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研究生: 陳鼎欣
論文名稱: 蛋白激酶-A與數個小分子抑制劑複合體之分子動力學模擬:結合能計算
Molecular Dynamics Simulation of Several Protein Kinase A - Inhibitor Complexs : Binding Energy Calculation
指導教授: 孫英傑
學位類別: 碩士
Master
系所名稱: 化學系
Department of Chemistry
論文出版年: 2010
畢業學年度: 98
語文別: 中文
論文頁數: 61
中文關鍵詞: 蛋白激酶-A小分子抑制劑分子動力學模擬結合能計算
論文種類: 學術論文
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  • 蛋白激酶 ( protein kinase ) 是生物體訊息傳導途徑的重要成員之一,藉由磷酸化特定蛋白質,調控細胞酵素及傳遞訊息。
    本研究中,我們的目的是利用分子動力學模擬方法,幫助設計PKA的抑製劑。首先我們從蛋白質資料庫(PDB)中選擇4個具有IC50值的PKA配體複合物,當中有其它類似的配體分子,再利用MM/PBSA計算小分子和PKA之間的結合自由能。
    四個結晶結構當中,除了2C1A模擬結果,與原有的IC50值相比不具正相關,其它三個結構與現有IC50值比,則得到良好的相關性。經過模擬計算,我們進行討論和分析,取代配體當中的那些官能基能提高整體的親合力。基於這些結果,我們進一步設計五個新配位分子。最後,得到了幾點改變官能基的建議:(1)添加甲基在鹵化苯基的環上,可以增加與疏水性空腔間的凡得瓦作用力。(2)添加羥基於小分子骨架,此羥基上的氧原子容易與ASN 168/ ASP 184產生強而穩定的氫鍵作用力。

    Protein kinase A plays significant role in a number of signaling pathways in cell, and is thought to be a potential drug target for treatments of several diseases by inhibiting its kinase activity.

    In the present study, we aimed to use molecular dynamics simulation method to aid in design of PKA inhibitors. We selected 4 ligand-PKA complexes, in which their ligands are analogous, from Protein data bank with available IC50 values, MM/PB(GB)SA was employed to investigate the binding between ligand and PKA. The calculated binding energies are in good accord with the available IC50 values of examined complexes except one. The calculated results were analyzed and discussed to aid in understanding which functional group substitutions can enhance the binding affinity. Based on these results,we further designed 5 new ligands to predict their binding affinities.

    The calculated results suggest the fillowing points to change the functional groups:
    (1) Adding a methyl group at the R1 or R3 position (see Figure in the text) of the single ring in the ligand can enhance the binding affinity. The van der Waals interaction is the main contributor in the total binding energy .
    (2) Adding a hydroxyl group at R5 position of the singl ring gave stable hydrogen bonds with the LYS 168 and ASP 184, increasing the binding affinity. These results together with the analysis above should be able to aid in design of PKA inhibitors analogous to the ligands investigated in the present study.

    圖目錄 ----------------------------------------------------------------------- Ⅳ 表目錄 ----------------------------------------------------------------------- Ⅵ 中文摘要 ------------------------------------------------------------------- Ⅶ 英文摘要Abstract ------------------------------------------------------- Ⅷ 第一章 緒論 ---------------------------------------------------------- 1 1-1 前言 --------------------------------------------------------------- 2 1-2 藥物分子與PKA結合位置--------------------------------- 3 1-3 Protein Kinase A訊息傳導途徑(Signaling pathway) ---------------------------------------------------------- 6 1-4 研究目標--------------------------------------------------------- 8 第二章 理論與方法 ---------------------------------------------- 9 2-1 分子動力學模擬 ( MD ) ----------------------------------- 2-1-1 分子動力學模擬理論----------------------------- 2-1-2 分子動力學模擬環境設定---------------------- 10 10 12 2-2 能量計算--------------------------------------------------------- 2-2-1 MM-PBSA 理論設定----------------------------- 14 14 2-3 氫鍵設定分析-------------------------------------------------- 15 第三章 計算結果與討論 -------------------------------------- 16 3-1 化合物與PKA複合物之模擬 --------------------------- 3-1-1 PKA與小分子結合模式 ----------------------- 3-1-2 模擬的結構偏差RMSd ----------------------- 17 17 20 3-2 PKA-小分子複合體結構實驗再現 -------------------- 21 3-2-1抑制劑與PKA之間作用力與結合強度相關性 ------------------------------------------------------------------ 21 3-3 胺基酸與小分子間的氫鍵作用分析-------------------- 3-3-1 1YDS模擬之氫鍵結合模式 ------------------- 3-3-2 1YDT模擬之氫鍵結合模式 ------------------- 25 26 28 3-3-3 2C1A模擬之氫鍵結合模式 ------------------- 30 3-3-4 2C1B模擬之氫鍵結合模式 ------------------- 33 3-4 官能基設計之模擬結果------------------------------------- 3-4-1 疏水效應----------------------------------------------- 3-4-2 疏水效應與官能基修飾(R1~R4) ------------- 35 36 38 3-4-3 氫鍵作用與官能基修飾(R5) ------------------- 39 3-5 新取代基分子預測 L-R1.3©5-(OH) ------------------- 41 第四章 結論 ---------------------------------------------------------- 45 附錄與參考文獻 ------------------------------------------------------ 48 圖目錄 圖1 Holoenzyme conformation -RIIα結構 -------------- 4 圖2 C-subunit 結合ATP ----------------------------------- 5 圖3 PKA抑制ERK訊息傳導途徑構 --------------------- 6 圖4 PKA與Wnt訊息傳遞途徑相互連繫 ---------------- 7 圖5 1ns 模擬後的總能量、溫度、壓力、體積、密度 13 圖6 四個小分子化合物結構 ------------------------------ 18 圖7 ( IQS.IQB.I5S.CQP )疊合情形 ---------------------- 18 圖8 四個分子與PKA結合位置 -------------------------- 19 圖9 PKA與四個結晶構形分子作用後的RMSd 圖 --- 20 圖10 四個小分子化合物官能基差異性 ------------------ 21 圖11 IQS與疏水性空腔示意圖 ------------------------- 23 圖12 IQB與疏水性空腔示意圖 ------------------------ 23 圖13 I5S與疏水性空腔示意圖 ------------------------- 24 圖14 CQP與疏水性空腔示意圖 ------------------------- 24 圖15 1YDS結晶結構與胺基酸間主要的氫鍵作用力 -- 27 圖16 1YDS模擬後與胺基酸間主要的氫鍵作用力 ----- 27 圖17 1YDT結晶結構與胺基酸間主要的氫鍵作用力 -- 29 圖18 1YDT模擬後與胺基酸間主要的氫鍵作用力 ----- 29 圖19 2C1A結晶結構與胺基酸間主要的氫鍵作用力 -- 31 圖20 2C1A模擬後與胺基酸間主要的氫鍵作用力 ----- 32 圖21 2C1B結晶結構與胺基酸間主要的氫鍵作用力 -- 34 圖22 2C1B模擬後與胺基酸間主要的氫鍵作用力 ----- 34 圖23 IQS與官能基替換的位置及標號R1~R5 -------- 35 圖24 R5官能基與胺基酸間主要的氫鍵作用力 --------- 39 圖25 新預測分子結構 --------------------------------------- 41 圖26 新預測分子與胺基酸間主要的氫鍵作用力 ------- 44 圖27 結晶結構△G與模擬得到的△G相關性 ------------ 45 圖28 化合物作用力整理示意圖 ---------------------------- 47 表目錄 表1 個別胺基酸作用貢獻能量計算------------------------- 22 表2 MM-PBSA 個別能量分解表---------------------------- 22 表3 模擬前後胺基酸與化合物可能存在的氫鍵---------- 25 表4 IQS與胺基酸產生氫鍵之百分比---------------------- 26 表5 IQB與胺基酸產生氫鍵之百分比---------------------- 28 表6 I5S與胺基酸產生氫鍵之百分比---------------------- 31 表7 CQP與胺基酸產生氫鍵之百分比-------------------- 33 表8 化合物與胺基酸序列較強VDW作用力------------- 37 表9 MM-PBSA計算甲基在不同位向修飾前、後能量- 38 表10 MM-PBSA計算增加羥基修飾前、後能量---------- 40 表11 疏水性空腔內的個別胺基酸貢獻 --------------------- 42 表12 MM-PBSA計算增加甲基及羥基修飾後能量 ------ 43 表13 各個化合物氫鍵作用力整理 --------------------------- 46

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