RRM
2008 Rustbelt RNA Meeting
RRM
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Poster abstracts
Abstract:
The clinical usefulness of aminoglycoside antibiotics has become limited due to an increase in antibiotic resistance. Resistance can occur if aminoglycosides become inactivated through enzymatic modification of their hydroxyl and amino groups, which can affect transport or ability of the compounds to bind to the target RNA. Recent approaches to overcome resistance have focused on simplifying the aminoglycosides and generating derivatives of the neamine core or 2-deoxystreptamine ring in order to maintain the minimal motif for binding, but avoid enzymatic modification. In this study, single-ring analogues of neamine were synthesized and ESI-MS was used to determine the binding affinity of the analogues to the decoding region A-site RNA from 16S rRNA (AS RNA). The data indicate that the 6-membered ring 2 moiety of neamine has weak binding to AS RNA, but there is no observed binding between the sugar moiety (ring 1) and AS RNA. In contrast, a synthetic ring 1 derivative shows moderate affinity to AS RNA (apparent Kd = 55 ± 4 µM) and the presence of a longer polyamine group at position N1 increases the binding affinity by 5.5 fold (apparent Kd = 10 ± 1µM). In contrast, blocking the polyamine group at the N1 position diminishes binding by five-fold. These data indicate that hydrogen-bond formation, as well as charge formation at the N1 position, is important for binding to AS RNA. The specificity of the tightest-binding derivative was tested using different RNA constructs (H69, H31, ssAS RNA, AS duplex RNA, and HS RNA). The preliminary data indicate that this neamine single-ring derivative has preferred binding to structured RNA as compared to ssRNA, as well as modest preference for AS RNA.
Keywords: aminoglycoside, antibiotics, ribosome
