Ligand Design for MetAP-2-targeting PROTAC^®

Nowadays, proteolysis targeting chimera (PROTAC^®) technology has received significant attention for therapeutic intervention based on regulation at protein levels. This technique creates bifunctional molecules consisting of an E3 ligase and a target protein that is to be degraded. The first bivalent molecule compound was reported in 2001, leading to the degradation of methionine aminopeptidase-2 (MetAP-2) by recruiting the ubiquitinated protein in a compound-dependent manner. As a famous and skillful supplier around the world, Creative Biolabs has extensive experience in target discovery and can provide sophisticated ligand design services for any cellular metabolic enzymes. Aided by us, PROTAC^®s can be manufactured to induce the ubiquitylation and degradation of target protein MetAP-2 in a cell-free system.

• Introduction to MetAP-2

Methionine aminopeptidases (MetAPs) are a type of intracellular metalloproteases that play a key role in protein maturation as they catalyze the removal of initiator methionine (Met) residue from newly synthesized proteins. In eukaryotes, there’re two classes of MetAPs identified by sequence analysis, types I (MetAP-1) and II (MetAP-2) respectively. MetAP-2 differs from MetAP-1 by a helical subdomain of ~60 residues in length inserted within the C-terminal domain of the former.

Fig.1 (A) Electron density of furnagillin in the catalytic pocket of human MetAP-2; (B) overall structure of the complex between human MetAP-2 and furnagillin. (Liu, 1998)

In humans, a full-length of MetAP-2 comprises 478 amino acids and the protein sequence is composed of a unique N-terminal region with one aspartate (Asp)-rich region, two lysine (Lys)-rich regions and a conserved C-terminal catalytic domain with a protease fold, called the “pita bread” fold. This catalytic fold seems to be conserved in all MetAPs, locating at a deep cleft in the C-terminal region of MetAPs and sharing identical metal-chelating residues that coordinate two neighbor metal ions. The N-terminal extension in MetAP-2 is not implicated in the protease activity, but it has a critical part in the regulation of the cell cycle and the global protein synthesis.

• MetAP-2-associated Diseases and Treatments

MetAP-2 is a bifunctional protein that is capable of regulating protein synthesis and post-translational processing. Another known function of this enzyme is the protection of eukaryotic initiation factor 2 (eIF2) from inhibitory phosphorylation. MetAP-2 is correlated with angiogenesis, whose inhibition induces cell cycle (late G1 phase) arrest, cytostasis in tumor cells in vitro, and blocking of tumor growth in vivo. To date, several fumagillin analogs (e.g. ovalicin, TNP-470, PPI-2458) have been found to be robust selective inhibitors of MetAP-2 and endothelial cell growth. Further, some reversible human MetAP-2 inhibitors (e.g. bengamides, triazole analogs) have shown their potential to inhibit angiogenesis and tumor cell proliferation in vivo as well.

• Ligand Design Services for MetAP-2 at Creative Biolabs

Fig.2 The first PROTAC^® for MetAP-2. (Wang, 2020)

PROTAC^®s are an emerging approach to inhibit the biological functions of scaffold proteins and aggregated proteins. They’re also promising therapeutic agents for cancer patients, considering its ability to selectively degrade desired proteins. A successful PROTAC^® ligand resides the E3 ligase in a proper distance and orientation to the target protein, enabling the latter to be ubiquitinated. The ubiquitinated protein is recognized by the proteasome and subsequently undergoes the process of degradation. Here, Creative Biolabs considers that PROTAC^®s are useful research tools to study cellular phenotypes and have greater opportunity to become powerful therapeutic solutions.

The first PROTAC^® describes how the Skp1-Cullin-F box E3 ligase complex was employed to degrade MetAP-2 protein. This has been achieved by a chimeric compound where the IκBα peptide and the antiangiogenic ovalicin were connected through a suberate linker. This construct was demonstrated to ubiquitinate and degrade target protein MetAP-2. Upon replacing the IκBα peptide with a small, cell-permeable molecule, PROTAC^®s can be effective therapeutic agents applied in many types of cancer. At Creative Biolabs, we’d like to design ideal ligands for MetAP-2 degradation based on its crystal structure. Remarkably, in the absence of small-molecule E3 binders, our experts have developed peptide-based PROTAC^®s that are sufficiently small to be cell-permeable.

• Advantages
  • Advanced PROTAC^® technical platforms enable rapid, sustained degradation of target proteins
  • Rational ligand design strategies to modify the potency and selectivity of specific proteins
  • More than 10 years of experience in molecular discovery and drug development

As a professional specialist in the drug industry, Creative Biolabs offers a comprehensive overview of recent developments in small molecule mediated protein degradation, including nuclear receptors, transcription factors, protein kinases, and metabolic enzymes. Here, we provide high-quality ligand design services for MetAP-2 with different forms, such as small molecules, peptides, and antibodies. For more details, please don’t hesitate to contact us.

References

1. Liu, S.; et al. Structure of human methionine aminopeptidase-2 complexed with fumagillin. Science. 1998, 282(5392): 1324-1327.
2. Wang, Y.; et al. Degradation of proteins by PROTAC^®s and other strategies. Acta Pharm Sin B. 2020, 10(2): 207-238.