细胞色素P450适配体的计算机辅助设计
Computer-aided design of aptamers for cytochrome p450.
作者信息
Shcherbinin Dmitrii S, Gnedenko Oksana V, Khmeleva Svetlana A, Usanov Sergey A, Gilep Andrei A, Yantsevich Aliaksei V, Shkel Tatsiana V, Yushkevich Ivan V, Radko Sergey P, Ivanov Alexis S, Veselovsky Alexander V, Archakov Alexander I
机构信息
Institute of Biomedical Chemistry RAMS, Pogodinskaya str., 10, Moscow 119121, Russia.
Institute of Biomedical Chemistry RAMS, Pogodinskaya str., 10, Moscow 119121, Russia.
出版信息
J Struct Biol. 2015 Aug;191(2):112-9. doi: 10.1016/j.jsb.2015.07.003. Epub 2015 Jul 10.
Aptamers are short single-stranded DNA or RNA oligonucleotides that can bind to their targets with high affinity and specificity. Usually, they are experimentally selected using the SELEX method. Here, we describe an approach toward the in silico selection of aptamers for proteins. This approach involves three steps: finding a potential binding site, designing the recognition and structural parts of the aptamers and evaluating the experimental affinity. Using this approach, a set of 15-mer aptamers for cytochrome P450 51A1 was designed using docking and molecular dynamics simulation. An experimental evaluation of the synthesized aptamers using SPR biosensor showed that these aptamers interact with cytochrome P450 51A1 with Kd values in the range of 10(-6)-10(-7) M.
适体是短的单链DNA或RNA寡核苷酸，能够以高亲和力和特异性结合其靶标。通常，它们是通过SELEX方法进行实验筛选的。在此，我们描述了一种用于蛋白质适体计算机辅助筛选的方法。该方法包括三个步骤：找到潜在的结合位点、设计适体的识别和结构部分以及评估实验亲和力。利用这种方法，通过对接和分子动力学模拟设计了一组针对细胞色素P450 51A1的15聚体适体。使用SPR生物传感器对合成的适体进行实验评估表明，这些适体与细胞色素P450 51A1相互作用，解离常数（Kd）值在10^(-6)-10^(-7) M范围内。
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