Identification of MMP-12 inhibitors by using biosensor-based screening of a fragment library.
Small inhibitors of matrix metalloproteinase 12 (MMP-12) have been identified with a biosensor-based screening strategy and a specifically designed fragment library. The interaction between fragments and three variants of the target and a reference protein with an active-site zinc ion was measured continuously by surface plasmon resonance. The developed experimental design overcame the inherent instability of MMP-12 and allowed the identification of fragments that interacted specifically with the active-site of MMP-12 but not with the reference protein. The interaction with MMP-12 for selected compounds were analyzed for concentration dependence and saturability. Compounds interacting distinctly with the target were further evaluated by an activity-based assay, verifying MMP-12 inhibition. Two effective inhibitors were identified, and the compound with highest affinity was confirmed to be a competitive inhibitor with an IC50 of 290 nM and a ligand efficiency of 0.7 kcal/mol heavy atom. This procedure integrates selectivity and binding site identification into the screening procedure and does not require structure determination.
Nordström
Helena
H
Department of Biochemistry and Organic Chemistry, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden.
Gossas
Thomas
T
Hämäläinen
Markku
M
Källblad
Per
P
Nyström
Susanne
S
Wallberg
Hans
H
Danielson
U Helena
UH
D001562:Benzimidazoles / Q000737:chemistry; D048588:Benzoxazines / Q000737:chemistry; D001665:Binding Sites; D015374:Biosensing Techniques; D024402:Carbonic Anhydrase II / Q000737:chemistry; D002257:Carbonic Anhydrase Inhibitors / Q000737:chemistry; D002413:Cations, Divalent; D015195:Drug Design; D006877:Hydroxamic Acids; D007211:Indoles / Q000737:chemistry; D007700:Kinetics; D008024:Ligands; D053508:Matrix Metalloproteinase 12 / Q000737:chemistry*; D061965:Matrix Metalloproteinase Inhibitors; D011485:Protein Binding; D011804:Quinolines / Q000737:chemistry; D054852:Small Molecule Libraries; D020349:Surface Plasmon Resonance; D013816:Thermodynamics; D013844:Thiazoles / Q000737:chemistry; D015032:Zinc / Q000737:chemistry
D001562:Benzimidazoles; D048588:Benzoxazines; D002257:Carbonic Anhydrase Inhibitors; D002413:Cations, Divalent; D006877:Hydroxamic Acids; D007211:Indoles; D008024:Ligands; D061965:Matrix Metalloproteinase Inhibitors; D011804:Quinolines; D054852:Small Molecule Libraries; D013844:Thiazoles; D053508:Matrix Metalloproteinase 12; D024402:Carbonic Anhydrase II; C119203:ilomastat; D015032:Zinc