Rapid Discovery of CD38 Inhibitor via DNA-Encoded Natural Product Library Screening.

Area of Science:

• Biochemistry
• Medicinal Chemistry
• Drug Discovery

Background:

• CD38 is a key enzyme in NAD+ metabolism and calcium signaling, implicated in multiple myeloma, metabolic decline, and neurodegenerative diseases.
• Current CD38 inhibitors, like monoclonal antibodies, have limitations, driving the need for novel small-molecule alternatives.

Purpose of the Study:

• To discover novel small-molecule CD38 inhibitors using DNA-encoded library (DEL) technology.
• To validate the efficacy and elucidate the mechanism of action of identified inhibitors.

Main Methods:

• High-throughput screening of a DEL library (>100,000 compounds) against recombinant human CD38.
• Surface plasmon resonance (SPR) for binding confirmation, enzymatic assays for activity inhibition, and structure-activity relationship (SAR) analysis.
• Molecular docking and molecular dynamics (MD) simulations to determine binding mechanisms.

Main Results:

• Identified eight hit compounds, including the repurposed antiparasitic drug Fenbendazole.
• SPR confirmed direct binding (KD: 7.74 × 10^-5 M to 2.15 × 10^-4 M).
• Fenbendazole and Flubendazole demonstrated dose-dependent inhibition of CD38 hydrolase and cyclase activities, with Flubendazole showing IC₅₀ values of 14.78 μM and 26.31 μM, respectively.

Conclusions:

• DEL technology is an effective platform for discovering CD38 inhibitors.
• Fenbendazole and Flubendazole represent promising scaffolds for developing new therapeutics for CD38-associated disorders.
• Van der Waals interactions and conserved aromatic residues are key to small-molecule binding in the CD38 active site.