NMR and amber analysis of the neamine pharmacophore for the design of novel aminoglycoside antibiotics

Andac C. A. , Stringfellow T. C. , Hornemann U., Noyanalpan N.

BIOORGANIC CHEMISTRY, vol.39, pp.28-41, 2011 (Journal Indexed in SCI) identifier identifier identifier

  • Publication Type: Article / Article
  • Volume: 39
  • Publication Date: 2011
  • Doi Number: 10.1016/j.bioorg.2010.10.002
  • Title of Journal : BIOORGANIC CHEMISTRY
  • Page Numbers: pp.28-41


The dependence of the solution structure of neamine on pH was determined by NMR and AMBER molecular dynamics methods at pD 3.3, pD 6.5, and pD 7.4 in D2O at 25 degrees C. Unlike neamine structures at pD 3.3 and 6.5, which essentially showed only one conformer, slowly exchanging primary, P-state, and secondary, S-state, neamine conformers populated on the NMR time scale at similar to 80% and similar to 20%, respectively, were detected at pD 7.4 with kinetic constants k(on(p -> S)) = 1.9771 s(-1) and k(off(s -> P)) = 1.1319 s(-1). A tertiary, T-state, neamine species populated at similar to 3% was also detected by NMR at pD 7.4. The pKa values determined by NMR titration experiments are pKa 1 6.44 +/- 0.13 for N3 of ring-II, pKa2 7.23 +/- 0.09 for N2' of ring-I, pKa3 7.77 +/- 0.19 for N1 of ring-II, and pKa1 8.08 +/- 0.15 for N6' of ring-I. Ring-I and ring-II of the P-state neamine and ring-I of the S and T-states of neamine possess the C-4(1) chair conformation between pD 3.3 and pD = 7.4. In contrast, ring-II of the S and T-states of neamine most likely adopt the (6)rH(1) half-chair conformation. The P and S-states of neamine exhibit a negative syn-psi glycosidic geometry. The exocyclic aminomethyl group of ring-I adopts the gt exocyclic rotamer conformation around physiological pHs while the gg exocyclic rotamer conformation predominates in acidic solutions near and below pH 4.5. Neamine exists in the P-state as a mixture of tetra-/tri-/di-protonated species between pD 4.5 and pD 7.4, while the S-state neamine exist only in a di-protonated species around physiological pDs. The existence of the S-state neamine may facilitate binding of neamine-like aminoglycosides by favorable entropy of binding to the A-site of 16S ribosomal RNA, suggesting that novel aminoglycoside compounds carrying a S-state neamine pharmacophore can be developed. (C) 2010 Elsevier Inc. All rights reserved.