Pseudokinases: From Allosteric Regulation of Catalytic Domains and the Formation of Macromolecular Assemblies to Emerging Drug Targets

Pseudokinases are a member of the kinase superfamily that lack one or more of the canonical residues required for catalysis. Protein pseudokinases are widely distributed across species and are present in proteins that perform a great diversity of roles in the cell. They represent approximately 10% to 40% of the kinome of a multicellular organism. In the human, the pseudokinase subfamily consists of approximately 60 unique proteins. Despite their lack of one or more of the amino acid residues typically required for the productive interaction with ATP and metal ions, which is essential for the phosphorylation of specific substrates, pseudokinases are important functional molecules that can act as dynamic scaffolds, competitors, or modulators of protein–protein interactions. Indeed, pseudokinase misfunctions occur in diverse diseases and represent a new therapeutic window for the development of innovative therapeutic approaches. In this contribution, we describe the structural features of pseudokinases that are used as the basis of their classification; analyse the interactome space of human pseudokinases and discuss their potential as suitable drug targets for the treatment of various diseases, including metabolic, neurological, autoimmune, and cell proliferation disorders.

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Development of Phosphodiesterase–Protein-Kinase Complexes as Novel Targets for Discovery of Inhibitors with Enhanced Specificity

International Journal of Molecular Sciences ◽

10.3390/ijms22105242 ◽

2021 ◽

Vol 22 (10) ◽

pp. 5242

Author(s):

Nikhil K. Tulsian ◽

Valerie Jia-En Sin ◽

Hwee-Ling Koh ◽

Ganesh S. Anand

Keyword(s):

Protein Interactions ◽

Cyclic Nucleotides ◽

Cyclic Nucleotide ◽

Drug Targets ◽

Cross Reactivity ◽

Nucleotide Receptors ◽

Protein Protein Interactions ◽

Macromolecular Assemblies ◽

Fluorescence Polarization Assay ◽

In Cells

Phosphodiesterases (PDEs) hydrolyze cyclic nucleotides to modulate multiple signaling events in cells. PDEs are recognized to actively associate with cyclic nucleotide receptors (protein kinases, PKs) in larger macromolecular assemblies referred to as signalosomes. Complexation of PDEs with PKs generates an expanded active site that enhances PDE activity. This facilitates signalosome-associated PDEs to preferentially catalyze active hydrolysis of cyclic nucleotides bound to PKs and aid in signal termination. PDEs are important drug targets, and current strategies for inhibitor discovery are based entirely on targeting conserved PDE catalytic domains. This often results in inhibitors with cross-reactivity amongst closely related PDEs and attendant unwanted side effects. Here, our approach targeted PDE–PK complexes as they would occur in signalosomes, thereby offering greater specificity. Our developed fluorescence polarization assay was adapted to identify inhibitors that block cyclic nucleotide pockets in PDE–PK complexes in one mode and disrupt protein-protein interactions between PDEs and PKs in a second mode. We tested this approach with three different systems—cAMP-specific PDE8–PKAR, cGMP-specific PDE5–PKG, and dual-specificity RegA–RD complexes—and ranked inhibitors according to their inhibition potency. Targeting PDE–PK complexes offers biochemical tools for describing the exquisite specificity of cyclic nucleotide signaling networks in cells.

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Protein Interaction Domains and Post-Translational Modifications: Structural Features and Drug Discovery Applications

Current Medicinal Chemistry ◽

10.2174/0929867326666190620101637 ◽

2020 ◽

Vol 27 (37) ◽

pp. 6306-6355 ◽

Cited By ~ 2

Author(s):

Marian Vincenzi ◽

Flavia Anna Mercurio ◽

Marilisa Leone

Keyword(s):

Drug Discovery ◽

Protein Interaction ◽

Protein Interactions ◽

Structural Information ◽

Protein Complexes ◽

Structural Features ◽

Protein Protein Interactions ◽

Modular Architecture ◽

Post Translational Modifications ◽

Interaction Domains

Background:: Many pathways regarding healthy cells and/or linked to diseases onset and progression depend on large assemblies including multi-protein complexes. Protein-protein interactions may occur through a vast array of modules known as protein interaction domains (PIDs). Objective:: This review concerns with PIDs recognizing post-translationally modified peptide sequences and intends to provide the scientific community with state of art knowledge on their 3D structures, binding topologies and potential applications in the drug discovery field. Method:: Several databases, such as the Pfam (Protein family), the SMART (Simple Modular Architecture Research Tool) and the PDB (Protein Data Bank), were searched to look for different domain families and gain structural information on protein complexes in which particular PIDs are involved. Recent literature on PIDs and related drug discovery campaigns was retrieved through Pubmed and analyzed. Results and Conclusion:: PIDs are rather versatile as concerning their binding preferences. Many of them recognize specifically only determined amino acid stretches with post-translational modifications, a few others are able to interact with several post-translationally modified sequences or with unmodified ones. Many PIDs can be linked to different diseases including cancer. The tremendous amount of available structural data led to the structure-based design of several molecules targeting protein-protein interactions mediated by PIDs, including peptides, peptidomimetics and small compounds. More studies are needed to fully role out, among different families, PIDs that can be considered reliable therapeutic targets, however, attacking PIDs rather than catalytic domains of a particular protein may represent a route to obtain selective inhibitors.

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Expanded: a gene involved in the control of cell proliferation in imaginal discs

Development ◽

10.1242/dev.118.4.1291 ◽

1993 ◽

Vol 118 (4) ◽

pp. 1291-1301 ◽

Cited By ~ 15

Author(s):

M. Boedigheimer ◽

A. Laughon

Keyword(s):

Cell Proliferation ◽

Protein Interactions ◽

Essential Gene ◽

Spontaneous Mutation ◽

Growth Control ◽

Imaginal Discs ◽

Apical Surface ◽

Protein Protein Interactions ◽

Acid Protein ◽

Disc Cells

The expanded gene was first identified by a spontaneous mutation that causes broad wings. We have identified an enhancer-trap insertion within expanded and used it to generate additional mutations, including one null allele. expanded is an essential gene, necessary for proper growth control of imaginal discs and, when mutant, causes either hyperplasia or degeneration depending on the disc. Wing overgrowth in expanded hypermorphs is limited to specific regions along the anterior-posterior and dorsal-ventral axis. expanded encodes a novel 1429 amino acid protein that is localized to the apical surface of disc cells and contains three potential SH3-binding sites. Together, these observations suggest that the Expanded protein engages in protein-protein interactions regulating cell proliferation in discs.

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Exploring Protein-Protein Interactions as Drug Targets for Anti-cancer Therapy with In Silico Workflows

Methods in Molecular Biology - Proteomics for Drug Discovery ◽

10.1007/978-1-4939-7201-2_15 ◽

2017 ◽

pp. 221-236 ◽

Cited By ~ 11

Author(s):

Alexander Goncearenco ◽

Minghui Li ◽

Franco L. Simonetti ◽

Benjamin A. Shoemaker ◽

Anna R. Panchenko

Keyword(s):

Cancer Therapy ◽

Protein Interactions ◽

In Silico ◽

Drug Targets ◽

Protein Protein Interactions ◽

Anti Cancer

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Protein–Protein Interactions in Translesion Synthesis

Molecules ◽

10.3390/molecules26185544 ◽

2021 ◽

Vol 26 (18) ◽

pp. 5544

Author(s):

Radha Charan Dash ◽

Kyle Hadden

Keyword(s):

Protein Interactions ◽

Acquired Resistance ◽

Translesion Synthesis ◽

Initial Response ◽

Structural Features ◽

Dna Lesions ◽

Protein Protein Interactions ◽

Dna Damage Tolerance ◽

Response To Chemotherapy ◽

Depth Analysis

Translesion synthesis (TLS) is an error-prone DNA damage tolerance mechanism used by actively replicating cells to copy past DNA lesions and extend the primer strand. TLS ensures that cells continue replication in the presence of damaged DNA bases, albeit at the expense of an increased mutation rate. Recent studies have demonstrated a clear role for TLS in rescuing cancer cells treated with first-line genotoxic agents by allowing them to replicate and survive in the presence of chemotherapy-induced DNA lesions. The importance of TLS in both the initial response to chemotherapy and the long-term development of acquired resistance has allowed it to emerge as an interesting target for small molecule drug discovery. Proper TLS function is a complicated process involving a heteroprotein complex that mediates multiple attachment and switching steps through several protein–protein interactions (PPIs). In this review, we briefly describe the importance of TLS in cancer and provide an in-depth analysis of key TLS PPIs, focusing on key structural features at the PPI interface while also exploring the potential druggability of each key PPI.

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Group I Metabotropic Glutamate Receptors and Interacting Partners: An Update

International Journal of Molecular Sciences ◽

10.3390/ijms23020840 ◽

2022 ◽

Vol 23 (2) ◽

pp. 840

Author(s):

Li-Min Mao ◽

Alaya Bodepudi ◽

Xiang-Ping Chu ◽

John Q. Wang

Keyword(s):

Synaptic Plasticity ◽

Protein Interactions ◽

Metabotropic Glutamate Receptors ◽

Adaptor Proteins ◽

Mammalian Brain ◽

Amino Acid Residues ◽

Protein Protein Interactions ◽

Metabotropic Glutamate ◽

Group I ◽

Associated Proteins

Group I metabotropic glutamate (mGlu) receptors (mGlu1/5 subtypes) are G protein-coupled receptors and are broadly expressed in the mammalian brain. These receptors play key roles in the modulation of normal glutamatergic transmission and synaptic plasticity, and abnormal mGlu1/5 signaling is linked to the pathogenesis and symptomatology of various mental and neurological disorders. Group I mGlu receptors are noticeably regulated via a mechanism involving dynamic protein–protein interactions. Several synaptic protein kinases were recently found to directly bind to the intracellular domains of mGlu1/5 receptors and phosphorylate the receptors at distinct amino acid residues. A variety of scaffolding and adaptor proteins also interact with mGlu1/5. Constitutive or activity-dependent interactions between mGlu1/5 and their interacting partners modulate trafficking, anchoring, and expression of the receptors. The mGlu1/5-associated proteins also finetune the efficacy of mGlu1/5 postreceptor signaling and mGlu1/5-mediated synaptic plasticity. This review analyzes the data from recent studies and provides an update on the biochemical and physiological properties of a set of proteins or molecules that interact with and thus regulate mGlu1/5 receptors.

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Characterization of COMMD protein–protein interactions in NF-κB signalling

Biochemical Journal ◽

10.1042/bj20051664 ◽

2006 ◽

Vol 398 (1) ◽

pp. 63-71 ◽

Cited By ~ 61

Author(s):

Prim de Bie ◽

Bart van de Sluis ◽

Ezra Burstein ◽

Karen J. Duran ◽

Ruud Berger ◽

...

Keyword(s):

Protein Interactions ◽

Copper Metabolism ◽

Nuclear Factor Κb ◽

Inhibitory Effect ◽

Protein Family ◽

Amino Acid Residues ◽

Protein Protein Interactions ◽

Necrosis Factor

COMMD [copper metabolism gene MURR1 (mouse U2af1-rs1 region 1) domain] proteins constitute a recently identified family of NF-κB (nuclear factor κB)-inhibiting proteins, characterized by the presence of the COMM domain. In the present paper, we report detailed investigation of the role of this protein family, and specifically the role of the COMM domain, in NF-κB signalling through characterization of protein–protein interactions involving COMMD proteins. The small ubiquitously expressed COMMD6 consists primarily of the COMM domain. Therefore COMMD1 and COMMD6 were analysed further as prototype members of the COMMD protein family. Using specific antisera, interaction between endogenous COMMD1 and COMMD6 is described. This interaction was verified by independent techniques, appeared to be direct and could be detected throughout the whole cell, including the nucleus. Both proteins inhibit TNF (tumour necrosis factor)-induced NF-κB activation in a non-synergistic manner. Mutation of the amino acid residues Trp24 and Pro41 in the COMM domain of COMMD6 completely abolished the inhibitory effect of COMMD6 on TNF-induced NF-κB activation, but this was not accompanied by loss of interaction with COMMD1, COMMD6 or the NF-κB subunit RelA. In contrast with COMMD1, COMMD6 does not bind to IκBα (inhibitory κBα), indicating that both proteins inhibit NF-κB in an overlapping, but not completely similar, manner. Taken together, these data support the significance of COMMD protein–protein interactions and provide new mechanistic insight into the function of this protein family in NF-κB signalling.

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