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 the experimental detection of H atoms owing to the well known limitations of X-ray crystallography. In the present work, it is demonstrated 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. A novel scoring method, called XModeScore, is described 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. It is shown that using XModeScore it is possible to consistently distinguish the correct bound protomeric/tautomeric modes based on routine X-ray data, even at lower resolutions of around 3 Å. These X-ray results are compared with the 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 entries 3hs4 and 4k0s), tautomerism in the 8HX ligand of urate oxidase (PDB entries 4n9s and 4n9m) and the protonation states of the catalytic aspartic acid found within the active site of an aspartic protease (PDB entry 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.
Highlights
Within structure-guided drug discovery (SGDD) and structurebased drug discovery (SBDD), accurate understanding of the protein–ligand complex structure, including the relevant proper protonation, is significant for obtaining meaningful results from docking/scoring, thermodynamic calculations, active-site exploration, lead optimization and, medicinal chemistry (Pospisil et al, 2003)
In the drug Mirapex, which is used to treat the symptoms of Parkinson’s disease, the important chemical activity is conferred by a single aminothiazole tautomeric state rather than an alternative imino tautomer (Varga et al, 2009); the selection of the wrong state during drug design would lead to irrelevant findings
The protonation state of AZM bound to human carbonic anhydrase II: Protein Data Bank (PDB) entry 3hs4 at 1.1 Aresolution
Summary
Within structure-guided drug discovery (SGDD) and structurebased drug discovery (SBDD), accurate understanding of the protein–ligand complex structure, including the relevant proper protonation, is significant for obtaining meaningful results from docking/scoring, thermodynamic calculations, active-site exploration, lead optimization and, medicinal chemistry (Pospisil et al, 2003). In the drug Mirapex, which is used to treat the symptoms of Parkinson’s disease, the important chemical activity is conferred by a single aminothiazole tautomeric state rather than an alternative imino tautomer (Varga et al, 2009); the selection of the wrong state during drug design would lead to irrelevant findings. Neutron diffraction is rarely feasible within industrial SBDD settings
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