De novo design of immunoglobulin-like domains

Abstract

Antibodies, and antibody derivatives such as nanobodies, contain immunoglobulin-like (Ig) β-sandwich scaffolds which anchor the hypervariable antigen-binding loops and constitute the largest growing class of drugs. Current engineering strategies for this class of compounds rely on naturally existing Ig frameworks, which can be hard to modify and have limitations in manufacturability, designability and range of action. Here, we develop design rules for the central feature of the Ig fold architecture—the non-local cross-β structure connecting the two β-sheets—and use these to design highly stable Ig domains de novo, confirm their structures through X-ray crystallography, and show they can correctly scaffold functional loops. Our approach opens the door to the design of antibody-like scaffolds with tailored structures and superior biophysical properties.

Wetting hysteresis induces effective unidirectional water transport through a fluctuating nanochannel

“…On the other hand, de novo protein designs have been actively proposed recently. [60][61][62] To the best of our knowledge, the design of proteins focusing on fluctuations has not yet been reported, but if, for example, photoswitching molecules can be grafted inside nanochannels or transmembrane proteins with gate structures exhibiting specific fluctuations can be designed from the amino acid sequence, water transport by the proposed mechanism will eventually be possible. Another technical implementation is to control channel wettability and pore size with time-dependent external stimuli.…”

The structural landscape of the immunoglobulin fold by large-scalede novodesign

“…Specifically, certain combinations of β-arch loop conformations, when compatible with β-strand length and sidechain orientations, strongly support the formation of the central cross-β motif within the core of Ig domains 10 . Based on these principles, we succeeded to de novo design 7-stranded Ig domains by a fragment-based computational approach using specific combinations of β-arch conformations 10 . However, the diversity of the designs was heavily constrained by the combinations of β-arch loop conformations considered, which exponentially grows with the number loop conformations per loop site.…”

A new dawn for monoclonal antibodies against antimicrobial resistant bacteria

“…Finally, computational models for high-resolution structural validation have also been recently used for de novo design of antibody-like domains. The approach developed in October 2022 by Chidyausiku and coworkers aimed to overcome the limits of mAb engineering by designing antibody-like scaffolds, not produced in nature, to graft loops containing the CDRs of functional antibodies (Chidyausiku et al, 2022 ). The gargantuan leap in solving three-dimensional structure of proteins marked a pivotal milestone in the field of mAb discovery, design and development which could be instrumental in the fight against AMR.…”