Calculation of Relative Hydration Free Energy Differences for Heteroaromatic Compounds:  Use in the Design of Adenosine Deaminase and Cytidine Deaminase Inhibitors

Heteroaromatic compounds frequently undergo reversible covalent hydration in aqueous solution with the extent of hydration dependent on the heterocycle and its substituents. Using a combined quantum mechanical and thermodynamic cycle perturbation (TCP) approach, relative hydration free energy differences (ΔΔGhyd) were calculated for a variety of pteridine, quinazoline, pyrimidine, and purine analogues. Good agreement with experimental data was obtained for heteroaromatic compounds exhibiting a wide range of hydration equilibrium constants (10-6−103). Differences in hydration were attributed to a multitude of molecular factors including both electronic and steric effects. Differences in the resonance energy lost during hydration of the heteroaromatic ring accounted for the 107-fold greater hydration of pteridine relative to 9-methylpurine (ΔΔGhyd (exp) ≈ −8.8 kcal/mol; ΔΔGhyd (calc) = −9.3 kcal/mol). An analysis of purine riboside and its 8-aza analogue showed that the 400-fold greater adenosine deaminase (ADA) inhibitor potency exhibited by the 8-aza analogue is accurately calculated by summing the hydration free energy difference with the relative binding free energy difference for the corresponding hydrated species. The greater inhibitor potency was attributed to increased hydration since hydration of 8-aza-9-methylpurine was strongly favored over 9-methylpurine (ΔΔGhyd = −7.1 kcal/mol), whereas the relative binding free energy calculated using the TCP method and the murine ADA structure favored the purine riboside hydrate (ΔΔGbind = 3.1 ± 0.7 kcal/mol). Increased desolvation costs for the 8-aza analogue and an unfavorable electrostatic interaction between the 8-nitrogen and Asp296 accounted for the loss in binding affinity. The combined results gave an apparent inhibition constant for the 8-aza analogue similar to the experimental value and demonstrated the potential importance of hydration free energy calculations in drug design.