Antiviral Drug Design Research Articles

A structural snapshot of the multiple working states of the Mpox virus helicase-primase D5.

The Mpox virus (or Monkeypox virus, MPXV) uses its own encoded proteins to form a replication machine that replicates the viral genome in the host cell cytoplasm, making this machinery a key target for antiviral drug design. The D5 (also known as the OPG117 or E5) protein, a bi-functional helicase-primase enzyme, is crucial in the MPXV replication machinery and genome uncoating process. Recently, cryo-electron microscopy (cryo-EM) structures of D5 in multiple states have been determined. These structures have elucidated the full trajectory of the MPXV D5 helicase-primase as it moves along single-stranded DNA, providing unprecedented advancements in the molecular dynamics and unwinding mechanism. This structural snapshot describes the structural features of the D5 protein and dissects the broader implications of its pivotal role in MPXV replication.

Early Steps of Individual Multireceptor Viral Interactions Dissected by High-Density, Multicolor Quantum Dot Mapping in Living Cells.

Viral capture and entry to target cells are the first crucial steps that ultimately lead to viral infection. Understanding these events is essential toward the design and development of suitable antiviral drugs and/or vaccines. Viral capture involves dynamic interactions of the virus with specific receptors in the plasma membrane of the target cells. In the last years, single virus tracking has emerged as a powerful approach to assess real time dynamics of viral processes in living cells and their engagement with specific cellular components. However, direct visualization of the early steps of multireceptor viral interactions at the single level has been largely impeded by the technical challenges associated with imaging individual multimolecular systems at relevant spatial (nanometer) and temporal (millisecond) scales. Here, we present a four-color, high-density quantum dot spatiotemporal mapping methodology to capture real-time interactions between individual virus-like-particles (VLPs) and three different viral (co-) receptors on the membrane of primary living immune cells derived from healthy donors. Together with quantitative tools, our approach revealed the existence of a coordinated spatiotemporal diffusion of the three different (co)receptors prior to viral engagement. By varying the temporal-windows of cumulated single-molecule localizations, we discovered that such a concerted diffusion impacts on the residence time of HIV-1 and SARS-CoV-2 VLPs on the host membrane and potential viral infectivity. Overall, our methodology offers the possibility for systematic analysis of the initial steps of viral-host interactions and could be easily implemented for the investigation of other multimolecular systems at the single-molecule level.

Mechanism of enterovirus VP0 maturation cleavage based on the structure of a stabilised assembly intermediate.

Molecular details of genome packaging are little understood for the majority of viruses. In enteroviruses (EVs), cleavage of the structural protein VP0 into VP4 and VP2 is initiated by the incorporation of RNA into the assembling virion and is essential for infectivity. We have applied a combination of bioinformatic, molecular and structural approaches to generate the first high-resolution structure of an intermediate in the assembly pathway, termed a provirion, which contains RNA and intact VP0. We have demonstrated an essential role of VP0 E096 in VP0 cleavage independent of RNA encapsidation and generated a new model of capsid maturation, supported by bioinformatic analysis. This provides a molecular basis for RNA-dependence, where RNA induces conformational changes required for VP0 maturation, but that RNA packaging itself is not sufficient to induce maturation. These data have implications for understanding production of infectious virions and potential relevance for future vaccine and antiviral drug design.

Analyzing and Critically Evaluating the Problems of Antiviral Chemotherapy

Antiviral chemotherapy, an indispensable tool in combating viral infections, faces numerous challenges that often undermine its overall effectiveness and application. This review critically examines the multifaceted issues associated with antiviral chemotherapy, drawing on comprehensive data from NCBI, PubMed, and other reputable academic sources. The primary purpose of this research is to analyze and evaluate key problems such as the development of drug resistance, narrow therapeutic windows, limited spectrum of activity, toxicity, high costs, viral latency, and the complexities inherent in combination therapy. These challenges necessitate a delicate and strategic balance in the development, regulation, and application of antiviral drugs. The research methodology included an exhaustive review of peer-reviewed articles and clinical studies sourced from PubMed and NCBI databases, focusing on ten critical challenges in antiviral chemotherapy. The findings underscore the persistent issue of drug resistance, particularly in RNA viruses like HIV and hepatitis C, which demand ongoing innovation in antiviral drug design and implementation. Additionally, the analysis reveals the significant risks posed by the narrow therapeutic index of many antiviral drugs, which often increases the likelihood of adverse effects, thus limiting their safe and effective use. The study also highlights the formidable challenges posed by viral latency and the limited efficacy of current therapies against emerging and re-emerging viral threats. This research significantly contributes to the understanding of the inherent limitations in existing antiviral therapies and underscores the pressing need for more effective, accessible, and safe treatments. The practical significance lies in offering insights that could guide future research, clinical practice, and policy decisions, ultimately improving global health outcomes in the fight against viral diseases.

From viruses to humans – Exploring the structure–function relationship of the Kesv protein for the future of biomedicine

Viruses often use ion channel proteins to initialise host infections. Defects in ion channel proteins are also linked to several metabolic disorders in humans. In that instance, modulation of ion channel activities becomes central to development of antiviral therapies and drug design. Kesv, a potassium-selective ion channel protein expressed by Ectocarpus siliculosus virus (EsV), possesses remarkable properties which can help to characterise the molecular basis of the functional processes relevant to virus biology and human physiology. The small structural features of this ion channel could serve as a fundamental primer to study more complex ion channels from humans. Therefore, in spite of their evolutionary distance, the potential link between viral and human ion channel proteins could provide opportunities for therapeutic and biotechnological applications.

Novel insights into the host cell glycan binding profile of human metapneumovirus.

Numerous viruses have been found to exploit glycoconjugates expressed on human cells as their initial attachment factor for viral entry and infection. The virus-cell glycointeractome, when characterized, may serve as a template for antiviral drug design. Heparan sulfate proteoglycans extensively decorate the human cell surface and were previously described as a primary receptor for human metapneumovirus (HMPV). After respiratory syncytial virus, HMPV is the second most prevalent respiratory pathogen causing respiratory tract infection in young children. To date, there is neither vaccine nor drug available to prevent or treat HMPV infection. Using a multidisciplinary approach, we report for the first time the glycointeractome of the HMPV fusion (F) protein, a viral surface glycoprotein that is essential for target-cell recognition, attachment, and entry. Our glycan microarray and surface plasmon resonance results suggest that Galβ1-3/4GlcNAc moieties that may be sialylated or fucosylated are readily recognized by HMPV F. The bound motifs are highly similar to the N-linked and O-linked glycans primarily expressed on the human lung epithelium. We demonstrate that the identified glycans have the potential to compete with the cellular receptors used for HMPV entry and consequently block HMPV infection. We found that lacto-N-neotetraose demonstrated the strongest HMPV binding inhibition in a cell infection assay. Our current findings offer an encouraging and novel avenue for the design of anti-HMPV drug candidates using oligosaccharide templates.IMPORTANCEAll cells are decorated with a dense coat of sugars that makes a sugar code. Many respiratory viruses exploit this sugar code by binding to these sugars to cause infection. Human metapneumovirus is a leading cause for acute respiratory tract infections. Despite its medical importance, there is no vaccine or antiviral drug available to prevent or treat human metapneumovirus infection. This study investigates how human metapneumovirus binds to sugars in order to more efficiently infect the human host. We found that human metapneumovirus binds to a diverse range of sugars and demonstrated that these sugars can ultimately block viral infection. Understanding how viruses can take advantage of the sugar code on our cells could identify new intervention and treatment strategies to combat viral disease.

How kelch domain-containing protein 3 distinguishes between the C-end degron of herpesviral protein UL49.5 and its mutants – Insights from molecular dynamics

The C-terminal residues of proteins can function as degrons recognized by ubiquitin ligases for proteasomal degradation. Kelch domain-containing protein 3 (KLHDC3) is a substrate receptor for E3 ubiquitin ligase (Cullin2-RING ligase) that targets the C-terminal degrons. UL49.5 is 96 amino-acid type 1 transmembrane protein from bovine herpesvirus 1. Herpesviruses have evolved highly effective strategies to evade the antiviral immune response. One of these strategies is inhibition of the antigen processing and presentation pathway by MHC I, thereby reducing the presentation of the antigenic peptides on the surface of the infected cell. Recently, it has been demonstrated that UL49.5 triggers TAP degradation via recruiting the E3 ubiquitin ligase to TAP. Moreover, the mutagenesis revealed that the mutations within the UL49.5 C-degron sequence (93RGRG96) affect binding of UL49.5 to KLHDC3.In this work the molecular dynamics of KLHDC3 in complexes with the C-terminal decapeptide of the herpesviral protein UL4.95 and its three mutants has been employed to provide a framework for understanding molecular recognition of UL49.5 by KLHDC3. The findings of this study give insights into the interactions of the various degrons with KLHDC3. During the molecular dynamics, an active RGKG mutant adopts a conformation similar to that of the wild type decapeptide, whereas the conformations of two inactive mutants, KGRG and RGRD are significantly different. Both R93K and G96D mutations impair the interactions of the C-terminal glycine with KLHDC3.The findings of this study expand the existing knowledge about the mechanism of protein recognition by Cullin2-RING ligases thus contributing to the design of antiviral and anticancer drugs that can selectively promote or inhibit degradation of the proteins of interest.

Understanding the SARS-CoV-2–Human Liver Interactome Using a Comprehensive Analysis of the Individual Virus–Host Interactions

Many metabolic processes at the molecular level support both viral attack strategies and human defenses during COVID-19. This knowledge is of vital importance in the design of antiviral drugs. In this study, we extracted 18 articles (2021–2023) from PubMed reporting the discovery of hub nodes specific for the liver during COVID-19, identifying 142 hub nodes. They are highly connected proteins from which to obtain deep functional information on viral strategies when used as functional seeds. Therefore, we evaluated the functional and structural significance of each of them to endorse their reliable use as seeds. After filtering, the remaining 111 hubs were used to obtain by STRING an enriched interactome of 1111 nodes (13,494 interactions). It shows the viral strategy in the liver is to attack the entire cytoplasmic translational system, including ribosomes, to take control of protein biosynthesis. We used the SARS2-Human Proteome Interaction Database (33,791 interactions), designed by us with BioGRID data to implement a reverse engineering process that identified human proteins actively interacting with viral proteins. The results show 57% of human liver proteins are directly involved in COVID-19, a strong impairment of the ribosome and spliceosome, an antiviral defense mechanism against cellular stress of the p53 system, and, surprisingly, a viral capacity for multiple protein attacks against single human proteins that reveal underlying evolutionary–topological molecular mechanisms. Viral behavior over time suggests different molecular strategies for different organs.

Selectively T cell phosphorylation activation of azvudine in the thymus tissue with immune protection effect

Thymus is the important immune organ, responsible for T cell development and differentiation. The lower circulating T counts have been observed in patients who died from COVID-19 compared with survivors. Azvudine, also known as FNC, is a thymus-homing anti-SARS-CoV-2 drug in treating COVID-19 patients. In this study, single-cell transcriptome, proteomics, and parallel reaction monitoring (PRM) were applied to insight into the activation process of FNC in rat and SARS-CoV-2 rhesus monkey thymus. The results indicated that thymic immune cells possess a robust metabolic capacity for cytidine-analogue drugs such as FNC. Key enzymes involved in the FNC phosphorylation process, such as Dck, Cmpk1, and Nme2, were highly expressed in CD4+ T cells, CD8+ T cells, and DP (CD4+ CD8+) cells. Additionally, FNC could upregulate multiple phosphorylated kinases in various cell types while downregulating the phosphatases, phosphoribosyl transferases, and deaminases, respectively. The robust phosphorylation capacity of the thymus for cytidine analogue drug FNC, and the activation effect of FNC on the NAs metabolism system potentially contribute to its enrichment in the thymus and immune protection effect. This suggests that it is crucial to consider the expression level of phosphorylation kinases when evaluating NA drug properties, as an important factor during antiviral drug design.

Structure of the recombinant RNA polymerase from African Swine Fever Virus

African Swine Fever Virus is a Nucleo-Cytoplasmic Large DNA Virus that causes an incurable haemorrhagic fever in pigs with a high impact on global food security. ASFV replicates in the cytoplasm of the infected cell and encodes its own transcription machinery that is independent of cellular factors, however, not much is known about how this system works at a molecular level. Here, we present methods to produce recombinant ASFV RNA polymerase, functional assays to screen for inhibitors, and high-resolution cryo-electron microscopy structures of the ASFV RNAP in different conformational states. The ASFV RNAP bears a striking resemblance to RNAPII with bona fide homologues of nine of its twelve subunits. Key differences include the fusion of the ASFV assembly platform subunits RPB3 and RPB11, and an unusual C-terminal domain of the stalk subunit vRPB7 that is related to the eukaryotic mRNA cap 2´-O-methyltransferase 1. Despite the high degree of structural conservation with cellular RNA polymerases, the ASFV RNAP is resistant to the inhibitors rifampicin and alpha-amanitin. The cryo-EM structures and fully recombinant RNAP system together provide an important tool for the design, development, and screening of antiviral drugs in a low biosafety containment environment.

Targeting the receptor binding domain and heparan sulfate binding for antiviral drug development against SARS-CoV-2 variants

The emergence of SARS-CoV-2 variants diminished the efficacy of current antiviral drugs and vaccines. Hence, identifying highly conserved sequences and potentially druggable pockets for drug development was a promising strategy against SARS-CoV-2 variants. In viral infection, the receptor-binding domain (RBD) proteins are essential in binding to the host receptor. Others, Heparan sulfate (HS), widely distributed on the surface of host cells, is thought to play a central role in the viral infection cycle of SARS-CoV-2. Therefore, it might be a reasonable strategy for antiviral drug design to interfere with the RBD in the HS binding site. In this study, we used computational approaches to analyze multiple sequences of coronaviruses and reveal important information about the binding of HS to RBD in the SARS-CoV-2 spike protein. Our results showed that the potential hot-spots, including R454 and E471, in RBD, exhibited strong interactions in the HS-RBD binding region. Therefore, we screened different compounds in the natural product database towards these hot-spots to find potential antiviral candidates using LibDock, Autodock vina and furthermore applying the MD simulation in AMBER20. The results showed three potential natural compounds, including Acetoside (ACE), Hyperoside (HYP), and Isoquercitrin (ISO), had a strong affinity to the RBD. Our results demonstrate a feasible approach to identify potential antiviral agents by evaluating the binding interaction between viral glycoproteins and host receptors. The present study provided the applications of the structure-based computational approach for designing and developing of new antiviral drugs against SARS-CoV-2 variants.

Structural and thermodynamic properties of conserved water molecules in Mpro native: A combined approach by MD simulation and Grid Inhomogeneous Solvation Theory.

The new viral strains of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) are continuously rising, becoming more virulent, and transmissible. Therefore, the development of new antiviral drugs is essential. Due to its significant role in the viral life cycle of SARS-CoV-2, the main protease (Mpro) enzyme is a leading target for antiviral drug design. The Mpro monomer consists of domain DI, DII, and DI-DII interface. Twenty-one conserved water molecules (W4-W24) are occupied at these domains according to multiple crystal structure analyses. The crystal and MD structures reveal the presence of eight conserved water sites in domain DI, DII and remaining in the DI-DII interface. Grid-based inhomogeneous fluid solvation theory (GIST) was employed on MD structures of Mpro native to predict structural and thermodynamic properties of each conserved water site for focusing to identify the specific conserved water molecules that can easily be displaced by proposed ligands. Finally, MD water W13 is emerged as a promising candidate for water mimic drug design due to its low mean interaction energy, loose binding character with the protein, and its involvement in a water-mediated H-bond with catalytic His41 via the interaction Thr25(OG)---W13---W---His41(NE2). In this context, water occupancy, relative interaction energy, entropy, and topologies of W13 are thermodynamically acceptable for the water displacement method. Therefore, the strategic use of W13's geometrical position in the DI domain may be implemented for drug discovery against COVID disease by designing new ligands with appropriately oriented chemical groups to mimic its structural, electronic, and thermodynamic properties.

Trapping a non-cognate nucleotide upon initial binding for replication fidelity control in SARS-CoV-2 RNA dependent RNA polymerase.

The RNA dependent RNA polymerase (RdRp) in SARS-CoV-2 is a highly conserved enzyme responsible for viral genome replication/transcription. To understand how the viral RdRp achieves fidelity control during such processes, here we computationally investigate the natural non-cognate vs. cognate nucleotide addition and selectivity during viral RdRp elongation. We focus on the nucleotide substrate initial binding (RdRp active site open) to the prechemical insertion (active site closed) of the RdRp. The current studies were first carried out using microsecond ensemble equilibrium all-atom molecular dynamics (MD) simulations. Due to the slow conformational changes (from open to closed) during nucleotide insertion and selection, enhanced or umbrella sampling methods have been further employed to calculate the free energy profiles of the nucleotide insertion. Our studies find notable stability of noncognate dATP and GTP upon initial binding in the active-site open state. The results indicate that while natural cognate ATP and Remdesivir drug analogue (RDV-TP) are biased toward stabilization in the closed state to facilitate insertion, the natural non-cognate dATP and GTP can be well trapped in off-path initial binding configurations and prevented from insertion so that to be further rejected. The current work thus presents the intrinsic nucleotide selectivity of SARS-CoV-2 RdRp for natural substrate fidelity control, which should be considered in antiviral drug design.

Evaluating mAbs binding abilities to Omicron subvariant RBDs: implications for selecting effective mAb therapies.

The ongoing evolution of the Omicron lineage of SARS-CoV-2 has led to the emergence of subvariants that pose challenges to antibody neutralization. Understanding the binding dynamics between the receptor-binding domains (RBD) of these subvariants spike and monoclonal antibodies (mAbs) is pivotal for elucidating the mechanisms of immune escape and for advancing the development of therapeutic antibodies. This study focused on the RBD regions of Omicron subvariants BA.2, BA.5, BF.7, and XBB.1.5, employing molecular dynamics simulations to unravel their binding mechanisms with a panel of six mAbs, and subsequently analyzing the origins of immune escape from energetic and structural perspectives. Our results indicated that the antibody LY-COV1404 maintained binding affinities across all studied systems, suggesting the resilience of certain antibodies against variant-induced immune escape, as seen with the mAb 1D1-Fab. The newly identified mAb 002-S21F2 showed a similar efficacy profile to LY-COV1404, though with a slightly reduced binding to BF.7. In parallel, mAb REGN-10933 emerged as a potential therapeutic candidate against BF.7 and XBB.1.5, reflecting the importance of identifying variant-specific antibody interactions, akin to the binding optimization observed in BA.4/5 and XBB.1.5. And key residues that facilitate RBD-mAb binding were identified (T345, L441, K444, V445, and T500), alongside residues that hinder protein-protein interactions (D420, L455, K440, and S446). Particularly noteworthy was the inhibited binding of V445 and R509 with mAbs in the presence of mAb 002-S21F2, suggesting a mechanism for immune escape, especially through the reduction of V445 hydrophobicity. These findings enhance our comprehension of the binding interactions between mAbs and RBDs, contributing to the understanding of immune escape mechanisms. They also lay the groundwork for the design and optimization of antiviral drugs and have significant implications for the development of treatments against current and future coronaviruses.

In silico analysis of non-structural protein 12 sequences from SARS-COV-2 found in Manaus, Amazonas, Brazil, reveals mutations linked to higher transmissibility.

The disease coronavirus COVID-19 has been the cause of millions of deaths worldwide. Among the proteins of SARS-CoV-2, non-structural protein 12 (NSP12) plays a key role during COVID infection and is part of the RNA-dependent RNA polymerase complex. The monitoring of NSP12 polymorphisms is extremely important for the design of new antiviral drugs and monitoring of viral evolution. This study analyzed the NSP12 mutations detected in circulating SARS-CoV-2 during the years 2020 to 2022 in the population of the city of Manaus, Amazonas, Brazil. The most frequent mutations found were P323L and G671S. Reports in the literature indicate that these mutations are related to transmissibility efficiency, which may have contributed to the extremely high numbers of cases in this location. In addition, two mutations described here (E796D and R914K) are close and have RMSD that is similar to the mutations M794V and N911K, which have been described in the literature as influential on the performance of the NSP12 enzyme. These data demonstrate the need to monitor the emergence of new mutations in NSP12 in order to better understand their consequences for the treatments currently used and in the design of new drugs.

Computer-Aided Prediction of the Interactions of Viral Proteases with Antiviral Drugs: Antiviral Potential of Broad-Spectrum Drugs.

Human society is facing the threat of various viruses. Proteases are promising targets for the treatment of viral infections. In this study, we collected and profiled 170 protease sequences from 125 viruses that infect humans. Approximately 73 of them are viral 3-chymotrypsin-like proteases (3CLpro), and 11 are pepsin-like aspartic proteases (PAPs). Their sequences, structures, and substrate characteristics were carefully analyzed to identify their conserved nature for proposing a pan-3CLpro or pan-PAPs inhibitor design strategy. To achieve this, we used computational prediction and modeling methods to predict the binding complex structures for those 73 3CLpro with 4 protease inhibitors of SARS-CoV-2 and 11 protease inhibitors of HCV. Similarly, the complex structures for the 11 viral PAPs with 9 protease inhibitors of HIV were also obtained. The binding affinities between these compounds and proteins were also evaluated to assess their pan-protease inhibition via MM-GBSA. Based on the drugs targeting viral 3CLpro and PAPs, repositioning of the active compounds identified several potential uses for these drug molecules. As a result, Compounds 1-2, modified based on the structures of Ray1216 and Asunaprevir, indicate potential inhibition of DENV protease according to our computational simulation results. These studies offer ideas and insights for future research in the design of broad-spectrum antiviral drugs.

Advances in virtual screening techniques for anti-viral drug design: A computational perspective

With the outbreak of the novel coronavirus, which has been found to mutate almost once a week, future viruses may mutate faster than we think. To deal with the mutation of the virus as soon as possible, the development of new drugs should be accelerated. The traditional drug research and development cycle is long, the cost is high, and the human resource consumption is large. Virtual screening technology has gradually become an indispensable link in the research and development of new drugs because of its high efficiency and low cost. This paper introduces the discovery, structure, symptoms and pathogenesis of 5 viruses (HIV, HBV, HCV, Ebola Virus, Coronavirus), and summarizes the application cases of virtual screening technology in the research and development of new antiviral drugs in recent years, to provide a reference for researchers.

Mangostenone Bioactive Compound from Garcinia mangostana L. as Antiviral Agent via Dual Inhibitors Against E6 HPV 16/18 Oncoprotein through Computational Simulation

HPV is a DNA virus from Papillomaviridae about 170 types have been identified and most of these viruses can triger cervial cancer disease. Types of HPV that can trigger cervical cancer consist of HPV-16 and HPV-18 with around 70% of cases, HPV-6 and HPV-11 only trigger genital warts. Types of HPV-16 and HPV-18 are high risk in triggering cervical cancer. High risk HPV types have the ability to interfere with the performance of tumor suppressors in cells through oncoprotein activity. E6 is a crucial oncoprotein because it allows degradation of tumor suppressors in host cells, E6 can be a major target in antiviral drug design. Inhibition of the E6 domain by antiviral candidate compounds is an important part of preventing the formation of the E6-p53 complex and preventing cancer development. Garcinia mangostana L. (Mangosteen) is a traditional medicine for treating bacterial, viral, fungal infections, as an antioxidant, and for degenerative diseases. This study aims to explore the potential of mangostenone compounds from Garcinia mangostana L. as HPV antivirals through inhibition of the E6 oncoprotein on HPV-16 and HPV-18 through in silico study. In silico analysis methods such as drug likeness, antiviral probability, docking simulation, chemical interaction analysis, and molecular visualization were used in this study to reveal HPV antiviral candidates from Mangostenone derivatives. Mangostenone derivative compounds from Garcinia mangostana L. can be antiviral candidates for HPV through a dual inhibitory mechanism by Mangostenone A. These compounds have strong activity through more negative binding affinity values and weak bonds such as hydrogen and hydrophobic bonds compared to other mangostenone derivative compounds.

Human antimicrobial peptide inactivation mechanism of enveloped viruses

HypothesisEnveloped viruses are pivotal in causing various illnesses, including influenza and COVID-19. The antimicrobial peptide LL-37, a critical part of the human innate immune system, exhibits potential as an antiviral agent capable of thwarting these viral threats. Its mode of action involves versatile and non-specific interactions that culminate in dismantling the viral envelope, ultimately rendering the viruses inert. However, the exact mechanism of action is not yet understood. ExperimentsHere, the mechanism of LL-37 triggered changes in the structure and function of an enveloped virus is investigated. The bacteriophage “Phi6” is used as a surrogate for pathogenic enveloped viruses. Small angle X-ray and neutron scattering combined with light scattering techniques demonstrate that LL-37 actively integrates into the virus’s lipid envelope. FindingsLL-37 addition to Phi6 leads to curvature modification in the lipid bilayer, ultimately separating the envelope from the nucleocapsid. Additional biological assays confirm the loss of virus infectivity in the presence of LL-37, which coincides with the structural transformations. The results provide a fundamental understanding of the structure-activity relationship related to enveloped viruses. The knowledge of peptide-virus interactions can guide the design of future peptide-based antiviral drugs and therapies.

Crystal structures of RNA-dependent RNA polymerases from Jingmen tick virus and Alongshan virus

Jingmenviruses are a group of flavi-like viruses with segmented genome and have been found in various types of hosts, including humans, cattle, monkeys, bats, rodents, sheep, ticks, mosquitoes and nematodes. Jingmenviruses, including the Jingmen tick virus (JMTV) and Alongshan virus (ALSV), have been associated with febrile illness and flu-like symptoms in humans. Viral polymerase plays critical roles in genome replication and transcription and is an ideal target for antiviral drugs. Here, we determined the crystal structures of RNA-dependent RNA polymerase (RdRp) domains of JMTV and ALSV at 2.6 Å and 3.2 Å resolutions, respectively. The overall structures of JMTV and ALSV RdRp domains are similar to those from the typical unsegmented viruses in Flaviviridae family, especially the Flavivirus genus. JMTV and ALSV RdRps can be divided into three subdomains and the catalytical Motif A-G are conserved like the typical flaviviruses, whereas the zinc-binding pockets are absent from the JMTV and ALSV RdRps. The 5′-ends of jingmenvirus genomes are varied in length and sequence, and a highly conserved 8-nucleotide element located on the tip of stem loop A was identified and shown to be required for binding with RdRp and performing de novo replication activity. These findings provide important structural insights into RdRp of segmented flavivirus and reveal the key region of virus genome responsible for replication initiation, which would promote molecular understanding of segmented flavivirus replication and the structure-based design of antiviral drugs against flaviviruses.