HIV integrase strand transfer inhibitors also inhibit cryptococcal growth

About This Grant

PROJECT SUMMARY/ABSTRACT Cryptococcus neoformans is the most common disseminated fungal pathogen in people living with HIV/AIDS, causing an estimated quarter million cases of cryptococcal meningitis annually and resulting in over 180,000 deaths worldwide. In the United States alone, the annual economic burden of cryptococcal disease exceeds $535 million. Despite the availability of antiretroviral therapy (ART) and antifungal drugs, mortality rates remain unacceptably high, ranging from 10–30% in medically advanced settings to 30–50% in resource-limited regions. Current antifungal therapies are constrained by toxicity, limited drug classes, emerging resistance, medication shortages, and reliance on host immune function. Thus, there is a critical need to identify new fungal pathways and targets to support antifungal drug development. We identified that multiple HIV integrase strand transfer inhibitors (INSTIs), including bictegravir, dolutegravir, raltegravir, elvitegravir, and cabotegravir, exhibit anti- cryptococcal activity in vitro, indicating a class effect. This activity was observed across multiple strains of C. gattii and C. deneoformans, but not against other fungal pathogens, suggesting species-specific effects. In combination studies, INSTIs demonstrated additive or synergistic interactions with amphotericin B, flucytosine, and fluconazole. In a murine model of cryptococcal infection, elvitegravir treatment resulted in a modest but statistically significant reduction in fungal burden, and combination treatment with fluconazole further enhanced fungal clearance relative to fluconazole alone. To investigate the fungal targets underlying these effects, we employed a structure-based computational approach using Foldseek to identify cryptococcal proteins with tertiary structural similarity to HIV-1 integrase. This analysis identified an uncharacterized protein in C. deneoformans containing an RNase H–like domain derived from a retrotransposon-associated protein. Orthologs of this domain were identified in C. neoformans (CKF44_05263 and CKF44_07425), but not in Candida albicans or Aspergillus fumigatus, consistent with the observed species-specific antifungal activity. In parallel, a transcription factor deletion screen identified 4 TFs, Fzc40, Fzc5, Hlh3, and Rds2, that contribute to resistance against multiple INSTIs. The proposed studies will use complementary genetic, biochemical, and transcriptomic approaches to define the cryptococcal genes and pathways mediating sensitivity and resistance to INSTIs and to determine whether CKF44_05263 and/or CKF44_07425 function as INSTI-responsive targets. While INSTIs are not proposed as direct therapeutics for cryptococcosis, these studies leverage INSTIs as chemical probes to uncover novel, druggable fungal pathways. Successful completion of this work will advance fundamental understanding of cryptococcal biology and provide a foundation for the rational development of new antifungal agents, directly aligning with NIAID’s mission to support fundamental discoveries and innovative research strategies to protect and improve human health.