AFFINITY CAPILLARY ELECTROPHORESIS MASS-SPECTROMETRY FOR SCREENING COMBINATORIAL LIBRARIES

A new methodology, affinity capillary electrophoresis-mass spectrometr y (ACE-MS), is introduced as a solution-based approach for screening c ombinatorial libraries for drug leads. The method allows on-line, one- step selection and structural identification of candidate ligands. ACE -MS is demonstrated using the binding of vancomycin to libraries of al l-D-tri- and tetrapeptides as a model system. Peptide libraries of dif ferent forms of Fmoc-DDXX and Fmoc-EXX containing up to 361 compounds were successfully employed to determine interacting structural motifs. A consensus structure of the strongest interacting peptides consisted of D-Ala at the C-terminus and an aromatic amino acid in the penultim ate position. Ligands with this structure bound more strongly to the r eceptor than the known ligand, D-Ala-D-Ala. A 1000 peptide library was also screened directly by ACE-MS. It was found that, for this and pot entially larger libraries, incorporating an affinity solid phase extra ction step prior to ACE-MS was effective in both removing a large numb er of non-interacting species as well as preconcentrating sample compo nents for sequence determination by MS.