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In Vitro Combinations of Baloxavir Acid and Other Inhibitors Against Seasonal Influenza a Viruses

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In Vitro Combinations of Baloxavir Acid and Other Inhibitors Against Seasonal Influenza a Viruses viruses Article In Vitro Combinations of Baloxavir Acid and Other Inhibitors against Seasonal Influenza A Viruses 1, 2,3, 2 2 Liva Checkmahomed y, Blandine Padey y , Andrés Pizzorno , Olivier Terrier , Manuel Rosa-Calatrava 2,4, Yacine Abed 1, Mariana Baz 1,* and Guy Boivin 1,* 1 Centre Hospitalier Universitaire de Québec—Centre Hospitalier de l’Université Laval (CHUQ-CHUL) and Laval University, Québec City, QC G1V 4G2, Canada; [email protected] (L.C.); [email protected] (Y.A.) 2 CIRI—Centre International de Recherche en Infectiologie, (Team VirPath), University Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS—Centre National de la Recherche Scientifique UMR5308, ENS de Lyon, F-69007 Lyon, France; [email protected] (B.P.); [email protected] (A.P.); [email protected] (O.T.); [email protected] (M.R.-C.) 3 Signia Therapeutics SAS, 69100 Villeurbane, France 4 VirNext, Faculté de Médecine RTH Laennec, Université Claude Bernard Lyon 1, Université de Lyon, 69008 Lyon, France * Correspondence: [email protected] (M.B.); [email protected] (G.B.) These authors contributed equally to this work. y Received: 21 September 2020; Accepted: 1 October 2020; Published: 8 October 2020 Abstract: Two antiviral classes, the neuraminidase inhibitors (NAIs) and polymerase inhibitors (baloxavir marboxil and favipiravir) can be used to prevent and treat influenza infections during seasonal epidemics and pandemics. However, prolonged treatment may lead to the emergence of drug resistance. Therapeutic combinations constitute an alternative to prevent resistance and reduce antiviral doses. Therefore, we evaluated in vitro combinations of baloxavir acid (BXA) and other approved drugs against influenza A(H1N1)pdm09 and A(H3N2) subtypes. The determination of an effective concentration inhibiting virus cytopathic effects by 50% (EC50) for each drug and combination indexes (CIs) were based on cell viability. CompuSyn software was used to determine synergism, additivity or antagonism between drugs. Combinations of BXA and NAIs or favipiravir had synergistic effects on cell viability against the two influenza A subtypes. Those effects were confirmed using a physiological and predictive ex vivo reconstructed human airway epithelium model. On the other hand, the combination of BXA and ribavirin showed mixed results. Overall, BXA stands as a good candidate for combination with several existing drugs, notably oseltamivir and favipiravir, to improve in vitro antiviral activity. These results should be considered for further animal and clinical evaluations. Keywords: baloxavir; combination; influenza; A(H1N1) virus; A(H3N2) virus; polymerase inhibitors; neuraminidase inhibitors; human airway epithelium 1. Introduction Since 1977, two subtypes of influenza A viruses, H1N1 and H3N2, along with influenza B viruses, have co-circulated in the human population. These viruses are responsible for seasonal epidemics and may cause global pandemics [1]. Influenza epidemics can lead to millions of cases of severe respiratory illnesses and to half a million deaths annually worldwide [2] representing a major public health challenge. Vaccination still remains the first line of prevention against seasonal influenza infections [3–5] but the protection conferred by actual vaccines varies from year to year due to the evolution of the circulating Viruses 2020, 12, 1139; doi:10.3390/v12101139 www.mdpi.com/journal/viruses Viruses 2020, 12, 1139 2 of 12 strain and the vaccine match [6,7]. Antivirals are recommended for the treatment of seasonal influenza viruses, especially in high risk populations (elderly, immunocompromised patients and subjects with co-morbidities) [8]. Neuraminidase inhibitors (NAIs), such as oseltamivir, zanamivir, peramivir and lanamivir, constitute the main recommended drugs for the treatment of influenza viruses in many countries [9–11]. These drugs inhibit the neuraminidase (a glycoprotein that enables the virus to be released from host cell) which reduces clinical illness [9,12]. In addition to this major class of antivirals, RNA-dependent RNA polymerase (RdRp) inhibitors are also approved in a few countries to treat influenza A and B viruses. Favipiravir (also known as T-705) is a purine nucleoside analog that is recognized as an alternative substrate by the viral polymerase and is incorporated into the nascent RNA, leading to RNA viral replication errors [13,14]. Recently, baloxavir marboxil (BXM; prodrug of baloxavir acid, BXA), a cap-dependent endonuclease inhibitor, has been licensed in a few countries including USA. This compound targets the endonuclease activity of the polymerase acidic (PA) subunit, resulting in the inhibition of RNA transcription and replication [14]. Not surprisingly, prolonged antiviral therapy may lead to the emergence of drug resistance. Indeed, H275Y, E119G, I427T or I223R (N1 numbering) substitutions, among others in the neuraminidase (NA) protein, induce single or multi-drug resistance [15–17]. Rapidly after licensure, the I38T PA substitution was shown to reduce sensitivity to BXM [18–21]. On the other hand, the K229R substitution in motif F of the PB1 subunit confers in vitro resistance to favipiravir [22]. Several in vitro and in vivo studies have shown that dual antiviral therapies may have a significant positive effect on the treatment of influenza infections [13,23–25] and could further delay the emergence of resistance. Indeed, combination therapy with BXM and oseltamivir was reported to produce synergistic responses against the influenza A/PR/8/34 strain and to reduce virus titers [26]. However, there is a lack of information about combination therapy between this new polymerase inhibitor and other approved drugs. Moreover, the impact of combining two polymerase inhibitors is still unknown. Therefore, we assessed the inhibitory effects of BXA with three NAIs (oseltamivir, zanamivir and peramivir) or two other polymerase inhibitors (favipiravir and ribavirin) in cell cultures and in human airway epithelia (HAE) infected with influenza A(H1N1)pdm09 and A(H3N2) viruses. 2. Materials and Methods 2.1. Cells, Viruses and Compounds Madin–Darby canine kidney cells over expressing the α2,6 sialic acid receptor (ST6-GalI-MDCK cells) (kindly provided by Y. Kawaoka from the University of Wisconsin, Madison, WI, USA [27]) were maintained in Minimum Essential medium (MEM) supplemented with 10% fetal bovine serum (FBS), HEPES (Invitrogen, Carlsbad, CA, USA) and 7.5 µg/mL of puromycin. MucilAirTM reconstituted HAE, issued from primary cells obtained from pools of nasal biopsies, were provided by Epithelix SARL (Geneva, Switzerland) and maintained in air–liquid interphase with specific culture medium in Costar Transwell inserts (Corning, NY, USA), according to the manufacturer’s instructions. The A/California/7/2009 (H1N1)pdm09, A/Switzerland/9715293/2013 (H3N2) and A/Texas/50/2012 (H3N2) influenza viruses were obtained from NIBSC (code numbers 15/252 and 14/224, respectively) and from the Centre National de Référence des Virus des Infections Respiratoires, Lyon, France Sud. Baloxavir acid was synthesized at Shionogi & Co., Ltd. (Osaka, Japan) and diluted in dimethyl sulfoxide (DMSO) to a stock concentration of 10 mM. Favipiravir (T-705) was purchased from Adooq Bioscience (Irvine, CA, USA) and diluted in DMSO to a stock concentration of 100 mM. Oseltamivir carboxylate (the active form of oseltamivir) was synthesized by Hoffmann-La Roche (Basel, Switzerland) and diluted in sterile water to a stock concentration of 10 mM. Zanamivir and ribavirin were purchased from Sigma (St-Louis, MO, USA) and diluted in sterile water and phosphate-buffered saline (PBS), respectively, to stock concentrations of 10 mM and 100 mM, respectively. Peramivir was synthesized by Biocryst (Durham, NC, USA) and diluted in sterile water to a stock concentration of 10 mM. Viruses 2020, 12, 1139 3 of 12 2.2. In Vitro Studies of Antiviral Combinations ST6-GalI-MDCK cells (5000 cells/well) were seeded in 96-well plates and inoculated with 200 Median Tissue Culture Infectious Dose per well (TCID50/well) of each of the influenza strains (A/California/7/2009 (H1N1)pdm09 and A/Switzerland/9715293/2013 (H3N2)). Infected cells were incubated for 60 min at 37 ◦C in a 5% CO2 atmosphere, followed by the addition of BXA, each NAI, favipiravir and ribavirin in two-fold serial dilutions. For A(H1N1)pdm09 infections, concentrations of 0.0175–10 nmol/L were used for BXA; 2.34–1000 nmol/L for oseltamivir; 2.34–1000 nmol/L for zanamivir; 0.468–400 nmol/L for peramivir; 78.125–80,000 nmol/L for favipiravir; 78.125–40,000 nmol/L for ribavirin, diluted in MEM and TPCK (L-1-Tosylamide-2-phenylethyl chloromethyl ketone) trypsin (1 mg/mL). For A(H3N2) infections, concentrations of 0.39–200 nmol/L were used for BXA; 7.8–4000 nmol/L for oseltamivir; 35.15–16,000 nmol/L for zanamivir; 1.56–800 nmol/L for peramivir; 312.5–160,000 nmol/L for favipiravir; 78.125–40,000 nmol/L for ribavirin, diluted in MEM and TPCK trypsin (1 mg/mL). These dilutions were based on Fukao et al. [26] and on our preliminary experiments. Forty-eight hours later, cell viability was assessed by adding 10 µL/well of 3-(4,5-dimethylthiazol-2yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium, inner salt (MTS) (Cell Titer 96 Aqueous One Solution Cell Proliferation Assay, Promega, Madison, WI, USA) and absorbance was measured at 490 nm with a plate reader. The percentage of cell survival was calculated as described elsewhere [28,29]. Then, 50% effective concentration (EC50) values were calculated for each viral strain using Prism software (GraphPad, v7). For two-drug combination studies, the EC50 value of each drug was used to determine an equipotent ratio between the two compounds. The synergism, additivity or antagonism were calculated using the combination index (CI) values, as reported by Chou [30]. Briefly, the weighted average CI (CIwt) was calculated for each combination as (CI50 + 2 CI75 + × 3 CI90 + 4 CI95)/10 to estimate drug combination effects at high levels of virus inhibition and to × × increase therapeutic relevance [31].
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