Antifungal discovery

Elucidating the mechanisms of echinocandin B biosynthesis under fatty acid feeding in Aspergillus nidulans based on genome and transcriptome sequencing

Echinocandin B (ECB), a non-ribosomal lipopeptide synthesized by ascomycete fungi, serves as a first-line therapeutic agent for invasive fungal infections. While the biosynthetic gene clusters of ECB have been identified in several Aspergillus species, the regulatory mechanisms governing its intracellular biosynthesis remain poorly understood, hindering the development of efficient ECB-producing cell factories. To address this issue, we elucidated the mechanisms underlying echinocandin B (ECB) biosynthesis in Aspergillus nidulans ZJB16068 under fatty acid feeding conditions through genome and transcriptome sequencing. The genome of ZJB16068 was sequenced using Oxford Nanopore Technology, yielding a 32.67 Mbp assembly with 11 scaffolds and a GC content of 50.23%. A total of 10,505 protein-coding genes were annotated, revealing 66 secondary metabolite gene clusters. Comparative transcriptomics between ZJB16068 and the reference strain ZJB0817 identified 2,342 differentially expressed genes (DEGs) under fatty acid supplementation. The KEGG analysis of the top 20 DEGs highlighted predominant metabolic pathways, including translation, energy metabolism, cofactor supply and lipid metabolism. We found that the up-regulation of genes related to the fatty acid metabolic pathway, pantothenic acid and CoA synthesis pathway accelerated the synthesis of acetyl-CoA, and the down-regulation of TCA pathway contributed to the throttling of acetyl-CoA. In addition, the genes involved in oxidative phosphorylation are fully upregulated, providing sufficient ATP for ECB synthesis. These pathways synergistically enhance the synthesis of ECB. These findings highlight the critical role of acetyl-CoA synthesis and energy supply in ECB synthesis and provide potential direction for future metabolic engineering aiming at increasing ECB production.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-025-04331-4.

Developing the trehalose biosynthesis pathway as an antifungal drug target

Invasive fungal infections are responsible for millions of deaths worldwide each year. Therefore, focusing on innovative approaches to developing therapeutics that target fungal pathogens is critical. Here, we discuss targeting the fungal trehalose biosynthesis pathway with antifungal therapeutics, which may lead to the improvement of human health globally, especially as fungal pathogens continue to emerge due to fluctuations in the climate.

Phenotypic landscape of a fungal meningitis pathogen reveals its unique biology

Cryptococcus neoformans is the most common cause of fungal meningitis and the top-ranked W.H.O. priority fungal pathogen. Only distantly related to model fungi, C. neoformans is also a powerful experimental system for exploring conserved eukaryotic mechanisms lost from specialist model yeast lineages. To decipher its biology globally, we constructed 4328 gene deletions and measured-with exceptional precision--the fitness of each mutant under 141 diverse growth-limiting in vitro conditions and during murine infection. We defined functional modules by clustering genes based on their phenotypic signatures. In-depth studies leveraged these data in two ways. First, we defined and investigated new components of key signaling pathways, which revealed animal-like pathways/components not predicted from studies of model yeasts. Second, we identified environmental adaptation mechanisms repurposed to promote mammalian virulence by C. neoformans, which lacks a known animal reservoir. Our work provides an unprecedented resource for deciphering a deadly human pathogen.

Advancements and challenges in antifungal therapeutic development

Over recent decades, the global burden of fungal disease has expanded dramatically. It is estimated that fungal disease kills approximately 1.5 million individuals annually; however, the true worldwide burden of fungal infection is thought to be higher due to existing gaps in diagnostics and clinical understanding of mycotic disease. The development of resistance to antifungals across diverse pathogenic fungal genera is an increasingly common and devastating phenomenon due to the dearth of available antifungal classes. These factors necessitate a coordinated response by researchers, clinicians, public health agencies, and the pharmaceutical industry to develop new antifungal strategies, as the burden of fungal disease continues to grow. This review provides a comprehensive overview of the new antifungal therapeutics currently in clinical trials, highlighting their spectra of activity and progress toward clinical implementation. We also profile up-and-coming intracellular proteins and pathways primed for the development of novel antifungals targeting their activity. Ultimately, we aim to emphasize the importance of increased investment into antifungal therapeutics in the current continually evolving landscape of infectious disease.

Molecular mechanisms governing antifungal drug resistance

Fungal pathogens are a severe public health problem. The leading causative agents of systemic fungal infections include species from the Candida, Cryptococcus, and Aspergillus genera. As opportunistic pathogens, these fungi are generally harmless in healthy hosts; however, they can cause significant morbidity and mortality in immunocompromised patients. Despite the profound impact of pathogenic fungi on global human health, the current antifungal armamentarium is limited to only three major classes of drugs, all of which face complications, including host toxicity, unfavourable pharmacokinetics, or limited spectrum of activity. Further exacerbating this issue is the growing prevalence of antifungal-resistant infections and the emergence of multidrug-resistant pathogens. In this review, we discuss the diverse strategies employed by leading fungal pathogens to evolve antifungal resistance, including drug target alterations, enhanced drug efflux, and induction of cellular stress response pathways. Such mechanisms of resistance occur through diverse genetic alterations, including point mutations, aneuploidy formation, and epigenetic changes given the significant plasticity observed in many fungal genomes. Additionally, we highlight recent literature surrounding the mechanisms governing resistance in emerging multidrug-resistant pathogens including Candida auris and Candida glabrata. Advancing our knowledge of the molecular mechanisms by which fungi adapt to the challenge of antifungal exposure is imperative for designing therapeutic strategies to tackle the emerging threat of antifungal resistance.

Photoinactivation of Planktonic Cells, Pseudohyphae, and Biofilms of Candida albicans Sensitized by a Free-Base Chlorin and Its Metal Complexes with Zn(II) and Pd(II)

Invasive candidiasis is an important cause of morbidity and mortality, and its occurrence is increasing due to the growing complexity of patients. In particular, Candida albicans exhibits several virulence factors that facilitate yeast colonization in humans. In this sense, the photodynamic inactivation of yeasts is a promising new alternative to eliminate fungal infections. Herein, the photodynamic activity sensitized by a free-base chlorin (TPCF16) and its complexes with Zn(II) (ZnTPCF16) and Pd(II) (PdTPCF16) was investigated in order to eliminate C. albicans under different forms of cell cultures. A decrease in cell survival of more than 5 log was found in planktonic cells incubated with 5 μM TPCF16 or ZnTPCF16 upon 15 min of white-light irradiation. The mechanism of action mainly involved a type II pathway in the inactivation of C. albicans cells. In addition, the photodynamic action induced by these chlorins was able to suppress the growth of C. albicans in a culture medium. These photosensitizers were also effective to photoinactivate C. albicans pseudohyphae suspended in PBS. Furthermore, the biofilms of C. albicans that incorporated the chlorins during the proliferation stage were completely eradicated using 5 μM TPCF16 or ZnTPCF16 after 60 min of light irradiation. The studies indicated that these chlorins are effective photosensitizing agents to eliminate C. albicans as planktonic cells, pseudohyphae, and biofilms.

Antifungal and Anti-Inflammatory Activities of PS1-2 Peptide against Fluconazole-Resistant Candida albicans

Clinically, fungal pneumonia rarely occurs in adults, and invasive fungal infections can cause substantial morbidity, and mortality due to sepsis and septic shock. In the present study, we have designed peptides that exhibit potent antifungal activities against fluconazole-resistant Candida albicans in physiological monovalent, and divalent ionic buffers, with minimal fungicidal concentrations ranging from 16 to 32 µM. None of these tested peptides resulted in the development of drug resistance similar to fluconazole. Among them, the PS1-2 peptide did not induce stimulation of macrophages by C. albicans, and it exerted antifungal and anti-inflammatory effects against C. albicans-induced intratracheal infection, in an acute lung injury mouse model. PS1-2 is likely a novel therapeutic agent for the control, and prevention of drug-resistant C. albicans infection, and our findings may be useful for designing antimicrobial peptides to combat fungal infection.