Novartis utilizes cryo-EM to understand new drug pathway for treating Chagas disease and sleeping sickness

Over a billion people across tropical and subtropical regions worldwide grapple with the severe health implications of kinetoplastid parasitic infections, including detrimental illnesses like Chagas disease and Human African Trypanosomiasis (HAT), also commonly referred to as sleeping sickness.

Current standard treatments such as benznidazole and nifurtimox for Chagas, despite being in use, pose their own set of problems, ranging from limited efficacy to severe side effects, often leading to treatment discontinuation. This scenario underscores a pressing need for more effective and manageable therapeutic alternatives.

Responding to this public health challenge, Novartis, along with public-private partnerships, has embarked on a journey to uncover new potential drugs leveraging phenotypic screening techniques. As part of a new study in the journal Science, they discovered compounds belonging to the cyanotriazoles (CTs) class, which showed promise as potential growth inhibitors for these parasites. Their efforts to identify and validate the drug target of CTs within the parasites fused phenotypic, genomic, and metabolomic analyses, revealing that CTs work by poisoning the parasite's topoisomerase.

Utilizing cryo-EM, the researchers validated that CTs function by selectively targeting and inhibiting kinetoplastid topoisomerase II. Structure determination by cryo-EM also revealed vital aspects of the compounds' potency and selectivity. Such knowledge is invaluable, not only for enhancing our current understanding, but also as a key foundation for the future development of more effective treatments for these devastating parasitic infections using structure-based drug design.

The key details in solving the cryo-EM structure of the Tc TopoII DNA binding domain, bound to dsDNA and CT1, are as follows:

• To mitigate the effect of preferred particle orientation, data was collected from both tilted and untilted perspectives.
• Movies for tilted and untilted datasets were recorded and processed simultaneously using the internally developed live analysis software, CryoFLARE.
• After separate processing of the tilted and untilted data, the optimal particles from each set were combined.
• The overall structural resolution achieved in this process was approximately 2.9 Å.
• For model refinement, the Alphafold structure of T. cruzi DNA Topoisomerase II was utilized as the starting model.

Useful links

1. Science research article: Cyanotriazoles are selective topoisomerase II poisons that rapidly cure trypanosome infections

2. Related perspective: A new class of antiparasitic drugs

3. CryoFLARE - The FMI Live Analysis and Reconstruction Engine