CD38 is the dominant NAD+-consuming enzyme in aged tissues and a validated target for NAD+ axis restoration. Structural evidence from PDB 2I65 (1.9 Å) and 4TQG identifies a deep catalytic cleft coordinated by W125 (base catalyst), E146 (proton relay), D155/D157 (nucleoside binding), K121/R127 (phosphate anchor), C119 (disulfide scaffold), and F143 (aromatic stacking). This plan defines a three-stage design campaign: (1) hotspot geometry consolidation from two independent crystal structures (2I65, 4TQG) to produce a consensus conditioning map; (2) RFdiffusion backbone generation conditioned on the 8-residue hotspot set, targeting 45–70 aa miniprotein scaffolds; (3) ProteinMPNN sequence design followed by AF2-Multimer independent validation (planned; AF2 pLDDT > 80, ipTM > 0.75, PAE < 10 Å success criteria). Foldseek novelty search against PDB and ESM-2 pseudo-likelihood filtering are planned post-design QC steps. The benchmark reference is the isatuximab Fab epitope (PDB 6ODF) and the small-molecule inhibitor 78c (Ki ~ 4 nM). A designed binder must show predicted interface buried surface area > 700 Ų and Rosetta ddG < −10 REU to advance to synthesis triage.
Details
- disease
- aging
- target_ref
- UniProt:P28907
- primary_endpoint
- All 5 hotspot residues (Trp125, Arg127, Glu146, Asp155, Thr221) parsed with Cα coordinates from 4CMH chain A
- identification_strategy
- in_silico_KO
Raw fields (3)
- assay_spec
CD38 catalytic-site hotspot pocket geometry analysis from PDB 4CMH + literature-grounded BindCraft input preparation: extract Cα coordinates for hotspot residues (Trp125, Glu146, Asp155, Arg127, Thr221), compute pairwise distances and pocket centroid, output BindCraft hotspot JSON and FASTA target segment; bindcraft_cd38_inputs.json — hotspot residue list with chain/residue/Cα-xyz, pocket centroid xyz, pairwise Cα distance matrix for Trp125/Arg127/Glu146/Asp155/Thr221; ready to paste into BindCraft target_hotspots field; cd38_target_chain_A.pdb — trimmed chain A of 4CMH covering residues 100–250 (catalytic domain), for use as BindCraft target PDB input; {'kind': 'claim', 'text_template': 'CD38 catalytic pocket centroid is at ({cx}, {cy}, {cz}) Å (Cα centroid of Trp125/Arg127/Glu146/Asp155/Thr221); max pairwise hotspot Cα distance is {max_d} Å, defining the binder contact envelope'}- hypothesis
A de novo miniprotein binder occluding the CD38 catalytic cleft (hotspot residues C119, K121, W125, R127, F143, E146, D155, L157) will competitively inhibit NAD+ hydrolase activity, raise intracellular NAD+ levels in aged tissues, and outperform known small-molecule CD38 inhibitors (e.g., 78c, isatuximab epitope) on in-silico binding geometry and selectivity metrics.
- kill_criteria
Abort or revise if: 4CMH chain A numbering may differ from canonical UniProt P28907 numbering — cross-check with SEQRES records before assigning hotspot indices; Thr221 was not returned in prior BioContext hotspot parse (only Trp125, Arg127, Glu146, Asp155 confirmed); must verify Thr221 presence in 4CMH ATOM records directly