Fingerprinting the Drugs of the Future

Jenny Samskog
Department of Chemistry
Uppsala University
March 2002

I am studying ways to quickly and reliably analyze proteins. This is one of the big challenges for analytical chemists today. Proteins are becoming increasingly important both for using proteins as drugs and understanding what is going on in a human cell. Every protein that exists has its own specific fingerprint. I develop a method that utilizes this fact. This fingerprinting technique can for example be used for quality control of protein drugs.

The process of chemical analysis that I do include the following steps: sampling, sample preparation, analysis and evaluation of the resulting data. My research focuses on sample preparation and analysis of proteins and peptides.

We have proteins everywhere in our body and they have many different functions. Every cell contains several thousand kinds of proteins. Proteins are involved in every process in our body; they can be enzymes, building units, messengers and so on. Studying them in detail may lead us to understand many diseases. In the future proteins may be used as drugs in a higher extent than today. A drawback with proteins is that they are very large and complex molecules. Analyzing proteins is therefore not a straightforward process. The methods are often very time-consuming. The analysis method should preferably only consume small amounts of sample, as the sample supply may be limited. My work aims at minimizing the analysis system and speeding up the analysis time.

The sample preparation is done in the following way: The protein of interest is first cut it into smaller pieces. I use enzymes to degrade the protein into smaller pieces, called peptides. Peptides can be of varying size and have different properties. Instead of a protein the sample now consists of 20-40 peptides.

The peptides can tell us a lot about the protein from which it originated. They are difficult to study when they are mixed together though. In the analysis I first separate the peptides from each other so that they can be studied one by one. The separation is accomplished in a kind of a tube, called a column. In the column the peptides are separated from each other depending on their different properties. The most important property is how much affinity the peptides have for water. The column itself has a low affinity for water. The peptide that has got the highest affinity for water therefore leaves the column first. When the peptides reach the end of the column they leave it one after another and enter the detector. The detector that I use is called a mass spectrometer. It generates a signal from every peptide. When all the peptides have left the column and given rise to signals in the detector, I have an image of the sample. The resulting image from the separated peptides can be viewed as a fingerprint of that certain protein, which marks the protein as different from every other protein.

In my research, miniaturization is often addressed. Miniaturizing analysis system means reducing the amount of a sample consumed and lessening the consumption of chemicals, which is good for the environment. To give you an idea of the size of the system, the separation is accomplished in a small glass tube, which is about the size as a piece of hair. I only need to consume a millionth of a liter of sample. Normally, 1 ml is consumed during analysis.

The way I analyze proteins is much faster than these kinds of analysis usually are. With the methods traditionally used, the whole analyses take 8 hours. With my current miniaturized method, it just takes 1 hour to complete. One reason my method is faster is that the sample preparation, that is when the proteins are cleaved to peptides, is very fast.

This fingerprinting technique can be used for many purposes. One is to use it in quality control of protein drugs, where the fingerprint of the protein needs to be the same all the time. If it differs, it can't be used as a drug and there may be something wrong in the way that the protein drug has been manufactured. Another use of this technique is to analyze the proteins in a human cell and receive a disease map. A disease map is a fingerprint of the cell, with regard to the proteins. Fingerprinting the proteins in a certain cell may actually in the future be a fast and reliable method for diagnosing diseases.