使用以配體為基準的三維結構活性關係研究人類 Cyclin-dependent Kinase 2之3-Amino-5 cyclopropylpyrazole衍生型抑制劑

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研究生：	蔡閔麒 Min-Chi Tsai
論文名稱：	使用以配體為基準的三維結構活性關係研究人類 Cyclin-dependent Kinase 2之3-Amino-5 cyclopropylpyrazole衍生型抑制劑 Ligand-based 3D-QSAR Studies on 3-Amino-5-cyclopropylpyrazole Derived Human Cyclin-dependent Kinase 2 Inhibitors
指導教授：	林志侯 Thy-Hou Lin
口試委員:
學位類別：	碩士 Master
系所名稱：	生命科學暨醫學院 - 分子醫學研究所 Institute of Molecular Medicine
論文出版年：	2008
畢業學年度：	96
語文別：	英文
論文頁數：	80
中文關鍵詞：	定量構效關係、比較分子場方法、比較分子相似性指標場、CDK2
外文關鍵詞：	QSAR, CoMFA, CoMSIA, CDK2
相關次數：	點閱：2 下載：0
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Abstract
Several three-dimensional quantitative structure-activity relationship (3D-QSAR) models have been constructed by the method of CoMFA (comparative molecular field analysis), CoMSIA (comparative molecular similarity indexes analysis), and Catalyst pharmacophore hypothesis, based on a series of 42 3-Amino-5-cyclopropylpyrazole derived inhibitors designed to inhibit the activity of human CDK2 (cyclin-dependent kinase 2), an enzyme involves in cell division cycle. Inhibition of CDK2 blocks cell cycle; thus CDK2 inhibitors are potential antitumor agents. The structures of these inhibitors were built from a structure template extracted from the crystal structure of human CDK2. The structures built were divided into the training and test sets for both the CoMFA and CoMSIA analyses with each consisted of 28 and 14 inhibitors, respectively. The structures were aligned through docking each inhibitor into the CDK2 active site by GOLD program. Some stepwise CoMSIAs were performed on the aligned training set on which the best CoMFA result was also obtained. The best CoMSIA model was identified from the stepwise analysis results and the corresponding pharmacophore features were used for constructing a pharmacophore hypothesis by the Catalyst program. Pharmacophore features obtained by CoMFA and CoMSIA were found to be in accord with each other and were both mapped onto the lipophilic potential surface and hydrogen bond donor/acceptor density map of CDK2 active site. These pharmacophore features were also compared with those obtained by the Catalyst program and mapped onto the molecular surface of CDK2 active site. A consensus 3D-QSAR model using combined CoMSIA and Catalyst analyses is also established. The possibility of using CoMSIA hydrogen bond and hydrophobic features from CoMSIA and Catalyst to design more potent CDK2 inhibitors was also discussed.

中文摘要
　　以一系列共42個人類的CDK2 3-Amino-5-cyclopropylpyrazole衍生型抑制劑為基礎，利用CoMFA、CoMSIA、及 Catalyst藥效基團特徵方法建立數個三度空間定量結構活性關係分析模型。CDK2參與細胞分裂周期，抑制CDK2即可抑制細胞分裂，因此其抑制劑為極具潛力的抗癌物。由一個人類的CDK2晶體結構內的抑制劑當模板，用GOLD軟體建立其餘抑制劑的三維結構。這一系列化合物分為訓練組28個及測試組14個以進行CoMFA、 CoMSIA、及 Catalyst分析。Catalyst部分則由最佳的CoMSIA結果來選擇使用的結構特性，所得結果皆套回CDK2活性區比對。也探討了從CoMSIA來選擇Catalyst要使用之結構特性的可行性。另外也建立了整合CoMSIA及Catalyst的三度空間定量結構活性分析模型。由本篇CoMFA、CoMSIA、及 Catalyst的結果，相信可藉CoMSIA分析所得的氫鍵特徵及CoMSIA與Catalyst分析所得的疏水作用力特徵，設計出效力更強之CDK2抑制劑。

Table of content

Abstract--------------------------------------------------i
List of tables-------------------------------------------iv
List of Figures-------------------------------------------v

Introduction----------------------------------------------1
Materials and Methods-------------------------------------5
  Introduction of software program used-------------------5
  Generation of ligand structures-------------------------8
  Construction of CoMFA and CoMSIA models-----------------9
  Generation of Catalyst hypotheses----------------------15
  Validation test of Catalyst hypotheses-----------------17
  Combination of CoMSIA and Catalyst hypotheses----------19

Results and Discussion-----------------------------------21
Docked conformation and statistics of CoMFA and CoMSIA---21
Mapping of CoMFA and CoMSIA models-----------------------23
Mapping of hypothesis generated by Catalyst--------------25
Features help to design more potent inhibitors-----------29
Compare CoMSIA and Catalyst characteristics--------------29
Find appropriate feature combination to improve activity prediction-----------------------------------------------30

Conclusion-----------------------------------------------33
Reference------------------------------------------------75



List of Tables

Table 1.  Structures of human CDK2 inhibitors studied----34

Table2. Summary of CoMFA and stepwise CoMSIA statistics for the training set CDK2 inhibitors-------------------------39

Table 3. Comparison of predicted activity by CoMFA, CoMSIA (A+D+H), and hypothesis 1 with actual activity of the training set inhibitors----- ----------------------------40

Table 4. Comparing predicted activity by CoMFA, CoMSIA (A+D+H), and Hypothesis 1 with actual activity of the test set inhibitors-------------------------------------------41

Table 5. Statistical result of top ten generated hypotheses----------------------------------------------------------42

Table 6. Validation of Hypothesis 1 by catScramble module in Catalyst 4.11 program---------------------------------43

Table 7. Summary and comparison of statistical values of each method used-----------------------------------------45



List of Figures

Figure 1. A QSAR table-----------------------------------48
Figure 2. The CoMFA process------------------------------49
Figure 3. Representation of formula for fit value calculation by Catalyst HypoGen module---50
Figure 4. Crystal structure of human CDK2/cyclin A complexed with two 26a inhibitor molecules in A chain and C chain----------------------------------------------------51
Figure 5. Comparison between the crystal structure of ligand 26a with the ligands generated by the GOLD program------------------------------------------------------------52

Figure 6. Overlap of all docked 42 CDK2 inhibitor structures by GOLD. The basic structure
3-aminopyrazolyl group of these inhibitors are roughly at the same position----------------------------------------53

Figure 7. Transparent view of the CoMFA contours with high potency compounds 4c (a) and 21a (b); low potency compound 14a (c) as well as neighboring residues from human CDK2--------------------------------------------------------------54

Figure 8. Transparent view of the CoMSIA contours with high potency compounds 4c (a) and 21a (b); low potency compound 14a (c) as well as neighboring residues from human CDK2--------------------------------------------------------------56

Figure 9. Projection of the CoMFA contours with compound 4c (a), 21a (b), and 14a (c) over electrostatic potential surface of human CDK2 active site------------------------58

Figure 10. Projection of the CoMSIA contours with compound 4c (a), 21a (b), and 14a (c) over lipophilic potential surface map of human CDK2 active site--------------------60

Figure 11. Projection of the CoMSIA contours with compound 4c (a), 21a (b), and 14a (c) over hydrogen bond donor density surface map of human CDK2 active site------------62

Figure 12. Linear regression of predicted and experimental activity (pIC50) from CoMFA (a) and CoMSIA (b) analyses of the training set-----------------------------------------64

Figure 13. Linear regression of predicted and experimental activity (pIC50) from CoMFA (a) and CoMSIA (b) analyses of the test set---------------------------------------------65

Figure 14. Correlation of predicted and experimental activity from Hypothesis 1 of the training set (a) and test set (b)--------------------------------------------------66

Figure 15. Linear regression of predicted and experimental activity (pIC50) from Catalyst HypoGen fit of the training set (a) and analyses of the test set (b)-----------------67

Figure 16. Linear regression of predicted and experimental activity (pIC50) from Method 1 (CoMSIA+whole catalyst features) of the training set (a) and analyses of the test set (b)--------------------------------------------------68

Figure 17. Linear regression of predicted and experimental activity (pIC50) from Method 2 (CoMSIA+three seperated  Catalyst features) of the training set (a) and analyses of the test set---------------------------------------------------------------------------------------------------------69

Figure 18. Mapping of the Hypo1 hypothesis onto the compound 4c (a), 21a (b), and 14a (c)--------------------------------------------------------------------------------70

Figure 19.Comparison of CoMSIA contour map (a) and Catalyst pharmacophore features map (b).--------------------------------------------------------------------------------------72

Figure 20.Solid view of projection of Hypothesis 1 onto the electrostatic potential surface (blue, positive potential; red, negative potential) of the CDK2 active site---------73

Figure 21.The most potent Inhibitor 4c with its potentially hydrogen bond forming residues Ile10 and Lys89-----------------------------------------------------------------------74

                                

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