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Zeba A, Sekar K, Ganjiwale A. M Protein from Dengue virus oligomerizes to pentameric channel protein: in silico analysis study. Genomics Inform 2023; 21:e41. [PMID: 37813637 PMCID: PMC10584644 DOI: 10.5808/gi.23035] [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: 04/25/2023] [Revised: 06/12/2023] [Accepted: 07/11/2023] [Indexed: 10/11/2023] Open
Abstract
The Dengue virus M protein is a 75 amino acid polypeptide with two helical transmembranes (TM). The TM domain oligomerizes to form an ion channel, facilitating viral release from the host cells. The M protein has a critical role in the virus entry and life cycle, making it a potent drug target. The oligomerization of the monomeric protein was studied using ab initio modeling and molecular dynamics (MD) simulation in an implicit membrane environment. The representative structures obtained showed pentamer as the most stable oligomeric state, resembling an ion channel. Glutamic acid, threonine, serine, tryptophan, alanine, isoleucine form the pore-lining residues of the pentameric channel, conferring an overall negative charge to the channel with approximate length of 51.9 Å. Residue interaction analysis (RIN) for M protein shows that Ala94, Leu95, Ser112, Glu124, and Phe155 are the central hub residues representing the physicochemical interactions between domains. The virtual screening with 165 different ion channel inhibitors from the ion channel library shows monovalent ion channel blockers, namely lumacaftor, glipizide, gliquidone, glisoxepide, and azelnidipine to be the inhibitors with high docking scores. Understanding the three-dimensional structure of M protein will help design therapeutics and vaccines for Dengue infection.
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Affiliation(s)
- Ayesha Zeba
- Department of Life Sciences, Bangalore University, Bangalore, Karnataka 560056, India
| | - Kanagaraj Sekar
- Laboratory for Structural Biology and Bio-computing, Computational and Data Sciences, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Anjali Ganjiwale
- Department of Life Sciences, Bangalore University, Bangalore, Karnataka 560056, India
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Dengue virus infection - a review of pathogenesis, vaccines, diagnosis and therapy. Virus Res 2023; 324:199018. [PMID: 36493993 DOI: 10.1016/j.virusres.2022.199018] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 10/19/2022] [Accepted: 12/04/2022] [Indexed: 12/12/2022]
Abstract
The transmission of dengue virus (DENV) from an infected Aedes mosquito to a human, causes illness ranging from mild dengue fever to fatal dengue shock syndrome. The similar conserved structure and sequence among distinct DENV serotypes or different flaviviruses has resulted in the occurrence of cross reaction followed by antibody-dependent enhancement (ADE). Thus far, the vaccine which can provide effective protection against infection by different DENV serotypes remains the biggest hurdle to overcome. Therefore, deep investigation is crucial for the potent and effective therapeutic drugs development. In addition, the cross-reactivity of flaviviruses that leads to false diagnosis in clinical settings could result to delay proper intervention management. Thus, the accurate diagnostic with high specificity and sensitivity is highly required to provide prompt diagnosis in respect to render early treatment for DENV infected individuals. In this review, the recent development of neutralizing antibodies, antiviral agents, and vaccine candidates in therapeutic platform for DENV infection will be discussed. Moreover, the discovery of antigenic cryptic epitopes, principle of molecular mimicry, and application of single-chain or single-domain antibodies towards DENV will also be presented.
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S AH, Pujar GV, Sethu AK, Bhagyalalitha M, Singh M. Dengue structural proteins as antiviral drug targets: Current status in the drug discovery & development. Eur J Med Chem 2021; 221:113527. [PMID: 34020338 DOI: 10.1016/j.ejmech.2021.113527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/30/2021] [Accepted: 04/20/2021] [Indexed: 01/04/2023]
Abstract
Dengue virus belongs to the class of RNA viruses and subclass of enveloped single-stranded positive-sense RNA virus. It causes dengue fever (DF), dengue hemorrhagic fever (DHF), or dengue shock syndrome (DSS), where DHF and DSS are life-threatening. Even though dengue is an age-old disease, it is still a mystery and continues to be a global threat. Numerous attempts have been carried out in the past few decades to eradicate the virus through vaccine and antiviral drugs, but still battle continues. In this review, the possible drug targets for discovery and development of potential antiviral drugs against structural proteins of dengue virus, the current development status of the antiviral drugs against dengue around the world, and challenges that need to be addressed to overcome the shortcomings in the process of drug discovery have been discussed.
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Affiliation(s)
- Akshatha H S
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Sri Shivarathreeshwara Nagara, Mysuru, 570015, India
| | - Gurubasavaraj V Pujar
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Sri Shivarathreeshwara Nagara, Mysuru, 570015, India.
| | - Arun Kumar Sethu
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Sri Shivarathreeshwara Nagara, Mysuru, 570015, India
| | - Meduri Bhagyalalitha
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Sri Shivarathreeshwara Nagara, Mysuru, 570015, India
| | - Manisha Singh
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Sri Shivarathreeshwara Nagara, Mysuru, 570015, India
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Blight J, Alves E, Reyes-Sandoval A. Considering Genomic and Immunological Correlates of Protection for a Dengue Intervention. Vaccines (Basel) 2019; 7:E203. [PMID: 31816907 PMCID: PMC6963661 DOI: 10.3390/vaccines7040203] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/25/2019] [Accepted: 11/27/2019] [Indexed: 01/18/2023] Open
Abstract
Over three billion are at risk of dengue infection with more than 100 million a year presenting with symptoms that can lead to deadly haemorrhagic disease. There are however no treatments available and the only licensed vaccine shows limited efficacy and is able to enhance the disease in some cases. These failures have mainly been due to the complex pathology and lack of understanding of the correlates of protection for dengue virus (DENV) infection. With increasing data suggesting both a protective and detrimental effect for antibodies and CD8 T-cells whilst having complex environmental dynamics. This review discusses the roles of genomic and immunological aspects of DENV infection, providing both a historical interpretation and fresh discussion on how this information can be used for the next generation of dengue interventions.
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Affiliation(s)
- Joshua Blight
- Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, South Kensington, London SW7 2AZ, UK; (J.B.); (E.A.)
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, The Henry Wellcome Building for Molecular Physiology, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Eduardo Alves
- Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, South Kensington, London SW7 2AZ, UK; (J.B.); (E.A.)
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, The Henry Wellcome Building for Molecular Physiology, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Arturo Reyes-Sandoval
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, The Henry Wellcome Building for Molecular Physiology, Roosevelt Drive, Oxford OX3 7BN, UK
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Faheem M, Barbosa Lima JC, Jamal SB, Silva PA, Barbosa JARG. An insight into dengue virus proteins as potential drug/vaccine targets. Future Virol 2019. [DOI: 10.2217/fvl-2019-0107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dengue virus (DENV) is an arbovirus that belongs to family flaviviridae. Its genome is composed of a single stranded RNA molecule that encodes a single polyprotein. The polyprotein is processed by viral and cellular proteases to generate ten viral proteins. There are four antigenically distinct serotypes of DENV (DENV1, DENV2, DENV3 and DENV4), which are genetically related. Although protein variability is a major problem in dengue treatment, the functional and structural studies of individual proteins are equally important in treatment development. The data accumulated on dengue proteins are significant to provide detailed understanding of viral infection, replication, host-immune evasion and pathogenesis. In this review, we summarized the detailed current knowledge about DENV proteins.
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Affiliation(s)
- Muhammad Faheem
- Laboratory of Biophysics, Department of Cellular Biology, University of Brasilia, Brasilia-DF 70910-900, Brazil
- Post-graduate program of Genomics Sciences & Biotechnology, Catholic University of Brasilia, Brasília-DF 70790-160, Brazil
| | - Jônatas Cunha Barbosa Lima
- Laboratory of Biophysics, Department of Cellular Biology, University of Brasilia, Brasilia-DF 70910-900, Brazil
| | - Syed Babar Jamal
- Department of Biological Sciences, National University of Medical Sciences, The Mall road, Rawalpindi, Punjab 46000, Pakistan
| | - Paula Andreia Silva
- Post-graduate program of Genomics Sciences & Biotechnology, Catholic University of Brasilia, Brasília-DF 70790-160, Brazil
| | - João Alexandre Ribeiro Gonçalves Barbosa
- Laboratory of Biophysics, Department of Cellular Biology, University of Brasilia, Brasilia-DF 70910-900, Brazil
- Post-graduate program of Genomics Sciences & Biotechnology, Catholic University of Brasilia, Brasília-DF 70790-160, Brazil
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Tripathi NK, Shrivastava A. Recent Developments in Recombinant Protein-Based Dengue Vaccines. Front Immunol 2018; 9:1919. [PMID: 30190720 PMCID: PMC6115509 DOI: 10.3389/fimmu.2018.01919] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Accepted: 08/03/2018] [Indexed: 12/11/2022] Open
Abstract
Recombinant proteins are gaining enormous importance these days due to their wide application as biopharmaceutical products and proven safety record. Various recombinant proteins of therapeutic and prophylactic importance have been successfully produced in microbial and higher expression host systems. Since there is no specific antiviral therapy available against dengue, the prevention by vaccination is the mainstay in reducing the disease burden. Therefore, efficacious vaccines are needed to control the spread of dengue worldwide. Dengue is an emerging viral disease caused by any of dengue virus 1-4 serotypes that affects the human population around the globe. Dengue virus is a single stranded RNA virus encoding three structural proteins (capsid protein, pre-membrane protein, and envelope protein) and seven non-structural proteins (NS1, NS2a, NS2b, NS3, NS4a, NS4b, NS5). As the only licensed dengue vaccine (Dengvaxia) is unable to confer balanced protection against all the serotypes, therefore various approaches for development of dengue vaccines including tetravalent live attenuated, inactivated, plasmid DNA, virus-vectored, virus-like particles, and recombinant subunit vaccines are being explored. These candidates are at different stages of vaccine development and have their own merits and demerits. The promising subunit vaccines are mainly based on envelope or its domain and non-structural proteins of dengue virus. These proteins have been produced in different hosts and are being investigated for development of a successful dengue vaccine. Novel immunogens have been designed employing various strategies like protein engineering and fusion of antigen with various immunostimulatory motif to work as self-adjuvant. Moreover, recombinant proteins can be formulated with novel adjuvants to enhance the immunogenicity and thus conferring better protection to the vaccinees. With the advent of newer and safer host systems, these recombinant proteins can be produced in a cost effective manner at large scale for vaccine studies. In this review, we summarize recent developments in recombinant protein based dengue vaccines that could lead to a good number of efficacious vaccine candidates for future human use and ultimately alternative dengue vaccine candidates.
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Affiliation(s)
- Nagesh K. Tripathi
- Bioprocess Scale Up Facility, Defence Research and Development Establishment, Gwalior, India
| | - Ambuj Shrivastava
- Division of Virology, Defence Research and Development Establishment, Gwalior, India
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Scott C, Griffin S. Viroporins: structure, function and potential as antiviral targets. J Gen Virol 2015; 96:2000-2027. [PMID: 26023149 DOI: 10.1099/vir.0.000201] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The channel-forming activity of a family of small, hydrophobic integral membrane proteins termed 'viroporins' is essential to the life cycles of an increasingly diverse range of RNA and DNA viruses, generating significant interest in targeting these proteins for antiviral development. Viroporins vary greatly in terms of their atomic structure and can perform multiple functions during the virus life cycle, including those distinct from their role as oligomeric membrane channels. Recent progress has seen an explosion in both the identification and understanding of many such proteins encoded by highly significant pathogens, yet the prototypic M2 proton channel of influenza A virus remains the only example of a viroporin with provenance as an antiviral drug target. This review attempts to summarize our current understanding of the channel-forming functions for key members of this growing family, including recent progress in structural studies and drug discovery research, as well as novel insights into the life cycles of many viruses revealed by a requirement for viroporin activity. Ultimately, given the successes of drugs targeting ion channels in other areas of medicine, unlocking the therapeutic potential of viroporins represents a valuable goal for many of the most significant viral challenges to human and animal health.
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Affiliation(s)
- Claire Scott
- Leeds Institute of Cancer & Pathology and Leeds CRUK Clinical Centre, Faculty of Medicine and Health, St James's University Hospital, University of Leeds, Beckett Street, Leeds LS9 7TF, UK
| | - Stephen Griffin
- Leeds Institute of Cancer & Pathology and Leeds CRUK Clinical Centre, Faculty of Medicine and Health, St James's University Hospital, University of Leeds, Beckett Street, Leeds LS9 7TF, UK
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Stolp ZD, Smurthwaite CA, Reed C, Williams W, Dharmawan A, Djaballah H, Wolkowicz R. A Multiplexed Cell-Based Assay for the Identification of Modulators of Pre-Membrane Processing as a Target against Dengue Virus. ACTA ACUST UNITED AC 2015; 20:616-26. [PMID: 25724189 PMCID: PMC4438100 DOI: 10.1177/1087057115571247] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 01/14/2015] [Indexed: 12/19/2022]
Abstract
The DenV pre-membrane protein (prM) is a crucial chaperone for the viral envelope protein, preventing premature fusion with vesicles during viral export. prM molecules in immature particles are cleaved by host proteases, leading to mature fusogenic virions. Blockade of prM cleavage would restrict fusion and represents a novel druggable opportunity against DenV. We have thus established a cell-based platform to monitor prM processing that relies on an engineered two-tag scaffold that travels to the cell surface through the secretory pathway. The assay discriminates between a single cell-surface tag when prM is cleaved and two tags when it is not, as detected through fluorescent-coupled antibodies by flow cytometry. The assay, miniaturized into a 96-well plate format, was multiplexed with the HIV-1 envelope boundary, also cleaved in the same pathway. A pilot screen against 1280 compounds was executed, leading to the identification of a potential active and corroborating the robustness of our assay for large-scale screening. We describe for the first time a cell-based assay that monitors DenV prM processing within the classical secretory pathway, which was exploited to identify a potential novel drug against DenV.
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Affiliation(s)
- Zachary D Stolp
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Connor Reed
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Wesley Williams
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Andre Dharmawan
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Roland Wolkowicz
- Department of Biology, San Diego State University, San Diego, CA, USA
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Nemésio H, Villalaín J. Membranotropic Regions of the Dengue Virus prM Protein. Biochemistry 2014; 53:5280-9. [DOI: 10.1021/bi500724k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Henrique Nemésio
- Instituto de Biología
Molecular y Celular, Universidad “Miguel Hernández”, E-03202 Elche-Alicante, Spain
| | - José Villalaín
- Instituto de Biología
Molecular y Celular, Universidad “Miguel Hernández”, E-03202 Elche-Alicante, Spain
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Abstract
Dengue virus (DENV) is an emerging mosquito-borne human pathogen that affects millions of individuals each year by causing severe and potentially fatal syndromes. Despite intense research efforts, no approved vaccine or antiviral therapy is yet available. Overcoming this limitation requires detailed understanding of the intimate relationship between the virus and its host cell, providing the basis to devise optimal prophylactic and therapeutic treatment options. With the advent of novel high-throughput technologies including functional genomics, transcriptomics, proteomics, and lipidomics, new important insights into the DENV replication cycle and the interaction of this virus with its host cell have been obtained. In this chapter, we provide a comprehensive overview on the current status of the DENV research field, covering every step of the viral replication cycle with a particular focus on virus-host cell interaction. We will also review specific chemical inhibitors targeting cellular factors and processes of relevance for the DENV replication cycle and their possible exploitation for the development of next generation antivirals.
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