Origin-1: A generative AI platform for de novo antibody design against novel epitopes
1 Origin-1 targets “zero-prior” epitopes: binding sites on antigens with no available antibody–antigen or protein–protein complex structures, and with limited homology (≤60% identity) to proteins that do have known complexes—setting up a stringent generalization test.
2 The platform combines two stages: AbsciGen (design) and AbsciBind (score/select). AbsciGen itself is modular: AbsciDiff generates epitope-conditioned all-atom antibody–antigen complex structures, then IgDesign2 designs paired heavy light CDR sequences to match those structures.
3 AbsciDiff is a diffusion-based all-atom generator fine-tuned from Boltz-1, modified for antibody docking/design with (i) antibody- and docking-specific masking/conditioning, (ii) explicit epitope conditioning via a token-wise epitope vector, (iii) an intermediate “sequence hypothesis” head with recycling, (iv) optimized equivariant kernels, and (v) optional structural templates (endogenous templating used in final training).
4 IgDesign2 is a “generate-and-refine” sequence designer: a GNN encoder captures 3D geometry, a causal transformer decoder autoregressively generates CDRs, then a paired antibody language model refines heavy light sequences with structure-aware fusion at every layer—aiming to avoid treating chains independently.
5 AbsciBind addresses a practical bottleneck: folding-model confidence metrics often underperform for antibody–antigen complexes. It derives from AF_Unmasked and computes an ipTM-style score with improved awareness of heavy/light chain arrangement plus an antibody-aligned normalization; the final AbsciBind Score averages global and antibody-aligned interface assessments.
6 In silico benchmarking vs RFantibody on 10 “zero-prior” targets: AbsciGen produced many more high-scoring candidates by AbsciBind Score (23.5% of designs ≥0.5 vs 0.8% for RFantibody) and higher mean AbsciBind Score overall, while also yielding more human-like sequences by OASis humanness percentiles.
7 Low-throughput experimental validation: with fewer than ~100 designs screened per target, Origin-1 produced specific binders for 4 targets (COL6A3, AZGP1, CHI3L2, IL36RA). Hits were filtered for specificity (including off-target proteins TL1A and PRLR) and confirmed via orthogonal assays (SPR, BLI, solution complexation).
8 Structural accuracy was validated by cryo-EM for designs against COL6A3, AZGP1, and an optimized IL36RA variant: 3.0–3.3 Å maps and high agreement with design models (DockQ 0.83–0.91), with sub-angstrom to ~1.5 Å-range CDR RMSDs reported across loops—supporting atomic fidelity of both docking pose and designed paratope geometry.
9 AI-guided affinity maturation: adapting Efficient Evolution with AbsciBind multiple protein language models, they improved weak binders and produced functional antagonists. For IL36RA, optimization yielded sub-nanomolar affinities and a best cellular potency EC50 of 12.3 nM; cross-reactivity to mouse IL36RA enabled functional testing in a mouse cell assay as well.
10 Developability profiling (polyreactivity, self-association, hydrophobicity, thermal stability, aggregation/polydispersity, purity) showed most binders were within therapeutically acceptable ranges; importantly, IL36RA variants retained generally similar developability despite >1000-fold affinity gains, highlighting an attempt to co-optimize binding and drug-like properties.
💻Code:
github.com/AbSciBio/origin-1
📜Paper:
biorxiv.org/content/10.64898…
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