1. Volume 24, Issue 11, Pages 1388-1400.e7 (November 2017)
Proteome-wide Map of Targets of T790M-EGFR-Directed Covalent Inhibitors 
Sherry Niessen, Melissa M. Dix, Sabrina Barbas, Zachary E. Potter, Shuyan Lu, Oleg Brodsky, Simon Planken, Douglas Behenna, Chau Almaden, Ketan S. Gajiwala, Kevin Ryan, RoseAnn Ferre, Michael R. Lazear, Matthew M. Hayward, John C. Kath, Benjamin F. Cravatt 
Cell Chemical Biology 
Volume 24, Issue 11, Pages e7 (November 2017)
DOI: /j.chembiol
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2. Cell Chemical Biology 2017 24, 1388-1400. e7DOI: (10. 1016/j. chembiol
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3. Figure 1
In Situ Proteome Reactivity of Third-Generation EGFR Inhibitors
(A) Chemical structures of third-generation, T790M-EGFR-directed inhibitors (1–3) and their corresponding alkyne-modified chemical probes (4–6) and selected second-generation EGFR chemical probes (7, 8).
(B) In situ proteome reactivity of second- and third-generation EGFR probes in human cancer cells. H1975 cells, which express double-mutant L858R/T790M EGFR, were treated with designated probes (1 μM, 1 hr) and analyzed by gel-based ABPP. Sample lanes marked with asterisks denote half sample loaded for better visualization. Coomassie stain of gels demonstrated equal loading (Figure S2C). B indicates blank lanes.
(C) Competitive profiling of the proteomic reactivity of probes 4–6 with corresponding parent inhibitors 1–3. H1975 cells were pre-treated with inhibitor (1–3; 10 μM, 2 hr) or DMSO followed by addition of probe (4–6; 1 μM, 4 hr) and then analyzed by gel-based ABPP. Specific competed protein targets are marked with <1–3 to indicate which of the inhibitor(s) competed probe labeling for these proteins. B indicates blank lanes. Coomassie stain of gels demonstrated equal loading (Figure S2C).
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4. Figure 2
Mapping Targets for Third-Generation EGFR Inhibitors by Quantitative Mass Spectrometry
(A) MS-based identification of proteins enriched by probes 4–6. ABPP-SILAC experiments in H1975 cells treated with probe (4–6; 1 μM, 4 hr) or DMSO. Data represent the mean SILAC ratio value (probe/DMSO) for proteins across three biological replicates. Probe-enriched targets are defined as those with mean SILAC ratio values ≥5 (red dashed line), with an additional requirement of being detected and quantified in at least two of the three biological replicates.
(B) High-occupancy targets of inhibitors 1–3 determined by competitive ABPP-SILAC. H1975 cells were pre-treated with inhibitor (1–3; 10 μM, 2 hr) or DMSO, followed by treatment with probe (4–6, respectively; 1 μM, 4 hr). Data represent the mean SILAC ratio value (DMSO + probe/inhibitor + probe) for proteins across three biological replicates. Black, blue, and red bars designate proteins competed by inhibitors 1, 2, and 3, respectively. High-occupancy competed proteins are defined as those with mean competition ratio values ≥5 (red dashed line), with an additional requirement of being detected and quantified in at least two of the three biological replicates. Competition ratios are plotted above and below the x axis for the indicated inhibitors as a log2 of the mean SILAC ratio (DMSO/inhibitor). NC, not competed; NF, not found.
(C) Heatmap illustrating competition ratios displayed in (B). Maximum quantifiable competition (SILAC competition ratio of 20) is shown in dark blue while minimum competition (SILAC competition ratio of 1) is shown in light blue. Gray designates proteins that were not enriched and detected by the indicated probe.
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5. Figure 3
Characterization of NT5DC1 and CHEK2 as Specific Off-Targets of Inhibitor 3
(A) Characterization of NT5DC1 as a specific off-target of inhibitor 3/probe 6. HEK293T cells recombinantly expressing NT5DC1 were pre-treated in situ with inhibitors (1–3; 10 μM, 2 hr) followed by probes (4–6; 1 μM 4 hr), and total cellular lysate was analyzed by gel-based ABPP (upper panel). Anti-NT5DC1 western blotting was used to confirm equivalent protein expression in each sample (lower panel). Gel-based ABPP experiments and western blots were performed in duplicate or triplicate with consistent results. Representative full-length labeled gel for NT5DC1 is shown in Figure S4A. Mock-transfected lanes are marked with the letter M.
(B) Characterization of CHEK2 as a specific off-target of inhibitor 3/probe 6. HEK293T cells recombinantly expressing FLAG-tagged CHEK2 were pre-treated in situ with inhibitors (1–3; 10 μM, 2 hr) followed by probes (4–6; 1 μM 4 hr), and soluble lysate was analyzed by gel-based ABPP (upper panel). Anti-FLAG western blotting was used to confirm equivalent protein expression in each sample (lower panel). Gel-based ABPP experiments and western blots were performed in duplicate or triplicate with consistent results. Representative full-length labeled gel for CHEK2 is shown in Figure S4B. Mock-transfected lanes are marked with the letter M.
(C) Inhibitor 3 targets C119 in NT5DC1. HEK293T cells recombinantly expressing NT5DC1 were treated in situ with DMSO or inhibitor 3 (10 μM, 4 hr). Cells were then lysed and treated with an iodoacetamide (IA)-alkyne probe (100 μM, 1 hr) and processed following previously described isoTOP-ABPP protocols (Backus et al., 2016). Shown are representative parent mass ion (MS1) ratios for tryptic peptides containing IA-reactive cysteine residues in NT5DC1, revealing that inhibitor 3 blocks IA labeling of C119, but not other quantified cysteines in this protein.
(D) HEK293T cells recombinantly expressing FLAG-tagged WT or C231A mutant CHEK2 were treated in situ with probe 6 (1 μM, 4 hr) and analyzed by gel-based ABPP (upper panel). Anti-FLAG western blotting was used to confirm equivalent protein expression in the samples (lower panel).
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6. Figure 4
Characterization of Cathepsin Off-Targets and Lysosomotropic Activity of Inhibitor 1/Probe 4
(A) Characterization of CTSC as a specific off-target of inhibitor 1/probe 4. HEK293T cells recombinantly expressing CTSC were treated in situ with inhibitors (1–3; 10 μM, 2 hr) followed by probes (4–6; 1 μM 4 hr), and the soluble lysate was analyzed by gel-based ABPP (upper panel). Anti-CTSC western blotting was used to confirm equivalent protein expression in the samples (lower panel). Representative full-length labeled gel for CTSC is shown in Figure S5A. Mock-transfected lanes are marked with the letter M.
(B) Comparison of in vitro versus in situ reactivity of probe 4 with CTSC. HEK293T cells recombinantly expressing CTSC were treated in situ (inhibitor 1: 10 μM, 2 hr; and/or probe 4: 1 μM, 4 hr) or in vitro (inhibitor 1: 10 μM, 1 hr; followed by probe 4: 5 μM, 1 hr or 1 μM, 3 hr) and analyzed by gel-based ABPP (upper panel). Anti-CTSC western blotting was used to confirm equivalent protein expression in the samples (lower panel). Mock-transfected lanes are marked with the letter M.
(C) Competitive ABPP of CTSC in vitro versus in situ with inhibitors 1–3 using the cathepsin-directed activity-based probe DCG-04. HEK293T cells recombinantly expressing CTSC were treated in situ with inhibitors 1–3 (10 μM, 2 hr) or in vitro with inhibitors 1–3 (10 μM, 1 hr) or E64 (10 μM, 1 hr) followed by DCG-04-rhodamine labeling in vitro (1 μM, 30 min), and analyzed by gel-based ABPP (upper panel). Anti-CTSC western blotting was used to confirm equivalent protein expression in the samples (lower panel). Mock-transfected lanes are marked with the letter M.
(D) In situ reactivity of CTSC with probe 4 post lysosomal neutralization. HEK293T cells recombinantly expressing CTSC were treated with NH4Cl (10 mM, 15 min) or bafilomycin A1 (10 nM, 15 min) prior to treatment with probe 4 (1 μM, 4 hr), after which cells were lysed and analyzed by gel-based ABPP (upper panel). Anti-CTSC western blotting was used to confirm equivalent protein expression in the samples (lower panel). Mock-transfected lanes are marked with the letter M.
(E) In situ reactivity of probe 4 post lysosomal neutralization in H1975 cells. H1975 cells were treated with NH4Cl (10 mM, 15 min) or bafilomycin A1 (10 nM, 15 min) prior to probe 4 labeling in situ (1 μM, 4 hr) and analyzed by gel-based ABPP (upper panel). The T790M-EGFR band is denoted with an arrowhead and the cathepsin band with an asterisk. Right panel shows representative tryptic peptide MS1 ratios for the indicated proteins from ABPP-SILAC experiments evaluating probe 4 reactivity in bafilomycin- versus DMSO-treated H1975 cells. Complete MS profile for bafilomycin-treated H1975 cells is displayed graphically in Figure S5G.
(F) LTR (LysoTracker red) staining of H1975 cells treated with inhibitors 1–3. H1975 cells were treated with indicated concentrations of inhibitors 1–3 (2 hr) and LTR staining was quantified. Data represent average values ± SEM for three independent experiments.
For (A) to (E), all gel-based ABPP experiments and western blots were performed in duplicate or triplicate with consistent results.
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7. Figure 5 Inhibitor 1 Targets Cathepsins In Vivo
(A) Characterization of mouse liver EGFR target engagement by inhibitor 1 in vivo. Four separate mice (marked as mouse 1 to mouse 4) were orally dosed with inhibitor 1 (25 mg/kg, 6 hr) or vehicle (8 mice in total), and the insoluble liver proteomes (pH 7.4) were incubated in vitro with probe 4 (5 μM for 1 hr) and analyzed by gel-based ABPP for EGFR target engagement (arrow, top gel). The same samples were analyzed by western blot for Y1068 phosphorylation (middle panel; pEGFR Y1068) and total EGFR levels (bottom panel; anti-EGFR).
(B) Mapping high-occupancy in vivo targets of inhibitor 1 in mouse liver by competitive ABPP with probe 4. Quantitative (ReDiMe) MS-based proteomics of inhibitor 1 blockade of probe 4-enriched targets, where mice liver samples were treated as described in (A). Shown is a ReDiMe ratio plot of quantified proteins, where inhibitor 1-competed targets are defined as those with a mean value ≥5 (red dashed line) and quantified in at least three of the four biological replicates. Only EGFR met these criteria and is labeled in red. Displayed to the right is an MS1 chromatogram for a representative EGFR tryptic peptide, with the average protein ratio for EGFR shown below it.
(C and D) Mapping cathepsin target engagement in vivo for inhibitor 1 using DCG-04 probes. Soluble liver proteomes (pH 5.0) from mice treated with vehicle and inhibitor 1 (25 mg/kg, 6 hr) were treated with rhodamine-tagged DCG-04 (1 μM, 30 min) and analyzed by gel-based ABPP, for which two exposures are shown (C), or with biotin-tagged DCG-04 (1 μM, 1 hr) and analyzed by MS (ReDiMe)-based ABPP (D). For (C), data for the four individual mice are shown (marked as mouse 1 to mouse 4) and western blotting was used to confirm equivalent CTSC protein expression in the samples (Anti-CTSC; bottom panel). Two exposures (high, h; low, l) are shown for the fluorescence gel image of liver cathepsins labeled by rhodamine-tagged DCG-04. Left panel of (D) shows an ReDiMe ratio plot of quantified proteins, where inhibitor 1-competed targets are defined as those with a mean value ≥2 (red dashed line) and quantified in at least three of the four biological replicates. CTSL1, CTSH, CTSC, and CTSF met these criteria and are highlighted in red. CTSS, CTSZ, and CTSB did not meet these criteria and are highlighted in blue. Right panel of (D) shows representative MS1 chromatograms for tryptic peptides from each identified cathepsin with the average protein ratios displayed below.
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