ChemGenex Therapeutics Inc. has three compounds in the clinic, and it’s only been three years since the chemical genomics company was founded by CEO Dennis Brown, who also was a co-founder of Matrix Pharmaceutical Inc.

ChemGenex, of Menlo Park, Calif., is focused, as the name suggests, on chemical genomics to find small-molecule drugs for cancer. By creating novel technologies and using genomics techniques with information tools, the company said it has been able to speed up the drug discovery process.

“We’ve been able to modernize and get compounds into the clinic in a very rapid fashion,” Brown said.

ChemGenex’s approach allows drug discovery to proceed in an almost circular fashion, Brown said, as opposed to a linear progression, which is more time consuming and risky, with perhaps years passing before a company knows if its compound will work.

“What is unique about our company is that the tools we are using, such as expression analysis, are not only exciting for target identification and potential lead compound hit identification, they are also a very powerful tool for development,” Brown said.

The company’s lead compound, Ceflatonin, is in Phase II trials for a number of leukemia indications, including acute promyelocytic leukemia. Ceflatonin is derived from a tree found in China.

“Its history is not dissimilar to Taxol,” Brown said.

In Phase I/II studies is a second compound, Quinamed, for hormone-refractory breast cancer, prostate cancer and brain cancer. Quinamed is a water-soluble isoquinoline, which the company said affects a number of critical nuclear targets, including topoisomerase and ribosylation.

ChemGenex’s compound CGX-6001 is in Phase I/II studies for prostate disease. CGX-6001 is an oral chemopotentiator that is designed to enhance the activity of established chemotherapeutics that affect tubulin and topoisomerases. Studies of the compound in other indications, including colorectal cancer, are scheduled to begin this year. The company also has other compounds in preclinical studies.

One ChemGenex option for Ceflatonin would be to develop its own sales force should it get FDA approval, although Brown said no decision has been made in that area. Quinamed, he said, represents a “larger market opportunity and will require a larger marketing force to fully develop its uniqueness and strength.” If the company did go with a worldwide partner, it would still want to retain commercialization rights in North America, he said.

ChemGenex formed a joint venture in April with Elan Corp. plc, of Dublin, Irleand, to develop cancer drugs. Elan contributed an anticancer agent with promising activity in hematological malignancies and solid tumors and also made an equity investment in ChemGenex.

To date, the company has raised $5 million, and it is in the process of trying to secure Series B funding, Brown said.

ChemGenex has 10 full-time employees, but through its network of contract research organization and contract employees, that number rises to about 15 to 20 individuals dedicated to the company’s work.