Partitioning the loss in vancomycin binding affinity for D-Ala-D-Lac into lost H-bond and repulsive lone pair contributions

The binding affinity of 4, which incorporates a methylene (CH2) in place of the key linking amide of Ac2-L-Lys-d-Ala-d-Ala, for vancomycin was compared with that of Ac2-L-Lys-d-Ala-d-Ala (3) and Ac2-L-Lys-d-Ala-d-Lac (5). The vancomycin affinity for 4 was approximately 10-fold less than that of 3, but 100-fold greater than that of 5. This suggests that the reduced binding affinity of 5 (4.1 kcal/mol) may be attributed to both the loss of a key H-bond (1.5 kcal/mol) and a destabilizing lone pair/lone pair electrostatic interaction introduced with the ester oxygen of 5 (2.6 kcal/mol) with the latter, not the H-bond, being responsible for the largest share of the 1000-fold reduction. Copyright © 2003 American Chemical Society.