Researchers develop method that simplifies the process of drug discovery and development

In the often lengthy process of discovering and developing a new drug, one of the key steps is to study how the drug affects different functions in the cells it comes into contact with. By using large-scale analysis of the genes that are activated or inactivated by the drug, or of the proteins produced in the cells, the overall cellular profile induced by the drug can be obtained. 

All approaches used generate large amounts of data, and require careful and detailed analysis of the information collected. A group of researchers at the National Institute of Health Dr. Ricardo Jorge, in Lisbon, led by FCT Researcher Rune Mattiesen, has now developed a method that simplifies the path followed in establishing the profile of a drug and allows better characterization of its effect in different compartments of the cell. The results have been published in the prestigious journal Nature Scientific Reports.

The team took a different approach to the conventional one, analyzing five subcellular fractions separately instead of whole cells. Biochemical extraction processes were applied to cells in culture, treated with a drug, to obtain the five fractions. These correspond to different cellular compartments: the nucleus (soluble component and insoluble component), mitochondria, microsomes (the vesicles that form from the endoplasmic reticulum of the cell), and microsomes+cytosol (the liquid that occupies the volume of the cell).

Rune Matthiesen and his team then applied the mass spectrometry technique to each fraction to analyze variations across the entire range of proteins in the cell, i.e. the proteome of the cell. With this approach they achieved greater coverage of the proteome when compared to non-fragmented samples: they identified 18,889 proteins, corresponding to 6,279 individual genes.

In addition, and crucially, they have achieved a more detailed analysis of the way in which the same or different proteins are regulated in different cellular compartments.

The results have already attracted the interest of pharmaceutical companies, and several other research groups, in Portugal and internationally.

The study was fully funded by FCT, through the FCT Investigator contract of Rune Matthiesen, the Studentship post-doctoral fellowship of Ana Sofia Carvalho (first author of the study) and an FCT Exploratory Project.

Images, from top to bottom:

• Representation of the increase (red) and decrease (green) of different protein classes (horizontal axis) by the drug, in the various cell fractions analyzed (vertical axis).
• Rune Mathiesen, FCT Researcher at the National Institute of Health Dr. Ricardo Jorge
• Ana Carvalho, post-doctoral researcher at the National Institute of Health Dr. Ricardo Jorge

(Credits: Rune Mathiesen, Ana Carvalho and Nature Scientific Reports)