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Bioactive compound identification without fractionation: an Ocimum spp. case study.

Evelyn J Abraham1, Kelsey Custer2, R Teal Jordan2

  • 1Intercollege Graduate Degree Program in Plant Biology, Pennsylvania State University, University Park, PA, 16802, USA.

Metabolomics : Official Journal of the Metabolomic Society
|November 15, 2025
PubMed
Summary

This study shows that metabolome-wide association studies can identify bioactive phytochemicals in whole plant extracts without fractionation. This approach successfully pinpointed gallic acid as a cytotoxic compound in Ocimum extracts.

Keywords:
BasilBiochemometricsCytotoxicityLASSO regressionMachine learningMetabolomicsOcimum

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Area of Science:

  • Phytochemistry
  • Metabolomics
  • Chemometrics

Background:

  • Understanding plant compounds is key for drug development.
  • Current methods using metabolomics and predictive modeling require fractionation, risking compound loss.

Purpose of the Study:

  • To assess if metabolome-wide association studies can identify bioactive phytochemicals in whole botanical extracts without prior fractionation.
  • To explore a novel approach for compound discovery in medicinal plants.

Main Methods:

  • Used 40 Ocimum extracts with varying bioactivity (MTT assay).
  • Combined metabolomic data (UPLC-MS/MS) with biochemometric modeling.
  • Applied chemometric tools and statistical filters for feature selection.

Main Results:

  • Generated ~1600 metabolite features.
  • Source-based filters and LASSO dimension reduction improved predictive model reliability.
  • Identified four biomarkers, including gallic acid, linked to bioactivity. Gallic acid's cytotoxicity was confirmed.

Conclusions:

  • Predictive modeling via metabolome-wide association studies on un-fractionated extracts can identify bioactive compounds.
  • This method offers a viable alternative to traditional fractionation techniques for phytochemical discovery.