Targeting the dimerization initiation site of HIV-1 RNA with aminoglycosides: from crystal to cell

• Published in: Nucleic acids research 2006-01, Vol.34 (8), p.2328-2339
• Main Authors: Ennifar, Eric, Paillart, Jean-Christophe, Bodlenner, Anne, Walter, Philippe, Weibel, Jean-Marc, Aubertin, Anne-Marie, Pale, Patrick, Dumas, Philippe, Marquet, Roland
• Format: Article
• Language: English
• Subjects: Aminoglycosides - chemistry; Anti-HIV Agents - chemistry; Binding Sites; Biochemistry, Molecular Biology; Cell Line; Crystallography, X-Ray; Dimerization; Drug Delivery Systems; HIV-1 - genetics; Humans; Life Sciences; Models, Molecular; RNA, Viral - chemistry; Virion - chemistry
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkl317

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.