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Nikoline Juul Nielsen, Post DocSoil and Environmental Chemistry (present)Bioorganic Chemistry (previous)

Exploratory Chemometrics and Analytical Chemistry – Looking for the Needle in the Haystack

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PhD in Natural Product Research

• Developing analytical tools (ways of measuring) and data processing tools (ways of interpreting data) for discovery of novel natural products

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Natural Products I - Drugs

S: de novo synthetic

N: Natural product

NM:Natural product mimic

ND:Natural product derived

S*:Synthetic, but NP pharmacophore

Newman and Cragg (2007): Journal of Natural Products, 70, 461-

Small molecule drugs approved 1981-2006 sorted by origin

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Natural Products II – Establishing biosynthetic pathways

Com

poun

d A

Com

poun

d B

Com

poun

d C

Aurof

usar

inEnz. 1 Enz. 2 Enz. 3

Com

poun

d C

O

OOHOH

O O

OOHO

OO

O

O OH O

OO

O

OOHOH

HO

Frandsen et al. (2006): Molecular Microbiology, vol. 61(4), pp. 1069-

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Natural Products III – Insect resistance factors in plants

Shinoda et al. (2002): J. Chem Ecol., 28(3), 587-Agerbirk et al. (2003): J. Chem Ecol., 29(6), 1417-Kuzina et al. (2009): Plant Phys., 151, 1977-Nielsen et al. (in press): J. Agric. Food. Chem.

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Natural Products IV – Small molecule endpoints from genes of unknown function

CMycelia CLiquid media

Overexpression Overexpression

Wildtype

Transporter deletion

Transporter deletion

Wildtype

DeletionDeletion

8.6 8.7 8.8 8.9 9 9.1 9.2 9.30

1000

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6000

a

13.9 14 14.1 14.2 14.3 14.4 14.50

0.5

1

1.5

2

2.5

3

x 104

b

m/z 683.5 rt 8.9 min

m/z 774.5 rt 14.1 min

Nielsen et al. (in press): Metabolomics

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Natural Products V – Plant biomarkers of environmental contamination

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How?

Meauring the organisms fingerprint i.e. as many analyte signal as possible and ideally all metabolites

Relating the fingerprints to a target vector i.e.

expected level of gene expression plant resistance to herbivores contaminant exposure level

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Measuring the organism metabolite fingerprints - Instrumentation

FLRDADUPLC ESI-TOF-MS

Chromatogram UV spectrum Mass-to-charge spectrum

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Measuring the organism metabolite fingerprints - Data

0 2000 4000 6000 8000 10000 12000 140000

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4000

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10000

12000

10

00

sca

ns

> 104 m/z values

Spectrum

Chromatogram0 200 400 600 800 1000 1200

0

500

1000

1500

2000

2500

3000

3500

4000

samples

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Relating the metabolite fingerprints to the target vector

Multivariate models can visualize the major variations in data e.g. Principal Component Analysis (PCA)

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Relating the metabolite fingerprints to the target vector

NoiseBaseline

Retention time shifts

Varying detector sensitivity

Artefacts in the chromatographic dimension

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My prime areas of interest

How to measure the entire set of metabolites i.e. increasing the information content of the data sets

How to fix up messy data i.e. for subsequent multivariate modelling

And this applies to a wide range of applications...

To characterize and identify targeted analytes from each application using e.g. NMR

Basically what we can do is finding out what metabolites from an organism are related to a treatment or an effect

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Acknowledgements:

The Research School of Environmental Chemistry, Microbiology and Toxicology

Any Questions?

TYFYA