Celgene-partnered Forma teams with Arpeggio to understand drug-target interactions

Drug discovery and early clinical development firm Forma Therapeutics, which counts Celgene and Boehringer Ingelheim among its collaborators, has tapped Arpeggio Biosciences’ capabilities in identifying drug candidates’ mechanism of action.

The partnership utilizes Arpeggio’s technology to identify the primary results of a drug’s impact on biological and genetic activity, to help Forma better understand the translational utility of its potential drug candidates.

Companies often use techniques like RNA-seq to perform cellular transcriptome profiling to investigate how a drug works in the biological system so that researchers can predict responsive patient populations before it heads into the clinic. The problem with RNA-seq is that it requires cells to be in the presence of the drug for a relatively long time before they can be collected to assess for mRNA changes. When these so-called “drug incubation periods” last too long, it’s difficult for scientists to differentiate primary targets from the many secondary and tertiary effects that have accumulated.

Arpeggio’s approach combines new RNA sequencing technologies with machine learning to shorten the time needed to capture significant quantities of biological information, the company told FierceBiotech. According to the company’s website introduction, its technology can measure changes in biological systems in less than 15 minutes of drug exposure, compared to over 12 hours required of RNA-seq. Its proprietary algorithms mine that data and help quickly identify the direct targets of a novel drug, which can then be used to continuously improve the sensitivity of its experiments, as well as understand transcription factor activity and various drugs’ mechanism of action.

The upstart was founded in 2017 based on research performed in the lab of Robin Dowell, Ph.D., a professor of molecular, cellular and developmental biology at the University of Colorado, Boulder.

“Using Arpeggio’s powerful combination of nascent RNA-sequencing combined with machine learning, we will be able to differentiate responses due to primary modulation of the therapeutic target, from secondary and tertiary effects,” said Forma President and CEO Steven Tregay, Ph.D., in a statement. “This will provide us invaluable information as we make critical decisions on candidates having potential for utility across a multitude of therapeutics diseases.”

Forma has already made its name in the industry with a strategic collaboration with Celgene first started in 2013, focused on protein homeostasis targets. In 2014, Celgene put down $225 million up front plus $375 million in milestones in a second deal to get Forma’s drug discovery engine to work on myriad areas. Both deals have achieved key milestones recently, and last August, Celgene came back to extend the 2014 pact with an additional $195 million, while also retaining its exclusive option to eventually acquire Forma.