Binding of sulfonamide and acetamide to the active-site zinc(2+) in carbonic anhydrase: a theoretical study

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Abstract
Self-consistent field molecular orbital (SCF MO) calculations at both 4-31 G and STO-3G levels have been used to examine the binding conformations of sulfonamide and acetamide compounds to the active site of carbonic anhydrase. The results are as follows: (1) sulfonamide binds to the Zn2+ ion in its deprotonated form through the sulfonamide nitrogen to the fourth coordination site of the metal ion; (2) acetamide as neutral species binds to the basic form of the enzyme through the carbonyl oxygen to the fifth coordination site of the metal ion; and (3) the acetamidate ion binds to the acid form of the enzyme through the amide nitrogen to form a tetracoordinated metal complex with three histidine ligands. Analysis of the effects of individual active-site residues on the binding conformations of these inhibitors suggest that metal alone favors bidentate coordination of sulfonamidate and acetamidate complexes and that electron donation from three histidine ligands to the metal ion determines the formation of a tetracoordinated metal complex, which is further stabilized by the presence of Thr 199, as it receives one hydrogen bond from the sulfonamide NH- or from the acetamide NH- and donates a backbone NH hydrogen bond to a sulfonamide oxygen. The calculated binding conformation of sulfonamide and the hydrogen-bonding interactions between sulfonamide and the enzyme are consistent with the X-ray diffraction study of the AMSulf-HCA II complex. However, no X-ray structures are available for amide-HCA II complexes. Finally, a three-step binding mechanism is proposed to explain the experimentally observed slow association kinetics of amide compounds: (1) initial binding of an amide compound through the carbonyl oxygen to the fifth coordination site of the metal ion; (2) proton transfer from the amide nitrogen to the metal-bound OH-; and (3) release of a metal-bound water molecule and subsequent coordination of the amidate compound through the amide nitrogen to the metal ion. The proton-transfer process of step 2 is considered to be rate limiting.