Search Results (187)

Cyclophilins (Cyps), a family of peptidyl-prolyl isomerases, play essential roles in the life cycle of coronaviruses by interacting with viral proteins and modulating host immune responses. In this systematic review, we examined cell culture, animal model, and clinical studies assessing the anti-viral efficacy of cyclosporine A (CsA, PubChem CID: 5284373) and its non-immunosuppressive derivatives against coronaviruses. CsA demonstrated robust anti-viral activity in vitro across a broad range of coronaviruses, including but not limited to HCoV-229E, SARS-CoV, MERS-CoV, and SARS-CoV-2, with potent EC₅₀ values in the low micromolar range. Non-immunosuppressive analogs such as Alisporivir and NIM811 exhibited similar inhibitory effects. In vivo, CsA treatment significantly reduced viral load, ameliorated lung pathology, and improved survival in coronavirus-infected animals. Clinical studies further indicated that CsA administration was associated with improved outcomes in COVID-19 patients, including reduced mortality and shorter hospital stays. Mechanistic studies revealed that CsA disrupts the formation of viral replication complexes, interferes with critical Cyp–viral protein interactions, and modulates innate immune signaling. These findings collectively demonstrate the therapeutic potential of cyclophilin inhibitors as broad-spectrum anti-virals against current and emerging coronaviruses. Full article

Background/Objectives: Viral respiratory infections have a significant impact on global health and the economy. While vaccines are effective in preventing infection, they might not be available or sufficient when used alone and must be complemented by specific therapeutic strategies. The development of new antiviral agents is increasingly important due to the continual emergence of novel respiratory pathogens. Previously we identified bovine lactoferrin (bLf)-derived tetrapeptides and peptidomimetics that showed potent in vitro activity against the influenza A virus in the picomolar range. Methods: Inspired by these results, in this study, we evaluated the antiviral potential of these compounds against HCoV-229E, a human coronavirus that can cause severe disease in immunocompromised individuals, using a compound repositioning approach. Results: Functional studies revealed that SK(N-Me)HS (3) interferes with viral entry and replication, while compound SNKHS (5) primarily blocks infection in the early stages. Biophysical analyses confirmed the occurrence of high-affinity binding to the viral spike protein, and computational studies suggested that the compounds target a region involved in conformational changes necessary for membrane fusion. Conclusions: These findings highlight these compounds as promising candidates for coronavirus entry inhibition and underscore the value of compound repurposing in antiviral development. Full article

Glycyrrhizic acid (GA) and its derivatives have been reported to have potent pharmacological effects against viral infections, including SARS-CoV and SARS-CoV-2. However, their antiviral mechanisms against coronaviruses are not fully understood. In this study, we found that diammonium glycyrrhizinate (DG) can effectively reduce infections of several human coronaviruses, including HCoV-OC43, HCoV-229E, and SARS-CoV-2, as well as newly emerged variants, with EC₅₀ values ranging from 115 to 391 μg/mL being recorded. Time-of-addition and pseudotype virus infection studies indicated that DG treatment dramatically inhibits the process of virus entry into cells. Furthermore, we demonstrated that DG broadly binds to the RBD of human coronaviruses, thereby blocking spike-mediated cellular entry, by using TR-FRET-based receptor-binding domain (RBD)-ACE2 interaction assay, capillary electrophoresis (CE), and surface plasmon resonance (SPR) assay. In support of this notion, studies of molecular docking and amino acid mutation showed that DG may directly bind to a conserved hydrophobic pocket of the RBD of coronaviruses. Importantly, intranasal administration of DG had a significant protective effect against viral infection in a HCoV-OC43 mouse model. Finally, we found that combinations of DG and other coronavirus inhibitors exhibited antiviral synergy. In summary, our studies strongly reveal that DG exerts broad-spectrum antiviral activity against human coronaviruses by interrupting spike-mediated cellular entry, demonstrating the pharmacological feasibility of using DG as a candidate for alternative treatment and prevention of coronavirus infection. Full article

Cell-based phenotypic screening of a privileged in-house library composed of pyridobenzothiazolone (PBTZ) analogues was conducted against representative viruses responsible for common respiratory tract infections in humans, i.e., respiratory syncytial virus (RSV), human coronavirus type OC43 (HCoV-OC43), and influenza virus type A (IFV-A). We identified a compound with broad-spectrum inhibitory activity against multiple strains of RSV, HCoV, and IFV, with EC₅₀ values in the low micromolar range and cell-independent activity. Its antiviral activity and cytocompatibility were confirmed in a fully differentiated 3D model of the bronchial epithelium mimicking the in vivo setting. The hit compound enters cells and localizes homogeneously in the cytosol, inhibiting replicative phases in a virus-specific manner. Overall, the selected PBTZ represents a good starting point for further preclinical development as a broad-spectrum antiviral agent that could address the continuous threat of new emerging pathogens and the rising issue of antiviral resistance. Full article

The human coronavirus 229E (HCoV-229E) is a member of the human coronavirus family that includes SARS-CoV-2, the causative agent of COVID-19. Developing antiviral strategies and compounds is crucial to treat and prevent HCoV-229E infections and the associated diseases. Ribozymes derived from ribonuclease P (RNase P) catalytic RNA represent a novel class of promising gene-targeting agents by cleaving their target mRNA and knocking down the expression of the target mRNA. However, it has not been reported whether RNase P ribozymes block the infection and replication of HCoV-229E. We report here the engineering of an anti-HCoV-229E RNase P ribozyme to target an overlapping region of viral genomic RNA and the mRNA encoding the nucleocapsid (N) protein, which is vital for viral replication and growth. The engineered ribozyme actively hydrolyzed the viral RNA target in vitro. HCoV-229E-infected cells expressing the engineered, catalytically active ribozyme exhibited a reduction of about 85% in viral RNA levels and N protein expression, and a reduction of about 750-fold in infectious particle production, compared to cells expressing no ribozymes or a control, catalytically inactive ribozyme. Our study provides the first direct evidence of the therapeutic potential of RNase P ribozymes against human coronaviruses such as HCoV-229E. Full article

Background: This study aims to evaluate the quality of treated wastewater flowing in the Zarqa River to determine its suitability for agricultural use. The assessment is based on physicochemical and biological parameters in accordance with Jordanian standards (JS 893:2021), the CCME water quality index, and the weighted arithmetic water quality index (WAWQI). Additionally, a microbial assessment was conducted to identify the presence of pathogens in the treated wastewater. Methods: A total of 168 water samples were collected from seven different sites along the Zarqa River over a 24-month period. This study focused on microbial assessment and selected parameters from the JS 893:2021, including total dissolved solids (TDSs), biochemical oxygen demand (BOD), dissolved oxygen (DO), chemical oxygen demand (COD), and E. coli levels. Furthermore, data were gathered on additional physicochemical parameters such as pH, mineral content (including Na, Ca, K, Mg, and Cl), salts (HCO₃, SO₄, NO₃, and PO₄), and heavy metals (Fe, Cu, Pb, Mn, and Co). The CCME water quality index and weighted arithmetic WQI scores were calculated to determine the water quality from all seven study sites. Results: In terms of Jordanian standards, Site 1 had the lowest TDS and DO values along with E. coli concentration. Further, in terms of minerals and salts, the maximum concentrations found for the sites are given herewith: Site 2 (K⁺ and NO₃), Site 3 (Cl⁻, Na⁺), Site 5 (Ca, HCO₃), and Site 7 (Mg²⁺, PO₄, and SO₄). In terms of pH, all the study sites had pH values within the acceptable range, i.e., between 6 and 9, for irrigation purposes. The concentrations of certain heavy metals, specifically lead (Pb), manganese (Mn), and cobalt (Co), were observed to be negligible. In contrast, Site 6 exhibited the highest concentration of iron (Fe) (0.0178 mg/L), while Site 5 recorded the maximum concentration of copper (Cu) (0.0210 mg/L) among the study locations. Site 1 demonstrated the most favorable water quality among the seven sites evaluated, whereas Site 6 exhibited the poorest water quality. Overall, the water quality from the majority of the sites was deemed suitable for drainage and for irrigating crops classified under the B category. However, based on the weighted arithmetic water quality index (WQI) values, none of the sites achieved a classification of good or excellent water quality, although the water quality at these sites may still be utilized for irrigation purposes. The current study is the first to report the presence of SARS-CoV-2 in Zarqa River water samples. Conclusions: The current study outcomes are promising and provide knowledgeable insights in terms of water quality parameters, while public health aspects should be considered when planning the WWTPs in parallel to reclaiming the wastewater for irrigation purposes. Full article

Background: There is an unmet medical need to develop a vaccine targeting endemic coronaviruses. Antigen-specific monoclonal antibodies (mAbs) are crucial for many assays to support vaccine development. Objective: In this study, we used the HuCal Fab phage display library with a diversity of 4.5 × 10¹⁰ to identify antibodies specific to the spike proteins of the four endemic coronaviruses: OC43, NL63, 229E, and HKU1. Methods: As proof of concept, we established a newly designed platform using a long-read NGS workflow for antibody discovery and compared the results against the traditional workflow using Sanger sequencing consisting of lengthy and laborious benchwork. Results: The long-read NGS workflow identified most of the antibodies seen from the Sanger sequencing workflow, and many more additional antigen-specific antibodies against the endemic coronaviruses. Overall efficiency improved up to three times, comparing the traditional workflow with the NGS workflow. Of the 113 NGS-derived mAbs isolated to bind the four endemic coronavirus spike proteins, 107/113 (94.7%) had potent ELISA binding affinities (EC50 < 150 ng/mL, or <1 nM), and 61/113 (54%) had extremely potent ELISA binding affinities (EC50 of <15 ng/mL, or <0.1 nM). Conclusions: We successfully developed and incorporated the long-read NGS workflow to generate target-specific antibodies with many antibodies at sub-nanomolar affinities that are likely missed by a traditional workflow. We identified strong neutralizing antibodies, proving that our endemic spike proteins are capable of generating antibodies that could offer protection against the endemic HCoVs. Full article

The effectiveness of copper-based composites, specifically cupric ion (Cu²⁺)-modified phyllosilicate minerals, was evaluated in reducing the concentration of infectious agents in the environment while minimizing metal ion release. The phyllosilicate minerals, vermiculite, exfoliated and unexfoliated, and sepiolite, all modified with Cu²⁺, were compared with copper oxide for their antiviral activity against non-enveloped porcine parvovirus (PPV) and enveloped human coronavirus 229E (HCoV). Sepiolite effectively removed PPV and HCoV from the solution, regardless of Cu²⁺ presence, while vermiculite showed substantial viral clearance only when Cu²⁺ was present. The kinetics of viral clearance was fast, with complete clearance within one hour in many cases. To better understand the mechanism of virus clearance, EDTA was added at different times during the clearance study for PPV. EDTA prevented virus clearance in all vermiculite samples, whereas sepiolite containing copper still demonstrated substantial virus clearance. The addition of BSA before the virus binding was able to block binding in all cases. It was determined that binding is the key mechanism, and PPV can be eluted from the minerals with EDTA and still be infectious. This study provides the potent antiviral mechanisms of Cu²⁺-modified phyllosilicate minerals, offering insights for designing paints and plastics for high-touch surfaces to reduce viral transmission and enhance public health significantly. Full article

In 2021, at the height of the COVID-19 pandemic, coronavirus research spiked, with over 83,000 original research articles related to the word “coronavirus” added to the online resource PubMed. Just 2 years later, in 2023, only 30,900 original research articles related to the word “coronavirus” were added. While, irrefutably, the funding of coronavirus research drastically decreased, a possible explanation for the decrease in interest in coronavirus research is that projects on SARS-CoV-2, the causative agent of COVID-19, halted due to the challenge of establishing a good cellular or animal model system. Most laboratories do not have the capabilities to culture SARS-CoV-2 ‘in house’ as this requires a Biosafety Level (BSL) 3 laboratory. Until recently, BSL 2 laboratory research on endemic coronaviruses was arduous due to the low cytopathic effect in isolated cell culture infection models and the lack of means to quantify viral loads. The purpose of this review article is to compare the human coronaviruses and provide an assessment of the latest techniques that use the endemic coronaviruses—HCoV-229E, HCoV-OC43, HCoV-NL63, and HCoV-HKU1—as lower-biosafety-risk models for the more pathogenic coronaviruses—SARS-CoV-2, SARS-CoV, and MERS-CoV. Full article

In order to detect and respond to invading pathogens, mammals have evolved a battery of pattern recognition receptors. Among these, RIG-I-like receptors (RLR) are cytosolic RNA sensors that play an essential role in the innate immune response against RNA viruses, including coronaviruses. In return, coronaviruses have acquired diverse strategies to impair RLR-mediated immune responses to enable productive infection. Viral innate immune evasion mechanisms have been well studied for highly pathogenic human coronaviruses (HCoVs), and often, these activities are thought to be linked to the severe symptoms these viruses can cause. Whether other coronaviruses, including human common cold coronaviruses, display similar activities has remained understudied. Here, we present evidence that the main protease (Mpro) of common cold HCoV-229E acts as an interferon (IFN) and NF-κB antagonist by disrupting RLR-mediated antiviral signalling. Furthermore, we show that HCoV-229E, HCoV-OC43 and MERS-CoV Mpros are able to directly cleave NEMO. We also show that HCoV-229E Mpro induces the cleavage and/or degradation of multiple other RLR pathway components, including MDA5, TBK1 and IKKε. Finally, we show that HCoV-229E infection leads to a delayed innate immune response that is accompanied by a decrease in NEMO protein levels. Our results suggest that NEMO degradation during HCoV-229E infection could be mediated, in part, by cellular degradation pathways, in addition to viral Mpro-mediated cleavage. Altogether, our research unveils innate immune evasion activities of the Mpros of low-pathogenic coronaviruses, which, despite their low pathogenicity, appear to share functionalities previously described for highly pathogenic HCoVs. Full article

Recently, previously known viruses have changed their pathogenicity and encompassed new types of host populations. An example of such an infection is that caused by SARS-CoV, belonging to the “well-known” coronavirus family. Another group of viruses that are of great importance to the human population are the herpes viruses. Due to increasing viral resistance to existing antiviral drugs, plant extracts are attracting increasing interest due to their complex composition and their simultaneous attack of different viral targets. Based on the above, we tested the antiviral potential of water–alcoholic extract obtained from a commercial sample of the plant Cistus incanus L. against the enveloped viruses SvHA1, SvHA2 (ACV resistant) and HCoV 229E. The results showed both complete inhibition of the intracellular stages of the viral replication and a strong effect on extracellular virions in the three viral models. In a study of the effect on the replication of SvHA 2, the calculated selectivity index was over 10. From the experiments on the virucidal effects on the two herpes viruses, it was found that the viral titer of the samples decreased by about 4 lg compared to the control sample. The extract is of interest for introduction into practice. Full article

The betacoronavirus genus contains five of the seven human coronaviruses, making it a particularly critical area of research to prepare for future viral emergence. We utilized three human betacoronaviruses, one from each subgenus—HCoV-OC43 (embecovirus), SARS-CoV-2 (sarbecovirus), and MERS-CoV (merbecovirus)—, to study betacoronavirus interactions with the PKR-like ER kinase (PERK) pathway of the integrated stress response (ISR)/unfolded protein response (UPR). The PERK pathway becomes activated by an abundance of unfolded proteins within the endoplasmic reticulum (ER), leading to phosphorylation of eIF2α and translational attenuation. We demonstrate that MERS-CoV, HCoV-OC43, and SARS-CoV-2 all activate PERK and induce responses downstream of p-eIF2α, while only SARS-CoV-2 induces detectable p-eIF2α during infection. Using a small molecule inhibitor of eIF2α dephosphorylation, we provide evidence that MERS-CoV and HCoV-OC43 maximize viral replication through p-eIF2α dephosphorylation. Interestingly, genetic ablation of growth arrest and DNA damage-inducible protein (GADD34) expression, an inducible protein phosphatase 1 (PP1)-interacting partner targeting eIF2α for dephosphorylation, did not significantly alter HCoV-OC43 or SARS-CoV-2 replication, while siRNA knockdown of the constitutive PP1 partner, constitutive repressor of eIF2α phosphorylation (CReP), dramatically reduced HCoV-OC43 replication. Combining GADD34 knockout with CReP knockdown had the maximum impact on HCoV-OC43 replication, while SARS-CoV-2 replication was unaffected. Overall, we conclude that eIF2α dephosphorylation is critical for efficient protein production and replication during MERS-CoV and HCoV-OC43 infection. SARS-CoV-2, however, appears to be insensitive to p-eIF2α and, during infection, may even downregulate dephosphorylation to limit host translation. Full article

The emergence of RNA viruses driven by global population growth and international trade highlights the urgent need for effective antiviral agents that can inhibit viral replication. Nucleoside analogs, which mimic natural nucleotides, have shown promise in targeting RNA-dependent RNA polymerases (RdRps). Starting from protected 5-iodouridine, we report the synthesis of hitherto unknown C5-substituted-(1,3-diyne)-uridines nucleosides and their phosphoramidate prodrugs. The modifications at C5 include 4-(trifluoromethyl)benzene (a), 4-pentyl-benzene (b), 3,5-dimethoxy-benzene (c), 4-(trifluoromethoxy)benzene (d), 3-aniline (e), 4-pyridine (f), 3-thiophene (g), C₆H₁₃ (h), 2-pyrimidine (i), cyclopropyl (j), and phenyl (k) groups. These compounds were synthesized using Sonogashira palladium-catalyzed reactions and nickel–copper-catalyzed C-H activation between various alkynes, yielding between 25% and 67%. The antiviral activities of obtained compounds were measured through HTS against RNA viruses including influenza H1N1 and H3N2, human respiratory syncytial virus (RSV), SARS-CoV-2, Zika, hepatitis C virus (HCV), Hepatitis E virus (HEV), as well as against coronavirus (HCoV-229E). Unfortunately, none of them showed promising antiviral activity, with less than 85% inhibition observed in the cell viability screening of infected cells. Full article

Ab initio calculations of cross sections for electron capture by protons in collisions with CO₂ are carried out at energies between 100 eV/u and 50 keV/u, employing a semiclassical method within the Franck–Condon framework. The scattering wave function is expanded in a set of ab initio electronic wave functions of the HCO₂⁺ supermolecule. The calculation is performed on several trajectory orientations to obtain orientation-averaged total cross sections. A two-state model with an exponential interaction between the entrance and the lowest charge transfer channel is proposed to describe the main aspects of the charge transfer process and to estimate the precision of the molecular expansion. The symmetry of the HOMO ${\pi }_g$ of CO₂ is relevant to choose the signs of the molecular functions and to set up the orientation average of the cross sections. Very good agreement is found with the experimental charge transfer cross sections. Full article

Human seasonal coronaviruses (hCoVs) are a group of viruses that affect the upper respiratory tract. While seasonal patterns and the annual variability of predominant hCoV species are well-documented, their genetic and species diversity in St. Petersburg and across Russia remains largely unexplored. In this study, we developed a two-pool, long-amplicon (900–1100 bp) PCR primer panel for the whole-genome sequencing of four seasonal hCoV species. The panel was validated using nasopharyngeal swab samples collected within the Global Influenza Hospital Surveillance Network (GIHSN) project. Over a period of six epidemiological seasons from 2017 to 2023, we retrospectively analyzed 14,704 nasopharyngeal swabs collected from patients hospitalized in St. Petersburg clinics. Of these samples, 5010 (34.07%) tested positive for respiratory viruses, with 424 (2.88% of all samples) identified as seasonal human coronaviruses. The assessment of species diversity showed that predominant hCoV species alternate between seasons. Whole-genome sequences for 85 seasonal human coronaviruses (hCoVs) with >70% genome coverage were obtained, including 23 hCoV-OC43, 6 hCoV-HKU1, 39 hCoV-229E, and 17 hCoV-NL63. These represent the first near-complete genomes of seasonal hCoVs from the Russian Federation, addressing a significant gap in the genomic epidemiology of these viruses. A detailed phylogenetic analysis of the sequenced genomes was conducted, highlighting the emergence of hCoV-229E subclades 7b.1 and 7b.2, which carry numerous substitutions in the Spike protein. Additionally, we sequenced a historical hCoV-229E isolate collected in the USSR in 1979, the oldest sequenced 229E virus from Eurasia, and demonstrated that it belongs to Genotype 2. The newly developed PCR-based sequencing protocol for seasonal hCoVs is straightforward and well-suited for genomic surveillance, providing a valuable tool to enhance our understanding of the genetic diversity of human seasonal coronaviruses. Full article