Short Interfering RNA Guide Strand Modifiers from Computational Screening

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• 作者：Kazumitsu Onizuka ; Jason G. Harrison ; Alexi A. Ball-Jones ; Jos茅 M. Ibarra-Soza ; Yuxuan Zheng ; Diana Ly ; Walter Lam ; Stephanie Mac ; Dean J. Tantillo ; Peter A. Beal
• 刊名：Journal of the American Chemical Society
• 出版年：2013
• 出版时间：November 13, 2013
• 年：2013
• 卷：135
• 期：45
• 页码：17069-17077
• 全文大小：489K
• 年卷期：v.135,no.45(November 13, 2013)
• ISSN：1520-5126

文摘

Short interfering RNAs (siRNAs) are promising drug candidates for a wide range of targets including those previously considered 鈥渦ndruggable鈥? However, properties associated with the native RNA structure limit drug development, and chemical modifications are necessary. Here we describe the structure-guided discovery of functional modifications for the guide strand 5鈥?end using computational screening with the high-resolution structure of human Ago2, the key nuclease on the RNA interference pathway. Our results indicate the guide strand 5鈥?end nucleotide need not engage in Watson鈥揅rick (W/C) H-bonding but must fit the general shape of the 5鈥?end binding site in MID/PIWI domains of hAgo2 for efficient knockdown. 1,2,3-Triazol-4-yl bases formed from the CuAAC reaction of azides and 1-ethynylribose, which is readily incorporated into RNA via the phosphoramidite, perform well at the guide strand 5鈥?end. In contrast, purine derivatives with modified Hoogsteen faces or N2 substituents are poor choices for 5鈥?end modifications. Finally, we identified a 1,2,3-triazol-4-yl base incapable of W/C H-bonding that performs well at guide strand position 12, where base pairing to target was expected to be important. This work expands the repertoire of functional nucleotide analogues for siRNAs.