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Journal of Clinical Periodontology Sep 2023Necroptosis participates in the pathogenesis of many inflammatory diseases, including periodontitis. Here, we aimed to investigate the role and mechanism of necroptosis...
AIM
Necroptosis participates in the pathogenesis of many inflammatory diseases, including periodontitis. Here, we aimed to investigate the role and mechanism of necroptosis inhibitors in attenuating periodontitis.
MATERIALS AND METHODS
The Gene Expression Omnibus (GEO) dataset GSE164241 was re-analysed to identify the role of necroptosis in periodontitis. Gingival specimens from healthy subjects or periodontitis patients were collected to evaluate the expression level of necroptosis-associated proteins. The therapeutic effect of necroptosis inhibitors on periodontitis was assessed in vivo and in vitro. Moreover, Transwell assays and Western blotting and siRNA transfection were used to identify the effects of necroptotic human gingival fibroblasts (hGFs) on THP-1 macrophages.
RESULTS
Re-analysis revealed that gingival fibroblasts (GFs) in periodontitis gingiva showed the highest area under the curve score of necroptosis. Elevated levels of necroptosis-associated proteins were identified in GFs in periodontitis gingiva collected from patients and mice. In ligature-induced periodontitis mice, local administration of receptor interacting protein kinase 3(RIPK3) inhibitor GSK'872 or sh-mixed-lineage kinase domain-like pseudokinase (Mlkl) markedly abrogated necroptosis and rescued periodontitis. Analogously, necroptosis inhibitors alleviated the inflammatory response and release of damage-associated molecular patterns in lipopolysaccharide- or LAZ (LPS + AZD'5582 + z-VAD-fmk, necroptosis inducer)-induced GFs and then reduced THP-1 cell migration and M1 polarization.
CONCLUSIONS
Necroptosis in GFs aggravated gingival inflammation and alveolar bone loss. Necroptosis inhibitors attenuate this process by modulating THP-1 macrophage migration and polarization. This study offers novel insights into the pathogenesis and potential therapeutic targets of periodontitis.
Topics: Humans; Mice; Animals; Protein Kinases; Gingiva; Necroptosis; Periodontitis; Fibroblasts; Gingivitis; Receptor-Interacting Protein Serine-Threonine Kinases
PubMed: 37366309
DOI: 10.1111/jcpe.13841 -
Biochemical Society Transactions Feb 2021The protein kinase C-related kinase (PRK) family of serine/threonine kinases, PRK1, PRK2 and PRK3, are effectors for the Rho family small G proteins. An array of studies... (Review)
Review
The protein kinase C-related kinase (PRK) family of serine/threonine kinases, PRK1, PRK2 and PRK3, are effectors for the Rho family small G proteins. An array of studies have linked these kinases to multiple signalling pathways and physiological roles, but while PRK1 is relatively well-characterized, the entire PRK family remains understudied. Here, we provide a holistic overview of the structure and function of PRKs and describe the molecular events that govern activation and autoregulation of catalytic activity, including phosphorylation, protein interactions and lipid binding. We begin with a structural description of the regulatory and catalytic domains, which facilitates the understanding of their regulation in molecular detail. We then examine their diverse physiological roles in cytoskeletal reorganization, cell adhesion, chromatin remodelling, androgen receptor signalling, cell cycle regulation, the immune response, glucose metabolism and development, highlighting isoform redundancy but also isoform specificity. Finally, we consider the involvement of PRKs in pathologies, including cancer, heart disease and bacterial infections. The abundance of PRK-driven pathologies suggests that these enzymes will be good therapeutic targets and we briefly report some of the progress to date.
Topics: Animals; Catalysis; Humans; Protein Conformation; Protein Kinase C; Protein Kinases; Signal Transduction; Structure-Activity Relationship
PubMed: 33522581
DOI: 10.1042/BST20200466 -
Methods in Enzymology 2022Pseudokinases regulate diverse cellular processes associated with normal cellular functions and disease. They are defined bioinformatically based on the absence of one... (Review)
Review
Pseudokinases regulate diverse cellular processes associated with normal cellular functions and disease. They are defined bioinformatically based on the absence of one or more catalytic residues that are required for canonical protein kinase functions. The ability to define pseudokinases based on primary sequence comparison has enabled the systematic mapping and cataloging of pseudokinase orthologs across the tree of life. While these sequences contain critical information regarding pseudokinase evolution and functional specialization, extracting this information and generating testable hypotheses based on integrative mining of sequence and structural data requires specialized computational tools and resources. In this chapter, we review recent advances in the development and application of open-source tools and resources for pseudokinase research. Specifically, we describe the application of an interactive data analytics framework, KinView, for visualizing the patterns of conservation and variation in the catalytic domain motifs of pseudokinases and evolutionarily related canonical kinases using a consistent set of curated alignments organized based on the widely used kinome evolutionary hierarchy. We also demonstrate the application of an integrated Protein Kinase Ontology (ProKinO) and an interactive viewer, ProtVista, for mapping and analyzing primary sequence motifs and annotations in the context of 3D structures and AlphaFold2 models. We provide examples and protocols for generating testable hypotheses on pseudokinase functions both for bench biologists and advanced users.
Topics: Catalytic Domain; Protein Kinases
PubMed: 35525549
DOI: 10.1016/bs.mie.2022.03.040 -
Drug Discovery Today Oct 2022Determining protein-ligand interaction characteristics and mechanisms is crucial to the drug discovery process. Here, we review recent progress and successful... (Review)
Review
Determining protein-ligand interaction characteristics and mechanisms is crucial to the drug discovery process. Here, we review recent progress and successful applications of a systematic protein-ligand interaction fingerprint (IFP) approach for investigating proteome-wide protein-ligand interactions for drug development. Specifically, we review the use of this IFP approach for revealing polypharmacology across the kinome, predicting promising targets from which to design allosteric inhibitors and covalent kinase inhibitors, uncovering the binding mechanisms of drugs of interest, and demonstrating resistant mechanisms of specific drugs. Together, we demonstrate that the IFP strategy is efficient and practical for drug design research for protein kinases as targets and is extensible to other protein families.
Topics: Drug Discovery; Ligands; Polypharmacology; Protein Kinase Inhibitors; Protein Kinases; Proteome
PubMed: 35850431
DOI: 10.1016/j.drudis.2022.07.004 -
International Journal of Molecular... Nov 2017With 1.67 million new cases and 522,000 deaths in the year 2012, breast cancer is the most common type of diagnosed malignancy and the second leading cause of cancer... (Review)
Review
With 1.67 million new cases and 522,000 deaths in the year 2012, breast cancer is the most common type of diagnosed malignancy and the second leading cause of cancer death in women around the world. Despite the success of screening programs and the development of adjuvant therapies, a significant percentage of breast cancer patients will suffer a metastatic disease that, to this day, remains incurable and justifies the research of new therapies to improve their life expectancy. Among the new therapies that have been developed in recent years, the emergence of targeted therapies has been a milestone in the fight against cancer. Over the past decade, many studies have shown a causal role of protein kinase dysregulations or mutations in different human diseases, including cancer. Along these lines, cancer research has demonstrated a key role of many protein kinases during human tumorigenesis and cancer progression, turning these molecules into valid candidates for new targeted therapies. The subsequent discovery and introduction in 2001 of the kinase inhibitor imatinib, as a targeted treatment for chronic myelogenous leukemia, revolutionized cancer genetic pathways research, and lead to the development of multiple small-molecule kinase inhibitors against various malignancies, including breast cancer. In this review, we analyze studies published to date about novel small-molecule kinase inhibitors and evaluate if they would be useful to develop new treatment strategies for breast cancer patients.
Topics: Animals; Antineoplastic Agents; Breast Neoplasms; Female; Humans; Protein Kinase Inhibitors; Protein Kinases
PubMed: 29186886
DOI: 10.3390/ijms18122543 -
Drug Resistance Updates : Reviews and... Mar 2018Herpesviruses thymidine kinase (TK) and protein kinase (PK) allow the activation of nucleoside analogues used in anti-herpesvirus treatments. Mutations emerging in these... (Review)
Review
Herpesviruses thymidine kinase (TK) and protein kinase (PK) allow the activation of nucleoside analogues used in anti-herpesvirus treatments. Mutations emerging in these two genes often lead to emergence of drug-resistant strains responsible for life-threatening diseases in immunocompromised populations. In this review, we analyze the binding of different nucleoside analogues to the TK active site of the three α-herpesviruses [Herpes Simplex Virus 1 and 2 (HSV-1 and HSV-2) and Varicella-Zoster Virus (VZV)] and present the impact of known mutations on the structure of the viral TKs. Furthermore, models of β-herpesviruses [Human cytomegalovirus (HCMV) and human herpesvirus-6 (HHV-6)] PKs allow to link amino acid changes with resistance to ganciclovir and/or maribavir, an investigational chemotherapeutic used in patients with multidrug-resistant HCMV. Finally, we set the basis for the understanding of drug-resistance in γ-herpesviruses [Epstein-Barr virus (EBV) and Kaposi's sarcoma associated herpesvirus (KSHV)] TK and PK through the use of animal surrogate models.
Topics: Animals; Antiviral Agents; Drug Design; Drug Resistance, Viral; Herpesviridae; Herpesviridae Infections; Humans; Mutation; Protein Conformation; Protein Kinases; Structure-Activity Relationship; Thymidine Kinase; Viral Proteins
PubMed: 29548479
DOI: 10.1016/j.drup.2018.01.003 -
Trends in Biochemical Sciences Apr 2019Since publication of the crystal structure of protein kinase (PK)A three decades ago, a structural portrait of the conserved kinase core has been drawn. The next... (Review)
Review
Since publication of the crystal structure of protein kinase (PK)A three decades ago, a structural portrait of the conserved kinase core has been drawn. The next challenge is to elucidate structures of full-length kinases and to address the intrinsically disordered regions (IDRs) that typically flank the core as well as the small linear motifs (SLiMs) that are embedded within the IDRs. It is increasingly apparent that unstructured regions integrate the kinase catalytic chassis into multienzyme-based regulatory networks. The extracellular signal-regulated kinase-ribosomal S6 PK-phosphoinositide-dependent kinase (ERK-RSK-PDK) complex is an excellent example to demonstrate how IDRs and SLiMs govern communication between four different kinase catalytic cores to mediate activation and how in molecular terms these promote the formation of kinase heterodimers in a context dependent fashion.
Topics: Humans; Intrinsically Disordered Proteins; Models, Molecular; Protein Domains; Protein Kinases
PubMed: 30611608
DOI: 10.1016/j.tibs.2018.12.002 -
Biochemical Society Transactions Jun 2017Protein phosphorylation, mediated by protein kinases, is a key event in the regulation of eukaryotic signal transduction. The majority of eukaryotic protein kinases... (Review)
Review
Protein phosphorylation, mediated by protein kinases, is a key event in the regulation of eukaryotic signal transduction. The majority of eukaryotic protein kinases perform phosphoryl transfer, assisted by two divalent metal ions. About 10% of all human protein kinases are, however, thought to be catalytically inactive. These kinases lack conserved residues of the kinase core and are classified as pseudokinases. Yet, it has been demonstrated that pseudokinases are critically involved in biological functions. Here, we show how pseudokinases have developed strategies by modifying amino acid residues in order to achieve stable, active-like conformations. This includes binding of the co-substrate ATP in a two metal-, one metal- or even no metal-binding mode. Examples of the respective pseudokinases are provided on a structural basis and compared with a canonical protein kinase, Protein Kinase A. Moreover, the functional roles of both independent metal-binding sites, Me1 and Me2, are discussed. Lack of phosphotransferase activity does not implicate a loss of function and can easily point to alternative roles of pseudokinases, i.e. acting as switches or scaffolds, and having evolved as components crucial for cellular cross-talk and signaling. Interestingly, pseudokinases are present in all kingdoms of life and their specific roles remain enigmatic. More studies are needed to unravel the crucial functions of those interesting proteins.
Topics: Amino Acid Motifs; Catalytic Domain; Cations, Divalent; Coenzymes; Coordination Complexes; Eukaryota; Evolution, Molecular; Humans; Metals; Protein Kinases; Signal Transduction
PubMed: 28620027
DOI: 10.1042/BST20160327 -
PeerJ 2023The Protein Kinase Ontology (ProKinO) is an integrated knowledge graph that conceptualizes the complex relationships among protein kinase sequence, structure, function,...
The Protein Kinase Ontology (ProKinO) is an integrated knowledge graph that conceptualizes the complex relationships among protein kinase sequence, structure, function, and disease in a human and machine-readable format. In this study, we have significantly expanded ProKinO by incorporating additional data on expression patterns and drug interactions. Furthermore, we have developed a completely new browser from the ground up to render the knowledge graph visible and interactive on the web. We have enriched ProKinO with new classes and relationships that capture information on kinase ligand binding sites, expression patterns, and functional features. These additions extend ProKinO's capabilities as a discovery tool, enabling it to uncover novel insights about understudied members of the protein kinase family. We next demonstrate the application of ProKinO. Specifically, through graph mining and aggregate SPARQL queries, we identify the p21-activated protein kinase 5 (PAK5) as one of the most frequently mutated dark kinases in human cancers with abnormal expression in multiple cancers, including a previously unappreciated role in acute myeloid leukemia. We have identified recurrent oncogenic mutations in the PAK5 activation loop predicted to alter substrate binding and phosphorylation. Additionally, we have identified common ligand/drug binding residues in PAK family kinases, underscoring ProKinO's potential application in drug discovery. The updated ontology browser and the addition of a web component, ProtVista, which enables interactive mining of kinase sequence annotations in 3D structures and Alphafold models, provide a valuable resource for the signaling community. The updated ProKinO database is accessible at https://prokino.uga.edu.
Topics: Humans; Protein Kinases; Ligands; Proteins; Phosphorylation; Neoplasms
PubMed: 38077442
DOI: 10.7717/peerj.16087 -
Frontiers in Immunology 2022Upon infection, the herpes viruses create a cellular environment suitable for survival, but innate immunity plays a vital role in cellular resistance to viral infection.... (Review)
Review
Upon infection, the herpes viruses create a cellular environment suitable for survival, but innate immunity plays a vital role in cellular resistance to viral infection. The UL13 protein of herpesviruses is conserved among all herpesviruses and is a serine/threonine protein kinase, which plays a vital role in escaping innate immunity and promoting viral replication. On the one hand, it can target various immune signaling pathways , such as the cGAS-STING pathway and the NF-κB pathway. On the other hand, it phosphorylates regulatory many cellular and viral proteins for promoting the lytic cycle. This paper reviews the research progress of the conserved herpesvirus protein kinase UL13 in immune escape and viral replication to provide a basis for elucidating the pathogenic mechanism of herpesviruses, as well as providing insights into the potential means of immune escape and viral replication of other herpesviruses that have not yet resolved the function of it.
Topics: Protein Kinases; Virus Replication; Simplexvirus; Protein Serine-Threonine Kinases; Viral Proteins
PubMed: 36531988
DOI: 10.3389/fimmu.2022.1088690