AminoX: Making Biologics Safer with Synthetic Biology and Advanced Chemistry

The Problem

Protein drugs that activate a patient’s immune system against a disease, including recombinant therapeutic proteins and antibodies are at the cutting-edge of biomedical research and often offer the most effective way to treat a large variety of medical illnesses and conditions. However, many of them also cause toxicities known as “immune-related adverse events” (irAEs), because they bind to their designated protein target also in tissues that are not affected by the disease, which can result in unwanted local and systemic immune responses. One example are immune checkpoint inhibitors (ICIs) that increase the progression-free survival of cancer patients, but can also lead to sometimes life-threatening acute irAEs in patients, which then are forced to discontinue their treatments.

Our Solution

The AminoX platform technology allows validated and newly developed protein drugs to only become active in the tumor microenvironment. It enables to design and build non-standard amino acids (nsAAs) into strategic positions of a therapeutic protein’s amino acid sequence to bring them into the proximity of amino acids of the bound target protein. In comparison to conventional protein drugs which only bind their target proteins transiently yet everywhere in the body, nsAA-containing protein drugs can provide stronger, longer-lasting, and locally restricted target inhibition.

To incorporate nsAAs into protein drugs, AminoX uses a synthetic biology approach that hacks the biological process cells use to synthesize their protein repertoire. In natural protein synthesis, the protein-synthesizing ribosome needs the supply of tRNAs that are loaded with any of the 20 natural amino acids, whereby each tRNA recognizes a specific codon in protein-encoding mRNA molecules and each amino acid corresponds to the codon information. While scanning a mRNA molecule, the ribosome follows the mRNA’s instruction codon-by-codon, continuously accepting corresponding amino acids from codon-specific so-called “amino acid-tRNA intermediates,” which it uses to elongate the protein sequence.

AminoX pioneers a method that enables the generation of functional “nsAA-tRNA intermediates” – a major bottleneck in the general engineering of nsAA-containing synthetic proteins. These synthetic intermediates can effectively hand over their nsAAs to the ribosome which, in a scalable and specialized cell-free synthesis process, adds them to the protein sequence when it encounters a specific codon engineered into a critical position of a drug-mRNA blueprint. AminoX takes machine learning approaches to identify new nsAA designs with therapeutic potential and candidate positions in protein sequences at which to insert nsAA. The efficiency of its optimized protein synthesis process allows the high-throughput testing of multiple variants of a protein drug containing nsAAs at different positions. This screening process is greatly accelerated by fluorogenic nsAAs that start to fluoresce once a bond to a target protein has been formed.

Product Journey

The AminoX team formed at the Wyss Institute when Erkin Kuru from George Church’s group, Helena de Puig from James Collins’ group, started to discuss the potential of nsAAs, which they have been already exploring for diagnostic applications, as means to create better therapeutics. Erkin Kuru is an expert in the development of nsAAs and the chemistry of in vitro protein synthesis, and Helena de Puig had previously developed smart materials with diagnostic capabilities using CRISPR technology. Erkin Kuru and Helena de Puig were joined by Michaël Moret, another member of Church’s group who complements the team with critical computational, machine learning, and drug discovery expertise. Other scientific team members are Allison Flores and Subhrajit Rout. On AminoX’s validation path and its first focus on irAEs and nsAA-enhanced immune checkpoint inhibitor drugs, the team is advised by Girija Goyal, a member of Donald Ingber’s group, on questions involving the human immune system, and Wyss technology development experts Sylvie Bernier and Ken Carlson, as well as business development expert Bill Bedell.

Impact

In approved therapies and clinical trials, irAEs resulting from on-target, off-tumor effects of current immune checkpoint inhibitors have required 15% of patients treated with an anti-CTLA4 inhibitor, 8% of patients treated with an anti-PD-1 inhibitor, and 36% of patients treated with a combination of the two to discontinue treatment; and immune-compromised individuals are often not included in clinical trials for this promising class of drugs due to the increased risk of irAEs. Based on its potential to overcome problems in drug toxicity and create superior protein drug variants in multiple therapeutic areas, AminoX was selected as a high-priority 2023 Wyss Institute Validation Project.