1
|
Bepler T, Barrera MD, Rooney MT, Xiong Y, Kuang H, Goodell E, Goodwin MJ, Harbron E, Fu R, Mihailescu M, Narayanan A, Cotten ML. Antiviral activity of the host defense peptide piscidin 1: investigating a membrane-mediated mode of action. Front Chem 2024; 12:1379192. [PMID: 38988727 PMCID: PMC11233706 DOI: 10.3389/fchem.2024.1379192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 05/08/2024] [Indexed: 07/12/2024] Open
Abstract
Outbreaks of viral diseases are on the rise, fueling the search for antiviral therapeutics that act on a broad range of viruses while remaining safe to human host cells. In this research, we leverage the finding that the plasma membranes of host cells and the lipid bilayers surrounding enveloped viruses differ in lipid composition. We feature Piscidin 1 (P1), a cationic host defense peptide (HDP) that has antimicrobial effects and membrane activity associated with its N-terminal region where a cluster of aromatic residues and copper-binding motif reside. While few HDPs have demonstrated antiviral activity, P1 acts in the micromolar range against several enveloped viruses that vary in envelope lipid composition. Notably, it inhibits HIV-1, a virus that has an envelope enriched in cholesterol, a lipid associated with higher membrane order and stability. Here, we first document through plaque assays that P1 boasts strong activity against SARS-CoV-2, which has an envelope low in cholesterol. Second, we extend previous studies done with homogeneous bilayers and devise cholesterol-containing zwitterionic membranes that contain the liquid disordered (Ld; low in cholesterol) and ordered (Lo, rich in cholesterol) phases. Using dye leakage assays and cryo-electron microscopy on vesicles, we show that P1 has dramatic permeabilizing capability on the Lo/Ld, an effect matched by a strong ability to aggregate, fuse, and thin the membranes. Differential scanning calorimetry and NMR experiments demonstrate that P1 mixes the lipid content of vesicles and alters the stability of the Lo. Structural studies by NMR indicate that P1 interacts with the Lo/Ld by folding into an α-helix that lies parallel to the membrane surface. Altogether, these results show that P1 is more disruptive to phase-separated than homogenous cholesterol-containing bilayers, suggesting an ability to target domain boundaries. Overall, this multi-faceted research highlights how a peptide that interacts strongly with membranes through an aromatic-rich N-terminal motif disrupt viral envelope mimics. This represents an important step towards the development of novel peptides with broad-spectrum antiviral activity.
Collapse
Affiliation(s)
- Tristan Bepler
- New York Structural Biology Center, New York, NY, United States
| | - Michael D. Barrera
- School of Systems Biology, George Mason University, Manassas, VA, United States
| | - Mary T. Rooney
- Department of Applied Science, William & Mary, Williamsburg, VA, United States
- Department of Chemistry, Hofstra University, Hempstead, NY, United States
| | - Yawei Xiong
- Department of Applied Science, William & Mary, Williamsburg, VA, United States
| | - Huihui Kuang
- New York Structural Biology Center, New York, NY, United States
| | - Evan Goodell
- Department of Applied Science, William & Mary, Williamsburg, VA, United States
| | - Matthew J. Goodwin
- Department of Chemistry, William & Mary, Williamsburg, VA, United States
| | - Elizabeth Harbron
- Department of Chemistry, William & Mary, Williamsburg, VA, United States
| | - Riqiang Fu
- National High Magnetic Field Laboratory, Tallahassee, FL, United States
| | - Mihaela Mihailescu
- Institute for Bioscience and Biotechnology Research, Rockville, MD, United States
| | - Aarthi Narayanan
- Department of Biology, George Mason University, Manassas, VA, United States
| | - Myriam L. Cotten
- Department of Applied Science, William & Mary, Williamsburg, VA, United States
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, United States
| |
Collapse
|
2
|
Ayusso GM, da Silva Sanches PR, Carvalho T, Santos IA, Martins DOS, Lima MLD, da Conceição PJP, Bittar C, Merits A, Cilli EM, Jardim ACG, Rahal P, Calmon MF. The Synthetic Peptide GA-Hecate and Its Analogs Inhibit Multiple Steps of the Chikungunya Virus Infection Cycle In Vitro. Pharmaceuticals (Basel) 2023; 16:1389. [PMID: 37895860 PMCID: PMC10610090 DOI: 10.3390/ph16101389] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 09/08/2023] [Accepted: 09/27/2023] [Indexed: 10/29/2023] Open
Abstract
Chikungunya virus (CHIKV) belongs to the Alphavirus genus and is responsible for significant outbreaks worldwide. Currently, there is no approved antiviral therapy against CHIKV. Bioactive peptides have great potential for new drug development. Here, we evaluated the antiviral activity of the synthetic peptide GA-Hecate and its analogs PSSct1905 and PSSct1910 against CHIKV infection. Initial screening showed that all three peptides inhibited the CHIKV replication cycle in baby hamster kidney fibroblast cells (BHK-21) and human hepatocarcinoma epithelial cells (Huh-7). GA-Hecate and its analog PSSct1905 were the most active, demonstrating suppression of viral infection by more than 91%. The analog PSSct1905 exhibited a protective effect in cells against CHIKV infection. We also observed that the analogs PSSct1905 and PSSct1910 affected CHIKV entry into both cell lines, inhibiting viral attachment and internalization. Finally, all tested compounds presented antiviral activity on the post-entry steps of CHIKV infection in all cells evaluated. In conclusion, this study highlights the potential of the peptide GA-Hecate and its analogs as novel anti-CHIKV compounds targeting different stages of the viral replication cycle, warranting the development of GA-Hecate-based compounds with broad antiviral activity.
Collapse
Affiliation(s)
- Gabriela Miranda Ayusso
- Institute of Biosciences, Letters and Exact Sciences, São Paulo State University, São José do Rio Preto 15054-000, SP, Brazil; (G.M.A.); (T.C.); (D.O.S.M.); (M.L.D.L.); (P.J.P.d.C.); (C.B.); (A.C.G.J.); (P.R.)
| | | | - Tamara Carvalho
- Institute of Biosciences, Letters and Exact Sciences, São Paulo State University, São José do Rio Preto 15054-000, SP, Brazil; (G.M.A.); (T.C.); (D.O.S.M.); (M.L.D.L.); (P.J.P.d.C.); (C.B.); (A.C.G.J.); (P.R.)
| | - Igor Andrade Santos
- Institute of Biomedical Sciences, Federal University of Uberlândia, Uberlândia 38408-100, MG, Brazil;
| | - Daniel Oliveira Silva Martins
- Institute of Biosciences, Letters and Exact Sciences, São Paulo State University, São José do Rio Preto 15054-000, SP, Brazil; (G.M.A.); (T.C.); (D.O.S.M.); (M.L.D.L.); (P.J.P.d.C.); (C.B.); (A.C.G.J.); (P.R.)
- Institute of Biomedical Sciences, Federal University of Uberlândia, Uberlândia 38408-100, MG, Brazil;
| | - Maria Letícia Duarte Lima
- Institute of Biosciences, Letters and Exact Sciences, São Paulo State University, São José do Rio Preto 15054-000, SP, Brazil; (G.M.A.); (T.C.); (D.O.S.M.); (M.L.D.L.); (P.J.P.d.C.); (C.B.); (A.C.G.J.); (P.R.)
| | - Pâmela Jóyce Previdelli da Conceição
- Institute of Biosciences, Letters and Exact Sciences, São Paulo State University, São José do Rio Preto 15054-000, SP, Brazil; (G.M.A.); (T.C.); (D.O.S.M.); (M.L.D.L.); (P.J.P.d.C.); (C.B.); (A.C.G.J.); (P.R.)
| | - Cíntia Bittar
- Institute of Biosciences, Letters and Exact Sciences, São Paulo State University, São José do Rio Preto 15054-000, SP, Brazil; (G.M.A.); (T.C.); (D.O.S.M.); (M.L.D.L.); (P.J.P.d.C.); (C.B.); (A.C.G.J.); (P.R.)
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Andres Merits
- Institute of Technology, University of Tartu, 50090 Tartu, Estonia;
| | - Eduardo Maffud Cilli
- Institute of Chemistry, São Paulo State University, Araraquara 14800-060, SP, Brazil;
| | - Ana Carolina Gomes Jardim
- Institute of Biosciences, Letters and Exact Sciences, São Paulo State University, São José do Rio Preto 15054-000, SP, Brazil; (G.M.A.); (T.C.); (D.O.S.M.); (M.L.D.L.); (P.J.P.d.C.); (C.B.); (A.C.G.J.); (P.R.)
- Institute of Biomedical Sciences, Federal University of Uberlândia, Uberlândia 38408-100, MG, Brazil;
| | - Paula Rahal
- Institute of Biosciences, Letters and Exact Sciences, São Paulo State University, São José do Rio Preto 15054-000, SP, Brazil; (G.M.A.); (T.C.); (D.O.S.M.); (M.L.D.L.); (P.J.P.d.C.); (C.B.); (A.C.G.J.); (P.R.)
| | - Marilia Freitas Calmon
- Institute of Biosciences, Letters and Exact Sciences, São Paulo State University, São José do Rio Preto 15054-000, SP, Brazil; (G.M.A.); (T.C.); (D.O.S.M.); (M.L.D.L.); (P.J.P.d.C.); (C.B.); (A.C.G.J.); (P.R.)
| |
Collapse
|
3
|
Hoffka G, Lountos GT, Needle D, Wlodawer A, Waugh DS, Tőzsér J, Mótyán JA. Self-inhibited State of Venezuelan Equine Encephalitis Virus (VEEV) nsP2 Cysteine Protease: A Crystallographic and Molecular Dynamics Analysis. J Mol Biol 2023; 435:168012. [PMID: 36792007 PMCID: PMC10758287 DOI: 10.1016/j.jmb.2023.168012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/15/2023]
Abstract
The Venezuelan equine encephalitis virus (VEEV) belongs to the Togaviridae family and is pathogenic to both humans and equines. The VEEV non-structural protein 2 (nsP2) is a cysteine protease (nsP2pro) that processes the polyprotein and thus it is a drug target for inhibitor discovery. The atomic structure of the VEEV nsP2 catalytic domain was previously characterized by both X-ray crystallography and computational studies. A modified nsP2pro harboring a N475A mutation in the N terminus was observed to exhibit an unexpected conformation: the N-terminal residues bind to the active site, mimicking binding of a substrate. The large conformational change of the N terminus was assumed to be induced by the N475A mutation, as N475 has an important role in stabilization of the N terminus and the active site. This conformation was first observed in the N475A mutant, but we also found it while determining a crystal structure of the catalytically active nsP2pro containing the wild-type N475 active site residue and K741A/K767A surface entropy reduction mutations. This suggests that the N475A mutation is not a prerequisite for self-inhibition. Here, we describe a high resolution (1.46 Å) crystal structure of a truncated nsP2pro (residues 463-785, K741A/K767A) and analyze the structure further by molecular dynamics to study the active and self-inhibited conformations of nsP2pro and its N475A mutant. A comparison of the different conformations of the N-terminal residues sheds a light on the interactions that play an important role in the stabilization of the enzyme.
Collapse
Affiliation(s)
- Gyula Hoffka
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Hungary; Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, Debrecen, Hungary
| | - George T Lountos
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Danielle Needle
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
| | - Alexander Wlodawer
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
| | - David S Waugh
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
| | - József Tőzsér
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Hungary
| | - János András Mótyán
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Hungary.
| |
Collapse
|
4
|
Yang M, Liu S, Zhang C. Antimicrobial peptides with antiviral and anticancer properties and their modification and nanodelivery systems. CURRENT RESEARCH IN BIOTECHNOLOGY 2023. [DOI: 10.1016/j.crbiot.2023.100121] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023] Open
|
5
|
The transcriptional landscape of Venezuelan equine encephalitis virus (TC-83) infection. PLoS Negl Trop Dis 2021; 15:e0009306. [PMID: 33788849 PMCID: PMC8041203 DOI: 10.1371/journal.pntd.0009306] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 04/12/2021] [Accepted: 03/12/2021] [Indexed: 01/10/2023] Open
Abstract
Venezuelan Equine Encephalitis Virus (VEEV) is a major biothreat agent that naturally causes outbreaks in humans and horses particularly in tropical areas of the western hemisphere, for which no antiviral therapy is currently available. The host response to VEEV and the cellular factors this alphavirus hijacks to support its effective replication or evade cellular immune responses are largely uncharacterized. We have previously demonstrated tremendous cell-to-cell heterogeneity in viral RNA (vRNA) and cellular transcript levels during flaviviral infection using a novel virus-inclusive single-cell RNA-Seq approach. Here, we used this unbiased, genome-wide approach to simultaneously profile the host transcriptome and vRNA in thousands of single cells during infection of human astrocytes with the live-attenuated vaccine strain of VEEV (TC-83). Host transcription was profoundly suppressed, yet “superproducer cells” with extremely high vRNA abundance emerged during the first viral life cycle and demonstrated an altered transcriptome relative to both uninfected cells and cells with high vRNA abundance harvested at later time points. Additionally, cells with increased structural-to-nonstructural transcript ratio exhibited upregulation of intracellular membrane trafficking genes at later time points. Loss- and gain-of-function experiments confirmed pro- and antiviral activities in both vaccine and virulent VEEV infections among the products of transcripts that positively or negatively correlated with vRNA abundance, respectively. Lastly, comparison with single cell transcriptomic data from other viruses highlighted common and unique pathways perturbed by infection across evolutionary scales. This study provides a high-resolution characterization of the VEEV (TC-83)-host interplay, identifies candidate targets for antivirals, and establishes a comparative single-cell approach to study the evolution of virus-host interactions. Little is known about the host response to Venezuelan Equine Encephalitis Virus (VEEV) and the cellular factors this alphavirus hijacks to support effective replication or evade cellular immune responses. Monitoring dynamics of host and viral RNA (vRNA) during viral infection at a single-cell level can provide insight into the virus-host interplay at a high resolution. Here, a single-cell RNA sequencing technology that detects host and viral RNA was used to investigate the interactions between TC-83, the vaccine strain of VEEV, and the human host during the course of infection of U-87 MG cells (human astrocytoma). Virus abundance and host transcriptome were heterogeneous across cells from the same culture. Subsets of differentially expressed genes, positively or negatively correlating with vRNA abundance, were identified and subsequently in vitro validated as candidate proviral and antiviral factors, respectively, in TC-83 and/or virulent VEEV infections. In the first replication cycle, “superproducer” cells exhibited rapid increase in vRNA abundance and unique gene expression patterns. At later time points, cells with increased structural-to-nonstructural transcript ratio demonstrated upregulation of intracellular membrane trafficking genes. Lastly, comparing the VEEV dataset with published datasets on other RNA viruses revealed unique and overlapping responses across viral clades. Overall, this study improves the understanding of VEEV-host interactions, reveals candidate targets for antiviral approaches, and establishes a comparative single-cell approach to study the evolution of virus-host interactions.
Collapse
|