Insights into the Mechanism of Streptonigrin-Induced Protein Arginine Deiminase Inactivation
Protein citrullination is just one of more than 200 known PTMs. This modification, catalyzed by the Protein Arginine Deiminases (PADs 1\xe2\x80\x934 and PAD6 in humans), converts the positively charged guanidinium group of an arginine residue into a neutral ureido-group. Given the strong links between dysregulated PAD activity and human disease, we initiated a program to develop PAD inhibitors as potential therapeutics for these and other diseases in which the PADs are thought to play a role. Streptonigrin which possesses both anti-tumor and anti-bacterial activity was later identified as a highly potent PAD4 inhibitor. In an effort to understand why streptonigrin is such a potent and selective PAD4 inhibitor, we explored its structure-activity relationships by examining the inhibitory effects of several analogues that mimic the A, B, C, and/or D rings of streptonigrin. We report the identification of the 7-amino-quinoline-5,8-dione core of streptonigrin as a highly potent pharmacophore that acts as a pan-PAD inhibitor.
1. Introduction<!>2.1. Library Screening<!>2.2. Reversibility Studies<!>2.3. Selectivity Studies<!>2.4. Gel-Based Competitive ABPP Studies<!>2.5. Substrate Protection Studies<!>2.6. MALDI Mass Spectrometry Analysis<!>2.7. Cell Proliferation Studies<!>3. Conclusion<!>4.1. Chemicals<!>4.2. Synthesis of Streptonigrin Analogues<!>4.3. Percent Inhibition Studies<!>4.4. IC50 Values<!>4.5. Irreversibility Studies<!>4.6. Gel-Based Competitive ABPP Studies<!>4.7. Streptonigrin Analogue Inactivation Studies<!>4.8. Substrate Protection Studies<!>4.9. MALDI Mass Spectrometry Analysis<!>4.10. XTT Assay
<p>Post-translational modifications (PTMs) are an added layer of regulation that finely tune the physiological functions of the cell. Protein citrullination is just one of more than 200 known PTMs. This modification, catalyzed by the Protein Arginine Deiminases (PADs 1–4 and PAD6 in humans), converts the positively charged guanidinium group of an arginine residue into a neutral ureido-group.1 As a consequence, this PTM can enhance or inhibit protein-protein interactions, and potentially disrupt protein-DNA and protein-RNA interactions. For example, citrullination of Arg2142 in the GRIP1 binding domain of p300 prevents the methylation of the same arginine residue by co-activator associated arginine methyltransferase 1 (CARM1), which consequently disrupts the interaction between p300 and GRIP1, a nuclear receptor co-activator.2 As a consequence, this modification leads to decreased expression of genes under the control of the estrogen receptor.2</p><p>With the potentially wide ranging effects of this PTM, it is unsurprising that several diseases (e.g., multiple sclerosis, rheumatoid arthritis (RA), and Colitis), are associated with aberrantly increased PAD activity.1 For example, the deterioration of the myelin sheath in multiple sclerosis correlates with the hyperdeimination of myelin basic protein.3 Since PAD2 is the predominant PAD in the brain, dysregulated PAD2 activity has been suggested to play a principle role in the onset and progression of this disease.3,4 In addition, one of the most well studied links between dysregulated PAD activity and human disease is the one that exists with RA. For example, the presence of a PAD4 mutation correlates with an increased risk of developing RA in Asian populations;5 these mutations are thought to increase PAD4 mRNA stability leading to the overexpression of PAD4.5 PAD2 also likely plays a role because both it and PAD4 are overexpressed in the synovial joints of these patients.6 Importantly, aberrant citrullination is associated with the development of anti-citrulline protein antibodies whose presence is highly diagnostic and predictive of RA.7,8</p><p>Given the strong links between dysregulated PAD activity and human disease, we initiated a program to develop PAD inhibitors as potential therapeutics for these and other diseases in which the PADs are thought to play a role. From our initial efforts, we identified Cl-amidine as an irreversible pan-PAD inhibitor9 and used it to show that the PADs play an important role in gene transcription and NET formation.10–15 For example, Cl-amidine was used to show that PAD2 activity is important for the high level of expression of estrogen receptor-α target genes via its ability to citrullinate histone H3 at R26.13 Additionally, Cl-amidine, or an analog, decrease disease severity in animal models of RA, spinal cord injury, ulcerative colitis, lupus and cancer, thereby helping to validate the PADs as therapeutic targets.16–21 2-chloroacetamidine, the reactive portion of Cl-amidine, was also recently shown to decrease disease severity in several animal models of multiple sclerosis.22</p><p>Although Cl-amidine has proven to be an extremely useful tool compound, it shows only modest selectivity between the PAD isozymes, and it is therefore difficult to use this compound to ascribe a particular function to a specific PAD. To identify PAD inhibitors with improved selectivity, we developed a Fluorescence-Polarization-Activity-based Protein Profiling (FluoPol-ABPP) based high-throughput screen to identify novel PAD inhibitors and chemotypes that could be further derivatized to generate highly potent and selective inhibitors.23 From an initial validation screen, we identified streptonigrin (Figure 1) as a potent and selective irreversible PAD4 inhibitor; streptonigrin preferentially inhibits PAD4 by 119-, 37-, and 126-fold versus PADs 1–3, respectively.23</p><p>Streptonigrin, a natural product produced by Streptomyces flocculus, possesses both anti-tumor and anti-bacterial activity. In eukaryotic cells, cytotoxicity is thought to primarily stem from effects on DNA stability, as this compound has been shown to induce strand breaks in a transition metal and NADH-dependent manner.24–26 Streptonigrin also inhibits topoisomerase II, which enhances the DNA damaging effects of this compound 27. The ability of streptonigrin to induce the formation of reactive oxygen species may also contribute to cell death.24 Given the fact that streptonigrin is a highly potent PAD4 inhibitor, the anti-neoplastic effects of this compound may also be due in part to its ability to inhibit PAD4.23</p><p>In an effort to understand why streptonigrin is such a potent and selective PAD4 inhibitor, we explored its structure-activity relationships by examining the inhibitory effects of several key partial structures that mimic the A, B, C, and/or D rings of streptonigrin (see Figure 1 for ring naming nomenclature). Herein, we report the results of these studies. Specifically, we show that the quinoline-5,8-dione portion of streptonigrin (A and B rings) is required for enzyme inactivation, that the pyridyl C ring and its substituents can significantly impact potency, and that rings C and D are likely required for isozyme selectivity. We also identified several derivatives from these efforts and report here that 7-amino-quinoline-5,8-diones are highly potent pan-PAD inhibitors(Compounds 3, 14, and 21) both in vitro and in cells.</p><!><p>Structurally, streptonigrin consists of four rings designated A, B, C, and D that correspond to the quinoline-5,8-dione (Ring A and B), the central pyridine (Ring C), and the substituted phenyl ring (Ring D). To determine the contributions of these components to the potency and selectivity of streptonigrin, we screeneda small, focused 32 member compound library that structurally mimics the A, B, C and D rings (Figure 2). For these studies, each member of the library (10 μM each) was tested against the active PAD isozymes, PADs 1, 2, 3, and 4 (PAD6 is not active) to obtain percent activity values (Table 1).7</p><p>Examining the structures of the most potent compounds, it is clear that the quinoline-5,8-dione portion is critical for the potency of streptonigrin, as analogues of the C and D rings (e.g., compounds 4, 6,7, and 8) showed little to no inhibition of the PADs. In contrast, the quinoline-5,8-dione moiety appears essential for potency as a number of analogs incorporating this functionality show strong inhibition of the PADs (e.g. compounds 3, 10, 14, 17, and 21). From this analysis, it is also clear that an oxidized quinoline-5,8-dione core is necessary for potent inhibition because napthoquinones (compound 19) show only modest inhibition (~50%) and non-oxidized quinolines (compounds 29 and 30), show no inhibition even when bound to pyridines (compounds 5 and 23), triazines (compounds 25 and 26) or more extended scaffolds (compound 24). Remarkably, removing the pyridyl nitrogen from the C ring led to loss in potency even with an analogue that contains the active 7-aminoquinoline-5,8-quinone (compound 22), indicating that ring C and its substituents can markedly influence potency.</p><p>Although the quinoline-5,8-dione core is essential for strong inhibition of the PADs (see data for compounds 3, 10, 14, 17, and 21), substitutions around the ring have a variety of effects on potency. For example, analogs in which the 6-methoxy group of the quinoline-5,8-dione is removed (compound 14) or replaced with a bromine (compound 21) either maintained or increased their potency for PADs 1–4.</p><p>Surprisingly, however, introduction of a bromine at the 6 or 7 positions on its own tempered the potency of several quinoline-5,8-diones (e.g., compounds 2, 9, 16, and 20) but this effect could be rescued by the introduction of an electron-donating group in combination with the bromine at either of these two positions (compare compounds 10 and 21 to compound 2). While the reason for this effect is not known, it is likely related to changes in the reactivity of the quinoline-5,8-dione for enzyme inactivation.</p><p>Based on both the percent activity (Table 1) screens and IC50 values (Supplementary Table 1), these studies identified analogues 1, 3, 10, 14, 17, and 21 as the most potent inhibitors of PADs 1–4. With the exception of analogue 10, the top hits all contain a 7-amino group. Further studies to prioritize these 7 compounds and characterize their mechanism(s) of inhibition are described below.</p><!><p>Given that quinoline-5,8-diones are known Michael acceptors and that streptonigrin irreversibly inhibits PAD4, the structures of the top hits suggested that their activity could be derived from their ability to irreversibly inhibit the PADs.23 To test this hypothesis, we treated PAD4 with an excess of compounds 3, 10, 14, 17, and 21 (100 μM) before dialysis to remove unbound inhibitor. These samples were then tested for the recovery of enzymatic activity (Figure 3A). The results indicate that little to no activity is recovered after dialysis confirming that these compounds are irreversible PAD4 inhibitors. To test whether this property was unique to PAD4, or shared amongst the other isozymes, we performed complementary experiments with PADs 1, 2, 3 and 4, focusing on 17, the most potent analogue. For these experiments, each of the PADs was incubated with a 170-fold excess of 17, and then dialyzed for 20 h (Figure 3B). Little to no activity was regained, thus confirming that these compounds irreversibly inhibit all of the active PAD isozymes. Note that the small amount of residual enzyme activity is most likely due to incomplete inactivation as the enzyme levels remained the same before and after dialysis.</p><!><p>To evaluate the selectivity amongst the active PAD isozymes, we determined kinact/KI(app) values(Table 2) for each of the top hits. Note that kinact/KI is a better measure of isozyme selectivity than IC50 because kinact/KI is a second order rate constant whereas IC50 values for irreversible inhibitors are a product of both reversible binding and time dependent irreversible inhibition. For 3, which is one of the simplest and most potent streptonigrin analogues, we also determined kinact, KI, and kinact/KI values for PADs 2 and 4. We focused on these two isozymes because they are the most relevant to human disease.1,7 For PAD4, inactivation by 3 yielded kinact, KI, and kinact/KI values of 0.12 ± 0.01 min−1, 20.1 ± 5.4 μM, and 5,700 M−1min−1, respectively(Figure 4). For PAD2, the values are 0.07 ± 0.003 min−1, 8.08 ± 1.7 μM, and 8,300 M−1 min−1, respectively. Note that the higher kinact/KI values obtained for PAD2 may relate to its ability to promote aggregation of this isozyme (Figure S1) but not PAD4 (Figure 5). Apparent kinact/KI values for the top hits mirrored the IC50 values as there was a ≤3-fold change in kinact/KI(app) values between the four different PAD isozymes (Table 2). In total, these data indicate that while highly potent, these analogues lack selectivity amongst the PADs.</p><!><p>To determine whether these analogues can prevent labeling of an active site residue, we used our previously described gel-based ABPP assay.23,28 Briefly, the PAD-targeted ABPPs, RFA and RCA covalently modify an active site cysteine and compete with an inhibitor for binding to the active site. Compounds that show strong inhibition will show minimal labeling by RFA and RCA, whereas weak inhibitors exhibit strong labeling by either of these probes.28,29 For these studies, the concentration of RFA was fixed at 10 μM and increasing amounts of streptonigrin, 3, and 17 were added to compete for ABPP labeling.</p><p>Note we focused here on 3 and 17 because 3 is one of the simpler analogues of the A, B and C rings whereas 17 is one of the most potent hits. As expected, increasing streptonigrin concentrations decreased the labeling of PADs 2 and 4 by RFA (Figure 5 and Figure S1). Like the parent compound, 3 and 17 also prevent labeling of PADs 2 and 4 by RFA suggesting that the quinoline-5,8-dione core covalently modifies an active site residue or alternatively prevents the adoption of the catalytically competent state (Figure 5 and Figure S1).</p><!><p>In addition to our competitive ABPP studies, we determined whether a PAD substrate, BAEE, can protect against the 3-induced inactivation of PAD4, similarly to streptonigrin.23 Typically substrate protection assays measure initial rates of activity using progress curves and varying concentrations of substrate; thus BAEE protection of the PAD active site from inactivation would result in faster initial rates of activity upon higher substrate concentrations. Surprisingly, little substrate protection was observed for the 3-induced inactivation of PAD4 (Figure S2). This result suggests PAD inactivation occurs not solely through modification of the active site but also by additional mechanisms.</p><!><p>To further interrogate the mechanism of streptonigrin inactivation, we examined the stoichiometry of inactivation by MADLI-MS. Upon treatment of recombinant WT-PAD4 with streptonigrin, 3, and 17 in a 1:10 ratio (enzyme:inhibitor), the mass of PAD4 was shifted by 710, 692, and 945 Da, respectively (Figure 6 and Table 3). Similarly, sized mass shifts were also observed for PAD2; the mass of PAD2 was increased by 469, 324, and 853 Da, respectively (Figure S3). These mass shifts are significantly higher than what one would expect for a 1:1 enzyme:inhibitor complex suggesting that multiple sites on the enzyme are modified. To determine whether one of those sites corresponds to the active site, we also examined the stoichiometry of the PAD2C647A and PAD4C645A mutants which are catalytically inactive due to a Cys to Ala substitution of the active site nucleophile. Interestingly, the mass shifts of these catalytically inactive mutants are also significantly higher than expected for a 1:1 stoichiometry and are consistent with multiple covalent modifications (Figure 6). Note that super oxide dismutase and catalase had no effect on enzyme inactivation (not shown), suggesting the >1:1 stoichiometry is not due to these compounds promoting enzyme oxidation. In total these results, coupled with our ABPP and substrate protection studies, suggest that streptonigrin, 3 and 17 inactivate the PADs through multiple covalent modifications both within and outside of the active sites of these enzymes.</p><!><p>When first discovered, streptonigrin was heralded for its antibiotic activity and efficacy as an anti-cancer agent. So much so, that the compound was almost immediately put into clinical trials, however, it became quite clear that the high toxicity and side effects of the compound outweighed its benefits as an anti-cancer agent.30 The mechanism(s) behind the cytotoxic nature of streptonigrin likely include DNA strand scission, Topoisomerase II-mediated DNA cleavage, the formation of DNA-damaging reactive oxygen species (ROS), and possibly PAD inhibition.23,24,27,31,32 To determine if our keyanalogues possess selective anti-proliferative activities that might show greater efficacy in PAD-associated cancers, we assessed their biological activities by measuring cell viability in U2OS cells, an osteosarcoma cell line that overexpresses PAD4 and NIH 3T3 cells, a mouse embryonic fibroblast cell line.11 At 10 μM, compound 3, 14 and 21 are most effective in killing both U2OS and NIH 3T3 cells with ≤30% of cells remaining viable. EC50 values for these compounds show that they possess a similar level of potency against U2OS and NIH 3T3 cells with ≤ 5-fold change in EC50 values amongst analogues (Figure 7 and Table 4). In comparison, 10 and 17 are moderately effective as both cells lines retain significant viability at 10 μM (Figure 7) and the EC50 value for 17 is 58.3 ± 8.7 μM in U20S cell(Figure 7 and Table 4). This phenomenon is also present in NIH 3T3 cells as cell viability is comparable to the DMSO control and an EC50 value of 61 ±10.1μM. The reduced potency of 17 may be due to a reduction in its bioavailability due to the presence of a negatively charged carboxylate.</p><!><p>In conclusion, we developed a structure-activity relationship for streptonigrin that has provided unique insights into the streptonigrin-induced inactivation of the PADs. Specifically, we identified the quinoline-5,8-dione core, in particular, the 7-amino-quinoline-5,8-dione scaffold, as critical for PAD inhibition. The lead compounds (3, 10, 14, 17, and 21) exhibit kinact/KI values that are comparable to our first and second generation mechanism-based inactivators, Cl-amidine9 and Thr-Asp-F-amidine (TDFA)33 whose kinact/KI values are 13,000 and 26,000 M−1min−1, respectively. Additional studies comparing the second order rate constants of inactivation (i.e., kinact/KI) indicate that the inter-isozyme selectivity is ≤5-fold. Thus, while these compounds lack selectivity, their high potency could allow these scaffolds to serve as pan-PAD inhibitors.</p><p>Although it remains unclear how streptonigrin inhibits the PADs, the fact that quinoline-5,8-dione scaffold contains Michael acceptors suggest that inhibition is due to the covalent modification of the enzyme, which was confirmed by MALDI-MS. Since the stoichiometry of modification by compounds 3 and 17 is >1, these data suggests a greater level of promiscuity associated with these streptonigrin analogues by contrast to its parent compound. We speculate that additional sites of modification may include other reactive non-disulfide bonded cysteines orlysine residues.</p><p>Finally, the cellular proliferation studies demonstrate that 3, 14, and 21 show a high degree of cytotoxicity towards both cancerous U2OS and normal NIH 3T3 cell lines. These results suggest cytotoxic properties associated with these analogues in addition to their ability to inhibit the PADs. In total, we have identified the quinoline-5,8-dione core as a potent PAD pharmacophore.</p><!><p>Dithiothreitol (DTT), 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES), ammonium iron (III) sulfate dodecahydrate, tris (2-carboxyethyl) phosphine (TCEP), and thiosemicarbazide were acquired from Sigma-Aldrich. Diacetyl monooxime (DAMO), N-α-Benzoyl-L-arginine ethyl ester (BAEE), and N-α-Benzoyl-L-arginine amide (BAA) were obtained from Acros. PADs 1–4 were purified analogously to previously described methods.33,34</p><!><p>Analogues (1, 2, 10, 13, 14,17 and 21) were prepared as previously disclosed or were available (3–9, 11, 12, 15, 16, 18–20, 22–30) from prior studies.35–4435–4041–44 Analogues 31 and 32 were prepared from analogue 2 as described below:</p><p>
</p><p>CeCl3 (12.0 mg, 0.049 mmol, 1.0 equiv) and NaOMe (25% in MeOH, 22 μL, 0.097 mmol, 2.0 equiv) were added sequentially to a stirred solution of methyl 7-bromo-5,7-dioxo-2-(2′-pyridyl)quinoline-6′-carboxylate (2, 18.2 mg, 0.049 mmol) in MeOH (0.7 mL). After 30 min, the reaction mixture was filtered through Celite and concentrated on a rotary evaporator. The resulting product was found to be sensitive to column chromatography and was used without further purification.</p><p>Sodium azide (6.9 mg, 0.11 mmol, 1.5 equiv) was added to a stirred solution of the crude 7-bromo-2-(6′-methoxycarbonyl-2′-pyridyl)-6-methoxy-quinoline-5,8-dione (28.7 mg, 0.07 mmol) in MeOH (2.5 mL) and DMF (2.5 mL) under Ar at RT in the dark. After 20 h, the reaction mixture was diluted with H2O (20 mL), and extracted with CH2Cl2 (5 × 15 mL). The combined organic extracts were washed with H2O (20 mL), dried (Na2SO4), and concentrated on a rotary evaporator. The crude azide was found to be sensitive to purification and was used without further purification.</p><p>10% Pd/C (5.4 mg) was added to a stirring suspension of the crude 7-azido-2-(6′-methoxycarbonyl-2′-pyridyl)-6-methoxy-quinoline-5,8-dione in EtOAc (5 mL) and EtOH (15 mL) under an H2 atmosphere in the dark at RT. The reaction mixture was then stirred at RT under Ar for 18 h. After 18 h, the reaction mixture was filtered through Celite. Flash chromatography (SiO2, EtOAc) provided 7-amino-2-(6′-methoxycarbonyl-2′-pyridyl)-6-methoxy-quinoline-5,8-dione (31) as a bright red solid (3.2 mg, 17%, over 3 steps):451H NMR (CDCl3, 400 MHz) δ 8.88 (d, J = 8.4 Hz, 1H), 8.84 (d, J = 8.0 Hz, 1H), 8.51 (d, J = 8.0 Hz, 1H), 8.20 (d, J = 7.6 Hz, 1H), 8.01 (t, J = 8.0 Hz, 1H), 4.11 (s, 3H), 4.05 (s, 3H); ESI-TOF HRMS m/z 340.0924 ([M + H]+, C17H13N3O5 + H+ requires 340.0928).</p><p>
</p><p>Na2S2O4 (1.2 mg, 0.0069 mmol, 1.1 equiv) in H2O (0.1 mL) was added to a stirred solution of 7-amino-2-(6′-methoxycarbonyl-2′-pyridyl)-6-methoxy-quinoline-5.8-dione (31, 2.2 mg) in THF–H2O (0.7 mL, 1:1) under Ar at RT. After 30 min, KOH (1 M in H2O, 53 μL, 0.053 mmol, 7.0 equiv) was added to the reaction mixture and stirring was continued at RT for 1 h. After 1 h, the reaction mixture was diluted with H2O (5 mL), acidified with addition of 10% aqueous HCl, and extracted with EtOAc (5 × 15 mL). The combined organic extracts were dried (Na2SO4) and concentrated on a rotary evaporator. Trituration of the crude residue with hexanes provided analogue 32 as an orange solid: 1H NMR (DMSO, 400 MHz) δ 8.84 (d, J = 8.0 Hz, 1H), 8.68 (d, J = 7.5 Hz, 1H), 8.45 (d, J = 8.5 Hz, 1H), 8.23 (t, J = 7.0 Hz, 1H), 8.18 (t, J = 8.0 Hz, 1H), 3.83 (s, 3H); ESI-TOF HRMS m/z 326.0778 ([M + H]+, C16H11N3O5 + H+ requires 326.0771).</p><!><p>The percent inhibition values for the streptonigrin analogues were determined in duplicateby incubating each compound (10 μM final) with recombinant wild-type PADs 1 and PAD4 (0.2 μM final) or PADs 2 and 3 (0.5 μM final) for 15 min in Reaction Buffer (10 mM CaCl2, 2 mM DTT, 50 mM NaCl, and 100 mM Tris-HCl, pH 7.6 ). BAEE (10 mM final) was then added to initiate the reaction. After 15 min, the reaction was quenched and citrulline production was measured with the COLDER assay using previously described methods.46,47</p><!><p>IC50 values were determined by incubating recombinant wild-type PADs 1 and 4 (0.2 μM final) or PADs 2 and 3 (0.5 μM final) with various concentrations of inhibitor for 15 min. BAEE (10 mM final) was then added and the reaction was allowed to proceed for 15 min before quenching with liquid N2. The experiments were completed in duplicate. IC50 values were determined by fitting an eight-point dilution curve to equation 1,</p><p>
(1)FractionalActivity=1/(1+[I]/IC50) using GraFit version 5.0.11.48 IC50 is defined as the concentration of inhibitor that provides 50% activity while [I] is the concentration of inhibitor.</p><!><p>Recombinant wild-type PAD4 and PAD2 (0.6 μM final) were incubated with streptonigrin, streptonigrin analogues, or no compound in Reaction Buffer (300 μL total reaction volume) for 1 h followed by dialysis into 2 L of Long-Term Storage Buffer (20 mM Tris-HCl, pH 7.6, 1 mM EDTA, 500 mM NaCl, 2 mM DTT, and 10% glycerol) for 20 h. Residual activity was measured as described above. Untreated controls for each of the isozymes were dialyzed separately and their percent activity remaining was set to 100%.</p><!><p>Recombinant wild-type PAD4 and PAD2 (2 μM final) were labeled with RFA (10 μM final) in the presence of calcium (10 mM final) and various concentrations of streptonigrin, 3 and 17 (0–50 μM final). Reactions were carried out in 50 mM HEPES, pH 7.6, 2 mM DTT, 50 mM NaCl for 1 h at 37 °C. 6X SDS-PAGE loading buffer (2.5 μL) was then added to each sample (20 μL final volume) to quench the reaction. The samples were boiled for 20 min and then the proteins were separated on a 12% SDS-PAGE gel. The relative fluorescence was visualized using a Typhoon imager and quantified with ImageQuant TL.</p><!><p>Inactivation reactions (100 mM Tris-HCl, pH 7.6, 10 mM CaCl2, and 2 mM DTT) were incubated with PAD isozymes (PADs 1 and 4 (2 μM final) or PADs 2 and 3 (5.0 μM final) for 10 min at 37 °C in 60 μL total volume. An aliquot (6 μL) of this mixture was then immediately added to Reaction Buffer containing BAEE (10 mM final) to measure the residual activity at various time points (0–60 min). These reaction mixtures (60 μL total volume) were pre-incubated at 37 °C for 10 min before adding aliquots from the inactivation mixture. The final reaction proceeded for 15 min at which point the reaction was stopped by flash freezing in liquid N2. Residual enzymatic activity was quantified using the methodology described above. The data obtained at each inactivator concentration were fit to equation 2,</p><p>
(2)v=v0e-kt using GraFit version 5.0.11. 48 where vo is the velocity, v is the initial velocity, k is the pseudo-first-order rate constant for inactivation, and t is time. The kinact/KI(app) values were determined by dividing the inactivation rate, kobs, by the concentration of inhibitor.</p><!><p>To evaluate the ability of substrate to protect against 3-induced inactivation, progress curves were generated with and without inactivator (0.5 μM final) at two different concentrations of substrate. For 3, BAEE concentrations of 2 mM (2Km for PAD4) and 10 mM (5Km for PAD4) were used. Reaction Buffer was pre-incubated for 10 min at 37 °C, and PAD4 (0.2 μM final) was added to initiate the reaction. Aliquots (60 μL) were taken at 0–8 min and data analysis was performed using equation 3,</p><p>
(3)Productformation=A0(1-e-kt)/k where A0 is the initial rate, k is the pseudo-first order rate constant for inactivation, and t is time.</p><!><p>Control and experimental reactions of PAD2 (3 Î¼M final) and PAD4 (3 Î¼M final) or their catalytically inactive mutants, PAD2 C647A (3 Î¼M final) and PAD4 C645A (5 Î¼M final) were incubated in a 1:10 ratio with streptonigrin or 3 in 100 mM HEPES, pH 7.6, 10 mM CaCl2, and 2 mM DTT for 1 h. These reactions were dialyzed in ddH2O overnight, concentrated and eluted in sinapinic acid for analysis on a Microflex MALDI-TOF mass spectrometer (Bruker Daltonics).</p><!><p>Mouse embryonic fibroblast NIH 3T3 and human osteosarcoma U2OS cell lines (2.5 x104 cells/mL) were treated with various concentrations of each streptonigrin analogue for 72 h in a 48 or 96-well plate. The 2,3-bis-(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide (XTT reagent) and N-methyl dibenzopyrazine methyl sulfate (PMS) activated solution (American Type Culture Collection) was added (50 Î¼L) and incubated 4 h for color formation. The orange-colored formazan containing solution was then measured at an absorbance of 475 nm using a spectrophotometer. EC50 values for cell growth inhibition were determined by fitting an eight-point dose response curves to equation 4,</p><p>
(4)Y=(Range/(1+([I]/EC50)s))+Background using GraFit 5.0.1148 where Range is the uninhibited value minus the background, and is s the slope factor.</p>