Think Twice: Understanding the High Potency of Bis(phenyl)methane Inhibitors of Thrombin

Impact of Ligand and Protein Desolvation on Ligand Binding to the S1 Pocket of Thrombin

“…This is in agreement with a previously performed alignment of thrombin crystal structures from the Protein Data Bank (PDB), 22 showing the remarkable flexibility of this glutamate. 23 Despite marginal changes, our structures exhibit only pronounced differences next to the modified P1 substituent.…”

Non-additivity of Functional Group Contributions in Protein–Ligand Binding: A Comprehensive Study by Crystallography and Isothermal Titration Calorimetry

“…A negligible heat of protonation has been observed experimentally for 4l. 14 As discussed in detail elsewhere, 14 this finding results from a rather complex protonation inventory that covers mutually compensating effects arising from deprotonation of His57 and protonation of the primary amino function of the ligand. Because a very similar pattern, and thus very similar pK a values are given with respect to titratable groups, we assume similar behavior, also resulting in buffer independence for the analogous inhibitors 4c and 4e.…”

“…Thrombin was selected as a model system because its binding site is well structured into three aligned subpockets and was used by us earlier for evaluating the binding properties of other systematically varied ligands. 14,15 Thrombin is readily accessible in significant quantities, crystal structure analysis is well established, and ITC yields reliable measurements. Furthermore, thrombin has been a prominent drug target for many years and it is therefore well known to many medicinal chemists, modelers and structural biologists.…”

Chasing Protons: How Isothermal Titration Calorimetry, Mutagenesis, and pKa Calculations Trace the Locus of Charge in Ligand Binding to a tRNA-Binding Enzyme

“…Recently, Baum et al observed the simultaneous superposition of a proton uptake and release reaction leading overall to a balanced proton inventory during ITC titrations. 8 This study underlines the importance to investigate congeneric ligand series, which differ only by small gradual changes varying the basic or acidic properties, respectively.…”