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研究生：	陳昭同 Chao-Tung Chen
論文名稱：	Sorafenib衍生物抑制劑與B-Raf蛋白質複合體和GSK3β-GSKIPide複合體之分子動力學模擬:結合自由能計算及複合體結構分析 Molecular Dynamics Simulation of B-Raf Kinase-Sorafenib Derivative Inhibitors and GSK3β-GSKIPide complexes:Binding Energy Calculation and Structural Analysis
指導教授：	孫英傑 Sun, Ying-Chieh
學位類別：	碩士 Master
系所名稱：	化學系 Department of Chemistry
論文出版年：	2011
畢業學年度：	99
語文別：	中文
論文頁數：	73
中文關鍵詞：	衍生物抑制劑、分子動力學、蛋白質激酶
論文種類：	學術論文
相關次數：	點閱：128 下載：0
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臨床統計上B-Raf 變異佔了人類所有癌症中的約7%，在黑色素瘤癌發現高達6成4有B-Raf 變異情形，其中B-Raf 變異以B-RafV600E為主要的變異型態。Sorafenib，在2005年被美國食品藥物管理局核准上市為B-Raf的標靶抑制劑，然而在臨床研究發現Sorafenib對
B-Raf選擇性並不高且有溶解度低不足的部分，2008一篇合成B-Raf衍生物抑制劑文獻提出其合成出在保有與Sorafenib相近IC50卻有較高溶解度的抑制劑。我們選出構型差異為在Benzimidazoles環氮上取代基分別為氫原子跟甲基的兩組抑制劑化合物與B-RafV600E進行模擬，利用MMPBSA計算結合自由能及結構分析來探討其實驗IC50具明顯差異的可能原因，模擬結果發現在兩組取代基為甲基的抑制劑化合物皆比取代基為氫原子的抑制劑化合物在凡得瓦作用力上穩定3.5~6kcal/mol，結構分析也確定抑制劑化合物甲基位置是處於較疏水性的環境中，最後我們也對五組從Docking其他構型與B-RafV600E進行模擬，從能量結果顯示挑選Docking中Fitness 1抑制劑化合物構型當做MD模擬的初始構型程序是合適的。

第一章  B-Raf與Sorafenib衍生物抑制劑複合體模擬.....................1
第一節  緒論…………………………………………………………..2
1-1   前言...............................................3
1-2     MAPK pathway 與標靶抑制劑..........................4
1-3     B-Raf kinase 變異..................................6
1-4     研究目標 ..........................................9

第二節 實驗與方法.......................................10
2-1 分子動力學模擬(Molecular dynamics)..................11
    2-1-1 分子動力學模擬理論............................11
    2-1-2 分子動力學模擬環境設定........................13
2-2 蛋白質結晶結構處理..................................14
    2-2-1 胺基酸活化片段序列補足........................14
    2-2-2 組胺酸構型調整................................17
2-3 能量計算............................................18
2-4 氫鍵分析設定.........................................19

第三節 結果與討論.......................................20
3-1四個Sorafenib衍生物抑制劑挑選.......................21
    3-1-1 Docking產生初始抑制劑結構.....................23
    3-1-2 Cheng-Prusoff equation近似....................24
3-2  B-RafV600E與BAY439006結合模擬結果討論................25
     3-2-1 RMSD與RMSF...................................26
     3-2-2 結合自由能計算 ...............................27
     3-2-3 氫鍵分析 .....................................28
3-3  B-RafV600E與Sorafenib衍生物抑制劑系統能量及構型
比較................................................30
     3-3-1  3-Br-bzle與3-Br-(N-methyl)bzle.........30
     3-3-2  2-Br-bzle與2-Br-(N-methyl)bzle.........35
     3-3-3  抑制劑化合物與鄰近疏水環境探討...............40
     3-3-4  抑制劑化合物與Sorafenib 中carboxamide
            構型比較.....................................41
3-4  衍生物抑制劑從分子嵌合產生的其他構型比較............43
第四節 結論..............................................48
第二章 GSK3β蛋白質激酶與GSKIPide複合體結合模式模擬……50
第一節   緒論............................................51
1-1   GSK3β跟Wnt 訊息傳遞路徑…………………………………52
1-2   GSK3β與三段胜肽鏈 Y2H細胞實驗…………………………55
1-3    研究目標............................................56

第二節 實驗與方法........................................57
2-1    蛋白質模擬環境系統設置………………………………………58
2-2    分子動力學模擬設定……………………………………………59

第三節   結果與討論......................................60
3-1     GSK3β-GSKIPide Cα RMSD...........................61
3-2     GSK3β-GSKIPide結構作用力分析.....................62
3-3     GSK3β-GSKIPide的V267G跟Y288 Cα RMSD 及結構作用力
 分析...............................................63
3-4     GSKIPide、AxinGID及FRATide與GSK3β作用力比較
      分析...............................................66
3-5    使用MMPBSA計算GSK3β-GSKIPide結合自由能 ......69

第四節  結論............................................70

參考文獻................................................71
                                

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