SOLVATION FREE ENERY OF THIENO [3, 2 - b] PYRIMIDINE ANALOGS COMPRISING INTERMOLECULAR SOLVATION AND INTRAMOLECULAR SELF-SOLVATION
Â Objective: The aim was to estimate the various physiochemical properties of a molecule and the de-solvation cost for its binding to macromolecular receptors, the solvation free energy is a fundamental thermodynamics that has to be used. Here, a new solvation free energy carried out through the improvement of the existing solute-solvent interaction model and test its applicability in estimating the solvation free energies of vascular endothelial growth factor receptor-2 (VEGFR-2) inhibitors are discussed.
Methods: The molecular dynamics program GROMACS, which is designed for free energy calculations and bond simulations, has been used to understand the solvation free energies.
Results: The estimates of the solvation free energies of VEGFR-2 inhibitor molecules showed a reasonable accuracy by combining the effects from the solvent exposed and self-solvation regions. This significant contribution of free energies is thus consistent with the stability of the inhibitors in the solvent.
Conclusion: The estimated solvation free energies from the new model illustrated a good association with the solute-solvent interaction. The current solvation model is thus expected to be more useful in supporting the stability of the inhibitors within a solvent.
Keywords: GROMACS, Solvation free energy, VEGFR-2.
Harding JH. Calculation of the free energy of defects in calcium fluoride. Phys Rev B Condens Matter 1985;32(10):6861-72.
Volpe CD, Siboni S. Some reflections on acid-base solid surface free energy theories J Colloid Interface Sci 1997;195(1):121-36.
Kentsis A, Gindin T, Mezei M, Osman R. Calculation of the free energy and cooperativity of protein folding. PLoS One 2007;2(5):e446.
Christen M, Christ CD, van Gunsteren WF. Free energy calculations using flexible-constrained, hard-constrained and non-constrained molecular dynamics simulations. Chemphyschem 2007;8(10):1557 64.
Makarewicz T, Kazmierkiewicz R. Molecular dynamics simulation by GROMACS using GUI plugin for PyMOL. J Chem Inf Model 2013;53(5):1229-34.
Wierzchowski SJ, Monson PA. Calculation of free energies and chemical potentials for gas hydrates using Monte Carlo simulations. J Phys Chem B 2007;111(25):7274-82.
Christ CD, van Gunsteren WF. Enveloping distribution sampling: A method to calculate free energy differences from a single simulation. J Chem Phys 2007;126(18):184110.
Brenner SL, McQuarrie DA. A self-consistent calculation of the free energy and electrostatic potential for a cylindrical polyion. J Theor Biol 1973;39(2):343-61.
Reinhardt WP, Miller MA, Amon LM. Why is it so difficult to simulate entropies, free energies, and their differences? Acc Chem Res 2001;34(7):607-14.
Hill TL. Approximate calculation of the electrostatic free energy of nucleic acids and other cylindrical macromolecules. Arch Biochem Biophys 1955;57(1):229-39.
Sugita Y, Kitao A. Improved protein free energy calculation by more accurate treatment of nonbonded energy: Application to chymotrypsin inhibitor 2, V57A. Proteins 1998;30(4):388-400.
Pohorille A, Jarzynski C, Chipot C. Good practices in free-energy calculations. J Phys Chem B 2010;114(32):10235-53.
Tyka MD, Sessions RB, Clarke AR. Absolute free-energy calculations of liquids using a harmonic reference state. J Phys Chem B 2007;111(32):9571-80.
Tateyama Y, Blumberger J, Ohno T, Sprik M. Free energy calculation of water addition coupled to reduction of aqueous RuO4-. J Chem Phys 2007;126(20):204506.
Pronk S, PÃ¡ll S, Schulz R, Larsson P, Bjelkmar P, Apostolov R, et al. GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics 2013;29(7):845-54.
Sumathy R, Ashwath SK, Bindroo BB, Gopalakrishnan VK. Theoretical modeling and docking studies of silkworm octopamine receptors. Int J Pharm Pharm Sci 2014;6(2):163-6.
SchÃ¼ttelkopf AW, van Aalten DM. PRODRG: A tool for high-throughputcrystallography of protein-ligand complexes. Acta Crystallogr D Biol Crystallogr 2004;60(Pt 8):1355-63.
Shamsudin Khan Y, GutiÃ©rrez-de-TerÃ¡n H, Boukharta L, Ã…qvist J. Toward an optimal docking and free energy calculation scheme in ligand design with application to COX-1 inhibitors. J Chem Inf Model 2014;54:1488-99.
Pellequer JL, Chen SW. Does conformational free energy distinguish loop conformations in proteins? Biophys J 1997;73(5):2359-75.
Xiong Y, Li Y, He H, Zhan CG. Theoretical calculation of the binding free energies for pyruvate dehydrogenase E1 binding with ligands. Bioorg Med Chem Lett 2007;17(18):5186-90.
Christ CD, Mark AE, van Gunsteren WF. Basic ingredients of free energy calculations: A review. J Comput Chem 2010;31(8):1569-82.
Villa A, Mark AE. Calculation of the free energy of solvation for neutral analogs of amino acid side chains. J Comput Chem 2002;23(5):548-53.
Mohanapriya A, Sajitha L, Sweta K, Nancy VK. Computational screening and evaluation of bioactive compounds against NS3 helicase of HCV. Int J Pharm Pharm Sci 2013;5(4):370-6.
Somani S, Gilson MK. Accelerated convergence of molecular free energy via superposition approximation-based reference states. J Chem Phys 2011;134(13):134107.
Stjernschantz E, Oostenbrink C. Improved ligand-protein binding affinity predictions using multiple binding modes. Biophys J 2010;98(11):2682-91.
Mon KK. Direct calculation of absolute free energy for lattice systems by Monte Carlo sampling of finite-size dependence. Phys Rev Lett 1985;54(25):2671-3.
Slater EC. Measurement and importance of phosphorylation potentials: Calculation of free energy of hydrolysis in cells. Methods Enzymol 1979;55:235-45.
Hamm RN, Turner JE, Ritchie RH, Wright HA. Calculation of heavy-ion tracks in liquid water. Radiat Res Suppl 1985;8:S20-6.
Weng Z, Delisi C, Vajda S. Empirical free energy calculation: Comparison to calorimetric data. Protein Sci 1997;6(9):1976-84.
Almarza NG. Computation of the free energy of solids. J Chem Phys 2007;126(21):211103.
Aragones JL, Noya EG, Valeriani C, Vega C. Free energy calculations for molecular solids using GROMACS. J Chem Phys 2013;139(3):034104.
How to Cite
The publication is licensed under CC By and is open access. Copyright is with author and allowed to retain publishing rights without restrictions.