肽脱甲酰化酶及其抑制剂的理论研究以及重—轻—重反应体系的共振研究
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摘要
本论文包括两部分工作。第一部分:用分子对接和分子动力学模拟方法研究肽脱甲酰化酶(Peptide deformylase,PDF)及其抑制剂的相互作用和性质;第二部分:用量子化学方法构建三原子及多原子体系的偏分势能面并研究散射共振态的形成机理,分述如下:
第一部分
抗感染药物在临床上的广泛使用导致耐药菌大量增生和蔓延,日益严重的细菌耐药性成为人类面临的严峻挑战之一,这就使新结构和新作用机制抗生素的开发成为非常迫切的问题。肽脱甲酰化酶(Peptide deformylase,PDF)是细菌生长过程中蛋白质合成所必需的一种酶,但在真核细胞蛋白质合成中并不需要,因此PDF成为抗菌药物潜在的作用靶点。
PDF抑制剂类抗生素是20世纪90年代末在国外新兴起的一个研究热点,因为PDF作为抑菌靶点的生化过程很明确,其晶体结构和活性部位也已经比较清楚。基因组分析表明PDF基因具有广泛的同源性,这使得PDF抑制剂类抗生素有可能成为一种广谱抗菌药物。目前British Biotech和Genesoft的BB-83698,Vicuron的VRC4887已进入临床研究,它们对革兰氏阳性菌和革兰氏阴性菌都有显著的抑制活性。所以PDF抑制剂的研究开发利用成为一个新兴的抗生素研究领域。
本论文从PDF晶体结构出发,采用对接和分子动力学模拟方法,研究了抑制剂与PDF之间的结合模式,探讨了结构与活性之间的关系。另外我们还考察了抑制剂的结合自由能,通过与抑制剂测定活性的比较,证明了分子动力学模拟的结果具有较高的参考价值。主要内容摘要如下:
第一章(绪论)。第一部分简要叙述了PDF及其抑制剂的研究现状。主要涉及到寻找新型抗菌药物的意义,PDF的发现史,PDF在细菌中的功能,PDF晶体结构和分类,PDF抑制剂类型和构效关系,临床药物的进展以及计算机辅助药物设计的概况。第二部分简要介绍了散射共振态研究的历史背景,共振态的分类,以及散射共振态的实验研究和理论研究的现状、最新动态及发展前景。
第二章,用对接的方法研究了异羟肟酸类衍生物与大肠杆菌PDF的结合模式和构效关系。抑制剂包括脯氨酸-3-烷基琥珀酰异羟肟酸类衍生物,N-烷基脲异羟肟酸类衍生物等四类异羟肟酸类衍生物。首先将所有的抑制剂与PDF进行对接,然后选取18个抑制剂建立起打分函数与IC_(50)的线性方程,并用该方程预测剩余5个抑制剂的抑制活性。通过比较结合模式,分析了它们的结构与活性关系。
第三章,用对接方法研究了不同类型的抑制剂与大肠杆菌PDF的结合模式和构效关系。抑制剂包括异羟肟酸类衍生物和N-甲酰羟胺类衍生物等四类PDF抑制剂。对接的结果显示,抑制剂复合物结合自由能的估算值与实验值具有很好的线性相关性。通过分析结合模式,发现一些新的结合口袋可用于抑制剂的设计。
第四章,用对接和分子动力学模拟方法研究了大环抑制剂与大肠杆菌PDF的结合模式。具有大环结构的模拟肽类抑制剂对革兰氏阳性菌和革兰氏阴性菌均表现出潜在的抑制作用。重点分析了环的大小对抑制剂的结合模式及结合自由能的影响,各复合物结合自由能的计算值接近于其实验值。
第五章,用对接和分子动力学模拟方法研究了BB-83698与嗜热脂肪芽孢杆菌PDF的结合模式。BB-83698是第一个进入临床测试的PDF抑制剂,而嗜热脂肪芽孢杆菌PDF被认为是最具有代表性的Ⅱ型PDF,因此讨论BB-83698与嗜热脂肪芽孢杆菌PDF之间的结合模式对于新型抑制剂的设计有着重要的意义。首先将BB-83698与PDF进行对接得到三种主要的结合模式,再用分子动力学模拟和结合自由能计算判断出最有利的结合模式,并与晶体结构进行比较。
第六章,用对接和分子动力学模拟方法研究了巯基肽类抑制剂与大肠杆菌PDF的结合模式。巯基肽立体异构体对革兰氏阳性菌和革兰氏阴性菌均表现出了一定的抑制活性,其中L型抑制剂具有更大的抑菌活性。模拟的结果显示结合自由能的计算值与实验值具有很好的线性相关性,从结合模式和能量两个方面分析了L型抑制剂与D型抑制剂结合能力的区别。
第七章,用对接和靶向动力学模拟方法研究了问号钩体PDF的底物口袋的变化。在放线酰胺素结合的PDF晶体复合物中,酶的底物口袋为半开状态。由于CD-loop环的限制,较小的开口使得抑制剂分子难以进入底物口袋。为了了解抑制剂与口袋结合的过程,我们对游离的以及放线酰胺素结合的PDF晶体复合物分别进行了分子动力学模拟。
第八章,用对接和分子动力学模拟的方法研究了底物、产物与大肠杆菌PDF结合的情况。在PDF参与的催化循环过程中,涉及到底物与PDF的结合以及产物的生成和释放,因此了解该过程中底物、产物与PDF的相互作用机理对于设计新型的PDF抑制剂有着重要的意义。我们对游离酶、底物复合物以及产物复合物的稳定构型进行了比较,分析了底物、产物与酶结合时引起的活性位点残基的变化,并将产物复合物的稳定构型与晶体复合物进行了比较。
第一部分的创新性研究成果表现在以下几个方面:
1.不同类型的异羟肟酸类衍生物其抑菌活性表现出较大差异。模拟结果显示①脯氨酸结构靠近Cys90,并与Pro94的吡咯环产生范德华作用。②N-烷基脲结构使P3′苯环能够与Ile44、Ile86和Leu125产生范德华作用和疏水作用,同时酚羟基还与Arg97形成新的氢键。③在α位引入OH、F等吸电子基,有利于抑制剂F1和F2与Gly45形成氢键。④异噁唑环侧链伸入S1′口袋,使抑制剂不能与Gly89形成氢键,同时也缺少相应的P3′侧链与酶作用。因此,在P2′位置引入脯氨酸结构或在P1′和P2′位置引入N-烷基脲结构或在α位引入吸电子基都有利于与酶的结合。而P3′侧链可以设计成既能形成氢键又具有疏水作用的基团,这将会显著地增强抑制剂的结合能力。
2.不同类型的抑制剂与大肠杆菌PDF进行对接时,发现位于活性位点附近的口袋A、B、C和D可用来容纳抑制剂的侧链。口袋A的残基包括Ile128、Cys129、Gln131、His132。口袋B的残基包括Ile44、Leu72和Cys129。口袋C由Gly43、Ile44、Gly45和Leu46组成。口袋D由Leu46、Cys90、Leu91、Ser92、Pro94、Glu95、Gln96和Leu141组成。在抑制剂3、8与酶的结合模式中,发现了新的结合口袋。该口袋一侧的残基包括Val16、Pro19、Ile57、Val59、Glu64、Arg113、Cys129、Met134、Val138、Lys140、Tyr145。而口袋另一侧的残基包括Glu76、Leu77、Lys80、Gld83、Arg109、Ala110、Phe118和Aso123。研究这些新发现的口袋的作用将有助于设计结合能力更强的抑制剂。
3.详细分析了环的大小对抑制剂结合模式的影响。模拟显示大环侧链都能不同程度地进入S1′口袋并与疏水残基作用。抑制剂1和2中的13和14元环离S1′口袋残基较远,使得抑制剂和口袋残基之间的作用要弱一些。6、7、8的结合模式相似,由于18到20元环不能全部被S1′口袋容纳,导致这三个抑制剂不能与活性位点形成必要的氢键、范德华作用和疏水作用。而抑制剂3、4、5都能很匹配地进入活性位点,一方面15、16、17元环侧链能更紧凑地与疏水残基作用;另一方面,抑制剂分子与Ile44、Gly45和Arg97之间的氢键增强了复合物的稳定性。
4.探讨BB-83698与嗜热脂肪芽孢杆菌PDF的结合模式将有助于更好地设计新型的抑制剂。模拟结果显示,模式2发生了较大的构型变化,抑制剂分子严重地偏离了晶体中配体的位置,不过最负的相对结合自由能暗示模式2可能是一个新的结合模式。模式3的结合模式和相对结合自由能表明该模式不利于抑制剂与酶的结合。模式1显示抑制剂与Ile59和Gly109之间的氢键增强了复合物的稳定性。另外,哌嗪环取代基与Pro57和Ile59之间的范德华作用以及苯并1,3-二氧杂戊烷取代基与Pro57、Ile59和Leu146之间的范德华作用对于抑制剂的结合是非常重要的。若在苯并1,3-二氧杂戊烷取代基上引入一些亲水性的基团则会显著地提高抑制剂的结合能力。
5.研究了巯基肽类立体异构体与大肠杆菌PDF的结合模式。动力学模拟显示,L型抑制剂能与酶产生更多的氢键、范德华作用和疏水作用。在P2′位置,L型抑制剂与Leu91产生范德华作用并与Cys90、Ile93、Glu95和Gln96形成氢键。而在P3′位置,L型抑制剂不仅能与疏水性的Ile44、Val62、Ile86、Leu125和Ile128作用,还能与亲水性的Glu42和Glu87作用。L型抑制剂的P2′和P3′侧链可以被修饰成多功能的基团以便与上述残基作用。尽管巯基肽类抑制剂的活性不如异羟肟酸类和N-甲酰羟胺类衍生物,立体选择性结合情况同样适用于这两类抑制剂。
6.采用对接和靶向动力学模拟方法分析了问号钩体PDF的构型变化。结果显示,Tyr71扮演了调节CD-loop环运动的作用,所得复合物的动力学平均结构接近于晶体结构。在游离酶中,Tyr71和Arg108之间氢键的形成导致了底物口袋的关闭。当放线酰胺素与酶结合时,Tyr71首先与放线酰胺素形成氢键,并在疏水簇的影响下,穿过整个底物口袋与Arg108形成氢键。最后,由于Tyr71离开Arg108导致了CD-loop环远离Arg108并形成半开的底物口袋。Tyr71的作用意味着,新的抑制剂的设计可以根据不同的目的对P3′侧链进行修饰。
7.底物、产物与PDF的动力学模拟结果显示,柔性的CD-loop区域有利于底物的结合和产物的释放。为使底物能顺利地进入活性位点,CD-loop与Glu42和Glu64等残基作用,使活性口袋入口的残基能向CD-loop方向移动,增大了活性口袋。同时,原先松散的疏水残基Ile86、Leu125和Ile128向底物方向靠近。底物脱甲酰化后,Leu91向P2′侧链方向移动,Ile86、Leu125和Ile128等残基与甲硫氨酸侧链形成稳定的疏水作用。Glu133侧链中的两个氧原子与铁一起移动,这对发挥其催化作用是十分重要的。当产物离开底物口袋时,CD-loop及底物口袋周围的残基逐渐远离产物,导致产物与酶之间的氢键、范德华作用和疏水作用逐渐减弱直至消失。这三个不同的模拟过程将有助于在更深层次上理解PDF的催化反应机理。
第二部分
散射共振态的研究一直是化学动力学研究的一个重要的前沿课题。散射共振态是化学反应过程中形成的准束缚态或暂稳态,它控制了化学反应的分支比,产物的能量分布和角分布等重要的特征性质。最近,对于散射共振态的实验研究取得了飞速发展。Neumark等人的光分离光谱研究和Liu等人的交叉分子束研究确凿无疑地证明了散射共振态的存在。然而对于散射共振态的形成机理等方面的理论研究还有很多问题尚未解决。
本论文对若干反应体系的散射共振态做了动力学理论研究,主要内容包括以下几个方面:
第九章,详细介绍了目前研究散射共振态的理论方法。理论研究主要包括势能面的构建和量子反应散射理论对散射共振态的计算。然后介绍了偏分势能面的理论基础和构建方法以及如何利用偏分势能面研究化学反应的散射共振态。
第十章,对H+NO、X+CH_4(X=H,F,Cl,Br)和OH+H_2O等若干反应体系,通过构建偏分势能面详细讨论了散射共振态寿命等重要特性,并将计算结果与文献报道的数据对照分析,对这类体系的分子束散射实验结果给出了较好的理论解释。
这一部分创新性的成果包括:
1.偏分势能面的建立。偏分势能面不同于传统意义上简单的减维势能面。我们所构建的偏分势能面是将垂直于反应坐标的振动模式(采用振动绝热近似)耦合到反应坐标上,结果是在势能中只包含反应坐标,于是可将比较复杂的反应体系得到合理的简化。偏分势能面过渡区域里的动力学势阱可以合理地解释散射共振态的形成机理,同时偏分势能面还提供了共振能数据。所以,偏分势能面是一个研究散射共振态的有利工具。
2.对H+NO→N+OH或O+NH反应体系的散射共振态进行了研究。将各垂直于反应坐标的振动模式(采用振动绝热近似)耦合到反应坐标上,每一条反应路径的两个过渡态区域均出现不对称势阱。正是由于这些势阱俘获了反应体系才形成准束缚态,该共振为Feshbach共振。利用偏分势能面我们估算出该体系的共振寿命为0.85 ps,与韩克利和Schatz的计算结果接近。
3.对重-轻-重X+CH_4→HX+CH_3(X=H,F,Cl,Br)反应体系的散射共振态进行了系统研究,总结出了相关的规律性。该类反应都属于不对称性的态态反应,沿反应路径的势能曲线具有不对称性,这些反应的偏分势能面曲线簇具有一定的相似性。但由于重原子的质量的不同,而使各反应的势能曲线上势阱的深度和宽度相差很大,从而生成的散射共振态的寿命也随着原子质量的增加而增加。其中Cl+CH_4→HCl+CH_3和Br+CH_4→HBr+CH_3两个反应属于共振态寿命较长的反应。
4.对重-轻-重反应体系OH+H_2O→H_2O+OH的散射共振态进行了研究,该反应属于对称性的态态反应,沿反应路径的势能曲线具有对称性。偏分势能面过渡态区域出现动力学势阱,于是可以解释散射共振态的形成,最后我们对该体系的共振态寿命进行了预测。
Two parts are included in this thesis:one part is about the interactions and character of peptide deformylase(PDF)and inhibitor by docking and molecular dynamics simulation(MD),and the other is about the partial potential energy surface (PPES)and formation mechanism of the scattering resonance states of three and polyatomic systems by quantum chemistry methods,and they are described as follows.
Part 1
With the wide-spread use of antibacterial drug,the increase of multi-drug resistant bacterial has been one of the rigorous challenges and created an urgent demand for new antibiotic with novel mechanisms of action and new structures.The absence of deformylase activity in mammal cells,coupled with the observation that the gene encoding PDF(def)is present in all sequenced pathogenic bacterial genomes,has made PDF an attractive target for antibacterial chemotherapy.
PDF and its inhibitor became a hot frontier research topic in the late 90s of 20th Century,for its clear biochemistry process,crystal structure and active site.High homology in gene of PDF makes the PDF inhibitor a class of potential broad-spectrum antibacterial agent.Bb-83698 from British Biotech& Genesoft and VRC-4887 from Vicuron have been under clinic trial and showed attractive effects for Gram-positive and gram-negative bacteria.So the discovery,development and application of PDF inhibitors have became a new active field of antibiotic research.
Based on the crystal structures of PDF,we investigate the binding modes between PDF and inhibitors,structure-activity relationship by docking and molecular dynamics simulation.In addition,for improvement of theoretical design and enhancement of deficiency for docking methods,we review the binding energy of target molecule with MD simulation.Followings are the abstracts of our studies.
Chapter 1 is the preface of the dissertation.In the part 1,we introduce the history development of PDF.We concentrate on the aspects of the function of PDF in bacteria,the structure and type of PDF,type and structure-activity relationship(SAR) of inhibitor,advance of clinical drug and computer-aided drug design.In the part 2, we introduce the history background,the classification,the current experimental and the theoretical research,and the tendency of the development of the scattering resonance states.
In chapter 2,we investigate the binding modes and SAR between different type of hydroxamic acids derivatives and PDF by docking methods.Four types of inhibitors, including proline-3-alkylsuccinyl and N-alkyl urea hydroxamic acids derivatives are investigated.Firstly these inhibitors are docked into PDF,then eighteen inhibitors are selected to build the linear equation between scoring function and IC_(50),finally the inhibitory activities of rest five inhibitors are predicted.By comparison of their binding modes,we can analyze their structure-activity relationships.
In chapter 3,we investigate the binding modes between different types of inhibitors and PDF,and SAR by docking methods.Four types of inhibitors,including hydroxamic acids derivatives and N-formylhydroxylamine derivatives,are investigated.The results show that there is a good linear relationship between AutoDock results and the experimental values.By comparison of their binding modes, some new binding pockets are found,which will be helpful for the design of new inhibitor.
In chapter 4,automated docking and molecular dynamics simulation are applied to investigate the binding of macrocyclic inhibitors to E.coli PDF.These macrocyclic peptidomimetic inhibitors show the potent inhibitory activities against Gram-positive and Gram-negative pathogens.We mainly analyze the effects of cycle size on the binding modes and binding free energy,and the predicted binding free energy approaches its experimental value.
In chapter 5,automated docking and molecular dynamics simulation are applied to investigate the binding of BB-83698 to the B.stea PDF.BB-83698 is a first potent PDF inhibitor to enter clinical trials,and B.Stea PDF is a representative typeⅡPDF, so it will be significant to explore the their binding modes.Firstly BB-83698 is docked into the active site of PDF,and three binding modes are obtained by scoring function.Then molecular dynamics simulation and binding free energy calculation are performed to judge most favorable for inhibitor binding,and the dynamics structure are also compared with that of crystal complex.
In chapter 6,the binding modes of the peptide thiol inhibitors and E.coli PDF are investigated by docking and molecular dynamics simulation.The stereoisomer shows potent antibacterial activities against Gram-positive bacteria and moderate activity against Gram-negative bacteria,in which the L-ligands are more biologically active than D-ligands.We analyze the effects of binding modes and free binding energy on inhibitory activity,AutoDock results are in good agreement with the experimental values,which demonstrates a good linear relationship.
In chapter 7,automated docking and targeted molecular dynamics simulation are applied to investigate the conformational changes of substrate pocket of LiPDF.In the actinonin-bound enzyme complex,the substrate pocket adopts a semi-open conformation.While the opening is not large enough for inhibitor entering,for the CD-loop restricts its access to the substrate pocke.To understand how the actinonin bind with substrate pocket,we perform a MD run separately on ligand-free and actinonin-bound LiPDF.
In chapter 8,automated docking and molecular dynamics simulation are applied to investigate the binding of substrate,product to E.coli PDF.The binding of substrate and the release of product are involved in the catalysis process of PDF,so it is important to understand the interaction mechanism between substrate,product and E. coli PDF,which is in favor of the design of new PDF inhibitor.We compare the stabilized conformations of free,substrate-bound and product-bound enzyme,analyze the conformational changes of residues around avtive site when substrate and product bind with enzyme,and also compare the conformation of product-bound complex with that of crystal complex.
The innovative points in the first part are summarized as follows:
1.The different types of hydroxamic acids derivatives show different inhibitory activities.①The proline group approaches Cys90 and makes van der Waals interacts with pyrrole group of Pro94.②The N-alkyl urea group makes the P3' phenyl group to form the van der Waals and hydrophobic interactions with Ile44,Ile86和Leu125, and phenolic hydroxyl can form the new hydrogen bond with Arg97.③If electron-withdrawing group such as OH or F is linked atαposition,F1 and F2 can form the new hydrogen bond with Gly45.④isoxazole side chain inserts into the Sl'pocket,which results in that the inhibitor can not form the new hydrogen bond with Gly89,and also no corresponding P3' side chain is used to interact with enzyme. So the introduction of electron-withdrawing group atαposition,N-alkyl urea group at P1' and P2' positions,or proline group at P2'position will in favor of the inhibitor binding to enzyme.In addition,the P3' side chain can be modified to make it form the hydrogen bond and hydrophobic interactions,which will improve the inhibitor's binding affinity greatly.
2.When the different types of inhibitors docked into E.coli PDF,there are four pockets(A,B,C and D)near the active site,which can accommodate the side chain of inhibitor.The residues in pocket A are Ile128,Cys129,Gln131 and His132.B is shallow and has less residues including Ile44,Leu72,Cys129.Pocket C is composed of Gly43,Ile44,Gly45和Leu46.D has the most residues such as Leu46,Cys90, Leu91,Ser92,Pro94,Glu95,Gln96 and Leu141.In the binding modes of 3,8 and PDF,new binding pocket are found.The residues on one side of the pocket include Val16,Pro19,Ile57,Val59,Glu64,Arg113,Cys129,Met134,Val138,Lys140,Tyr145. Those on the other side are Glu76,Leu77,Lys80,Gld83,Arg109,Ala110,Phe118 and Aso123.Considering the interactions between pockets and inhibitor will be helpful in designing the inhibitor with high binding affinity.
3.We discuss the effects of cycle size on inhibitory activity in detail.The results show that,a common character is that macrocycle inserts into the S1'pocket and interacts with hydrophobic residues.The 13-and 14-membered maerocycles of 1 and 2 lie away from S1' pocket residues,and their interactions are very weak.6 to 8 have the similar binding mode,their macrocycles can't be completely accommodated by the S1'pocket,and the necessary hydrogen bonds,van der Waals interactions and hydrophobic interactions can't be formed with the active site.While compounds 3 to5 fit nicely into active site.On one hand,compounds their macrocycles of 3 to 5 make more close contacts with the hydrophobic residues.On the other hand,the more hydrogen bonds between inhibitor and Ile44,Gly45 and Arg97 make the complex more stable.
4.Exploring the binding modes between BB-83698 and B.stea PDF will be in favor of the design of new inhibitor.The results show that large conformational changes take place for Mode 2,leading the ligand to deviate from the crystal positions of the complex greatly,while most negative relative binding free energy indicates it may be a new binding mode.The binding mode and binding free energy of Mode 3 show this mode is not favorable for inhibitor's binding to PDF.The average structure of the Mode 1 complex suggests that the fundamental hydrogen bond interactions between inhibitor and Ile59 and Gly109 stabilize the binding of ligand to protein.In addition,the close interactions between piperazine ring and Pro57 and Ile59 and between the benzo-[1,3]-dioxole group and Pro57,Ile59 and Leu146 seem to be very important for the binding of inhibitor to B.Stea PDF.The introduction of hydrophilic group onto the benzo-[1,3]-dioxole ring will probably greatly increase the binding affinity of ligand.
5.The binding modes of thiol stereoisomers are investigated.The results show that the L-ligands have more hydrogen bonds,van der Waals interactions and hydrophobic interactions with E.coli PDF than those of D-ligands.At the P2' position, L-ligands can makes van der Waals interactions with Leu91 and hydrogen bonds with Cys90,Ile93,Glu95 and Gln96.P3' side chain of L-ligand interacts with not only hydrophobic residues Ile44,Va162,Ile86,Leu125 and Ile128 but also with hydrophilic residues Glu42 and Glu87.The above results indicate that the P2' and P3' side chain of L-ligand can be modified into the multifunctional grouPs in favor of interaction with above mentioned residues.Although the peptide thiol inhibitor has weaker inhibitory activity than hydroxamic acids derivatives and N-formylhydroxylamine derivatives,the stereochemistry is also fit for them.
6.This chapter analyzes the conformational changes of LiPDF by docking and targeted MD methods.The results show that Tyr71 plays an important role of mediating the movements of CD-loop.The average structure obtained from the MD simulation approaches its crystal structure.In the free LiPDF,the hydrogen bond between Tyr71 and Arg108 results in the closure of the substrate pocket.In the presence of actinonin,Tyr71 firstly hydrogen-bonds with actinonin,then it goes across the substrate pocket and hydrogen-bonds with Arg108.The re-opening of the substrate pocket occurs with the breaking of the hydrogen bond between Tyr71 and Arg108 and leaving of CD-loop from Arg108.The hydrophilicity of Tyr71 suggests us that new inhibitor can be modified at P3' according to its different purposes.
7.The dynamics simulation of substrate,product and PDF complexes shows that the larger flexibility of CD-loop is helpful for the binding of substrate and release of product.To make the substrate enter into the active site,the CD-loop interacts with Glu42 and Glu64,which forces the residues around the binding pocket to move towards CD-loop,and the pocket becomes larger,at the same time,the loose residues Ile86、Leu125 and Ile128 approach substrate.After the deformyling of substrate, Leu91 moves to P2' side chain,and Ile86,Leu125 and Ile128 form the hydrophobic interactions with the side chain of Methionine.The two oxygen atoms of Glu133 move together with iron,which is necessary for the catalysis of Glu133.When the product leaves the active pocket,CD-loop and the residues around the active pocket begin to leave from product,and the hydrogen bonds,van der Waals interactions and hydrophobic interactions between product and enzyme become weak gradually and disappear finally.These three different simulations will be helpful for further understanding the catalytic mechanism of PDF.
Part 2
The research on the scattering resonance state is always the important frontier work in the chemical dynamics research area.The scattering resonance state is the quasi-bound state or transient steady state formed in chemical reactions,which controls some key properties of the reaction system,i.e.,the ratio of the products,the distribution of the energy and the space of the products.In most recent years,the rapid developments of the experimental research on the scattering resonance states accelerate the theoretical research work consumedly.The most remarkable achievements are the high-resolution threshold photodetachment spectroscopy results of the D M Neumark et al.and the crossed molecular beams experiments performed by Kopin Liu,which prove the opinion about the existence of scattering resonance state.But there are still lots of unsolved problems of the theoretical research on the formation mechanism of scattering resonance states.
The main contents are introduced as follows.
In chapter 9 we introduce the current theoretical methods by which the scattering resonance states are investigated.The theoretical research mainly involves the construction of the potential energy surface and the calculation of the resonance states with the quantum reactive scattering theory.Then the theoretical basis and the construction method of the partial potential energy surface(PPES)are introduced in detail.At last we explain how to investigate the scattering resonance states in the chemical reactions with the PPES.
In chapter 10,by the PPESs of these systems constructed here,we discuss some important characters(like resonance lifetime,etc.)of the scattering resonance states in H+NO、X+CH_4(X=H,F,Cl,Br)and OH+H_2Oreaction systems.And then we compare the results with the data reported in the literature,and give the reasonable explanation for the experimental results about molecular beam of these systems.
The innovative points in these results are summarized as follows:
1.The first point is the construction of the PPES.The PPES is not equal to the traditional simple reduced-dimensional potential energy surface(RD-PES).The PPESs constructed here are the productions of the coupling of the vibrational freedom and the minimum energy reactive pathway,and the potential energy of the system only includes the reactive coordinate s.So the complicated problems of the PESs are reduced reasonably.The dynamics potential well in PPES gives us reasonable explanation of the formation mechanism of the scattering resonance states,and some interrelated data such as resonance energy are obtained by the calculations on the PPESs.Therefore,the PPES should be a useful tool for the research on the scattering resonance states.
2.The scattering resonance states of the H+NO→N+OH or O+NH are investigated.The asymmetrical wells are emerged in the transition state region for every reaction pathway,when coupling of both the translation along the reaction coordinate and vibration(adopting vibrational adiabatic approximation)perpendicular to reaction coordinate is adopted.We see that just the dynamic Eying Lake traps the reaction system and forms quasi-bound state,so this resonance is called Feshbach resonance.Using the PPES,we estimate the lifetime of the complex is 0.85 ps,which approaches Han K.L.and Schatz's computational results.
3.Systemic investigation was done for the scattering resonance states of the HLH systems,X+CH_4→HX+CH_3(X=H,F,Cl,Br),and the rules relevant to these systems were summarized.All these reactions belong to asymmetrical state-to-state reactions with the potential curves which are asymmetric along the reactive coordinate.So the curves in the PPESs of these reactions also have considerable similarity.On the other hand,because of the difference of the mass of the heavy atoms,there is remarkable difference in depth and width of the potential well on the potential curves between these reactions.And the lifetime of the scattering resonance state increases with the increase of the mass of the heavy atoms correspondingly.Among these reactions,the two reactions Cl+CH_4→HCl+CH_3 and Br+CH_4→HBr+CH_3 are the ones with long lifetime resonance states.
4.The investigation is done for the scattering resonance states of OH+H_2O→H_2O+OH LHL reaction system.All reactions belong to symmetrical state-to-state reactions with the potential curves which are symmetric along the reactive coordinate. The potential well can explain the formation mechanism of the scattering resonance state.Finally,the lifetime of the scattering resonance state is estimated.
第一部分
抗感染药物在临床上的广泛使用导致耐药菌大量增生和蔓延,日益严重的细菌耐药性成为人类面临的严峻挑战之一,这就使新结构和新作用机制抗生素的开发成为非常迫切的问题。肽脱甲酰化酶(Peptide deformylase,PDF)是细菌生长过程中蛋白质合成所必需的一种酶,但在真核细胞蛋白质合成中并不需要,因此PDF成为抗菌药物潜在的作用靶点。
PDF抑制剂类抗生素是20世纪90年代末在国外新兴起的一个研究热点,因为PDF作为抑菌靶点的生化过程很明确,其晶体结构和活性部位也已经比较清楚。基因组分析表明PDF基因具有广泛的同源性,这使得PDF抑制剂类抗生素有可能成为一种广谱抗菌药物。目前British Biotech和Genesoft的BB-83698,Vicuron的VRC4887已进入临床研究,它们对革兰氏阳性菌和革兰氏阴性菌都有显著的抑制活性。所以PDF抑制剂的研究开发利用成为一个新兴的抗生素研究领域。
本论文从PDF晶体结构出发,采用对接和分子动力学模拟方法,研究了抑制剂与PDF之间的结合模式,探讨了结构与活性之间的关系。另外我们还考察了抑制剂的结合自由能,通过与抑制剂测定活性的比较,证明了分子动力学模拟的结果具有较高的参考价值。主要内容摘要如下:
第一章(绪论)。第一部分简要叙述了PDF及其抑制剂的研究现状。主要涉及到寻找新型抗菌药物的意义,PDF的发现史,PDF在细菌中的功能,PDF晶体结构和分类,PDF抑制剂类型和构效关系,临床药物的进展以及计算机辅助药物设计的概况。第二部分简要介绍了散射共振态研究的历史背景,共振态的分类,以及散射共振态的实验研究和理论研究的现状、最新动态及发展前景。
第二章,用对接的方法研究了异羟肟酸类衍生物与大肠杆菌PDF的结合模式和构效关系。抑制剂包括脯氨酸-3-烷基琥珀酰异羟肟酸类衍生物,N-烷基脲异羟肟酸类衍生物等四类异羟肟酸类衍生物。首先将所有的抑制剂与PDF进行对接,然后选取18个抑制剂建立起打分函数与IC_(50)的线性方程,并用该方程预测剩余5个抑制剂的抑制活性。通过比较结合模式,分析了它们的结构与活性关系。
第三章,用对接方法研究了不同类型的抑制剂与大肠杆菌PDF的结合模式和构效关系。抑制剂包括异羟肟酸类衍生物和N-甲酰羟胺类衍生物等四类PDF抑制剂。对接的结果显示,抑制剂复合物结合自由能的估算值与实验值具有很好的线性相关性。通过分析结合模式,发现一些新的结合口袋可用于抑制剂的设计。
第四章,用对接和分子动力学模拟方法研究了大环抑制剂与大肠杆菌PDF的结合模式。具有大环结构的模拟肽类抑制剂对革兰氏阳性菌和革兰氏阴性菌均表现出潜在的抑制作用。重点分析了环的大小对抑制剂的结合模式及结合自由能的影响,各复合物结合自由能的计算值接近于其实验值。
第五章,用对接和分子动力学模拟方法研究了BB-83698与嗜热脂肪芽孢杆菌PDF的结合模式。BB-83698是第一个进入临床测试的PDF抑制剂,而嗜热脂肪芽孢杆菌PDF被认为是最具有代表性的Ⅱ型PDF,因此讨论BB-83698与嗜热脂肪芽孢杆菌PDF之间的结合模式对于新型抑制剂的设计有着重要的意义。首先将BB-83698与PDF进行对接得到三种主要的结合模式,再用分子动力学模拟和结合自由能计算判断出最有利的结合模式,并与晶体结构进行比较。
第六章,用对接和分子动力学模拟方法研究了巯基肽类抑制剂与大肠杆菌PDF的结合模式。巯基肽立体异构体对革兰氏阳性菌和革兰氏阴性菌均表现出了一定的抑制活性,其中L型抑制剂具有更大的抑菌活性。模拟的结果显示结合自由能的计算值与实验值具有很好的线性相关性,从结合模式和能量两个方面分析了L型抑制剂与D型抑制剂结合能力的区别。
第七章,用对接和靶向动力学模拟方法研究了问号钩体PDF的底物口袋的变化。在放线酰胺素结合的PDF晶体复合物中,酶的底物口袋为半开状态。由于CD-loop环的限制,较小的开口使得抑制剂分子难以进入底物口袋。为了了解抑制剂与口袋结合的过程,我们对游离的以及放线酰胺素结合的PDF晶体复合物分别进行了分子动力学模拟。
第八章,用对接和分子动力学模拟的方法研究了底物、产物与大肠杆菌PDF结合的情况。在PDF参与的催化循环过程中,涉及到底物与PDF的结合以及产物的生成和释放,因此了解该过程中底物、产物与PDF的相互作用机理对于设计新型的PDF抑制剂有着重要的意义。我们对游离酶、底物复合物以及产物复合物的稳定构型进行了比较,分析了底物、产物与酶结合时引起的活性位点残基的变化,并将产物复合物的稳定构型与晶体复合物进行了比较。
第一部分的创新性研究成果表现在以下几个方面:
1.不同类型的异羟肟酸类衍生物其抑菌活性表现出较大差异。模拟结果显示①脯氨酸结构靠近Cys90,并与Pro94的吡咯环产生范德华作用。②N-烷基脲结构使P3′苯环能够与Ile44、Ile86和Leu125产生范德华作用和疏水作用,同时酚羟基还与Arg97形成新的氢键。③在α位引入OH、F等吸电子基,有利于抑制剂F1和F2与Gly45形成氢键。④异噁唑环侧链伸入S1′口袋,使抑制剂不能与Gly89形成氢键,同时也缺少相应的P3′侧链与酶作用。因此,在P2′位置引入脯氨酸结构或在P1′和P2′位置引入N-烷基脲结构或在α位引入吸电子基都有利于与酶的结合。而P3′侧链可以设计成既能形成氢键又具有疏水作用的基团,这将会显著地增强抑制剂的结合能力。
2.不同类型的抑制剂与大肠杆菌PDF进行对接时,发现位于活性位点附近的口袋A、B、C和D可用来容纳抑制剂的侧链。口袋A的残基包括Ile128、Cys129、Gln131、His132。口袋B的残基包括Ile44、Leu72和Cys129。口袋C由Gly43、Ile44、Gly45和Leu46组成。口袋D由Leu46、Cys90、Leu91、Ser92、Pro94、Glu95、Gln96和Leu141组成。在抑制剂3、8与酶的结合模式中,发现了新的结合口袋。该口袋一侧的残基包括Val16、Pro19、Ile57、Val59、Glu64、Arg113、Cys129、Met134、Val138、Lys140、Tyr145。而口袋另一侧的残基包括Glu76、Leu77、Lys80、Gld83、Arg109、Ala110、Phe118和Aso123。研究这些新发现的口袋的作用将有助于设计结合能力更强的抑制剂。
3.详细分析了环的大小对抑制剂结合模式的影响。模拟显示大环侧链都能不同程度地进入S1′口袋并与疏水残基作用。抑制剂1和2中的13和14元环离S1′口袋残基较远,使得抑制剂和口袋残基之间的作用要弱一些。6、7、8的结合模式相似,由于18到20元环不能全部被S1′口袋容纳,导致这三个抑制剂不能与活性位点形成必要的氢键、范德华作用和疏水作用。而抑制剂3、4、5都能很匹配地进入活性位点,一方面15、16、17元环侧链能更紧凑地与疏水残基作用;另一方面,抑制剂分子与Ile44、Gly45和Arg97之间的氢键增强了复合物的稳定性。
4.探讨BB-83698与嗜热脂肪芽孢杆菌PDF的结合模式将有助于更好地设计新型的抑制剂。模拟结果显示,模式2发生了较大的构型变化,抑制剂分子严重地偏离了晶体中配体的位置,不过最负的相对结合自由能暗示模式2可能是一个新的结合模式。模式3的结合模式和相对结合自由能表明该模式不利于抑制剂与酶的结合。模式1显示抑制剂与Ile59和Gly109之间的氢键增强了复合物的稳定性。另外,哌嗪环取代基与Pro57和Ile59之间的范德华作用以及苯并1,3-二氧杂戊烷取代基与Pro57、Ile59和Leu146之间的范德华作用对于抑制剂的结合是非常重要的。若在苯并1,3-二氧杂戊烷取代基上引入一些亲水性的基团则会显著地提高抑制剂的结合能力。
5.研究了巯基肽类立体异构体与大肠杆菌PDF的结合模式。动力学模拟显示,L型抑制剂能与酶产生更多的氢键、范德华作用和疏水作用。在P2′位置,L型抑制剂与Leu91产生范德华作用并与Cys90、Ile93、Glu95和Gln96形成氢键。而在P3′位置,L型抑制剂不仅能与疏水性的Ile44、Val62、Ile86、Leu125和Ile128作用,还能与亲水性的Glu42和Glu87作用。L型抑制剂的P2′和P3′侧链可以被修饰成多功能的基团以便与上述残基作用。尽管巯基肽类抑制剂的活性不如异羟肟酸类和N-甲酰羟胺类衍生物,立体选择性结合情况同样适用于这两类抑制剂。
6.采用对接和靶向动力学模拟方法分析了问号钩体PDF的构型变化。结果显示,Tyr71扮演了调节CD-loop环运动的作用,所得复合物的动力学平均结构接近于晶体结构。在游离酶中,Tyr71和Arg108之间氢键的形成导致了底物口袋的关闭。当放线酰胺素与酶结合时,Tyr71首先与放线酰胺素形成氢键,并在疏水簇的影响下,穿过整个底物口袋与Arg108形成氢键。最后,由于Tyr71离开Arg108导致了CD-loop环远离Arg108并形成半开的底物口袋。Tyr71的作用意味着,新的抑制剂的设计可以根据不同的目的对P3′侧链进行修饰。
7.底物、产物与PDF的动力学模拟结果显示,柔性的CD-loop区域有利于底物的结合和产物的释放。为使底物能顺利地进入活性位点,CD-loop与Glu42和Glu64等残基作用,使活性口袋入口的残基能向CD-loop方向移动,增大了活性口袋。同时,原先松散的疏水残基Ile86、Leu125和Ile128向底物方向靠近。底物脱甲酰化后,Leu91向P2′侧链方向移动,Ile86、Leu125和Ile128等残基与甲硫氨酸侧链形成稳定的疏水作用。Glu133侧链中的两个氧原子与铁一起移动,这对发挥其催化作用是十分重要的。当产物离开底物口袋时,CD-loop及底物口袋周围的残基逐渐远离产物,导致产物与酶之间的氢键、范德华作用和疏水作用逐渐减弱直至消失。这三个不同的模拟过程将有助于在更深层次上理解PDF的催化反应机理。
第二部分
散射共振态的研究一直是化学动力学研究的一个重要的前沿课题。散射共振态是化学反应过程中形成的准束缚态或暂稳态,它控制了化学反应的分支比,产物的能量分布和角分布等重要的特征性质。最近,对于散射共振态的实验研究取得了飞速发展。Neumark等人的光分离光谱研究和Liu等人的交叉分子束研究确凿无疑地证明了散射共振态的存在。然而对于散射共振态的形成机理等方面的理论研究还有很多问题尚未解决。
本论文对若干反应体系的散射共振态做了动力学理论研究,主要内容包括以下几个方面:
第九章,详细介绍了目前研究散射共振态的理论方法。理论研究主要包括势能面的构建和量子反应散射理论对散射共振态的计算。然后介绍了偏分势能面的理论基础和构建方法以及如何利用偏分势能面研究化学反应的散射共振态。
第十章,对H+NO、X+CH_4(X=H,F,Cl,Br)和OH+H_2O等若干反应体系,通过构建偏分势能面详细讨论了散射共振态寿命等重要特性,并将计算结果与文献报道的数据对照分析,对这类体系的分子束散射实验结果给出了较好的理论解释。
这一部分创新性的成果包括:
1.偏分势能面的建立。偏分势能面不同于传统意义上简单的减维势能面。我们所构建的偏分势能面是将垂直于反应坐标的振动模式(采用振动绝热近似)耦合到反应坐标上,结果是在势能中只包含反应坐标,于是可将比较复杂的反应体系得到合理的简化。偏分势能面过渡区域里的动力学势阱可以合理地解释散射共振态的形成机理,同时偏分势能面还提供了共振能数据。所以,偏分势能面是一个研究散射共振态的有利工具。
2.对H+NO→N+OH或O+NH反应体系的散射共振态进行了研究。将各垂直于反应坐标的振动模式(采用振动绝热近似)耦合到反应坐标上,每一条反应路径的两个过渡态区域均出现不对称势阱。正是由于这些势阱俘获了反应体系才形成准束缚态,该共振为Feshbach共振。利用偏分势能面我们估算出该体系的共振寿命为0.85 ps,与韩克利和Schatz的计算结果接近。
3.对重-轻-重X+CH_4→HX+CH_3(X=H,F,Cl,Br)反应体系的散射共振态进行了系统研究,总结出了相关的规律性。该类反应都属于不对称性的态态反应,沿反应路径的势能曲线具有不对称性,这些反应的偏分势能面曲线簇具有一定的相似性。但由于重原子的质量的不同,而使各反应的势能曲线上势阱的深度和宽度相差很大,从而生成的散射共振态的寿命也随着原子质量的增加而增加。其中Cl+CH_4→HCl+CH_3和Br+CH_4→HBr+CH_3两个反应属于共振态寿命较长的反应。
4.对重-轻-重反应体系OH+H_2O→H_2O+OH的散射共振态进行了研究,该反应属于对称性的态态反应,沿反应路径的势能曲线具有对称性。偏分势能面过渡态区域出现动力学势阱,于是可以解释散射共振态的形成,最后我们对该体系的共振态寿命进行了预测。
Two parts are included in this thesis:one part is about the interactions and character of peptide deformylase(PDF)and inhibitor by docking and molecular dynamics simulation(MD),and the other is about the partial potential energy surface (PPES)and formation mechanism of the scattering resonance states of three and polyatomic systems by quantum chemistry methods,and they are described as follows.
Part 1
With the wide-spread use of antibacterial drug,the increase of multi-drug resistant bacterial has been one of the rigorous challenges and created an urgent demand for new antibiotic with novel mechanisms of action and new structures.The absence of deformylase activity in mammal cells,coupled with the observation that the gene encoding PDF(def)is present in all sequenced pathogenic bacterial genomes,has made PDF an attractive target for antibacterial chemotherapy.
PDF and its inhibitor became a hot frontier research topic in the late 90s of 20th Century,for its clear biochemistry process,crystal structure and active site.High homology in gene of PDF makes the PDF inhibitor a class of potential broad-spectrum antibacterial agent.Bb-83698 from British Biotech& Genesoft and VRC-4887 from Vicuron have been under clinic trial and showed attractive effects for Gram-positive and gram-negative bacteria.So the discovery,development and application of PDF inhibitors have became a new active field of antibiotic research.
Based on the crystal structures of PDF,we investigate the binding modes between PDF and inhibitors,structure-activity relationship by docking and molecular dynamics simulation.In addition,for improvement of theoretical design and enhancement of deficiency for docking methods,we review the binding energy of target molecule with MD simulation.Followings are the abstracts of our studies.
Chapter 1 is the preface of the dissertation.In the part 1,we introduce the history development of PDF.We concentrate on the aspects of the function of PDF in bacteria,the structure and type of PDF,type and structure-activity relationship(SAR) of inhibitor,advance of clinical drug and computer-aided drug design.In the part 2, we introduce the history background,the classification,the current experimental and the theoretical research,and the tendency of the development of the scattering resonance states.
In chapter 2,we investigate the binding modes and SAR between different type of hydroxamic acids derivatives and PDF by docking methods.Four types of inhibitors, including proline-3-alkylsuccinyl and N-alkyl urea hydroxamic acids derivatives are investigated.Firstly these inhibitors are docked into PDF,then eighteen inhibitors are selected to build the linear equation between scoring function and IC_(50),finally the inhibitory activities of rest five inhibitors are predicted.By comparison of their binding modes,we can analyze their structure-activity relationships.
In chapter 3,we investigate the binding modes between different types of inhibitors and PDF,and SAR by docking methods.Four types of inhibitors,including hydroxamic acids derivatives and N-formylhydroxylamine derivatives,are investigated.The results show that there is a good linear relationship between AutoDock results and the experimental values.By comparison of their binding modes, some new binding pockets are found,which will be helpful for the design of new inhibitor.
In chapter 4,automated docking and molecular dynamics simulation are applied to investigate the binding of macrocyclic inhibitors to E.coli PDF.These macrocyclic peptidomimetic inhibitors show the potent inhibitory activities against Gram-positive and Gram-negative pathogens.We mainly analyze the effects of cycle size on the binding modes and binding free energy,and the predicted binding free energy approaches its experimental value.
In chapter 5,automated docking and molecular dynamics simulation are applied to investigate the binding of BB-83698 to the B.stea PDF.BB-83698 is a first potent PDF inhibitor to enter clinical trials,and B.Stea PDF is a representative typeⅡPDF, so it will be significant to explore the their binding modes.Firstly BB-83698 is docked into the active site of PDF,and three binding modes are obtained by scoring function.Then molecular dynamics simulation and binding free energy calculation are performed to judge most favorable for inhibitor binding,and the dynamics structure are also compared with that of crystal complex.
In chapter 6,the binding modes of the peptide thiol inhibitors and E.coli PDF are investigated by docking and molecular dynamics simulation.The stereoisomer shows potent antibacterial activities against Gram-positive bacteria and moderate activity against Gram-negative bacteria,in which the L-ligands are more biologically active than D-ligands.We analyze the effects of binding modes and free binding energy on inhibitory activity,AutoDock results are in good agreement with the experimental values,which demonstrates a good linear relationship.
In chapter 7,automated docking and targeted molecular dynamics simulation are applied to investigate the conformational changes of substrate pocket of LiPDF.In the actinonin-bound enzyme complex,the substrate pocket adopts a semi-open conformation.While the opening is not large enough for inhibitor entering,for the CD-loop restricts its access to the substrate pocke.To understand how the actinonin bind with substrate pocket,we perform a MD run separately on ligand-free and actinonin-bound LiPDF.
In chapter 8,automated docking and molecular dynamics simulation are applied to investigate the binding of substrate,product to E.coli PDF.The binding of substrate and the release of product are involved in the catalysis process of PDF,so it is important to understand the interaction mechanism between substrate,product and E. coli PDF,which is in favor of the design of new PDF inhibitor.We compare the stabilized conformations of free,substrate-bound and product-bound enzyme,analyze the conformational changes of residues around avtive site when substrate and product bind with enzyme,and also compare the conformation of product-bound complex with that of crystal complex.
The innovative points in the first part are summarized as follows:
1.The different types of hydroxamic acids derivatives show different inhibitory activities.①The proline group approaches Cys90 and makes van der Waals interacts with pyrrole group of Pro94.②The N-alkyl urea group makes the P3' phenyl group to form the van der Waals and hydrophobic interactions with Ile44,Ile86和Leu125, and phenolic hydroxyl can form the new hydrogen bond with Arg97.③If electron-withdrawing group such as OH or F is linked atαposition,F1 and F2 can form the new hydrogen bond with Gly45.④isoxazole side chain inserts into the Sl'pocket,which results in that the inhibitor can not form the new hydrogen bond with Gly89,and also no corresponding P3' side chain is used to interact with enzyme. So the introduction of electron-withdrawing group atαposition,N-alkyl urea group at P1' and P2' positions,or proline group at P2'position will in favor of the inhibitor binding to enzyme.In addition,the P3' side chain can be modified to make it form the hydrogen bond and hydrophobic interactions,which will improve the inhibitor's binding affinity greatly.
2.When the different types of inhibitors docked into E.coli PDF,there are four pockets(A,B,C and D)near the active site,which can accommodate the side chain of inhibitor.The residues in pocket A are Ile128,Cys129,Gln131 and His132.B is shallow and has less residues including Ile44,Leu72,Cys129.Pocket C is composed of Gly43,Ile44,Gly45和Leu46.D has the most residues such as Leu46,Cys90, Leu91,Ser92,Pro94,Glu95,Gln96 and Leu141.In the binding modes of 3,8 and PDF,new binding pocket are found.The residues on one side of the pocket include Val16,Pro19,Ile57,Val59,Glu64,Arg113,Cys129,Met134,Val138,Lys140,Tyr145. Those on the other side are Glu76,Leu77,Lys80,Gld83,Arg109,Ala110,Phe118 and Aso123.Considering the interactions between pockets and inhibitor will be helpful in designing the inhibitor with high binding affinity.
3.We discuss the effects of cycle size on inhibitory activity in detail.The results show that,a common character is that macrocycle inserts into the S1'pocket and interacts with hydrophobic residues.The 13-and 14-membered maerocycles of 1 and 2 lie away from S1' pocket residues,and their interactions are very weak.6 to 8 have the similar binding mode,their macrocycles can't be completely accommodated by the S1'pocket,and the necessary hydrogen bonds,van der Waals interactions and hydrophobic interactions can't be formed with the active site.While compounds 3 to5 fit nicely into active site.On one hand,compounds their macrocycles of 3 to 5 make more close contacts with the hydrophobic residues.On the other hand,the more hydrogen bonds between inhibitor and Ile44,Gly45 and Arg97 make the complex more stable.
4.Exploring the binding modes between BB-83698 and B.stea PDF will be in favor of the design of new inhibitor.The results show that large conformational changes take place for Mode 2,leading the ligand to deviate from the crystal positions of the complex greatly,while most negative relative binding free energy indicates it may be a new binding mode.The binding mode and binding free energy of Mode 3 show this mode is not favorable for inhibitor's binding to PDF.The average structure of the Mode 1 complex suggests that the fundamental hydrogen bond interactions between inhibitor and Ile59 and Gly109 stabilize the binding of ligand to protein.In addition,the close interactions between piperazine ring and Pro57 and Ile59 and between the benzo-[1,3]-dioxole group and Pro57,Ile59 and Leu146 seem to be very important for the binding of inhibitor to B.Stea PDF.The introduction of hydrophilic group onto the benzo-[1,3]-dioxole ring will probably greatly increase the binding affinity of ligand.
5.The binding modes of thiol stereoisomers are investigated.The results show that the L-ligands have more hydrogen bonds,van der Waals interactions and hydrophobic interactions with E.coli PDF than those of D-ligands.At the P2' position, L-ligands can makes van der Waals interactions with Leu91 and hydrogen bonds with Cys90,Ile93,Glu95 and Gln96.P3' side chain of L-ligand interacts with not only hydrophobic residues Ile44,Va162,Ile86,Leu125 and Ile128 but also with hydrophilic residues Glu42 and Glu87.The above results indicate that the P2' and P3' side chain of L-ligand can be modified into the multifunctional grouPs in favor of interaction with above mentioned residues.Although the peptide thiol inhibitor has weaker inhibitory activity than hydroxamic acids derivatives and N-formylhydroxylamine derivatives,the stereochemistry is also fit for them.
6.This chapter analyzes the conformational changes of LiPDF by docking and targeted MD methods.The results show that Tyr71 plays an important role of mediating the movements of CD-loop.The average structure obtained from the MD simulation approaches its crystal structure.In the free LiPDF,the hydrogen bond between Tyr71 and Arg108 results in the closure of the substrate pocket.In the presence of actinonin,Tyr71 firstly hydrogen-bonds with actinonin,then it goes across the substrate pocket and hydrogen-bonds with Arg108.The re-opening of the substrate pocket occurs with the breaking of the hydrogen bond between Tyr71 and Arg108 and leaving of CD-loop from Arg108.The hydrophilicity of Tyr71 suggests us that new inhibitor can be modified at P3' according to its different purposes.
7.The dynamics simulation of substrate,product and PDF complexes shows that the larger flexibility of CD-loop is helpful for the binding of substrate and release of product.To make the substrate enter into the active site,the CD-loop interacts with Glu42 and Glu64,which forces the residues around the binding pocket to move towards CD-loop,and the pocket becomes larger,at the same time,the loose residues Ile86、Leu125 and Ile128 approach substrate.After the deformyling of substrate, Leu91 moves to P2' side chain,and Ile86,Leu125 and Ile128 form the hydrophobic interactions with the side chain of Methionine.The two oxygen atoms of Glu133 move together with iron,which is necessary for the catalysis of Glu133.When the product leaves the active pocket,CD-loop and the residues around the active pocket begin to leave from product,and the hydrogen bonds,van der Waals interactions and hydrophobic interactions between product and enzyme become weak gradually and disappear finally.These three different simulations will be helpful for further understanding the catalytic mechanism of PDF.
Part 2
The research on the scattering resonance state is always the important frontier work in the chemical dynamics research area.The scattering resonance state is the quasi-bound state or transient steady state formed in chemical reactions,which controls some key properties of the reaction system,i.e.,the ratio of the products,the distribution of the energy and the space of the products.In most recent years,the rapid developments of the experimental research on the scattering resonance states accelerate the theoretical research work consumedly.The most remarkable achievements are the high-resolution threshold photodetachment spectroscopy results of the D M Neumark et al.and the crossed molecular beams experiments performed by Kopin Liu,which prove the opinion about the existence of scattering resonance state.But there are still lots of unsolved problems of the theoretical research on the formation mechanism of scattering resonance states.
The main contents are introduced as follows.
In chapter 9 we introduce the current theoretical methods by which the scattering resonance states are investigated.The theoretical research mainly involves the construction of the potential energy surface and the calculation of the resonance states with the quantum reactive scattering theory.Then the theoretical basis and the construction method of the partial potential energy surface(PPES)are introduced in detail.At last we explain how to investigate the scattering resonance states in the chemical reactions with the PPES.
In chapter 10,by the PPESs of these systems constructed here,we discuss some important characters(like resonance lifetime,etc.)of the scattering resonance states in H+NO、X+CH_4(X=H,F,Cl,Br)and OH+H_2Oreaction systems.And then we compare the results with the data reported in the literature,and give the reasonable explanation for the experimental results about molecular beam of these systems.
The innovative points in these results are summarized as follows:
1.The first point is the construction of the PPES.The PPES is not equal to the traditional simple reduced-dimensional potential energy surface(RD-PES).The PPESs constructed here are the productions of the coupling of the vibrational freedom and the minimum energy reactive pathway,and the potential energy of the system only includes the reactive coordinate s.So the complicated problems of the PESs are reduced reasonably.The dynamics potential well in PPES gives us reasonable explanation of the formation mechanism of the scattering resonance states,and some interrelated data such as resonance energy are obtained by the calculations on the PPESs.Therefore,the PPES should be a useful tool for the research on the scattering resonance states.
2.The scattering resonance states of the H+NO→N+OH or O+NH are investigated.The asymmetrical wells are emerged in the transition state region for every reaction pathway,when coupling of both the translation along the reaction coordinate and vibration(adopting vibrational adiabatic approximation)perpendicular to reaction coordinate is adopted.We see that just the dynamic Eying Lake traps the reaction system and forms quasi-bound state,so this resonance is called Feshbach resonance.Using the PPES,we estimate the lifetime of the complex is 0.85 ps,which approaches Han K.L.and Schatz's computational results.
3.Systemic investigation was done for the scattering resonance states of the HLH systems,X+CH_4→HX+CH_3(X=H,F,Cl,Br),and the rules relevant to these systems were summarized.All these reactions belong to asymmetrical state-to-state reactions with the potential curves which are asymmetric along the reactive coordinate.So the curves in the PPESs of these reactions also have considerable similarity.On the other hand,because of the difference of the mass of the heavy atoms,there is remarkable difference in depth and width of the potential well on the potential curves between these reactions.And the lifetime of the scattering resonance state increases with the increase of the mass of the heavy atoms correspondingly.Among these reactions,the two reactions Cl+CH_4→HCl+CH_3 and Br+CH_4→HBr+CH_3 are the ones with long lifetime resonance states.
4.The investigation is done for the scattering resonance states of OH+H_2O→H_2O+OH LHL reaction system.All reactions belong to symmetrical state-to-state reactions with the potential curves which are symmetric along the reactive coordinate. The potential well can explain the formation mechanism of the scattering resonance state.Finally,the lifetime of the scattering resonance state is estimated.
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