臺灣博碩士論文加值系統

mTOR(mammalian target of rapamycin)在生物體中以mTORC1(mammalian target of
rapamycin complex 1)及mTORC2(mammalian target of rapamycin complex 2)兩種不同的
形式作用。兩者的訊息傳遞路徑有所不同，但皆與細胞的生長、代謝、增殖等調控息息
相關，倘若此部分出現異常，可能導致癌症發生，因此抑制mTOR 可有效控制並治療
此類型之癌症。
mTOR 抑制物可依作用標的分為兩大類，rapamycin-binding domain 抑制物(又稱
rapalogs)及kinase domain(ATP-binding domain)抑制物。前者僅可抑制mTORC1，後者則
可同時抑制mTORC1 及mTORC2。因此，近期mTOR 抑制物之設計多以kinase domain
作為藥物作用標的。由於mTOR 的kinase domain 與PI3K(phosphoinositol 3-kinase)有高
度相似性，通常mTOR kinase domain 抑制物也會對PI3K 造成影響，設計對mTOR 具
有選擇性的抑制物可避免這種情況。
惠氏研究(Wyeth Research)於2009 年發表一系列對mTOR 有選擇性之kinsae domain
抑制物，其對mTOR 及PI3K 的生物活性資料亦非常完整，但是尚無三維構效關係
(three-dimensional quantitative structure-activity relationship, 3D-QSAR)方面的分析。本研
究將惠氏研究發表83 個pyrazolopyrimidines 抑制物，以3D-QSAR 方式計算其於三維空
間中的各特性描述場與抑制能力間的關係。在此同時，以蛋白質同源模擬方法建立出
mTOR 的三維結構。將3D-QSAR 模型與mTOR 三維結構疊合，猜測抑制物與目標蛋白
可能的結合模式，用以說明3D-QSAR 場圖與目標蛋白間的關係，並將抑制物取代基的
特性及相對應的蛋白質部位的特性作系統性的整理。
由所建立的3D-QSAR 模型得知，如要增加抑制物對mTOR 的活性，R1 在phenylring
之後需加上urea group，以提供氫鍵給體與mTOR 的Asp2195 作用，R2 需設計為
piperidine 連接pyridine，以提供負電取代基與His2247 作用。避免藥物對PI3K 造成影
響，則R1 不宜過長，R2 piperidin 與pyridine 中央應設計為carbonyl group。藉由本研
究，希望此模型可為未來mTOR 抑制物之開發提供參考，並對相關病症之治療有所貢
獻。

mTOR (mammalian target of rapamycin), a key regulator of growth, metabolism, and
proliferation, exists as two forms of protein complexes, mTORC1 (mammalian target of
rapamycin complex 1) and mTORC2 (mammalian target of rapamycin complex 2). Since
mTORC1 and mTORC2 are highly involved in mediation of PI3K (phosphoinositol 3-kinase)
signaling pathways that are deregulated in human tumors, they have been recognized as
cancer treatment targets. According to the inhibition domains, mTOR inhibitors are
categorized into rapamycin-binding domain inhibitors and of kinase domain (ATP-binding
domain) inhibitors. The former targets at mTORC1, whereas the latter, which has been more
widely studied in recent years, targets at both mTORC1 and mTORC2. Because of close
similarity between kinase domains of mTOR and PI3K, inhibitors toward mTOR inevitably
show certain degree of inhibition on PI3K. Delicate design of mTOR inhibitors is expected to
achieve a higher therapeutic index for enhanced clinical efficacy.
Herein 3D-QSAR (three-dimensional quantitative structure-activity relationship)
modeling is applied to investigate 83 pyrazolopyrimidine derivatives, which were published
in 2009 and expected to serve as selective mTOR kinase domain inhibitors by Wyeth
Research. Due to the lack of known mTOR structure, homology method is adopted to build
mTOR in complex with one studied compound to provide details of possible binding mode
and further to be correlated with the 3D-QSAR models.
The constructed models suggest that R1 with a urea-modified benzene moiety enhances
the hydrogen bonding interaction with mTOR Asp2195, whereas R2 carrying a piperidine in
connection with a pyridine boosts the electrostatic interaction with mTOR His2247. On the
other hand, the size of substituent on R1 and the connector between piperidine and pyridine
on R2 play essential roles in PI3K/mTOR selectivity.

目錄 ........................................................................................................................ i
表目錄 .................................................................................................................. iv
圖目錄 ................................................................................................................... v
中文摘要 ............................................................................................................... 1
英文摘要 ............................................................................................................... 2
第一章、前言 ....................................................................................................... 3
1.1 mTOR簡介 .......................................................................................... 3
1.2 三維構效關係(3D-QSAR)簡介 .......................................................... 8
1.3 蛋白質同源模擬簡介 ....................................................................... 12
1.4 研究動機及研究目的 ....................................................................... 14
第二章、材料與方法 ......................................................................................... 15
2.1 材料 .................................................................................................... 15
2.2 3D-QSAR模型建立步驟及參數設定 .............................................. 23
2.3 蛋白質同源模擬方法 ....................................................................... 25
2.4 蛋白質同源模擬後之能量最小化與結構合理性評估 ................... 27
2.5 3D-QSAR模型與mTOR同源模擬蛋白質疊合 ............................... 27
第三章、3D-QSAR結果與討論 ........................................................................ 28
3.1 化合物疊合結果 ............................................................................... 28
3.2 PLS統計結果 ..................................................................................... 29
3.2.1 以mTOR為作用標的之3D-QSAR模型 ................................ 29
3.2.2 以PI3K為作用標的之3D-QSAR模型 ................................... 29
3.2.3 選擇性(selectivity)之3D-QSAR模型 .................................... 30
3.3 3D-QSAR模型預測能力 .................................................................. 30
3.3.1 以mTOR為作用標的之3D-QSAR模型 ................................ 30
3.3.2 以PI3K為作用標的之3D-QSAR模型 ................................... 32
3.3.3 選擇性(selectivity)之3D-QSAR模型 .................................... 32
3.4 場圖結果與討論 ............................................................................... 34
3.4.1 以mTOR為標的之3D-QSAR場圖結果與討論 .................... 34
3.4.2 以PI3K為標的之3D-QSAR場圖結果與討論 ...................... 41
3.4.3 選擇性(selectivity)之3D-QSAR場圖結果與討論 ................ 48
3.5 3D-QSAR模型比較........................................................................... 54
第四章、蛋白質同源模擬結果與討論 ............................................................ 57
4.1 mTOR蛋白質序列搜尋結果 ............................................................ 57
4.2 mTOR蛋白質序列與3IBE中PI3K序列的比對結果 ...................... 58
4.3 mTOR同源模擬結構 ........................................................................ 59
4.4 mTOR同源模擬蛋白質結構合理性評估 ........................................ 60
4.5 mTOR模型與蛋白質疊合的相關討論 ............................................ 61
第五章、結論 ..................................................................................................... 62
第六章、參考文獻 ............................................................................................. 64

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