June 1, 2009 (Vol. 29, No. 11)

Firm’s KINOMEscan Measures the Active Site of the Enzyme rather than the Activity

For some companies, the third incarnation holds the key to success. Ambit Biosciences, founded in 2000 as Aventa, set out to build a comprehensive database of proteins and small molecule interactions. The founders believed that drug researchers would pay to search the database and select small molecules to inhibit biological targets. “At the time, the biotechnology bubble was inflating and lots of money was pouring into genomic and proteomic technologies that promised to accelerate drug discovery,” says Scott Salka, CEO.

The biotechnology bubble burst, however, and the company was forced to shift  gears. After operating briefly without a name, the company evolved into Ambit Biosciences in 2003 to focus on kinases as drug targets. It leveraged some of its initial technology to create a high-throughput screening (HTS) platform to select small molecule kinase inhibitors.

Kinases are a rich area for therapeutic drug development, with more than 500 kinases identified and more than 50 kinase inhibitors in clinical trials or approved by the FDA. Ambit’s expertise not only fuels its own pipeline, but also assists a growing list of customers to identify potential drugs, Salka says.

Ambit’s lead compound, AC220, is a second-generation class III receptor tyrosine kinase inhibitor that acts on FLT3-dependent tumors. Up to 40% of patients with acute myeloid leukemia (AML) have mutations in the receptor tyrosine kinase FLT3.

Based on the results of its Phase I trial, Ambit met with the FDA to discuss the possibility of conducting a registration trial of AC220 as a monotherapy for elderly AML patients. “If the outcome is good, we could get approval to sell the drug for elderly AML patients after only two clinical trials,” comments Salka.

In general, no good treatments exist for patients with AML older than 60 years. Elderly AML patients do not tolerate standard chemotherapy, and their life expectancy is less than six months after being diagnosed. “The clinical data we generated to date for AC220 opens the way for a potential major advance in the treatment of AML,” adds Salka.

Small molecule-kinase interaction maps for three approved kinase inhibitors across a panel of 317 human kinases.
(Adapted and reproduced with permission from Science and Cell Signaling Technology)

Flexible High-Throughput Platform

The success of AC220 also validates Ambit’s KINOMEscan™ profiling and drug-optimization platform. AC220 was identified using KINOMEscan, and it was designed, synthesized, screened, characterized, and optimized at Ambit. KINOMEscan is an active-site dependent, competition binding assay in which human kinases of interest are tagged with DNA, and a known ligand is immobilized on a solid support. Using real-time quantitative PCR, the amount of kinase bound to the immobilized ligand is measured in the presence and absence of a test compound. KINOMEscan includes a growing panel of more than 400 kinases, including all known clinically relevant kinases and mutations and inactive forms.

The technology replaces slow and time-consuming enzyme activity assays for evaluating potential kinase inhibitors. KINOMEscan consists of a set of HTS assays that measure binding at the active site of an enzyme, rather than enzyme activity. The degree of binding near the active site approximates the extent of inhibition of enzyme activity. “It took us a few years to broadly confirm that binding was a substitute for enzyme inhibition,” continues Salka. The assay is now widely accepted by drug discovery researchers, he adds.

Selectivity scores calculated for binding interactions with Kdscan assay platform.

Profiling Data

Ambit scientists published kinase profiling data for 38 well-known kinase inhibitors in January 2008, including details of a novel approach for quantifying the interactions between compounds and the human kinome. The approach allows for the systematic analysis of high-throughput kinase-profiling data and dramatically improves the efficiency of selecting and optimizing high-quality drug candidates from kinase-based compound libraries.

About 100 clients have contracted with Ambit to screen samples with KINOMEscan, including Roche, Cephalon, Astra-Zeneca, and Bristol-Myers Squibb, Salka reports. Customers send molecules of interest to Ambit, and a report is generated in one to two weeks.

“Many compounds at biotechnology and pharmaceutical companies that are moving their way through clinical development were selected and optimized with KINOMEscan,” Salka says. The process is flexible—customers can scan one compound against one kinase assay or 10,000 compounds against all 442 assays included in the HTS platform.

Rounding out Ambit’s in-house pipeline is AC480, a panHER kinase inhibitor for solid tumors in Phase II trials. By mid-2009, Ambit hopes to extend the testing of AC480 to glioblastoma patients. A BRAF kinase inhibitor was developed in partnership with Cephalon. Many tumors show mutations in the BRAF kinase, including melanoma and colon tumors. Inhibitors of Aurora, JAK2, and CSF1R kinases are also in development for inflammatory diseases and various types of cancers.

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