovery step in our SELEX to direct aptamers to the surface of erythrocytes infected with P. falciparum. The selected aptamers bind with high affinity (low nanomolar Kd values) and selectivity to exposed surface proteins of both laboratory parasite strains as well isolates from patients in Asia and Africa with clinical malaria. The results obtained in this study potentially open new approaches to malaria diagnosis and surveillance. [ABSTRACT FROM AUTHOR]

Thyroid eye disease (TED) affects 25–50% of patients with Graves' Disease. In TED, collagen accumulation leads to an expansion of the extracellular matrix (ECM) which causes destructive tissue remodeling. The purpose of this study was to investigate the therapeutic potential of activating the aryl hydrocarbon receptor (AHR) to limit ECM accumulation in vitro. The ability of AHR to control expression of matrix metalloproteinase-1 (MMP1) was analyzed. MMP1 degrades collagen to prevent excessive ECM. Human orbital fibroblasts (OFs) were treated with the pro-scarring cytokine, transforming growth factor beta (TGFβ) to induce collagen production. The AHR ligand, 6-formylindolo[3,2b]carbazole (FICZ) was used to activate the AHR pathway in OFs. MMP1 protein and mRNA levels were analyzed by immunosorbent assay, Western blotting and quantitative PCR. MMP1 activity was detected using collagen zymography. AHR and its transcriptional binding partner, ARNT were depleted using siRNA to determine their role in activating expression of MMP1. FICZ induced MMP1 mRNA, protein expression and activity. MMP1 expression led to a reduction in collagen 1A1 levels. Furthermore, FICZ-induced MMP1 expression required both AHR and ARNT, demonstrating that the AHR-ARNT transcriptional complex is necessary for expression of MMP1 in OFs. These data show that activation of the AHR by FICZ increases MMP1 expression while leading to a decrease in collagen levels. Taken together, these studies suggest that AHR activation could be a promising target to block excessive collagen accumulation and destructive tissue remodeling that occurs in fibrotic diseases such as TED. [ABSTRACT FROM AUTHOR]

Small-molecule agonism of peroxisome proliferator-activated receptor α (PPARα), a ligand-activated transcriptional factor involved in regulating fatty acid metabolism, is an important approach for treating dyslipidemia. Here, we determined the structures of the ligand-binding domain (LBD) of PPARα in complex with 1H-pyrazolo[3,4-b]pyridine-4-carboxylic acid derivatives, which were recently identified as PPARα-selective activators with markedly different structures from those of the well-known PPARα agonists fibrates. The crystal structures of the complexes showed that they form a canonical hydrogen-bond network involving helix 12 in the LBD, which is thought to be essential for PPARα activation, as also observed for fibrates. However, the phenyl side chain of the compounds occupies a small cavity between Ile272 and Ile354, which is rarely accessed by fibrates. This unique feature may be essential for subtype selectivity and combine with the well-characterized binding mode of fibrates to improve activity. These findings demonstrate the advantage of using 1H-pyrazolo-[3,4-b]pyridine as a skeleton of PPARα agonists and provide insight into the design of molecules for treating dyslipidemia. [ABSTRACT FROM AUTHOR]

The transporter Multidrug Resistance Protein 1 (MRP1, ABCC1) is implicated in multidrug resistant (MDR) phenotype of cancer cells. Glutathione (GSH) plays a key role in MRP1 transport activities. In addition, a ligand-stimulated GSH transport which triggers the death of cells overexpressing MRP1, by collateral sensitivity (CS), has been described. This CS could be a way to overcome the poor prognosis for patients suffering from a chemoresistant cancer. The molecular mechanism of such massive GSH transport and its connection to the other transport activities of MRP1 are unknown. In this context, we generated MRP1/MRP2 chimeras covering different regions, MRP2 being a close homolog that does not trigger CS. The one encompassing helices 16 and 17 led to the loss of CS and MDR phenotype without altering basal GSH transport. Within this region, the sole restoration of the original G1228 (D1236 in MRP2) close to the extracellular loop between the two helices fully rescued the CS (massive GSH efflux and cell death) but not the MDR phenotype. The flexibility of that loop and the binding of a CS agent like verapamil could favor a particular conformation for the massive transport of GSH, not related to other transport activities of MRP1. [ABSTRACT FROM AUTHOR]

The alpha-2,8-linked form of the polysaccharide polysialic acid (PSA) has widespread implications in physiological and pathological processes, ranging from neurological development to disease progression. Though the high electronegativity and excluded volume of PSA often promotes interference of biomolecular interactions, PSA-binding ligands have important implications for both biological processes and biotechnological applications. As such, the design, identification, and characterisation of novel ligands towards PSA is critical for expanding knowledge of PSA interactions and achieving selective glycan targeting. Here, we report on a rational approach for the identification of alpha-2,8-PSA-binding peptides, involving design from the endogenous ligand Siglec-11 and multi-platform characterisation of peptide binding. Microarray-based examination of peptides revealed charge and sequence characteristics influencing peptide affinity to PSA, and carbohydrate–peptide binding was further quantified with a novel fluorescence anisotropy assay. PSA-binding peptides exhibited specific binding to polymeric SA, as well as different degrees of selective binding in various conditions, including competition with PSA of alternating 2,8/9-linkages and screening with PSA-expressing cells. A computational study of Siglec-11 and Siglec-11-derived peptides offered synergistic insight into ligand binding. These results demonstrate the potential of PSA-binding peptides for selective targeting and highlight the importance of the approaches described herein for the study of carbohydrate interactions. [ABSTRACT FROM AUTHOR]

A computational technique for predicting the DTIs has now turned out to be an indispensable job during the process of drug finding. It tapers the exploration room for interactions by propounding possible interaction contenders for authentication through experiments of wet-lab which are known for their expensiveness and time consumption. Chemogenomics, an emerging research area focused on the systematic examination of the biological impact of a broad series of minute molecular-weighting ligands on a broad raiment of macromolecular target spots. Additionally, with the advancement in time, the complexity of the algorithms is increasing which may result in the entry of big data technologies like Spark in this field soon. In the presented work, we intend to offer an inclusive idea and realistic evaluation of the computational Drug Target Interaction projection approaches, to perform as a guide and reference for researchers who are carrying out work in a similar direction. Precisely, we first explain the data utilized in computational Drug Target Interaction prediction attempts like this. We then sort and explain the best and most modern techniques for the prediction of DTIs. Then, a realistic assessment is executed to show the projection performance of several illustrative approaches in various situations. Ultimately, we underline possible opportunities for additional improvement of Drug Target Interaction projection enactment and also linked study objectives. [ABSTRACT FROM AUTHOR]

A copper (I) polymer, [Cu2Mg(pzdc)2(H2O)5•2H2O]n (pzdc = 2,3-Pyrazinedicarboxylic acid), was synthesized by solvothermal method. The complex was characterized using X-ray diffraction (XRD), fourier transform infrared spectroscopy (FT-IR), ultraviolet-visible spectrophotometry (UV-Vis), and element analysis. X-ray crystal structure analysis reveals that the complex is a two-dimensional coordination polymer. The photophysical and luminescent properties of the complex were investigated. At room temperature, the complex exhibits reversible double strands cyclic voltammogram and displays efficient blue emission with peak maxima at 468 nm. Catalytic liquid phase oxidation of dyes and glyphosate was carried out using the copper (I) polymer as catalyst and H2O2 as oxidant. Degradation efficiencies were evaluated by varying the reaction conditions (i.e. illumination and oxidant). In the degradation reactions, the polymer exhibits high degradation efficiency within a short reaction time under the optimum reaction conditions. Furthermore, the reusability of the catalyst is excellent, showing no activity loss in four repeated cycles. The possible reaction mechanism catalyzed by the polymer was inferred on the basis of the results of electron spin resonance (ESR), electrochemical and ion chromatography analyses (IC). [ABSTRACT FROM AUTHOR]

Primary production by phytoplankton represents a major pathway whereby atmospheric CO2 is sequestered in the ocean, but this requires iron, which is in scarce supply. As over 99% of iron is complexed to organic ligands, which increase iron solubility and microbial availability, understanding the processes governing ligand dynamics is of fundamental importance. Ligands within humic-like substances have long been considered important for iron complexation, but their role has never been explained in an oceanographically consistent manner. Here we show iron co-varying with electroactive humic substances at multiple open ocean sites, with the ratio of iron to humics increasing with depth. Our results agree with humic ligands composing a large fraction of the iron-binding ligand pool throughout the water column. We demonstrate how maximum dissolved iron concentrations could be limited by the concentration and binding capacity of humic ligands, and provide a summary of the key processes that could influence these parameters. If this relationship is globally representative, humics could impose a concentration threshold that buffers the deep ocean iron inventory. This study highlights the dearth of humic data, and the immediate need to measure electroactive humics, dissolved iron and iron-binding ligands simultaneously from surface to depth, across different ocean basins. [ABSTRACT FROM AUTHOR]

Morphine and structurally-derived compounds are µ opioid receptor (µOR) agonists, and the most effective analgesic drugs. However, their usefulness is limited by serious side effects, including dependence and abuse potential. The N-substituent in morphinans plays an important role in opioid activities in vitro and in vivo. This study presents the synthesis and pharmacological evaluation of new N-phenethyl substituted 14-O-methylmorphinan-6-ones. Whereas substitution of the N-methyl substituent in morphine (1) and oxymorphone (2) by an N-phenethyl group enhances binding affinity, selectivity and agonist potency at the µOR of 1a and 2a, the N-phenethyl substitution in 14-methoxy-N-methylmorphinan-6-ones (3 and 4) converts selective µOR ligands into dual µ/δOR agonists (3a and 4a). Contrary to N-methylmorphinans 1–4, the N-phenethyl substituted morphinans 1a–4a produce effective and potent antinociception without motor impairment in mice. Using docking and molecular dynamics simulations with the µOR, we establish that N-methylmorphinans 1–4 and their N-phenethyl counterparts 1a–4a share several essential receptor-ligand interactions, but also interaction pattern differences related to specific structural features, thus providing a structural basis for their pharmacological profiles. The emerged structure-activity relationships in this class of morphinans provide important information for tuning in vitro and in vivo opioid activities towards discovery of effective and safer analgesics. [ABSTRACT FROM AUTHOR]

Abdominal aortic aneurysm (AAA) is an irreversible bulge in the artery with higher prevalence among the elderlies. Increase of the aneurysm diameter by time is a fatal phenomenon which will lead to its sidewall rupture. Invasive surgical treatments are vital in preventing from AAA development. These approaches however have considerable side effects. Targeted drug delivery using microbubbles (MBs) has been recently employed to suppress the AAA growth. The present study is aimed to investigate the surface adhesion of different types of drug-containing MBs to the inner wall of AAA through ligand-receptor binding, using fluid-structure interaction (FSI) simulation by using a patient CT-scan images of the vascular system. The effect of blood flow through AAA on MBs delivery to the intended surface was also addressed. For this purpose, the adherence of four types of MBs with three different diameters to the inner surface wall of AAA was studied in a patient with 40-mm diameter aneurysm. The effects of the blood mechanical properties on the hematocrit (Hct) percentage of patients suffering from anemia and diabetes were studied. Moreover, the impact of variations in the artery inlet velocity on blood flow was addressed. Simulation results demonstrated the dependency of the surface density of MBs (SDM) adhered on the AAA lumen to the size and the type of MBs. It was observed that the amount of SDM due to adhesion on the AAA lumen for one of the commercially-approved MBs (Optison) with a diameter of 4.5 μm was higher than the other MBs. Furthermore, we have shown that the targeted drug delivery to the AAA lumen is more favorable in healthy individuals (45% Hct) compared to the patients with diabetes and anemia. Also, it was found that the targeted drug delivery method using MBs on the patients having AAA with complicated aneurysm shape and negative inlet blood flow velocity can be severely affected. [ABSTRACT FROM AUTHOR]

Heme-copper oxygen reductases are terminal respiratory enzymes, catalyzing the reduction of dioxygen to water and the translocation of protons across the membrane. Oxygen consumption is inhibited by various substances. Here we tested the relatively unknown inhibition of cytochrome c oxidase (CcO) with isocyanate. In contrast to other more common inhibitors like cyanide, inhibition with cyanate was accompanied with the rise of a metal to ligand charge transfer (MLCT) band around 638 nm. Increasing the cyanate concentration furthermore caused selective reduction of heme a. The presence of the CT band allowed for the first time to directly monitor the nature of the ligand via surface-enhanced resonance Raman (SERR) spectroscopy. Analysis of isotope sensitive SERR spectra in comparison with Density Functional Theory (DFT) calculations identified not only the cyanate monomer as an inhibiting ligand but suggested also presence of an uretdion ligand formed upon dimerization of two cyanate ions. It is therefore proposed that under high cyanate concentrations the catalytic site of CcO promotes cyanate dimerization. The two excess electrons that are supplied from the uretdion ligand lead to the observed physiologically inverse electron transfer from heme a3 to heme a. [ABSTRACT FROM AUTHOR]

Aedes aegypti is the primary vector for transmission of Dengue, Zika and chikungunya viruses. Previously it was shown that Dengue virus infection of the mosquito led to an in increased expression of the odorant binding protein 22 (AeOBP22) within the mosquito salivary gland and that siRNA mediated knockdown of AeOBP22 led to reduced mosquito feeding behaviors. Insect OBPs are implicated in the perception, storage and transport of chemosensory signaling molecules including air-borne odorants and pheromones. AeOBP22 is unusual as it is additionally expressed in multiple tissues, including the antenna, the male reproductive glands and is transferred to females during reproduction, indicating multiple roles in the mosquito life cycle. However, it is unclear what role it plays in these tissues and what ligands it interacts with. Here we present solution and X-ray crystallographic studies that indicate a potential role of AeOBP22 binding to fatty acids, and that the specificity for longer chain fatty acids is regulated by a conformational change in the C-terminal tail that leads to creation of an enlarged binding cavity that enhances binding affinity. This study sheds light onto the native ligands for AeOBP22 and provides insight into its potential functions in different tissues. [ABSTRACT FROM AUTHOR]