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Mapping the Targets of Antimalarial Compounds Through Chemical Profiling

Final Report Summary - MALARIA TARGETS ID (Mapping the Targets of Antimalarial Compounds Through Chemical Profiling.)

Malaria is a devastating parasitic infectious disease killing around half a million people every year and affecting close to 250 million worldwide. The recent emergence of drug resistance against the newest antimalarial therapies has made the identification of novel drug targets extremely urgent. In an effort to synergise basic research with antimalarials drug development the pharmaceutical industry identified thousands of new compounds with antimalarial activity. These hits represent a treasure-throve of chemical tools to study parasite biology and identify new targets. However, in order to harness the potential benefits of these compounds it is crucial to understand how these small molecules kill the malaria parasite.

Our group has been using chemical biology approaches to identify the targets of some of these bioactive compounds with the goal of validating new antimalarial targets. In particular, we use small molecule tools called activity-based probes (ABPs) that allow us to simultaneously monitor the activity of dozens of enzymes in the malaria parasites. We have used this method to determine whether any small molecule from a collection of 400 anti-parasitic compounds, known as the Malaria Box, was able to inhibit enzymes belonging to two families that are essential for parasite development, namely metabolic serine hydrolases and cysteine proteases. While none of the compounds was able to robustly inhibit any cysteine protease, three of them consistently targeted three unknown serine hydrolases. We then used a quantitative chemical proteomics approach to identify these potential targets by measuring whether increasing concentrations of compound decrease the level of ABP labelling of any serine hydrolase in the malaria proteome. Interestingly, two serine hydrolases (abH112 and abH114) are inhibited in a dose-dependent manner. We have generated conditional knockout lines for these two genes and are currently determining their biological functions and testing whether they are the targets responsible for the antimalarial activity of the selected compounds. Importantly, these two serine hydrolases have been annotated as essential genes based on a recent genetic screen, and might therefore be potential antimalarial targets.

We also applied a similar quantitative chemical proteomic method to identify all serine hydrolases in the malaria parasite and determine how their activity changes during the asexual replication cycle, which consists of red blood cell (RBC) invasion, parasite growth and replication within RBCs, and escape from the host cells for further RBC invasion. The exponential replication of parasites during this erythrocytic cycle is responsible for all the pathology associated with malaria. Our chemical proteomic approach has identified 29 different serine hydrolases that are active at different stages of parasite development. Interesting, we observed a substantial number of enzymes that seem to be specifically activated at the time of RBC invasion. We think these enzymes might be important for establishing an adequate metabolic niche within newly infected RBCs to allow initial parasite development. We have selected three of these parasite serine hydrolases and generated conditional knockout lines to determine whether they are essential for parasite development and to study their biological functions.

Interestingly, our chemical proteomics approach also identified 8 host serine hydrolases that are active in infected RBCs. More importantly, we have shown that selective inhibitors of two of these host enzymes have antimalarial activity, suggesting that the parasite co-opts the activity of human serine hydrolases to develop within infected RBCs. We are currently investigating whether these compounds do indeed prevent parasite development by targeting human enzymes. This result can have great implication in terms of drug development given that it would be much more difficult for the parasite to develop resistance to a drug that targets a human enzyme rather than a parasite one. Overall, we are currently performing follow-up work on two human and five parasite enzymes to determine whether they are essential for parasite development and potential drug targets.

For further information about this project contact Dr Edgar Deu at the Francis Crick Institute, London (edgar.deu@crick.ac.uk) or visit https://www.crick.ac.uk/research/labs/edgar-deu/areas-of-interest/chemical-biology.