Repurposing dye ligands as antivirals via a docking approach on viral membrane and globular proteins - SARS-CoV-2 and HPV-16

A series of dye ligands are docked to three different proteins, E and 3a of severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) and E6 of human papilloma virus type 16 (HPV-16) using three different software. A four-level selection algorithm is used based on nonparametric statistics of numerical key values such as the "rank" derived from (i) averaged estimated binding energies (EBEs) and (ii) absolute EBE value of each of the software, (iii) frequency of ranking and (iv) rank of the area-under-curve values (AUCs) from decoy docking. A series of repurposing drugs and known antivirals used in experimental studies are docked for comparison. One dye ligand is ranked best for all proteins using the selection algorithm levels i - iii. Another three dye ligands are ranked top for the proteins individually when using all four levels.

Loading-device effects on the protein-unfolding mechanisms using molecular-dynamic simulations

Experimental force spectroscopy has been effectively utilized for measuring structural characterization of biomolecules and mechanical properties of biomaterials. Specifically, atomic force microscopy (AFM) has been widely used to portray biomolecular characterization in single-molecule experiment by observing the unfolding behavior of the proteins. Not only the experimental techniques enable us to characterize globular protein, but computational methods like molecular dynamics (MD) also gives insight into understanding biomolecular structures. To better comprehend the behavior of biomolecules, conditions such as pulling velocities and loading rates are put to the test, yet there are still limitations in understanding the unfolding behavior of biomolecules with the effect of different loading devices. In this study, we performed an all-atom MD and steered molecular dynamics (SMD) simulations considering different loading device effects such as "soft" and "stiff" to characterize the anisotropic unfolding behavior of ubiquitin protein. We found out the anisotropic unfolding pathways of the protein through the broken number of hydrogen bonds and geometric secondary structures of the biomolecule. Our study provides the importance for usage of various loading-devices on biomolecules when analyzing the structural compositions and the characteristics of globular biomolecules.

Monitoring of nanoclay-protein adsorption isotherms via fluorescence techniques

The investigation of nanoparticles and their interaction with bio-macromolecules have become an important issue; the widely discussed protein corona around nanoparticles and their biological fate in general have drawn particular attention. Here, we focus on nanoclay dispersions and the use of solvatochromic fluorescent dyes (Dansyl and Coumarin 153) for monitoring the interaction with two model proteins, bovine serum albumin and β-lactoglobulin. On one hand, these dyes are poorly emissive in water, but experience a boost in their fluorescence when adsorbed into the hydrophobic domains of proteins. On the other hand, (nano)clays and clay minerals have previously been investigated in terms of their individual protein adsorption isotherms and their usefulness for the solubilization of water-insoluble dyes into an aqueous environment. In the following, we have combined all three individual parts (nanoclay, fluorophore and protein) in dispersions in a wide range of concentration ratios to systematically study the various adsorption processes via fluorescence techniques. In order to clarify the extent of dye diffusion and adsorption-desorption equilibria in the investigations, nanoclay hybrids with an adsorbed dye (Coumarin 153) and a covalently conjugated dye (Dansyl) were compared. The results suggest that the fluorescence progression of protein titration curves correlate with the amount of protein adsorbed, matching their reported adsorption isotherms on hectorite clays. Furthermore, experimental data on the protein monolayer formation around the nanoclays could be extracted due to only minor alterations of the dispersions' optical quality and transparency. In this manner, a fluorescence-based monitor for the formation of the globular protein layer around the nanoclay was realized.

Denatured globular protein and bile salt-coated nanoparticles for poorly water-soluble drugs: Penetration across the intestinal epithelial barrier into the circulation system and enhanced oral bioavailability

Oral drug delivery is the most preferred route for patients; however, the low solubility of drugs and the resultant poor absorption compromise the benefits of oral administration. On the other hand, for years, the overwhelmingly accepted mechanism for enhanced oral absorption using lipid nanocarriers was based on the process of lipid digestion and drug solubilization in the small intestine. Few reports indicated that other bypass pathways are involved in drug absorption in the gastrointestinal tract (GIT) for oral delivery of nanocarriers. Herein, we report a new nanoemulsion system with a denatured globular protein with a diameter of 30 nm, soybean protein isolates (SPI), and bile salt as emulsifiers, aiming to enhance the absorption of insoluble drugs and explore other pathways for absorption. A BCS class II drug, fenofibrate (FB), was used as the model drug. The SPI and bile salt-coated Ns with a diameter of approximately 150 nm were prepared via a high-pressure homogenizing procedure. Interestingly, the present Ns could be converted to solid dosage form using fluid-bed coating technology, maintaining a nanoscale size. Most importantly, in a model of in situ rat intestinal perfusion, Ns could penetrate across the intestinal epithelial barrier into the systemic circulation and then obtain biodistribution into other tissues. In addition, Ns significantly improved FB oral absorption, exhibited as a greater than 2- and 2.5-fold increase in Cmax and AUC0-t, respectively, compared to the suspension formulation. Overall, the present Ns are promising nanocarriers for the oral delivery of insoluble drugs, and the penetration of intact Ns across the GIT barrier into systemic circulation may be a new strategy for improved drug absorption with the use of nanocarriers.