Discovery of a non-nucleoside RNA polymerase inhibitor for blocking Zika virus replication through in silico screening

Pattnaik, Aryamav; Palermo, Nicholas Y.; Sahoo, Bikash R.; Yuan, Zhe; Hu, Duoyi; Annamalai, Arun S.; Vu, Hiep L.X.; Correas, Ignacio; Prathipati, Pavan Kumar; Destache, Christopher J.; Li, Qingsheng; Osorio, Fernando A.; Pattnaik, Asit K.; Xiang, Shi Hua

doi:10.1016/j.antiviral.2017.12.016

Cited by 55 publications

(42 citation statements)

References 52 publications

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“…4b). To confirm that these differences were due to decreased RNA replication rather than defects at other stages of the viral life cycle, we treated infected sphingolipid-depleted and normal cells with an inhibitor of ZIKV RNA polymerase (TPB) 49 and measured intracellular replication relative to non-TPB-treated cells at 8 hpi (Fig. 4c).…”

Section: Resultsmentioning

confidence: 98%

A global lipid map defines a network essential for Zika virus replication

Leier

Weinstein

Kyle

et al. 2020

Preprint

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26Zika virus (ZIKV), an arbovirus of global concern, remodels intracellular membranes to form 27 replication sites. How ZIKV dysregulates lipid networks to allow this, and consequences for 28 disease, is poorly understood. Here, we performed comprehensive lipidomics to create a lipid 29 network map during ZIKV infection. We found that ZIKV significantly alters host lipid 30 composition, with the most striking changes seen within subclasses of sphingolipids. Ectopic 31 expression of ZIKV NS4B protein resulted in similar changes, demonstrating a role for NS4B in 32 modulating sphingolipid pathways. Disruption of sphingolipid biosynthesis in various cell types, 33including human neural progenitor cells, blocked ZIKV infection. Additionally, the sphingolipid 34 ceramide redistributes to ZIKV replication sites and increasing ceramide levels by multiple 35 pathways sensitizes cells to ZIKV infection. Thus, we identify a sphingolipid metabolic network 36 with a critical role in ZIKV replication and show that ceramide flux is a key mediator of ZIKV 37 infection. Results 112 ZIKV alters the lipid landscape of host cells 113To understand how cellular lipid metabolism is altered by ZIKV infection, we carried out 114 a global lipidomic survey of the model Huh7 human hepatic carcinoma cell line 20 infected for 24 115 or 48 hours with Asian lineage ZIKV strain FSS13025 (Fig. 1a). Lipids extracted from 116 populations of mock and infected cells (n = 5 biological replicates per condition) were analyzed 117 with electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) (Supplementary Data 118 1 and Supplementary Fig. 1a-f). We identified 340 lipid species spanning the phospholipid, 119 sphingolipid, glycerolipid, and sterol classes for which pairwise comparisons of normalized 120 abundance between mock and infected cells could be made (Supplementary Data 1). Of these, 121 80 species (23.5%) showed significant changes in abundance by 24 hours post-infection (hpi) 122 and 172 species (50.6%) were significantly altered by 48 hpi (P < 0.05, ANOVA or g-test) 123( Supplementary Data 1). Principal component analysis (PCA) of these observations confirmed 124 that infection status (mock or ZIKV) and timepoint (24 or 48 hpi) accounted most of these 125 changes, with changes in lipid composition between mock and infected cells increasing over 126 time (Fig. 1b). 127Next, we examined how ZIKV-induced changes in host lipid composition broke down by 128 subclass and species (Fig. 1c, d). A map of the pairwise correlations of all 340 species at 48 hpi 129 ( Supplementary Fig. 2a) revealed that lipid subclasses largely fell into two groups of species 130 that were either enriched or depleted in abundance ( Supplementary Fig. 2b), suggesting that 131 individual metabolic pathways are up-or down-regulated to create a specific lipid milieu around 132 the events of the viral replication cycle. Supporting this, many of the trends we observed were 133 consistent with earlier reports of functional roles for lipids during flavivirus infection. In ...

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Section: Resultsmentioning

confidence: 98%

A global lipid map defines a network essential for Zika virus replication

Leier

Weinstein

Kyle

et al. 2020

Preprint

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“…First, we included 13 diverse structural analogues of 1a ( 1a – 1o ): these compounds have been previously identified in our group as potent inhibitors of the replication of hepatitis C virus, which is also a flavivirus [ 18 ]. In addition, we screened a second series of 11 non-nucleoside compounds, 2a – 2m : 2a has been previously reported as a potent inhibitor of ZIKV replication in Vero cells, with efficacy in reducing ZIKV viremia in vivo in an immunocompetent mouse model, and a mechanism of action pointing towards inhibition of the viral RNA-dependent RNA polymerase (RdRp) [ 19 ]. Different structural analogues of 2a , among which we selected 2b – 2m , have been recently explored in our research group for their inhibition of human norovirus (hNoV) RdRp, and their ability to interfere with hNoV replication in a replicon system [ 20 ].…”

Section: Resultsmentioning

confidence: 99%

Novel Nucleoside Analogues as Effective Antiviral Agents for Zika Virus Infections

et al. 2020

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Previously considered a neglected flavivirus, Zika virus has recently emerged as a public health concern due to its ability to spread rapidly and cause severe neurological disorders, such as microcephaly in newborn babies from infected mothers, and Guillain-Barré syndrome in adults. Despite extensive efforts towards the identification of effective therapies, specific antivirals are still not available. As part of ongoing medicinal chemistry studies to identify new antiviral agents, we screened against Zika virus replication in vitro in a targeted internal library of small-molecule agents, comprising both nucleoside and non-nucleoside agents. Among the compounds evaluated, novel aryloxyphosphoramidate prodrugs of the nucleosides 2′-C-methyl-adenosine, 2-CMA, and 7-deaza-2′C-methyl-adenosine, 7-DMA, were found to significantly inhibit the virus-induced cytopathic effect in multiple relevant cell lines. In addition, one of these prodrugs exhibits a synergistic antiviral effect against Zika virus when applied in combination with an indirect antiviral agent, a l-dideoxy bicyclic pyrimidine nucleoside analogue, which potently inhibits vaccinia and measles viruses in vitro by targeting a host pathway. Our findings provide a solid basis for further development of an antiviral therapy for Zika virus infections, possibly exploiting a dual approach combining two different agents, one targeting the viral polymerase (direct-acting antiviral), the second targeting a host-directed autophagy mechanism.

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“…Furthermore, in vivo studies (25 mg/kg) in animals (immunocompetent mice) infected with ZIKV and treating with the compound, TPB showed a reduction of 40-fold plasma viral load compared to the untreated controls. In addition, PK analysis of the compound in the same animal in post-injection period was also found to retain it in the mouse plasma at 150-100 ng/mL level for 10-12 h. Thus, TPB appears to be a promising compound against ZIKV infection [130].…”

Section: [103]mentioning

confidence: 83%

“…Non-nucleoside RNA polymerase inhibitors: By in silico screening of a compound library of 100,000 small molecules based on Zika RNA-dependent RNA polymerase (RdRp) structure, ten lead compounds were reported in a recent study [130]. Through in vitro tests in Vero cell assays, one of these compounds, 3-chloro-N-[(amino)carbonothioyl]-1-benzothiophene-2-carbox-amide (TPB), a non-nucleoside, was found to inhibit ZIKV replication with an EC50 in submicromolar concentration (0.94 µM) [130]. In silico molecular docking evaluations suggest that the compound binds to the catalytic site of the ZIKV RdRp, acting as an allosteric agent to block the viral RNA synthesis.…”

Section: [103]mentioning

confidence: 99%

Computer-Assisted and Data Driven Approaches for Surveillance, Drug Discovery, and Vaccine Design for the Zika Virus

et al. 2019

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Human life has been at the edge of catastrophe for millennia due diseases which emerge and reemerge at random. The recent outbreak of the Zika virus (ZIKV) is one such menace that shook the global public health community abruptly. Modern technologies, including computational tools as well as experimental approaches, need to be harnessed fast and effectively in a coordinated manner in order to properly address such challenges. In this paper, based on our earlier research, we have proposed a four-pronged approach to tackle the emerging pathogens like ZIKV: (a) Epidemiological modelling of spread mechanisms of ZIKV; (b) assessment of the public health risk of newly emerging strains of the pathogens by comparing them with existing strains/pathogens using fast computational sequence comparison methods; (c) implementation of vaccine design methods in order to produce a set of probable peptide vaccine candidates for quick synthesis/production and testing in the laboratory; and (d) designing of novel therapeutic molecules and their laboratory testing as well as validation of new drugs or repurposing of drugs for use against ZIKV. For each of these stages, we provide an extensive review of the technical challenges and current state-of-the-art. Further, we outline the future areas of research and discuss how they can work together to proactively combat ZIKV or future emerging pathogens.

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Discovery of a non-nucleoside RNA polymerase inhibitor for blocking Zika virus replication through in silico screening

Cited by 55 publications

References 52 publications

A global lipid map defines a network essential for Zika virus replication

A global lipid map defines a network essential for Zika virus replication

Novel Nucleoside Analogues as Effective Antiviral Agents for Zika Virus Infections

Computer-Assisted and Data Driven Approaches for Surveillance, Drug Discovery, and Vaccine Design for the Zika Virus

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