CD38 is the dominant NAD+-consuming ectoenzyme in aged tissues, responsible for the majority of NAD+ depletion observed with aging. Its catalytic cleft has been structurally characterized at 1.9 Å (PDB 2I65). Prior art is dominated by small-molecule inhibitors (78c, apigenin, luteolinidin); no clinical-grade protein binder exists. This plan initiates a de novo protein binder design campaign: (1) extend hotspot profiling to additional CD38 structures capturing inhibitor-bound conformations (4F45, 6WV5); (2) retrieve IC50 benchmarks from BindingDB for reference comparator selection; (3) run BindCraft conditioned on the catalytic-cleft hotspot set; (4) validate top designs by AF2-Multimer (independent of the design model); (5) rank by ipTM, pLDDT > 80, PAE < 10 Å, and Rosetta ddG; (6) emit lead candidate as protein_design artifact. Success criterion: at least one designed binder with predicted KD < 100 nM (by AF3-Multimer pAE proxy), confirmed by Foldseek novelty search (no PDB hit > 30% sequence identity at the interface).
Details
- disease
- aging
- target_ref
- UniProt:P28907 / PDB:5F1K
- primary_endpoint
- Predicted binding affinity (KD proxy from Boltz/Chai ipTM) and AF2-Multimer ipTM >= 0.70 for the lead CD38 binder candidate.
- identification_strategy
- in_silico_KO
Raw fields (3)
- assay_spec
Planned: (1) BindCraft run conditioned on CD38 catalytic-cleft hotspot geometry from pdb_hotspot_profile output; (2) AF2-Multimer forward-fold validation of top-10 BindCraft candidates (pLDDT > 80, ipTM > 0.7 success threshold); (3) Rosetta ddG refinement of AF2-validated binders; (4) Foldseek structure search for novelty vs PDB; (5) ESM-2 perplexity filter (perplexity < 10 pass). Success criterion: at least one candidate with predicted KD < 100 nM by Boltz/Chai complex scoring, RMSD < 2 Å from design model in AF2 forward fold, and no structural homolog in PDB with TM-score > 0.5.
- hypothesis
A de novo protein binder targeting the CD38 catalytic cleft (residues ~155-157, 179, 196, 233, 275, 287) will competitively inhibit NAD+-consuming hydrolase activity with sub-micromolar potency, restore intracellular NAD+ pools in aged tissues, and exhibit selectivity over structurally related BST1 (CD157) through hotspot-specific contacts not shared in the BST1 active site.
- kill_criteria
Abort or revise if: BindCraft compute on 8 trajectories may exceed sandbox wall-time; decompose to 4+4 if needed; 2I65 is an apo structure with substrate analog — binder may clash with NAD/cADPR substrate; validate with substrate-bound structure 2O3U if available; ESM-2 perplexity threshold of 10 is conservative; if all fail, relax to 12 before discarding batch