scholarly journals Interaction of I50V Mutant and I50L/A71V Double Mutant HIV-Protease with Inhibitor TMC114 (Darunavir): Molecular Dynamics Simulation and Binding Free Energy Studies

2012 ◽  
Vol 116 (6) ◽  
pp. 1884-1900 ◽  
Author(s):  
Biswa Ranjan Meher ◽  
Yixuan Wang
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulation ◽  
Double Mutant ◽  
Binding Free Energy ◽  
Hiv Protease ◽  
Dynamics Simulation

scholarly journals Hydrogen Bond Stability of Quinazoline Derivatives Compounds in Complex against EGFR using Molecular Dynamics Simulation

2019 ◽  
Vol 19 (2) ◽  
pp. 461
Author(s):  
Herlina Rasyid ◽  
Bambang Purwono ◽  
Thomas S Hofer ◽  
Harno Dwi Pranowo
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Free Energy ◽  
Molecular Dynamics Simulation ◽  
Binding Free Energy ◽  
Dynamics Simulation ◽  
Inhibition Mechanism ◽  
Energy Calculation ◽  
Protein Receptor ◽  
The Stability

Lung cancer was a second common cancer case due to the high cigarette smoking activity both in men and women. One of protein receptor which plays an important role in the growth of the tumor is Epidermal Growth Factor Receptor (EGFR). EGFR protein is the most frequent protein mutation in cancer and promising target to inhibit the cancer growth. In this work, the stability of the hydrogen bond as the main interaction in the inhibition mechanism of cancer will be evaluated using molecular dynamics simulation. There were two compounds (A1 and A2) as new potential inhibitors that were complexed against the EGFR protein. The dynamic properties of each complexed were compared with respect to erlotinib against EGFR. The result revealed that both compounds had an interaction in the main catalytic area of protein receptor which is at methionine residue. Inhibitor A1 showed additional interactions during simulation time but the interactions tend to be weak. Inhibitor A2 displayed a more stable interaction. Following dynamics simulation, binding free energy calculation was performed by two scoring techniques MM/GB(PB)SA method and gave a good correlation with the stability of the complex. Furthermore, potential inhibitor A2 had a lower binding free energy as a direct consequence of the stability of hydrogen bond interaction.

Binding Free Energy and the structural changes determination in hGH protein with different concentrations of copper ions (A molecular dynamics simulation study)

2016 ◽  
Vol 15 (05) ◽  
pp. 1650045 ◽  
Author(s):  
Elham Tazikeh-Lemeski
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulation ◽  
Surface Area ◽  
Structural Changes ◽  
Copper Ions ◽  
Binding Free Energy ◽  
Free Energy Calculations ◽  
Dynamics Simulation ◽  
Solvent Accessible Surface Area

In this study, we estimated the optimum concentration of copper ions that are effective in the stability and the structural changes of human growth hormone (hGH) protein in the combination of different concentrations of these ions at the molecular level using molecular dynamics simulation by Gromacs 4.6.5 software. Moreover, to estimate the binding affinity of copper ions to hGH protein, binding free energies is calculated by the molecular mechanics Poisson–Boltzmann Surface Area (MM-PBSA). The analysis of molecular dynamics (MD) trajectories as dictionary of the secondary structure of protein (DSSP), solvent accessible surface area (SASA) and binding free energy calculations show that hGH protein structure is more stabilized by increasing a limited concentration of copper ions. These findings align with our previous experimental studies.

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