Specificity-driven protein binder design with Odin-Multi

Abstract

A useful protein binder is defined as much by what it does not bind as by what it does. Some applications call for one binder to cover a family of related targets; others require it to distinguish a single member from near-identical relatives. Yet, widely used deep-learning-based de novo design methods typically optimise one interaction at a time, leaving cross-reactivity and specificity to emerge during downstream screening. Here we present Odin-Multi, a binder design framework that optimises a shared binder sequence against several complexes simultaneously, applying attractive objectives to on-targets and repulsive objectives to off-targets. We benchmarked Odin-Multi in silico across three systems representing distinct cross-reactivity and specificity challenges: class B1 G protein-coupled receptors (GPCRs), testing cross-reactivity across multiple therapeutically relevant receptors; short-chain three-finger toxins, testing cross-reactivity across homologous toxin family members; and peptide-MHC (pMHC) complexes, testing specificity between near-identical target and off-target surfaces. For pairs of related class B1 GPCRs, 83.5 to 96.8% of jointly optimised designs exceeded an interaction-confidence threshold for both targets, compared with 6.8 to 36.3% of designs from single-target campaigns. For two short-chain three-finger neurotoxins, 9.2% of jointly optimised designs exceeded the corresponding threshold for both targets, compared with 0.8% of designs optimised against one toxin alone. Finally, in a pMHC specificity benchmark where target and off-target differed only in a single peptide residue, counter-selection increased the fraction of designs satisfying both the target-confidence criterion and a target-to-off-target interaction-confidence ratio of 2.5 from 6.0% to 14.2%. Experimental screening produced leads consistent with both design regimes in the two systems tested in vitro. We identified a cross-reactive toxin minibinder showing apparent nanomolar binding to the neurotoxin Erabutoxin A and to a candidate NK-shNTx-containing fraction from Naja kaouthia venom (higher-affinity fitted components of 11.95 and 34.43 nM, respectively), and a pMHC minibinder with greater target-to-off-target discrimination than a previously reported design. By treating cross-reactivity and specificity as explicit design objectives rather than screening outcomes, Odin-Multi widens the range of binding behaviours accessible to computational design.