•A computational approach was tried to find the evolutionarily related fold of the RAP proteins through the structural and sequence-based analysis, found various protein folds that are very close to ...the RAP folds.•Remote homolog datasets were used potentially to develop different support vector machine (SVM) methods to recognize the homologous RAP fold.•This study to show how 1lre-RAP SVM models recognize other proteins and How the other proteins SVM models recognize 1lre-RAP proteins. To answer these questions, different SVM based methods and confusion matrix based prediction score graphs were generated.•According to the structural, sequence alignment and SVM recognition BAR/IMD domain-like fold (PDB identifier 2efl-A) and Multiheme cytochromes (PDB identifier 4rkm-H) protein folds are evolutionarily related to 1lre-RAP fold.
The receptor-associated protein (RAP) is an inhibitor of endocytic receptors that belong to the lipoprotein receptor gene family. In this study, a computational approach was tried to find the evolutionarily related fold of the RAP proteins. Through the structural and sequence-based analysis, found various protein folds that are very close to the RAP folds. Remote homolog datasets were used potentially to develop a different support vector machine (SVM) methods to recognize the homologous RAP fold. This study helps in understanding the relationship of RAP homologs folds based on the structure, function and evolutionary history.
Experimental and theoretical investigations on the molecular structure, electronic and vibrational characteristics of 2-Amino-3-bromo-5-nitropyridine are presented. The vibrational frequencies were ...obtained by DFT/B3LYP calculations employing 6–311++G (d, p) basis set. This was compared with experimental FT-IR and FT-Raman spectral data. Simulated FT-IR (4000–400cm−1) and FT-Raman spectra (4000–100cm−1) showed good agreement with the observed spectra. The molecular equilibrium geometry of the title compound was fully optimized. Quantum chemical calculations of the equilibrium geometry and the complete vibrational assignments of wavenumbers using potential energy distribution (PED) were calculated with scaled quantum mechanics. HOMO–LUMO energies, energy gap (ΔE), electronegativity (χ), chemical potential (μ), global hardness (η), softness (S) and the Fukui function were calculated for the title molecule. The title compound has a low softness value (0.239) and the calculated value of electrophilicity index (5.905) describes the biological activity. The stability and charge delocalization of the title molecule were studied by Natural Bond Orbital (NBO) analysis, Non-Linear Optical (NLO) behaviour in terms of first order hyperpolarizability, dipole moment and anisotropy of polarizability and Molecular Electrostatic Potential (MEP) were accounted. The computed values of μ, α and β for the title molecule are 1.851 Debye, 1.723×10−23esu and 7.428×10−30esu respectively. The high β value and non-zero value of μ indicate that the title compound might be a good candidate for NLO material. Thermodynamic properties of the title molecule were studied for different temperatures thereby revealing the correlations between heat capacity (C), entropy (S) and enthalpy changes (H) with temperatures. Docking studies of the title compound were scrutinized to predict the preferred binding orientation, affinity and activity of the given compound. The title compound was docked into the active site of the protein 5FCT which belongs to the class of proteins exhibiting the property as a Dihydrofolate synthase inhibitor. A minimum binding energy of −5.9kcal/mol and intermolecular energy of −6.5kcal/mol is seen in the interaction.
Quantum chemical calculations of the equilibrium geometry, harmonic vibrational frequencies, Infrared intensities and Raman activity of 2-Amino-3-bromo-5-nitropyridine in the ground state were carried out by using density functional theory (DFT/B3LYP) method with 6–311++G (d, p) basis set. The theoretical and experimental spectrograms for FT-IR, FT-Raman of the title compound haven been constructed. Docking into the active site of the protein 5FCT which belongs to the class of proteins exhibiting the property as a Dihydrofolate synthase inhibitor was studied. Display omitted
•Spectroscopic properties of C5H4BrN3O2 were examined by FT-IR, FT-Raman techniques and DFT methods.•Hyperpolarizability, donor acceptor interactions, HOMO-LUMO, MEP distribution, have been studied.•Thermodynamic properties and chemical reactivity with Fukui functions have been calculated.•Docking studies and binding energy calculations were accounted.
A high perovskite activity is sought for use in magnetic applications. In this paper, we present the simple synthesis of (2.5% and 5%) Tellurium-impregnated-LaCoO3 (Te-LCO), Te and LaCoO3 (LCO) by ...using a ball mill, chemical reduction, and hydrothermal synthesis, respectively. We also explored the structure stability along with the magnetic properties of Te-LCO. Te has a rhombohedral crystal structure, whereas Te-LCO has a hexagonal crystal system. The reconstructed Te was imbued with LCO that was produced by hydrothermal synthesis; as the concentration of the imbuing agent grew, the material became magnetically preferred. According to the X-ray photoelectron spectra, the oxidation state of the cobaltite is one that is magnetically advantageous. As a result of the fact that the creation of oxygen-deficient perovskites has been shown to influence the mixed (Te4+/2−) valence state of the incorporated samples, it is abundantly obvious that this process is of utmost significance. The TEM image confirms the inclusion of Te in LCO. The samples start out in a paramagnetic state (LCO), but when Te is added to the mixture, the magnetic state shifts to a weak ferromagnetic one. It is at this point that hysteresis occurs due to the presence of Te. Despite being doped with Mn in our prior study, rhombohedral LCO retains its paramagnetic characteristic at room temperature (RT). As a result, the purpose of this study was to determine the impacts of RT field dependency of magnetization (M-H) for Te-impregnated LCO in order to improve the magnetic properties of RT because it is a low-cost material for advanced multi-functional and energy applications.
CuMn2O4 nanoparticles were successfully synthesized by adopting solvothermal method with optimum hydrothermal processing temperature maintained at 160 °C for 12 h. The synthesized CuMn2O4 ...nanoparticles structure, morphology, optical and electrochemical properties were analyzed with respect to varying the hydrothermal temperature. The product dominant XRD peak observed at 35.8° matches well with corresponding planes of standard data. The IR vibrational modes of Mn-O and Cu-O band were authenticated by the peak appearance at 526 and 630 cm−1. The rice-like morphology formation of CuMn2O4 nanoparticles prepared at 160 °C hydrothermal processing temperature revealed the superior behavior of electrochemical properties. The electrochemical studies carried out to estimate the specific capacitance of CuMn2O4 nanoparticles (MX3) at low scan rate 10 mV/s showed an excellent specific capacitance value of 520.4 F/g. The GCD studies of synthesized rice-like morphology CuMn2O4 nanoparticles (MX3) revealed superior specific capacitance of 577.9 F g−1 at 0.5 A g−1 and retain its 98% capacitance as 571.6 F g−1 at 1 A g−1 current density.
•Rice-like CuMn2O4 nanoparticles at 160 °C hydrothermal processing temperature.•Superior excellent specific capacitance of 577.9 F/g at 0.5 A/g.•Product retains its 98% capacitance as 571.6 F g−1 at 1 Ag-1 current density.
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•The molecular structure was optimized and the band gap energy was calculated.•UV spectral analysis was made and the charge transfer due to excitation was studied.•ESP, ELF and LOL ...maps generated reveals the charge distribution on the surface.•Fukui functions and reactivity descriptors were calculated.•Molecular docking studies confirmed the antiviral activity of the compound.
Valacyclovir is the l-valyl ester prodrug of the antiviral drug acyclovir that exhibits activity against Herpes simplex virus types and varicella zoster virus. An explicit surface analysis on the title compound was carried out theoretically using the wavefunction analyser multiwfn software, inorder to study the reactivity of the compound. The input wavefunction files were generated by Gaussian 09W software using B3LYP/6-311++G(d,p) as the basis set. The structure of the title compound was optimized; wave function analyses and the molecular docking studies were completed. The UV spectrum was experimentally recorded in solvent phase and in addition to it the electronic absorption spectrum of the compound was evaluated by TD-DFT in the gas and solvent phase. The ESP (Electrostatic potential) map points out the surface extremas where the global surface minimum is seen at the oxygen atom with the value −61.5675 and global surface maximum near the hydrogen atom with the value 67.862. The energy band gap obtained from the HOMO-LUMO gap (E = 3.6023 eV) were found to be in agreement with the energy gap (E = 3.6174 eV) calculated using λmax from the UV spectrum. The electron-hole distribution of the molecule indicated a charge transfer within the molecule. Electron Localization Function, Local Orbital Localizer, Thermodynamic functions were discussed. The reactive sites of the compound were studied from the fukui function calculations and chemical descriptors define the reactivity of the molecule on the whole. The antiviral activities of the title compound against various viral proteins (VZV, HSV, Dengue) were studied using molecular docking.
Nanotheranostics is to apply and further develop nanomedicine strategies for advanced theranostics. This review summarizes the various nanocarriers developed so far in the literature for ...nanotheranostics, which include polymer conjugations, dendrimers, micelles, liposomes, metal and inorganic nanoparticles, carbon nanotubes, and nanoparticles of biodegradable polymers for sustained, controlled and targeted co-delivery of diagnostic and therapeutic agents for better theranostic effects with fewer side effects. The theranostic nanomedicine can achieve systemic circulation, evade host defenses and deliver the drug and diagnostic agents at the targeted site to diagnose and treat the disease at cellular and molecular level. The therapeutic and diagnostic agents are formulated in nanomedicine as a single theranostic platform, which can then be further conjugated to biological ligand for targeting. Nanotheranostics can also promote stimuli-responsive release, synergetic and combinatory therapy, siRNA co-delivery, multimodality therapies, oral delivery, delivery across the blood-brain barrier as well as escape from intracellular autophagy. The fruition of nanotheranostics will be able to provide personalized therapy with bright prognosis, which makes even the fatal diseases curable or at least treatable at the earliest stage.
A growing number of cohort studies suggest a potential role of dairy consumption in type 2 diabetes (T2D) prevention. The strength of this association and the amount of dairy needed is not clear.
We ...performed a meta-analysis to quantify the associations of incident T2D with dairy foods at different levels of intake.
A systematic literature search of the PubMed, Scopus, and Embase databases (from inception to 14 April 2015) was supplemented by hand searches of reference lists and correspondence with authors of prior studies. Included were prospective cohort studies that examined the association between dairy and incident T2D in healthy adults. Data were extracted with the use of a predefined protocol, with double data-entry and study quality assessments. Random-effects meta-analyses with summarized dose-response data were performed for total, low-fat, and high-fat dairy, (types of) milk, (types of) fermented dairy, cream, ice cream, and sherbet. Nonlinear associations were investigated, with data modeled with the use of spline knots and visualized via spaghetti plots.
The analysis included 22 cohort studies comprised of 579,832 individuals and 43,118 T2D cases. Total dairy was inversely associated with T2D risk (RR: 0.97 per 200-g/d increment; 95% CI: 0.95, 1.00;P= 0.04;I(2)= 66%), with a suggestive but similar linear inverse association noted for low-fat dairy (RR: 0.96 per 200 g/d; 95% CI: 0.92, 1.00;P= 0.072;I(2)= 68%). Nonlinear inverse associations were found for yogurt intake (at 80 g/d, RR: 0.86 compared with 0 g/d; 95% CI: 0.83, 0.90;P< 0.001;I(2)= 73%) and ice cream intake (at ∼10 g/d, RR: 0.81; 95% CI: 0.78, 0.85;P< 0.001;I(2)= 86%), but no added incremental benefits were found at a higher intake. Other dairy types were not associated with T2D risk.
This dose-response meta-analysis of observational studies suggests a possible role for dairy foods, particularly yogurt, in the prevention of T2D. Results should be considered in the context of the observed heterogeneity.
•Quantum chemical calculations on energy and molecular structure of the compound.•Stability is assessed using HOMO-LUMO values and significant electronic characteristics.•Chemical structure and ...reactivity, topological analyses carried out.•UV–vis absorption spectra were obtained employing the TD-DFT technique for various solvents.•Molecular docking simulations, drug likeness parameters, ADMET and mol inspiration values were reported.
Theoretical studies of 6-Bromo-7-methylimidazo1,2-a pyridine employing density functional theory has been accomplished in this present work. The caption compound's molecular geometry and optimal structure were computed. The significant bonding sites and weak interactions in the molecule were also presented utilising multiwave function, along with the electron-hole dispersal for the excited states and topological analyses (ELF, LOL, and RDG). NLO predictions, orbital HOMO-LUMO investigations and MEP findings by DFT method, IEFPCM model were executed in green solvents comprising water, ethanol, acetone and heptane and also in gas phase. The least HOMO-LUMO gap was obtained for heptane (3.8426). Among the solvents chosen, water is found to have the highest value of dipole moment (1.192707), polarizability (7.3045 × 10-23 esu) and first order hyperpolarizability (5.43313 × 10-30 esu). The molecule's consistency ensuing from the hyper conjugative relation and charge delocalization were examined exercising NBO scrutiny. UV – Vis spectra have been reconnoitred with the aid of the TD-SCF approach, IEFPCM model. ADMET and drug-likeness were employed to assess the biological properties. Finally, the headline compound was docked into the effective locations of 4LRI protein (antiviral-cmv property), 4HJ2 and 2VL3 proteins (Thioredoxin inhibitor property). Additionally, target proteins stability has been ascertained using Ramachandran plots.
Ce doped ZnO nanoparticles (Zn
1−x
Ce
x
O, x = 0.0, 0.05 and 0.1) have been synthesized by sol–gel method at annealing temperature of 500 °C for 1 h under Ar atmosphere. The synthesized samples have ...been characterized by powder X-ray diffraction (XRD), energy dispersive X-ray studies, UV–Visible spectrophotometer and fourier transform infrared (FTIR) spectroscopy. The XRD measurements indicate that the prepared nanoparticles have a hexagonal wurtzite structure and CeO
2
crystallites. The calculated average crystalline varied from 21.97 to 15.62 nm with increase in Ce concentrations. The increase in lattice parameters reveals the substitution of Ce into ZnO lattice. The presence of functional groups and the chemical bonding is confirmed by FTIR spectra. PL spectra of the Zn
1−x
Ce
x
O system show that the shift in near band edge emission from 386 to 363 nm and a shift in blue band emission from 517 to 485 nm which confirms the substitution of Ce into the ZnO lattice.
In this present study, an amalgamation of experimental and theoretical investigation on the molecular structure, MEP, ELF, LOL, NBO, drug likeness and molecular docking study with spectroscopic ...investigation (FT-IR, FT-Raman and UV–vis) of Tinidazole, an anti-protozoal compound has been reported.
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•Optimized the molecular structure. Spectroscopic (FT-IR, FT-Raman and UV-vis) experimental data were compared with the theoretical data and assigned.•NBO analysis carried out confirming charge delocalization and stability of the molecule. Surface reactivity was studied and the reactive sites were located based on Fukui indices.•Ligand-protein interactions of anti-infective (Malaria), anti-fungal (Invasive aspergillosis) and anti-mycobacterial (Mycobacterium tuberculosis) activities were confirmed using molecular docking analysis. 2D protein-ligand interaction profile images have been created.•Drug likeness analysis was performed to confirm the active potential pharmaceutical activity.
1-(2-ethylsulfonylethyl)-2-methyl-5-nitro-imidazole (1EMI) C8H13N3O4S also known as Tinidazole, selected for its antiprotozoal property is extensively used for spectroscopic elucidations and computational aspects using density functional methods. Along with spectral conclusions, further investigations on fundamental reactive properties such as electrical, optical, nonlinear combined with DFT simulations were performed. Molecular docking procedure supports the results of chosen appropriate antiprotozoal agent based on ligand-protein interactions. Experimental and simulated (B3LYP/6-311++G (d,p)) IR and Raman spectra showed concurrence. NLO analysis through first order hyperpolarizability parameter helps in finding the potential of 1EMI as a good NLO candidate. Charge delocalization and the stability of the compound were discussed using natural bond orbital (NBO) analysis. Furthermore, Electron localization function (ELF), local orbital locator (LOL), and Frontier molecular orbitals (FMO) were studied. Besides, Mulliken population analysis on atomic charges, Energy gap, chemical potential, global hardness, softness, ionization potential, electronegativity, electrophilicity index along thermodynamic parameters (enthalpy, entropy and heat capacity) have been calculated. Drug likeness parameters and molecular docking approach enabled to check pharmaceutical potential and biological activity of 1EMI. The biological activity of 1EMI through ligand and protein interactions have been confirmed theoretically for the treatment of Malaria, Invasive aspergillosis and Mycobacterium tuberculosis with respect to chosen proteins. Three different activity targets and protein interactions are quite successful revealing the bond distances, intermolecular energy, binding energy and inhibition constant. 2D interaction profile image of the two maximum interacted proteins and also Ramachandran plot used to show stereochemistry of selected protein. The activities of 1EMI were studied in accordance with literature survey and the results were presented.
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