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Ligand Binding Sites

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...

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Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked. In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...

Ligand Binding and Linkage

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Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked. In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...

Ligand Binding Sites

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Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...

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Updated: Jun 17, 2026

Targeted Antibody Blocking by a Dual-Functional Conjugate of Antigenic Peptide and Fc-III Mimetics DCAF

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Exploiting the DCAF16-SPIN4 interaction to identify DCAF16 ligands for PROTAC development.

Isabella A Riha¹, Miguel A Campos^1,2, Xiaokang Jin¹

¹Department of Chemistry, Northwestern University Evanston IL 60208 USA zhang@northwestern.edu.

RSC Medicinal Chemistry

|December 18, 2024

Summary

Researchers developed a new assay to find DCAF16 binders for targeted protein degradation. A compound was identified that degrades FKBP12 via PROTAC technology, advancing drug discovery.

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Area of Science:

Biochemistry
Medicinal Chemistry
Molecular Biology

Background:

Traditional drugs target protein activity, but some proteins lack suitable sites.
Targeted protein degradation (TPD) offers an alternative by directing proteins for degradation.
DCAF16 is an E3 ligase with potential for TPD via PROTAC and molecular glue mechanisms.

Purpose of the Study:

To develop a homogeneous time resolved fluorescence (HTRF) assay for discovering DCAF16 binders.
To identify novel compounds that interact with DCAF16.
To explore the potential of DCAF16 binders in targeted protein degradation strategies.

Main Methods:

Development of a homogeneous time resolved fluorescence (HTRF) assay.
Screening of an in-house electrophile library against DCAF16.
Chemical modification of a DCAF16 binder into a Proteolysis-Targeting Chimera (PROTAC).

Main Results:

Identification of two diastereomeric compounds binding to DCAF16.
One compound was found to engage DCAF16 covalently at cysteines C177-179.
The covalent DCAF16 binder was successfully converted into a PROTAC that degrades FKBP12.

Conclusions:

The developed HTRF assay is effective for discovering DCAF16 binders.
Covalent engagement of DCAF16 is a viable strategy for targeted protein degradation.
This work expands the utility of DCAF16 in developing novel PROTACs for therapeutic applications.