Prospects for pharmacological targeting of pseudokinases

Abstract

Pseudokinases are members of the protein kinase superfamily but signal primarily through noncatalytic mechanisms. Many pseudokinases contribute to the pathologies of human diseases, yet they remain largely unexplored as drug targets owing to challenges associated with modulation of their biological functions. Our understanding of the structure and physiological roles of pseudokinases has improved substantially over the past decade, revealing intriguing similarities between pseudokinases and their catalytically active counterparts. Pseudokinases often adopt conformations that are analogous to those seen in catalytically active kinases and, in some cases, can also bind metal cations and/or nucleotides. Several clinically approved kinase inhibitors have been shown to influence the noncatalytic functions of active kinases, providing hope that similar properties in pseudokinases could be pharmacologically regulated. In this Review, we discuss known roles of pseudokinases in disease, their unique structural features and the progress that has been made towards developing pseudokinase-directed therapeutics.

Emerging concepts in pseudoenzyme classification, evolution, and signaling

“…More broadly among pseudoenzymes, such functions likely speak to a noncatalytic substrate binding to an ancestral enzyme, which has evolved to perform a catalytic function, as has been demonstrated during in vitro evolution experiments (48,49) and by using structural features to evolve canonical activity in the pseudokinase CASK (Ca 2+ /calmodulin-activated serine/threonine kinase), where four amino acid substitutions are required to regenerate an Mg-ATPdependent enzyme (50). In a similar vein, improving the curation of (nonkinase) pseudoenzyme families will provide the scientific community with valuable information to understand the evolution of these proteins, the etiology of related diseases, and the development and repurposing of pseudoenzyme-targeted drugs, a useful bonus in carefully conducted pseudoenzyme studies (7,51,52).…”

“…Formally, we propose that pseudoenzymes be defined as "the predicted catalytically defective counterparts of enzymes owing to an absence of one or more catalytic residue". It should come as no surprise that, in some cases, in which this simple description is applied, residual catalytic activities have been reported among proteins defined as pseudoenzymes (mainly pseudokinases), including the isolated pseudokinase domains for human epidermal growth factor receptor 3 (HER3, also known as EGFR3 or ERBB3), Janus kinase 2 [JAK2; pseudokinase domain called JAK homology-2 (JH2)], CASK, and Tribbles 2 (TRIB2) (7,50,64,65). However, because these very modest catalytic activities are either dispensable for biological function or not conserved in vitro among paralogous proteins across species (such as HER3/EGFR3[2) (24), this vestigial (or residual) catalytic activity is probably not a defining feature of their biological function.…”

“…Genomic sequencing and annotation and the subsequent mining of datasets from varied organisms confirm that most well-characterized enzyme families encode pseudoenzyme homologs, which are predicted to be enzymatically inactive due to the loss of at least one key catalytic amino acid residue. This basic description, garnered from primary sequencing data, has allowed the bioinformatic identification of pseudoenzyme genes (all of which are transcribed as mRNAs and translated into proteins) in >20 different protein families (1), including well-studied paradigms among the pseudokinases, pseudophosphatases, and pseudoproteases (2)(3)(4)(5)(6)(7)(8)(9)(10). As detailed in Table 1, subtle changes in catalytic and substrate-binding sites have likely led to the appearance of pseudoenzymes from classical enzyme templates, almost certainly after gene duplication events.…”

KinCon: Cell‐based recording of full‐length kinase conformations

“…In addition, we show basal KinCon conformations with kinases from the mTOR pathway, some CDKs, and with kinases upstream of AMPK. It should be noted that the KinCon reporter principle may also provide functional insights into pseudokinase conformation dynamics . Recently, it has been demonstrated that nucleotide binding, substrate interactions, or small molecule interactions alter non‐catalytic protein‐interaction modules of pseudokinase .…”

Cell-Free Protein Synthesis: A Promising Option for Future Drug Development

“…Proteins whose functionality is not well characterized form a large percentage of entries in many of the currently available biological databases, including the Protein Data Bank (PDB), and there is a constantly growing demand for reliable and fast synthesis and characterization methods. When it comes to drug discovery, proteins are key components as they can have therapeutic potential themselves (e.g., antibodies, coagulation factors, hormones, growth factors, enzymes, and antimicrobial peptides), but also because they could serve as drug targets for diverse diseases (as ion channels, receptors, enzymes, and transporters, for example) [1][2][3][4][5][6][7]. A large proportion of approved pharmaceutical drugs target human proteins.…”