Sea Squirt Microbiome Yields Compound Effective against Deadly Strain of Fungal Pathogen
By combing the ocean for new antimicrobials, scientists at the University of Wisconsin-Madison have discovered an antifungal compound that efficiently targets potentially deadly, multidrug-resistant strains of the fungal pathogen Candida auris, without toxic side effects in mice.
The new molecule was discovered in the microbiome of a sea squirt from the Florida Keys, as part of the team’s effort to identify novel antimicrobials from understudied ecosystems. Scientists named the antifungal turbinmicin, after the sea squirt Ecteinascidia turbinate, from which it was isolated. Discovery of turbinmicin is the most tangible output to date, of the group’s five-year, $30 million NIH grant, to identify useful new antimicrobial drugs from bacteria living in overlooked environments.
“Bacteria in particular are rich sources of molecules,” said Tim Bugni, PhD, a professor in the UW-Madison School of Pharmacy who led the turbinmicin project. “But a lot of the terrestrial ecosystems have been pretty heavily mined for drug discovery. There’s immense bacterial diversity in the marine environment and it’s barely been investigated at all.”
Bugni and colleagues describe their discovery of turbinmicin, and the results of in vivo tests in mice, in a paper in Science, which is titled, “A marine microbiome antifungal targets urgent-threat drug-resistant fungi.”
Infectious fungal diseases are among the deadliest threats to global human health, the authors wrote, and nearly 2 million people die globally, every year, from fungal infections. Multidrug-resistance Candida auris, for example, has become a major global threat. “Most recently, the pandrug-resistant “killer fungus,” C. auris, has emerged and is spreading in health care facilities worldwide, prompting an urgent threat alert from the Centers for Disease Control and Prevention (CDC).”
Today, there are only three classes of antifungal drugs that are available for clinical use, and disease-causing fungi continue to evolve resistance to those drugs that are available to fight them. As a result, more people are dying from previously treatable diseases, such as candidiasis or aspergillosis, which are caused by common fungi that sometimes turn virulent. Developing new antifungal agents has proven challenging, and the majority of existing antimicrobials were isolated from soil-dwelling bacteria, so as scientists have continued probing these bacteria for new drugs, they often turned up the same molecules over and over again. “The development of new antifungals has been hampered, in part, by the evolutionary history fungi and animals share, limiting treatment options to drugs because of limited efficacy and/or toxic side effects,” the team noted.
For the newly reported studies, Bugni partnered with UW School of Medicine and Public Health infectious disease professor David Andes, PhD, UW-Madison bacteriology professor Cameron Currie, PhD, and their colleagues, to search neglected ecosystems. Specifically, they undertook genomic, metabolomic and antimicrobial screening of bacteria isolated from a variety of marine animals in the search for new antimicrobial compound from this understudied ecosystem.
To identify turbinmicin, the research team began by collecting ocean-dwelling invertebrates from the Florida Keys between 2012 and 2016. From these animals, they identified and grew nearly 1,500 strains of actinobacteria, the same group of bacteria that has produced many clinical antibiotics. Using their screening method, they prioritized 174 strains to test against drug-resistant Candida, an increasingly prominent disease-causing fungus. “To identify antifungal candidates, we implemented a discovery platform that leverages
liquid chromatography–mass spectrometry (LC-MS)–based metabolomics, genomics, and antimicrobial activity screening of metabolomics arrays from bacterial isolates from the microbiome of marine animals,” the researchers wrote. Bugni further noted, “Candida auris in particular is pretty nasty.” Nearly half of patients with systemic Candida infection die. “The Candida auris strain we targeted in this paper is resistant to all three classes” of existing antifungals.”
Turbinmicin stood out for its effectiveness. “One hit from a Micromonospora sp. was prioritized on the basis of potency, MS, and nuclear magnetic resonance,” the team commented. “This led to the discovery of the antifungal agent that we named turbinmicin.” The researchers tested purified turbinmicin against a slate of 39 fungi isolated from patients. These strains represented diverse species and, collectively demonstrated all of the known resistance mechanisms that fungi have evolved to existing drugs. In lab experiments, turbinmicin halted or killed nearly all of the fungal strains at low concentrations, indicating a potent effect. Similar experiments in mice infected with drug-resistant strains of Candida auris and with a particularly difficult-to-treat strain of the filamentous fungal pathogen, Aspergillus fumigatus, also demonstrated turbinmicin’s ability to attack resistant fungi.
Because fungi and animals are closely related, and thus share similar cellular machinery, antifungals can prove toxic to animals as well as to their target fungi. “A major developmental challenge for antifungal agents is the establishment of their safety in humans and ability to evade or forestall resistance mechanisms,” the investigators stated. But encouragingly, turbinmicin did not show toxic side effects in mice, even at concentrations 1000 times higher than the minimum dose. The effective dose would work out to tens of milligrams for an average-weight adult, less than the concentration of many other antibiotics. “Studies to map turbinmicin’s potential for toxicity are warranted, but the results of mousemodels are thus far promising,” the team said.
Experiments in yeast led by UW-Madison genetics professor Anjon Audhya, PhD, indicated that turbinmicin targets the cellular packaging and organizational system of fungi. The compound appears to block the action of a protein, Sec14p, that is involved in the vesicular trafficking pathway, with the end result that yeast like Candida cannot bud to reproduce. “Our data implicate Sec14p as the primary antifungal target of turbinmicin: potential off-target effects appear to be limited and devoid of downstream toxicities,” the scientists stated. Other kinds of fungi, when exposed to turbinmicin, may have a difficult time shuttling cellular contents around to grow.
The researchers have submitted a patent for turbinmicin and are now looking to improve the molecule by making small alterations to its structure that could increase its effectiveness as a drug. However, while turbinmicin is a promising drug candidate, additional study of the molecule and extensive preclinical research must be performed before a new drug can become available. “Careful attention to monitoring for adverse effects with more prolonged treatments similar to those required for management of fungal disease in patients (typically 2 to 6 weeks), as well as studies in additional animal species, will be needed before further development toward human administration,” the investigators stated.
Nevertheless, as the team concluded, “The promising in vitro and in vivo activity against urgent fungal pathogens, mammalian safety, and exploitation of Sec14p as a target argue for further preclinical development of turbinmicin as an antifungal lead.”
The discovery of turbinmicin also serves as a proof-of-concept for the collaboration’s efforts to explore new ecosystems and screen thousands of candidates to identify new, effective antimicrobial candidates. “Now we have the tools to sort through candidates, find promising strains and produce molecules to do animal studies,” said Bugni. “That’s the key for targeting multi-drug resistance: you need unique molecules.”