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Tillquist RC, Lladser ME. Low-dimensional representation of genomic sequences. J Math Biol 2019; 79:1-29. [PMID: 30929047 DOI: 10.1007/s00285-019-01348-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 11/12/2018] [Indexed: 01/09/2023]
Abstract
Numerous data analysis and data mining techniques require that data be embedded in a Euclidean space. When faced with symbolic datasets, particularly biological sequence data produced by high-throughput sequencing assays, conventional embedding approaches like binary and k-mer count vectors may be too high dimensional or coarse-grained to learn from the data effectively. Other representation techniques such as Multidimensional Scaling (MDS) and Node2Vec may be inadequate for large datasets as they require recomputing the full embedding from scratch when faced with new, unclassified data. To overcome these issues we amend the graph-theoretic notion of "metric dimension" to that of "multilateration." Much like trilateration can be used to represent points in the Euclidean plane by their distances to three non-colinear points, multilateration allows us to represent any node in a graph by its distances to a subset of nodes. Unfortunately, the problem of determining a minimal subset and hence the lowest dimensional embedding is NP-complete for general graphs. However, by specializing to Hamming graphs, which are particularly well suited to representing biological sequences, we can readily generate low-dimensional embeddings to map sequences of arbitrary length to a real space. As proof-of-concept, we use MDS, Node2Vec, and multilateration-based embeddings to classify DNA 20-mers centered at intron-exon boundaries. Although these different techniques perform comparably, MDS and Node2Vec potentially suffer from scalability issues with increasing sequence length whereas multilateration provides an efficient means of mapping long genomic sequences.
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Affiliation(s)
- Richard C Tillquist
- Department of Computer Science, The University of Colorado, Boulder, CO, 80309-0526, USA
| | - Manuel E Lladser
- Department of Applied Mathematics, The University of Colorado, Boulder, CO, 80309-0526, USA.
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52
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Nitsche C. Proteases from dengue, West Nile and Zika viruses as drug targets. Biophys Rev 2019; 11:157-165. [PMID: 30806881 DOI: 10.1007/s12551-019-00508-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 02/13/2019] [Indexed: 12/13/2022] Open
Abstract
Proteases from flaviviruses have gained substantial interest as potential drug targets to combat infectious diseases caused by dengue, West Nile, Zika and related viruses. Despite nearly two decades of drug discovery campaigns, promising lead compounds for clinical trials have not yet been identified. The main challenges for successful lead compound development are associated with limited drug-likeness of inhibitors and structural ambiguity of the protease target. This brief review focuses on the available information on the structure of flavivirus proteases and their interactions with inhibitors and attempts to point the way forward for successful identification of future lead compounds.
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Affiliation(s)
- Christoph Nitsche
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia.
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Abdulrahman AY, Khazali AS, Teoh TC, Rothan HA, Yusof R. Novel Peptides Inhibit Zika NS2B-NS3 Serine Protease and Virus Replication in Human Hepatic Cell Line. Int J Pept Res Ther 2019. [DOI: 10.1007/s10989-019-09808-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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54
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Morazzani EM, Compton JR, Leary DH, Berry AV, Hu X, Marugan JJ, Glass PJ, Legler PM. Proteolytic cleavage of host proteins by the Group IV viral proteases of Venezuelan equine encephalitis virus and Zika virus. Antiviral Res 2019; 164:106-122. [PMID: 30742841 DOI: 10.1016/j.antiviral.2019.02.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 01/13/2019] [Accepted: 02/01/2019] [Indexed: 12/12/2022]
Abstract
The alphaviral nonstructural protein 2 (nsP2) cysteine proteases (EC 3.4.22.-) are essential for the proteolytic processing of the nonstructural (ns) polyprotein and are validated drug targets. A common secondary role of these proteases is to antagonize the effects of interferon (IFN). After delineating the cleavage site motif of the Venezuelan equine encephalitis virus (VEEV) nsP2 cysteine protease, we searched the human genome to identify host protein substrates. Here we identify a new host substrate of the VEEV nsP2 protease, human TRIM14, a component of the mitochondrial antiviral-signaling protein (MAVS) signalosome. Short stretches of homologous host-pathogen protein sequences (SSHHPS) are present in the nonstructural polyprotein and TRIM14. A 25-residue cyan-yellow fluorescent protein TRIM14 substrate was cleaved in vitro by the VEEV nsP2 protease and the cleavage site was confirmed by tandem mass spectrometry. A TRIM14 cleavage product also was found in VEEV-infected cell lysates. At least ten other Group IV (+)ssRNA viral proteases have been shown to cleave host proteins involved in generating the innate immune responses against viruses, suggesting that the integration of these short host protein sequences into the viral protease cleavage sites may represent an embedded mechanism of IFN antagonism. This interference mechanism shows several parallels with those of CRISPR/Cas9 and RNAi/RISC, but with a protease recognizing a protein sequence common to both the host and pathogen. The short host sequences embedded within the viral genome appear to be analogous to the short phage sequences found in a host's CRISPR spacer sequences. To test this algorithm, we applied it to another Group IV virus, Zika virus (ZIKV), and identified cleavage sites within human SFRP1 (secreted frizzled related protein 1), a retinal Gs alpha subunit, NT5M, and Forkhead box protein G1 (FOXG1) in vitro. Proteolytic cleavage of these proteins suggests a possible link between the protease and the virus-induced phenotype of ZIKV. The algorithm may have value for selecting cell lines and animal models that recapitulate virus-induced phenotypes, predicting host-range and susceptibility, selecting oncolytic viruses, identifying biomarkers, and de-risking live virus vaccines. Inhibitors of the proteases that utilize this mechanism may both inhibit viral replication and alleviate suppression of the innate immune responses.
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Affiliation(s)
- Elaine M Morazzani
- United States Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - Jaimee R Compton
- Center for Bio/molecular Science and Engineering, U.S. Naval Research Laboratory, Washington, DC 20375, USA
| | - Dagmar H Leary
- Center for Bio/molecular Science and Engineering, U.S. Naval Research Laboratory, Washington, DC 20375, USA
| | | | - Xin Hu
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, Rockville, MD 20850, USA
| | - Juan J Marugan
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, Rockville, MD 20850, USA
| | - Pamela J Glass
- United States Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - Patricia M Legler
- Center for Bio/molecular Science and Engineering, U.S. Naval Research Laboratory, Washington, DC 20375, USA.
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55
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Tahir Ul Qamar M, Maryam A, Muneer I, Xing F, Ashfaq UA, Khan FA, Anwar F, Geesi MH, Khalid RR, Rauf SA, Siddiqi AR. Computational screening of medicinal plant phytochemicals to discover potent pan-serotype inhibitors against dengue virus. Sci Rep 2019; 9:1433. [PMID: 30723263 PMCID: PMC6363786 DOI: 10.1038/s41598-018-38450-1] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 12/19/2018] [Indexed: 02/07/2023] Open
Abstract
Emergence of Dengue as one of the deadliest viral diseases prompts the need for development of effective therapeutic agents. Dengue virus (DV) exists in four different serotypes and infection caused by one serotype predisposes its host to another DV serotype heterotypic re-infection. We undertook virtual ligand screening (VLS) to filter compounds against DV that may inhibit inclusively all of its serotypes. Conserved non-structural DV protein targets such as NS1, NS3/NS2B and NS5, which play crucial role in viral replication, infection cycle and host interaction, were selected for screening of vital antiviral drug leads. A dataset of plant based natural antiviral derivatives was developed. Molecular docking was performed to estimate the spatial affinity of target compounds for the active sites of DV’s NS1, NS3/NS2B and NS5 proteins. The drug likeliness of the screened compounds was followed by ADMET analysis whereas the binding behaviors were further elucidated through molecular dynamics (MD) simulation experiments. VLS screened three potential compounds including Canthin-6-one 9-O-beta-glucopyranoside, Kushenol W and Kushenol K which exhibited optimal binding with all the three conserved DV proteins. This study brings forth novel scaffolds against DV serotypes to serve as lead molecules for further optimization and drug development against all DV serotypes with equal effect against multiple disease causing DV proteins. We therefore anticipate that the insights given in the current study could be regarded valuable towards exploration and development of a broad-spectrum natural anti-dengue therapy.
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Affiliation(s)
| | - Arooma Maryam
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Iqra Muneer
- School of Life Sciences, University of Science and Technology of China, Hefei, P.R. China
| | - Feng Xing
- College of Informatics, Huazhong Agricultural University, Wuhan, P.R. China
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Faheem Ahmed Khan
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education China, Huazhong Agricultural University, Wuhan, P.R. China
| | - Farooq Anwar
- Department of Chemistry, University of Sargodha, Sargodha, Pakistan
| | - Mohammed H Geesi
- Department of Chemistry, College of Sciences and Humanities, Prince Sattam Bin Abdulaziz University, Al Kharj, Saudi Arabia.
| | - Rana Rehan Khalid
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Sadaf Abdul Rauf
- Department of Computer Science, Fatima Jinnah Women University, Rawalpindi, Pakistan
| | - Abdul Rauf Siddiqi
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan.
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56
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Ahmad Z, Poh CL. The Conserved Molecular Determinants of Virulence in Dengue Virus. Int J Med Sci 2019; 16:355-365. [PMID: 30911269 PMCID: PMC6428985 DOI: 10.7150/ijms.29938] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 12/17/2018] [Indexed: 12/22/2022] Open
Abstract
Dengue virus belongs to the Flaviviridae family which also includes viruses such as the Zika, West Nile and yellow fever virus. Dengue virus generally causes mild disease, however, more severe forms of the dengue virus infection, dengue haemorrhagic fever (DHF) and dengue haemorrhagic fever with shock syndrome (DSS) can also occur, resulting in multiple organ failure and even death, especially in children. The only dengue vaccine available in the market, CYD-TDV offers limited coverage for vaccinees from 9-45 years of age and is only recommended for individuals with prior dengue exposure. A number of mutations that were shown to attenuate virulence of dengue virus in vitro and/or in vivo have been identified in the literature. The mutations which fall within the conserved regions of all four dengue serotypes are discussed. This review hopes to provide information leading to the construction of a live attenuated dengue vaccine that is suitable for all ages, irrespective of the infecting dengue serotype and prior dengue exposure.
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Affiliation(s)
- Zuleeza Ahmad
- Centre for Virus and Vaccine Research, School of Science and Technology, Sunway University, 47500 Subang Jaya, Selangor, Malaysia
| | - Chit Laa Poh
- Centre for Virus and Vaccine Research, School of Science and Technology, Sunway University, 47500 Subang Jaya, Selangor, Malaysia
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57
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Dengue drug discovery: Progress, challenges and outlook. Antiviral Res 2018; 163:156-178. [PMID: 30597183 DOI: 10.1016/j.antiviral.2018.12.016] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 12/22/2018] [Accepted: 12/25/2018] [Indexed: 12/14/2022]
Abstract
In the context of the only available vaccine (DENGVAXIA) that was marketed in several countries, but poses higher risks to unexposed individuals, the development of antivirals for dengue virus (DENV), whilst challenging, would bring significant benefits to public health. Here recent progress in the field of DENV drug discovery made in academic laboratories and industry is reviewed. Characteristics of an ideal DENV antiviral molecule, given the specific immunopathology provoked by this acute viral infection, are described. New chemical classes identified from biochemical, biophysical and phenotypic screens that target viral (especially NS4B) and host proteins, offer promising opportunities for further development. In particular, new methodologies ("omics") can accelerate the discovery of much awaited flavivirus specific inhibitors. Challenges and opportunities in lead identification activities as well as the path to clinical development of dengue drugs are discussed. To galvanize DENV drug discovery, collaborative public-public partnerships and open-access resources will greatly benefit both the DENV research community and DENV patients.
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58
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Norazharuddin H, Lai NS. Roles and Prospects of Dengue Virus Non-structural Proteins as Antiviral Targets: An Easy Digest. Malays J Med Sci 2018; 25:6-15. [PMID: 30914859 PMCID: PMC6419879 DOI: 10.21315/mjms2018.25.5.2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Accepted: 03/21/2018] [Indexed: 12/13/2022] Open
Abstract
Dengue is a neglected disease caused by the infection of dengue virus which is transmitted by Aedes mosquitoes and to some, it could be fatal. Regardless of the enormous work devoted to research for the treatment of dengue, to this day there is no cure, and treatment is solely limited to supportive care by treating the symptoms. The inhibition of the viral RNA non-structural enzymes has been the most popular approach amongst the strategies applied to the search and development of dengue antivirals. This review is a compact digest of what is already known of the roles and the prospects of the dengue virus non-structural proteins NS1, NS2BNS3, NS4A, NS4B and NS5 as the targets for antiviral studies including the recent progress that has been published regarding their roles.
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Affiliation(s)
- Hannah Norazharuddin
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800 USM, Pulau Pinang, Malaysia
| | - Ngit Shin Lai
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800 USM, Pulau Pinang, Malaysia
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59
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Zhu G, Pan A, Grüber G, Lu L. Conformational states of Zika virus non-structural protein 3 determined by molecular dynamics simulations with small-angle X-Ray scattering data. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 143:13-19. [PMID: 30291845 DOI: 10.1016/j.pbiomolbio.2018.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 09/17/2018] [Accepted: 09/29/2018] [Indexed: 11/16/2022]
Abstract
Zika virus (ZIKV) has become a great public health emergency. Its non-structural protein 3 (NS3) is a key enzyme in viral replication and has been considered as a potential therapeutic target. A conformational characterization of ZIKV NS3 is critical for a comprehensive understanding of its molecular interactions and functions. However, the high conformational flexibility of solution NS3 obstacles the structural characterization of NS3 solely from the experimental observable that averages over its heterogeneous conformations. Here, we employed replica exchange with solute tempering (REST) method to simulate the di-domain protein ZIKV NS3. Three independent MD simulations identified a conserved conformational ensemble of NS3, consisting of a major conformational state and several minor states from compact to loose conformations. The major state agrees well with the scattering profile from small-angle X-ray scattering (SAXS) experiments. Moreover, the simulated ensemble is supported by a direct data-fitting result that requires both short- and long-range structural contacts to recover the experimental data. We discussed the interplay between simulation and experiment in ensemble construction of flexible biomolecules and shed light on the physically derived conformational ensembles.
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Affiliation(s)
- Guanhua Zhu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Ankita Pan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Lanyuan Lu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore.
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60
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Hill ME, Kumar A, Wells JA, Hobman TC, Julien O, Hardy JA. The Unique Cofactor Region of Zika Virus NS2B-NS3 Protease Facilitates Cleavage of Key Host Proteins. ACS Chem Biol 2018; 13:2398-2405. [PMID: 30080377 DOI: 10.1021/acschembio.8b00508] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Zika virus is an emerging mosquito-borne pathogen capable of severely damaging developing fetuses as well as causing neurological abnormalities in adults. The molecular details of how Zika virus causes pathologies that are unique among the flavivirus family remain poorly understood and have contributed to the lack of Zika antiviral therapies. To elucidate how Zika virus protease (ZVP) affects host cellular pathways and consequent pathologies, we used unbiased N-terminomics to identify 31 human proteins cleaved by the NS2B-NS3 protease. In particular, autophagy-related protein 16-1 (ATG16L1) and eukaryotic translation initiation factor 4 gamma 1 (eIF4G1) are dramatically depleted during Zika virus infection. ATG16L1 and eIF4G1 mediate type-II interferon production and host-cell translation, respectively, likely aiding immune system evasion and driving the Zika life cycle. Intriguingly, the NS2B cofactor region from Zika virus protease is essential for recognition of host cell substrates. Replacing the NS2B region in another flavivirus protease enabled recognition of novel Zika-specific substrates by hybrid proteases, suggesting that the cofactor is the principal determinant in ZVP substrate selection.
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Affiliation(s)
- Maureen E. Hill
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Anil Kumar
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - James A. Wells
- Department of Pharmaceutical Chemistry and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158, United States
| | - Tom C. Hobman
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Olivier Julien
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Jeanne A. Hardy
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
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Structurally- and dynamically-driven allostery of the chymotrypsin-like proteases of SARS, Dengue and Zika viruses. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 143:52-66. [PMID: 30217495 PMCID: PMC7111307 DOI: 10.1016/j.pbiomolbio.2018.08.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 08/09/2018] [Accepted: 08/24/2018] [Indexed: 01/19/2023]
Abstract
Coronavirus 3C-like and Flavivirus NS2B-NS3 proteases utilize the chymotrypsin fold to harbor their catalytic machineries but also contain additional domains/co-factors. Over the past decade, we aimed to decipher how the extra domains/co-factors mediate the catalytic machineries of SARS 3C-like, Dengue and Zika NS2B-NS3 proteases by characterizing their folding, structures, dynamics and inhibition with NMR, X-ray crystallography and MD simulations, and the results revealed: 1) the chymotrypsin fold of the SARS 3C-like protease can independently fold, while, by contrast, those of Dengue and Zika proteases lack the intrinsic capacity to fold without co-factors. 2) Mutations on the extra domain of SARS 3C-like protease can transform the active catalytic machinery into the inactive collapsed state by structurally-driven allostery. 3) Amazingly, even without detectable structural changes, mutations on the extra domain are sufficient to either inactivate or enhance the catalytic machinery of SARS 3C-like protease by dynamically-driven allostery. 4) Global networks of correlated motions have been identified: for SARS 3C-like protease, N214A inactivates the catalytic machinery by decoupling the network, while STI/A and STIF/A enhance by altering the patterns of the network. The global networks of Dengue and Zika proteases are coordinated by their NS2B-cofactors. 5) Natural products were identified to allosterically inhibit Zika and Dengue proteases through binding a pocket on the back of the active site. Therefore, by introducing extra domains/cofactors, nature develops diverse strategies to regulate the catalytic machinery embedded on the chymotrypsin fold through folding, structurally- and dynamically-driven allostery, all of which might be exploited to develop antiviral drugs.
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Yusufzai SK, Osman H, Khan MS, Abd Razik BM, Ezzat MO, Mohamad S, Sulaiman O, Gansau JA, Parumasivam T. 4-Thiazolidinone coumarin derivatives as two-component NS2B/NS3 DENV flavivirus serine protease inhibitors: synthesis, molecular docking, biological evaluation and structure-activity relationship studies. Chem Cent J 2018; 12:69. [PMID: 29896651 PMCID: PMC5997609 DOI: 10.1186/s13065-018-0435-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 05/12/2018] [Indexed: 12/04/2022] Open
Abstract
A series of novel 4-thiazolidinone inhibitors SKYa-SKYg, containing coumarin as a core structure were synthesized via facile and efficient method. The structures of the synthesized compounds were established by extensive spectroscopic studies (FT IR, 1D NMR, 2D NMR, LC-MS) and elemental analysis. All the synthesized hybrids were further evaluated for their potential as anti-tubercular agents against Mycobacterium tuberculosis H37Rv ATCC 25618, and anti-bacterial agents against Escherichia coli, Enterobacter aerogenes, Salmonella typhi, Streptococcus pneumoniae and Staphylococcus aureus. Interestingly, the hybrids displayed potent bioactivity. However, compounds SKYc, SKYd, and SKYe appeared to be more effective against the tested bacterial strains, among which compound SKYb showed the highest inhibition against all the bacterial strains ranging from 41 to 165 μg/mL, as compared to the standards, streptomycin, kanamycin and vancomycin. Moreover, derivative SKYa was found to be the strongest against M. tuberculosis (83 μg/mL). Additionally, the anti-dengue potential of the coumarin hybrids as two-component NS2B/NS3 DENV flavivirus serine protease inhibitors was calculated using computational molecular docking approach, with reference to the standards 4-hydroxypanduratin, panduratin and ethyl 3-(4-(hydroxymethyl)-2-methoxy-5-nitrophenoxy)propanoate with DS of - 3.379, - 3.189 and - 3.381, respectively. The docking results revealed that the synthesized hybrids exhibited potent anti-dengue activity among which compounds SKYf, SKYd, SKYc and SKYe were found to be the best ones with docking scores of - 4.014, - 3.964, - 3.905 and - 3.889. In summary, we discovered 4-thiazolidinone coumarin derivatives as a new scaffold that may eventually yield useful compounds in the treatment of bacterial and viral infections.
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Affiliation(s)
- Samina Khan Yusufzai
- School of Chemical Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia
- School of Industrial Technology, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Hasnah Osman
- School of Chemical Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia.
| | - Mohammad Shaheen Khan
- Industrial Chemistry Programme, Faculty of Science and Natural Resources, Universiti Malaysia Sabah, 88400, Kota Kinabalu, Sabah, Malaysia
| | - Basma M Abd Razik
- College of Pharmacy, Al-Mustansiriyah University, Baghdad, 10001, Iraq
| | - Mohammed Oday Ezzat
- College of Education for Women, University of Anbar, Ramadi, Anbar, 31001, Iraq
| | - Suriyati Mohamad
- School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Othman Sulaiman
- School of Industrial Technology, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Jualang Azlan Gansau
- Biotechnology Programme, Faculty of Science and Natural Resources, Universiti Malaysia Sabah, 88400, Kota Kinabalu, Sabah, Malaysia
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Synthesis, X-ray crystallographic study, pharmacology and docking of hydrazinyl thiazolyl coumarins as dengue virus NS2B/NS3 serine protease inhibitors. Med Chem Res 2018. [DOI: 10.1007/s00044-018-2179-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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64
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Peng M, Swarbrick CMD, Chan KWK, Luo D, Zhang W, Lai X, Li G, Vasudevan SG. Luteolin escape mutants of dengue virus map to prM and NS2B and reveal viral plasticity during maturation. Antiviral Res 2018; 154:87-96. [PMID: 29665375 DOI: 10.1016/j.antiviral.2018.04.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 04/10/2018] [Accepted: 04/13/2018] [Indexed: 10/17/2022]
Abstract
We previously showed that luteolin, a well-known plant-derived component found in the "heat clearing" class of Traditional Chinese Medicine (TCM) herbs, is an uncompetitive inhibitor (Ki 58.6 μM) of the host proprotein convertase furin, an endoprotease that is required for maturation of flaviviruses in the trans-Golgi compartment. Luteolin also weakly inhibited recombinant dengue virus NS2B/NS3 protease (Ki 140.36 μM) non-competitively. In order to further explore the mechanism of inhibition we isolated resistant mutants by continuous passaging of DENV2 in the presence of increasing concentrations of luteolin. Nucleotide sequence analysis of the luteolin-resistant escape mutants revealed nucleotide changes that lead to amino acid substitutions in the prM (T79R) and NS2B (I114M) genes. These mutations were introduced into a DENV2 infectious clone and tested for replication in Huh-7 cells. Interestingly we found that the replication kinetics of prM T19R-NS2B I114M double-mutant (DM) was similar to wild-type virus (WT). On the other hand the prM T79R single mutant (SM1) was attenuated and the NS2B I114M single mutant (SM2) showed enhanced replication. Time of drug addition assay with luteolin showed that the mutant viruses were able to produce more mature virions than WT in the order DM > SM2>SM1>WT. Exogenous addition of furin to purified immature WT or mutant viruses revealed that luteolin blocked the prM cleavage of WT and SM2 at a similar level. On the other hand the SM1 immature virus showed some cleavage while the DM immature virus revealed efficient furin cleavage of prM even in the presence of 50 μM luteolin. Our findings suggest that luteolin inhibition of furin may occur at host/pathogen interface that permits the virus to escape the suppression by mutating key residue that may lead to an altered interface.
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Affiliation(s)
- Minhua Peng
- Program in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore; Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | | | - Kitti Wing-Ki Chan
- Program in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore; Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921, Singapore
| | - Wei Zhang
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Xiaoping Lai
- Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Geng Li
- Center for Animal Experiment, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Subhash G Vasudevan
- Program in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore; Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore.
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Tian YS, Zhou Y, Takagi T, Kameoka M, Kawashita N. Dengue Virus and Its Inhibitors: A Brief Review. Chem Pharm Bull (Tokyo) 2018; 66:191-206. [PMID: 29491253 DOI: 10.1248/cpb.c17-00794] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The global occurrence of viral infectious diseases poses a significant threat to human health. Dengue virus (DENV) infection is one of the most noteworthy of these infections. According to a WHO survey, approximately 400 million people are infected annually; symptoms deteriorate in approximately one percent of cases. Numerous foundational and clinical investigations on viral epidemiology, structure and function analysis, infection source and route, therapeutic targets, vaccines, and therapeutic drugs have been conducted by both academic and industrial researchers. At present, CYD-TDV or Dengvaxia® is the only approved vaccine, but potent inhibitors are currently under development. In this review, an overview of the viral life circle and the history of DENVs is presented, and the most recently reported antiviral candidates and newly discovered promising targets are focused and summarized. We believe that these successes and failures have enabled progress in anti-DENV drug discovery and hope that our review will stimulate further innovation in this area.
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Affiliation(s)
- Yu-Shi Tian
- Graduate School of Pharmaceutical Sciences, Osaka University
| | - Yi Zhou
- Graduate School of Pharmaceutical Sciences, Osaka University
| | - Tatsuya Takagi
- Graduate School of Pharmaceutical Sciences, Osaka University
| | - Masanori Kameoka
- Department of International Health, Kobe University Graduate School of Health Sciences
| | - Norihito Kawashita
- Graduate School of Pharmaceutical Sciences, Osaka University.,Faculty of Sciences and Engineering, Kindai University
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66
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Stabell AC, Meyerson NR, Gullberg RC, Gilchrist AR, Webb KJ, Old WM, Perera R, Sawyer SL. Dengue viruses cleave STING in humans but not in nonhuman primates, their presumed natural reservoir. eLife 2018; 7:31919. [PMID: 29557779 PMCID: PMC5860865 DOI: 10.7554/elife.31919] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 02/08/2018] [Indexed: 12/25/2022] Open
Abstract
Human dengue viruses emerged from primate reservoirs, yet paradoxically dengue does not reach high titers in primate models. This presents a unique opportunity to examine the genetics of spillover versus reservoir hosts. The dengue virus 2 (DENV2) - encoded protease cleaves human STING, reducing type I interferon production and boosting viral titers in humans. We find that both human and sylvatic (reservoir) dengue viruses universally cleave human STING, but not the STING of primates implicated as reservoir species. The special ability of dengue to cleave STING is thus specific to humans and a few closely related ape species. Conversion of residues 78/79 to the human-encoded 'RG' renders all primate (and mouse) STINGs sensitive to viral cleavage. Dengue viruses may have evolved to increase viral titers in the dense and vast human population, while maintaining decreased titers and pathogenicity in the more rare animals that serve as their sustaining reservoir in nature.
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Affiliation(s)
- Alex C Stabell
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, United States
| | - Nicholas R Meyerson
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, United States
| | - Rebekah C Gullberg
- Arthropod-borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, United States
| | - Alison R Gilchrist
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, United States
| | - Kristofor J Webb
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, United States
| | - William M Old
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, United States
| | - Rushika Perera
- Arthropod-borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, United States
| | - Sara L Sawyer
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, United States
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67
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The Structure of the Zika Virus Protease, NS2B/NS3pro. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1062:131-145. [DOI: 10.1007/978-981-10-8727-1_10] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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68
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The Transactions of NS3 and NS5 in Flaviviral RNA Replication. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1062:147-163. [PMID: 29845531 DOI: 10.1007/978-981-10-8727-1_11] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Dengue virus (DENV) replication occurs in virus-induced vesicles that contain the replication complex (RC) where viral RNA, viral proteins and host proteins participate in RNA-RNA, RNA-protein and protein-protein interactions to ensure viral genome synthesis. However, the details of the multitude of interactions involved in the biogenesis of the infectious virion are not fully understood. In this review, we will focus on the interaction between non-structural (NS) proteins NS3 and NS5, as well as their interactions with viral RNA and briefly also the interaction of NS5 with the host nuclear transport receptor protein importin-α. The multifunctional NS3 protease/helicase and NS5 methyltransferase (MTase)/RNA-dependent RNA polymerase (RdRp) contain all the enzymatic activities required to synthesize the viral RNA genome. The success stories of drug discovery and development with Hepatitis C virus (HCV), a member of the Flaviviridae family, has led to the view that DENV NS3 and NS5 may be attractive antiviral drug targets. However, more than 10 years of intensive research effort by Novatis has revealed that they are not "low hanging fruits" and therefore, the search for potent directly acting antivirals (DAAs) remains a pipeline goal for several medium to large drug discovery enterprises. The effort to discover DAAs for DENV has been boosted by the epidemic outbreak of the closely related flavivirus member - Zika virus (ZIKV). Because the viral RNA replication occurs within a molecular machine that is composed several viral and host proteins, much interest has turned to characterising functionally essential protein-protein interactions in order to identify potential allosteric inhibitor binding sites within the RC.
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69
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Huang YW, Lee CT, Wang TC, Kao YC, Yang CH, Lin YM, Huang KS. The Development of Peptide-based Antimicrobial Agents against Dengue Virus. Curr Protein Pept Sci 2018; 19:998-1010. [PMID: 29852867 PMCID: PMC6446661 DOI: 10.2174/1389203719666180531122724] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 04/20/2018] [Accepted: 05/25/2018] [Indexed: 11/22/2022]
Abstract
Dengue fever has become an imminent threat to international public health because of global warming and climate change. The World Health Organization proclaimed that more than 50% of the world's population is at risk of dengue virus (DENV) infection. Therefore, developing a clinically approved vaccine and effective therapeutic remedy for treating dengue fever is imperative. Peptide drug development has become a novel pharmaceutical research field. This article reviews various peptidesbased antimicrobial agents targeting three pathways involved in the DENV lifecycle. Specifically, they are peptide vaccines from immunomodulation, peptide drugs that inhibit virus entry, and peptide drugs that interfere with viral replication. Many antiviral peptide studies against DENV have been conducted in animal model trials, and progression to clinical trials for these promising peptide drugs is anticipated.
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Affiliation(s)
| | | | | | | | | | | | - Keng-Shiang Huang
- Address correspondence to this author at the School of Chinese Medicine for Post-Baccalaureate, I-Shou University, Kaohsiung, Taiwan;, Tel: +886-988-399-979; E-mail:
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70
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Hsieh MS, Chen MY, Hsieh CH, Pan CH, Yu GY, Chen HW. Detection and quantification of dengue virus using a novel biosensor system based on dengue NS3 protease activity. PLoS One 2017; 12:e0188170. [PMID: 29161301 PMCID: PMC5697845 DOI: 10.1371/journal.pone.0188170] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 11/01/2017] [Indexed: 01/08/2023] Open
Abstract
Background The traditional methods, plaque assays and immuno-focus assays, used to titrate infectious dengue virus (DENV) particles are time consuming and labor intensive. Here, we developed a DENV protease activity detection system (DENPADS) to visualize DENV infection in cells based on dengue protease activity. Methodology/Principal findings Dengue NS3 protease cleaves NS4B-NS5. BHK-21 cells stably expressing the sensor module comprising DENV-2 NS4 and the 10 amino-terminal amino acids of NS5 (N10NS5) fused with the SV40 nuclear localization signal (NLS) and Cre recombinase (Cre), were generated. Cre is constrained outside the nucleus in the absence of NS3 activity but translocates into the nucleus through NS4B-NS5 cleavage when cells are infected with DENV. Nuclear translocation of Cre can trigger the reporter system, which contains a cis-loxP-flanked mCherry with three continuous stop codons following an SV40 polyA tail cDNA upstream of EGFP or mHRP cDNA. Our results show that DENPADS is an efficient and accurate method to titrate 4 DENV serotypes in 24 hours. Compared with current virus titration methods, the entire process is easy to perform, and the data are easily acquired. Conclusions/Significance In this study, we demonstrate that DENPADS can be used to detect dengue viral infection through a fluorescence switch or HRP activity in the infected cells. This approach is sensitive with less incubation time and labor input. In addition, DENPADS can simultaneously evaluate the efficacy and cytotoxicity of potential anti-DENV candidates. Overall, DENPADS is a useful tool for dengue research.
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Affiliation(s)
- Ming-Shu Hsieh
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan, ROC
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan, ROC
| | - Mei-Yu Chen
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan, ROC
| | - Chun-Hsiang Hsieh
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan, ROC
| | - Chien-Hsiung Pan
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan, ROC
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan, ROC
| | - Guann-Yi Yu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan, ROC
| | - Hsin-Wei Chen
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan, ROC
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan, ROC
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan, ROC
- * E-mail:
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71
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Halim SA, Khan S, Khan A, Wadood A, Mabood F, Hussain J, Al-Harrasi A. Targeting Dengue Virus NS-3 Helicase by Ligand based Pharmacophore Modeling and Structure based Virtual Screening. Front Chem 2017; 5:88. [PMID: 29164104 PMCID: PMC5671650 DOI: 10.3389/fchem.2017.00088] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 10/16/2017] [Indexed: 12/25/2022] Open
Abstract
Dengue fever is an emerging public health concern, with several million viral infections occur annually, for which no effective therapy currently exist. Non-structural protein 3 (NS-3) Helicase encoded by the dengue virus (DENV) is considered as a potential drug target to design new and effective drugs against dengue. Helicase is involved in unwinding of dengue RNA. This study was conducted to design new NS-3 Helicase inhibitor by in silico ligand- and structure based approaches. Initially ligand-based pharmacophore model was generated that was used to screen a set of 1201474 compounds collected from ZINC Database. The compounds matched with the pharmacophore model were docked into the active site of NS-3 helicase. Based on docking scores and binding interactions, 25 compounds are suggested to be potential inhibitors of NS3 Helicase. The pharmacokinetic properties of these hits were predicted. The selected hits revealed acceptable ADMET properties. This study identified potential inhibitors of NS-3 Helicase in silico, and can be helpful in the treatment of Dengue.
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Affiliation(s)
- Sobia A Halim
- Department of Biochemistry, Kinnaird College for Women, Lahore, Pakistan
| | - Shanza Khan
- Department of Biochemistry, Kinnaird College for Women, Lahore, Pakistan
| | - Ajmal Khan
- Department of Chemistry, COMSATS Institute of Information Technology, Abbottabad, Pakistan.,UoN Chair of Oman Medicinal Plants and Marine Products, University of Nizwa, Nizwa, Oman
| | - Abdul Wadood
- Department of Biochemistry, Shankar Campus, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Fazal Mabood
- Department of Biological Sciences and Chemistry, College of Arts and Sciences, University of Nizwa, Nizwa, Oman
| | - Javid Hussain
- Department of Biological Sciences and Chemistry, College of Arts and Sciences, University of Nizwa, Nizwa, Oman
| | - Ahmed Al-Harrasi
- UoN Chair of Oman Medicinal Plants and Marine Products, University of Nizwa, Nizwa, Oman
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72
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Chew MF, Poh KS, Poh CL. Peptides as Therapeutic Agents for Dengue Virus. Int J Med Sci 2017; 14:1342-1359. [PMID: 29200948 PMCID: PMC5707751 DOI: 10.7150/ijms.21875] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 09/01/2017] [Indexed: 12/19/2022] Open
Abstract
Dengue is an important global threat caused by dengue virus (DENV) that records an estimated 390 million infections annually. Despite the availability of CYD-TDV as a commercial vaccine, its long-term efficacy against all four dengue virus serotypes remains unsatisfactory. There is therefore an urgent need for the development of antiviral drugs for the treatment of dengue. Peptide was once a neglected choice of medical treatment but it has lately regained interest from the pharmaceutical industry following pioneering advancements in technology. In this review, the design of peptide drugs, antiviral activities and mechanisms of peptides and peptidomimetics (modified peptides) action against dengue virus are discussed. The development of peptides as inhibitors for viral entry, replication and translation is also described, with a focus on the three main targets, namely, the host cell receptors, viral structural proteins and viral non-structural proteins. The antiviral peptides designed based on these approaches may lead to the discovery of novel anti-DENV therapeutics that can treat dengue patients.
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Affiliation(s)
- Miaw-Fang Chew
- Research Centre for Biomedical Sciences, Sunway University, Bandar Sunway, Selangor 47500, Malaysia
| | - Keat-Seong Poh
- Department of Surgery, Faculty of Medicine, University of Malaya, Jalan Universiti, Kuala Lumpur, 50603, Malaysia
| | - Chit-Laa Poh
- Research Centre for Biomedical Sciences, Sunway University, Bandar Sunway, Selangor 47500, Malaysia
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73
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Boldescu V, Behnam MAM, Vasilakis N, Klein CD. Broad-spectrum agents for flaviviral infections: dengue, Zika and beyond. Nat Rev Drug Discov 2017; 16:565-586. [PMID: 28473729 PMCID: PMC5925760 DOI: 10.1038/nrd.2017.33] [Citation(s) in RCA: 198] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Infections with flaviviruses, such as dengue, West Nile virus and the recently re-emerging Zika virus, are an increasing and probably lasting global risk. This Review summarizes and comments on the opportunities for broad-spectrum agents that are active against multiple flaviviruses. Broad-spectrum activity is particularly desirable to prepare for the next flaviviral epidemic, which could emerge from as-yet unknown or neglected viruses. Potential molecular targets for broad-spectrum antiflaviviral compounds include viral proteins, such as the viral protease or polymerase, and host targets that are exploited by these viruses during entry and replication, including α-glucosidase and proteins involved in nucleoside biosynthesis. Numerous compounds with broad-spectrum antiviral activity have already been identified by target-specific or phenotypic assays. For other compounds, broad-spectrum activity can be anticipated because of their mode of action and molecular targets.
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Affiliation(s)
- Veaceslav Boldescu
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
- Laboratory of Organic Synthesis and Biopharmaceuticals, Institute of Chemistry of the Academy of Sciences of Moldova, Academiei 3, 2028 Chisinau, Moldova
| | - Mira A. M. Behnam
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Nikos Vasilakis
- Dept. of Pathology and Center for Biodefense and Emerging Infectious Diseases, Center for Tropical Diseases and Institute for Human Infections and Immunity, 2.138D Keiller Bldg, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555–0609, USA
| | - Christian D. Klein
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
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74
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Roy A, Lim L, Srivastava S, Lu Y, Song J. Solution conformations of Zika NS2B-NS3pro and its inhibition by natural products from edible plants. PLoS One 2017; 12:e0180632. [PMID: 28700665 PMCID: PMC5503262 DOI: 10.1371/journal.pone.0180632] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 06/19/2017] [Indexed: 12/20/2022] Open
Abstract
The recent Zika viral (ZIKV) epidemic has been associated with severe neurological pathologies such as neonatal microcephaly and Guillain-Barre syndrome but unfortunately no vaccine or medication is effectively available yet. Zika NS2B-NS3pro is essential for the proteolysis of the viral polyprotein and thereby viral replication. Thus NS2B-NS3pro represents an attractive target for anti-Zika drug discovery/design. Here, we have characterized the solution conformations and catalytic parameters of both linked and unlinked Zika NS2B-NS3pro complexes and found that the unlinked complex manifested well-dispersed NMR spectra. Subsequently with selective isotope-labeling using NMR spectroscopy, we demonstrated that C-terminal residues (R73-K100) of NS2B is highly disordered without any stable tertiary and secondary structures in the Zika NS2B-NS3pro complex in the free state. Upon binding to the well-characterized serine protease inhibitor, bovine pancreatic trypsin inhibitor (BPTI), only the extreme C-terminal residues (L86-K100) remain disordered. Additionally, we have identified five flavonoids and one natural phenol rich in edible plants including fruits and vegetables, which inhibit Zika NS2B-NS3pro in a non-competitive mode, with Ki ranging from 770 nM for Myricetin to 34.02 μM for Apigenin. Molecular docking showed that they all bind to a pocket on the back of the active site and their structure-activity relationship was elucidated. Our study provides valuable insights into the solution conformation of Zika NS2B-NS3pro and further deciphers its susceptibility towards allosteric inhibition by natural products. As these natural product inhibitors fundamentally differ from the currently-known active site inhibitors in terms of both inhibitory mode and chemical scaffold, our finding might open a new avenue for development of better allosteric inhibitors to fight ZIKV infection.
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Affiliation(s)
- Amrita Roy
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Liangzhong Lim
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Shagun Srivastava
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Yimei Lu
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Jianxing Song
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
- * E-mail:
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75
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Peng M, Watanabe S, Chan KWK, He Q, Zhao Y, Zhang Z, Lai X, Luo D, Vasudevan SG, Li G. Luteolin restricts dengue virus replication through inhibition of the proprotein convertase furin. Antiviral Res 2017; 143:176-185. [DOI: 10.1016/j.antiviral.2017.03.026] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 02/14/2017] [Accepted: 03/29/2017] [Indexed: 11/17/2022]
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76
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Characterization of the Zika virus two-component NS2B-NS3 protease and structure-assisted identification of allosteric small-molecule antagonists. Antiviral Res 2017; 143:218-229. [PMID: 28461069 DOI: 10.1016/j.antiviral.2017.04.015] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 04/20/2017] [Accepted: 04/26/2017] [Indexed: 11/22/2022]
Abstract
The recent re-emergence of Zika virus (ZIKV)1, a member of the Flaviviridae family, has become a global emergency. Currently, there are no effective methods of preventing or treating ZIKV infection, which causes severe neuroimmunopathology and is particularly harmful to the developing fetuses of infected pregnant women. However, the pathology induced by ZIKV is unique among flaviviruses, and knowledge of the biology of other family members cannot easily be extrapolated to ZIKV. Thus, structure-function studies of ZIKV proteins are urgently needed to facilitate the development of effective preventative and therapeutic agents. Like other flaviviruses, ZIKV expresses an NS2B-NS3 protease, which consists of the NS2B cofactor and the NS3 protease domain and is essential for cleavage of the ZIKV polyprotein precursor and generation of fully functional viral proteins. Here, we report the enzymatic characterization of ZIKV protease, and we identify structural scaffolds for allosteric small-molecule inhibitors of this protease. Molecular modeling of the protease-inhibitor complexes suggests that these compounds bind to the druggable cavity in the NS2B-NS3 protease interface and affect productive interactions of the protease domain with its cofactor. The most potent compound demonstrated efficient inhibition of ZIKV propagation in vitro in human fetal neural progenitor cells and in vivo in SJL mice. The inhibitory scaffolds could be further developed into valuable research reagents and, ultimately, provide a roadmap for the selection of efficient inhibitors of ZIKV infection.
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77
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Dengue Virus NS2B/NS3 Protease Inhibitors Exploiting the Prime Side. J Virol 2017; 91:JVI.00045-17. [PMID: 28298600 DOI: 10.1128/jvi.00045-17] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 03/07/2017] [Indexed: 12/12/2022] Open
Abstract
The mosquito-transmitted dengue virus (DENV) infects millions of people in tropical and subtropical regions. Maturation of DENV particles requires proper cleavage of the viral polyprotein, including processing of 8 of the 13 substrate cleavage sites by dengue virus NS2B/NS3 protease. With no available direct-acting antiviral targeting DENV, NS2/NS3 protease is a promising target for inhibitor design. Current design efforts focus on the nonprime side of the DENV protease active site, resulting in highly hydrophilic and nonspecific scaffolds. However, the prime side also significantly modulates DENV protease binding affinity, as revealed by engineering the binding loop of aprotinin, a small protein with high affinity for DENV protease. In this study, we designed a series of cyclic peptides interacting with both sides of the active site as inhibitors of dengue virus protease. The design was based on two aprotinin loops and aimed to leverage both key specific interactions of substrate sequences and the entropic advantage driving aprotinin's high affinity. By optimizing the cyclization linker, length, and amino acid sequence, the tightest cyclic peptide achieved a Ki value of 2.9 μM against DENV3 wild-type (WT) protease. These inhibitors provide proof of concept that both sides of DENV protease active site can be exploited to potentially achieve specificity and lower hydrophilicity in the design of inhibitors targeting DENV.IMPORTANCE Viruses of the flaviviral family, including DENV and Zika virus transmitted by Aedes aegypti, continue to be a threat to global health by causing major outbreaks in tropical and subtropical regions, with no available direct-acting antivirals for treatment. A better understanding of the molecular requirements for the design of potent and specific inhibitors against flaviviral proteins will contribute to the development of targeted therapies for infections by these viruses. The cyclic peptides reported here as DENV protease inhibitors provide novel scaffolds that enable exploiting the prime side of the protease active site, with the aim of achieving better specificity and lower hydrophilicity than those of current scaffolds in the design of antiflaviviral inhibitors.
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78
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El Sahili A, Lescar J. Dengue Virus Non-Structural Protein 5. Viruses 2017; 9:E91. [PMID: 28441781 PMCID: PMC5408697 DOI: 10.3390/v9040091] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 04/15/2017] [Accepted: 04/20/2017] [Indexed: 12/17/2022] Open
Abstract
The World Health Organization estimates that the yearly number of dengue cases averages 390 million. This mosquito-borne virus disease is endemic in over 100 countries and will probably continue spreading, given the observed trend in global warming. So far, there is no antiviral drug available against dengue, but a vaccine has been recently marketed. Dengue virus also serves as a prototype for the study of other pathogenic flaviviruses that are emerging, like West Nile virus and Zika virus. Upon viral entry into the host cell and fusion of the viral lipid membrane with the endosomal membrane, the viral RNA is released and expressed as a polyprotein, that is then matured into three structural and seven non-structural (NS) proteins. The envelope, membrane and capsid proteins form the viral particle while NS1-NS2A-NS2B-NS3-NS4A-NS4B and NS5 assemble inside a cellular replication complex, which is embedded in endoplasmic reticulum (ER)-derived vesicles. In addition to their roles in RNA replication within the infected cell, NS proteins help the virus escape the host innate immunity and reshape the host-cell inner structure. This review focuses on recent progress in characterizing the structure and functions of NS5, a protein responsible for the replication and capping of viral RNA that represents a promising drug target.
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Affiliation(s)
- Abbas El Sahili
- School of Biological Sciences, Nanyang Technological University, Nanyang Institute for Structural Biology, Experimental Medicine Building, 59 Nanyang Drive, Singapore 636921, Singapore.
| | - Julien Lescar
- School of Biological Sciences, Nanyang Technological University, Nanyang Institute for Structural Biology, Experimental Medicine Building, 59 Nanyang Drive, Singapore 636921, Singapore.
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79
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Aguirre S, Luthra P, Sanchez-Aparicio MT, Maestre AM, Patel J, Lamothe F, Fredericks AC, Tripathi S, Zhu T, Pintado-Silva J, Webb LG, Bernal-Rubio D, Solovyov A, Greenbaum B, Simon V, Basler CF, Mulder LCF, García-Sastre A, Fernandez-Sesma A. Dengue virus NS2B protein targets cGAS for degradation and prevents mitochondrial DNA sensing during infection. Nat Microbiol 2017; 2:17037. [PMID: 28346446 DOI: 10.1038/nmicrobiol.2017.37] [Citation(s) in RCA: 274] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 02/17/2017] [Indexed: 12/19/2022]
Abstract
During the last few decades, the global incidence of dengue virus (DENV) has increased dramatically, and it is now endemic in more than 100 countries. To establish a productive infection in humans, DENV uses different strategies to inhibit or avoid the host innate immune system. Several DENV proteins have been shown to strategically target crucial components of the type I interferon system. Here, we report that the DENV NS2B protease cofactor targets the DNA sensor cyclic GMP-AMP synthase (cGAS) for lysosomal degradation to avoid the detection of mitochondrial DNA during infection. Such degradation subsequently results in the inhibition of type I interferon production in the infected cell. Our data demonstrate a mechanism by which cGAS senses cellular damage upon DENV infection.
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Affiliation(s)
- Sebastian Aguirre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029-6574, USA
| | - Priya Luthra
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029-6574, USA
| | - Maria T Sanchez-Aparicio
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029-6574, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029-6574, USA
| | - Ana M Maestre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029-6574, USA
| | - Jenish Patel
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029-6574, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029-6574, USA.,Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029-6574, USA
| | - Francise Lamothe
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029-6574, USA
| | - Anthony C Fredericks
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029-6574, USA.,Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029-6574, USA
| | - Shashank Tripathi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029-6574, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029-6574, USA
| | - Tongtong Zhu
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029-6574, USA.,Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029-6574, USA
| | - Jessica Pintado-Silva
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029-6574, USA.,Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029-6574, USA
| | - Laurence G Webb
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029-6574, USA.,Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029-6574, USA
| | - Dabeiba Bernal-Rubio
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029-6574, USA
| | - Alexander Solovyov
- Tisch Cancer Institute, Division of Hematology and Medical Oncology, Department of Medicine, Department of Pathology and Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029-6574, USA
| | - Benjamin Greenbaum
- Tisch Cancer Institute, Division of Hematology and Medical Oncology, Department of Medicine, Department of Pathology and Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029-6574, USA
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029-6574, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029-6574, USA.,Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York 10029-6574, USA
| | - Christopher F Basler
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029-6574, USA
| | - Lubbertus C F Mulder
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029-6574, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029-6574, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029-6574, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029-6574, USA.,Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York 10029-6574, USA
| | - Ana Fernandez-Sesma
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029-6574, USA.,Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029-6574, USA.,Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York 10029-6574, USA
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80
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da Fonseca NJ, Lima Afonso MQ, Pedersolli NG, de Oliveira LC, Andrade DS, Bleicher L. Sequence, structure and function relationships in flaviviruses as assessed by evolutive aspects of its conserved non-structural protein domains. Biochem Biophys Res Commun 2017; 492:565-571. [PMID: 28087275 DOI: 10.1016/j.bbrc.2017.01.041] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 01/09/2017] [Indexed: 10/20/2022]
Abstract
Flaviviruses are responsible for serious diseases such as dengue, yellow fever, and zika fever. Their genomes encode a polyprotein which, after cleavage, results in three structural and seven non-structural proteins. Homologous proteins can be studied by conservation and coevolution analysis as detected in multiple sequence alignments, usually reporting positions which are strictly necessary for the structure and/or function of all members in a protein family or which are involved in a specific sub-class feature requiring the coevolution of residue sets. This study provides a complete conservation and coevolution analysis on all flaviviruses non-structural proteins, with results mapped on all well-annotated available sequences. A literature review on the residues found in the analysis enabled us to compile available information on their roles and distribution among different flaviviruses. Also, we provide the mapping of conserved and coevolved residues for all sequences currently in SwissProt as a supplementary material, so that particularities in different viruses can be easily analyzed.
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Affiliation(s)
- Néli José da Fonseca
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Av. Antônio Carlos, 6627, Belo Horizonte, 31270-901, Brazil.
| | - Marcelo Querino Lima Afonso
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Av. Antônio Carlos, 6627, Belo Horizonte, 31270-901, Brazil.
| | - Natan Gonçalves Pedersolli
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Av. Antônio Carlos, 6627, Belo Horizonte, 31270-901, Brazil.
| | - Lucas Carrijo de Oliveira
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Av. Antônio Carlos, 6627, Belo Horizonte, 31270-901, Brazil.
| | - Dhiego Souto Andrade
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Av. Antônio Carlos, 6627, Belo Horizonte, 31270-901, Brazil.
| | - Lucas Bleicher
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Av. Antônio Carlos, 6627, Belo Horizonte, 31270-901, Brazil.
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81
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Abstract
Viruses are major pathogenic agents that can cause a variety of diseases, such as AIDS, hepatitis, respiratory diseases, and many more, in humans, plants, and animals. The most prominent of them have been adenoviruses, alphaviruses, flaviviruses, hepatitis C virus, herpesviruses, human immunodeficiency virus of type 1, and picornaviruses. This chapter presents an introductory remark on such viruses, mechanisms of their invasion, and diseases related to them. The inhibition of these viruses is of great concern to human beings. Each of these viruses encodes one or more proteases that play crucial roles in their replication, and thus they are important targets for the design and development of potent antiviral agents. The chapter, therefore, also introduces the readers to such proteases and their structures and functions. This chapter is thus a prelude to the remaining chapters in the book, which present in detail about the different viruses and their proteases.
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Affiliation(s)
- Anjana Sharma
- Meerut Institute of Engineering and Technology, Meerut, Uttar Pradesh, India
| | - Satya P. Gupta
- National Institute of Technical Teachers’ Training and Research, Bhopal, Madhya Pradesh, India
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82
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Rut W, Zhang L, Kasperkiewicz P, Poreba M, Hilgenfeld R, Drąg M. Extended substrate specificity and first potent irreversible inhibitor/activity-based probe design for Zika virus NS2B-NS3 protease. Antiviral Res 2016; 139:88-94. [PMID: 28034744 DOI: 10.1016/j.antiviral.2016.12.018] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 12/19/2016] [Accepted: 12/21/2016] [Indexed: 11/29/2022]
Abstract
Zika virus is spread by Aedes mosquitoes and is linked to acute neurological disorders, especially to microcephaly in newborn children and Guillan-Barré Syndrome. The NS2B-NS3 protease of this virus is responsible for polyprotein processing and therefore considered an attractive drug target. In this study, we have used the Hybrid Combinatorial Substrate Library (HyCoSuL) approach to determine the substrate specificity of ZIKV NS2B-NS3 protease in the P4-P1 positions using natural and a large spectrum of unnatural amino acids. Obtained data demonstrate a high level of specificity of the S3-S1 subsites, especially for basic amino acids. However, the S4 site exhibits a very broad preference toward natural and unnatural amino acids with selected D-amino acids being favored over L enantiomers. This information was used for the design of a very potent phosphonate inhibitor/activity-based probe of ZIKV NS2B-NS3 protease.
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Affiliation(s)
- Wioletta Rut
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Linlin Zhang
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany; German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, 23562 Lübeck, Germany
| | - Paulina Kasperkiewicz
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland; NCI-designated Cancer Center, Sanford-Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Marcin Poreba
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland; NCI-designated Cancer Center, Sanford-Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Rolf Hilgenfeld
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany; German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, 23562 Lübeck, Germany
| | - Marcin Drąg
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland.
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83
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Phoo WW, Li Y, Zhang Z, Lee MY, Loh YR, Tan YB, Ng EY, Lescar J, Kang C, Luo D. Structure of the NS2B-NS3 protease from Zika virus after self-cleavage. Nat Commun 2016; 7:13410. [PMID: 27845325 PMCID: PMC5116066 DOI: 10.1038/ncomms13410] [Citation(s) in RCA: 163] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 09/30/2016] [Indexed: 12/22/2022] Open
Abstract
The recent outbreak of Zika virus (ZIKV) infections in the Americas represents a serious threat to the global public health. The viral protease that processes viral polyproteins during infection appears as an attractive drug target. Here we report a crystal structure at 1.84 Å resolution of ZIKV non-structural protein NS2B-NS3 protease with the last four amino acids of the NS2B cofactor bound at the NS3 active site. This structure represents a post-proteolysis state of the enzyme during viral polyprotein processing and provides insights into peptide substrate recognition by the protease. Nuclear magnetic resonance (NMR) studies and protease activity assays unravel the protein dynamics upon binding the protease inhibitor BPTI in solution and confirm this finding. The structural and functional insights of the ZIKV protease presented here should advance our current understanding of flavivirus replication and accelerate structure-based antiviral drug discovery against ZIKV. The proteases of flaviviruses are promising targets for development of specific antiviral drugs. Here, the authors report a high resolution crystal structure of the NS2B-NS3 protease of Zika virus that provides insight into substrate and inhibitor binding.
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Affiliation(s)
- Wint Wint Phoo
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 636921, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Yan Li
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis way, Nanos, #03-01, Singapore 138669, Singapore
| | - Zhenzhen Zhang
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Michelle Yueqi Lee
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis way, Nanos, #03-01, Singapore 138669, Singapore
| | - Ying Ru Loh
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis way, Nanos, #03-01, Singapore 138669, Singapore
| | - Yaw Bia Tan
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Elizabeth Yihui Ng
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis way, Nanos, #03-01, Singapore 138669, Singapore
| | - Julien Lescar
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 636921, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore
| | - CongBao Kang
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis way, Nanos, #03-01, Singapore 138669, Singapore
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 636921, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore
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84
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Gruba N, Rodriguez Martinez JI, Grzywa R, Wysocka M, Skoreński M, Burmistrz M, Łęcka M, Lesner A, Sieńczyk M, Pyrć K. Substrate profiling of Zika virus NS2B-NS3 protease. FEBS Lett 2016; 590:3459-3468. [PMID: 27714789 DOI: 10.1002/1873-3468.12443] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 09/12/2016] [Accepted: 09/22/2016] [Indexed: 01/05/2023]
Abstract
Zika virus (ZIKV), isolated from macaques in Uganda in 1947, was not considered to be a dangerous human pathogen. However, this view has recently changed as ZIKV infections are now associated with serious pathological disorders including microcephaly and Guillain-Barré syndrome. Similar to other viruses in the Flaviviridae family, ZIKV expresses the serine protease NS3 which is responsible for viral protein processing and replication. Herein, we report the expression of an active NS3pro domain fused with the NS2B cofactor (NS2BLN NS3pro ) in a prokaryotic expression system and profile its specificity for synthesized FRET-type substrate libraries. Our findings pave way for screening potential intracellular substrates of NS3 and for developing specific inhibitors of this ZIKV protease.
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Affiliation(s)
- Natalia Gruba
- Department of Biochemistry, Faculty of Chemistry, University of Gdansk, Poland
| | | | - Renata Grzywa
- Division of Medicinal Chemistry and Microbiology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Magdalena Wysocka
- Department of Biochemistry, Faculty of Chemistry, University of Gdansk, Poland
| | - Marcin Skoreński
- Division of Medicinal Chemistry and Microbiology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Michał Burmistrz
- Department of Microbiology, Faculty of Biochemistry Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.,Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Maria Łęcka
- Division of Medicinal Chemistry and Microbiology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Adam Lesner
- Department of Biochemistry, Faculty of Chemistry, University of Gdansk, Poland.
| | - Marcin Sieńczyk
- Division of Medicinal Chemistry and Microbiology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw, Poland.
| | - Krzysztof Pyrć
- Department of Microbiology, Faculty of Biochemistry Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland. .,Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
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85
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Chen X, Yang K, Wu C, Chen C, Hu C, Buzovetsky O, Wang Z, Ji X, Xiong Y, Yang H. Mechanisms of activation and inhibition of Zika virus NS2B-NS3 protease. Cell Res 2016; 26:1260-1263. [PMID: 27752039 DOI: 10.1038/cr.2016.116] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Xia Chen
- School of Life Sciences, Tianjin University, Tianjin 300072, China.,Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
| | - Kailin Yang
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH 44195, USA
| | - Chen Wu
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Cheng Chen
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Can Hu
- School of Life Sciences, Tianjin University, Tianjin 300072, China.,Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
| | - Olga Buzovetsky
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Zefang Wang
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Xiaoyun Ji
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Haitao Yang
- School of Life Sciences, Tianjin University, Tianjin 300072, China.,Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
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86
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Lin KH, Nalivaika EA, Prachanronarong KL, Yilmaz NK, Schiffer CA. Dengue Protease Substrate Recognition: Binding of the Prime Side. ACS Infect Dis 2016; 2:734-743. [PMID: 27657335 DOI: 10.1021/acsinfecdis.6b00131] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Dengue virus (DENV), transmitted predominantly in tropical and subtropical regions by the mosquito Aedes aegypti, infects millions of people and leads to dengue fever and thousands of deaths each year. There are no direct-acting antivirals to combat DENV, and molecular and structural knowledge is required to develop such compounds. The dengue NS2B/NS3 protease is a promising target for direct-acting antivirals, as viral polyprotein cleavage during replication is required for the maturation of the viral particle. The NS2B/NS3 protease processes 8 of the 13 viral polyprotein cleavage sites to allow viral maturation. Although these sites share little sequence homology beyond the P1 and P2 positions, most are well conserved among the serotypes. How the other substrate residues, especially at the P' side, affect substrate recognition remains unclear. We exploited the tight-binding general serine protease inhibitor aprotinin to investigate protease-substrate interactions at the molecular level. We engineered aprotinin's binding loop with sequences mimicking the P' side of DENV substrates. P' residues significantly modulate substrate affinity to protease, with inhibition constants varying from nanomolar to sub-millimolar. Structural and dynamic analysis revealed the molecular basis of this modulation and allowed identifying optimal residues for each of the P' positions. In addition, isothermal titration calorimetry showed binding to be solely entropy driven for all constructs. Potential flaviviral P' side inhibitors could benefit from mimicking the optimal residues at P' positions and incorporate hydrophobicity and rigidity to maintain entropic advantage for potency.
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Affiliation(s)
- Kuan-Hung Lin
- Department of Biochemistry
and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Ellen A. Nalivaika
- Department of Biochemistry
and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Kristina L. Prachanronarong
- Department of Biochemistry
and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Nese Kurt Yilmaz
- Department of Biochemistry
and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Celia A. Schiffer
- Department of Biochemistry
and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
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87
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Song Q, Zhang X, Li N, Shen J, Cheng J. A propeptide-independent protease from Tannerella sp.6_1_58FAA_CT1 displays trypsin-like specificity. J Basic Microbiol 2016; 57:50-56. [PMID: 27714828 DOI: 10.1002/jobm.201600486] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 09/18/2016] [Indexed: 11/06/2022]
Abstract
Despite the absence of any homologs of Tannerella forsythia KLIKK proteases in Tannerella sp.6_1_58FAA_CT1, the strain possesses a putative cysteine protease (G9S4N1) closely related to RgpB of Porphyromonas gingivalis. G9S4N1 lacks obvious propeptide that behaves as inhibitor of proteases and was proven to be a propeptide-independent protease. Unlike RgpB, which exclusively cleaves ArgXaa bonds, G9S4N1 exhibits both arginine- and citrulline-specific activities. Mutations of Asp177, a potential P1-Arg binding site, to uncharged or positively charged residues did not alter the substrate specificity of G9S4N1 significantly. Moreover, a group of arginine-specific proteases from different species including porcine trypsin, bovine thrombin, and a trypsin-like serine protease of dengue 2 virus CF40-Gly-NS3pro185 also display different specificity toward citrulline residue, suggesting that citrulline-modified protein might have different roles and destiny in biological processes involving various proteases.
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Affiliation(s)
- Qitao Song
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, P. R. China
| | - Xiaoyue Zhang
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, P. R. China
| | - Na Li
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, P. R. China
| | - Jie Shen
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, P. R. China
| | - Jiansong Cheng
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, P. R. China
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88
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Identification of fused bicyclic derivatives of pyrrolidine and imidazolidinone as dengue virus-2 NS2B-NS3 protease inhibitors. Eur J Med Chem 2016; 125:751-759. [PMID: 27721158 DOI: 10.1016/j.ejmech.2016.09.063] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Revised: 09/19/2016] [Accepted: 09/20/2016] [Indexed: 11/23/2022]
Abstract
A series of fused ring derivatives of pyrrolidine and imidazolidinone were designed, synthesized, characterized and assayed against the DENV-2 NS2B-NS3 protease and wild-type DENV-2 virus. The linear dipeptide compound 1 and the non-peptidic fused ring compound 2 show comparable activities against DENV-2 NS2B-NS3 protease and wild-type DENV-2 virus in a viral replication assay. The preliminary SAR reveals that a substituent and its stereochemistry at C-3 position, substitution (X) at N-2 arene and a linker (Y) between C-3 position and its attached arene are important for the fused-ring scaffold of pyrrolidino [1,2-c]imidazolidinone to block the active site of NS2B-NS3 protease. This promising structural core will facilitate the discovery of non-peptidic, potent NS2B-NS3 protease inhibitors to stop dengue virus infections.
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89
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Ulanday GEL, Okamoto K, Morita K. Development and utility of an in vitro, fluorescence-based assay for the discovery of novel compounds against dengue 2 viral protease. Trop Med Health 2016; 44:22. [PMID: 27551237 PMCID: PMC4979183 DOI: 10.1186/s41182-016-0025-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 07/18/2016] [Indexed: 11/27/2022] Open
Abstract
Background Dengue disease is one of the most significant vector-borne illnesses in the world. The emergence and re-emergence of dengue infections in many parts of the world affect millions annually and continue to burden public health systems especially in low-income populations. Advances in dengue vaccine development showed promising results; however, protection seems to be suboptimal. There is no licensed chemotherapeutic agent against dengue to date. An ideal scenario of combinatorial vaccination of high-risk individuals and chemotherapy of the diseased during outbreaks may compensate for the meager protection offered by the vaccine. The dengue virus protease is important to viral replication and, as such, has been identified as a potential target for antivirals. It is, therefore, our objective to establish and optimize an appropriate screening method for use during the early stages of drug development for dengue. Methods In this study, we developed and optimized a biochemical assay system for use in screening compound libraries against dengue virus protease. We tested the selected protease inhibitors with a cell-based assay to determine inhibition of viral replication. Results We have presented direct plots of substrate kinetics data showing an apparent inhibition of the protease at excessive substrate concentrations. The most common sources of interference that may have affected the said observation were elucidated. Finally, a screen was done on an existing compound library using the developed method. The compounds selected in this study showed inhibitory activity against both the recombinant dengue protease and cell-based infectivity assays. Conclusions Our study shows the practicality of a customized biochemical assay to find possible inhibitors of dengue viral protease during the initial stages of drug discovery. Electronic supplementary material The online version of this article (doi:10.1186/s41182-016-0025-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gianne Eduard L Ulanday
- Department of Virology, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523 Japan ; Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Kenta Okamoto
- Department of Virology, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523 Japan
| | - Kouichi Morita
- Department of Virology, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523 Japan ; Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan ; Leading Graduate School Program, Nagasaki University, Nagasaki, Japan
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90
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Balasubramanian A, Manzano M, Teramoto T, Pilankatta R, Padmanabhan R. High-throughput screening for the identification of small-molecule inhibitors of the flaviviral protease. Antiviral Res 2016; 134:6-16. [PMID: 27539384 DOI: 10.1016/j.antiviral.2016.08.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 08/13/2016] [Indexed: 01/18/2023]
Abstract
The mosquito-borne dengue virus serotypes 1-4 (DENV1-4) and West Nile virus (WNV) cause serious illnesses worldwide associated with considerable morbidity and mortality. According to the World Health Organization (WHO) estimates, there are about 390 million infections every year leading to ∼500,000 dengue haemorrhagic fever (DHF) cases and ∼25,000 deaths, mostly among children. Antiviral therapies could reduce the morbidity and mortality associated with flaviviral infections, but currently there are no drugs available for treatment. In this study, a high-throughput screening assay for the Dengue protease was employed to screen ∼120,000 small molecule compounds for identification of inhibitors. Eight of these inhibitors have been extensively analyzed for inhibition of the viral protease in vitro and cell-based viral replication using Renilla luciferase reporter replicon, infectivity (plaque) and cytotoxicity assays. Three of these compounds were identified as potent inhibitors of DENV and WNV proteases, and viral replication of DENV2 replicon and infectious RNA. Fluorescence quenching, kinetic analysis and molecular modeling of these inhibitors into the structure of NS2B-NS3 protease suggest a mode of inhibition for three compounds that they bind to the substrate binding pocket.
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Affiliation(s)
| | - Mark Manzano
- Department of Microbiology and Immunology, Georgetown University, Washington, D.C., USA
| | - Tadahisa Teramoto
- Department of Microbiology and Immunology, Georgetown University, Washington, D.C., USA
| | - Rajendra Pilankatta
- Department of Microbiology and Immunology, Georgetown University, Washington, D.C., USA
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91
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Timiri AK, Sinha BN, Jayaprakash V. Progress and prospects on DENV protease inhibitors. Eur J Med Chem 2016; 117:125-43. [DOI: 10.1016/j.ejmech.2016.04.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 03/28/2016] [Accepted: 04/04/2016] [Indexed: 12/17/2022]
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92
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Liew LSY, Lee MY, Wong YL, Cheng J, Li Q, Kang C. Selection of suitable detergents for obtaining an active dengue protease in its natural form from E. coli. Protein Expr Purif 2016; 121:141-8. [DOI: 10.1016/j.pep.2016.02.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 01/18/2016] [Accepted: 02/01/2016] [Indexed: 01/05/2023]
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93
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Abstract
INTRODUCTION Flaviviruses are major causes of infectious disease. The vast global, social and economic impact due to morbidity and mortality associated with diseases caused by these viruses urgently demands effective therapeutic interventions. There is currently no specific antiviral therapy available for the effective clinical treatment of infections by any of the flaviviridae. Development of more effective vaccines and antiviral agents for the prevention and treatment of most flavivirus infections remains a clear public health priority in the 21st century. AREAS COVERED This review describes some of the recent discoveries in the field of flavivirus inhibitor development, with a particular focus on targeting viral proteins. Emphasis is placed on the advances published during the 2012-2015 period. EXPERT OPINION The field of drug discovery targeting viral proteins has progressed slowly in recent years. New information, particularly on structures, location and mechanisms of action of established protein targets have been reported. There have also been studies on repurposing known drugs as templates for targeting flavivirus proteins and these hits could be promising templates for developing new more potent inhibitors. Further research should be conducted to improve in vitro assays that better reflect the conditions found in cellular environments.
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Affiliation(s)
- W Mei Kok
- a Division of Chemistry and Structural Biology, Institute for Molecular Bioscience , The University of Queensland , Brisbane , Australia
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94
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Hassandarvish P, Rothan HA, Rezaei S, Yusof R, Abubakar S, Zandi K. In silico study on baicalein and baicalin as inhibitors of dengue virus replication. RSC Adv 2016. [DOI: 10.1039/c6ra00817h] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The dengue virus (DENV) is an important human arbovirus that belongs to the Flaviviridae.
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Affiliation(s)
- Pouya Hassandarvish
- Tropical Infectious Disease Research and Education Centre
- Department of Medical Microbiology Faculty of Medicine
- University of Malaya
- 50603 Kuala Lumpur
- Malaysia
| | - Hussin A. Rothan
- Department of Molecular Medicine
- Faculty of Medicine
- University of Malaya
- 50603 Kuala Lumpur
- Malaysia
| | - Sahar Rezaei
- Medical Laboratory Sciences Department
- Tarleton State University
- Fort Worth
- USA
| | - Rohana Yusof
- Department of Molecular Medicine
- Faculty of Medicine
- University of Malaya
- 50603 Kuala Lumpur
- Malaysia
| | - Sazaly Abubakar
- Tropical Infectious Disease Research and Education Centre
- Department of Medical Microbiology Faculty of Medicine
- University of Malaya
- 50603 Kuala Lumpur
- Malaysia
| | - Keivan Zandi
- Tropical Infectious Disease Research and Education Centre
- Department of Medical Microbiology Faculty of Medicine
- University of Malaya
- 50603 Kuala Lumpur
- Malaysia
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95
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Koh-Stenta X, Joy J, Wang SF, Kwek PZ, Wee JLK, Wan KF, Gayen S, Chen AS, Kang C, Lee MA, Poulsen A, Vasudevan SG, Hill J, Nacro K. Identification of covalent active site inhibitors of dengue virus protease. DRUG DESIGN DEVELOPMENT AND THERAPY 2015; 9:6389-99. [PMID: 26677315 PMCID: PMC4677662 DOI: 10.2147/dddt.s94207] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Dengue virus (DENV) protease is an attractive target for drug development; however, no compounds have reached clinical development to date. In this study, we utilized a potent West Nile virus protease inhibitor of the pyrazole ester derivative class as a chemical starting point for DENV protease drug development. Compound potency and selectivity for DENV protease were improved through structure-guided small molecule optimization, and protease-inhibitor binding interactions were validated biophysically using nuclear magnetic resonance. Our work strongly suggests that this class of compounds inhibits flavivirus protease through targeted covalent modification of active site serine, contrary to an allosteric binding mechanism as previously described.
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Affiliation(s)
- Xiaoying Koh-Stenta
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (ASTAR), Singapore
| | - Joma Joy
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (ASTAR), Singapore
| | - Si Fang Wang
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (ASTAR), Singapore
| | - Perlyn Zekui Kwek
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (ASTAR), Singapore
| | - John Liang Kuan Wee
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (ASTAR), Singapore
| | - Kah Fei Wan
- Novartis Institute for Tropical Diseases, Singapore
| | - Shovanlal Gayen
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (ASTAR), Singapore
| | - Angela Shuyi Chen
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (ASTAR), Singapore
| | - CongBao Kang
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (ASTAR), Singapore
| | - May Ann Lee
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (ASTAR), Singapore
| | - Anders Poulsen
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (ASTAR), Singapore
| | - Subhash G Vasudevan
- Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore
| | - Jeffrey Hill
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (ASTAR), Singapore
| | - Kassoum Nacro
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (ASTAR), Singapore
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96
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Behnam MAM, Graf D, Bartenschlager R, Zlotos DP, Klein CD. Discovery of Nanomolar Dengue and West Nile Virus Protease Inhibitors Containing a 4-Benzyloxyphenylglycine Residue. J Med Chem 2015; 58:9354-70. [PMID: 26562070 DOI: 10.1021/acs.jmedchem.5b01441] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The dengue virus (DENV) and West Nile Virus (WNV) NS2B-NS3 proteases are attractive targets for the development of dual-acting therapeutics against these arboviral pathogens. We present the synthesis and extensive biological evaluation of inhibitors that contain benzyl ethers of 4-hydroxyphenylglycine as non-natural peptidic building blocks synthesized via a copper-complex intermediate. A three-step optimization strategy, beginning with fragment growth of the C-terminal 4-hydroxyphenylglycine to the benzyloxy ether, followed by C- and N-terminal optimization, and finally fragment merging generated compounds with in vitro affinities in the low nanomolar range. The most promising derivative reached Ki values of 12 nM at the DENV-2 and 39 nM at the WNV proteases. Several of the newly discovered protease inhibitors yielded a significant reduction of dengue and West Nile virus titers in cell-based assays of virus replication, with an EC50 value of 3.4 μM at DENV-2 and 15.5 μM at WNV for the most active analogue.
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Affiliation(s)
- Mira A M Behnam
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University , Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Dominik Graf
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University , Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University , Im Neuenheimer Feld 345, 69120 Heidelberg, Germany.,German Center for Infection Research, Heidelberg University , Im Neuenheimer Feld 345, 69120 Heidelberg, Germany
| | - Darius P Zlotos
- Department of Pharmaceutical Chemistry, The German University in Cairo , New Cairo City, 11835 Cairo, Egypt
| | - Christian D Klein
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University , Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
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97
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Policresulen, a novel NS2B/NS3 protease inhibitor, effectively inhibits the replication of DENV2 virus in BHK-21 cells. Acta Pharmacol Sin 2015; 36:1126-36. [PMID: 26279156 DOI: 10.1038/aps.2015.56] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 05/08/2015] [Indexed: 12/17/2022] Open
Abstract
AIM Dengue is a severe epidemic disease caused by dengue virus (DENV) infection, for which no effective treatment is available. The protease complex, consisting of nonstructural protein 3 (NS3) and its cofactor NS2B, plays a pivotal role in the replication of DENV, thus may be a potential target for anti-DENV drugs. Here, we report a novel inhibitor of DENV2 NS2B/NS3 protease and its antiviral action. METHODS An enzymatic inhibition assay was used for screening DENV2 NS2B/NS3 inhibitors. Cytotoxicity to BHK-21 cells was assessed with MTT assay. Antiviral activity was evaluated in BHK-21 cells transfected with Rlu-DENV-Rep. The molecular mechanisms of the antiviral action was analyzed using surface plasmon resonance, ultraviolet-visible spectral analysis and differential scanning calorimetry assays, as well as molecular docking analysis combined with site-directed mutagenesis. RESULTS In our in-house library of old drugs (~1000 compounds), a topical hemostatic and antiseptic 2-hydroxy-3,5-bis[(4-hydroxy-2-methyl-5-sulfophenyl)methyl]-4-methyl-benzene-sulfonic acid (policresulen) was found to be a potent inhibitor of DENV2 NS2B/NS3 protease with IC50 of 0.48 μg/mL. Furthermore, policresulen inhibited DENV2 replication in BHK-21 cells with IC50 of 4.99 μg/mL, whereas its IC50 for cytotoxicity to BHK-21 cells was 459.45 μg/mL. Policresulen acted as a competitive inhibitor of the protease, and slightly affected the protease stability. Using biophysical technology-based assays and molecular docking analysis combined with site-directed mutagenesis, we demonstrated that the residues Gln106 and Arg133 of DENV2 NS2B/NS3 protease directly interacted with policresulen via hydrogen bonding. CONCLUSION Policresulen is a potent inhibitor of DENV2 NS2B/NS3 protease that inhibits DENV2 replication in BHK-21 cells. The binding mode of the protease and policresulen provides useful hints for designing new type of inhibitors against the protease.
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98
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Context-Dependent Cleavage of the Capsid Protein by the West Nile Virus Protease Modulates the Efficiency of Virus Assembly. J Virol 2015; 89:8632-42. [PMID: 26063422 DOI: 10.1128/jvi.01253-15] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 06/02/2015] [Indexed: 12/31/2022] Open
Abstract
UNLABELLED The molecular mechanisms that define the specificity of flavivirus RNA encapsulation are poorly understood. Virions composed of the structural proteins of one flavivirus and the genomic RNA of a heterologous strain can be assembled and have been developed as live attenuated vaccine candidates for several flaviviruses. In this study, we discovered that not all combinations of flavivirus components are possible. While a West Nile virus (WNV) subgenomic RNA could readily be packaged by structural proteins of the DENV2 strain 16681, production of infectious virions with DENV2 strain New Guinea C (NGC) structural proteins was not possible, despite the very high amino acid identity between these viruses. Mutagenesis studies identified a single residue (position 101) of the DENV capsid (C) protein as the determinant for heterologous virus production. C101 is located at the P1' position of the NS2B/3 protease cleavage site at the carboxy terminus of the C protein. WNV NS2B/3 cleavage of the DENV structural polyprotein was possible when a threonine (Thr101 in strain 16681) but not a serine (Ser101 in strain NGC) occupied the P1' position, a finding not predicted by in vitro protease specificity studies. Critically, both serine and threonine were tolerated at the P1' position of WNV capsid. More extensive mutagenesis revealed the importance of flanking residues within the polyprotein in defining the cleavage specificity of the WNV protease. A more detailed understanding of the context dependence of viral protease specificity may aid the development of new protease inhibitors and provide insight into associated patterns of drug resistance. IMPORTANCE West Nile virus (WNV) and dengue virus (DENV) are mosquito-borne flaviviruses that cause considerable morbidity and mortality in humans. No specific antiflavivirus therapeutics are available for treatment of infection. Proteolytic processing of the flavivirus polyprotein is an essential step in the replication cycle and is an attractive target for antiviral development. The design of protease inhibitors has been informed by insights into the molecular details of the interactions of proteases and their substrates. In this article, studies of the processing of WNV and DENV capsid proteins by the WNV protease identified an unexpected contribution of the sequence surrounding critical residues within the cleavage site on protease specificity. This demonstration of context-dependent protease cleavage has implications for the design of chimeric flaviviruses, new therapeutics, and the interpretation of flavivirus protease substrate specificity studies.
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99
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Yotmanee P, Rungrotmongkol T, Wichapong K, Choi SB, Wahab HA, Kungwan N, Hannongbua S. Binding specificity of polypeptide substrates in NS2B/NS3pro serine protease of dengue virus type 2: A molecular dynamics Study. J Mol Graph Model 2015; 60:24-33. [PMID: 26086900 DOI: 10.1016/j.jmgm.2015.05.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 05/14/2015] [Accepted: 05/15/2015] [Indexed: 02/05/2023]
Abstract
The pathogenic dengue virus (DV) is a growing global threat, particularly in South East Asia, for which there is no specific treatment available. The virus possesses a two-component (NS2B/NS3) serine protease that cleaves the viral precursor proteins. Here, we performed molecular dynamics simulations of the NS2B/NS3 protease complexes with six peptide substrates (capsid, intNS3, 2A/2B, 4B/5, 3/4A and 2B/3 containing the proteolytic site between P(1) and P(1)' subsites) of DV type 2 to compare the specificity of the protein-substrate binding recognition. Although all substrates were in the active conformation for cleavage reaction by NS2B/NS3 protease, their binding strength was somewhat different. The simulated results of intermolecular hydrogen bonds and decomposition energies suggested that among the ten substrate residues (P(5)-P(5)') the P(1) and P(2) subsites play a major role in the binding with the focused protease. The arginine residue at these two subsites was found to be specific preferential binding at the active site with a stabilization energy of <-10 kcal mol(-1). Besides, the P(3), P(1)', P(2)' and P(4)' subsites showed a less contribution in binding interaction (<-2 kcal mol(-1)). The catalytic water was detected nearby the carbonyl oxygen of the P(1) reacting center of the capsid, intNS3, 2A/2B and 4B/5 peptides. These results led to the order of absolute binding free energy (ΔGbind) between these substrates and the NS2B/NS3 protease ranked as capsid>intNS3>2A/2B>4B/5>3/4A>2B/3 in a relative correspondence with previous experimentally derived values.
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Affiliation(s)
- Pathumwadee Yotmanee
- Department of Chemistry, Faculty of Science, Ramkhamhaeng University, Bangkok 10240, Thailand; Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Thanyada Rungrotmongkol
- Ph.D. Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Kanin Wichapong
- Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sy Bing Choi
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor 11800, Pulau Pinang, Malaysia; Natural Product and Drug Discovery Centre, Malaysian Institutes of Pharmaceuticals and Nutraceuticals, National Institutes of Biotechnology Malaysia, Ministry of Science, Technology and Innovation, Block 5-A, Halaman Bukit Gambir, 11700, Penang, Malaysia
| | - Habibah A Wahab
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor 11800, Pulau Pinang, Malaysia; Natural Product and Drug Discovery Centre, Malaysian Institutes of Pharmaceuticals and Nutraceuticals, National Institutes of Biotechnology Malaysia, Ministry of Science, Technology and Innovation, Block 5-A, Halaman Bukit Gambir, 11700, Penang, Malaysia.
| | - Nawee Kungwan
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Supot Hannongbua
- Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
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100
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Luo D, Vasudevan SG, Lescar J. The flavivirus NS2B-NS3 protease-helicase as a target for antiviral drug development. Antiviral Res 2015; 118:148-58. [PMID: 25842996 DOI: 10.1016/j.antiviral.2015.03.014] [Citation(s) in RCA: 194] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 03/20/2015] [Accepted: 03/26/2015] [Indexed: 11/30/2022]
Abstract
The flavivirus NS3 protein is associated with the endoplasmic reticulum membrane via its close interaction with the central hydrophilic region of the NS2B integral membrane protein. The multiple roles played by the NS2B-NS3 protein in the virus life cycle makes it an attractive target for antiviral drug discovery. The N-terminal region of NS3 and its cofactor NS2B constitute the protease that cleaves the viral polyprotein. The NS3 C-terminal domain possesses RNA helicase, nucleoside and RNA triphosphatase activities and is involved both in viral RNA replication and virus particle formation. In addition, NS2B-NS3 serves as a hub for the assembly of the flavivirus replication complex and also modulates viral pathogenesis and the host immune response. Here, we review biochemical and structural advances on the NS2B-NS3 protein, including the network of interactions it forms with NS5 and NS4B and highlight recent drug development efforts targeting this protein. This article forms part of a symposium in Antiviral Research on flavivirus drug discovery.
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Affiliation(s)
- Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, 61 Biopolis Drive, Proteos Building, #07-03, Singapore 138673, Singapore.
| | - Subhash G Vasudevan
- Program in Emerging Infectious Diseases, DUKE-NUS Graduate Medical School, 8 College Road, Singapore 169857, Singapore.
| | - Julien Lescar
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; UPMC UMRS CR7 - CNRS ERL 8255-INSERM U1135 Centre d'Immunologie et des Maladies Infectieuses, Centre Hospitalier Universitaire Pitié-Salpêtrière, Faculté de Médecine Pierre et Marie Curie, Paris, France.
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