Metabolomics and dereplication strategies in the discovery of natural product derived drugs

Abstract

Metabolomics is the technology designed to provide general qualitative and quantitative profile of metabolites in organisms exposed to different conditions. Metabolomics is applied in many aspects of natural drug discoveries, particularly in bioactivity screening to improve dereplication and identification procedures. Fast dereplication of known compounds and identification of lead bioactive metabolites is important in the primary stages of metabolomics profiling prior to an intensive isolation work. Two levels of metabolomics were used in this study. First was metabolites fingerprinting which aimed for rapid classification of samples by comparing the metabolites patterns or fingerprints. Second was metabolites profiling and dereplication study for class of compounds related to a specific pathway in order to individually identify and quantify these metabolites. This study involved isolation of endophytic fungus Aspergillus aculeatus from Egyptian medicinal plants, Terminalia laxiflora. Identification of the strains has been achieved through molecular biological methods. Metabolomic profiling, using NMR and HR-MS were done at different stages of the growth phase for both solid and liquid culture media. Dereplication studies were accomplished by utilizing the MZmine 2.10 software with aid of the AntiBase and DNP databases. By end of the dereplication process metabolites were sorted out into three levels; level 1: identified compounds, level 2: putatively annotated compound class and level 3: completely unidentified and unclassified compounds. Multivariate data analysis was employed by using PCA in order to classify samples into groups, trends and outliers, which maximize the information, can be obtained from spectral data. OPLS-DA was used to correlate the chemical profile with tested biological activity. Metabolomics has been shown to be a powerful facilitator in the discovery of natural products, which are considered an excellent source for novel leads

LC-HRMS-Database Screening Metrics for Rapid Prioritization of Samples to Accelerate the Discovery of Structurally New Natural Products

“…This meant determination of chemical diversity, which usually occurred after extraction, isolation, and purification had been performed, resulted in high redundancy rates. To overcome this problem, several dereplication methods have been developed. , One example is the use of genetic information on the organism particularly in microorganisms. ,,, However, challenges remain, as it has been shown that even strains with similar 16S gene sequences do not necessarily produce the same chemistry, , indicating that the induction and/or activation of biosynthetic machinery for natural product production is far more complex than originally thought and relies on a complex interaction of environmental, chemical, biochemical, and biological stimuli. , Even if the organism’s metabolome is successfully stimulated, the next challenge is detection and identification of new secondary metabolites that are often produced in small quantities, in a background of known metabolites present in higher quantities. It is therefore imperative to devise new strategies that rapidly identify known compounds early on in the project, so that resources can be concentrated only on the discovery of structurally new or novel ones.…”

“…13,16 One example is the use of genetic information on the organism 17 particularly in microorganisms. 8,13,18,19 However, challenges remain, as it has been shown that even strains with similar 16S gene sequences do not necessarily produce the same chemistry, 20,21 indicating that the induction and/or activation of biosynthetic machinery for natural product production is far more complex than originally thought and relies on a complex interaction of environmental, chemical, biochemical, and biological stimuli. 8,22 Even if the organism's metabolome is successfully stimulated, the next challenge is detection and identification of new secondary metabolites that are often produced in small quantities, in a background of known metabolites present in higher quantities.…”

Database for Rapid Dereplication of Known Natural Products Using Data from MS and Fast NMR Experiments

“…Dereplication is now defined as the elimination of known active substances from consideration when a bioactive mixture is being investigated . Since 1978 a diversity of dereplication strategies have been reported. − These strategies generally rely upon the ability to match molecular features present in unknown bioactive NPs (either spectroscopic/spectrometric or structural) with data stored in spectroscopic (containing MS and/or 13 C NMR data of NPs) and/or structural databases. A dereplication strategy is generally implemented after initial screening of extracts or semipurified fractions, and the most widely used involve the so-called hyphenated techniques, in which a separation device (a chromatograph) is coupled with spectrometers such as MS, UV, IR, and NMR and analysis of the spectra obtained provides structural information on the compounds present in mixtures. ,− UV and IR provide the least discriminatory spectroscopic data and can really be used only for dereplication in combination with other spectroscopic data.…”