Interplay of halogen bonding and solvation in protein–ligand binding

Summary Halogen bonding is increasingly utilized in efforts to achieve high affinity and selectivity of molecules designed to bind proteins, making it paramount to understand the relationship between structure, dynamics, and thermodynamic driving forces. We present a detailed analysis addressing this problem using a series of protein–ligand complexes involving single halogen substitutions — F, Cl, Br, and I — and nearly identical structures. Isothermal titration calorimetry reveals an increasingly favorable binding enthalpy from F to I that correlates with the halogen size and σ-hole electropositive character, but is partially counteracted by unfavorable entropy, which is constant from F to Cl and Br, but worse for I. Consequently, the binding free energy is roughly equal for Cl, Br, and I. QM and solvation-free-energy calculations reflect an intricate balance between halogen bonding, hydrogen bonds, and solvation. These advances have the potential to aid future drug design initiatives involving halogenated compounds.


Supporting information
Table S1.Collection statistics and model qualities for galectin-3C in complexes S2      (A) Overview of estimated R1 relaxation rate constants for all 5 protein-ligand complexes, H (blue), F (teal), Cl (purple), Br (green), and I (pink).The color-coded circles at the bottom of the plot indicate, for each residue, the protein-ligand complexes for which R1 could be measured.(B) Box plots comparing the distribution of R1 values for each protein-ligand complex.On each box, the central mark is the median (2nd quantile, q2) and the edges of the box are the 25th and 75th percentiles (1st and 3rd quantiles, q1 and q3, respectively).The whiskers extend to the most extreme data points that are not considered outliers.The outliers are plotted individually using the '+' symbol.The extremes of the whiskers correspond to q3 + 1.5 × (q3 -q1) and q1 -1.5 × (q3 -q1).
Table S2.Calibration of the EP model for the three ligands Cl, Br, and I. Related to figure 10.

Figure S1 .Figure S4 .Figure S5 .
Figure S1. 1 H-15 N HSQC of galectin-3C in complexes and the apo state S3 Figure S2. 1 H and 15 N chemical shift perturbations versus the enthalpy of binding S4 Figure S3. 15N R1 relaxation rate constants for the H, F, Cl, Br, and I-complexes S5TableS2.Calibration of the EP model for the three ligands with Cl, Br, and I S6
Figure S2. 1 H and 15 N chemical shift perturbations.Related to figure 6.

Figure S4 .
Figure S4.Correlation between the calculated water -T∆Stot and the experimental total -T∆SITC, using different MM parameters for Cl, Br and I. Related to figure 10.

Figure S5 .
Figure S5.Superposition of the crystal structures and the water densities from the MD simulations.Related to figure 9.

Table S1 .
Collection statistics and model qualities for galectin-3C in complex with H, F, Cl, Br, and I. Related to figures 3-5.

Table S3
Comparison of FEP and experimental (ITC)results for the relative binding affinities.Related to figure10.All energies and uncertainties are given in kJ/mol.