Dioxane enhanced immobilization of urease on alkyl modified nano-porous silica using reversible denaturation approach

Protein click chemistry and its potential for medical applications

A revolution in chemical biology occurred with the introduction of click chemistry. Click chemistry plays an important role in protein chemistry modifications, providing specific, sensitive, rapid, and easy-to-handle methods. Under physiological conditions, click chemistry often overlaps with bioorthogonal chemistry, defined as reactions that occur rapidly and selectively without interfering with biological processes. Click chemistry is used for the posttranslational modification of proteins based on covalent bond formations. With the contribution of click reactions, selective modification of proteins would be developed, representing an alternative to other technologies in preparing new proteins or enzymes for studying specific protein functions in different biological processes. Click-modified proteins have potential in diverse applications such as imaging, labeling, sensing, drug design, and enzyme technology. Due to the promising role of proteins in disease diagnosis and therapy, this review aims to highlight the growing applications of click strategies in protein chemistry over the last two decades, with a special emphasis on medicinal applications.

Stacking of nanorings to generate nanotubes for acceleration of protein refolding

Self-assembly and photoisomerization of azobenzene-based amphiphilic molecules produced nanorings with an inner diameter of 25 nm and lengths of <40 nm. The nanorings, which consisted of a single bilayer membrane of the amphiphiles, retained their morphology in the presence of a stacking inhibitor; whereas in the absence of the inhibitor, the nanorings stacked into short nanotubes (<500 nm). When subjected to mild heat treatment, these nanotubes joined end-to-end to form nanotubes with lengths of several tens of micrometers. The nanorings and the short and long nanotubes were able to encapsulate proteins and thereby suppress aggregation induced by thermal denaturation. In addition, the nanotubes accelerated refolding of denatured proteins by encapsulating them and then releasing them into the bulk solution; refolding occurred simultaneously with release. In contrast, the nanorings did not accelerate protein refolding. Refolding efficiency increased with increasing nanotube length, indicating that the re-aggregation of the proteins was strictly inhibited by lowering the concentration of the proteins in the bulk solution as the result of the slow release from the longer nanotubes. The migration of the proteins through the long, narrow nanochannels during the release process will also contribute to refolding.

New 1,2,3-triazole-(thio)barbituric acid hybrids as urease inhibitors: Design, synthesis, in vitro urease inhibition, docking study, and molecular dynamic simulation

A new series of 1,2,3-triazole-(thio)barbituric acid hybrids 8a-n was designed and synthesized on the basis of potent pharmacophores with urease inhibitory activity. Therefore, these compounds were evaluated against Helicobacter pylori urease. The obtained result demonstrated that all the synthesized compounds, 8a-n, were more potent than the standard urease inhibitor, hydroxyurea. Moreover, among them, compounds 8a, 8c-e, 8g,h, and 8k,l exhibited higher urease inhibitory activities than the other standard inhibitor used: thiourea. Docking studies were performed with the synthesized compounds. Furthermore, molecular dynamic simulation of the most potent compounds, 8e and 8l, showed that these compounds interacted with the conserved residues Cys592 and His593, which belong to the active site flap and are essential for enzymatic activity. These interactions have two consequences: (a) blocking the movement of a flap at the entrance of the active site channel and (b) stabilizing the closed active site flap conformation, which significantly reduces the catalytic activity of urease. Calculation of the physicochemical and topological properties of the synthesized compounds 8a-n predicted that all these compounds can be orally active. The ADME prediction of compounds 8a-n was also performed.

Spectroscopic and mechanistic analysis of the interaction between Jack bean urease and polypseudorotaxane fabricated with bis-thiolated poly(ethylene glycol) and α-cyclodextrin

Self-assembled polypseudorotaxanes (PPRXs) fabricated with α-cyclodextrin and poly(ethylene glycol) (PEG) or its thiolated derivatives were candidate functional materials for enzyme soft-immobilization, encapsulation and controlled-release. The study of their interaction with Jack bean urease (JBU) indicated that they inconspicuously influenced the activity and stability of JBU during long storage, up to 30 days. The macro-species were inaccessible to JBU's active site and the steric effect might play a significant role in the stabilization of JBU, when compared with the small-molecular sulfhydryl inhibitor thioglycolic acid. Circular dichroism and fluorescence spectra analyses revealed that thiolated PEG₄₀₀-(SH)₂ and its assembly PPRX₄₀₀(SH) brought in perturbations to certain α-helical or β-sheet domains of JBU, making JBU's conformation more flexible. The resulting partial unfolding of domains exposed several hydrophobic clusters and varied JBU's surface hydrophobicity. It also rendered the chromophores more hydrophilic and more bared to the polar environment, leading to the typical bathochromic-shift and quenching in intrinsic and synchronous fluorescence spectra. Moreover, the surface hydrophobicity profile of JBU was depicted by fluorescent probe monitoring and the unique "hydrophobic cave" motif was proposed by analyzing JBU's structural data from the Protein Data Bank. It should be pointed out that conformational variations mainly occurred at the surface region of JBU, while the buried active bi-nickel center was not markedly influenced by the macro-species. The results demonstrated that the PPRXs might act as a proper carrier for JBU encapsulation or soft-immobilization.

Glycolipid-based nanostructures with thermal-phase transition behavior functioning as solubilizers and refolding accelerators for protein aggregates

The self-assembly of synthetic glycolipids produced nanostructures such as vesicles and nanotubes consisting of bilayer membranes, which underwent a gel-to-liquid crystalline thermal phase transition. Vesicles formed at temperatures above the thermal phase transition temperatures (T_g-l) could solubilize aggregates of denatured proteins by trapping them in the fluid bilayer membranes. Cooling to temperatures below T_g-l caused a morphological transformation into nanotubes that accompanied the thermal phase transition from the fluid to the solid state. This phenomenon allowed the trapped proteins to be quickly released into the bulk solution and simultaneously facilitated the refolding of the proteins. The refolding efficiency strongly depended on the electrostatic attraction between the bilayer membranes of the nanostructures and the proteins. Because of the long shape (>400 nm) of the nanotubes, simple membrane filtration through a pore size of 200 nm led to complete separation and recovery of the refolded proteins (3-9 nm sizes).

Effect of Photoinduced Size Changes on Protein Refolding and Transport Abilities of Soft Nanotubes

Self-assembly of azobenzene-modified amphiphiles (Glyn Azo, n=1-3) in water at room temperature in the presence of a protein produced nanotubes with the protein encapsulated in the channels. The Gly2 Azo nanotubes (7 nm internal diameter [i.d.]) promoted refolding of some encapsulated proteins, whereas the Gly3 Azo nanotubes (13 nm i.d.) promoted protein aggregation. Although the 20 nm i.d. channels of the Gly1 Azo nanotubes were too large to influence the encapsulated proteins, narrowing of the i.d. to 1 nm by trans-to-cis photoisomerization of the azobenzene units of the Gly1 Azo monomers packed in the solid bilayer membranes led to a squeezing out of the proteins into the bulk solution and simultaneously enhanced their refolding ratios. In contrast, photoinduced transformation of the Gly2 Azo nanotubes to short nanorings (<40 nm) with a large i.d. (28 nm) provided no further refolding assistance. We thus demonstrate that pertubation by the solid bilayer membrane wall of the nanotubes is important to accelerate refolding of the denatured proteins during their transport in the narrow nanotube channels.

Nanomaterials for biocatalyst immobilization – state of the art and future trends

Advantages, drawbacks and trends in nanomaterials for enzyme immobilization.

Large scale screening of commonly used Iranian traditional medicinal plants against urease activity

Background and purpose of the study

H. pylori infection is an important etiologic impetus usually leading to gastric disease and urease enzyme is the most crucial role is to protect the bacteria in the acidic environment of the stomach. Then urease inhibitors would increase sensitivity of the bacteria in acidic medium.

Methods

137 Iranian traditional medicinal plants were examined against Jack bean urease activity by Berthelot reaction. Each herb was extracted using 50% aqueous methanol. The more effective extracts were further tested and their IC₅₀ values were determined.

Results

37 plants out of the 137 crude extracts revealed strong urease inhibitory activity (more than 70% inhibition against urease activity at 10 mg/ml concentration). Nine of the whole studied plants crude extracts were found as the most effective with IC₅₀ values less than 500 μg/ml including; Rheum ribes, Sambucus ebulus, Pistachia lentiscus, Myrtus communis, Areca catechu, Citrus aurantifolia, Myristica fragrans, Cinnamomum zeylanicum and Nicotiana tabacum.

Conclusions

The most potent urease inhibitory was observed for Sambucus ebulus and Rheum ribes extracts with IC₅₀ values of 57 and 92 μg/ml, respectively.

Soft nanotube hydrogels functioning as artificial chaperones

Self-assembly of rationally designed asymmetric amphiphilic monomers in water produced nanotube hydrogels in the presence of chemically denatured proteins (green fluorescent protein, carbonic anhydrase, and citrate synthase) at room temperature, which were able to encapsulate the proteins in the one-dimensional channel of the nanotube consisting of a monolayer membrane. Decreasing the concentrations of the denaturants induced refolding of part of the encapsulated proteins in the nanotube channel. Changing the pH dramatically reduced electrostatic attraction between the inner surface mainly covered with amino groups of the nanotube channel and the encapsulated proteins. As a result, the refolded proteins were smoothly released into the bulk solution without specific additive agents. This recovery procedure also transformed the encapsulated proteins from an intermediately refolding state to a completely refolded state. Thus, the nanotube hydrogels assisted the refolding of the denatured proteins and acted as artificial chaperones. Introduction of hydrophobic sites such as a benzyloxycarbony group and a tert-butoxycarbonyl group onto the inner surface of the nanotube channels remarkably enhanced the encapsulation and refolding efficiencies based on the hydrophobic interactions between the groups and the surface-exposed hydrophobic amino acid residues of the intermediates in the refolding process. Refolding was strongly dependent on the inner diameters of the nanotube channels. Supramolecular nanotechnology allowed us to not only precisely control the diameters of the nanotube channels but also functionalize their surfaces, enabling us to fine-tune the biocompatibility. Hence, these nanotube hydrogel systems should be widely applicable to various target proteins of different molecular weights, charges, and conformations.