Comparative Analysis of The Kinomes of Plasmodium Falciparum, Plasmodium Vivax And Their Host Homo Sapiens

Background: Novel antimalarials should be effective across all species of malaria parasites that infect humans, especially the two species that bear the most impact, Plasmodium falciparum and Plasmodium vivax. Protein kinases encoded by pathogens, as well as host kinases required for survival of intracellular pathogens, carry considerable potential as targets for antimalarial intervention 1,2. To date, no comprehensive P. vivax kinome assembly has been conducted; and the P. falciparum kinome, first assembled in 2004, requires an update. The present study, aimed to fill these gaps, utilises a recently published structurally-validated multiple sequence alignment (MSA) of the human kinome 3. This MSA is used as a scaffold to assist the alignment of all protein kinase sequences from P. falciparum and P. vivax, and (where possible) their assignment to specific kinase groups/families.Results: We were able to assign six P. falciparum previously classified as OPK or ‘orphans’ (i.e. with no clear phylogenetic relation to any of the established ePK groups) to one of the aforementioned ePK groups. Direct phylogenetic comparison established that despite an overall high level of similarity between the P. falciparum and P. vivax kinomes, which will help in selecting targets for intervention, there are differences that may underlie the biological specificities of these species. Furthermore, we highlight a number of Plasmodium kinases that have a surprisingly high level of homology with their human counterparts and therefore not well suited as targets for drug discovery.Conclusions: Direct comparison of the kinomes of Homo sapiens, P. falciparum and P. vivax sheds additional light on the previously documented divergence of many P. falciparum and P. vivax kinases from those of their human host. We provide the first direct kinome comparison between the phylogenetically distinct species of P. falciparum and P. vivax, illustrating the key similarities and differences which must be considered in the context of kinase-directed antimalarial drug discovery, and discuss the divergences and similarities between the human and Plasmodium kinomes to inform future searches for selective antimalarial intervention.

Using the Structural Kinome to Systematize Kinase Drug Discovery

Kinase-targeted drug design is challenging. It requires designing inhibitors that can bind to specific kinases, when all kinase catalytic domains share a common folding scaffold that binds ATP. Thus, obtaining the desired selectivity, given the whole human kinome, is a fundamental task during early-stage drug discovery. This begins with deciphering the kinase-ligand characteristics, analyzing the structure–activity relationships and prioritizing the desired drug molecules across the whole kinome. Currently, there are more than 300 kinases with released PDB structures, which provides a substantial structural basis to gain these necessary insights. Here, we review in silico structure-based methods – notably, a function-site interaction fingerprint approach used in exploring the complete human kinome. In silico methods can be explored synergistically with multiple cell-based or protein-based assay platforms such as KINOMEscan. We conclude with new drug discovery opportunities associated with kinase signaling networks and using machine/deep learning techniques broadly referred to as structural biomedical data science.

A subcellular map of the human kinome

The human kinome comprises 538 kinases playing essential functions by catalyzing protein phosphorylation. Annotation of subcellular distribution of the kinome greatly facilitates investigation of normal and disease mechanisms. Here, we present Kinome Atlas (KA), an image-based map of the kinome annotated to 10 cellular compartments. 456 epitope-tagged kinases, representing 85% of the human kinome, were expressed in HeLa cells and imaged by immunofluorescent microscopy under a similar condition. KA revealed kinase family-enriched subcellular localizations, and discovered a collection of new kinase localizations at mitochondria, plasma membrane, extracellular space, and other structures. Furthermore, KA demonstrated the role of liquid-liquid phase separation in formation of kinase condensates. Identification of MOK as a mitochondrial kinase revealed its function in cristae dynamics, respiration, and oxidative stress response. Although limited by possible mislocalization due to overexpression or epitope tagging, this subcellular map of the kinome can be used to refine regulatory mechanisms involving protein phosphorylation.

Exploring the understudied human kinome for research and therapeutic opportunities

ABSTRACTThe functions of protein kinases have been widely studied and many kinase inhibitors have been developed into FDA-approved therapeutics. A substantial fraction of the human kinome is nonetheless understudied. In this perspective, members of the NIH Understudied Kinome Consortium mine publicly available databases to assess the functionality of these understudied kinases as well as their potential to be therapeutic targets for drug discovery campaigns. We start with a re-analysis of the kinome as a whole and describe criteria for creating an inclusive set of 710 kinase domains as well as a curated set of 557 protein kinase like (PKL) domains. We define an understudied (‘dark’) kinome by quantifying the public knowledge on each kinase with a PKL domain using an automatic reading machine. We find a substantial number are essential in the Cancer Dependency Map and differentially expressed or mutated in disease databases such as The Cancer Genome Atlas. Based on this and other data, it seems likely that the dark kinome contains biologically important genes, a subset of which may be viable drug targets.

The first eukaryotic kinome tree illuminates the dynamic history of present-day kinases

Eukaryotic Protein Kinases (ePKs) are essential for eukaryotic cell signalling. Several phylogenetic trees of the ePK repertoire of single eukaryotes have been published, including the human kinome tree. However, a eukaryote-wide kinome tree was missing due to the large number of kinases in eukaryotes. Using a pipeline that overcomes this problem, we present here the first eukaryotic kinome tree. The tree reveals that the Last Eukaryotic Common Ancestor (LECA) possessed at least 92 ePKs, much more than previously thought. The retention of these LECA ePKs in present-day species is highly variable. Fourteen human kinases with unresolved placement in the human kinome tree were found to originate from three known ePK superfamilies. Further analysis of ePK superfamilies shows that they exhibit markedly diverse evolutionary dynamics between the LECA and present-day eukaryotes. The eukaryotic kinome tree thus unveils the evolutionary history of ePKs, but the tree also enables the transfer of functional information between related kinases.

Novel method to identify group-specific non-catalytic pockets of human kinome for drug design

Kinase proteins have been intensively investigated as drug targets for decades because of their crucial involvement in many biological pathways. We developed hybrid approach to identify non-catalytic pockets and will benefit the kinome drug design.

Sequential phosphorylation of NDEL1 by the DYRK2-GSK3β complex is critical for neuronal morphogenesis

Neuronal morphogenesis requires multiple regulatory pathways to appropriately determine axonal and dendritic structures, thereby to enable the functional neural connectivity. Yet, however, the precise mechanisms and components that regulate neuronal morphogenesis are still largely unknown. Here, we newly identified the sequential phosphorylation of NDEL1 critical for neuronal morphogenesis through the human kinome screening and phospho-proteomics analysis of NDEL1 from mouse brain lysate. DYRK2 phosphorylates NDEL1 S336 to prime the phosphorylation of NDEL1 S332 by GSK3β. TARA, an interaction partner of NDEL1, scaffolds DYRK2 and GSK3β to form a tripartite complex and enhances NDEL1 S336/S332 phosphorylation. This dual phosphorylation increases the filamentous actin dynamics. Ultimately, the phosphorylation enhances both axonal and dendritic outgrowth and promotes their arborization. Together, our findings suggest the NDEL1 phosphorylation at S336/S332 by the TARA-DYRK2-GSK3β complex as a novel regulatory mechanism underlying neuronal morphogenesis.