Virtual screening of anti-HIV1 compounds against SARS-CoV-2: machine learning modeling, chemoinformatics and molecular dynamics simulation based analysis.

COVID-19 caused by the SARS-CoV-2 is a current global challenge and urgent discovery of potential drugs to combat this pandemic is a need of the hour. 3-chymotrypsin-like cysteine protease (3CLpro) enzyme is the vital molecular target against the SARS-CoV-2. Therefore, in the present study, 1528 anti-HIV1compounds were screened by sequence alignment between 3CLpro of SARS-CoV-2 and avian infectious bronchitis virus (avian coronavirus) followed by machine learning predictive model, drug-likeness screening and molecular docking, which resulted in 41 screened compounds. These 41 compounds were re-screened by deep learning model constructed considering the IC50 values of known inhibitors which resulted in 22 hit compounds. Further, screening was done by structural activity relationship mapping which resulted in two structural clefts. Thereafter, functional group analysis was also done, where cluster 2 showed the presence of several essential functional groups having pharmacological importance. In the final stage, Cluster 2 compounds were re-docked with four different PDB structures of 3CLpro, and their depth interaction profile was analyzed followed by molecular dynamics simulation at 100 ns. Conclusively, 2 out of 1528 compounds were screened as potential hits against 3CLpro which could be further treated as an excellent drug against SARS-CoV-2.

Natural product-derived phytochemicals as potential agents against coronaviruses: A review.

Coronaviruses are responsible for a growing economic, social and mortality burden, as the causative agent of diseases such as severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), avian infectious bronchitis virus (IBV) and COVID-19. However, there is a lack of effective antiviral agents for many coronavirus strains. Naturally existing compounds provide a wealth of chemical diversity, including antiviral activity, and thus may have utility as therapeutic agents against coronaviral infections. The PubMed database was searched for papers including the keywords coronavirus, SARS or MERS, as well as traditional medicine, herbal, remedy or plants, with 55 primary research articles identified. The overwhelming majority of publications focussed on polar compounds. Compounds that show promise for the inhibition of coronavirus in humans include scutellarein, silvestrol, tryptanthrin, saikosaponin B2, quercetin, myricetin, caffeic acid, psoralidin, isobavachalcone, and lectins such as griffithsin. Other compounds such as lycorine may be suitable if a therapeutic level of antiviral activity can be achieved without exceeding toxic plasma concentrations. It was noted that the most promising small molecules identified as coronavirus inhibitors contained a conjugated fused ring structure with the majority being classified as being polyphenols.

Antiviral activities of Cholistani plants against common poultry viruses.

Herbal medicines are becoming more popular and acceptable day by day due to their effectiveness, limited side effects, and cost-effectiveness. Cholistani plants are reported as a rich source of antibacterial, antifungal, antiprotozoal, antioxidant, and anticancer agents. The current study has evaluated antiviral potential of selected Cholistani plants. The whole plants were collected, ground and used in extract formation with n-hexane, ethyl acetate and n-butanol. All the extracts were concentrated by using a rotary evaporator and concentrate was finally dissolved in an appropriate vol of the same solvent. All of the extracts were tested for their antiviral potential by using 9-11 days old chick embryonated eggs. Each extract was tested against the Avian Influenza virus H9N2 strain (AIV), New Castle Disease virus Lasoota strain (NDV), Infectious bronchitis virus (IBV) and an Infectious bursal disease virus (IBDV). Hemagglutination test (HA) and Indirect Hemagglutination (IHA) tests were performed for different viruses. The overall order of the antiviral potential of Cholistani plants against viruses was NDV>IBV>IBDV>AIV. In terms of antiviral activity from extracts, the order of activity was n-butanol>ethyl acetate>n-hexane. The medicinal plants Achyranthes aspera, Neuroda procumbens, Panicum antidotale, Ochthochloa compressa and Suaeda fruticose were very effective against all four poultry viruses through their extracts. The low IC50 values of these extracts confirm the high antiviral potential against these viruses. It is worth to mention that Achyranthes aspera was found positive against IBDV through all its extracts which overcome the problem of unavailability of any known drug against IBDV. In short, the study proved that Cholistani plants are rich source of antiviral agent and their extracts can be used as good source of antiviral drugs both in crude and in purified form.

In vitro antiviral activity of fifteen plant extracts against avian infectious bronchitis virus.

BACKGROUND: Avian infectious bronchitis (IB) is a disease that can result in huge economic losses in the poultry industry. The high level of mutations of the IB virus (IBV) leads to the emergence of new serotypes and genotypes, and limits the efficacy of routine prevention. Medicinal plants, or substances derived from them, are being tested as options in the prevention of infectious diseases such as IB in many countries. The objective of this study was to investigate extracts of 15 selected medicinal plants for anti-IBV activity. RESULTS: Extracts of S. montana, O. vulgare, M. piperita, M. officinalis, T. vulgaris, H. officinalis, S. officinalis and D. canadense showed anti-IBV activity prior to and during infection, while S. montana showed activity prior to and after infection. M. piperita, O. vulgare and T. vulgaris extracts had > 60 SI. In further studies no virus plaques (plaque reduction rate 100%) or cytopathogenic effect (decrease of TCID50 from 2.0 to 5.0 log10) were detected after IBV treatment with extracts of M. piperita, D. canadense and T. vulgaris at concentrations of extracts ≥0.25 cytotoxic concentration (CC50) (P < 0.05). Both PFU number and TCID50 increased after the use of M. piperita, D. canadense, T. vulgaris and M. officinalis extracts, the concentrations of which were 0.125 CC50 and 0.25 CC50 (P < 0.05). Real-time PCR detected IBV RNA after treatment with all plant extracts using concentrations of 1:2 CC50, 1:4 CC50 and 1:8 CC50. Delta cycle threshold (Ct) values decreased significantly comparing Ct values of 1:2 CC50 and 1:8 CC50 dilutions (P < 0.05). CONCLUSIONS: Many extracts of plants acted against IBV prior to and during infection, but the most effective were those of M. piperita, T. vulgaris and D. canadense .

Chromatographic Data Segmentation Method: A Hybrid Analytical Approach for the Investigation of Antiviral Substances in Medicinal Plant Extracts.

The methodology described in this article will significantly reduce the time required for understanding the relations between chromatographic data and bioactivity assays. The methodology is a hybrid of hypothesis-based and data-driven scientific approaches. In this work, a novel chromatographic data segmentation method is proposed, which demonstrates the capability of finding what volatile substances are responsible for antiviral and cytotoxic effects in the medicinal plant extracts. Up until now, the full potential of the separation methods has not been exploited in the life sciences. This was due to the lack of data ordering methods capable of adequately preparing the chromatographic information. Furthermore, the data analysis methods suffer from multidimensionality, requiring a large number of investigated data points. A new method is described for processing any chromatographic information into a vector. The obtained vectors of highly complex and different origin samples can be compared mathematically. The proposed method, efficient with relatively small sized data sets, does not suffer from multidimensionality. In this novel analytical approach, the samples did not need fractionation and purification, which is typically used in hypothesis-based scientific research. All investigations were performed using crude extracts possessing hundreds of phyto-substances. The antiviral properties of medicinal plant extracts were investigated using gas chromatography-mass spectrometry, antiviral tests, and proposed data analysis methods. The findings suggested that (i) ß- cis-caryophyllene, linalool, and eucalyptol possess antiviral activity, while (ii) thujones do not, and (iii) α-thujone, ß-thujone, cis- p-menthan-3-one, and estragole show cytotoxic effects.

Astragalus polysaccharides inhibit avian infectious bronchitis virus infection by regulating viral replication.

The avian coronavirus causes infectious bronchitis (IB), which is one of the most serious diseases affecting the avian industry worldwide. However, there are no effective strategies for controlling the IB virus (IBV) at present. Therefore, development of novel antiviral treatment strategies is urgently required. As reported, astragalus polysaccharides (APS) have potential antiviral effects against several viruses; however, the antiviral effect of APS against IBV remains unclear. In this study, we explored whether APS had the potential to inhibit IBV infectionby utilizing several in vitro experimental approaches. To this end, the effect of APS on the replication of IBV was examined in chicken embryo kidney (CEK) cells. Viral titers were calculated by using the plaque formation assay, and the cytotoxicity of APS was tested by utilizing a Cell Counting Kit-8 assay. The expression of viral mRNA and cytokine (IL-1ß, IL-6, IL-8 and TNF-α) mRNA transcripts was determined by real-time quantitative RT-PCR(qRT-PCR). IBV titers in infected CEK cells treated with APS were significantly reduced in a dose-dependent manner, indicating that APS inhibited IBV replication in vitro. We also found that the decreased viral replication after APS treatment was associated with reduced mRNA levels of the cytokines IL-1B, IL-6, IL-8 and TNF-α. In conclusion, these results suggest that APS exhibit antiviral activities against IBV and it may represent a potential therapeutic agent for inhibiting the replication of IBV.

Sambucus nigra extracts inhibit infectious bronchitis virus at an early point during replication.

BACKGROUND: Infectious bronchitis virus (IBV) is a pathogenic chicken coronavirus. Currently, vaccination against IBV is only partially protective; therefore, better preventions and treatments are needed. Plants produce antimicrobial secondary compounds, which may be a source for novel anti-viral drugs. Non-cytotoxic, crude ethanol extracts of Rhodiola rosea roots, Nigella sativa seeds, and Sambucus nigra fruit were tested for anti-IBV activity, since these safe, widely used plant tissues contain polyphenol derivatives that inhibit other viruses. RESULTS: Dose-response cytotoxicity curves on Vero cells using trypan blue staining determined the highest non-cytotoxic concentrations of each plant extract. To screen for IBV inhibition, cells and virus were pretreated with extracts, followed by infection in the presence of extract. Viral cytopathic effect was assessed visually following an additional 24 h incubation with extract. Cells and supernatants were harvested separately and virus titers were quantified by plaque assay. Variations of this screening protocol determined the effects of a number of shortened S. nigra extract treatments. Finally, S. nigra extract-treated virions were visualized by transmission electron microscopy with negative staining.Virus titers from infected cells treated with R. rosea and N. sativa extracts were not substantially different from infected cells treated with solvent alone. However, treatment with S. nigra extracts reduced virus titers by four orders of magnitude at a multiplicity of infection (MOI) of 1 in a dose-responsive manner. Infection at a low MOI reduced viral titers by six orders of magnitude and pretreatment of virus was necessary, but not sufficient, for full virus inhibition. Electron microscopy of virions treated with S. nigra extract showed compromised envelopes and the presence of membrane vesicles, which suggested a mechanism of action. CONCLUSIONS: These results demonstrate that S. nigra extract can inhibit IBV at an early point in infection, probably by rendering the virus non-infectious. They also suggest that future studies using S. nigra extract to treat or prevent IBV or other coronaviruses are warranted.

Ameliorative effect of a microbial feed additive on infectious bronchitis virus antibody titer and stress index in broiler chicks fed deoxynivalenol.

Although acute mycotoxicoses are rare in poultry production, chronic exposure to low levels of mycotoxins is responsible for reduced productivity and increased susceptibility to infectious diseases. Deoxynivalenol (DON) is known to modulate immune function, but only a few studies have investigated the effect of DON on the vaccinal immune response. In addition, the effects of Mycofix select (Biomin GmbH, Herzogenburg, Austria) supplementation to DON-contaminated broiler diets have not yet been demonstrated. Therefore, an experiment with 1-d-old male broilers (Ross 308) was carried out to examine the effects of feeding DON-contaminated low-protein grower diets on performance, serum biochemical parameters, lymphoid organ weight, and antibody titers to infectious bronchitis vaccination in serum and to evaluate the effects of Mycofix select dietary supplementation in either the presence or absence of DON in broilers. In total, thirty-two 1-d-old broiler chicks were randomly assigned to 1 of the 4 dietary treatments for 5 wk. The dietary treatments were 1) control; 2) artificially contaminated diets with 10 mg of DON/kg of diet; 3) DON-contaminated diets supplemented with Mycofix select; and 4) control diet supplemented with Mycofix select. Feeding of contaminated diets decreased (P = 0.000) the feed intake, BW (P = 0.001), BW gain (P = 0.044), and feed efficiency during the grower phase. Deoxynivalenol affected the blood biochemistry, whereas plasma total protein and uric acid concentrations in birds fed contaminated grains were decreased compared with those of the controls. Moreover, in birds fed contaminated feeds, there was a tendency to reduce triglycerides in the plasma (P = 0.090), suggesting that DON in the diets affected protein and lipid metabolism in broiler chickens. The feeding of contaminated diets altered the immune response in broilers by reducing the total lymphocyte count. Similarly, the antibody response against infectious bronchitis vaccination antigens was decreased (P = 0.003) after feeding contaminated diets, compared with the controls. Moreover, contamination of the broiler diet with DON increased the heteropil:lymphocyte ratio (stress index), suggesting that DON elevated the physiological stress responses of broilers. However, feeding of DON-containing diets did not alter the other plasma constituents, including activities of enzymes. Mycofix select addition to the DON-contaminated feed led to normal immunological and physiological functions in broilers that were comparable with those of the control group, indicating that the addition of the additive to the DON-contaminated feed of the broilers effectively alleviated the alterations caused by DON. It was concluded that broiler performance and some blood and immunological parameters were adversely affected by feeding diets contaminated with the Fusarium mycotoxin DON. However, the dietary Mycofix select supplementation as a detoxifying agent was successful in overcoming the mycotoxin-related effects.

In vitro and in vivo effects of Houttuynia cordata on infectious bronchitis virus.

Avian infectious bronchitis virus (IBV), a coronavirus, causes infectious bronchitis leading to enormous economic loss in the poultry industry worldwide. Houttuynia cordata (Saururaceae) (HC) is a traditional Chinese medicine used in China. In the present study, the effect of HC on cell infection by IBV was determined using plaque assay and reverse transcription-polymerase chain reaction. The inhibitory effect of HC on IBV infection in ovo and in vivo was analysed using specific pathogen free (SPF) chicken embryos and chickens. Moreover, the effect of HC on cell apoptosis induced by IBV was investigated. Results showed that HC had more than 90% inhibition rate against IBV infection in Vero cells and chicken embryo kidney cells, and decreased more than 90% apoptotic cells caused by IBV. HC fully protected the SPF embryos, and had more than 50% protection rate in SPF chickens, against IBV challenge.

Comparative anti-infectious bronchitis virus (IBV) activity of (-)-pinene: effect on nucleocapsid (N) protein.

In the present study, anti-IBV (infectious bronchitis virus) activities of (-)-pinenes were studied by MTT assay, as well as docking and molecular dynamic (MD) simulations. The CC50 values of (-)-α-pinene and (-)-ß-pinene were above 10 mM. And the maximum noncytotoxic concentrations (TD0) of (-)-α-pinene and (-)-ß-pinene were determined as 7.88 ± 0.06 and 6.09 ± 0.31 mM, respectively. The two compounds were found to inhibit IBV with an IC50 of 0.98 ± 0.25 and 1.32 ± 0.11 mM. The MTT assay showed that the inhibitions of (-)-pinenes against IBV appear to occur moderately before entering the cell but are much stronger occur after penetration of the virus into the cell. Molecular simulations indicated that (-)-α-pinene and (-)-ß-pinene specifically interact with the active site which is located at the N terminus of phosphorylated nucleocapsid (N) protein, with the former being more potent than the latter. The binding energies of them are -36.83 and -35.59 kcal mol-1, respectively. Results presented here may suggest that (-)-α-pinene and (-)-ß-pinene possess anti-IBV properties, and therefore are a potential source of anti-IBV ingredients for the pharmaceutical industry.

Forsythoside a inhibits the avian infectious bronchitis virus in cell culture.

Forsythoside A is a polyphenolic constituent of the fruits of Forsythia suspensa Vahl. which is widely used as an antiinflammatory agent in traditional Chinese medicine. In the present study, the effects of forsythoside A on cell infection by avian infectious bronchitis virus were assessed. A real-time fluorescence quantitative PCR assay was used to determine mRNA content of IBV N gene. The pretreatment of cells with forsythoside A, adding forsythoside A post infection of cells, and treatment of virus with forsythoside A were analysed. The inhibitory effect of forsythoside A was confirmed by infecting primary chicken embryo kidney cells. Infected cells were inhibited by forsythoside A treatment. The data indicated that forsythoside A has the potential to prevent IBV infection in vitro. Copyright © 2010 John Wiley & Sons, Ltd.

Avian coronavirus infectious bronchitis virus susceptibility to botanical oleoresins and essential oils in vitro and in vivo.

Anti-coronaviral activity of a mixture of oleoresins and essential oils from botanicals, designated QR448(a), was examined in vitro and in vivo. Treatment of avian infectious bronchitis virus (IBV) with QR448(a) reduced the virus titer as measured in two laboratory host systems, Vero E6 cells and embryonating eggs. The effect of QR448(a) on IBV in chickens was also investigated. Administering QR448(a) to chickens at a 1:20 dilution by spray, 2h before challenge with IBV was determined to be the most effective treatment. Treatment decreased the severity of clinical signs and lesions in the birds, and lowered the amount of viral RNA in the trachea. Treatment with QR448(a) protected chickens for up to 4 days post-treatment from clinical signs of disease (but not from infection) and decreased transmission of IBV over a 14-day period. Anti-IBV activity of QR448(a) was greater prior to virus attachment and entry indicating that the effect is virucidal. In addition, QR448(a) had activity against both Massachusetts and Arkansas type IB viruses, indicating that it can be expected to be effective against IBV regardless of serotype. To our knowledge, this is the first report on the in vivo use of a virucidal mixture of compounds effective against the coronavirus IBV.

The polypeptides of infectious bronchitis virus (IBV-41 strain).

The Massachusetts strain of avian infectious bronchitis virus was purified from embryonated hens' eggs. Four major species of apparent mol. wt. 90 000, 52 000, 29 000 and 26 000 were resolved by SDS-polyacrylamide gel electrophoresis. Omission of reducing agent failed to resolve the 29 000 mol. wt. component. Labelling of acrylamide gels with 125I-concanavalin A indicated that polypeptides of mol. wt. 90 000, 29 000 and 26 000 were glycosylated and, in the absence of reducing agent, that the 29 000 species migrated as a dimer in the 5000 mol. wt. region. Purified IBV radio-iodinated with Bolton and Hunter reagent, which banded as a single peak of radioactivity in Metrizamide gradients, was found to contain bands of radioactivity when analysed by SDS-PAGE, corresponding to the polypeptides of mol. wt. 90 000, 52 000 and 29 000 resolved in stained gels. Disruption of IBV particles in Triton X-100 released two subviral particles, a 16 nm spike which comprised polypeptides of 90 000, 52 000 and 29 000 mol. wt. and another denser spherical particle of 25 to 45 nm which contained RNA and the 52 000 and 26 000 polypeptides.