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Volume 37 Issue 4
July  2022
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Meng-Xin Chen, Xiao-Dong Zhu, Hao Zhang, Zhen Liu, Yuan-Ning Liu. SMRI: A New Method for siRNA Design for COVID-19 Therapy[J]. Journal of Computer Science and Technology, 2022, 37(4): 991-1002. DOI: 10.1007/s11390-021-0826-x
Citation: Meng-Xin Chen, Xiao-Dong Zhu, Hao Zhang, Zhen Liu, Yuan-Ning Liu. SMRI: A New Method for siRNA Design for COVID-19 Therapy[J]. Journal of Computer Science and Technology, 2022, 37(4): 991-1002. DOI: 10.1007/s11390-021-0826-x
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SMRI: A New Method for siRNA Design for COVID-19 Therapy

  • 1College of Software, Jilin University, Changchun 130012, China
    2Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education, Jilin University, Changchun 130012, China
    3College of Computer Science and Technology, Jilin University, Changchun 130012, China
    4Graduate School of Engineering, Nagasaki Institute of Applied Science, Nagasaki 851-0193, Japan

Funds: The work was supported by Jilin Provincial Key Laboratory of New Biometrics Technology, the National Natural Science Foundation of China under Grant No. 61471181, and the Jilin Province Industrial Innovation Special Fund Project of China under Grant Nos. 2019C053-2 and 2019C053-6.
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  • Author Bio:

    Yuan-Ning Liu received his B.S. degree, M.S. degree in computer application and Ph.D. degree in communication information system from Jilin University, Changchun. He is currently a professor of computer science of Jilin University, Changchun. His current research interests are software engineering, RNA interference, pattern recognition, and bioinformatics.

  • Corresponding author:

    Yuan-Ning Liu E-mail: liuyn@jlu.edu.cn

  • Received Date: July 22, 2020
  • Revised Date: August 23, 2021
  • Accepted Date: August 30, 2021
  • Published Date: July 24, 2022
    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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