Homology modeling and molecular docking studies to decrease glutamine affinity of Yarrowia lipolytica L-asparaginase.

Area of Science:

• Biochemistry
• Molecular Biology
• Computational Chemistry

Background:

• L-Asparaginase is crucial for treating leukemias and lymphomas.
• Off-target L-glutamine affinity of L-asparaginase causes adverse side effects.
• Need for modified L-asparaginase with improved specificity and stability.

Purpose of the Study:

• To computationally model and design Yarrowia lipolytica L-asparaginase (YL-ASNase) mutants.
• Objective: Reduce L-glutamine affinity and enhance L-asparagine affinity and enzyme stability.
• Aim: Develop potential therapeutic candidates with fewer side effects.

Main Methods:

• Protein modeling and molecular docking using AutoDock Vina.
• Assessment of wild-type and mutant YL-ASNase interactions with L-asparagine and L-glutamine.
• Molecular dynamics simulations and MM/GBSA free energy calculations for stability analysis.

Main Results:

• Three mutants (T171S, T171S-N60A, T171A-T223A) showed increased L-asparagine affinity and decreased L-glutamine affinity compared to wild-type.
• Mutant T171S-N60A exhibited enhanced stability and preferential binding to L-asparagine over L-glutamine.
• Computational results suggest these mutants are promising for therapeutic applications.

Conclusions:

• Engineered YL-ASNase mutants demonstrate improved substrate specificity and stability.
• These mutants hold potential as therapeutic agents for leukemia and lymphoma with reduced side effects.
• Further in vitro and in vivo validation is required to confirm functional properties.