Antiviral activity of chitosan nanoparticles encapsulating silymarin (Sil-CNPs) against SARS-CoV-2 (in silico and in vitro study).

To develop a specific treatment against COVID-19, we investigated silymarin-chitosan nanoparticles (Sil-CNPs) as an antiviral agent against SARS-CoV-2 using in silico and in vitro approaches. Docking of Sil and CNPs was carried out against SARS-CoV-2 spike protein using AutoDock Vina. CNPs and Sil-CNPs were prepared by the ionic gelation method and characterized by TEM, FT-IR, zeta analysis, and the membrane diffusion method to determine the drug release profile. Cytotoxicity was tested on both Vero and Vero E6 cell lines using the MTT assay. Minimum binding energies with spike protein and ACE2 were -6.6, and -8.0 kcal mol-1 for CNPs, and -8.9, and -9.7 kcal mol-1 for Sil, respectively, compared to -6.6 and -8.4 kcal mol-1 respectively for remdesivir (RMV). CNPs and Sil-CNPs were prepared at sizes of 29 nm and 82 nm. The CC50 was 135, 35, and 110 µg mL-1 for CNPs, Sil, and Sil-CNPs, respectively, on Vero E6. The IC50 was determined at concentrations of 0.9, 12 and 0.8 µg mL-1 in virucidal/replication assays for CNPs, Sil, and Sil-CNPs respectively using crystal violet. These results indicate antiviral activity of Sil-CNPs against SARS-CoV-2.

Inhibition of SARS-CoV-2 spike protein entry using biologically modified polyacrylonitrile nanofibers: in vitro study towards specific antiviral masks.

With the increase of the contagiousness rates of Coronavirus disease (COVID-19), new strategies are needed to halt virus spread. Blocking virus entry by capturing its spike (S) protein is one of the effective approaches that could help in eliminating or reducing transmission rate of viruses. Herein, we aim to develop a nanofiber-based filter for protective face masks, composed of polyacrylonitrile (PAN) nanofibers (NFs)-loaded with Angiotensin Converting Enzyme-2 (ACE-2) for capturing the spike protein of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) and blocking its entry. Docking simulations were performed to evaluate interactions of PAN with target proteins of both SARS-CoV-2 and Human Adenovirus type 5 (ADV-5) which was used as an in vitro model of human respiratory viruses. Scanning electron microscopy (SEM) and Fourier transformed infrared (FT-IR) spectroscopy was employed to investigate the surface morphology and to analyze the functional groups of the NFs, respectively. The mechanical properties of the electrospun NFs were investigated, according to which the tensile strengths of PAN and modified PAN NFs were 4.9 ± 1.2 GPa and 4.5 GPa. Additionally, elongations at break were 25 ± 2.5% to 24 ± 1.48% for PAN and modified PAN NFs. The tensile strength test showed good mechanical characteristics of the NFs. The ACE-2-loaded NFs were shown to be safe, with promising antiviral activity towards ADV-5. Meanwhile, a binding affinity study between the spike protein and ACE-2 was performed and the dissociation constant (K D) was found to be 1.1 nM. Accordingly, the developed antiviral filters have a potential role to stand as a base for combating various human respiratory viruses.

Zinc Oxide Nanoparticle-Loaded Electrospun Polyvinylidene Fluoride Nanofibers as a Potential Face Protector against Respiratory Viral Infections.

ZnO-NPs loaded polyvinylidene fluoride (PVDF) composite nanofibers were fabricated by electrospinning and optimized using different concentrations (0, 2, and 5 wt %) of ZnO-NPs. Characterization techniques, for example, FTIR, SEM, XRD, and tensile strength analysis were performed to analyze the composite nanofibers. Molecular docking calculations were performed to evaluate the binding affinity of PVDF and ZnO@PVDF against the hexon protein of adenovirus (PDB ID: 6CGV). The cytotoxicity of tested materials was evaluated using MTT assay, and nontoxic doses subjected to antiviral evaluation against human adenovirus type-5 as a human respiratory model were analyzed using quantitative polymerase chain reaction assay. IC50 values were obtained at concentrations of 0, 2, and 5% of ZnO-loaded PVDF; however, no cytotoxic effect was detected for the nanofibers. In 5% ZnO-loaded PVDF nanofibers, both the viral entry and its replication were inhibited in both the adsorption and virucidal antiviral mechanisms, making it a potent antiviral filter/mask. Therefore, ZnO-loaded PVDF nanofiber is a potentially prototyped filter embedded in a commercial face mask for use as an antiviral mask with a pronounced potential to reduce the spreading of infectious respiratory diseases, for example, COVID-19 and its analogues.

Computational Approach for Probing Redox Potential for Iron-Sulfur Clusters in Photosystem I.

Photosystem I is a light-driven electron transfer device. Available X-ray crystal structure from Thermosynechococcus elongatus showed that electron transfer pathways consist of two nearly symmetric branches of cofactors converging at the first iron-sulfur cluster FX, which is followed by two terminal iron-sulfur clusters FA and FB. Experiments have shown that FX has lower oxidation potential than FA and FB, which facilitates the electron transfer reaction. Here, we use density functional theory and Multi-Conformer Continuum Electrostatics to explain the differences in the midpoint Em potentials of the FX, FA and FB clusters. Our calculations show that FX has the lowest oxidation potential compared to FA and FB due to strong pairwise electrostatic interactions with surrounding residues. These interactions are shown to be dominated by the bridging sulfurs and cysteine ligands, which may be attributed to the shorter average bond distances between the oxidized Fe ion and ligating sulfurs for FX compared to FA and FB. Moreover, the electrostatic repulsion between the 4Fe-4S clusters and the positive potential of the backbone atoms is lowest for FX compared to both FA and FB. These results agree with the experimental measurements from the redox titrations of low-temperature EPR signals and of room temperature recombination kinetics.

The Delta Variant Mutations in the Receptor Binding Domain of SARS-CoV-2 Show Enhanced Electrostatic Interactions with the ACE2.

Mutations in the receptor binding domain (RBD) in SARS-CoV-2 are shown to enhance its replication, transmissibility, and binding to host cells. Recently, a new strain is reported in India that includes a mutation (T478K, and L452R) in the RBD, that is possibly increasing the infection rate. Here, using Molecular Mechanics (MM) and Monte Carlo (MC) sampling, we show that the double mutant variant of SARS-CoV-2 induced conformational change in ACE2-E37, which enhanced the electrostatic interactions by the formation of a salt-bridge with SARS-CoV-2-R403. In addition, we observed that the double mutated structure induced a significant change in the salt-bridge electrostatic interaction between RBD-T500 and ACE2-D355. Where that this interaction lost more than 70% of its value compared to its value in WT protein.

The new SARS-CoV-2 strain shows a stronger binding affinity to ACE2 due to N501Y mutant.

SARS-CoV-2 is a global challenge due to its ability to spread much faster than the SARS-CoV, which was attributed to the mutations in the receptor binding domain (RBD). These mutations enhanced the electrostatic interactions. Recently, a new strain is reported in the UK that includes a mutation (N501Y) in the RBD, that is possibly increasing the infection rate. Here, using Molecular Dynamics simulations (MD) and Monte Carlo (MC) sampling, we show that the N501 mutation enhanced the electrostatic interactions due to the formation of a strong hydrogen bond between SARS-CoV-2-T500 and ACE2-D355 near the mutation site. In addition, we observed that the electrostatic interactions between the SARS-CoV-2 and ACE2 in the wild type and the mutant are dominated by salt-bridges formed between SARS-CoV-2-K417 and ACE2-D30, SARS-CoV-2-K458, ACE2-E23, and SARS-CoV-2-R403 and ACE2-E37. These interactions contributed more than 40% of the total binding energies.

ACE2 coding variants in different populations and their potential impact on SARS-CoV-2 binding affinity.

The susceptibility of different populations to SARS-CoV-2 infection is not yet understood. Here, we combined ACE2 coding variants' analysis in different populations and computational chemistry calculations to probe the effects on SARS-CoV-2/ACE2 interaction. ACE2-K26R; which is most frequent in Ashkenazi Jewish population decreased the SARS-CoV-2/ACE2 electrostatic attraction. On the contrary, ACE2-I468V, R219C, K341R, D206G, G211R increased the electrostatic attraction; ordered by binding strength from weakest to strongest. The aforementioned variants are most frequent in East Asian, South Asian, African and African American, European, European and South Asian populations, respectively.