Viscoelastic Supramolecular Hyaluronan-Peptide Cross-Linked Hydrogels.

Viscoelasticity plays a key role in hydrogel design. We designed a physically cross-linked hydrogel with tunable viscoelasticity, comprising supramolecular-assembled peptides coupled to hyaluronan (HA), a native extracellular matrix component. We then explored the structural and molecular mechanisms underlying the mechanical properties of a series of these HA-peptide hydrogels. By modifying the peptide sequence, we modulated both long- and short-time stress relaxation rates as a way to target viscoelasticity with limited impact on stiffness, leading to gels that relax up to 60% of stress in 10 min. Gels with the highest viscoelasticity exhibited large mesh sizes and ß-sheet secondary structures. The stiffness of the gel correlated with hydrogen bonding between the peptide chains. These gels are cytocompatible: highly viscoelastic gels that mimic the native skin microenvironment promote dermal fibroblast cell spreading. Moreover, HA-peptide gels enabled cell encapsulation, as shown with primary human T cells. Overall, these physically-cross-linked hydrogels enable tunable viscoelasticity that can be used to modulate cell morphology.

Transfer-based nuclear magnetic resonance uncovers unique mechanisms for protein-polymer and protein-nanoparticle binding behavior.

Nanoparticle-based drug delivery systems have shown increasing popularity as a means to improve patient outcomes by improving the effectiveness of active pharmaceutical ingredients (APIs). Similarly, nanoparticles have shown success in targeting alternative routes of API administration, such as applying mucoadhesion or mucopenetration to mucosal drug delivery to enhance uptake. While there are many promising examples of mucoadhesive nanomedicines in literature, there are also many examples of contradictory mucoadhesive binding behavior, most prominently in cases using the same nanoparticle materials. We have uncovered mechanistic insights in polymer-protein binding systems using nOe transfer-based NMR and sought to leverage them to explore nanoparticle-protein interactions. We tested several polymer-coated nanoparticles and micellar polymer nanoparticles and evaluated their binding with mucin proteins. We uncovered that the composition and interaction intimacy of polymer moieties that promote mucin binding change when the polymers are incorporated onto nanoparticle surfaces compared to polymer in solution. This change from solution state to nanoparticle coating can enable switching of behavior of these materials from inert to binding, as we observed in polyvinyl pyrrolidone. We also found the nanoparticle core was influential in determining the binding fate of polymer materials, whereas the nanoparticle size did not possess a clear correlation in the ranges we tested (60-270 nm). These experiments demonstrate that identical polymers may switch their binding behavior to mucin as a function of conformational changes that are induced by incorporating the polymers onto the surface of nanoparticles. These NMR-derived insights could be further leveraged to optimize nanoparticle formulations and guide polymer-mediated mucoadhesion.

Isomerization of bioactive acylhydrazones triggered by light or thiols.

The acylhydrazone unit is well represented in screening databases used to find ligands for biological targets, and numerous bioactive acylhydrazones have been reported. However, potential E/Z isomerization of the C=N bond in these compounds is rarely examined when bioactivity is assayed. Here we analysed two ortho-hydroxylated acylhydrazones discovered in a virtual drug screen for modulators of N-methyl-D-aspartate receptors and other bioactive hydroxylated acylhydrazones with structurally defined targets reported in the Protein Data Bank. We found that ionized forms of these compounds, which are populated under laboratory conditions, photoisomerize readily and the isomeric forms have markedly different bioactivity. Furthermore, we show that glutathione, a tripeptide involved with cellular redox balance, catalyses dynamic E⇄Z isomerization of acylhydrazones. The ratio of E to Z isomers in cells is determined by the relative stabilities of the isomers regardless of which isomer was applied. We conclude that E/Z isomerization may be a common feature of the bioactivity observed with acylhydrazones and should be routinely analysed.

Investigating the Molecular Mechanism of Protein-Polymer Binding with Direct Saturation Compensated Nuclear Magnetic Resonance.

Herein, we describe a new technique, direct saturation compensated transfer (DISCO) NMR, to characterize protein-macromolecule interactions. DISCO enables the direct observation of intermolecular interactions and is used to investigate mucoadhesion, a type of polymer-protein interaction that is widely implemented in drug delivery but remains poorly understood. In a model system of bovine submaxillary mucin and poly(acrylic acid), DISCO identifies selective backbone interactions that facilitate mucoadhesion through chain interpenetration. DISCO demonstrated distinct patterns of molecular selectivity between mucoadhesive polymers when applied to hydroxypropyl cellulose and carboxymethyl cellulose and that functionalizing adhesive polymers with strongly interacting moieties may be detrimental to the overall adhesive interaction. Additionally, DISCO was used to estimate polymer-protein dissociation constants using individual proton signals as reporters. Overall, DISCO can be used as a label-free screening tool to generate polymer-specific binding fingerprints to map and quantify interactions between macromolecules.

Minimizing the risk of deducing wrong natural product structures from NMR data.

There continues to be a disturbing number of natural products reported in the literature whose structures are incorrect. At least in part, this reflects the fact that many natural product chemists have limited formal nuclear magnetic resonance training. Gaps in training and lack of awareness regarding the challenges and ambiguities associated with two-dimensional nuclear magnetic resonance data interpretation can easily lead to errors in structure elucidation. The purpose of this tutorial is to point out some of these issues, highlight the kinds of errors that have been made and provide specific advice on how to avoid these missteps such that the risk of reporting a wrong structure is minimized.

Synthesis, Crystallography, and Anti-Leukemic Activity of the Amino Adducts of Dehydroleucodine.

Dehydroleucodine is a bioactive sesquiterpene lactone. Herein, four dehydroleucodine amino derivatives were synthesized using the amines proline, piperidine, morpholine, and tyramine, and spectroscopic methods and single-crystal X-ray diffraction unambiguously established their structures. The cytotoxic activity of these compounds was evaluated against eight acute myeloid leukemia cell lines, and their toxicity to peripheral blood mononuclear cells was also determined. The proline adduct was the most active compound, it showed anti-leukemic activity, upregulated heme oxygenase 1 (HMOX1) and the primary stress-inducible isoform of the heath shock 70 kDa protein 1 (HSPA1A), and downregulated NFkB1 transcription, it was also found to be about 270 times more water soluble than dehydroleucodine.

The role of computer-assisted structure elucidation (CASE) programs in the structure elucidation of complex natural products.

Covering: up to the end of December, 2018 There are still a disturbing number of incorrect natural product structure elucidations reported in the literature. The use of Computer-Assisted Structure Elucidation (CASE) programs can minimize this risk by generating all structures that are consistent with the input data and by ranking these structures in order of probability. They can successfully determine structures for complex natural products, with the possible exception of compounds with very few protons. Current CASE programs utilize mainly 2D COSY and HMBC correlation data for structure generation with a starting assumption that all observed peaks are due to pairs of atoms no more than 3 bonds apart. We discuss these assumptions and the problems that occur when they are violated. We also discuss the advantages and disadvantages of other types of 2D data that could be included at the structure generation stage. Four different CASE programs are described with particular emphasis on how they deal with the presence of longer range correlation peaks. These programs provide only planar skeletal structures. However, a new program that relies on different types of stereospecific NMR data to determine 3D structures is also described. Other types of computer assistance for structure elucidation are discussed, including the increasing use of theoretical DFT calculations to determine 3D structures and to predict chemical shifts. Finally, we suggest possible improvements in these programs and suggest that a challenge match between the developers of current CASE programs would be useful.

A model for C-F activation by electrophilic phosphonium cations.

The synthesis of the electrophilic phosphonium cation (EPC) salt [C10H6(CF3)PF(C6F5)2][B(C6F5)4] 4 was achieved via oxidation of phosphine [C10H6(CF3)P(C6F5)2] 2 with XeF2 to form phosphorane [C10H6(CF3)PF2(C6F5)2] 3 and subsequent fluoride ion abstraction. Structural and spectroscopic characterization of 4 provides evidence of an interaction between the CF3 functionality and the phosphonium centre. AIM and NBO analyses also support donation from a lone pair on a fluorine atom of the CF3 group to the P-F σ* orbital of the fluorophosphonium unit, consistent with previously proposed mechanisms for main group C-F bond activations.

Stereochemical inversion of (S)-reticuline by a cytochrome P450 fusion in opium poppy.

The gateway to morphine biosynthesis in opium poppy (Papaver somniferum) is the stereochemical inversion of (S)-reticuline since the enzyme yielding the first committed intermediate salutaridine is specific for (R)-reticuline. A fusion between a cytochrome P450 (CYP) and an aldo-keto reductase (AKR) catalyzes the S-to-R epimerization of reticuline via 1,2-dehydroreticuline. The reticuline epimerase (REPI) fusion was detected in opium poppy and in Papaver bracteatum, which accumulates thebaine. In contrast, orthologs encoding independent CYP and AKR enzymes catalyzing the respective synthesis and reduction of 1,2-dehydroreticuline were isolated from Papaver rhoeas, which does not accumulate morphinan alkaloids. An ancestral relationship between these enzymes is supported by a conservation of introns in the gene fusions and independent orthologs. Suppression of REPI transcripts using virus-induced gene silencing in opium poppy reduced levels of (R)-reticuline and morphinan alkaloids and increased the overall abundance of (S)-reticuline and its O-methylated derivatives. Discovery of REPI completes the isolation of genes responsible for known steps of morphine biosynthesis.

Optical control of protein-protein interactions via blue light-induced domain swapping.

The design of new optogenetic tools for controlling protein function would be facilitated by the development of protein scaffolds that undergo large, well-defined structural changes upon exposure to light. Domain swapping, a process in which a structural element of a monomeric protein is replaced by the same element of another copy of the same protein, leads to a well-defined change in protein structure. We observe domain swapping in a variant of the blue light photoreceptor photoactive yellow protein in which a surface loop is replaced by a well-characterized protein-protein interaction motif, the E-helix. In the domain-swapped dimer, the E-helix sequence specifically binds a partner K-helix sequence, whereas in the monomeric form of the protein, the E-helix sequence is unable to fold into a binding-competent conformation and no interaction with the K-helix is seen. Blue light irradiation decreases the extent of domain swapping (from Kd = 10 µM to Kd = 300 µM) and dramatically enhances the rate, from weeks to <1 min. Blue light-induced domain swapping thus provides a novel mechanism for controlling of protein-protein interactions in which light alters both the stability and the kinetic accessibility of binding-competent states.

CRAPT: an improved version of APT with compensation for variations in JCH.

A modified version of the attached proton test (APT) sequence for (13)C spectral editing, which we call CRisis-APT (CRAPT), is developed and tested on representative organic compounds. CRAPT incorporates (13)C compensation for refocusing inefficiency with synchronized inversion sweeps (CRISIS) pulses in combination with (1)H broadband inversion pulses to give improved compensation for variations in (1)JCH along with improved refocusing efficiency. It is shown that CRAPT gives edited (13)C spectra with only small losses in sensitivity (between 8% and 15% for strychnine, 1, menthol, 2, cholecalciferol, 3, and isotachysterol, 4), compared with basic (13)C spectra obtained on the same compounds. CRAPT also gives significantly better signal/noise than DEPTQ for nonprotonated carbons. Therefore, we conclude that CRAPT is an improvement over APT or DEPTQ or a combination of DEPT135 with a full (13)C spectrum for routine (13)C spectral editing of organic compounds.

A circularly permuted photoactive yellow protein as a scaffold for photoswitch design.

Upon blue light irradiation, photoactive yellow protein (PYP) undergoes a conformational change that involves large movements at the N-terminus of the protein. We reasoned that this conformational change might be used to control other protein or peptide sequences if these were introduced as linkers connecting the N- and C-termini of PYP in a circular permutant. For such a design strategy to succeed, the circularly permuted PYP (cPYP) would have to fold normally and undergo a photocycle similar to that of the wild-type protein. We created a test cPYP by connecting the N- and C-termini of wild-type PYP (wtPYP) with a GGSGGSGG linker polypeptide and introducing new N- and C-termini at G115 and S114, respectively. Biophysical analysis indicated that this cPYP adopts a dark-state conformation much like wtPYP and undergoes wtPYP-like photoisomerization driven by blue light. However, thermal recovery of dark-state cPYP is ∼10-fold faster than that of wtPYP, so that very bright light is required to significantly populate the light state. Targeted mutations at M121E (M100 in wtPYP numbering) were found to enhance the light sensitivity substantially by lengthening the lifetime of the light state to ∼10 min. Nuclear magnetic resonance (NMR), circular dichroism, and UV-vis analysis indicated that the M121E-cPYP mutant also adopts a dark-state structure like that of wtPYP, although protonated and deprotonated forms of the chromophore coexist, giving rise to a shoulder near 380 nm in the UV-vis absorption spectrum. Fluorine NMR studies with fluorotryptophan-labeled M121E-cPYP show that blue light drives large changes in conformational dynamics and leads to solvent exposure of Trp7 (Trp119 in wtPYP numbering), consistent with substantial rearrangement of the N-terminal cap structure. M121E-cPYP thus provides a scaffold that may allow a wider range of photoswitchable protein designs via replacement of the linker polypeptide with a target protein or peptide sequence.

Bending rigid molecular rods: formation of oligoproline macrocycles.

Bent but not broken: cyclic oligoprolines are accessed in a reaction that effectively bends rigid oligoproline peptides (see scheme; TBDMS=tert-butyldimethylsilyl). The stitching is accomplished during macrocyclization enabled by aziridine aldehydes and isocyanides. Molecular modeling studies suggest that electrostatic attraction between the termini of the linear peptide is pivotal for macrocyclization. The macrocycles were studied by circular dichroism with a polyproline II structure being observed in larger macrocycles.

Structural and optical characterization of dissolved organic matter from the lower Athabasca River, Canada.

Dissolved organic matter (DOM) is a ubiquitous constituent of natural waters and is comprised of a variety of chemically heterogeneous molecular structures and functional groups. DOM is often considered to be a major ligand for metals in most natural waters and its reactivity is thought to be strongly dependent on its chemical composition and structure. In this study, a combination of UV/visible, emission excitation matrix fluorescence (EEM) and (1)H NMR spectroscopies were used to characterize DOM from the Athabasca River (Alberta, Canada). The chemical characterization of river DOM showed that the most upstream samples located in agricultural areas were blue-shifted and less aromatic and contained more hydrogens connected with oxygen functional groups than those in the wetland dominated area in the Athabasca oil sand deposit region. The presence of paramagnetic ions (Fe and Al) was not found to significantly affect the structural composition of DOM as revealed by (1)H NMR. Such change in the quality of DOM may have a profound impact on metal binding in the Athabasca River watershed.

An Apparent Size-Exclusion Quantification Limit Reveals a Molecular Weight Limit in the Synthesis of Externally Initiated Polythiophenes.

We report the linear and nonlinear regions of the relationship between number average molecular weight determined by gel permeation chromatography (GPC) and 1H NMR end-group analysis for a series of o-tolyl-initiated poly(3-hexylthiophene)s (P3HTs). For conjugated polymers with chains that are 39-138 repeat units in length (6.5-23 kDa), GPC systematically overestimates the number average molecular weight (Mn) by a factor of 1.3 ± 0.1 (standard error), and GPC and 1H NMR end-group analysis correlate in a linear manner. For chains 138-1130 (23-188 kDa) repeat units in length, we observe a nonlinear relationship between GPC and end-group analysis. Static light-scattering experiments confirm that at high molecular weight (>70 kDa) decreasing the catalyst loading does not appreciably increase the polymer chain length. Thus, we conclude that there is a molecular weight limit in the synthesis of externally initiated polythiophenes and a propensity for the growth of nonexternally initiated chains which increases as a function of Mn. This is significant as external initiation has been reported to result in nearly 100% externally initiated chains as well as reduce the possibility of chain-chain coupling in a typical synthesis. Our data show that 100% external initiation only holds true for polymers that are less than 40 kDa and encourages caution when determining Mn by NMR using this synthetic methodology at high molecular weights.

The toxicity of titanium dioxide nanopowder to early life stages of the Japanese medaka (Oryzias latipes).

In this study, fertilized Japanese medaka (Oryzias latipes) embryos were exposed from fertilization to 5 d post-hatch using static non-renewal assays to aqueous suspensions of titanium dioxide nanoparticles (nTiO2) ranging in nominal concentrations between 0 and 14 µg mL⁻¹. The average size of the nTiO2 in the stock solution before addition to the test treatments was 87 nm (±14 nm). TiO2 materials accumulated in a concentration dependent manner on the chorionic filaments of developing medaka embryos with evidence of pericardial edema occurring during embryo development. However, no significant (p > 0.05) increases in mortality relative to control treatments were observed for the nTiO2 exposed embryos. A concentration dependent increase in cumulative percent hatch was observed at 11 d, indicating that exposure to increasing concentrations of nTiO2 resulted in the premature hatch of medaka embryos. Post-hatch, a significant proportion of sac fry from the nTiO2 exposure groups exhibited moribund swimming behavior and these individuals also experienced greater mortality at 15 d post-hatch. Combined, these results demonstrate that exposure to nTiO2 can impact the development of early life stages of fish.

Experimental characterization of the mechanism of perfluorocarboxylic acids' liver protein bioaccumulation: the key role of the neutral species.

Perfluorocarboxylic acids (PFCAs) of chain length greater than seven carbon atoms bioconcentrate in the livers of fish. However, a mechanistic cause for the empirically observed increase in the bioconcentration potential of PFCAs as a function of chain length has yet to be determined. To this end, recombinant rat liver fatty acid-binding protein (L-FABP) was purified, and its interaction with PFCAs was characterized in an aqueous system at pH 7.4. Relative binding affinities of L-FABP with PFCAs of carbon chain lengths of five to nine were established fluorimetrically. The energetics, mechanism, and stoichiometry of the interaction of perfluorooctanoic acid (PFOA) with L-FABP were examined further by isothermal titration calorimetry (ITC) and electrospray ionization combined with tandem mass spectrometry (ESI-MS/MS). Perfluorooctanoic acid was shown to bind to L-FABP with an affinity approximately an order of magnitude less than the natural ligand, oleic acid, and to have at least 3:1 PFOA:L-FABP stoichiometry. Two distinct modes of PFOA binding to L-FABP were observed by ESI-MS/MS analysis; in both cases, PFOA binds solely as the neutral species under typical physiological pH and aqueous concentrations of the anion. A comparison of their chemical and physical properties with other well-studied biologically relevant chemicals showed that accumulation of PFCAs in proteins as the neutral species is predictable. For example, the interaction of PFOA with L-FABP is almost identical to that of the acidic ionizing drugs ketolac, ibuprofen, and warfarin that show specificity to protein partitioning with a magnitude that is proportional to the K(OW) (octanol-water partitioning) of the neutral species. The experimental results suggest that routine pharmacochemical models may be applicable to predicting the protein-based bioaccumulation of long-chain PFCAs.

Empirically predicted 13C NMR chemical shifts for 8-hydroxyflavone starting from 7,8,4'-trihydroxyflavone and from 7,8-dihydroxyflavone.

8-Hydroxyflavone is not found in nature. While the (13)C chemical shifts of 8-hydroxyflavone have been reported previously, the observed (13)C chemical shifts were not assigned. A previously reported empirical predictive tool has been applied in reverse in order to deconvolute the (13)C chemical shifts for 8-hydroxyflavone from each of those of 7,8,4'-trihydroxyflavone and 7,8-dihydroxyflavone together with those of 7-hydroxyflavone, 4'-hydroxyflavone, and flavone. The two sets of calculated (13)C chemical shifts for 8-hydroxyflavone are in good agreement with each other in that the average absolute difference is 0.4 ppm. The previously reported but unassigned (13)C chemical shifts for 8-hydroxyflavone have been assigned by matching them with the averages of the two sets of calculated (13)C chemical shifts for 8-hydroxyflavone such that the minimum average absolute difference is 0.63 ppm. The assigned (13)C chemical shifts of 8-hydroxyflavone may be used, along with the (13)C chemical shifts of the remaining monohydroxyflavones, as part of a predictive tool to rapidly assess the (13)C NMR spectra of C8-hydroxylated flavonoids.

Experimental pKa determination for perfluorooctanoic acid (PFOA) and the potential impact of pKa concentration dependence on laboratory-measured partitioning phenomena and environmental modeling.

An accurately measured equilibrium acid dissociation constant (pKa) is essential for understanding and predicting the fate of perfluorocarboxylic acids (PFCAs) in the environment. The aqueous pKa of perfluorooctanoic acid (PFOA) has been determined potentiometrically using a standard water-methanol mixed solvent approach and was found to be 3.8 +/- 0.1. The acidity of PFOA is thus considerably weaker than its shorter-chain PFCA homologues. This was attributed to differences in molecular and electronic structure, coupled with solvation effects. The pKa of PFOA was suppressed to approximately 2.3 at higher concentrations because of the aggregation of perfluorooctanoate (PFO). Often, PFCA partion coefficients are determined at concentrations above those found in the environment. Thus, it was suggested that a pKa correction factor, which accounts for this concentration-dependent shift in acid/base equilibrium, should be applied to PFCA partition efficients before they are implemented in environmental fate models. A pKa of 3.8 +/- 0.1 suggests that a considerable concentration of the PFCA exists as the neutral species in the aqueous environment for example, in typical Ontario rainwater, it is approximately 17%. Transport, fate, and partitioning models have often ignored the presence this species completely. The environmental dissemination of PFCAs could, in part, be explained by considering the role of the neutral species.

A predictive tool for assessing (13)C NMR chemical shifts of flavonoids.

Herein are presented the (1)H and (13)C NMR data for seven monohydroxyflavones (3-, 5-, 6-, 7-, 2'-, 3'-, and 4'-hydroxyflavone), five dihydroxyflavones (3,2'-, 3,3'-, 3,4'-, 3,6-, 2',3'-dihydroxyflavone), a trihydroxyflavone (apigenin; 5,7,4'-trihydroxyflavone), a tetrahydroxyflavone (luteolin; 5,7,3',4'-tetrahydroxyflavone), and three glycosylated hydroxyflavones (orientin; luteolin-6C-beta-D-glucoside, homoorientin; luteolin-8C-beta-D-glucoside, vitexin; apigenin-8C-beta-D-glucoside). When these NMR spectra are compared, it is possible to assess the impact of flavone modification and to elucidate detailed structural and electronic information for these flavonoids. A simple predictive tool for assigning flavonoid (13)C chemical shifts, which is based on the cumulative differences between the monohydroxyflavones and flavone (13)C chemical shifts, is demonstrated. The tool can be used to accurately predict (13)C flavonoid chemical shifts and it is expected to be useful for rapid assessment of flavonoid (13)C NMR spectra and for assigning substitution patterns in newly isolated flavonoids.