Novel matrix metalloproteinase inhibitors: Generation of lead compounds by the in silico fragment-based approach

Discovery process of a new chemical lead to identify matrix metalloproteinase inhibitors using the in silico fragment-based approach is reported. Generation of structurally new matrix metalloproteinase inhibitors was successfully carried out using an in silico technique. In order to identify the small fragment interacting with residues in the S1′ pocket of MMP-1 through hydrogen bonds, we performed in silico screening using the LUDI program. As a result, acetyl-l-alanyl-(N-methyl)amide (Ac-l-Ala-NHMe) was selected to link with another fragment, hydroxamic acid that interacted with catalytic zinc. By this approach, the l-glutamic acid derivative 2b was discovered to be a new type of matrix metalloproteinase inhibitor. Further transformation to reduce its peptidic nature and improve activity yielded nonpeptidic lead compounds as inhibitors of MMP-1, -2, -3, and -9.