In Silico-Driven THIOMAB Approach for Stable PROTAC Conjugates by Docking Payloads in Antibody Cavities

The heterobifunctional proteolysis targeting chimeras (PROTACs) are a class of emerging therapeutic modalities that enable selective degradation of target proteins in cells. As antibody payloads, they offer several advantages compared to conventional chemical toxins, such as catalytic nature, potent and long-lasting activity, and precise selectivity to avoid systemic toxicity. However, the relatively large size and high hydrophobicity of these chimeric payloads may result in challenging the stability of antibodies, which complicates the in vivo performance. In this work, we use the highly hydrophobic GNE-987 as model PROTAC to evaluate a THIOMAB approach for mitigating the conjugate’s hydrophobicity while maintaining the therapeutic potency. We describe an in silico method to select the less hydrophobic site in an antibody and employ the stable tetrapeptide-aminomethoxy linker to conjugate the PROTAC payloads. The resulting degrader-antibody conjugate (J591 DAC) displays antigen-dependent BRD4 degradation and potent cytotoxic activity in PSMA-positive cancer cells. Finally, this DAC, bearing two highly hydrophobic PROTACs, also exhibits a long blood retention and strong antitumor efficacy in mouse models, likely owing to the homogeneous and stable conjugation from the THIOMAB approach. This work provides an example of the design and construction of antibody conjugates with highly hydrophobic payloads.