1
|
Zhang T, Han Y, Huang W, Wei H, Zhao Y, Shu L, Guo Y, Ye B, Zhou J, Liu J. Neutralizing antibody responses against contemporary and future influenza A(H3N2) viruses in paradoxical clades elicited by repeated and single vaccinations. J Med Virol 2024; 96:e29743. [PMID: 38884419 DOI: 10.1002/jmv.29743] [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: 03/06/2024] [Revised: 05/16/2024] [Accepted: 06/05/2024] [Indexed: 06/18/2024]
Abstract
As one of the most effective measures to prevent seasonal influenza viruses, annual influenza vaccination is globally recommended. Nevertheless, evidence regarding the impact of repeated vaccination to contemporary and future influenza has been inconclusive. A total of 100 subjects singly or repeatedly immunized with influenza vaccines including 3C.2a1 or 3C.3a1 A(H3N2) during 2018-2019 and 2019-2020 influenza season were recruited. We investigated neutralization antibody by microneutralization assay using four antigenically distinct A(H3N2) viruses circulating from 2018 to 2023, and tracked the dynamics of B cell receptor (BCR) repertoire for consecutive vaccinations. We found that vaccination elicited cross-reactive antibody responses against future emerging strains. Broader neutralizing antibodies to A(H3N2) viruses and more diverse BCR repertoires were observed in the repeated vaccination. Meanwhile, a higher frequency of BCR sequences shared among the repeated-vaccinated individuals with consistently boosting antibody response was found than those with a reduced antibody response. Our findings suggest that repeated seasonal vaccination could broaden the breadth of antibody responses, which may improve vaccine protection against future emerging viruses.
Collapse
MESH Headings
- Humans
- Influenza A Virus, H3N2 Subtype/immunology
- Influenza Vaccines/immunology
- Influenza Vaccines/administration & dosage
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/blood
- Antibodies, Viral/immunology
- Influenza, Human/prevention & control
- Influenza, Human/immunology
- Influenza, Human/virology
- Adult
- Cross Reactions/immunology
- Male
- Female
- Vaccination
- Middle Aged
- Young Adult
- Neutralization Tests
- Receptors, Antigen, B-Cell/immunology
- Receptors, Antigen, B-Cell/genetics
- Adolescent
Collapse
Affiliation(s)
- Ting Zhang
- Collaborative Innovation Centre of Regenerative Medicine and Medical Bioresource Development and Application Co-constructed by the Province and Ministry, Guangxi Medical University, Nanning, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Research Unit of Adaptive Evolution and Control of Emerging Viruses (2018RU009), Chinese Academy of Medical Sciences, Beijing, China
| | - Yang Han
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Research Unit of Adaptive Evolution and Control of Emerging Viruses (2018RU009), Chinese Academy of Medical Sciences, Beijing, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Weijuan Huang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hejiang Wei
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yingze Zhao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Research Unit of Adaptive Evolution and Control of Emerging Viruses (2018RU009), Chinese Academy of Medical Sciences, Beijing, China
| | - Liumei Shu
- Department of Health Care, Beijing Daxing District Hospital, Beijing, China
| | - Yaxin Guo
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Research Unit of Adaptive Evolution and Control of Emerging Viruses (2018RU009), Chinese Academy of Medical Sciences, Beijing, China
| | - Beiwei Ye
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Research Unit of Adaptive Evolution and Control of Emerging Viruses (2018RU009), Chinese Academy of Medical Sciences, Beijing, China
| | - Jianfang Zhou
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jun Liu
- Collaborative Innovation Centre of Regenerative Medicine and Medical Bioresource Development and Application Co-constructed by the Province and Ministry, Guangxi Medical University, Nanning, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Research Unit of Adaptive Evolution and Control of Emerging Viruses (2018RU009), Chinese Academy of Medical Sciences, Beijing, China
| |
Collapse
|
2
|
Pushan SS, Samantaray M, Rajagopalan M, Ramaswamy A. Structural dynamics of influenza A (H1N1) hemagglutinin protein: a comparative study of Indian (2018) isolate with its evolutionary neighbor, Californian (2009) strain. J Biomol Struct Dyn 2024:1-14. [PMID: 38379377 DOI: 10.1080/07391102.2024.2317985] [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: 11/09/2023] [Accepted: 02/07/2024] [Indexed: 02/22/2024]
Abstract
This work highlights the structure and dynamics of two trimeric HA proteins of the H1N1 virus from different origins, the pandemic Californian (HACal) and its closest Indian neighbor (HAInd), reported in 2009 and 2018, respectively. Because of mutation, HAInd acquires new N-glycosylation and epitope binding sites along with mutations at RBD, which might trigger an altered viral-host interaction mechanism. Molecular dynamics simulations performed on HA trimers for a period of 250 ns reveal the highly dynamic nature of HACal trimers inherited by the flexibility of HA monomers. In the trimer, the dynamics of one monomer are more pronounced compared to others, and the enhanced dynamics of RBD especially gain attention as they plays a key role during fusion. Conversely, the mutant HAInd trimer effectively establishes more H-bond interactions, and accordingly, the trimer undergoes more stabilized dynamics with a relatively lower amplitude of RBD dynamics, as endorsed by the reduced RMSD, Rg, and SASA variations. The cooperative and anti-cooperative motions dissected for the subdomains of both strains also reveal a prominent anticorrelative motion of RBD against other subdomains. In agreement, the free energy landscape of stable HAInd is also characterized by a single lowest wide energy basin instead of the two minimum energy basins of the HACal trimer. In essence, the mutant HAInd acquires a highly stable conformation with novel functional features, which calls for (i) further investigation on the emerging mutation-mediated variation in viral-host binding mechanism and (ii) the need for further design of site-specific potential inhibitors to face future challenges.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Shilpa Sri Pushan
- Department of Bioinformatics, Pondicherry University (A Central University), Kalapet, Puducherry, India
| | - Mahesh Samantaray
- Department of Bioinformatics, Pondicherry University (A Central University), Kalapet, Puducherry, India
| | - Muthukumaran Rajagopalan
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur
| | - Amutha Ramaswamy
- Department of Bioinformatics, Pondicherry University (A Central University), Kalapet, Puducherry, India
| |
Collapse
|
3
|
Pushan SS, Samantaray M, Rajagopalan M, Ramaswamy A. Evolution of Indian Influenza A (H1N1) Hemagglutinin Strains: A Comparative Analysis of the Pandemic Californian HA Strain. Front Mol Biosci 2023; 10:1111869. [PMID: 37006623 PMCID: PMC10061220 DOI: 10.3389/fmolb.2023.1111869] [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: 11/30/2022] [Accepted: 02/20/2023] [Indexed: 03/18/2023] Open
Abstract
The need for a vaccine/inhibitor design has become inevitable concerning the emerging epidemic and pandemic viral infections, and the recent outbreak of the influenza A (H1N1) virus is one such example. From 2009 to 2018, India faced severe fatalities due to the outbreak of the influenza A (H1N1) virus. In this study, the potential features of reported Indian H1N1 strains are analyzed in comparison with their evolutionarily closest pandemic strain, A/California/04/2009. The focus is laid on one of its surface proteins, hemagglutinin (HA), which imparts a significant role in attacking the host cell surface and its entry. The extensive analysis performed, in comparison with the A/California/04/2009 strain, revealed significant point mutations in all Indian strains reported from 2009 to 2018. Due to these mutations, all Indian strains disclosed altered features at the sequence and structural levels, which are further presumed to be associated with their functional diversity as well. The mutations observed with the 2018 HA sequence such as S91R, S181T, S200P, I312V, K319T, I419M, and E523D might improve the fitness of the virus in a new host and environment. The higher fitness and decreased sequence similarity of mutated strains may compromise therapeutic efficacy. In particular, the mutations observed commonly, such as serine-to-threonine, alanine-to-threonine, and lysine-to-glutamine at various regions, alter the physico-chemical features of receptor-binding domains, N-glycosylation, and epitope-binding sites when compared with the reference strain. Such mutations render diversity among all Indian strains, and the structural and functional characterization of these strains becomes inevitable. In this study, we observed that mutational drift results in the alteration of the receptor-binding domain, the generation of new variant N-glycosylation along with novel epitope-binding sites, and modifications at the structural level. Eventually, the pressing need to develop potentially distinct next-generation therapeutic inhibitors against the HA strains of the Indian influenza A (H1N1) virus is also highlighted here.
Collapse
Affiliation(s)
- Shilpa Sri Pushan
- Department of Bioinformatics, Pondicherry University, Puducherry, India
| | - Mahesh Samantaray
- Department of Bioinformatics, Pondicherry University, Puducherry, India
| | - Muthukumaran Rajagopalan
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, India
| | - Amutha Ramaswamy
- Department of Bioinformatics, Pondicherry University, Puducherry, India
| |
Collapse
|
4
|
Unique Mode of Antiviral Action of a Marine Alkaloid against Ebola Virus and SARS-CoV-2. Viruses 2022; 14:v14040816. [PMID: 35458549 PMCID: PMC9028129 DOI: 10.3390/v14040816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/24/2022] [Accepted: 04/02/2022] [Indexed: 11/16/2022] Open
Abstract
Lamellarin α 20-sulfate is a cell-impenetrable marine alkaloid that can suppress infection that is mediated by the envelope glycoprotein of human immunodeficiency virus type 1. We explored the antiviral action and mechanisms of this alkaloid against emerging enveloped RNA viruses that use endocytosis for infection. The alkaloid inhibited the infection of retroviral vectors that had been pseudotyped with the envelope glycoprotein of Ebola virus and SARS-CoV-2. The antiviral effects of lamellarin were independent of the retrovirus Gag-Pol proteins. Interestingly, although heparin and dextran sulfate suppressed the cell attachment of vector particles, lamellarin did not. In silico structural analyses of the trimeric glycoprotein of the Ebola virus disclosed that the principal lamellarin-binding site is confined to a previously unappreciated cavity near the NPC1-binding site and fusion loop, whereas those for heparin and dextran sulfate were dispersed across the attachment and fusion subunits of the glycoproteins. Notably, lamellarin binding to this cavity was augmented under conditions where the pH was 5.0. These results suggest that the final action of the alkaloid against Ebola virus is specific to events following endocytosis, possibly during conformational glycoprotein changes in the acidic environment of endosomes. Our findings highlight the unique biological and physicochemical features of lamellarin α 20-sulfate and should lead to the further use of broadly reactive antivirals to explore the structural mechanisms of virus replication.
Collapse
|
5
|
Coutinho JVP, Macedo-da-Silva J, Mule SN, Kronenberger T, Rosa-Fernandes L, Wrenger C, Palmisano G. Glycoprotein molecular dynamics analysis: SARS-CoV-2 spike glycoprotein case study. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 131:277-309. [PMID: 35871894 PMCID: PMC9181370 DOI: 10.1016/bs.apcsb.2022.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Molecular Dynamics (MD) is a method used to calculate the movement of atoms and molecules broadly applied to several aspects of science. It involves computational simulation, which makes it, at first glance, not easily accessible. The rise of several automated tools to perform molecular simulations has allowed researchers to navigate through the various steps of MD. This enables to elucidate structural properties of proteins that could not be analyzed otherwise, such as the impact of glycosylation. Glycosylation dictates the physicochemical and biological properties of a protein modulating its solubility, stability, resistance to proteolysis, interaction partners, enzymatic activity, binding and recognition. Given the high conformational and compositional diversity of the glycan chains, assessing their influence on the protein structure is challenging using conventional analytical techniques. In this manuscript, we present a step-by-step workflow to build and perform MD analysis of glycoproteins focusing on the SPIKE glycoprotein of SARS-CoV-2 to appraise the impact of glycans in structure stabilization and antibody occlusion.
Collapse
Affiliation(s)
| | - Janaina Macedo-da-Silva
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Simon Ngao Mule
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Thales Kronenberger
- Department of Internal Medicine VIII, University Hospital Tuebingen, Tuebingen, Germany,Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard-Karls-Universität, Tuebingen, Germany,Cluster of Excellence iFIT (EXC 2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tuebingen, Tuebingen, Germany,Tuebingen Center for Academic Drug Discovery & Development (TüCAD2), Tuebingen, Germany
| | - Livia Rosa-Fernandes
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Carsten Wrenger
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Giuseppe Palmisano
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil,Faculty of Science and engineering, Macquarie University, Sydney, NSW, Australia,Corresponding author:
| |
Collapse
|
6
|
Tomar DS, Licari G, Bauer J, Singh SK, Li L, Kumar S. Stress-dependent flexibility of a full-length human monoclonal antibody: Insights from molecular dynamics to support biopharmaceutical development. J Pharm Sci 2021; 111:628-637. [PMID: 34742728 DOI: 10.1016/j.xphs.2021.10.039] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/30/2021] [Accepted: 10/30/2021] [Indexed: 01/15/2023]
Abstract
After several decades of advancements in drug discovery, product development of biopharmaceuticals remains a time- and resource-consuming endeavor. One of the main reasons is associated to the lack of fundamental understanding of conformational dynamics of such biologic entities, and how they respond to various stresses encountered during manufacturing. In this work, we have studied the conformational dynamics of human IgG1κ b12 monoclonal antibody (mAb) using molecular dynamics simulations. The hundreds of nanoseconds long trajectories reveal that b12 mAb is highly flexible. Its variable domains show greater conformational fluctuations than the constant domains. Additionally, it collapses towards a more globular shape in response to thermal stress, leading to decrease in the total solvent exposed surface area and radius of gyration. This behavior is more pronounced for the deglycosylated b12 mAb, and it appears to correlate with increase in inter-domain contacts between specific regions of the antibody. Conformational fluctuations also cause temporary formation and disruption of hydrophobic and charged patches on the antibody surface, which is particularly important for the prediction of CMC properties during development phases of antibody-based biotherapeutics. The insights gained through these simulations may help the development of biologic drugs, especially with regards to manufacturing processes where antibodies may undergo significant thermal stress.
Collapse
Affiliation(s)
- Dheeraj S Tomar
- Biotherapeutics Pharmaceutical Sciences Research and Development, Pfizer Inc., 700 Chesterfield Parkway West, Chesterfield, MO, 63017, USA
| | - Giuseppe Licari
- Pharmaceuticals Development Biologicals, Boehringer Ingelheim Pharmaceuticals, Inc., D-88397 Biberach an der Riss, Germany
| | - Joschka Bauer
- Pharmaceuticals Development Biologicals, Boehringer Ingelheim Pharmaceuticals, Inc., D-88397 Biberach an der Riss, Germany
| | - Satish K Singh
- Biotherapeutics Pharmaceutical Sciences Research and Development, Pfizer Inc., 700 Chesterfield Parkway West, Chesterfield, MO, 63017, USA
| | - Li Li
- Biotherapeutics Pharmaceutical Sciences Research and Development, Pfizer Inc., 1 Burtt Road, Andover, Massachusetts, 01810, USA
| | - Sandeep Kumar
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, CT 06877.
| |
Collapse
|
7
|
Kotani O, Suzuki Y, Saito S, Ainai A, Ueno A, Hemmi T, Sano K, Tabata K, Yokoyama M, Suzuki T, Hasegawa H, Sato H. Structure-Guided Creation of an Anti-HA Stalk Antibody F11 Derivative That Neutralizes Both F11-Sensitive and -Resistant Influenza A(H1N1)pdm09 Viruses. Viruses 2021; 13:v13091733. [PMID: 34578314 PMCID: PMC8473006 DOI: 10.3390/v13091733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/24/2021] [Accepted: 08/26/2021] [Indexed: 12/05/2022] Open
Abstract
The stalk domain of influenza virus envelope glycoprotein hemagglutinin (HA) constitutes the axis connecting the head and transmembrane domains, and plays pivotal roles in conformational rearrangements of HA for virus infection. Here we characterized molecular interactions between the anti-HA stalk neutralization antibody F11 and influenza A(H1N1)pdm09 HA to understand the structural basis of the actions and modifications of this antibody. In silico structural analyses using a model of the trimeric HA ectodomain indicated that the F11 Fab fragment has physicochemical properties, allowing it to crosslink two HA monomers by binding to a region near the proteolytic cleavage site of the stalk domain. Interestingly, the F11 binding allosterically caused a marked suppression of the structural dynamics of the HA cleavage loop and flanking regions. Structure-guided mutagenesis of the F11 antibody revealed a critical residue in the F11 light chain for the F11-mediated neutralization. Finally, the mutagenesis led to identification of a unique F11 derivative that can neutralize both F11-sensitive and F11-resistant A(H1N1)pdm09 viruses. These results raise the possibility that F11 sterically and physically disturbs proteolytic cleavage of HA for the ordered conformational rearrangements and suggest that in silico guiding experiments can be useful to create anti-HA stalk antibodies with new phenotypes.
Collapse
Affiliation(s)
- Osamu Kotani
- Center for Pathogen Genomics, National Institute of Infectious Diseases, Tokyo 208-0011, Japan; (M.Y.); (H.S.)
- Correspondence: (O.K.); (S.S.)
| | - Yasushi Suzuki
- Center for Influenza and Respiratory Virus Research, National Institute of Infectious Diseases, Tokyo 208-0011, Japan; (Y.S.); (H.H.)
| | - Shinji Saito
- Department of Pathology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan; (A.A.); (A.U.); (T.H.); ka-- (K.S.); (K.T.); (T.S.)
- Correspondence: (O.K.); (S.S.)
| | - Akira Ainai
- Department of Pathology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan; (A.A.); (A.U.); (T.H.); ka-- (K.S.); (K.T.); (T.S.)
| | - Akira Ueno
- Department of Pathology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan; (A.A.); (A.U.); (T.H.); ka-- (K.S.); (K.T.); (T.S.)
| | - Takuya Hemmi
- Department of Pathology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan; (A.A.); (A.U.); (T.H.); ka-- (K.S.); (K.T.); (T.S.)
| | - Kaori Sano
- Department of Pathology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan; (A.A.); (A.U.); (T.H.); ka-- (K.S.); (K.T.); (T.S.)
| | - Koshiro Tabata
- Department of Pathology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan; (A.A.); (A.U.); (T.H.); ka-- (K.S.); (K.T.); (T.S.)
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Hokkaido 001-0020, Japan
| | - Masaru Yokoyama
- Center for Pathogen Genomics, National Institute of Infectious Diseases, Tokyo 208-0011, Japan; (M.Y.); (H.S.)
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan; (A.A.); (A.U.); (T.H.); ka-- (K.S.); (K.T.); (T.S.)
| | - Hideki Hasegawa
- Center for Influenza and Respiratory Virus Research, National Institute of Infectious Diseases, Tokyo 208-0011, Japan; (Y.S.); (H.H.)
| | - Hironori Sato
- Center for Pathogen Genomics, National Institute of Infectious Diseases, Tokyo 208-0011, Japan; (M.Y.); (H.S.)
| |
Collapse
|
8
|
Chitranshi N, Kumar A, Sheriff S, Gupta V, Godinez A, Saks D, Sarkar S, Shen T, Mirzaei M, Basavarajappa D, Abyadeh M, Singh SK, Dua K, Zhang KYJ, Graham SL, Gupta V. Identification of Novel Cathepsin B Inhibitors with Implications in Alzheimer's Disease: Computational Refining and Biochemical Evaluation. Cells 2021; 10:cells10081946. [PMID: 34440715 PMCID: PMC8391575 DOI: 10.3390/cells10081946] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 07/23/2021] [Accepted: 07/27/2021] [Indexed: 02/07/2023] Open
Abstract
Amyloid precursor protein (APP), upon proteolytic degradation, forms aggregates of amyloid β (Aβ) and plaques in the brain, which are pathological hallmarks of Alzheimer’s disease (AD). Cathepsin B is a cysteine protease enzyme that catalyzes the proteolytic degradation of APP in the brain. Thus, cathepsin B inhibition is a crucial therapeutic aspect for the discovery of new anti-Alzheimer’s drugs. In this study, we have employed mixed-feature ligand-based virtual screening (LBVS) by integrating pharmacophore mapping, docking, and molecular dynamics to detect small, potent molecules that act as cathepsin B inhibitors. The LBVS model was generated by using hydrophobic (HY), hydrogen bond acceptor (HBA), and hydrogen bond donor (HBD) features, using a dataset of 24 known cathepsin B inhibitors of both natural and synthetic origins. A validated eight-feature pharmacophore hypothesis (Hypo III) was utilized to screen the Maybridge chemical database. The docking score, MM-PBSA, and MM-GBSA methodology was applied to prioritize the lead compounds as virtual screening hits. These compounds share a common amide scaffold, and showed important interactions with Gln23, Cys29, His110, His111, Glu122, His199, and Trp221. The identified inhibitors were further evaluated for cathepsin-B-inhibitory activity. Our study suggests that pyridine, acetamide, and benzohydrazide compounds could be used as a starting point for the development of novel therapeutics.
Collapse
Affiliation(s)
- Nitin Chitranshi
- Faculty of Medicine, Health and Human Sciences, Macquarie University, F10A, 2 Technology Place, North Ryde, NSW 2109, Australia; (S.S.); (A.G.); (D.S.); (S.S.); (T.S.); (M.M.); (D.B.); (S.L.G.)
- Correspondence: (N.C.); (V.G.); Tel.: +61-(02)-9850-2804 (N.C.)
| | - Ashutosh Kumar
- Center for Biosystems Dynamics Research, Laboratory for Structural Bioinformatics, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Kanagawa, Japan; (A.K.); (K.Y.J.Z.)
| | - Samran Sheriff
- Faculty of Medicine, Health and Human Sciences, Macquarie University, F10A, 2 Technology Place, North Ryde, NSW 2109, Australia; (S.S.); (A.G.); (D.S.); (S.S.); (T.S.); (M.M.); (D.B.); (S.L.G.)
| | - Veer Gupta
- School of Medicine, Faculty of Health, Deakin University, Geelong, VIC 3220, Australia;
| | - Angela Godinez
- Faculty of Medicine, Health and Human Sciences, Macquarie University, F10A, 2 Technology Place, North Ryde, NSW 2109, Australia; (S.S.); (A.G.); (D.S.); (S.S.); (T.S.); (M.M.); (D.B.); (S.L.G.)
| | - Danit Saks
- Faculty of Medicine, Health and Human Sciences, Macquarie University, F10A, 2 Technology Place, North Ryde, NSW 2109, Australia; (S.S.); (A.G.); (D.S.); (S.S.); (T.S.); (M.M.); (D.B.); (S.L.G.)
| | - Soumalya Sarkar
- Faculty of Medicine, Health and Human Sciences, Macquarie University, F10A, 2 Technology Place, North Ryde, NSW 2109, Australia; (S.S.); (A.G.); (D.S.); (S.S.); (T.S.); (M.M.); (D.B.); (S.L.G.)
| | - Ting Shen
- Faculty of Medicine, Health and Human Sciences, Macquarie University, F10A, 2 Technology Place, North Ryde, NSW 2109, Australia; (S.S.); (A.G.); (D.S.); (S.S.); (T.S.); (M.M.); (D.B.); (S.L.G.)
| | - Mehdi Mirzaei
- Faculty of Medicine, Health and Human Sciences, Macquarie University, F10A, 2 Technology Place, North Ryde, NSW 2109, Australia; (S.S.); (A.G.); (D.S.); (S.S.); (T.S.); (M.M.); (D.B.); (S.L.G.)
| | - Devaraj Basavarajappa
- Faculty of Medicine, Health and Human Sciences, Macquarie University, F10A, 2 Technology Place, North Ryde, NSW 2109, Australia; (S.S.); (A.G.); (D.S.); (S.S.); (T.S.); (M.M.); (D.B.); (S.L.G.)
| | - Morteza Abyadeh
- Cell Science Research Center, Department of Molecular Systems Biology, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran 1665659911, Iran;
| | - Sachin K. Singh
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara 144411, Punjab, India;
| | - Kamal Dua
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Ultimo, NSW 2007, Australia;
- Australian Research Centre in Complementary and Integrative Medicine, Faculty of Health, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Kam Y. J. Zhang
- Center for Biosystems Dynamics Research, Laboratory for Structural Bioinformatics, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Kanagawa, Japan; (A.K.); (K.Y.J.Z.)
| | - Stuart L. Graham
- Faculty of Medicine, Health and Human Sciences, Macquarie University, F10A, 2 Technology Place, North Ryde, NSW 2109, Australia; (S.S.); (A.G.); (D.S.); (S.S.); (T.S.); (M.M.); (D.B.); (S.L.G.)
| | - Vivek Gupta
- Faculty of Medicine, Health and Human Sciences, Macquarie University, F10A, 2 Technology Place, North Ryde, NSW 2109, Australia; (S.S.); (A.G.); (D.S.); (S.S.); (T.S.); (M.M.); (D.B.); (S.L.G.)
- Correspondence: (N.C.); (V.G.); Tel.: +61-(02)-9850-2804 (N.C.)
| |
Collapse
|
9
|
Piantham C, Ito K. Modeling the selective advantage of new amino acids on the hemagglutinin of H1N1 influenza viruses using their patient age distributions. Virus Evol 2021; 7:veab049. [PMID: 34285812 PMCID: PMC8286795 DOI: 10.1093/ve/veab049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
In 2009, a new strain of H1N1 influenza A virus caused a pandemic, and its descendant strains are causing seasonal epidemics worldwide. Given the high mutation rate of influenza viruses, variant strains having different amino acids on hemagglutinin (HA) continuously emerge. To prepare vaccine strains for the next influenza seasons, it is an urgent task to predict which variants will be selected in the viral population. An analysis of 24,681 pairs of an amino acid sequence of HA of H1N1pdm2009 viruses and its patient age showed that the empirical fixation probability of new amino acids on HA significantly differed depending on their frequencies in the population, patient age distributions, and epitope flags. The selective advantage of a variant strain having a new amino acid was modeled by linear combinations of patients age distributions and epitope flags, and then the fixation probability of the new amino acid was modeled using Kimura’s formula for advantageous selection. The parameters of models were estimated from the sequence data and models were tested with four-fold cross validations. The frequency of new amino acids alone can achieve high sensitivity, specificity, and precision in predicting the fixation of a new amino acid of which frequency is more than 0.11. The estimated parameter suggested that viruses with a new amino acid having a frequency in the population higher than 0.11 have a significantly higher selective advantage compared to viruses with the old amino acid at the same position. The model considering the Z-value of patient age rank-sums of new amino acids predicted amino acid substitutions on HA with a sensitivity of 0.78, specificity of 0.86, and precision of 0.83, showing significant improvement compared to the constant selective advantage model, which used only the frequency of the amino acid. These results suggested that H1N1 viruses tend to be selected in the adult population, and frequency of viruses having new amino acids and their patient ages are useful to predict amino acid substitutions on HA.
Collapse
Affiliation(s)
- Chayada Piantham
- Division of Bioinformatics, Graduate School of Infectious Diseases, Hokkaido University, Sapporo 0600818, Japan
| | - Kimihito Ito
- Division of Bioinformatics, International Institute for Zoonosis Control, Hokkaido University, Sapporo 0010020, Japan
| |
Collapse
|
10
|
Identification of a Novel Cis-Acting Regulator of HIV-1 Genome Packaging. Int J Mol Sci 2021; 22:ijms22073435. [PMID: 33810482 PMCID: PMC8036536 DOI: 10.3390/ijms22073435] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/19/2021] [Accepted: 03/24/2021] [Indexed: 12/17/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) uptakes homo-dimerized viral RNA genome into its own particle. A cis-acting viral RNA segment responsible for this event, termed packaging signal (psi), is located at the 5′-end of the viral genome. Although the psi segment exhibits nucleotide variation in nature, its effects on the psi function largely remain unknown. Here we show that a psi sequence from an HIV-1 regional variant, subtype D, has a lower packaging ability compared with that from another regional variant, HIV-1 subtype B, despite maintaining similar genome dimerization activities. A series of molecular genetic investigations narrowed down the responsible element of the selective attenuation to the two sequential nucleotides at positions 226 and 227 in the psi segment. Molecular dynamics simulations predicted that the dinucleotide substitution alters structural dynamics, fold, and hydrogen-bond networks primarily of the psi-SL2 element that contains the binding interface of viral nucleocapsid protein for the genome packaging. In contrast, such structural changes were minimal within the SL1 element involved in genome dimerization. These results suggest that the psi 226/227 dinucleotide pair functions as a cis-acting regulator to control the psi structure to selectively tune the efficiency of packaging, but not dimerization of highly variable HIV-1 genomes.
Collapse
|
11
|
Sano K, Saito S, Suzuki T, Kotani O, Ainai A, van Riet E, Tabata K, Saito K, Takahashi Y, Yokoyama M, Sato H, Maruno T, Usami K, Uchiyama S, Ogawa-Goto K, Hasegawa H. An influenza HA stalk reactive polymeric IgA antibody exhibits anti-viral function regulated by binary interaction between HA and the antibody. PLoS One 2021; 16:e0245244. [PMID: 33412571 PMCID: PMC7790537 DOI: 10.1371/journal.pone.0245244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 12/23/2020] [Indexed: 01/12/2023] Open
Abstract
IgA antibodies, which are secreted onto the mucosal surface as secretory IgA antibodies (SIgAs), play an important role in preventing influenza virus infection. A recent study reported that anti-hemagglutinin (HA) head-targeting antibodies increase anti-viral functions such as hemagglutination inhibition (HI) and virus neutralization (NT), in addition to HA binding activity (reactivity) via IgA polymerization. However, the functional properties of anti-viral IgA antibodies with mechanisms of action distinct from those of anti-HA head-targeting antibodies remain elusive. Here, we characterized the functional properties of IgG, monomeric IgA, and polymeric IgA anti-HA stalk-binding clones F11 and FI6, and B12 (a low affinity anti-HA stalk clone), as well as Fab-deficient (ΔFab) IgA antibodies. We found that IgA polymerization impacts the functional properties of anti-HA stalk antibodies. Unlike anti-HA head antibodies, the anti-viral functions of anti-HA stalk antibodies were not simply enhanced by IgA polymerization. The data suggest that two modes of binding (Fab paratope-mediated binding to the HA stalk, and IgA Fc glycan-mediated binding to the HA receptor binding site (RBS)) occur during interaction between anti-stalk HA IgA antibodies and HA. In situations where Fab paratope-mediated binding to the HA stalk exceeded IgA Fc glycan-mediated binding to HA RBS, IgA polymerization increased anti-viral functions. By contrast, when IgA Fc glycan-mediated binding to the HA RBS was dominant, anti-viral activity will fall upon IgA polymerization. In summary, the results suggest that coordination between these two independent binding modules determines whether IgA polymerization has a negative or positive effect on the anti-viral functions of anti-HA stalk IgA antibodies.
Collapse
Affiliation(s)
- Kaori Sano
- Department of Pathology, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
- Division of Infectious Diseases Pathology, Department of Global Infectious Diseases, Tohoku Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Shinji Saito
- Influenza Virus Research Center, National Institute of Infectious Diseases, Musashimurayama, Tokyo, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Osamu Kotani
- Pathogen Genomics Center, National Institute of Infectious Diseases, Musashimurayama, Tokyo, Japan
| | - Akira Ainai
- Department of Pathology, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Elly van Riet
- Influenza Virus Research Center, National Institute of Infectious Diseases, Musashimurayama, Tokyo, Japan
| | - Koshiro Tabata
- Department of Pathology, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Kumpei Saito
- Department of Pathology, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Yoshimasa Takahashi
- Department of Immunology, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Masaru Yokoyama
- Pathogen Genomics Center, National Institute of Infectious Diseases, Musashimurayama, Tokyo, Japan
| | - Hironori Sato
- Pathogen Genomics Center, National Institute of Infectious Diseases, Musashimurayama, Tokyo, Japan
| | - Takahiro Maruno
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
| | - Kaede Usami
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
| | - Susumu Uchiyama
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi, Japan
| | - Kiyoko Ogawa-Goto
- Nippi Research Institute of Biomatrix, Nippi Incorporated, Toride, Ibaraki, Japan
| | - Hideki Hasegawa
- Department of Pathology, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
- Division of Infectious Diseases Pathology, Department of Global Infectious Diseases, Tohoku Graduate School of Medicine, Sendai, Miyagi, Japan
- Influenza Virus Research Center, National Institute of Infectious Diseases, Musashimurayama, Tokyo, Japan
- Global Virus Network, Baltimore, MD, United States of America
| |
Collapse
|
12
|
Gouma S, Kim K, Weirick ME, Gumina ME, Branche A, Topham DJ, Martin ET, Monto AS, Cobey S, Hensley SE. Middle-aged individuals may be in a perpetual state of H3N2 influenza virus susceptibility. Nat Commun 2020; 11:4566. [PMID: 32917903 PMCID: PMC7486384 DOI: 10.1038/s41467-020-18465-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 08/17/2020] [Indexed: 12/20/2022] Open
Abstract
Influenza virus exposures in childhood can establish long-lived memory B cell responses that can be recalled later in life. Here, we complete a large serological survey to elucidate the specificity of antibodies against contemporary H3N2 viruses in differently aged individuals who were likely primed with different H3N2 strains in childhood. We find that most humans who were first infected in childhood with H3N2 viral strains from the 1960s and 1970s possess non-neutralizing antibodies against contemporary 3c2.A H3N2 viruses. We find that 3c2.A H3N2 virus infections boost non-neutralizing H3N2 antibodies in middle-aged individuals, potentially leaving many of them in a perpetual state of 3c2.A H3N2 viral susceptibility.
Collapse
MESH Headings
- Adolescent
- Adult
- Aged
- Aged, 80 and over
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/blood
- Antibodies, Viral/immunology
- Antigens, Viral/immunology
- Child
- Child, Preschool
- Disease Susceptibility
- Female
- Hemagglutinin Glycoproteins, Influenza Virus/immunology
- Humans
- Infant
- Influenza A Virus, H3N2 Subtype/immunology
- Influenza, Human/immunology
- Male
- Middle Aged
- Models, Biological
- Philadelphia
- Recombinant Proteins
- Seasons
- Young Adult
Collapse
Affiliation(s)
- Sigrid Gouma
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kangchon Kim
- Department of Ecology & Evolution, University of Chicago, Chicago, IL, 60637, USA
| | - Madison E Weirick
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Megan E Gumina
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Angela Branche
- Division of Infectious Diseases, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - David J Topham
- Department of Medicine and Department of Microbiology and Immunology, David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Emily T Martin
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Arnold S Monto
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Sarah Cobey
- Department of Ecology & Evolution, University of Chicago, Chicago, IL, 60637, USA
| | - Scott E Hensley
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| |
Collapse
|
13
|
Jia WQ, Feng XY, Liu YY, Han ZZ, Jing Z, Xu WR, Cheng XC. Identification of Phosphoinositide-3 Kinases Delta and Gamma Dual Inhibitors Based on the p110δ/γ Crystal Structure. LETT DRUG DES DISCOV 2020. [DOI: 10.2174/1570180816666190730163431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Phosphoinositide-3 kinases (PI3Ks) are key signaling molecules that affect
a diverse array of biological processes in cells, including proliferation, differentiation, survival, and
metabolism. The abnormal activity of PI3K signals is closely related to the occurrence of many diseases,
which has become a very promising drug target, especially for the treatment of cancer.
PI3Kδ/γ inhibitors can reduce toxicity concerns for chronic indications such as asthma and rheumatoid
arthritis compared with pan PI3Ks inhibitors.
Methods:
With the aim of finding more effective PI3Kδ/γ dual inhibitors, virtual screening,
ADMET prediction Molecular Dynamics (MD) simulations and MM-GBSA were executed based
on the known p110δ/γ crystal structure. Compound ZINC28564067 with high docking score and
low toxicity was obtained.
Results:
By MD simulations and MM-GBSA, we could observe that ZINC28564067 had more favorable
conformation binding to the PI3Kδ/γ than the original ligands.
Conclusion:
The results provided a rapid approach for the discovery of novel PI3Kδ/γ dual inhibitors
which might be a potential anti-tumor lead compound.
Collapse
Affiliation(s)
- Wen-Qing Jia
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Xiao-Yan Feng
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Ya-Ya Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Zhen-Zhen Han
- Baokang Hospital, Tianjin University of Traditional Chinese Medicine, Tianjin 300193, China
| | - Zhi Jing
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Wei-Ren Xu
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin 300193, China
| | - Xian-Chao Cheng
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| |
Collapse
|
14
|
Gouma S, Weirick M, Hensley SE. Antigenic assessment of the H3N2 component of the 2019-2020 Northern Hemisphere influenza vaccine. Nat Commun 2020; 11:2445. [PMID: 32415074 PMCID: PMC7229105 DOI: 10.1038/s41467-020-16183-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 04/19/2020] [Indexed: 11/13/2022] Open
Abstract
The 2019–2020 Northern Hemisphere influenza vaccine includes antigens from 3c3.A H3N2 viruses; however, over half of circulating H3N2 viruses belong to subclade 3c2.A1b. Here, we analyze antibody responses elicited by the egg-adapted 3c3.A H3N2 vaccine strain in ferrets and humans. We find that this vaccine strain elicits antibodies that have reduced reactivity to a wild-type 3c3.A strain and very limited reactivity to 3c2.A strains, including the currently circulating 3c2.A1b strain. Vaccine mismatch and changes in antigenicity due to vaccine strain egg adaptation can affect seasonal influenza vaccine effectiveness. Here, Gouma et al. show that the egg-adapted 3c3.A H3N2 vaccine strain elicits antibodies with limited reactivity to a wildtype 3c3.A strain and currently circulating 3c2.A H3N2 strains.
Collapse
Affiliation(s)
- Sigrid Gouma
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Madison Weirick
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Scott E Hensley
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
15
|
Feng XY, Ding TT, Liu YY, Xu WR, Cheng XC. In-silico identification of peroxisome proliferator-activated receptor (PPAR)α/γ agonists from Ligand Expo Components database. J Biomol Struct Dyn 2020; 39:1853-1864. [DOI: 10.1080/07391102.2020.1745279] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Xiao-Yan Feng
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Ting-Ting Ding
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Ya-Ya Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Wei-Ren Xu
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin, China
| | - Xian-Chao Cheng
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| |
Collapse
|
16
|
Allosteric Regulation of HIV-1 Capsid Structure for Gag Assembly, Virion Production, and Viral Infectivity by a Disordered Interdomain Linker. J Virol 2019; 93:JVI.00381-19. [PMID: 31189701 DOI: 10.1128/jvi.00381-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 06/04/2019] [Indexed: 12/12/2022] Open
Abstract
The retroviral Gag capsid (Gag-CA) interdomain linker is an unstructured peptide segment connecting structured N-terminal and C-terminal domains. Although the region is reported to play roles in virion morphogenesis and infectivity, underlying molecular mechanisms remain unexplored. To address this issue, we determined biological and molecular phenotypes of HIV-1 CA linker mutants by experimental and in silico approaches. Among the nine linker mutants tested, eight exhibited attenuation of viral particle production to various extents mostly in parallel with a reduction in viral infectivity. Sucrose density gradient, confocal microscopy, and live-cell protein interaction analyses indicated that the defect is accompanied by attenuation of Gag-Gag interactions following Gag plasma membrane targeting in the cells. In silico analyses revealed distinct distributions of interaction-prone hydrophobic patches between immature and mature CA proteins. Molecular dynamics simulations predicted that the linker mutations can allosterically alter structural fluctuations, including the interaction surfaces apart from the mutation sites in both the immature and mature CA proteins. These results suggest that the HIV-1 CA interdomain linker is a cis-modulator of the CA interaction surfaces to optimize efficiency of Gag assembly, virion production, and viral infectivity.IMPORTANCE HIV-1 particle production and infection are highly ordered processes. Viral Gag proteins play a central role in the assembly and disassembly of viral molecules. Of these, capsid protein (CA) is a major contributor to the Gag-Gag interactions. CA consists of two structured domains, i.e., N-terminal (NTD) and C-terminal (CTD) domains, connected by an unstructured domain named the interdomain linker. While multiple regions in the NTD and CTD are reported to play roles in virion morphogenesis and infectivity, the roles of the linker region in Gag assembly and virus particle formation remain elusive. In this study, we showed by biological and molecular analyses that the linker region functions as an intramolecular modulator to tune Gag assembly, virion production, and viral infectivity. Our study thus illustrates a hitherto-unrecognized mechanism, an allosteric regulation of CA structure by the disordered protein element, for HIV-1 replication.
Collapse
|
17
|
Protein kinase A inhibits tumor mutator APOBEC3B through phosphorylation. Sci Rep 2019; 9:8307. [PMID: 31165764 PMCID: PMC6549188 DOI: 10.1038/s41598-019-44407-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 05/14/2019] [Indexed: 12/26/2022] Open
Abstract
APOBEC3B cytidine deaminase (A3B) catalyzes cytosine into uracil in single-strand DNA and induces C-to-T mutations in genomic DNA of various types of tumors. Accumulation of APOBEC signature mutations is correlated with a worse prognosis for patients with breast cancer or multiple myeloma, suggesting that A3B activity might be a cause of the unfavorable DNA mutations and clonal evolution in these tumors. Phosphorylation of conserved threonine residues of other cytidine deaminases, activation induced deaminase (AID) and APOBEC3G, inhibits their activity. Here we show that protein kinase A (PKA) physically binds to A3B and phosphorylates Thr214. In vitro deaminase assays and foreign DNA editing assays in cells confirm that phosphomimetic A3B mutants, T214D and T214E, completely lose deaminase activity. Molecular dynamics simulation of A3B phosphorylation reveals that Thr214 phosphorylation disrupts binding between the phospho-A3B catalytic core and ssDNA. These mutants still inhibit retroviral infectivity at least partially, and also retain full anti-retrotransposition activity. These results imply that PKA-mediated phosphorylation inhibits A3B mutagenic activity without destructing its innate immune functions. Therefore, PKA activation could reduce further accumulation of mutations in A3B overexpressing tumors.
Collapse
|
18
|
Cueno ME, Shiotsu H, Nakano K, Sugiyama E, Kikuta M, Usui R, Oya R, Imai K. Structural significance of residues 158-160 in the H3N2 hemagglutnin globular head: A computational study with implications in viral evolution and infection. J Mol Graph Model 2019; 89:33-40. [PMID: 30849718 DOI: 10.1016/j.jmgm.2019.02.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 01/28/2019] [Accepted: 02/18/2019] [Indexed: 01/14/2023]
Abstract
Influenza A H3N2 has been linked to annual outbreaks within the human population attributable to continuous structural changes. H3N2 HA contains well identified antigenic sites and receptor-binding sites (RBS) that are possibly correlated to viral evolution and infection. However, the structural significance of amino acid residues associated with both viral evolution and infection were not fully demonstrated. Throughout this study, we generated and analyzed H3N2 HA models that represented the clade 3C.2 population (comprised of clades 3C.2, 3C.2a, and 3C.21 from the transitioning 2014-2018 H3N2 strains) and 3C.3a (from the 2016 H3N2 strain). Model quality estimation, structural analyses and superimposition, and network analytics of H3N2 HA1 evolution were performed. We found that the structural properties of residues 158-160 could influence the overall HA backbone. More specifically, amino acid substitutions at residues 159-160 affected the amino acid orientation at residue 158, thereby, causing the overall HA backbone structure to vary. Our results were consistent with 1968-2018 HA1 evolution. Taken together, we propose that our results would highlight the structural significance of residues 158-160 in HA1 for both antigenic drift and RBS.
Collapse
Affiliation(s)
- Marni E Cueno
- Department of Microbiology, Nihon University School of Dentistry, Tokyo, 101-8310, Japan; Immersion Physics Class, Department of Science, Tokyo Gakugei University International Secondary School, Tokyo, 178-0063, Japan; Immersion Biology Class, Department of Science, Tokyo Gakugei University International Secondary School, Tokyo, 178-0063, Japan.
| | - Hayato Shiotsu
- Immersion Physics Class, Department of Science, Tokyo Gakugei University International Secondary School, Tokyo, 178-0063, Japan
| | - Karin Nakano
- Immersion Physics Class, Department of Science, Tokyo Gakugei University International Secondary School, Tokyo, 178-0063, Japan
| | - Emiko Sugiyama
- Immersion Biology Class, Department of Science, Tokyo Gakugei University International Secondary School, Tokyo, 178-0063, Japan
| | - Mari Kikuta
- Immersion Biology Class, Department of Science, Tokyo Gakugei University International Secondary School, Tokyo, 178-0063, Japan
| | - Rikuya Usui
- Immersion Physics Class, Department of Science, Tokyo Gakugei University International Secondary School, Tokyo, 178-0063, Japan
| | - Riku Oya
- Immersion Physics Class, Department of Science, Tokyo Gakugei University International Secondary School, Tokyo, 178-0063, Japan
| | - Kenichi Imai
- Department of Microbiology, Nihon University School of Dentistry, Tokyo, 101-8310, Japan
| |
Collapse
|
19
|
Knapp B, Ospina L, Deane CM. Avoiding False Positive Conclusions in Molecular Simulation: The Importance of Replicas. J Chem Theory Comput 2018; 14:6127-6138. [PMID: 30354113 DOI: 10.1021/acs.jctc.8b00391] [Citation(s) in RCA: 170] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Molecular simulations are a computational technique used to investigate the dynamics of proteins and other molecules. The free energy landscape of these simulations is often rugged, and minor differences in the initial velocities, floating-point precision, or underlying hardware can cause identical simulations (replicas) to take different paths in the landscape. In this study we investigated the magnitude of these effects based on 310 000 ns of simulation time. We performed 100 identically parametrized replicas of 3000 ns each for a small 10 amino acid system as well as 100 identically parametrized replicas of 100 ns each for an 827 residue T-cell receptor/MHC system. Comparing randomly chosen subgroups within these replica sets, we estimated the reproducibility and reliability that can be achieved by a given number of replicas at a given simulation time. These results demonstrate that conclusions drawn from single simulations are often not reproducible and that conclusions drawn from multiple shorter replicas are more reliable than those from a single longer simulation. The actual number of replicas needed will always depend on the question asked and the level of reliability sought. On the basis of our data, it appears that a good rule of thumb is to perform a minimum of five to 10 replicas.
Collapse
Affiliation(s)
- Bernhard Knapp
- Bioinformatics and Immunoinformatics Research Group, Department of Basic Sciences , International University of Catalonia , 08195 Barcelona , Spain.,Protein Informatics Group, Department of Statistics , University of Oxford , Oxford OX1 3LB , United Kingdom
| | - Luis Ospina
- Protein Informatics Group, Department of Statistics , University of Oxford , Oxford OX1 3LB , United Kingdom.,Alliance Manchester Business School , University of Manchester , Manchester M13 9SS , United Kingdom
| | - Charlotte M Deane
- Protein Informatics Group, Department of Statistics , University of Oxford , Oxford OX1 3LB , United Kingdom
| |
Collapse
|
20
|
Allen JD, Ross TM. H3N2 influenza viruses in humans: Viral mechanisms, evolution, and evaluation. Hum Vaccin Immunother 2018; 14:1840-1847. [PMID: 29641358 PMCID: PMC6149781 DOI: 10.1080/21645515.2018.1462639] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Annual seasonal influenza vaccines are composed of two influenza A strains representing the H1N1 and H3N2 subtypes, and two influenza B strains representing the Victoria and Yamagata lineages. Strains from these Influenza A and Influenza B viruses currently co-circulate in humans. Of these, strains associated with the H3N2 subtype are affiliated with severe influenza seasons. H3N2 influenza viruses pre-dominated during 3 of the last 5 quite severe influenza seasons. During the 2016/2017 flu season, the H3N2 component of the influenza vaccine exhibited a poor protective efficacy (∼28-42%) against preventing infection of co-circulating strains. Since their introduction to the human population in 1968, H3N2 Influenza viruses have rapidly evolved both genetically and antigenically in an attempt to escape host immune pressures. As a result, these viruses have added numerous N-linked glycans to the viral hemagglutinin (HA), increased the overall net charge of the HA molecule, changed their preferences in receptor binding, and altered the ability of neuraminidase (NA) to agglutinate red blood cells prior to host entry. Over time, these adaptations have made characterizing these viruses increasingly difficult. This review investigates these recent changes in modern H3N2 influenza viruses and explores the methods that researchers are currently developing in order to study these viruses.
Collapse
Affiliation(s)
- James D Allen
- a Center for Vaccines and Immunology, University of Georgia , Athens , GA , USA
| | - Ted M Ross
- a Center for Vaccines and Immunology, University of Georgia , Athens , GA , USA.,b Department of Infectious Diseases , University of Georgia , Athens , GA , USA
| |
Collapse
|
21
|
Yang JR, Hsu SZ, Kuo CY, Huang HY, Huang TY, Wang HC, Liu MT. An epidemic surge of influenza A(H3N2) virus at the end of the 2016-2017 season in Taiwan with an increased viral genetic heterogeneity. J Clin Virol 2017; 99-100:15-21. [PMID: 29278832 DOI: 10.1016/j.jcv.2017.12.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 12/04/2017] [Accepted: 12/21/2017] [Indexed: 11/29/2022]
Abstract
BACKGROUND The epidemic of the 2016-2017 influenza season in Taiwan started early with moderate activity and was predominated by the influenza A(H3N2) virus. However, the influenza activity increased dramatically during the late stage of the 2016-2017 season. OBJECTIVES The genetic and antigenic characteristics of the influenza A(H3N2) virus circulating in Taiwan during the 2016-2017 season were investigated. The relationship between virus clades and the patients' 2016-2017 vaccination histories was determined. STUDY DESIGN Respiratory samples from patients with influenza-like illness in the community, clustered outbreaks, and inpatients with severe complications were tested for influenza virus. Influenza gene sequencing, phylogenetic analysis and hemagglutination inhibition assay were performed. RESULTS A total of 1185, 690 and 353 cases of outpatients, inpatients and cluster events were tested positive for the A(H3N2) virus in this report. Multiple clades of the H3N2 virus co-circulated. New genetic variants were detected, including clade 3C.2a.1 with additional N121 K, K92R or T135 K mutations, 3C.2a.3a with T135 K and R150 K mutations and 3C.2a.4. The proportions of N121 K and T135 K mutations were continuously increasing. Most of the viruses (85.4%, 111/130) were antigenically related to the current vaccine strain. Infection by different clade H3N2 viruses did not correlate with immunization with the 2016-2017 vaccine. CONCLUSIONS The data in this study indicate that antigenic drift is not the primary determinant of the epidemic wave at the end of the 2016-2017 season. The fitness changes in new variants, waning immunity and climatic changes are considered as possible contributors to the resurgence of the influenza A(H3N2) virus.
Collapse
Affiliation(s)
- Ji-Rong Yang
- Centers for Disease Control, Taipei, Taiwan, ROC
| | - Shu-Zhen Hsu
- Centers for Disease Control, Taipei, Taiwan, ROC
| | - Chuan-Yi Kuo
- Centers for Disease Control, Taipei, Taiwan, ROC
| | | | | | | | | |
Collapse
|
22
|
Jia WQ, Jing Z, Liu X, Feng XY, Liu YY, Wang SQ, Xu WR, Liu JW, Cheng XC. Virtual identification of novel PPARα/γ dual agonists by scaffold hopping of saroglitazar. J Biomol Struct Dyn 2017; 36:3496-3512. [DOI: 10.1080/07391102.2017.1392363] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Wen-Qing Jia
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Zhi Jing
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Xin Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Xiao-Yan Feng
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Ya-Ya Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Shu-Qing Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Wei-Ren Xu
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin, China
| | - Jian-Wen Liu
- State Key Laboratory of Bioreactor Engineering & Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Xian-Chao Cheng
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| |
Collapse
|