Essential oil constituents of regional ethnomedicinal plants as potential inhibitors of SARS-CoV-2 M: an integrated molecular docking, molecular dynamics and QM/MM study.

The scientific community has achieved a remarkable milestone by creating efficacious vaccines against the SARS-CoV-2 virus. The treatment alternatives are still restricted, though. The bioactive ingredients present in natural plants are known to exhibit diverse pharmacological effects against many diseases.

A Study Modeling Bridged Nucleic Acid-Based ASOs and Their Impact on the Structure and Stability of ASO/RNA Duplexes.

Antisense medications treat diseases that cannot be treated using traditional pharmacological technologies. Nucleotide monomers of bare and phosphorothioate (PS)-modified LNA, N-MeO-amino-BNA, 2',4'-BNA[NH], 2',4'-BNA[NMe], and N-Me-aminooxy-BNA antisense modifications were considered for a detailed DFT-based quantum chemical study to estimate their molecular-level structural and electronic properties. Oligomer hybrid duplex stability is described by performing an elaborate MD simulation study by incorporating the PS-LNA and PS-BNA antisense modifications onto 14-mer ASO/RNA hybrid gapmer type duplexes targeting protein PTEN mRNA nucleic acid sequence (5'--3'/3'-GAAUCGUGACCGGA-5').

Antihyperglycemic Potential of Quercetin-3-glucoside Isolated from Seedpods via the SIRT1/AMPK/GLUT4 Signaling Cascade.

(Lam.) de Wit, a traditional medicinal plant, has been reported among the ethnic communities of Mexico, Indonesia, China, and India for the treatment of diabetes, obesity, and related complications. This study investigates the antihyperglycemic activity of the plant and its isolated active compound quercetin-3-glucoside.

Oxidation pathways and kinetics of the 1,1,2,3-tetrafluoropropene (CFCF-CHF) reaction with Cl-atoms and subsequent aerial degradation of its product radicals in the presence of NO.

To give a comprehensive account of the environmental acceptability of 1,1,2,3-tetrafluoropropene (CFCF-CHF) in the troposphere, we have examined the oxidation reaction pathways and kinetics of CFCF-CHF initiated by Cl-atoms using the second-order Møller-Plesset perturbation (MP2) theory along with the 6-31+G(d,p) basis set. We also performed single-point energy calculations to further refine the energies at the CCSD(T) level along with the basis sets 6-31+G(d,p) and 6-311++G(d,p). The estimation of the relative energies and thermodynamic parameters of the CFCF-CHF + Cl reaction clearly shows that Cl-atom addition reaction pathways are more dominant compared to H-abstraction reaction pathways.

Inhibitory potential of furanocoumarins against cyclin dependent kinase 4 using integrated docking, molecular dynamics and ONIOM methods.

Cyclin Dependent Kinase 4 (CDK4) is vital in the process of cell-cycle and serves as a G1 phase checkpoint in cell division. Selective antagonists of CDK4 which are in use as clinical chemotherapeutics cause various side-effects in patients. Furanocoumarins induce anti-cancerous effects in a range of human tumours.

Reaction Mechanism and Kinetics for the Selective Hydrogenation of Carbon Dioxide to Formic Acid and Methanol over the [Cu] Dimer.

With the rapid growth of industrialization, deforestation, and burning of fossil fuels, undeniably there has been an incredible escalation of the CO concentration in the atmosphere. In order to mitigate the problem, the capture and utilization of CO in different value-added chemicals have thus remained topics of concerned research for more than a decade. Accordingly, we have performed molecular -level catalytic hydrogenation of CO to formic acid using bare [Cu] dimers as catalysts.

Design of LNA Analogues Using a Combined Density Functional Theory and Molecular Dynamics Approach for RNA Therapeutics.

Antisense therapeutics treat a wide spectrum of diseases, many of which cannot be addressed with the current drug technologies. In the quest to design better antisense oligonucleotide drugs, we propose five novel LNA analogues (A1-A5) for modifying antisense oligonucleotides and establishing each with the five standard nucleic acids: adenine (A), guanine (G), cytosine (C), thymine (T), and uracil (U). Monomer nucleotides of these modifications were considered for a detailed Density Functional Theory (DFT)-based quantum chemical analysis to determine their molecular-level structural and electronic properties.

Regioselective Friedel-Crafts Acylation Reaction Using Single Crystalline and Ultrathin Nanosheet Assembly of Scrutinyite-SnO.

Peculiar physicochemical properties of two-dimensional (2D) nanomaterials have attracted research interest in developing new synthetic technology and exploring their potential applications in the field of catalysis. Moreover, ultrathin metal oxide nanosheets with atomic thickness exhibit abnormal surficial properties because of the unique 2D confinement effect. In this work, we present a facile and general approach for the synthesis of single crystalline and ultrathin 2D nanosheets assembly of scrutinyite-SnO through a simple solvothermal method.

Incorporation of transition to transversion ratio and nonsense mutations, improves the estimation of the number of synonymous and non-synonymous sites in codons.

A common approach to estimate the strength and direction of selection acting on protein coding sequences is to calculate the dN/dS ratio. The method to calculate dN/dS has been widely used by many researchers and many critical reviews have been made on its application after the proposition by Nei and Gojobori in 1986. However, the method is still evolving considering the non-uniform substitution rates and pretermination codons.

Glycome Profiling and Bioprospecting Potential of the Himalayan Buddhist Handmade Paper of Tawang Region of Arunachal Pradesh.

The paper and pulp industry (PPI) is one of the largest industries that contribute to the growing economy of the world. While wood remains the primary raw material of the PPIs, the demand for paper has also grown alongside the expanding global population, leading to deforestation and ecological imbalance. Wood-based paper production is associated with enormous utilization of water resources and the release of different wastes and untreated sludge that degrades the quality of the environment and makes it unsafe for living creatures.

Stem Region of tRNA Genes Favors Transition Substitution Towards Keto Bases in Bacteria.

Transversion and transition mutations have variable effects on the stability of RNA secondary structure considering that the former destabilizes the double helix geometry to a greater extent by introducing purine:purine (R:R) or pyrimidine:pyrimidine (Y:Y) base pairs. Therefore, transversion frequency is likely to be lower than that of transition in the secondary structure regions of RNA genes. Here, we performed an analysis of transition and transversion frequencies in tRNA genes defined well with secondary structure and compared with the intergenic regions in five bacterial species namely Escherichia coli, Klebsiella pneumoniae, Salmonella enterica, Staphylococcus aureus and Streptococcus pneumoniae using a large genome sequence data set.

Integrated pretreatment of banana agrowastes: Structural characterization and enhancement of enzymatic hydrolysis of cellulose obtained from banana peduncle.

An integrated treatment coupling alkali, steam explosion and ammonia/chlorine-free bleaching with sequential mild acid pretreatment were performed to isolate and characterize cellulose from banana agrowastes followed by optimized enzymatic hydrolysis to glucose. The cellulose yield, compositional, microstructural, and morphological analysis initially obtained from three post-harvest banana agrowastes (peel, pseudostem, and peduncle) were surveyed. Isolation parameters for banana peduncle agrowastes, the most efficient precursor, were reconfigured for acid hydrolysis by applying an orthogonal L array of Taguchi design.

Light-induced synthesis of unsymmetrical organic carbonates from alcohols, methanol and CO under ambient conditions.

The present work describes the first visible light-assisted, metal-free and organic base 1,1,3,3-tetramethyl guanidine (TMG) mediated synthesis of unsymmetrical methyl aryl/alkyl carbonates from the reaction of alcohols, methanol, and CO in high to excellent yields under atmospheric pressure and ambient temperature conditions.

Immunoinformatics mapping of potential epitopes in SARS-CoV-2 structural proteins.

All approved coronavirus disease 2019 (COVID-19) vaccines in current use are safe, effective, and reduce the risk of severe illness. Although data on the immunological presentation of patients with COVID-19 is limited, increasing experimental evidence supports the significant contribution of B and T cells towards the resolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Despite the availability of several COVID-19 vaccines with high efficacy, more effective vaccines are still needed to protect against the new variants of SARS-CoV-2.

Structural insight into locked nucleic acid based novel antisense modifications: A DFT calculations at monomer and MD simulations at oligomer level.

In the present study, five novel LNA based antisense modifications have been proposed. A conformational search was carried out using TANGO, followed by geometry optimization using MOPAC. Based on their electronic energies the most stable conformation for each modification was identified.

Atmospheric insight into the reaction mechanism and kinetics of isopropenyl methyl ether (i-PME) initiated by OH radicals and subsequent oxidation of product radicals.

Studies on primary gas-phase reactions of emitted saturated and unsaturated ethers with oxidants and subsequent secondary reactions of product radicals with O in the presence of NO are important in their atmospheric chemical processes. To accomplish these findings, we have examined the chemistry of OH-initiated oxidation of isopropenyl methyl ether (i-PME) CHC(CH)OCH by electronic structure ca using density functional theory. Our energetic calculations show that OH additions to carbon-carbon double bonds of i-PME are more favorable reaction pathways than H-abstraction reactions from the various CH sites of the titled molecule.

Computational modelling of nanotube delivery of anti-cancer drug into glutathione reductase enzyme.

Density functional theory method combined with docking and molecular dynamics simulations are used to understand the interaction of carmustine with human glutathione reductase enzyme. The active site of the enzyme is evaluated by docking simulation is used for molecular dynamics simulation to deliver the carmustine molecule by (5,5) single walled carbon nanotube (SWCNT). Our model of carmustine in the active site of GR gives a negative binding energy that is further refined by QM/MM study in gas phase and solvent phase to confirm the stability of the drug molecule inside the active site.

Tuning the transition barrier of H dissociation in the hydrogenation of CO to formic acid on Ti-doped SnO clusters.

A density functional theory study has been performed to investigate cation-doped Sn2O4 clusters for selective catalytic reduction of CO2. We study the influence of Si and Ti dopants on the height of the H2 dissociation barrier for the doped systems, and then the subsequent mechanism for the conversion of CO2 into formic acid (FA) via a hydride pinning pathway. The lowest barrier height for H2 dissociation is observed across the 'Ti-O' bond of the Ti-doped Sn2O4 cluster, with a negatively charged hydride (Ti-H) formed during the heterolytic H2 dissociation, bringing selectivity towards the desired FA product.

Unveiling the Role of Hydrogen Bonding and -Tensor in the Interaction of Ru-Bis-DMSO with Amino Acid Residue and Human Serum Albumin.

Density functional theory calculations have been carried out to observe the role of hydrogen bonding in hydrolysis and the coordination mechanism of three amino acid residues (histidine, cysteine, and alanine) with Ru-bis-DMSO complex via which the complex tends to interact with the HSA protein receptor. The interaction mechanism shows that ruthenium complexes prefer to bind protein receptor through cysteine and histidine residues rather than through alanine, which has been confirmed by DFT evaluated H-bonding and -tensor analysis. The number of H-bonds plays a major role in stabilizing the intermediates and transition states involved in the Ru-bis-DMSO and amino acid residue interactions.

Greener production of microcrystalline cellulose (MCC) from Saccharum spontaneum (Kans grass): Statistical optimization.

In this study, microcrystalline cellulose (MCC) was isolated from Saccharum spontaneum by integrating alkaline delignification, chlorine-free bleaching, and acid hydrolysis treatments, through an environment friendly and sustainable method. To minimize acid concentrations, the acid hydrolysis conditions were optimized using Taguchi orthogonal L design that evaluated the influences of reaction time, temperature, acid concentration and solution to pulp ratio on the physical and chemical characteristics of MCC. The cellulose source at its different stages of processing was submitted to various analytical techniques for morphological and physiochemical investigations.

Recent Advances in Nanoarchitectonics of SnO₂ Clusters and Their Applications in Catalysis.

Tin dioxide nanoclusters are very effective as catalysts for various reactions including CO₂ conversion and Friedel-Crafts acylation for pharmaceuticals. The nanoarchitectonics of SnO₂ could be controlled by different synthetic strategies. In the current article, we have presented synthesis of SnO₂ nanoclusters and their applications in catalysis.

Design of Potential IKK-β Inhibitors using Molecular Docking and Molecular Dynamics Techniques for their Anti-cancer Potential.

Aim And Objective: To evaluate a set of seventy phytochemicals for their potential ability to bind the inhibitor of nuclear factor kappaB kinase beta (IKK-β) which is a prime target for cancer and inflammatory diseases.

Materials And Methods: Seventy phytochemicals were screened against IKK-β enzyme using DFT-based molecular docking technique and the top docking hits were carried forward for molecular dynamics (MD) simulation protocols. The ADME-Toxicity analysis was also carried out for the top docking hits.

Atmospheric oxidation of HFE-7300 [n-CFCF(OCH)CF(CF)] initiated by OH/Cl oxidants and subsequent degradation of its product radical: a DFT approach.

To understand the atmospheric chemistry of hydrofluoroethers, we have studied the oxidation of a highly fluorinated compound n-CFCF(OCH)CF(CF) (HFE-7300) by OH/Cl oxidants. Here, we have employed M06-2X functional along with a 6-31 + G(d,p) basis set to obtain the optimized structures, various forms of energies, and different modes of frequencies for all species. We have characterized energies of all species on the potential energy surface, and it indicates that H-abstraction from n-CFCF(OCH)CF(CF) by Cl atom is kinetically more dominant than the H-abstraction reaction initiated by OH radical.

Oxidation pathways, kinetics and branching ratios of chloromethyl ethyl ether (CMEE) initiated by OH radicals and the fate of its product radical: an insight from a computational study.

The OH-initiated oxidation reactions of chloromethyl ethyl ether (CH2ClOCH2CH3) have been presented by using quantum calculation methods. The Minnesota functional (M06-2X) of the density functional theory method along with a polarization and diffuse 6-311++G(d,p) basis set is chosen for optimization and frequency calculations for H-abstractions from CH2ClOCH2CH3 molecules by OH radicals. Furthermore, the CCSD(T) method along with the same basis set is used for energy refinement of all optimized structures to obtain more accurate energies of the species.

Mechanistic investigation of the atmospheric oxidation of bis(2-chloroethyl) ether (ClCHCHOCHCHCl) by OH and NO radicals and Cl atoms: a DFT approach.

The oxidation of bis(2-chloroethyl) ether (ClCHCHOCHCHCl) in the atmosphere, as initiated by various oxidants (OH and NO radicals and Cl atoms), was examined using the functional M06-2X in conjunction with the basis set 6-31 + G(d,p). We explored the oxidation pathways and reaction energies (enthalpies and Gibb's free energies) for the abstraction of H from the -CHCl and -OCH sites of ClCHCHOCHCHCl by oxidants. The energy profile shows that H abstraction from the -OCH site of the title molecule by each atmospheric oxidant is more likely than H abstraction from the other site.