In silico design and ADMET evaluation of new inhibitors for PIM1 kinase using QSAR studies, molecular docking, and molecular dynamic simulation.

The proviral Integration site of Moloney (PIM) kinase is highly expressed in various diseases, including cancer, making the development of selective inhibitors for this protein important. A series of PIM1 inhibitors, triazolo [4, 3-b] pyridazin-3-yl-quinoline derivatives, have been studied to design new inhibitors. The activity and structural features of these derivatives were investigated to understand their interactions with PIM1 using molecular docking, molecular dynamic simulation, and QSAR techniques.

Development of a sensitive ds-DNA/Au NPs/ PGE biosensor for determination of Buprenorphine using electrochemical and molecular dynamic simulation investigation.

A sensitive electrochemical DNA biosensor has been developed for the detection of Buprenorphine (Bu), a narcotic pain reliever. To achieve this, double-stranded DNA (ds-DNA) was immobilized on a pencil graphite electrode that was modified with gold nanoparticles (Au NPs/PGE). The gold nanoparticles enhanced the performance of the DNA biosensor.

The Binding Mechanism Between Cyclodextrins and Anticancer Drug Noscapine: A Spectroscopic and Molecular Docking Study.

In this paper the binding of noscapine (NOS) as an anticancer drug with poor bioavailability and low solubility with beta and methyl-beta cyclodextrins (β-CD and M-β-CD) as the biocompatible drug carriers were discussed using ultraviolet-visible, fluorescence and nuclear magnetic resonance spectroscopy, as well as molecular docking. The absorption of NOS changed when it was bound to both cyclodextrins, resulting in a hyperchromic shift. It formed a 1:1 stoichiometry inclusion complex with both cyclodextrins according to the Benesi-Hildebrand equation.

Dual-template imprinted polymer electrochemical sensor for simultaneous determination of malathion and carbendazim using graphene quantum dots.

Malathion (MAL) and carbendazim (CBZ) are organophosphate pesticides and fungicides, respectively. They are often used simultaneously in agriculture, and both have been shown to have harmful effects on humans and animals. Therefore, it is important to be able to measure both of these toxins simultaneously in order to assess their potential risks.

Research and study of 2-((4,6 dimethyl pyrimidine-2-yle) thio)-N-phenyl acetamide derivatives as inhibitors of sirtuin 2 protein for the treatment of cancer using QSAR, molecular docking and molecular dynamic simulation.

Phenyl acetamide derivatives have a wide range of biological activities, so their research and development can be useful and effective for the design production of new drugs. In this project, quantitative structure-activity relationship (QSAR) was performed. For modeling two methods of multiple linear regression (MLR) and nonlinear regression of support vector machine (SVR) were used.

A new electrochemical DNA biosensor for determination of anti-cancer drug chlorambucil based on a polypyrrole/flower-like platinum/NiCoO/pencil graphite electrode.

In the current study, DNA immobilization was performed on pencil graphite (PG) modified with a polypyrrole (PPy) and flower-like Pt/NiCoO (FL-Pt/NiCoO) nanocomposite, as a new sensitive electrode to detect chlorambucil (CHB). Energy dispersive X-ray (EDX) analysis, X-ray diffraction (XRD) and scanning electron microscopy (SEM) techniques were employed to characterize the synthesized FL-Pt/NiCoO and PPy/FL-Pt/NiCoO nanocomposites. Moreover, differential pulse voltammetry (DPV) was selected to assess the guanine and adenine electrochemical responses on the DNA sensor.

Fabrication of platinum-doped NiCoO nanograss modified electrode for determination of carbendazim.

In this study, a platinum-doped nickel cobaltite nanograss (Pt-doped NiCoO NG) with its own unique structural features was initially synthesized, utilizing a simple hydrothermal method and then applied as a novel platform for the detection of carbendazim (CHNO; CBZ). To this end, the CBZ electrochemical signals were evaluated by means of differential pulse voltammetry (DPV), demonstrating the acceptable catalytic effect of the Pt-doped NiCoO NG/screen-printed electrode (SPE) on the CBZ oxidation signal. Under the optimized conditions, CBZ was subsequently quantified by the Pt-doped NiCoO NG/SPE with a wide linear range (0.

Development of a new electrochemical DNA biosensor based on Eu-doped NiO for determination of amsacrine as an anti-cancer drug: Electrochemical, spectroscopic and docking studies.

The present research reported a new electrochemical biosensor based on ds-DNA/Eu doped NiO/CPE to detect amsacrine. Therefore, UV-Vis spectrophotometry, docking, and differential pulse voltammetry (DPV) have been used to study the interactions between amsacrine and dsDNA. Then, experimental parameters affected DNA immobilization and interactions between amsacrine and ds-DNA have been optimized.

Investigation of the mechanism of enantioseparation of some drug compounds by considering the mobile phase in HPLC by molecular dynamics simulation.

The separation mechanism of chiral drugs in high-pressure liquid chromatography is yet ambiguous. Computational chemistry helps to gain insights about chiral drug separations. The interaction between the 13 drug enantiomers and cellulose tris (3, 5-dimethyl phenyl carbamate) (chiral cel OD) as chiral stationary phase in 3 mobile phases was assayed by AutoDock and LAMMPS simulations.

study combining QSAR, docking and molecular dynamics simulation on 2,4-disubstituted pyridopyrimidine derivatives.

2,4-Disubstituted pyridopyrimidine derivatives were studied against ABCG2 enzyme. The modeling of pyridopyrimidine derivatives were done using two methods of multiple linear regression and support vector regression and four molecular descriptors of BIC4, log , VRA2, and binding energy were selected for modeling. The statistical results were satisfactory.

Molecular docking, molecular dynamics simulations and QSAR studies on some of 2-arylethenylquinoline derivatives for inhibition of Alzheimer's amyloid-beta aggregation: Insight into mechanism of interactions and parameters for design of new inhibitors.

Alzheimer's disease is characterized using amyloid-beta (Aβ) aggregation. The present work was carried out to extend and design a novel quantitative structure-activity relationship (QSAR) model on inhibition efficiency of some of new 2-arylethenylquinoline derivatives against the Aβ peptide aggregation. The QSAR study, molecular docking and molecular dynamics (MD) simulations were performed to explore the influence of the structural features and investigate the molecular mechanism of ligands interactions with the Aβ peptide.

3D protein structure prediction using Imperialist Competitive algorithm and half sphere exposure prediction.

Predicting the native structure of proteins based on half-sphere exposure and contact numbers has been studied deeply within recent years. Online predictors of these vectors and secondary structures of amino acids sequences have made it possible to design a function for the folding process. By choosing variant structures and directs for each secondary structure, a random conformation can be generated, and a potential function can then be assigned.

Application of multivariate image analysis in modeling (13) C-NMR chemical shifts of mono substituted pyridines.

Multivariate image analysis (MIA) descriptors have been applied to the quantitative structure-property relationship (QSPR) study of (13) C-NMR chemical shifts of 2-mono substituted pyridines. In this method, descriptors are generated from pixels of images and are analyzed with different multivariate methods. Correlation ranking-principal component regression and correlation ranking-principal component-artificial neural networks were applied in constructing predictor models.

Application of multivariate image analysis in QSPR study of 13C chemical shifts of naphthalene derivatives: a comparative study.

A new implemented QSPR method, whose descriptors achieved from bidimensional images, was applied for predicting (13)C NMR chemical shifts of 25 mono substituted naphthalenes. The resulted descriptors were subjected to principal component analysis (PCA) and the most significant principal components (PCs) were extracted. MIA-QSPR (multivariate image analysis applied to quantitative structure-property relationship) modeling was done by means of principal component regression (PCR) and principal component-artificial neural network (PC-ANN) methods.

Quantitative structure-retention relationship study of some phenol derivatives in gas chromatography.

A quantitative structure-retention relationship (QSRR) model has been developed for the gas chromatographic retention times of 37 phenolic derivatives in a DB-5 non-polar column (95% dimethyl and 5% diphenyl-polysiloxane). As a first step, multiple linear regression (MLR) was employed to gain informative descriptors that can predict the retention times of these compounds. Descriptors appearing in the MLR model are categorized as topological and geometric parameters that comply with the applied column.

Modeling the antileishmanial activity screening of 5-nitro-2-heterocyclic benzylidene hydrazides using different chemometrics methods.

QSAR analysis for modeling the antileishmanial activity screening of a series of 49 nitro derivatives of Hydrazides were carried out using different Chemometrics methods. First, a large number of descriptors were calculated using Hyperchem, Mopac and Dragon softwares. Then, a suitable number of these descriptors were selected using multiple linear regression (MLR) technique.