Identification of Novel Influenza Polymerase PB2 Inhibitors Using a Cascade Docking Virtual Screening Approach

To discover novel inhibitors that target the influenza polymerase basic protein 2 (PB2) cap-binding domain (CBD), commercial ChemBridge compound libraries containing 384,796 compounds were screened using a cascade docking of LibDock–LigandFit–GOLD, and 60 compounds were selected for testing with cytopathic effect (CPE) inhibition assays and surface plasmon resonance (SPR) assay. Ten compounds were identified to rescue cells from H1N1 virus-mediated death at non-cytotoxic concentrations with EC₅₀ values ranging from 0.30 to 67.65 μM and could bind to the PB2 CBD of H1N1 with Kd values ranging from 0.21 to 6.77 μM. Among these, four compounds (11D4, 12C5, 21A5, and 21B1) showed inhibition of a broad spectrum of influenza virus strains, including oseltamivir-resistant ones, the PR/8-R292K mutant (H1N1, recombinant oseltamivir-resistant strain), the PR/8-I38T mutant (H1N1, recombinant baloxavir-resistant strain), and the influenza B/Lee/40 virus strain. These compounds have novel chemical scaffolds and relatively small molecular weights and are suitable for optimization as lead compounds. Based on sequence and structure comparisons of PB2 CBDs of various influenza virus subtypes, we propose that the Phe323/Gln325, Asn429/Ser431, and Arg355/Gly357 mutations, particularly the Arg355/Gly357 mutation, have a marked impact on the selectivities of PB2 CBD-targeted inhibitors of influenza A and influenza B.     

Synthesis and Antiviral Evaluation of Nucleoside Analogues Bearing One Pyrimidine Moiety and Two D-Ribofuranosyl Residues

A series of 1,2,3-triazolyl nucleoside analogues in which 1,2,3-triazol-4-yl-β-d-ribofuranosyl fragments are attached via polymethylene linkers to both nitrogen atoms of the heterocycle moiety (uracil, 6-methyluracil, thymine, quinazoline-2,4-dione, alloxazine) or to the C-5 and N-3 atoms of the 6-methyluracil moiety was synthesized. All compounds synthesized were evaluated for antiviral activity against influenza virus A/PR/8/34/(H1N1) and coxsackievirus B3. Antiviral assays revealed three compounds, 2i, 5i, 11c, which showed moderate activity against influenza virus A H1N1 with IC₅₀ values of 57.5 µM, 24.3 µM, and 29.2 µM, respectively. In the first two nucleoside analogues, 1,2,3-triazol-4-yl-β-d-ribofuranosyl fragments are attached via butylene linkers to N-1 and N-3 atoms of the heterocycle moiety (6-methyluracil and alloxazine, respectively). In nucleoside analogue 11c, two 1,2,3-triazol-4-yl-2′,3′,5′-tri-O-acetyl-β-d-ribofuranose fragments are attached via propylene linkers to the C-5 and N-3 atoms of the 6-methyluracil moiety. Almost all synthesized 1,2,3-triazolyl nucleoside analogues showed no antiviral activity against the coxsackie B3 virus. Two exceptions are 1,2,3-triazolyl nucleoside analogs 2f and 5f, in which 1,2,3-triazol-4-yl-2′,3′,5′-tri-O-acetyl-β-d-ribofuranose fragments are attached to the C-5 and N-3 atoms of the heterocycle moiety (6-methyluracil and alloxazine respectively). These compounds exhibited high antiviral potency against the coxsackie B3 virus with IC₅₀ values of 12.4 and 11.3 µM, respectively, although both were inactive against influenza virus A H1N1. According to theoretical calculations, the antiviral activity of the 1,2,3-triazolyl nucleoside analogues 2i, 5i, and 11c against the H1N1 (A/PR/8/34) influenza virus can be explained by their influence on the functioning of the polymerase acidic protein (PA) of RNA-dependent RNA polymerase (RdRp). As to the antiviral activity of nucleoside analogs 2f and 5f against coxsackievirus B3, it can be explained by their interaction with the coat proteins VP1 and VP2.     

Discovery of New Ginsenol-Like Compounds with High Antiviral Activity

A number of framework amides with a ginsenol backbone have been synthesized using the Ritter reaction. We named the acetamide as Ginsamide. A method was developed for the synthesis of the corresponding amine and thioacetamide. The new compounds revealed a high activity against H1N1 influenza, which was confirmed using an animal model. Biological experiments were performed to determine the mechanism of action of the new agents, a ginsamide-resistant strain of influenza virus was obtained, and the pathogenicity of the resistant strain and the control strain was studied. It was shown that the emergence of resistance to Ginsamide was accompanied by a reduction in the pathogenicity of the influenza virus.     

Synthesis of Pyrimidine Conjugates with 4-(6-Amino-hexanoyl)-7,8-difluoro-3,4-dihydro-3-methyl-2H-[1,4]benzoxazine and Evaluation of Their Antiviral Activity

A series of pyrimidine conjugates containing a fragment of racemic 7,8-difluoro-3,4-dihydro-3-methyl-2H-[1,4]benzoxazine and its (S)-enantiomer attached via a 6-aminohexanoyl fragment were synthesized by the reaction of nucleophilic substitution of chlorine in various chloropyrimidines. The structures of the synthesized compounds were confirmed by ¹H, ¹⁹F, and ¹³C NMR spectral data. Enantiomeric purity of optically active derivatives was confirmed by chiral HPLC. Antiviral evaluation of the synthesized compounds has shown that the replacement of purine with a pyrimidine fragment leads to a decrease in the anti-herpesvirus activity compared to the lead compound, purine conjugate. The studied compounds did not exhibit significant activity against influenza A (H1N1) virus.     

2,5-Diketopiperazine Derivatives as Potential Anti-Influenza (H5N2) Agents: Synthesis,Biological Evaluation,and Molecular Docking Study

2,5-Diketopiperazine derivatives, consisting of benzylidene and alkylidene substituents at 3 and 6 positions, have been considered as a core structure for their antiviral activities. Herein, the novel N-substituted 2,5-Diketopiperazine derivatives were successfully prepared and their antiviral activities against influenza virus were evaluated by monitoring viral propagation in embryonated chicken eggs. It was found that (3Z,6Z)-3-benzylidene-6-(2-methyl propylidene)-4-substituted-2,5-Diketopiperazines (13b–d), (3Z,6E)-3-benzylidene-6-(2-methylpropyli dene)-1-(1-ethyl pyrrolidine)-2,5-Diketopiperazine (14c), and Lansai-C exhibited negative results in influenza virus propagation at a concentration of 25 µg/mL. Additionally, molecular docking study revealed that 13b–d and 14c bound in 430-cavity of neuraminidase from H5N2 avian influenza virus and the synthesized derivatives also strongly interacted with the key amino acid residues, including Arg371, Pro326, Ile427, and Thr439.     

Features of oxa-bridge cleavage in hexahydro-3a,6-epoxyisoindol-1(4H)-ones: A concise method to access acetylisoindolones possessing anti-viral activity

Unusual stereo- and regioselective methods for epoxy-bridge cleavage in perhydro-3a,6-epoxyisoindolones, under the action of the BF₃·Et₂O/Ac₂O system, were discovered. The reaction pathway strongly depends on the characteristics of the isoindolone ring substituents and allows the synthesis of a wide diversity of isoindole-containing heterocycles. The obtained isoindolinones belong to a new class of anti-viral agents possessing a high activity against influenza virus A/Puerto Rico/8/34 (H1N1) in in vitro experiments.     

Wickerols A and B: novel anti-influenza virus diterpenes produced by Trichoderma atroviride FKI-3849

Wickerols A and B were produced by a fungus, Trichoderma atroviride FKI-3849. Wickerol A showed potent anti-influenza virus activity against strain A/PR/8/34 (H1N1), whereas wickerol B exhibited weaker impact. The anti-influenza virus spectrum between wickerols A and B was different. The cyclization mechanism of the wickerol carbon-skeleton was investigated by incorporation of ¹³C-labeled acetate. A pathway through the verticillyl cation was predicted.     

Antiinfluenza virus activity of a bacteriocin produced by Lactobacillus delbrueckii

A novel antibacterial substance produced by Lactobacillus delbrueckii has been isolated and characterized (1). The inhibitory agent corresponded to the criteria for bacteriocins. It was active against lactic acid bacteria (LAB) species and several food-borne pathogens. The cell-free supernatant was purified by HPLC gel-filtration. Three preparations at different purification steps were tested for activity on the reproduction of influenza virus A/chicken/Germany, strain Weybridge (H7N7) and strain Rostock (H7N1) in cell cultures of chicken embryo fibroblasts (CEF). The inhibitory effect was shown to be highly selective and specific. Expression of viral glycoproteins hemagglutinin, neuraminidase, and nucleoprotein on the surface of infected cells, virus-induced cytopathic effect, infectious virus yield, and hemagglutinin production were all reduced at nontoxic concentrations of the crude preparation (B1). B1 did not protect cells from infection, did not affect adsorption, and slightly inhibited viral penetration into infected cells. The purification did not enhance the cellular toxicity and increased about 870-fold the virus-inhibitory activity. No inactivating effect on extracellular virus was found.     

New triterpenoid saponins from the roots of Platycodon grandiflorum

Bioassay-directed fractionation of the antiviral active fraction of the roots of Platycodon grandiflorum leads to the isolation of three new triterpenoid saponins, platycosides G1-G3 (1-3), as well as two known saponins, platycodin D3 (4), and platycoside E (5). The structures of the new compounds were elucidated on the basis of their spectral data and chemical evidences. The isolated saponins were tested for their antiviral activities against respiratory syncytial virus (RSV), herpes simplex type 1 virus (HSV-1) and influenza type A virus (Flu A). Compound 4 showed weak anti-RSV activity.     

Microbial biotransformations in water/organic solvent system. Enantioselective reduction of aromatic β- and γ-nitroketones

The production of single enantiomers of γ- and β-nitroalcohols by microbial bioreduction has been studied. A restricted screening among 14 yeasts was performed using 1-phenyl-4-nitro-1-butanone 1 as substrate. Pichia minuta (CBS 1708) and Pichia etchellsii (CBS 2011) gave the highest enantiopreference for (S)-alcohol 3 formation (e.e. 85% and 80%, respectively), while Kluyveromyces marxianus (CBS 397) was the only strain able to preferentially furnish the (R) enantiomer (e.e. 70%). These three microorganisms, along with baker's yeast, were then employed in reactions performed in water/organic solvent systems using different solvents (hexane, benzene and dibutyl ether) affording alcohol 3 in high enantiomeric excesses (>95–97%). These strains were also employed to reduce 1-phenyl-3-nitro-1-propanone 2, maintaning the same stereobias observed with γ-nitroketone 1 and showing high enantioselectivity in both simple aqueous (>85–97%) and biphasic media (>97%).     

Aspergilazine A,a diketopiperazine dimer with a rare N-1 to C-6 linkage,from a marine-derived fungus Aspergillus taichungensis

A novel diketopiperazine (DKP) dimer, aspergilazine A (1), dimerized by two DKP units via a rare N-1 to C-6 linkage, was isolated from the marine-derived fungus Aspergillus taichungensis ZHN-7-07. The structure was determined by the combination of spectroscopic and Marfey’s methods. Biological evaluation indicated that aspergilazine A (1) had a weak activity against influenza A (H₁N₁) virus.     

The effect of preparation procedure and composition of water-ethanol suspensions of amorphous silica on their aggregative stability and kinetics of coagulation

The method of flow ultramicroscopy is employed to study the effect of the composition and preparation procedure of dilute water-ethanol suspensions of two samples of amorphous silica (fractionated fused quartz and monodisperse amorphous silica) on the kinetics of their coagulation. It is revealed that all suspensions prepared by the addition of silica powders to water-ethanol mixtures with ethanol contents of 96 and 40 vol % are stable with respect to aggregation, as the suspensions prepared by the addition of aliquots of concentrated dispersions of the aforementioned silica samples in 96% ethanol aged for different time periods to water-ethanol mixtures containing 96 vol % ethanol. At a 40-vol % content of ethanol in the mixture, the coagulation whose character (including “superfast” coagulation) substantially depends on the time of aging of initial concentrated silica dispersions occurs. Furthermore, kinetic studies are performed for the coagulation of dilute silica suspensions prepared by the addition of silica powders to water-ethanol solutions containing 40 vol % of ethanol and traces (<1 ppm) of poly(ethoxysilane), poly(acrylic acid), and a supernatant prepared by the centrifugation of concentrated silica dispersion in 96% ethanol aged for more than 3 months. It is found that the addition of aliquots of the aforementioned ethanol solutions to silica suspensions in 40% ethanol, which are initially stable with respect to aggregation, causes their superfast coagulation.     

Ultrastructural Damages to H1N1 Influenza Virus Caused by Vapor Essential Oils

Influenza viruses are transmitted from human to human via airborne droplets and can be transferred through contaminated environmental surfaces. Some works have demonstrated the efficacy of essential oils (EOs) as antimicrobial and antiviral agents, but most of them examined the liquid phases, which are generally toxic for oral applications. In our study, we describe the antiviral activity of Citrus bergamia, Melaleuca alternifolia, Illicium verum and Eucalyptus globulus vapor EOs against influenza virus type A. In the vapor phase, C. bergamia and M. alternifolia strongly reduced viral cytopathic effect without exerting any cytotoxicity. The E. globulus vapor EO reduced viral infection by 78% with no cytotoxicity, while I. verum was not effective. Furthermore, we characterized the EOs and their vapor phase by the head-space gas chromatography–mass spectrometry technique, observing that the major component found in each liquid EO is the same one of the corresponding vapor phases, with the exception of M. alternifolia. To deepen the mechanism of action, the morphological integrity of virus particles was checked by negative staining transmission electron microscopy, showing that they interfere with the lipid bilayer of the viral envelope, leading to the decomposition of membranes. We speculated that the most abundant components of the vapor EOs might directly interfere with influenza virus envelope structures or mask viral structures important for early steps of viral infection.     

Diels-Alder adducts of 3-N-substituted derivatives of (−)-Cytisine as influenza A/H1N1 virus inhibitors; stereodifferentiation of antiviral properties and preliminary assessment of action mechanism

The synthesis and anti-influenza activity study of Diels-Alder adducts of 3-N-substituted derivatives of (−)-cytisine with N-substituted maleimides are described. Synthesized compounds were studied for antiviral activity against influenza virus A/California/07/09 (H1N1)pdm09 in MDCK. The values of CC₅₀, IC₅₀ and selectivity indexes (SI) of obtained derivatives were determined. It was shown that anti-influenza activity of ‘α-endo’ adducts is higher (SI of three samples is 79 and higher) than activity of ‘β-endo’ adducts. By means of ‘time-of-addition’ experiment it was established that the leading compound (3aS,4R,8S,12R,12aR,12bS)-10-benzyl-2-phenyloctahydro-1H-4,12a-etheno-8,12-methanopyrrolo[3′,4':3,4]pyrido[1,2-a][1,5]diazocine-1,3,5(4H)-trione (16a) demonstrates anti-influenza activity at the middle and late stages of the virus life cycle. The possibility of interaction of synthesized derivatives with the active sites of the PA_N and PB2 was estimated via in silico approach. The difference in the locations of ‘α-endo’ and ‘β-endo’ adducts in PB2 active site (5JUN) is offered as an explanation of the dependence of their virus-inhibiting properties on stereochemistry.     

Synthesis of Four Pentacyclic Triterpene–Sialylglycopeptide Conjugates and Their Affinity Assays with Hemagglutinin

Influenza outbreaks pose a serious threat to human health. Hemagglutinin (HA) is an important target for influenza virus entry inhibitors. In this study, we synthesized four pentacyclic triterpene conjugates with a sialylglycopeptide scaffold through the Cu(I)-catalyzed alkyne-azide cycloaddition reaction (CuAAC) and prepared affinity assays of these conjugates with two HAs, namely H1N1 (A/WSN/1933) and H5N1 (A/Hong Kong/483/97), respectively. With a dissociation constant (K_D) of 6.89 μM, SCT-Asn-betulinic acid exhibited the strongest affinity with the H1N1 protein. Furthermore, with a K_D value of 9.10 μM, SCT-Asn-oleanolic acid exhibited the strongest affinity with the H5N1 protein. The conjugates considerably enhanced antiviral activity, which indicates that pentacyclic triterpenes can be used as a ligand to improve the anti-influenza ability of the sialylglycopeptide molecule by acting on the HA protein.     

Reversed phase monolithic analytical columns for the determination of HA1 subunit of influenza virus haemagglutinin

Monoliths are chromatographic stationary phases, which were specially designed for efficient purification of large biomolecules, like proteins, viruses and DNA. In this work, the small scale monolithic butyl (C4) and styrene-divinyl benzene (SDVB) columns were applied for reversed phase analyses of various degraded influenza viruses. The binding of the HA1 subunit of haemagglutinin to the monolithic columns was confirmed by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) and the Western blot. The working linear range was determined as 1.60 × 10¹⁰ viral particles/mL to at least 1.64 × 10¹¹ viral particles/mL, the limit of detection was found to be 2.56 × 10⁹ virus particles/mL and the limit of quantification was 5.12 × 10⁹ virus particles/mL. The analytical HPLC method developed with the H1N1 virus was also applicable for the analytics of the HA1 subunit of H3N2 influenza virus and the influenza B virus.     

Synthesis and anti-influenza activity of 2-cyanoethoxy and 2-(1<Emphasis Type="Italic">H</Emphasis>-tetrazol-5-yl)ethoxy derivatives of dammarane-type triterpenoids

A series of 3-(2-1Н-tetrazol-5-ylethoxy- and 2-1Н-tetrazol-5-ylethoxyimino) derivatives of dammarane triterpenoids was synthesized by azidation of 3-(2-cyanoethoxy- and 2-cyanoethoxyimino)-dammaranes. The anti-influenza activity of the prepared tetrazolyldammaranes and intermediate compounds against influenza virus А H1N1 was tested. A considerable antiviral activity was observed for 20(S)-3-(2-1Н-tetrazol-5-ylethoxyimino)-25,26,27-trinor-20,24-olidedammarane (SI 26).     

Expression of Avian Influenza Virus (H5N1) Hemagglutinin and Matrix Protein 1 in Pichia pastoris and Evaluation of their Immunogenicity in Mice

The conventional avian influenza vaccines rely on development of neutralizing antibodies against the HA and NA antigens. However, these antigens are highly variable, and hence there is a need for better vaccine candidates which would offer broader protection in animals. The M1 of avian influenza is another major structural protein that has conserved epitopes that are reported to induce CD8+ T cells and can contribute to protection against morbidity and mortality from influenza. Hence in an effort to study the immune response of rM1 either alone or in combination with rHA, the hemagglutinin (HA) and matrix protein (M1) of A/Hatay/2004/H5N1 strain of avian influenza were expressed in Pichia pastoris as his-tagged proteins and purified through Ni-NTA chromatography. The His-tag was removed using TEV protease cleavage site and the immunogenicity of purified rHA and rM1 either alone or in combination was determined in mice. One group of mice was immunized with 5 μg of purified rHA, the other group was immunized with rM1, and a third group of mice were immunized with 5 μg of rHA and rM1. All the animals were boosted twice, once on 28 days postimmunization (dpi) and the second on 42 dpi. The immune response was evaluated by enzyme-linked immunosorbent assay (ELISA) and hemagglutination inhibition (HI) assay. The group of mice immunized with rHA and rM1 together showed significantly higher immune response against rHA and rM1 than mice immunized with either HA or M1 antigens. The addition of rM1 with rHA resulted in increased HI titer in animals immunized with both the antigens. These results suggest that the HA and M1 expressed in P. pastoris can be utilized in combination for the development of faster and cost-effective vaccines for circulating and newer strains of avian influenza and would aid in combating the disease in a pandemic situation, in which production time matters greatly.     

A network-based pharmacology study of active compounds and targets of Fritillaria thunbergii against influenza

Seasonal and pandemic influenza infections are serious threats to public health and the global economy. Since antigenic drift reduces the effectiveness of conventional therapies against the virus, herbal medicine has been proposed as an alternative. Fritillaria thunbergii (FT) have been traditionally used to treat airway inflammatory diseases such as coughs, bronchitis, pneumonia, and fever-based illnesses. Herein, we used a network pharmacology-based strategy to predict potential compounds from Fritillaria thunbergii (FT), target genes, and cellular pathways to better combat influenza and influenza-associated diseases. We identified five compounds, and 47 target genes using a compound-target network (C-T). Two compounds (beta-sitosterol and pelargonidin) and nine target genes (BCL2, CASP3, HSP90AA1, ICAM1, JUN, NOS2, PPARG, PTGS1, PTGS2) were identified using a compound-influenza disease target network (C-D). Protein-protein interaction (PPI) network was constructed and we identified eight proteins from nine target genes formed a network. The compound-disease-pathway network (C-D-P) revealed three classes of pathways linked to influenza: cancer, viral diseases, and inflammation. Taken together, our systems biology data from C-T, C-D, PPI and C-D-P networks predicted potent compounds from FT and new therapeutic targets and pathways involved in influenza.