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Zafrens Bets on Drug Discovery Market With High-Throughput Cell-Based Assay Platform


NEW YORK – Life sciences technology startup Zafrens launched this week with $23 million in financing to commercialize its high-throughput, multiomic cell analysis platform for drug discovery services.

The San Diego-based company said it plans to generate revenues through pharma partnerships while continuing to use its platform internally to garner biological and clinical insights.

Traditional drug discovery focuses heavily on small molecule compounds, "and all the experiments are done in 96-well plates," said Zafrens CEO and Cofounder Swamy Vijayan. "The thought was, could we simplify drug discovery using multiomics tools?"

Zafrens was incorporated in the summer of 2021 and started operations in January 2022. Besides Vijayan, its cofounders include Yi Zhang, executive VP of engineering; Kayj Shannon, VP of corporate development; and Ravi Ramenani, director of applications.

Vijayan had previously worked at Illumina and subsequently helped establish two other firms, Omniome and Plexium. Omniome had developed a sequencing-by-binding platform and was later acquired by Pacific Biosciences. Meanwhile, Plexium invented technologies to enable high-throughput DNA-encoded compounds for cell-based drug discovery.

"We can do high-throughput cell-based assays, but then you still have to spend a lot of time worrying about, 'Is this compound going to be toxic? What is the mechanism by which this compound has an effect on the cell?'" Vijayan said. "It was an opportunity again for the early [Zafrens] team, and I started thinking about [how we could] compress more stages of drug discovery using omics tools."

Zafrens' foundational technology is a high-throughput microfluidic chip-based platform named Z-Screen. Each chip contains 50,000 to 200,000 microwells with imaging and multiomic capabilities integrated into every well.

"The thing we want to emphasize is, any experiment you can do in the 96-well plate format, we can do [on our platform] without any robots," Vijayan said.

Using an approach the company plans to publish in the future, the platform can sort 50,000 to 200,000 single cells into barcoded microwells. The platform also enables co-culture experiments, where individual cells can interact with other cell types, so researchers can observe their interactions and measure secretions longitudinally.

In addition, the platform can combine functional analysis of live cells via imaging with multiomics assays, which cover the whole transcriptome and a number of proteins. The mRNA analysis involves a proprietary library prep method that is integrated into the platform’s chip engineering, followed by sequencing on Illumina devices.

Finally, Zafrens' technology can carry out perturbation experiments on individual cells using small molecules, peptides, or genetic material.

The company has synthesized about 11 million compounds on beads, each with a unique QR code, that can be tracked and placed into individual wells. Since the compounds are photocleavable, they can be released to target cells upon light activation. Cellular responses to the compounds can then be measured simultaneously by imaging or sequencing-based expression profiling, Vijayan said.

"What would typically be multiple stages of drug discovery, we end up doing in one experiment because we integrated multiomics at scale," he noted.

While the platform can assay single cells, Vijayan emphasized that he does not consider Zafrens a single-cell company. "Our approach is to isolate a lot of single cells but study them functionally and longitudinally in the context of other cells and other kinds of microenvironments," he said.

Zafrens started to build its platform in 2022 and "had most of the components working" by the middle of this year, he said. The company has also been optimizing different applications, such as for T cells and small molecules, with partners.

Zafrens' current business model is to earn revenues through pharmaceutical partnerships while advancing internal projects, Vijayan said.

At the moment, the firm is focusing on developing the platform for analyzing RNA regulation, which is likely going to be its first commercial service. In addition, Zafrens is advancing the platform for small molecule and T-cell therapeutics applications.

The company currently does not have plans to sell its platform, Vijayan noted.

To date, Zafrens has raised $23 million in financing, led by Prime Movers Lab. BlueYard Capital, Kofa Healthcare, Global Brains, FoundersX Ventures, Alix Ventures, Possible Ventures, Iaso Ventures, and Hawktail Ventures are also investors in the company.

Vijayan said the bulk of the money will be used to continue advancing the company’s platform, as well as forging partnerships with pharma companies. Zafrens is already working with three unnamed partners at an early stage, he added.

Most of the company's technology has been developed in-house. It has filed "a handful of" provisional patent applications covering technologies pertinent to the Z-Screen platform, Vijayan said.

Other companies, such as Recursion, 10x Genomics, Eikon Therapeutics, and Bruker's PhenomeX (formerly Berkeley Lights), have also been developing platforms and assays for the cell-based multiomic drug discovery space. However, Vijayan asserted that "none of these companies are considered competitors," given that the firm is "pioneering a new approach to drug discovery that is distinct in the simultaneous scale and resolution."

The company currently has about 30 employees, including engineers, biologists, and chemists, and plans to further build out its computational team.

"Ultimately, our value is to show we can find good molecules," Vijayan said. "We want to play in that niche where we bring our expertise in multiomics to advance therapeutics for patients and compress the timeline it takes [to develop them]."