Ennifar Eric, Paillart Jean-Christophe, Bodlenner Anne, Walter Philippe, Weibel Jean-Marc, Aubertin Anne-Marie, Pale Patrick, Dumas Philippe, Marquet Roland
UPR 9002 du CNRS conventionnée à l'Université Louis Pasteur, IBMC 15 rue René Descartes, 67084, Strasbourg cedex, France.
Nucleic Acids Res. 2006 May 5;34(8):2328-39. doi: 10.1093/nar/gkl317. Print 2006.
The kissing-loop complex that initiates dimerization of genomic RNA is crucial for Human Immunodeficiency Virus Type 1 (HIV-1) replication. We showed that owing to its strong similitude with the bacterial ribosomal A site it can be targeted by aminoglycosides. Here, we present its crystal structure in complex with neamine, ribostamycin, neomycin and lividomycin. These structures explain the specificity for 4,5-disubstituted 2-deoxystreptamine (DOS) derivatives and for subtype A and subtype F kissing-loop complexes, and provide a strong basis for rational drug design. As a consequence of the different topologies of the kissing-loop complex and the A site, these aminoglycosides establish more contacts with HIV-1 RNA than with 16S RNA. Together with biochemical experiments, they showed that while rings I, II and III confer binding specificity, rings IV and V are important for affinity. Binding of neomycin, paromomycin and lividomycin strongly stabilized the kissing-loop complex by bridging the two HIV-1 RNA molecules. Furthermore, in situ footprinting showed that the dimerization initiation site (DIS) of HIV-1 genomic RNA could be targeted by these aminoglycosides in infected cells and virions, demonstrating its accessibility.
引发基因组RNA二聚化的吻式环复合物对于1型人类免疫缺陷病毒（HIV-1）的复制至关重要。我们发现，由于其与细菌核糖体A位点高度相似，它可被氨基糖苷类药物靶向。在此，我们展示了其与新霉素、核糖霉素、新霉素和青紫霉素形成复合物的晶体结构。这些结构解释了对4,5-二取代2-脱氧链霉胺（DOS）衍生物以及A亚型和F亚型吻式环复合物的特异性，并为合理药物设计提供了坚实基础。由于吻式环复合物和A位点的拓扑结构不同，这些氨基糖苷类药物与HIV-1 RNA形成的接触比与16S RNA更多。结合生化实验，结果表明虽然I、II和III环赋予结合特异性，但IV和V环对亲和力很重要。新霉素、巴龙霉素和青紫霉素的结合通过桥接两个HIV-1 RNA分子，强烈稳定了吻式环复合物。此外，原位足迹实验表明，HIV-1基因组RNA的二聚化起始位点（DIS）在受感染细胞和病毒颗粒中可被这些氨基糖苷类药物靶向，证明了其可及性。
