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)
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)
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)
We used electrophoresis for three purposes: (i) estimation of the mean pore size of polyacrylamide gels via measuring electrophoretic mobility of globular proteins of known sizes in combination with simple sieve (cylindrical and slit) models; (ii) determination of the average size of protein molecules (native or denatured) by the use of the same models;(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)
The chaperone action of alpha-cyclodextrin (alpha-CyD), based on providing beneficial microenvironment of hydrophobic nanocavity to form molecular complex with alcohol dehydrogenase (ADH) was examined by experimental and computational techniques. The results of UV-vis and dynamic light scattering (DLS) indicated that the chaperone-like activity of alpha-CyD(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)