STUDI INTERAKSI QUINPIROLE DENGAN RESEPTOR DOPAMIN D3 MENGGUNAKAN METODE DOCKING MOLEKULER DAN SIMULASI DINAMIKA MOLEKULER; INTERACTION STUDY OF QUINPIROLE WITH DOPAMINE D3 RECEPTOR USING MOLECULAR DOCKING METHOD AND MOLECULAR DYNAMICS SIMULATION

Fitriani, Dini, Ria Armunanto

2015 | Skripsi | FMIPA UGM

Molecular docking and molecular dynamics simulation eticlopride and quinpirole d with dopamine D3 receptor have been conducted. Molecular docking was conducted to look for RMSD ETQ d based on its similarity to the d ETQ experiments. Molecular docking of quinpirole d use scoring method to determine the best conformation. Molecular dynamics simulations performed to predict the solubility of the d and protein-d complexes in aqueous solvent with free energy perturbation method (FEP) in NPT state. RMSD (Root Mean Square Deviation) was calculated to determine the protein structure changes during molecular dynamics simulations in NPT (constant Number of particles, Volume and Pressure) state. Equilibration is often conducted in two phases. The first phase is conducted under an NVT (constant Number of particles, Volume, and Temperature). The second phase is conducted under an NPT. The results showed that the RMSD of ETQ d molecular docking is 0,59 Å. Quinpirole first conformation has the lowest score is -77,42 kJ/mol is the best conformation of quinpirole. Based on the research for the results obtained docking quinpirole 2 hydrogen bonds with a distance of 1,9 Å and 2,6 Å. Result of molecular dynamics simulation the estimates solvation free energy in water for quinpirole is -176,66 ± 0,25 kJ / mol. ETQ solubility is higher than the quinpirole solubility due ETQ more likely to be able to form hydrogen bonds with the solvent

Kata Kunci : Molecular docking; molecular dynamics simulation; eticlopride; quinpirole; RMSD