February 1, 2008 (Vol. 28, No. 3)

Former Fee-for-Service Company Now Offers Plethora of Technologies As Well

When Protagen (www.protagen.com) was awarded cGMP certification for protein analysis, it became one of a select group of protein products and service organizations capable of offering therapeutic protein manufacturers certified analyses of commercial batches of protein-based drugs, according to Christoph Hüls, Ph.D., CEO.

The achievement marks a major milestone for Protagen, a company that has offered fee-for-service protein analysis to academia and industry since its inception in 1997. The firm now also offers a myriad of protein biochip, antibody development, biomarker discovery, and bioinformatics products and services worldwide.

Most recently, Protagen introduced a new bio-IT software product, Modiro™ – The PTM-Explorer, developed as a high-performance algorithm for identifying post-translational modifications (PTM) in large MS/MS data sets in a single step. “Utilizing mass spectrometry data from all leading instrument manufacturers, the software uses a number of search strategies to discover unsuspected and unknown mass shifts, sequence errors (isoforms), unspecific enzymatic cleavage, and transpeptidation products,” Dr. Hüls states.

Protagen claims that, compared with standard database search tools, Modiro cuts manual-results evaluation time down to minutes, even for LC-MS/MS analysis, and can nearly double the number of explained spectra. “Modiro is a valuable tool for both research and preclinical drug development to help unravel the function of proteins,” says Dr. Hüls. “We have already verified the ability of the tool to uncover protein PTMs that have never been identified before.

“The product is aimed at academic as well as preclinical proteomics research labs involved in the study of protein activity important for pathway elucidation in system biology or mode-of-action studies for new drugs under development.”

Modiro is the latest product in a portfolio of products and services Protagen has developed to expedite protein therapeutics research and product development, and maximize levels of meaningful data.

“Protagen has more than 10 years experience in the protein analysis field. During the last five years we have expanded our focus from one of primarily fee-for-service analytics, to include product development in its own right,” Dr. Hüls points out. “Our long-term partnership with Bruker Daltronics (www.bdal.com) was instrumental in the development of Modiro, which can be easily integrated into the latest ProteinScape 1.3.”

Expanding into the field of protein biochips, IP licensed in from academic institutes has also enabled the company to develop new chip-based technologies for antibody development and autoantibody biomarker discovery.”

UNIchip Products

Embodied in the UNIchip® product family, launched in 2005, Protagen’s protein chip technology has been developed to carry out a range of antibody analyses including specificity and off-target antibody activity, enzyme substrate/inhibitor identification, quantitative antibody fingerprinting, biomarker discovery, ELISAs, and protein-protein interactions.

“We are all aware of the potentially serious side effects of antibody therapeutics. UNIchip is a new technology that can test for the off-target activity of antibody candidates, helping to ensure safer testing in the clinical setting,” maintains Dr. Hüls.

Within the UNIchip family, the UNIchip AV-series is designed primarily for quantitative antibody characterization. Each UNIchip is spotted with 400 different human proteins and specific control proteins, allowing researchers to generate a specific antibody fingerprint and help identify the off-target-activity of an examined antibody.

Three different UNIchip AV protein biochips are available: UNIchip AV-400 comprises a cross section of cellular proteins; UNIchip AV-VAR EP includes extracellular proteins; and UNIchip AV-VAR MP is spotted with membrane proteins. Protagen also offers a full, flexible UNIchip service package, including study design, chip production, incubation, scanning, and data analysis.

“The successful UNIchip technology has aided development of our UNIarray™ biomarker discovery and verification program, an approach that enables the systematic identification of autoantibodies in patient sera for diagnostic and prognostic purposes,” Dr. Hüls continues.

UNIarray allows for the identification of diagnostic autoantibody signatures, which serve as biomarkers that can be used for patient stratification in clinical studies, treatment selection, or monitoring disease progression or therapeutic efficacy.

Utilized through in-house programs to find new biomarkers for diseases including multiple sclerosis, rheumatoid arthritis, juvenile idiopathic arthritis, and Alzheimer’s disease, UNIarray is also offered to the diagnostic and pharmaceutical industry through a collaborative business model.

Once the partner-specific concept has been arranged, Protagen then carries out Macroarray screening to find biomarker candidates, which are verified using protein microarrays. A biochip prototype and initial clinical testing are then carried out, and a final biochip assembled for use in a clinical setting.

“It’s a unique concept and a new business model for us that could potentially lead to faster, more accurate diagnostics,” maintains Dr. Hüls. “Our most advanced in-house program in multiple sclerosis has already generated promising results, and, despite only recently launching UNIarray, we are already in discussions with potential partners.”

The company is able to offer a range of protein identification, characterization and analytics services, from 1-D and 2-D gel electrophoresis and MALDI-MS/MS or LC-ESI-MS/MS, to N- and C- terminal sequencing via ISD (in-source-decay), amino acid analysis, and a full and flexible Macroarray service for antigen identification, based on its UNIclone® technology.

“The range of technologies and services Protagen offers, together with our drive to develop new products to speed the development of more effective, safer protein therapeutics, keeps us at the forefront of protein sciences,” explains Dr. Hüls “Proteomics hasn’t necessarily delivered in the past, partly because we needed to make more effort to ensure the quality and reproducibility of studies; but also because the focus on high throughput has been to the detriment of high performance. We need to start looking more at the quality and meaningfulness of results, rather than just sift through quantities of data.”

It’s a sentiment embodied in Protagen’s evolution over the last 10 years. “We are actively moving to offer the protein R&D sectors high-quality products and services that will make a real difference to the diagnosis and treatment of diseases. Our UNIchip and more recent Modiro and UNIarray technologies are prime examples and will help us move our business forward, as we continue product development over the coming years.”

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