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1.
Proc Natl Acad Sci U S A ; 121(20): e2321260121, 2024 May 14.
Article En | MEDLINE | ID: mdl-38722807

Protein capsids are a widespread form of compartmentalization in nature. Icosahedral symmetry is ubiquitous in capsids derived from spherical viruses, as this geometry maximizes the internal volume that can be enclosed within. Despite the strong preference for icosahedral symmetry, we show that simple point mutations in a virus-like capsid can drive the assembly of unique symmetry-reduced structures. Starting with the encapsulin from Myxococcus xanthus, a 180-mer bacterial capsid that adopts the well-studied viral HK97 fold, we use mass photometry and native charge detection mass spectrometry to identify a triple histidine point mutant that forms smaller dimorphic assemblies. Using cryoelectron microscopy, we determine the structures of a precedented 60-mer icosahedral assembly and an unexpected 36-mer tetrahedron that features significant geometric rearrangements around a new interaction surface between capsid protomers. We subsequently find that the tetrahedral assembly can be generated by triple-point mutation to various amino acids and that even a single histidine point mutation is sufficient to form tetrahedra. These findings represent a unique example of tetrahedral geometry when surveying all characterized encapsulins, HK97-like capsids, or indeed any virus-derived capsids reported in the Protein Data Bank, revealing the surprising plasticity of capsid self-assembly that can be accessed through minimal changes in the protein sequence.


Capsid Proteins , Capsid , Cryoelectron Microscopy , Point Mutation , Capsid/metabolism , Capsid/chemistry , Capsid/ultrastructure , Capsid Proteins/genetics , Capsid Proteins/chemistry , Capsid Proteins/metabolism , Myxococcus xanthus/genetics , Myxococcus xanthus/metabolism , Models, Molecular
2.
Bioorg Chem ; 147: 107415, 2024 Jun.
Article En | MEDLINE | ID: mdl-38701597

The tobacco mosaic virus coat protein (TMV-CP) is indispensable for the virus's replication, movement and transmission, as well as for the host plant's immune system to recognize it. It constitutes the outermost layer of the virus particle, and serves as an essential component of the virus structure. TMV-CP is essential for initiating and extending viral assembly, playing a crucial role in the self-assembly process of Tobacco Mosaic Virus (TMV). This research employed TMV-CP as a primary target for virtual screening, from which a library of 43,417 compounds was sourced and SH-05 was chosen as the lead compound. Consequently, a series of α-amide phosphate derivatives were designed and synthesized, exhibiting remarkable anti-TMV efficacy. The synthesized compounds were found to be beneficial in treating TMV, with compound 3g displaying a slightly better curative effect than Ningnanmycin (NNM) (EC50 = 304.54 µg/mL) at an EC50 of 291.9 µg/mL. Additionally, 3g exhibited comparable inactivation activity (EC50 = 63.2 µg/mL) to NNM (EC50 = 67.5 µg/mL) and similar protective activity (EC50 = 228.9 µg/mL) to NNM (EC50 = 219.7 µg/mL). Microscale thermal analysis revealed that the binding of 3g (Kd = 4.5 ± 1.9 µM) to TMV-CP showed the same level with NNM (Kd = 5.5 ± 2.6 µM). Results from transmission electron microscopy indicated that 3g could disrupt the structure of TMV virus particles. The toxicity prediction indicated that 3g was low toxicity. Molecular docking showed that 3g interacted with TMV-CP through hydrogen bond, attractive charge interaction and π-Cation interaction. This research provided a novel α-amide phosphate structure target TMV-CP, which may help the discovery of new anti-TMV agents in the future.


Antiviral Agents , Capsid Proteins , Phosphates , Tobacco Mosaic Virus , Tobacco Mosaic Virus/drug effects , Antiviral Agents/pharmacology , Antiviral Agents/chemistry , Antiviral Agents/chemical synthesis , Phosphates/chemistry , Phosphates/pharmacology , Structure-Activity Relationship , Molecular Structure , Capsid Proteins/antagonists & inhibitors , Capsid Proteins/chemistry , Capsid Proteins/metabolism , Drug Design , Microbial Sensitivity Tests , Amides/chemistry , Amides/pharmacology , Amides/chemical synthesis , Dose-Response Relationship, Drug , Drug Discovery , Molecular Docking Simulation
3.
Vet Res ; 55(1): 63, 2024 May 17.
Article En | MEDLINE | ID: mdl-38760810

The maintenance of viral protein homeostasis depends on the interaction between host cell proteins and viral proteins. As a molecular chaperone, heat shock protein 70 (HSP70) has been shown to play an important role in viral infection. Our results showed that HSP70 can affect translation, replication, assembly, and release during the life cycle of duck hepatitis A virus type 1 (DHAV-1). We demonstrated that HSP70 can regulate viral translation by interacting with the DHAV-1 internal ribosome entry site (IRES). In addition, HSP70 interacts with the viral capsid proteins VP1 and VP3 and promotes their stability by inhibiting proteasomal degradation, thereby facilitating the assembly of DHAV-1 virions. This study demonstrates the specific role of HSP70 in regulating DHAV-1 replication, which are helpful for understanding the pathogenesis of DHAV-1 infection and provide additional information about the role of HSP70 in infection by different kinds of picornaviruses, as well as the interaction between picornaviruses and host cells.


HSP70 Heat-Shock Proteins , Hepatitis Virus, Duck , Internal Ribosome Entry Sites , Virus Replication , Hepatitis Virus, Duck/physiology , Hepatitis Virus, Duck/genetics , HSP70 Heat-Shock Proteins/metabolism , HSP70 Heat-Shock Proteins/genetics , Animals , Viral Structural Proteins/metabolism , Viral Structural Proteins/genetics , Ducks , Poultry Diseases/virology , Picornaviridae Infections/veterinary , Picornaviridae Infections/virology , Picornaviridae Infections/metabolism , Capsid Proteins/metabolism , Capsid Proteins/genetics , Hepatitis, Viral, Animal/virology , Hepatitis, Viral, Animal/metabolism , Protein Biosynthesis
5.
Nat Commun ; 15(1): 3780, 2024 May 06.
Article En | MEDLINE | ID: mdl-38710714

Recombinant adeno-associated viruses (rAAVs) have emerged as promising gene therapy vectors due to their proven efficacy and safety in clinical applications. In non-human primates (NHPs), rAAVs are administered via suprachoroidal injection at a higher dose. However, high doses of rAAVs tend to increase additional safety risks. Here, we present a novel AAV capsid (AAVv128), which exhibits significantly enhanced transduction efficiency for photoreceptors and retinal pigment epithelial (RPE) cells, along with a broader distribution across the layers of retinal tissues in different animal models (mice, rabbits, and NHPs) following intraocular injection. Notably, the suprachoroidal delivery of AAVv128-anti-VEGF vector completely suppresses the Grade IV lesions in a laser-induced choroidal neovascularization (CNV) NHP model for neovascular age-related macular degeneration (nAMD). Furthermore, cryo-EM analysis at 2.1 Å resolution reveals that the critical residues of AAVv128 exhibit a more robust advantage in AAV binding, the nuclear uptake and endosome escaping. Collectively, our findings highlight the potential of AAVv128 as a next generation ocular gene therapy vector, particularly using the suprachoroidal delivery route.


Choroidal Neovascularization , Dependovirus , Genetic Therapy , Genetic Vectors , Retinal Pigment Epithelium , Animals , Dependovirus/genetics , Genetic Vectors/genetics , Genetic Vectors/administration & dosage , Genetic Therapy/methods , Mice , Retinal Pigment Epithelium/metabolism , Retinal Pigment Epithelium/virology , Choroidal Neovascularization/therapy , Choroidal Neovascularization/genetics , Rabbits , Humans , Gene Transfer Techniques , Macular Degeneration/therapy , Macular Degeneration/genetics , Macular Degeneration/pathology , Disease Models, Animal , Capsid Proteins/genetics , Capsid Proteins/metabolism , Transduction, Genetic , Vascular Endothelial Growth Factor A/genetics , Vascular Endothelial Growth Factor A/metabolism , Mice, Inbred C57BL , Retina/metabolism , Retina/virology , Male , HEK293 Cells
6.
Methods Mol Biol ; 2807: 153-161, 2024.
Article En | MEDLINE | ID: mdl-38743227

Recent evidence has shown that uncoating and reverse transcription precede nuclear import. These recent breakthroughs have been made possible through the development of innovative biochemical and imaging techniques. This method outlines the biochemical assay used for detecting the presence of the HIV-1 core in the nuclear compartment. In this procedure, human cells are infected with HIV-1NL4-3, with or without the inclusion of PF74, a small molecule that inhibits core entry into the nuclear compartment. Subsequently, cells are separated into cytosolic and nuclear fractions. To assess whether the capsid protein has reached the nuclear compartment, cytosolic and nuclear fractions are subjected to Western blot analysis, utilizing antibodies specific to the HIV-1 capsid protein p24. To validate the true origin of these fractions, Western blot analysis employing antibodies against cytosolic and nuclear markers are also performed. In summary, this assay provides a reliable and efficient means to detect the presence of the HIV-1 capsid protein in the nucleus during infection under various conditions.


Capsid , Cell Nucleus , HIV Infections , HIV-1 , Humans , Cell Nucleus/metabolism , HIV Infections/virology , HIV Infections/metabolism , Capsid/metabolism , HIV Core Protein p24/metabolism , HIV Core Protein p24/analysis , Capsid Proteins/metabolism , Blotting, Western/methods , Phenylalanine/metabolism , Phenylalanine/analogs & derivatives , Cell Line
7.
Sci Rep ; 14(1): 10253, 2024 05 04.
Article En | MEDLINE | ID: mdl-38704431

The tegument protein pp150 of Human Cytomegalovirus (HCMV) is known to be essential for the final stages of virus maturation and mediates its functions by interacting with capsid proteins. Our laboratory has previously identified the critical regions in pp150 important for pp150-capsid interactions and designed peptides similar in sequence to these regions, with a goal to competitively inhibit capsid maturation. Treatment with a specific peptide (PepCR2 or P10) targeted to pp150 conserved region 2 led to a significant reduction in murine CMV (MCMV) growth in cell culture, paving the way for in vivo testing in a mouse model of CMV infection. However, the general pharmacokinetic parameters of peptides, including rapid degradation and limited tissue and cell membrane permeability, pose a challenge to their successful use in vivo. Therefore, we designed a biopolymer-stabilized elastin-like polypeptide (ELP) fusion construct (ELP-P10) to enhance the bioavailability of P10. Antiviral efficacy and cytotoxic effects of ELP-P10 were studied in cell culture, and pharmacokinetics, biodistribution, and antiviral efficacy were studied in a mouse model of CMV infection. ELP-P10 maintained significant antiviral activity in cell culture, and this conjugation significantly enhanced P10 bioavailability in mouse tissues. The fluorescently labeled ELP-P10 accumulated to higher levels in mouse liver and kidneys as compared to the unconjugated P10. Moreover, viral titers from vital organs of MCMV-infected mice indicated a significant reduction of virus load upon ELP-P10 treatment. Therefore, ELP-P10 has the potential to be developed into an effective antiviral against CMV infection.


Antiviral Agents , Cytomegalovirus Infections , Elastin , Muromegalovirus , Peptides , Phosphoproteins , Viral Matrix Proteins , Animals , Elastin/chemistry , Elastin/metabolism , Cytomegalovirus Infections/drug therapy , Cytomegalovirus Infections/virology , Mice , Antiviral Agents/pharmacology , Antiviral Agents/pharmacokinetics , Antiviral Agents/chemistry , Peptides/pharmacology , Peptides/chemistry , Muromegalovirus/drug effects , Humans , Capsid Proteins/metabolism , Capsid Proteins/chemistry , Cytomegalovirus/drug effects , Capsid/metabolism , Capsid/drug effects , Recombinant Fusion Proteins/pharmacology , Recombinant Fusion Proteins/pharmacokinetics , Disease Models, Animal , Elastin-Like Polypeptides
8.
Virology ; 595: 110093, 2024 Jul.
Article En | MEDLINE | ID: mdl-38692134

Oncolytic virotherapy stands out as a burgeoning and promising therapeutic paradigm, harnessing the intrinsic cytotoxicity of oncolytic viruses for selective replication and dissemination within tumors. The primary mode of action revolves around the direct eradication of tumor cells. In our previous investigations, we formulated an oncolytic herpes simplex virus type 2 (OH2) and substantiated its anti-tumor efficacy both in vivo and in vitro. Subsequently, we embarked on a phase I/II clinical trial in China (NMPA, 2018L02743) and the USA (FDA, IND 27137) to assess OH2's safety, biodistribution, and anti-tumor activity as a standalone agent in patients with advanced solid tumors. In this investigation, our primary focus was to comprehend the influence of the major capsid protein VP5 of OH2 on its efficacy as an antitumor agent. Our findings underscore that the VP5 protein significantly amplifies OH2's oncolytic impact on A549 cells. Additionally, we observed that VP5 actively promotes the induction of apoptosis in A549 cells, both in vivo and in vitro. Through comprehensive transcriptional sequencing, we further authenticated that the VP5 protein triggers apoptosis-related signaling pathways and Gene Ontology (GO) terms in A549 cells. Moreover, we scrutinized differentially expressed genes in the p53-dependent apoptosis pathway and conducted meticulous in vitro validation of these genes. Subsequently, we delved deeper into unraveling the functional significance of the TP53I3 gene and conclusively affirmed that the VP5 protein induces apoptosis in A549 cells through the TP53I3 gene. These revelations illuminate the underlying mechanisms of OH2's antitumor activity and underscore the pivotal role played by the VP5 protein. The outcomes of our study harbor promising implications for the formulation of effective oncolytic virotherapy strategies in cancer treatment.


Apoptosis , Herpesvirus 2, Human , Oncolytic Virotherapy , Oncolytic Viruses , Humans , Oncolytic Viruses/genetics , Oncolytic Viruses/physiology , A549 Cells , Oncolytic Virotherapy/methods , Animals , Herpesvirus 2, Human/physiology , Herpesvirus 2, Human/genetics , Capsid Proteins/genetics , Capsid Proteins/metabolism , Mice , Xenograft Model Antitumor Assays
9.
Int J Mol Sci ; 25(9)2024 Apr 29.
Article En | MEDLINE | ID: mdl-38732084

Bacteriophage fitness is determined by factors influencing both their replication within bacteria and their ability to maintain infectivity between infections. The latter becomes particularly crucial under adverse environmental conditions or when host density is low. In such scenarios, the damage experienced by viral particles could lead to the loss of infectivity, which might be mitigated if the virus undergoes evolutionary optimization through replication. In this study, we conducted an evolution experiment involving bacteriophage Qß, wherein it underwent 30 serial transfers, each involving a cycle of freezing and thawing followed by replication of the surviving viruses. Our findings show that Qß was capable of enhancing its resistance to this selective pressure through various adaptive pathways that did not impair the virus replicative capacity. Notably, these adaptations predominantly involved mutations located within genes encoding capsid proteins. The adapted populations exhibited higher resistance levels than individual viruses isolated from them, and the latter surpassed those observed in single mutants generated via site-directed mutagenesis. This suggests potential interactions among mutants and mutations. In conclusion, our study highlights the significant role of extracellular selective pressures in driving the evolution of phages, influencing both the genetic composition of their populations and their phenotypic properties.


Freezing , Mutation , RNA Phages/genetics , RNA Phages/physiology , Adaptation, Physiological/genetics , Evolution, Molecular , Virus Replication/genetics , Capsid Proteins/genetics
10.
J Med Virol ; 96(4): e29510, 2024 Apr.
Article En | MEDLINE | ID: mdl-38573018

Hepatitis B virus (HBV) infection poses a significant burden on global public health. Unfortunately, current treatments cannot fully alleviate this burden as they have limited effect on the transcriptional activity of the tenacious covalently closed circular DNA (cccDNA) responsible for viral persistence. Consequently, the HBV life cycle should be further investigated to develop new anti-HBV pharmaceutical targets. Our previous study discovered that the host gene TMEM203 hinders HBV replication by participating in calcium ion regulation. The involvement of intracellular calcium in HBV replication has also been confirmed. In this study, we found that transient receptor potential vanilloid 4 (TRPV4) notably enhances HBV reproduction by investigating the effects of several calcium ion-related molecules on HBV replication. The in-depth study showed that TRPV4 promotes hepatitis B core/capsid protein (HBc) protein stability through the ubiquitination pathway and then promotes the nucleocapsid assembly. HBc binds to cccDNA and reduces the nucleosome spacing of the cccDNA-histones complex, which may regulate HBV transcription by altering the nucleosome arrangement of the HBV genome. Moreover, our results showed that TRPV4 promotes cccDNA-dependent transcription by accelerating the methylation modification of H3K4. In conclusion, TRPV4 could interact with HBV core protein and regulate HBV during transcription and replication. These data suggest that TRPV4 exerts multifaceted HBV-related synergistic factors and may serve as a therapeutic target for CHB.


Antineoplastic Agents , Hepatitis B , Humans , Ubiquitin , Capsid , Capsid Proteins , Hepatitis B virus/genetics , TRPV Cation Channels/genetics , Calcium , Nucleosomes , Methylation , Membrane Proteins
11.
J Biomed Sci ; 31(1): 34, 2024 Apr 01.
Article En | MEDLINE | ID: mdl-38561844

BACKGROUND: It is generally believed that hepatitis B virus (HBV) core protein (HBc) dephosphorylation (de-P) is important for viral DNA synthesis and virion secretion. HBV polymerase contains four domains for terminal protein, spacer, reverse transcriptase, and RNase H activities. METHODS: HBV Polymerase mutants were transfected into HuH-7 cells and assayed for replication and HBc de-P by the Phos-tag gel analysis. Infection assay was performed by using a HepG2-NTCP-AS2 cell line. RESULTS: Here, we show that a novel phosphatase activity responsible for HBc de-P can be mapped to the C-terminal domain of the polymerase overlapping with the RNase H domain. Surprisingly, while HBc de-P is crucial for viral infectivity, it is essential for neither viral DNA synthesis nor virion secretion. The potential origin, significance, and mechanism of this polymerase-associated phosphatase activity are discussed in the context of an electrostatic homeostasis model. The Phos-tag gel analysis revealed an intriguing pattern of "bipolar distribution" of phosphorylated HBc and a de-P HBc doublet. CONCLUSIONS: It remains unknown if such a polymerase-associated phosphatase activity can be found in other related biosystems. This polymerase-associated phosphatase activity could be a druggable target in clinical therapy for hepatitis B.


Capsid , Hepatitis B virus , Hepatitis B virus/genetics , Capsid/metabolism , Virus Assembly/genetics , DNA, Viral , RNA, Viral/metabolism , Capsid Proteins/metabolism , Virus Replication/genetics , Ribonuclease H/metabolism , Phosphoric Monoester Hydrolases/metabolism
12.
PLoS One ; 19(4): e0301340, 2024.
Article En | MEDLINE | ID: mdl-38625924

A safe, highly immunogenic multivalent vaccine to protect against all nine serotypes of African horse sickness virus (AHSV), will revolutionise the AHS vaccine industry in endemic countries and beyond. Plant-produced AHS virus-like particles (VLPs) and soluble viral protein 2 (VP2) vaccine candidates were developed that have the potential to protect against all nine serotypes but can equally well be formulated as mono- and bi-valent formulations for localised outbreaks of specific serotypes. In the first interferon α/ß receptor knock-out (IFNAR-/-) mice trial conducted, a nine-serotype (nonavalent) vaccine administered as two pentavalent (5 µg per serotype) vaccines (VLP/VP2 combination or exclusively VP2), were directly compared to the commercially available AHS live attenuated vaccine. In a follow up trial, mice were vaccinated with an adjuvanted nine-serotype multivalent VP2 vaccine in a prime boost strategy and resulted in the desired neutralising antibody titres of 1:320, previously demonstrated to confer protective immunity in IFNAR-/- mice. In addition, the plant-produced VP2 vaccine performed favourably when compared to the commercial vaccine. Here we provide compelling data for a nonavalent VP2-based vaccine candidate, with the VP2 from each serotype being antigenically distinguishable based on LC-MS/MS and ELISA data. This is the first preclinical trial demonstrating the ability of an adjuvanted nonavalent cocktail of soluble, plant-expressed AHS VP2 proteins administered in a prime-boost strategy eliciting high antibody titres against all 9 AHSV serotypes. Furthermore, elevated T helper cells 2 (Th2) and Th1, indicative of humoral and cell-mediated memory T cell immune responses, respectively, were detected in mouse serum collected 14 days after the multivalent prime-boost vaccination. Both Th2 and Th1 may play a role to confer protective immunity. These preclinical immunogenicity studies paved the way to test the safety and protective efficacy of the plant-produced nonavalent VP2 vaccine candidate in the target animals, horses.


African Horse Sickness Virus , African Horse Sickness , Viral Vaccines , Animals , Mice , Horses , African Horse Sickness Virus/genetics , African Horse Sickness/prevention & control , Vaccines, Combined , Chromatography, Liquid , Capsid Proteins , Tandem Mass Spectrometry , Antibodies, Viral
13.
Cell Host Microbe ; 32(4): 441-442, 2024 Apr 10.
Article En | MEDLINE | ID: mdl-38604120

The size of the nuclear pore should, in principle, prevent HIV-1 entry. However, HIV-1 capsid is able to gain nuclear pore entry. In a recent issue of Nature, Fu et al. and Dickson et al. demonstrate that the HIV-1 capsid mimics the nuclear transport protein karyopherins to access host nuclei.


HIV Infections , Nuclear Pore , Humans , Capsid/metabolism , Capsid Proteins/metabolism , HIV Infections/metabolism , Active Transport, Cell Nucleus , Cell Nucleus/metabolism , Nuclear Pore Complex Proteins/metabolism
14.
PLoS Pathog ; 20(4): e1011750, 2024 Apr.
Article En | MEDLINE | ID: mdl-38574119

Rotaviruses infect cells by delivering into the cytosol a transcriptionally active inner capsid particle (a "double-layer particle": DLP). Delivery is the function of a third, outer layer, which drives uptake from the cell surface into small vesicles from which the DLPs escape. In published work, we followed stages of rhesus rotavirus (RRV) entry by live-cell imaging and correlated them with structures from cryogenic electron microscopy and tomography (cryo-EM and cryo-ET). The virus appears to wrap itself in membrane, leading to complete engulfment and loss of Ca2+ from the vesicle produced by the wrapping. One of the outer-layer proteins, VP7, is a Ca2+-stabilized trimer; loss of Ca2+ releases both VP7 and the other outer-layer protein, VP4, from the particle. VP4, activated by cleavage into VP8* and VP5*, is a trimer that undergoes a large-scale conformational rearrangement, reminiscent of the transition that viral fusion proteins undergo to penetrate a membrane. The rearrangement of VP5* thrusts a 250-residue, C-terminal segment of each of the three subunits outward, while allowing the protein to remain attached to the virus particle and to the cell being infected. We proposed that this segment inserts into the membrane of the target cell, enabling Ca2+ to cross. In the work reported here, we show the validity of key aspects of this proposed sequence. By cryo-EM studies of liposome-attached virions ("triple-layer particles": TLPs) and single-particle fluorescence imaging of liposome-attached TLPs, we confirm insertion of the VP4 C-terminal segment into the membrane and ensuing generation of a Ca2+ "leak". The results allow us to formulate a molecular description of early events in entry. We also discuss our observations in the context of other work on double-strand RNA virus entry.


Rotavirus , Rotavirus/genetics , Capsid Proteins/metabolism , Capsid/metabolism , Calcium/metabolism , Liposomes/analysis , Liposomes/metabolism
15.
Int J Mol Sci ; 25(7)2024 Mar 23.
Article En | MEDLINE | ID: mdl-38612429

Norovirus (NoV) genogroup II, polymerase type P31, capsid genotype 4, Sydney_2012 variant (GII.P31/GII.4_Sydney_2012) has been circulating at high levels for over a decade, raising the question of whether this strain is undergoing molecular alterations without demonstrating a substantial phylogenetic difference. Here, we applied next-generation sequencing to learn more about the genetic diversity of 14 GII.P31/GII.4_Sydney_2012 strains that caused epidemics in a specific region of Japan, with 12 from Kyoto and 2 from Shizuoka, between 2012 and 2022, with an emphasis on amino acid (aa) differences in all three ORFs. We found numerous notable aa alterations in antigenic locations in the capsid region (ORF2) as well as in other ORFs. In all three ORFs, earlier strains (2013-2016) remained phylogenetically distinct from later strains (2019-2022). This research is expected to shed light on the evolutionary properties of dominating GII.P31/GII.4_Sydney_2012 strains, which could provide useful information for viral diarrhea prevention and treatment.


Evolution, Molecular , Norovirus , Japan/epidemiology , Phylogeny , Biological Evolution , Capsid Proteins/genetics , Norovirus/genetics
16.
Int J Mol Sci ; 25(7)2024 Mar 27.
Article En | MEDLINE | ID: mdl-38612545

HIV-1 capsid protein (CA) is the molecular target of the recently FDA-approved long acting injectable (LAI) drug lenacapavir (GS-6207). The quick emergence of CA mutations resistant to GS-6207 necessitates the design and synthesis of novel sub-chemotypes. We have conducted the structure-based design of two new sub-chemotypes combining the scaffold of GS-6207 and the N-terminal cap of PF74 analogs, the other important CA-targeting chemotype. The design was validated via induced-fit molecular docking. More importantly, we have worked out a general synthetic route to allow the modular synthesis of novel GS-6207 subtypes. Significantly, the desired stereochemistry of the skeleton C2 was confirmed via an X-ray crystal structure of the key synthetic intermediate 22a. Although the newly synthesized analogs did not show significant potency, our efforts herein will facilitate the future design and synthesis of novel subtypes with improved potency.


Anti-HIV Agents , HIV-1 , Capsid Proteins/genetics , HIV-1/genetics , Molecular Docking Simulation , Anti-HIV Agents/pharmacology , Mutation
17.
Biochem Biophys Res Commun ; 710: 149878, 2024 May 28.
Article En | MEDLINE | ID: mdl-38608492

Sapovirus (SaV) is a nonenveloped RNA virus that causes acute gastroenteritis in humans. Although SaV is a clinically important pathogen in children, an effective vaccine is currently unavailable. The capsid protein VP1 of SaVs forms the outer shell of the virion and is highly diverse, as often seen in the virion-surface proteins of RNA viruses, creating an obstacle for vaccine development. We here report a unique phenomenon pertaining to the variation of SaV VP1. Phylogenetic and information entropy analyses using full-length VP1 sequences from a public database consistently showed that the amino acid sequences of the VP1 protein have been highly conserved over more than 40 years in the major epidemic genotype GI.1 but not in GI.2. Structural modeling showed that even the VP1 P2 subdomain, which is arranged on the outermost shell of the virion and presumably exposed to anti-SaV antibodies, remained highly homogeneous in GI.1 but not in GI.2. These results suggest strong evolutionary constraints against amino acid changes in the P2 subdomain of the SaV GI.1 capsid and illustrate a hitherto unappreciated mechanism, i.e., preservation of the VP1 P2 subdomain, involved in SaV survival. Our findings could have important implications for the development of an anti-SaV vaccine.


Sapovirus , Vaccines , Child , Humans , Sapovirus/genetics , Capsid Proteins/genetics , Phylogeny , Amino Acids/genetics , Genotype , Feces
18.
Arch Virol ; 169(5): 105, 2024 Apr 18.
Article En | MEDLINE | ID: mdl-38637359

In this study, we identified a novel double-strand RNA (dsRNA) mycovirus in Pyricularia oryzae, designated "Magnaporthe oryzae partitivirus 4" (MoPV4). The genome of MoPV4 consists of a dsRNA-1 segment encoding an RNA-dependent RNA polymerase (RdRP) and a dsRNA-2 segment encoding a capsid protein (CP). Phylogenetic analysis indicated that MoPV4 belongs to the genus Gammapartitivirus within family Partitiviridae. The particles of MoPV4 are isometric with a diameter of about 32.4 nm. Three-dimensional structure predictions indicated that the RdRP of MoPV4 forms a classical right-handed conformation, while the CP has a reclining-V shape.


Ascomycota , Fungal Viruses , RNA Viruses , RNA, Viral/genetics , Phylogeny , RNA Viruses/genetics , Capsid Proteins/genetics , RNA-Dependent RNA Polymerase/genetics , Genome, Viral , Fungal Viruses/genetics , RNA, Double-Stranded/genetics , Open Reading Frames
19.
J Virol ; 98(5): e0006824, 2024 May 14.
Article En | MEDLINE | ID: mdl-38661364

The portal protein of tailed bacteriophage plays essential roles in various aspects of capsid assembly, motor assembly, genome packaging, connector formation, and infection processes. After DNA packaging is complete, additional proteins are assembled onto the portal to form the connector complex, which is crucial as it bridges the mature head and tail. In this study, we report high-resolution cryo-electron microscopy (cryo-EM) structures of the portal vertex from bacteriophage lambda in both its prohead and mature virion states. Comparison of these structures shows that during head maturation, in addition to capsid expansion, the portal protein undergoes conformational changes to establish interactions with the connector proteins. Additionally, the independently assembled tail undergoes morphological alterations at its proximal end, facilitating its connection to the head-tail joining protein and resulting in the formation of a stable portal-connector-tail complex. The B-DNA molecule spirally glides through the tube, interacting with the nozzle blade region of the middle-ring connector protein. These insights elucidate a mechanism for portal maturation and DNA translocation within the phage lambda system. IMPORTANCE: The tailed bacteriophages possess a distinct portal vertex that consists of a ring of 12 portal proteins associated with a 5-fold capsid shell. This portal protein is crucial in multiple stages of virus assembly and infection. Our research focused on examining the structures of the portal vertex in both its preliminary prohead state and the fully mature virion state of bacteriophage lambda. By analyzing these structures, we were able to understand how the portal protein undergoes conformational changes during maturation, the mechanism by which it prevents DNA from escaping, and the process of DNA spirally gliding.


Bacteriophage lambda , Capsid Proteins , Capsid , Cryoelectron Microscopy , Virion , Virus Assembly , Bacteriophage lambda/physiology , Bacteriophage lambda/genetics , Capsid Proteins/metabolism , Capsid Proteins/chemistry , Virion/metabolism , Virion/ultrastructure , Capsid/metabolism , Capsid/ultrastructure , DNA, Viral/genetics , DNA, Viral/metabolism , DNA Packaging , Models, Molecular , Protein Conformation
20.
J Virol ; 98(5): e0021224, 2024 May 14.
Article En | MEDLINE | ID: mdl-38591886

Porcine rotaviruses (PoRVs) cause severe economic losses in the swine industry. P[7] and P[23] are the predominant genotypes circulating on farms, but no vaccine is yet available. Here, we developed a bivalent subunit PoRV vaccine using truncated versions (VP4*) of the VP4 proteins from P[7] and P[23]. The vaccination of mice with the bivalent subunit vaccine elicited more robust neutralizing antibodies (NAbs) and cellular immune responses than its components, even at high doses. The bivalent subunit vaccine and inactivated bivalent vaccine prepared from strains PoRVs G9P[7] and G9P[23] were used to examine their protective efficacy in sows and suckling piglets after passive immunization. The immunized sows showed significantly elevated NAbs in the serum and colostrum, and the suckling piglets acquired high levels of sIgA antibodies from the colostrum. Challenging subunit-vaccinated or inactivated-vaccinated piglets with homologous virulent strains did not induce diarrhea, except in one or two piglets, which had mild diarrhea. Immunization with the bivalent subunit vaccine and inactivated vaccine also alleviated the microscopic lesions in the intestinal tissues caused by the challenge with the corresponding homologous virulent strain. However, all the piglets in the challenged group displayed mild to watery diarrhea and high levels of viral shedding, whereas the feces and intestines of the piglets in the bivalent subunit vaccine and inactivated vaccine groups had lower viral loads. In summary, our data show for the first time that a bivalent subunit vaccine combining VP4*P[7] and VP4*P[23] effectively protects piglets against the diarrhea caused by homologous virulent strains.IMPORTANCEPoRVs are the main causes of diarrhea in piglets worldwide. The multisegmented genome of PoRVs allows the reassortment of VP4 and VP7 genes from different RV species and strains. The P[7] and P[23] are the predominant genotypes circulating in pig farms, but no vaccine is available at present in China. Subunit vaccines, as nonreplicating vaccines, are an option to cope with variable genotypes. Here, we have developed a bivalent subunit candidate vaccine based on a truncated VP4 protein, which induced robust humoral and cellular immune responses and protected piglets against challenge with homologous PoRV. It also appears to be safe. These data show that the truncated VP4-protein-based subunit vaccine is a promising candidate for the prevention of PoRV diarrhea.


Antibodies, Neutralizing , Antibodies, Viral , Capsid Proteins , Rotavirus Infections , Rotavirus Vaccines , Rotavirus , Swine Diseases , Vaccines, Subunit , Animals , Swine , Rotavirus/immunology , Antibodies, Neutralizing/blood , Antibodies, Neutralizing/immunology , Swine Diseases/prevention & control , Swine Diseases/virology , Swine Diseases/immunology , Capsid Proteins/immunology , Capsid Proteins/genetics , Antibodies, Viral/blood , Antibodies, Viral/immunology , Vaccines, Subunit/immunology , Vaccines, Subunit/administration & dosage , Rotavirus Infections/prevention & control , Rotavirus Infections/veterinary , Rotavirus Infections/immunology , Rotavirus Infections/virology , Rotavirus Vaccines/immunology , Rotavirus Vaccines/administration & dosage , Mice , Female , Mice, Inbred BALB C , Vaccines, Synthetic/immunology , Vaccines, Synthetic/administration & dosage , Diarrhea/prevention & control , Diarrhea/virology , Diarrhea/veterinary , Diarrhea/immunology , Genotype , Immunity, Cellular , Vaccination
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