Using antibodies to control chemical reactivity

In this work we demonstrated how to repurpose IgG antibodies to boost different chemical reactions and synthesize functional molecules.

The work has recently been published in Nature Communications. Follow this link to read the full article or read Lorena’s post below for a summary.

The environment in the interior of a cell consists of a solution full of molecules that interact in an ordered and harmonic fashion, with bio-chemical reactions happening at the right place and at the right time. One of the ways by which Nature achieves this high coordination is through proximity: the reactants are brought into a confined space that boosts their effective concentration and allows them to react.

The way Nature controls the chemical reactivity inside a cell is what any organic chemist dreams of: multiple reactions that can be specifically controlled in complex mixtures without any cross-reactivity. Inspired by this mechanism, we have demonstrated that it is possible to use biomolecules with bivalent binding (i.e. IgG antibodies) to induce proximity between reactants and thus control their chemical reactivity. To do this we took advantage of the versatility of synthetic DNA oligonucleotides and the predictability of DNA-DNA interactions. More precisely, we employed two synthetic DNA oligonucleotides each of them modified at one end with a chemical reactive group. These two DNA strands were also modified at the other end with a recognition element (i.e. an antigen) for a specific IgG antibody. Under diluted conditions, the two reactive groups cannot react with each other as their encounter is highly improbable. However, things change when the specific IgG antibody targeting the antigens at the ends of the DNA strands is present in solution. The bivalent binding characteristic from IgG antibodies allows for the colocalization of the two reactive groups. As a result, the chemical reaction can occur, and a product is obtained (Figure 1).

Figure 1. IgG antibodies induce proximity between reactants (reactive groups linked to complementary DNA strands) thus triggering a chemical reaction.

Because we can very easily change the antigens and the reactive groups on the DNA strands, we can make the system responsive to different antibodies and also trigger different reactions. Everything is triggered by the very specific recognition event between the antibody and the antigen so we can design parallel systems so that multiple reactions could be controlled in the same solution by different antibodies (Figure 2).

Figure 2. **Orthogonal control of reactions mediated by different specific antibodies**. Two systems with complementary DNA pairs each labeled with a specific recognition element (DIG and DNP) were used in the same solution. One strand from each complementary pair was also labeled with a different fluorophore to differentiate the products.

However, not all the research involved in this project was limited to the wet lab. We happily collaborated with a professor in theoretical organic chemistry that, based on some of our experimental results, could model the system in a very accurate way. It was mind-blowing to see that the events that happen in solution, which in my mind were pictured in a very simplistic way, could be mathematically described by kilometer-long equations.

He developed a kinetic model that predicts the final yield of the reaction depending on the affinity of the DNA system and the type of antibody used to induce proximity between reactants (Figure 3). To see how theory fitted the experimental data somehow felt like putting in the last piece of a puzzle.

Figure 3. **Plot of reaction yield vs. the inverse of dissociation constant.** For each pair of dots, the dot on the left and on the right correspond to the experimental yield in the absence and presence of the anti-DIG antibody, respectively. The solid curve is the theoretical yield obtained by fitting the experimental points to the kinetic model of the system.

Finally, we explored the possibility to generate functional molecules such as therapeutic agents using these antibody-templated reactions. As a proof of principle, we demonstrated the formation of an anticoagulant drug able to inhibit the activity of thrombin, a key enzyme of blood coagulation and an important target for the treatment of thrombosis. We demonstrated that a specific IgG antibody can trigger the formation of the anticoagulant agent, which was further proven to efficiently inhibit the activity of thrombin.

In summary, we show that the natural function of IgG antibodies can be repurposed to control the reaction between two reactive groups in solution. The potential ability of IgG antibodies to control chemical reactions would allow the formation of different molecules, ranging from imaging to therapeutic agents, only when a specific diagnostic IgG antibody is present. We envision that this strategy might find applications in diagnostics and therapeutics.

Written by Lorena Baranda Pellejero, PhD student in Francesco Ricci’s research group at UNITOV

Reference: Baranda Pellejero, L., Mahdifar, M., Ercolani, G. et al. Using antibodies to control DNA-templated chemical reactions. Nat Commun 11, 6242 (2020). https://doi.org/10.1038/s41467-020-20024-3

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