Accelrys, Sun create 3D proteome map for Neisseria meningitidis

Accelrys, a wholly-owned subsidiary of Pharmacopeia Inc. (Princeton, NJ), announced that through its technology collaboration with Sun Microsystems Inc., Accelrys has successfully mapped 70% of the Neisseria meningitidis genome with functional annotations. This creates a wealth of opportunity for mining new protein drug targets for the treatment and prevention of bacterial meningitis. The new map represents a substantial improvement in the functional assignment of 54% of the genome reported previously, and has resulted in over 300 new assignments of proteins that could be targeted for therapeutic intervention. The need for treatment options for meningococcal infection persists, since the role of the bacterium Neisseria meningitidis in causing bacterial meningitis and septicemia (severe conditions that can result in brain damage, coma, and even death) is well established.

Utilizing a 24 cpu Sun Enterprise 6500 system, Accelrys scientists were able to analyze the Neisseria meningitidis genome using GeneAtlas(TM), Accelrys' leading edge protein annotation tools to facilitate the search for new drugs to fight the disease. The combination of multiple annotation approaches within the GeneAtlas technology provides for more robust assignment of protein function, which is beneficial in guiding future experimentation to further validate putative drug targets. Several known targets, such as outer membrane proteins, iron-dependent regulator proteins and lipoproteins, were annotated with this technology. Importantly, GeneAtlas' inclusion of 3D annotation tools provides access to model structures for many of the protein targets that can be used subsequently in the drug discovery process.

"The combination of robust assignment of protein function with the 3D annotations generated by GeneAtlas has provided novel annotations for many proteins in Neisseria meningitidis," commented Dr. Scott Kahn, Senior Vice President, Life Sciences, at Accelrys. "We continue to work with Sun in our efforts to further leverage chemical knowledge for the annotation of genomic data, a process called chemical genomics, with the goal of enabling researchers to advance novel gene targets through to the lead identification phase of the drug discovery process more rapidly."

"Accelrys' GeneAtlas technology nicely illustrates the power that SUN's computing platform can provide in helping to solve some of the world's toughest challenges in the life sciences field," said Dr. Siamak H. Zadeh, Group Marketing Manager of Life Sciences at Sun Microsystems, Inc. "Building upon Sun's pioneering involvement in the bioinformatics and genomics areas, this work with Accelrys is extending our impact into proteomics, demonstrating our ongoing commitment in helping to solve some of the world's most critical computational challenges in life science."

Pharmacopeia (www.pharmacopeia.com) is a leader in enabling science and technology that accelerates and improves the drug discovery and chemical development processes. Pharmacopeia's software subsidiary, Accelrys, develops and commercializes molecular modeling and simulation software for the life sciences and materials research, cheminformatics and decision support systems, and bioinformatics tools including gene sequence analysis. The business also provides consulting services to its customers in drug discovery and chemical development. Pharmacopeia's Drug Discovery segment integrates proprietary small molecule combinatorial and medicinal chemistry, high-throughput screening, in-vitro pharmacology, computational methods and informatics to discover and optimize lead compounds and to accelerate customers' drug discovery efforts. Pharmacopeia employs approximately 750 people, generated 2000 revenues of approximately $119 million, and is headquartered in Princeton, NJ.

Source: Pharmacopeia, Inc.