基于D1蛋白酶结构的抑制剂先导化合物的设计与合成
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摘要
D1蛋白酶(CtpA)是广泛存在于绿色植物叶绿素中的一种多肽加工酶。D1蛋白酶的功能是剪切D1蛋白前体(pD1)8～16个氨基酸延伸端,形成用于PSⅡ氧释放中心(OEC)锰簇原子组装的成熟D1蛋白(mD1)。现有研究表明,D1蛋白酶是绿色植物进行光合作用所必需,并且具有低含量,高同源性,分布广的特点,可以作为新型广谱高效除草剂的新型靶标。基于D1蛋白酶结构开展新型除草剂先导化合物的设计和合成,对于满足当前农业生产对高效低毒除草剂的需求和解决除草剂使用出现的越来越严重的抗性问题具有重要意义。
目前仅仅有一篇D1蛋白酶抑制剂的研究报道,尚没有关于D1蛋白酶抑制剂的商业化品种。本文的前期工作在斜生栅藻D1蛋白酶晶体结构数据的基础上,同源模建高等植物菠菜D1蛋白酶的三维结构,通过虚拟筛选获得了多个系列的化合物作为D1蛋白酶抑制剂先导化合物的结构信息。本文通过合理设计和合成,得到四大类化合物合计90个,所有目标化合物经~1H NMR、MS验证,部分化合物同时经元素分析,~(13)C NMR验证,并获得了结构较为复杂的异嗯唑噻唑哌啶脲类部分代表性化合物的晶体,通过单晶X-射线衍射进一步确证了其分子结构。对全部化合物进行了活体生物活性测试,部分化合物进行了离体生物活性研究,初步确认了异噁唑噻唑哌啶脲化合物具有D1蛋白酶抑制剂先导化合物的特征,为进一步的研究奠定了良好的基础。本文具体内容如下:
1、阐述了基于靶标大分子结构的农药研发策略,系统综述了D1蛋白酶及其抑制剂的研究现状,提出了本论文的研究思路和研究方案。
2、利用1,3-偶极环加成形成异噁唑环,以酰胺键与赖氨酰脲连接,获得了异噁唑酰赖氨酰脲类目标化合物共21个(ILU 1～21)。采用平皿法测定了这些化合物对两种模式植物油菜和稗草的抑制活性,初步探讨了这个系列化合物的分子结构与生物活性的关系。研究发现,化合物脲端取代基不变,异噁唑苯基取代基邻对位都为氯时,化合物除草活性较高;异噁唑苯基取代基不变,脲端中含有杂环吗啡啉时,化合物具有比较好的生物活性。该骨架化合物中,改变脲基的取代基对化合物活性影响较大。
3、利用β-二酮酯与羟胺环化得到异噁唑甲酸酯,酯氨解后,通过Lawesson试剂转化为硫酰胺,与卤代酮反应得到异噁唑噻唑甲酸酯,经过肼解,与相应的酰氯或异氰酸酯反应得到异噁唑基噻唑甲酰肼类目标化合物共14个(ITH 1～14)。活体生物活性测试表明,酰肼脲类化合物活性普遍优于比酰肼酰基类。该骨架部分化合物对油菜和稗草的除草活性表现出一定的选择性。该两类化合物溶解性都较差,需要进一步优化其结构来提高这类化合物的生物利用度。
4、利用1,3-偶极环加成和Hansztch噻唑合成法得到异噁唑基噻唑基哌啶衍生物,与酰氯、异氰酸酯或异硫氰酸酯反应,得到两类合计43个异噁唑基噻唑基哌啶基碳酰胺或硫代碳酰胺目标化合物(ITP 1～43)。第二类化合物为刚性结构的异噁唑并环己烷并噻唑的哌啶碳酰胺化合物。活体生物活性测试表明,第二类目标化合物的除草活性有普遍的提高。综合比较两类化合物的生物活性与结构的关系,可知在异噁唑苯环上有取代基时,苯环2,4位是比较重要的取代基引入位置,且氟原子的引入能提高化合物活性;在脲端,对氟苯基的引入能够改善化合物活性;异噁唑环及哌啶酰胺的结构可能是比较重要的结构单元。刚性六元环连接异噁唑和噻唑环也在一定程度上提高化合物对油菜的抑制率。
5、利用咪唑啉三酮与胺偶联,亚胺基还原后与相应的酰氯反应得到5-氨基咪唑啉2,4-二酮类化合物共12个(H1～12)。活性测试显示,环上3位甲酰基取代的化合物活性优于苯基取代的化合物活性。环外5位NH上取代基变化对化合物活性有较大影响。咪唑啉-2,4-二酮环上3位和环外5位NH可能是重要的衍生位置。
6、在实验室前期生物提纯天然菠菜D1蛋白酶和重组菠菜D1蛋白酶的工作基础上,利用HPLC技术,测定异噁唑噻唑哌啶类化合物ITP 16,ITP 21,ITP 22,ITP 26,ITP 29,ITP 42,ITP43对D1蛋白酶水解24肽的抑制作用,其中ITP21对D1蛋白酶的抑制常数K_i值为1.3μM,属竞争性抑制。利用表面等离子共振(SPR)技术测定了化合物ITP21与D1蛋白酶的抑制作用。数据显示,在0.1 mM浓度下,化合物对酶的抑制率为47%。经过两种离体活性方法的测定,初步确定了异噁唑噻唑类化合物的作用靶标为D1蛋白酶。
D1 protease(CtpA),a kind of C-terminal processing protease,widely exists in the chloroplast of green plants.It cleaves 8～16 amino acid residues of the precursor D1 protein(pD1) to form mature D1 protein(mD1),and this process is necessary for assembling the manganese cluster in the oxygen-evolving center of PSⅡ.Because of its necessary for the photosynthetic reaction in plants, low amount,high homology in organisms,D1 protease has been predicted to be an ideal herbicidal target.To meet the need of high-efficient and environment-friendly herbicides in modern agriculture and solve the problem of herbicidal resistance,it will possess great significance for rational design and synthesis of hit compounds targeting D1 protease.
At present there is only one report concerning the D1 protease inhibitors,and there are no commercial inhibitors targeting D1 protease.In our previous work,the homology model of spinach D1 protease was built on the basis of the crystal structure of D1 protease from Scenedesmus obliquus. With the three-dimension structure of this spinach D1 protease model,virtual screening was performed by docking of small molecules from various compound libraries into the active site of the Dlprotease model and subsequent evaluating of the predicted bioactivities with scoring functions. Thus several types of hit compounds were identified.In this thesis,four series of compounds were rationally designed on the basis of the hit compounds for chemical synthesis,and total 90 compounds were synthesized.The molecular structures of all the target compounds were verified with ~1HNMR and MS,and some were also confirmed with ~(13)CNMR and elemental analysis.With X-ray crystallography,the complex structures of isoxazolythiazolyl piperidine derivatives were determined. The herbicidal activities of the target compounds were tested and showed moderate and good herbicidal efficacies.In order to validate the hit,some compounds were also tested their in vitro inhibition effects against the native or recombinant D1 protease with HPLC and SPR methodologies.
This dissertation may be summarized as followings.
1.This dissertation first made an investigation of the strategy for the structure-based design of pesticide.A systematic review was made on the research of D1 protease as the herbicidal target and progress on the inhibitors targeting D1 protease.The research strategies and plans were proposed for this dissertation.
2.By taking use of the isoxazolecarboxylic acid formed via 1,3-dipolar cycloaddition followed by oxidation and the subsequent amidation withε-lysinylurea units,totally 21 compounds(ILU 1～21) were synthesized.The herbicidal efficacies of these compounds were tested against the growth rates of two model plants rape and barnyard grass.The structure-activity relationship was preliminarily discussed.Among these compounds,when the urea moieties were same,the compound with 2,4-dichloro substituent on the phenyl of isoxazole had better herbicidal activity.While when the isoxazole moieties had the same substituent,the urea moiety containing morpholine possessed better herbicidal efficacies.Changing the substituent of urea moiety will influence the biological activity of compounds to a great extent.
3.Totally 21 compounds(ITH 1～14),namely isoxazolylthiazolecarbohydrazine derivatives, were rational designed and synthesized.The synthesis was accomplished via the subsequent formation of isoxazole ring,thiazole ring,and carbohydrazine.The isoxazole moieties were formed via the condensation of P-diketone ester and hydroxylamine,while the isoxazolylthiazolecarboxylic esters were formed via amidation and thiolation with the Lawesson's reagent and subsequent condensation with 2-chloroacetoacetic ester(Hansztch reaction).The isoxazolylthiazolecarboxylic esters were subjected to react with hydrazines followed by acylation or aminocarbohydrazine,and finally the isoxazolylthiazolecarbohydrazine derivatives were obtained.Biological test showed that the title compounds with urea moieties possessed better activities.Some compounds show good biological selectivity.However,since the water solubilities of these compounds were relatively low and the redesign is necessary for these compounds to improve their bioavailability.
4.With the use of 1,3-dipolar cycloaddition and Hansztch reaction as like as the procedures mentioned above,the 4-isoxazolylthiazolylpiperidines as intermediates were obtained.The piperidine moieties in these intermediates were subjected to react with acyl chlorides,isocyantes or isothiocyanate to afford two classes of target compounds,totally 43 compounds(ITP 1～43).The second class of compounds possesses an isoxazolocyclohexanothiazole rigid moiety,which was expected to endow these compounds with higher bioactivities,and the bioassays demonstrated this expectation.The structure-activity relationship shows that the ortho- and para- position of phenyl on the isoxazole ring are important and the fluorine atom located at the ortho-position will promote the bioactivity of compounds;The p-F phenyl possessing the urea motiey alsohas the same effect.The isoxazole and piperidine moieties should be important units of the compounds,and the rigid cyclohexanyl connecting the isoxazole and thiazole will increase the compounds inhibiting efficiency to the growth of rape.
5.A series of 5-aminoimidazoline-2,4-dione derivatives were rationally designed and synthesized. The synthesis was accomplished via the coupling of triones with amine,followed by reduction of the imine group and acylations with acyl chlorides.Thus totally twelve 5-aminoimidazoline-dione derivatives(H1～12) were obtained.The hydantoin with N-acyl aryl group had the better biological activities than N-aryl substituented compounds.The substitutents of 5-NH will influence the herbicidal activities of compounds.In order to get higher bioactivity of compounds the 3th position of the ring and the 5-NH will be important positions to vary different substituents.
6.On the basis of our previous work for the isolation,purification and expression of spinach D1 protease,the isoxazolylthiazolyl piperidine carboxamides,ITP 16,ITP 21,ITP 22,ITP 26,ITP 29, ITP 42,ITP 43,were measured their in vitro inhibition efficacies against D1 protease by the HPLC method.One of these compounds,ITP 21,was demonstrated to possess an inhibitor constant(K_i) 1.3μM.The result showed the compound possessed effective inhibition to CtpA with a competitive inhibition.On the other hand,the inhibiting efficacy ratio of the compound ITP 21 was tested with the competitive strategy by surface plasmon resonance technology,and it was shown that this compound possessed an in vitro inhibition efficacy 47%at the concentration of 0.1 mM.All the results from the in vivo and in vitro tests show that the compounds containing isoxazolylthiazolyl piperidine carboxamides may be the potential compounds targeting D1 protease directly.
目前仅仅有一篇D1蛋白酶抑制剂的研究报道,尚没有关于D1蛋白酶抑制剂的商业化品种。本文的前期工作在斜生栅藻D1蛋白酶晶体结构数据的基础上,同源模建高等植物菠菜D1蛋白酶的三维结构,通过虚拟筛选获得了多个系列的化合物作为D1蛋白酶抑制剂先导化合物的结构信息。本文通过合理设计和合成,得到四大类化合物合计90个,所有目标化合物经~1H NMR、MS验证,部分化合物同时经元素分析,~(13)C NMR验证,并获得了结构较为复杂的异嗯唑噻唑哌啶脲类部分代表性化合物的晶体,通过单晶X-射线衍射进一步确证了其分子结构。对全部化合物进行了活体生物活性测试,部分化合物进行了离体生物活性研究,初步确认了异噁唑噻唑哌啶脲化合物具有D1蛋白酶抑制剂先导化合物的特征,为进一步的研究奠定了良好的基础。本文具体内容如下:
1、阐述了基于靶标大分子结构的农药研发策略,系统综述了D1蛋白酶及其抑制剂的研究现状,提出了本论文的研究思路和研究方案。
2、利用1,3-偶极环加成形成异噁唑环,以酰胺键与赖氨酰脲连接,获得了异噁唑酰赖氨酰脲类目标化合物共21个(ILU 1～21)。采用平皿法测定了这些化合物对两种模式植物油菜和稗草的抑制活性,初步探讨了这个系列化合物的分子结构与生物活性的关系。研究发现,化合物脲端取代基不变,异噁唑苯基取代基邻对位都为氯时,化合物除草活性较高;异噁唑苯基取代基不变,脲端中含有杂环吗啡啉时,化合物具有比较好的生物活性。该骨架化合物中,改变脲基的取代基对化合物活性影响较大。
3、利用β-二酮酯与羟胺环化得到异噁唑甲酸酯,酯氨解后,通过Lawesson试剂转化为硫酰胺,与卤代酮反应得到异噁唑噻唑甲酸酯,经过肼解,与相应的酰氯或异氰酸酯反应得到异噁唑基噻唑甲酰肼类目标化合物共14个(ITH 1～14)。活体生物活性测试表明,酰肼脲类化合物活性普遍优于比酰肼酰基类。该骨架部分化合物对油菜和稗草的除草活性表现出一定的选择性。该两类化合物溶解性都较差,需要进一步优化其结构来提高这类化合物的生物利用度。
4、利用1,3-偶极环加成和Hansztch噻唑合成法得到异噁唑基噻唑基哌啶衍生物,与酰氯、异氰酸酯或异硫氰酸酯反应,得到两类合计43个异噁唑基噻唑基哌啶基碳酰胺或硫代碳酰胺目标化合物(ITP 1～43)。第二类化合物为刚性结构的异噁唑并环己烷并噻唑的哌啶碳酰胺化合物。活体生物活性测试表明,第二类目标化合物的除草活性有普遍的提高。综合比较两类化合物的生物活性与结构的关系,可知在异噁唑苯环上有取代基时,苯环2,4位是比较重要的取代基引入位置,且氟原子的引入能提高化合物活性;在脲端,对氟苯基的引入能够改善化合物活性;异噁唑环及哌啶酰胺的结构可能是比较重要的结构单元。刚性六元环连接异噁唑和噻唑环也在一定程度上提高化合物对油菜的抑制率。
5、利用咪唑啉三酮与胺偶联,亚胺基还原后与相应的酰氯反应得到5-氨基咪唑啉2,4-二酮类化合物共12个(H1～12)。活性测试显示,环上3位甲酰基取代的化合物活性优于苯基取代的化合物活性。环外5位NH上取代基变化对化合物活性有较大影响。咪唑啉-2,4-二酮环上3位和环外5位NH可能是重要的衍生位置。
6、在实验室前期生物提纯天然菠菜D1蛋白酶和重组菠菜D1蛋白酶的工作基础上,利用HPLC技术,测定异噁唑噻唑哌啶类化合物ITP 16,ITP 21,ITP 22,ITP 26,ITP 29,ITP 42,ITP43对D1蛋白酶水解24肽的抑制作用,其中ITP21对D1蛋白酶的抑制常数K_i值为1.3μM,属竞争性抑制。利用表面等离子共振(SPR)技术测定了化合物ITP21与D1蛋白酶的抑制作用。数据显示,在0.1 mM浓度下,化合物对酶的抑制率为47%。经过两种离体活性方法的测定,初步确定了异噁唑噻唑类化合物的作用靶标为D1蛋白酶。
D1 protease(CtpA),a kind of C-terminal processing protease,widely exists in the chloroplast of green plants.It cleaves 8～16 amino acid residues of the precursor D1 protein(pD1) to form mature D1 protein(mD1),and this process is necessary for assembling the manganese cluster in the oxygen-evolving center of PSⅡ.Because of its necessary for the photosynthetic reaction in plants, low amount,high homology in organisms,D1 protease has been predicted to be an ideal herbicidal target.To meet the need of high-efficient and environment-friendly herbicides in modern agriculture and solve the problem of herbicidal resistance,it will possess great significance for rational design and synthesis of hit compounds targeting D1 protease.
At present there is only one report concerning the D1 protease inhibitors,and there are no commercial inhibitors targeting D1 protease.In our previous work,the homology model of spinach D1 protease was built on the basis of the crystal structure of D1 protease from Scenedesmus obliquus. With the three-dimension structure of this spinach D1 protease model,virtual screening was performed by docking of small molecules from various compound libraries into the active site of the Dlprotease model and subsequent evaluating of the predicted bioactivities with scoring functions. Thus several types of hit compounds were identified.In this thesis,four series of compounds were rationally designed on the basis of the hit compounds for chemical synthesis,and total 90 compounds were synthesized.The molecular structures of all the target compounds were verified with ~1HNMR and MS,and some were also confirmed with ~(13)CNMR and elemental analysis.With X-ray crystallography,the complex structures of isoxazolythiazolyl piperidine derivatives were determined. The herbicidal activities of the target compounds were tested and showed moderate and good herbicidal efficacies.In order to validate the hit,some compounds were also tested their in vitro inhibition effects against the native or recombinant D1 protease with HPLC and SPR methodologies.
This dissertation may be summarized as followings.
1.This dissertation first made an investigation of the strategy for the structure-based design of pesticide.A systematic review was made on the research of D1 protease as the herbicidal target and progress on the inhibitors targeting D1 protease.The research strategies and plans were proposed for this dissertation.
2.By taking use of the isoxazolecarboxylic acid formed via 1,3-dipolar cycloaddition followed by oxidation and the subsequent amidation withε-lysinylurea units,totally 21 compounds(ILU 1～21) were synthesized.The herbicidal efficacies of these compounds were tested against the growth rates of two model plants rape and barnyard grass.The structure-activity relationship was preliminarily discussed.Among these compounds,when the urea moieties were same,the compound with 2,4-dichloro substituent on the phenyl of isoxazole had better herbicidal activity.While when the isoxazole moieties had the same substituent,the urea moiety containing morpholine possessed better herbicidal efficacies.Changing the substituent of urea moiety will influence the biological activity of compounds to a great extent.
3.Totally 21 compounds(ITH 1～14),namely isoxazolylthiazolecarbohydrazine derivatives, were rational designed and synthesized.The synthesis was accomplished via the subsequent formation of isoxazole ring,thiazole ring,and carbohydrazine.The isoxazole moieties were formed via the condensation of P-diketone ester and hydroxylamine,while the isoxazolylthiazolecarboxylic esters were formed via amidation and thiolation with the Lawesson's reagent and subsequent condensation with 2-chloroacetoacetic ester(Hansztch reaction).The isoxazolylthiazolecarboxylic esters were subjected to react with hydrazines followed by acylation or aminocarbohydrazine,and finally the isoxazolylthiazolecarbohydrazine derivatives were obtained.Biological test showed that the title compounds with urea moieties possessed better activities.Some compounds show good biological selectivity.However,since the water solubilities of these compounds were relatively low and the redesign is necessary for these compounds to improve their bioavailability.
4.With the use of 1,3-dipolar cycloaddition and Hansztch reaction as like as the procedures mentioned above,the 4-isoxazolylthiazolylpiperidines as intermediates were obtained.The piperidine moieties in these intermediates were subjected to react with acyl chlorides,isocyantes or isothiocyanate to afford two classes of target compounds,totally 43 compounds(ITP 1～43).The second class of compounds possesses an isoxazolocyclohexanothiazole rigid moiety,which was expected to endow these compounds with higher bioactivities,and the bioassays demonstrated this expectation.The structure-activity relationship shows that the ortho- and para- position of phenyl on the isoxazole ring are important and the fluorine atom located at the ortho-position will promote the bioactivity of compounds;The p-F phenyl possessing the urea motiey alsohas the same effect.The isoxazole and piperidine moieties should be important units of the compounds,and the rigid cyclohexanyl connecting the isoxazole and thiazole will increase the compounds inhibiting efficiency to the growth of rape.
5.A series of 5-aminoimidazoline-2,4-dione derivatives were rationally designed and synthesized. The synthesis was accomplished via the coupling of triones with amine,followed by reduction of the imine group and acylations with acyl chlorides.Thus totally twelve 5-aminoimidazoline-dione derivatives(H1～12) were obtained.The hydantoin with N-acyl aryl group had the better biological activities than N-aryl substituented compounds.The substitutents of 5-NH will influence the herbicidal activities of compounds.In order to get higher bioactivity of compounds the 3th position of the ring and the 5-NH will be important positions to vary different substituents.
6.On the basis of our previous work for the isolation,purification and expression of spinach D1 protease,the isoxazolylthiazolyl piperidine carboxamides,ITP 16,ITP 21,ITP 22,ITP 26,ITP 29, ITP 42,ITP 43,were measured their in vitro inhibition efficacies against D1 protease by the HPLC method.One of these compounds,ITP 21,was demonstrated to possess an inhibitor constant(K_i) 1.3μM.The result showed the compound possessed effective inhibition to CtpA with a competitive inhibition.On the other hand,the inhibiting efficacy ratio of the compound ITP 21 was tested with the competitive strategy by surface plasmon resonance technology,and it was shown that this compound possessed an in vitro inhibition efficacy 47%at the concentration of 0.1 mM.All the results from the in vivo and in vitro tests show that the compounds containing isoxazolylthiazolyl piperidine carboxamides may be the potential compounds targeting D1 protease directly.
引文
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