Skip to main content

Main menu

  • Home
  • Articles
    • Current
    • Special Feature Articles - Most Recent
    • Special Features
    • Colloquia
    • Collected Articles
    • PNAS Classics
    • List of Issues
  • Front Matter
    • Front Matter Portal
    • Journal Club
  • News
    • For the Press
    • This Week In PNAS
    • PNAS in the News
  • Podcasts
  • Authors
    • Information for Authors
    • Editorial and Journal Policies
    • Submission Procedures
    • Fees and Licenses
  • Submit
  • Submit
  • About
    • Editorial Board
    • PNAS Staff
    • FAQ
    • Accessibility Statement
    • Rights and Permissions
    • Site Map
  • Contact
  • Journal Club
  • Subscribe
    • Subscription Rates
    • Subscriptions FAQ
    • Open Access
    • Recommend PNAS to Your Librarian

User menu

  • Log in
  • My Cart

Search

  • Advanced search
Home
Home
  • Log in
  • My Cart

Advanced Search

  • Home
  • Articles
    • Current
    • Special Feature Articles - Most Recent
    • Special Features
    • Colloquia
    • Collected Articles
    • PNAS Classics
    • List of Issues
  • Front Matter
    • Front Matter Portal
    • Journal Club
  • News
    • For the Press
    • This Week In PNAS
    • PNAS in the News
  • Podcasts
  • Authors
    • Information for Authors
    • Editorial and Journal Policies
    • Submission Procedures
    • Fees and Licenses
  • Submit
Research Article

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

Katarzyna M. Romek, Pierrick Nun, Gérald S. Remaud, Virginie Silvestre, Germain Sotoing Taïwe, Florine Lecerf-Schmidt, Ahcène Boumendjel, Michel De Waard, and Richard J. Robins
  1. aElucidation of Biosynthesis by Isotopic Spectrometry Group, Interdisciplinary Chemistry: Synthesis, Analysis, Modeling, CNRS–University of Nantes Unité Mixte de Recherche 6230, F-44322 Nantes, France;
  2. bLaboratory for Isotope Effects Studies, Department of Chemistry, Institute of Applied Radiation Chemistry, Lodz University of Technology, 90-924 Lodz, Poland;
  3. cDepartment of Zoology and Animal Physiology, University of Buea, Buea, Cameroon;
  4. dDepartment of Medicinal Chemistry, University Grenoble Alpes–CNRS Unité Mixte de Recherche 5063, F-38041 Grenoble, France;
  5. eGrenoble Institute of Neuroscience, Unit Inserm U836, F-38700 La Tronche, France;
  6. fUniversity Joseph Fourier, F-38041 Grenoble, France

See allHide authors and affiliations

PNAS July 7, 2015 112 (27) 8296-8301; first published June 23, 2015; https://doi.org/10.1073/pnas.1506011112
Katarzyna M. Romek
aElucidation of Biosynthesis by Isotopic Spectrometry Group, Interdisciplinary Chemistry: Synthesis, Analysis, Modeling, CNRS–University of Nantes Unité Mixte de Recherche 6230, F-44322 Nantes, France;
bLaboratory for Isotope Effects Studies, Department of Chemistry, Institute of Applied Radiation Chemistry, Lodz University of Technology, 90-924 Lodz, Poland;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Pierrick Nun
aElucidation of Biosynthesis by Isotopic Spectrometry Group, Interdisciplinary Chemistry: Synthesis, Analysis, Modeling, CNRS–University of Nantes Unité Mixte de Recherche 6230, F-44322 Nantes, France;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Gérald S. Remaud
aElucidation of Biosynthesis by Isotopic Spectrometry Group, Interdisciplinary Chemistry: Synthesis, Analysis, Modeling, CNRS–University of Nantes Unité Mixte de Recherche 6230, F-44322 Nantes, France;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Virginie Silvestre
aElucidation of Biosynthesis by Isotopic Spectrometry Group, Interdisciplinary Chemistry: Synthesis, Analysis, Modeling, CNRS–University of Nantes Unité Mixte de Recherche 6230, F-44322 Nantes, France;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Germain Sotoing Taïwe
cDepartment of Zoology and Animal Physiology, University of Buea, Buea, Cameroon;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Florine Lecerf-Schmidt
dDepartment of Medicinal Chemistry, University Grenoble Alpes–CNRS Unité Mixte de Recherche 5063, F-38041 Grenoble, France;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Ahcène Boumendjel
dDepartment of Medicinal Chemistry, University Grenoble Alpes–CNRS Unité Mixte de Recherche 5063, F-38041 Grenoble, France;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Michel De Waard
eGrenoble Institute of Neuroscience, Unit Inserm U836, F-38700 La Tronche, France;
fUniversity Joseph Fourier, F-38041 Grenoble, France
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Richard J. Robins
aElucidation of Biosynthesis by Isotopic Spectrometry Group, Interdisciplinary Chemistry: Synthesis, Analysis, Modeling, CNRS–University of Nantes Unité Mixte de Recherche 6230, F-44322 Nantes, France;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: Richard.ROBINS@univ-nantes.fr
  1. Edited by Jerrold Meinwald, Cornell University, Ithaca, NY, and approved May 28, 2015 (received for review March 26, 2015)

  • Article
  • Figures & SI
  • Info & Metrics
  • PDF
Loading

Significance

The extraction of tramadol from the roots of Nauclea latifolia excited great interest worldwide. This was the first time that a widely marketed synthetic drug was found as an apparently natural product at high abundance. In this article, we describe the position-specific distribution of 13C in this tramadol. As a conventional approach to study its probable biosynthetic precursors, enzymatic steps, and intermediate metabolites is not currently feasible, we herein propose the concept of a retro-biosynthesis by examining the position-specific isotope distribution within the molecule and rationally interpreting the data in terms of known plant biochemical processes that may be involved in a biosynthesis of tramadol. Thus, clear guidance is given for future labeling studies.

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 13C NMR spectrometry make possible the measurement of the nonstatistical position-specific natural abundance distribution of 13C (δ13Ci) within the molecule with better than 1‰ precision. Very substantial variation in the 13C positional distribution is found: between δ13Ci = −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 18O/16O 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 13C 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

Footnotes

  • ↵1To whom correspondence should be addressed. Email: Richard.ROBINS{at}univ-nantes.fr.
  • Author contributions: P.N., G.S.R., A.B., M.D.W., and R.J.R. designed research; K.M.R., V.S., G.S.T., and F.L.-S. performed research; G.S.R. contributed new reagents/analytic tools; P.N., G.S.R., and R.J.R. analyzed data; and P.N., G.S.R., and R.J.R. wrote the paper.

  • The authors declare no conflict of interest.

  • This article is a PNAS Direct Submission.

View Full Text
PreviousNext
Back to top
Article Alerts
Email Article

Thank you for your interest in spreading the word on PNAS.

NOTE: We only request your email address so that the person you are recommending the page to knows that you wanted them to see it, and that it is not junk mail. We do not capture any email address.

Enter multiple addresses on separate lines or separate them with commas.
A retro-biosynthetic approach to the prediction of biosynthetic pathways from position-specific isotope analysis as shown for tramadol
(Your Name) has sent you a message from PNAS
(Your Name) thought you would like to see the PNAS web site.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Citation Tools
PSIA to predict biosynthetic pathways
Katarzyna M. Romek, Pierrick Nun, Gérald S. Remaud, Virginie Silvestre, Germain Sotoing Taïwe, Florine Lecerf-Schmidt, Ahcène Boumendjel, Michel De Waard, Richard J. Robins
Proceedings of the National Academy of Sciences Jul 2015, 112 (27) 8296-8301; DOI: 10.1073/pnas.1506011112

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
Request Permissions
Share
PSIA to predict biosynthetic pathways
Katarzyna M. Romek, Pierrick Nun, Gérald S. Remaud, Virginie Silvestre, Germain Sotoing Taïwe, Florine Lecerf-Schmidt, Ahcène Boumendjel, Michel De Waard, Richard J. Robins
Proceedings of the National Academy of Sciences Jul 2015, 112 (27) 8296-8301; DOI: 10.1073/pnas.1506011112
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
  • Tweet Widget
  • Facebook Like
  • Mendeley logo Mendeley

Article Classifications

  • Biological Sciences
  • Biochemistry
Proceedings of the National Academy of Sciences: 112 (27)
Table of Contents

Submit

Sign up for Article Alerts

Jump to section

  • Article
    • Abstract
    • Results and Discussion
    • Conclusion
    • Methods
    • Acknowledgments
    • Footnotes
    • References
  • Figures & SI
  • Info & Metrics
  • PDF

You May Also be Interested in

Water from a faucet fills a glass.
News Feature: How “forever chemicals” might impair the immune system
Researchers are exploring whether these ubiquitous fluorinated molecules might worsen infections or hamper vaccine effectiveness.
Image credit: Shutterstock/Dmitry Naumov.
Reflection of clouds in the still waters of Mono Lake in California.
Inner Workings: Making headway with the mysteries of life’s origins
Recent experiments and simulations are starting to answer some fundamental questions about how life came to be.
Image credit: Shutterstock/Radoslaw Lecyk.
Cave in coastal Kenya with tree growing in the middle.
Journal Club: Small, sharp blades mark shift from Middle to Later Stone Age in coastal Kenya
Archaeologists have long tried to define the transition between the two time periods.
Image credit: Ceri Shipton.
Mouse fibroblast cells. Electron bifurcation reactions keep mammalian cells alive.
Exploring electron bifurcation
Jonathon Yuly, David Beratan, and Peng Zhang investigate how electron bifurcation reactions work.
Listen
Past PodcastsSubscribe
Panda bear hanging in a tree
How horse manure helps giant pandas tolerate cold
A study finds that giant pandas roll in horse manure to increase their cold tolerance.
Image credit: Fuwen Wei.

Similar Articles

Site Logo
Powered by HighWire
  • Submit Manuscript
  • Twitter
  • Facebook
  • RSS Feeds
  • Email Alerts

Articles

  • Current Issue
  • Special Feature Articles – Most Recent
  • List of Issues

PNAS Portals

  • Anthropology
  • Chemistry
  • Classics
  • Front Matter
  • Physics
  • Sustainability Science
  • Teaching Resources

Information

  • Authors
  • Editorial Board
  • Reviewers
  • Subscribers
  • Librarians
  • Press
  • Cozzarelli Prize
  • Site Map
  • PNAS Updates
  • FAQs
  • Accessibility Statement
  • Rights & Permissions
  • About
  • Contact

Feedback    Privacy/Legal

Copyright © 2021 National Academy of Sciences. Online ISSN 1091-6490