A retro-biosynthetic approach to the prediction of biosynthetic pathways from position-specific isotope analysis as shown for tramadol

Proc Natl Acad Sci U S A. 2015 Jul 7;112(27):8296-301. doi: 10.1073/pnas.1506011112. Epub 2015 Jun 23.

Abstract

Tramadol, previously only known as a synthetic analgesic, has now been found in the bark and wood of roots of the African medicinal tree Nauclea latifolia. At present, no direct evidence is available as to the biosynthetic pathway of its unusual skeleton. To provide guidance as to possible biosynthetic precursors, we have adopted a novel approach of retro-biosynthesis based on the position-specific distribution of isotopes in the extracted compound. Relatively recent developments in isotope ratio monitoring by (13)C NMR spectrometry make possible the measurement of the nonstatistical position-specific natural abundance distribution of (13)C (δ(13)Ci) within the molecule with better than 1‰ precision. Very substantial variation in the (13)C positional distribution is found: between δ(13)Ci = -11 and -53‰. Distribution is not random and it is argued that the pattern observed can substantially be interpreted in relation to known causes of isotope fractionation in natural products. Thus, a plausible biosynthetic scheme based on sound biosynthetic principals of precursor-substrate relationships can be proposed. In addition, data obtained from the (18)O/(16)O ratios in the oxygen atoms of the compound add support to the deductions made from the carbon isotope analysis. This paper shows how the use of (13)C NMR at natural abundance can help with proposing a biosynthetic route to compounds newly found in nature or those difficult to tackle by conventional means.

Keywords: NMR spectrometry; Nauclea latifolia; position-specific isotope analysis; retro-biosynthesis; tramadol.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biosynthetic Pathways*
  • Carbon / metabolism
  • Carbon Isotopes / metabolism
  • Isotope Labeling / methods*
  • Magnetic Resonance Spectroscopy / methods*
  • Mass Spectrometry
  • Molecular Structure
  • Oxygen / metabolism
  • Oxygen Isotopes / metabolism
  • Plant Bark / chemistry
  • Plant Roots / chemistry
  • Rubiaceae / chemistry
  • Tramadol / chemistry
  • Tramadol / isolation & purification
  • Tramadol / metabolism*
  • Wood / chemistry

Substances

  • Carbon Isotopes
  • Oxygen Isotopes
  • Tramadol
  • Carbon
  • Oxygen