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Wickenhagen A, van Tol S, Munster V. Molecular determinants of cross-species transmission in emerging viral infections. Microbiol Mol Biol Rev 2024:e0000123. [PMID: 38912755 DOI: 10.1128/mmbr.00001-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024] Open
Abstract
SUMMARYSeveral examples of high-impact cross-species transmission of newly emerging or re-emerging bat-borne viruses, such as Sudan virus, Nipah virus, and severe acute respiratory syndrome coronavirus 2, have occurred in the past decades. Recent advancements in next-generation sequencing have strengthened ongoing efforts to catalog the global virome, in particular from the multitude of different bat species. However, functional characterization of these novel viruses and virus sequences is typically limited with regard to assessment of their cross-species potential. Our understanding of the intricate interplay between virus and host underlying successful cross-species transmission has focused on the basic mechanisms of entry and replication, as well as the importance of host innate immune responses. In this review, we discuss the various roles of the respective molecular mechanisms underlying cross-species transmission using different recent bat-borne viruses as examples. To delineate the crucial cellular and molecular steps underlying cross-species transmission, we propose a framework of overall characterization to improve our capacity to characterize viruses as benign, of interest, or of concern.
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Affiliation(s)
- Arthur Wickenhagen
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Sarah van Tol
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Vincent Munster
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
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2
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Fan P, Sun M, Zhang X, Zhang H, Liu Y, Yao Y, Li M, Fang T, Sun B, Chen Z, Chi X, Chen L, Peng C, Chen Z, Zhang G, Ren Y, Liu Z, Li Y, Li J, Li E, Guan W, Li S, Gong R, Zhang K, Yu C, Chiu S. A potent Henipavirus cross-neutralizing antibody reveals a dynamic fusion-triggering pattern of the G-tetramer. Nat Commun 2024; 15:4330. [PMID: 38773072 PMCID: PMC11109247 DOI: 10.1038/s41467-024-48601-w] [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: 03/08/2024] [Accepted: 05/06/2024] [Indexed: 05/23/2024] Open
Abstract
The Hendra and Nipah viruses (HNVs) are highly pathogenic pathogens without approved interventions for human use. In addition, the interaction pattern between the attachment (G) and fusion (F) glycoproteins required for virus entry remains unclear. Here, we isolate a panel of Macaca-derived G-specific antibodies that cross-neutralize HNVs via multiple mechanisms. The most potent antibody, 1E5, confers adequate protection against the Nipah virus challenge in female hamsters. Crystallography demonstrates that 1E5 has a highly similar binding pattern to the receptor. In cryo-electron microscopy studies, the tendency of 1E5 to bind to the upper or lower heads results in two distinct quaternary structures of G. Furthermore, we identify the extended outer loop β1S2-β1S3 of G and two pockets on the apical region of fusion (F) glycoprotein as the essential sites for G-F interactions. This work highlights promising drug candidates against HNVs and contributes deeper insights into the viruses.
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Grants
- the Defense Industrial Technology Development Program, Grant No. JCKY2020802B001
- the Ministry of Science and Technology of China,Grant No. 2022YFC2303700; the Fundamental Research Funds for the Central Universities, Grant No. WK9100000032
- Hubei Jiangxia Laboratory, Grant No. JXBS002
- the Ministry of Science and Technology of China,Grant No. 2022YFC2303700, Grant No. 2022YFA1302700; the Strategic Priority Research Program of the Chinese Academy of Sciences, Grant No. XDB0490000; the Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Grant No. QYPY20220019; the Fundamental Research Funds for the Central Universities, Grant No. WK9100000044
- the Strategic Priority Research Program of the Chinese Academy of Sciences,Grant No. XDB0490000
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Affiliation(s)
- Pengfei Fan
- Laboratory of Advanced Biotechnology, Institute of Biotechnology, Beijing, China.
| | - Mengmeng Sun
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Xinghai Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Huajun Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Yujiao Liu
- Laboratory of Advanced Biotechnology, Institute of Biotechnology, Beijing, China
| | - Yanfeng Yao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Ming Li
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Ting Fang
- Laboratory of Advanced Biotechnology, Institute of Biotechnology, Beijing, China
| | - Bingjie Sun
- Laboratory of Advanced Biotechnology, Institute of Biotechnology, Beijing, China
| | - Zhengshan Chen
- Laboratory of Advanced Biotechnology, Institute of Biotechnology, Beijing, China
| | - Xiangyang Chi
- Laboratory of Advanced Biotechnology, Institute of Biotechnology, Beijing, China
| | - Li Chen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Cheng Peng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Zhen Chen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Guanying Zhang
- Laboratory of Advanced Biotechnology, Institute of Biotechnology, Beijing, China
| | - Yi Ren
- Laboratory of Advanced Biotechnology, Institute of Biotechnology, Beijing, China
| | - Zixuan Liu
- Laboratory of Advanced Biotechnology, Institute of Biotechnology, Beijing, China
| | - Yaohui Li
- Laboratory of Advanced Biotechnology, Institute of Biotechnology, Beijing, China
| | - Jianmin Li
- Laboratory of Advanced Biotechnology, Institute of Biotechnology, Beijing, China
| | - Entao Li
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Wuxiang Guan
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Shanshan Li
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, MOE Key Laboratory for Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Department of Urology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Rui Gong
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.
| | - Kaiming Zhang
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, MOE Key Laboratory for Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
- Department of Urology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
| | - Changming Yu
- Laboratory of Advanced Biotechnology, Institute of Biotechnology, Beijing, China.
| | - Sandra Chiu
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
- Key Laboratory of Anhui Province for Emerging and Reemerging Infectious Diseases, Hefei, 230027, Anhui, China.
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3
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Wang C, Li M, Wang Y, Ding Q, Fan S, Lan J. Structural insights into the Langya virus attachment glycoprotein. Structure 2024:S0969-2126(24)00180-1. [PMID: 38815575 DOI: 10.1016/j.str.2024.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 03/23/2024] [Accepted: 05/03/2024] [Indexed: 06/01/2024]
Abstract
Langya virus (LayV) was recently detected in patients with acute pneumonic diseases in China. Genome alignment indicated that LayV is a type of zoonotic henipavirus (HNV) that might also infect domestic animals. Previous studies revealed that HNVs mainly use ephrin-B1, ephrin-B2, or ephrin-B3 as cell receptors and the attachment glycoprotein (G) is the host cell receptor-binding protein. However, the LayV receptor remains unknown. Here, we present the 2.77 Å crystal structure of the LayV G C-terminal domain (CTD). We show that the LayV G protein CTD possesses a similar architecture as the Mojiang virus (MojV) G protein but is markedly different from the Nipah virus (NiV), Hendra virus (HeV), and Cedar virus (CedV) G proteins. Surface plasmon resonance (SPR) experiments indicate that LayV G does not bind ephrin-B proteins. Steric hindrance may prevent interactions between LayV G and ephrin-B. Our data might facilitate drug development targeting LayV.
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Affiliation(s)
- Chenghai Wang
- School of Biomedical Sciences, Hunan University, Changsha, China
| | - Min Li
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yufan Wang
- School of Biomedical Sciences, Hunan University, Changsha, China
| | - Qiang Ding
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Shilong Fan
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.
| | - Jun Lan
- School of Biomedical Sciences, Hunan University, Changsha, China.
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4
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Li X, Fang Y, Huang X, Zhao Y, Wan C. A Luciferase Immunosorbent Assay Based on Attachment Glycoprotein for the Rapid and Easy Detection of Nipah Virus IgG Antibodies. Microorganisms 2024; 12:983. [PMID: 38792812 PMCID: PMC11124132 DOI: 10.3390/microorganisms12050983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/07/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
Nipah virus (NiV) is a virulent zoonotic disease whose natural host is the fruit bat (Pteropus medius), which can coexist with and transmit the virus. Due to its high pathogenicity, wide host range, and pandemic potential, establishing a sensitive, specific, and rapid diagnostic method for NiV is key to preventing and controlling its spread and any outbreaks. Here, we established a luciferase immunosorbent assay (LISA) based on the NiV attachment glycoprotein (G) to detect NiV-specific immunoglobulin G by expressing a fusion protein of nanoluciferase (NanoLuc) and the target antigen. Sensitivity analysis was performed and compared to an indirect enzyme-linked immunosorbent assay (ELISA), and specificity and cross-reactivity assessments were performed using NiV-positive horse serum and Ebola virus-, Crimean-Congo hemorrhagic fever virus-, and West Nile virus-positive horse sera. The optimal structural domain for NiV detection was located within amino acids 176-602 of the NiV G protein head domain. Moreover, the LISA showed at least fourfold more sensitivity than the indirect ELISA, and the cross-reactivity results suggested that the LISA had good specificity and was capable of detecting NiV-specific immunoglobulin G in both mouse and horse serum. In conclusion, the establishment of a rapid, simple NiV LISA using the G protein head domain provides a resource for NiV monitoring.
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Affiliation(s)
- Xinyue Li
- BSL-3 Laboratory, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China; (X.L.); (Y.F.); (X.H.)
| | - Yuting Fang
- BSL-3 Laboratory, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China; (X.L.); (Y.F.); (X.H.)
| | - Xinyi Huang
- BSL-3 Laboratory, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China; (X.L.); (Y.F.); (X.H.)
| | - Yongkun Zhao
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China
| | - Chengsong Wan
- BSL-3 Laboratory, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China; (X.L.); (Y.F.); (X.H.)
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5
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Albiheyri R, Ahmad V, Khan MI, Alzahrani FA, Jamal QMS. Investigating the Antiviral Properties of Nyctanthes arbor-tristis Linn against the Ebola, SARS-CoV-2, Nipah, and Chikungunya Viruses: A Computational Simulation Study. Pharmaceuticals (Basel) 2024; 17:581. [PMID: 38794151 PMCID: PMC11124395 DOI: 10.3390/ph17050581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/26/2024] Open
Abstract
Background: The hunt for naturally occurring antiviral compounds to combat viral infection was expedited when COVID-19 and Ebola spread rapidly. Phytochemicals from Nyctanthes arbor-tristis Linn were evaluated as significant inhibitors of these viruses. Methods: Computational tools and techniques were used to assess the binding pattern of phytochemicals from Nyctanthes arbor-tristis Linn to Ebola virus VP35, SARS-CoV-2 protease, Nipah virus glycoprotein, and chikungunya virus. Results: Virtual screening and AutoDock analysis revealed that arborside-C, beta amyrin, and beta-sitosterol exhibited a substantial binding affinity for specific viral targets. The arborside-C and beta-sitosterol molecules were shown to have binding energies of -8.65 and -9.11 kcal/mol, respectively, when interacting with the major protease. Simultaneously, the medication remdesivir exhibited a control value of -6.18 kcal/mol. The measured affinity of phytochemicals for the other investigated targets was -7.52 for beta-amyrin against Ebola and -6.33 kcal/mol for nicotiflorin against Nipah virus targets. Additional molecular dynamics simulation (MDS) conducted on the molecules with significant antiviral potential, specifically the beta-amyrin-VP35 complex showing a stable RMSD pattern, yielded encouraging outcomes. Conclusions: Arborside-C, beta-sitosterol, beta-amyrin, and nicotiflorin could be established as excellent natural antiviral compounds derived from Nyctanthes arbor-tristis Linn. The virus-suppressing phytochemicals in this plant make it a compelling target for both in vitro and in vivo research in the future.
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Affiliation(s)
- Raed Albiheyri
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Varish Ahmad
- Health Information Technology Department, The Applied College, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
- Centre for Artificial Intelligence in Precision Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Mohammad Imran Khan
- Research Center, King Faisal Specialist Hospital and Research Center, Jeddah 21499, Saudi Arabia;
| | - Faisal A. Alzahrani
- Department of Biochemistry, Faculty of Science, Embryonic Stem Cell Unit, King Fahad Center for Medical Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Qazi Mohammad Sajid Jamal
- Department of Health Informatics, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
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6
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Cui C, Hao P, Jin C, Xu W, Liu Y, Li L, Du S, Shang L, Jin X, Jin N, Wang J, Li C. Interaction of Nipah Virus F and G with the Cellular Protein Cortactin Discovered by a Proximity Interactome Assay. Int J Mol Sci 2024; 25:4112. [PMID: 38612921 PMCID: PMC11012870 DOI: 10.3390/ijms25074112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
Nipah virus (NiV) is a highly lethal zoonotic virus with a potential large-scale outbreak, which poses a great threat to world health and security. In order to explore more potential factors associated with NiV, a proximity labeling method was applied to investigate the F, G, and host protein interactions systematically. We screened 1996 and 1524 high-confidence host proteins that interacted with the NiV fusion (F) glycoprotein and attachment (G) glycoprotein in HEK293T cells by proximity labeling technology, and 863 of them interacted with both F and G. The results of GO and KEGG enrichment analysis showed that most of these host proteins were involved in cellular processes, molecular binding, endocytosis, tight junction, and other functions. Cytoscape software (v3.9.1) was used for visual analysis, and the results showed that Cortactin (CTTN), Serpine mRNA binding protein 1 (SERBP1), and stathmin 1 (STMN1) were the top 20 proteins and interacted with F and G, and were selected for further validation. We observed colocalization of F-CTTN, F-SERBP1, F-STMN1, G-CTTN, G-SERBP1, and G-STMN1 using confocal fluorescence microscopy, and the results showed that CTTN, SERBP1, and STMN1 overlapped with NiV F and NiV G in HEK293T cells. Further studies found that CTTN can significantly inhibit the infection of the Nipah pseudovirus (NiVpv) into host cells, while SERBP1 and STMN1 had no significant effect on pseudovirus infection. In addition, CTTN can also inhibit the infection of the Hendra pseudovirus (HeVpv) in 293T cells. In summary, this study revealed that the potential host proteins interacted with NiV F and G and demonstrated that CTTN could inhibit NiVpv and HeVpv infection, providing new evidence and targets for the study of drugs against these diseases.
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Affiliation(s)
- Chunmei Cui
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (C.C.); (P.H.); (W.X.); (L.L.); (S.D.); (N.J.)
- Preventive Veterinary Medicine Laboratory of Agricultural College, Yanbian University, Yanji 133000, China;
| | - Pengfei Hao
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (C.C.); (P.H.); (W.X.); (L.L.); (S.D.); (N.J.)
| | - Chaozhi Jin
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; (C.J.); (Y.L.); (L.S.)
| | - Wang Xu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (C.C.); (P.H.); (W.X.); (L.L.); (S.D.); (N.J.)
| | - Yuchen Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; (C.J.); (Y.L.); (L.S.)
| | - Letian Li
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (C.C.); (P.H.); (W.X.); (L.L.); (S.D.); (N.J.)
| | - Shouwen Du
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (C.C.); (P.H.); (W.X.); (L.L.); (S.D.); (N.J.)
| | - Limin Shang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; (C.J.); (Y.L.); (L.S.)
| | - Xin Jin
- Preventive Veterinary Medicine Laboratory of Agricultural College, Yanbian University, Yanji 133000, China;
| | - Ningyi Jin
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (C.C.); (P.H.); (W.X.); (L.L.); (S.D.); (N.J.)
| | - Jian Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; (C.J.); (Y.L.); (L.S.)
| | - Chang Li
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (C.C.); (P.H.); (W.X.); (L.L.); (S.D.); (N.J.)
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7
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Oguntuyo KY, Haas GD, Azarm KD, Stevens CS, Brambilla L, Kowdle SS, Avanzato VA, Pryce R, Freiberg AN, Bowden TA, Lee B. Structure-guided mutagenesis of Henipavirus receptor-binding proteins reveals molecular determinants of receptor usage and antibody-binding epitopes. J Virol 2024; 98:e0183823. [PMID: 38426726 PMCID: PMC10949843 DOI: 10.1128/jvi.01838-23] [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: 11/30/2023] [Accepted: 02/05/2024] [Indexed: 03/02/2024] Open
Abstract
Nipah virus (NiV) is a highly lethal, zoonotic Henipavirus (HNV) that causes respiratory and neurological signs and symptoms in humans. Similar to other paramyxoviruses, HNVs mediate entry into host cells through the concerted actions of two surface glycoproteins: a receptor-binding protein (RBP) that mediates attachment and a fusion glycoprotein (F) that triggers fusion in an RBP-dependent manner. NiV uses ephrin-B2 (EFNB2) and ephrin-B3 (EFNB3) as entry receptors. Ghana virus (GhV), a novel HNV identified in a Ghanaian bat, uses EFNB2 but not EFNB3. In this study, we employ a structure-informed approach to identify receptor-interfacing residues and systematically introduce GhV-RBP residues into a NiV-RBP backbone to uncover the molecular determinants of EFNB3 usage. We reveal two regions that severely impair EFNB3 binding by NiV-RBP and EFNB3-mediated entry by NiV pseudotyped viral particles. Further analyses uncovered two-point mutations (NiVN557SGhV and NiVY581TGhV) pivotal for this phenotype. Moreover, we identify NiV interaction with Y120 of EFNB3 as important for the usage of this receptor. Beyond these EFNB3-related findings, we reveal two domains that restrict GhV binding of EFNB2, confirm the HNV-head as an immunodominant target for polyclonal and monoclonal antibodies, and describe putative epitopes for GhV- and NiV-specific monoclonal antibodies. Cumulatively, the work presented here generates useful reagents and tools that shed insight to residues important for NiV usage of EFNB3, reveal regions critical for GhV binding of EFNB2, and describe putative HNV antibody-binding epitopes. IMPORTANCE Hendra virus and Nipah virus (NiV) are lethal, zoonotic Henipaviruses (HNVs) that cause respiratory and neurological clinical features in humans. Since their initial outbreaks in the 1990s, several novel HNVs have been discovered worldwide, including Ghana virus. Additionally, there is serological evidence of zoonotic transmission, lending way to concerns about future outbreaks. HNV infection of cells is mediated by the receptor-binding protein (RBP) and the Fusion protein (F). The work presented here identifies NiV RBP amino acids important for the usage of ephrin-B3 (EFNB3), a receptor highly expressed in neurons and predicted to be important for neurological clinical features caused by NiV. This study also characterizes epitopes recognized by antibodies against divergent HNV RBPs. Together, this sheds insight to amino acids critical for HNV receptor usage and antibody binding, which is valuable for future studies investigating determinants of viral pathogenesis and developing antibody therapies.
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Affiliation(s)
| | - Griffin D. Haas
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Kristopher D. Azarm
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Christian S. Stevens
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Luca Brambilla
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Shreyas S. Kowdle
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Victoria A. Avanzato
- Division of Structural Biology, Wellcome Center for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Rhys Pryce
- Division of Structural Biology, Wellcome Center for Human Genetics, University of Oxford, Oxford, United Kingdom
| | | | - Thomas A. Bowden
- Division of Structural Biology, Wellcome Center for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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8
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Guo Y, Wu S, Li W, Yang H, Shi T, Ju B, Zhang Z, Yan R. The cryo-EM structure of homotetrameric attachment glycoprotein from langya henipavirus. Nat Commun 2024; 15:812. [PMID: 38280880 PMCID: PMC10821904 DOI: 10.1038/s41467-024-45202-5] [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: 07/07/2023] [Accepted: 01/18/2024] [Indexed: 01/29/2024] Open
Abstract
Langya Henipavirus (LayV) infection is an emerging zoonotic disease that has been causing respiratory symptoms in China since 2019. For virus entry, LayV's genome encodes the fusion protein F and the attachment glycoprotein G. However, the structural and functional information regarding LayV-G remains unclear. In this study, we revealed that LayV-G cannot bind to the receptors found in other HNVs, such as ephrin B2/B3, and it shows different antigenicity from HeV-G and NiV-G. Furthermore, we determined the near full-length structure of LayV-G, which displays a distinct mushroom-shaped configuration, distinguishing it from other attachment glycoproteins of HNV. The stalk and transmembrane regions resemble the stem and root of mushroom and four downward-tilted head domains as mushroom cap potentially interact with the F protein and influence membrane fusion process. Our findings enhance the understanding of emerging HNVs that cause human diseases through zoonotic transmission and provide implication for LayV related vaccine development.
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Affiliation(s)
- Yingying Guo
- Department of Biochemistry, School of Medicine, Key University Laboratory of Metabolism and Health of Guangdong, Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, China.
| | - Songyue Wu
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, China
- The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Wenting Li
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, China
- The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Haonan Yang
- Department of Biochemistry, School of Medicine, Key University Laboratory of Metabolism and Health of Guangdong, Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, China
| | - Tianhao Shi
- Department of Biochemistry, School of Medicine, Key University Laboratory of Metabolism and Health of Guangdong, Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, China
| | - Bin Ju
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, China.
- The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, China.
| | - Zheng Zhang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, China.
- The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, China.
| | - Renhong Yan
- Department of Biochemistry, School of Medicine, Key University Laboratory of Metabolism and Health of Guangdong, Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, China.
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9
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May AJ, Acharya P. Structural Studies of Henipavirus Glycoproteins. Viruses 2024; 16:195. [PMID: 38399971 PMCID: PMC10892422 DOI: 10.3390/v16020195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 01/19/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
Henipaviruses are a genus of emerging pathogens that includes the highly virulent Nipah and Hendra viruses that cause reoccurring outbreaks of disease. Henipaviruses rely on two surface glycoproteins, known as the attachment and fusion proteins, to facilitate entry into host cells. As new and divergent members of the genus have been discovered and structurally characterized, key differences and similarities have been noted. This review surveys the available structural information on Henipavirus glycoproteins, complementing this with information from related biophysical and structural studies of the broader Paramyxoviridae family of which Henipaviruses are members. The process of viral entry is a primary focus for vaccine and drug development, and this review aims to identify critical knowledge gaps in our understanding of the mechanisms that drive Henipavirus fusion.
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Affiliation(s)
- Aaron J. May
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA
- Department of Biochemistry, Duke University, Durham, NC 27710, USA
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA
- Department of Biochemistry, Duke University, Durham, NC 27710, USA
- Department of Surgery, Duke University, Durham, NC 27710, USA
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10
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Hoque AF, Rahman MM, Lamia AS, Islam A, Klena JD, Satter SM, Epstein JH, Montgomery JM, Hossain ME, Shirin T, Jahid IK, Rahman MZ. In silico prediction of interaction between Nipah virus attachment glycoprotein and host cell receptors Ephrin-B2 and Ephrin-B3 in domestic and peridomestic mammals. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 116:105516. [PMID: 37924857 DOI: 10.1016/j.meegid.2023.105516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/11/2023] [Accepted: 10/18/2023] [Indexed: 11/06/2023]
Abstract
Nipah virus (NiV) is a lethal bat-borne zoonotic virus that causes mild to acute respiratory distress and neurological manifestations in humans with a high mortality rate. NiV transmission to humans occurs via consumption of bat-contaminated fruit and date palm sap (DPS), or through direct contact with infected individuals and livestock. Since NiV outbreaks were first reported in pigs from Malaysia and Singapore, non-neutralizing antibodies against NiV attachment Glycoprotein (G) have also been detected in a few domestic mammals. NiV infection is initiated after NiV G binds to the host cell receptors Ephrin-B2 and Ephrin-B3. In this study, we assessed the degree of NiV host tropism in domestic and peridomestic mammals commonly found in Bangladesh that may be crucial in the transmission of NiV by serving as intermediate hosts. We carried out a protein-protein docking analysis of NiV G complexes (n = 52) with Ephrin-B2 and B3 of 13 domestic and peridomestic species using bioinformatics tools. Protein models were generated by homology modelling and the structures were validated for model quality. The different protein-protein complexes in this study were stable, and their binding affinity (ΔG) scores ranged between -8.0 to -19.1 kcal/mol. NiV Bangladesh (NiV-B) strain displayed stronger binding to Ephrin receptors, especially with Ephrin-B3 than the NiV Malaysia (NiV-M) strain, correlating with the observed higher pathogenicity of NiV-B strains. From the docking result, we found that Ephrin receptors of domestic rat (R. norvegicus) had a higher binding affinity for NiV G, suggesting greater susceptibility to NiV infections compared to other study species. Investigations for NiV exposure to domestic/peridomestic animals will help us knowing more the possible role of rats and other animals as intermediate hosts of NiV and would improve future NiV outbreak control and prevention in humans and domestic animals.
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Affiliation(s)
- Ananya Ferdous Hoque
- Infectious Diseases Division (IDD), icddr,b, 68, Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka 1212, Bangladesh
| | - Md Mahfuzur Rahman
- Infectious Diseases Division (IDD), icddr,b, 68, Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka 1212, Bangladesh; Department of Microbiology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Ayeasha Siddika Lamia
- Infectious Diseases Division (IDD), icddr,b, 68, Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka 1212, Bangladesh
| | - Ariful Islam
- EcoHealth Alliance, 520 8th Ave Ste. 1200, New York, NY 10018, USA
| | - John D Klena
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, GA 30333, USA
| | - Syed Moinuddin Satter
- Infectious Diseases Division (IDD), icddr,b, 68, Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka 1212, Bangladesh
| | | | - Joel M Montgomery
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, GA 30333, USA
| | - Mohammad Enayet Hossain
- Infectious Diseases Division (IDD), icddr,b, 68, Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka 1212, Bangladesh
| | - Tahmina Shirin
- Institute of Epidemiology, Disease Control and Research (IEDCR), Mohakhali, Dhaka 1212, Bangladesh
| | - Iqbal Kabir Jahid
- Department of Microbiology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Mohammed Ziaur Rahman
- Infectious Diseases Division (IDD), icddr,b, 68, Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka 1212, Bangladesh.
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11
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Narayanan KK, Amaya M, Tsang N, Yin R, Jays A, Broder CC, Shukla D, Procko E. Sequence basis for selectivity of ephrin-B2 ligand for Eph receptors and pathogenic henipavirus G glycoproteins. J Virol 2023; 97:e0062123. [PMID: 37931130 PMCID: PMC10688352 DOI: 10.1128/jvi.00621-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 09/13/2023] [Indexed: 11/08/2023] Open
Abstract
IMPORTANCE Ephrin-B2 (EFNB2) is a ligand for six Eph receptors in humans and regulates multiple cell developmental and signaling processes. It also functions as the cell entry receptor for Nipah virus and Hendra virus, zoonotic viruses that can cause respiratory and/or neurological symptoms in humans with high mortality. Here, we investigate the sequence basis of EFNB2 specificity for binding the Nipah virus attachment G glycoprotein over Eph receptors. We then use this information to engineer EFNB2 as a soluble decoy receptor that specifically binds the attachment glycoproteins of the Nipah virus and other related henipaviruses to neutralize infection. These findings further mechanistic understanding of protein selectivity and may facilitate the development of diagnostics or therapeutics against henipavirus infection.
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Affiliation(s)
| | - Moushimi Amaya
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, Maryland, USA
| | - Natalie Tsang
- Department of Biochemistry, University of Illinois, Urbana, Illinois, USA
| | - Randy Yin
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Alka Jays
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Christopher C. Broder
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, Maryland, USA
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana, Illinois, USA
- Cancer Center at Illinois, University of Illinois, Urbana, Illinois, USA
| | - Erik Procko
- Department of Biochemistry, University of Illinois, Urbana, Illinois, USA
- Cancer Center at Illinois, University of Illinois, Urbana, Illinois, USA
- Cyrus Biotechnology, Seattle, Washington, USA
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12
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Oguntuyo KY, Haas GD, Azarm KD, Stevens CS, Brambilla L, Kowdle S, Avanzato VA, Pryce R, Freiberg AN, Bowden TA, Lee B. Structure guided mutagenesis of Henipavirus Receptor Binding Proteins reveals molecular determinants of receptor usage and antibody binding epitopes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.22.568281. [PMID: 38045373 PMCID: PMC10690272 DOI: 10.1101/2023.11.22.568281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Nipah virus (NiV) is a highly lethal, zoonotic henipavirus (HNV) that causes respiratory and neurological signs and symptoms in humans. Similar to other paramyxoviruses, HNVs mediate entry into host cells through the concerted actions of two surface glycoproteins: a receptor binding protein (RBP) that mediates attachment and a fusion glycoprotein (F) that triggers fusion in an RBP-dependent manner. NiV uses ephrin-B2 (EFNB2) and ephrin-B3 (EFNB3) as entry receptors. Ghana virus (GhV), a novel HNV identified in a Ghanaian bat, use EFNB2 but not EFNB3. In this study, we employ a structure-informed approach to identify receptor interfacing residues and systematically introduce GhV-RBP residues into a NiV-RBP backbone to uncover the molecular determinants of EFNB3 usage. We reveal two regions that severely impair EFNB3 binding by NiV-RBP and EFNB3-mediated entry by NiV pseudotyped viral particles. Further analyses uncovered two point mutations (NiVN557SGhV and NiVY581TGhV) pivotal for this phenotype. Moreover, we identify NiV interaction with Y120 of EFNB3 as important for usage of this receptor. Beyond these EFNB3-related findings, we reveal two domains that restrict GhV binding of EFNB2, identify the HNV-head as an immunodominant target for polyclonal and monoclonal antibodies, and describe putative epitopes for GhV and NiV-specific monoclonal antibodies. Cumulatively, the work presented here generates useful reagents and tools that shed insight to residues important for NiV usage of EFNB3, reveals regions critical for GhV binding of EFNB2, and describes putative HNV antibody binding epitopes.
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Affiliation(s)
- K Y Oguntuyo
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - G D Haas
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - K D Azarm
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - C S Stevens
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - L Brambilla
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - S Kowdle
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - V A Avanzato
- Division of Structural Biology, Wellcome Center for Human Genetics, University of Oxford, OX3 7BN Oxford, United Kingdom
| | - R Pryce
- Division of Structural Biology, Wellcome Center for Human Genetics, University of Oxford, OX3 7BN Oxford, United Kingdom
| | - A N Freiberg
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - T A Bowden
- Division of Structural Biology, Wellcome Center for Human Genetics, University of Oxford, OX3 7BN Oxford, United Kingdom
| | - B Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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13
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Debroy B, De A, Bhattacharya S, Pal K. In silico screening of herbal phytochemicals to develop a Rasayana for immunity against Nipah virus. J Ayurveda Integr Med 2023; 14:100825. [PMID: 38048723 PMCID: PMC10746367 DOI: 10.1016/j.jaim.2023.100825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 09/09/2023] [Accepted: 10/27/2023] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND The first emergence of the Nipah virus (NiV) in 1998 from Malaysia became a major concern when it came to light and resurfaced on different occasions thereafter. NiV is a bat-borne zoonotic and pleomorphic virus that causes severe infection in human and animal hosts. Studies revealed fruit bats are the major reservoirs as natural hosts and pigs as intermediate hosts for the spread of this infection. This became a major concern as the disease was characterized by high pathogenicity varying from 40% to 80% depending on its acuteness. Moreover, the solemnity lies in the fact that the infection transcends from being a mere mild illness to an acute respiratory infection leading to fatal encephalitis with a reportedly high mortality rate. Currently, there is no treatment or vaccine available against the NiV. Many antiviral drugs have been explored and developed but with limited efficacy. METHODOLOGY In search of high-affinity ayurvedic alternatives, we conducted a pan-proteome in silico exploration of the NiV proteins for their interaction with the best-suited phytoconstituents. The toxicity prediction of thirty phytochemicals based on their LD50 value identified thirteen potential candidates. Molecular docking studies of those thirteen phytochemicals with five important NiV proteins identified Tanshinone I as the potential compound with a high binding affinity. RESULTS The pharmacokinetics and pharmacodynamics studies also aided in determining the absorption, distribution, metabolism, excretion, and toxicity of the selected phytoconstituent. Interestingly, docking studies also revealed Rosmariquinone as a potent alternative to the antiviral drug Remdesivir binding the same pocket of RNA-dependent RNA polymerase of the NiV. A molecular dynamics simulation study of the surface glycoprotein of NiV against Tanshinone I showed a stable complex formation and significant allosteric changes in the protein structure, implying that these phytochemicals could be a natural alternative to synthetic drugs against NiV. CONCLUSION This study provides preliminary evidence based on in silico analysis that the herbal molecules showed an effect against NiV. However, it is essential to further evaluate the efficacy of this approach through cell-based experiments, organoid models, and eventually clinical trials.
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Affiliation(s)
- Bishal Debroy
- Department of Biological Sciences, School of Life Science and Biotechnology, Adamas University, Barasat-Barrackpore Road, Kolkata, West Bengal, 700126, India
| | - Arkajit De
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Barasat-Barrackpore Road, Kolkata, West Bengal, 700126, India
| | - Somdatta Bhattacharya
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Barasat-Barrackpore Road, Kolkata, West Bengal, 700126, India
| | - Kuntal Pal
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Barasat-Barrackpore Road, Kolkata, West Bengal, 700126, India; School of Biosciences and Technology (SBST), Vellore Institute Technology, Vellore, Tamil Nadu, 632014, India.
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14
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Stelfox AJ, Oguntuyo KY, Rissanen I, Harlos K, Rambo R, Lee B, Bowden TA. Crystal structure and solution state of the C-terminal head region of the narmovirus receptor binding protein. mBio 2023; 14:e0139123. [PMID: 37737607 PMCID: PMC10653815 DOI: 10.1128/mbio.01391-23] [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: 06/09/2023] [Accepted: 07/05/2023] [Indexed: 09/23/2023] Open
Abstract
IMPORTANCE Genetically diverse paramyxoviruses are united in their presentation of a receptor-binding protein (RBP), which works in concert with the fusion protein to facilitate host-cell entry. The C-terminal head region of the paramyxoviral RBP, a primary determinant of host-cell tropism and inter-species transmission potential, forms structurally distinct classes dependent upon protein and glycan receptor specificity. Here, we reveal the architecture of the C-terminal head region of the RBPs from Nariva virus (NarV) and Mossman virus (MosV), two archetypal rodent-borne paramyxoviruses within the recently established genus Narmovirus, family Paramyxoviridae. Our analysis reveals that while narmoviruses retain the general architectural features associated with paramyxoviral RBPs, namely, a six-bladed β-propeller fold, they lack the structural motifs associated with known receptor-mediated host-cell entry pathways. This investigation indicates that the RBPs of narmoviruses exhibit pathobiological features that are distinct from those of other paramyxoviruses.
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Affiliation(s)
- Alice J. Stelfox
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- European Molecular Biology Laboratory, Grenoble, France
| | | | - Ilona Rissanen
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland
| | - Karl Harlos
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Robert Rambo
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Oxford, United Kingdom
| | - Benhur Lee
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Thomas A. Bowden
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
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15
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Naeem I, Mateen RM, Sibtul Hassan S, Tariq A, Parveen R, Saqib MAN, Fareed MI, Hussain M, Afzal MS. In silico identification of potential drug-like molecules against G glycoprotein of Nipah virus by molecular docking, DFT studies, and molecular dynamic simulation. J Biomol Struct Dyn 2023; 41:7104-7118. [PMID: 36036362 DOI: 10.1080/07391102.2022.2115557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/16/2022] [Indexed: 10/15/2022]
Abstract
Nipah virus (NiV) is a novel zoonotic pathogen that belongs to the Paramyxovirus family. The pathogen has infected a number of people in countries like Bangladesh, India, Singapore, and Malaysia with high mortality rates. Although the NiV has been classified as a biosafety level four pathogen (BSL-4), there is no drug approved for treatment against it. In this study, the G glycoprotein of the NiV was chosen as an antiviral target. Based on ADMET criteria, BBB- and BBB + group compounds were screened out of the Gold & platinum Asinex library containing 211620 compounds. After careful evaluation, the selected ligands were then virtually screened to identify the potential inhibitors against the G glycoprotein of the NiV through molecular docking, density functional theory (DFT), and molecular dynamic (MD) simulation studies. In our study we identified 5-(1,3-Benzodioxol-5-yl)-2-[(3-fluorobenzyl)sulfanyl]-5,8-dihydropyrido[2,3-d]pyrimidine-4,7(1H,6H)-dione (from BBB- group) and 7,7-Dimethyl-1-(4-methylphenyl)-3-(4-morpholinylcarbonyl)-7,8-dihydro-2,5(1H,6H)-quinolinedione) (from BBB + group) as potential compounds for the prevention and treatment of NiV related diseases.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Iqra Naeem
- Department of Life Science, School of Science, University of Management and Technology (UMT), Lahore, Punjab, Pakistan
| | - Rana Muhammad Mateen
- Department of Life Science, School of Science, University of Management and Technology (UMT), Lahore, Punjab, Pakistan
- Center for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Syed Sibtul Hassan
- Department of Life Science, School of Science, University of Management and Technology (UMT), Lahore, Punjab, Pakistan
| | - Asma Tariq
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
| | - Rukhsana Parveen
- Center for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | | | - Muhammad Irfan Fareed
- Department of Life Science, School of Science, University of Management and Technology (UMT), Lahore, Punjab, Pakistan
| | - Mureed Hussain
- Department of Life Science, School of Science, University of Management and Technology (UMT), Lahore, Punjab, Pakistan
| | - Muhammad Sohail Afzal
- Department of Life Science, School of Science, University of Management and Technology (UMT), Lahore, Punjab, Pakistan
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16
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Huang X, Li Y, Li R, Wang S, Yang L, Wang S, Yin Y, Zai X, Zhang J, Xu J. Nipah virus attachment glycoprotein ectodomain delivered by type 5 adenovirus vector elicits broad immune response against NiV and HeV. Front Cell Infect Microbiol 2023; 13:1180344. [PMID: 37577376 PMCID: PMC10413271 DOI: 10.3389/fcimb.2023.1180344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 07/04/2023] [Indexed: 08/15/2023] Open
Abstract
Nipah virus (NiV) and Hendra virus (HeV) are newly emerging dangerous zoonotic pathogens of the Henipavirus genus of the Paramyxoviridae family. NiV and HeV (HNVs) which are transmitted by bats cause acute respiratory disease and fatal encephalitis in humans. To date, as there is a lack of antiviral drugs or effective antiviral therapies, the development of vaccines against those two viruses is of primary importance, and the immunogen design is crucial to the success of vaccines. In this study, the full-length protein (G), the ectodomain (Ge) and the head domain (Gs) of NiV attachment glycoprotein were delivered by the replication-defective type 5 adenovirus vector (Ad5) respectively, and the recombinant Ad5-NiV vaccine candidates (Ad5-NiVG, Ad5-NiVGe and Ad5-NiVGs) were constructed and their immunogenicity were evaluated in mice. The results showed that all the vaccine candidates stimulated specific humoral and cellular immune responses efficiently and rapidly against both NiV and HeV, and the Ad5-NiVGe elicited the strongest immune responses after a single-dose immunization. Furthermore, the potent conserved T-cell epitope DTLYFPAVGFL shared by NiV and HeV was identified in the study, which may provide valid information on the mechanism of HNVs-specific cellular immunity. In summary, this study demonstrates that the Ad5-NiVGe could be a potent vaccine candidate against HNVs by inducing robust humoral and cellular immune responses.
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Affiliation(s)
- Xiaoyan Huang
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yaohui Li
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Ruihua Li
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Shaoyan Wang
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Lu Yang
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Shuyi Wang
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Ying Yin
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Xiaodong Zai
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Jun Zhang
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Junjie Xu
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China
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17
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May AJ, Pothula KR, Janowska K, Acharya P. Structures of Langya Virus Fusion Protein Ectodomain in Pre- and Postfusion Conformation. J Virol 2023; 97:e0043323. [PMID: 37278642 PMCID: PMC10308951 DOI: 10.1128/jvi.00433-23] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 05/13/2023] [Indexed: 06/07/2023] Open
Abstract
Langya virus (LayV) is a paramyxovirus in the Henipavirus genus, closely related to the deadly Nipah (NiV) and Hendra (HeV) viruses, that was identified in August 2022 through disease surveillance following animal exposure in eastern China. Paramyxoviruses present two glycoproteins on their surface, known as attachment and fusion proteins, that mediate entry into cells and constitute the primary antigenic targets for immune response. Here, we determine cryo-electron microscopy (cryo-EM) structures of the uncleaved LayV fusion protein (F) ectodomain in pre- and postfusion conformations. The LayV-F protein exhibits pre- and postfusion architectures that, despite being highly conserved across paramyxoviruses, show differences in their surface properties, in particular at the apex of the prefusion trimer, that may contribute to antigenic variability. While dramatic conformational changes were visualized between the pre- and postfusion forms of the LayV-F protein, several domains remained invariant, held together by highly conserved disulfides. The LayV-F fusion peptide (FP) is buried within a highly conserved, hydrophobic interprotomer pocket in the prefusion state and is notably less flexible than the rest of the protein, highlighting its "spring-loaded" state and suggesting that the mechanism of pre-to-post transition must involve perturbations to the pocket and release of the fusion peptide. Together, these results offer a structural basis for how the Langya virus fusion protein compares to its Henipavirus relatives and propose a mechanism for the initial step of pre- to postfusion conversion that may apply more broadly to paramyxoviruses. IMPORTANCE The Henipavirus genus is quickly expanding into new animal hosts and geographic locations. This study compares the structure and antigenicity of the Langya virus fusion protein to other henipaviruses, which have important vaccine and therapeutic development implications. Furthermore, the study proposes a new mechanism to explain the early steps of the fusion initiation process that can be more broadly applied to the Paramyxoviridae family.
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Affiliation(s)
- Aaron J. May
- Duke Human Vaccine Institute, Durham, North Carolina, USA
- Duke University, Department of Biochemistry, Durham, North Carolina, USA
| | | | | | - Priyamvada Acharya
- Duke Human Vaccine Institute, Durham, North Carolina, USA
- Duke University, Department of Biochemistry, Durham, North Carolina, USA
- Duke University, Department of Surgery, Durham, North Carolina, USA
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18
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Saha N, Baek DS, Mendoza RP, Robev D, Xu Y, Goldgur Y, De La Cruz MJ, de Stanchina E, Janes PW, Xu K, Dimitrov DS, Nikolov DB. Fully human monoclonal antibody targeting activated ADAM10 on colorectal cancer cells. Biomed Pharmacother 2023; 161:114494. [PMID: 36917886 PMCID: PMC10499537 DOI: 10.1016/j.biopha.2023.114494] [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: 01/09/2023] [Revised: 02/27/2023] [Accepted: 03/07/2023] [Indexed: 03/14/2023] Open
Abstract
Metastasis and chemoresistance in colorectal cancer are mediated by certain poorly differentiated cancer cells, known as cancer stem cells, that are maintained by Notch downstream signaling initiated upon Notch cleavage by the metalloprotease ADAM10. It has been shown that ADAM10 overexpression correlates with aberrant signaling from Notch, erbBs, and other receptors, as well as a more aggressive metastatic phenotype, in a range of cancers including colon, gastric, prostate, breast, ovarian, uterine, and leukemia. ADAM10 inhibition, therefore, stands out as an important and new approach to deter the progression of advanced CRC. For targeting the ADAM10 substrate-binding region, which is located outside of the catalytic domain of the protease, we generated a human anti-ADAM10 monoclonal antibody named 1H5. Structural and functional characterization of 1H5 reveals that it binds to the substrate-binding cysteine-rich domain and recognizes an activated ADAM10 conformation present on tumor cells. The mAb inhibits Notch cleavage and proliferation of colon cancer cell lines in vitro and in mouse models. Consistent with its binding to activated ADAM10, the mAb augments the catalytic activity of ADAM10 towards small peptide substrates in vitro. Most importantly, in a mouse model of colon cancer, when administered in combination with the therapeutic agent Irinotecan, 1H5 causes highly effective tumor growth inhibition without any discernible toxicity effects. Our singular approach to target the ADAM10 substrate-binding region with therapeutic antibodies could overcome the shortcomings of previous intervention strategies of targeting the protease active site with small molecule inhibitors that exhibit musculoskeletal toxicity.
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Affiliation(s)
- Nayanendu Saha
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, United States.
| | - Du-San Baek
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Rachelle P Mendoza
- Department of Pathology, University of Chicago, Chicago, IL 60637, United States
| | - Dorothea Robev
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, United States
| | - Yan Xu
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH 43210, United States
| | - Yehuda Goldgur
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, United States
| | - M Jason De La Cruz
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, United States
| | - Elisa de Stanchina
- Antitumor Assessment Facility, Memorial Sloan Kettering Cancer Center, New York, NY 10065, United States
| | - Peter W Janes
- Tumour Targeting Program, Olivia Newton-John Cancer Research Institute and School of Cancer Medicine, La Trobe University, Heidelberg, Victoria 3084, Australia
| | - Kai Xu
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH 43210, United States; Department of Microbial Infection and Immunity, Ohio State University, Columbus, OH 43210, United States
| | - Dimiter S Dimitrov
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Dimitar B Nikolov
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, United States.
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19
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Narayanan KK, Amaya M, Tsang N, Yin R, Jays A, Broder CC, Shukla D, Procko E. The Sequence Basis for Selectivity of Ephrin-B2 Ligand for Eph Receptors and Pathogenic Henipavirus G Glycoproteins: Selective Ephrin-B2 Decoys for Nipah and Hendra Virus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.26.538420. [PMID: 37162958 PMCID: PMC10168364 DOI: 10.1101/2023.04.26.538420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Ephrin-B2 (EFNB2) is a ligand for six Eph receptors in humans and functions as a cell entry receptor for several henipaviruses including Nipah virus (NiV), a pathogenic zoonotic virus with pandemic potential. To understand the sequence basis of promiscuity for EFNB2 binding to the attachment glycoprotein of NiV (NiV-G) and Eph receptors, we performed deep mutagenesis on EFNB2 to identify mutations that enhance binding to NiV-G over EphB2, one of the highest affinity Eph receptors. The mutations highlight how different EFNB2 conformations are selected by NiV-G versus EphB2. Specificity mutations are enriched at the base of the G-H binding loop of EFNB2, especially surrounding a phenylalanine hinge upon which the G-H loop pivots, and at a phenylalanine hook that rotates away from the EFNB2 core to engage Eph receptors. One EFNB2 mutant, D62Q, possesses pan-specificity to the attachment glycoproteins of closely related henipaviruses and has markedly diminished binding to the six Eph receptors. However, EFNB2-D62Q has high residual binding to EphB3 and EphB4. A second deep mutational scan of EFNB2 identified combinatorial mutations to further enhance specificity to NiV-G. A triple mutant of soluble EFNB2, D62Q-Q130L-V167L, has minimal binding to Eph receptors but maintains binding, albeit reduced, to NiV-G. Soluble EFNB2 decoy receptors carrying the specificity mutations were potent neutralizers of chimeric henipaviruses. These findings demonstrate how specific residue changes at the shared binding interface of a promiscuous ligand (EFNB2) can influence selectivity for multiple receptors, and may also offer insight towards the development of henipavirus therapeutics and diagnostics.
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Affiliation(s)
| | - Moushimi Amaya
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda MD, USA
| | - Natalie Tsang
- Department of Biochemistry, University of Illinois, Urbana IL, USA
| | - Randy Yin
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda MD, USA
| | - Alka Jays
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda MD, USA
| | - Christopher C. Broder
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda MD, USA
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana, IL, USA
- Cancer Center at Illinois, University of Illinois, Urbana IL, USA
| | - Erik Procko
- Department of Biochemistry, University of Illinois, Urbana IL, USA
- Cancer Center at Illinois, University of Illinois, Urbana IL, USA
- Cyrus Biotechnology, Seattle WA, USA
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20
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Yan L, Sterling SL, Fusco DL, Chan YP, Xu K, Laing ED, Broder CC. Recombinant Soluble Henipavirus Glycoprotein Preparation. Methods Mol Biol 2023; 2682:33-58. [PMID: 37610572 DOI: 10.1007/978-1-0716-3283-3_3] [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] [Indexed: 08/24/2023]
Abstract
Henipaviruses possess two envelope glycoproteins, the attachment (G) and the fusion (F) proteins that mediate cellular entry and are the major targets of virus-neutralizing antibody responses. Recombinant expression technologies have been used to produce soluble G and F proteins (sG and sF) that retain native-like oligomeric conformations and epitopes, which are advantageous for the development and characterization of vaccines and antiviral antibody therapeutics. In addition to Hendra virus and Nipah virus tetrameric sG and trimeric sF production, we also describe the expression and purification of Cedar virus tetrameric sG and Ghana virus trimeric sF glycoproteins. These henipavirus glycoproteins were also used as immunizing antigens to generate monoclonal antibodies, and binding was demonstrated with a pan-henipavirus multiplex microsphere immunoassay.
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Affiliation(s)
- Lianying Yan
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD, USA
| | - Spencer L Sterling
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD, USA
| | - Deborah L Fusco
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD, USA
| | - Yee-Peng Chan
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD, USA
| | - Kai Xu
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
- Center for Retrovirus Research, The Ohio State University, Columbus, OH, USA
| | - Eric D Laing
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD, USA
| | - Christopher C Broder
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD, USA.
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21
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Glycoprotein attachment with host cell surface receptor ephrin B2 and B3 in mediating entry of nipah and hendra virus: a computational investigation. J CHEM SCI 2022; 134:114. [DOI: 10.1007/s12039-022-02110-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/23/2022] [Accepted: 10/13/2022] [Indexed: 11/25/2022]
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22
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Liew YJM, Ibrahim PAS, Ong HM, Chong CN, Tan CT, Schee JP, Gómez Román R, Cherian NG, Wong WF, Chang LY. The Immunobiology of Nipah Virus. Microorganisms 2022; 10:microorganisms10061162. [PMID: 35744680 PMCID: PMC9228579 DOI: 10.3390/microorganisms10061162] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/31/2022] [Accepted: 06/03/2022] [Indexed: 12/23/2022] Open
Abstract
Nipah virus (NiV) is a highly lethal zoonotic paramyxovirus that emerged in Malaysia in 1998. It is a human pathogen capable of causing severe respiratory infection and encephalitis. The natural reservoir of NiV, Pteropus fruit bats, remains a continuous virus source for future outbreaks, although infection in the bats is largely asymptomatic. NiV provokes serious disease in various mammalian species. In the recent human NiV outbreaks in Bangladesh and India, both bats-to-human and human-to-human transmissions have been observed. NiV has been demonstrated to interfere with the innate immune response via interferon type I signaling, promoting viral dissemination and preventing antiviral response. Studies of humoral immunity in infected NiV patients and animal models have shown that NiV-specific antibodies were produced upon infection and were protective. Studies on cellular immunity response to NiV infection in human and animal models also found that the adaptive immune response, specifically CD4+ and CD8+ T cells, was stimulated upon NiV infection. The experimental vaccines and therapeutic strategies developed have provided insights into the immunological requirements for the development of successful medical countermeasures against NiV. This review summarizes the current understanding of NiV pathogenesis and innate and adaptive immune responses induced upon infection.
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Affiliation(s)
- Yvonne Jing Mei Liew
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (Y.J.M.L.); (P.A.S.I.); (H.M.O.); (C.N.C.); (W.F.W.)
- Deputy Vice Chancellor’s Office (Research & Innovation), Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Puteri Ainaa S. Ibrahim
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (Y.J.M.L.); (P.A.S.I.); (H.M.O.); (C.N.C.); (W.F.W.)
| | - Hui Ming Ong
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (Y.J.M.L.); (P.A.S.I.); (H.M.O.); (C.N.C.); (W.F.W.)
| | - Chee Ning Chong
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (Y.J.M.L.); (P.A.S.I.); (H.M.O.); (C.N.C.); (W.F.W.)
| | - Chong Tin Tan
- Division of Neurology, Department of Medicine, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (C.T.T.); (J.P.S.)
| | - Jie Ping Schee
- Division of Neurology, Department of Medicine, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (C.T.T.); (J.P.S.)
| | - Raúl Gómez Román
- Vaccine Research and Development, Coalition for Epidemic Preparedness Innovation (CEPI), Askekroken 11, 0277 Oslo, Norway; (R.G.R.); (N.G.C.)
| | - Neil George Cherian
- Vaccine Research and Development, Coalition for Epidemic Preparedness Innovation (CEPI), Askekroken 11, 0277 Oslo, Norway; (R.G.R.); (N.G.C.)
| | - Won Fen Wong
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (Y.J.M.L.); (P.A.S.I.); (H.M.O.); (C.N.C.); (W.F.W.)
| | - Li-Yen Chang
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (Y.J.M.L.); (P.A.S.I.); (H.M.O.); (C.N.C.); (W.F.W.)
- Correspondence:
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23
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Wang Z, Dang HV, Amaya M, Xu Y, Yin R, Yan L, Hickey AC, Annand EJ, Horsburgh BA, Reid PA, Smith I, Eden JS, Xu K, Broder CC, Veesler D. Potent monoclonal antibody-mediated neutralization of a divergent Hendra virus variant. Proc Natl Acad Sci U S A 2022; 119:e2122769119. [PMID: 35617431 PMCID: PMC9295758 DOI: 10.1073/pnas.2122769119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 04/16/2022] [Indexed: 12/27/2022] Open
Abstract
Hendra virus (HeV) and Nipah virus (NiV) are deadly zoonotic Henipaviruses (HNVs) responsible for recurrent outbreaks in humans and domestic species of highly fatal (50 to 95%) disease. A HeV variant (HeV-g2) of unprecedented genetic divergence has been identified in two fatally diseased horses, and in two flying fox species in regions of Australia not previously considered at risk for HeV spillover. Given the HeV-g2 divergence from HeV while retaining equivalent pathogenicity and spillover potential, understanding receptor usage and antigenic properties is urgently required to guide One Health biosecurity. Here, we show that the HeV-g2 G glycoprotein shares a conserved receptor tropism with prototypic HeV and that a panel of monoclonal antibodies recognizing the G and F glycoproteins potently neutralizes HeV-g2– and HeV G/F–mediated entry into cells. We determined a crystal structure of the Fab fragment of the hAH1.3 antibody bound to the HeV G head domain, revealing an antigenic site associated with potent cross-neutralization of both HeV-g2 and HeV. Structure-guided formulation of a tetravalent monoclonal antibody (mAb) mixture, targeting four distinct G head antigenic sites, results in potent neutralization of HeV and HeV-g2 and delineates a path forward for implementing multivalent mAb combinations for postexposure treatment of HNV infections.
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Affiliation(s)
- Zhaoqian Wang
- Department of Biochemistry, University of Washington, Seattle, WA 98195
| | - Ha V. Dang
- Department of Biochemistry, University of Washington, Seattle, WA 98195
| | - Moushimi Amaya
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD 20814
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20814
| | - Yan Xu
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210
| | - Randy Yin
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD 20814
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20814
| | - Lianying Yan
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD 20814
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20814
| | - Andrew C. Hickey
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20814
- US Public Health Services Commissioned Corps, Rockville, MD 20852
| | - Edward J. Annand
- Sydney School of Veterinary Science, University of Sydney, Sydney, 2570 NSW, Australia
- Sydney Institute for Infectious Diseases, University of Sydney, Sydney, 2006 NSW, Australia
- Black Mountain Laboratories, Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Canberra, 2601 ACT, Australia
- Equine Veterinary and One Health Epidemiology, EquiEpiVet, Aireys Inlet, Surf Coast, 3231 VIC, Australia
| | - Bethany A. Horsburgh
- University of Sydney School of Medicine, Sydney, 2006 NSW, Australia
- Westmead Institute for Medical Research, Sydney, 2145 NSW, Australia
| | - Peter A. Reid
- Private Equine Veterinary Practice, Brisbane, 4034 QLD, Australia
| | - Ina Smith
- Black Mountain Laboratories, Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Canberra, 2601 ACT, Australia
| | - John-Sebastian Eden
- University of Sydney School of Medicine, Sydney, 2006 NSW, Australia
- Westmead Institute for Medical Research, Sydney, 2145 NSW, Australia
| | - Kai Xu
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210
| | - Christopher C. Broder
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD 20814
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195
- HHMI, University of Washington, Seattle, WA 98195
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24
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Lawrence P, Escudero-Pérez B. Henipavirus Immune Evasion and Pathogenesis Mechanisms: Lessons Learnt from Natural Infection and Animal Models. Viruses 2022; 14:v14050936. [PMID: 35632678 PMCID: PMC9146692 DOI: 10.3390/v14050936] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/27/2022] [Accepted: 04/27/2022] [Indexed: 02/01/2023] Open
Abstract
Nipah henipavirus (NiV) and Hendra henipavirus (HeV) are zoonotic emerging paramyxoviruses causing severe disease outbreaks in humans and livestock, mostly in Australia, India, Malaysia, Singapore and Bangladesh. Both are bat-borne viruses and in humans, their mortality rates can reach 60% in the case of HeV and 92% for NiV, thus being two of the deadliest viruses known for humans. Several factors, including a large cellular tropism and a wide zoonotic potential, con-tribute to their high pathogenicity. This review provides an overview of HeV and NiV pathogenicity mechanisms and provides a summary of their interactions with the immune systems of their different host species, including their natural hosts bats, spillover-hosts pigs, horses, and humans, as well as in experimental animal models. A better understanding of the interactions between henipaviruses and their hosts could facilitate the development of new therapeutic strategies and vaccine measures against these re-emerging viruses.
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Affiliation(s)
- Philip Lawrence
- Science and Humanities Confluence Research Centre (EA 1598), Catholic University of Lyon (UCLy), 69002 Lyon, France
- Correspondence: (P.L.); (B.E.-P.)
| | - Beatriz Escudero-Pérez
- WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
- German Centre for Infection Research (DZIF), Partner Site Hamburg-Luebeck-Borstel, 38124 Braunschweig, Germany
- Correspondence: (P.L.); (B.E.-P.)
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25
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Wang Z, Amaya M, Addetia A, Dang HV, Reggiano G, Yan L, Hickey AC, DiMaio F, Broder CC, Veesler D. Architecture and antigenicity of the Nipah virus attachment glycoprotein. Science 2022; 375:1373-1378. [PMID: 35239409 DOI: 10.1126/science.abm5561] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nipah virus (NiV) and Hendra virus (HeV) are zoonotic henipaviruses (HNVs) responsible for outbreaks of encephalitis and respiratory illness. The entry of HNVs into host cells requires the attachment (G) and fusion (F) glycoproteins, which are the main targets of antibody responses. To understand viral infection and host immunity, we determined a cryo-electron microscopy structure of the NiV G homotetrameric ectodomain in complex with the nAH1.3 broadly neutralizing antibody Fab fragment. We show that a cocktail of two nonoverlapping G-specific antibodies neutralizes NiV and HeV synergistically and limits the emergence of escape mutants. Analysis of polyclonal serum antibody responses elicited by vaccination of macaques with NiV G indicates that the receptor binding head domain is immunodominant. These results pave the way for implementing multipronged therapeutic strategies against these deadly pathogens.
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Affiliation(s)
- Zhaoqian Wang
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Moushimi Amaya
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD 20814, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20814, USA
| | - Amin Addetia
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Ha V Dang
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Gabriella Reggiano
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Lianying Yan
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD 20814, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20814, USA
| | - Andrew C Hickey
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD 20814, USA.,U.S. Public Health Services Commissioned Corps, Rockville, MD 20852, USA
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Christopher C Broder
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD 20814, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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26
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Loomis RJ, DiPiazza AT, Falcone S, Ruckwardt TJ, Morabito KM, Abiona OM, Chang LA, Caringal RT, Presnyak V, Narayanan E, Tsybovsky Y, Nair D, Hutchinson GB, Stewart-Jones GBE, Kueltzo LA, Himansu S, Mascola JR, Carfi A, Graham BS. Chimeric Fusion (F) and Attachment (G) Glycoprotein Antigen Delivery by mRNA as a Candidate Nipah Vaccine. Front Immunol 2021; 12:772864. [PMID: 34956199 PMCID: PMC8692728 DOI: 10.3389/fimmu.2021.772864] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 11/12/2021] [Indexed: 12/12/2022] Open
Abstract
Nipah virus (NiV) represents a significant pandemic threat with zoonotic transmission from bats-to-humans with almost annual regional outbreaks characterized by documented human-to-human transmission and high fatality rates. Currently, no vaccine against NiV has been approved. Structure-based design and protein engineering principles were applied to stabilize the fusion (F) protein in its prefusion trimeric conformation (pre-F) to improve expression and increase immunogenicity. We covalently linked the stabilized pre-F through trimerization domains at the C-terminus to three attachment protein (G) monomers, forming a chimeric design. These studies detailed here focus on mRNA delivery of NiV immunogens in mice, assessment of mRNA immunogen-specific design elements and their effects on humoral and cellular immunogenicity. The pre-F/G chimera elicited a strong neutralizing antibody response and a superior NiV-specific Tfh and other effector T cell response compared to G alone across both the mRNA and protein platforms. These findings enabled final candidate selection of pre-F/G Fd for clinical development.
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Affiliation(s)
- Rebecca J. Loomis
- Viral Pathogenesis Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States,*Correspondence: Barney S. Graham, ; Rebecca J. Loomis,
| | - Anthony T. DiPiazza
- Viral Pathogenesis Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | | | - Tracy J. Ruckwardt
- Viral Pathogenesis Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Kaitlyn M. Morabito
- Viral Pathogenesis Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Olubukola M. Abiona
- Viral Pathogenesis Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Lauren A. Chang
- Viral Pathogenesis Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Ria T. Caringal
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | | | | | - Yaroslav Tsybovsky
- Vaccine Research Center Electron Microscopy Unit, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Deepika Nair
- Viral Pathogenesis Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Geoffrey B. Hutchinson
- Viral Pathogenesis Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Guillaume B. E. Stewart-Jones
- Virology Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Lisa A. Kueltzo
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | | | - John R. Mascola
- Virology Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | | | - Barney S. Graham
- Viral Pathogenesis Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States,*Correspondence: Barney S. Graham, ; Rebecca J. Loomis,
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27
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Saha N, Xu K, Zhu Z, Robev D, Kalidindi T, Xu Y, Himanen J, de Stanchina E, Pillarsetty NVK, Dimitrov DS, Nikolov DB. Inhibitory monoclonal antibody targeting ADAM17 expressed on cancer cells. Transl Oncol 2021; 15:101265. [PMID: 34768098 PMCID: PMC8592942 DOI: 10.1016/j.tranon.2021.101265] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/28/2021] [Accepted: 11/04/2021] [Indexed: 11/26/2022] Open
Abstract
A novel anti-ADAM17 monoclonal antibody, D8P1C1, has been developed. D8P1C1 inhibits the proteolysis of peptide substrates by ADAM17. D8P1C1 inhibits the proliferation of cancer cells and tumor growth inhibition in vivo. D8P1C1 preferentially recognizes ADAM17 on cancer cells. Negative stain EM analysis reveals that D8P1C1 binds to the ADAM17 protease domain.
ADAM17 is upregulated in many cancers and in turn activates signaling pathways, including EGFR/ErbB, as well as those underlying resistance to targeted anti-EGFR therapies. Due to its central role in oncogenic pathways and drug resistance mechanisms, specific and efficacious monoclonal antibodies against ADAM17 could be useful for a broad patient population with solid tumors. Hence, we describe here an inhibitory anti-ADAM17 monoclonal antibody, named D8P1C1, that preferentially recognizes ADAM17 on cancer cells. D8P1C1 inhibits the catalytic activity of ADAM17 in a fluorescence-based peptide cleavage assay, as well as the proliferation of a range of cancer cell lines, including breast, ovarian, glioma, colon and the lung adenocarcinoma. In mouse models of triple-negative breast cancer and ovarian cancer, treatment with the mAb results in 78% and 45% tumor growth inhibition, respectively. Negative staining electron microscopy analysis of the ADAM17 ectodomain in complex with D8P1C1 reveals that the mAb binds the ADAM17 protease domain, consistent with its ability to inhibit the ADAM17 catalytic activity. Collectively, our results demonstrate the therapeutic potential of the D8P1C1 mAb to treat solid tumors.
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Affiliation(s)
- Nayanendu Saha
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, United States
| | - Kai Xu
- Department of Veterinary Bioscience, Ohio State University, Columbus, OH 43210, United States
| | - Zhongyu Zhu
- Lentigen, a Miltenyi Biotec Company, Gaithersburg, MD 20878, United States
| | - Dorothea Robev
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, United States
| | - Teja Kalidindi
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, United States
| | - Yan Xu
- Department of Veterinary Bioscience, Ohio State University, Columbus, OH 43210, United States
| | - Juha Himanen
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, United States
| | - Elisa de Stanchina
- Antitumor Assessment Facility, Memorial Sloan Kettering Cancer Center, New York, NY 10065, United States
| | | | - Dimiter S Dimitrov
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Dimitar B Nikolov
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, United States
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28
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Combinatorial F-G Immunogens as Nipah and Respiratory Syncytial Virus Vaccine Candidates. Viruses 2021; 13:v13101942. [PMID: 34696372 PMCID: PMC8537613 DOI: 10.3390/v13101942] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/10/2021] [Accepted: 09/21/2021] [Indexed: 01/21/2023] Open
Abstract
Nipah virus (NiV) and respiratory syncytial virus (RSV) possess two surface glycoproteins involved in cellular attachment and membrane fusion, both of which are potential targets for vaccines. The majority of vaccine development is focused on the attachment (G) protein of NiV, which is the immunodominant target. In contrast, the fusion (F) protein of RSV is the main target in vaccine development. Despite this, neutralising epitopes have been described in NiV F and RSV G, making them alternate targets for vaccine design. Through rational design, we have developed a vaccine strategy applicable to phylogenetically divergent NiV and RSV that comprises both the F and G proteins (FxG). In a mouse immunization model, we found that NiV FxG elicited an improved immune response capable of neutralising pseudotyped NiV and a NiV mutant that is able to escape neutralisation by two known F-specific antibodies. RSV FxG elicited an immune response against both F and G and was able to neutralise RSV; however, this was inferior to the immune response of F alone. Despite this, RSV FxG elicited a response against a known protective epitope within G that is conserved across RSV A and B subgroups, which may provide additional protection in vivo. We conclude that inclusion of F and G antigens within a single design provides a streamlined subunit vaccine strategy against both emerging and established pathogens, with the potential for broader protection against NiV.
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Yeo YY, Buchholz DW, Gamble A, Jager M, Aguilar HC. Headless Henipaviral Receptor Binding Glycoproteins Reveal Fusion Modulation by the Head/Stalk Interface and Post-receptor Binding Contributions of the Head Domain. J Virol 2021; 95:e0066621. [PMID: 34288734 PMCID: PMC8475510 DOI: 10.1128/jvi.00666-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/13/2021] [Indexed: 11/20/2022] Open
Abstract
Cedar virus (CedV) is a nonpathogenic member of the Henipavirus (HNV) genus of emerging viruses, which includes the deadly Nipah (NiV) and Hendra (HeV) viruses. CedV forms syncytia, a hallmark of henipaviral and paramyxoviral infections and pathogenicity. However, the intrinsic fusogenic capacity of CedV relative to NiV or HeV remains unquantified. HNV entry is mediated by concerted interactions between the attachment (G) and fusion (F) glycoproteins. Upon receptor binding by the HNV G head domain, a fusion-activating G stalk region is exposed and triggers F to undergo a conformational cascade that leads to viral entry or cell-cell fusion. Here, we demonstrate quantitatively that CedV is inherently significantly less fusogenic than NiV at equivalent G and F cell surface expression levels. We then generated and tested six headless CedV G mutants of distinct C-terminal stalk lengths, surprisingly revealing highly hyperfusogenic cell-cell fusion phenotypes 3- to 4-fold greater than wild-type CedV levels. Additionally, similarly to NiV, a headless HeV G mutant yielded a less pronounced hyperfusogenic phenotype compared to wild-type HeV. Further, coimmunoprecipitation and cell-cell fusion assays revealed heterotypic NiV/CedV functional G/F bidentate interactions, as well as evidence of HNV G head domain involvement beyond receptor binding or G stalk exposure. All evidence points to the G head/stalk junction being key to modulating HNV fusogenicity, supporting the notion that head domains play several distinct and central roles in modulating stalk domain fusion promotion. Further, this study exemplifies how CedV may help elucidate important mechanistic underpinnings of HNV entry and pathogenicity. IMPORTANCE The Henipavirus genus in the Paramyxoviridae family includes the zoonotic Nipah (NiV) and Hendra (HeV) viruses. NiV and HeV infections often cause fatal encephalitis and pneumonia, but no vaccines or therapeutics are currently approved for human use. Upon viral entry, Henipavirus infections yield the formation of multinucleated cells (syncytia). Viral entry and cell-cell fusion are mediated by the attachment (G) and fusion (F) glycoproteins. Cedar virus (CedV), a nonpathogenic henipavirus, may be a useful tool to gain knowledge on henipaviral pathogenicity. Here, using homotypic and heterotypic full-length and headless CedV, NiV, and HeV G/F combinations, we discovered that CedV G/F are significantly less fusogenic than NiV or HeV G/F, and that the G head/stalk junction is key to modulating cell-cell fusion, refining the mechanism of henipaviral membrane fusion events. Our study exemplifies how CedV may be a useful tool to elucidate broader mechanistic understanding for the important henipaviruses.
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Affiliation(s)
- Yao Yu Yeo
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - David W. Buchholz
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Amandine Gamble
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, USA
| | - Mason Jager
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Hector C. Aguilar
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
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Abstract
Hendra virus (HeV) and Nipah virus (NiV) are bat-borne zoonotic para-myxoviruses identified in the mid- to late 1990s in outbreaks of severe disease in livestock and people in Australia and Malaysia, respectively. HeV repeatedly re-emerges in Australia while NiV continues to cause outbreaks in South Asia (Bangladesh and India), and these viruses have remained transboundary threats. In people and several mammalian species, HeV and NiV infections present as a severe systemic and often fatal neurologic and/or respiratory disease. NiV stands out as a potential pandemic threat because of its associated high case-fatality rates and capacity for human-to-human transmission. The development of effective vaccines, suitable for people and livestock, against HeV and NiV has been a research focus. Here, we review the progress made in NiV and HeV vaccine development, with an emphasis on those approaches that have been tested in established animal challenge models of NiV and HeV infection and disease.
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Affiliation(s)
- Moushimi Amaya
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, USA;
| | - Christopher C Broder
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, USA;
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Sendai Virus-Vectored Vaccines That Express Envelope Glycoproteins of Respiratory Viruses. Viruses 2021; 13:v13061023. [PMID: 34072332 PMCID: PMC8230104 DOI: 10.3390/v13061023] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/10/2021] [Accepted: 05/21/2021] [Indexed: 01/01/2023] Open
Abstract
Human respiratory syncytial virus (HRSV), human metapneumovirus (HMPV), and human parainfluenza viruses (HPIVs) are leading causes of respiratory disease in young children, the elderly, and individuals of all ages with immunosuppression. Vaccination strategies against these pneumoviruses and paramyxoviruses are vast in number, yet no licensed vaccines are available. Here, we review development of Sendai virus (SeV), a versatile pediatric vaccine that can (a) serve as a Jennerian vaccine against HPIV1, (b) serve as a recombinant vaccine against HRSV, HPIV2, HPIV3, and HMPV, (c) accommodate foreign genes for viral glycoproteins in multiple intergenic positions, (d) induce durable, mucosal, B-cell, and T-cell immune responses without enhanced immunopathology, (e) protect cotton rats, African green monkeys, and chimpanzees from infection, and (f) be formulated into a vaccine cocktail. Clinical phase I safety trials of SeV have been completed in adults and 3–6-year-old children. Clinical testing of SeVRSV, an HRSV fusion (F) glycoprotein gene recombinant, has also been completed in adults. Positive results from these studies, and collaborative efforts with the National Institutes of Health and the Serum Institute of India assist advanced development of SeV-based vaccines. Prospects are now good for vaccine successes in infants and consequent protection against serious viral disease.
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Dang HV, Cross RW, Borisevich V, Bornholdt ZA, West BR, Chan YP, Mire CE, Da Silva SC, Dimitrov AS, Yan L, Amaya M, Navaratnarajah CK, Zeitlin L, Geisbert TW, Broder CC, Veesler D. Broadly neutralizing antibody cocktails targeting Nipah virus and Hendra virus fusion glycoproteins. Nat Struct Mol Biol 2021; 28:426-434. [PMID: 33927387 DOI: 10.1038/s41594-021-00584-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 03/17/2021] [Indexed: 02/02/2023]
Abstract
Hendra virus (HeV) and Nipah virus (NiV) are henipaviruses (HNVs) causing respiratory illness and severe encephalitis in humans, with fatality rates of 50-100%. There are no licensed therapeutics or vaccines to protect humans. HeV and NiV use a receptor-binding glycoprotein (G) and a fusion glycoprotein (F) to enter host cells. HNV F and G are the main targets of the humoral immune response, and the presence of neutralizing antibodies is a correlate of protection against NiV and HeV in experimentally infected animals. We describe here two cross-reactive F-specific antibodies, 1F5 and 12B2, that neutralize NiV and HeV through inhibition of membrane fusion. Cryo-electron microscopy structures reveal that 1F5 and 12B2 recognize distinct prefusion-specific, conserved quaternary epitopes and lock F in its prefusion conformation. We provide proof-of-concept for using antibody cocktails for neutralizing NiV and HeV and define a roadmap for developing effective countermeasures against these highly pathogenic viruses.
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Affiliation(s)
- Ha V Dang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Robert W Cross
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA.,Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX, USA
| | - Viktoriya Borisevich
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | | | | | - Yee-Peng Chan
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD, USA
| | - Chad E Mire
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA.,Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX, USA
| | | | - Antony S Dimitrov
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD, USA
| | - Lianying Yan
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD, USA
| | - Moushimi Amaya
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD, USA
| | | | | | - Thomas W Geisbert
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA.,Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX, USA
| | - Christopher C Broder
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
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Novel Roles of the N1 Loop and N4 Alpha-Helical Region of the Nipah Virus Fusion Glycoprotein in Modulating Early and Late Steps of the Membrane Fusion Cascade. J Virol 2021; 95:JVI.01707-20. [PMID: 33568505 DOI: 10.1128/jvi.01707-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 01/27/2021] [Indexed: 11/20/2022] Open
Abstract
Nipah virus (NiV) is a zoonotic bat henipavirus in the family Paramyxoviridae NiV is deadly to humans, infecting host cells by direct fusion of the viral and host cell plasma membranes. This membrane fusion process is coordinated by the receptor-binding attachment (G) and fusion (F) glycoproteins. Upon G-receptor binding, F fuses membranes via a cascade that sequentially involves F-triggering, fusion pore formation, and viral or genome entry into cells. Using NiV as an important paramyxoviral model, we identified two novel regions in F that modulate the membrane fusion cascade. For paramyxoviruses and other viral families with class I fusion proteins, the heptad repeat 1 (HR1) and HR2 regions in the fusion protein prefusion conformation bind to form a six-helix bundle in the postfusion conformation. Here, structural comparisons between the F prefusion and postfusion conformations revealed that a short loop region (N1) undergoes dramatic spatial reorganization and a short alpha helix (N4) undergoes secondary structural changes. The roles of the N1 and N4 regions during the membrane fusion cascade, however, remain unknown for henipaviruses and paramyxoviruses. By performing alanine scanning mutagenesis and various functional analyses, we report that specific residues within these regions alter various steps in the membrane fusion cascade. While the N1 region affects early F-triggering, the N4 region affects F-triggering, F thermostability, and extensive fusion pore expansion during syncytium formation, also uncovering a link between F-G interactions and F-triggering. These novel mechanistic roles expand our understanding of henipaviral and paramyxoviral F-triggering, viral entry, and cell-cell fusion (syncytia), a pathognomonic feature of paramyxoviral infections.IMPORTANCE Henipaviruses infect bats, agriculturally important animals, and humans, with high mortality rates approaching ∼75% in humans. Known human outbreaks have been concentrated in Southeast Asia and Australia. Furthermore, about 20 new henipaviral species have been recently discovered in bats, with geographical spans in Asia, Africa, and South America. The development of antiviral therapeutics requires a thorough understanding of the mechanism of viral entry into host cells. In this study, we discovered novel roles of two regions within the fusion protein of the deadly henipavirus NiV. Such roles were in allowing viral entry into host cells and cell-cell fusion, a pathological hallmark of this and other paramyxoviruses. These novel roles were in the previously undescribed N1 and N4 regions within the fusion protein, modulating early and late steps of these important processes of viral infection and henipaviral disease. Notably, this knowledge may apply to other henipaviruses and more broadly to other paramyxoviruses.
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Functional Analysis of the Fusion and Attachment Glycoproteins of Mojiang Henipavirus. Viruses 2021; 13:v13030517. [PMID: 33809833 PMCID: PMC8004131 DOI: 10.3390/v13030517] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 03/16/2021] [Accepted: 03/17/2021] [Indexed: 01/30/2023] Open
Abstract
Mojiang virus (MojV) is the first henipavirus identified in a rodent and known only by sequence data, whereas all other henipaviruses have been isolated from bats (Hendra virus, Nipah virus, Cedar virus) or discovered by sequence data from material of bat origin (Ghana virus). Ephrin-B2 and -B3 are entry receptors for Hendra and Nipah viruses, but Cedar virus can utilize human ephrin-B1, -B2, -A2 and -A5 and mouse ephrin-A1. However, the entry receptor for MojV remains unknown, and its species tropism is not well characterized. Here, we utilized recombinant full-length and soluble forms of the MojV fusion (F) and attachment (G) glycoproteins in membrane fusion and receptor tropism studies. MojV F and G were functionally competent and mediated cell–cell fusion in primate and rattine cells, albeit with low levels and slow fusion kinetics. Although a relative instability of the pre-fusion conformation of a soluble form of MojV F was observed, MojV F displayed significantly greater fusion activity when heterotypically paired with Ghana virus G. An exhaustive investigation of A- and B-class ephrins indicated that none serve as a primary receptor for MojV. The MojV cell fusion phenotype is therefore likely the result of receptor restriction rather than functional defects in recombinant MojV F and G glycoproteins.
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Sehnal D, Svobodová R, Berka K, Rose AS, Burley SK, Velankar S, Koča J. High-performance macromolecular data delivery and visualization for the web. Acta Crystallogr D Struct Biol 2020; 76:1167-1173. [PMID: 33263322 PMCID: PMC7709201 DOI: 10.1107/s2059798320014515] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/01/2020] [Indexed: 11/11/2022] Open
Abstract
Biomacromolecular structural data make up a vital and crucial scientific resource that has grown not only in terms of its amount but also in its size and complexity. Furthermore, these data are accompanied by large and increasing amounts of experimental data. Additionally, the macromolecular data are enriched with value-added annotations describing their biological, physicochemical and structural properties. Today, the scientific community requires fast and fully interactive web visualization to exploit this complex structural information. This article provides a survey of the available cutting-edge web services that address this challenge. Specifically, it focuses on data-delivery problems, discusses the visualization of a single structure, including experimental data and annotations, and concludes with a focus on the results of molecular-dynamics simulations and the visualization of structural ensembles.
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Affiliation(s)
- David Sehnal
- CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL–EBI), Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom
| | - Radka Svobodová
- CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Karel Berka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, Šlechtitelů 241/27, 779 00 Olomouc, Czech Republic
| | - Alexander S. Rose
- Research Collaboratory for Structural Bioinformatics (RCSB), San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, San Diego, CA 92093-0743, USA
| | - Stephen K. Burley
- RCSB Protein Data Bank, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854-8076, USA
- Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, 195 Little Albany Street, New Brunswick, NJ 08903-2681, USA
- RCSB Protein Data Bank, San Diego Supercomputer Center and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0654, USA
| | - Sameer Velankar
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL–EBI), Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom
| | - Jaroslav Koča
- CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
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Tit-Oon P, Tharakaraman K, Artpradit C, Godavarthi A, Sungkeeree P, Sasisekharan V, Kerdwong J, Miller NL, Mahajan B, Khongmanee A, Ruchirawat M, Sasisekharan R, Fuangthong M. Prediction of the binding interface between monoclonal antibody m102.4 and Nipah attachment glycoprotein using structure-guided alanine scanning and computational docking. Sci Rep 2020; 10:18256. [PMID: 33106487 PMCID: PMC7588459 DOI: 10.1038/s41598-020-75056-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 09/21/2020] [Indexed: 11/08/2022] Open
Abstract
Nipah Virus (NiV) has been designated as a priority disease with an urgent need for therapeutic development by World Health Organization. The monoclonal antibody m102.4 binds to the immunodominant NiV receptor-binding glycoprotein (GP), and potently neutralizes NiV, indicating its potential as a therapeutic agent. Although the co-crystal structure of m102.3, an m102.4 derivative, in complex with the GP of the related Hendra Virus (HeV) has been solved, the structural interaction between m102.4 and NiV is uncharacterized. Herein, we used structure-guided alanine-scanning mutagenesis to map the functional epitope and paratope residues that govern the antigen-antibody interaction. Our results revealed that the binding of m102.4 is mediated predominantly by two residues in the HCDR3 region, which is unusually small for an antibody-antigen interaction. We performed computational docking to generate a structural model of m102.4-NiV interaction. Our model indicates that m102.4 targets the common hydrophobic central cavity and a hydrophilic rim on the GP, as observed for the m102.3-HeV co-crystal, albeit with Fv orientation differences. In summary, our study provides insight into the m102.4-NiV interaction, demonstrating that structure-guided alanine-scanning and computational modeling can serve as the starting point for additional antibody reengineering (e.g. affinity maturation) to generate potential therapeutic candidates.
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Affiliation(s)
- Phanthakarn Tit-Oon
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Kannan Tharakaraman
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | | | - Abhinav Godavarthi
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, 10210, Thailand
- Yale University, New Haven, CT, 06520, USA
| | - Pareenart Sungkeeree
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Varun Sasisekharan
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Jarunee Kerdwong
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Nathaniel Loren Miller
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Bhuvna Mahajan
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Amnart Khongmanee
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Mathuros Ruchirawat
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Ram Sasisekharan
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Mayuree Fuangthong
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, 10210, Thailand.
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Loomis RJ, Stewart-Jones GBE, Tsybovsky Y, Caringal RT, Morabito KM, McLellan JS, Chamberlain AL, Nugent ST, Hutchinson GB, Kueltzo LA, Mascola JR, Graham BS. Structure-Based Design of Nipah Virus Vaccines: A Generalizable Approach to Paramyxovirus Immunogen Development. Front Immunol 2020; 11:842. [PMID: 32595632 PMCID: PMC7300195 DOI: 10.3389/fimmu.2020.00842] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 04/14/2020] [Indexed: 12/18/2022] Open
Abstract
Licensed vaccines or therapeutics are rarely available for pathogens with epidemic or pandemic potential. Developing interventions for specific pathogens and defining generalizable approaches for related pathogens is a global priority and inherent to the UN Sustainable Development Goals. Nipah virus (NiV) poses a significant epidemic threat, and zoonotic transmission from bats-to-humans with high fatality rates occurs almost annually. Human-to-human transmission of NiV has been documented in recent outbreaks leading public health officials and government agencies to declare an urgent need for effective vaccines and therapeutics. Here, we evaluate NiV vaccine antigen design options including the fusion glycoprotein (F) and the major attachment glycoprotein (G). A stabilized prefusion F (pre-F), multimeric G constructs, and chimeric proteins containing both pre-F and G were developed as protein subunit candidate vaccines. The proteins were evaluated for antigenicity and structural integrity using kinetic binding assays, electron microscopy, and other biophysical properties. Immunogenicity of the vaccine antigens was evaluated in mice. The stabilized pre-F trimer and hexameric G immunogens both induced serum neutralizing activity in mice, while the post-F trimer immunogen did not elicit neutralizing activity. The pre-F trimer covalently linked to three G monomers (pre-F/G) induced potent neutralizing antibody activity, elicited responses to the greatest diversity of antigenic sites, and is the lead candidate for clinical development. The specific stabilizing mutations and immunogen designs utilized for NiV were successfully applied to other henipaviruses, supporting the concept of identifying generalizable solutions for prototype pathogens as an approach to pandemic preparedness.
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Affiliation(s)
- Rebecca J. Loomis
- Viral Pathogenesis Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Guillaume B. E. Stewart-Jones
- Virology Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Ria T. Caringal
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Kaitlyn M. Morabito
- Viral Pathogenesis Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Jason S. McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States
| | - Amy L. Chamberlain
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Sean T. Nugent
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Geoffrey B. Hutchinson
- Viral Pathogenesis Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Lisa A. Kueltzo
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - John R. Mascola
- Virology Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Barney S. Graham
- Viral Pathogenesis Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
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Fc-Based Recombinant Henipavirus Vaccines Elicit Broad Neutralizing Antibody Responses in Mice. Viruses 2020; 12:v12040480. [PMID: 32340278 PMCID: PMC7232446 DOI: 10.3390/v12040480] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 04/05/2020] [Accepted: 04/21/2020] [Indexed: 12/26/2022] Open
Abstract
The genus Henipavirus (HNVs) includes two fatal viruses, namely Nipah virus (NiV) and Hendra virus (HeV). Since 1994, NiV and HeV have been endemic to the Asia–Pacific region and responsible for more than 600 cases of infections. Two emerging HNVs, Ghana virus (GhV) and Mojiang virus (MojV), are speculated to be associated with unrecognized human diseases in Africa and China, respectively. Despite many efforts to develop vaccines against henipaviral diseases, there is presently no licensed human vaccine. As HNVs are highly pathogenic and diverse, it is necessary to develop universal vaccines to prevent future outbreaks. The attachment enveloped glycoprotein (G protein) of HNVs mediates HNV attachment to the host cell’s surface receptors. G proteins have been used as a protective antigen in many vaccine candidates for HNVs. We performed quantitative studies on the antibody responses elicited by the G proteins of NiV, HeV, GhV, and MojV. We found that the G proteins of NiV and HeV elicited only a limited cross-reactive antibody response. Further, there was no cross-protection between MojV, GhV, and highly pathogenic HNVs. We then constructed a bivalent vaccine where the G proteins of NiV and HeV were fused with the human IgG1 Fc domain. The immunogenicity of the bivalent vaccine was compared with that of monovalent vaccines. Our results revealed that the Fc-based bivalent vaccine elicited a potent antibody response against both NiV and HeV. We also constructed a tetravalent Fc heterodimer fusion protein that contains the G protein domains of four HNVs. Immunization with the tetravalent vaccine elicited broad antibody responses against NiV, HeV, GhV, and MojV in mice, indicating compatibility among the four antigens in the Fc-fusion protein. These data suggest that our novel bivalent and tetravalent Fc-fusion proteins may be efficient candidates to prevent HNV infection.
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Azarm KD, Lee B. Differential Features of Fusion Activation within the Paramyxoviridae. Viruses 2020; 12:v12020161. [PMID: 32019182 PMCID: PMC7077268 DOI: 10.3390/v12020161] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/25/2020] [Accepted: 01/29/2020] [Indexed: 12/13/2022] Open
Abstract
Paramyxovirus (PMV) entry requires the coordinated action of two envelope glycoproteins, the receptor binding protein (RBP) and fusion protein (F). The sequence of events that occurs during the PMV entry process is tightly regulated. This regulation ensures entry will only initiate when the virion is in the vicinity of a target cell membrane. Here, we review recent structural and mechanistic studies to delineate the entry features that are shared and distinct amongst the Paramyxoviridae. In general, we observe overarching distinctions between the protein-using RBPs and the sialic acid- (SA-) using RBPs, including how their stalk domains differentially trigger F. Moreover, through sequence comparisons, we identify greater structural and functional conservation amongst the PMV fusion proteins, as compared to the RBPs. When examining the relative contributions to sequence conservation of the globular head versus stalk domains of the RBP, we observe that, for the protein-using PMVs, the stalk domains exhibit higher conservation and find the opposite trend is true for SA-using PMVs. A better understanding of conserved and distinct features that govern the entry of protein-using versus SA-using PMVs will inform the rational design of broader spectrum therapeutics that impede this process.
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Navaratnarajah CK, Generous AR, Yousaf I, Cattaneo R. Receptor-mediated cell entry of paramyxoviruses: Mechanisms, and consequences for tropism and pathogenesis. J Biol Chem 2020; 295:2771-2786. [PMID: 31949044 DOI: 10.1074/jbc.rev119.009961] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Research in the last decade has uncovered many new paramyxoviruses, airborne agents that cause epidemic diseases in animals including humans. Most paramyxoviruses enter epithelial cells of the airway using sialic acid as a receptor and cause only mild disease. However, others cross the epithelial barrier and cause more severe disease. For some of these viruses, the host receptors have been identified, and the mechanisms of cell entry have been elucidated. The tetrameric attachment proteins of paramyxoviruses have vastly different binding affinities for their cognate receptors, which they contact through different binding surfaces. Nevertheless, all input signals are converted to the same output: conformational changes that trigger refolding of trimeric fusion proteins and membrane fusion. Experiments with selectively receptor-blinded viruses inoculated into their natural hosts have provided insights into tropism, identifying the cells and tissues that support growth and revealing the mechanisms of pathogenesis. These analyses also shed light on diabolically elegant mechanisms used by morbilliviruses, including the measles virus, to promote massive amplification within the host, followed by efficient aerosolization and rapid spread through host populations. In another paradigm of receptor-facilitated severe disease, henipaviruses, including Nipah and Hendra viruses, use different members of one protein family to cause zoonoses. Specific properties of different paramyxoviruses, like neurotoxicity and immunosuppression, are now understood in the light of receptor specificity. We propose that research on the specific receptors for several newly identified members of the Paramyxoviridae family that may not bind sialic acid is needed to anticipate their zoonotic potential and to generate effective vaccines and antiviral compounds.
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Affiliation(s)
| | - Alex R Generous
- Mayo Clinic Graduate School of Biomedical Sciences, Virology and Gene Therapy Track, Mayo Clinic, Rochester, Minnesota 55905
| | - Iris Yousaf
- Mayo Clinic Graduate School of Biomedical Sciences, Virology and Gene Therapy Track, Mayo Clinic, Rochester, Minnesota 55905
| | - Roberto Cattaneo
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota 55905.
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Pryce R, Azarm K, Rissanen I, Harlos K, Bowden TA, Lee B. A key region of molecular specificity orchestrates unique ephrin-B1 utilization by Cedar virus. Life Sci Alliance 2020; 3:e201900578. [PMID: 31862858 PMCID: PMC6925387 DOI: 10.26508/lsa.201900578] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/03/2019] [Accepted: 12/04/2019] [Indexed: 01/13/2023] Open
Abstract
The emergent zoonotic henipaviruses, Hendra, and Nipah are responsible for frequent and fatal disease outbreaks in domestic animals and humans. Specificity of henipavirus attachment glycoproteins (G) for highly species-conserved ephrin ligands underpins their broad host range and is associated with systemic and neurological disease pathologies. Here, we demonstrate that Cedar virus (CedV)-a related henipavirus that is ostensibly nonpathogenic-possesses an idiosyncratic entry receptor repertoire that includes the common henipaviral receptor, ephrin-B2, but, distinct from pathogenic henipaviruses, does not include ephrin-B3. Uniquely among known henipaviruses, CedV can use ephrin-B1 for cellular entry. Structural analyses of CedV-G reveal a key region of molecular specificity that directs ephrin-B1 utilization, while preserving a universal mode of ephrin-B2 recognition. The structural and functional insights presented uncover diversity within the known henipavirus receptor repertoire and suggest that only modest structural changes may be required to modulate receptor specificities within this group of lethal human pathogens.
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Affiliation(s)
- Rhys Pryce
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | | | - Ilona Rissanen
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
- Helsinki Institute for Life Science, University of Helsinki, Biocenter 3, Helsinki, Finland
| | - Karl Harlos
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Thomas A Bowden
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Benhur Lee
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Virus Network Center of Excellence, Center for Virology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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Sen N, Kanitkar TR, Roy AA, Soni N, Amritkar K, Supekar S, Nair S, Singh G, Madhusudhan MS. Predicting and designing therapeutics against the Nipah virus. PLoS Negl Trop Dis 2019; 13:e0007419. [PMID: 31830030 PMCID: PMC6907750 DOI: 10.1371/journal.pntd.0007419] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 11/04/2019] [Indexed: 11/28/2022] Open
Abstract
Despite Nipah virus outbreaks having high mortality rates (>70% in Southeast Asia), there are no licensed drugs against it. In this study, we have considered all 9 Nipah proteins as potential therapeutic targets and computationally identified 4 putative peptide inhibitors (against G, F and M proteins) and 146 small molecule inhibitors (against F, G, M, N, and P proteins). The computations include extensive homology/ab initio modeling, peptide design and small molecule docking. An important contribution of this study is the increased structural characterization of Nipah proteins by approximately 90% of what is deposited in the PDB. In addition, we have carried out molecular dynamics simulations on all the designed protein-peptide complexes and on 13 of the top shortlisted small molecule ligands to check for stability and to estimate binding strengths. Details, including atomic coordinates of all the proteins and their ligand bound complexes, can be accessed at http://cospi.iiserpune.ac.in/Nipah. Our strategy was to tackle the development of therapeutics on a proteome wide scale and the lead compounds identified could be attractive starting points for drug development. To counter the threat of drug resistance, we have analysed the sequences of the viral strains from different outbreaks, to check whether they would be sensitive to the binding of the proposed inhibitors.
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Affiliation(s)
- Neeladri Sen
- Indian Institute of Science Education and Research, Pune, India
| | | | | | - Neelesh Soni
- Indian Institute of Science Education and Research, Pune, India
| | | | - Shreyas Supekar
- Indian Institute of Science Education and Research, Pune, India
| | - Sanjana Nair
- Indian Institute of Science Education and Research, Pune, India
| | - Gulzar Singh
- Indian Institute of Science Education and Research, Pune, India
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Bhattacharya S, Dhar S, Banerjee A, Ray S. Detailed Molecular Biochemistry for Novel Therapeutic Design Against Nipah and Hendra Virus: A Systematic Review. Curr Mol Pharmacol 2019; 13:108-125. [PMID: 31657692 DOI: 10.2174/1874467212666191023123732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 10/13/2019] [Accepted: 10/15/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Nipah virus (NiV) and Hendra virus (HeV) of genus Henipavirus are the deadliest zoonotic viruses, which cause severe respiratory ailments and fatal encephalitis in humans and other susceptible animals. The fatality rate for these infections had been alarmingly high with no approved treatment available to date. Viral attachment and fusion with host cell membrane is essential for viral entry and is the most essential event of viral infection. Viral attachment is mediated by interaction of Henipavirus attachment glycoprotein (G) with the host cell receptor: Ephrin B2/B3, while viral fusion and endocytosis are mediated by the combined action of both viral glycoprotein (G) and fusion protein (F). CONCLUSION This review highlights the mechanism of viral attachment, fusion and also explains the basic mechanism and pathobiology of this infection in humans. The drugs and therapeutics used either experimentally or clinically against NiV and HeV infection have been documented and classified in detail. Some amino acid residues essential for the functionality of G and F proteins were also emphasized. Therapeutic designing to target and block these residues can serve as a promising approach in future drug development against NiV and HeV.
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Affiliation(s)
| | - Shreyeshi Dhar
- Amity Institute of Biotechnology, Amity University, Kolkata, India
| | - Arundhati Banerjee
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, Nadia, India
| | - Sujay Ray
- Amity Institute of Biotechnology, Amity University, Kolkata, India
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Structural and functional analyses reveal promiscuous and species specific use of ephrin receptors by Cedar virus. Proc Natl Acad Sci U S A 2019; 116:20707-20715. [PMID: 31548390 PMCID: PMC6789926 DOI: 10.1073/pnas.1911773116] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Cedar virus (CedV) is a bat-borne henipavirus related to Nipah virus (NiV) and Hendra virus (HeV), zoonotic agents of fatal human disease. CedV receptor-binding protein (G) shares only ∼30% sequence identity with those of NiV and HeV, although they can all use ephrin-B2 as an entry receptor. We demonstrate that CedV also enters cells through additional B- and A-class ephrins (ephrin-B1, ephrin-A2, and ephrin-A5) and report the crystal structure of the CedV G ectodomain alone and in complex with ephrin-B1 or ephrin-B2. The CedV G receptor-binding site is structurally distinct from other henipaviruses, underlying its capability to accommodate additional ephrin receptors. We also show that CedV can enter cells through mouse ephrin-A1 but not human ephrin-A1, which differ by 1 residue in the key contact region. This is evidence of species specific ephrin receptor usage by a henipavirus, and implicates additional ephrin receptors in potential zoonotic transmission.
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Duro N, Varma S. Role of Structural Fluctuations in Allosteric Stimulation of Paramyxovirus Hemagglutinin-Neuraminidase. Structure 2019; 27:1601-1611.e2. [DOI: 10.1016/j.str.2019.07.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 05/29/2019] [Accepted: 07/15/2019] [Indexed: 11/29/2022]
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An antibody against the F glycoprotein inhibits Nipah and Hendra virus infections. Nat Struct Mol Biol 2019; 26:980-987. [PMID: 31570878 PMCID: PMC6858553 DOI: 10.1038/s41594-019-0308-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 08/21/2019] [Indexed: 12/02/2022]
Abstract
Nipah virus (NiV) and Hendra virus (HeV) are zoonotic henipaviruses (HNVs) responsible for outbreaks of encephalitis and respiratory illness with fatality rates of 50–100%. No vaccines or licensed therapeutics currently exist to protect humans against NiV or HeV. HNVs enter host cells by fusing the viral and cellular membranes via the concerted action of the attachment (G) and fusion (F) glycoproteins, the main targets of the humoral immune response. Here, we describe the isolation and humanization of a potent monoclonal antibody cross-neutralizing NiV and HeV. Cryo-electron microscopy, triggering and fusion studies show the antibody binds to a prefusion-specific quaternary epitope, conserved in NiV F and HeV F glycoproteins, and prevents membrane fusion and viral entry. This work supports the importance of the HNV prefusion F conformation for eliciting a robust immune response and paves the way for using this antibody for prophylaxis and post-exposure therapy with NiV- and HeV-infected individuals. An antibody that recognizes the F glycoproteins from Nipah and Hendra viruses can neutralize both viruses and recognizes a quaternary epitope in the prefusion F trimer, preventing conformational changes required for fusion.
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Li K, Yan S, Wang N, He W, Guan H, He C, Wang Z, Lu M, He W, Ye R, Veit M, Su S. Emergence and adaptive evolution of Nipah virus. Transbound Emerg Dis 2019; 67:121-132. [PMID: 31408582 PMCID: PMC7168560 DOI: 10.1111/tbed.13330] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 07/24/2019] [Accepted: 07/27/2019] [Indexed: 12/11/2022]
Abstract
Since its first emergence in 1998 in Malaysia, Nipah virus (NiV) has become a great threat to domestic animals and humans. Sporadic outbreaks associated with human-to-human transmission caused hundreds of human fatalities. Here, we collected all available NiV sequences and combined phylogenetics, molecular selection, structural biology and receptor analysis to study the emergence and adaptive evolution of NiV. NiV can be divided into two main lineages including the Bangladesh and Malaysia lineages. We formly confirmed a significant association with geography which is probably the result of long-term evolution of NiV in local bat population. The two NiV lineages differ in many amino acids; one change in the fusion protein might be involved in its activation via binding to the G protein. We also identified adaptive and positively selected sites in many viral proteins. In the receptor-binding G protein, we found that sites 384, 386 and especially 498 of G protein might modulate receptor-binding affinity and thus contribute to the host jump from bats to humans via the adaption to bind the human ephrin-B2 receptor. We also found that site 1645 in the connector domain of L was positive selected and involved in adaptive evolution; this site might add methyl groups to the cap structure present at the 5'-end of the RNA and thus modulate its activity. This study provides insight to assist the design of early detection methods for NiV to assess its epidemic potential in humans.
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Affiliation(s)
- Kemang Li
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Shiyu Yan
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Ningning Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Wanting He
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Haifei Guan
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Chengxi He
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Zhixue Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Meng Lu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Wei He
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Rui Ye
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Michael Veit
- Institute for Virology, Center for Infection Medicine, Veterinary Faculty, Free University Berlin, Berlin, Germany
| | - Shuo Su
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
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Ropón-Palacios G, Chenet-Zuta ME, Olivos-Ramirez GE, Otazu K, Acurio-Saavedra J, Camps I. Potential novel inhibitors against emerging zoonotic pathogen Nipah virus: a virtual screening and molecular dynamics approach. J Biomol Struct Dyn 2019; 38:3225-3234. [DOI: 10.1080/07391102.2019.1655480] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Georcki Ropón-Palacios
- Laboratório de Modelagem Computacional – LaModel, Instituto de Ciências Exatas – ICEx, Universidade Federal de Alfenas – UNIFAL-MG, Alfenas, Minas Gerais, Brazil
| | - Manuel E. Chenet-Zuta
- Facultad de Psicología, Universidad Nacional Autónoma de México, Distrito Federal, México
| | - Gustavo E. Olivos-Ramirez
- Laboratorio de Evaluación de Los Recursos Acuáticos y Cultivo de Especies Auxiliares, Departamento Académico de Biología, Microbiología y Biotecnología, Facultad de Ciencias, Universidad Nacional Del Santa, Nuevo Chimbote, Perú
| | - Kewin Otazu
- Facultad de Ciencias Biológicas, Universidad Nacional Del Altiplano, Puno, Perú
| | - Jorge Acurio-Saavedra
- Laboratorio de Genética Molecular, Departamento de Biología, Facultad de Ciencias, Universidad Nacional de San Antonio Abad del Cusco, Cusco, Perú
| | - Ihosvany Camps
- Laboratório de Modelagem Computacional – LaModel, Instituto de Ciências Exatas – ICEx, Universidade Federal de Alfenas – UNIFAL-MG, Alfenas, Minas Gerais, Brazil
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Bae SE, Kim SS, Moon ST, Cho YD, Lee H, Lee JY, Shin HY, Lee HJ, Kim YB. Construction of the safe neutralizing assay system using pseudotyped Nipah virus and G protein-specific monoclonal antibody. Biochem Biophys Res Commun 2019; 513:781-786. [PMID: 30995971 DOI: 10.1016/j.bbrc.2019.03.212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 03/30/2019] [Indexed: 12/26/2022]
Abstract
Nipah virus (NiV) is a recently emerged paramyxovirus that causes acute respiratory illness and fatal encephalitis in a broad spectrum of vertebrates, including humans. Due to its high pathogenicity and mortality rates, NiV requires handling in biosafety level-4 (BSL-4) containment facilities and no effective vaccines or therapeutic agents are currently available. Since current diagnostic tests for detecting serum neutralizing antibodies against NiV mainly employ live viruses, establishment of more safe and robust alternative diagnostic methods is an essential medical requirement. Here, we have developed a pseudotyped NiV and closely related Hendra virus (HeV) expressing envelope attachment (G) and fusion (F) glycoproteins using the Moloney murine leukemia virus (MuLV) packaging system. We additionally generated polyclonal antibodies (pAbs) against NiV-G and HeV-G and assessed their neutralizing activities for potential utilization in the pseudovirus-based neutralization assay and further application in the serum diagnostic test. To enhance the specificity of neutralizing antibody and sensitivity of the serological diagnostic test, monoclonal antibodies (mAbs) against NiV-G were generated, and among which four out of six mAb clones showed significant reactivity. Specifically, the 7G9 clone displayed the highest sensitivity. The selected mAb clones showed no cross-reactivity with HeV-G and efficient neutralizing activities against pseudotyped NiV. These results validate the safety and specificity of neutralization assays against NiV and HeV and present a useful tool to design effective vaccines and serological diagnosis.
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Affiliation(s)
- Seong Eun Bae
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea; Department of Bio-industrial Technologies, Konkuk University, Seoul, 05029, Republic of Korea.
| | - Seong Su Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea; Department of Bio-industrial Technologies, Konkuk University, Seoul, 05029, Republic of Korea.
| | - Seong Tae Moon
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea; Department of Bio-industrial Technologies, Konkuk University, Seoul, 05029, Republic of Korea.
| | - Yeon Dong Cho
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea; Department of Bio-industrial Technologies, Konkuk University, Seoul, 05029, Republic of Korea.
| | - Hansaem Lee
- Division of Emerging Infectious Disease & Vector Research, Center for Infectious Diseases Research, Chungbuk, 28159, Republic of Korea.
| | - Joo-Yeon Lee
- Division of Emerging Infectious Disease & Vector Research, Center for Infectious Diseases Research, Chungbuk, 28159, Republic of Korea.
| | - Ha Youn Shin
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea.
| | - Hee-Jung Lee
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea.
| | - Young Bong Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea; Department of Bio-industrial Technologies, Konkuk University, Seoul, 05029, Republic of Korea.
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van Beusekom B, Wezel N, Hekkelman ML, Perrakis A, Emsley P, Joosten RP. Building and rebuilding N-glycans in protein structure models. Acta Crystallogr D Struct Biol 2019; 75:416-425. [PMID: 30988258 PMCID: PMC6465985 DOI: 10.1107/s2059798319003875] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 03/20/2019] [Indexed: 01/16/2023] Open
Abstract
N-Glycosylation is one of the most common post-translational modifications and is implicated in, for example, protein folding and interaction with ligands and receptors. N-Glycosylation trees are complex structures of linked carbohydrate residues attached to asparagine residues. While carbohydrates are typically modeled in protein structures, they are often incomplete or have the wrong chemistry. Here, new tools are presented to automatically rebuild existing glycosylation trees, to extend them where possible, and to add new glycosylation trees if they are missing from the model. The method has been incorporated in the PDB-REDO pipeline and has been applied to build or rebuild 16 452 carbohydrate residues in 11 651 glycosylation trees in 4498 structure models, and is also available from the PDB-REDO web server. With better modeling of N-glycosylation, the biological function of this important modification can be better and more easily understood.
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Affiliation(s)
- Bart van Beusekom
- Department of Biochemistry, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Natasja Wezel
- Department of Biochemistry, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Maarten L. Hekkelman
- Department of Biochemistry, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Anastassis Perrakis
- Department of Biochemistry, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Paul Emsley
- MRC Laboratory for Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, England
| | - Robbie P. Joosten
- Department of Biochemistry, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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