title: Active-site MMP-selective antibody inhibitors discovered from convex paratope synthetic libraries.
abstract: Proteases are frequent pharmacological targets, and their inhibitors are valuable drugs in multiple pathologies. The catalytic mechanism and the active-site fold, however, are largely conserved among the protease classes, making the development of the selective inhibitors exceedingly challenging. In our departure from the conventional strategies, we reviewed the structure of known camelid inhibitory antibodies, which block enzyme activities via their unusually long, convex-shaped paratopes. We synthesized the human Fab antibody library (over 1.25 × 109individual variants) that carried the extended, 23- to 27-residue, complementarity-determining region (CDR)-H3 segments. As a proof of principle, we used the catalytic domain of matrix metalloproteinase-14 (MMP-14), a promalignant protease and a drug target in cancer, as bait. In our screens, we identified 20 binders, of which 14 performed as potent and selective inhibitors of MMP-14 rather than as broad-specificity antagonists. Specifically, Fab 3A2 bound to MMP-14 in the vicinity of the active pocket with a high 4.8 nM affinity and was similarly efficient (9.7 nM) in inhibiting the protease cleavage activity. We suggest that the convex paratope antibody libraries described here could be readily generalized to facilitate the design of the antibody inhibitors to many additional enzymes.
authors.affiliation: Department of Chemical and Environmental Engineering, University of California, Riverside, CA 92521.
authors.forename: Dong Hyun
authors.initials: DH
authors.lastname: Nam
authors.affiliation: Department of Chemical and Environmental Engineering, University of California, Riverside, CA 92521.
authors.forename: Carlos
authors.initials: C
authors.lastname: Rodriguez
authors.affiliation: Inflammatory and Infectious Disease Center and Cancer Research Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037.
authors.forename: Albert G
authors.initials: AG
authors.lastname: Remacle
authors.affiliation: Inflammatory and Infectious Disease Center and Cancer Research Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037.
authors.forename: Alex Y
authors.initials: AY
authors.lastname: Strongin
authors.affiliation: Department of Chemical and Environmental Engineering, University of California, Riverside, CA 92521; xge@engr.ucr.edu.
authors.forename: Xin
authors.identifier: 0000-0001-7491-7805
authors.initials: X
authors.lastname: Ge
mesh_terms: D020816:Amino Acid Motifs; D000818:Animals; D000906:Antibodies / Q000737:chemistry; D001666:Binding Sites, Antibody; D002162:Camelus; D020134:Catalytic Domain; D022801:Complementarity Determining Regions / Q000737:chemistry; D004926:Escherichia coli; D006801:Humans; D007140:Immunoglobulin Fab Fragments / Q000737:chemistry; D020128:Inhibitory Concentration 50; D053511:Matrix Metalloproteinase 14 / Q000737:chemistry / Q000276:immunology*; D061965:Matrix Metalloproteinase Inhibitors / Q000737:chemistry*; D051379:Mice; D008968:Molecular Conformation; D019151:Peptide Library; D020349:Surface Plasmon Resonance
chemical_list: D000906:Antibodies; D022801:Complementarity Determining Regions; D007140:Immunoglobulin Fab Fragments; D061965:Matrix Metalloproteinase Inhibitors; D019151:Peptide Library; C507086:MMP14 protein, human; D053511:Matrix Metalloproteinase 14
keywords: MMP; convex paratope; inhibitory antibody; long CDR; synthetic library