Coronavirus envelope protein: current knowledge

Highly versatile small virus-encoded proteins in cellular membranes: A structural perspective on how proteins' inherent conformational plasticity couples with host membranes' properties to control cellular processes

We investigated several small viral proteins that reside and function in cellular membranes. These proteins belong to the viroporin family because they assemble into ion-conducting oligomers. However, despite forming similar oligomeric structures with analogous functions, these proteins have diverse amino acid sequences. In particular, the amino acid compositions of the proposed channel-forming transmembrane (TM) helices are vastly different-some contain residues (e.g., His, Trp, Asp, Ser) that could facilitate cation transport. Still, other viroporins' TM helices encompass exclusively hydrophobic residues; therefore, it is difficult to explain their channels' activity, unless other mechanisms (e.g., involving a negative lipid headgroups and/or membrane destabilization) take place. For this study, we selected the M2, Vpu, E, p13II, p7, and 2B proteins from the influenza A, HIV-1, human T-cell leukemia, hepatitis C, and picorna viruses, respectively. We provide a brief overview of the current knowledge about these proteins' structures as well as remaining questions about more comprehensive understanding of their structures, conformational dynamics, and function. Finally, we outline strategies to utilize a multi-prong structural and computational approach to overcome current deficiencies in the knowledge about these proteins.

In silico evaluation of S-adenosyl-L-homocysteine analogs as inhibitors of nsp14-viral cap N7 methyltranferase and PLpro of SARS-CoV-2: synthesis, molecular docking, physicochemical data, ADMET and molecular dynamics simulations studies

A series of S-adenosyl-L-homosysteine (SAH) analogs, with modification in the base and sugar moiety, have been designed, synthesized and screened as nsp14 and PLpro inhibitors of severe acute respiratory syndrome corona virus (SARS-CoV-2). The outcomes of ADMET (Adsorption, Distribution, Metabolism, Excretion, and Toxicity) studies demonstrated that the physicochemical properties of all analogs were permissible for development of these SAH analogs as antiviral agents. All molecules were screened against different SARS-CoV-2 targets using molecular docking. The docking results revealed that the SAH analogs interacted well in the active site of nsp14 protein having H-bond interactions with the amino acid residues Arg289, Val290, Asn388, Arg400, Phe401 and π-alkyl interactions with Arg289, Val290 and Phe426 of Nsp14-MTase site. These analogs also formed stable H-bonds with Leu163, Asp165, Arg167, Ser246, Gln270, Tyr274 and Asp303 residues of PLpro proteins and found to be quite stable complexes therefore behaved as probable nsp14 and PLpro inhibitors. Interestingly, analog 3 showed significant in silico activity against the nsp14 N7 methyltransferase of SARS-CoV-2. The molecular dynamics (MD) and post-MD results of analog 3 unambiguously established the higher stability of the nsp14 (N7 MTase):3 complex and also indicated its behavior as probable nsp14 inhibitor like the reference sinefungin. The docking and MD simulations studies also suggested that sinefungin did act as SARS-CoV-2 PLpro inhibitor as well. This study's findings not only underscore the efficacy of the designed SAH analogs as potent inhibitors against crucial SARS-CoV-2 proteins but also pinpoint analog 3 as a particularly promising candidate. All the study provides valuable insights, paving the way for potential advancements in antiviral drug development against SARS-CoV-2.

Flow cytometric analysis of the SARS coronavirus 2 antibodies in human plasma

COVID-19 is an infectious disease caused by the severe acute respiratory syndrome coronavirus (SARS-CoV-2). Anti-SARS-CoV-2 antibodies can provide information on patient immunity, identify asymptomatic patients, and track the spread of COVID-19. Efforts have been made to develop methods to detect anti-SARS-CoV-2 antibodies in humans. Here, we describe a flow cytometric assay for the simultaneous detection of anti-SARS-CoV-2 IgG and IgM in human plasma. To assess the antibody response against the different SARS-CoV-2 structural proteins, five viral recombinant proteins, including spike protein subunit 1 (S1), N-terminal domain of S1 (S1A), spike receptor-binding domain (RBD), spike protein subunit 2 (S2), and nucleocapsid protein (N), were generated. A comparison of the antibody profiles detected by the assay with plasma from 100 healthy blood donors collected prior to the COVID-19 pandemic and plasma from 100 virologically confirmed COVID-19 patients demonstrated a clear discrimination between the two groups. Among the COVID-19 patients, the antibody responses for the viral proteins, as determined by their prevalence, were anti-RBD IgG = anti-N IgG > anti-S1 IgG > anti-S1A IgG > anti-S2 IgG, and anti-RBD IgM > anti-S1 IgM > anti-N IgM > anti-S2 IgM. The prevalence of anti-SARS-CoV-2 IgG and IgM was not associated with sex, age, race, days after the onset of symptoms, or severity of illness, except for a higher prevalence of anti-S2 IgG being observed in men than in women. The levels of anti-RBD IgG were higher in patients 65 years and older and in patients who had severe symptoms. Similarly, patients who had severe symptoms exhibited higher levels of anti-S1 and anti-S1A IgG than patients who had mild or moderate symptoms. The levels of anti-RBD IgM tended to be higher in men but did not differ among age, race, days after the onset of symptoms, or severity of illness. Our study indicates that the flow cytometric assay, especially using RBD as target antigen, can be used to detect simultaneously anti-SARS-CoV-2 IgG and IgM antibodies in human plasma.

Solid-State NMR of Virus Membrane Proteins

Enveloped viruses encode ion-conducting pores that permeabilize the host cell membranes and mediate the budding of new viruses. These viroporins are some of the essential membrane proteins of viruses, and have high sequence conservation, making them important targets of antiviral drugs. High-resolution structures of viroporins are challenging to determine by X-ray crystallography and cryoelectron microscopy, because these proteins are small, hydrophobic, and prone to induce membrane curvature. Solid-state NMR (ssNMR) spectroscopy is an ideal method for elucidating the structure, dynamics, and mechanism of action of viroporins in phospholipid membranes. This Account describes our investigations of influenza M2 proteins and the SARS-CoV-2 E protein using solid-state NMR.M2 proteins form acid-activated tetrameric proton channels that initiate influenza uncoating in the cell. 15N and 13C exchange NMR revealed that M2 shuttles protons into the virion using a crucial histidine, whose imidazole nitrogens pick up and release protons on the microsecond time scale at acidic pH. This proton exchange is synchronized with and facilitated by imidazole reorientation, which is observed in NMR spectra. Quantitative 15N NMR spectra yielded the populations of neutral and cationic histidines as a function of pH, giving four proton dissociation constants (pKa's). The pKa's of influenza AM2 indicate that the +3 charged channel has the highest time-averaged single-channel conductance; thus the third protonation event defines channel activation. In comparison, influenza BM2 exhibits lower pKa's due to a second, peripheral histidine, which accelerates proton dissociation from the central proton-selective histidine. Amantadine binding to AM2 suppressed proton exchange and imidazole reorientation, indicating that this antiviral drug acts by inhibiting proton shuttling. Solid-state NMR 13C-2H distance measurements revealed that amantadine binds the N-terminal pore of the channel near a crucial Ser31, whose mutation to asparagine causes amantadine resistance in circulating influenza A viruses. A second binding site, on the lipid-facing surface of the protein, only occurs when amantadine is in large excess in lipid bilayers. M2 not only functions as a proton channel but also conducts membrane scission during influenza budding in a cholesterol-dependent manner. Solid-state NMR distance experiments revealed that two cholesterol molecules bind asymmetrically to the surface of the tetrameric channel, thus recruiting the protein to the cholesterol-rich budding region of the cell membrane to cause membrane scission.To accelerate full structure determination of viroporins, we developed a suite of 19F solid-state NMR techniques that measure interatomic distances to 1-2 nm. Using this approach, we determined the atomic structures of influenza BM2, SARS-CoV-2 E, and EmrE, a multidrug-resistance bacterial transporter. pH-induced structural changes of these proteins gave detailed insights into the activation mechanisms of BM2 and E and the proton-coupled substrate transport mechanism of EmrE. The SARS-CoV-2 E protein forms pentameric helical bundles whose structures are distinct between the closed state at neutral pH and the open state at acidic pH. These 19F-enabled distance NMR experiments are also instrumental for identifying the binding mode and binding site of hexamethylene amiloride in E, paving the way for developing new antiviral drugs that target these pathogenic virus ion channels.

Recent Advances in Antiviral Drug Delivery Strategies

Viral infectious diseases have long posed significant challenges to public health, leading to substantial morbidity and mortality worldwide. Recent outbreaks, including those caused by coronaviruses, have highlighted the urgent need for more effective antiviral treatments. Existing therapies, while numerous, face limitations such as drug resistance, toxicity, poor bioavailability, and non-specific targeting, which hinder their effectiveness against new and emerging viruses. This review focuses on the latest advances in nanoplatform technologies designed to enhance drug solubility, provide sustained or targeted delivery, and improve the efficacy of antiviral therapies. Additionally, we explore how these technologies can be integrated with novel strategies like genetic modulation to combat viral infections more effectively. The review also discusses the potential of these innovations in addressing the challenges posed by current antiviral therapies and their implications for future clinical applications.

Subcellular localization of SARS-CoV-2 E and 3a proteins along the secretory pathway

SARS-CoV-2 E and 3a proteins are important for the assembly, budding, and release of viral particles. These two transmembrane proteins have been implicated in forming channels in the membrane that allow the transport of ions to favor viral replication. During an active infection, both proteins generally localize to the endoplasmic reticulum (ER), ER-Golgi intermediate compartment (ERGIC), and the Golgi where viral assembly occurs. The ER and Golgi are critical for the proper packaging and trafficking of cellular proteins along the secretory pathways which determine a protein's final destination inside or outside of the cell. The SARS-CoV-2 virus primarily infects epithelial cells that are highly secretory in nature such as those in the lung and gut. Here we quantified the distribution of SARS-CoV-2 E and 3a proteins along the secretory pathways in a human intestinal epithelial cell line. We used NaturePatternMatch to demonstrate that epitope-tagged E and 3a proteins expressed alone via transient transfection have a similar immunoreactivity pattern as E and 3a proteins expressed by wild-type viral infection. While E and 3a proteins localized with all selected cellular markers to varying degrees, 3a protein displayed a higher correlation coefficient with the Golgi, early/late endosome, lysosome, and plasma membrane when compared to E protein. This work is the first to provide quantification of the subcellular distribution of E and 3a proteins along the multiple components of the secretory pathway and serves as a basis to develop models for examining how E and 3a alter proteostasis within these structures and affect their function.

The antiviral effects and underlying mechanisms of probiotics on viral infections

In public health emergencies, viral diseases like influenza and COVID-19 have become a major concern. One of the proposed responses to this concern is the use of probiotics. Probiotics have a potent role in arming our bodies to combat viral infections. They affect the innate and adaptive immune systems in various ways. Accumulating studies has shown that probiotics can reduce the possibility of infection or the duration of respiratory symptoms by modulating the functions of the immune system. This review aims to summarize the impacts of probiotics on respiratory viral infections and their potential antiviral mechanisms. Therefore, we herein discussed probiotics in relation to lung immunity, distinct types of respiratory viral infections (VRIs), including influenza, rhinoviruses, respiratory syncytial virus, and upper respiratory viral infections, and lastly, probiotics and their effects on COVID-19. However, more studies are needed to explore the antiviral mechanisms of probiotics.

Investigation of ritonavir analogs antiretroviral natural compounds against SARS-CoV-2 envelope protein

Since the pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first reported from Wuhan, China, there has been a surge in scientific research to find a permanent cure for the disease. The main challenge in effective drug discovery is the continuously mutating nature of the SARS-CoV-2 virus. Thus, we have used the I-TASSER modeling to predict the structure of the SARS-CoV-2 viral envelope protein followed by combinatorial computational assessment to predict its putative potential small molecule inhibitors. As early treatment with ritonavir in combination was associated with faster time to clinical improvement and/or virological clearance, we aimed to retrieve analogs of ritonavir to find ideal inhibitors for SARS-CoV-2 viral envelope protein. The collected ligands were screened against the predicted binding pocket of viral envelope protein using extra precision (XP) docking protocol and the first four best-docked compounds were studied for complex stability using 300 ns all-atom molecular dynamics simulations embedding within the cellular membrane. Among the selected compounds, ZINC64859171 and ZINC1221429 showed considerable stability and interactions by comparison to the reference compound, i.e., Ritonavir (ZINC3944422). Moreover, the post-simulation analysis suggested the considerable binding affinity and induced conformation changes in the respective docked complexes against Ritonavir. Altogether, the obtained results demonstrated the putative potential of screened ritonavir analogs, i.e., ZINC64859171, against the envelope protein of SARS-CoV-2 and can be considered for further drug development in the treatment of the COVID-19 pandemic.Communicated by Ramaswamy H. Sarma.

Silver Nanoparticles-Functionalized Textile against SARS-CoV-2: Antiviral Activity of the Capping Oleylamine Molecule

COVID-19 disease, triggered by SARS-CoV-2 virus infection, has led to more than 7.0 million deaths worldwide, with a significant fraction of recovered infected people reporting postviral symptoms. Smart surfaces functionalized with nanoparticles are a powerful tool to inactivate the virus and prevent the further spreading of the disease. Literature reports usually focus on the role of nanomaterial composition and size dispersion in evaluating their efficacy against SARS-CoV-2. Here, the anti-SARS-CoV-2 activity of oleylamine (OAm) used as a capping agent of silver nanoparticles is quantified for the first time. Spherical hydrophobic nanoparticles with 8 ± 2 nm diameter were prepared and characterized by Fourier transform infrared, dynamic light scattering, and transmission electron microscopy techniques. Biological assays showed that microgram amounts of nanoparticles, deposited on nonwoven textile obtained from surgical masks, efficiently inactivated up to 99.6(2)% of the virus with just 2 min of exposure. The virucidal activity of the corresponding amount of free OAm has been determined as well, reaching up to 67(1)% of activity for an exposure time of 10 min. Inductively coupled plasma optical emission spectrometry results pointed out a low leaching out of the nanoparticles in contact with water or culture medium. All in all, these results propose the capping molecules as an important chemical variable to be taken into account in the design of fast, efficient, and long-lasting anti-SARS-CoV-2 coatings.

Combined mutations in nonstructural protein 14, envelope, and membrane proteins mitigate the neuropathogenicity of SARS-CoV-2 Omicron BA.1 in K18-hACE2 mice

We previously reported that mutations outside the spike protein play a role in the attenuation of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron BA.1 variant in human ACE2 transgenic mice (K18-hACE2). Here, we assessed the pathogenicity of SARS-CoV-2 (WA1/2020) containing mutations from the Omicron BA.1 variant in K18-hACE2 mice. At an infection dose of 104 plaque-forming units (PFU), WA1 virus carrying Omicron BA.1 Nsp14(I42V), E(T9I), M(D3G/Q19E/A63T), but not Nsp6(Δ105-107, I189V), substitutions showed significant reduction in lethality. Interestingly, reduction of viral load is more pronounced in the brains than in the lungs. Subsequent analyses suggest that BA.1 E(T9I) and M(D3G/Q19E/A63T) substitutions result in less efficient packaging of virus-like particles. Given that Nsp14(I42V), E(T9I), M(Q19E/A63T) are well preserved in subsequent omicron subvariants, including currently circulating variants, our findings highlight the importance of understanding how non-spike mutations affect the pathogenicity of SARS-CoV-2 variants.

IMPORTANCE

Inoculation of transgenic mice expressing human angiotensin-converting enzyme 2 (hACE2) with SARS-CoV-2 often leads to a fatal brain infection. Omicron BA.1 variant, however, was found to be non-lethal in this model. Here, we systematically assessed the effect of individual mutations of Omicron BA.1 on the pathogenicity of the virus in hACE2 transgenic mice and found that combination of 5 mutations of Nsp14, E, and M of BA.1 variant significantly lowered brain viral load and reduced lethality. These results provide new insights into how SARS-CoV-2 Omicron BA.1 is attenuated.

Evaluation of Genomic Surveillance of SARS-CoV-2 Virus Isolates and Comparison of Mutational Spectrum of Variants in Bangladesh

The SARS-CoV-2-induced disease, COVID-19, remains a worldwide public health concern due to its high rate of transmission, even in vaccinated and previously infected people. In the endemic state, it continues to cause significant pathology. To elu- cidate the viral mutational changes and screen the emergence of new variants of concern, we conducted this study in Bangladesh. The viral RNA genomes extracted from 25 ran- domly collected samples of COVID-19-positive patients from March 2021 to February 2022 were sequenced using Illumina COVID Seq protocol and genomic data processing, as well as evaluations performed in DRAGEN COVID Lineage software. In this study, the percentage of Delta, Omicron, and Mauritius variants identified were 88%, 8%, and 4%, respectively. All of the 25 samples had 23,403 A>G (D614G, S gene), 3037 C>T (nsp3), and 14,408 C>T (nsp12) mutations, where 23,403 A>G was responsible for increased transmis- sion. Omicron had the highest number of unique mutations in the spike protein (i.e., sub- stitutions, deletions, and insertions), which may explain its higher transmissibility and immune-evading ability than Delta. A total of 779 mutations were identified, where 691 substitutions, 85 deletions, and 3 insertion mutations were observed. To sum up, our study will enrich the genomic database of SARS-CoV-2, aiding in treatment strategies along with understanding the virus's preferences in both mutation type and mutation site for predicting newly emerged viruses' survival strategies and thus for preparing to coun- teract them.

Towards developing multistrain PEDV vaccines: Integrating basic concepts and SARS-CoV-2 pan-sarbecovirus strategies

Porcine epidemic diarrhea virus (PEDV) is a major pathogen impacting the global pig industry, with outbreaks causing significant financial losses. The genetic variability of PEDV has posed challenges for vaccine development since its identification in the 1970s, a problem that intensified with its global emergence in the 2010s. Since current vaccines provide limited cross-protection against PEDV strains, and the development of multistrain PEDV vaccines remains an underexplored area of research, there is an urgent need for improved vaccine solutions. The rapid development of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines and ongoing pan-sarbecovirus vaccine research, have demonstrated the potential of next-generation vaccine platforms and novel antigen design strategies. These advancements offer valuable insights for the development of multistrain PEDV vaccines. This review summarizes key aspects of PEDV virology and explores multistrain vaccine development considering SARS-CoV-2 vaccine innovations, proposing a framework for developing next-generation PEDV vaccine solutions.

Swine Acute Diarrhea Syndrome Coronavirus: An Overview of Virus Structure and Virus-Host Interactions

SADS-CoV, a recently identified Rhinolophus bat coronavirus HKU2-associated swine coronavirus, is a malignant pathogen that causes acute diarrhea, severe diarrhea, and weight loss in infected piglets. The virus was first detected in Guangdong Province, China, in 2017 and has since been observed in Jiangxi, Fujian, and Guangxi Provinces. In 2023, the virus was detected in Henan Province, in inland China. This virus can infect various cell lines, including human cell lines, showing significant potential for cross-species transmission and posing a possible zoonotic threat. However, the molecular biology of SADS-CoV remains largely unknown, and there are no commercially available therapeutics or vaccines to prevent SADS-CoV infection. In this review, an update on progress in SADS-CoV research is provided, with a focus on the history of outbreaks, the characteristics of the virus, its interactions with the host, and developments in therapeutics and vaccines.

Polar Networks Mediate Ion Conduction of the SARS-CoV-2 Envelope Protein

The SARS-CoV-2 E protein conducts cations across the cell membrane to cause pathogenicity to infected cells. The high-resolution structures of the E transmembrane domain (ETM) in the closed state at neutral pH and in the open state at acidic pH have been determined. However, the ion conduction mechanism remains elusive. Here, we use solid-state NMR spectroscopy to investigate the side chain structure, dynamics, and interactions of five polar residues at the N-terminal entrance of the channel and three polar residues at the C-terminal end. The chemical shifts of the N-terminal Glu8 reveal that the Glu side chain interacts with protons, Ca2+ and two neighboring Thr residues, and adopts distinct motionally averaged conformational ensembles. These polar interactions are sensitive to the presence of negatively charged lipids in the membrane. A T9I mutation, prevalent in the Omicron variants of SARS-CoV-2 E, perturbs these interactions and partially immobilizes the N-terminal segment. Deeper into the channel, two polar residues, Asn15 and Ser16, form interhelical hydrogen bonds in the closed state but become separated by water molecules in the open state. This is manifested by Asn15-Ser16 correlation signals at neutral pH and the loss of these correlations and the appearance of water cross peaks with Ser16 at acidic pH in the presence of Ca2+. Finally, the guanidinium side chain of the C-terminal Arg38 undergoes fast reorientations in the closed state but becomes more restricted in the open state. These results provide evidence for a dynamic and hydrogen-bonded N-terminal polar network that recruits and relays protons and Ca2+ in a lipid-dependent manner. Once inside, the ions permeate past the hydrophobic middle of the transmembrane domain with the help of enhanced hydrophilicity of the C-terminal channel lumen due to the insertion of the Arg38 side chain into the pore.

Conformational dynamics of the membrane protein of MERS-CoV in comparison with SARS-CoV-2 in ERGIC complex

The present study explores the conformational dynamics of the membrane protein of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) within the Endoplasmic Reticulum-Golgi Intermediate Compartment (ERGIC) complex using an all-atomistic molecular dynamics simulation approach. Significant structural changes were observed in the N-terminal, C-terminal, transmembrane, and beta-sheet sandwich domains of the MERS-CoV membrane protein. This study also highlights the structural similarities between the MERS-CoV and the SARS-CoV-2 membrane proteins, particularly in how both exhibit a distinct kink in the transmembrane helix caused by aromatic residue-lipid interactions. A structural expansion below the transmembrane and above the beta-sheet sandwich domain within the dimer was observed in all the M-proteins. This site on the beta-sheet sandwich domains near the C-terminal end could serve as a potential drug-binding site. Notably, a stable helical structure was identified in the C-terminal domain of the MERS-CoV membrane protein, whereas a proper secondary structural conformation was not observed in the SARS-CoV-2 membrane protein. Further, the SARS-CoV-2 membrane protein exhibited stronger binding to the lipid bilayer than the MERS-CoV, indicating its greater structural stability within the ERGIC complex. The structural similarity between the membrane protein of MERS-CoV and SARS-CoV-2 suggests the feasibility of employing a common inhibitor against these beta-coronaviruses. Furthermore, this analysis enhances our understanding of the membrane protein's interactions with proteins and lipids, paving the way for therapeutic developments against these viruses.

SARS-CoV-2 Is an Electricity-Driven Virus

One of the most important and challenging biological events of recent times has been the pandemic caused by SARS-CoV-2. Since the underpinning argument behind this book is the ubiquity of electrical forces driving multiple disparate biological events, consideration of key aspects of the SARS-CoV-2 structural proteins is included. Electrical regulation of spike protein, nucleocapsid protein, membrane protein, and envelope protein is included, with several of their activities regulated by LLPS and the multivalent and π-cation and π-π electrical forces that drive phase separation.

Risk impact of SARS-CoV-2 coronavirus and spike protein on cardiac tissue: a comprehensive review

The global COVID-19 pandemic, caused by SARS-CoV-2, has led to significant morbidity and mortality, with a profound impact on cardiovascular health. This review investigates the mechanisms of SARS-CoV-2's interaction with cardiac tissue, particularly emphasizing the role of the Spike protein and ACE2 receptor in facilitating viral entry and subsequent cardiac complications. We dissect the structural features of the virus, its interactions with host cell receptors, and the resulting pathophysiological changes in the heart. Highlighting SARS-CoV-2's broad organ tropism, especially its effects on cardiomyocytes via ACE2 and TMPRSS2, the review addresses how these interactions exacerbate cardiovascular issues in patients with pre-existing conditions such as diabetes and hypertension. Additionally, we assess both direct and indirect mechanisms of virus-induced cardiac damage, including myocarditis, arrhythmias, and long-term complications such as 'long COVID'. This review underscores the complexity of SARS-CoV-2's impact on the heart, emphasizing the need for ongoing research to fully understand its long-term effects on cardiovascular health. Key words: COVID-19, Heart, ACE2, Spike protein, Cardiomyocytes, Myocarditis, Long COVID.

Microfluidic methods for the diagnosis of acute respiratory tract infections

Acute respiratory tract infections (ARTIs) are caused by sporadic or pandemic outbreaks of viral or bacterial pathogens, and continue to be a considerable socioeconomic burden for both developing and industrialized countries alike. Diagnostic methods and technologies serving as the cornerstone for disease management, epidemiological tracking, and public health interventions are evolving continuously to keep up with the demand for higher sensitivity, specificity and analytical throughput. Microfluidics is becoming a key technology in these developments as it allows for integrating, miniaturizing and automating bioanalytical assays at an unprecedented scale, reducing sample and reagent consumption and improving diagnostic performance in terms of sensitivity, throughput and response time. In this article, we describe relevant ARTIs-pneumonia, influenza, severe acute respiratory syndrome, and coronavirus disease 2019-along with their pathogenesis. We provide a summary of established methods for disease diagnosis, involving nucleic acid amplification techniques, antigen detection, serological testing as well as microbial culture. This is followed by a short introduction to microfluidics and how flow is governed at low volume and reduced scale using centrifugation, pneumatic pumping, electrowetting, capillary action, and propagation in porous media through wicking, for each of these principles impacts the design, functioning and performance of diagnostic tools in a particular way. We briefly cover commercial instruments that employ microfluidics for use in both laboratory and point-of-care settings. The main part of the article is dedicated to emerging methods deriving from the use of miniaturized, microfluidic systems for ARTI diagnosis. Finally, we share our thoughts on future perspectives and the challenges associated with validation, approval, and adaptation of microfluidic-based systems.

Docking heparan sulfate-based ligands as a promising inhibitor for SARS-CoV-2

CONTEXT

Heparan sulfate (HS) linear polysaccharide glycosaminoglycan compound is linked to components from the cell surface and the extracellular matrix. HS mediates SARS-CoV-2 infection through spike protein binding to cell surface receptors and is required to bind ACE2, prompting the need for electronic structure and molecular docking evaluation of this core system to exploit this attachment in developing new derivatives. Therefore, we have studied five molecules based on HS using molecular docking and electronic structure analysis. Non-covalent interaction analysis shows hydrogen bonding and van der Waals interactions in the binding to RBD-ACE2 interface and 3CLpro. SDM3 and SDM1 molecules present the lowest gap, including solvent effect under 154.6 kcal/mol, and exhibit the most reactivity behavior in this group, potentially leading to enhanced interaction in docking studies.

METHODS

Heparan sulfate and four derivatives were optimized using B3LYP functional with two basis sets 6-31 + G(d,p) and def2SVP. Electronic structure was used to explore the main interactions and the reactivity of these molecules, and these optimized structures were used in the molecular docking study against 3CLpro, RBD, and ACE2.

Structural proteins of human coronaviruses: what makes them different?

Following COVID-19 outbreak with its unprecedented effect on the entire world, the interest to the coronaviruses increased. The causative agent of the COVID-19, severe acute respiratory syndrome coronavirus - 2 (SARS-CoV-2) is one of seven coronaviruses that is pathogenic to humans. Others include SARS-CoV, MERS-CoV, HCoV-HKU1, HCoV-OC43, HCoV-NL63 and HCoV-229E. The viruses differ in their pathogenicity. SARS-CoV, MERS-CoV, and SARS-CoV-2 are capable to spread rapidly and cause epidemic, while HCoV-HKU1, HCoV-OC43, HCoV-NL63 and HCoV-229E cause mild respiratory disease. The difference in the viral behavior is due to structural and functional differences. All seven human coronaviruses possess four structural proteins: spike, envelope, membrane, and nucleocapsid. Spike protein with its receptor binding domain is crucial for the entry to the host cell, where different receptors on the host cell are recruited by different viruses. Envelope protein plays important role in viral assembly, and following cellular entry, contributes to immune response. Membrane protein is an abundant viral protein, contributing to the assembly and pathogenicity of the virus. Nucleocapsid protein encompasses the viral RNA into ribonucleocapsid, playing important role in viral replication. The present review provides detailed summary of structural and functional characteristics of structural proteins from seven human coronaviruses, and could serve as a practical reference when pathogenic human coronaviruses are compared, and novel treatments are proposed.

Elevated serum mtDNA in COVID-19 patients is linked to SARS-CoV-2 envelope protein targeting mitochondrial VDAC1, inducing apoptosis and mtDNA release

Mitochondria dysfunction is implicated in cell death, inflammation, and autoimmunity. During viral infections, some viruses employ different strategies to disrupt mitochondria-dependent apoptosis, while others, including SARS-CoV-2, induce host cell apoptosis to facilitate replication and immune system modulation. Given mitochondrial DNAs (mtDNA) role as a pro-inflammatory damage-associated molecular pattern in inflammatory diseases, we examined its levels in the serum of COVID-19 patients and found it to be high relative to levels in healthy donors. Furthermore, comparison of serum protein profiles between healthy individuals and SARS-CoV-2-infected patients revealed unique bands in the COVID-19 patients. Using mass spectroscopy, we identified over 15 proteins, whose levels in the serum of COVID-19 patients were 4- to 780-fold higher. As mtDNA release from the mitochondria is mediated by the oligomeric form of the mitochondrial-gatekeeper-the voltage-dependent anion-selective channel 1 (VDAC1)-we investigated whether SARS-CoV-2 protein alters VDAC1 expression. Among the three selected SARS-CoV-2 proteins, small envelope (E), nucleocapsid (N), and accessory 3b proteins, the E-protein induced VDAC1 overexpression, VDAC1 oligomerization, cell death, and mtDNA release. Additionally, this protein led to mitochondrial dysfunction, as evidenced by increased mitochondrial ROS production and cytosolic Ca2+ levels. These findings suggest that SARS-CoV-2 E-protein induces mitochondrial dysfunction, apoptosis, and mtDNA release via VDAC1 modulation. mtDNA that accumulates in the blood activates the cGAS-STING pathway, triggering inflammatory cytokine and chemokine expression that contribute to the cytokine storm and tissue damage seen in cases of severe COVID-19.

Productive infection of the retinal pigment epithelium by SARS-CoV-2: Initial effects and consideration of long-term consequences

As the SARS-CoV-2 coronavirus continues to evolve and infect the global population, many individuals are likely to suffer from post-acute sequelae of SARS-CoV-2 infection (PASC). Manifestations of PASC include vision symptoms, but little is known about the ability of SARS-CoV-2 to infect and impact the retinal cells. Here, we demonstrate that SARS-CoV-2 can infect and perturb the retinal pigment epithelium (RPE) in vivo, after intranasal inoculation of a transgenic mouse model of SARS-CoV-2 infection, and in cell culture. Separate lentiviral studies showed that SARS-CoV-2 Spike protein mediates viral entry and replication in RPE cells, while the Envelope and ORF3a proteins induce morphological changes. Infection with major variants of SARS-CoV-2 compromised the RPE barrier function and phagocytic capacity. It also caused complement activation and production of cytokines and chemokines, resulting in an inflammatory response that spread across the RPE layer. This inflammatory signature has similarities to that associated with the onset of age-related macular degeneration (AMD), a major cause of human blindness, resulting from RPE pathology that eventually leads to photoreceptor cell loss. Thus, our findings suggest that post-acute sequelae of SARS-CoV-2 infection of the RPE may have long-term implications for vision, perhaps comparable to the increased occurrence of AMD found among individuals infected by HIV, but with greater public health consequences due to the much larger number of SARS-CoV-2 infections.

Interaction between coronaviruses and the autophagic response

In recent years, the emergence and widespread dissemination of the coronavirus SARS-CoV-2 has posed a significant threat to global public health and social development. In order to safely and effectively prevent and control the spread of coronavirus diseases, a profound understanding of virus-host interactions is paramount. Cellular autophagy, a process that safeguards cells by maintaining cellular homeostasis under diverse stress conditions. Xenophagy, specifically, can selectively degrade intracellular pathogens, such as bacteria, fungi, viruses, and parasites, thus establishing a robust defense mechanism against such intruders. Coronaviruses have the ability to induce autophagy, and they manipulate this pathway to ensure their efficient replication. While progress has been made in elucidating the intricate relationship between coronaviruses and autophagy, a comprehensive summary of how autophagy either benefits or hinders viral replication remains elusive. In this review, we delve into the mechanisms that govern how different coronaviruses regulate autophagy. We also provide an in-depth analysis of virus-host interactions, particularly focusing on the latest data pertaining to SARS-CoV-2. Our aim is to lay a theoretical foundation for the development of novel coronavirus vaccines and the screening of potential drug targets.

NK Cell and Monocyte Dysfunction in Multisystem Inflammatory Syndrome in Children

Multisystem inflammatory syndrome in children (MIS-C) is a severe complication of SARS-CoV-2 infection characterized by multiorgan involvement and inflammation. Testing of cellular function ex vivo to understand the aberrant immune response in MIS-C is limited. Despite strong Ab production in MIS-C, SARS-CoV-2 nucleic acid testing can remain positive for 4-6 wk postinfection. Therefore, we hypothesized that dysfunctional cell-mediated Ab responses downstream of Ab production may be responsible for delayed clearance of viral products in MIS-C. In MIS-C, monocytes were hyperfunctional for phagocytosis and cytokine production, whereas NK cells were hypofunctional for both killing and cytokine production. The decreased NK cell cytotoxicity correlated with an NK exhaustion marker signature and systemic IL-6 levels. Potentially providing a therapeutic option, cellular engagers of CD16 and SARS-CoV-2 proteins were found to rescue NK cell function in vitro. Taken together, our results reveal dysregulation in Ab-mediated cellular responses of myeloid and NK cells that likely contribute to the immune pathology of this disease.

Molecular targets in SARS-CoV-2 infection: An update on repurposed drug candidates

The 2019 widespread contagion of the human coronavirus novel type (SARS-CoV-2) led to a pandemic declaration by the World Health Organization. A daily increase in patient numbers has formed an urgent necessity to find suitable targets and treatment options for the novel coronavirus (COVID-19). Despite scientists' struggles to discover quick treatment solutions, few effective specific drugs are approved to control SARS-CoV-2 infections thoroughly. Drug repositioning or Drug repurposing and target-based approaches are promising strategies for facilitating the drug discovery process. Here, we review current in silico, in vitro, in vivo, and clinical updates regarding proposed drugs for prospective treatment options for COVID-19. Drug targets that can direct pharmaceutical sciences efforts to discover new drugs against SARS-CoV-2 are divided into two categories: Virus-based targets, for example, Spike glycoprotein and Nucleocapsid Protein, and host-based targets, for instance, inflammatory cytokines and cell receptors through which the virus infects the cell. A broad spectrum of drugs has been found to show anti-SARS-CoV-2 potential, including antiviral drugs and monoclonal antibodies, statins, anti-inflammatory agents, and herbal products.

Broad Adaptability of Coronavirus Adhesion Revealed from the Complementary Surface Affinity of Membrane and Spikes

Coronavirus stands for a large family of viruses characterized by protruding spikes surrounding a lipidic membrane adorned with proteins. The present study explores the adhesion of transmissible gastroenteritis coronavirus (TGEV) particles on a variety of reference solid surfaces that emulate typical virus-surface interactions. Atomic force microscopy informs about trapping effectivity and the shape of the virus envelope on each surface, revealing that the deformation of TGEV particles spans from 20% to 50% in diameter. Given this large deformation range, experimental Langmuir isotherms convey an unexpectedly moderate variation in the adsorption-free energy, indicating a viral adhesion adaptability which goes beyond the membrane. The combination of an extended Helfrich theory and coarse-grained simulations reveals that, in fact, the envelope and the spikes present complementary adsorption affinities. While strong membrane-surface interaction lead to highly deformed TGEV particles, surfaces with strong spike attraction yield smaller deformations with similar or even larger adsorption-free energies.

Unraveling the role of the nucleocapsid protein in SARS-CoV-2 pathogenesis: From viral life cycle to vaccine development

BACKGROUND

The nucleocapsid protein (N protein) is the most abundant protein in SARS-CoV-2. Viral RNA and this protein are bound by electrostatic forces, forming cytoplasmic helical structures known as nucleocapsids. Subsequently, these nucleocapsids interact with the membrane (M) protein, facilitating virus budding into early secretory compartments.

SCOPE OF REVIEW

Exploring the role of the N protein in the SARS-CoV-2 life cycle, pathogenesis, post-sequelae consequences, and interaction with host immunity has enhanced our understanding of its function and potential strategies for preventing SARS-CoV-2 infection.

MAJOR CONCLUSION

This review provides an overview of the N protein's involvement in SARS-CoV-2 infectivity, highlighting its crucial role in the virus-host protein interaction and immune system modulation, which in turn influences viral spread.

GENERAL SIGNIFICANCE

Understanding these aspects identifies the N protein as a promising target for developing effective antiviral treatments and vaccines against SARS-CoV-2.

Coronavirus nucleocapsid protein enhances the binding of p-PKCα to RACK1: Implications for inhibition of nucleocytoplasmic trafficking and suppression of the innate immune response

The hallmark of coronavirus infection lies in its ability to evade host immune defenses, a process intricately linked to the nuclear entry of transcription factors crucial for initiating the expression of antiviral genes. Central to this evasion strategy is the manipulation of the nucleocytoplasmic trafficking system, which serves as an effective target for the virus to modulate the expression of immune response-related genes. In this investigation, we discovered that infection with the infectious bronchitis virus (IBV) dynamically impedes the nuclear translocation of several transcription factors such as IRF3, STAT1, STAT2, NF-κB p65, and the p38 MAPK, leading to compromised transcriptional induction of key antiviral genes such as IFNβ, IFITM3, and IL-8. Further examination revealed that during the infection process, components of the nuclear pore complex (NPC), particularly FG-Nups (such as NUP62, NUP153, NUP42, and TPR), undergo cytosolic dispersion from the nuclear envelope; NUP62 undergoes phosphorylation, and NUP42 exhibits a mobility shift in size. These observations suggest a disruption in nucleocytoplasmic trafficking. Screening efforts identified the IBV nucleocapsid (N) protein as the agent responsible for the cytoplasmic distribution of FG-Nups, subsequently hindering the nuclear entry of transcription factors and suppressing the expression of antiviral genes. Interactome analysis further revealed that the IBV N protein interacts with the scaffold protein RACK1, facilitating the recruitment of activated protein kinase C alpha (p-PKCα) to RACK1 and relocating the p-PKCα-RACK1 complex to the cytoplasm. These observations are conserved across diverse coronaviruses N proteins. Concurrently, the presence of both RACK1 and PKCα/β proved essential for the phosphorylation and cytoplasmic dispersion of NUP62, the suppression of antiviral cytokine expression, and efficient virus replication. These findings unveil a novel, highly effective, and evolutionarily conserved mechanism.

Palmitoylation of SARS-CoV-2 Envelope protein is central to virus particle formation

The Envelope (E) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an integral structural protein in the virus particles. However, its role in the assembly of virions and the underlying molecular mechanisms are yet to be elucidated, including whether the function of E protein is regulated by post-translational modifications. In the present study, we report that SARS-CoV-2 E protein is palmitoylated at C40, C43, and C44 by palmitoyltransferases zDHHC3, 6, 12, 15, and 20. Mutating these three cysteines to serines (C40/43/44S) reduced the stability of E protein, decreased the interaction of E with structural proteins Spike, Membrane, and Nucleocapsid, and thereby inhibited the production of virus-like particles (VLPs) and VLP-mediated luciferase transcriptional delivery. Specifically, the C40/43/44S mutation of E protein reduced the density of VLPs. Collectively, these results demonstrate that palmitoylation of E protein is vital for its function in the assembly of SARS-CoV-2 particles.IMPORTANCEIn this study, we systematically examined the biochemistry of palmitoylation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) E protein and demonstrated that palmitoylation of SARS-CoV-2 E protein is required for virus-like particle (VLP) production and maintaining normal particle density. These results suggest that palmitoylated E protein is central for proper morphogenesis of SARS-CoV-2 VLPs in densities required for viral infectivity. This study presents a significant advancement in the understanding of how palmitoylation of viral proteins is vital for assembling SARS-CoV-2 particles and supports that palmitoyl acyltransferases can be potential therapeutic targets for the development of SARS-CoV-2 inhibitors.

TLR2/NF-κB signaling in macrophage/microglia mediated COVID-pain induced by SARS-CoV-2 envelope protein

Pain has become a major symptom of long COVID-19 without effective therapy. Apart from viral infection pathological process, SARS-CoV-2 membranal proteins (envelope [S2E], spike [S2S] and membrane [S2M]) also present pro-inflammatory feature independently. Here, we aim to uncover the neuroinflammatory mechanism of COVID-pain induced by SARS-CoV-2 membranal proteins. We detected the three proteins in both peripheral sensory ganglions and spinal dorsal horn of COVID-19 donors. After intradermal and intrathecal injection, only S2E triggered pain behaviors, accompanied with upregulated-phosphorylation nuclear factor kappa B (NF-κB), which was significantly attenuated by minocycline in mice. We further identified Toll-like receptor 2 (TLR2) among TLRs as the target of S2E to evoke inflammatory responses leading to COVID-pain. This study identified the nociceptive effect of S2E through directly interacting with macrophage/microglia TLR2 and inducing the following NF-κB inflammatory storm. Clearing away S2E and inhibiting macrophage/microglia TLR2 served as perspective therapeutic strategies for COVID-19 pain.

Coronavirus envelope protein activates TMED10-mediated unconventional secretion of inflammatory factors

The precise cellular mechanisms underlying heightened proinflammatory cytokine production during coronavirus infection remain incompletely understood. Here we identify the envelope (E) protein in severe coronaviruses (SARS-CoV-2, SARS, or MERS) as a potent inducer of interleukin-1 release, intensifying lung inflammation through the activation of TMED10-mediated unconventional protein secretion (UcPS). In contrast, the E protein of mild coronaviruses (229E, HKU1, or OC43) demonstrates a less pronounced effect. The E protein of severe coronaviruses contains an SS/DS motif, which is not present in milder strains and facilitates interaction with TMED10. This interaction enhances TMED10-oligomerization, facilitating UcPS cargo translocation into the ER-Golgi intermediate compartment (ERGIC)-a pivotal step in interleukin-1 UcPS. Progesterone analogues were identified as compounds inhibiting E-enhanced release of proinflammatory factors and lung inflammation in a Mouse Hepatitis Virus (MHV) infection model. These findings elucidate a molecular mechanism driving coronavirus-induced hyperinflammation, proposing the E-TMED10 interaction as a potential therapeutic target to counteract the adverse effects of coronavirus-induced inflammation.

Viral fingerprints of the ion channel evolution: compromise of complexity and function

Evolution from precellular supramolecular assemblies to cellular world originated from the ability to make a barrier between the interior of the cell and the outer environment. This step resulted from the possibility to form a membrane, which preserves the cell like a wall of the castle. However, every castle needs gates for trading, i.e. in the case of cell, for controlled exchange of substances. These 'gates' should have the mechanism of opening and closing, guards, entry rules, and so on. Different structures are known to be able to make membrane permeable to various substances, from ions to macromolecules. They are amphipathic peptides, their assemblies, sophisticated membrane channels with numerous transmembrane domains, etc. Upon evolving, cellular world preserved and selected many variants, which, finally, have provided both prokaryotes and eukaryotes with highly selective and regulated ion channels. However, various simpler variants of ion channels are found in viruses. Despite the origin of viruses is still under debates, they have evolved parallelly with the cellular forms of life. Being initial form of the enveloped organisms, reduction of protocells or their escaped parts, viruses might be fingerprints of the evolutionary steps of cellular structures like ion channels. Therefore, viroporins may provide us a necessary information about selection between high functionality and less complex structure in supporting all the requirements for controlled membrane permeability. In this review we tried to elucidate these compromises and show the possible way of the evolution of ion channels, from peptides to complex multi-subunit structures, basing on viral examples.

Exploring the binding dynamics of covalent inhibitors within active site of PLpro in SARS-CoV-2

In the global fight against the COVID-19 pandemic caused by the highly transmissible SARS-CoV-2 virus, the search for potent medications is paramount. With a focused investigation on the SARS-CoV-2 papain-like protease (PLpro) as a promising therapeutic target due to its pivotal role in viral replication and immune modulation, the catalytic triad of PLpro comprising Cys111, His272, and Asp286, highlights Cys111 as an intriguing nucleophilic center for potential covalent bonds with ligands. The detailed analysis of the binding site unveils crucial interactions with both hydrophobic and polar residues, demonstrating the structural insights of the cavity and deepening our understanding of its molecular landscape. The sequence of PLpro among variants of concern (Alpha, Beta, Gamma, Delta and Omicron) and the recent variant of interest, JN.1, remains conserved with no mutations at the active site. Moreover, a thorough exploration of apo, non-covalently bound, and covalently bound PLpro conformations exposes significant conformational changes in loop regions, offering invaluable insights into the intricate dynamics of ligand-protein complex formation. Employing strategic in silico medication repurposing, this study swiftly identifies potential molecules for target inhibition. Within the domain of covalent docking studies and molecular dynamics, using reported inhibitors and clinically tested molecules elucidate the formation of stable covalent bonds with the cysteine residue, laying a robust foundation for potential therapeutic applications. These details not only deepen our comprehension of PLpro inhibition but also play a pivotal role in shaping the dynamic landscape of COVID-19 treatment strategies.

A Gain-of-Function Cleavage of TonEBP by Coronavirus NSP5 to Suppress IFN-β Expression

Human coronaviruses (HCoVs) modify host proteins to evade the antiviral defense and sustain viral expansion. Here, we report tonicity-responsive enhancer (TonE) binding protein (TonEBP) as a cellular target of HCoVs. TonEBP was cleaved into N-terminal and C-terminal fragments (TonEBP NT and TonEBP CT, respectively) by NSP5 from all the HCoVs tested. This cleavage resulted in the loss of TonEBP's ability to stimulate the TonE-driven transcription. On the other hand, TonEBP NT promoted viral expansion in association with the suppression of IFN-β expression. TonEBP NT competed away NF-κB binding to the PRD II domain on the IFN-β promoter. A TonEBP mutant resistant to the cleavage by NSP5 did not promote the viral expansion nor suppress the IFN-β expression. These results demonstrate that HCoVs use a common strategy of targeting TonEBP to suppress the host immune defense.

Porcine ex-vivo intestinal mucus has age-dependent blocking activity against transmissible gastroenteritis virus

Transmissible gastroenteritis virus (TGEV) causes high mortality in young piglets (< 3 days of age). With aging, the susceptibility/morbidity/mortality rates drop. We previously hypothesized that the age-related changes in the intestinal mucus could be responsible for this resistance. Hence, this study investigated the effect of porcine intestinal mucus from 3-day and 3-week-old pigs on the free mobility of the virulent TGEV Miller strain, and on the infection in swine testicle (ST) cells. Single particle tracking (SPT) revealed that TGEV had significantly higher diffusion coefficients in 3-day mucus compared to 3-week mucus. TGEV and charged and uncharged control nanoparticles diffused freely in 3-day mucus but were hindered by 3-week mucus in the diffusion model; TGEV mimicked the diffusion behavior of negatively charged carboxylated particles. Inoculation of ST cells with TGEV in the presence of 3-week mucus resulted in a significantly lower average number of infected cells (30.9 ± 11.9/5 fields) compared with 3-day mucus (84.6 ± 16.4/5 fields). These results show that 3-week mucus has a significant TGEV-blocking activity compared to 3-day mucus in free diffusion and infection of the underlying susceptible cells. Additionally, a label-free proteomics analysis revealed an increased expression of mucin 13, known for negatively regulating the tight junctions in intestinal epithelium, in 3-day-old pigs. In 3-week-old pigs, a higher expression of mucin 2, a type of secreted mucin which is known for inhibiting coronavirus infection, was observed. Concludingly, this study demonstrated a protective effect of 3-week mucus against viral infections.

SARS-CoV-2 envelope protein alters calcium signaling via SERCA interactions

The clinical management of severe COVID-19 cases is not yet well resolved. Therefore, it is important to identify and characterize cell signaling pathways involved in virus pathogenesis that can be targeted therapeutically. Envelope (E) protein is a structural protein of the virus, which is known to be highly expressed in the infected host cell and is a key virulence factor; however, its role is poorly characterized. The E protein is a single-pass transmembrane protein that can assemble into a pentamer forming a viroporin, perturbing Ca2+ homeostasis. Because it is structurally similar to regulins such as, for example, phospholamban, that regulate the sarco/endoplasmic reticulum calcium ATPases (SERCA), we investigated whether the SARS-CoV-2 E protein affects the SERCA system as an exoregulin. Using FRET experiments we demonstrate that E protein can form oligomers with regulins, and thus can alter the monomer/multimer regulin ratio and consequently influence their interactions with SERCAs. We also confirm that a direct interaction between E protein and SERCA2b results in a decrease in SERCA-mediated ER Ca2+ reload. Structural modeling of the complexes indicates an overlapping interaction site for E protein and endogenous regulins. Our results reveal novel links in the host-virus interaction network that play an important role in viral pathogenesis and may provide a new therapeutic target for managing severe inflammatory responses induced by SARS-CoV-2.

Oligomeric State and Drug Binding of the SARS-CoV-2 Envelope Protein Are Sensitive to the Ectodomain

The envelope (E) protein of SARS-CoV-2 is the smallest of the three structural membrane proteins of the virus. E mediates budding of the progeny virus in the endoplasmic reticulum Golgi intermediate compartment of the cell. It also conducts ions, and this channel activity is associated with the pathogenicity of SARS-CoV-2. The structural basis for these functions is still poorly understood. Biochemical studies of E in detergent micelles found a variety of oligomeric states, but recent 19F solid-state NMR data indicated that the transmembrane domain (ETM, residues 8-38) forms pentamers in lipid bilayers. Hexamethylene amiloride (HMA), an E inhibitor, binds the pentameric ETM at the lipid-exposed helix-helix interface. Here, we investigate the oligomeric structure and drug interaction of an ectodomain-containing E construct, ENTM (residues 1-41). Unexpectedly, 19F spin diffusion NMR data reveal that ENTM adopts an average oligomeric state of dimers instead of pentamers in lipid bilayers. A new amiloride inhibitor, AV-352, shows stronger inhibitory activity than HMA in virus-like particle assays. Distance measurements between 13C-labeled protein and a trifluoromethyl group of AV-352 indicate that the drug binds ENTM with a higher stoichiometry than ETM. We measured protein-drug contacts using a sensitivity-enhanced two-dimensional 13C-19F distance NMR technique. The results indicate that AV-352 binds the C-terminal half of the TM domain, similar to the binding region of HMA. These data provide evidence for the existence of multiple oligomeric states of E in lipid bilayers, which may carry out distinct functions and may be differentially targeted by antiviral drugs.

Bioproduction and immunogenic evaluation of SARS-CoV-2 prototype vaccine in silkworm BmN cells

COVID-19, caused by the novel coronavirus SARS-CoV-2, has presented a significant challenge to global health, security, and the economy. Vaccination is considered a crucial measure in preventing virus transmission. The silkworm bioreactor has gained widespread usage in antigen presentation, monoclonal antibody preparation, and subunit vaccine development due to its safety, efficiency, convenience, and cost-effectiveness. In this study, we employed silkworm BmN cells and the silkworm MultiBac multigene co-expression system to successfully produce two prototype vaccines: a recombinant baculovirus vector vaccine (NPV) co-displaying the SARS-CoV-2 virus capsid protein and a capsid protein virus-like particle (VLP) vaccine. Following the purification of these vaccines, we immunized BALB/c mice to evaluate their immunogenicity. Our results demonstrated that both VLP and NPV prototype vaccines effectively elicited robust immune responses in mice. However, when equal inoculation doses between groups were compared, the recombinant NPV vaccine exhibited significantly higher serum antibody titers and increased expression of spleen cytokines and lymphocyte immune regulatory factors compared to the VLP group. These results suggested an increased immune efficacy of the recombinant NPV vaccine. Conversely, the VLP prototype vaccine displayed more pronounced effects on lymphocyte cell differentiation induction. This study successfully constructed two distinct morphological recombinant vaccine models and systematically elucidated their differences in humoral immune response and lymphocyte differentiation rate. Furthermore, it has fully harnessed the immense potential of silkworm bioreactors for vaccine research and development, providing valuable technical insights for studying mutated viruses like coronaviruses.

Membrane remodeling and trafficking piloted by SARS-CoV-2

The molecular mechanisms underlying SARS-CoV-2 host cell invasion and life cycle have been studied extensively in recent years, with a primary focus on viral entry and internalization with the aim of identifying antiviral therapies. By contrast, our understanding of the molecular mechanisms involved in the later steps of the coronavirus life cycle is relatively limited. In this review, we describe what is known about the host factors and viral proteins involved in the replication, assembly, and egress phases of SARS-CoV-2, which induce significant host membrane rearrangements. We also discuss the limits of the current approaches and the knowledge gaps still to be addressed.

Boosting immunity: synergistic antiviral effects of luteolin, vitamin C, magnesium and zinc against SARS-CoV-2 3CLpro

SARS-CoV-2 was first discovered in 2019 and has disseminated throughout the globe to pandemic levels, imposing significant health and economic burdens. Although vaccines against SARS-CoV-2 have been developed, their long-term efficacy and specificity have not been determined, and antiviral drugs remain necessary. Flavonoids, which are commonly found in plants, fruits, and vegetables and are part of the human diet, have attracted considerable attention as potential therapeutic agents due to their antiviral and antimicrobial activities and effects on other biological activities, such as inflammation. The present study uses a combination of biochemical, cellular, molecular dynamics, and molecular docking experiments to provide compelling evidence that the flavonoid luteolin (2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4H-chromen-4-one) has antiviral activity against SARS-CoV-2 3-chymotrypsin-like protease (3CLpro) that is synergistically enhanced by magnesium, zinc, and vitamin C. The IC50 of luteolin against 2 µM 3CLpro is 78 µM and decreases 10-fold to 7.6 µM in the presence of zinc, magnesium, and vitamin C. Thermodynamic stability analyses revealed that luteolin has minimal effects on the structure of 3CLpro, whereas metal ions and vitamin C significantly alter the thermodynamic stability of the protease. Interactome analysis uncovered potential host-virus interactions and functional clusters associated with luteolin activity, supporting the relevance of this flavone for combating SARS-CoV-2 infection. This comprehensive investigation sheds light on luteolin's therapeutic potential and provides insights into its mechanisms of action against SARS-CoV-2. The novel formulation of luteolin, magnesium, zinc, and vitamin C may be an effective avenue for treating COVID-19 patients.

Membrane Activity and Viroporin Assembly for the SARS-CoV-2 E Protein Are Regulated by Cholesterol

The SARS-CoV-2 E protein is an enigmatic viral structural protein with reported viroporin activity associated with the acute respiratory symptoms of COVID-19, as well as the ability to deform cell membranes for viral budding. Like many viroporins, the E protein is thought to oligomerize with a well-defined stoichiometry. However, attempts to determine the structure of the protein complex have yielded inconclusive results, suggesting several possible oligomers, ranging from dimers to pentamers. Here, we combined patch-clamp, confocal fluorescence microscopy on giant unilamellar vesicles, and atomic force microscopy to show that E protein can exhibit two modes of membrane activity depending on membrane lipid composition. In the absence or the presence of a low content of cholesterol, the protein forms short-living transient pores, which are seen as semi-transmembrane defects in a membrane by atomic force microscopy. Approximately 30 mol% cholesterol is a threshold for the transition to the second mode of conductance, which could be a stable pentameric channel penetrating the entire lipid bilayer. Therefore, the E-protein has at least two different types of activity on membrane permeabilization, which are regulated by the amount of cholesterol in the membrane lipid composition and could be associated with different types of protein oligomers.

Anti-SARS-CoV-2 activity of microwave solvolysis lignin from woody biomass

The global pandemic caused by the novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has had profoundly detrimental effects on our society. To combat this highly pathogenic virus, we turned our attention to an abundant renewable natural aromatic polymer found in wood. Through a chemical modification of Eucalyptus and Japanese cedar wood via acidic microwave solvolysis in equivolume mixture of 2 % (w/w) aqueous H2SO4, ethylene glycol, and toluene at 190 °C. Subsequently, we separated the resulting solvolysis products through extractions with toluene, ethyl acetate, and ethanol. Among these products, the ethyl acetate extract from Eucalyptus wood (eEAE) demonstrated the highest inhibition effects against the novel SARS-CoV-2. We further divided eEAE into four fractions, and a hexane extract from the ethanol-soluble portion, termed eEAE3, exhibited the most substantial inhibitory rate at 93.0 % when tested at a concentration of 0.5 mg/mL. Analyzing eEAE3 using pyrolysis gas chromatography-mass spectrometry revealed that its primary components are derived from lignin. Additionally, 1H-13C edited-heteronuclear single quantum coherence nuclear magnetic resonance analysis showed that the solvolysis process cleaved major lignin interunit linkages. Considering the abundance and renewability of lignin, the lignin-derived anti-SARS-CoV-2 agent presents a promising potential for application in suppressing infections within our everyday environment.

The SARS-CoV-2 nucleoprotein associates with anionic lipid membranes

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a lipid-enveloped virus that acquires its lipid bilayer from the host cell it infects. SARS-CoV-2 can spread from cell to cell or from patient to patient by undergoing assembly and budding to form new virions. The assembly and budding of SARS-CoV-2 is mediated by several structural proteins known as envelope (E), membrane (M), nucleoprotein (N), and spike (S), which can form virus-like particles (VLPs) when co-expressed in mammalian cells. Assembly and budding of SARS-CoV-2 from the host ER-Golgi intermediate compartment is a critical step in the virus acquiring its lipid bilayer. To date, little information is available on how SARS-CoV-2 assembles and forms new viral particles from host membranes. In this study, we used several lipid binding assays and found the N protein can strongly associate with anionic lipids including phosphoinositides and phosphatidylserine. Moreover, we show lipid binding occurs in the N protein C-terminal domain, which is supported by extensive in silico analysis. We demonstrate anionic lipid binding occurs for both the free and the N oligomeric forms, suggesting N can associate with membranes in the nucleocapsid form. Based on these results, we present a lipid-dependent model based on in vitro, cellular, and in silico data for the recruitment of N to assembly sites in the lifecycle of SARS-CoV-2.

Vitamin D supplementation and calcium: Many-faced gods or nobody in fighting against Corona Virus Disease 2019

In December 2019, Corona Virus Disease 2019 (COVID-19) was first identified and designated as a pandemic in March 2020 due to rapid spread of the virus globally. At the beginning of the pandemic, only a few treatment options, mainly focused on supportive care and repurposing medications, were available. Due to its effects on immune system, vitamin D was a topic of interest during the pandemic, and researchers investigated its potential impact on COVID-19 outcomes. However, the results of studies about the impact of vitamin D on the disease are inconclusive. In the present narrative review, different roles of vitamin D regarding the COVID-19 have been discussed to show that vitamin D supplementation should be recommended carefully.

The mutual lipid-mediated effect of the transmembrane domain of SARS-CoV-2 E-protein and glycyrrhizin nicotinate derivatives on the localization in the lipid bilayer

Glycyrrhizinic acid (GA) is one of the active substances in licorice root. It exhibits antiviral activity against various enveloped viruses, for example, SARS-CoV-2. GA derivatives are promising biologically active compounds from perspective of developing broad-spectrum antiviral agents. Given that GA nicotinate derivatives (Glycyvir) demonstrate activity against various DNA- and RNA-viruses, a search for a possible mechanism of action of these compounds is required. In the present paper, the interaction of Glycyvir with the transmembrane domain of the SARS-CoV-2 E-protein (ETM) in a model lipid membrane was investigated by NMR spectroscopy and molecular dynamics simulation. The lipid-mediated influence on localization of the SARS-CoV-2 E-protein by Glycyvir was observed. The presence of Glycyvir leads to deeper immersion of the ETM in lipid bilayer. Taking into account that E-protein plays a significant role in virus production and takes part in virion assembly and budding, the data on the effect of potential antiviral agents on ETM localization and structure in the lipid environment may provide a basis for further studies of potential coronavirus E-protein inhibitors.

A glimpse into viral warfare: decoding the intriguing role of highly pathogenic coronavirus proteins in apoptosis regulation

Coronaviruses employ various strategies for survival, among which the activation of endogenous or exogenous apoptosis stands out, with viral proteins playing a pivotal role. Notably, highly pathogenic coronaviruses such as SARS-CoV-2, SARS-CoV, and MERS-CoV exhibit a greater array of non-structural proteins compared to low-pathogenic strains, facilitating their ability to induce apoptosis via multiple pathways. Moreover, these viral proteins are adept at dampening host immune responses, thereby bolstering viral replication and persistence. This review delves into the intricate interplay between highly pathogenic coronaviruses and apoptosis, systematically elucidating the molecular mechanisms underpinning apoptosis induction by viral proteins. Furthermore, it explores the potential therapeutic avenues stemming from apoptosis inhibition as antiviral agents and the utilization of apoptosis-inducing viral proteins as therapeutic modalities. These insights not only shed light on viral pathogenesis but also offer novel perspectives for cancer therapy.

Mapping Vulnerability to Potential Crisis Events in Surabaya City: A GIS-Based Approach

Background

This study aims to develop a vulnerability map for Surabaya using GIS-based Multi-Criteria Decision Analysis (MCDA) to assess the city's vulnerability to COVID-19.

Methods

Six key factors influencing vulnerability were identified and their relative importance determined through the Analytic Hierarchy Process (AHP) pairwise comparison matrix. GIS was utilized to classify Surabaya's vulnerability into five levels: very low, low, medium, high, and very high.

Results

The resulting vulnerability map provides essential insights for decision-makers, healthcare professionals, and disaster management teams. It enables strategic resource allocation, targeted interventions, and formulation of comprehensive response strategies tailored to specific needs of vulnerable districts.

Conclusions

Through these measures, Surabaya can enhance its resilience and preparedness, ensuring the well-being of its residents in the face of potential emergency outbreaks.

SARS-CoV-2 superinfection in CD14+ monocytes with latent human cytomegalovirus (HCMV) promotes inflammatory cascade

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiologic agent of coronavirus disease 2019 (COVID-19), has posed significant challenges to global health. While much attention has been directed towards understanding the primary mechanisms of SARS-CoV-2 infection, emerging evidence suggests co-infections or superinfections with other viruses may contribute to increased morbidity and mortality, particularly in severe cases of COVID-19. Among viruses that have been reported in patients with SARS-CoV-2, seropositivity for Human cytomegalovirus (HCMV) is associated with increased COVID-19 risk and hospitalization. HCMV is a ubiquitous beta-herpesvirus with a seroprevalence of 60-90 % worldwide and one of the leading causes of mortality in immunocompromised individuals. The primary sites of latency for HCMV include CD14+ monocytes and CD34+ hematopoietic cells. In this study, we sought to investigate SARS-CoV-2 infection of CD14+ monocytes latently infected with HCMV. We demonstrate that CD14+ cells are susceptible and permissive to SARS-CoV-2 infection and detect subgenomic transcripts indicative of replication. To further investigate the molecular changes triggered by SARS-CoV-2 infection in HCMV-latent CD14+ monocytes, we conducted RNA sequencing coupled with bioinformatic differential gene analysis. The results revealed significant differences in cytokine-cytokine receptor interactions and inflammatory pathways in cells superinfected with replication-competent SARS-CoV-2 compared to the heat-inactivated and mock controls. Notably, there was a significant upregulation in transcripts associated with pro-inflammatory response factors and a decrease in anti-inflammatory factors. Taken together, these findings provide a basis for the heightened inflammatory response, offering potential avenues for targeted therapeutic interventions among HCMV-infected severe cases of COVID-19. SUMMARY: COVID-19 patients infected with secondary viruses have been associated with a higher prevalence of severe symptoms. Individuals seropositive for human cytomegalovirus (HCMV) infection are at an increased risk for severe COVID-19 disease and hospitalization. HCMV reactivation has been reported in severe COVID-19 cases with respiratory failure and could be the result of co-infection with SARS-CoV-2 and HCMV. In a cell culture model of superinfection, HCMV has previously been shown to increase infection of SARS-CoV-2 of epithelial cells by upregulating the human angiotensin-converting enzyme-2 (ACE2) receptor. In this study, we utilize CD14+ monocytes, a major cell type that harbors latent HCMV, to investigate co-infection of SARS-CoV-2 and HCMV. This study is a first step toward understanding the mechanism that may facilitate increased COVID-19 disease severity in patients infected with SARS-CoV-2 and HCMV.

Antiviral activity of the host defense peptide piscidin 1: investigating a membrane-mediated mode of action

Outbreaks of viral diseases are on the rise, fueling the search for antiviral therapeutics that act on a broad range of viruses while remaining safe to human host cells. In this research, we leverage the finding that the plasma membranes of host cells and the lipid bilayers surrounding enveloped viruses differ in lipid composition. We feature Piscidin 1 (P1), a cationic host defense peptide (HDP) that has antimicrobial effects and membrane activity associated with its N-terminal region where a cluster of aromatic residues and copper-binding motif reside. While few HDPs have demonstrated antiviral activity, P1 acts in the micromolar range against several enveloped viruses that vary in envelope lipid composition. Notably, it inhibits HIV-1, a virus that has an envelope enriched in cholesterol, a lipid associated with higher membrane order and stability. Here, we first document through plaque assays that P1 boasts strong activity against SARS-CoV-2, which has an envelope low in cholesterol. Second, we extend previous studies done with homogeneous bilayers and devise cholesterol-containing zwitterionic membranes that contain the liquid disordered (Ld; low in cholesterol) and ordered (Lo, rich in cholesterol) phases. Using dye leakage assays and cryo-electron microscopy on vesicles, we show that P1 has dramatic permeabilizing capability on the Lo/Ld, an effect matched by a strong ability to aggregate, fuse, and thin the membranes. Differential scanning calorimetry and NMR experiments demonstrate that P1 mixes the lipid content of vesicles and alters the stability of the Lo. Structural studies by NMR indicate that P1 interacts with the Lo/Ld by folding into an α-helix that lies parallel to the membrane surface. Altogether, these results show that P1 is more disruptive to phase-separated than homogenous cholesterol-containing bilayers, suggesting an ability to target domain boundaries. Overall, this multi-faceted research highlights how a peptide that interacts strongly with membranes through an aromatic-rich N-terminal motif disrupt viral envelope mimics. This represents an important step towards the development of novel peptides with broad-spectrum antiviral activity.

SARS-CoV-2 envelope protein regulates innate immune tolerance

Severe COVID-19 often leads to secondary infections and sepsis that contribute to long hospital stays and mortality. However, our understanding of the precise immune mechanisms driving severe complications after SARS-CoV-2 infection remains incompletely understood. Here, we provide evidence that the SARS-CoV-2 envelope (E) protein initiates innate immune inflammation, via toll-like receptor 2 signaling, and establishes a sustained state of innate immune tolerance following initial activation. Monocytes in this tolerant state exhibit reduced responsiveness to secondary stimuli, releasing lower levels of cytokines and chemokines. Mice exposed to E protein before secondary lipopolysaccharide challenge show diminished pro-inflammatory cytokine expression in the lung, indicating that E protein drives this tolerant state in vivo. These findings highlight the potential of the SARS-CoV-2 E protein to induce innate immune tolerance, contributing to long-term immune dysfunction that could lead to susceptibility to subsequent infections, and uncovers therapeutic targets aimed at restoring immune function following SARS-CoV-2 infection.