Carmot Therapeutics, a small company located in San Francisco’s Mission Bay, has developed a very innovative drug discovery technology, called Chemotype Evolution (CE), that relies on fragment-based discovery but is different from traditional FBDD and HTS approaches in important ways.
The first important innovation is that CE relies on a “bait” molecule as a starting point for screening. The bait can be a known ligand, cofactor, or inhibitor. The bait is then derivatized with a linker moiety that allows it to become chemically bonded with every fragment in a proprietary library. This process generates a screening library that contains thousands of bait-fragment hybrids. These hybrids are then screened against the target for binding using either biophysical or biochemical screening techniques in a high-throughput plate format.
The most powerful aspect of CE is the ability to iterate over chemical space, allowing access to an exponential number of possible fragment-bait hybrids. The method can be iterated with new “baits” derived from the best fragment hits of the previous round. Thus, instead of having 7,000 fragments in your library, after 3 iterations you access 7,000^3 possible combinations (343 billion possible compounds), selecting only the most target-relevant chemotypes at each stage.
The CE approach is similar in concept to the “tethering” approach pioneered at Sunesis, but differs in the fact that no protein engineering of cysteine residues needs to be performed. The bait molecule performs the role of the engineered cys, providing a “handle” that binds to the target and selects for complementary fragment binders.
Carmot Therapeutics just embarked upon their first major industry collaboration with the January 2014 announcement of a partnership with Amgen to use CE technology against two challenging targets. Identifying leads and developing hits will be carried out jointly between the companies, while clinical trials will proceed at Amgen. I think Carmot is definitely a company to watch given its innovative and potentially paradigm-shifting discovery technology and increasing interest from big pharma.