Ab initio calculations at the MP2/6-31G* level have shown that variously substituted di- and trifluorobenzenes form non-covalent complexes with benzene that adopt either aromatic-aromatic or H-F binding, the choice being determined by the pattern of fluorination. The binding energies of these structures are from 3.4 to 4.5 kcal mol(-1). This range is large enough to account for observed variations in the binding affinity of a library of fluoroaromatic inhibitors of carbonic anhydrase. This enzyme has an aromatic amino acid at a central position in the active site. The diverse modes of binding of the dimers also suggest that aggregates of fluorobenzenes might adopt specified 3-dimensional shapes in the solid state.

QSAR has been used to elucidate the origin of the hydrophobicity and binding affinity of a small library of fluoroaromatic inhibitors of F131V carbonic anhydrase II. Our analysis predicted the presence of a twisted amide conformation for several bound inhibitors, which we confirmed crystallographically. We also determined that the hydrophobicity of the inhibitors as a whole results from the fragment hydrophobicities of their fluorobenzyl rings, corrected for field effects and the presence of an intramolecular F.H contact in solution. The loss of this interaction on binding to the enzyme makes the affinity sensitive to the same terms, but with the opposite dependence on the F.H contact. In the case of the four inhibitors bound as twisted amides, this F.H contact must be retained to some extent in the bound state in order for their affinities to be consistent with our QSAR analysis of the entire set of 17 molecules.

We have developed a versatile tool for the delivery of inhibitors of carbonic anhydrase II, which allows modification of a hydrophobic drug with either a water-solubilizing, photolabile cage or a hydrophobic, photolabile cage. The former mask is useful for direct delivery of hydrophobic molecules in an aqueous prodrug form. The latter may find application if delivery from a surface is desirable. In our system, where the target enzyme is found in the eye, both approaches may be useful for the delivery of hydrophobic drugs having subnanomolar dissociation constants from the enzyme.

Intermolecular interactions of eleven different fluoroaromatic inhibitors are probed within the scaffolding of the crystal lattice of Phe-131-->Val carbonic anhydrase II. The degree and pattern of fluorine substitution on the inhibitor benzyl ring modulate its size, shape, and electronic character. In turn, these properties affect the geometry of intermolecular interactions between the fluoroaromatic rings of two different inhibitor molecules bound in the crystal lattice, as determined by X-ray crystallography. Depending on the degree and pattern of fluorine substitution, we observe a face-to-face (aromatic-aromatic) interaction, an atom-to-face (carbonyl-aromatic) interaction, or no interaction at all. These interaction geometries are analyzed with regard to van der Waals, electrostatic, and possible charge-transfer effects. For the aromatic-aromatic interactions investigated in this study, with aromatic ring quadrupoles specifically "tuned" by the degree and pattern of fluorination, the structural results suggest that London forces and charge-transfer complexation dominate over weakly polar electrostatic interactions in the association of aromatic ring pairs.

Carbonic anhydrase II (CAII) is a zinc metalloenzyme that catalyzes the hydration of CO2 to yield bicarbonate and a proton. N-(4-Sulfamylbenzoyl)benzylamine (SBB) is a tight-binding inhibitor of human CAII with K-d = 2.1 nM. Previous X-ray crystallographic work shows that the benzyl ring of SBB makes an edge-to-face interaction with Phe-131 in the enzyme active site. We have manipulated the electrostatics of this interaction by systematically substituting electronegative fluorine atoms for the benzyl ring hydrogens of SBB. Crystal structures of 10 enzyme-inhibitor complexes have been determined to atomic resolution. Analysis of these structures reveals that the main contributions to enzyme-inhibitor affinity can be approximated by a combination of dipole-induced dipole, dipole-quadrupole, and quadrupole-quadrupole interactions. Surprisingly, different electrostatic components dominate affinity in different enzyme-inhibitor pairs.

Ab initio (HF) and density functional theory (DFT) calculations of F-19 NMR chemical shifts were performed for models of fluoroaromatic inhibitors of carbonic anhydrase II (CA). DFT gave slightly better agreement with the experimentally measured chemical shifts of the actual inhibitors, suggesting that intramolecular dispersion does contribute significantly to the chemical shifts in these molecules. HF and DFT calculations for the stacked complex of hexafluorobenzene with benzene gave excellent agreement with experimental F-19 chemical shifts in this system. The fact that both approaches to this calculation were successful suggests that intermolecular dispersion is not an important contributor to F-19 chemical shifts in this system. Electron transfer and electrostatics must, therefore, be responsible for the changes in the F-19 NMR spectra observed on complexation. Finally, an unsuccessful attempt was made to apply HF and DFT methods to the calculation of the F-19 chemical shift of a pentafluorobenzyl-derived CA inhibitor bound to the protein in close proximity to a phenylalanine residue. A model of the inhibitor's aromatic ring interacting with the protein's aromatic residue gave a calculated chemical shift change that was much greater than that observed experimentally. Effects on the chemical shift from the field due to atoms omitted from the calculation, as well as from extensive rovibrational freedom, cannot easily be addressed in calculations of these large systems and are the likely reasons for the failure of these calculations.

Linear free energy relationships between binding affinity and hydrophobicity for a library of fluoroaromatic inhibitors of F131V carbonic anhydrase II (CA) implicate three modes of interaction. X-ray crystal structures suggest that F131 interacts with fluoroaromatic inhibitors, while P202, on the opposite side of the active site cleft, serves as the site of the hydrophobic contact in the case of the F131V mutant. 2-Fluorinated compounds bind more tightly, perhaps due to the field effect of the nearby fluorine on the acidity of the amide proton.