Karim Mahnam

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In this study, homology modeling, molecular docking and molecular dynamics simulation were performed to explore structural features and binding mechanism of some inhibitors of chemokine receptor type 5 (CCR5), and to construct a model for designing new CCR5 inhibitors for preventing HIV attachment to the host cell. A homology modeling procedure was employed(More)
Partial least squares (PLS) method as ligand-based method was applied for building quantitative structure–activity relationships (QSAR) regression model to predict the inhibitory activity of some A2B antagonists. The accuracy and predictability of the developed model were evaluated by several validation methods using external and internal test sets and also(More)
The electrostatic interaction of amino acid lysines 190, 195 and 199 of human serum albumin (HSA) with bilirubin have been investigated using molecular dynamic simulations, QM and QM/MM minimization methods. In this study two methodological approaches have been employed. In the first approach X-ray structure and the structure obtained from the molecular(More)
The kinetic and thermodynamic effects of aspirin and diclofenac on the activity of adenosine deaminase (ADA) were studied in 50 mM phosphate buffer pH = 7.5 at 27 and 37 degrees C, using UV-Vis spectrophotometry and isothermal titration calorimetry (ITC). Aspirin exhibits competitive inhibition at 27 and 37 degrees C and the inhibition constants are 42.8(More)
Structural integrity of microtubule protein (MTP) is pivotal for its physiological roles. Disruption of the MTP network is known to be involved in neurodegenerative disorders. The gum resin of plants of the boswellia species, with β-boswellic acid (BBA) as the major component, has long been used in Ayurveda and Oriental Medicine to prevent amnesia. In the(More)
A QSAR study of 74 derivatives of 1,3,8-substituted-9-deazaxanthines as potent and selective A2B adenosine receptor (A2BAR) antagonists is described. pKi of all the studied compounds were acquired by three linear and nonlinear methods namely stepwise multiple linear regression, partial least squares (PLS), and general regression neural networks (GRNN). The(More)
Selective A(2B) receptor antagonists and agonists may play a role in important pathologies such as gastrointestinal, neurological (i.e., Alzheimer disease and dementia) and hypersensitive disorders (i.e., asthma), diabetes, atherosclerosis, restenosis and cancer. Hence, it is regarded as a good target for the development of clinically useful agents. In this(More)
Effects of sodium dodecyl sulfate, dodecyltrimethylammonium bromide, sodium chloride, sodium sulfate, methanol and ethanol, on the structure and activity of adenosine deaminase (ADA) were investigated by UV-Vis, circular dichroism spectrophotometry and molecular dynamics (MDs) studies. Relative activity, experimental and computational helix content, total(More)
The improved Cd(2+) surface affinity characteristics of a mutated cyanobacterial metallothionein SmtA (K45C) were investigated via experimental and theoretical methods. Molecular dynamics simulations were carried out using a model of Cd(2+) and other ions enclosed in a fully hydrated simulation box with the wild-type or mutated SmtA protein. The theoretical(More)
The non-covalent interaction between single-walled carbon nanotube and surfactant peptides makes them soluble in biological media to be used in nano-medicine, drug delivery and gene therapy. Pervious study has shown that two important parameters in binding peptides into nanotubes are hydrophobic effect and the number of aromatic amino acids. Ten surfactant(More)