XModeScore: a novel method for accurate protonation/tautomer-state determination using quantum-mechanically driven...

Area of Science:

• Structural Biology
• Computational Chemistry
• Drug Discovery

Background:

• Accurate protein-ligand complex structures are crucial for structure-guided drug discovery.
• Experimental determination of hydrogen atom positions, vital for protonation and tautomerism, is limited by X-ray crystallography.
• Conventional methods struggle to definitively establish ligand protonation states and tautomers.

Purpose of the Study:

• To demonstrate that semiempirical quantum mechanics-based macromolecular crystallographic refinement can identify ligand protonation and tautomer states.
• To introduce XModeScore, a novel scoring method for analyzing protomeric/tautomeric modes.
• To validate XModeScore's ability to distinguish correct bound states using routine X-ray data.

Main Methods:

• Developed XModeScore, which refines ligand modes against X-ray data using the PM6 Hamiltonian.
• Scored refined modes using a combination of ligand strain energy and difference electron density analysis.
• Compared XModeScore results from X-ray data with neutron diffraction data for three different systems.

Main Results:

• XModeScore successfully identified correct protomeric/tautomeric modes from X-ray data, even at resolutions as low as 3 Å.
• Results from X-ray data using XModeScore consistently matched the correct protonation states determined by neutron diffraction.
• The method proved effective for acetazolamide, 8HX ligand, and aspartic acid residues.

Conclusions:

• Semiempirical quantum mechanics-based refinement is sensitive to protonation/tautomer states.
• XModeScore provides a reliable method for determining ligand protonation states and tautomers from X-ray data.
• This approach offers a more accessible alternative to neutron diffraction for studying these crucial molecular features in drug discovery.