Structural behavior of monomer of SARS-CoV-2 spike protein during initial stage of adsorption on graphene

Organic-inorganic biohybrid films from wool-keratin/jellyfish-collagen/silica/boron via sol-gel reactions for soft tissue engineering applications

Therapeutic angiogenesis is pivotal in creating effective tissue-engineered constructs that deliver nutrients and oxygen to surrounding cells. Hence, biomaterials that promote angiogenesis can enhance the efficacy of various medical treatments, encompassing tissue engineering, wound healing, and drug delivery systems. Considering these, we propose a rapid method for producing composite silicon-boron-wool keratin/jellyfish collagen (Si-B-WK/JFC) inorganic-organic biohybrid films using sol-gel reactions. In this approach, reactive tetraethyl orthosilicate and boric acid (pKa ⩾ 9.24) were used as silicon and boron sources, respectively, and a solid-state gel was formed through the condensation reaction of these reactive groups with the keratin/collagen mixture. Once the resulting gel was thoroughly suspended in water, the films were prepared by a casting/solvent evaporation methodology. The fabricated hybrid films were characterized structurally and mechanically. In addition, angiogenic characteristics were determined by the in ovo chick chorioallantoic membrane assay, which revealed an increased vascular network within the Si-B-WK/JFC biohybrid films. In conclusion, it is believed that Si-B-WK/JFC biohybrid films with mechanical and pro-angiogenic properties have the potential to be possessed in soft tissue engineering applications, especially wound healing.

On the Sensitivity and Affinity of Gold, Silver, and Platinum Surfaces against the SARS-CoV-2 Virus: A Comparative Computational Study

The novel coronavirus disease and its complications have motivated the design of new sensors with the highest sensitivity, and affinity for the detection of the SARS-CoV-2 virus is considered in many research studies. In this research article, we employ full atomistic molecular dynamics (MD) models to study the interactions between the receptor binding domain (RBD) and spike protein of the coronavirus and different metals such as gold (Au), platinum (Pt), and silver (Ag) to analyze their sensitivity against this virus. The comparison between the RBD interactions with ACE2 (angiotensin-converting enzyme 2) and different metals indicates that metals have remarkable effects on the structural features and dynamical properties of the RBD. The binding site of the RBD has more affinity to the surfaces of gold, platinum, and silver than to the other parts of the protein. Moreover, the initial configuration of the RBD relative to the metal surface plays an important role in the stability of metal complexes with the RBD. The binding face of the protein to the metal surface has been changed in the presence of different metals. In other words, the residues of the RBD that participate in RBD interactions with the metals are different irrespective of the initial configurations in which the [Asn, Thr, Tyr], [Ser, Thr, Tyr], and [Asn, Asp, Tyr] residues of the protein have a greater affinity to Ag, Au, and Pt, respectively. The corresponding metals have a considerable affinity to the RBD, which due to strong interactions with the protein can change the secondary structure and structural features. Based on the obtained results during the complexation process between the protein and metals, the helical structure of the protein changes to the bend and antiparallel β-sheets. The calculated binding energies for the RBD complexes with silver, gold, and platinum are -95.03, -138.03, and -133.96 kcal·mol-1, respectively. The adsorption process of the spike protein on the surfaces of different metals represents similar results and indicates that the entire spike protein of the coronavirus forms a more stable complex with the gold surface compared with other metals. Moreover, the RBD of the spike protein has more interactions with the surfaces than with the other parts of the protein. Therefore, it is possible to predict the properties of the coronavirus on the metal surface based on the dynamical behavior of the RBD. Overall, our computational results confirm that the gold surface can be considered as an outstanding substrate for developing new sensors with the highest sensitivity against SARS-CoV-2.

Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2

Despite tremendous efforts in the past two years, our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus-host interactions, immune response, virulence, transmission, and evolution is still very limited. This limitation calls for further in-depth investigation. Computational studies have become an indispensable component in combating coronavirus disease 2019 (COVID-19) due to their low cost, their efficiency, and the fact that they are free from safety and ethical constraints. Additionally, the mechanism that governs the global evolution and transmission of SARS-CoV-2 cannot be revealed from individual experiments and was discovered by integrating genotyping of massive viral sequences, biophysical modeling of protein-protein interactions, deep mutational data, deep learning, and advanced mathematics. There exists a tsunami of literature on the molecular modeling, simulations, and predictions of SARS-CoV-2 and related developments of drugs, vaccines, antibodies, and diagnostics. To provide readers with a quick update about this literature, we present a comprehensive and systematic methodology-centered review. Aspects such as molecular biophysics, bioinformatics, cheminformatics, machine learning, and mathematics are discussed. This review will be beneficial to researchers who are looking for ways to contribute to SARS-CoV-2 studies and those who are interested in the status of the field.

Potential of graphene based photocatalyst for antiviral activity with emphasis on COVID-19: A review

Coronavirus disease-2019 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been one of the most challenging worldwide epidemics of recent times. Semiconducting materials (photocatalysts) could prove effectual solar-light-driven technology on account of variant reactive oxidative species (ROS), including superoxide (^•O₂ ^- ) and hydroxyl (^•OH) radicals either by degradation of proteins, DNA, RNA, or preventing cell development by terminating cellular membrane. Graphene-based materials have been exquisitely explored for antiviral applications due to their extraordinary physicochemical features including large specific surface area, robust mechanical strength, tunable structural features, and high electrical conductivity. Considering that, the present study highlights a perspective on the potentials of graphene based materials for photocatalytic antiviral activity. The interaction of virus with the surface of graphene based nanomaterials and the consequent physical, as well as ROS induced inactivation process, has been highlighted and discussed. It is highly anticipated that the present review article emphasizing mechanistic antiviral insights could accelerate further research in this field.

Structure and Orientation of the SARS-Coronavirus-2 Spike Protein at Air-Water Interfaces

The SARS coronavirus 2 (SARS-CoV-2) spike protein is located at the outermost perimeter of the viral envelope and is the first component of the virus to make contact with surrounding interfaces. The stability of the spike protein when in contact with surfaces plays a deciding role for infection pathways and for the viability of the virus after surface contact. While cryo-EM structures of the spike protein have been solved with high resolution and structural studies in solution have provided information about the secondary and tertiary structures, only little is known about the folding when adsorbed to surfaces. We here report on the secondary structure and orientation of the S1 segment of the spike protein, which is often used as a model protein for in vitro studies of SARS-CoV-2, at the air-water interface using surface-sensitive vibrational sum-frequency generation (SFG) spectroscopy. The air-water interface plays an important role for SARS-CoV-2 when suspended in aerosol droplets, and it serves as a model system for hydrophobic surfaces in general. The SFG experiments show that the S1 segment of the spike protein remains folded at the air-water interface and predominantly binds in its monomeric state, while the combination of small-angle X-ray scattering and two-dimensional infrared spectroscopy measurements indicate that it forms hexamers with the same secondary structure in aqueous solution.

High performance flame-retardant organic-inorganic hybrid epoxy composites with POSS and DOPO-based co-curing agent

Polyhedral oligomeric silsesquioxane (POSS) and a highly effective 9,10-dihydro-9-oxa-10-phosphaphenanthrene-10-oxide (DOPO)-based flame retardant co-curing agent (D-bp) were chemically introduced into the 4,4′-diaminodiphenyl methane (DDM)/diglycidyl ether of bisphenol A (DGEBA) epoxy system to create organic–inorganic hybrid epoxy composites with simultaneously improved flame retardancy and mechanical properties. The results revealed that POSS/D-bp/DGEBA hybrid composites exhibited excellent comprehensive performance, in which the V-0 criterion of the UL-94 test was passed and the peak of heat release rate (P-HRR) was significantly decreased from 939 to 371 kW m⁻² when the phosphorus content was only 0.25 wt%. The glass transition temperature (T_g) increased by 16.2 °C and obvious improvement in the mechanical properties was also evidenced.

This paper introduces flame-retardant organic–inorganic hybrid epoxy composites possessing excellent comprehensive performance, which results from the phosphorus–silicon synergistic flame retardant effect of the glycidyl POSS and DOPO derivative.

Interaction between SARS-CoV-2 spike glycoprotein and human skin models: a molecular dynamics study

The possibility of contamination of human skin by infectious virions plays an important role in indirect transmission of respiratory viruses but little is known about the fundamental physico-chemical aspects of the virus-skin interactions. In the case of coronaviruses, the interaction with surfaces (including the skin surface) is mediated by their large glycoprotein spikes that protrude from (and cover) the viral envelope. Here, we perform all atomic simulations between the SARS-CoV-2 spike glycoprotein and human skin models. We consider an "oily" skin covered by sebum and a "clean" skin exposing the stratum corneum. The simulations show that the spike tries to maximize the contacts with stratum corneum lipids, particularly ceramides, with substantial hydrogen bonding. In the case of "oily" skin, the spike is able to retain its structure, orientation and hydration over sebum with little interaction with sebum components. Comparison of these results with our previous simulations of the interaction of SARS-CoV-2 spike with hydrophilic and hydrophobic solid surfaces, suggests that the "soft" or "hard" nature of the surface plays an essential role in the interaction of the spike protein with materials.