Identification of fragments targeting SMYD3 using highly sensitive kinetic and multiplexed biosensor-based screening

Area of Science:

• Biochemistry
• Drug Discovery
• Structural Biology

Background:

• SMYD3 is a potential anticancer drug target due to its roles in carcinogenesis.
• Understanding SMYD3 ligand interactions is crucial for developing effective anticancer therapies.
• Current knowledge is limited regarding ligands targeting different sites or modes of action on SMYD3.

Purpose of the Study:

• To identify novel ligands for SMYD3.
• To differentiate ligands binding to the active site versus other sites.
• To select ligands based on kinetic properties, not just affinity.

Main Methods:

• Screening of a 1056-membered fragment library using a grating coupled interferometry (GCI)-based biosensor.
• A multiplexed experimental design was employed, screening SMYD3 alone and with a blocked active site.
• Hit selection prioritized dissociation rates, followed by X-ray crystallography for structural analysis.

Main Results:

• 20 fragments were identified as SMYD3 binders.
• Half of the hits targeted the active site, while the other half targeted different sites.
• The GCI biosensor provided exceptional sensitivity and time resolution, enabling kinetic rate constant estimation for fragments.

Conclusions:

• The developed biosensor assay and multiplexed approach represent a paradigm shift in fragment screening.
• This method allows for the rational selection of ligands targeting specific sites on SMYD3.
• The ability to quantify kinetic rates for fragment binding is a significant advancement in drug discovery.