dUMP/F-dUMP Binding to Thymidylate Synthase: Human Versus Mycobacterium tuberculosis

Area of Science:

• Biochemistry
• Structural Biology
• Computational Biology

Background:

• Thymidylate synthase is crucial for DNA synthesis, making it a target for tuberculosis drugs.
• Mycobacterium tuberculosis thymidylate synthase (MtbThyX) differs structurally from human thymidylate synthase (hThyA).
• Current inhibitors like Fluorodeoxyuridylate (F-dUMP) lack selectivity, highlighting the need for better drug design.

Purpose of the Study:

• To understand the atomic-level dynamics and energetics of substrate/inhibitor binding to MtbThyX and hThyA.
• To quantitatively estimate ligand selectivity between deoxyuridine monophosphate (dUMP) and F-dUMP for both enzymes.
• To provide insights for designing novel, selective thymidylate synthase inhibitors.

Main Methods:

• Utilized extensive computer simulations (approximately 4.5 μs) based on experimentally determined protein-ligand complex structures.
• Analyzed ligand binding preferences and energetics for MtbThyX and hThyA with dUMP and F-dUMP.
• Investigated the structural features, such as the ligand-binding pocket environment and specific amino acid residues, influencing selectivity.

Main Results:

• MtbThyX prefers the deprotonated (enolate) form of dUMP, while hThyA binds the keto form.
• Computed energetics indicate MtbThyX exhibits lower selectivity between dUMP and F-dUMP, favoring F-dUMP over hThyA.
• Tyrosine at position 135 (Y135) in hThyA plays a key role in enhancing selectivity; MtbThyX has a dry binding pocket, unlike the wetter pocket of hThyA.

Conclusions:

• The distinct binding mechanisms and energetics of MtbThyX and hThyA offer opportunities for developing selective inhibitors.
• Understanding the role of specific residues like Y135 and the nature of the binding pocket (dry vs. wet) is critical for rational drug design.
• Targeting MtbThyX with selective inhibitors could lead to more effective treatments for tuberculosis.