Enter Host Cells Research Articles

Porphyromonas gingivalis gingipain potentially activates influenza A virus infectivity through proteolytic cleavage of viral hemagglutinin.

Influenza is a worldwide health problem that causes significant morbidity and mortality among the elderly; therefore, its prevention is important. During influenza virus infection, the cleavage of hemagglutinin (HA) is essential for the virus to enter host cells. Influenza virus-bacteria interactions influence the pathogenicity of infections, and specific bacteria contribute to the severity of the disease by participating in HA cleavage. Poor oral hygiene and the presence of oral bacteria are associated with influenza. Porphyromonas gingivalis, a periodontopathic bacterium, is particularly associated with influenza; however, the underlying mechanisms remain unclear. In the present study, we observed P. gingivalis culture supernatant promoted viral release and cell-to-cell spread of the infection. Further investigation revealed that the supernatant contained cleaved HA. Therefore, we focused on gingipains (Rgp and Kgp) which are trypsin-like proteases produced by P. gingivalis. We determined that the Rgp inhibitor inhibited both HA cleavage and the increase in virus release associated with the P. gingivalis culture supernatant, whereas such effects were not observed with the Kgp inhibitor. In addition, Rgp-deficient P. gingivalis culture supernatant failed to cleave HA, enhance virus spread, or increase virus release. In contrast, Kgp-deficient P. gingivalis culture supernatant cleaved HA and promoted infection. These results indicated that P. gingivalis-secreted Rgp has the potential to activate influenza virus infectivity through HA cleavage, suggesting that understanding the effects of P. gingivalis on influenza virus infection will contribute to the establishment of influenza prevention measures.

Discovery of pentacyclic triterpene conjugates as HBV polymerase/NTCP dual-targeting inhibitors with potent anti-HBV activities.

The inhibition of HBV DNA and elimination of HBsAg has already been established as an indicator for HBV clinic cure, and a novel dual-targeting inhibitors of HBV polymerase/entry are designed and synthesized in this study. Pentacyclic triterpenes (PTs) scaffold of exhibiting a high affinity to NTCP, including glycyrrhitinic acid (GA), oleanolic acid (OA), ursolic acid (UA), and betulinic acid (BA) were linked neatly with the nucleoside drug zidovudine (AZT) through a molecular hybrid strategy to synthesize twenty of PTs-AZT conjugates for targeting HBV polymerase as well as sodium taurocholate cotransporting polypeptide (NTCP). The conjugates showed significant inhibitory effects on the secretion of HBsAg and HBeAg in HepG2.2.15 cells, and the activity on HBsAg were better. Moreover, HBV DNA replication was also notably suppressed after incubated with the conjugates. The IC50 value of BA-AZT1 on HBsAg inhibition was 0.65±0.07μM, and it was 284.2 times and 442.2 times higher comparing to corresponding parent compound BA and AZT. Additionally, the therapeutic index (TI) was also improved by 87.8 times than AZT. And the IC50 value of BA-AZT1 on inhibition of HBV DNA replication was 0.70±0.02μM, 10.4 times higher than that of AZT besides conspicuous TI. Molecular docking suggested that AZT skeleton of conjugate BA-AZT1 interacted with B region of HBV Polymerase reverse transcription region, and BA structure simultaneously targeted to C region of polymerase via hydrophobic chain, establishing strong binding interactions with the HBV Pol protein. In addition, docked with NTCP, BA-AZT1 with flat pentacyclic structure inserted into the interface and also formed hydrogen bonds, hydrophobic and van der Waals forces with the amino residue 157-165 of NTCP. Further SPR analysis demonstrated the binding affinity of BA-AZT1 to C region of polymerase was 19.55μM, stronger than 53.21μM of BA and 31.82μM of AZT. BA-AZT1 selectively bound to the 157-165 epitopes of NTCP receptors in host cell but not PreS1 of virus. As a result, we deduced that the designed conjugates targeted NTCP and HBV polymerase, not only prevented HBV from entering host cells via selective binding NTCP, but also inhibited HBV DNA replication through obstructing the function of HBV polymerase, and it could potentially serve as a promising dual-functional and dual-target inhibitor with both replication and entry inhibition to exert anti-HBV activity.

Immunoisolation of Plant Endosomal Vesicles to Explore Uptake of Pathogen Effector Proteins During Infection of Nicotiana benthamiana.

Endocytosis is an essential cellular process that uptakes substances into cells at the plasma membrane from the extracellular space and plays a major role in plant development and responses to environmental stimuli. Research has shown that plant membrane-resident proteins are endocytosed and transported into plant endosomes in response to pathogen-secreted elicitors. However, there is no conclusive experimental evidence demonstrating how secreted cytoplasmic effectors from oomycetes and fungi enter host cells during infection. The adapted protocol in this chapter describes endosome isolation using immunopurification with the aim to co-capture Phytophthora infestans RXLR effectors during infection. This protocol can be widely used in the isolation and purification of different subtypes of endosomal vesicles that uptake extracellular molecules during pathogen infection and in response to environmental stimuli.

Vimentin as a contributing factor in SARS-CoV-2-induced orchitis on postmortem testicular autopsy of COVID-19 cases: A case-control study

Background: Coronavirus disease 2019 (COVID-19) was identified in China in late December 2019 and led to a pandemic that resulted in millions of confirmed cases and deaths. The causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), uses distinct receptors and co-receptors to enter host cells. Vimentin has emerged as a potential co-receptor for SARS-CoV-2 due to the high level of vimentin expression in testis tissue. Objective: The present study investigated the link between vimentin expression level and SARS-CoV-2-induced orchitis. Materials and Methods: In this case-control study, testis autopsy samples were collected immediately after the death of both COVID-19 cases and a control group that included individuals who died due to accidental causes. Gene expression and immunohistochemical assays were conducted to evaluate the level of vimentin expression, cell proliferation, and leukocyte infiltration. Results: A significant expression of vimentin and infiltration of immune cells (CD68+, CD38+, and CD138+) in the testicular tissue of COVID-19 cases, along with extensive immunoglobulin G precipitation and reduced inhibin expression (p = 0.001) were observed. Additionally, gene expression analysis revealed increased expression of vimentin and decreased expression of the proliferation markers Ki67 and proliferating cell nuclear antigen, suggesting that SARS-CoV-2 may disrupt spermatogenesis through immune responses and the arrest of cell proliferation. Conclusion: There may be a strong link between vimentin expression and COVID-19-induced orchitis. Further studies are needed to confirm these findings. Considering some limitations, vimentin can be used as a biomarker option for testicular damage following COVID-19-induced orchitis.

The biological and psychological impact of the Coronavirus disease-19 pandemic on the characteristics of the menstrual cycle.

The Coronavirus disease-19 (COVID-19) pandemic was declared in March 2020 by the World Health Organization. The severe acute respiratory syndrome-coronavirus-2 virus enters host cells through angiotensin-converting enzyme 2 receptors and transmembrane serine protease type II that are expressed in pulmonary alveoli, as well as in hepatocytes, endothelium, ovaries, uterus, vagina, thyroid, and other tissues. In addition to viral injury, the COVID-19 pandemic, through protective measures such as social isolation and lockdown, has promoted a scenario of psychosocial stress, especially in women. In this context of isolation, anxiety, fear, and mental distress, there is dysregulation of the hypothalamic-pituitary-adrenal axis and subsequent gonadal side effects. Furthermore, studies report an association between COVID-19 and temporary menstrual cycle alterations such, as increased cycle duration, decreased cycle duration, increased menstrual flow, dysmenorrhea, and amenorrhea. Regarding COVID-19 vaccination, menstrual irregularities have been observed in about half of the women, predominantly with a decrease in cycle duration and increased menstrual flow, but without fertility sequelae. The aim of this study was to review the most up-to-date information on the relationship between the COVID-19 pandemic and menstrual irregularities.

Comparative Analysis of Host Cell Entry Efficiency and Neutralization Sensitivity of Emerging SARS-CoV-2 Lineages KP.2, KP.2.3, KP.3, and LB.1.

New SARS-CoV-2 lineages continue to evolve and may exhibit new characteristics regarding host cell entry efficiency and potential for antibody evasion. Here, employing pseudotyped particles, we compared the host cell entry efficiency, ACE2 receptor usage, and sensitivity to antibody-mediated neutralization of four emerging SARS-CoV-2 lineages, KP.2, KP.2.3, KP.3, and LB.1. The XBB.1.5 and JN.1 lineages served as controls. Our findings reveal that KP.2, KP.2.3, KP.3, and LB.1 lineages enter host cells efficiently and in an ACE2-dependent manner, and that KP.3 is more adept at entering Calu-3 lung cells than JN.1. However, the variants differed in their capacity to employ ACE2 orthologues from animal species for entry, suggesting differences in ACE2 interactions. Moreover, we demonstrate that only two out of seven therapeutic monoclonal antibody (mAbs) in preclinical development retain robust neutralizing activity against the emerging JN.1 sublineages tested, while three mAbs displayed strongly reduced neutralizing activity and two mAbs lacked neutralizing activity against any of the lineages tested. Furthermore, our results show that KP.2, KP.2.3, KP.3, and LB.1 lineages evade neutralization by antibodies induced by infection or vaccination with greater efficiency than JN.1, particularly in individuals without hybrid immunity. This study indicates that KP.2, KP.2.3, KP.3, and LB.1 differ in ACE2 interactions and the efficiency of lung cell entry and suggest that evasion of neutralizing antibodies drove the emergence of these variants.

Association of ACE2 Gene Variants with Adverse Perinatal Outcomes in COVID-19 Infected Pregnant Women in Kazakhstan.

SARS-CoV-2 utilizes the angiotensin-converting enzyme 2 (ACE2) receptors located on membranes to enter host cells. Nevertheless, the ACE2 gene primarily encodes for a zinc metalloproteinase, which is a part of the renin-angiotensin system (RAS). ACE2 downregulation results in the deregulation of RAS in favor of pro-fibrosis, pro-apoptosis, oxidative stress, pro-inflammation, aldosterone production and release, and blood vessel contraction axis. ACE2 is highly expressed in the placenta. There are both axes of the RAS system in the placenta. This study aims to assess the perinatal outcomes with ACE2 receptor polymorphisms in pregnant women infected with SARS-CoV-2 during pregnancy. The case-control study was conducted to determine the association of ACE2 single-nucleotide polymorphisms in 171 COVID-19-positive pregnant subjects and 112 control subjects. The recessive mutations of rs2158082 and rs4830974 were associated with an increased risk of low birthweight and preterm birth, whereas the dominant mutation of rs2285666 (CT + TT) was associated with decreased odds of low birthweight. COVID-19 was not a significant factor contributing to the adverse perinatal outcomes in our sampling. These findings may help to clarify the controversy regarding the increased risk of adverse perinatal outcomes observed during COVID-19 as well as provide new perspectives for research on the genetic factors associated with a higher risk of adverse perinatal outcomes.

Molecular mechanism and structure-guided humanization of a broadly neutralizing antibody against SFTSV.

Severe fever with thrombocytopenia syndrome virus (SFTSV) is a novel tick-borne bunyavirus that causes severe fever with thrombocytopenia syndrome (SFTS), with a high mortality rate of up to 30%. The envelope glycoproteins of SFTSV, glycoprotein N (Gn) and glycoprotein C (Gc), facilitate the recognition of host receptors and the process of membrane fusion, allowing the virus to enter host cells. We previously reported a monoclonal antibody, mAb 40C10, capable of neutralizing different genotypes of SFTSV and SFTSV-related viruses. However, the specific neutralization mechanism is poorly understood. In this study, we elucidated the high-resolution structure of the SFTSV Gn head domain in complex with mAb 40C10, confirming that the binding epitope in the domain I region of SFTSV Gn, and it represented that a novel binding epitope of SFTSV Gn was identified. Through in-depth structural and sequence analyses, we found that the binding sites of mAb 40C10 are relatively conserved among different genotypes of SFTSV and SFTSV-related Heartland virus and Guertu virus, elucidating the molecular mechanism underlying the broad-spectrum neutralizing activity of mAb 40C10. Furthermore, we humanized of mAb 40C10, which is originally of murine origin, to reduce its immunogenicity. The resulting nine humanized antibodies maintained potent affinity and neutralizing activity. One of the humanized antibodies exhibited neutralizing activity at picomolar IC50 values and demonstrated effective therapeutic and protective effects in a mouse infection model. These findings provide a novel target for the future development of SFTSV vaccines or drugs and establish a foundation for the research and development of antibody therapeutics for clinical applications.

The Role of ACE2 in Neurological Disorders: From Underlying Mechanisms to the Neurological Impact of COVID-19.

Angiotensin-converting enzyme 2 (ACE2) has become a hot topic in neuroscience research in recent years, especially in the context of the global COVID-19 pandemic, where its role in neurological diseases has received widespread attention. ACE2, as a multifunctional metalloprotease, not only plays a critical role in the cardiovascular system but also plays an important role in the protection, development, and inflammation regulation of the nervous system. The COVID-19 pandemic further highlights the importance of ACE2 in the nervous system. SARS-CoV-2 enters host cells by binding to ACE2, which may directly or indirectly affect the nervous system, leading to a range of neurological symptoms. This review aims to explore the function of ACE2 in the nervous system as well as its potential impact and therapeutic potential in various neurological diseases, providing a new perspective for the treatment of neurological disorders.

Applications of reinforcement learning, machine learning, and virtual screening in SARS-CoV-2-related proteins

Similarly, to all coronaviruses, SARS-CoV-2 uses the S glycoprotein to enter host cells, which contains two functional domains: S1 and S2 receptor binding domain (RBD). Angiotensin-converting enzyme 2 (ACE2) is recognizable by the S proteins on the surface of the SARS-CoV-2 virus. The SARS-CoV-2 virus causes SARS, but some mutations in the RBD of the S protein markedly enhance their binding affinity to ACE2. Searching for new compounds in COVID-19 is an important initial step in drug discovery and materials design. Still, the problem is that this search requires trial-and-error experiments, which are costly and time-consuming. In the automatic molecular design method based on deep reinforcement learning, it is possible to design molecules with optimized physical properties by combining a newly devised coarse-grained representation of molecules with deep reinforcement learning. Also, structured-based virtual screening uses protein 3D structure information to evaluate the binding affinity between proteins and compounds based on physicochemical interactions such as van der Waals forces, Coulomb forces, and hydrogen bonds, and select drug candidate compounds. In addition, AlphaFold can predict 3D protein structures, given the amino acid sequence, and the protein building blocks. Ensemble docking, in which multiple protein structures are generated using the molecular dynamics method and docking calculations are performed for each, is often performed independently of docking calculations. In the future, the AlphaFold algorithm can be used to predict various protein structures related to COVID-19.

MβCD inhibits SFTSV entry by disrupting lipid raft structure of the host cells

Severe fever with thrombocytopenia syndrome virus (SFTSV), recently named as Dabie bandavirus, belongs to the family Phenuiviridae of the order Bunyavirales, is a newly-identified bunyavirus with a case fatality rate of up to 30%, posing a serious threat to public health. Lipid rafts on plasm membranes are important for the entry of enveloped viruses; however, the role of lipid rafts in bunyavirus entry remains unclear. In this study, we found that methyl-beta-cyclodextrin (MβCD), a drug that disrupts cholesterol in lipid rafts of cell membranes, inhibits SFTSV infection. Additionally, there is a back-complementary effect of SFTSV infection upon the addition of cholesterol. Moreover, the concentration of SFTSV particles in lipid rafts during entry directly indicated the role of lipid rafts as a gateway, whereas MβCD could inhibit SFTSV entry by affecting the structure of lipid rafts. In an in vivo study, MβCD also reduced the susceptibility of mice to SFTSV infection. Our results suggest that SFTSV can interact with Talin1 proteins on lipid rafts to enter host cells by endocytosis of lipid rafts and reveal the potential therapeutic value of MβCD for SFTSV infection.

RNA-Seq analysis reveals the different mechanisms triggered by bovine and equine after infection with FMDV.

Foot-and-mouth disease virus (FMDV) is an important pathogen of the MicroRNA virus family. Infection of livestock can cause physical weakness, weight loss, reduced milk production, and a significant reduction in productivity for an extended period. It also causes a high mortality rate in young animals, seriously affecting livestock production. The host range of FMDV is mainly limited to cloven-hoofed animals such as cattle and sheep, while odd-toed ungulates such as horses and donkeys have natural resistance to FMDV. The mechanism underlying this resistance in odd-toed ungulates remains unclear. This study aimed to analyze the differences between FMDV-infected cattle and horses to provide valuable insights into the host-FMDV interaction mechanisms, thereby contributing to the control of foot-and-mouth disease and promoting the development of the livestock industry. We observed the distribution of integrins, which help FMDV enter host cells, in the nasopharyngeal tissues of cattle and horses using immunohistochemistry. Then, we employed high-throughput RNA sequencing (RNA-Seq) to study the changes in host gene expression in the nasopharyngeal epithelial tissues of cattle and horses after FMDV infection. We performed enrichment analysis of GO and KEGG pathways after FMDV infection and validated related genes through qPCR. The immunohistochemical results showed that both cattle and horses had four integrin receptors that could assist FMDV entry into host cells. The transcriptome analysis revealed that after FMDV infection, pro-apoptotic genes such as caspase-3 (CASP3) and cytochrome C (CYCS) were upregulated in cattle, while apoptosis-inhibiting genes such as NAIP and BCL2A1 were downregulated. In contrast, the expression trend of related genes in horses was opposite to that in cattle. Additionally, autophagy-related genes such as beclin 1, ATG101, ATG4B, ATG4A, ATG13, and BCL2A1 were downregulated in cattle after FMDV infection, indicating that cattle did not clear the virus through autophagy. However, key autophagy genes including ATG1, ATG3, ATG9, ATG12, and ATG16L1 were significantly upregulated in horses after viral infection. Both water buffaloes and Mongolian horses express integrin receptors that allow FMDV entry into cells. Therefore, the resistance of Mongolian horses to FMDV may result from more changes in intracellular mechanisms, including processes such as autophagy and apoptosis. Significant differences were observed between water buffaloes and Mongolian horses in these processes, suggesting that these processes influence FMDV replication and synthesis.

Quantitatively Dissecting Triple Roles of Dynactin in Dynein-Driven Transport of Influenza Virus by Quantum Dot-Based Single-Virus Tracking.

After entering host cells by endocytosis, influenza A virus (IAV) is transported along microfilaments and then transported by dynein along microtubules (MTs) to the perinuclear region for genome release. Understanding the mechanisms of dynein-driven transport is significant for a comprehensive understanding of IAV infection. In this work, the roles of dynactin in dynein-driven transport of IAV were quantitatively dissected in situ using quantum dot-based single-virus tracking. It was revealed that dynactin was essential for dynein to transport IAV toward the nucleus. After virus entry, virus-carrying vesicles bound to dynein and dynactin before being delivered to MTs. The attachment of dynein to the vesicles was dependent on dynactin and its subunits, p150Glued and Arp1. Once viruses reached MTs, dynactin-assisted dynein initiates retrograde transport of IAV. Importantly, the retrograde transport of viruses could be initiated at both plus ends (32%) and other regions on MTs (68%). Subsequently, dynactin accompanied and assisted dynein to persistently transport the virus along MTs in the retrograde direction. This study revealed the dynactin-dependent dynein-driven transport process of IAV, enhancing our understanding of IAV infection and providing important insights into the cell's endocytic transport mechanism.

Molecular basis of convergent evolution of ACE2 receptor utilization among HKU5 coronaviruses.

DPP4 was considered a canonical receptor for merbecoviruses until the recent discovery of African bat-borne MERS-related coronaviruses using ACE2. The extent and diversity with which merbecoviruses engage ACE2 and their receptor species tropism remain unknown. Here, we reveal that HKU5 enters host cells utilizing Pipistrellus abramus (P.abr) and several non-bat mammalian ACE2s through a binding mode distinct from that of any other known ACE2-using coronaviruses. These results show that several merbecovirus clades independently evolved ACE2 utilization, which appears to be a broadly shared property among these pathogens, through an extraordinary diversity of ACE2 recognition modes. We show that MERS-CoV and HKU5 have markedly distinct antigenicity, due to extensive genetic divergence, and identified several HKU5 inhibitors, including two clinical compounds. Our findings profoundly alter our understanding of coronavirus evolution and pave the way for developing countermeasures against viruses poised for human emergence.

Correlation between Exposure to UFP and ACE/ACE2 Pathway: Looking for Possible Involvement in COVID-19 Pandemic.

The overlap between the geographic distribution of COVID-19 outbreaks and pollution levels confirmed a correlation between exposure to atmospheric particulate matter (PM) and the SARS-CoV-2 pandemic. The RAS system is essential in the pathogenesis of inflammatory diseases caused by pollution: the ACE/AngII/AT1 axis activates a pro-inflammatory pathway, which is counteracted by the ACE2/Ang(1-7)/MAS axis, which activates an anti-inflammatory and protective pathway. However, ACE2 is also known to act as a receptor through which SARS-CoV-2 enters host cells to replicate. Furthermore, in vivo systems have demonstrated that exposure to PM increases ACE2 expression. In this study, the effects of acute and sub-acute exposure to ultrafine particles (UFP), originating from different anthropogenic sources (DEP and BB), on the levels of ACE2, ACE, COX-2, HO-1, and iNOS in the lungs and other organs implicated in the pathogenesis of COVID-19 were analyzed in the in vivo BALB/c male mice model. Exposure to UFP alters the levels of ACE2 and/or ACE in all examined organs, and exposure to sub-acute DEP also results in the release of s-ACE2. Furthermore, as evidenced in this and our previous works, COX-2, HO-1, and iNOS levels also demonstrated organ-specific alterations. These proteins play a pivotal role in the UFP-induced inflammatory and oxidative stress responses, and their dysregulation is linked to the development of severe symptoms in individuals infected with SARS-CoV-2, suggesting a heightened vulnerability or a more severe clinical course of the disease. UFP and SARS-CoV-2 share common pathways; therefore, in a "risk stratification" concept, daily exposure to air pollution may significantly increase the likelihood of developing a severe form of COVID-19, explaining, at least in part, the greater lethality of the virus observed in highly polluted areas.

An N-terminal heptad repeat trimer-based peptide fusion inhibitor exhibits potent anti-H1N1 activity

Influenza viruses are susceptible to seasonal influenza, which has repeatedly caused global pandemics and jeopardized human health. Vaccines are only used as preventive medicine due to the extreme mutability of influenza viruses, and antiviral medication is the most significant clinical treatment to reduce influenza morbidity and mortality. Nevertheless, the clinical application of anti-influenza virus agents is characterized by the narrow therapeutic time window, the susceptibility to drug resistance, and relatively limited effect on severe influenza. Therefore, it is of great significance to develop novel anti-influenza virus drugs to fulfill the urgent clinical needs. Influenza viruses enter host cells through the hemagglutinin (HA) mediated membrane fusion process, and fusion inhibitors function antivirally by blocking hemagglutinin deformation, promising better therapeutic efficacy and resolving drug resistance, with targets different from marketed medicines. Previous studies have shown that unnatural peptides derived from Human Immunodeficiency Virus Type 1 (HIV-1) membrane fusion proteins exhibit anti-HIV-1 activity. Based on the similarity of the membrane fusion protein deformation process between HIV-1 and H1N1, we selected sequences derived from the gp41 subunit in the HIV-1 fusion protein, and then constructed N-trimer spatial structure through inter-helical isopeptide bond modification, to design the novel anti-H1N1 fusion inhibitors. The results showed that the novel peptides could block 6-HB formation during H1N1 membrane fusion procedure, and thus possessed significant anti-H1N1 activity, comparable to the positive control oseltamivir. Our study demonstrates the design viability of peptide fusion inhibitors based on similar membrane fusion processes among viruses, and furthermore provides an important idea for the novel anti-H1N1 inhibitors development.

COVID-19 and Prostatitis: A Review of Current Evidence.

Coronavirus disease 2019 (COVID-19), a highly contagious viral disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), poses a global health threat. The virus enters host cells by binding with angiotensin-converting enzyme 2 (ACE2), which is then facilitated by the protease activity of transmembrane serine protease 2 (TMPRSS2). It triggers a cytokine storm that eventually leads to cell apoptosis, tissue damage, and organ failure. Therefore, any organs in the human body that have both receptors are highly susceptible to COVID-19 infection, potentially resulting in multiple-organ failure. The prostate has been reported to express high levels of ACE2 and TMPRSS2. While there are limited studies regarding the association between COVID-19 and prostatitis, the possibility that SARS-CoV-2 could cause prostatitis cannot be denied. Thus, through this review, a better insight into the associations of SAR-CoV-2 can be provided.

The Roles of Endocytosis and Autophagy at the Cellular Level During Influenza Virus Infection: A Mini-Review.

Acute respiratory infections contribute to morbidity and mortality worldwide. The common cause of this deadly disease is a virus, and one of the most commonly found is the influenza virus. Influenza viruses have several capabilities in infection, including utilizing the host's machinery to survive within cells and replicate safely. This review aims to examine the literature on how influenza viruses use host machinery, including endocytosis and autophagy, for their internalization and replication within cells. This review method involves a literature search by examining articles published in the PubMed and Scopus databases. The keywords used were "Endocytosis" OR "Autophagy" AND "Influenza Virus". Eighteen articles were included due to inclusion and exclusion criteria. GTPases switch, and V-ATPase plays a key role in the endocytic machinery hijacked by influenza viruses to enter host cells. On the other hand, LC3 and Atg5 facilitate influenza-induced apoptosis via the autophagic pathway. In conclusion, influenza viruses primarily use clathrin-mediated endocytosis to enter cells and avoid degradation during endosomal maturation by exiting endosomes for transfer to the nucleus for replication. It also uses autophagy to induce apoptosis to continue replication. The capability of the influenza viruses to hijack endocytosis and autophagy mechanisms could be critical points for further research. Therefore, we discuss how the influenza virus utilizes both endocytosis and autophagy and the approach for a new strategic therapy targeting those mechanisms.

The Malaria Box molecules: a source for targeting the RBD and NTD cryptic pocket of the spike glycoprotein in SARS-CoV-2.

SARS-CoV-2, responsible for COVID-19, has led to over 500 million infections and more than 6 million deaths globally. There have been limited effective treatments available. The study aims to find a drug that can prevent the virus from entering host cells by targeting specific sites on the virus's spike protein. We examined 13,397 compounds from the Malaria Box library against two specific sites on the spike protein: the receptor-binding domain (RBD) and a predicted cryptic pocket. Using virtual screening, molecular docking, molecular dynamics, and MMPBSA techniques, they evaluated the stability of two compounds. TCMDC-124223 showed high stability and binding energy in the RBD, while TCMDC-133766 had better binding energy in the cryptic pocket. The study also identified that the interacting residues are conserved, which is crucial for addressing various virus variants. The findings provide insights into the potential of small molecules as drugs against the spike protein.

Biophysical principles predict fitness of SARS-CoV-2 variants

SARS-CoV-2 employs its spike protein's receptor binding domain (RBD) to enter host cells. The RBD is constantly subjected to immune responses, while requiring efficient binding to host cell receptors for successful infection. However, our understanding of how RBD's biophysical properties contribute to SARS-CoV-2's epidemiological fitness remains largely incomplete. Through a comprehensive approach, comprising large-scale sequence analysis of SARS-CoV-2 variants and the identification of a fitness function based on binding thermodynamics, we unravel the relationship between the biophysical properties of RBD variants and their contribution to viral fitness. We developed a biophysical model that uses statistical mechanics to map the molecular phenotype space, characterized by dissociation constants of RBD to ACE2, LY-CoV016, LY-CoV555, REGN10987, and S309, onto an epistatic fitness landscape. We validate our findings through experimentally measured and machine learning (ML) estimated binding affinities, coupled with infectivity data derived from population-level sequencing. Our analysis reveals that this model effectively predicts the fitness of novel RBD variants and can account for the epistatic interactions among mutations, including explaining the later reversal of Q493R. Our study sheds light on the impact of specific mutations on viral fitness and delivers a tool for predicting the future epidemiological trajectory of previously unseen or emerging low-frequency variants. These insights offer not only greater understanding of viral evolution but also potentially aid in guiding public health decisions in the battle against COVID-19 and future pandemics.