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New Approaches to Structure-Based Discovery of Dengue Protease Inhibitors
2009
Infectious Diseases - Drug Targets
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This review discusses current and newly implemented structure-based computational efforts to discover antivirals that target the DENV NS3 protease, although it is clear that these computational tools can ...
Dengue virus (DENV), a member of the family Flaviviridae, presents a tremendous threat to global health since an estimated 2.5 billion people worldwide are at risk for epidemic transmission. ...
Comparison of the dengue NS3 protease [63] and the dengue NS2B-NS3 protease [68] . Ribbon diagram representation of (A) NS3 and (B) NS2B-NS3 proteins. ...
doi:10.2174/1871526510909030327
pmid:19519486
fatcat:z3g7wb3fonhcdddlw56axh2jfu
Designing cyclic peptide inhibitor of dengue virus NS3-NS2B protease by using molecular docking approach
2010
Bioinformation
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Seven cyclopentapeptide inhibitors were designed in this study against dengue virus type 2 (DEN-2) NS3-NS2B protease: CKRRC, CGRRC, CRGRC, CRTRC, CTRRC, CKRKC and CRRKC. ...
Thus, the cyclopentapeptide is proposed as a potential inhibitor to the NS3-NS2B protease activities of DEN-2. ...
Acknowledgement: We are grateful to Ridla Bakri PhD, Chairman of Department of Chemistry, Faculty of Mathematics and Natural Science, University of Indonesia for his support of this research. ...
doi:10.6026/97320630005250
pmid:21364826
pmcid:PMC3055701
fatcat:acfpya66qje2zd7ekalyye7yh4
Molecular Dynamics of the Dengue Virus NS3/NS2B Protease in Presence of Inhibitor or Substrate
2014
Biophysical Journal
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The computationally less expensive empirical ligand and structure based methods require training a predictive model to yield accurate free energy estimates. ...
In addition, these studies can provide fundamental insights into how ligand binding regulates protein function. ...
doi:10.1016/j.bpj.2013.11.1534
fatcat:sgm4xg6bcra6xalkjle32meoyu
Insights to Substrate Binding and Processing by West Nile Virus NS3 Protease through Combined Modeling, Protease Mutagenesis, and Kinetic Studies
2006
Journal of Biological Chemistry
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Using a combination of molecular fitting of substrates to the active site of the crystal structure of NS3, site-directed enzyme and cofactor mutagenesis, and kinetic studies on proteolytic processing of ...
A key enzyme that is essential for viral replication is the viral protease NS2B-NS3, which is highly conserved among all flaviviruses. ...
Recently reported crystal structures for NS2B/NS3 proteases of both WNV and Den2 (6) provide new structural insights to flaviviral proteases in ligand-bound conformations. ...
doi:10.1074/jbc.m607641200
pmid:17052977
fatcat:mhjzkbo67rhtrolmjxnfdapl4y
Interactomics of Blebbistatin
2013
Biophysical Journal
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hand, a nutrient-how the receptor senses these agonists in healthy and diseased states. ...
extracellular domain (ECD) of CaSR with various spectroscopic methods including the tryptophan fluorescence titration, circular dichroism (CD) and nuclear magnetic resonance (NMR) as well as molecular ...
Drugs for the Discovery of Inhibitors of Dengue Virus NS2B-NS3 Protease by Docking, Consensus Scoring, and Molecular Dynamics Simulations Aldo Segura-Cabrera, Carlos A. ...
doi:10.1016/j.bpj.2012.11.2252
fatcat:ln3pjsxi2fcsfcp4ta5cam4g6a
In Silico Prediction of the Phosphorylation of NS3 as an Essential Mechanism for Dengue Virus Replication and the Antiviral Activity of Quercetin
2021
Biology
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Dengue virus infection is a global health problem for which there have been challenges to obtaining a cure. ...
We employed computational methods based on structure-function relationships between human host kinases and viral nonstructural protein 3 (NS3) to understand viral replication inhibitors' therapeutic effect ...
Appendix A Figure 1 . 1 NS3 crystal structure. (A) The crystal structure of the NS3 Protease-Helicase from Dengue virus (PDB: 2VBC). The Protease domain (N-terminal, residues 20-168) is shown in red. ...
doi:10.3390/biology10101067
pmid:34681164
fatcat:i4wpxf3lpng4pghcgy2k244d4y
Mechanisms of Proteolytic Enzymes and Their Inhibition in QM/MM Studies
2021
International Journal of Molecular Sciences
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In line with this, computational chemistry based on experimental structures came up with studies on all major protease classes in recent years; examples of aspartic, metallo-, cysteine, serine, and threonine ...
In this overview, a few examples demonstrate the high potential of the QM/MM approach for sophisticated pharmaceutical compound design and supporting functions in the analysis of biomolecular structures ...
Similarly, the reaction mechanism of the HCIV-related NS3 protease of the Dengue virus with its cofactor NS2B exhibited a stepwise nucleophilic attack and protonation at the scissile bond during the acylation ...
doi:10.3390/ijms22063232
pmid:33810118
pmcid:PMC8004986
fatcat:4gc4ck72uvg7xonbaveqtss5bq
Molecular dynamics suggests antiviral compounds active against Dengue Virus show similar binding patterns to Zika Virus proteins
[article]
2018
bioRxiv
pre-print
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Here we have applied these methods on compounds that were previously shown to be active against Dengue virus in vitro, taking the structural information of such compounds and applying docking methods to ...
A molecular dynamics approach was also used to refine the docking results. ...
of the helicase activity of the NS3 protein, thus providing further insights into the action mechanisms of each compound against Dengue virus, as originally suggested by the respective authors of each ...
doi:10.1101/309351
fatcat:j35dvkyndnhpdbo4qmxxsukxgq
Genetic and structural analyses of ssRNA viruses pave the way for the discovery of novel antiviral pharmacological targets
2021
Molecular Omics
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In the era of big data and artificial intelligence a lot of new discoveries have influenced the field of antiviral drug design and pharmacophore identification. Viruses have always been a... ...
disruption of the NS2B-NS3 interaction emerges as a possible alternative approach in the design of anti-flaviviral drugs. ...
Flavivirus protease is a complex between the NS3 protein and a hydrophobic core within the viral NS2B protein, which acts as an essential cofactor. ...
doi:10.1039/d0mo00173b
pmid:33725065
fatcat:edvbbsxm4zf5pect65nzb5rtnq
Molecular docking and QSAR theoretical model for prediction of phthalazinone derivatives as new class of potent dengue virus inhibitors
2020
Beni-Suef University Journal of Basic and Applied Sciences
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The improvement of existing agents that can inhibit the dengue virus is therefore of utmost importance. ...
Also, in this study, molecular docking simulation was carried between dengue virus serotype 2 protease (PDB CODE: 6mol) and some selected phthalazinone derivatives (compounds 1, 2, 7, 11, and 21). ...
Figures 2a, b, 6a-d, and 7a ,b showed prepared structure of the target (NS2B-NS3) and 3D structure of the prepared ligand 21, 2D interaction type for ligand 1, 2, 7, and 11 with different amino acids in ...
doi:10.1186/s43088-020-00073-9
fatcat:6oicuqdoojcqbmg6zrpdsdgbju
Discovery of novel West Nile Virus protease inhibitor based on isobenzonafuranone and triazolic derivatives of eugenol and indan-1,3-dione scaffolds
2019
PLoS ONE
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The West Nile Virus (WNV) NS2B-NS3 protease is an attractive target for the development of therapeutics against this arboviral pathogen. ...
Molecular docking calculations predicted a recognition pattern involving the residues His51 and Ser135, which are members of the catalytic triad of the WNV NS2B-NS3 protease. ...
Viral protease performs the cleavage of some sites: NS2A-NS2B, NS2B-NS3, NS3-NS4A and NS4B-NS5. ...
doi:10.1371/journal.pone.0223017
pmid:31557229
pmcid:PMC6762200
fatcat:4bqa2u4l2rg3fa2duux4nqsq6e
Peptide-Based Subunit Vaccine Design of T- and B-Cells Multi-Epitopes against Zika Virus Using Immunoinformatics Approaches
2019
Microorganisms
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In this study, a collection of Zika proteomes was used to find the best candidates for T- and B-cell epitopes using the immunoinformatics approach. ...
The Zika virus disease, also known as Zika fever is an arboviral disease that became epidemic in the Pacific Islands and had spread to 18 territories of the Americas in 2016. ...
The structure for NS2B was obtained from a complexed structure with the protease domain of dengue NS3 [113] . ...
doi:10.3390/microorganisms7080226
pmid:31370224
pmcid:PMC6722788
fatcat:s7jcassopfhylgj426zduliini
Facile Synthesis and In Vitro Activity of N-Substituted 1,2-Benzisothiazol-3(2H)-ones against Dengue Virus NS2BNS3 Protease
2021
Pathogens
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Several new N-substituted 1,2-benzisothiazol-3(2H)-ones (BITs) were synthesised through a facile synthetic route for testing their anti-dengue protease inhibition. ...
Thus, the synthesised BITs were tested for inhibitory activity against the recombinant dengue virus serotype-2 (DENV-2) NS2BNS3 protease. ...
Acknowledgments: The assistance and support of Heike Oberwinkler and Melissa Zimniak in designing and executing the in-vitro studies are greatly acknowledged. ...
doi:10.3390/pathogens10040464
pmid:33921368
fatcat:aufujbzicre6xakbu63riirwvm
Computational approach to decipher cellular interactors and drug targets during co-infection of SARS-CoV-2, Dengue, and Chikungunya virus
2021
VirusDisease
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The co-occurrence of the Dengue virus (DENV) and Chikungunya virus (CHIKV) has been into existence, but recently the co-infection of DENV and SARS-CoV-2 has been reported. ...
In total, 17 interacting host proteins were identified showing association with envelope, structural, non-structural, and accessory proteins. ...
Funding The research was funded by Council of Scientific and Industrial Research (CSIR) for providing financial support (ack. no. 113486/2K18/1). ...
doi:10.1007/s13337-021-00665-8
pmid:33723515
pmcid:PMC7945596
fatcat:jlkz664pzzczjavdn3uzje6gdm
Computer-Assisted and Data Driven Approaches for Surveillance, Drug Discovery, and Vaccine Design for the Zika Virus
2019
Pharmaceuticals
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Modern technologies, including computational tools as well as experimental approaches, need to be harnessed fast and effectively in a coordinated manner in order to properly address such challenges. ...
In this paper, based on our earlier research, we have proposed a four-pronged approach to tackle the emerging pathogens like ZIKV: (a) Epidemiological modelling of spread mechanisms of ZIKV; (b) assessment ...
Importantly, three of these NS proteins, NS2B-NS3 protease, NS3 helicase, and NS5 methyltransferase are available with ligands, ATP and RNA in the data bank. ...
doi:10.3390/ph12040157
pmid:31623241
pmcid:PMC6958466
fatcat:unxtxxjpznazvcdphl7zacxdhu
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