Access Type

Open Access Dissertation

Date of Award

January 2020

Degree Type


Degree Name




First Advisor

David . Crich


The ever-increasing threat posed by multidrug-resistant infectious bacteria necessitates

the development of novel antibiotics. Aminoglycoside antibiotics are growing in interest due to

their broad spectrum of activity, lack of known drug related allergies, low manufacturing cost,

and their well-studied mechanism of action. The simplification of rational drug design due to the

well-studied mechanism of action is the key to overcoming the issues presented by these drugs,

namely ototoxicity and nephrotoxicity.

A study of the effect of the conformation of the aminoglycoside ring I side chain is

described wherein it was discovered that an increase in a particular conformation augments the

antibacterioribosomal and antibacterial activity of paromomycin, as well as decreasing the

toxicity to human ribosomes.

Chapter one introduces the aminoglycoside antibiotics and describes advantages and

disadvantages of their clinical use. Various resistance mechanisms arising from target


modification, altered transport, and aminoglycoside modifying enzymes are discussed as is the

mechanism of bacterial inhibition and how this is related to toxicity in human cells.

Chapter two describes the synthesis of paromomycin and neomycin derivatives alkylated

at C-6’ with both the (R) and (S) configurations as well as NMR spectroscopic studies of the side

chain conformation of these derivatives. These derivatives were subjected to cell free ribosomal

translation assays using M. smegmatis ribosomes with decoding A-sites of the wild type, human

mitochondrial, mutant human mitochondrial, and human cytosolic ribosomes, as well as to

bacterial MIC assays using E. coli and ESKAPE pathogens. The (R) configuration results in a higher

solution state population of the bound conformation resulting in higher activity than the

equivalent modification with the (S) configuration, which reduces the population of the bound

conformation in solution.

Chapter three describes the synthesis of paromomycin derivatives where ring I was fused

to an additional ring by bridging O-4’ and C-6’, such that the conformation of the C5-C6 bond is

locked. Conformational analysis by NMR spectroscopy shows a progression from the preferred

solution state conformation of the ring I side chain to the ideal bound conformation as a function

of the size of the fused ring. These derivatives were subjected to the cell free ribosomal assays

and bacterial MIC assays. It was found that as the conformation of the locked side chain

approached the ideal gauche, trans conformation the activity increased, leading to the conclusion

that the gt conformation is the bound conformation.

Chapter four discusses the effect of the 4’-substituent on the population of ring I side

chain conformers in an attempt to rationalize the differences in activity between paromomycin,

4’-deoxy paromomycin, and 4’-deoxy-4’-propyl paromomycin (propylamycin), a recently


published synthetic aminoglycoside demonstrating equal activity to paromomycin and reduced

toxicity in an animal model. Models of ring I of 4’-deoxy paromomycin and propylamycin were

synthesized with and without selective deuteration at the side chain carbon. NMR spectroscopic

studies of the relative populations of conformers of the ring I side chain for these models were

conducted leading to the conclusion that the substituent at the 4’-position has minimal effect on

the relative populations of the side chain conformers of ring I: any differences in activity between

these compounds are due to other factors.