Fruit Bromelain-Derived Peptide Potentially Restrains the Attachment of SARS-CoV-2 Variants to hACE2: A Pharmacoinformatics Approach

Before entering the cell, the SARS-CoV-2 spike glycoprotein receptor-binding domain (RBD) binds to the human angiotensin-converting enzyme 2 (hACE2) receptor. Hence, this RBD is a critical target for the development of antiviral agents. Recent studies have discovered that SARS-CoV-2 variants with mutations in the RBD have spread globally. The purpose of this in silico study was to determine the potential of a fruit bromelain-derived peptide. DYGAVNEVK. to inhibit the entry of various SARS-CoV-2 variants into human cells by targeting the hACE binding site within the RBD. Molecular docking analysis revealed that DYGAVNEVK interacts with several critical RBD binding residues responsible for the adhesion of the RBD to hACE2. Moreover, 100 ns MD simulations revealed stable interactions between DYGAVNEVK and RBD variants derived from the trajectory of root-mean-square deviation (RMSD), radius of gyration (Rg), and root-mean-square fluctuation (RMSF) analysis, as well as free binding energy calculations. Overall, our computational results indicate that DYGAVNEVK warrants further investigation as a candidate for preventing SARS-CoV-2 due to its interaction with the RBD of SARS-CoV-2 variants.

Investigation of Structural, Electronic and Thermoelectric Properties of Two-Dimensional Graphdiyne/Borophene Monolayers and Hetero-bilayers

The integration of dissimilar 2D materials is important for nanoelectronic and thermoelectric applications. Among different polymorphs and different bond geometries, borophene and graphdiyne are two promising candidates for these applications. In the present paper, we have studied hetero-bilayers comprising graphdiyne-borophene (GDY-BS) sheets. Three structural models, namely S0, S1 and S2 have been used for borophene sheets. The optimum interlayer distance for the hetero-bilayers was obtained through binding energy calculations. Then, the structure and electronic properties of the monolayers and hetero-bilayers were individually examined and compared. Graphdiyne monolayer was shown to be a semiconductor with a band gap of 0.43 eV, while the borophene monolayers, as well as all studied hetero-bilayers showed metallic behavior. The thermoelectric properties of borophene and graphdiyne monolayers and the graphdiyne-borophene bilayers were calculated on the basis of the semi-classical Boltzmann theory. The results showed signs of improvement in the conductivity behavior of the hetero-bilayers. Furthermore, considering the increase in Seebeck coefficient and the conductivity for all the structures after calculating figure of merit and power factor, a higher power factor and more energy generation were observed for bilayers. These results show that the GDY-BS hetero-bilayers can positively affect the performance of thermoelectric devices,

Confined Monolayer Ice Between CaF2 (111) and Graphene: Structure and Stability

Water monolayer can form in layered confined systems. Here, CaF2 (111) and graphene are chosen as modeling systems to explore the structure and stability of confined monolayer water. First, water molecules tend to intercalate into a confined space between graphene and CaF2, rather than on a bare surface of graphene. Water molecules can move fast in the confined space due to a low diffusion barrier. These water molecules are likely to aggregate together, forming monolayer ice. Four ice phases including ice II, ice III, ice IV, and ice Ih are compared in this confined system. Intriguingly, all the ice phases undergo very small deformation, indicating the 2D monolayer ice can be stable in the CaF2–graphene–confined system. Beyond, projected band structures are also plotted to understand the electronic behavior of these confined ice phases. Nearly all the bands originated from confined ices are flat and locate about 2–3 eV below the Fermi level. Binding energy calculations suggest that the stability sequence in this confined system as follows: Ih-up ≈ Ih-down ≈ II < IV < III. Our results bring new insights into the formation of water monolayer production in such a confined condition.

Accelerating the Discovery of the Beyond Rule of Five Compounds That Have High Affinities Toward SARS-CoV-2 Spike RBD

<div><div><div><p>The battle against SARS-CoV-2 coronavirus is the focal point for the global pandemic that has affected millions of lives worldwide. The need for effective and selective therapeutics for the treatment of the disease caused by SARS-CoV-2 is critical. Herein, we performed computational de novo design incorporating molecular docking studies, molecular dynamics simulations, absolute binding energy calculations, and steered molecular dynamics simulations for the discovery of potential compounds with high affinity towards SARS-CoV-2 spike RBD. By leveraging ZINC15 database, a total of 1282 in-clinical and FDA approved drugs were filtered out from nearly 0.5 million protomers of relatively large compounds (MW > 500, and LogP ≤ 5). Our results depict plausible mechanistic aspects related to the blockage of SARS-CoV-2 spike RBD by the top hits discovered. We found that the most promising candidates, namely, ZINC95628821, ZINC95617623, ZINC3979524, and ZINC261494658, strongly bind to the spike RBD and interfere with the human ACE2 receptor. These findings accelerate the rational design of selective inhibitors targeting the spike RBD protein of SARS-CoV-2.</p></div></div></div>

The Sabatier Principle in Electrocatalysis: Basics, Limitations, and Extensions

The Sabatier principle, which states that the binding energy between the catalyst and the reactant should be neither too strong nor too weak, has been widely used as the key criterion in designing and screening electrocatalytic materials necessary to promote the sustainability of our society. The widespread success of density functional theory (DFT) has made binding energy calculations a routine practice, turning the Sabatier principle from an empirical principle into a quantitative predictive tool. Given its importance in electrocatalysis, we have attempted to introduce the reader to the fundamental concepts of the Sabatier principle with a highlight on the limitations and challenges in its current thermodynamic context. The Sabatier principle is situated at the heart of catalyst development, and moving beyond its current thermodynamic framework is expected to promote the identification of next-generation electrocatalysts.

Residual np-interaction and mass predictions in transfermium region

We study the consistency of local mass relation approach in its application to prediction of nuclear masses in the region of superheavy elements. Binding energy calculations are carried out for nuclei with [Formula: see text] using formulas for evaluation of residual [Formula: see text]-interaction. The results are found to be in good agreement with the experimental data AME2016. We also make predictions for characteristics of [Formula: see text]-decay in isotopes [Formula: see text]–106, [Formula: see text]–157.

Arthropod Ectoparasites Have Potential to Bind SARS-CoV-2 via ACE

Coronavirus-like organisms have been previously identified in Arthropod ectoparasites (such as ticks and unfed cat flea). Yet, the question regarding the possible role of these arthropods as SARS-CoV-2 passive/biological transmission vectors is still poorly explored. In this study, we performed in silico structural and binding energy calculations to assess the risks associated with possible ectoparasite transmission. We found sufficient similarity between ectoparasite ACE and human ACE2 protein sequences to build good quality 3D-models of the SARS-CoV-2 Spike:ACE complex to assess the impacts of ectoparasite mutations on complex stability. For several species (e.g., water flea, deer tick, body louse), our analyses showed no significant destabilisation of the SARS-CoV-2 Spike:ACE complex, suggesting these species would bind the viral Spike protein. Our structural analyses also provide structural rationale for interactions between the viral Spike and the ectoparasite ACE proteins. Although we do not have experimental evidence of infection in these ectoparasites, the predicted stability of the complex suggests this is possible, raising concerns of a possible role in passive transmission of the virus to their human hosts.