Abstract
Purpose :
Usher syndrome type 1B (USH1B), caused by mutations in the MYO7A gene, results in hearing and vision loss. MYO7A ~7kbp gene size cannot be packaged within a single adeno-associated virus (AAV) vector (Fig. 1) for effective treatment. We suggest a de-novo protein design based approach to generating compact MYO7A replacement. Our approach generates a fully functional compact MYO7A enabling its packaging into a single AAV for potential therapeutic applications.
Methods :
Our approach is based on two key steps: modeling and generation. In the modeling step we explicitly define the binding modes, interacting rotamers, of MYO7A to its binding partners SANS and Harmonin (Fig 2A). To that end we use genotype-phenotype (ClinVar), structure (RCSB, AlphaFold2, RosettaFold), and dynamics (GROMACS) analysis. Next, a generative AI protein design algorithm, RFDiffusion, creates compact scaffolds that stabilize the selected function critical rotamers. Sequences are generated (proteinMPNN) and distilled by re-predicting structure and properties of the generated sequences. The top in-silico scoring candidates are synthesized to validate their expression and binding mode using BioLayer Interferometry (BLI).
Results :
Our FERM1-SANS interaction analysis identified 11 out of 627 critical residues to preserve and generated 20k mini-FERM1 constructs ranging in size of 220-250aa, a 5/2 compression ratio. 23 top scoring candidates were selected for in-vitro testing. 23/23 of the designs expressed, were soluble and stable, and had a clear band on SDS-PAGE. 15/23 (65%) demonstrated clear BLI signal indicative of binding to the SANS protein (Fig. 2B), some with affinities, approaching that of the wild-type MF1. Top selected FERM1 and FERM2 (to be tested) domains will be taken for reconstruction of the functional compact MYO7A protein for AAV packaging and further in-vitro and in-vivo testing.
Conclusions :
Overall our innovative approach holds great promise for developing single AAV Usher 1B gene therapy. The successful miniaturization of MYO7A, achieved through the utilization of computational modeling and advanced protein design techniques, signifies a breakthrough that propels the advancement of next-generation minigens.
This abstract was presented at the 2024 ARVO Annual Meeting, held in Seattle, WA, May 5-9, 2024.