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Zhao Z, Cao L, Sun Z, Liu W, Li X, Fang K, Shang X, Hu J, Chen H, Lou Z, Qian P. A Structure-Guided Genetic Modification Strategy: Developing Seneca Valley Virus Therapy against Nonsensitive Nonsmall Cell Lung Carcinoma. J Virol 2023; 97:e0045923. [PMID: 37097154 PMCID: PMC10231241 DOI: 10.1128/jvi.00459-23] [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: 03/30/2023] [Accepted: 04/03/2023] [Indexed: 04/26/2023] Open
Abstract
Numerous studies have illustrated that the Seneca Valley virus (SVV) shows sufficient oncolytic efficacy targeting small cell lung cancer (SCLC). However, the therapeutics of nonsmall cell lung carcinoma (NSCLC, accounts for 85% of lung cancer cases) using oncolytic virus have been resisting due to the filtration of neutralizing antibody and limited reproduction capacity. Here, we employed structural biology and reverse genetics to optimize novel oncolytic SVV mutants (viral receptor-associated mutant SVV-S177A and viral antigenic peptide-related variant SVV-S177A/P60S) with increased infectivity and lower immunogenicity. The results of the NSCLC-bearing athymic mouse model demonstrated that wild-type (wt) SVV-HB extended the median overall survival (mOS) from 11 days in the PBS group to 19 days. Notably, the newly discovered mutations significantly (P < 0.001) prolonged the mOS from 11 days in the control cohort to 23 days in the SVV-S177A cohort and the SVV-S177A/P60S cohort. Taken together, we present a structure-guided genetic modification strategy for oncolytic SVV optimization and provide a candidate for developing oncolytic viral therapy against nonsensitive NSCLC. IMPORTANCE Nonsmall cell lung cancer (NSCLC) accounts for approximately 85% of lung cancer cases (more than 1.85 million cases with 1.48 million deaths in 2020). In the present study, two novel oncolytic SVV mutants modified based on structural biology and reverse genetics (viral receptor-associated mutant SVV-S177A and viral antigenic peptide-related mutant SVV-S177A/P60S) with increased infectivity or lower immunogenicity significantly (P < 0.001) prolonged the mOS from 11 days in the control cohort to 23 days in the SVV-S177A cohort and the SVV-S177A/P60S cohort in the NSCLC-bearing athymic mouse model, which may provide the direction for modifying SVV to improve the effect of oncolysis.
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Affiliation(s)
- Zekai Zhao
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Lin Cao
- Ministry of Education Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Response, College of Life Sciences, and State Key Laboratory of Medicinal Chemical Biology Nankai University, Tianjin, China
| | - Zixian Sun
- Ministry of Education Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China
- Department of Basic Research, Guangzhou Laboratory, Guangzhou, China
| | - Wenqiang Liu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xiangmin Li
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Kui Fang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xianfei Shang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Junjie Hu
- Hubei Colorectal Cancer Clinical Research Center, Hubei Cancer Hospital, Wuhan, China
| | - Huanchun Chen
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zhiyong Lou
- Ministry of Education Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China
| | - Ping Qian
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
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Matsumoto S, Ishida S, Terayama K, Okuno Y. Quantitative analysis of protein dynamics using a deep learning technique combined with experimental cryo-EM density data and MD simulations. Biophys Physicobiol 2023; 20:e200022. [PMID: 38496243 PMCID: PMC10941960 DOI: 10.2142/biophysico.bppb-v20.0022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 05/12/2023] [Indexed: 03/19/2024] Open
Abstract
Protein functions associated with biological activity are precisely regulated by both tertiary structure and dynamic behavior. Thus, elucidating the high-resolution structures and quantitative information on in-solution dynamics is essential for understanding the molecular mechanisms. The main experimental approaches for determining tertiary structures include nuclear magnetic resonance (NMR), X-ray crystallography, and cryogenic electron microscopy (cryo-EM). Among these procedures, recent remarkable advances in the hardware and analytical techniques of cryo-EM have increasingly determined novel atomic structures of macromolecules, especially those with large molecular weights and complex assemblies. In addition to these experimental approaches, deep learning techniques, such as AlphaFold 2, accurately predict structures from amino acid sequences, accelerating structural biology research. Meanwhile, the quantitative analyses of the protein dynamics are conducted using experimental approaches, such as NMR and hydrogen-deuterium mass spectrometry, and computational approaches, such as molecular dynamics (MD) simulations. Although these procedures can quantitatively explore dynamic behavior at high resolution, the fundamental difficulties, such as signal crowding and high computational cost, greatly hinder their application to large and complex biological macromolecules. In recent years, machine learning techniques, especially deep learning techniques, have been actively applied to structural data to identify features that are difficult for humans to recognize from big data. Here, we review our approach to accurately estimate dynamic properties associated with local fluctuations from three-dimensional cryo-EM density data using a deep learning technique combined with MD simulations.
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Affiliation(s)
| | - Shoichi Ishida
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan
| | - Kei Terayama
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Center for Computational Science, Kobe, Hyogo 650-0047, Japan
| | - Yasuhshi Okuno
- Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
- RIKEN Center for Computational Science, Kobe, Hyogo 650-0047, Japan
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Shen M, Ding P, Luan G, Du T, Deng S. The antiviral activity of a small molecule drug targeting the NSP1-ribosome complex against Omicron, especially in elderly patients. Front Cell Infect Microbiol 2023; 13:1141274. [PMID: 36960047 PMCID: PMC10027911 DOI: 10.3389/fcimb.2023.1141274] [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: 01/10/2023] [Accepted: 02/14/2023] [Indexed: 03/09/2023] Open
Abstract
Introduction With the emergence of SARS-CoV-2 mutant strains, especially the epidemic of Omicron, it continues to evolve to strengthen immune evasion. Omicron BQ. 1 and XBB pose a serious threat to the current COVID-19 vaccine (including bivalent mRNA vaccine for mutant strains) and COVID-19-positive survivors, and all current therapeutic monoclonal antibodies are ineffective against them. Older people, those with multimorbidity, and those with specific underlying health conditions remain at increased risk of COVID-19 hospitalization and death after the initial vaccine booster. However, small-molecule drugs for conserved targets remain effective and urgently needed. Methods The non-structural protein of SARS-CoV-2 non-structural protein 1(Nsp1) can bind to the host 40S ribosomal subunit and activate the nuclease to hydrolyze the host RNA, while the viral RNA is unaffected, thus hijacking the host system. First, the present study analyzed mutations in the Nsp1 protein and then constructed a maximum-likelihood phylogenetic tree. A virtual drug screening method based on the Nsp1 structure (Protein Data Bank ID: 7K5I) was constructed, 7495 compounds from three databases were collected for molecular docking and virtual screening, and the binding free energy was calculated by the MM/GBSA method. Results Our study shows that Nsp1 is relatively conserved and can be used as a comparatively fixed drug target and that therapies against Nsp1 will target all of these variants. Golvatinib, Gliquidone, and Dihydroergotamine were superior to other compounds in the crystal structure of binding conformation and free energy. All effectively interfered with Nsp1 binding to 40S protein, confirming the potential inhibitory effect of these three compounds on SARS-CoV-2. Discussion In particular, Golwatinib provides a candidate for treatment and prophylaxis in elderly patients with Omicjon, suggesting further evaluation of the anti-SARS-CoV-2 activity of these compounds in cell culture. Further studies are needed to determine the utility of this finding through prospective clinical trials and identify other meaningful drug combinations.
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Affiliation(s)
- Min Shen
- Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, Sichuan, China
- Vincent Mary School of Science and Technology, Assumption University, Bangkok, Thailand
| | - Ping Ding
- Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, Sichuan, China
| | - Guangxin Luan
- Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, Sichuan, China
| | - Ting Du
- Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, Sichuan, China
| | - Shanshan Deng
- Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, Sichuan, China
- *Correspondence: Shanshan Deng,
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Qiao J, Zhao C. Therapeutic effect of adenosylmethionine on viral hepatitis and related factors inducing diseas. Am J Transl Res 2021; 13:9485-9494. [PMID: 34540070 PMCID: PMC8430085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 02/01/2021] [Indexed: 06/13/2023]
Abstract
OBJECTIVE To analyze the therapeutic efficacy of adenosylmethionine on viral hepatitis and the related factors inducing disease. METHODS From May 2018 to April 2019, 137 patients with viral hepatitis who received treatment in our hospital were selected and assigned to two groups according to different treatment methods. In the control group (CG), 61 cases were treated with routine liver protection and enzyme reduction. In the research group, 76 cases were treated with adenosylmethionine on the basis of the CG. After therapy, the total response rate was analyzed in both groups, and the adverse reactions were observed during the treatment. The liver function indexes [albumin (ALB), alanine aminotransferase (ALT), glutamic acid transaminase (AST) and total bilirubin (TBIL)], liver fiber indicators [hyaluronic acid (HA), laminin (LN), type III procollagen (PCIII), type IV collagen (IV-C)], inflammatory factors [interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α)] were compared in both groups before and after therapy. ELISA was applied to detect inflammatory factors in both groups before and after treatment. Logistic analysis was applied to analyze the independent risk factors affecting the curative effect of patients with viral hepatitis. RESULTS After therapy, the total response rate of patients in RG was obviously higher than that in CG; The total incidence of adverse effects in RG was obviously lower than that in CG; The improvement of liver function indexes and liver fiber indicators in RG was better than that in CG; The expression of inflammatory factors in RG was obviously lower than that in CG. Logistic analysis revealed that patients' age (>40 years old), drinking history, family history, low improvement of hepatic function and hepatic fibrosis, high level of inflammatory cytokines and routine treatment were independent prognostic factors affecting patients with viral hepatitis. CONCLUSION Adenosylmethionine intervention can promote disease recovery, reduce inflammation level and improve liver function damage for patients with viral hepatitis.
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Affiliation(s)
- Jinggui Qiao
- Department of Gastroenterology, Xi'an Gaoxing Hospital Xi'an 710000, Shaanxi Province, China
| | - Congya Zhao
- Department of Gastroenterology, Xi'an Gaoxing Hospital Xi'an 710000, Shaanxi Province, China
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Abe H, Ushijima Y, Bikangui R, Ondo GN, Zadeh VR, Pemba CM, Mpingabo PI, Igasaki Y, de Vries SG, Grobusch MP, Loembe MM, Agnandji ST, Lell B, Yasuda J. First evidence for continuous circulation of hepatitis A virus subgenotype IIA in Central Africa. J Viral Hepat 2020; 27:1234-1242. [PMID: 32564517 PMCID: PMC7586949 DOI: 10.1111/jvh.13348] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 05/30/2020] [Accepted: 06/08/2020] [Indexed: 12/22/2022]
Abstract
Although a high seroprevalence of antibodies against hepatitis A virus (HAV) has been estimated in Central Africa, the current status of both HAV infections and seroprevalence of anti-HAV antibodies remains unclear due to a paucity of surveillance data available. We conducted a serological survey during 2015-2017 in Gabon, Central Africa, and confirmed a high seroprevalence of anti-HAV antibodies in all age groups. To identify the currently circulating HAV strains and to reveal the epidemiological and genetic characteristics of the virus, we conducted molecular surveillance in a total of 1007 patients presenting febrile illness. Through HAV detection and sequencing, we identified subgenotype IIA (HAV-IIA) infections in the country throughout the year. A significant prevalence trend emerged in the young child population, presenting several infection peaks which appeared to be unrelated to dry or rainy seasons. Whole-genome sequencing and phylogenetic analyses revealed local HAV-IIA evolutionary events in Central Africa, indicating the circulation of HAV-IIA strains of a region-specific lineage. Recombination analysis of complete genome sequences revealed potential recombination events in Gabonese HAV strains. Interestingly, Gabonese HAV-IIA possibly acquired the 5'-untranslated region (5'-UTR) of the rare subgenotype HAV-IIB in recent years, suggesting the present existence of HAV-IIB in Central Africa. These findings indicate a currently stable HAV-IIA circulation in Gabon, with a high risk of infections in children aged under 5 years. Our findings will enhance the understanding of the current status of HAV infections in Central Africa and provide new insight into the molecular epidemiology and evolution of HAV genotype II.
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Affiliation(s)
- Haruka Abe
- Department of Emerging Infectious DiseasesInstitute of Tropical Medicine (NEKKEN)Nagasaki UniversityNagasakiJapan
| | - Yuri Ushijima
- Department of Emerging Infectious DiseasesInstitute of Tropical Medicine (NEKKEN)Nagasaki UniversityNagasakiJapan
| | - Rodrigue Bikangui
- Centre de Recherches Médicales de LambarénéLambarénéGabon,Institute for Tropical MedicineUniversity of TübingenTübingenGermany
| | | | - Vahid R. Zadeh
- Department of Emerging Infectious DiseasesInstitute of Tropical Medicine (NEKKEN)Nagasaki UniversityNagasakiJapan,Graduate School of Biomedical SciencesNagasaki UniversityNagasakiJapan
| | - Christelle M. Pemba
- Department of Emerging Infectious DiseasesInstitute of Tropical Medicine (NEKKEN)Nagasaki UniversityNagasakiJapan,Graduate School of Biomedical SciencesNagasaki UniversityNagasakiJapan
| | - Patrick I. Mpingabo
- Department of Emerging Infectious DiseasesInstitute of Tropical Medicine (NEKKEN)Nagasaki UniversityNagasakiJapan,Graduate School of Biomedical SciencesNagasaki UniversityNagasakiJapan
| | - Yui Igasaki
- Department of Emerging Infectious DiseasesInstitute of Tropical Medicine (NEKKEN)Nagasaki UniversityNagasakiJapan
| | - Sophia G. de Vries
- Centre de Recherches Médicales de LambarénéLambarénéGabon,Division of Internal MedicineDepartment of Infectious DiseasesCenter of Tropical Medicine and Travel MedicineAmsterdam University Medical CentersUniversity of AmsterdamAmsterdamNetherlands
| | - Martin P. Grobusch
- Centre de Recherches Médicales de LambarénéLambarénéGabon,Institute for Tropical MedicineUniversity of TübingenTübingenGermany,Division of Internal MedicineDepartment of Infectious DiseasesCenter of Tropical Medicine and Travel MedicineAmsterdam University Medical CentersUniversity of AmsterdamAmsterdamNetherlands
| | | | - Selidji T. Agnandji
- Centre de Recherches Médicales de LambarénéLambarénéGabon,Institute for Tropical MedicineUniversity of TübingenTübingenGermany
| | - Bertrand Lell
- Centre de Recherches Médicales de LambarénéLambarénéGabon,Division of Infectious Diseases and Tropical MedicineMedical University of ViennaViennaAustria
| | - Jiro Yasuda
- Department of Emerging Infectious DiseasesInstitute of Tropical Medicine (NEKKEN)Nagasaki UniversityNagasakiJapan,Graduate School of Biomedical SciencesNagasaki UniversityNagasakiJapan,National Research Center for the Control and Prevention of Infectious Diseases (CCPID)Nagasaki UniversityNagasakiJapan
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7
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Wang K, Zhu L, Sun Y, Li M, Zhao X, Cui L, Zhang L, Gao GF, Zhai W, Zhu F, Rao Z, Wang X. Structures of Echovirus 30 in complex with its receptors inform a rational prediction for enterovirus receptor usage. Nat Commun 2020; 11:4421. [PMID: 32887891 PMCID: PMC7474057 DOI: 10.1038/s41467-020-18251-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 08/12/2020] [Indexed: 01/27/2023] Open
Abstract
Receptor usage that determines cell tropism and drives viral classification closely correlates with the virus structure. Enterovirus B (EV-B) consists of several subgroups according to receptor usage, among which echovirus 30 (E30), a leading causative agent for human aseptic meningitis, utilizes FcRn as an uncoating receptor. However, receptors for many EVs remain unknown. Here we analyzed the atomic structures of E30 mature virion, empty- and A-particles, which reveals serotype-specific epitopes and striking conformational differences between the subgroups within EV-Bs. Of these, the VP1 BC loop markedly distinguishes E30 from other EV-Bs, indicative of a role as a structural marker for EV-B. By obtaining cryo-electron microscopy structures of E30 in complex with its receptor FcRn and CD55 and comparing its homologs, we deciphered the underlying molecular basis for receptor recognition. Together with experimentally derived viral receptor identifications, we developed a structure-based in silico algorithm to inform a rational prediction for EV receptor usage. Echovirus 30 (E30) belongs to the Enterovirus-B group and causes aseptic meningitis in humans. Here, the authors present the cryo-EM structures of the E30 E-particle, A-particle and the mature virion, as well as structures of E30 in complex with its receptor FcRn and CD55, and furthermore they describe a structure-based algorithm that allows the prediction of EV receptor usage.
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Affiliation(s)
- Kang Wang
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,NHC Key Laboratories of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, 210009, China.,State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences and College of Pharmacy and Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, 300353, China
| | - Ling Zhu
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yao Sun
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Minhao Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin Zhao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lunbiao Cui
- NHC Key Laboratories of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, 210009, China
| | - Li Zhang
- NHC Key Laboratories of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, 210009, China
| | - George F Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Weiwei Zhai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Fengcai Zhu
- NHC Key Laboratories of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, 210009, China.
| | - Zihe Rao
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences and College of Pharmacy and Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, 300353, China
| | - Xiangxi Wang
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. .,State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences and College of Pharmacy and Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, 300353, China.
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Co-Occurrence of Hepatitis A Infection and Chronic Liver Disease. Int J Mol Sci 2020; 21:ijms21176384. [PMID: 32887515 PMCID: PMC7504211 DOI: 10.3390/ijms21176384] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 08/23/2020] [Accepted: 09/01/2020] [Indexed: 02/06/2023] Open
Abstract
Hepatitis A virus (HAV) infection occasionally leads to a critical condition in patients with or without chronic liver diseases. Acute-on-chronic liver disease includes acute-on-chronic liver failure (ACLF) and non-ACLF. In this review, we searched the literature concerning the association between HAV infection and chronic liver diseases in PubMed. Chronic liver diseases, such as metabolic associated fatty liver disease and alcoholic liver disease, coinfection with other viruses, and host genetic factors may be associated with severe hepatitis A. It is important to understand these conditions and mechanisms. There may be no etiological correlation between liver failure and HAV infection, but there is an association between the level of chronic liver damage and the severity of acute-on-chronic liver disease. While the application of an HAV vaccination is important for preventing HAV infection, the development of antivirals against HAV may be important for preventing the development of ACLF with HAV infection as an acute insult. The latter is all the more urgent given that the lives of patients with HAV infection and a chronic liver disease of another etiology may be at immediate risk.
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Chen S, Zhang W, Min J, Liu K. Lesson from a Fab-enabled co-crystallization study of TDRD2 and PIWIL1. Methods 2020; 175:72-78. [PMID: 31288074 DOI: 10.1016/j.ymeth.2019.07.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 06/30/2019] [Accepted: 07/03/2019] [Indexed: 10/26/2022] Open
Abstract
The interaction of Tudor domain-containing proteins (TDRDs) with P-element-induced wimpy testis (PIWI) proteins plays critical roles in transposon silencing and spermatogenesis. Most human TDRDs recognize PIWI proteins in a methylarginine-dependent manner via their extended Tudor (eTudor) domains, except TDRD2, which prefers an unmethylated PIWI protein. In order to illustrate the recognition of unmethylated PIWI proteins by TDRD2, we extensively tried co-crystallization of the TDRD2 eTudor with different PIWIL1 peptides, but to no avail. Recombinant antigen-binding fragments (Fabs) have been used to crystallize some difficult proteins in the past, so we generated Fab against the TDRD2 eTudor protein using a phage-display antibody library, and one of these Fab fragments indeed facilitated the co-crystallization of TDRD2 and PIWIL1. Structural analysis of Fab, the TDRD2 eTudor domain in complex with an unmethylated PIWIL1-derived peptide revealed that the PIWIL1 residues G3 through R8 bound between the Tudor core and SN domain of TDRD2. The C-terminal residues of the PIWIL1 peptide were not resolved, presumably due to steric competition with the heavy chain of the Fab. We propose Fab-assisted crystallization as a tool not only for structural studies of single proteins, but also for analysis of interactions between proteins and their ligands in cases where co-crystallization of native protein complexes fails.
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Affiliation(s)
- Sizhuo Chen
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Weilian Zhang
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Jinrong Min
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China; Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada; Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Ke Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China; Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.
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Li N, Li Z, Fu Y, Cao S. Cryo-EM Studies of Virus-Antibody Immune Complexes. Virol Sin 2020; 35:1-13. [PMID: 31916022 PMCID: PMC7035235 DOI: 10.1007/s12250-019-00190-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 11/25/2019] [Indexed: 01/25/2023] Open
Abstract
Antibodies play critical roles in neutralizing viral infections and are increasingly used as therapeutic drugs and diagnostic tools. Structural studies on virus-antibody immune complexes are important for better understanding the molecular mechanisms of antibody-mediated neutralization and also provide valuable information for structure-based vaccine design. Cryo-electron microscopy (cryo-EM) has recently matured as a powerful structural technique for studying bio-macromolecular complexes. When combined with X-ray crystallography, cryo-EM provides a routine approach for structurally characterizing the immune complexes formed between icosahedral viruses and their antibodies. In this review, recent advances in the structural understanding of virus-antibody interactions are outlined for whole virions with icosahedral T = pseudo 3 (picornaviruses) and T = 3 (flaviviruses) architectures, focusing on the dynamic nature of viral shells in different functional states. Glycoprotein complexes from pleomorphic enveloped viruses are also discussed as immune complex antigens. Improving our understanding of viral epitope structures using virus-based platforms would provide a fundamental road map for future vaccine development.
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Affiliation(s)
- Na Li
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Wuhan, 430071, China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhiqiang Li
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Wuhan, 430071, China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan Fu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Wuhan, 430071, China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Sheng Cao
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Wuhan, 430071, China. .,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China.
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Abstract
Picornaviruses are small, icosahedral, nonenveloped, positive-sense, single-stranded RNA viruses that form one of the largest and most important viral families. Numerous Picornaviridae members pose serious health or agricultural threats, causing diseases such as poliomyelitis, hepatitis A, or foot-and-mouth disease. The antigenic characterization of picornavirus capsids plays an important role in understanding the mechanism of viral neutralization and the conformational changes associated with genome release, and it can point to regions which can be targeted by small-molecule compounds to be developed as antiviral inhibitors. In a recent study, Cao and colleagues applied this strategy to hepatitis A virus (HAV) and used cryo-electron microscopy (cryo-EM) to characterize a well-conserved antigenic site recognized by several monoclonal antibodies. They further used computational approaches to identify a small-molecule drug with a strong inhibitory effect on cell attachment. This Primer explores the implications of a recent structural characterization of picornavirus capsid antigenicity, which points to regions that can be targeted by small-molecule antiviral inhibitors.
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