Ligand Design for DAPK1-targeting PROTAC^®

The structure of death-associated protein kinase 1 (DAPK1) could be used as the starting point for designing of bioavailable DAPK1 ligand. Armed with our advanced platform, Creative Biolabs offers the comprehensive ligand development services with the help of computer-aided drug design strategies such as fragment-based ligand design, ligand protein binding simulation, protein ligand docking calculation, and prediction. We now provide services about DAPK1 ligand design for DAPK1-targeting proteolysis targeting chimeras (PROTAC^®) development. These ligands include but are not limited to small molecule inhibitors, peptides, engineered antibodies, and (modified) natural products.

Introduction to DAPK1

DAPK1 acts as a critical component in the endoplasmic reticulum stress-induced cell death pathway and it is also a mediator of the pro-apoptotic pathway, participating in multiple cell death processes induced by various internal and external apoptotic stimulants. DAPK1 regulates the caspase-independent and caspase-dependent cell death signal. The DAPK1 structure is shown in Fig.1. Each DAPK1 domain plays a unique role in its catalytic activity, stability, localization, and interaction with its substrates or binding partners.

Fig.1 Schematic depiction of the DAPK1 structure. (Singh, 2016)

DAPK1 plays an important role in tumor suppression. DAPK1 expression is downregulated in a wide variety of cancer types such as lung cancer, cervical carcinoma, lymphoma, nasopharyngeal carcinoma, and gastrointestinal tumors. DAPK1 promoter regions are significantly methylated in almost 30 different human tumor types compared with their corresponding normal tissue. Besides, DAPK1 has also been associated with the pathogenesis of neuronal disorders such as epilepsy, Alzheimer’s disease, and ischemic brain injury. This may be due to its ability to induce neuronal cell death in response to ceramide, ischemia and glutamate toxicity.

Ligands Design Services for DAPK1

1. Small Molecule Inhibitor Ligand

To identify small molecule inhibitors for DAPK1, Creative Biolabs has performed a high throughput screening campaign using an in-house chemical library and identified several compounds as a novel class of DAPK1 inhibitors. They exhibited potent inhibitory activity against DAPK1. Based on enzyme kinetics and molecular docking studies, we propose that some compounds may bind to the ATP-binding site of the enzyme, while others are non-ATP-competitive inhibitors. These non-ATP-competitive inhibitors act as a protein-protein interaction inhibitor by hindering the DAPK1 kinase reaction through preventing the binding of DAPK1 substrates. Commercial potent and selective inhibitors of DAPK1 are also available for you, such as TC-DAPK 6, HS-38.

2. Peptide Ligand

The tumor modifier p21 protein has the most highly conserved elements of a DAPK consensus substrate, including a basic core followed by a hydrophobic core. Therefore, the p21 protein was synthesized in overlapping fragments to acquire a panel of peptide ligands for testing in DAPK1 binding. Several distinct p21 derived peptide fragments were found to bind to DAPK1. DAPK-1 stimulatory peptides attenuate tryptic cleavage of DAPK-1 by altering DAPK-1 conformation and locking the enzyme onto its substrate through binding.



3. Antibody Ligand

Our strategies which are used to identify novel antibody or antibody-based ligands include nuclear magnetic resonance (NMR), surface plasmon resonance (SPR), thermal shift, DNA-encoded libraries of small molecules and small-molecule microarrays. Their incorporation into PROTAC^® molecules will promote your drug development.

4. Natural Product

According to the reported research, some natural products could be used as ligands targeting DAPK1. Creative Biolabs can also provide modification end engineering services based on the natural product scaffold. By using these scaffold-based ligands, Creative Biolabs and coworkers have produced the DAPK1 degrader by conjugation of the ligands to the thalidomide derivative and pomalidomide.

Features of Our Innovative Services

• No inhibition of any other DAPK family members
• Available peptide ligands and inhibitor ligands
• Compound profiling prediction
• Chemical and physiological properties prediction
• PROTAC^® modeling

Creative Biolabs offers custom services for the design and synthesis of degrader building blocks particularly target ligand design for your targeted protein degradation research. Additionally, we can partner with your discovery project for the custom design and synthesis of active degraders. If you are interested in our ligand design services for DAPK1-targeting PROTAC^®, please feel free to contact us for more information.

Reference

1. Singh, P.; et al. Death associated protein kinase 1 (DAPK1): a regulator of apoptosis and autophagy. Frontiers in molecular neuroscience. 2016, 9: 46.