Publication: XModeScore: A novel method for accurate protonation/tautomer state determination using quantum mechanically (QM) driven, macromolecular X-ray crystallographic refinement

April 01, 2016

Abstract: Gaining an understanding of the protein:ligand complex structure along with the proper protonation and explicit solvent effects can be important in obtaining meaningful results in structure-guided drug discovery and structure-based drug discovery. Unfortunately, protonation and tautomerism are difficult to establish with conventional methods because of difficulties in experimental detection of hydrogen atoms due to well-known limitations of X-ray crystallography. In the present work, we demonstrate that semiempirical, quantum mechanics-based macromolecular crystallographic refinement is sensitive to the choice of a protonation state/tautomer form of ligands and residues and can therefore be used to explore potential states. We describe a novel scoring method, called XModeScore, which enumerates the possible protomeric/tautomeric modes, refines each mode against X-ray diffraction data with the semiempirical quantum mechanics (PM6) Hamiltonian, and scores each mode using a combination of energetic strain (or ligand strain) and rigorous statistical analysis of the difference electron density distribution. We show that with XModeScore we are able to consistently distinguish the correct bound protomeric/tautomeric modes based on routine X-ray data - even at lower resolution around 3Å. These X-ray results are compared with results obtained from much more expensive and laborious neutron diffraction studies for three different examples: tautomerism in the acetazolamide ligand of human carbonic anhydrase II (PDB 3HS4 and 4K0S), tautomerism in the 8HX ligand of urate oxidase (PDB 4N9S and 4N9M), and protonation states of the catalytic aspartic acid found within the active site of an aspartic protease (PDB 2JJJ). In each case, XModeScore applied to the X-ray diffraction data is able to determine the correct protonation state as defined by the neutron diffraction data. The impact of QM-based refinement versus conventional refinement on XModeScore is also discussed.

Authors:  O. Y. Borbulevych, R. I. Martin, I. Tickle, and L. M. Westerhoff

Reference: Acta Cryst. (2016). D72, 586-598. (paper available for free download under Open Access)

Software Availability: link

Need background? See our previous publication!