Biochemical Screening of Five Protein Kinases from Plasmodium falciparum against 14,000 Cell-Active Compounds

Abstract

In 2010 the identities of thousands of anti-Plasmodium compounds were released publicly to facilitate malaria drug development. Understanding these compounds’ mechanisms of action—i.e., the specific molecular targets by which they kill the parasite—would further facilitate the drug development process. Given that kinases are promising anti-malaria targets, we screened ~14,000 cell-active compounds for activity against five different protein kinases. Collections of cell-active compounds from GlaxoSmithKline (the ~13,000-compound Tres Cantos Antimalarial Set, or TCAMS), St. Jude Children’s Research Hospital (260 compounds), and the Medicines for Malaria Venture (the 400-compound Malaria Box) were screened in biochemical assays of Plasmodium falciparum calcium-dependent protein kinases 1 and 4 (CDPK1 and CDPK4), mitogen-associated protein kinase 2 (MAPK2/MAP2), protein kinase 6 (PK6), and protein kinase 7 (PK7). Novel potent inhibitors (IC50 < 1 μM) were discovered for three of the kinases: CDPK1, CDPK4, and PK6. The PK6 inhibitors are the most potent yet discovered for this enzyme and deserve further scrutiny. Additionally, kinome-wide competition assays revealed a compound that inhibits CDPK4 with few effects on ~150 human kinases, and several related compounds that inhibit CDPK1 and CDPK4 yet have limited cytotoxicity to human (HepG2) cells. Our data suggest that inhibiting multiple Plasmodium kinase targets without harming human cells is challenging but feasible.

PubChem BioAssay: 2017 update

“…Nature Cell Biology led this effort by recommending RNAi data deposition to public repository, which recently also started to call small molecule data sharing. Other open access journals, such as PLoS One, joined the force lately for recommending data sharing via public repository and brought in the deposition of several small molecule data sets in PubChem (16,17). Assay data contributed by these sources are linked to the respective publications indexed in PubMed (16–36), allowing PubChem users to access the articles for additional information, and vice versa, PubMed users also gain access to the research data in the BioAssay archive supporting machine readable format.…”

“…Other open access journals, such as PLoS One, joined the force lately for recommending data sharing via public repository and brought in the deposition of several small molecule data sets in PubChem (16,17). Assay data contributed by these sources are linked to the respective publications indexed in PubMed (16–36), allowing PubChem users to access the articles for additional information, and vice versa, PubMed users also gain access to the research data in the BioAssay archive supporting machine readable format. All BioAssay depositors and the associated information, such as affiliations, summary of data submissions may be viewed at the PubChem Data Source page at: https://pubchem.ncbi.nlm.nih.gov/sources/, whereas data sources are grouped by geographic location and various other categories.…”

Evaluation of the anti-malarial activity and cytotoxicity of 2,4-diamino-pyrimidine-based kinase inhibitors

“…A number of studies aimed at improving our understanding of the approximately 65 Pf specific kinases have been reported, many of which share considerable homology with human kinases [10,16,19]. This has led to a kinase screening campaign [20] and SAR studies on specific protein kinases, including PfCDPK1 [21,22], PfPK5 [23] and PfPK7 [24]. Nevertheless, it is not yet established which parasite kinase rep-resents the most valid target [10], or whether polypharmacology approaches could represent a useful approach, as found for cancer [25].…”

“…In 2010, GlaxoSmithKline reported the results of screening of almost 2 million compounds to identify anti-malarial hits. Approximately 13,500 compounds with activity at P. falciparum (Pf) 3D7, multidrug resistant Dd2 Pf strain and for cytotoxicity in the HepG2 cell line were released in the public domain [26].In2016, these hits were re-assessed at five Pf kinases (PfCDPK1, PfCDPK4, PfPK6, PfPK7 and PfMAPK2) and led to the identification of twelve series with potential for optimization [20].…”

In silico Screening and Evaluation of Plasmodium falciparum Protein Kinase 5 (PK5) Inhibitors

“…[4][5][6][7] The P. falciparum genome encodes for 86 protein kinases,m any of which are thought to be essential based on genetic [8][9][10] and chemical inhibition studies. [11,12] Thus, the Plasmodium kinome remains ar ich yet largely untapped area for novel drugt arget development. [12][13][14] In contrast to human kinases,t he biological functions of many Plasmodium kinases are unresolved due to the lack of molecular and chemicalt ools to probe mechanisms.…”