Researchers find a potential treatment for mitochondrial damage that causes disease

Not just a power plant 

Although mitochondria are best known for producing energy, that’s not their only role. “They’re so busy! This organelle is so critical,” Mochly-Rosen said. For instance, they’re responsible for constructing some of the cell’s molecular building blocks and for deliberately killing cells whose DNA is damaged. 

For a long time, scientists assumed that mitochondria were confined to their host cells, but they recently discovered this isn’t true. “Now we know they can exit one cell and enter another one,” Mochly-Rosen said. “When bad mitochondria do this to a healthy cell, they can kill it. When healthy mitochondria do it to a sick cell, they can help it heal.”

Seventeen years ago, Mochly-Rosen and her colleagues trained a microscope on cells from a rat with high blood pressure and discovered that the mitochondria were fragmented into small pieces. This set off a quest to find out what was happening and how to prevent or fix it.

Hijacking fission

Mitochondria are often depicted as little jellybeans whose shape never changes, said Suman Pokhrel, who was a PhD student at SLAC and Stanford at the time he led the study. But in real life they form an ever-changing, fibril-like network. Thousands of them surround the nucleus of each cell, and they’re constantly dividing and fusing with each other. Mitochondria need to maintain a balance between division and fusion to stay healthy, increase their numbers and make enough energy.

In healthy mitochondria, a protein called Drp1 attaches to the mitochondrial membrane and initiates division via a go-between protein called Mff. But when mitochondria send out distress signals – for instance, if they’ve been attacked by a reactive oxygen molecule like hydrogen peroxide and can’t repair the damage fast enough – Drp1 attaches to a protein called Fis1 and uses it as a go-between instead. 

Fis1 directs mitochondrial fission in yeast, but in humans it only brings grief. It hijacks the normal process mitochondria use to divide neatly in half and instead squeezes them into uneven pieces that fragment into even smaller ones that don’t produce enough energy. 

One obvious solution would be to block Drp1 from coupling with Fis1, Pokhrel said. But incapacitating Drp1 was out of the question because cells need it for other things, including normal cell division. And the surface of the Fis1 molecule doesn’t have any obvious pocket where a drug could dock. As Pokhrel puts it, “Both are essentially undruggable.”

But maybe, he thought, Fis1 molecules that have been activated into their mitochondria-chopping state would have a place where a drug molecule could plug in to prevent or reverse the damage. 

A well-hidden Achilles heel 

Finding this weak spot and a potential drug to target it required more than three years of work that Pokhrel performed with Mochly-Rosen and SLAC/Stanford Professor Soichi Wakatsuki as his PhD advisers, along with colleagues Gwangbeom Heo from Stanford, Irimpan Mathews and Tsutomu Matsui from SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL) and Shun Yokoi and Ayori Mitsutake from Meiji University in Japan. 

Through repeated rounds of computer simulations, biochemical experiments, X-ray crystallography and scattering at SSRL, and other techniques, the team learned how Fis1 changes shape in response to oxidative stress.

“The stress response process of Fis1 has turned out be pretty complex,” Wakatsuki said, “and untangling it required tour-de-force multidisciplinary efforts.”

First, one of Fis1’s six squiggly components, or helices, unwinds and moves away a bit. When that happens, a single site in Fis1 called Cys41 is exposed. It’s a type of amino acid, cysteine, that can sense oxidative cell damage, and thus a potential target for drugs. 

These exposed Cys41 sites then link pairs of Fis1 molecules together, and this paired configuration allows them to grab Drp1 and begin the abnormal fission process that leaves mitochondria in fragments.

If a drug could be found that attaches to Cys41 and keeps the Fis1 molecules from forming pairs, it could prevent stress-induced mitochondrial fragmentation, Wakatsuki said. 

The team screened 6,000 molecules to find one that would fit the Cys41 site and found a match: SP11. When they added SP11 to cultured human kidney cells whose mitochondria had been fragmented by exposure to hydrogen peroxide, the mitochondria returned to normal.

In their report, the research team noted that SP11 includes a compound called phenothiazine that’s connected to a chemical “warhead” – a bit that can fit into a molecular pocket and engage with Cys41. Several phenothiazine-based drugs are approved by the Food and Drug Administration as treatments for nausea, vomiting, allergies and neurological conditions, they added, so it’s likely that SP11 also has good drug-like properties. As with all medications, it would take much more research and development to tailor SP11 for safely treating specific health conditions. 

This work was supported in part by the Assistant Secretary of Defense for Health Affairs endorsed by the Department of Defense (W81XWH-22-1-0203). Opinions, interpretations, conclusions and recommendations are not necessarily endorsed by the Assistant Secretary of Defense for Health Affairs or the Department of Defense. SSRL is a DOE Office of Science user facility, and the SSRL Structural Molecular Biology Program is supported by the DOE Office of Science, and by the National Institutes of Health, National Institute of General Medical Sciences. 

Citation: Suman Pokhrel et al., Nature Communications, 6 May 2025 (10.1038/s41467-025-59434-6)

For questions or comments, contact SLAC Strategic Communications & External Affairs at communications@slac.stanford.edu.