Surface Plasmon Resonance Based Enzymatic Assay

High-throughput assays for screening potential inhibitors of proteases are known. An example of such an assay is the scintillation proximity assay (SPA). SPA technology involves the use of beads coated with scintillant. Bound to the beads are acceptor molecules such as antibodies, receptors or enzyme substrates which interact with ligands or enzymes in a reversible manner.

For a typical protease assay the substrate peptide is biotinylated at one end and the other end is radiolabelled with low energy emitters such as .sup.125 I or .sup.3 H. The labeled substrate is then incubated with the enzyme. Avidin coated SPA beads are then added which bind to the biotin. When the substrate peptide is cleaved by the protease, the radioactive emitter is no longer in proximity to the scintillant bead and no light emission takes place. Inhibitors of the protease will leave the substrate intact and can be identified by the resulting light emission which takes place in their presence.

The SPA assay works well. However, labeling of the substrate could result in inactivation of the substrate. In addition, radiolabeled emitters may pose both health and environmental concern. Therefore there is a need for producing a high-throughput assay which does not require the use of radioactive substances.

The present invention fills this need by providing for a method for determining if a substrate is cleaved by an enzyme using surface plasmon resonance. According to the process of the present invention, the substrate and the protease are placed together in solution in a reaction vessel under conditions wherein the protease can cleave the substrate after which the reaction is stopped. The solution containing the protease and substrate are then brought into contact with a ligand bound to a sensor chip, wherein the ligand is able to bind to the substrate, and wherein the mass of the intact substrate versus the mass of the cleaved substrate is detected by surface plasmon resonance technology.

The present invention is further comprised of a method of determining if a test substance is a protease inhibitor. The test substance is placed in solution in the reaction vessel with the protease and the substrate. The solution containing the protease, substrate and test substance are then brought into contact with a ligand bound to a sensor chip, wherein the ligand is able to bind to the substrate, and wherein the mass of the substrate versus the mass of the cleaved substrate is detected by surface plasmon resonance technology. If the substrate is cleaved as determined by its decrease in mass as detected by surface plasmon resonance technology then the test substance is not a protease inhibitor. On the other hand if the substrate is a protease inhibitor, then the substrate does not have a decrease in mass as is determined by surface plasmon resonance.

FIG. 1 schematically depicts the HCV genome.

FIG. 2 depicts the recombinant synthesis of plasmid pBJ1015.

FIG. 3 depicts the recombinant synthesis of plasmid pTS56-9.

FIG. 4 depicts the recombinant synthesis of plasmid pJB1006.

FIG. 5 depicts the recombinant synthesis of plasmid pBJ1022.

FIG. 6 depicts the recombinant synthesis of plasmid pNB(-V)182.DELTA.4AHT.

FIG. 7 depicts the recombinant synthesis of plasmid pT5His/HIV/183.

FIG. 8 schematically depicts a high throughput assay for determining if a substrate is cleaved by an HCV protease or discovering HCV protease inhibitors using surface plasmon resonance technology.

FIG. 8A illustrates the outcome expected in the absence of an uninhibited HCV protease, while

FIG. 8B illustrates the outcome expected in the presence of an active HCV protease.

FIG. 9 schematically depicts a high throughput assay for determining if a substrate is cleaved by a CMV protease or discovering CMV protease inhibitors using surface plasmon resonance technology.

FIG. 9A illustrates the outcome expected in the absence of an uninhibited CMV protease, while

FIG. 9B illustrates the outcome expected in the presence of an active CMV protease.

A novel, high throughput enzymatic assay utilizing the surface plasmon resonance technology (SPR) has been successfully developed. Using this assay, and a dedicated BIAcore.TM. instrument, at least 1000 samples per week can be screened for either their enzymatic activity or their inhibitory effects toward the enzymatic activity, in a 96 well plate format. This methodology is readily adaptable to any enzyme-substrate reaction. We have successfully used this methodology to develop high throughput assays for CMV and HCV proteases. The advantage of this assay over the currently available SPA assay is that it does not require a radiolabeled peptide substrate.

BIAcore.TM. is a processing unit for Biospecific Interaction Analysis. The processing unit integrates an optical detection system with an autosampler and a microfluidic system. BIAcore.TM. uses the optical phenomena, surface plasmon resonance to monitor interaction between biomolecules. SPR is a resonance phenomenon between incoming photons and electrons on the surface of thin metal film. Resonance occurs at a sharply defined angle of incident light. At this angle, called the resonance angle, energy is transferred to the electrons in the metal film, resulting in a decreased intensity of the reflected light. SPR response depends on a change in refractive index in the close vicinity of the sensor chip surface, and is proportional to the mass of analyte bound to the surface. BIAcore continuously measure the resonance angle by a relative scale of resonance units (RU) and displays it as an SPR signal in a sensorgram, where RU are plotted as a function of time.

In addition, BIAcore.TM. uses continuous flow technology. One interactant is immobilized irreversibly on the sensor chip, comprising of a non-crosslinked carboxymethylated dextran providing a hydrophilic environment for bimolecular interaction. Solution containing the other interactant flow continuously over the sensor chip surface. As molecules from the solution bind to the immobilized ligand, the resonance angle changes resulting in a signal registered by the instrument.

In contrast to many current high throughput assays based on technologies that require radiolabeling of one of the reactants studied, in BIAcore.TM. no need for radiolabelling exists. This important advantage allows for development of assays for studying reactions where labeling of one of the component is either not feasible or would interfere with the true interaction of biomolecules targeted for screening.

Since the commercial availability of the BIAcore.TM., the surface plasmon resonance technology has been extensively and primarily been used to study the interaction of biomolecules i.e. protein-protein, protein-DNA, protein-antibody, peptide-antibody, etc. in real time. To our knowledge, there are currently no published methodologies for use of the SPR technology, specifically in a high throughput fashion for following the extent of enzyme-substrate reaction, determination of catalytic activity of enzymes, determination of enzyme kinetics and ultimately screening for inhibitors of enzymatic activity. Here, we disclose a novel methodology which when used in conjunction with SPR technology allows for rapid screening of inhibitors of enzymatic activity. In this methodology, the enzymatic reactions are carried out outside of the BIAcore, i.e. in reaction tubes or 96-well tissue culture plates, as it is conventionally done for any of the currently available high throughput assays. The SPR is only used as a detection means for determination of the amount of an intact substrate remaining in a solution with and without the enzyme after the reaction is quenched.

In order to measure the amount of the intact substrate prior to the addition of enzyme, a means of capturing the substrate onto the sensor chip had to be established. In addition, to satisfy the requirement for a high throughput assay on the BIAcore, the substrate needed to be removed from the surface subsequent to completion of analysis. This is required since the same surface will be used for the subsequent reactions. To accomplish these two requirements, a phosphotyrosine is synthetically attached to one end of the substrate. The phosphotyrosine was chosen due to the commercial availability of an anti-phosphotyrosine monoclonal antibody. The antibody is covalently attached to the sensor chip by standard amine coupling chemistry. The anti-phosphotyrosine antibody, bound permanently to the chip is used to capture the phosphotyrosine-containing substrate in a reversible manner. The antibody-phosphotyrosine interaction is ultimately used to capture and release the peptide substrate when desired by regeneration of the surface with various reagents i.e. 2 M MgCl.sub.2.

Introduction of the intact peptide onto the antibody surface results in a larger mass which is detected by the instrument. To follow the extent of peptide cleavage, a mixture of peptide substrate and enzyme is incubated for the desired time and then quenched. Introduction of this mixture containing the cleaved peptide and the intact peptide to a regenerated antibody surface results in a lower mass value than that detected for a sample containing only intact peptide. The difference in the two values is then used to calculate the exact amount of intact peptide remaining after cleavage by the enzyme.

Although the reduction in mass can be directly followed with many large substrates, due to the small mass of a typical synthetic peptide substrate (10-20 amino acids, 1-3 Daltons), the mass difference, and thus the signal difference between the intact and cleaved peptide is very small within the signal to noise ratio of the instrument. To circumvent this low sensitivity, we synthesized a biotin molecule on the N-terminal of the peptide. By addition and thus tagging of peptide with streptavidin prior to injection of tagged peptide onto the antibody surface of the chip, the signal due to the presence of streptavidin will be higher. Using this approach, a cleaved peptide lacking the N-terminal half, tagged with streptavidin will result in a much lower signal.

The following examples are included to illustrate the present invention using hepatitis C protease and its substrates and the cytomegalovirus protease and its substrates.

The present example illustrates a method for determining if a compound can be useful as an HCV protease inhibitor using the surface plasmon resonance assay. FIGS. 8A, 8B, 9A and 9B. illustrate the technique.

Procedure for Coupling Anti-phosphotyrosine Mab to the Sensor Chip

The anti-phosphotyrosine Mab is coupled to the carboxymethylated dextran surface of a sensor chip in the following manner. The flow rate used throughout the coupling procedure is 5 .mu.l/min. The surface is first activated with a 35 .mu.l injection of NHS/EDC (N-hydroxysuccinimide/N-dimethyllaminopropyl-N'-ethylcarbodiimide-HCl). This is followed by a 40 ml injection of Mab 4G10 at 50 .mu.g/ml in 10 mM sodium acetate buffer, pH=4.0. Any remaining activated esters are then blocked by the injection of 35 .mu.l of 1 M ethanolamine. These conditions result in the immobilization of approximately 7,500 response units (420 .mu.M) of antibody.

Binding of Peptide and Regeneration of Mab 4G10 Surface

The flow rate used throughout the BIAcore analysis run is 5 .mu.l/min. A 4 .mu.l injection containing streptavidin-tagged peptide (peptide concentration at 2 .mu.M, streptavidin binding sites concentration at 9 .mu.M) is carried out. The amount of streptavidin-tagged peptide bound to the antibody surface (in response units) is measured 30 seconds after the injection is complete.

Regeneration of sensor chip surface

Regeneration of the Mab 4G10 surface is achieved using a 4 .mu.l pulse of 2 M MgCl.sub.2 after each peptide injection. Surfaces regenerated up to 500 times still showed 100% binding of tagged peptide.

Determination of the Optimal Concentration of Peptide and Streptavidin

To determine the optimal peptide concentration, a standard curve was generated using various amounts of peptide (0-10 .mu.M) in the presence of excess streptavidin. A value in the linear range, 2 .mu.M, was chosen for standard assay conditions.

The amount of streptavidin required to completely tag the peptide was determined using a peptide concentration of 2.5 .mu.M and titrating the amount of streptavidin (.mu.M of binding sites). All the peptides were shown to be completely tagged when streptavidin concentrations greater than 3 .mu.M (approximately equimolar to the peptide concentration) were used. A streptavidin concentration of 9 .mu.M (a 4.5 fold excess) was chosen for standard assay conditions.

The HCV protease 5A/5B peptide substrate, DTEDVVACSMSYTWTGK (SEQ ID NO 18), with phosphotyrosine at the C-terminal and biotin at the N-terminal is synthesized. Anti-phosphotyrosine monoclonal antibody, 4G10 was coupled to the sensor chip.

In the absence of HCV protease, the intact streptavidin-tagged biotinylated phosphotyrosine peptide results in a large signal (large mass unit/large response units) through its interaction with the anti-phosphotyrosine monoclonal antibody.

The protease-catalyzed hydrolysis of the phosphotyrosine-biotinylated peptide was carried out in a 96 well plate. The reaction was stopped with an equal volume of the quenching buffer containing mercuribenzoate. Streptavidin was added to tag the peptide which binds to the biotin. The cleaved peptide which lacks the tagged streptavidin (less mass) results in the loss of response units.

Using this assay, numerous compounds can be tested for their inhibitory activity since the antibody surface can be regenerated repetitively with 2 M MgCl.sub.2.

The peptide cleavage activity by HCV protease can be monitored in a time dependent manner using the BIAcore-based methodology. Using the concentrated enzyme and the BIAcore substrate, Biotin-DTEDVVAC SMSYTWTGK-pY (SEQ ID NO 17), 50% substrate cleavage is achieved within 1 hour using the BIAcore-based HCV assay. Based on the amount of enzyme, His-NS3(183).DELTA.4AHT needed to reach a 50% cleavage within 2 hours, a time scale desired for a development of a high throughput assay, we estimate that 1 liter of fermentation of the His-NS3(183).DELTA.4AHT construct results in enough protease to run at least 100 reactions on the BIAcore.

Reactions are prepared in a 96-well tissue culture plate using the Reaction Buffer (50 mM HEPES, pH 7.4, 20% glycerol, 150 mM NaCl, 1 mM EDTA, 0.1% Tween-20,1 mM DTT ) as diluent. The final reaction volume is 100 .mu.l. Sample with the peptide alone (Biotin-DTEDVVAC SMSYTWTGKpY) is prepared by addition of 10 .mu.l of peptide stock at 100 .mu.M (prepared in the reaction buffer) to 90 .mu.l of reaction buffer, so that the final concentration of peptide is 10 .mu.M. Samples comprised of peptide and the enzyme are prepared by addition of 10 .mu.l of peptide stock at 100 .mu.M and 10 .mu.l of partially purified His-NS3 (183)-.DELTA.4A-HT stock at 1.7 mg/ml (both prepared in the reaction buffer) to 80 .mu.l of reaction buffer, so that the final concentration of peptide and the enzyme is 10 and 0.1 .mu.M respectively. The reaction is held at 30.degree. C. for the specified time and then quenched. Quenching is achieved by transferring a 20-.mu.l aliquot of the reaction mixture to a new tissue culture plate containing an equal volume of PMB Quenching Buffer (50 mM HEPES, pH 7.8, 150 mM NaCl, 5 mM P-Hydroxymercuribenzoic Acid, and 13 mM EDTA).

To prepare the quenched reaction mixture for injection onto the sensor surface, 30 .mu.l PMB BIAcore Buffer (50 mM HEPES, pH 7.4, 1 M NaCl) and 30 .mu.l of streptavidin at 0.5 mg/ml in water is added to the 40 .mu.l of the quenched reaction mixture to a final volume of 100 .mu.l. In this step, all the peptides are tagged with streptavidin prior to the injection of samples. Finally, 4 .mu.l of this sample is injected over the antiphosphotyrosine surface for determination of the intact versus cleaved peptide. The final concentration of peptide and the streptavidin in the BIAcore sample is 2 and 9 .mu.M respectively.

Experimental Conditions:

Reactions are prepared in a 96-well tissue culture plate using the Reaction Buffer (50 mM HEPES, pH=7.4,25% Glycerol, 1 mM DTT) as diluent. The final reaction volume is 100 .mu.L. Sample with the peptide alone (Biotin-RGVVNA SCRLAKY (SEQ ID NO: 31) is prepared by addition of 10 .mu.l of peptide stock at 100 mM (prepared in the reaction buffer) to 90 .mu.l of reaction buffer, so that the final concentration of peptide is 10 .mu.M. Samples comprised of peptide and the enzyme are prepared by addition of 10 .mu.l of peptide stock at 100 .mu.M and 10 .mu.l of enzyme stock at 1 mM (both prepared in the reaction buffer) to 80 .mu.l of reaction buffer, so that the final concentration of peptide and the enzyme is 10 and 0.1 .mu.M respectively. The reaction is held at 25.degree. C. for the specified time and then quenched. Quenching is achieved by transferring a 20-.mu.l aliquot of the reaction mixture to a new tissue culture plate containing an equal volume of PMB Quenching Buffer (50 mM HEPES, pH 7.8, 150 mM NaCl, 5 mM p-Hydroxymercuribenzoic Acid, and 13 mM EDTA).

To prepare the quenched reaction mixture for injection onto the sensor surface, 30 .mu.l PMB BIAcore Buffer (50 mM HEPES, pH 7.4, 1 M NaCl) and 30 .mu.l of streptavidin at 0.5 mg/ml in water is added to the 40 .mu.l of the quenched reaction mixture to a final volume of 100 .mu.l. In this step, all the peptides are tagged with streptavidin prior to the injection of samples. Finally, 4 .mu.l of this sample, is injected over the antiphosphotyrosine surface for determination of the intact versus cleaved peptide. The final concentration of peptide and the streptavidin in the BIAcore sample is 2 and 9 .mu.M respectively.

I. Comparison of HPLC and BIAcore Methodology

A set of CMV protease reaction samples were analyzed by both standard HPLC methodology and the above described BIAcore based method. Values for the amount of intact peptide substrate remaining at each time point were determined using both methods. The extent of enzyme catalysis as measured by the BIAcore method were identical to that measured by the standard HPLC method typically used in the field of enzyme catalysis.

HPLC Substrate: A-G-V-V-N-A-S-S-R-L-A (SEQ ID NO: 32)

BIAcore Substrate: (Biotin)-R-G-V-V-N-A-S-S-R-L-A-K-(pY) (SEQ ID NO: 31)

Substrate concentration: 100 .mu.M

Enzyme:

CMV Protease See Baum, Ellen et al., J. Virology January 1993 pages 497-506.

A. Refolded wild type: 0.5 .mu.M

Time points: 10, 20, 30, 45, 70, and 100 min

Temperature: 25.degree. C.

Reaction conditions:

50 mM HEPES, pH 7.5

150 mM NaCl

1 mM DTT

25% glycerol

II. Determination of kinetic parameters for the hydrolysis of CMV maturation site substrate by various human CMV protease forms

HCMV protease activity was determined by monitoring the cleavage of the peptide using the BIAcore-based methodology as described. The concentration of peptides used for the calculation of kinetics parameters was determined by amino acid composition analysis. 12 different concentrations of substrate, from 10 .mu.M to 3.2 mM were used for k.sub.m calculation (see below). Hydrolysis at each peptide concentration was monitored at six different time points (see below). A total of 96 samples were processed in a 96 well-plate format in 12 hours for determination of kinetic parameters for each enzyme. Kinetic parameters (km, V.sub.max, K.sub.cat) were determined by fitting directly the velocity (initial rates at <15% of the total substrate hydrolysis) versus substrate concentration data to Michaelis-Menton equation using both BIAevaluation program (Pharmecia Biosensor) and K.cat program (BioMetallics, Inc.).

Substrate: A-G-V-V-N-A-S-S-R-L-A (SEQ ID NO: 32)

Enzyme concentration:

Substrate concentration: 10, 13, 16, 22, 35, 60, 110, 210, 410, 810, 1610, 3210 .mu.M

Time points: 1, 5, 10, 15, 20, 25 min

Temperature: 22.degree. C.

Reaction conditions:

50 mM HEPES, pH 7.5

150 mM NaCl

1 mM DTT

25% glycerol

III. Validation of Enzyme Kinetics and Inhibition Determined Using BIAcore-based CMV Assay

A. Effect of Enzyme Concentration and Time of Reaction on Cleavage of Native Peptide Substrate

Experimental Conditions:

Summary:

Using the native substrate, cleavage of the substrate is linear with respect to protease concentration (within the 0.02 to 0.08 .mu.M range) and time (within 1 to 4 hour range). A standard BIAcore-based CMV assay using the native substrate is carried out for 2 hours at 0.06 .mu.M resulting in 50% cleavage of the substrate.

B. Effect of Enzyme Concentration and Time of Reaction on Cleavage of P2' Serine Analog Substrate

Experimental Conditions:

Summary:

Using the serine substrate, cleavage of the substrate is linear with respect to protease concentration (within the 0.1 to 0.5 .mu.M range) and time (within 1 to 4 hour range). A standard BIAcore-based CMV assay using the serine analog is carried out for 2 hours at 0.5 .mu.M resulting in 50% cleavage of the substrate.

C. Effect of Substrate Concentration on Rate of Hydrolysis

Experimental Conditions:

Summary:

The rate of hydrolysis of CMV peptide substrate is linear with respect to substrate concentrations up to 60 .mu.M. The concentration of substrate used in a standard BIAcore-based assay is 10 .mu.M.

D. Effect of Dithiothreitol on CMV Protease Activity

Experimental Conditions:

Protease:

1. Break cells in the presence of DTT

2. Purify supernatant on Anion Exchange Column in the presence of DTT

3. Purify protease on Phenyl Sepharose with and without DTT.

Summary

The CMV protease, purified in the absence of DTT lacks catalytic activity as judged in a 20-hour assay as compared to an active preparation, purified in the presence of DTT. Addition of DTT to the inactive protease results in a complete reactivation of the protease. Thus, presence of DTT in the CMV assay is essential for the catalytic activity of CMV protease.

E. Minimum Requirement of DTT for CMV Protease Activity

Experimental Conditions:

A stock preparation of CMV protease, purified entirely in the presence of DTT, and subsequently stored with DTT (final concentration=2 mM) was used. For the assay, titration of DTT from 800 .mu.M down to 4 .mu.M was carried out so that the final concentration of enzyme in all reaction was 0.04 .mu.M. All reactions were stopped at various times (1, 2, 3, and 4 hours) by addition of equal volume of 5 mM mercuribenzoate.

Summary:

A 200-fold reduction of DTT concentration from 800 .mu.M to 4 .mu.M lowers the percent cleavage of the native substrate by only 12% at 2 hours, a time period for a standard BIAcore assay resulting in a 50% cleavage of the substrate. This reduction in percent cleavage can easily be recovered by increasing the time of the reaction from 2 to 3 hours. Thus currently, the BIAcore based CMV assay can be carried out at DTT concentration as low as 4 .mu.M. By increasing the time of the reaction, concentration of DTT may further be lowered if desired.

F. CMV Protease Inhibition Study with Compound 33277-129-2 assayed in the presence of 4 and 800 .mu.M DTT using BIAcore-based CMV Assay

Experimental Conditions:

Summary:

The compound 33277-129-2 is shown to inhibit the CMV protease activity by 40% at .about.12 .mu.M and 60% at .about.100 .mu.M in the presence of 4 .mu.M DTT. The percent inhibition by this compound is lowered to 33% at 12 .mu.M and 40% at 100 .mu.M in the presence of 800 mM DTT.

IV. Competitive Inhibition of CMV Protease Activity by Maturation Site Peptide Analogs Monitored on BIAcore

The apparent affinity (km) of the purified double mutant form of CMV protease, A143V/V209A for the maturation site peptide, AGVVNASSRLA (P2' serine analog) was determined to be 900 .mu.M at 22.degree. C. using the BIAcore-based CMV assay (Table 1).

Various analogs of this substrate were then characterized in order to further define the amino acids crucial for hydrolysis versus those involved in enzyme binding. To address this issue, the interaction of native maturation site peptide (GVVNASCRLA) and four of its mutant analogs with the enzyme were studied by both directly monitoring the hydrolysis of each peptide by the enzyme on the HPLC, and the competition of each peptide with the biotinylated native substrate using the CMV assay developed on the BIAcore.

The HPLC results indicate that three out of four analogs tested (analogs A, C, D) were not hydrolyzed by the enzyme as monitored on HPLC. Two of the three non-hydrolyzable peptides (analogs A, D) were synthesized with only a single amino acid mutation where as analog C was synthesized so two of its amino acids were mutated to two non-native amino acids.

The mechanism behind the loss of hydrolysis for analog A and C versus analog D was deciphered by the competition studies carried out using the BIAcore-based CMV assay. The results of this assay show that the peptide substrate analogs A and C retain their binding ability to the enzyme but they are not hydrolyzed. These peptides inhibited the enzyme activity by competing with the biotinylated native substrate with a similar IC-50 to that of the native peptide (IC-50.sub.native .about.1 mM; IC-50.sub.mutants .about.1.5 mM). On the other hand, the results of the competition assay indicate that the lack of any observed hydrolysis for the peptide substrate analog D (as monitored on HPLC) is due to the loss of its binding ability to the enzyme as this peptide is not capable of competing with the biotinylated native peptide as detected on the BIAcore.

A. Plasmid constructions.

Several plasmids were designed and constructed using standard recombinant DNA techniques (Sambrook,Fritsch & Maniatis) to express the HCV protease in E. coli (FIG. 2-7). All HCV specific sequences originated from the parental plasmid pBRTM/HCV 1-3011 (Grakoui et al.1993). To express the N-terminal 183 amino acid versions of the protease, a stop codon was inserted into the HCV genome using synthetic oligonucleotides (FIG. 3). The plasmids designed to express the N-terminal 246 amino acid residues were generated by the natural Nco1 restriction site at the C-terminus.

i) Construction of the plasmid pBJ1015 (FIG. 2)

The plasmid pBRTM/HCV 1-3011 containing the entire HCV genome (Grakoui A., et al., J. Virol. 67: 1385-1395) was digested with the restriction enzymes Sca I and Hpa I and the 7138 bp (base pair) DNA fragment was isolated and cloned to the Sma I site of pSP72 (Promega) to produce the plasmid, pRJ201. The plasmid pRJ 201 was digested with Msc I and the 2106 bp Msc I fragment was isolated and cloned into the Sma I site of the plasmid pBD7. The resulting plasmid pMBM48 was digested with Kas I and Nco I, and the 734 bp DNA fragment after blunt ending with Klenow polymerase was isolated and cloned into Nco I digested, klenow polymerase treated pTrc HIS B seq expression plasmid (Invitrogen). The ligation regenerated a Nco I site at the 5' end and Nsi I site at the 3' end of HCV sequence. The plasmid pTHB HCV NS3 was then digested with Nco I and Nsi I, and treated with klenow polymerase and T4 DNA polymerase, to produce a blunt ended 738 bp DNA fragment which was isolated and cloned into Asp I cut, klenow polymerase treated expression plasmid pQE30 (HIV). The resulting plasmid pBJ 1015 expresses HCV NS3 (246 amino acids) protease.

(ii) Construction of the plasmid pTS 56-9 with a stop codon after amino acid 183 (FIG. 3)

The plasmid pTHB HCV NS3 was digested with Nco I, treated with klenow polymerase, then digested with Bst Y I; and the DNA fragment containing HCV sequence was isolated and cloned into Sma I and Bgl II digested pSP72. The resulting plasmid pTS 49-27 was then digested with Bgl II and Hpa I and ligated with a double stranded oligonucleotide:

to produce pTS 56-9.

Thus, a stop codon was placed directly at the end of DNA encoding the protease catalytic domain of the NS3 protein. This enabled the HCV protease to be expressed independently from the helicase domain of the NS3 protein.

(iii) Construction of the plasmid pjB 1006 Fused with a peptide of positively charged amino acids at the carboxy terminus of NS3 183 (FIG. 4).

The plasmid pTS 56-9 was digested with Sph I and Bgl II and the DNA fragment containing HCV sequence was isolated and cloned into a Sph I, Bgl II cut pSP72. The resulting plasmid pJB 1002 digested with Age I and HpaI and ligated to a double stranded oligonucleotide,

to construct pJB 1006. This fused the hydrophilic, solubilizing motif onto the NS3 protease.

(iv) Construction of the plasmid pBJ 1022 expressing His-NS3(183)-HT in E.coli (FIG. 5)

The plasmid pJB 1006 was digested with NgoM I and Nhe I and the 216 bp DNA fragment was isolated and cloned into Ngo M I, Nhe I cut pBJ 1015 to construct plasmid pBJ 1019. The plasmid pBJ 1019 was digested with Nar I and Pvu II, and treated with Klenow polymerase to fill in 5' ends of Nar I fragments. The expression plasmid pQE31 (Invitrogen) was digested with BamH I, blunt ended with Klenow polymerase. The 717 bp Nar I- Pvu II DNA fragment was isolated and ligated to the 2787 bp BamH I/Klenowed--Msc I (Bal I) fragment of the expression plasmid pQE31 (Invitrogen). The recombinant plasmid, pBJ 1022, obtained after transformation into E.coli expresses His NS3(2-183)-HT which does not contain any HIV protease cleavage site sequence. The plasmid also contains a large deletion in the CAT (Chloramphenicol Acetyl Transferase) gene.

(v) Construction of the plasmid pNB(-V)182-.DELTA.4A HT (FIG. 6)

The plasmid pMBM 48 was digested with Eag I and Xho I, treated with Klenow polymerase and the 320 bp DNA fragment was isolated and cloned into BamH I cut, blunt ended pSP 72 to construct the plasmid pJB1004. The 320 bp fragment encodes 7 amino acid from carboxy terminal of NS3(631), all of NS4A, and the amino terminal 46 amino acid of NS4B. The recombinant plasmid pJB1004 was digested with Eag I and Cel 2, blunt ended with Klenow polymerase. The 220 bp DNA fragment was isolated and cloned into the expression plasmid pQE30 which was digested with BamH I and blunt ended with Klenow polymerase prior to ligation. The resulting plasmid pJB 1011 was digested with NgoM I and Hind III and ligated to a double stranded oligonucleotide,

to construct the plasmid pNB 4A HT. The plasmid pNB 4AHT was digested with Msl I and Xba I. The 1218 bp DNA fragment was isolated and cloned into Age I cut, klenow polymerase treated, Xba I cut vector DNA of pBJ 1019. The ligation results in a substitution of the 183rd amino acid residue valine by a glycine residue in NS3, and a deletion of amino terminal three amino acid residues of NS4A at the junction. The recombinant plasmid pNB182.DELTA.4A HT comprising NS3(182aa)-G-NS4A(4-54 amino acid) does not contain NS3/NS4A cleavage site sequence at the junction and is not cleaved by the autocatalytic activity of NS3. Finally the plasmid pNB182.DELTA.4A HT (SEQ ID NO 8) was digested with Stu I and Nhe I, the 803 bp DNA fragment was isolated and cloned into Stu I and Nhe I cut plasmid pBJ 1022. The resulting plasmid pNB(-V)182-.DELTA.4A HT contains a deletion of the HIV sequence from the amino terminus end of the NS3 sequence and in the CAT gene (SEQ ID NO 27).

(vi) Construction of the plasmid pT5 His HIV-NS3 (FIG. 7)

The plasmid pTS56-9 was digested with Bgl II, and treated with Klenow polymerase to fill in 5' ends. The plasmid was then digested with NgoM I and the blunt ended Bgl II/NgoMI fragment containing the NS3 sequence was isolated and ligated to the SglI, Klenow treated NgmMI cut and Sal I klenowed pBJ 1015. The resulting plasmid is designated pT5His HIV 183.

Purification of His182HT (SEQ ID NO 4) and His (-V)182.DELTA.4AHT (SEO ID NO 8)

The recombinant plasmids pBJ1022 and pNB(-V)182.DELTA.4A were used to transform separate cultures of E. coli strain M15 [pREP4] (Qiagen), which over-expresses the lac repressor, according to methods recommended by the manufacturer. M15 [pREP4] bacteria harboring recombinant plasmids were grown overnight in broth containing 20 g/L bactotrypton, 5 g/L bacto-yeast extract, 10 g/L NaCl and supplemented with 100 .mu.g/ml ampicillin and 25 .mu.g/ml kanamycin. Cultures were diluted down to O.D.600 of 0.1, then grown at 30.degree. C. to O.D.600 of 0.6 to 0.8, after which IPTG was added to a final concentration of 1 mM. At post-induction 2 to 3 hours, the cells were harvested by pelleting, and the cell pellets were washed with 100 mM Tris, pH 7.5. Cell lysates were prepared as follows: to each ml equivalent of pelleted fermentation broth was added 50 .mu.l sonication buffer (50 mM sodium phosphate, pH 7.8, 0.3M NaCl) with 1 mg/ml lysozyme; cell suspension was placed on ice for 30 min. Suspension was then brought to a final concentration of 0.2% Tween-20, 10 mM dithiothreitol (DTT), and sonicated until cell breakage was complete. Insoluble material was pelleted at 12,000.times.g in a microcentrifuge for 15 minutes, the soluble portion was removed to a separate tube and the soluble lysate was then brought to a final concentration of 10% glycerol. Soluble lysates from cells expressing the plasmids produce strongly immunoreactive bands of the predicted molecular weight. Soluble lysates prepared for Ni.sup.2+ column purification were prepared with 10 mM .beta.-mercaptoethanol (BME) instead of DTT. Lysates were stored at -80.degree. C.

Purification using Ni.sup.2+ -Nitrosyl acetic acid (NTA) agarose (QIAGEN)

The proteins were then purified by placing the extracted lysate on an NTA agarose column. NTA agarose column chromatography was used because the histidine tag which was fused to the N-terminus of the proteases readily binds to the nickel column. This produces a powerful affinity chromatographic technique for rapidly purifying the soluble protease. The column chromatography was performed in a batch mode. The Ni.sup.2+ NTA resin (3 ml) was washed twice with 50 ml of Buffer A (50 mM sodium phosphate pH 7.8 containing 10% glycerol, 0.2% Tween-20, 10 mM BME). The lysate obtained from a 250 ml fermentation (12.5 ml) was incubated with the resin for one hour at 4.degree. C. The flow through was collected by centrifugation. The resin was packed into a 1.0.times.4 cm column and washed with buffer A until the baseline was reached. The bound protein was then eluted with a 20 ml gradient of imidazole (0-0.5M) in buffer A. Eluted fractions were evaluated by SDS-PAGE and western blot analysis using a rabbit polyclonal antibody to His-HIV 183.

Purification using POROS metal-chelate affinity column

In an alternative method to purify the proteins the lysate containing the proteins were applied to a POROS metal-chelate affinity column. Perfusion chromatography was performed on a POROS MC metal chelate column (4.6.times.50 mm, 1.7 ml) precharged with Ni.sup.2+. The sample was applied at 10 ml/min and the column was washed with buffer A. The column was step eluted with ten column volumes of buffer A containing 25 mM imidazole. The column was further eluted with a 25 column volume gradient of 25-250 mM imidazole in buffer A. All eluted fractions were evaluated by SDS-PAGE and western blot analysis using rabbit polyclonal antibody.

The peptides 5A/5B and 4B/5A substrates (SEQ ID NOs 16, 18, 19, 20 and 21) were synthesized using Fmoc chemistry on an ABI model 431A peptide synthesizer. The manufacture recommended FastMoc.TM. activation strategy (HBTU/HOBt) was used for the synthesis of 4A activator peptide. A more powerful activator, HATU with or without the additive HOAt were employed to assemble 5A/5B substrate peptides on a preloaded Wang resin. The peptides were cleaved off the resin and deprotected by standard TFA cleavage protocol. The peptides were purified on reverse phase HPLC and confirmed by mass spectrometric analysis.

To test the proteolytic activity of the HCV NS3 protease the DTEDVVCC SMSYTWTGK (SEQ ID NO 16) and soluble HCV NS3 (SEQ ID NO 27) were placed together in an assay buffer. The assay buffer was 50 mM sodium phosphate pH 7.8, containing 15% glycerol, 10 mM DTT, 0.2% Tween20 and 200 mM NaCI). The protease activity of SEQ ID NO 27 cleaved the substrate into two byproduct peptides, namely 5A and 5B. The substrate and two byproduct peptides were separated on a reversed-phase HPLC column. (Dynamax, 4.6.times.250 mm) with a pore size of 300 .ANG. and a particle size of 5 .mu.m. The column was equilibrated with 0.1% TFA (Solvent A) at a flow rate of 1 ml per minute. The substrate and the product peptide standards were applied to the column equilibrated in A. Elution was performed with a acetonitrile gradient (Solvent B=100% acetonitrile in A). Two gradients were used for elution (5% to 70% B in 50 minutes followed by 70% to 100% B in 10 minutes).

In another experiment, partially purified SEQ ID NO 27 or vector control was incubated with 100 .mu.M of substrate for 3, 7 and 24 hours at 30.degree. C. The reaction mixture was quenched by the addition of TFA to 0.01% and applied to the reversed-phase HPLC column. The fractions from each run were evaluated by mass spectrometry and sequencing.

The present example describes a novel process for the refolding of HCV NS3 protease which does not have a solubilizing motif from an E.coli inclusion body pellet. This procedure can be used to generate purified enzyme for activity assays and structural studies.

Extraction and Purification of His-HIV 183 from the E.coli inclusion body pellet

E. coli cells harboring the plasmid for HisHIV183 was used to transform a culture of E. coli strain M15 [pREP] (Qiagen), which over-expresses the lac repressor, according to methods recommended by commercial source. M15 [pREP] bacteria harboring recombinant plasmids were grown overnight in 20-10-5 broth supplemented with 100 .mu.g/ml ampicillin and 25 .mu.g/ml kanamycin. Cultures were diluted to O.D.600 of 0.1, then grown at 37.degree. C. to O.D.600 of 0.6 to 0.8, after which IPTG was added to a final concentration of 1 mM. At post-induction 2 to 3 hours, the cells were harvested by pelleting, and the cell pellets were washed with 100 mM Tris, pH 7.5. were pelleted by centrifugation. The cell pellet was resuspended in 10 ml of 0.1M Tris-HCl, 5 mM EDTA, pH 8.0 (Buffer A) for each gm wet weight of pellet. The pellet was homogenized and resuspended using a Dounce homogenizer. The suspension was clarified by centrifugation at 20,000.times.g for 30 minutes at 4.degree. C. The pellet was sequentially washed with the following five buffers:

1. Buffer A

2. 1.0M sodium chloride (NaCl) in buffer A

3. 1.0% Triton X-100 in buffer A

4. Buffer A

5. 1.0 M Guanidine HCl (GuHCl) in buffer A.

The washed pellet was solubilized with 5M GuHCl, 1% beta mercaptoethanol in buffer A (3 ml per gm wet wt. of pellet) using a Dounce homogenizer and centrifuged at 100,000.times.g for 30 minutes at 4.degree. C. Purification of denatured HisHIV183 from high molecular weight aggregates was accomplished by size exclusion on a SEPHACRYL S-300 gel filtration column.

In particular, an 8 ml sample of the 5.0M GuHCl E. coli extract was applied to a 160 ml Pharmacia S-300 column (1.6.times.100 cm) at a flow rate of 1.0 ml/min. The column buffer was comprised of 5.0 M GuHCl, 0.1 M Tris-HCl, pH 8.0, and 5.0 mM EDTA. The fraction size was 5.0 ml.

Appropriate fractions were pooled based on the results of SDS-PAGE, as well as N-terminal sequence analysis of the protein transferred to a Pro-Blot.

Detergent-assisted refolding of HCV-protease

The protein was concentrated by ultrafiltration using a 43 mm Amicon YM10 membrane to 1.0 mg per ml in 5M GuHCl, 0.1M Tris-HCl pH 8.0, 1.0 mM EDTA, 1.0% beta-mercaptoethanol. It was then diluted 50-fold to 0.1M GuHCl in refolding buffer (100 mM sodium phosphate pH 8.0, 10 mM DTT, 0.1% lauryl maltoside) and the mixture was incubated on ice for at least one hour. A 25 ml sample containing 500 .mu.g of the protein in the refolding buffer was applied to a Pro-RPC HR 3/5 reversed phase chromatography column. The applied sample contained 500 .mu.g protein in 25 ml of refolding buffer. To the column was then applied a solution B comprised of 99.9% H.sub.2 O+0.1% trifluoroacetic acid (TFA). A 10 ml volume of solution C [10% H.sub.2 O, 90% acetonitrile (AcN)+0.1% TFA] was applied to the column at a 0-60% gradient into solution B at a flow rate of 0.5 ml/min. and a fraction size of 0.5 ml. The fractions were monitored at A214; 2.0 absorbance units full scale (AUFS).

Fractions containing the protein (corresponding to peak 1) were pooled for renaturation by stepwise dialysis. The fractions were first dialysed in 0.1% TFA in 25% glycerol overnight at 4.degree. C.; then dialyzed in 0.01% TFA in 25% glycerol overnight at 4.degree. C.; then dialyzed in 0.001% TFA in 25% glycerol for 3.0 hours; then dialyzed for 3 hours at 4.degree. C. in 50 mM NaPO.sub.4, pH 6.0, 10 mM dithiotreitol (DTT) in 25% glycerol. The protein was then dialyzed for 3.0 hours at 4.degree. C. in 50 mM NaPO.sub.4, pH 7.0, 0.15 M NaCl, 10 mM DTT in 25% glycerol; and then finally dialyzed in 50 mM NaPO.sub.4, pH 7.8, 0.3 M NaCl, 10 mM DTT, 0.2% Tween 20 in 25% glycerol. This resulted in purified, refolded, soluble, active HCV NS3 protease.

Far UV circular dichroism (CD) analysis of the protein was used to monitor the refolding from an acid denatured state to a folded state at neutral pH. The protein recovery was monitored by a UV scan and SDS-PAGE analysis.

Results:

Detergent-assisted Refolding of His-HIV183

HisHIV183 was quantitatively extracted from an E. coli inclusion body pellet. SDS-PAGE analysis at the various stages of extraction shows that sequential washes are essential to remove significant amounts of the contaminating proteins. HisHIV183 was extracted from the washed inclusion body pellet in the presence of 5M GuHCl. The 5M GuHCl extract was applied to a SEPHACRYL S-300 column and the appropriate fractions were pooled based on SDS-PAGE analysis. The amino acid sequence of the first ten residues was verified.

Refolding was performed at very low concentrations of protein, in the presence of DTT, lauryl maltoside and glycerol at 4.degree. C. The diluted protein was concentrated on a Pro-RPC reversed phase column. Two peaks were obtained based on the UV and protein profile. Only Peak 1 has yielded soluble protein after stepwise dialysis. Far UV CD spectral analysis was used to monitor refolding from a denatured state at acid pH to a folded state at neutral pH. At pH 7.4, the protein was found to exhibit significant amounts of secondary structure that is consistent with that of beta sheet protein. At low pH, the CD spectrum showed that it is fully random coil, having a minimal molar ellipticity at 200 nm. The ratio of this minimum at 200 nm to that of the shoulder at 220 nm is approximately 4:1. This ratio decreased when the secondary structure formation occurred at neutral pH.

A UV scan at each step of dialysis showed that the protein recovery was >90% up to pH 7.4 and that there was no light scattering effect due to protein aggregates. SDS-PAGE analysis also indicated that there was no loss of protein up to pH 7.0 during refolding. Precipitation of protein occurred at the last step of dialysis, and the soluble protein was clarified by centrifugation. The overall protein recovery was about 0.10%. The refolded protein was found to be active in a trans-cleavage assay using the in vitro-translated 5A/5B substrate in the presence of 4A peptide.