Automating DNA Synthesis Boosts Drug Discovery – Genetic Engineering & Biotechnology News

Software

By Jyotsna Venugopal, PhD

Jyotsna Venugopal, PhD
Telesis Bio

Since its introduction 20 years ago, the field of synthetic biology has shown remarkable progress. For example, it has generated increasingly sophisticated synthetic DNA and RNA solutions, supporting increasingly ambitious research projects. And now it is beginning to enable applications in drug discovery.

Synthetic biology follows an iterative three-part cycle: design, build, and test. It has enabled the systematic interrogation of the genome to identify key molecules and their corresponding functions. It has also started to drive innovations in a range of applications. These applications include the engineering of proteins for agricultural products, the development of therapeutic antibodies, and the production of next-generation adoptive cell therapies.

Such applications are so demanding that continued progress depends on tools that can enable more efficient synthetic biology workflows. Synthetic biology must keep pace with other technologies such as rapid sequencing, machine learning, bioinformatics, and biophysical screening. Otherwise, these technologies will be limited in their ability to accelerate the design and testing of candidate sequences. In pharmaceutical and biotechnology companies, where all parts of the workflow must be robust to meet demand, eliminating synthetic biology bottlenecks is key to accelerating discovery.

Current synthetic biology solutions for discovery workflows pose many limitations, whether the workflows are for engineered proteins, therapeutic antibodies, or cell-based immunotherapies. Turnaround times for synthesis or cloning projects can be unpredictable. All too often, the turnaround times are too long, especially for complex projects.

Outsourcing these projects to a service provider often leads to a lack of control over workflows and involves the sharing of proprietary biological information or material with external parties, raising security issues. Keeping the projects in-house and using conventional molecular biology techniques to synthesize constructs poses its own difficulties. These include complex manual workflows, lavish time investments from expert personnel, and inconsistencies in the accuracy of results. Such difficulties limit the adoption and application of synthetic biology for discovery.

Fortunately, these difficulties may be addressed by recent advances in automated synthetic biology platforms. Innovative solutions that combine the reliability and speed of automation with industry-leading synthesis chemistry are bringing synthetic biology back into laboratories, enabling rapid overnight synthesis with barely any hands-on time required.

Synthetic biology bottlenecks have constrained discovery screening workflows. However, these bottlenecks are being eliminated now that synthetic biology platforms are being automated. Indeed, these platforms are bringing about a new age of discovery.

Telesis Bio (formerly Codex DNA) recently introduced the BioXp 9600, a next-generation high-throughput platform for synthetic biology workflows. The BioXp 9600 system, which incorporates proprietary Gibson Assembly and two-step error-correction technology, is designed to provide overnight, automated synthesis of genes, clones, DNA libraries, and mRNA. BioXp kits include custom reagents to build, amplify, and assemble DNA fragments, clones, and variant libraries.

Antibody discovery

Pharmaceutical and biotechnology companies have been hard-pressed to develop new antibody-based therapeutics. Earlier generations of antibody-based therapeutics addressed simple targets. But new drug candidates are trying to address more complex targets such as G protein–coupled receptors and ion channels.

To boost antibody discovery success rates, scientists have adopted synthetic biology. The goal is to screen many more candidates to identify higher-quality antibody leads for challenging targets.

The discovery process begins with sequencing and ends with screening, two highly efficient techniques. But the discovery process also involves another technique: the cloning and expression of heavy and light chain variable sequences. This technique is less efficient. Indeed, it makes for a rate-limiting step.

During this step, codon-optimized candidates must be synthesized and cloned into plasmids. Once those candidates are screened, the process begins again with new sequences designed based on which ones performed best.

With traditional DNA synthesis via outsourcing, this iterative process might add months to the discovery workflows due to long synthesis lead times for large numbers of complex antibody sequences each time new candidates must be synthesized and cloned. In an industry facing challenging timelines, the ability to support higher throughputs efficiently and seamlessly across workflows is important to quickly comb through enough candidates and generate leads.

With in-house DNA synthesis using an automated benchtop system, new candidates can be built, cloned, and amplified in just a few days with minimal user interaction. Moreover, in-house automation helps researchers ensure that valuable proprietary vector information remains protected through the discovery process.

Protein or enzyme engineering

A mainstay in the drug discovery and development process, enzyme engineering is widely used to improve purity, yield, and production reliability for protein-based drug candidates. The process typically involves a discovery phase to find a template candidate, followed by iterative cycles of engineering for each desired trait. Engineering is often performed through the synthesis of variant libraries, giving scientists the opportunity to study how performance varies among enzymes that have slightly different sequences.

The longer each cycle takes to complete and inform the next cycle, the more the entire enzyme engineering process delays the identification of a lead candidate for development. That’s why scientists are so focused on finding ways to shorten cycle time. There is no way to run cycles in parallel, as the outcome of each cycle is used as the basis for the next. Given the time pressures of drug development, scientists usually must make an unfortunate compromise—screening fewer variants than they would like and accepting that the results may be suboptimal.

Here, too, an automated platform for in-house DNA synthesis can make a real difference. The ability to synthesize several variant libraries—both high-diversity and low-diversity libraries—in just a day or two can shave weeks or months off each cycle, allowing scientists to test enzyme activity and design another round of candidates far more quickly.

Immunotherapy discovery

Synthetic biology is also being used to streamline a much newer class of treatments: patient-specific immunotherapies. In this growing area, scientists have already demonstrated the value of synthetic biology approaches for screening and optimizing T-cell receptors (TCRs) and chimeric antigen receptors (CARs).

With TCRs, for instance, screening for tumor reactivity is often conducted by generating TCR construct cell lines in Jurkat, and then generating a yeast display or mammalian cell line libraries. After that, TCRs are engineered into autologous peripheral T cells, and then the modified T cells are expanded and infused back into the patient. The process of building candidate TCR constructs can be dramatically accelerated with automated in-house DNA synthesis, reducing a weeks-long process to just a few days.

Similarly, workflows designed to generate CARs for potential use in CAR T-cell therapies are slowed by traditional DNA synthesis and its long turnaround times. These therapies need to be designed and manufactured quickly for optimal patient care. Access to high-throughput benchtop automation workflows in synthetic biology helps accelerate discovery by lowering the barrier to complex TCR discovery and CAR engineering workflows, and by giving valuable time back to researchers juggling multiple priorities.

Technical limitations

When pharmaceutical and biotechnology firms adopt synthetic biology for more parts of the drug discovery and development process, they tend to rely heavily on outsourced solutions. Besides posing practical challenges, such solutions are simply suboptimal.

As sequences become more complex, lead times for synthetic DNA become more of a challenge, especially in higher-throughput discovery projects, where lead times are already unpredictable and longer than desired, especially when vendors are involved. From the time a scientist orders a sequence—usually in response to a specific need in the drug discovery process—weeks or months may pass before a vendor returns a construct. In this model, scientists also lose the power to control their discovery workflow, relying entirely on providers to troubleshoot or move things forward when challenges arise in the synthesis process.

Outsourcing is sometimes limited to fragment synthesis to mitigate costs. In these cases, downstream fragment assembly, cloning, and sequencing can slow the discovery process if, for example, the entry of a particular DNA construct into the workflow is delayed. At a time when the pressure is on pharmaceutical and biotechnology companies to get new treatments to market faster, such delays are untenable.

Recent improvements

In the past few years, scientists in the synthetic biology field have finally used an alternative to DNA synthesis vendors. New automated benchtop instruments have enabled researchers to build DNA constructs in their own laboratories.

Automated synthetic biology platforms can produce dozens of constructs or libraries in a single overnight workflow. Some of these platforms offer automated error-correction capabilities. By preventing minor errors from compounding, these platforms increase the likelihood of generating highly accurate DNA products that do not require extensive quality control steps. These platforms are designed to run independently. Accordingly, they can minimize the hands-on time required of users.

When DNA is built in-house, it is easier to protect intellectual property because designed sequences remain under tight control. They don’t have to be shared with a vendor.

Finally, automated systems can improve workflow control and increase throughput in the “build” phase of synthetic biology’s design-build-test cycle, ensuring that it matches the efficiency of the design and test phases. Helping the build phase keep up with the other phases is particularly important for a few key applications where synthetic biology is already being implemented in pharmaceutical companies’ pipelines.

Looking ahead

Synthetic biology promises to enhance drug discovery workflows, especially now that automated DNA synthesis platforms are entering laboratories. These are benchtop platforms, and they will soon be employed across a broad range of applications. Because they can deliver highly accurate constructs while reducing turnaround times and lowering costs, these platforms are in a position to help pharmaceutical and biotechnology companies expand their pipelines.

Jyotsna Venugopal, PhD, is director of product marketing at Telesis Bio.