酮脂酰合成酶FabH抑制剂设计及作用机制研究

发布时间：2018-03-16 20:28

本文选题：FabH　切入点：4VM　出处：《天津理工大学》2017年硕士论文　论文类型：学位论文

【摘要】：首先,本文分别应用分子动力学模拟实验及MM-PBSA方法研究了ecFabH单体及4VM类衍生物存在时复合物体系的RMSD、Rg、RMSF、蛋白二级结构、关键残基质心距及相对结合自由能随模拟时间变化规律。其次,从ChemDiv库中筛选FabH抑制剂,借助FAF-DRUGS3进行ADME/T预测,采用多种分子对接软件进行结合能评价,筛选得到35个具有潜在成药性且结合能较低的分子,以此总结出FabH抑制剂应有的结构特性。最后,基于本组历年来合成的数百个有抗菌生物活性的化合物与FabH进行分子对接筛选,选取结合能较低且结构合适的化合物,基于此新设计一系列新型FabH抑制剂并进行对接筛选,经过进一步改造得到目标化合物125,并分别选取化合物A6、95、125进行分子动力学模拟实验,研究其微观作用机制。分子动力学研究表明:无抑制剂存在时,FabH单体体系稳定性较差,活性口袋残基波动较大,FabH活性口袋处α螺旋有轻微向外扩张趋势,以便为了底物或配体更好的进入。当抑制剂4VK、4LB、4VL或4VM存在时,均可使FabH活性口袋入口处α螺旋收紧,从而阻挡底物乙酰-CoA的进入,尤其是4VM既可与活性位点残基形成氢键结合等相互作用,又能很好地占据本该属于底物乙酰-CoA的位置,这种“雀占鸠巢”的稳定结合作用,决定了其可作为一个高效的FabH抑制剂。虚拟筛选得到的化合物在结构上有如下特征:抑制剂在活性位点附近的部分,含有氢键供体或受体部分,能与FabH酶的活性位点催化三联体Cys112-His244-Asn274形成氢键作用,相当于产生一个“锚”结构,将其牢牢固定在催化三联体附近,抑制剂的其余部分沿着细长的活性口袋向外延伸,并可与附近残基作用,抑制剂末端部分最好也含有氢键供体或受体,以便能和通道入口处富含Arg的区域结合,从而产生更加紧密的结合,牢牢占据活性通道而阻止酶底物乙酰-CoA的进入,达到抑制效果。新设计得到的FabH抑制剂125与ecFabH有很高的亲和性,分子动力学模拟实验证实,发现FabH活性口袋处残基Trp32、Ile33、Arg36、Thr37、Ile155、Ile157、Met207、Asn210、Val212、Phe213、Asn247、Phe304在抑制剂结合中有重要作用,化合物125可很好的与上述残基形成相互作用,可基于此利用模板定位法、原子生长法及分子碎片法等全新药物设计方法,设计出新型FabH抑制剂。
[Abstract]:Firstly, molecular dynamics simulation and MM-PBSA method were used to study the secondary structure of RMSDX RMSF, protein in the complex system of ecFabH monomer and 4VM derivative. The centroid distance of the key residues and the relative binding free energy varied with the simulated time. Secondly, the FabH inhibitors were screened from the ChemDiv library, the ADME/T was predicted by FAF-DRUGS3, and the binding energy was evaluated by a variety of molecular docking software. 35 molecules with potential drug potential and low binding energy were screened to summarize the structural properties of FabH inhibitors. Based on the molecular docking screening of hundreds of antimicrobial bioactive compounds with FabH over the years, a series of novel FabH inhibitors were designed and screened based on the selection of compounds with low binding energy and suitable structure. After further modification, the target compound 125 was obtained, and the molecular dynamics simulation experiment was carried out on the compound A6O95H125.The molecular dynamics study showed that the stability of the monomers of Fabh was poor when there was no inhibitor. The residue of active pocket fluctuates greatly. The 伪 helix in the active pocket of Fabh has a slight outward expansion trend in order to better enter the substrate or ligand. The 伪 helix at the entrance of the active pocket of FabH can be tightened when the inhibitor 4VKO 4LBN 4VL or 4VM exists. Thus blocking the entry of substrate acetyl-CoA, especially 4VM can not only form hydrogen bond binding with active site residues, but also occupy the position that belongs to substrate acetyl-CoA. It is determined that it can be used as an efficient FabH inhibitor. The compounds obtained by virtual screening have the following structural characteristics: the inhibitor is located near the active site and contains the hydrogen bond donor or receptor part. It can catalyze the hydrogen bond formation of triplet Cys112-His244-Asn274 with the active site of FabH enzyme, which is equivalent to producing an "anchor" structure, which is firmly immobilized near the catalytic triad, and the rest of the inhibitor extends outward along the slender active pocket. And can interact with nearby residues, and the end of the inhibitor preferably also contains a hydrogen bond donor or receptor to bind to a region rich in Arg at the entrance of the channel, resulting in closer binding. The new FabH inhibitor 125 has high affinity to ecFabH, which is confirmed by molecular dynamics simulation. It was found that the residue of Trp32AIle3C3HN Arg36Th r37C Ile155H Met207Asn210AV 212Phe213Asn247Phe304 plays an important role in inhibitor binding. Compound 125 can interact well with the above residues, which can be used to design new drugs, such as template localization method, atomic growth method and molecular fragment method. A new type of FabH inhibitor was designed.
【学位授予单位】：天津理工大学
【学位级别】：硕士
【学位授予年份】：2017
【分类号】：R91

【相似文献】