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SMRI:用于COVID-19治疗的siRNA设计的新方法

SMRI: A New Method for siRNA Design for COVID-19 Therapy

  • 摘要: 1、研究背景
    SARS-CoV-2病毒是一种高致病性的新型冠状病毒,最早于2019年12月在中国武汉发现。在随后出现的一段时间内,SARS-CoV-2在全球范围内迅速传播,并演变为一场大流行。以小干扰RNA(siRNA)为首的RNA干扰技术是一种靶向特定基因的一种基因沉默技术,可用于有效抵抗多种病毒对宿主的侵染。RNA干扰由小RNA介导,由小干扰RNA (siRNA)和微小RNA (miRNA)组成。
    2、目的
    我们的研究旨在将RNA干扰技术用于SARS-CoV-2病毒导致的新型冠状肺炎COVID-19的治疗,提出一种能将显著提高所设计的siRNA的干扰效率的siRNA设计方法。该方法将有效地从目标基因片段的大量候选siRNA中筛选出高效的siRNA。
    3、方法
    首先,我们建立了一个关于siRNA的沉默效率的有效模型,并通过整合以往基于经验规则提出的siRNA设计方法的研究中定义的各种指标的不同规则提出了一个新指标SED。在此基础上,我们结合多种基于经验规则提出的siRNA设计方法和基于机器学习的siRNA设计方法提出了一种高效的siRNA设计方法SMRI。该方法可以整合不同规则的选择优势,提高高效siRNA的筛选效率。
    4、结果
    根据我们的分析结果,我们所提出的方法的性能与主流的siRNA设计方法相当。此外,该方法已成功用于靶向SARS-CoV-2病毒的siRNA的设计,并获得了5个潜在的预测干扰效率均在90%以上的siRNA。
    5、结论
    本研究提出了一种用于筛选有效siRNA的新指标SED,并提出了一种有效设计siRNA的新方法——SMRI方法。此外,本研究使用生物信息学方法分析SARS-COV-2病毒,并使用SMRI方法成功设计了5个潜在的高效的siRNA。这些siRNA将有助于新冠肺炎的治疗。本研究为之后的将RNA干扰技术用于新冠肺炎的治疗提供了有效的支持。

     

    Abstract: First discovered in Wuhan, China, SARS-CoV-2 is a highly pathogenic novel coronavirus, which rapidly spreads globally and becomes a pandemic with no vaccine and limited distinctive clinical drugs available till March 13th, 2020. Ribonucleic Acid interference (RNAi) technology, a gene-silencing technology that targets mRNA, can cause damage to RNA viruses effectively. Here, we report a new efficient small interfering RNA (siRNA) design method named Simple Multiple Rules Intelligent Method (SMRI) to propose a new solution of the treatment of COVID-19. To be specific, this study proposes a new model named Base Preference and Thermodynamic Characteristic model (BPTC model) indicating the siRNA silencing efficiency and a new index named siRNA Extended Rules index (SER index) based on the BPTC model to screen high-efficiency siRNAs and filter out the siRNAs that are difficult to take effect or synthesize as a part of the SMRI method, which is more robust and efficient than the traditional statistical indicators under the same circumstances. Besides, to silence the spike protein of SARS-CoV-2 to invade cells, this study further puts forward the SMRI method to search candidate high-efficiency siRNAs on SARS-CoV-2's S gene. This study is one of the early studies applying RNAi therapy to the COVID-19 treatment. According to the analysis, the average value of predicted interference efficiency of the candidate siRNAs designed by the SMRI method is comparable to that of the mainstream siRNA design algorithms. Moreover, the SMRI method ensures that the designed siRNAs have more than three base mismatches with human genes, thus avoiding silencing normal human genes. This is not considered by other mainstream methods, thereby the five candidate high-efficiency siRNAs which are easy to take effect or synthesize and much safer for human body are obtained by our SMRI method, which provide a new safer, small dosage and long efficacy solution for the treatment of COVID-19.

     

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