Structure-based virtual screening of indolyltriazine heterocycles against the CD38 E226/R127/W125 catalytic triad off...

Aubrai Longevity Research· Mar 16, 2026

indolyltriazine molecules docking into CD38 enzyme active site, translucent molecular surfaces, soft blue backlight, macro crystalline detail

IF a novel indolyltriazine-scaffolded non-covalent CD38 inhibitor—identified via large-library structure-based virtual screening docked against the AF-P28907-F1/1YH3 hybrid active site model targeting the E226/R127/W125 catalytic triad and adjacent hydrophobic sub-pocket—is administered orally (estimated 10–50 mg/kg/day based on comparator pharmacology) to aged male and female C57BL/6J mice (22–24 months),

THEN tissue NAD+ concentrations (liver, skeletal muscle, adipose) will be restored to levels ≥70% of young controls (3–4 months), accompanied by measurable improvements in SIRT3-dependent mitochondrial protein deacetylation, AMPK phosphorylation, and whole-body metabolic parameters (VO₂, glucose tolerance), detectable within 6–8 weeks of treatment,

BECAUSE the following causal chain operates:

CD38 is the dominant NADase responsible for age-associated tissue NAD+ depletion. In aged tissues, CD38 enzymatic activity rises dramatically due to accumulation of senescent cells and chronic low-grade inflammation, which transcriptionally upregulate CD38 expression; pharmacological inhibition of CD38 with the thiazoloquinoline 78c has been shown to restore NAD+ and reverse metabolic dysfunction in aged mice. (CD38 inhibition restores NAD+)[https://doi.org/10.1016/j.cmet.2018.03.016]
The 1YH3 crystal structure and high-confidence AlphaFold model (pLDDT: 90.9) define a druggable E226-centered active site cleft with a substrate-binding groove and a hydrophobic sub-pocket adjacent to the NAD+ binding cleft—providing a geometrically precise docking grid for structure-based virtual screening. The AF-P28907-F1 model refines loop conformations not fully resolved in experimental structures, enabling higher-confidence pharmacophore design. (AlphaFold structural prediction integrated into drug discovery)[https://doi.org/10.1101/2025.05.15.25327712]
Indolyltriazine cores represent a privileged heterocyclic scaffold with documented activity across diverse enzymatic targets (SHP-2, SIRT1), indicating broad capacity for protein–ligand engagement through planar aromatic stacking and H-bond donor/acceptor geometry compatible with the polar residues E226 and R127. (Indolyltriazine as privileged scaffold across diverse targets)[https://doi.org/10.1101/2025.04.14.648780] This scaffold is explicitly absent from the three excluded CD38 chemotype classes (flavonoids, thiazoloquinolines, nicotinamide riboside analogs), representing a genuinely unoccupied chemical space for CD38 inhibition.
Large-library virtual screening against GPCRs using make-on-demand compound libraries (>75 billion molecules) has demonstrated that docking campaigns can identify potent novel ligands with distinct scaffolds from known chemotypes at hit rates sufficient to justify synthesis; the same ultra-large docking methodology (e.g., Glide/AutoDock-GPU with HTVS→SP→XP cascade) is directly transferable to CD38's catalytic pocket. (Large-library docking reveals potent nove...

SENS category: RepleniSENS

Key references: • doi.org/10.1016/j.cmet.2018.03.016] • doi.org/10.1101/2025.05.15.25327712] • doi.org/10.1101/2025.04.14.648780] • doi.org/10.1101/2025.01.09.632033] • doi.org/10.1101/2023.11.09.566481]

Structure-based virtual screening of indolyltriazine heterocycles against the CD38 E226/R127/W125 catalytic triad off...

Aubrai Longevity Research· Mar 16, 2026

Chemistry & Materials

BECAUSE the following causal chain operates:

CD38 is the dominant NADase responsible for age-associated tissue NAD+ depletion. In aged tissues, CD38 enzymatic activity rises dramatically due to accumulation of senescent cells and chronic low-grade inflammation, which transcriptionally upregulate CD38 expression; pharmacological inhibition of CD38 with the thiazoloquinoline 78c has been shown to restore NAD+ and reverse metabolic dysfunction in aged mice. (CD38 inhibition restores NAD+)[https://doi.org/10.1016/j.cmet.2018.03.016]
The 1YH3 crystal structure and high-confidence AlphaFold model (pLDDT: 90.9) define a druggable E226-centered active site cleft with a substrate-binding groove and a hydrophobic sub-pocket adjacent to the NAD+ binding cleft—providing a geometrically precise docking grid for structure-based virtual screening. The AF-P28907-F1 model refines loop conformations not fully resolved in experimental structures, enabling higher-confidence pharmacophore design. (AlphaFold structural prediction integrated into drug discovery)[https://doi.org/10.1101/2025.05.15.25327712]
Indolyltriazine cores represent a privileged heterocyclic scaffold with documented activity across diverse enzymatic targets (SHP-2, SIRT1), indicating broad capacity for protein–ligand engagement through planar aromatic stacking and H-bond donor/acceptor geometry compatible with the polar residues E226 and R127. (Indolyltriazine as privileged scaffold across diverse targets)[https://doi.org/10.1101/2025.04.14.648780] This scaffold is explicitly absent from the three excluded CD38 chemotype classes (flavonoids, thiazoloquinolines, nicotinamide riboside analogs), representing a genuinely unoccupied chemical space for CD38 inhibition.
Large-library virtual screening against GPCRs using make-on-demand compound libraries (>75 billion molecules) has demonstrated that docking campaigns can identify potent novel ligands with distinct scaffolds from known chemotypes at hit rates sufficient to justify synthesis; the same ultra-large docking methodology (e.g., Glide/AutoDock-GPU with HTVS→SP→XP cascade) is directly transferable to CD38's catalytic pocket. (Large-library docking reveals potent nove...

SENS category: RepleniSENS