人类核糖核苷酸还原酶的模拟分子对接
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摘要
核糖核苷酸还原酶(RR)是人类体内唯一的催化4种核糖核苷酸还原、生成相应的脱氧核糖核苷酸的酶。研究表明,人体小亚基R2能促进各种致癌基因的转变,提高癌细胞的入侵能力。因此通过,研究R2抑制剂,抑制肿瘤细胞的生成和转移,已成为治愈人类癌肿的靶点研究之一,越来越受到关注。本文从结构生物信息学的角度研究人体中RR的小亚基R2蛋白质。首先,我们应用metaPocket2.0找出R2表面上可能的小分子作用位点,应用AutoDock Vina蛋白质与小分子对接软件对ZINC、DrugBank和PDB数据库中大规模的小分子进行了虚拟筛选,筛选出9个可用于实验验证的小分子化合物。我们筛选出一个新的R2抑制剂,格列喹酮,它与2个活性位点的结合亲和力值最好,为下一步实验验证提供依据。接着,我们应用ZDOCK蛋白质-蛋白质对接软件进行R1和R2模拟对接,并利用metaPPI预测出R1和R2上的蛋白质结合位点,构造出4种RR全酶模型。最后,通过从结构和序列上比较人类R2与大肠杆菌的R2,以及通过KFC、FlodX、HOTPOINT和HotSpot Wizard4种软件预测,得到了R2二聚体结合表面上的1对热点氨基酸A_PHE101-D_PHE101,它们在氨基酸序列上和空间结构上都是完全对称的。本文的结果可为后续实验筛选作用于R2的小分子药物及研究R2二聚体形成机制提供可靠的理论依据,具有一定的参考意义。
Ribonucleotide Reductase (RR) is the unique enzyme responsible for the conversion of ribonucleotides to2'-deoxyribonucleotides in human. Study have shown that small subunit R2can promote the transformation of various oncogenes and enhance the invasion ability of cancer cells. Therefore, the study of R2inhibitor, to inhibit the generation and transfer oftumor cells, has become one of the target for research to cure human cancer, and got more and more attention.In this article, we mainly focus the small submit R2of RR in Homo Sapiens by computational structural bioinformatics approaches. First, we applied metaPocket to identify potential ligand binding pockets on R2submit surface. Then we used AutoDock Vina to screen a large number of compounds from ZINC、DrugBank and PDB database that might bind to those pockets. Nine small molecules were screened out, which can be further validated experimentally to inhibit R2. The new R2inhibitor(gliquidone) with the best binding affinity values of the two active sites of R2provided the basis for further experimental verification. Secondly, we applied ZDOCK to build up the complex structure of RR from R1and R2. The protein binding sites of R1and R2were prediction by metaPPI.4good models of RR complex structure were obtained in the end. Last, by comparing structure and sequence of R2in Homo sapiens and in E. coli,, and hotspot residues predicted by KFC、FlodX、HOTPOINT and HotSpot Wizard, we got a pair of hotspot residues A_PHE101-D_PHE101in the interface of R2, and they are perfectly symmetrical on theamino acid sequence and spatial structure. The computational results in this work need to be validated by experiments and might provide insights to inhibit R2functions and R2dimerization mechanism.
Ribonucleotide Reductase (RR) is the unique enzyme responsible for the conversion of ribonucleotides to2'-deoxyribonucleotides in human. Study have shown that small subunit R2can promote the transformation of various oncogenes and enhance the invasion ability of cancer cells. Therefore, the study of R2inhibitor, to inhibit the generation and transfer oftumor cells, has become one of the target for research to cure human cancer, and got more and more attention.In this article, we mainly focus the small submit R2of RR in Homo Sapiens by computational structural bioinformatics approaches. First, we applied metaPocket to identify potential ligand binding pockets on R2submit surface. Then we used AutoDock Vina to screen a large number of compounds from ZINC、DrugBank and PDB database that might bind to those pockets. Nine small molecules were screened out, which can be further validated experimentally to inhibit R2. The new R2inhibitor(gliquidone) with the best binding affinity values of the two active sites of R2provided the basis for further experimental verification. Secondly, we applied ZDOCK to build up the complex structure of RR from R1and R2. The protein binding sites of R1and R2were prediction by metaPPI.4good models of RR complex structure were obtained in the end. Last, by comparing structure and sequence of R2in Homo sapiens and in E. coli,, and hotspot residues predicted by KFC、FlodX、HOTPOINT and HotSpot Wizard, we got a pair of hotspot residues A_PHE101-D_PHE101in the interface of R2, and they are perfectly symmetrical on theamino acid sequence and spatial structure. The computational results in this work need to be validated by experiments and might provide insights to inhibit R2functions and R2dimerization mechanism.
引文
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