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Carrimycin inhibits coronavirus replication by decreasing the efficiency of programmed–1 ribosomal frameshifting through directly binding to the rna pseudoknot of viral frameshift-stimulatory element

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Acta Pharmaceutica Sinica B 2024年第6期14卷 2567-2580页

作者： Hongying Li Jianrui Li Jiayu Li Hu Li Xuekai Wang Jing Jiang Lei Lei Han Sun Mei Tang Biao Dong Weiqing He Shuyi Si Bin Hong Yinghong Li Danqing Song Zonggen Peng Yongsheng Che Jian-Dong Jiang CAMS Key Laboratory of Antiviral Drug Research Institute of Medicinal BiotechnologyChinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100050China Beijing Key Laboratory of Antimicrobial Agents Institute of Medicinal BiotechnologyChinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100050China Key Laboratory of Biotechnology of Antibiotics the National Health and Family Planning Commission(NHFPC)Institute of Medicinal BiotechnologyChinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100050China

The pandemic of SARS-CoV-2 worldwide with successive emerging variants urgently calls for small-molecule oral drugs with broad-spectrum antiviral ***,we show that carrimycin,a new macrolide antibiotic in the clinic and an antiviral candidate for SARS-CoV-2 in phase III trials,decreases the efficiency of programmed–1 ribosomal frameshifting of coronaviruses and thus impedes viral replication in a broad-spectrum *** binds directly to the coronaviral frameshift-stimulatory element(FSE)rna pseudoknot,interrupting the viral protein translation switch from ORF1a to ORF1b and thereby reducing the level of the core components of the viral replication and transcription *** carrimycin with known viral replicase inhibitors yielded a synergistic inhibitory effect on *** the FSE mechanism is essential in all coronaviruses,carrimycin could be a new broad-spectrum antiviral drug for human coronaviruses by directly targeting the conserved coronaviral FSE *** finding may open a new direction in antiviral drug discovery for coronavirus variants.

关键词： Carrimycin Coronavirus Broad-spectrum antiviral activity Programmed-1 ribosomal frameshifting rna pseudoknot Antiviral agent rna target Synergistic inhibitory effect

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Molecular Dynamics Simulation of rna pseudoknot Unfolding Pathway

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Wuhan University Journal of Natural Sciences 2013年第2期18卷 133-141页

作者： GUO Yun ZHANG Wenbing School of Physics and Technology Wuhan University

Many biological functions of rna molecules are re- lated to their pseudoknot structures. It is significant for predicting the structure and function of rna that learning about the stability and the process of rna pseudoknot folding and unfolding. The structural features of mouse mammary tumor virus （MMTV） rna pseudoknot in different ion concentration, the unfolding process of the rna pseudoknot, and the two hairpin helices that constitute the rna pseudoknot were studied with all atom molecule dynam- ics simulation method in this paper. We found that the higher cation concentration can cause structure of the rna molecules more stable, and ions played an indispensable role in keeping the structure of rna molecules stable; the unfolding process of hair- pin structure was corresponding to the antiprocess of its folding process. The main pathway of pseudoknot unfolding was that the inner base pair opened first, and then, the two helices, which formed the rna pseudoknot opened decussately, while the folding pathway of the rna pseudoknot was a helix folding after forma- tion of the other helix. Therefore, the unfolding process of rna pseudoknot is different from the antiprocess of its folding process, and the unfolding process of each helix in the rna pseudoknot is similar to the hairpin structure＇s unfolding process, which means that both are the unzipping process.

关键词： rna pseudoknot molecular dynamics simulation stability unfolding pathway

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Tertiary Structure Formation in Simian Retrovirus Type 1 rna pseudoknot Increases Mechanical Stability and-1 Ribosomal Frameshifting Efficiency

Tertiary Structure Formation in Simian Retrovirus Type 1 RNA...

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中国化学会-生物物理化学专业委员会第四届全国生物物理化学会议

作者：钟振声杨丽霞陈刚 Nanyang Technological University

Many rna viruses including Simian Retrovirus type 1(SRV-1) utilize minus-one ribosomal frameshifting as an alternative translation mechanism to generate stable ratios of structural and catalytic proteins. The detailed mechanism of minus-one ribosomal frameshifting is still not well understood. The SRV-1 frameshifting pseudoknot is located in the overlapping region of gag and pol genes and plays critical roles in stimulating frameshifting. We applied single-molecule force spectroscopy and steered molecular dynamics simulation to probe the mechanical stability of the wildtype SRV-1 frameshifting rna pseudoknot and its mutants. In addition, we carried out ensemble thermal denaturation and native polyacrylamide gel electrophoresis studies. Our studies reveal that the minor-groove base triple formation in the pseudoknot enhances the structural compactness and mechanical stability. The-1 frameshifting efficiency is positively correlated with one-step unfolding rupture force and inversely correlated with the unfolding rate, consistent with the fact that ribosome is a force-generating molecular motor with helicase activity.

关键词： rna pseudoknot Ribosomal frameshifting Optical tweezers

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Tertiary Structure Formation in SRV-1 rna pseudoknot Increases Mechanical Stability and-1 Ribosomal Frameshifting Efficiency

Tertiary Structure Formation in SRV-1 RNA Pseudoknot Increas...

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中国化学会-生物物理化学专业委员会第四届全国生物物理化学会议

作者：钟振声杨丽霞陈刚 Nanyang Technological University

关键词： rna pseudoknot ribosomal frameshifting optical tweezers

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