Chronic stress enhances progression of periodontitis via α1-adrenergic signaling: a potential target for periodontal disease therapy

This study assessed the roles of chronic stress (CS) in the stimulation of the sympathetic nervous system and explored the underlying mechanisms of periodontitis. Using an animal model of periodontitis and CS, the expression of tyrosine hydroxylase (TH) and the protein levels of the α1-adrenergic receptor (α1-AR) and β2-adrenergic receptor (β2-AR) were assessed. Furthermore, human periodontal ligament fibroblasts (HPDLFs) were stimulated with lipopolysaccharide (LPS) to mimic the process of inflammation. The proliferation of the HPDLFs and the expression of α1-AR and β2-AR were assessed. The inflammatory-related cytokines interleukin (IL)-1β, IL-6 and IL-8 were detected after pretreatment with the α1/β2-AR blockers phentolamine/propranolol, both in vitro and in vivo. Results show that periodontitis under CS conditions enhanced the expression of TH, α1-AR and β2-AR. Phentolamine significantly reduced the inflammatory cytokine levels. Furthermore, we observed a marked decrease in HPDLF proliferation and the increased expression of α1-ARfollowing LPS pretreatment. Pretreatment with phentolamine dramatically ameliorated LPS-inhibited cell proliferation. In addition, the blocking of α1-ARsignaling also hindered the upregulation of the inflammatory-related cytokines IL-1β, IL-6 and IL-8. These results suggest that CS can significantly enhance the pathological progression of periodontitis by an α1-adrenergic signaling-mediated inflammatory response. We have identified a potential therapeutic target for the treatment of periodontal disease, particularly in those patients suffering from concurrent CS.     

Binding affinity prediction for binary drug–target interactions using semi-supervised transfer learning

Journal of Computer-Aided Molecular Design - In the field of drug–target interactions prediction, the majority of approaches formulated the problem as a simple binary classification task....     

Nitazoxanide and azithromycin for the early treatment of COVID-19: A multi-spectroscopic,biochemical and computational drug–drug interaction study

Herein, we present an experimental and theoretical drug–drug interaction study between nitazoxanide (NTZ) and azithromycin (AZT) in an aqueous solution. Interaction was studied by using UV/Vis, fluorescence, attenuated total reflectance-fourier transform infrared (ATR-FTIR), and circular dichroism (CD) spectroscopy, while molecular docking studies were performed to establish the interaction computationally. A bright yellow color was observed when the two drugs interacted, giving a hyperchromic band at 420 nm. The rate of absorbance was linearly increased by increasing drug concentrations and in a time-dependent manner. Stability of the interaction complex (i.e., NTZ: AZT) was measured at variable temperatures (25–80°C), pH (5.0–10.0) and ionic strength (0.05–2.0 M NaCl), and not only proved stable but also retained antimicrobial potential with reduced cellular toxicity. Mole ratio and Job's method of continuous variations were used to establish the binding stoichiometry and found to be 2:1. The calculated binding constant (k_b = 8,400 M⁻¹) and Gibb's free energy (ΔG° = −22.4 KJ/mol) also suggested an energetically favorable interaction. FTIR spectra of NTZ: AZT complex in comparison with two drugs alone revealed significant interaction which was nicely complemented by molecular docking studies. Interaction was also successfully demonstrated in presence of carrier protein HSA and by spiking the two drugs in real samples of human plasma and urine.     

Virtual screening using a conformationally flexible target protein: models for ligand binding to p38α MAPK

We have used virtual screening to develop models for the binding of aryl substituted heterocycles to p38α MAPK. Virtual screening was conducted on a number of p38α MAPK crystal structures using a library of 46 known p38α MAPK inhibitors containing a heterocyclic core substituted by pyridine and fluorophenyl rings (structurally related to SB203580) and a set of decoy compounds. Multiple protonation states and tautomers of active and decoy compounds were considered. Each docking model was evaluated using receiver operating characteristic (ROC) curves and enrichment factors. The two best performing single crystal structures were found to be 1BL7 and 2EWA, with enrichment factors of 14.1 and 13.0 at 2 % of the virtual screen respectively. Ensembles of up to four receptors of similar conformations were generated, generally giving good or very good performances with high ROC AUCs and good enrichment. The 1BL7-2EWA ensemble was able to outperform each of its constituent receptors and gave high enrichment factors of 17.3, 12.0, 8.0 at 2, 5 and 10 % respectively, of the virtual screen. A ROC AUC of 0.94 was obtained for this ensemble. This method may be applied to other proteins where there are a large number of inhibitor classes with different binding site conformations.     

A flow-injection ultrafiltration sampling chemiluminescence system for on-line determination of drug–protein interaction

A flow-injection ultrafiltration sampling chemiluminescence system for on-line determination of cimetidine–bovine serum albumin (BSA) interaction is proposed in this paper. Cimetidine can be oxidized by N-bromosuccinimide (NBS) and sensitized by fluorescein to produce high chemiluminescence emission in basic media. The concentration of cimetidine is linear with the CL intensity in the range 3×10^–7–1×10^–4 mol L^–1 with a detection limit of 1×10^–7 mol L^–1 (3). The drug and protein were mixed in different molar ratios in 0.067 mol L^–1 phosphate buffer, pH 7.4, and incubated at 37 °C in a water bath. The ultrafiltration probe was utilized to sample the mixed solution at a flow rate of 5 µL min^–1. The data obtained by the proposed ultrafiltration flow-injection chemiluminescence method was analyzed with Scrathard analysis and a Klotz plot. The estimated association constant (K) and the number of the binding site (n) on one molecule of BSA by Scrathard analysis and Klotz plot were 3.15×10⁴ L mol^–1 and 0.95, 3.25×10⁴ L mol^–1 and 0.92, respectively. The proposed system proved that flow-injection chemiluminescence analysis coupled with on-line ultrafiltration sampling is a simple and reliable technique for the study of drug–protein interaction.     

Screening for disease-markers and investigating drug effects by proteome profiling: can it meet expectations?

Drugs exert their functions mainly by affecting proteins. Therefore, it seems straightforward to focus on proteins in order to investigate drug effects. Unfortunately, proteins are of very high complexity, rendering it much more difficult to screen for protein alterations as compared to gene regulation. However, the efficiency and applicability of proteome analysis has been dramatically increased recently. We are on the way to be able to comprehensively assess disease-related proteome alterations, which may become an essential source of information for knowledge-based drug design. This review will provide an overview of current techniques in proteome analysis, focusing on screening technologies for biomedical research. An outlook at the future potential of proteomics supported by modern bioinformatics will highlight why proteomics is worth the effort.     

Sol–gel behavior of a novel nanodroplet biomaterial for drug delivery

Nanodroplets can be considered as those nano/microemulsions in which the oil itself forms the active agent and the droplet size ambits in the nanometer range. Eugenol is an anti-inflammatory agent and its nanodroplet gel (NDG) has immense potential for topical use. Topical gels oblige some rheological characteristics to nail down the demands of proper application, stability and storage. Thus, the purpose of our study was to comprehend the effect of eugenol on the sol–gel tranisition properties of its NDGs. Towards this goal nanodroplets of eugenol were prepared and evaluated and the three selected nanodroplet formulations with 5, 10 and 5% v/v eugenol were converted into topical gel formulation using 1% w/w Carbopol 940. The NDGs were characterized using frequency sweep, creep recovery and thixotropy. All these tests pointed out that eugenol concentration has significant effect on the sol–gel behavior of NDGs. The NDGs exhibited more viscous (sol) properties than elastic (gel) properties as observed from the frequency sweep studies. The thixotropy of the NDGs was found to decrease with increase in eugenol concentration. Efforts have been made to explain the study results using mechanistic approach. The outcomes of our research studies could be of great use in future endeavors towards development of a topical NDG of eugenol with tailored sol–gel behavior.     

JR 400–NaAOT interaction: a detailed thermodynamic study of polymer–surfactant interaction bearing opposite charges

The present study entails interaction between the cationic polymer N,N-dimethylhydroxyethyl cellulose (JR 400) and the double-tailed anionic surfactant Na-bis-2-ethyhexylsulphosuccinate (NaAOT). This oppositely charged polymer and surfactant are expected to cause coacervation and precipitation; hence, we have observed formation of thick solution similar to diluted gel at [JR 400]?~?0.01 and 0.10 %?w/v in aqueous solution. Viscometry, conductometry, tensiometry, and microcalorimetry techniques are used to monitor the interaction process. The results are explained in the light of both intrachain and interchain linking by way of NaAOT reverse micelle formation. Adsorption of NaAOT monomers onto the charged side chains of the polymer shields interchain electrostatic repulsion, leading to the formation of hydrophobic microdomains and microscopic heterogeneity in the solution. The morphologies of the domains depend on the level of addition of NaAOT in the system. The different stages of physiochemical changes that arise in solution have been identified by the use of different techniques, and correlations of the results have been attempted in terms of pragmatic models.     

Ranking and similarity for quantitative structure–retention relationship models in predicting Lee retention indices of polycyclic aromatic hydrocarbons

Quantitative structure–(chromatographic) retention relationship (QSRR) models for prediction of Lee retention indices for polycyclic aromatic hydrocarbons (PAHs) were gathered from the literature and the predictive performances of models were compared. Numerous Lee retention indices (46) were served as a reliable basis for ranking by a recently developed novel method of ordering based on the sum of ranking differences (SRD) [TrAC, Trends Anal. Chem. 29 (2010) 101–109], by which the best model can be selected easily. Two kinds of references for ranking were accepted, average (consensus) and the experimental retention indices. Leave-many-out cross validation of the SRD procedure provides an easy way to group similar models. Significant differences among models can be revealed by using Wilcoxon's matched pair test.     

99mTc–meropenem as a potential SPECT imaging probe for tumor hypoxia

Meropenem was successfully radiolabeled with ^99mTc in high labeling yield (92 ± 2%) and stability (~6 h). ^99mTc–meropenem showed high accumulation in tumor hypoxic tissue (4.193% injected dose/g organ). ^99mTc–meropenem showed high ability to differentiate the tumor tissue from inflamed or infected tissues in different mice models as its T/NT ratio ~4 in case of tumor mice model while T/NT ratio ~1 in case of inflamed mice model. So, ^99mTc–meropenem showed high selectivity in comparison with FDG-PET and ^99mTc-nitroimidazole analogues. Thus, ^99mTc–meropenem could be used as a selective potential imaging agent for diagnosis of tumor hypoxia.     

Theoretical designs for germaacetylene (RC≡GeR'): a new target for synthesis

The effect of substitution on the potential energy surfaces of RC≡GeR (R = F, H, OH, CH(3), SiH(3), Tbt, Ar*, SiMe(SitBu(3))(2) and SiiPrDis(2)) was explored using density functional theories (B3LYP/LANL2DZdp and B3PW91/6-31G(d)). Our theoretical studies indicate that all the triply bonded RC≡GeR species prefer to adopt trans-bent geometry, which is in agreement with the theoretical model (mode (B)). Additionally, we show that the stabilities of the RC≡GeR species bearing smaller substituents (R = F, H, OH, CH(3) and SiH(3)) decrease in the order R(2)C=Ge: > RC≡GeR > :C=GeR(2). On the other hand, the triply bonded RC≡GeR molecules with bulkier substituents (R = Tbt, Ar*, SiMe(SitBu(3))(2), SiiPrDis(2)) were found to possess the global minimum on the singlet potential energy surface and are both kinetically and thermodynamically stable. That is to say, both electronic and steric effects of bulky substituents play a crucial role in making triply bonded germaacetylenes (RC≡GeR) an interesting synthetic target.     

Structure-based grafting and identification of kinase–inhibitors to target mTOR signaling pathway as potential therapeutics for glioblastoma

Mammalian target of rapamycin (mTOR), a key mediator of PI3K/Akt/mTOR signaling pathway, has recently emerged as a compelling molecular target in glioblastoma. The mTOR is a member of serine/threonine protein kinase family that functions as a central controller of growth, proliferation, metabolism and angiogenesis, but its signaling is dysregulated in various human diseases especially in certain solid tumors including the glioblastoma. Here, considering that there are various kinase inhibitors being approved or under clinical or preclinical development, it is expected that some of them can be re-exploited as new potent agents to target mTOR for glioblastoma therapy. To achieve this, a synthetic pipeline that integrated molecular grafting, consensus scoring, virtual screening, kinase assay and structure analysis was described to systematically profile the binding potency of various small-molecule inhibitors deposited in the protein kinase–inhibitor database against the kinase domain of mTOR. Consequently, a number of structurally diverse compounds were successfully identified to exhibit satisfactory inhibition profile against mTOR with IC₅₀ values at nanomolar level. In particular, few sophisticated kinase–inhibitors as well as a flavonoid myricetin showed high inhibitory activities, which could thus be considered as potential lead compounds to develop new potent, selective mTOR–inhibitors. Structural examination revealed diverse nonbonded interactions such as hydrogen bonds, hydrophobic forces and van der Waals contacts across the complex interface of mTOR with myricetin, conferring both stability and specificity for the mTOR–inhibitor binding.     

Protamine-stabilized gold nanoclusters as a fluorescent nanoprobe for lead(II) via Pb(II)–Au(I) interaction

The authors report on a one-pot approach for synthesizing highly fluorescent protamine-stabilized gold nanoclusters. These are shown to be a viable nanoprobe for selective and sensitive fluorometric determination of lead(II) via quenching of fluorescence via Pb(II)-Au(I) interaction. Under optimized conditions, fluorescence measured at excitation/emission peaks of 300/599 nm drops in the 80 nM–15 μM lead(II) concentration range. The detection limit is 24 nM, and relative standard deviations (for n?=?11) at concentrations of 0.10, 4.0 and 15 μM are 1.6, 2.5 and 1.9%, respectively. The relative recoveries of added lead(II) in the water samples ranged from 97.9?±?2.29% to 101.2?±?1.83%.

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Graphical abstract Lead(II) ions are found to be able to selectively and sensitively quench the fluorescence of the protamine-gold nanoclusters (PRT-AuNCs). Thereby, an inexpensive, selective and sensitive lead(II) assay was established.

     

Density functional theory of freezing of a system of conjugated oligomers parameterised via Gay–Berne potential

Density functional theory (DFT) of freezing is used to study the isotropic–nematic, isotropic–smectic A and nematic–smectic A phase transitions in a system of large, semi-flexible conjugated oligomers parameterised within Gay–Berne (GB) potential. The pair correlation functions of the isotropic fluid, used as structural inputs in the DFT, are calculated by solving the Percus–Yevick integral equation theory. Large number of spherical harmonic coefficients of each orientation-dependent functions has been considered to ensure the numerical accuracy at different densities and temperatures for the system of these model GB ellipsoids having large aspect ratio (length-to-breadth ratio). We found that the system of GB ellipsoids parameterised for conjugated oligomers shows stable isotropic, nematic and smectic A phases. At low temperatures, on increasing the density, isotropic fluid makes a direct transition to smectic A phase. Nematic phase get stabilised in between the isotropic and smectic A phases on increasing the temperature. Using the transition parameter obtained through the DFT, we have plotted the temperature–density and pressure–temperature phase diagrams which are found to be qualitatively similar to the one obtained in simulations for the systems with low aspect ratio GB particles.     

Metallomics in drug development: characterization of a liposomal cisplatin drug formulation in human plasma by CE–ICP–MS

A capillary electrophoresis inductively coupled plasma mass spectrometry method for separation of free cisplatin from liposome-encapsulated cisplatin and protein-bound cisplatin was developed. A liposomal formulation of cisplatin based on PEGylated liposomes was used as model drug formulation. The effect of human plasma matrix on the analysis of liposome-encapsulated cisplatin and intact cisplatin was studied. The presence of 1 % of dextran and 4 mM of sodium dodecyl sulfate in HEPES buffer was demonstrated to be effective in improving the separation of liposomes and cisplatin bound to proteins in plasma. A detection limit of 41 ng/mL of platinum and a precision of 2.1 % (for 10 μg/mL of cisplatin standard) were obtained. Simultaneous measurements of phosphorous and platinum allows the simultaneous monitoring of the liposomes, liposome-encapsulated cisplatin, free cisplatin and cisplatin bound to plasma constituents in plasma samples. It was demonstrated that this approach is suitable for studies of the stability of liposome formulations as leakage of active drug from the liposomes and subsequent binding to biomolecules in plasma can be monitored. This methodology has not been reported before and will improve characterization of liposomal drugs during drug development and in studies on kinetics.

Determination of fingerprints contents of different extracts and parts of six endemic Salvia taxa by GC–MS: Source species for valuable compounds with drug or drug potential

Public use of Salvia species and their importance in the scientific world is continually increasing. It is known that this use and the importance of Salvia species are mostly due to the terpenoid compounds that they contain. In this context, the terpenoid–steroid–flavonoid contents of extracts of six endemic Salvia (S. kurdica, S. pseudeuphratica, S. rosifolia, S. siirtica, S. cerino-pruinosa var. cerino-pruinosa and S. cerino-pruinosa var. elazigensis) species prepared with different solvents were determined by gas chromatography–mass spectrometry. Within the framework of the ingredient analysis, content analysis of the ethanol extracts of the root, branch, leaf and flower parts of the species collected in the same period between 2015 and 2017 years was performed. In general, extracts prepared with chloroform and ethanol were found to contain a wide variety of compounds while petroleum ether extracts were found to contain much less varied compounds. In addition, in general, root extracts are richer in terpenoid compounds than aerial part extracts. Some species can be used as source species in terms of ferruginol, cryptanol, 6,7-dehydroroyleanone, lup-(20)29-ene-2α-hydroxy-3β-acetate, salvigenin and β-sitosterol contents (52,114.28, 75,979.08, 101,247.41, 40,071.29, 33,952.13 and 34,010.90 μg analyte/g extract, respectively).