Papers by Jahan B Ghasemi
Current Analytical Chemistry, 2010
The growth inhibiting activity of 27 derivatives of N-benzyl-2-bromo-3, 3-dimethylbutanamide havi... more The growth inhibiting activity of 27 derivatives of N-benzyl-2-bromo-3, 3-dimethylbutanamide having various substituents at the a-position and the benzene ring of the Nbenzyl group against bulrush, Scirpus juncoides, was determined in the vial test. The structure-activity relationships were analyzed quantitatively by physicochemical substituent parameters and multiple regression analysis. The variation in the activity of N-(ca-substituted benzyl) derivatives was shown to be related parabolically with variation in the steric dimension of the substituents. The greater the hydrophobicity of substituents is, the greater the activity is. The variation in the steric dimension of the benzene ring substituents was responsible for the activity of N-(1-methyl-l-substituted phenylethyl) derivatives.
3D-QSAR studies on the toxicity of substituted benzenes to Tetrahymena pyriformis: CoMFA, CoMSIA and VolSurf approaches
Ecotoxicology and Environmental Safety, 2014
Thermodynamic studies of molecular interactions in mixtures of o-toulidine with pyridine and picolines: Excess molar volumes, excess molar enthalpies, and excess isentropic compressibilities
Journal of Chemical Thermodynamics, 2011
Excess molar enthalpies, HE data of {o-toluidine (i)+pyridine or α-, β-, or γ-picoline (j)} binar... more Excess molar enthalpies, HE data of {o-toluidine (i)+pyridine or α-, β-, or γ-picoline (j)} binary mixtures at a temperature of 308.15K; densities, ρ speeds of sound, u of the same mixtures at a temperature of (298.15, 303.15, and 308.15)K have been measured over entire mole fraction range. The measured densities and speeds of sound data have been utilized to determine
New Journal of Chemistry
Detection and determination of metal cations in different real samples are important matters in v... more Detection and determination of metal cations in different real samples are important matters in various fields of experimental science. Herein, graphitic carbon nitride (g-C3N4) doped with boron was facilely prepared...
Current Neuropharmacology
Background: Neurodegenerative diseases such as Alzheimer's disease (AD), amyotrophic lateral scle... more Background: Neurodegenerative diseases such as Alzheimer's disease (AD), amyotrophic lateral sclerosis, Parkinson's disease (PD), spinal cerebellar ataxias, and spinal and bulbar muscular atrophy are described by slow and selective degeneration of neurons and axons in the central nervous system (CNS) and constitute one of the major challenges of modern medicine. Computeraided or in silico drug design methods have matured into powerful tools for reducing the number of ligands that should be screened in experimental assays. Methods: In the present review, the authors provide a basic background about neurodegenerative diseases and in silico techniques in the drug research. Furthermore, they review the various in silico studies reported against various targets in neurodegenerative diseases, including homology modeling, molecular docking, virtual high-throughput screening, quantitative structure activity relationship (QSAR), hologram quantitative structure activity relationship (HQSAR), 3D pharmacophore mapping, proteochemometrics modeling (PCM), fingerprints, fragment-based drug discovery, Monte Carlo simulation, molecular dynamic (MD) simulation, quantum-mechanical methods for drug design, support vector machines, and machine learning approaches. Results: Detailed analysis of the recently reported case studies revealed that the majority of them use a sequential combination of ligand and structure-based virtual screening techniques, with particular focus on pharmacophore models and the docking approach. Conclusion: Neurodegenerative diseases have a multifactorial pathoetiological origin, so scientists have become persuaded that a multi-target therapeutic strategy aimed at the simultaneous targeting of multiple proteins (and therefore etiologies) involved in the development of a disease is recommended in future.
Application of genetic algorithm and multivariate methods for the detection and measurement of milk‐surfactant adulteration by attenuated total reflection and near‐infrared spectroscopy
Journal of the Science of Food and Agriculture
Simultaneous removal of crystal violet and methyl green in water samples by functionalised SBA-15
International Journal of Environmental Analytical Chemistry
Deposited CuBi2O4 and Bi3ClO4 nanoparticles on g-C3N4 nanosheet: a promising visible light-induced photocatalyst toward the removal of tetracycline hydrochloride and rhodamine B
Journal of Materials Science
Sensors
The presented manuscript reports the simultaneous detection of a ternary mixture of the benzodiaz... more The presented manuscript reports the simultaneous detection of a ternary mixture of the benzodiazepines diazepam, lorazepam, and flunitrazepam using an array of voltammetric sensors and the electronic tongue principle. The electrodes used in the array were selected from a set of differently modified graphite epoxy composite electrodes; specifically, six electrodes were used incorporating metallic nanoparticles of Cu and Pt, oxide nanoparticles of CuO and WO3, plus pristine electrodes of epoxy-graphite and metallic Pt disk. Cyclic voltammetry was the technique used to obtain the voltammetric responses. Multivariate examination using Principal Component Analysis (PCA) justified the choice of sensors in order to get the proper discrimination of the benzodiazepines. Next, a quantitative model to predict the concentrations of mixtures of the three benzodiazepines was built employing the set of voltammograms, and was first processed with the Discrete Wavelet Transform, which fed an artifi...
Design of pyrimidine-based scaffolds as potential anticancer agents for human DHFR: three-dimensional quantitative structure–activity relationship by docking derived grid-independent descriptors
Journal of the Iranian Chemical Society
Food Science and Technology Research
This study aimed to develop a new prebiotic dairy dessert by adding different concentration of ce... more This study aimed to develop a new prebiotic dairy dessert by adding different concentration of cereal flours (10 _ 16% w/w), inulin (6 and 8% w/w) and sugar (2 and 4% w/w) into dairy dessert formulation. A mixture design approach was used to create nine formulation of dessert samples. Desserts were evaluated by consumers who were asked to answer a check-all-that-apply (CATA) question. Water holding capacity (WHC) and syneresis values were also measured. Based on our results different concentration of flour, inulin and sugar resulted in different sensory and rheological properties. Dessert samples with higher content of inulin and sugar had lesser consistency coefficient and storage modulus. Samples with higher level of flour and lower level of inulin and sugar had good physical stability and presented appropriate sensory characteristics. Results showed that data from both consumers' response to CATA question and rheological measurements presented the same information.
Synthesis of magnetically modified mesoporous nanoparticles and their application in simultaneous determination of Pb(II), Cd(II) and Cu(II)
Research on Chemical Intermediates
Journal of Chemometrics
Dihydrofolate reductase (DHFR) is an essential enzyme in the folate metabolism pathway and an imp... more Dihydrofolate reductase (DHFR) is an essential enzyme in the folate metabolism pathway and an important target of antineoplastic, antimicrobial, antiprotozoal, and antiinflammatory drugs. Despite the clinical effectiveness of current antifolate treatments, new drugs are needed to be designed due to developing resistance of this enzyme through multiple-site mutagenesis. Understanding the factors affecting the ligand binding selectivity profiles among DHFR families is critical for the design of novel potent and selective inhibitors, with the least side effects, against DHFR of pathogens. Hybrid scaffolds containing pyrimidine ring are effective in DHFR inhibition. In this study, using proteochemometric (PCM) modeling, we designed and evaluated new potent pyrimidine scaffold-based inhibitors via 3-dimensional alignmentfree GRid-INdependent Descriptors (GRIND), VolSurf molecular, and sequence-based (z-scale) descriptors to provide ligand and receptor descriptors, respectively. Validation and robustness of the model were confirmed by venetian blinds cross-validation and Y-scrambling approaches, respectively. Applicability domain (AD) analysis was performed to estimate the likelihood of reliable prediction for compounds. To show the applicability of the PCM model, new ligands were designed using structural data retrieved from this model. Inhibitory activities of the designs were then predicted, and selectivity ratio profiles were investigated. Finally, potent and highly selective inhibitors were identified regarding the protozoan parasite Toxoplasma gondii, followed by evaluating the ADMET parameters of the ligands.
High-throughput Docking and Molecular Dynamics Simulations towards the Identification of Novel Peptidomimetic Inhibitors against CDC7
Molecular Informatics
Simultaneous sensitive determination of benzenediol isomers using multiwall carbon nanotube–ionic liquid modified carbon paste electrode by a combination of artificial neural network and fast Fourier transform admittance voltammetry
New Journal of Chemistry
A novel electrochemical method for the simultaneous determination of catechol, hydroquinone, and ... more A novel electrochemical method for the simultaneous determination of catechol, hydroquinone, and resorcinol.
Editorial: In Silico Methodologies Applied to Drug Discovery
Combinatorial chemistry & high throughput screening, 2018
Dynamic structure based pharmacophore modeling of the Acetylcholinesterase reveals several potential inhibitors
Journal of biomolecular structure & dynamics, Jan 17, 2018
Acetylcholinesterase is a critical enzyme that regulates neurotransmission by catalyzing the brea... more Acetylcholinesterase is a critical enzyme that regulates neurotransmission by catalyzing the breakdown of neurotransmitter acetylcholine in synapses of the nervous system. It is an important target for therapeutic drugs that treat Alzheimer's disease. Since, the degree of flexibility of the side chains of the residues in the active-site gorge of Acetylcholinesterase is diverse it results in different bound ligand conformations. The side-chain conformations of Ser293, Tyr341, Leu76, and Val73 are flexible, while the side-chain conformations of Tyr72, Tyr 124, Ser125, Phe295, and Arg296 appear to be fixed. In this study, multi-conformation dynamic pharmacophore models from the donepezyl-binding pocket based on highly populated structures chosen from molecular dynamics simulations were used for screening compounds that can properly bind acetylcholinesterase. Based on these structures, three pharmacophore models were generated. Consequently, 14 hits were retrieved as final candidate...
Docking of Natural Products against Neurodegenerative Diseases: General Concepts
Combinatorial chemistry & high throughput screening, Jan 13, 2018
Since antiquity, humanity has used medicinal plant preparations to cure its ills, and, as researc... more Since antiquity, humanity has used medicinal plant preparations to cure its ills, and, as research has progressed, new technologies have enabled more investigations on natural compounds which originate from plants, fungi, and marine species. The health benefits that these natural products provide have become a motive for treatment studies of various diseases. Among them, the neurodegenerative diseases like Alzheimer's and Parkinson's, a major age-related neurodegenerative disorder. Studies with natural products for neurodegenerative diseases (particularly through molecular docking) search for, and then focus on those ligands which offer effective inhibition of the enzymes monoamine oxidase and acetylcholinesterase. This review introduces the main concepts involved in docking studies with natural products: and also in our group, which has conducted a docking study of natural products isolated from Tetrapterys mucronata for inhibition of acetylcholinesterase.
Spectrophotometric Determination of Trace Amounts of Palladium with Molybdate and Rhodamine B in the Presence of PVA
Analytical Letters
A new spectrophotometric reagent for the determination of trace amounts of fluoride has been intr... more A new spectrophotometric reagent for the determination of trace amounts of fluoride has been introduced. This method is based on the decolorization of a complex of Al(III) with xylenol orange (XO) as an ultra-sensitive colored reagent. Since the Al-XO complex plays an important role in this method, the protonation and complexation of XO with Al(III) at an ionic strength of 0.1 mol L(-1) at 25 degrees C has been studied by a spectrophotometric global analysis method. The EQUISPEC program was used to evaluate the protonation constants of XO and the stability constants of the formed complexes with Al(III). The protonation and the stability constants of the major complex species such as ML, MLH and MLH2, were determined. Finally, a spectrophotometric method for the assay of fluoride based on a decrease of the color intensity of the Al-XO complex, in an aqueous solution has been designed. The effects of some important variables on the determination of fluoride based on the proposed method were investigated. The method was applied to the determination of fluoride under the optimum conditions (pH 5.2, ionic strength 0.1 mol L(-1), 25 degrees C). The determination of fluoride in the range of 0.08-1.4 microg mL(-1) (SD = 1.2%) was successfully performed. Interferences of Fe(III) were easily eliminated by using ascorbic acid. The proposed method was applied to the determination of trace amounts of fluoride content of some real water samples.
Journal of enzyme inhibition and medicinal chemistry, 2017
A 3D-QSAR modeling was performed on a series of diarylpyrazole-benzenesulfonamide derivatives act... more A 3D-QSAR modeling was performed on a series of diarylpyrazole-benzenesulfonamide derivatives acting as inhibitors of the metalloenzyme carbonic anhydrase (CA, EC 4.2.1.1). The compounds were collected from two datasets with the same scaffold, and utilized as a template for a new pharmacophore model to screen the ZINC database of commercially available derivatives. The datasets were divided into training, test, and validation sets. As the first step, comparative molecular field analysis (CoMFA), CoMFA region focusing and comparative molecular similarity indices analysis (CoMSIA) in parallel with docking studies were applied to a set of 41 human (h) CA II inhibitors. The validity and the prediction capacity of the resulting models were evaluated by leave-one-out (LOO) cross-validation approach. The reliability of the model for the prediction of possibly new CA inhibitors was also tested.
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Papers by Jahan B Ghasemi