Volume 22, Issue 11, Pages 1442-1452 (November 2015) Combinatorial Screening Identifies Novel Promiscuous Matrix Metalloproteinase Activities that Lead to Inhibition of the Therapeutic Target IL-13  Carole Urbach, Nathaniel C. Gordon, Ian Strickland, David Lowne, Cathy Joberty-Candotti, Richard May, Athula Herath, DirkJan Hijnen, Judith L. Thijs, Carla A. Bruijnzeel-Koomen, Ralph R. Minter, Florian Hollfelder, Lutz Jermutus  Chemistry & Biology  Volume 22, Issue 11, Pages 1442-1452 (November 2015) DOI: 10.1016/j.chembiol.2015.09.013 Copyright © 2015 Elsevier Ltd Terms and Conditions

Figure 1 A Matrix for Empirical Exploration of Promiscuous Proteolysis Reactions (A) Digestions were set up with a target/enzyme ratio of 20:1 for 3 and 24 hr, at 37°C, and analyzed by SDS-PAGE. (B) The site of cleavage, when specific (i.e. target cleaved into two fragments), was determined by MALDI (example: cleavage of IL-13 by MMP-8). (C) The matrix describes a qualitative assessment of each proteolytic combination as revealed by SDS-PAGE. Not cleaved: no observed proteolysis. Site-specific cleavage: two proteolytic fragments observed by SDS-PAGE, indicating rapid (observable after 3 hr) and site-specific proteolysis. Non-specific cleavage: the appearance of multiple bands on SDS-PAGE is observed. Low activity: proteolysis may be site specific, but products are less than 50% of starting material after 24 hr. Low activity and non-specific: non-specific proteolysis accounts for less than 50% of starting material after 24 hr. Chemistry & Biology 2015 22, 1442-1452DOI: (10.1016/j.chembiol.2015.09.013) Copyright © 2015 Elsevier Ltd Terms and Conditions

Figure 2 Quantification of Protease Activity by In Vitro and Biological Assays Silver-stained SDS-PAGE and bioassays of proteolyzed IL-13, IL-6, and MCP-1. (A) SDS-PAGE gels of proteolysis reactions are shown for three substrate/protease pairs. Lane 1, protein substrate control; lane 2, proteolysis reaction mix stopped by addition of appropriate inhibitor; lane 3, proteolysis mix control whereby inhibitors and protein substrate were added before the protease; lane 4, protease and inhibitor control. (B) TF-1 proliferation assays for IL-13 and IL-6 show stimulation of the tritiated thymidine incorporation by TF-1 cells in a dose-dependent manner, as shown by increase in counts per minute (CPM). An FLIPR assay for MCP-1 shows calcium release through binding to a calcium-sensitive fluorescent dye. Upon MCP-1-receptor binding, intracellular calcium is released, thereby increasing fluorescence intensity. Four samples corresponding to lanes 1, 2, 3, and 4 of the SDS-PAGE gels were tested, where P is the protease and I the appropriate inhibitor. Data shown are means ± SEM in duplicate and measured at the same time. Chemistry & Biology 2015 22, 1442-1452DOI: (10.1016/j.chembiol.2015.09.013) Copyright © 2015 Elsevier Ltd Terms and Conditions

Figure 3 Hydrolysis of IL-13 by the Catalytic Domains of MMPs 5 μM IL-13 was incubated with 250 nM MMP for (A) 3 hr and (B) 24 hr, at 37°C in PBS, 1 mM CaCl2, 20 μM ZnCl2 (pH 7.4), and reaction products were analyzed by SDS-PAGE. I is intact IL-13 and F1 and F2 are the main products generated by proteolysis. Chemistry & Biology 2015 22, 1442-1452DOI: (10.1016/j.chembiol.2015.09.013) Copyright © 2015 Elsevier Ltd Terms and Conditions

Figure 4 Hydrolysis of IL-13 by MMPs in BAL of Humanized IL-13 Mice 1 μM MMP-1, -8, 12, -20, or PBS were incubated for 24 hr at 37°C in ovalbumin-challenged mice expressing human IL-13. Levels of IL-13 were measured by sandwich ELISA. Data shown are means ± SD in duplicate and measured at the same time. Chemistry & Biology 2015 22, 1442-1452DOI: (10.1016/j.chembiol.2015.09.013) Copyright © 2015 Elsevier Ltd Terms and Conditions

Figure 5 MMP-8 Expression in Patients with Moderate to Severe Atopic Dermatitis and Normal Healthy Controls The serum level of MMP-8 was measured using the Luminex platform. Each point represents a single atopic dermatitis patient (n = 196) or healthy control (n = 30). Geometric mean and 95% confidence interval are shown. ∗∗∗∗P ≤ 0.0001. Chemistry & Biology 2015 22, 1442-1452DOI: (10.1016/j.chembiol.2015.09.013) Copyright © 2015 Elsevier Ltd Terms and Conditions