Molecular docking aided machine learning for the identification of potential VEGFR inhibitors against renal cell carcinoma.

Renal cell carcinoma is a highly vascular tumor associated with vascular endothelial growth factor (VEGF) expression. The Vascular Endothelial Growth Factor -2 (VEGF-2) and its receptor was identified as a potential anti-cancer target, and it plays a crucial role in physiology as well as pathology. Inhibition of angiogenesis via blocking the signaling pathway is considered an attractive target.

Design, synthesis and in silico molecular docking evaluation of novel 1,2,3-triazole derivatives as potent antimicrobial agents.

Chalcone and triazole scaffolds have demonstrated a crucial role in the advancement of science and technology. Due to their significance, research has proceeded on the design and development of novel benzooxepine connected to 1,2,3-triazolyl chalcone structures. The new chalcone derivatives produced by benzooxepine triazole methyl ketone and different aromatic carbonyl compounds are discussed in this paper.

The identification of c-Abl inhibitors as potential agents for Parkinson's disease: a preliminary in silico approach.

Parkinson's disease (PD) is the most common movement disorder worldwide. PD is primarily associated with the mutation, overexpression, and phosphorylation of α-synuclein. At the molecular level, the upstream protein c-Abl, a tyrosine kinase, has been shown to regulate α-synuclein activation and expression patterns.

A Highly Selective Schiff Base Based Chemodosimeter for the Detection of Perfluorooctanoic Acid by Optical Biosensor.

A simple imine derivative based sensor (IDP) has been synthesized and characterized by  H NMR,  C NMR and mass spectral techniques. IDP is more capable of detecting perfluorooctanoic acid (PFOA) in a selective and sensitive manner. The PFOA as a biomarker interacts with IDP and shows "TURN-ON" response by colorimetric and fluorimetric method.

Construction of Mechanically Interlocked Fluorescence Photoswitchable [2]Rotaxane with Aggregation-Induced Emission and Molecular Shuttling Behaviors.

Here, we report the design, synthesis, and optical behaviors of a multistimuli responsive [2]rotaxane system constructed from noncovalent interactions between diarylethene (DAE)-based axle and a tetraphenylethene (TPE)-based macrocycle using a snapping supramolecular assembly approach. The shuttling behavior of the macrocycle (-) between dialkylammonium and urea stations could be realized by the influence of acid-base stimuli using H NMR spectroscopy. Switching between the open-form (OF) [2]rotaxanes ( and ) is highly reversible using external chemical stimuli.

Green synthesis of naphthyl derivative as an optical sensor for the detection of l-carnitine in food samples.

An economical and green approach to the synthesis of naphthyl derivative for detection of l-carnitine (3-hydroxy-4-N-trimethyl-aminobutyrate) is practically important. We developed a naphthyl derivative as a probe showing 'turn-on' response towards l-carnitine selectively at pH 7.2 through ICT mechanism with a good limit of detection (LOD) of 0.

Highly Sensitive and Selective Detection of Melatonin in Biofluids by Antipyrine Based Fluorophore.

A simple fluorescent based organic fluorophore was synthesized and it shows significant fluorescent intensity with melatonin (MLN). Hence, it was applicable to the detection of MLN by colorimetric and fluorimetric techniques at neutral pH. Under optimized experimental condition, the synthesized organic fluorophore detects MLN selectively in the presence of other interfering biomolecules through ICT mechanism.

Effective Detection of Phenylalanine Using Pyridine Based Sensor.

Pyridine based organic molecule as probe has been synthesized for the detection of phenylalanine (PA) biomarker. The synthesized probe is characterized by H and C NMR and mass spectroscopic studies. The photophysical properties for the probe has recorded by colorimetric and fluorimetric techniques.

Development of Optical Biosensor for the Detection of Glutamine in Human Biofluids Using Merocyanine Dye.

Merocyanine dye based fluorescent organic compound has been synthesized for the detection of glutamine. The probe showed remarkable fluorescent intensity with glutamine through ICT (Intermolecular Charge Transfer Mechanism). Hence, it is tested for the detection of glutamine using colorimetric and fluorimetric techniques in physiological and neutral pH (7.

Eco-Friendly Sustainable Poly(benzoxazine--urethane) with Room-Temperature-Assisted Self-Healing Based on Supramolecular Interactions.

This work is an attempt to develop bio-based eco-friendly poly(benzoxazine--urethane) [poly(U--CDL-aee)] materials using cardanol-based benzoxazines (CDL) and hexamethylene diisocyanate (HMDI) to check their self-healing ability and thermal properties. CDL monomers were synthesized using cardanol, amino ethoxyethanol (aee) or 3-aminopropanol (3-ap), and paraformaldehyde through the Mannich reaction. Later, CDL-aee or CDL-3-ap monomers were copolymerized with a urethane precursor (HMDI), followed by ring-opening polymerization through thermal curing.

Atomistic simulation on flavonoids derivatives as potential inhibitors of bacterial gyrase of .

The bacterial DNA gyrase is an attractive target to identify the novel antibacterial agents. The flavonoid derivatives possess various biological activities such as antimicrobial, anti-inflammatory and anticancer activities. The aim of present study is to identify the potential molecule from flavonoid derivatives against using atomistic simulation namely Molecular Docking, Quantum Chemical and Molecular Dynamics.

Diversiform Nanostructures Constructed from Tetraphenylethene and Pyrene-Based Acid/Base Controllable Molecular Switching Amphiphilic [2]Rotaxanes with Tunable Aggregation-Induced Static Excimers.

Dual-emissive tetraphenylethene (TPE) and pyrene-containing amphiphilic molecules are of great interest because they can be integrated to form stimuli responsive materials with various biological applications. Herein, we report the study of mechanically interlocked molecules (MIMs) with aggregation-induced static excimer emission (AISEE) property through a series of TPE and pyrene-based amphiphilic [2]rotaxanes, where -butylcalix[4]arene with hydrophobic nature was used as the macrocycle. Evidently, by adorning TPE and pyrene units in [2]rotaxanes , , , and , they display remarkable emission bands in 70% of water fraction () in tetrahydrofuran (THF)/water mixture, which could be attributed to the restricted intramolecular rotation of phenyl groups, whereas prominent blue-shifted excimer emission of pyrene started to appear as reached 80% for and 90% for , , and , which was ascribed to the favorable π-π stacking and hydrophobic interactions of the pyrene rings that enabled their static excimer formation.

Rationally designed imidazole derivative as colorimetric and fluorometric sensor for selective, qualitative and quantitative cyanide ion detection in real time samples.

A new imidazole derivative of 1,2-diaminoanthraquinone and fluorene-2-carboxaldehyde was designed as a sensor B2 to selectively detect the cyanide (CN) ion through colorimetric and/or fluorometric methods. The photochemical characterizations of sensor B2 were tested using absorption and emission spectral studies in CHCN-HO (8:2) semi-aqueous medium. An excited state proton transfer process (ESIPT) was proved by theoretical and spectral studies.

Highly Selective and Sensitive Colorimetric and Fluorimetric Sensor for Cu.

A newly designed fluorescent and colorimetric probe was synthesized and selective detection of cu was successful in aqueous medium. The design strategy exhibited strongly fluorescent when binding with cu based on the change in structure between spirocyclic to a non-cyclic form of rhodamine based dye. The UV visible spectra of probe (6GS2) exhibited three absorption peaks at 229, 309 and 530 nm respectively.

Molecular docking and ADMET analysis of hydroxamic acids as HDAC2 inhibitors.

Histone deacetylase (HDAC2) belongs to the hydrolase family and a promising target for cancers. We reported 96 hydroxamic compounds optimized using hydrogen-donors, hydrophobic and electron withdrawing groups followed by molecular docking studies. The optimized compounds show good LibDock score and H-bond interaction in the active site of HDAC2.

Simultaneous Production and Surface Functionalization of Silver Nanoparticles for Label-free Colorimetric Detection of Copper Ion.

In this work, a simple method was developed to simultaneously fabricate silver nanoparticles (AgNPs) and modify their surfaces with recognition functional groups for colorimetric detection of Cu ions. To prepare the AgNPs with proper functional group on their surface for detection of Cu ions, photochemical reaction was employed and a photoactive species of tyrosine (Tyr) was used to trigger the photoreduction of AgNPs, while the oxidized Tyr (Tyr) was used to functionalize the AgNPs surface at the same time. To understand the behaviors, the prepared color AgNPs colloidal solution was characterized by UV-visible spectrometer, FT-IR spectrometer, dynamic light scattering (DLS), X-ray photoelectron spectrometer (XPS) and density functional theory (DFT).

Quantum mechanistic insights on aryl propargyl ether Claisen rearrangement.

The mechanism of aryl propargyl ether Claisen rearrangement in gas and solvent phase was investigated using DFT methods. Solvent phase calculations are carried out using N,N-diethylaniline as a solvent in the PCM model. The most favorable pathways involve a [3,3]-sigmatropic reaction followed by proton transfer in the first two steps and then deprotonation or [1,5]-sigmatropic reaction.

Spectroscopic probe on N-H⋯N, N-H⋯O and controversial C-H⋯O contact in A-T base pair: a DFT study.

DNA base pair A-T has been investigated by IR and NMR spectroscopy using DFT methods. The results have been analyzed in terms of infrared vibrational frequencies and (1)H NMR chemical shifts. Different types of interactions N-H⋯N, N-H⋯O and C-H⋯O types have been investigated in DNA base pairs.

Quantum mechanical calculations for the misincorporation of nucleotides opposite mutagenic 3,N4-ethenocytosine.

The ubiquitous nature and persistence of exocyclic DNA adducts suggest their involvement as initiators of carcinogenesis. We have investigated the misincorporation properties of the exocyclic DNA adduct, 3,N(4)-ethenocytosine, using DFT and DFT-D methods. Computational investigations have been carried out by using the B3LYP, M062X, and wB97XD methods with the 6-31+G* basis set to determine the hydrogen bonding strengths, binding energy, and physical parameters.

Computational investigation on microsolvation of the osmolyte glycine betaine [GB (H(2)O)(1-7)].

The preferential interactions of glycine betaine (GB) with solvent components and the effect of solvent on its stability have been examined. In particular, the microsolvation of organic osmolyte and widely important osmoprotectant in nature as glycine betaine has been reported by using M06 method. A number of configurations (b(X) (a-z)) of the clusters for one to seven water molecules (× = 1-7) have been considered for the microsolvation.

Model calculations for the misincorporation of nucleotides opposite five-membered exocyclic DNA adduct: N(2),3-ethenoguanine.

Five-membered exocyclic DNA adducts are biologically very significant because of their potential to block DNA replication and transcription. N(2),3-Ethenoguanine (N(2,3)-εG) has been identified in the liver DNA of vinyl chloride-exposed rats as a five-membered DNA adduct. Singer et al.

On the chemical stabilities of ionic liquids.

Ionic liquids are novel solvents of interest as greener alternatives to conventional organic solvents aimed at facilitating sustainable chemistry. As a consequence of their unusual physical properties, reusability, and eco-friendly nature, ionic liquids have attracted the attention of organic chemists. Numerous reports have revealed that many catalysts and reagents were supported in the ionic liquid phase, resulting in enhanced reactivity and selectivity in various important reaction transformations.