Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 113, Issue 52, Pages 14970-14975Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.1609375114
Keywords
inhibitory antibody; long CDR; synthetic library; convex paratope; MMP
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Funding
- National Science Foundation [1453645]
- NIH [R01 GM115672]
- California Breast Cancer Research Program Developmental and Exploratory Award [21IB-0104]
- Directorate For Engineering [1453645] Funding Source: National Science Foundation
- Div Of Chem, Bioeng, Env, & Transp Sys [1453645] Funding Source: National Science Foundation
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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 x 10(9) individual 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.
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