Researchers create compound that combats drug-resistant malaria parasites, spares human cells

Teasing apart subtle differences between a protein-shredding structure found in malaria parasites and in human cells enabled researchers to design a compound targeting the parasite without harming human tissue.

Matthew Bogyo and his colleagues found a way to design a compound that can kill malarial microorganisms without harming human cells.
Steve Fisch

Stanford University School of Medicine investigators have designed a compound that kills the parasitic microorganisms responsible for malaria but avoids harming human cells.

The compound exploits tiny structural differences between the parasitic and human versions of an intercellular protein-recycling machine called the proteasome.

Malaria, one of the world’s most devastating infectious diseases, exacts a yearly toll of more than 400,000 deaths, mostly of children younger than 5. Mortality rates are dropping because of large-scale global intervention efforts, but malaria’s prevalence remains stubbornly high, with hundreds of millions of people newly infected each year in sub-Saharan Africa and Southeast Asia. 

Some 2.3 billion people — one-third of the Earth’s people — are at risk for infection with the parasite.

Bloods cells pillaged

Malaria is caused by protozoans of the genus Plasmodium. Five different species of Plasmodium are known to cause malaria in humans, with most deaths caused by one species, P. falciparum. Transmitted by mosquitos, the microbes invade the body, first holing up in the liver and then penetrating and replicating in red blood cells, which they ultimately destroy as they break out in search of new red blood cells to pillage.

“This penetration/replication/breakout cycle is rapid — every 48 hours — providing the opportunity for large numbers of mutations that can produce drug resistance,” said Matthew Bogyo, PhD, professor of pathology. Consequently, several generations of antimalarial drugs have long since been rendered useless, he said.

Resistance to current front-line antimalarial drugs, known as artemisinins, is spreading and has been observed in a half-dozen Southeast Asian countries. But in a study to be published Feb. 11 in Nature, Bogyo and his colleagues showed, using laboratory-adapted clinical samples from Southeast Asia, that the new compound can effectively kill artemisinin-resistant malaria parasites and that low doses of the drug can further sensitize them to killing by artemisinin.

Bogyo shares senior authorship of the study with Paula da Fonseca, PhD, of the MRC Laboratory of Molecular Biology in Cambridge, UK. The lead author is Stanford graduate student Hao Li.

Protein chewers

Proteins, which perform the vast majority of the work done inside a cell, are assembled from building blocks called amino acids, which are linked together in a linear sequence like beads in a necklace. 

The proteasome, a barrel-shaped cluster of proteins, chews up other proteins by breaking those amino-acid links. Proteasomes abound in all human cells and in all protozoans. They are crucial to the elimination of faulty proteins and to cell replication. So blocking their function wreaks havoc within a cell. 

But compounds previously found to block proteasome activity in P. falciparum have tended to inhibit the human version of the proteasome, too, resulting in toxicity that would be unacceptable in a malaria drug. 

In the new study, the Stanford team produced highly purified preparations of both human and P. falciparum proteasomes and then “fed” those two preparations a set of protein fragments collectively containing a vast variety of amino-acid linkages “in order to see which amino-acid linkages these proteasomes like to chew up,” Bogyo said.

Clogging up the works

The team identified 117 amino-acid linkages that are readily chewed up by P. falciparum proteasomes but not so well by human proteasomes, and 153 where the reverse is the case. They used this information to design tiny protein snippets that failed to interact with human proteasomes but that, instead of getting chopped up by P. falciparum proteasomes, would gum up parts of them responsible for cleaving certain amino-acid links.

“They just stick and don’t get released,” Bogyo said. The clogged catalytic sites are now unable to break apart the linkages they were designated to cleave.

Next, the UK group investigated the basis for this selectivity by using a high-resolution version of electron microscopy to map the detailed structure of the parasite and human proteasomes. This allowed Bogyo’s team to optimize the protein snippets they were using as parasite-selective proteasome inhibitors. The three-amino-acid snippet they ultimately focused on, called WLL, was able to gum up two different catalytic regions in P. falciparum proteasomes without any effect on those of cultured human cells. There was a 600-fold difference in WLL’s potency at killing the parasitic cells over the human cells.

Reducing parasites in mice

In experiments with mice with a murine version of malaria-inducing Plasmodium, the researchers saw a nearly complete reduction of parasites with both single and multiple doses of WLL. Still other tests, performed on artemisinin-resistant parasites infecting human red blood cells in laboratory cultures, suggested that the WLL compound was equally effective at killing artemisinin-resistant parasites and artemisinin-sensitive parasites. 

Bogyo pointed out that the artemisinin family of drugs work by modifying proteins in the parasite. Resistance occurs when the parasites’ proteasomes are able to recycle those modified proteins. But this means that artemisinin-treated parasites are particularly sensitive to disruption of normal protein function.

“The compounds we’ve derived can kill artemisinin-resistant parasites because those parasites have an increased need for highly efficient proteasomes,” he said. “So, combining the proteasome inhibitor with artemisinin should make it possible to block the onset of resistance. That will, in turn, allow the continued use of that front-line malaria treatment, which has been so effective up until now.”

Clinical trials of compounds derived from this research remain several years away, Bogyo cautioned.

Other Stanford co-authors are postdoctoral scholars Wouter van der Linden, PhD, Euna Yoo, PhD, and Ian Foe, PhD. 

Researchers from the University of California–San Francisco and the University of Melbourne in Australia contributed to the study.

The study was funded by the National Institutes of Health (grants R01AI078947 and R01EB005011); the Medical Research Council in the UK; Singapore’s Agency of Science, Technology and Research; and the Netherlands Organization for Scientific Research.

Stanford’s departments of Pathology and of Chemical and Systems Biology also supported the work.

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