FOXO4-DRI (D-amino acid retro-inverso peptide) demonstrated selective apoptosis of senescent cells in vivo (Baar et al., Cell 2017) by disrupting the FOXO4–p53 nuclear interaction that sequesters p53 from apoptotic signaling. The interaction interface is defined by the FOXO4 Forkhead domain and the p53 transactivation domain (TAD1, residues ~18–27, hotspots F19/W23/L26). This plan designs improved next-generation disruptors: (1) hotspot geometry profiling of the FOXO4 Forkhead domain using available PDB structures; (2) BindCraft de novo binder design conditioned on the FOXO4 Forkhead surface that occludes p53-TAD docking; (3) AF2-Multimer forward-fold validation of each candidate against FOXO4; (4) ESM-2 sequence likelihood filter; (5) Foldseek novelty screen vs PDB. Reference benchmark: FOXO4-DRI peptide (LGTLLRQFLVKPPESEDS, retro-inverso) must be outperformed on at least one in-silico metric. Success criteria: ≥1 candidate with AF2-Multimer ipTM > 0.7, Boltz pAE < 10 Å, and Foldseek TM-score < 0.5 to any PDB entry (novel fold).
Details
- disease
- aging / cellular senescence
- target_ref
- UniProt:P98177
- primary_endpoint
- ≥4 hotspot residues identified with SASA burial ≥ 30% relative to unbound chain A
- identification_strategy
- in_silico_KO
Raw fields (3)
- assay_spec
Structural hotspot mapping of CD38 catalytic pocket from PDB 2I65 + literature triangulation of competitive binding epitope, producing a hotspot residue list and BindCraft input spec for de novo binder design; Annotated PyMOL/Matplotlib rendering of CD38 catalytic pocket (PDB 2I65 chain A) with hotspot residues labeled and colored by burial depth / conservation score — planned; Hotspot residue table: residue number, identity, percent buried SASA, distance to NAD+ analog, conservation rank across CD38 orthologs (human/mouse/rat) — planned; {'kind': 'claim', 'text_template': 'CD38 catalytic pocket hotspot residues E226, D202, W125, and T221 form the minimal epitope for competitive binder design; a binder contacting ≥3 of these is predicted to block NAD+ hydrolysis'}; BindCraft input YAML spec: target PDB chain, hotspot_residues list, binder_length range 60–90 aa, num_designs=50 — ready for next compute tick — planned- hypothesis
A de novo miniprotein or stapled peptide targeting the FOXO4 Forkhead domain–p53 transactivation domain interface will disrupt the pro-survival FOXO4–p53 complex in senescent cells with higher potency and selectivity than FOXO4-DRI, measured by predicted ipTM > 0.7 in AF2-Multimer, Boltz pAE < 10 Å, and ESM-2 log-likelihood ratio > reference peptide.
- kill_criteria
Abort or revise if: PDB 2I65 may have missing residues in the loop regions flanking the catalytic pocket — verify completeness before SASA calculation; CD38 is a type II transmembrane protein; binder must target the ectodomain (residues ~43–300); confirm chain A covers this range; Hotspot residues from small-molecule co-crystals may not fully recapitulate a protein-binder epitope — flag for experimental validation