Structural characterization of Group II introns bound to small molecule inhibitors

Fungal diseases have long existed as a global health problem, causing well over a million deaths annually and causing severe diseases in more than a billion people. These numbers are an underestimation due to misdiagnosis and underdiagnosis, owing to the absence of accurate and affordable diagnostic tools. Invasive candidiasis, caused by bloodstream infection of Candida sp., is one of the most prevalent fungal diseases, with an estimated annual incidence of more than 1.5 million and a staggering mortality rate of 63.6%. These fungal pathogens have become increasingly problematic and prevalent in patients with compromised immune systems, such as those with HIV/AIDS and those undergoing cancer therapy. Current methods of treating fungal diseases are limited – polyenes, azoles, allylamines, echinocandins and flucytosine are widely in use for treatment. Each of these drug classes comes with its own set of adverse side effects, ranging from mild (skin rashes and irritation) to severe (nephrotoxicity and hepatotoxicity).

Challenging this limited repertoire of antifungals is another pressing problem – drug resistance. Resistance is acquired through drug target alteration, target overexpression, enhanced efflux pump activity or through activation of cellular stress pathways. Development of new antifungal drugs is particularly challenging due to the close evolutionary relationship between fungi and humans, implicating the limited number of exclusive fungal drug targets. Therefore, in the current setting, it is essential to recognize new fungal-specific drug targets and develop new drug molecules against the deadly pathogens.

Fungal pathogens contain Group I and II introns within mitochondrial rRNA and genes which are essential for respiration and survival. Respiration is absolutely necessary for pathogenic fungi to form biofilms, which also contribute to antifungal drug resistance. Timely splicing of these introns is essential for gene expression and survival of these organisms within the host. Structural studies of these introns over the past two decades have revealed that these RNA molecules form elaborate tertiary structures which enable them to carry out their own splicing. These introns contain several structural motifs that can be targeted with inhibitors. In addition, these RNA molecules are absent in humans, making them potential targets for drug design.

My PhD project will focus on characterizing molecular interactions between Group II introns from pathogenic fungi, specifically Candida sp. and small molecule inhibitors that will be selected through High Throughput Screening (HTS), defining Structure-Activity Relationships (SAR) and optimization of potency. Combining biochemical and integrative structural biology approaches, it will be possible to determine how the compounds impede catalysis. This data can be a stepping stone for the rational design of new small molecule inhibitors that can effectively prevent the growth of pathogenic fungi.