Evolution of malaria protein family offers new drug targets

Researchers from the Francis Crick Institute and the Gulbenkian Institute for Molecular Medicine (GIMM) have shown that the evolution of a family of exported proteins in the malaria-causing parasite Plasmodium falciparum enabled it to infect humans.

Targeting these proteins may hold promise for identifying new drugs that are less susceptible to resistance.

Malaria infects over 200 million and kills over 500,000 people every year. It is caused by Plasmodium parasites infecting red blood cells and being transmitted from host to host by mosquitos. There are available treatments, but drug resistance is an ongoing problem.

In research published today in Nature Microbiology, a team of malaria researchers at the Crick, now based at GIMM, investigated the deadliest Plasmodium species, P. falciparum, which causes over 95% of malaria deaths.

Parasitic tools to target human cells

During a malaria infection, the P. falciparum parasite injects 10% of its proteins into host red blood cells, remodelling these cells so they stick to the blood vessels and to each other, eventually causing blood clots.

These exported proteins include a family called FIKK kinases, which modify host molecules or other exported parasite proteins to activate or inactivate them.

The team looked at over two thousand P. falciparum samples from people infected with malaria, finding that out of 21 FIKK kinases, 18 were protected against harmful mutations, suggesting they are necessary for the parasite to infect humans and likely helped it evolve.

The researchers then expressed the FIKK kinases in bacteria to see what each one does. This experiment showed that the FIKK kinases all had different protein targets in the cell.

To their surprise, the scientists demonstrated that one FIKK kinase specifically targets an amino acid called tyrosine, which hasn't been shown before in parasites. They believe this kinase evolved to interact with specific host cell signalling pathways that use tyrosine.

Using a combination of computational and laboratory tools, including the protein structure prediction software AlphaFold 2, the scientists revealed that the specificity of FIKK kinases for different protein targets is linked to small changes in a flexible 'loop region'.

Even though these small changes allow different kinases to recognise different proteins, the team identified some recurring structures in the loop regions, which make FIKK kinases different from human kinases and offer a potential way to target them.

Blocking all FIKK kinases

In search of a way to disrupt the FIKK kinases, the team screened a library of molecules known to block human kinases, in collaboration with GlaxoSmithKline. They identified three promising molecules and then found that two blocked most FIKK kinases in a test tube.

As blocking all FIKK kinases at once could be a promising treatment strategy to ease malaria symptoms, the next steps will be drug development to modify these compounds so they can be used in people.

Moritz Treeck, head of the Cell Biology of Host-Pathogen Interaction Laboratory, formerly at the Crick and now at the Gulbenkian Institute for Molecular Medicine, said: "About 1 million years ago, Plasmodium crossed from birds into great apes. With this cross, the FIKK kinase family expanded to enable infection of our closest relatives. A relatively short time ago, Plasmodium falciparum crossed from great apes to humans, and we've shown that the kinases needed for survival in great apes are still required for survival in humans. This suggests that targeting shared properties of FIKK kinases could stop P. falciparum from remodelling the host cell."

Hugo Belda, former postdoctoral research assistant at the Crick, now postdoctoral researcher at GIMM and co-first author with David Bradley, said: "This project has been very collaborative across multiple institutions and disciplines, resulting in a holistic investigation into P. falciparum evolution. Current drugs mostly target single proteins, which makes the emergence of drug resistance more likely. Developing compounds which target several proteins at once, like those blocking all FIKK kinases, may be one way to tackle this problem."

The majority of the research took place at the Crick, with some experiments taking place at GIMM. The researchers worked with the Crick's Protein-Protein Interaction Laboratory led by Louise Walport, as well as the Structural Biology, Chemical Biology, Flow Cytometry and Proteomics teams, Crick-GSK LinkLabs and Christian Landry's team at Université Laval in Canada.