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Helena Danielson1 1 Department of Biochemistry and Organic Chemistry, Uppsala University, Sweden 2 Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, Uppsala University

Trang 1

residues in hepatitis C virus nonstructural protein 3

Go¨ran Dahl1, Anja Sandstro¨m2, Eva A˚ kerblom2

and U Helena Danielson1

1 Department of Biochemistry and Organic Chemistry, Uppsala University, Sweden

2 Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, Uppsala University, Sweden

The bifunctional nonstructural protein 3 (NS3,

EC 3.4.21.98) from hepatitis C virus (HCV) is an

inter-esting enzyme biochemically, and is of importance for

anti-HCV drug discovery It has an N-terminal domain

that constitutes a serine protease with a typical

chymo-trypsin fold, and a C-terminal superfamily 2 DExH⁄

D-box RNA helicase domain Furthermore, the

prote-ase domain contains a structural zinc atom and needs

to interact with the viral nonstructural protein 4A

(NS4A) in order to be fully functional The protease

activity of NS3 is responsible for cleaving the viral

polyprotein of HCV, whereas the helicase is

responsi-ble for unwinding douresponsi-ble-stranded RNA Thus, the

two enzyme activities of the NS3 protein are involved

in critical steps of viral replication, making them both

attractive anti-HCV drug targets (for reviews, see [1] and [2])

From a biochemical point of view, it is not clear why the two enzymes are fused into a single protein The active sites of each of the enzymes are located in the respective domains, and truncated variants of NS3, containing either the protease or the helicase alone, are functional on their own However, the truncated protease has slightly different kinetic prop-erties and the helicase has a lower activity compared with the full-length enzyme [3–5], suggesting that there may be a functional justification for the con-struction

Nevertheless, for practical reasons, most researchers working on the discovery of drugs against either of the

Keywords

full length; hepatitis C virus; inhibition;

nonstructural protein 3; protease

Correspondence

U H Danielson, Department of

Biochemistry and Organic Chemistry,

Uppsala University, BMC, Box576,

SE-751 23 Uppsala, Sweden

Fax: +46 18 558431

Tel: +46 18 4714545

E-mail: Helena.Danielson@bioorg.uu.se

(Received 4 May 2007, revised 17 August

2007, accepted 25 September 2007)

doi:10.1111/j.1742-4658.2007.06120.x

This study of the full-length bifunctional nonstructural protein 3 from hep-atitis C virus (HCV) has revealed that residues in the helicase domain affect the inhibition of the protease Two residues (Q526 and H528), appar-ently located in the interface between the S2 and S4 binding pockets of the substrate binding site of the protease, were selected for modification, and three enzyme variants (Q526A, H528A and H528S) were expressed, puri-fied and characterized The substitutions resulted in indistinguishable Km values and slightly lower kcatvalues compared to the wild-type The Ki val-ues for a series of structurally diverse protease inhibitors were affected by the substitutions, with increases or decreases up to 10-fold The inhibition profiles for H528A and H528S were different, confirming that not only did the removal of the imidazole side chain have an effect, but also that minor differences in the nature of the introduced side chain influenced the charac-teristics of the enzyme These results indicate that residues in the helicase domain of nonstructural protein 3 can influence the protease, supporting our hypothesis that full-length hepatitis C virus nonstructural protein 3 should be used for protease inhibitor optimization and characterization Furthermore, the data suggest that inhibitors can be designed to interact with residues in the helicase domain, potentially leading to more potent and selective compounds

Abbreviations

HCV, hepatitis C virus; NS3, nonstructural protein 3; NS4A, nonstructural protein 4A.

Trang 2

itors is not feasible, and many have apparently

discon-tinued their anti-HCV NS3 protease drug discovery

programmes However, when the first and, so far, only

crystal structure of the full-length NS3 was published,

it revealed that the protease active site was situated in

the interface between the helicase and the protease

domains, creating a well-defined binding cleft (Fig 1A)

[7] Indeed, it appears that certain residues in the

heli-case domain may interact directly with substrates or

product-based inhibitors binding in this cleft [7] As a

consequence, we have concluded that the full-length

protein is the most relevant model system for NS3

Moreover, despite the lower yields and stabilities

com-pared with those obtained with the truncated protease,

it is the protein that has been used in all of our studies

of the NS3 protease [8–13]

Nevertheless, we are interested in determining the

functional importance of the helicase domain for the

activity and inhibition of the protease, and have

focused on the identification of specific helicase

resi-dues which may be involved In the crystal structure of

the full-length enzyme, the C-terminus is located in the

substrate binding site and the helicase clearly interacts

with the C-terminus of NS3 (Fig 1B) [7] By structural

modelling of an inhibitor binding to full-length NS3,

In order to experimentally determine the importance

of these residues, we have substituted the side chains

of these residues for side chains with other functional properties, and have analysed how this affects protease activity and inhibition For the analysis of modified inhibition characteristics, a set of 11 inhibitors with varying structure, mechanism and potency was used (Fig 2) BILN 2061 was the first HCV NS3 protease inhibitor to reach clinical trials [14], but was later with-drawn because of cardiac toxicity in rhesus monkeys [15] Nevertheless, it is a useful model compound as it

is one of the most potent inhibitors of HCV NS3 today, and is a macrocyclic compound, in contrast to other inhibitors used here VX-950 was the second inhibitor to reach clinical trials and is therefore also a useful reference compound [16] It is a linear mecha-nism-based inhibitor with an electrophilic C-terminus, and is thus different mechanistically from BILN 2061 and the other compounds studied here The other inhibitors were selected from the compounds previ-ously tested against the wild-type enzyme They include tri- and tetrapeptides with either a carboxylic acid or an acyl sulfonamide as their C-terminus [11– 13], and hexapeptides with P2 and P4 residues of dif-ferent polarity and size [8,10]

H528

Q526 D81 H57 S139

Fig 1 Structure of full-length HCV NS3 (A) Complete HCV NS3 with the protease domain (red), helicase domain (blue) and NS4A cofactor fused to the N-terminus (green) (PDB: 1CU1) [7] The structural zinc atom in the protease domain and a phos-phate group in the helicase domain are also visible The interface region between the helicase and the protease domains is framed and shown in detail in (B) The cata-lytic triad, H57, D81 and S139, in the pro-tease domain, and the conserved helicase residues, Q526 and H528, are shown in a ball-and-stick representation The blue strand represents the C-terminus of NS3, and shows the substrate binding site of the protease.

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Fig 2 Structures of the studied inhibitors The arrows indicate the a-carbon of the P1 residue of the inhibitor The P2, P3, P4, P5 and P6 side chains can be deduced from the nomenclature by Schechter and Berger [20].

Trang 4

Q526 and H528 were substituted for residues for side

chains with different interaction characteristics Three

single mutants, coding for the enzyme variants Q526A,

H528A and H528S, were created The alanine

substitu-tion replaces the original side chain with a small

hydrophobic moiety, whereas the serine substitution

also introduces alternative hydrogen bonding

capabili-ties

Full-length Q526A, H528A and H528S HCV NS3

were successfully constructed, expressed and purified

Expression resulted in around 150–200 lg of enzyme

per litre of cell culture for all variants and the

wild-type Purities were over 98% in all cases, as judged by

the single band on a silver-stained SDS⁄ PAGE gel

(Fig 3) An automatic chromatographic procedure

gave a highly reproducible purification

Kinetic characterization of NS3 protease variants

The three substitutions in the helicase domain of NS3

did not influence the Km values significantly, but kcat

values were reduced (Table 1) Assuming a normal

dis-tribution, the wild-type has a significantly higher kcat

value compared with the helicase variants at a 95% confidence level

Inhibition of NS3 protease variants The effect of changes in the helicase residues on the inhibition of the protease was investigated for the three variants and a series of inhibitors Inhibition constants (Ki) were determined for all variants and inhibitors (Fig 4)

The data showed that the substitutions of Q526 and H528 did not generally have a large or consistent effect

on the inhibition, but there were some notable effects and trends The Q526A and H528A substitutions had little impact on the inhibition of the enzyme by BILN 2061, but the H528S substitution reduced the potency of the inhibitor As a result, the Ki value for BILN 2061 differed 10-fold depending on whether the residue in position 528 was alanine or serine A similar profile was also seen with compound 9, the second most potent inhibitor By contrast, VX-950 was not affected by any of the investigated substitutions The effect of substituting either Q526 or H528 was found to be more diverse for the less potent com-pounds The inhibition by compounds 4 and 6 was not affected to any large extent by any of the substitutions, whereas compounds 2 and 5 became more effective for all variants The H528A substitution decreased the Ki values for compounds 1 and 3, but the Q526A and H528S substitutions had no effect All substitutions reduced the inhibition by compound 7, and both Q526A and H528A reduced it for compound 8 It should be noted that the differences between the values were larger than those deduced from the differences in bar lengths in the logarithmic graph

Discussion

This study has shown that residues in the helicase domain of full-length NS3 from HCV can directly influence the protease Modifications of the side chains

of two residues (Q526 and H528) were found to influ-ence the effect of some protease inhibitors The Km

97 kDa 66 45

30 20.1 14.4

Fig 3 Purification of HCV NS3 protease A silver-stained

SDS ⁄ PAGE gel from a typical purification procedure (in this case

the H528A variant): Lane 1, immobilized ion affinity chromatography

(IMAC) flow-through; lane 2, IMAC eluate; lane 3, IMAC eluate

after buffer change; lane 4, PolyU flow-through; lane 5, PolyU

elu-ate; lane 6, molecular weight marker (LMW-SDS Marker kit, GE

Healthcare).

kcat(s ) 0.53 ± 0.03 0.30 ± 0.04 0.32 ± 0.02 0.37 ± 0.04

k cat ⁄ K m (l M )1Æs)1)

1.96 ± 0.45 0.79 ± 0.37 1.10 ± 0.28 0.84 ± 0.58

Trang 5

and kcat⁄ Kmvalues for the enzyme variants were

indis-tinguishable from those of the wild-type, even though

the kcat values were significantly lower However, this

is not considered to be of great importance and could

be a result of differences in the active enzyme

concen-tration

The effect of changing residues in the helicase

domain on inhibition was dependent on both the

sub-stitution and the inhibitor Subsub-stitution of Q526 with

alanine had only minor effects, despite earlier

specula-tions that this residue is located in the interface

between the S2 and S4 binding pockets of the

full-length enzyme, and therefore would be critical for

interaction with product-based inhibitors [7,10]

Substi-tuting H528 with alanine resulted in increased

inhibi-tion for all compounds except three, whose inhibiinhibi-tion

was more or less unchanged The increase was largest

for compounds with a P4 side chain Under the present

conditions (pH 7.4), H528 is expected to be essentially

uncharged and to act either as a hydrogen bond donor,

interacting with the carbonyl oxygen of the P4 residue

on the inhibitor, or as a hydrogen bond acceptor for

the P4 NH of the inhibitor Although some of the

inhibitors were only tripeptides, they all had at least

the equivalent of a P4 carbonyl group, and the

substi-tution of H528 with alanine or serine could thus be

expected to weaken the inhibition, but not to increase

it Apparently, other interactions play a significant

role, where, for example, the hydrophobic alanine

resi-due contributes more than a potential hydrogen bond

from the histidine When H528 was replaced with

ser-ine, the effect was more varied; both enhanced and

reduced inhibition were detected However, compounds

lacking a P4 residue and containing large P2 side

chains were affected the most by this substitution,

lead-ing to reduced potencies This effect became less and

less pronounced as the overall potency of the inhibitors

decreased It is not clear why the nature of the residue

at position 528 results in such different effects, espe-cially for BILN 2061, but these observations imply that the initial structural model [10] does not adequately describe the forces involved It should be noted that, even though a 10-fold change in Ki is significant, the change in binding energy is small and equal to approx-imately the loss of a hydrogen bond [17]

Drug discovery is a technique in which modified variants of enzymes are often used in order to increase stability, yield or other parameters to produce an effi-cient process However, it is critical that the modifica-tion does not compromise the informamodifica-tion obtained when using the variant for drug discovery purposes Although the data presented here are based on a lim-ited number of compounds and only two helicase resi-dues, the experimental observations indicate that the helicase can influence protease inhibitors Therefore, the use of truncated NS3, containing only the protease domain, for the identification and optimization of HCV NS3 protease inhibitors is a procedure that may

be inappropriate The data also suggest that inhibitors can be designed to interact with residues in the helicase domain, potentially leading to more potent and selec-tive compounds

Conclusion

The strategy used in this study has demonstrated that specific amino acids in the helicase of full-length HCV NS3 can influence the inhibition of the protease As a consequence, anti-HCV protease drug discovery using full-length HCV NS3 as a model system for inhibition studies may be more appropriate than using the trun-cated protease In addition, protease inhibitor design can make use of the helicase domain as a novel anchor point for inhibitors

Fig 4 Effect of HCV NS3 helicase domain

substitutions Q526A, H528A and H528S on

the potency of NS3 protease inhibitors.

Error bars represent the standard deviations.

The scale on the y-axis ranges from 10 p M

(top) to 10 l M (bottom) on a logarithmic

scale Blue, wild-type; red, Q526A; yellow,

H528A; green, H528S.

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GCAGACCATCTTGAAT-3¢), H528A forward primer

(5¢-TCCCGTGTGTCAAGACGCTCTTGAAT-3¢) or H528S

forward primer (5¢-TCCCGTGTGTCAAGACTCTCTTG

AAT-3¢) and reverse primer (5¢-AGTCCCGGGGTGTT

CATGTATGCTC-3¢) Each PCR vial contained 50 ng of

template DNA, 0.2 mm dNTPs, 0.2 lm forward primer,

0.2 lm reverse primer (Thermo Electron GmbH, Ulm,

Ger-many) and 1.25 U Pfu Turbo DNA polymerase

(Strata-gene, La Jolla, CA, USA) in 50 lL Pfu Buffer [200 mm

Tris⁄ HCl pH 8.8, 20 mm MgSO4, 100 mm KCl, 100 mm

(NH4)2SO4, 1% Triton X-100, 1 mgÆmL)1 nuclease free

BSA (Stratagene)] The primers were phosphorylated at the

5¢-end to promote recircularization The vials were

sub-jected to 1 min of melting at 95C, 1 min of annealing at

73C and 15 min of extension at 72 C in 25 cycles using a

thermal cycler (GeneAmp PCR system 2400, Perkin-Elmer,

Boston, MA, USA) After this, 20 U DpnI restriction

enzyme (New England Biolabs, Beverly, MA, USA) was

added and the vials were left at 37C for 1 h The DNA

was then purified on a 1% Tris, borate, EDTA agarose gel,

and fragments corresponding to the PCR products were cut

out and purified using the GeneClean gel extraction kit

(Qbiogene, Illkirch Cedex, France) The purified PCR

prod-uct was then blunt-end ligated using the T4 rapid DNA

ligation kit (Roche Diagnostics Scandinavia AB, Bromma,

Sweden) and transformed to thermocompetent TOP10 cells

The DNA was sequenced using a Mega BACE 1000

sequencer (GE Healthcare, Uppsala, Sweden)

Expression and purification

The expression and purification of HCV NS3 variants were

performed essentially as described previously [9] That is,

6· 500 mL TOP10 cells with A600¼ 0.7 were induced

with 0.002% (w⁄ v) l-(+)-arabinose overnight at 21 C,

150 r.p.m The cells were then harvested and resuspended

in lysation buffer [25 mm Hepes pH 7.6, 0.3 m NaCl, 20%

glycerol, 10 mm b-mercaptoethanol and 0.1% Chaps

(Ana-trace, Maumee, OH, USA)] and 2 lgÆmL)1 DNAse I

(Roche Diagnostics Scandinavia AB) Lysation was

initi-ated by adding 1 mgÆmL)1 lysozyme (Sigma-Aldrich

Swe-den AB, Stockholm, SweSwe-den), and thereafter the cells were

sonicated The lysate was centrifuged at 25 000 g for

40 min, and the cleared supernatant was loaded on to a

10 mL chelating Sepharose fast flow gel (GE Healthcare)

loaded with Ni2+, and washed with buffer A (50 mm Hepes

pH 7.6, 0.3 m NaCl, 26% glycerol, 10 mm

b-mercaptoetha-nol and 0.1% Chaps), buffer A supplemented with 1 m

HiTrap desalting column (GE Healthcare) The sample was loaded on to a 2.5 mL PolyU gel (GE Healthcare), and the gel was washed with buffer B before purified enzyme was finally eluted with buffer B supplemented with 1 m NaCl All chromatographic steps were performed with an A¨KTA Explorer (GE Healthcare) The eluted fractions with highest absorbance at 280 nm were pooled and stored at ) 80 C The protein concentration was determined using a Brad-ford-based assay (Bio-Rad, Sundbyberg, Sweden), and the purity was estimated with SDS⁄ PAGE using the PHAST system and 8–25% precast PHAST gels and silver staining (GE Healthcare)

Enzymatic characterization

Protease activity was measured as described previously [9] That is, the hydrolysis of a depsipeptide substrate, Ac-Asp-Glu-Asp(EDANS)-Glu-Glu-Abu-w-[COO]Ala-Ser-Lys(DABCYL)-NH2 (AnaSpec, San Jose, CA, USA), was recorded continuously over time with a fluorescence plate reader (Fluoroskan Ascent Labsystems, Stockholm, Swe-den) Each sample well contained 276.5 lL assay buffer (50 mm Hepes pH 7.5, 10 mm dithiothreitol, 40% (w⁄ v) glycerol, 0.1% n-octyl-b-d-glucoside), 9.25 lL dimethylsulf-oxide, 0.75 lL of 10 mm peptide cofactor KKGSVVIV-GRIVLSGK in dimethylsulfoxide and 3.5 lL of 6 lgÆmL)1 NS3 (1 nm final concentration), and was incubated at 30C for 10 min before the reaction was started by the addition

of 10 lL substrate to a final concentration between 0.25 and 4 lm All measurements were performed in triplicate

Kmand kcatvalues were estimated by fitting the Michaelis– Menten equation to the data by simulated annealing (GOSA, Bio-Log, Ramonville, France) kcat⁄ Kmvalues were calculated from the estimated kcatand Kmvalues

Inhibitors and inhibition measurements

Eleven inhibitors were used in this study (Fig 2) They included the clinical compounds BILN 2061 [14] and

VX-950 [16], compounds 2, 3, 4, 5 (compounds 16, 4, 9 and 1, respectively, in [10]), compound 6 (compound 18a in [13]), compounds 7, 8, 9 (compound 20, 29 and 31, respectively,

in [12]) and the commercially available reference compound

1 (Product no N-1725, Bachem, Weil am Rein, Germany) (entry 14 in Table 4 in [18])

The inhibitors were dissolved in dimethylsulfoxide and preincubated with enzyme and NS4A cofactor at 30C for 10 min in the same buffer conditions as stated for the

Trang 7

activity assay The reaction was started by the addition of

10 lL substrate to a final concentration of 0.5 lm Pilot

measurements over a large concentration range were

per-formed in order to estimate IC20 and IC80 Six inhibitor

concentrations between IC20and IC80with constant enzyme

and substrate amounts were used All measurements were

performed in triplicate The Ki and Vmax values were

esti-mated by fitting Eqn (1) (adapted from [19]) to the data

using simulated annealing (GOSA, Bio-Log)

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Acknowledgements

We would like to thank Gun Stenberg for her help in

primer design, and Robert Roẽnn and Pernilla Oẽrtqvist

(Department of Medicinal Chemistry, Pharmaceutical

Organic Chemistry, Uppsala University, Sweden) for

compounds 6, 7, 8 and 9 We would also like to thank

Boehringer Ingelheim for the kind gift of BILN 2061

and the VIRGIL DrugPharm Team for VX-950 This

work was conducted with support from the VIRGIL

European Union Network of Excellence

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