"Hidden Antibiotics": A New Class of Antifungal Substances Found in a Common Fungus

Scientists have shown that if you do not test "raw" extracts of microorganisms as a whole, but first separate them into fractions and quickly filter out known molecules using mass spectra, then hidden active substances begin to emerge in the same samples. This is how they came across coniotins - rare linear lipopeptibiotics from the fungus Coniochaeta hoffmannii. Coniotin A turned out to be active against the "problem four" from the WHO list: Candida auris, Candida albicans, Cryptococcus neoformans and Aspergillus fumigatus; moreover, it hits the β-glucan of the cell wall, which causes the cell to "rebuild" the wall and become more vulnerable to caspofungin. The work was published in Nature Communications.

Background

• Why does everyone need new antifungals so much? In the clinic, there are actually several main classes of systemic agents (azoles, polyenes, echinocandins; recently added ibrexafungerp, rezafungin, etc.), and resistance is growing faster than "chemistry" with new targets appears. Reviews of the pipeline emphasize: there is progress, but the window of opportunity is still narrow.
• Why Candida auris? It is a nosocomial yeast with frequent multidrug resistance, hospital outbreaks, and severe outcomes; WHO has classified it as a critical priority along with C. albicans, A. fumigatus, and C. neoformans. CDC guidelines specifically emphasize susceptibility testing and resistance monitoring.
• The problem of echinocandins (caspofungin, etc.). They are the "mainstay" of invasive candidiasis therapy: they block the synthesis of β-1,3-D-glucan in the cell wall. But FKS1 mutations that reduce sensitivity to echinocandins are increasingly found in C. auris - hence the interest in molecules that "hook" the action of caspofungin or bypass its weak points.
• Where new molecular skeletons might come from. Historically, natural products of fungi and bacteria are the main source of anti-infective chemotypes. But “crude” extracts are often cluttered with dominant known compounds. Therefore, modern screens rely on preliminary fractionation and dereplication according to LC-MS/MS and molecular networks (GNPS, SNAP-MS) to quickly filter out the “very familiar” and catch rare metabolites.
• Who are peptaibiotics? These are linear nonribosomal peptides rich in the unusual amino acid Aib, most often in fungi of the genus Trichoderma; the class is known for its membrane activity and resistance to proteolysis. Lipopeptaibiotics are their "fat-tailed" variety. Against this background, the discovery of coniotins in Coniochaeta expands the geography of the class and provides a new chemical "skeleton".
• What the current paper adds. The authors showed that a library of prefractionated microbial extracts + rapid MS dereplication dramatically increased the yield of “really new” candidates, and on this platform they isolated coniotins A–D — lipopeptaibiotics active against C. auris and other clinically important fungi. The target is cell wall β-glucan; the effect leads to synergy with caspofungin. This is both a new mechanism (membrane activity was more often described for peptaibiotics) and a practical idea for combinations where echinocandins “sag”.
• Why all this in practice. C. auris with FKS mutations and biofilms already limits the choice of therapy; new molecules that interfere with the wall architecture and enhance echinocandins are a promising way to reduce the risk of treatment failure and bypass resistance.

How the "newbie" was found

The researchers assembled a library of prefractionated extracts from bacteria and fungi and ran them against two Candida species, C. auris and C. albicans. This approach dramatically increased the number of hits compared to crude extracts and allowed for rapid dereplication of known classes (enniatins, surfactins, tunicamycins) from MS/MS fingerprints, focusing on the unknown activity peak from Coniochaeta. Guided by the activity of the fractions, the team isolated four related molecules, coniotins A–D. Their ancestry was confirmed by a hybrid PKS–NRPS cluster (~182 kb; 21 NRPS modules — exactly 21 amino acid residues of the peptide). The cluster contains many unusual amino acids (e.g., α-aminobutyric acid, Aib), which is typical for peptibiotics and is associated with their resistance to proteolysis.

How much does it "take" the fungus (MIC from the table)

In sensitivity tests (microbroth dilution), coniotin A showed:

• C. auris (resistant clinical isolates): MIC 8 μg/mL in three strains; 4 μg/mL in one. For comparison, caspofungin in these strains: MIC 64 μg/mL, and fluconazole - >64 μg/mL.
• A. fumigatus (including FluR): MIC 4 μg/mL; fluconazole is ineffective (>64 μg/mL) and caspofungin is weak (64 μg/mL).
• C. neoformans H99: MIC 4 μg/ml.

A separate advantage is selectivity: on human erythrocytes, hemolysis began only at >256 μg/ml, which is significantly “further” than therapeutic levels for amphotericin B (8 μg/ml in the same test).

How it works

Coniotin A does not accumulate inside the cell and hits the surface:

• Binds to cell wall β-glucan (pull-down mass spectrometry),
• Prevents β-1,3-glucanase from breaking down laminarin and inhibits the activation of factor G (Glucatell® reagent),
• It induces a wall remodeling response (chitin growth, thickened septa) and morphological disruptions that are visible in confocal and TEM images.
  As a result, C. auris becomes more sensitive to caspofungin: in a checkerboard, the combination dramatically lowers the caspofungin MIC down to the CLSI clinical threshold of 2 μg/mL for “severe” isolates.

Are there any live models?

Yes, but not in mammals yet: in a C. elegans model, coniotin A (8 μg/ml) reduced colonization by C. albicans and extended the lifespan of worms infected with multidrug-resistant C. auris when compared to amphotericin B and control. This is a quick “tech demo” of potential; mammals are the next step.

Why is this important?

• New classes are urgently needed. The clinic has only three main groups of systemic antifungals in its arsenal; resistance is growing, and Candida auris is a critical priority in the WHO list. Therefore, any “new skeleton” of a molecule with a different mechanism is worth its weight in gold.
• The platform is also a godsend. The approach itself — cheap fractionation + fast MS screening and dereplication — helps to catch rare, “muffled” metabolites that are lost against the background of dominant compounds in the crude extract. This is scalable for academic labs, not just for large pharma screens.
• Combinations with echinocandins: A precise hit to the surface β-glucan anchors caspofungin to its target—a logical strategy for overcoming C. auris resistance.

A fly in the ointment and plans

There is no data in mammals yet: we need to check the pharmacokinetics, toxicology, therapeutic window and choose a form (most likely parenteral or topical, given the physical chemistry of the molecule). The structure and contact with β-glucan need to be clarified at the NMR/crystallography level, and the “risk of resistance” under prolonged pressure needs to be checked. But already now coniotins look like real candidates for preclinical use, and the platform itself is a route to other “hidden” natural antifungals.

Source: Chen X. et al. Coniontins, lipopetaibiotics active against Candida auris identified from a microbial natural product fractionation library. Nature Communications 16, 7337 (2025), published 8 August 2025. MIC table and key mechanism experiments in the main article.