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      Off-Target In Vitro Profiling Demonstrates that Remdesivir Is a Highly Selective Antiviral Agent

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          Abstract

          Remdesivir (RDV, GS-5734), the first FDA-approved antiviral for the treatment of COVID-19, is a single diastereomer monophosphoramidate prodrug of an adenosine analogue. It is intracellularly metabolized into the active triphosphate form, which in turn acts as a potent and selective inhibitor of multiple viral RNA polymerases.

          ABSTRACT

          Remdesivir (RDV, GS-5734), the first FDA-approved antiviral for the treatment of COVID-19, is a single diastereomer monophosphoramidate prodrug of an adenosine analogue. It is intracellularly metabolized into the active triphosphate form, which in turn acts as a potent and selective inhibitor of multiple viral RNA polymerases. RDV has broad-spectrum activity against members of the coronavirus family, such as SARS-CoV-2, SARS-CoV, and MERS-CoV, as well as filoviruses and paramyxoviruses. To assess the potential for off-target toxicity, RDV was evaluated in a set of cellular and biochemical assays. Cytotoxicity was evaluated in a set of relevant human cell lines and primary cells. In addition, RDV was evaluated for mitochondrial toxicity under aerobic and anaerobic metabolic conditions, and for the effects on mitochondrial DNA content, mitochondrial protein synthesis, cellular respiration, and induction of reactive oxygen species. Last, the active 5′-triphosphate metabolite of RDV, GS-443902, was evaluated for potential interaction with human DNA and RNA polymerases. Among all of the human cells tested under 5 to 14 days of continuous exposure, the 50% cytotoxic concentration (CC 50) values of RDV ranged from 1.7 to >20 μM, resulting in selectivity indices (SI, CC 50/EC 50) from >170 to 20,000, with respect to RDV anti-SARS-CoV-2 activity (50% effective concentration [EC 50] of 9.9 nM in human airway epithelial cells). Overall, the cellular and biochemical assays demonstrated a low potential for RDV to elicit off-target toxicity, including mitochondria-specific toxicity, consistent with the reported clinical safety profile.

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          Most cited references31

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          Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.

          The two most commonly used methods to analyze data from real-time, quantitative PCR experiments are absolute quantification and relative quantification. Absolute quantification determines the input copy number, usually by relating the PCR signal to a standard curve. Relative quantification relates the PCR signal of the target transcript in a treatment group to that of another sample such as an untreated control. The 2(-Delta Delta C(T)) method is a convenient way to analyze the relative changes in gene expression from real-time quantitative PCR experiments. The purpose of this report is to present the derivation, assumptions, and applications of the 2(-Delta Delta C(T)) method. In addition, we present the derivation and applications of two variations of the 2(-Delta Delta C(T)) method that may be useful in the analysis of real-time, quantitative PCR data. Copyright 2001 Elsevier Science (USA).
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            Remdesivir for the Treatment of Covid-19 — Final Report

            Abstract Background Although several therapeutic agents have been evaluated for the treatment of coronavirus disease 2019 (Covid-19), none have yet been shown to be efficacious. Methods We conducted a double-blind, randomized, placebo-controlled trial of intravenous remdesivir in adults hospitalized with Covid-19 with evidence of lower respiratory tract involvement. Patients were randomly assigned to receive either remdesivir (200 mg loading dose on day 1, followed by 100 mg daily for up to 9 additional days) or placebo for up to 10 days. The primary outcome was the time to recovery, defined by either discharge from the hospital or hospitalization for infection-control purposes only. Results A total of 1063 patients underwent randomization. The data and safety monitoring board recommended early unblinding of the results on the basis of findings from an analysis that showed shortened time to recovery in the remdesivir group. Preliminary results from the 1059 patients (538 assigned to remdesivir and 521 to placebo) with data available after randomization indicated that those who received remdesivir had a median recovery time of 11 days (95% confidence interval [CI], 9 to 12), as compared with 15 days (95% CI, 13 to 19) in those who received placebo (rate ratio for recovery, 1.32; 95% CI, 1.12 to 1.55; P<0.001). The Kaplan-Meier estimates of mortality by 14 days were 7.1% with remdesivir and 11.9% with placebo (hazard ratio for death, 0.70; 95% CI, 0.47 to 1.04). Serious adverse events were reported for 114 of the 541 patients in the remdesivir group who underwent randomization (21.1%) and 141 of the 522 patients in the placebo group who underwent randomization (27.0%). Conclusions Remdesivir was superior to placebo in shortening the time to recovery in adults hospitalized with Covid-19 and evidence of lower respiratory tract infection. (Funded by the National Institute of Allergy and Infectious Diseases and others; ACTT-1 ClinicalTrials.gov number, NCT04280705.)
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              Liver injury in COVID-19: management and challenges

              In December, 2019, an outbreak of a novel coronavirus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2], previously 2019-nCoV) started in Wuhan, China, and has since become a global threat to human health. The number of confirmed cases of 2019 coronavirus disease (COVID-19) has reached 87 137 worldwide as of March 1, 2020, according to WHO COVID-19 situation report 41; most of these patients are in Wuhan, China. Many cases of COVID-19 are acute and resolve quickly, but the disease can also be fatal, with a mortality rate of around 3%. 1 Onset of severe disease can result in death due to massive alveolar damage and progressive respiratory failure. 2 SARS-CoV-2 shares 82% genome sequence similarity to SARS-CoV and 50% genome sequence homology to Middle East respiratory syndrome coronavirus (MERS-CoV)—all three coronaviruses are known to cause severe respiratory symptoms. Liver impairment has been reported in up to 60% of patients with SARS 3 and has also been reported in patients infected with MERS-CoV. 4 At least seven relatively large-scale case studies have reported the clinical features of patients with COVID-19.1, 5, 6, 7, 8, 9, 10 In this Comment, we assess how the liver is affected using the available case studies and data from The Fifth Medical Center of PLS General Hospital, Beijing, China. These data indicate that 2–11% of patients with COVID-19 had liver comorbidities and 14–53% cases reported abnormal levels of alanine aminotransferase and aspartate aminotransferase (AST) during disease progression (table ). Patients with severe COVID-19 seem to have higher rates of liver dysfunction. In a study in The Lancet by Huang and colleagues, 5 elevation of AST was observed in eight (62%) of 13 patients in the intensive care unit (ICU) compared with seven (25%) of 28 patients who did not require care in the ICU. Moreover, in a large cohort including 1099 patients from 552 hospitals in 31 provinces or provincial municipalities, more severe patients with disease had abnormal liver aminotransferase levels than did non-severe patients with disease. 1 Furthermore, in another study, 8 patients who had a diagnosis of COVID-19 confirmed by CT scan while in the subclinical phase (ie, before symptom onset) had significantly lower incidence of AST abnormality than did patients diagnosed after the onset of symptoms. Therefore, liver injury is more prevalent in severe cases than in mild cases of COVID-19. Table Comorbidity with liver disease and liver dysfunction in patients with SARS-CoV-2 infection Patients with SARS-CoV-2 infection Patients with pre-existing liver conditions Patients with abnormal liver function Notes Guan et al 1 1099 23 (2·3%) AST abnormal (22·2%), ALT abnormal (21·3%) Elevated levels of AST were observed in 112 (18·2%) of 615 patients with non-severe disease and 56 (39·4%) of 142 patients with severe disease. Elevated levels of ALT were observed in 120 (19·8%) of patients with non-severe disease and 38 (28·1%) of 135 patients with severe disease. Huang et al 5 41 1 (2·0%) 15 (31·0%) Patients with severe disease had increased incidence of abnormal liver function. Elevation of AST level was observed in eight (62%) of 13 patients in the ICU compared with seven (25%) 25 patients who did not require care in the ICU. Chen et al 6 99 NA 43 (43·0%) One patient with severe liver function damage. Wang et al 7 138 4 (2·9%) NA .. Shi et al 8 81 7 (8·6%) 43 (53·1%) Patients who had a diagnosis of COVID-19 confirmed by CT scan while in the subclinical phase had significantly lower incidence of AST abnormality than did patients diagnosed after the onset of symptoms. Xu et al 9 62 7 (11·0%) 10 (16·1%) .. Yang et al 10 52 NA 15 (29·0%) No difference for the incidences of abnormal liver function between survivors (30%) and non-survivors (28%). Our data (unpublished) 56 2 (3·6%) 16 (28·6%) One fatal case, with evaluated liver injury. 13 AST= aspartate aminotransferase. ALT= alanine aminotransferase. ICU=intensive care unit. Liver damage in patients with coronavirus infections might be directly caused by the viral infection of liver cells. Approximately 2–10% of patients with COVID-19 present with diarrhoea, and SARS-CoV-2 RNA has been detected in stool and blood samples. 11 This evidence implicates the possibility of viral exposure in the liver. Both SARS-CoV-2 and SARS-CoV bind to the angiotensin-converting enzyme 2 (ACE2) receptor to enter the target cell, 7 where the virus replicates and subsequently infects other cells in the upper respiratory tract and lung tissue; patients then begin to have clinical symptoms and manifestations. Pathological studies in patients with SARS confirmed the presence of the virus in liver tissue, although the viral titre was relatively low because viral inclusions were not observed. 3 In patients with MERS, viral particles were not detectable in liver tissue. 4 Gamma-glutamyl transferase (GGT), a diagnostic biomarker for cholangiocyte injury, has not been reported in the existing COVID-19 case studies; we found that it was elevated in 30 (54%) of 56 patients with COVID-19 during hospitalisation in our centre (unpublished). We also found that elevated alkaline phosphatase levels were observed in one (1·8%) of 56 patients with COVID-19 during hospitalisation. A preliminary study (albeit not peer-reviewed) suggested that ACE2 receptor expression is enriched in cholangiocytes, 12 indicating that SARS-CoV-2 might directly bind to ACE2-positive cholangiocytes to dysregulate liver function. Nevertheless, pathological analysis of liver tissue from a patient who died from COVID-19 showed that viral inclusions were not observed in the liver. 13 It is also possible that the liver impairment is due to drug hepatotoxicity, which might explain the large variation observed across the different cohorts. In addition, immune-mediated inflammation, such as cytokine storm and pneumonia-associated hypoxia, might also contribute to liver injury or even develop into liver failure in patients with COVID-19 who are critically ill. Liver damage in mild cases of COVID-19 is often transient and can return to normal without any special treatment. However, when severe liver damage occurs, liver protective drugs have usually been given to such patients in our unit. Chronic liver disease represents a major disease burden globally. Liver diseases including chronic viral hepatitis, non-alcoholic fatty liver disease, and alcohol-related liver disease affect approximately 300 million people in China. Given this high burden, how different underlying liver conditions influence liver injury in patients with COVID-19 needs to be meticulously evaluated. However, the exact cause of pre-existing liver conditions has not been outlined in the case studies of COVID-19 and the interaction between existing liver disease and COVID-19 has not been studied. Immune dysfunction—including lymphopenia, decreases of CD4+ T-cell levels, and abnormal cytokine levels (including cytokine storm)—is a common feature in cases of COVID-19 and might be a critical factor associated with disease severity and mortality. For patients with chronic hepatitis B in immunotolerant phases or with viral suppression under long-term treatment with nucleos(t)ide analogues, evidence of persistent liver injury and active viral replication after co-infection with SARS-CoV-2 need to be further investigated. In patients with COVID-19 with autoimmune hepatitis, the effects of administration of glucocorticoids on disease prognosis is unclear. Given the expression of the ACE2 receptor in cholangiocytes, whether infection with SARS-CoV-2 aggravates cholestasis in patients with primary biliary cholangitis, or leads to an increase in alkaline phosphatase and GGT, also needs to be monitored. Moreover, patients with COVID-19 with liver cirrhosis or liver cancer might be more susceptible to SARS-CoV-2 infection because of their systemic immunocompromised status. The severity, mortality, and incidence of complications in these patients, including secondary infection, hepatic encephalopathy, upper gastrointestinal bleeding, and liver failure, need to be examined in large-cohort clinical studies. Considering their immunocompromised status, more intensive surveillance or individually tailored therapeutic approaches is needed for severe patients with COVID-19 with pre-existing conditions such as advanced liver disease, especially in older patients with other comorbidities. Further research should focus on the causes of liver injury in COVID-19 and the effect of existing liver-related comorbidities on treatment and outcome of COVID-19.
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                Author and article information

                Journal
                Antimicrob Agents Chemother
                Antimicrob Agents Chemother
                aac
                aac
                AAC
                Antimicrobial Agents and Chemotherapy
                American Society for Microbiology (1752 N St., N.W., Washington, DC )
                0066-4804
                1098-6596
                23 November 2020
                20 January 2021
                February 2021
                20 January 2021
                : 65
                : 2
                : e02237-20
                Affiliations
                [a ]Gilead Sciences, Inc., Foster City, California, USA
                Author notes
                Address correspondence to Joy Y. Feng, joy.feng@ 123456gilead.com .
                [*]

                Present address: Ona Barauskas, Vir Biotechnology, San Francisco, California, USA; Michel Perron, Janssen BioPharma Inc., Janssen Pharmaceutical Companies, South San Francisco, California, USA.

                Citation Xu Y, Barauskas O, Kim C, Babusis D, Murakami E, Kornyeyev D, Lee G, Stepan G, Perron M, Bannister R, Schultz BE, Sakowicz R, Porter D, Cihlar T, Feng JY. 2021. Off-target in vitro profiling demonstrates that remdesivir is a highly selective antiviral agent. Antimicrob Agents Chemother 65:e02237-20. https://doi.org/10.1128/AAC.02237-20.

                Author information
                https://orcid.org/0000-0003-4837-1911
                Article
                02237-20
                10.1128/AAC.02237-20
                7849018
                33229429
                b4472f68-1d73-4fd5-891d-6da5dced78b1
                Copyright © 2021 Xu et al.

                This article is made available via the PMC Open Access Subset for unrestricted noncommercial re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.

                History
                : 22 October 2020
                : 4 November 2020
                : 20 November 2020
                Page count
                Figures: 5, Tables: 6, Equations: 6, References: 31, Pages: 14, Words: 9319
                Funding
                Funded by: Gilead Sciences (Gilead), https://doi.org/10.13039/100005564;
                Award Recipient : Award Recipient : Award Recipient : Award Recipient : Award Recipient : Award Recipient : Award Recipient : Award Recipient : Award Recipient : Award Recipient : Award Recipient : Award Recipient : Award Recipient : Award Recipient : Award Recipient :
                Categories
                Antiviral Agents
                Custom metadata
                February 2021

                Infectious disease & Microbiology
                covid-19,sars-cov-2,antiviral agents,mitochondria,mitochondrial respiration,nucleoside analogs,remdesivir,toxicity

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