Stearoyl-CoA desaturase inhibition blocks formation of hepatitis C virus-induced specialized membranes

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1 StearoyloA desaturase inhibition blocks formation of hepatitis virusinduced specialized membranes Rodney K. Lyn 1,2, Ragunath Singaravelu 1,3, Stacia Kargman 4, Shifawn Hara 1, Helen han 4, Renata balla 4, Zheng Huang 4, Daniel M. Jones 5, Andrew Ridsdale 1, Rodney S. Russell 5, Anthony Partridge 4 * & John Paul Pezacki 1,2,3 * 1 ational Research ouncil of anada, ttawa, ntario, anada. 2 Department of hemistry, and 3 Department of Biochemistry, Microbiology and Immunology, University of ttawa, ttawa, anada. 4 Merck Research Laboratories, Merck & o., Kenilworth,.J., USA. 5 Immunology and Infectious Diseases, aculty of Medicine, Memorial University of ewfoundland, St. John s, ewfoundland, anada. urrent address for H: Alexion Pharmaceuticals, Montreal, anada; R: Inception Sciences anada Inc., Vancouver, anada; ZH: Eli Lilly hina Research & Development enter, Shanghai, hina; AP: Pharmaron, Beijing, hina. orrespondence and requests for materials should be addressed to A.P. (Anthony.Partridge@pharmaron.com) or J.P.P. (John.Pezacki@nrccnrc.gc.ca).

2 Relative ell Viability Supplementary igure S ompound [SD] (nm) A (nm) Supplementary igure S1: ytotoxicity assay for inhibitor A. The toxicity of inhibitor A was evaluated via an MTT assay following a 96 hour treatment in Huh7SGR cells. Results confirm no significant cytotoxicity was observed at the concentrations tested.

3 Supplementary igure S2 A H stearic acid SD1 H oleic acid B mau stearic acid oleic acid min Supplementary igure S2: Measuring SD1 cellbased enzymatic activity by labeling of stearic acid. (a) SD1 enzymatic assays were performed by treatment of cells with stearic acid. An organic extraction was performed to isolate lipids, and the conversion rate to oleic acid was subsequently measured via reverse phase HPL. Detection was performed using a scintillation analyzer. (b) An illustration of a typical chromatogram is shown.

4 Supplementary igure S3 A B Huh nm 500 nm 1000 nm Huh7.5 GR 500 nm 1000 nm ellular lipid volume (%) ellular lipid volume (%) 100 nm D nm 15 nm ompound B treatment 50 nm nm 15 nm 50 nm ompound B treatment Supplementary igure S3: S3 protease inhibitor has no effect on LD phenotype. (a) Huh7.5 and (b) Huh7.5GR cells were treated with various concentrations of inhibitor B: 50nM, 15nM, and 5nM and nontreated (mock) of the inhibitor B. 96 hours posttreatment, cells were fixed and imaged by ARS microscopy. Representative images are shown for each concentrations (n=2). Scale bar = 10μm. The LD density was measured by voxel analysis under multiple field of views for (c) Huh7.5 cells (n>10) and (d) Huh7.5GR cells (n>10). The bar graphs illustrate the average cellular lipid volume measured by voxel analysis with error bars representing the standard error of the mean.

5 % change in HV expression in Dig vs Diguc HV expression relative to mock HV expression relative to mock Supplementary igure S4 A ompound A Digitonin uclease P B Dig Diguc P40 P= DigucP40 uc SD SDDig SDDiguc SDP40 SDDigucP40 : % ompound A inhibitor: % Inhibitor SD A Supplementary igure S4: HV RA susceptibility to exogenously added nuclease after inhibiting SD1. (a) Huh7SGR cells were treated with vehicle (DMS) (Lanes 16) or a concentration of inhibitor A yielding a 50% reduction in HV RA levels (Lanes 711) for 96 hours. RTPR was performed to illustrate the relative differences in HV RA abundance (n=4). The second trial (2) was shown as a representative image in igure 2. (b) The densitometry for each trial in (a) is quantified and individually shown. (c) The change in HV RA abundance between digitonin and digitonin nuclease treatments for both mock and inhibitor A treated cells is shown. This graph demonstrates that SD1 inhibition with inhibitor A increases susceptibility of HV RA to exogenously added nucleases in digitonin permeabilized cells.

6 Supplementary igure S5 Supplementary igure S5: Electron microscopy shows that high dose treatment with inhibitor A reduces the appearance of membranous webs and the size and number of lipid droplets in Huh7SGR cells. Huh7SGR cells treated for 96h with vehicle (DMS) (ab) or 500nM inhibitor A (cd) were fixed and processed for EM. ne representative cell is shown for each treatment at magnifications of 1500X (a,c) and 2500X (b,d) MW: membranous webs, LD: lipid droplets, : nucleus

7 Supplementary Table S1: Palmitoleic acid or oleic acid treatment rescues SD inhibitors antiviral effect. Inhibition Rescue E 50 (nm) Inhibitor Structure Gt1b Gt1a Gt1b 50%HS 10% BS 100 µm leic acid 100 µm Palmitoleic acid H > D >40000 H E H >40000 Br > H 3 H 3 H H G > >40000 >40000 H H Br >40000 H 2 S

8 Supplementary Table S2: SD inhibitors do not directly repress HV S3 protease and S5B polymerase activity in vitro. Inhibitor Structure S3 E 50 (nm) S5B E 50 (nm) H > H E > >80000 Br H 3 H 3 H H > G H > H H 2 S Br > >80000

9 Supplementary Table S3: List of primers Primer ame 18S rra WD 18S rra REV HV IRES WD HV IRES REV JH1 HV IRES REV ucleotide Sequence GGATGGGGGGTTATT AATTGTAATTGTGTGT GTTGGGAAGGTGAGTA GAAATTAGGATT GAAATGGGGGATA