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Unraveling Common Patterns and Differences among Cruzipains through Molecular Dynamics Simulations and Structural

Lucianna Helene S Santos¹, Augusto César Broilo Campos², Viviane Corrêa Santos²

¹Institut Pasteur de Montevideo, Mataojo 2020, Montevideo 11400, Uruguay.

|May 19, 2025

Summary

Novel drug development for Chagas disease (CD) is crucial. Four Cruzipain subtypes show distinct active site features, suggesting varied substrate binding and potential for targeted therapies against this neglected tropical disease.

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Area of Science:

Biochemistry
Parasitology
Computational Biology

Background:

Chagas disease (CD) is a neglected tropical disease requiring new treatments.
Cruzipain, a cysteine protease, is a key drug target for CD.
Bioinformatics identified four Cruzipain subtypes with active site variations.

Purpose of the Study:

To investigate the impact of substitutions on Cruzipain subtypes.
To analyze structural and functional differences in Cruzipain active sites.

Main Methods:

Employed molecular dynamics simulations.
Conducted varied structural analyses on Cruzipain subtype representatives.
Utilized virtual probes to assess active site characteristics.

Main Results:

Substitutions did not significantly alter overall protease flexibility or conformation.
Observed differences in active site electrostatic potentials, cavity volumes, and probe interactions.
Identified distinct alterations in active site subsites, particularly the S2 subsite.

Conclusions:

Cruzipain subtypes exhibit unique active site characteristics despite similar overall structures.
These differences may influence substrate specificity, ligand binding, and therapeutic effectiveness for Chagas disease.
Findings support the development of subtype-specific inhibitors for Chagas disease treatment.