How can drug developers design therapies around cellular networks rather than a single target?

That is the question Arpeggio Biosciences is seeking to answer — and with a new influx of funds. The Boulder, Colorado-based startup announced the close of a $17 million Series A financing round on Wednesday, bringing its total funding to date to more than $20 million.

The funding was led by Builders VC, with participation from Khosla Ventures, TechU Ventures, FundersClub, Alice Zhang, Fifty Years, Tencent, ATEM Capital, Formic Ventures, Tau Ventures, Milad Alucozai of BoxOne Ventures and
and Matthew De Silva of Longtail Capital.

Arpeggio is a preclinical therapeutics company whose technology platform is focused on measuring the transcriptome — which refers to the full range of mRNA molecules expressed by an organism — at scale. It was founded in 2018 by CEO Joey Azofeifa and CTO Tim Read. The pair met at the University of Colorado, where they were completing PhD research that dealt with the intersection of machine learning and transcriptomics (the study of the transcriptome). 

The startup’s founders launched the company because they were interested in the idea of designing therapies to elicit specific effects on the transcriptome, which Azofeifa called “kind of a crazy idea,” in a recent interview.

“Typically when we think about drug development, we think about one protein or one enzyme at a time,” he said. “But if there’s one thing that the human genome has taught us, it’s that one gene does not equal one disease. It’s really a whole network of many small genetic changes that can give rise to something like autoimmunity or cancer metastasis.”

Arpeggio has built technology that can monitor activity of more than 100,000 mRNA transcripts from diseased and healthy cells after they are exposed to stimuli like small molecules, biologics or antisense oligonucleotides. The startup uses machine learning to reconstruct the biological networks affected by the stimuli and matches molecules to diseases where they could be therapeutically beneficial. This technology can illuminate new mechanisms of how drugs work, according to Azofeifa.

The startup will put half of the funds it raised toward maturing its own drug pipeline. It is currently working with contract research organizations to design better molecules for the treatment of mesenchymal tumors, Azofeifa said. 

Arpeggio will use the other to scale its partnerships with pharma companies. Under these partnerships, pharma companies send Arpeggio drugs so it can assess the impact these treatments have on the transcriptome, and the startup sells that intelligence back to these drugmakers. 

The company has partnered with more that 40 pharma companies so far, including Forma Therapeutics, Intrinsic Medicine and Treventis. The company could also go on to co-develop drugs with its pharma partners in the future — a scenario in which Arpeggio would collect royalties or milestone payments for drug success, Azofeifa pointed out.

While there are plenty of companies that do drug screens, such as Recursion Pharmaceuticals and Insilico Medicine, Azofeifa contends that Arpeggio is the only one focusing on the effect drugs have on the transcriptome. Other companies can measure things like whether a drug kills cells or whether it activates the immune system, but he said they do not “capture the true effect that drugs can have on the entire network of RNA.”

Photo: Christoph Burgstedt, Getty Images