Simulation of Molecular Dynamics of SARS-CoV-2 S-Protein in the Presence of Multiple Arbidol Molecules: Interactions and Binding Mode Insights

In this work, we evaluated the antiviral activity of Arbidol (Umifenovir) against SARS-CoV-2 using a pseudoviral system with the glycoprotein S of the SARS-CoV-2 virus on its surface. In order to search for binding sites to protein S of the virus, we described alternative binding sites of Arbidol in RBD and in the ACE-2-RBD complex. As a result of our molecular dynamics simulations combined with molecular docking data, we note the following fact: wherever the molecules of Arbidol bind, the interaction of the latter affects the structural flexibility of the protein. This interaction may result both in a change in the shape of the domain–enzyme binding interface and simply in a change in the structural flexibility of the domain, which can subsequently affect its affinity to the enzyme. In addition, we examined the possibility of Arbidol binding in the stem part of the surface protein. The possibility of Arbidol binding in different parts of the protein is not excluded. This may explain the antiviral activity of Arbidol. Our results could be useful for researchers searching for effective SARS-CoV-2 virus inhibitors targeting the viral entry stage.

Design of a MOF based on octa-nuclear zinc clusters realizing both thermal stability and structural flexibility

A octa-nuclear zinc (Zn8) cluster-based two-fold interpenetrated metal−organic framework (MOF) of [(CH3)2NH2]2[Zn8O3(FDC)6]·7DMF (denoted as Zn8-as; H2FDC = 9H-fluorene-2,7-dicarboxylic acid; DMF = N,N-dimethylformamide) was synthesized by reactions of a hard base...

Synthetic uranium oxide hydrate materials: Current advances and future perspectives

Uranium oxide hydrate (UOH) materials, a group of minerals and synthetic phases, have attracted recent attention due to their highly structural flexibility and diversity, as well as their primary relationship...

Structural flexibility of the SARS-CoV-2 genome relevant to variation, replication, pathogenicity, and immune evasion.

The SARS-CoV-2 pandemic continues to be driven by viral variants. Most research has focused on structural proteins and on site-specific mutations. Here, we describe recombination events involving genomic terminal sequences in SARS-CoV-2 and related viruses leading to structural rearrangements in terminal and coding regions and discuss their potential contributions to viral variation, replication, pathogenicity, and immune evasion.

Guide RNA acrobatics: positioning consecutive uridines for pseudouridylation by H/ACA pseudouridylation loops with dual guide capacity

Site-specific pseudouridylation of human ribosomal and spliceosomal RNAs is directed by H/ACA guide RNAs composed of two hairpins carrying internal pseudouridylation guide loops. The distal “antisense” sequences of the pseudouridylation loop base-pair with the target RNA to position two unpaired target nucleotides 5′-UN-3′, including the 5′ substrate U, under the base of the distal stem topping the guide loop. Therefore, each pseudouridylation loop is expected to direct synthesis of a single pseudouridine (Ψ) in the target sequence. However, in this study, genetic depletion and restoration and RNA mutational analyses demonstrate that at least four human H/ACA RNAs (SNORA53, SNORA57, SCARNA8, and SCARNA1) carry pseudouridylation loops supporting efficient and specific synthesis of two consecutive pseudouridines (ΨΨ or ΨNΨ) in the 28S (Ψ3747/Ψ3749), 18S (Ψ1045/Ψ1046), and U2 (Ψ43/Ψ44 and Ψ89/Ψ91) RNAs, respectively. In order to position two substrate Us for pseudouridylation, the dual guide loops form alternative base-pairing interactions with their target RNAs. This remarkable structural flexibility of dual pseudouridylation loops provides an unexpected versatility for RNA-directed pseudouridylation without compromising its efficiency and accuracy. Besides supporting synthesis of at least 6% of human ribosomal and spliceosomal Ψs, evidence indicates that dual pseudouridylation loops also participate in pseudouridylation of yeast and archaeal rRNAs.

Research on Structural Flexibility and Acceptance Model (SFAM) Reconstruction Based on Disruption Innovation in the Social Humanities and Education Sector

The research objectives are as follows: (1) Developing a flexible structural model of the relationship between variables. (2) Develop a structural model that is robust with the assumptions of normality and homoscedasticity. (3) Obtain estimator properties from the flexible and robust SFAM structural model. (4) Obtaining hypothesis testing of each relationship constructed from a flexible and robust SFAM structural model. This research is integrated with a flexible and robust model approach based on nonparametric smoothing spline (RNSS) regression analysis which can capture the form of relationships that depend on empirical data, and the robustness of the model based on the distribution assumption and the assumption of homoscedasticity error variance. There are at least three transformation methods, namely SRS, MSI, and RASCH, which will be used in the development of the Structural Flexibility and Acceptance Model (SFAM). The results obtained from the research progress report are obtaining the development of a flexible structural model of the form of the relationship between variables, obtaining the development of a robust structural model of the assumptions of normality and homoscedasticity, obtaining the estimator properties of the flexible and robust SFAM structural model, and obtaining hypothesis testing. of each relationship constructed from a flexible and robust SFAM structural model. The originality of the theory in this study is very visible in the discovery of a new model, namely SFAM which can accommodate several things, which are the weaknesses of several existing analysis tools such as reciprocal and recursive models, more than one endogenous variable, flexible and robust models, overcoming inadmissible solutions, reflective indicators, formative , and reflective/formative (on the second-order), metric and non-metric data, and simultaneous processing of the input score data (through transformation to scale).

A SUSTAINABLE HOMESTEAD PROTOTYPE IN SUNDARBANS Disaster adaptability through alternative building materials

Sundarbans as the primary coastal defense of Bangladesh against various natural disaster encounters recurrent homelessness due to these calamities, resulting in cutting down forests for housing materials from the only nearby resource. The traditional vernacular practice and socio-cultural studies show a symbiotic relationship between the forest and inhabitants, but the ecological imbalance created by climate change made life difficult for them, whose livelihood solely depends on the forest as well. The inability to reuse the building materials any disaster causes an ever-increasing cycle of carbon footprint. Regarding these, the non-experimental research aims to build such a homestead prototype that creates an adaptable solution. The existing building practices consist of non-reusable materials, poor structural integrity, and lack of sustainable approaches, thus unfit to withstand the increasing disasters and calamities. The approach discussed here utilizes plastic waste, drums, bamboo for disaster adaptability, structural flexibility, rainwater harvesting, solar, and biogas energy for a sustainable lifestyle. So, the goal is to provide a sustainable solution for the economically challenged population. This prototype creates an adaptive strategy for mitigating the disastrous events in Sundarbans to promote resilience and sustainability.