Targeting non-structural proteins and 3CLpro in SARS-CoV-2 virus using phytochemicals from medicinal plants - In-silico approach

In the present study, the main protease 3CL^pro and non-structural protein (NSP-12 with co-factors 7 and 8) trimer complex are used to study the protein-drug interactions with the phytochemicals from Ocimum Sanctum, Tinospora Cordifolia, Glycyrrhiza Glabra, and Azadirachta Indica. Which can give insight to be used as potent antiviral drugs against SARS-CoV-2. Twenty phytochemicals, five from each plant species, known for their wide range of biological activities were chosen from the literature. The in-silico study was carried out using virtual screening tools and the top five, which showed the least binding energies, were selected. Molecular docking tools revealed that gedunin and epoxy azadiradione proved to be excellent inhibitors for 3CL^pro and so did Tinosporide for non-structural-protein complex. Further, the best-hit phytochemicals with respect to structure similarities with FDA drugs and investigatory drugs, were considered for comparative study. Molecular docking was done to check the drug-protein interactions and to check the inhibitory responses of these drugs against the viral protein. The analyses showed that the phytochemicals had similar responses on the protein complex but with exceptionally higher inhibitory responses hence which may be taken for further clinical study.     

The mutual responses of higher plants to environment: physiological and microbiological aspects

Higher plants are different from animals in many aspects, but the important difference may be that plants are more easily influenced by environment. Plants have a series of fine mechanisms for responding to environmental changes, which has been established during their long-period evolution and artificial domestication. The relationship between higher plants and environment is influenced mutually. The component in environment provides higher plants with nutrients for shaping themselves and higher plants simultaneously bring photosynthetic products and metabolites to surroundings, which is the most important part of natural circle. Photosynthetic products are realized mainly by physiological mechanisms, and microbiological aspects in environment (for instance, soil environment) impact the above processes greatly. The complete understanding of the relationship will extremely promote the sustainable utilization of plant resources and make the best use of its current potential under different scales.     

Analysis of gene expression as a new tool in ecotoxicology and environmental monitoring

Pollution affects biological mechanisms in exposed biota, with adverse effects on tissue, organism and, eventually, entire ecosystem levels. Ecotoxicological biomarkers reflect these pollutant-induced physiological alterations, usually by measuring changes in the activity of specific enzymes, or alterations in hormone or protein levels. New, robust polymerase-chain-reaction (PCR)-based methodologies for quantifying specific messenger-RNA molecules have allowed the development of a new family of biomarkers based on analysis of gene-expression patterns. These gene-expression biomarkers have already been applied to many aspects of risk assessment, from toxicological analyses of new substances to in-field monitoring schemes. We review the fundamentals of these techniques, their application in different environmental surveys, their limitations and the outlook for their use in the future.     

Identification of cellulose synthase(s) in higher plants: sequence analysis of processive β-glycosyltransferases with the common motif ’D, D, D35Q(R,Q)XRW‘

More than ten β-glycosyltransferases are now recognized that have limited similarity to the amino acid sequence of cellulose synthase from Acetobacter xylinum. Using hydrophobic cluster analysis (HCA), we recently identified two domains and putative catalytic residues in the processive β-glycosyltransferases. In this study, we have found expressed sequence tags (ESTs) from higher plants (Arabidopsis thaliana, Brassica campestris, and Oryza sativa) that exhibit a limited sequence similarity to the A. xylinum cellulose synthase. These ESTs contain some of the conserved residues identified in the processive β-glycosyltransferases. Complete sequencing of an EST clone (T88271) from A. thaliana led to the identification of all the conserved residues in the derived truncated polypeptide which appears to be part of a putative cellulose synthase. Sequence comparison of proteins with known function and several unidentified proteins have the ‘D, D, D35Q(R,Q)XRW’ motif which is considered a strong predictor for β-glycosyltransferasesthat includes, among other proteins, cellulose and chitin synthases. The first two conserved aspartic acid residues in this motif were analysed by site-directed mutagenesis, and their replacement by another amino acid led to a loss of cellulose synthase activity in A. xylinum, suggesting that they are essential for enzyme activity. A correlation between the second residue (R or Q) in the Q(R,Q)XRW sequence and the synthesis of along glucan chain (polysaccharide) or a short glucan chain(oligosaccharide) suggests that this residue may be involved in the degree of processivity This revised version was published online in August 2006 with corrections to the Cover Date.     

Spectra and structure of organophosphorus compounds: XLIX. Microwave,infrared, and Raman spectra,electric dipole moment,molecular structure,and ab initio calculations of dimethylphosphonothioic fluoride

The microwave spectra of (CH₃)₂PSF, (CH₃)(CD₃)PSF, (CD₃)₂PSF, and (CH₃)₂P³⁴SF have been investigated from 20.0 to 40.0 GHz. Botha-type R branch andc-type Q branch transitions have been measured in the ground states of each isotopic species. From a least-square adjustment to fit 12 rotational constants, the following structural parameters were obtained:r(P–F)=1.582 ± 0.003 Å;r(P=S)=1.902 ± 0.001 Å;r(P-C)=1.800 ± 0.001 Å;r(C-H)=1.088 ± 0.002 Å; HCP=109.28 ± 0.12°; SPF=114.50 ± 0.13°; and SPC=116.33 ± 0.06°. From Stark effect measurements, the dipole moment components have been determined to be ¦ _a ¦ =3.556 ± 0.005; ¦ _c ¦=2.026 ± 0.009; and ¦ _t ¦=4.093 ± 0.009 (D). The Raman spectra (3200 to 100 cm^–1) of each isotopic species have been measured for the solid, and liquid and qualitative depolarization values obtained. Additionally, the mid-infrared spectra (3200 to 500 cm^–1) of the solids have been recorded. Proposed assignments of the normal modes have been made on the basis of Raman depolarization values and group frequencies which are supported by normal coordinate analysis utilizing an ab initio force field. Optimized structural parameters have been obtained with both the 3-21G^* and 6-31G^* basis sets. These results are compared to the corresponding quantities for several similar molecules.For part XLVIII, seeJ. Raman Spectrosc.1922,23, 107.     

Disordered proteins and network disorder in network descriptions of protein structure, dynamics and function: hypotheses and a comprehensive review

During the last decade, network approaches became a powerful tool to describe protein structure and dynamics. Here we review the links between disordered proteins and the associated networks, and describe the consequences of local, mesoscopic and global network disorder on changes in protein structure and dynamics. We introduce a new classification of protein networks into 'cumulus-type', i.e., those similar to puffy (white) clouds, and 'stratus-type', i.e., those similar to flat, dense (dark) low-lying clouds, and relate these network types to protein disorder dynamics and to differences in energy transmission processes. In the first class, there is limited overlap between the modules, which implies higher rigidity of the individual units; there the conformational changes can be described by an 'energy transfer' mechanism. In the second class, the topology presents a compact structure with significant overlap between the modules; there the conformational changes can be described by 'multi-trajectories'; that is, multiple highly populated pathways. We further propose that disordered protein regions evolved to help other protein segments reach 'rarely visited' but functionally-related states. We also show the role of disorder in 'spatial games' of amino acids; highlight the effects of intrinsically disordered proteins (IDPs) on cellular networks and list some possible studies linking protein disorder and protein structure networks.     

Thorium compounds with non-metals: Electronic structure, chemical bond, and physicochemical properties

The current state of research on the nature of the chemical bond and the physicochemical properties of binary Th-X (X = H, B, C, N, O, P, S, As, Se, Sb) and ternary (carbonitrides, thorates, and silicates) thorium compounds by modern ab initio methods of the band structure theory is reviewed. The possibilities of the ab initio band structure methods in describing the structural states, phase stability, elasticity characteristics, X-ray emission, absorption, and photoelectron spectra of thorium-containing systems are discussed.     

Transport phenomenon as a function of counter and co-ions in solution: chronopotentiometric behavior of anion exchange membrane in different aqueous electrolyte solutions

Anion exchange membrane has been investigated in different electrolyte solutions by chronopotentiometry to explore the influence of co-ion and counterion of the exchange group of the membrane, on the transport phenomena. Chloride, nitrate, sulfate and acetate in sodium salts were used as counterions and sodium, potassium, calcium and ammonium in chloride salts were used as co-ions. The membrane showed a potential drop (E₀) in all these electrolytes when a constant current was applied across it, which remained constant for a period less than τ, called the transition time and rose gradually to a maximum (E_max) value. The parameters such as τ, E₀ and E_max and the potential jump (ΔE) and τ and the inflection zone (Δt) along the time axis have been measured and compared at an applied current density (I) of 10 mA cm⁻² in 10 mM solutions. The values of τ^1/2/z_A[A₀] or τ^1/2/z_C[C₀], with or , E₀ and ΔE with or (where r_A and r_C are the ionic radii of counter and co-ions, respectively) have been correlated. Permselectivity (P) and transference number of the membrane with respect to each one of the above electrolytes have been evaluated and discussed.     

Local structure and oxidation state of uranium in some ternary oxides: X-ray absorption analysis

We investigated the local atomic and electronic structures of two related systematic sets of ternary uranium oxides, NaUO₃-KUO₃-RbUO₃ and BaUO₃-Ba₂U₂O₇-BaUO₄, by measuring the X-ray absorption near edge structure (XANES). The results are compared with calculations based on a self-consistent real space full multiple scattering analysis. We found a very good agreement between measured and calculated spectra, which indicates that the uranium ions are in a pure U⁵⁺ oxidation state in these compounds. The low energy shoulder observed in the U L₃ edge XANES is an intrinsic feature of the uranium unoccupied 6d electronic states of the U⁵⁺ ions within the studied materials. Specific double shoulder features in the higher energy range of the U L₃ edge XANES can be interpreted as indicative of the pure cubic perovskite structure.