Tobramycin-RNA aptamer

Apr 24, 2024 • Linfei Li, Yuhang Luo

Timeline

Description

In 1995, Wang, Y et al. isolated aptamers with high affinity tobramycin binding sites using in vitro selection techniques. Subsequently, Jiang, LPatel et al. elucidated the structure of the aptamer with tobramycin using multidimensional NMR spectroscopy and molecular dynamics calculations^[1,2,3].

SELEX

An RNA diversity library was used to select for sequences capable of binding to the aminoglycoside antibiotic tobramycin.After six cycles of selection, 82 % of the RNA bound to tobramycin specifically. The selected RNA was reverse-transcribed into DNA, which was then cloned. At low selection stringency, an extremely large number of clones, on the order of 107, produced RNAs capable of binding tobramycin with Kds in the PM range (values similar to that observed for the binding of tobramycin to Escherichia coli ribosomes). Sequencing of 18 of the clones revealed no obvious consensus sequence. At higher selection stringencies (Kds in the nM range) only two consensus sequences for binding were observed^[1].
Detailed information are accessible on SELEX page.

Structure

2D representation

Here we use ribodraw to complete the figure, through the 3D structure information.

Tobramycin-RNA aptamer I: 5'-GGCACGAGGUUUAGCUACACUCGUGCC-3'^[2]
Tobramycin-RNA aptamer II: 5'-ACUUGGUUUAGGUAAUGAGU-3'^[3]

3D visualisation

Jiang, L., Suri, A. K., Fiala, R., & Patel, D. J.et al.described a solution-structure determination of the tobramycin-RNA aptamer complex, obtained using NMR and molecular dynamics. The PDB ID of this structure is 1TOB^[2].
Additional available structures that have been solved and detailed information are accessible on Structures page.
Jiang, L., & Patel, D. J. et al. described the structure of the complex was calculated by NMR and the X-PLOR 3.1 programme, and molecular dynamics constraints were performed to demonstrate the solution structure of the complex of the aminoglycoside antibiotic tobramycin in conjunction with stem-loop RNA. The PDB ID of this structure is 2TOB^[3].
Additional available structures that have been solved and detailed information are accessible on Structures page.

Binding pocket

Left: Surface representation of the binding pocket of the aptamer generated from PDB ID: 1TOB by NMR. Tobramycin (shown in sticks) is labeled in yellow. Right: The hydrogen bonds of binding sites of the aptamer bound with tobramycin.


Left: Surface representation of the binding pocket of the aptamer generated from PDB ID: 2TOB by NMR. Tobramycin (shown in sticks) is labeled in yellow. Right: The hydrogen bonds of binding sites of the aptamer bound with tobramycin.

Ligand information

SELEX ligand

Wang, Y., & Rando, R. R et al.used an RNA diversity library to screen for sequences that bind to aminoglycoside antibiotics.After six cycles of screening, 82% of the RNA binds specifically to tobramycin. The screened RNAs were reverse transcribed into DNA and then cloned. Cloning at lower selection stringency yielded RNAs capable of binding tobramycin with Kds in the PM range (values similar to those for tobramycin binding to tobramycin). Sequencing of 18 clones showed no apparent consensus sequence. At higher selection stringency (Kds in the nM range), only two bound consensus sequences were observed^[1].

Structure ligand

Tobramycin is an aminoglycoside antibiotic used to treat cystic fibrosis-associated bacterial, lower respiratory tract, urinary tract, eye, skin, bone, and skin structure infections.-----From Drugbank

PubChem CID	Molecular Formula	MW	CAS	Solubility	Drugbank ID
36294	C18H37N5O9	467.5 g/mol	32986-56-4	53.7 g/L (in water)	DB00684

Similar compound

We screened the compounds with great similarity to tobramycin by using the ZINC database and showed some of the compounds' structure diagrams. For some CAS numbers not available,we will supplement them with Pubchem CID.

Zinc_id	Named	CAS	Pubchem CID	Structure
ZINC8551162	(2R,3S,4R,5S,6S)-4-amino-2-[(1R,2R,3R,4S,6R)-4,6-diamino-3-[(2S,3S,5S,6S)-3-amino-6-(aminomethyl)-5-hydroxyoxan-2-yl]oxy-2-hydroxycyclohexyl]oxy-6-(hydroxymethyl)oxane-3,5-dio	NA	92331686
ZINC8551164	(2R,3S,4R,5S,6S)-4-amino-2-[(1R,2R,3R,4S,6R)-4,6-diamino-3-[(2R,3S,5S,6S)-3-amino-6-(aminomethyl)-5-hydroxyoxan-2-yl]oxy-2-hydroxycyclohexyl]oxy-6-(hydroxymethyl)oxane-3,5-diol	NA	92331688
ZINC8551165	(2R,3S,4R,5S,6S)-4-amino-2-[(1R,2R,3R,4S,6R)-4,6-diamino-3-[(2R,3S,5S,6R)-3-amino-6-(aminomethyl)-5-hydroxyoxan-2-yl]oxy-2-hydroxycyclohexyl]oxy-6-(hydroxymethyl)oxane-3,5-diol	NA	92331689
ZINC8551163	(2R,3S,4R,5S,6S)-4-amino-2-[(1R,2R,3R,4S,6R)-4,6-diamino-3-[(2S,3S,5S,6R)-3-amino-6-(aminomethyl)-5-hydroxyoxan-2-yl]oxy-2-hydroxycyclohexyl]oxy-6-(hydroxymethyl)oxane-3,5-diol	NA	92331687
ZINC8214692	Tobramycin	32986-56-4	36294
ZINC43562055	(2S,3R,4R,5S,6S)-2-(Aminomethyl)-6-[(1R,2R,3S,4R,6S)-4,6-diamino-3-[(2S,3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-2-hydroxycyclohexyl]oxyoxane-3,4,5-triol	NA	11274101
ZINC8214590	Kanamycin	59-01-8	6032
ZINC53132258	Bekanamycin	4696-76-8	439318
ZINC8214383	Dibekacin	34493-98-6	470999

References

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Wang, Y., & Rando, R. R.
Chemistry & biology, 2(5), 281–290. (1995)
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Jiang, L., Suri, A. K., Fiala, R., & Patel, D. J.
SChemistry & biology, 4(1), 35–50. (1997)
[3] Solution structure of the tobramycin-RNA aptamer complex.
Jiang, L., & Patel, D. J.
Nature structural biology, 5(9), 769–774. (1998)
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