Merck

Bioretrosynthetic construction of a didanosine biosynthetic pathway.

Nature chemical biology (2014-03-25)
William R Birmingham, Chrystal A Starbird, Timothy D Panosian, David P Nannemann, T M Iverson, Brian O Bachmann
ABSTRACT

Concatenation of engineered biocatalysts into multistep pathways markedly increases their utility, but the development of generalizable assembly methods remains a major challenge. Herein we evaluate 'bioretrosynthesis', which is an application of the retrograde evolution hypothesis, for biosynthetic pathway construction. To test bioretrosynthesis, we engineered a pathway for synthesis of the antiretroviral nucleoside analog didanosine (2',3'-dideoxyinosine). Applying both directed evolution- and structure-based approaches, we began pathway construction with a retro-extension from an engineered purine nucleoside phosphorylase and evolved 1,5-phosphopentomutase to accept the substrate 2,3-dideoxyribose 5-phosphate with a 700-fold change in substrate selectivity and threefold increased turnover in cell lysate. A subsequent retrograde pathway extension, via ribokinase engineering, resulted in a didanosine pathway with a 9,500-fold change in nucleoside production selectivity and 50-fold increase in didanosine production. Unexpectedly, the result of this bioretrosynthetic step was not a retro-extension from phosphopentomutase but rather the discovery of a fortuitous pathway-shortening bypass via the engineered ribokinase.

MATERIALS
Product Number
Brand
Product Description

Didanosine for system suitability, European Pharmacopoeia (EP) Reference Standard
Sigma-Aldrich
2′,3′-Dideoxyinosine, ≥98% (HPLC)
Didanosine, European Pharmacopoeia (EP) Reference Standard