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

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 C i ) within the molecule with better than 1‰ precision. Very substantial variation in the 13 C positional distribution is found: between δ 13 C i = −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 precursorsubstrate 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.NMR spectrometry | position-specific isotope analysis | retro-biosynthesis | tramadol | Nauclea latifolia

Non-statistical 13C Fractionation Distinguishes Co-incident and Divergent Steps in the Biosynthesis of the Alkaloids Nicotine and Tropine

“…This also parallels the relative depletion in a number of O-methyl groups, for example, ferulic acid (33). In tramadol, the N-Me 2 is also depleted relative to the part of the molecule considered to be derived from L-lysine by ϳ12‰ (20), which encouraged us to consider AdoMet as its probable origin. The O-methyl group of tramadol was also relatively depleted, although only by ϳ7‰.…”

“…In a recent article (20) applying this tactic to a newly discovered natural product, we were able to propose a credible biosynthetic route based on the observed pattern of the site-specific 13 C/ 12 C ratios. However, in that study, no direct underlying biological chemistry is yet available to substantiate the proposed reaction scheme.…”

The new face of isotopic NMR at natural abundance

“…Isotopic analysis makes it possible to characterize reaction mechanisms and distinguish between different biosynthetic origins . A recent work carried out by Romek et al . examined position‐specific isotope composition (δ 13 C i ) within tramadol.…”

Computer-generated isotope model achieves experimental accuracy of filiation for position-specific isotope analysis

“…(Gauchotte-Lindsay and Turnbull, 2016;Eiler, 2013) PSIA is able to obtain information about the origin of specific atoms in a given compound, but often requires more separation steps and more sample mass for similar precision. (Schmidt et al, 2004;Romek et al, 2015) PSIA can involve destructive or nondestructive means. One widespread non-destructive technique for measuring intramolecular enrichment is nuclear magnetic resonance (NMR).…”