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University of Pennsylvania, Diversa, Graffinity Pharmaceuticals, NeoGenesis Pharmaceuticals


Penn Proteomics Finds a Home

The University of Pennsylvania’s new proteomics facility has found a permanent home, the facility’s director Ian Blair told ProteoMonitor last week. The Dean of Penn’s School of Medicine, has allocated the proteomics facility 2,500 square feet of space in the Biomedical Research Building, which the facility will inhabit by February 2003, Blair said. Penn has pledged $5 million towards the new proteomics laboratory.

The proteomics research center will include 2D gel separations and imaging software from Amersham Biosciences and GeneBio, two Applied Biosystems Voyager DE Pro MALDI-TOFs, two ABI QSTAR Q-TOFs, and two LCQ Deca ion traps from Thermo Finnigan, as reported previously. Blair, also a professor of pharmacology and director of the center for cancer pharmacology at Penn, said the proteomics facility will be a component of the Genomics Institute, headed by biologist David Roos.


Diversa to Apply Proteomics to Genomes To Life

San Diego-based Diversa said last week that the Department of Energy, through its Genomes to Life program, had awarded the company $3.3 million to use its proteomics and genome sequencing technologies to study microbes with potential applications to environmental remediation. The award is part of a five-year, $36.6 million grant the DOE awarded the Lawrence Berkely National Laboratory.

In addition to comparing the genome sequences of microbes that respond to toxic environments, Diversa will also study the protein expression profiles of microbial cells. The company will have rights to license and commercialize any enzymes discovered or evaluated as part of its research and development efforts.


Lilly to Collaborate with Graffinity

Graffinity Pharmaceuticals has agreed to use its chemical genomics technology in an attempt to identify small molecule hit compounds for a selection of Eli Lilly’s therapeutic targets, Heidelberg, Germany-based Graffinity said last week. Graffinity’s chemical genomics technology involves the use of chemical microarrays, drug fragment libraries, and label-free imaging of protein-ligand interactions to search for hits to drug targets.

The companies did not disclose the nature of Lilly’s targets or financial details of the transaction, but Victor Matassa, Graffinity’s vice president for research and development, said in a statement that “the partnership has the potential to generate long term value” for his company.

Graffinity also has collaborations with Pfizer, Aventis Pharma, Boehringer Ingelheim, Celera, Biosearch Italia, and Structural Genomix.


NeoGenesis Collaborates with Mass General

Cambridge, Mass.-based NeoGenesis Pharmaceuticals and Massachusetts General Hospital molecular biologist Brian Seed have signed an agreement to jointly study potential drug targets and therapeutics for cancer and inflammatory diseases, NeoGenesis said last week. Under the four-year agreement, Mass General will use a proteomics strategy to supply protein targets to NeoGenesis, which will attempt to select lead compounds from its library of 10 million small molecules, the company said. Mass General will then use disease-based assays and animal models to validate the lead compounds.

According to NeoGenesis, Seed’s lab has the ability to produce and characterize hundreds of disease-associated proteins.


LifeSpan Signs Sankyo to Drug Target Database

LifeSpan BioSciences said last week that Japanese pharma Sankyo had subscribed to the nuclear receptor module of LifeSpan’s DrugTarget database, a collection of protein expression and localization information. The two companies did not disclose financial terms of the agreement.

Sankyo said in a statement that it subscribed to the nuclear receptor module of the database because the company is interested in pursuing nuclear receptor targets for diseases such as diabetes mellitus, cancer, and obesity. Sankyo already subscribes to the GPCR module of LifeSpan’s database.

Lifespan’s database includes proprietary immunohistochemical data, obtained using specific antibodies to determine protein localization in normal and diseased human tissues, as well as manually curated public sequence and localization data on more than 2,000 human genes from eight gene families. Other modules of the database include ion channels, protein kinases, protein phosphatases, phosphodiesterases, transporters, and proteases.


GeneFormatics Signs De Novo Pharmaceuticals as Partner

In its second partnership with a pharma company in the last four weeks, GeneFormatics has agreed to search for inhibitors to matrix metalloproteinases for Cambridge, UK-based De Novo Pharmaceuticals, the companies said last week. Specifically, GeneFormatics will study potential inhibitors to the M10 family of matrix metalloproteinases.

The agreement calls for GeneFormatics to identify all members of the M10 family, and characterize the structure and chemistry of the proteins’ active sites. De Novo will then perform docking models and run virtual screens of small molecules against the proteins to identify small molecules that inhibit their function. The two companies did not disclose financial details. Two weeks ago, GeneFormatics announced a drug discovery collaboration with Arakis, a specialty pharmaceutical company based in Little Chesterford, UK.


Pfizer Extends Collaboration with Compugen

Pfizer has agreed to extend its partnership with Compugen, the Tel Aviv, Israel-based company said last week. Specifically, the agreement provides Pfizer with a license to use Compugen’s LEADS computational biology software, and Z4000 and Z3, two 2D gel analysis software packages. Compugen did not disclose financial details.

The collaboration between the two companies dates to 1998, when Compugen began working with the Parke-Davis division of Warner-Lambert, which was acquired by Pfizer in 2000.

The Scan

NFTs for Genome Sharing

Nature News writes that non-fungible tokens could be a way for people to profit from sharing genomic data.

Wastewater Warning System

Time magazine writes that cities and college campuses are monitoring sewage for SARS-CoV-2, an approach officials hope lasts beyond COVID-19.

Networks to Boost Surveillance

Scientific American writes that new organizations and networks aim to improve the ability of developing countries to conduct SARS-CoV-2 genomic surveillance.

Genome Biology Papers on Gastric Cancer Epimutations, BUTTERFLY, GUNC Tool

In Genome Biology this week: recurrent epigenetic mutations in gastric cancer, correction tool for unique molecular identifier-based assays, and more.