Secondary metabolite pipeline

Secondary metabolite pipeline

Discovery and exploitation of novel marine products and biomolecules

Despite their high potential for biotechnological and pharmaceutical applications, only a small fraction of compounds that marine microbes are capable of producing have been isolated so far. Natural product discovery pipelines involve distinct technologies and expertise in areas such as compound extraction, fractionation, isolation and purification, determination of biological activities, as well as structural characterization.

The expertise required for successful natural product discovery from marine organisms exists in different European research institutions, but is often fragmented and not always easily accessible for external scientists. Hence, the EMBRIC secondary metabolite pipeline offers access to marine microbe collections and scientific networks to facilitate exploration of novel lead compounds or bioactive molecules that can potentially be used in health care, nutrition, as well as for immune-modulation in agriculture and aquaculture. The pipeline covers the entire project workflow from the isolation of the novel natural product all the way to optimization of desired compound properties.



Bioprofiling of marine extracts

Initial investigation of marine extracts in order to quickly check for interesting bioactivities. If interesting properties are discovered, follow-up experiments are suggested to the user.

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Compound identification

Compound identification includes extract preparation, fractionation of extracts, MS, NMR and chemical structure elucidation.

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It is crucial to figure out as soon as possible whether the newly isolated natural product has been described before in order to avoid wasting time and resources on known chemical entities. This is done using database-based approaches.

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Hit optimisation

While displaying certain desired properties, the initially isolated natural product likely needs to be optimized further in order to improve properties such as for example solubility, potency etc.

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Visibility in European compound collections

Once a natural product with desirable properties has been characterised and is available in sufficient quantities, it might be of interest to the scientist to expose the natural product to as many biological assays as possible in order to get a comprehensive overview of its properties. Compound collections accessed by many users over time represent an attractive means to do so. If desired, newly identified compounds can be added to such compound collections.

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Possible research workflows with this pipeline


Example 1

A scientist could for example have a newly isolated natural product from a marine organism but no idea what that newly isolated substance can do. EMBRIC could offer initial Bioprofiling of that substance in order to get a better idea of what the substance might be good for. We would suggest to the user to get in touch with the HZI and the FMP in order to initiate Bioprofiling experiments. The HZI has strong expertise in ant-infectious assays, the FMP can offer for example cytotoxicity measurements.


Example 2

If you have a bioactive marine extract but you do not know the active component, we can help you to identify the active compound. In addition, as soon as structural and other information becomes available, we will use database-based approached for rapid dereplication experiments. This ensures that only novel chemical entities will be pursuit further and thus saves valuable resources and time.


Example 3

If you have a thoroughly characterized natural product and want to expose it to a variety of biological assays, we can help you to deposit your compound in compound collections. Once archived, your compound will be screened in all subsequent assays, and you will be contacted once your substance generates a hit in one of the biological assays encountered.


Contact person for questions and inquiries

Philip Gribbon
Fraunhofer ScreeningPort IME
Tel:        +49 (0)40 3037640


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