Reframe de novo generation into the repurposing frame per the founder's
idea: use a pocket-conditioned generative model (TargetDiff/DiffSBDD/
Pocket2Mol) to propose an idealised binder as a SEARCH BEACON, then
retrieve the nearest EXISTING drugs by chemical similarity (Tanimoto/
embedding) as repurposing candidates — the generated molecule is never
synthesised.
Caveats kept honest: generated molecules used only as beacons (often
synthetically invalid); similarity != activity, so retrieved neighbours
still must be docked + pass the binding recovery test; open question
whether it beats brute-force docking the existing library. Explore only
after the §12.3-12.4 docking baseline is validated. §12.7 exclusion
reworded to point here.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Add a scoped (not committed) follow-on track pivoting modality from
expression-connectivity to structure-based drug-target binding, motivated
by the empirical finding that the expression modality is signal-dead for
this task (relational-only supervised AUC = 0.49, chance).
§12 covers: the evidence for the pivot, a sickle-specific druggable target
shortlist with known-binder positive controls (Hb/voxelotor, PKR/mitapivat,
DNMT1/decitabine, LSD1, HDAC, EHMT2, PDE9), method (classical docking
baseline -> AF3-class co-folding: Boltz-2/Chai-1/DiffDock), a pre-registered
binding recovery test, integration with the expression layer as the real
prize, honest pitfalls (binding != efficacy, BCL11A untractable, GPU breaks
the all-local assumption), and open decisions before committing.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
