Plexxikon CEO Peter Hirth thinks his company is an example of the third generation of biotechnology companies.

Having had success as president of Sugen Inc. from its founding to its acquisition by Pharmacia Corp. in 1999, Hirth is taking his nearly 20 years of pharmaceutical and biotech experience and focusing on Plexxikon and its Scaffold Discovery Factory.

Founded in January 2001 in Berkeley, Calif., privately held Plexxikon opened its doors for business in June after receiving a Series A financing of $8.2 million in May. Hirth is now arranging a Series B financing, which he hopes to close soon.

Besides Hirth, other founders include Tom Kassberg, vice president, commercial and business development at Plexxikon; Song-Hou Kim, chemistry professor at the University of California at Berkeley; and Joseph Schlessinger, professor and chair of the department of pharmacology at Yale University Medical School.

Plexxikon’s approach rests on scaffolds, or basic chemical structures from which specific drug leads for druggable targets can be developed. The Plexxikon approach relies on bioinformatics tools, high-throughput co-complexing of ligands with proteins, large-scale protein production, high-throughput co-crystallization, use of surrogate proteins and in silico methods, and automated co-structure determination.

Plexxikon’s Scaffold Discovery Factory is designed to discover low-molecular-weight scaffolds that act on protein families that share common folds. Plexxikon has initiated discovery programs in the first four protein families and selected compound collections for screening.

Hirth said the work is important because so many protein families have been only marginally explored, such as the kinases, and Plexxikon wants to chart the territory.

“We think there is a unique window of opportunity now to file patents against as many protein families and scaffolds as [we] can get,” he said, noting that one scaffold can lead to multiple products.

Hirth said the first goal is filing patents and gaining control of the company’s discoveries and showing that they can be turned into leads. But Hirth also said he expects to be at 80 employees by year’s end.

“We will only vertically integrate within a year or two after we have mined the chemical universe,” he said.

Plexxikon already has strategic alliances with two companies and one academic institution, including an agreement with Scynexis Chemistry & Automation Inc., of Research Triangle Park, N.C., to access Scynexis’ Medchem-Factory technology. This will provide Plexxikon with dedicated chemistry processes using technology from chemists experienced in automation and high-throughput discovery chemistry.

The company also has an alliance with University of California, Berkeley, and the Phenix Consortium. Phenix provides Plexxikon with third-generation automation tools for high-throughput X-ray structure determination.

Hirth said Plexxikon would like to collaborate with people who have validated targets and drive the companies into clinical and preclinical studies.

“[We have had] interesting discussions where companies have issues achieving desired selectivity for the compounds,” he said.