Method of screening inhibitor of caspase activity by lipopolysaccharide

Abstract

Provided are a method of screening an inhibitor of caspase activity by lipopolysaccharide and a method of screening a therapeutic agent for inflammatory diseases or sepsis using the same. Accordingly, it is possible to develop a caspase-4-specific inhibitor.

Claims

1. A method of screening for an inhibitor of caspase-4 activity, wherein the caspase-4 is activated by lipopolysaccharide (LPS), the method comprising: incubating a mixture comprising a caspase-4-derived polypeptide, lipopolysaccharide (LPS), and a test material, wherein the caspase-4-derived polypeptide comprises a caspase activation and recruitment domain (CARD) labeled with a fluorescent material, wherein the CARD has an amino acid sequence selected from the group consisting of SEQ ID NOs: 1, 7 and 9, wherein a pH of the mixture is 5.5 to 9.5 and the incubation is conducted at 0 C. to 40 C.; measuring a fluorescence polarization (FP) value of the mixture: selecting the test material as an inhibitor of binding of CARD and LPS, when the measured FP value is lowered, as compared with that of a negative control not treated with the test material; and calculating, from the measured FP value, an inhibition rate of binding of CARD and LPS; wherein the CARD has a peptide tag at the N-terminus and having cysteine (Cys) inserted between the C-terminus of the peptide tag and the N-terminus of the CARD.

2. The method of claim 1, wherein the fluorescent material is conjugated through cysteine.

3. The method of claim 1, wherein the mixture does not comprise bovine serum albumin (BSA), a surfactant, a divalent cation, or a combination thereof.

4. The method of claim 1, wherein pH of the mixture is 7.0.

5. The method of claim 1, wherein the incubating of the mixture is performed at 37 C.

6. The method of claim 1, wherein the mixture comprises 0% (w/v) to 10% (w/v) of dimethyl sulfoxide (DMSO).

7. The method of claim 1, further comprising: after said selection of the test material, adding LPS and the test material to caspase-expressing cells; measuring caspase activity of the cells; and selecting the test material as an inhibitor of caspase activity in said cells, when the measured caspase activity is lowered, as compared with that of a negative control not treated with the test material.

Description

BRIEF DESCRIPTION OF THE DRAWINGS

(1) The above and other aspects, features, and advantages of certain embodiments of the disclosure will be more apparent from the following description taken in conjunction with the accompanying drawings, in which:

(2) FIG. 1A shows illustrations of prepared constructs, FIG. 1B shows graphs showing tryptophan emission spectra of full-length C258A-Casp-4, CARD, and CARD-C258A-Casp-4 with LPS-Ra (0 M to 50 M), and FIG. 1C shows SPR sensorgrams of full-length C258A-Casp-4, CARD, and CARD-C258A-Casp-4 binding to E. coli LPS(O55:B5) immobilized on a CM5 chip sensor;

(3) FIG. 2A shows an illustration of CARD variants in which cysteine is inserted, FIG. 2B shows a graph showing an FP binding assay of ALEXA FLOUR 488-labeled CARD variants for LPS, FIG. 2C shows an illustration of an ALEXA FLOUR 488-labeled CARD variant and Coomassie blue staining (left) and fluorescence (right) images of an SDS-PAGE gel of M1C-CARD purified by Ni-NTA column chromatography (lane 1) and SUPERDEX 200 column chromatography (lane 2) and after labeling with ALEXA FLUOR 488 (lane 3), FIG. 2D shows illustrations of binding of CARD and LPS and a method of screening for inhibitors using the same, and FIG. 2E shows an FP binding curve of ALEXA FLUOR 488-CARD or ALEXA FLUOR 488 alone (dye) depending on LPS concentrations;

(4) FIGS. 3A to 3E show FP binding curves with respect to additives, incubation time, pH, different concentrations of LPS-Ra, and different concentrations of DMSO, respectively, and FIG. 3F shows a graph showing Z factor depending on 0% to 10% DMSO;

(5) FIG. 4 shows a graph showing results of screening of a library of FDA-approved drugs (1,443 drugs) for inhibition of binding of CARD and LPS;

(6) FIGS. 5A to 5C show graphs showing results of FP competition assays of nine screened hit compounds; and

(7) FIG. 6A shows a graph showing Casp-4 activity depending on the presence of LPS in Casp-4-expressing HEK293T cells, FIG. 6B shows a graph showing inhibition of Casp-4 activity in the presence of LPS and screened hit compounds in which the dashed line indicates 50% inhibition, and FIG. 6C shows a graph showing activity of activated Casp-4 in the presence of four screened compounds.

DETAILED DESCRIPTION

(8) Reference will now be made in detail to embodiments, examples of which are illustrated in the accompanying drawings, wherein like reference numerals refer to like elements throughout. In this regard, the present embodiments may have different forms and should not be construed as being limited to the descriptions set forth herein. Accordingly, the embodiments are merely described below, by referring to the figures, to explain aspects of the present description. As used herein, the term and/or includes any and all combinations of one or more of the associated listed items. Expressions such as at least one of, when preceding a list of elements, modify the entire list of elements and do not modify the individual elements of the list.

(9) Hereinafter, the present disclosure will be described in more detail with reference to Examples. However, these Examples are only for illustrating the present disclosure, and the scope of the present disclosure is not limited thereto.

Example 1. Measurement of Binding Affinity of Caspase-4 and LPS

(1) Preparation of Casp-4 Variants

(10) Catalytically inactive full-length Casp-4 (1-377, C258A modification, referred to as C258A-Casp-4), CARD(1-80), and CARD truncated Casp-4 (81-377, C258A modification, referred to as CARD-C258A-Casp-4) were prepared.

(11) Genes, each encoding C258A-Casp-4 or CARD, were cloned into NdeI and HindIII restriction sites of a pET28b vector having His6 tag at the N-terminus. CARD-C258A-Casp-4, activated Casp-4(81-377)(p20/p10), three types of cysteine-inserted CARD(1-80) variants (Cys-His-CARD, His-Cys-CARD (M1C-CARD), and His-CARD-Cys) were prepared using a QUIKCHANGE Mutagenesis kit (Agilent Technologies). Schematic illustrations of the prepared constructs are shown in FIGS. 1A and 2A.

(12) All constructs were transformed into CLEARCOLI BL21(DE3)(Lucigen), respectively. When OD.sub.600 reached 0.8, 0.2 mM IPTG (isopropyl--D-1-thiogalactopyranoside) induction was performed, and then cells were inoculated in an LB medium supplemented with 50 g/mL of kanamycin and cultured at 18 C. overnight.

(13) The cultured cells were harvested, and the harvested cells were sonicated in a buffer A (25 mM Tris-HCl pH 8.0, 300 mM NaCl, 20 mM imidazole) containing 5 mM beta-mercaptoethanol (-mercaptoethanol: 2ME, Bio-Rad) (for full length Casp-4 C258A, 1% (v/v) TWEEN 20 (Bio-Rad) was supplemented). Thermostable CARD (1-80) and cysteine-inserted CARD variants were further incubated at 70 C. for 30 minutes after sonication. Each lysate was centrifuged at 4 C. and 12,000g for 40 minutes, and each supernatant was loaded on a HISTRAP column (Cytiva) equilibrated with buffer A. The recombinant proteins were sequentially washed with 10 column volumes (CV) of buffer A, 10 CVs of buffer A and 0.1% (v/v) TWEEN 20, and 50 CVs of a mixture (a volume ratio of 9:1) of buffer A and buffer B (25 mM Tris-HCl pH 8.0, 300 mM NaCl, 300 mM imidazole). After washing, the recombinant proteins were eluted with a gradient of increasing concentration of buffer B. Thereafter, the recombinant proteins were purified using a SUPERDEX 200 gel-filtration column (Cytiva) equilibrated with buffer C (50 mM Tris-HCl pH 7.0, 150 mM NaCl) at 4 C.

(2) Analysis of Binding Affinity of Casp-4 and LPS

(14) It was reported that caspase-4 (Casp-4) interacts with LPS through its CARD domain. To examine whether the interaction between CARD and LPS is related with binding affinity of Casp-4 and LPS, apparent equilibrium dissociation constants (K.sub.d.sup.app) of CARD and LPS were measured.

(15) Apparent dissociation constants were measured by tryptophan fluorescence spectrometry. When LPS is bound, the fluorescence emission spectrum of the tryptophan residue in the LPS-binding protein shows a blue-shift and the fluorescence intensity tends to increase. Apparent dissociation constant values were calculated by analyzing the fluorescence emission spectra.

(16) Fluorescence spectra were obtained with a FluoroMate FS-2 fluorescence spectrophotometer (Sinco) equipped with a quartz cuvette with a 5 mm path length. 1 M of the recombinant protein was mixed with increasing concentrations of LPS-Ra (in the range of 0 M to 50 M) in an HBS-E buffer (10 mM HEPES pH 7.5, 150 mM NaCl, 3 mM EDTA), and incubated at 37 C. for 30 minutes. The sample was excited at 280 nm, and emission spectra at 300 nm to 500 nm were recorded with an excitation/emission slit width of 2.5/5 nm, respectively. The fluorescence intensity of the sample was corrected by subtracting the background intensity of LPS alone. A difference in the fluorescence intensity at 334 nm was expressed as a function of LPS-Ra concentration, and the apparent equilibrium dissociation constant (K.sub.d.sup.app) was calculated from the nonlinear regression curve fit, as analyzed in GRAPHPAD PRISM 8. Graphs showing the emission spectra of the tryptophan residue in full-length C258A-Casp-4, CARD, and CARD-C258A-Casp-4 in LPS-Ra (0 M to 50 M) are shown in FIG. 1B. As shown in FIG. 1B, upon LPS binding, blue shifts were found (2.05 nm and 11.8 nm, respectively) and the fluorescence intensity increased in a concentration-dependent manner. The K.sub.d.sup.app values calculated from the fluorescence spectra of C258A-Casp-4 and CARD were 5.30.5 M and 6.50.8 M, respectively.

(17) In addition, the binding affinity between Casp-4 and LPS was determined by a surface plasmon resonance (SPR) experiment. The SPR experiment was performed at 25 C. using a BIACORE T200 (Cytiva). A filtered and degassed running buffer (HBS-E) was prepared prior to use. Amine-derived LPS O55:B5 (NH-LPS, Sigma-Aldrich) was prepared by a method described in P. T. Wong et al., J Mater Chem B, 2015, 3, 1149-1156, herein incorporated by reference. NH-LPS was immobilized on a CM5 sensor chip (Cytiva) using an amine coupling method (480 RU), and blocked with 1 M ethanolamine (pH 8.5). Purified proteins of the indicated concentration were injected, and the resulting sensorgrams were analyzed using a BIACORE T200 Evaluation software. The SPR sensorgrams are shown in FIG. 1C. As shown in FIG. 1C, the dissociation constants of C258A-Casp-4 and CARD were 2.4 M and 2.1 M, respectively.

(18) However, as shown in FIGS. 1B and 1C, the binding between CARD-C258A-Casp-4 and LPS was not identified in both methods.

(19) Therefore, it was confirmed that CARD may be used in an assay to monitor the binding between LPS and Casp-4.

(3) Fluorescent Dye Labeling and Fluorescence Polarization Analysis of CARD Variants

(20) The labeling efficiency of each CARD was evaluated using ALEXA FLUOR 488 which is a thiol-reactive fluorescent dye, and the dynamic range of the fluorescence polarization signal of the construct upon binding to LPS was measured.

(21) To evaluate the labeling efficiency of CARD, variants (His-Cys-CARD, M1C-CARD) including cysteine at the N-terminal (Cys-His-CARD), at the C-terminal (His-CARD-Cys), or between the N-terminal His6 tag and CARD were prepared (FIG. 2A), using the fact that CARD does not include a cysteine residue.

(22) The cysteine-inserted CARD variants were incubated overnight at 4 C. with the addition of buffer C supplemented with a 5-fold molar excess of ALEXA FLUOR 488 C5 maleimide (Invitrogen) and a 10-fold molar excess of TCEP. Dyes not used for labeling were removed by using a PD-10 desalting column (Cytiva) and a 10K centrifugal filter (Millipore) until no dye was detected in the filtrate. The labeled CARD was identified by SDS electrophoresis (FIG. 2C).

(23) The labeling efficiency was calculated according to the Lambert-Beer law using absorbance measured at 280 nm and 489 nm using a UV/Vis spectrophotometer (BIOCHROM LIBRA S22). Absorbance at 280 nm provided by Alexa-Fluor 488 was corrected using a correction factor of 0.11.

(24) The labeling efficiency is shown in Table 1.

(25) TABLE-US-00001 TABLE 1 Labeling Cysteine-inserted CARD variant efficiency (%) Cys-His-CARD 24% His-Cys-CARD (M1C-CARD) 86% His-CARD-Cys 7.8%

(26) To examine whether it is possible to screen agents inhibiting binding between CARD and LPS through fluorescence polarization of the CARD variants, a fluorescence polarization-based analysis between CARD and LPS was performed (FIG. 2B). Binding between CARD and LPS and use thereof for screening of inhibitors' are illustrated in FIG. 2D.

(27) Fluorescence polarization (FP) was measured with an APPLISKAN microplate reader (ThermoFisher) using 485 nm excitation and 535 nm emission filters. The FP value was calculated according to the following equation: FP (mP)=1000(I.sub.sGI.sub.p)/(I.sub.s+GI.sub.p). In the equation, I.sub.s represents a parallel (equivalent) emission intensity, I.sub.p represents a perpendicular emission intensity, and G represents a lattice coefficient 0.877.

(28) FP binding assay was performed by adding 200 L of a reaction mixture to each well of a black 96-well plate (SPL Life Sciences). The reaction mixture includes 50 nM ALEXA FLUOR 488-CARD (tracer) with increasing concentrations of LPS-Ra (in the range of 0 M to 12.8 M, a molecular weight of LPS-Ra is assumed to be 3,835 g/mole, Sigma-Aldrich) in a buffer C or an indicated buffer. The reaction mixture was incubated at 37 C. for 30 minutes to 4 hours before reaction. FP values are expressed as a function of LPS-Ra concentration. FP binding curves of His-Cys-CARD (ALEXA FLUOR 488-CARD) or ALEXA FLUOR 488 alone (dye) with respect to the concentrations of LPS are shown in FIG. 2E.

(29) Apparent equilibrium dissociation constants (K.sub.d.sup.app) were calculated from the nonlinear regression curve fit, as analyzed in GRAPHPAD PRISM 8 from the FP binding curves.

(30) Reproducible separation of the FP values for binding of LPS and ALEXA FLOUR 488-CARD and controls at different concentrations (0% to 10%) of DMSO (Sigma-Aldrich) were evaluated using Z factor. The Z factor was calculated by the following equation: 1(3SD.sub.s+3SD.sub.p)/|.sub.s.sub.p|. In the equation, SD.sub.s and SD.sub.p represent standard deviations of a sample and a positive control (without LPS), and .sub.s and .sub.p represent averages of FP values obtained from the sample and the positive control (without LPS), respectively.

(31) As shown in Table 1 and FIG. 2B, His-Cys-CARD showed the highest labeling efficiency (about 86%), showed the largest difference in polarization signal, and showed a sigmoidal FP binding curve with increasing fluorescence intensity. The K.sub.d.sup.app value determined for ALEXA FLOUR 488-CARD and LPS was 2.20.2 M when 50 nM ALEXA FLOUR 488-CARD was used (FIG. 2E).

(32) Therefore, it was confirmed that ALEXA FLUOR 488-labeled His-Cys-CARD (ALEXA FLOUR 488-CARD) had a detectable wide window for the binding between CARD and LPS, and thus ALEXA FLOUR 488-CARD was selected as a tracer for high-throughput inhibitor screening assays.

(4) Optimization of FP Analysis Method for Application to High-Throughput Inhibitor Screening Assay

(33) To optimize high-throughput screening (HTS) of inhibitors, additives, incubation time, pH, and DMSO concentrations were optimized.

(34) An FP binding curve from FP values measured with buffer C (50 mM Tris-HCl pH 7.0, 150 mM NaCl) supplemented with additives such as 0.1 mg/mL BSA, 0.01% NP-40, or 1 mM MC (MgCl.sub.2+CaCl.sub.2) is shown in FIG. 3A. An FP binding curve from FP values measured by incubating ALEXA FLOUR 488-CARD serially diluted with buffer C for 0.5 hours to 4 hours is shown in FIG. 3B (grey area: range of 20 nM to 50 nM). An FP binding curve from FP values measured with buffers of different pHs is shown in FIG. 3C. An FP binding curve from FP values measured by incubating different concentrations of LPS-Ra in buffer C for 0.5 hours to 4 hours is shown in FIG. 3D. An FP binding curve from FP values measured with buffer C supplemented with different concentrations of DMSO is shown in FIG. 3E. In addition, LPS-Ra concentration-dependent Z factor was evaluated in buffer C supplemented with 0% to 10% DMSO. Unless otherwise mentioned, reactions were incubated at 37 C. for 1 hour.

(35) As shown in FIG. 3A, the binding of CARD and LPS was inhibited by the presence of BSA, NP-40, or divalent cations. Based on the results of FIGS. 3B to 3D, the assay was set up with use of 50 nM ALEXA FLUOR 499-CARD at pH 7.0, 150 mM NaCl, and 37 C. In addition, as shown in FIGS. 3E and 3F, as the concentration of DMSO increased, the dynamic range of the FP value slightly decreased, but the K.sub.d.sup.app value maintained in the similar range up to 10% DMSO, and 1.6 M of LPS-Ra was selected as a minimum concentration to yield a Z coefficient of 0.7, which is a statistical cutoff value providing reproducible separation between target and control within a wide range of DMSO concentrations.

(5) Screening for Inhibitor of Binding of CARD and LPS

(36) After constructing HTS, a library of 1,443 FDA-approved drugs was screened to select hit compounds inhibiting 50% of FP signal.

(37) For the HTS method, 0.8 L of FDA-approved drug (2.5 mM in DMSO, Selleckchem) was added to each well of a 96-well plate containing 50 nM tracer and 1.6 M LPS-Ra using a pipetting device (Mosquito, sptlabtech) to prepare a final volume of 200 L per well. Each plate contained a negative control (DMSO with LPS) and a positive control (DMSO without LPS). FP was measured using APPLISKAN after incubation at 37 C. for 1 hour. A final inhibition rate was calculated by the following equation: inhibition rate (%)=100((mP.sub.negativemP.sub.test compound)/(mP.sub.negativemP.sub.positive)). In the equation, mP.sub.negative represents an FP value of a negative control, mP.sub.positive is an FP value of a positive control, and mP.sub.test compound is an FP value of a sample containing a test compound. The 50% inhibition rate was arbitrarily chosen as a threshold.

(38) The results of screening by the HTS method are shown in FIG. 4. Among the hit compounds, 32 compounds were selected (hit rate: about 2.2%), excluding 25 pan-assay interference compounds (PAINS) and fluorescence quenchers.

(39) IC.sub.50 value of each hit compound was determined using an FP competition assay in the presence of the hit compound serially diluted from 50 M to 0.022 M with 6.4 M (about twice the K.sub.d.sup.app value) of LPS-Ra and 0 nM of ALEXA FLOUR 488-CARD. In detail, the FP competition assay was performed by mixing 50 nM of tracer, 6.4 M of LPS-Ra, and 3-fold serially diluted hit compound (50 M to 0.022862 M) in buffer C. The mixture was incubated at 37 C. for 1 hour before measurement. FP values were expressed as a function of compound concentrations, and IC.sub.50 values were obtained from a sigmoidal curve fit, as analyzed in GRAPHPAD PRISM 8.

(40) As shown in FIGS. 5A to 5C, 9 compounds (C-5: Crystal violet, C-6: Mitoxantrone, C-19: Entrectinib, C-15: Sotrastaurin, C-11: Eltrombopag Olamine, C-13: Enzastaurin, C-7: Eltrombopag, C-16: Ceritinib, C-8: Ethacridine lactate) out of 32 compounds showed FP signal decreases in a concentration-dependent manner within the IC.sub.50 value of M level.

(6) Inhibition of Casp-4 Activity by Screened Compounds

(41) Autolytic activation of Casp-4 requires interaction with cytoplasmic LPS, and therefore, it was examined whether, when a hit compound inhibits the interaction between LPS and CARD, subsequent Casp-4 activation and its catalytic activity are inhibited by the hit compound.

(42) Genes, each encoding a wild-type Casp-4 or a C258A-Casp-4 inactive variant, were cloned into KpnI and XbaI restriction sites of a p3FLAG-CMV-10 vector. HEK293T cells cultured in a DMEM medium (Welgene) supplemented with 10% (v/v) heat-inactivated FBS (Gibco), 100 U/mL penicillin and 100 U/mL streptomycin were transfected with each construct using LIPOFECTAMINE 2000 (ThermoFisher). 24 hours after transfection, cells were re-inoculated into a black, flat-bottomed 96-well culture dish (SPL life sciences) at a density of 10.sup.5 cells per well. After incubation for 2 hours for cell adhesion, the culture supernatant was replaced by an activity assay buffer [(0.01% (w/v) digitonin(Sigma-Aldrich), 10 mM DTT, 100 M Ac-WEHD-AMC(Enzo-life science), 10 M LPS-Ra, and 50 M of the hit compound, or buffer C supplemented with an equal volume of DMSO]. For the assay of active Casp-4 (p20/p10), 1 M of purified p20/p10 was assayed using the same assay buffer. Hydrolysis of fluorescent 7-amino-4-methylcoumarin (AMC, Sigma-Aldrich) was monitored with APPLISKAN at room temperature using 326 nm excitation and 460 nm emission filters at the predetermined time intervals. The amount of free AMC hydrolyzed by Casp-4 was calculated using a standard curve prepared with AMC serially diluted with the assay buffer containing each hit compound.

(43) Activities of the full-length Casp-4 and activated p20/p10 Casp-4 in the presence of LPS (activator) with or without the screened compound (inhibitor) are shown in FIGS. 6A to 6C.

(44) As shown in FIG. 6A, Casp-4 or C258A-Casp-4 had no activity in the absence of LPS, whereas the activity of Casp-4 dramatically increased in the presence of LPS. Based on this, the Casp-4 inhibitory effects of 9 hit compounds were examined, and the results are shown in FIG. 6B. DMSO as a negative control and LPS-sequestering antibiotic polymyxin B (PMB) as a positive control were used. As shown in FIG. 6B, 4 hit compounds out of 9 hit compounds inhibited Casp-4 activity by 50% or more at a concentration of 50 M. However, when activated Casp-4 (P20/p10) was used, the Casp-4 inhibitory effect by the compound was not identified (FIG. 6C).

(45) Therefore, it was found that it is possible to screen inhibitors specifically inhibiting the binding of LPS and CARD, thereby inhibiting the activity of Casp-4, through the established HTS method, in order to develop drugs for treatment of inflammation and sepsis caused by LPS.

(46) According to the method of screening an inhibitor of caspase activity by lipopolysaccharide and the method of screening a therapeutic agent for inflammatory diseases or sepsis using the same, a caspase-4-specific inhibitor may be developed.

(47) It should be understood that embodiments described herein should be considered in a descriptive sense only and not for purposes of limitation. Descriptions of features or aspects within each embodiment should typically be considered as available for other similar features or aspects in other embodiments. While one or more embodiments have been described with reference to the figures, it will be understood by those of ordinary skill in the art that various changes in form and details may be made therein without departing from the spirit and scope of the disclosure as defined by the following claims.