In silico analysis of plasmodium falciparum CDPK5 protein through molecular modeling, docking and dynamics

CACTI: an in silico chemical analysis tool through the integration of chemogenomic data and clustering analysis

It is well-accepted that knowledge of a small molecule's target can accelerate optimization. Although chemogenomic databases are helpful resources for predicting or finding compound interaction partners, they tend to be limited and poorly annotated. Furthermore, unlike genes, compound identifiers are often not standardized, and many synonyms may exist, especially in the biological literature, making batch analysis of compounds difficult. Here, we constructed an open-source annotation and target hypothesis prediction tool that explores some of the largest chemical and biological databases, mining these for both common name, synonyms, and structurally similar molecules. We used this Chemical Analysis and Clustering for Target Identification (CACTI) tool to analyze the Pathogen Box collection, an open-source set of 400 drug-like compounds active against a variety of microbial pathogens. Our analysis resulted in 4,315 new synonyms, 35,963 pieces of new information and target prediction hints for 58 members.Scientific contributionsWith the employment of this tool, a comprehensive report with known evidence, close analogs and drug-target prediction can be obtained for large-scale chemical libraries that will facilitate their evaluation and future target validation and optimization efforts.

An update on cerebral malaria for therapeutic intervention

BACKGROUND

Cerebral malaria is often pronounced as a major life-threatening neurological complication of Plasmodium falciparum infection. The complex pathogenic landscape of the parasite and the associated neurological complications are still not elucidated properly. The growing concerns of drugresistant parasite strains along with the failure of anti-malarial drugs to subdue post-recovery neuro-cognitive dysfunctions in cerebral malaria patients have called for a demand to explore novel biomarkers and therapeutic avenues. Due course of the brain infection journey of the parasite, events such as sequestration of infected RBCs, cytoadherence, inflammation, endothelial activation, and blood-brain barrier disruption are considered critical.

METHODS

In this review, we briefly summarize the diverse pathogenesis of the brain-invading parasite associated with loss of the blood-brain barrier integrity. In addition, we also discuss proteomics, transcriptomics, and bioinformatics strategies to identify an array of new biomarkers and drug candidates.

CONCLUSION

A proper understanding of the parasite biology and mechanism of barrier disruption coupled with emerging state-of-art therapeutic approaches could be helpful to tackle cerebral malaria.

CDPKs: The critical decoders of calcium signal at various stages of malaria parasite development

Calcium ions are used as important signals during various physiological processes. In malaria parasites, Plasmodium spp., calcium dependent protein kinases (CDPKs) have acquired the unique ability to sense and transduce calcium signals at various critical steps during the lifecycle, either through phosphorylation of downstream substrates or mediating formation of high molecular weight protein complexes. Calcium signaling cascades establish important crosstalk events with signaling pathways mediated by other secondary messengers such as cyclic adenosine monophosphate (cAMP) and cyclic guanosine monophosphate (cGMP). CDPKs play critical roles at various important physiological steps during parasite development in vertebrates and mosquitoes. They are also important for transmission of the parasite between the two hosts. Combined with the fact that CDPKs are not present in humans, they continue to be pursued as important targets for development of anti-malarial drugs.

Parasite and Host Erythrocyte Kinomics of Plasmodium Infection

Malaria remains a heavy public health and socioeconomic burden in tropical and subtropical regions. Increasing resistance against front-line treatments implies that novel targets for antimalarial intervention are urgently required. Protein kinases of both the parasites and their host cells possess strong potential in this respect. We present an overview of the updated kinome of Plasmodium falciparum, the species that is the largest contributor to malaria mortality, and of current knowledge pertaining to the function of parasite-encoded protein kinases during the parasite's life cycle. Furthermore, we detail recent advances in drug initiatives targeting Plasmodium kinases and outline the potential of protein kinases in the context of the growing field of host-directed therapies, which is currently being explored as a novel way to combat parasite drug resistance.

Characterization of Three Calcium-Dependent Protein Kinases of Cryptosporidium parvum

In Cryptosporidium spp., calcium-dependent protein kinases (CDPKs) are considered promising targets for the development of pharmaceutical interventions. Whole-genome sequencing has revealed the presence of 11 CDPKs in Cryptosporidium parvum (CpCDPKs). In this study, we expressed recombinant CpCDPK4, CpCDPK5, and CpCDPK6 in Escherichia coli. The biological characteristics and functions of these CpCDPKs were examined by using quantitative reverse transcription PCR (qRT-PCR), immunofluorescence microscopy, and an in vitro neutralization assay. The expression of the CpCDPK4 gene peaked at 12 h post-infection, the CpCDPK5 gene peaked at 12 and 48 h, and the CpCDPK6 gene peaked at 2–6 h. CpCDPK4 protein was located in the anterior and mid-anterior regions of sporozoites, and CpCDPK5 protein was located over the entire sporozoites, while CpCDPK6 protein was expressed in a spotty pattern. Immune sera of CpCDPK4 and CpCDPK6 exhibited significant inhibitory effects on host cell invasion, while the immune sera of CpCDPK5 had no effects. These differences in protein localization, gene expressions, and neutralizing capacities indicated that the CpCDPK proteins may have different roles during the lifecycle of Cryptosporidium spp.

An Update on Development of Small-Molecule Plasmodial Kinase Inhibitors

Malaria control relies heavily on the small number of existing antimalarial drugs. However, recurring antimalarial drug resistance necessitates the continual generation of new antimalarial drugs with novel modes of action. In order to shift the focus from only controlling this disease towards elimination and eradication, next-generation antimalarial agents need to address the gaps in the malaria drug arsenal. This includes developing drugs for chemoprotection, treating severe malaria and blocking transmission. Plasmodial kinases are promising targets for next-generation antimalarial drug development as they mediate critical cellular processes and some are active across multiple stages of the parasite's life cycle. This review gives an update on the progress made thus far with regards to plasmodial kinase small-molecule inhibitor development.

A computational approach to validate novel drug targets of gentianine from Swertiya chirayita in Plasmodium falciparum

Gentianine is one of the compounds found in the plant Swertiya chirayita that is known for its antimalarial activity. However, its exact molecular mechanism of action is yet to be understood. In our present study, we applied several computational approaches to filter out and determine possible targets of gentianine in Plasmodium falciparum 3D7. Protein-protein networks formed the basis of one of our strategies along with orthologous protein analysis to establish essentiality. Out of 6 essential proteins from unique pathways, haloacid dehalogenase like-hydrolase (PfHAD1), phosphoenolpyruvate carboxykinase (PfPEPCK) and fumarate hydratase (PfFH) were screened as drug targets through this approach. Through our other strategy we established the predicted IC50 (PIC50) value of gentianine with a set of molecular descriptors from 123 Pathogen Box anti-malarial compounds. Afterwards through 2D structural similarity, L-lactate dehydrogenase (PfLDH) was established as another possible target. In our work, we performed in silico docking and analysed the binding of gentianine to the proteins. All of the proteins were reported with favourable binding results and were considered for complex molecular dynamics simulation approach. Our research clears up the molecular mechanism of antimalarial activity of gentianine to some extent paving way for experimental validation of the same in future.

Screening the Medicines for Malaria Venture Pathogen Box for invasion and egress inhibitors of the blood stage of Plasmodium falciparum reveals several inhibitory compounds

With emerging resistance to frontline treatments, it is vital that new drugs are identified to target Plasmodium falciparum. One of the most critical processes during parasites asexual lifecycle is the invasion and subsequent egress of red blood cells (RBCs). Many unique parasite ligands, receptors and enzymes are employed during egress and invasion that are essential for parasite proliferation and survival, therefore making these processes druggable targets. To identify potential inhibitors of egress and invasion, we screened the Medicines for Malaria Venture Pathogen Box, a 400 compound library against neglected tropical diseases, including 125 with antimalarial activity. For this screen, we utilised transgenic parasites expressing a bioluminescent reporter, nanoluciferase (Nluc), to measure inhibition of parasite egress and invasion in the presence of the Pathogen Box compounds. At a concentration of 2 µM, we found 15 compounds that inhibited parasite egress by >40% and 24 invasion-specific compounds that inhibited invasion by >90%. We further characterised 11 of these inhibitors through cell-based assays and live cell microscopy, and found two compounds that inhibited merozoite maturation in schizonts, one compound that inhibited merozoite egress, one compound that directly inhibited parasite invasion and one compound that slowed down invasion and arrested ring formation. The remaining compounds were general growth inhibitors that acted during the egress and invasion phase of the cell cycle. We found the sulfonylpiperazine, MMV020291, to be the most invasion-specific inhibitor, blocking successful merozoite internalisation within human RBCs and having no substantial effect on other stages of the cell cycle. This has significant implications for the possible development of an invasion-specific inhibitor as an antimalarial in a combination based therapy, in addition to being a useful tool for studying the biology of the invading parasite.