CD38 is the dominant NAD-consuming ectoenzyme in aged tissues; its activity rises with age and is a primary driver of the NAD+ decline associated with mitochondrial dysfunction, senescence, and frailty. Eight catalytic-cleft hotspot residues (C119, K121, D155, D156, D179, P184, A200, N229) have been geometrically profiled from PDB 2I65 (1.9 Å resolution, NMN co-crystal). Candidate interface residues flanking the hotspots (I122, C201, L157, V185, D154/155/156, P118) were identified. The design campaign will: (1) condition RFdiffusion backbone generation on the 8 hotspot centroids; (2) sequence-design with ProteinMPNN (T=0.1, 32 sequences/backbone); (3) filter by ESM-2 pseudo-log-likelihood > -1.5; (4) validate top candidates with AF2-Multimer (ipTM > 0.7, pLDDT > 80); (5) rank by ipSAE and Rosetta interface ddG; (6) run Foldseek novelty search against PDB to confirm non-redundancy. Reference inhibitors from BindingDB (IC50 baseline) define the bar each design must clear. Known prior art: daratumumab (anti-CD38 antibody, myeloma), 78c (small-molecule CD38i), quercetin (weak NAD+ axis modulator). Success criterion: at least one binder with predicted KD < 100 nM by AF3-Multimer PAE proxy, structurally distinct from any PDB deposited antibody paratope (Foldseek TM-score < 0.5 vs nearest hit).
Details
- disease
- aging / nad+ decline / metabolic frailty
- target_ref
- UniProt:P28907 / PDB:2I65
- primary_endpoint
- At least 1 of 3 AF2-Multimer forward-fold predictions returns ipTM ≥ 0.75 AND pAE interface ≤ 10 Å
- identification_strategy
- in_silico_KO
Raw fields (3)
- assay_spec
BindCraft single-pass binder design against NAMPT catalytic cleft (PDB:2GVJ hotspots Q168/K228/V274/A306/I309/G383); 6 designs, 70-90 aa, then ESM-2 pseudo-perplexity filter (keep top 3), then AF2-Multimer ipTM forward-fold validation (pass threshold: ipTM ≥ 0.75); FASTA file of 6 BindCraft-designed binder sequences targeting NAMPT cleft (planned); ESM-2 pseudo-perplexity scores for all 6 designs; top 3 flagged for forward-fold (planned); AF2-Multimer complex prediction PDB + ipTM/pAE scores for top 3 ESM-filtered designs (planned); Lead NAMPT binder candidate: sequence, ipTM, pAE, ESM-2 perplexity rank, and go/no-go recommendation for wet-lab synthesis (planned)
- hypothesis
A de novo protein binder designed against the CD38 catalytic cleft (hotspot residues C119, K121, D155, D156, D179, P184, A200, N229 from PDB 2I65) will competitively inhibit NAD+ hydrolysis with sub-micromolar affinity, restoring NAD+ levels in aged tissues. Binders designed via RFdiffusion conditioned on these hotspots and validated independently by AF2-Multimer will achieve ipTM > 0.7 and predicted interface ddG < -8 kcal/mol.
- kill_criteria
Abort or revise if: PDB:2GVJ chain A hotspot numbering may differ from UniProt canonical numbering — verify residue mapping before passing to BindCraft conditioning; BindCraft may reject designs with cleft geometry that is too enclosed (FK866 binding pocket is small for a peptide binder — may need to relax hotspot contact constraints to 3 of 6 residues); AF2-Multimer ipTM threshold of 0.75 is aggressive for a first-pass screen; if 0 of 3 pass, fall back to 0.65 and flag as provisional