Chagas disease is a potentially life-threatening illness caused by the parasite, Trypanosoma cruzi, and is transmitted to humans through triatomine blood-sucking bugs that are commonly referred to as “kissing bugs” or “vampire bugs.” While it was once confined to the Americas, worldwide travel has spread the disease, which is now endemic to approximately 20 countries. Currently, the World Health Organization (WHO) estimates that 10-13 million people are chronically infected, around 90 million people are exposed to the risk of the infection, and nearly 21,000 people die each year as a result, making effective treatment a necessity.
Current treatments are largely effective in the first phase (acute) of the infection but have significantly diminished efficacy in the subsequent phase (chronic) of Chagas disease. Moreover, these drugs, which were developed in the 60s, are associated with severe adverse effects.
Now, investigators from the Advanced Computational Drug Discovery Unit at Tokyo Tech and the School of Tropical Medicine and Global Health at Nagasaki University have just established a multimodal integrated approach to develop potential new anti-Chagas therapies by combining the principles of 3D structure-based drug design with in vitro testing methods and X-ray crystallography. This approach narrows the range of potential drug candidates more efficiently. Findings from the new study were published today in Scientific Reports in an article entitled “In Silico, In Vitro, X-Ray Crystallography, and Integrated Strategies for Discovering Spermidine Synthase Inhibitors for Chagas Disease.”
In the current study, the researchers used virtual screening by TSUBAME at Tokyo Tech, one of the world’s top, large-scale supercomputers. They selected their target protein, T. cruzi spermidine synthase (SpdSyn), based on specific structural features and properties indicating its importance for survival in another Trypanosoma species. If the protein is required for survival of a species, inhibiting that protein could be a potential mechanism of action for a drug with activity against the parasite that causes Chagas disease.
“To develop a novel anti-Chagas drug, we virtually screened 4.8 million small molecules against spermidine synthase (SpdSyn) as the target protein using our supercomputer ‘TSUBAME2.5’ and conducted in vitro enzyme assays to determine the half-maximal inhibitory concentration values,” the authors wrote. “We identified four hit compounds that inhibit T. cruzi SpdSyn (TcSpdSyn) by in silico and in vitro screening. We also determined the TcSpdSyn–hit compound complex structure using X-ray crystallography, which shows that the hit compound binds to the putrescine-binding site and interacts with Asp171 through a salt bridge.”
The research team focused on SpdSyn as the target protein, as sourced from the in-house web system iNTRODB, which facilitates the selection of drug target proteins for neglected tropical diseases, particularly for trypanosomiasis. This system provides information on trypanosomal proteins with useful annotations, including the protein structure from the Protein Data Bank (PDB) and the protein inhibitors from ChEMBL.
Following selection, potential drug candidate inhibitors were identified through a screening search known as docking simulation—a structure-based drug design approach using 3D simulations to computationally match drug compounds to SpdSyn. The team successfully identified four drug-like compounds that were virtual “matches,” then evaluated their inhibition activity in vitro and compared the results with those of a positive control. To further test potential activity and binding, the investigators employed X-ray crystallography to confirm these four compounds in complex with the protein structure. Through interaction analyses for each compound, the researchers found that all four compounds interacted with the proposed target binding sites through the same amino acid, Asp171. Additionally, molecular simulation suggested additional interacting sites for each compound that was not predicted by docking simulation.
The research team believes that the study’s results are indicative of the promise that docking simulation holds for the identification of potential drug-like inhibitors of the target protein and therapies for Chagas disease. They hope to demonstrate the general applicability of their approach, opening doors to the discovery of treatments for other diseases.