A Cell Protection Screen Reveals Potent Inhibitors of Multiple Stages of the Hepatitis C Virus Life Cycle

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A Cell Protection Screen Reveals Potent Inhibitors of Multiple Stages of the Hepatitis C Virus Life Cycle A cell protection screen reveals potent inhibitors of multiple stages of the hepatitis C virus life cycle Karuppiah Chockalingama, Rudo L. Simeona, Charles M. Riceb, and Zhilei Chena,1 aArtie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843; and bCenter for the Study of Hepatitis C, The Rockefeller University, New York, NY 10065 Contributed by Charles M. Rice, December 30, 2009 (sent for review December 16, 2009) The hepatitis C virus (HCV) life cycle involves multiple steps, but against different aspects of the HCV life cycle. In particular, we most current drug candidates target only viral replication. The reasoned that n4mBid cells should be able to report the presence inability to systematically discover inhibitors targeting multiple of anti-HCV molecules via increased cell viability relative to steps of the HCV life cycle has hampered antiviral development. We untreated cells in the presence of HCV infection. Such an assay present a simple screen for HCV antivirals based on the alleviation should be simple, quick, cost-effective, and, importantly, should of HCV-mediated cytopathic effect in an engineered cell line— obviate the need for a separate assay to assess drug hits for cyto- n4mBid. This approach obviates the need for a secondary screen toxic effects because toxic drugs should not produce a positive cell to avoid cytotoxic false-positive hits. Application of our screen to viability readout. 1280 compounds, many in clinical trials or approved for therapeutic use, yielded >200 hits. Of the 55 leading hits, 47 inhibited one or Results and Discussion more aspects of the HCV life cycle by >40%. Six compounds blocked Viral Inhibitors Effectively Protect n4mBid Cells from HCV Infection. HCV entry to levels similar to an antibody (JS-81) targeting the HCV To verify that inhibition of different aspects of the HCV life cycle entry receptor CD81. Seven hits inhibited HCV replication and/or can alleviate the HCV-induced cytopathic effect experienced by infectious virus production by >100-fold, with one (quinidine) inhib- n4mBid cells, we tested the effect of known HCV replication, iting infectious virus production by 450-fold relative to HCV repli- entry, and assembly/release inhibitors on n4mBid cell viability in cation levels. This approach is simple and inexpensive and should the presence of HCV infection. N4mBid cells were seeded in 96- enable the rapid discovery of new classes of HCV life cycle inhibitors. well plates in the presence of both Jc1 HCVcc (14) and small molecules, and cell viability was quantified 4 days later (Fig. 1A). cell death | drug | high throughput | rescue | virus assembly For small-molecule cytotoxicity profiles, regular growth media was used in place of HCVcc. The HCV replication inhibitors VX-950 epatitis C virus (HCV) infection is a major public health (15), 2′-C-methyladenosine (2′CMA) (16), and cyclosporin A (17), Hproblem, putting ~180 million infected individuals worldwide targeting the NS3-4A protease, NS5B RNA-dependent RNA (3% of the world’s population) at risk for developing cirrhosis, polymerase, and a required cellular factor [cyclophilin A (18)], hepatocellular carcinoma, and liver failure. Chronic hepatitis C is respectively, each produced a strong dose-dependent increase in a leading cause for liver transplantation in the Western world. The n4mBid cell viability following HCV infection. A recombinant current standard IFN-based therapy is costly, time-consuming, monoclonal antibody (mAb JS-81) against the essential HCV entry riddled with serious side effects, and cures only ∼50% of patients factor CD81 (19) also exhibited a dose-dependent protection of infected with the most common genotype. Although it is antici- n4mBid cells from the HCV cytopathic effect, as did the HCV fi pated that small molecules that effectively inhibit the HCV life assembly/release-speci c inhibitor naringenin (20) and the cyto- α B cycle can complement or even replace IFN therapy, no anti-HCV kine IFN -2a (Fig. 1 ). drugs have yet been approved for human use. Efforts to develop HCV antivirals mostly target only viral replication due to wide- Library Screening for Antivirals Using n4mBid Cells. We next screened the LOPAC1280 library consisting of 1280 compounds spread dependence on the HCV replicon model (1–4), which known to be pharmacologically active in a variety of cellular effectively reproduces the RNA replication aspects of the HCV processes for molecules able to protect n4mBid cells from the life cycle but does not allow screens to identify inhibitors of entry HCV cytopathic effect. Many of the compounds in this library or infectious virus assembly and release. are approved for human therapeutic use in clinical trials or are The identification of a genotype 2a isolate of HCV that repro- structurally related to clinically approved molecules. Fig. S1 duces the entire viral life cycle in cell culture (5–7) promised to shows a set of representative cell viability results obtained from accelerate the discovery of antivirals targeting all aspects of HCV this screen. In total, >200 molecules mediated a statistically growth in a more true-to-life model system. Several recent reports significant increase in cell viability relative to untreated cells in describe systems that can in principle screen for inhibitors targeting response to HCV infection. Among the 56 hits that most strongly different steps of the HCV life cycle via the prevention of the protected n4mBid cells from the HCV cytopathic effect, we spread of cell culture-derived hepatitis C virus (HCVcc) infection fi – identi ed the known HCV inhibitors cyclosporin A (17), MK- in a cell monolayer (8 11). Very recently, one such screen based on 886 (12, 21), and TTNPB (22), as well as five additional com- a colorimetric readout following immunostaining with an anti-E2 fi pounds recently found in an anti-HCV drug screen targeting antibody identi ed inhibitors of multiple stages of the HCV life multiple aspects of the HCV life cycle (12). Numerous other cycle (12). Although effective, this approach is labor-intensive and molecules with reported anti-HCV activity appeared as weaker not readily amenable to high-throughput application, requiring antibodies and 12 washing steps in addition to a secondary screen to assess drug cytotoxicity. — — Author contributions: K.C. and Z.C. designed research; K.C. and R.L.S. performed research; We previously created a cell line n4mBid that sensitively C.M.R. contributed new reagents/analytic tools; K.C. and Z.C. analyzed data; C.M.R. pro- reports HCV infection via a cell death phenotype by introducing a vided conceptual advice; and K.C. and Z.C. wrote the paper. HCV NS3-4A protease-cleavable derivative of the proapoptotic The authors declare no conflict of interest. factor Bid, mBid (13), into the highly HCV-permissive hepatoma 1To whom correspondence should be addressed. E-mail: [email protected]. cell line Huh-7.5. In the present study, we demonstrate the utility This article contains supporting information online at www.pnas.org/cgi/content/full/ of the n4mBid cell line as a medium for the discovery of inhibitors 0915117107/DCSupplemental. 3764–3769 | PNAS | February 23, 2010 | vol. 107 | no. 8 www.pnas.org/cgi/doi/10.1073/pnas.0915117107 Downloaded by guest on September 28, 2021 Fig. 1. A n4mBid cell protection anti-HCV drug screen reports the presence of inhibitors targeting multiple stages of the HCV life cycle. (A) Schematic of screen. (B) Effect of known anti-HCV molecules on rescuing n4mBid cells from the HCV-induced cytopathic effect. (Upper) Drug dose–responses reporting n4mBid cell viability in the presence of HCV infection. (Lower) Drug cytotoxicity in the absence of HCV infection. (i and v) HCV replication inhibitors 2′CMA (•), VX-950 (▲), and cyclosporin A (■). (ii and vi) HCV entry-blocking anti-human CD81 mAb, JS-81. (iii and vii) The HCV assembly/release inhibitor naringenin. (iv and viii) IFNα-2a. Cell viability is presented as a percentage of mock-treated cells in the absence of both HCV infection and inhibitors. Values are the mean ± SD of two independent experiments carried out in duplicate. hits in our screen. A handful of known HCV inhibitors present molecules may interfere with mBid-mediated apoptosis, thus within the library did not protect n4mBid cells from HCV-mediated protecting cells from HCV-mediated cell death without specifi- cell death. This phenomenon is likely due to a combination of two cally influencing the HCV life cycle. Screening hits that enhance factors: (i) an extent of HCV life cycle inhibition insufficient to infectious HCV production (Table 1) may act, at least in part, alleviate the HCV cytopathic effect and (ii) drug cytotoxicity. For through alleviation of a cytopathic effect downstream of HCV example, the estrogen receptor antagonist tamoxifen, a HCV rep- infection rather than directly targeting the HCV life cycle, thus lication inhibitor present in the library, did not appear as a hit, likely increasing HCV productivity by making the producer cells less due to its significant cytotoxicity even while inhibiting HCV repli- susceptible to HCV-induced stress. cation at 1 μM(23). We commenced characterization of the leading 55 drug hits from Effect of Selected Inhibitors on Viral Entry. Several of the HCV our screen (excluding cyclosporin A) by measuring their dose- inhibitor hits from our screen strongly inhibited entry of HCVpp dependent effects on the protection of n4mBid cells from the HCV into Huh-7.5 cells (Table 1 and Fig. S3). Six of these compounds cytopathic effect, as well as on HCV-independent cellular cytotox- exhibited a strong dose-dependent inhibition of HCVpp entry icity, confirming that all of the leading 55 drug hits mediated a dose- without significant cytotoxicity (Fig. 2). Five of these six compounds dependent protection phenotype from HCV-triggered cell death inhibited HCVpp entry without significantly affecting entry of VSV- (Fig.
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