NEW YORK – Proteomics firm Nautilus Biotechnology continues to struggle with the development of reagents for its single-molecule proteomics platform.
During a conference call Tuesday following release of the company's Q3 2024 financial results, CEO Sujal Patel said Nautilus has experienced higher-than-expected failure rates for the affinity agents used by the platform.
Nautilus' technology uses chips functionalized with DNA origami structures that allow researchers to deposit single proteins in extremely dense arrays, enabling single-molecule analysis of as many as 10 billion individual proteins. The Seattle-based company analyzes the arrayed proteins by iteratively staining the sample with semi-specific probes and then using machine learning to make identifications of the individual proteins based on the patterns of probe binding observed.
The company has had difficulty producing these probes. In 2022, for instance, Patel noted that development deals with outside firms including Abcam had not been as productive as hoped. During the Q3 call, he highlighted setbacks to the firm's internal probe development efforts, observing that it was seeing high failure rates when trying to move candidate probes to what he called "platform-ready" status.
"We always expected that there would be some fallout between probe candidate and platform-ready probe, but currently that fallout rate is too high," Patel said.
He added that Nautilus plans in the coming months to focus on its probe development workflows with the goal of hitting a roughly 33 percent success rate for moving candidate probes to platform-ready status.
Patel also said Nautilus aims to launch its proteomic platform in late 2025, though he said it was possible this could be pushed to 2026. He declined to say exactly when the company expects to demonstrate the platform's ability to measure on the order of 500 to 2,000 proteins in a complex sample, which he called a "critical milestone."
Nautilus has pushed back its timelines several times since launching. The company initially said it aimed to measure 2,500 proteins per run by early 2022, to measure up to 10,000 proteins per run by late 2022, and to analyze full proteomes by the middle of 2023. In 2022, it pushed a planned 2023 launch to mid-2024. In August 2023, it announced that while it continued to target mid-2024 for its launch, it was scaling back the specifications for the initial version of the platform. At the beginning of 2024, it again pushed back the launch timeline, this time to 2025.
In the meantime, Nautilus continues to develop its platform's capabilities for targeted analysis with an initial emphasis on profiling the proteoforms of the tau protein, which is linked to various neurodegenerative diseases, including Alzheimer's disease.
At the recent annual meeting of the Human Proteome Organization, the company presented on a new tau proteoform assay that Chief Scientist Parag Mallick said during the Q3 call can measure up to 2,048 proteoforms of tau.
In addition, Nautilus has signed research agreements with Amgen, Genentech, and MD Anderson for use of its technology for targeted applications.
For Q3 2024, Nautilus reported a net loss of $16.4 million, up 3 percent from a net loss of $15.9 million in the year-ago period. It did not post any revenues during the quarter ended Sept. 30.
Nautilus reported a loss per share of $.13 for Q3 2024, beating the consensus Wall Street estimate of $.16 per share and matching its loss per share in Q3 2023.
Nautilus's R&D spending in Q3 was $12.3 million, up 3 percent from $12.0 million a year ago, while general and administrative costs were down 4 percent to $6.8 million from $7.1 million.
Nautilus ended the quarter with $4.4 million in cash and cash equivalents and $136.2 million in short-term investments.
In Tuesday morning trading on the Nasdaq, Nautilus shares were down 5 percent at $2.66.