GOALI: Methods for designing antibodies specific for intrinsically disordered proteins

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1605266 Tessier, Peter M. A grand, unmet challenge in the field of biotechnology is to be able to reliably design antibodies that recognize pre-selected epitopes within diverse biomolecules. This project has broad implications for understanding fundamental principles for designing binding proteins that can be used for a wide range of applications. This GOALI project will also expose graduate students to the biotech industry through research experiences at Pfizer, short courses taught by Pfizer scientists, and regular interactions with Pfizer scientists. Another key focus of this proposal is to develop science outreach programs to underrepresented minorities and other disadvantaged students in New York's Capital Region.This collaborative GOALI project between academia (Rensselaer Polytechnic Institute) and industry (Pfizer) is aimed at overcoming the limitations of using immunization to generate antibodies specific for intrinsically disordered proteins. The proposed method for designing antibodies is inspired by the natural hydrogen bonding interactions between beta-strands within folded proteins. This approach is based on mining the Protein Data Bank for small peptides (3-6mers) within beta-strands that are naturally paired to segments of the target epitope in neighboring beta-strands. By identifying multiple small peptides that are complementary to the target epitope and which overlap with each other, larger complementary peptides will be generated. These peptides will be evaluated for their ability to mediate antibody binding to the target epitope when grafted into the complementarity determining regions (CDRs) of antibody fragments. Moreover, molecular modeling and directed evolution methods will be used to identify mutations in the grafted complementary peptides and neighboring CDRs that further increase binding affinity. Finally, solubilizing mutations in and near the CDRs will be introduced to overcome the hydrophobic nature of the grafted peptides.This award by the Biotechnology and Biochemical Engineering Program of the CBET Division is co-funded by the GOALI Program of the Division of Industrial Innovation and Partnerships and by the Biomaterials Program of the Division of Materials Research.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.