Design improved FOXO4-DRI-style peptide disruptors of the FOXO4 forkhead domain (FHD) – p53 DBD interaction. Approach: (1) characterize the FOXO4 FHD hotspot geometry from NMR ensemble PDB:2LZB; (2) extract p53-contacting residues; (3) plan BindCraft binder campaign conditioned on the FHD hotspot; (4) validate top candidates with AF2-Multimer forward fold; (5) score ESM-2 perplexity and Foldseek novelty vs FOXO4-DRI reference. Success criterion: planned BindCraft design with AF2-Multimer ipTM > 0.7 and Foldseek TM-score < 0.5 vs known senolytics.
Details
- disease
- aging, cellular senescence
- target_ref
- UniProt:P98177 / UniProt:P04637 / PDB:2LZB
- kill_criteria
- AF2-Multimer ipTM < 0.55 across all candidates OR Foldseek search returns TM-score > 0.7 hit in PDB (prior art collision) OR ESM-2 perplexity > 15 (sequence implausibility).
- timeline_weeks
- 6
- primary_endpoint
- Planned: AF2-Multimer ipTM > 0.7 for top binder candidate vs FOXO4 FHD hotspot; ESM-2 pseudo-perplexity < 8; Foldseek TM-score < 0.5 vs PDB (novelty).
- identification_strategy
- in_silico_KO
Raw fields (2)
- assay_spec
Planned competitive bar resolution: BindingDB IC50 sweep (P28907, limit=20) + Kd sweep (P28907, limit=20) + PubMed search (CD38 protein binder inhibitor nanomolar) + EuropePMC search (CD38 NADase inhibitor protein binder aging NAD+). Success criterion: at least one affinity entry with IC50 < 10 µM or Kd < 1 µM to ground competitive bar. BindCraft conditioning remains: PDB 2I65 chain A, hotspot_residues=[119,121,155,156,157,179,201], neighbor_radius=5.0 Å, n_designs=50, length 60-120 aa, pLDDT>80, ipTM>0.7.
- hypothesis
A de novo protein binder targeting the CD38 catalytic cleft (centered on the C2 subdomain residues E226, W125, D155, N157, T221, W189) can competitively inhibit NAD+ hydrolase activity with Kd < 10 nM, sufficient to restore tissue NAD+ levels in aged animals without broad immunosuppression.