Structure-based pharmacophore modeling, virtual screening and simulation studies for the identification of potent anticancerous phytochemical lead targeting cyclin-dependent kinase 2

Cyclin-dependent kinases are of critical importance in directing various cell cycle phases making them as potential tumor targets. Cyclin-dependent kinase 2 (CDK2) in particular plays a significant part during cell cycle events and its imbalance roots out tumorogenic environment. Herein, we built a structure-based pharmacophore model complementing the ATP pocket site of CDK2 with four pharmacophoric features, using a series of structures obtained from cluster analysis during MD simulation assessment. This was followed by its validation and further database screening against Taiwan indigenous plants database (5284 compounds). The screened compounds were subjected toward Lipinski's rule (RO5) and ADMET filter followed by docking analysis and simulation study. In filtering hits (10 compounds) via molecular docking against CDK2, Schinilenol with -8.1 kcal/mol fetched out as a best lead phytoinhibitor in the presence of standard drug (Dinaciclib). Additionally, pharmacophore mapping analysis also indicated relative fit values of dinaciclib and schinilenol as 2.37 and 2.31, respectively. Optimization, flexibility prediction and the stability of CDK2 in complex with the ligands were also ascertained by means of molecular dynamics for 50 ns, which further proposed schinilenol having better binding stability than dinaciclib with RMSD values ranging from 0.31 to 0.34 nm. Reactivity site, biological activity detection and cardiotoxicity assessment also proposed schinilenol as a better phytolead inhibitor than the existing dinaciclib. Abbreviations: CDK2: Cyclin dependent kinase2; ATP: Adenosine triphosphate; MD: Molecular dynamics, RO5: Rule of five; ADMET: Absorption, distribution, metabolism, and excretion; RMSD: Root mean square deviation; DS: Discovery Studio; SOM: Site of metabolism; RBPM: receptor based pharmacophore model; TIP: Schinilenol; hERG: human Ether-à-go-go - Related GeneCommunicated by Ramaswamy H. Sarma.

Direct sunlight-driven enhanced photocatalytic performance of V2O5 nanorods/ graphene oxide nanocomposites for the degradation of Victoria blue dye

Herein, we report the synthesis and characterizations of Vanadium pentoxide (V₂O₅) nanorods/graphene oxide (GO) nanocomposite as efficient direct solar light driven photocatalyst for the enhanced degradation of victoria blue (VB) dye. The nanocomposite was synthesized by sonochemical process and characterized using several analytical methods in order to study the structural, morphological, compositional, optical and photocatalytic properties. The X-ray diffraction studies confirmed the orthorhombic structure of V₂O₅ while the morphological examinations revealed the growth of V₂O₅ nanorods and 2D GO sheets. Interestingly, the UV studies ratify that the bandgap of the nanocomposite was reduced compared to pure GO and V₂O₅. Interestingly, the interaction of the V₂O₅ nanorods with the graphene oxide substrate and its effect on the electronic properties of the combined system, have been examined by means of theoretical calculations, based on the so called Geometry, Frequency, Noncovalent, eXtended Tight Binding (GFN-xTB) method. Studying the photocatalytic behavior of nanocomposite, we observe an almost complete degradation (97.95%) of Victoria Blue (VB) dye under direct sunlight illumination within just 90 min. The outstanding nanocomposite photocatalytic efficiency was due to the excellent transfer of interfacial charge and the suppressed recombination of charge-carrier. The kinetics of the degradation process was also analyzed by calculating the rate constant and half-life time. Finally, a possible mechanism has also been discussed for the degradation process of VB dye using nanocomposite under direct sunlight irradiation.

Synthesis and Characterization of CuO Rods for Enhanced Visible Light Driven Dye Degradation

Here, we report simple and efficient method to synthesize CuO rods using copper acetate, hexamethylenetetramine (HMTA) and sodium hydroxide (NaOH) solutions via hydrothermal process followed by calcination. The Field emission scanning electron microscopy images revealed that synthesized CuO rods were 2-4μm thick with several micrometers long and grown into high density. The as-synthesized CuO rods were characterized by X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), UV-visible spectroscopy and Energy dispersive X-ray analysis (EDS) which confirmed the formation of highly crystalline, single phase pure CuO rods with monoclinic structures. The photocatalytic capability of synthesized CuO rods was executed by monitoring the degradation of methylene blue (MB) dye under visible light illumination. The results showed MB dye degraded about ~70% in just 100 min and followed first order reaction kinetics with rate constant k = 0.01123 mint.1 and R² = 0.9880.

Synthesis and Characterizations of Nitrogen (N) Doped Strontium Titanate (SrTiO₃) Nanoparticles for Enhanced Visible Light Driven Photocatalytic Degradation

Highly crystalline bare and N-doped SrTiO₃ nanoparticles were effectively synthesized with strontium acetate, titanium isopropoxide, hexamethylenetetramine as precursor via citric acid assisted hydrothermal process followed by calcination. The hydrothermally synthesized bare and N-doped SrTiO₃ NPs possessed monodispersity throughout with particle size diameter 50±5 nm but because of annealing at 750 °C temperature the synthesized NPs got agglomerate which created rough surface and induces oxygen vacancy in the NPs. Introducing N^3- ions impurity into SrTiO₃ lattice tailored the electronic band structure of SrTiO₃ and extends its absorption into the visible region. It would display the p-type conductivity and facilitate the photoinduced electron-hole pairs towards respective site which diminishes the chances of recombination of electron-hole pairs that enhances photocatalytic degradation reaction. The results showed MB degraded about ~88 in just 140 min and followed first order reaction kinetics with rate constant k = 0.01489 mint^-1.

Quantitative structure activity relationship and molecular simulations for the exploration of natural potent VEGFR-2 inhibitors: an in silico anti-angiogenic study

VEGFR-2 has recently become an eye-catching molecular target for the novel therapeutic designs against cancer for its well known role in persuading angiogenesis in tumor cells. The current study set sights on the exploration of novel potent natural compound targeting VEGFR-2 via computational ligand-based modeling and database screening followed by binding pattern analysis, reactivity site prediction and MD simulation studies. The known 53 VEGFR-2 inhibitors (with IC50 ranging from 0.7 nM to 9700 nM) were headed for development of Ligand based pharmacophore model using 3 D QSAR pharmacophore generation module of DS Client. Training set inhibitors (23 compounds) were exploited to create pharmacophore model based on their chemical features. The model was validated through 30 test set inhibitors and exploited further for screening of 62,082 natural compounds from InterBioscreen natural compound database. Screened compounds further went through Drug-Likeliness study, ADMET prediction, Binding pattern analysis, In silico prediction of reactivity sites, Biological activity spectra prediction, pan assay interference compound identification and MD simulation analysis. Out of 5 screened compounds, Compound A and Compound B exhibited highest binding energy judged against the standard drug "Sorafenib". On further conducting reactivity site prediction, BAS prediction, and pan assay interference compound identification, Compound B exhibited better result which was carried forward for MD simulation study for 50 ns. MD simulation results suggested that Compound B exhibited more stable binding to the active site of VEGFR-2 without causing any conformational changes in protein-ligand complex. Thereby, the investigation proposes Compound B to hold potent antiangiogenic potential targeting VEGFR-2. [Formula: see text] Communicated by Ramaswamy H. Sarma.

Highly porous ZnO nanosheets self-assembled in rosette-like morphologies for dye-sensitized solar cell application

Facile and direct growth of highly porous ZnO nanosheets self-assembled in rosette-like morphologies on ITO for high performance dye-sensitized solar cell application.

Efficient degradation of Methylene Blue dye over highly reactive Cu doped strontium titanate (SrTiO3) nanoparticles photocatalyst under visible light

Visible light induced photocatalysts of Cu doped SrTiO3 (Cu/SrTiO3) nanoparticles with the size -60-75 nm were prepared via facile sol-gel method. The morphological, optical, crystalline properties and compositions of synthesized Cu/SrTiO3 nanoparticles were thoroughly characterized by field emission scanning electron microscopy (FE-SEM), powder X-ray diffraction (XRD), ultra violet-visible spectroscopy (UV-Vis) and energy dispersive X-ray (EDX). A significant red shift in the UV-diffused reflectance spectrum was observed and the absorption edge shifted to visible region by the Cu doping. Surprisingly, the band gap of SrTiO3 was changed from 3.2 eV drop to 2.96 eV. The photocatalytic activity of the synthesized Cu/SrTiO3 nanoparticles was demonstrated for the degradation of Methylene Blue dye under visible light irradiation. The formation of new acceptor region in Cu/SrTiO3 was responsible for high photocatalytic activity of Cu/SrTiO3 nanoparticles. The results showed that the Methylene Blue dye was degraded by -66% within time span of 2 h over the Cu/SrTiO3 nanoparticles. This dye degradation reaction followed the Langmuir-Hinshelwood kinetics and also exhibited first order reaction rate. The calculated rate constant for the degradation reaction following first order kinetics was k = 0.0016 min(-1).