The fight against fungi

Damian Krysan had already fielded three phone calls about fungal infections when C&EN caught up with him on a Friday afternoon in early January. Krysan, an organic chemist turned pediatrician who studies pathogenic fungi at the University of Iowa, says the calls weren’t about the kinds of infections people think of when they hear “fungus”—a gnarly toenail growth or a childhood case of thrush. They were about rare, potentially life-threatening systemic fungal infections, which can attack internal organs, including the brain, heart, and lungs.

Krysan recalled one young patient he’d seen months before with a mold growth that was eating away at her jaw. Krysan had to explain to her family that there were no medicines that could treat the infection. Surgery was their only option. “You basically try to cut out as much as you can,” Krysan says. “And then hope.” The girl died.

It’s just one tragic example of a growing problem: systemic fungal infections are becoming more common, and doctors’ meager medical options for treating them are increasingly ineffective. “Our society has a lot of trust in our ability to do pretty amazing things with technology, but we have real holes,” Krysan says. “I would argue that there’s no part of medicine that has made as little progress in the last 35 to 40 years than the treatment of fungal infections.”

But there is some good news. A handful of scientists in academia and at small companies are working to increase the power of the antifungal stockpile. They’re designing drugs to go after new antifungal targets, creating new classes of drugs to attack existing targets, and modifying antifungal drugs to make them more selective or easier to take. The success or failure of these compounds, both as viable fungal fighters and as pharmaceutical investments, will become apparent in the next couple of years as they face approval from regulators and a tough marketplace for anti-infectives.

The trouble with fungi

Fungi are all around us. Whether they’re yeast, mold, or mushrooms, millions of fungal species live in our soil, grow on our bodies, and generate spores that we inhale and exhale with every breath. Of those millions of fungi, only a few hundred can infect people. And people with healthy immune systems usually fight those infections handily, which makes systemic fungal infections rare.

However, when they do strike, systemic fungal infections are exceptionally dangerous. They have extraordinarily high mortality rates—about 15 to 50%, according to the Global Action Fund for Fungal Infections (GAFFI)—and kill more than 1 million people each year.

Among hospital-acquired infections, systemic fungal infections are the deadliest, according to David Andes, an infectious disease specialist at the University of Wisconsin–Madison who studies antifungal drugs and drug resistance. “It’s not even close,” he says. About 5% of hospitalized patients in the US who get bacterial infections die from them, according to the Centers for Disease Control and Prevention. About 50% of hospitalized people who get fungal infections don’t survive, even with treatment, Andes says.

Most of those people were already very sick. Fungal infections tend to strike people with compromised immune systems, a group that has expanded in the past few decades, thanks to medicines that keep people alive but at the cost of weakening their immune response. Such medicines include some cancer chemotherapies and drugs that prevent the body from rejecting organ transplants.

“To put it really bluntly, there are many patients we see now who never would have lived long enough to get a fungal infection,” the University of Iowa’s Krysan says. “We keep expanding the pool of patients who are at risk for these. But we have done zero to improve our ability to actually treat them once they occur.”

A dearth of drugs

Krysan and other scientists who work on drugs for pathogenic fungi point out that it’s been 20 years since a drug in a new class of antifungals, the echinocandins, was approved by the US Food and Drug Administration. That 2001 approval brought the grand total of FDA-approved antifungal drug classes to four—all of which have downsides.

The echinocandins inhibit the enzyme that makes β-glucan, an essential component of the fungal cell wall. Human cells don’t have cell walls, so the enzyme is an attractive target for drugmakers. But certain fungi, including Cryptococcus, have shown resistance to the echinocandins. Cryptococcus is a fungal pathogen that often infects people with untreated HIV and kills around 125,000 people each year, according to GAFFI. The echinocandins also have to be given via intravenous infusion, which means they have to be administered in a doctor’s office or hospital. So they aren’t typically used to prevent fungal infections in vulnerable people who aren’t already in the hospital.

Polyenes, the oldest class of antifungal drugs, also have to be given intravenously. These drugs—the best known of which is amphotericin B—have been around since the 1950s. They kill fungi by binding to ergosterol, a sterol in the fungal cell membrane. This strips the ergosterol away and punches holes in the membrane so that it becomes leaky enough to fail. But the polyenes also interact with cholesterol in human cell membranes, which can have lethal side effects. Amphotericin B’s kidney toxicity is so notorious that doctors often refer to the drug as “ampho-terrible B.”

The third major class of antifungals are the azoles—the only antifungal on the market that can be taken as pills. The compounds also disrupt ergosterol, but instead of interacting directly with the sterol, they block the fungal cytochrome P450–dependent enzymes involved in making ergosterol, ultimately compromising the fungal cell membrane’s integrity. But humans also have myriad cytochrome P450–dependent enzymes, and the azoles’ tendency to inhibit those often leads to liver toxicity. The azoles also often interact with other drugs, including the immunosuppressant tacrolimus, which is used by people who are prone to fungal infections.

Flucytosine stands alone in the fourth class of antifungal agents. This compound mucks up both fungal DNA and RNA synthesis. But fungi develop resistance to it so quickly that it is almost never used on its own.

Drug resistance is a problem with all the antifungals, but it’s particularly problematic for the azoles. Many are static rather than cidal agents, which means they arrest fungal growth but don’t kill the fungus, explains Leah Cowen, who studies the biology and evolution of fungal pathogens at the University of Toronto. If a drug doesn’t kill the fungus, she says, “you’re really providing ample selection for that population to evolve resistance.” The situation is worsened by the agricultural use of azoles, in which they are commonly applied to plants like tulip bulbs.

With so few classes of drugs, doctors are concerned about the number of drug-resistant fungal infections—in healthy people as well as sick people.

“We’re seeing patients on a regular basis that we don’t have an effective therapy for,” the University of Wisconsin’s Andes says. For example, doctors have struggled to treat infections from Candida auris, a yeast that emerged about a decade ago and can’t be killed by any of the approved antifungal agents.

Making a good antifungal agent is tough because people and fungi are closely related, Cowen explains. Both are eukaryotes and share many of the same biological pathways. This similarity makes it challenging to find safe drugs.

“You can find antifungal molecules,” the University of Iowa’s Krysan says. “The problem is they are going to kill the patient before they kill the bug.”

Jose L. Lopez-Ribot, who studies fungal infections at the University of Texas at San Antonio, says that to create antifungal drugs, drugmakers exploited some differences between humans and fungi. Fungal cells have walls, whereas human cells do not, and fungal cell membranes contain ergosterol, whereas human cell membranes use cholesterol. But Lopez-Ribot says these differences are often subtle, and “there are not that many selective targets that you can exploit from the point of view of antifungal drug development. That’s the main reason for the very small arsenal of antifungal drugs that we currently have.”

If we want to improve antifungal resources and overcome drug resistance, doctors and scientists say, we need to look for new targets. “A couple more drugs with a couple of different mechanisms of action, used in both prophylaxis or in treatment, or in combination, may become very attractive to treat these fungal infections,” says John R. Perfect, a physician at Duke University who specializes in fungal infections, “because they’re not going to go away.”

Taking a new tack

Scientists have tried to tackle the enzyme Gwt1 as an antifungal target for decades. But it’s only in the past few years that a small molecule that inhibits this enzyme­—Amplyx Pharmaceuticals’ fosmanogepix—has made it into the clinic. Gwt1 is an enzyme in the endoplasmic reticulum that’s involved in anchoring mannoproteins to the cell wall. Mannoproteins act as armor for fungal cells, explains Ciara Kennedy, Amplyx’s president and CEO. Mannoproteins decorate the cell surface and are constantly shed and replaced. Without them, fungal cells can’t invade organs and become susceptible to the host’s immune system.

The enzyme has been challenging to crack because it has 13 helices, each of which crosses the endoplasmic reticulum’s membrane, making it tough to get a crystal structure. Medicinal chemists often rely on these structures to determine the best way to inhibit an enzyme. Around 20 years ago, the pharmaceutical company Eisai in Japan had a project to find molecules that could inhibit Gwt1. The company deployed an army of medicinal chemists and ultimately came up with fosmanogepix, Kennedy says. “Essentially it was brute-force chemistry to get the right structure.”

By inhibiting Gwt1, fosmanogepix causes mannoproteins to get stuck inside the endoplasmic reticulum, which stresses the cell, Kennedy says. “At the same time, the cell surface is being depleted of mannoproteins,” she says, which weakens the cell’s wall enough that the cell is no longer able to infect other cells or evade the host’s immune system. “So by addressing this one target, you get this sort of double whammy,” Kennedy says.

Fosmanogepix is a prodrug with an N-phosphonooxymethylene group that gets cleaved by phosphatase enzymes. It selectively inhibits Gwt1, and in experiments in cells and animals, it doesn’t show any activity against the mammalian version of the enzyme.

The compound, which Amplyx licensed from Eisai in 2015, can be dosed intravenously or orally, giving doctors options, Kennedy says. It has completed Phase 2 clinical trials for invasive Candida albicans infections and is in Phase 2 trials to treat other types of fungal infections, including those by Candida auris. Beyond the ongoing Phase 2 trials of fosmanogepix, Amplyx is exploring other antifungal therapies based on a similar mechanism of action.

Another antifungal target that has scientists excited is dihydroorotate dehydrogenase (DHODH), an enzyme that’s involved in the biosynthesis of pyrimidine, a key component in DNA and RNA. The first compound to address this target is F2G’s olorofim. Unlike broad-spectrum antifungals, olorofim kills only a few fungi, most notably Aspergillus, a common fungus that produces spores and is linked to roughly 200,000 infections annually. It has also been shown to kill the fungus that causes valley fever, a disease that can affect the brain and can sometimes be tough to treat.

Scientists at F2G screened more than 340,000 compounds to find molecules that could kill Aspergillus. Medicinal chemistry work from an initial hit in that screen led them to olorofim. At the time, F2G scientists didn’t know how the compound worked, but they later determined that it inhibits DHODH. Olorofim is 2,200 times as selective for the fungal enzyme as it is for human DHODH.

“Lots of things go wrong in the cell if we inhibit this enzyme,” says Jason Oliver, F2G’s head of biochemistry and molecular biology. Blocking fungal DHODH disrupts DNA and RNA synthesis, Oliver says. And when scientists look under a microscope at filamentous fungi, such as Aspergillus, that have been exposed to olorofim, they see the fungi stop growing, swell, and burst. Because olorofim can be taken orally, patients don’t have to be in the hospital to get the antifungal treatment, says Mike Birch, F2G’s chief operating officer. The compound could be given as a protective measure to people who may be susceptible to fungal infections—for example, people who are undergoing chemotherapy for certain cancers. F2G expects olorofim to begin Phase 3 trials, the final stretch before regulatory review, for invasive Aspergillus infections later this year, Birch says.

Fresh takes on old targets

Scientists are also looking at new ways to broach established targets. At Scynexis, scientists are exploring ibrexafungerp, a compound that blocks the same enzyme that the echinocandins do but has a completely different structure. Ibrexafungerp is a derivative of the natural product enfumafungin, a compound that has antifungal activity but is metabolized too quickly to be practical. In collaboration with Merck & Co., Scynexis researchers modified the enfumafungin structure to produce a molecule that is stabler and can be given both orally and intravenously.

“By having distinct structural features, we have qualities in terms of both efficacy and safety that are quite differentiated from standard of care that is being currently used,” says Rajeshwar Motheram, vice president of pharmaceutical development at Scynexis. The FDA is considering whether to approve ibrexafungerp for the treatment of vaginal yeast infections, and Phase 3 trials for the treatment of systemic fungal infections, including Candida auris, are ongoing.

Cidara Therapeutics is exploring echinocandin derivatives. The company’s clinical candidate rezafungin is a derivative of anidulafungin, a compound originally discovered at Eli Lilly and Company and currently marketed by Pfizer. Chemists placed a choline group at a critical point on the molecule, a feature that stabilizes the echinocandin ring and prevents metabolic breakdown of the molecule, explains Cidara’s president and CEO, Jeff Stein.

That stability also means the broad-spectrum antifungal drug candidate, currently in Phase 3 studies, has to be given only once a week—an improvement over the daily intravenous dosing of existing echinocandins, which must be administered in the hospital. If the drug is approved, patients could get the therapy on an outpatient basis by visiting their doctors for a weekly infusion.

Scientists are also working to improve azole-based compounds. For example, Mycovia Pharmaceuticals is developing compounds with more potency and fewer side effects than the azoles currently approved to treat fungal infections. While the azoles on the market have either imidazole or triazole groups, Mycovia’s drug candidates oteseconazole and VT-1598 are tetrazoles. They were designed to tightly bind to fungal cytochrome P450 but to not bind to the human cytochrome P450 enzymes, which account for the azole antifungals’ side effects, says Mycovia’s chief operating officer, Thorsten Degenhardt.

Oteseconazole recently completed Phase 3 trials for chronic vaginal yeast infections, and Mycovia plans to submit a new drug application for the compound with the FDA this year. VT-1598 is in Phase 1 trials for several types of invasive fungal infections.

The next hurdle

While doctors and scientists eagerly await the approval of more antifungals, drugmakers note that getting an antifungal through clinical trials is arduous and does not guarantee commercial success.

One of the main challenges with clinical trials of antifungals is that the people who get fungal infections are already very sick and usually in the hospital intensive care unit. So it can be hard to disentangle whether a patient dies because the medicine didn’t work or because the underlying disease was too advanced.

Setting up the trials is a complicated process, Amplyx’s Kennedy says. “You set up your clinical trial sites, and then unfortunately have to wait for a patient to get into trouble and need your help.” Even then, she says, there’s a leap of faith involved. “We’re asking patients and physicians to try a new-mechanism-of-action drug that may well save their life, but we don’t have all of the data yet to show that it’s going to work.”

Because patients are so sick, getting their consent to enroll them in a trial is often difficult, Cidara’s Stein says. And because delaying antifungal treatment makes it more likely that a patient will die from the infection, doctors often give an approved antifungal as soon as they suspect a fungal infection. But, Stein says, testing an experimental antifungal after giving an approved drug makes for murky results.

On top of that, Stein says, it takes about 72 h to culture fungus from blood. And you need the results of that culture to enroll someone in a clinical trial. The upshot is that you have to enroll a patient in the clinical trial on the same day that the blood culture is positive. This is logistically challenging but also means that the drug candidate is being tested late in the course of the infection.

A financial component also holds back antifungal drug development: many investors and companies don’t see it as profitable. A relatively small number of people need antifungal drugs, and they typically take the drugs for just a short period, which limits how much money a company can make.

Kennedy points out that several companies working on antibacterial drugs have done a lot of work to get their compound approved and have still failed “because those products are not being used in the hospital setting because pharmacists or physicians are worried about resistance” and use old, generic drugs first. “If you invest the hundreds of millions of dollars needed to get a drug approved, and then you’re showing sales revenues of $10 to $20 million a year—that’s not an equation that works for anybody, including savvy investors.”

Without those financial incentives, scientists worry that antifungal development isn’t the priority it should be. “For those of us who have been involved in the field of infectious diseases, very often you feel that we’re almost like an afterthought,” the University of Texas at San Antonio’s Lopez-Ribot says.

But he wonders if the COVID-19 pandemic might change how pharmaceutical companies, funding agencies, and the general public think about and invest in therapies for infectious disease, including fungal infections. “We have this false sense that we have conquered infectious disease with the antibiotic era,” he says. “This pandemic is reminding us that infectious disease is the type of thing that could really wipe us out.”