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

Multinuclear Nuclear Magnetic Resonance Spectroscopy Is Used to Determine Rapidly and Accurately the Individual pKa Values of 2-Deoxystreptamine, Neamine, Neomycin, Paromomycin, and Streptomycin

“…In acid, it essentially showed only one conformer. 28 The pK a values determined by NMR titration experiments are as follows: pK a 1 = 6.44 ± 0.13 for N-3 of ring-II, pK a 2 = 7.23 ± 0.09 for N-2′ of ring-I, pK a 3 = 7.77 ± 0.19 for N-1 of ring-II, and pK a 4 = 8.08 ± 0.15 for N-6′ of ring-I. 28 In this work, using δ x , we determined the pK a values of neamine to be N-3 = 6.51, N-2′ = 7.11, N-1 = 7.60, and N-6′ = 8.31.…”

“…28 The pK a values determined by NMR titration experiments are as follows: pK a 1 = 6.44 ± 0.13 for N-3 of ring-II, pK a 2 = 7.23 ± 0.09 for N-2′ of ring-I, pK a 3 = 7.77 ± 0.19 for N-1 of ring-II, and pK a 4 = 8.08 ± 0.15 for N-6′ of ring-I. 28 In this work, using δ x , we determined the pK a values of neamine to be N-3 = 6.51, N-2′ = 7.11, N-1 = 7.60, and N-6′ = 8.31. Therefore, neamine exists as a mixture of tetra−/tri−/diprotonated species between pD 4.5 and 7.4, but it really is only a diprotonated species around physiological pDs.…”

“…This may facilitate the binding of neaminelike aminoglycosides by favorable entropy of binding to the Asite of 16S rRNA, suggesting that novel aminoglycoside compounds carrying such a neamine-based pharmacophore can be developed. 28 Such binding complexes are stabilized by the formation of multiple interactions with receptors. The crystal structures of complexes between aminoglycoside antibiotics, e.g., neamine and neomycin B, and oligonucleotides containing the decoding A-site of bacterial ribosomes have been reported at resolutions of 2.2−3.0 Å with up to eight conserved hydrogen bonds in the observed complexes.…”

“…These pK a values are consistent in magnitude and in assignment order with those reported in the literature. 28 3. pK a Values of the Individual Amino Groups of Neomycin. Neomycin is the most basic aminoglycoside with its six primary amino group substituents on two amino sugar rings, D-neosamine and L-neosamine, and the central cyclohexane ring (a 4,5-O-disubstituted 2-deoxystreptamine).…”

A study on the structure, mechanism, and biochemistry of kanamycin B dioxygenase (KanJ)—an enzyme with a broad range of substrates

“…Using a computational model derived from the obtained crystal structures, we tested plausible mechanisms of the decisive reaction steps elicited by the reactive ferryl species. Assuming the C2’‐bound amino group of kanamycin B is positively charged (pKa = 7.23 for neamine [51]), the barrier for OH rebound is much higher than the barrier for deprotonation of amine group and subsequent electron transfer, which leads to protonated imine intermediate product. For the form of the substrate with the key amino group deprotonated (C2’‐NH 2 ), the first step, that is, H atom abstraction, triggers immediate formation of an imine intermediate product.…”