|Challenge: The design of superior biologic therapeutics such as monoclonal antibodies, single-domain antibodies, and engineered proteins requires optimizing their ability to bind to disease targets. Antibodies offer many advantages over small molecules in treating diseases, but the process for generating them is complex, expensive and often requires further steps of affinity maturation to achieve the desired level of potency. Molecular modeling can accelerate the discovery and development of therapeutic antibodies and can help re-engineer and improve existing ones that have sub-optimal properties.
Solution: The principal Investigator has developed a platform called ADAPT (Assisted Design of Antibodies and Protein Therapeutics) to rapidly design antibodies against specific targets. It interleaves computational predictions with experimental validation for focused step-wise affinity maturation from single-point to quadruple mutants. An exhaustive single-mutant virtual scan of all CDR (complementarity determining region) loops is carried out using consensus scoring functions. Selected mutants from the top-scoring ones are experimentally tested. Virtual screening of double mutants comprised of validated single mutants is then carried out. Selected double mutants are validated and the process is iterated to generate triple and quadruple mutants. Significant improvement in affinity is typically obtained with 30-50 mutants designed and tested.
Achievements/Impact: As a proof of concept, the platform was applied to antibodies against VEGF-A and HER2, both therapeutic targets in cancer. Enhancements in binding affinity by as much as 100-fold over the parent antibody were obtained with triple mutants. Post-project, ADAPT has been used to enhance the binding affinity of a single-domain antibody against C. difficile toxin A by 10-fold. It has also been used to introduce a pH-switch to an antibody against HER2, making it more specific to cancer cells versus normal cells, mitigating its potential adverse side effects.
The platform should reduce the cost of therapeutic antibody development, while generating highly specific, high affinity drug candidates for the pharma industry.