Discovery of novel potential CRBN modulators through structure-based virtual screening and bioassay

Area of Science:

• Biochemistry
• Molecular Biology
• Drug Discovery

Background:

• The Cereblon (CRBN) protein is an E3 ubiquitin ligase crucial for the ubiquitin-proteasome system in eukaryotic cells.
• Small molecules modulating CRBN can induce target protein ubiquitination and degradation, offering therapeutic potential for tumors and immune diseases.
• Existing CRBN modulators often feature a glutarimide skeleton, prompting the search for novel chemical scaffolds.

Purpose of the Study:

• To discover novel and potent CRBN modulators beyond the typical glutarimide structure.
• To identify compounds with potential antitumor and immunomodulatory activities.
• To investigate the binding interactions of novel CRBN modulators with the CRBN protein.

Main Methods:

• Utilized Lipinski's and Veber's rules for drug-likeness assessment.
• Performed pharmacophore-based and docking-based virtual screening.
• Conducted ADMET screening for pharmacokinetic properties.
• Evaluated antitumor activity using MTS assays.
• Employed molecular dynamics (MD) simulations and binding free energy calculations.
• Verified CRBN binding using a luciferase complementation assay.

Main Results:

• Identified and evaluated 11 candidate CRBN modulators.
• AN7535 demonstrated potent antitumor activity against HL-60 (IC50 = 0.72 μM) and SMMC-7721 (IC50 = 1.438 μM) cell lines.
• AO6355 exhibited significant antitumor activity against SMMC-7721 (IC50 = 7.469 μM).
• MD simulations and binding free energy calculations indicated that AN7535 and AO6355 stabilize CRBN and possess favorable binding affinity.
• Luciferase complementation assay confirmed AN7535 binding to CRBN (IC50 = 215.9 μM).

Conclusions:

• Successfully identified novel CRBN modulators, AN7535 and AO6355, with significant antitumor potential.
• These compounds exhibit favorable binding characteristics with the CRBN protein, suggesting a viable mechanism of action.
• The findings support the development of new CRBN-targeting small molecules for cancer and immune system disease therapies.