Computationally Designed Bispecific Antibodies Using Negative State Repertoires
By Andrew Leaver-Fay, K. Froning, S. Atwell, H. Aldaz, A. Pustilnik, F. Lu, F. Huang, R. Yuan, Saleema Hassanali, A. K. Chamberlain and 3 more. 2016
53 citations recorded by the source corpus.
A challenge in the structure-based design of specificity is modeling the negative states, i.e. the complexes that you do not want to form. This is a difficult problem because mutations predicted to destabilize the negative state might be accommodated by small conformational rearrangements. To overcome this challenge, we employ an iterative strategy that cycles between sequence design and protein docking in order to build up an ensemble of alternative negative state conformations for use in specificity prediction. We have applied our technique to the design of heterodimeric CH3 interfaces in the Fc region of antibodies. Combining computationally- and rationally-designed mutations produced unique designs with heterodimer purities greater than 90%. Asymmetric Fc crystallization was able to resolve the interface mutations; the heterodimer structures confirmed that the interfaces formed as designed. With these CH3 mutations, and those made at the heavy-/light-chain interface, we demonstrate one-step synthesis of four fully IgG bispecific antibodies.
Subfields: Biomedical Engineering, Molecular Biology, Radiology, Nuclear Medicine and Imaging
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In Radiology, Nuclear Medicine and Imaging
Citations in the corpus
- Protein sequence design by conformational landscape optimization (2021, background): “Multistate design (10 – 12) can be carried out to maximize the energy gap between the desired conformation and other specified conformations, but the latter must be known in advance and be relatively few in number for such calculations to be tractable.”
- Essentials of de novo protein design: Methods and applications (2018, methodology): “It is worth noting that certain design problems, such as optimizing binding specificities, by definition require to include negative design and, for that purpose, multistate design methods have been developed, 57 – 59 but these are beyond the scope of this review.”