Tools to Unravel Proteins at Forefront of Biotech
Monday December 3 7:27 PM ET
By Deena Beasley
dailynews.yahoo.com
LOS ANGELES (Reuters) - Protein is not only a vital part of our diet -- it may be the key to unlocking human biology, putting the emerging field of tools to decipher and catalog proteins at the forefront of drug research.
The publication of the decoded human genome this year was hailed widely as a milestone in biology, but the far more complex task of teasing from genes the specks of data that some believe will revolutionize medicine is at an earlier stage.
The human genetic map shows there are some 35,000 genes responsible for instructing proteins, which come in a far greater number of variations.
Proteins are the targets of most drug discovery efforts but only a few thousand are well understood. Drug companies want to identify exactly which proteins are responsible for signaling things like cancer cell growth so they can make drugs to combat or disable them.
By identifying these proteins, doctors would also have a way to detect disease or know ahead of time whether a certain patient will respond to a drug.
``Drug companies have a lot of new targets. What they don't have are serious new technologies to help them with the later stages of the development process,'' said N. Leigh Anderson, head of the proteomics unit of Large Scale Biology Inc., one company in the field.
$6 BILLION MARKET
Tracking and sorting the thousands of proteins in our bodies is a task of awesome technical complexity, requiring a special combination of biological and computing skills.
DNA microarrays, or biochips, are readily available for sorting tens of thousands of genes simultaneously, but there is still no dominant technology for identifying or characterizing proteins, which consist of myriad patterns of 20 amino acids folded into delicate three-dimensional shapes. The shape determines their function.
Gel electrophoresis is the standard process for separating proteins based on their charge and mass. Mass spectrometry can then identify the proteins by analyzing their components. Additional lab experiments are needed to observe how the proteins interact and to see their structure.
The proteomics technologies market -- chips, databases and arrays -- surged past the $1.5 billion mark this year and could reach nearly $6 billion in the next five years, according to the market research firm Kalorama Information.
Players include companies like Ciphergen Biosystems Inc. (Nasdaq:CIPH), Zyomyx Inc., Phylos Inc. and Large Scale Biology
(Nasdaq:LSBC), to name a few.
Fremont, California-based Ciphergen's chip technology, which combines mass spectrometry with an array platform, is not high-density like microarrays now commonly used to analyze genes. The technique allows scientists to place a crude biological sample, such as blood, in one spot and to see all the proteins in the sample, said Richard Rubin, chief marketing officer at Ciphergen.
VERY DELICATE
``DNA chips and protein chips have the same fundamental concept, but the underlying technology is very different. DNA can be treated almost harshly, but proteins are very delicate,'' said Lawrence Cohen, chief executive at Zyomyx.
The Hayward, California-based company is working on a high-throughput protein chip. ``Once you've got a clue, our chip can differentiate the proteins,'' the CEO said, noting that Zyomyx expects to launch test versions of its chips next year.
Large Scale Biology, which has its proteomics unit in Germantown, Maryland, is focused primarily on developing content for chips. ``We are acquiring knowledge about which proteins you want to measure,'' said proteomics chief Anderson.
Anderson expects protein biochips will be used extensively in research by late next year, but it will be much longer before regulators approve their use to diagnose, treat or prevent disease.
``It is such a complicated and major step forward in medical practice, but the advantages are so great it will obviously be done,'' he said.
A more immediate use for the chips could be in clinical trials, Anderson said. ``Currently, patients in clinical trials are monitored by conventional medical means. We believe that using antibody arrays to measure proteins would detect any kind of toxicity problems,'' he explained.
The protein chips could also be used to determine quickly whether a trial patient responds to treatment. ``This would not only improve the quality of trials, it would increase the number of trials that can be conducted,'' Anderson said.
Lexington, Massachusetts-based Phylos is another company positioned as a provider of content material to makers of protein chips.
Chief Executive Ashley Lawton said the company's technology for rapidly selecting specific proteins will likely be used in microarray formats within the next couple of years, and has applications in a wide range of other formats.
``The field is so complex, there is probably room for a lot of technologies,'' said Rubin at Ciphergen. |
