METAP1 Human

What is METAP1 and what is its primary function in human cells?

Human Methionine Aminopeptidase 1 (METAP1) is a critical enzyme responsible for cleaving N-terminal methionine residues from nascent proteins, a process known as N-terminal methionine excision (NME). This post-translational modification is essential for proper protein maturation, function, and stability . METAP1 belongs to the family of methionine aminopeptidases that catalyze this crucial first step in protein processing. The removal of the initiator methionine exposes the second amino acid, which can then be subject to further modifications such as myristoylation, acetylation, or methylation, depending on the protein . METAP1 primarily functions in the cytosol and plays vital roles in cell cycle progression, cell proliferation, enzyme function, protein stability, and cellular localization .

How does METAP1 differ structurally and functionally from METAP2?

Structurally, METAP1 and METAP2 share a conserved catalytic domain but differ in their N-terminal regions. While type 1 MetAPs (including METAP1) lack the N-terminal extension characteristic of type 2 MetAPs, human METAP2 contains an N-terminal domain with a positively charged Lys-rich region .

Functionally, proteomics analysis has shown that METAP2 preferentially processes substrates with Val or Thr as the second amino acid (iMet-Val and iMet-Thr) . METAP1's catalytic site has more steric restrictions compared to METAP2, potentially influencing its substrate specificity. Despite significant overlap in substrate specificity, they maintain distinct functions: METAP1 is more involved in basic cellular processes including cell cycle progression and protein stability, whereas METAP2 has been specifically implicated in angiogenesis, B-cell differentiation, and cell-specific cytotoxicity .

A notable distinction is that METAP2, not METAP1, is the molecular target of the anti-angiogenesis inhibitor TNP-470, which has been investigated for cancer treatment .

What are the key cellular processes regulated by METAP1?

According to the research findings, METAP1 regulates several crucial cellular processes:

These functions highlight METAP1's role as a critical regulator of proteome diversity and function. The removal of the initiator methionine creates the necessary N-terminal state for further modifications that ultimately determine protein fate, function, and interactions within cellular networks.

What experimental models are commonly used to study METAP1 function?

Several experimental models have proven valuable for investigating METAP1 function:

• Yeast models: Deletion studies in yeast have shown that removing METAP1 leads to a slow growth phenotype that can be rescued by overexpressing METAP2, demonstrating the essential nature of the NME process .

• Structural studies: High-resolution structural analysis has been employed to understand MetAP function, as demonstrated in studies of mitochondrial MetAP1D structures in its apo-, cobalt-, and methionine-bound states .

• Synthetic biology approaches: Advanced platforms combining metagenomics and synthetic biology have been used to discover novel inhibitors of METAP1 .

• In vitro enzymatic assays: These are used to measure METAP1 activity and evaluate inhibitor potency, as indicated in the development of metapeptin B with "sub-micromolar potency" .

• Proteomics analysis: Used to determine substrate specificity of human MetAPs and to identify the proteome-wide effects of METAP1 activity .

How do researchers distinguish between METAP1 and METAP1D activity in experimental settings?

Researchers differentiate between cytosolic METAP1 and mitochondrial METAP1D activities through several approaches:

• Structural analysis: High-resolution structural studies have revealed "distinct structural disparities within the active-site pocket primarily contributed by two specific loops" between cytosolic METAP1 and mitochondrial METAP1D . These structural differences can be exploited in experimental designs.

• Subcellular localization: Since METAP1D is localized to mitochondria while METAP1 is cytosolic, subcellular fractionation techniques can physically separate these isozymes for individual study.

• Specific substrate interactions: The structural disparities in the active-site pocket suggest that differential substrate preferences could be used to develop assays that preferentially measure one isozyme's activity over the other .

What are the established methods for identifying novel inhibitors of METAP1?

According to the search results, several sophisticated approaches are being employed to discover novel METAP1 inhibitors:

Metagenomic Natural Product Discovery Platform: This end-to-end discovery platform enables targeted discovery of novel natural products that can modulate METAP1 . This platform combines:

• Large-scale metagenomic sequencing of soil samples, creating a database containing >1.4Tb of assembled sequences and >6.8M predicted biosynthetic gene clusters (BGCs)

• Bioinformatic strategies leveraging self-resistance enzymes (SREs) to identify BGCs predicted to encode novel inhibitors

• In silico search strategies to prioritize promising candidates

• Heterologous expression systems for producing the encoded molecules

• Untargeted discovery workflows for novel metabolites

• Computational approaches to assign observed bioactivity to specific metabolites

This integrated approach led to the discovery of metapeptin B, a novel cyclic depsipeptide inhibitor of METAP1 with sub-micromolar potency and strong selectivity for METAP1 over METAP2 .

What are the current challenges in developing selective METAP1 inhibitors for cancer therapy?

Several challenges exist in developing selective METAP1 inhibitors for cancer therapy:

• Selectivity issues: Achieving selectivity between METAP1 and METAP2 is significant, as highlighted by the specific mention that metapeptin B demonstrates "strong selectivity for HsMetAP1 over HsMetAP2" . This suggests many compounds may inhibit both isozymes, potentially leading to off-target effects.

• Structural similarities: MetAP isozymes "share a predominantly conserved structure" , which complicates the design of selective inhibitors targeting only METAP1.

• Chemical space limitations: Traditional approaches to inhibitor discovery have limitations, necessitating "next-gen" discovery platforms that overcome "many of the challenges constraining traditional methods" . This suggests difficulty in identifying compounds with appropriate drug-like properties from conventional chemical libraries.

• Bioinformatic challenges: Current computational approaches have had "limited success in developing computational approaches that can accurately predict the structure of the encoded small molecule" , making it difficult to efficiently prioritize promising candidates.

How do researchers differentiate between the roles of METAP1 and METAP2 in N-terminal protein processing?

Researchers use multiple approaches to differentiate between METAP1 and METAP2 roles:

• Proteomics analysis: Substrate specificity studies have revealed that "MetAP2 prefers iMet-Val and iMet-Thr" while also showing that "substrate specificity is significantly overlapping for human MetAP1 and MetAP2" . This approach can identify both shared and unique substrates.

• Structural studies: Research has shown "a potential difference in the substrate specificity of their catalytic sites due to more steric restrictions in MetAP1" , providing a structural basis for functional differences.

• Genetic manipulation: Studies in yeast demonstrate that "deleting MetAP1 in yeast leads to a slow growth phenotype which can be rescued by overexpressing MetAP2" , showing functional redundancy but also suggesting unique roles for each enzyme.

• Selective inhibitors: Compounds like metapeptin B with "strong selectivity for HsMetAP1 over HsMetAP2" and TNP-470, which targets "human MetAP2, not human MetAP1" , provide pharmacological tools to distinguish the consequences of inhibiting each isozyme specifically.

What is the significance of METAP1 as a cancer target?

METAP1 has been identified as a "validated oncology target" with "strong associations across a wide range of solid tumor cancers" . The development of targeted inhibitors suggests its importance in cancer biology, with one study specifically mentioning its associations with solid tumors referencing works by Frottin et al. (2016) and Behan et al. (2019) .

While METAP2 inhibitors have advanced further in clinical development for various indications including cancer, obesity, Prader-Willi Syndrome, and autoimmunity , the focus on discovering selective METAP1 inhibitors like metapeptin B indicates the distinct therapeutic potential of targeting this isozyme specifically in oncology applications.

How does inhibition of METAP1 differ from inhibition of METAP2 in therapeutic contexts?

Therapeutic targeting of these isozymes shows distinct patterns:

These differences likely reflect the distinct biological roles of these isozymes, with METAP1 more involved in fundamental cellular processes and METAP2 having more specialized functions in processes like angiogenesis.

What emerging approaches might improve our understanding of METAP1 biology?

Several emerging research directions could advance our understanding of METAP1:

• Structural biology: Further high-resolution structural studies, similar to those conducted for mitochondrial MetAP1D , could provide deeper insights into the mechanisms of substrate recognition and catalysis by METAP1.

• Metagenomics-based discovery: The "next-gen" discovery platform described as overcoming "many of the challenges constraining traditional methods" suggests that mining metagenomic data will continue to yield novel insights and inhibitors .

• Comparative isozyme studies: More detailed analysis of the "distinct structural disparities within the active-site pocket" between METAP1 variants could inform more selective targeting strategies.

• Integration with other N-terminal modification pathways: Further investigation of how METAP1 activity coordinates with downstream modification enzymes responsible for "myristoylation, acetylation, methylation, or other chemical reactions" could provide a more holistic understanding of N-terminal protein processing regulation.

What technological advances are needed to better study METAP1 in complex biological systems?

Based on the challenges identified in the search results, several technological advances would benefit METAP1 research:

• Improved computational prediction tools: Current limitations in "accurately predict[ing] the structure of the encoded small molecule" suggest a need for better computational approaches for predicting natural product structures from genomic data.

• Advanced proteomics techniques: More sensitive methods to identify and quantify N-terminal methionine excision events in complex proteomes would enhance our understanding of METAP1's substrate landscape.

• Selective probes and reporters: Development of highly selective chemical probes or biosensors for METAP1 activity would enable more precise studies in live cells and complex systems.

• Systems biology integration: Techniques that can place METAP1 activity within the broader context of cellular proteostasis networks would provide more comprehensive insights into its biological significance.