Benchling launches purpose-built tools to accelerate RNA R&D

The new RNA capabilities are available to scientists using Benchling’s R&D cloud across the globe.

The platform is the first purpose-built offering on the market to help R&D organizations accelerate the delivery of drug candidates, said the developer.

Comprising an RNA-aware registry with visualization tools for oligo and mRNA design and the only tool with support for chemical modification of mRNA sequences, RNA biologists and chemists can now collaborate more efficiently, standardize their work across teams, and develop drug candidates faster, said the technology provider.

“With Benchling’s new RNA capabilities, scientists can now design, develop, and test a new mRNA vaccine or RNA cancer treatment from start to finish on a single platform,”​ said Ashu Singhal, co-founder and president of Benchling.

The company said scientists working on RNA and mRNA therapeutics, RNA-based gene therapy, and gene editing, globally, will benefit from:

• Faster RNA design: “Scientists can design RNA sequences more efficiently with easy navigation between monomer- and sequence-level views. They can use “find and replace” to execute chemical modifications more easily across entire sequences and reduce the need for manual, tedious effort.” ​
• Simplified collaboration: “All teams across the entire RNA R&D lifecycle can now operate on a single platform.”  ​
• Higher quality data and insights: “Scientists can now standardize and improve accuracy of RNA sequence design, including management of chemical modifications and uniqueness checks during registration. The standardization and centralization ensure high data integrity and improve data traceability. Any changes in structure can be directly associated with experimental results. As a result, scientists can aggregate data faster and make more data-driven decisions easily.” ​

Overcoming R&D limitations​

Prem Mohanty, product manager, Benchling, said RNA drug development often involves teams of biologists, chemists, bioinformaticists, and immunologists. Each team performs different experiments and uses advanced analytical instruments, generating vast amounts of diverse data that all need to be collected, stored, analyzed, and transferred to and between each group. “That scenario opens the door to a lot of silos and to a high volume of handovers and touch points, which in turn can lead to bad data,”​ he told BioPharma-Reporter.

While RNA therapeutics hold tremendous potential to impact human health, he said the R&D tools to create, test, and develop these molecules have been severely limited - traditional chemistry tools cannot model the intricacies of RNA biology, while biology tools ignore the chemistry involved with RNA modifications altogether, so scientists have had to contend with manual, low-throughput, and disconnected software to manage their R&D work.

“Scientists also have to use a variety of generic, siloed tools such as cheminformatics tools to design and chemically modify RNA sequences, biology-based tools to model sequence-level information, and/or generic sample management systems to model inventory needs. ​

“Use of spreadsheets is also rampant to track chemical modifications of RNA sequences, maintain inventory information, and bring together results from multiple sources. This leads to a variety of pain points such as the lack of standardization of sequence design across a team, duplication of effort, errors in monomer and sequence design, missing or incomplete experimental context, and significant time spent on non-value-added tasks including finding, aggregating, and cleaning data.   ​

“When scientists are spending more time on logistical tasks, they’re spending less time doing the science. Some 64% of scientists think their data collection hinders data analysis. And one final data point – on average, data has three to five different touch points across different teams and departments. We’ve seen the power that collaboration tools like Salesforce, AWS and Google Productivity Suite have had on making other industries more efficient and smarter, biotech and specifically RNA R&D can benefit from an R&D cloud as well.”​

In terms of how Benchling looked to overcome those challenges, he explained:

“We can’t help but see this scenario from the lens of a tech company, and these are the sort of challenges where we really thrive: improving collaboration, workflows, and information sharing. For us at Benchling, it was about the important role we could play, bringing better software to the science of RNA. ​

“As with any emerging science, it was also about the velocity and enthusiasm in RNA. So many of our customers are either adding more RNA therapeutics work into their pipeline or it's the sole-focus of their company. And while we’ve seen tremendous breakthroughs with mRNA for COVID-19, we all know the powerhouse potential of RNA — it’s extremely versatile and can be used across a variety of categories, from cancer treatments to rare diseases to something as immediately practical as the omicron booster. In other words, we didn’t want to miss the party.”​

“With our new launch, we’re providing tools purpose-built to design natural and modified RNA sequences and to store small molecule entities. Scientists access their biological constructs and chemical entities from a single, connected registry that offers complete experimental context for efficient collaboration and richer insights. Working from one central source of truth, one collaboration and data platform, makes their work more seamless, accurate and efficient.”​

Last June, the company launched technology focused on oligonucleotides, shorter strand RNA or DNA. “That was an important first step and gave our customers many of the tools to collaborate better across biology and chemistry and to work with designing and testing RNA and DNA oligonucleotides. But now with our recent launch, we are extending our capabilities to support longer length RNA such as mRNA in addition to revamping some of our design tooling across RNA oligos and sequences,”​ continued Mohanty.

End users ​

There are 1,000+ known companies working across RNA therapeutics, gene therapy and gene editing today, he said, and specifically 200+ known companies working on mRNA.

“This includes emerging companies and the big players. We know that nearly half of the top 50 global biopharma companies are involved in RNA work through their own pipelines, M&A, or strategic alliances. ​

“The end-users for our RNA solutions at these companies are RNA biologists, CRISPR scientists, research scientists, analytical scientists, and chemists. RNA therapeutics include a diverse group of therapeutic molecules that range from mRNA vaccines, antisense oligos, RNA-based gene therapy, and guide RNA-based CRISPR complexes to several other innovative RNA molecules. And this is a field that’s just getting started, it’s the tip of the iceberg with RNA therapies.”​

The new RNA capabilities are powered by Benchling molecular biology and registry applications: “They allow scientists to design, analyze, and register natural and chemically modified mRNA/RNA. Beyond this - because the Benchling R&D cloud has a scientifically aware data layer - scientists can now also use mRNA/RNA across their entire scientific workflow to capture data against RNA molecules and small molecule conjugates, improve traceability of RNA and related samples, and connect results with RNA structure. We also understand that our customers might have varying IT needs, so we provide our solution on a trusted, open platform that is extensible and can integrate with existing IT infrastructure, equipment, and instruments.”​