From Proteopedia

Geneticin

Geneticin, also known as gentamicin or G418, belongs to a group of positively charged sugar derivatives known as aminoglycosides. Aminoglycosides contain three rings that possess hydroxyl, ammonium, and methyl groups.^[1] This group of proteins bind to different regions of the 30S particle of the ribosome interfering with protein synthesis. The different regions of the ribosome they bind to depend on their chemical structures. Because geneticin is capable of binding to the 80S ribosome, it is known to be toxic to eukaryotic organisms. However, studies have shown that geneticin can be used in medicine to treat parasites and in the treatment of genetic disorders.

Structure

Aminoglycosides all contain a central 2-deoxystreptamine, or 2-DOS or Ring II, containing an ammonium group on either side of the deoxy carbon and attached to Ring I at position 4. This structure forms ^[2] The neamine moiety forms base pairs with C1407-G1494 and the non-Watson-Crick pair U1406-U1495, of the decoding site RNA. Since these base pairs are conserved in both the prokaryotes and eukaryotes, molecular discrimination of the bacterial target is provided by the sugar substituents occuring at positions 4-, 5-, and 6- of the neamine moiety.^[3]

When geneticin is bound to the eubacterial decoding A site, the complex is comprised of a double helix with 16 Watson-Crick pairs, two UU pairs, two unpaired and four adenine bases.^[1] The neamine moiety binds to two A sites of the RNA and influences the adenine bases 1492 and 1943 of each site to turn away from the helix forming base triples with G-C pairs. In site I and II, 14 hydrogen bonds occur between geneticin and the base atoms and phosphate oxygen atoms of the A site. ^[1] The flipped out adenine bases allow Ring I to intercalate inside the helix and is further stabilized by stacking against G1491. The phosphate groups of the bulged adenine bases are hydrogen bonded to two hydroxyl groups. Also found in the paromycin and tobramycin complexes, intramolecular hydrogen bonds occur between Ring II and the other two rings and ammonium N3 is completely dehydrated. ^[1]

There are a few noted differences in structure of geneticin compared to those of tobramycin and paromycin. These differences are essentially found in Ring III. In geneticin, the exocyclic C'6 is chiral. Also, the additional methyl group at C7' induces a smaller propeller twist angle of the base pairs..^[1]

Function

Geneticin, and other aminoglycosides, inhibit bacterial protein synthesis and are commonly used to treat infections induced by Gram-negative bacteria, such as Escherichia coli. ^[4] They prevent the ability of tRNA to bind to the A site of the bacterial 16S rRNA ribosome by binding to the A site. Aminoglycosides are toxic to mammalian systems, primarily through kidney and ear-associated illnesses.^[1] Geneticin is more toxic to eukaroytic organisms than paromomycin, especially in the absence of an inactivating enzyme or targeted drug.6 Geneticin was discovered to be a weak non-competitive inhibitor of orthnithine decarboxylase found in Trypanosoma brucei, however, the structural analysis of bound ornithine decarboxylase to geneticin has provided a basis into the enzyme's function. ^[5]

Implications

Geneticin has been used in a study for current drug therapy that targets ornithine decarboxylase for treatment of African sleeping sickness. Because of geneticin's distinctive functional groups responsible for point mutations associated with resistance or phylogentic variations, geneticin is a good model to use for understanding its associated toxicity at the ribosomal level.^[1] Also, the conserved U-U pair has revealed an important role and should be considered when developing new antibacterial drugs. ^[1]

References

1. ↑ ^{1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7} Vicens Q, Westhof E. Crystal structure of geneticin bound to a bacterial 16S ribosomal RNA A site oligonucleotide. J Mol Biol. 2003 Feb 28;326(4):1175-88. PMID:12589761
2. ↑ Francois B, Russell RJ, Murray JB, Aboul-ela F, Masquida B, Vicens Q, Westhof E. Crystal structures of complexes between aminoglycosides and decoding A site oligonucleotides: role of the number of rings and positive charges in the specific binding leading to miscoding. Nucleic Acids Res. 2005 Oct 7;33(17):5677-90. Print 2005. PMID:16214802 doi:33/17/5677
3. ↑ Han Q, Zhao Q, Fish S, Simonsen KB, Vourloumis D, Froelich JM, Wall D, Hermann T. Molecular recognition by glycoside pseudo base pairs and triples in an apramycin-RNA complex. Angew Chem Int Ed Engl. 2005 Apr 29;44(18):2694-700. PMID:15849690 doi:10.1002/anie.200500028
4. ↑ Morris JC, Ping-Sheng L, Zhai HX, Shen TY, Mensa-Wilmot K. Phosphatidylinositol phospholipase C is activated allosterically by the aminoglycoside G418. 2-deoxy-2-fluoro-scyllo-inositol-1-O-dodecylphosphonate and its analogs inhibit glycosylphosphatidylinositol phospholipase C. J Biol Chem. 1996 Jun 28;271(26):15468-77. PMID:8663028
5. ↑ Jackson LK, Goldsmith EJ, Phillips MA. X-ray structure determination of Trypanosoma brucei ornithine decarboxylase bound to D-ornithine and to G418: insights into substrate binding and ODC conformational flexibility. J Biol Chem. 2003 Jun 13;278(24):22037-43. Epub 2003 Apr 2. PMID:12672797 doi:10.1074/jbc.M300188200

6 Griffiths, J.K., Balakrishnan, R., Widmer, G., and Tzipori, S. 1998. Paromomycin and Geneticin inhibit intracellular Cryotosporidium parvum without trafficking through the host cell cytoplasm: implications for drug delivery. Infection and Immunity. 66:3874-3883.