Antibody-catalyzed removal of the p-nitrobenzyl ester protecting group: the molecular basis of broad substrate specificity

Antibody catalysts for the removal of the p-nitrobenzyl ester protecting group have been generated to accommodate a broad range of substrates. Antibody 7B9, which was elicited against p-nitrobenzyl phosphonate 1, catalyzed the hydrolyses of p-nitrobenzyl monoesters of nonsubstituted, and beta- and gamma-substituted glutaric acids with almost identical Km and kcat values. In addition, 7B9 displayed substrate tolerance towards the a-substituents and accepted the p-nitrobenzyl esters of Leu, Norleu, and Phe. To define the molecular basis of the broad substrate tolerance, we have cloned and sequenced the antibody and constructed a model of the active-site-hapten complex. The model showed a relatively shallow pocket of the antigen-combining site that accommodates the p-nitrobenzyl moiety, and this is consistent with the observed substrate specificity. Thus, in the antibody-catalyzed reaction, the alpha-, beta-, and gamma-substituents of the substrates should be outside the combining site and ignored by the antibody recognition. A structural comparison of 7B9 with antibody D2.3, elicited against the structurally similar haptenic phosphonate, suggests the significance of the linker moiety in hapten design, which endows antibody catalysts with broad substrate specificity. These investigations provide new strategies for the generation of catalytic antibodies that accept a broad range of substrates for practical applications in organic synthetic chemistry.