Carbohydrates play a critical role in the activity of many important biological agents and pharmaceuticals, and small alterations in their structures can have a significant impact on their efficacy. Hence, it is not necessarily unexpected that naturally occurring glycans and sugar appendages are so structurally diverse. What is surprising, however, is that most of these unusual carbohydrates are biosynthesized from a relatively small pool of common sugars via a series of reactions that often include new and unusual chemical transformations. By exploiting the machinery of these pathways, it is possible to enhance or vary the biological activities of the glycosylated compounds and apply the principles learned to new systems. However, in order to fully realize the potential of such an approach, the biosynthetic pathways must be characterized and the underlying chemistry thoroughly understood. In this spirit, we have identified several systems to be investigated in the next funding period. The first specific aim is the mechanistic study of the five- to four-membered ring contraction at the heart of oxetanocin A and albucidin biosynthesis. The enzymes involved in these reactions are members of the B12- dependent radical SAM family that has only recently been discovered and remains very poorly understood. The ultimate goal of the work proposed is to determine the mechanism of the highly unusual ring contraction as well as the roles played by the B12 cofactor and the radical SAM machinery. The second specific aim is focused on understanding the mechanism by which glycosidic linkages are oxidatively cyclized to form the characteristic spirocyclic ortho-?-lactones of the orthosomycin class of antibiotics and in particular hygromycin B. This is an unprecedented transformation in carbohydrate biochemistry that is likely to involve radical intermediates and be of value to the discovery of new orthosomycin antibiotics. The third specific aim seeks to complete the description of gentamicin biosynthesis. The final uncharacterized process in this pathway is a unique ?,?-dideoxygenation that stands in contrast to all previously characterized monodeoxygenation reactions involving carbohydrates. While there is little information about how this dideoxygenation might be accomplished, genetic analyses suggest the involvement of exciting radical chemistry. Through the collective application of our expertise in deoxysugar biosynthesis, chemical synthesis and enzymology, we aim to investigate the uncharacterized enzymes in the pathway to resolve this question.
These research aims have been selected on the basis of their novelty, implications for the fields of mechanistic enzymology and natural product biosynthesis as well as potential utility in biomedical and biotechnological research at the basic and translational levels.

Public Health Relevance

Carbohydrates with chemically complex and unusual structures play a central role in drug design, because they often represent critical structural features necessary for the antimicrobial or anticancer properties of the active pharmaceutical ingredient. The carbohydrate-containing natural products proposed for study herein have been specifically selected not only for their antibacterial (hygromycins and gentamicins) and antiviral (oxetanocin and albucidin) properties, but also because of the unprecedented chemistry involved in their biosynthesis. Addressing the gaps in our understanding of natural product biosynthesis and mechanistic enzymology that these compounds represent is thus the focal point of the current proposal. Pursuing these questions will expand our understanding of complex mechanistic enzymology and thereby continue to develop the biochemical foundation on which new pharmaceuticals are discovered and improved.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
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Macromolecular Structure and Function A Study Section (MSFA)
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Fabian, Miles
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University of Texas Austin
Schools of Pharmacy
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Lin, Geng-Min; Romo, Anthony J; Liem, Priscilla H et al. (2017) Identification and Interrogation of the Herbicidin Biosynthetic Gene Cluster: First Insight into the Biosynthesis of a Rare Undecose Nucleoside Antibiotic. J Am Chem Soc 139:16450-16453
Kim, Hak Joong; Liu, Yung-Nan; McCarty, Reid M et al. (2017) Reaction Catalyzed by GenK, a Cobalamin-Dependent Radical S-Adenosyl-l-methionine Methyltransferase in the Biosynthetic Pathway of Gentamicin, Proceeds with Retention of Configuration. J Am Chem Soc 139:16084-16087
Ko, Yeonjin; Wang, Shao-An; Ogasawara, Yasushi et al. (2017) Identification and Characterization of Enzymes Catalyzing Pyrazolopyrimidine Formation in the Biosynthesis of Formycin A. Org Lett 19:1426-1429
Bridwell-Rabb, Jennifer; Zhong, Aoshu; Sun, He G et al. (2017) A B12-dependent radical SAM enzyme involved in oxetanocin A biosynthesis. Nature 544:322-326
Lin, Chia-I; McCarty, Reid M; Liu, Hung-Wen (2017) The Enzymology of Organic Transformations: A Survey of Name Reactions in Biological Systems. Angew Chem Int Ed Engl 56:3446-3489
Lin, Geng-Min; Sun, He G; Liu, Hung-Wen (2016) Study of Uridine 5'-Diphosphate (UDP)-Galactopyranose Mutase Using UDP-5-Fluorogalactopyranose as a Probe: Incubation Results and Mechanistic Implications. Org Lett 18:3438-41
Ushimaru, Richiro; Lin, Chia-I; Sasaki, Eita et al. (2016) Characterization of Enzymes Catalyzing Transformations of Cysteine S-Conjugated Intermediates in the Lincosamide Biosynthetic Pathway. Chembiochem 17:1606-11
Jackson, David R; Yu, Xia; Wang, Guojung et al. (2016) Insights into Complex Oxidation during BE-7585A Biosynthesis: Structural Determination and Analysis of the Polyketide Monooxygenase BexE. ACS Chem Biol 11:1137-47
Kim, Hak Joong; LeVieux, Jake; Yeh, Yu-Cheng et al. (2016) C3'-Deoxygenation of Paromamine Catalyzed by a Radical S-Adenosylmethionine Enzyme: Characterization of the Enzyme AprD4 and Its Reductase Partner AprD3. Angew Chem Int Ed Engl 55:3724-8
Bridwell-Rabb, Jennifer; Kang, Gyunghoon; Zhong, Aoshu et al. (2016) An HD domain phosphohydrolase active site tailored for oxetanocin-A biosynthesis. Proc Natl Acad Sci U S A 113:13750-13755

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