Ion Transport, Selectivity, and Electronic Polarization in Fluoride Channels

Fluoride channels (Fluc) export toxic F- from the cytoplasm. Crystallography and mutagenesis have identified several conserved residues crucial for fluoride transport, but the transport mechanism at the molecular level has remained elusive. Herein we have applied constant-pH molecular dynamics and free energy sampling methods to investigate fluoride transfer through a Fluc protein from Escherichia coli. We find that fluoride is facile to transfer in its charged form, i.e., F-, by traversing through a non-bonded network. The extraordinary F- selectivity is gained by the hydrogen-bonding capability of the central binding site and the Coulombic filter at the channel entrance. The F- transfer rate calculated using an electronically polarizable force field is significantly more accurate compared to the experimental value than that calculated using a more standard additive force field, suggesting an essential role for electronic polarization in the F- - Fluc interactions.

Histidine Protonation Controls Structural Heterogeneity in the Cyanobacteriochrome AnPixJg2

Cyanobacteriochromes are compact and spectrally diverse photoreceptor proteins that bind a linear tetrapyrrole as a chromophore. They show photochromicity by having two stable states that can be interconverted by the photoisomerization of the chromophore. Hence, these photochemical properties make them an attractive target for biotechnological applications. However, their application is impeded by structural heterogeneity that reduces the yield of the photoconversion. The heterogeneity can originate either from the chromophore structure or the protein environment. Here, we study the origin of the heterogeneity in AnPixJg2, a representative member of the red/green cyanobacteriochrome family, that has a red absorbing parental state and a green absorbing photoproduct state. Using molecular dynamics simulations and umbrella sampling we have identified the protonation state of a conserved histidine residue as a trigger for structural heterogeneity. When the histidine is in a neutral form, the chromophore structure is homogenous, while in a positively charged form, the chromophore is heterogeneous with two different conformations. We have identified a correlation between the protonation of the histidine and the structural heterogeneity of the chromophore by detailed characterization of the interactions in the protein binding site. Our findings reconcile seemingly contradicting spectroscopic studies that attribute the heterogeneity to different sources. Furthermore, we predict that circular dichroism can be used as a diagnostic tool to distinguish different substates.Significance statementCyanobacteriochromes are photoreceptor proteins that have attracted attention for their immense potential in bioimaging and optogenetics applications. This is due to their desirable properties such as compactness, photochromicity and diverse spectral tuning. Despite these advantages, nature has set a limitation in the form of structural heterogeneity that presents a drawback for its application in biotechnology. We have identified a histidine residue in the vicinity of the chromophore as the origin of the heterogeneity in red/green CBCRs. The protonation state of this conserved histidine alters an extended network of protein-chromophore interactions and induces heterogeneity. Furthermore, theoretical CD spectroscopy has revealed easy identification of heterogeneity. Hence, our study paves the way for rational design and optimization of protein properties.

Capsaicin-Cyclodextrin Complex Enhances Mepivacaine Targeting and Improves Local Anesthesia in Inflamed Tissues

Acidic environments, such as in inflamed tissues, favor the charged form of local anesthetics (LA). Hence, these drugs show less cell permeation and diminished potency. Since the analgesic capsaicin (CAP) triggers opening of the TRPV1 receptor pore, its combination with LAs could result in better uptake and improved anesthesia. We tested the above hypothesis and report here for the first time the analgesia effect of a two-drug combination (LA and CAP) on an inflamed tissue. First, CAP solubility increased up to 20 times with hydroxypropyl-beta-cyclodextrin (HP-β-CD), as shown by the phase solubility study. The resulting complex (HP-β-CD-CAP) showed 1:1 stoichiometry and high association constant, according to phase-solubility diagrams and isothermal titration calorimetry data. The inclusion complex formation was also confirmed and characterized by differential scanning calorimetry (DSC), X-ray diffraction, and 1H-NMR. The freeze-dried complex showed physicochemical stability for at least 12 months. To test in vivo performance, we used a pain model based on mouse paw edema. Results showed that 2% mepivacaine injection failed to anesthetize mice inflamed paw, but its combination with complexed CAP resulted in pain control up to 45 min. These promising results encourages deeper research of CAP as an adjuvant for anesthesia in inflamed tissues and cyclodextrin as a solubilizing agent for targeting molecules in drug delivery.

Multiwalled Carbon Nanotubes-CeO2 Nanorods: A “Nanonetwork” Modified Electrode for Detecting Trace Rifampicin

Herein, a “nanonetwork” modified electrode was fabricated based on multiwalled carbon nanotubes and CeO2 nanorods. Scanning electron microscopy, X-ray powder diffraction and zeta potential were employed to characterize this electrode. Multiwalled carbon nanotubes negatively charged and CeO2 nanorods positively charged form “nanonetwork” via electrostatic interaction. The performance of the CeO2 nanorods-based electrode remarkably improved due to the introduction of multiwalled carbon nanotubes. The detection of rifampicin (RIF) was used as a model system to probe this novel electrode. The results showed a significant electrocatalytic activity for the redox reaction of RIF. Differential pulse voltammetry was used to detect rifampicin, the reduction peak current of rifampicin linear with the logarithm of their concentrations in the range of 1.0 × 10−13–1.0 × 10−6 mol/L, The linear equation is ip = 6.72 + 0. 46lgc, the detect limit is 3.4 × 10−14 mol/L (S/N = 3). Additionally, the modified electrode exhibits enduring stability, excellent reproducibility, and high selectivity. This strategy can be successfully used to detect trace rifampicin in samples with satisfactory results.

Fast Identification of Possible Drug Treatment of Coronavirus Disease -19 (COVID-19) Through Computational Drug Repurposing Study

<p>The recent outbreak of novel coronavirus disease -19 (COVID-19) calls for and welcomes possible treatment strategies using drugs on the market. It is very efficient to apply computer-aided drug design techniques to quickly identify promising drug repurposing candidates, especially after the detailed 3D-structures of key virous proteins are resolved. Taking the advantage of a recently released crystal structure of COVID-19 protease in complex with a covalently-bonded inhibitor, N3,¹ I conducted virtual docking screening of approved drugs and drug candidates in clinical trials. For the top docking hits, I then performed molecular dynamics simulations followed by binding free energy calculations using an endpoint method called MM-PBSA-WSAS.^2-4 Several promising known drugs stand out as potential inhibitors of COVID-19 protease, including Carfilzomib, Eravacycline, Valrubicin, Lopinavir and Elbasvir. Carfilzomib, an approved anti-cancer drug acting as a proteasome inhibitor, has the best MM-PBSA-WSAS binding free energy, -13.82 kcal/mol. Streptomycin, an antibiotic and a charged molecule, also demonstrates some inhibitory effect, even though the predicted binding free energy of the charged form (-3.82 kcal/mol) is not nearly as low as that of the neutral form (-7.92 kcal/mol). One bioactive, PubChem 23727975, has a binding free energy of -12.86 kcal/mol. Detailed receptor-ligand interactions were analyzed and hot spots for the receptor-ligand binding were identified. I found that one hotspot residue HIS41, is a conserved residue across many viruses including COVID-19, SARS, MERS, and HCV. The findings of this study can facilitate rational drug design targeting the COVID-19 protease.</p><p> </p>

Fast Identification of Possible Drug Treatment of Coronavirus Disease -19 (COVID-19) Through Computational Drug Repurposing Study

<p>The recent outbreak of novel coronavirus disease -19 (COVID-19) calls for and welcomes possible treatment strategies using drugs on the market. It is very efficient to apply computer-aided drug design techniques to quickly identify promising drug repurposing candidates, especially after the detailed 3D-structures of key virous proteins are resolved. Taking the advantage of a recently released crystal structure of COVID-19 protease in complex with a covalently-bonded inhibitor, N3,¹ I conducted virtual docking screening of approved drugs and drug candidates in clinical trials. For the top docking hits, I then performed molecular dynamics simulations followed by binding free energy calculations using an endpoint method called MM-PBSA-WSAS.^2-4 Several promising known drugs stand out as potential inhibitors of COVID-19 protease, including Carfilzomib, Eravacycline, Valrubicin, Lopinavir and Elbasvir. Carfilzomib, an approved anti-cancer drug acting as a proteasome inhibitor, has the best MM-PBSA-WSAS binding free energy, -13.82 kcal/mol. Streptomycin, an antibiotic and a charged molecule, also demonstrates some inhibitory effect, even though the predicted binding free energy of the charged form (-3.82 kcal/mol) is not nearly as low as that of the neutral form (-7.92 kcal/mol). One bioactive, PubChem 23727975, has a binding free energy of -12.86 kcal/mol. Detailed receptor-ligand interactions were analyzed and hot spots for the receptor-ligand binding were identified. I found that one hotspot residue HIS41, is a conserved residue across many viruses including COVID-19, SARS, MERS, and HCV. The findings of this study can facilitate rational drug design targeting the COVID-19 protease.</p><p> </p>

Cocrystal solubility-pH and drug solubilization capacity of sodium dodecyl sulfate – mass action model for data analysis and simulation to improve design of experiments

This review discusses the disposition of the anionic surfactant, sodium dodecyl sulfate (SDS; i.e., sodium lauryl sulfate), to solubilize sparingly-soluble drugs above the surfactant critical micelle concentration (CMC), as quantitated by the solubilization capacity (k). A compilation of 101 published SDS k values of mostly poorly-soluble drug molecules was used to develop a prediction model as a function of the drug’s intrinsic solubility, S0, and its calculated H-bond acceptor/donor potential. In almost all cases, the surfactant was found to solubilize the neutral form of the drug. Using the mass action model, the k values were converted to drug-micelle stoichiometric binding constants, Kn, corresponding to drug-micelle equilibria in drug-saturated solutions. An in-depth case study (data from published sources) considered the micellization reactions as a function of pH of a weak base, B, (pKa 3.58, S0 52 μg/mL), where at pH 1 the BH.SDS salt was predicted to precipitate both below and above the CMC. At low SDS concentrations, two drug salts were predicted to co-precipitate: BH.Cl and BH.SDS. Solubility products of both were determined from the analysis of the reported solubility-surfactant data. Above the CMC, in a rare example, the charged form of the drug (BH+) appeared to be strongly solubilized by the surfactant. The constant for that reaction was also determined. At pH 7, the reactions were simpler, as only the neutral form of the drug was solubilized, to a significantly lesser extent than at pH 1. Case studies also featured examples of solubilization of solids in the form of cocrystals. For many cocrystal systems studied in aqueous solution, the anticipated supersaturated state is not long-lasting, as the drug component precipitates to a thermodynamically stable form, thus lowering the amount of the active ingredient available for intestinal absorption. Use of surfactant can prevent this. A recently-described method for predicting the solubility product of cocrystals (coupled with predicted k values described here) allowed for simulations of solubility-pH speciation profiles of cocrystal systems in the presence of SDS. Well in advance of any actual measurements, these simulations can be used to probe conditions favorable to the design of cocrystal experiments where SDS stabilizes cocrystal suspensions against drug precipitation over a predicted range of pH values.

Gothic possessives, adjectives, and other modifiers in-ata

The paradigm of some possessive pronouns, adjectives, and some other modifiers in Gothic contains an instance of morphological variation in the neuter nominative and accusative singular, where the bare stem of the modifier alternates with the pronominally inflected form in-ata(for example,juggversusjuggata‘young’). In an effort to account for this morphological variation, this paper examines the evidence for the competition between the bare stem and inflected forms in-ataattested in the Gothic New Testament. Further, it assesses the synchronic and diachronic implications of the variation with a view to gaining a better understanding of the development of the Germanic strong modifier inflection. It demonstrates that-atais a stylistically charged form observed in specific contexts and grammatical environments. From a diachronic point of view, the evidence of-atasheds light on the development of the Germanic strong modifier inflection, pointing toward a lexical diffusion-type development, with the inflection of demonstrative pronouns spreading across the lexicon of modifiers through possessive pronouns and quantifiers to adjectives and participles.*

Anionic coordination complexes of C60 and C70 with cyclopentadienyl and pentamethylcyclopentadienyl molybdenum dicarbonyl

Crystalline molybdenum η2-complexes with fullerenes C60 and C70 in the neutral and negatively charged form were obtained and studied.