How an Inhibitor Bound to Subunit Interface Alters Triosephosphate Isomerase Dynamics

Area of Science:

• Biochemistry
• Parasitology
• Computational Biology

Background:

• Triosephosphate isomerase (TIM) is essential for Trypanosoma cruzi, the parasite causing Chagas disease.
• Certain benzothiazole derivatives inhibit TIM by targeting a tunnel region near the dimer interface, distinct from the active site.
• The precise mechanism of inhibition by these compounds, such as bt10, remains unclear.

Purpose of the Study:

• To elucidate the inhibitory mechanism of the benzothiazole derivative bt10 on Trypanosoma cruzi TIM.
• To investigate the allosteric effects of bt10 binding on TIM's structure and dynamics.
• To identify key binding sites and their impact on enzyme function.

Main Methods:

• Multiple 100-ns molecular dynamics (MD) simulations of apo and complex TIM structures.
• Elastic network modeling (ENM), including mixed coarse-grained ENM on MD snapshots.
• Residue-based ENM scanning to identify critical binding regions.

Main Results:

• Bt10 binding stabilized aromatic clusters and enhanced intersubunit hydrogen bonds at the dimer interface, suggesting allosteric modulation.
• MD simulations and ENM revealed altered collective dynamics, including shifts in eigenvalues, due to bt10's constraining effect.
• Allosteric changes in the catalytic loop's dynamics, flexibility, and correlations were observed, impacting active site accessibility.
• Residue-based ENM scanning identified the tunnel region as a crucial allosteric binding site.

Conclusions:

• The benzothiazole derivative bt10 inhibits Trypanosoma cruzi TIM via an allosteric mechanism, not by direct active site blockade.
• Binding in the tunnel region allosterically modulates the enzyme's global dynamics, including the catalytic loop.
• These findings provide a deeper understanding of TIM inhibition and potential avenues for Chagas disease therapeutics.