利用熱力學積分分子動力學模擬計算GSK-3β 激酶與配體複合體之相對結合自由能：含嘧啶環的化合物

Abstract

在阿茲海默症可能的發病機制探討中，人體腦部神經元中GSK-3β激酶蛋白過度磷酸化下游的tau蛋白被認為是其中一種主要的原因。透過抑制GSK-3β激酶可能減緩阿茲海默症症狀，甚至能達到治療成效。由於小分子與蛋白複合體間的結合自由能是反映抑制強度的重要物理量，本研究中使用熱力學積分分子動力學模擬輔助設計GSK-3β的競爭性抑制劑。此方法是利用參考分子與待測分子分別對目標蛋白的結合情況，去預測相對結合自由能(ΔΔG)。我們首先計算已知結晶構型及結合親和力的抑制劑。計算的結果與實驗值相差0.4 kcal/mol，顯示結果與實驗值吻合。接著我們利用同樣的計算流程預測自資料庫挑出的9個分子與已知結晶構型的參考分子ZRM之ΔΔG值。一開始本研究先假定分子的結合模式與ZRM相同，在這9個分子的計算結果當中，計算值均落在1.4-5.0 kcal/mol，是值得進行實驗測試的化合物。此外，本研究也探討了利用分子嵌合計算與這些結合構型的ΔΔG值，結果顯示9個分子有8個以原先類似ZRM的結合模式相同。這些預測小分子與蛋白之結合親和力與結合模式的結果將能輔助類似物分子抑制劑的設計。Among the proposed possible mechanisms of occurrence of Alzheimer’s disease (AD), over-phosphorylation of tau protein of neurons in human brain by GSK-3β kinase is considered to be one of the main causes. Inhibition of GSK-3β kinase activity may alleviate symptom of AD or even cure. In this study, thermodynamic integration-molecular dynamics simulation is used to aid in design of GSK-3β kinase inhibitors undergoing competitive inhibition mechanism for which binding free energy of ligand-protein complex is a key parameter reflecting the inhibition strength. This method predicts relative binding free energy (ΔΔG) of a compound and a reference compound binding with a target protein. For calibration purpose, computations for known inhibitors with crystal structure and binding affinity available were carried out first. The computed value deviated from experimental value by 0.4 kcal/mol, showing good agreement with experimental result. With the same computational protocol, we carry out computations to predict ΔΔG for 9 compounds analogous to a reference compound, referring to ZRM compound which has crystal structure available, first with the assumption that their binding modes are the same with ZRM’s. Among these 9 compounds, the best result was 1.4 kcal/mol and the compound was recommended for enzyme assay. To explore further, we investigated ΔΔG at different binding conformations obtained from docking computation. The results showed that 8 compounds adopted ZRM-like binding mode. Only 1 compound adopted different binding mode. The predicted binding affinities and binding modes should be useful in further design of inhibitors analogous to the examined compounds.