The global spread of SARS-CoV-2 requires an urgent need to find effective therapeutics for the treatment of COVID-19. We developed a data-driven drug repositioning framework, which applies both machine learning and statistical analysis approaches to systematically integrate and mine large-scale knowledge graph, literature and transcriptome data to discover the potential drug candidates against SARS-CoV-2. The retrospective study using the past SARS-CoV and MERS-CoV data demonstrated that our machine learning based method can successfully predict effective drug candidates : bioRxiv preprint against a specific coronavirus. Our in silico screening followed by wet-lab validation indicated that a poly-ADP-ribose polymerase 1 (PARP1) inhibitor, CVL218, currently in Phase I clinical trial, may be repurposed to treat COVID-19. Our in vitro assays revealed that CVL218 can exhibit effective inhibitory activity against SARS-CoV-2 replication without obvious cytopathic effect. In addition, we showed that CVL218 is able to suppress the CpG-induced IL-6 production in peripheral blood mononuclear cells, suggesting that it may also have anti-inflammatory effect that is highly relevant to the prevention immunopathology induced by SARS-CoV-2 infection. Further pharmacokinetic and toxicokinetic evaluation in rats and monkeys showed a high concentration of CVL218 in lung and observed no apparent signs of toxicity, indicating the appealing potential of this drug for the treatment of the pneumonia caused by SARS-CoV-2 infection. Moreover, molecular docking simulation suggested that CVL218 may bind to the N-terminal domain of nucleocapsid (N) protein of SARS-CoV-2, providing a possible model to explain its antiviral action. We also proposed several possible mechanisms to explain the antiviral activities of PARP1 inhibitors against SARS-CoV-2, based on the data present in this study and previous evidences reported in the literature. In summary, the PARP1 inhibitor CVL218 discovered by our data-driven drug repositioning framework can serve as a potential therapeutic agent for the treatment of COVID-19.

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The effects of ultrasound on the molecular weight, structure, and antioxidant potential of a fucoidan found in Isostichopus badionotus were investigated. The results showed the molecular weight (Mw) of fucoidan decreased obviously after ultrasound treatment. Higher ultrasonic intensity, lower temperature, and lower fucoidan concentrations led to a more effective sonochemical effect. The kinetic model for fucoidan degradation fitted to 1/M(wt)-1/M(w0) = kt at the tested temperature. The optimized degradation conditions by response surface methodology (RSM) were temperature, 12 °C, and intensity, 508 W/cm². Structural analysis by FTIR and NMR indicated the fucoidan kept the linear tetrasaccharide repeating units as the original polysaccharides after the ultrasound treatment, with only slight destruction of the middle nonsulfated fucose units. Antioxidant activity assay showed the antioxidant activity was slightly improved by the ultrasound treatment. The results suggested that ultrasound treatment is an effective approach to decrease the M(w) of fucoidan with only minor structural destruction.

Understanding the phase separation characteristics of nucleocapsid protein provides a new therapeutic opportunity against SARS-CoV-2 Dear EditorTo date, tens of millions of people have been infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing the outbreak of the respiratory disease named the coronavirus disease 2019 . As a newly emerged member of the coronavirus family, SARS-CoV-2 is an enveloped positive-strand RNA virus, which has probably the largest genome (approximately 30 kb) among all RNA viruses. The nucleocapsid (N) protein of SARS-CoV-2 is mainly responsible for recognizing and wrapping viral RNA into helically symmetric structures (Malik, 2020). It was also reported that N protein can boost the efficiency of transcription and replication of viral RNA, implying its vital and multifunctional roles in the life cycle of coronavirus (Surjit and Lal, 2008;Chang et al., 2014). Recently, several independent research teams have reported that N protein of SARS-CoV-2 is capable of undergoing liquid-liquid phase separation (LLPS) (Iserman et al., 2020;Perdikari et al., 2020;Savastano et al., 2020).Here, we comprehensively determined the characteristics of the phase separation driven by the N protein of SARS-CoV-2 (termed SARS-CoV-2 N), and found that LLPS is involved in the interplay between the N protein-viral RNA complex of SARS-CoV-2 (termed SARS-CoV-2 N-RNA) and other viral proteins, such as nsp12. Importantly, we identified two small molecules targeting the SARS-CoV-2 N protein, which can intervene the phase separation properties of the N protein-viral RNA-nsp12 (termed SARS-CoV-2 N-RNA-nsp12) complex, thus probably improving the accessibility of other antiviral drugs (e.g., remdesivir) to their viral targets (e. g., nsp12/RdRp).First, IUPred2 (Erdos and Dosztanyi, 2020) and PLAAC (Lancaster et al., 2014) programs showed that SARS-CoV-2 N is highly disordered, and contains three intrinsically disordered regions (IDRs), with one also displaying prion-like activity (Figs. 1A and S1). Then, we expressed and purified the recombinant SARS-CoV-2 N protein with an mEGFP-tag (a monomeric variant of EGFP, A206K) or a His-tag using a prokaryotic expression system to understand the properties of N-driven LLPS in vitro (Fig. S2A and S2B). Confocal fluorescence microscopy showed that SARS-CoV-2 N was readily self-associated to form numerous micron-sized spherical condensates (Fig. 1B and 1C). Further time-lapse observations revealed that the SARS-CoV-2 N condensates fused and coalesced into larger ones upon their intersections (Fig. 1D and Video S1), verifying the liquid-like properties of SARS-CoV-2 N condensates. We also used fluorescence recovery after photobleaching (FRAP) to deeply study the dynamics of internal molecules within the N protein condensates. Recovery of fluorescence within the bleached regions (Fig. 1E) showed that SARS-CoV-2 N can partially freely diffuse within the condensed phase, consistent with their liquid-like behavior. In addition, phase condensation of SARS-CoV-2 ...

Chikungunya virus (CHIKV) is an arthritogenic alphavirus that causes debilitating musculoskeletal disease. CHIKV displays broad cell, tissue, and species tropism, which may correlate with the attachment factors and entry receptors used by the virus. Cell-surface glycosaminoglycans (GAGs) have been identified as CHIKV attachment factors. However, the specific types of GAGs and potentially other glycans to which CHIKV binds and whether there are strain-specific differences in GAG binding is not fully understood. To identify the types of glycans bound by CHIKV, we conducted glycan microarray analyses and discovered that CHIKV preferentially binds GAGs. Microarray results also indicate that sulfate groups on GAGs are essential for CHIKV binding and that CHIKV binds most strongly to longer GAG chains of heparin and heparan sulfate. To determine whether GAG-binding capacity varies among CHIKV strains, a representative strain from each genetic clade was tested. While all strains directly bound to heparin and chondroitin sulfate in ELISAs and depended on heparan sulfate for efficient cell-binding and infection, we observed some variation by strain. Enzymatic removal of cell-surface GAGs and genetic ablation that diminishes GAG expression reduced CHIKV binding and infectivity of all strains. Collectively, these data demonstrate that GAGs are the preferred glycan bound by CHIKV, enhance our understanding of the specific GAG moieties required for CHIKV binding, define strain differences in GAG engagement, and provide further evidence for a critical function of GAGs in CHIKV cell attachment and infection. IMPORTANCE Alphavirus infections are a global health threat, contributing to outbreaks of disease in many parts of the world. Recent epidemics caused by CHIKV, an arthritogenic alphavirus, resulted in more than 8.5 million cases as the virus has spread into new geographic regions, including the Western Hemisphere. CHIKV causes disease in the majority of people infected, leading to severe and debilitating arthritis. Despite the severity of CHIKV disease, there are no licensed therapeutics. Since attachment factors and receptors are determinants of viral tropism and pathogenesis, understanding these virus-host interactions can enhance our knowledge of CHIKV infection. We analyzed over 670 glycans and identified GAGs as the main glycan bound by CHIKV. We defined specific GAG components required for CHIKV binding and assessed strain-specific differences in GAG-binding capacity. These studies provide insight about cell-surface molecules that CHIKV binds, which could facilitate the development of antiviral therapeutics targeting the CHIKV attachment step.

The fresh water clam Corbicula fluminea is currently one of the most economically important aquatic species in China because of its nutritional value and pharmacological activity. In order to explore the potential of C. fluminea as a natural resource of bioactive compounds, a papain-released polysaccharide designated CFPS-2 was isolated. Chemical composition analysis indicated that CFPS-2 contained glucosamine, glucose, galactose, fucose, protein and sulfate groups, with an average molecular weight of about 22 kDa. Furthermore, the antioxidant and antitumor activities, in vitro, of the polysaccharide fractions (crude CFPS and purified CFPS-2) were evaluated. CFPS-2, which exhibited strong antioxidant activities in a dose dependent manner also showed significant inhibitory effects on growth of human gastric cancer cells (SGC7901) and human ovarian carcinoma cells (SKOV3 and A2780). The present results suggest that CFPS-2 could be a potential candidate for the development of novel functional food ingredient.

The global spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires an urgent need to find effective therapeutics for the treatment of coronavirus disease 2019 (COVID-19). In this study, we developed an integrative drug repositioning framework, which fully takes advantage of machine learning and statistical analysis approaches to systematically integrate and mine large-scale knowledge graph, literature and transcriptome data to discover the potential drug candidates against SARS-CoV-2. Our in silico screening followed by wet-lab validation indicated that a poly-ADP-ribose polymerase 1 (PARP1) inhibitor, CVL218, currently in Phase I clinical trial, may be repurposed to treat COVID-19. Our in vitro assays revealed that CVL218 can exhibit effective inhibitory activity against SARS-CoV-2 replication without obvious cytopathic effect. In addition, we showed that CVL218 can interact with the nucleocapsid (N) protein of SARS-CoV-2 and is able to suppress the LPS-induced production of several inflammatory cytokines that are highly relevant to the prevention of immunopathology induced by SARS-CoV-2 infection.

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