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').

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.

Reverse vaccinology and immunoinformatics approach to design a chimeric epitope vaccine against .

Scrub typhus is a vector-borne infectious disease caused by and it is reportedly associated with up to 20 % of hospitalized cases of febrile illnesses. The major challenge of vaccine development is the lack of identified antigens that can induce both heterotypic and homotypic immunity including the production of antibodies, cytotoxic T lymphocyte, and helper T lymphocytes. We employed a comprehensive immunoinformatic prediction algorithm to identify immunogenic epitopes of the 56-kDa type-specific cell membrane surface antigen and surface cell antigen A of .

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.

Oxido- and mixed-ligand peroxido complexes of niobium(V) as potent phosphatase inhibitors and efficient catalysts for eco-friendly styrene epoxidation.

The present study describes the facile synthesis and comprehensive characterization of new oxido and peroxidoniobium(V) complexes with biogenic ligands, maltol (malt) and deferiprone (def) in their co-ordination sphere, ., [NbO(malt)]·9HO (1), Na[Nb(O)(malt)]·HO (2) and Na[Nb(O)(def)]·2HO (3). The complexes were characterized using various analytical and spectroscopic techniques (FTIR, Raman, NMR, UV-visible, TGA, ICP-OES and elemental analysis).

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.

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.

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.