Abstract
Objective: Cyclin-dependent kinases (CDKs, play important roles in cell cycle regulation. Since deregulation of cyclins and/or alteration or absence of inhibitors has been associated with many cancers, there is strong interest in CDKs inhibitors that could play an necessary role in the discovery of a new family of antitumor agents. Material and Methods: Molecular modeling is used to design new materials, which the correct prediction of physical properties of realistic systems is required. Gromacs is an tool to perform molecular dynamics simulations and energy minimization of bimolecular systems which commonly consists of several tens to thousands of amino acid residues. From the simulations the first 100 ps were regarded as equilibration, leaving 900 ps for analysis purposes. Results: Thermodynamic properties density, potential energy, temperature, and pressure are given. In this results tetramethyl ((1,4-phenylenebis (azanediyl)) bis ((4-chlorophenyl) methylene)) bis (phosphonate) was found to be the better selective known inhibitor for cyclin-dependent kinase2 because it shown lowest energy.Conclusion: The phosphoric acid moiety is considered to bind to the affected protein more actively than the corresponding carboxylic acid because of its di anionic character.
Highlights
Understanding the function of biomolecules using the available structural data is one of the grand objections of the current century
Since deregulation of cyclins and/or alteration or absence of inhibitors has been associated with many cancers, there is strong interest in Cyclin-dependent kinases (CDKs) inhibitors that could play an necessary role in the discovery of a new family of antitumor agents [8]
Molecular dynamics becomes the most effective way to express the details of the flow and to study many fundamental Nano fluid problems, which can be acutely difficult to investigate by other means [10]
Summary
Understanding the function of biomolecules using the available structural data is one of the grand objections of the current century. To rapid developments in computer technology, the growth in the field, in particular in molecular dynamics (MD) simulations, has been phenomenal [1]. From the early 1980s, three MD simulation packages with their associated force fields have prominent themselves, namely, AMBER, CHARMM and GROMACS. At present most of the simulation work on biomolecules is carried out using one of these packages.The force fields frequently used in molecular dynamics simulations of proteins are optimized under bulk conditions [2]. CDK misregulation is indicated in a number of disease states, and in particular cancer. To advance such studies, small molecule cyclin-dependent kinase inhibitors would be worthy biochemical tools [3]
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