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In silico virtual screening approaches for anti-viral drug discovery
2012
Drug Discovery Today : Technologies
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Virtual in silico screening has repeatedly proven to be useful to meet the special challenges of antiviral drug discovery. ...
Large virtual compound libraries are filtered by different computational screening methods such as docking, ligand-based similarity searches or pharmacophore-based screening, reducing the number of candidate ...
s contribution to this work. ...
doi:10.1016/j.ddtec.2012.07.009
pmid:24990575
pmcid:PMC7105918
fatcat:jcea6cudwve6jiqf3yb4usn66e
Interactions of HIV-1 Capsid with Host Factors and TheirImplications for Developing Novel Therapeutics
2021
Viruses
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used to identify host factors that interact with capsid. ...
Conventional anti-retroviral therapies primarily target HIV-1 enzymes. Insights of capsid structure have resulted in a first-in-class, long-acting capsid-targeting inhibitor, GS-6207 (Lenacapavir). ...
Silvas for her support in generating capsid core and CA structures in Figures 2D and 3D .
Conflicts of Interest: The authors declare no conflict of interest. ...
doi:10.3390/v13030417
pmid:33807824
fatcat:adop23yeanacznp2uvmmdqlu5m
Top-Down and Bottom-Up Proteomics Methods to Study RNA Virus Biology
2021
Viruses
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implications to identify novel tractable antiviral targets. ...
identification of antiviral targets. ...
Acknowledgments: We thank members of the Dynamics of Viral Structures and Systems Arbovirology laboratories for helpful discussions and apologize to those colleagues, whose work could not be cited due ...
doi:10.3390/v13040668
pmid:33924391
fatcat:km5ey3omwrc3hfqsw6afrro5dq
Antiviral Stratagems against HIV-1 Using RNA Interference (RNAi) Technology
2013
Evolutionary Bioinformatics
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In this regard, targeting multiple HIV sites in the context of a combinatorial RNAi-based approach may efficiently stop viral propagation at an early stage. ...
in the fight against the HIV-1 virus. ...
Acknowledgements The authors would like to sincerely thank Prof. ...
doi:10.4137/ebo.s11412
pmid:23761954
pmcid:PMC3662398
fatcat:cwdzs6bpingihci5fejcacusca
Identification of a Broad-Spectrum Viral Inhibitor Targeting a Novel Allosteric Site in the RNA-Dependent RNA Polymerases of Dengue Virus and Norovirus
2020
Frontiers in Microbiology
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virtual screening to discover compounds that can inhibit the RdRps of both hNV and DENV. ...
In this study, we take advantage of the structurally equivalent site in the dengue virus (DENV) RdRp, the N-pocket, and in the human norovirus (hNV) RdRp, the B-site, and performed a parallel structure-based ...
Structure-Based Virtual Screening To identify compounds that inhibit RdRps of both DENV and hNV, we performed structure-based virtual screening against TargetMol's Bioactive compound library plus (7568 ...
doi:10.3389/fmicb.2020.01440
pmid:32670253
pmcid:PMC7330483
fatcat:xzlrsh27erddle53c5aj2x4utm
Energy Based Pharmacophore Modelling and Docking Studies for Determining Potent Inhibitor Against M2 Proton Channel of Influenza Virus
2018
Indian Journal of Pharmaceutical Education and Research
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Keeping this in our minds, an investigation was performed to determine potent inhibitors of M2 protein using computational strategies like e-pharmacophore based virtual screening and molecular docking. ...
Due to its primal role in the life cycle of influenza A virus, it is targeted by many potent drugs like amantadine and rimantadine. ...
Figure 1 : 1 Virtual screening workflow of the lead identification based on e-pharmacophore based drug design. ...
doi:10.5530/ijper.52.3.59
fatcat:o5ksv7gp7fgltj2rp3uecwtehy
Immunity and Viral Infections: Modulating Antiviral Response via CRISPR–Cas Systems
2021
Viruses
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Understanding and exploiting virus–host interactions is instrumental for identifying host factors involved in viral replication, developing effective antiviral agents, and mitigating the severity of virus-borne ...
The diversity of CRISPR systems and CRISPR-based tools enables the specific modulation of innate immune responses and has contributed impressively to the fields of virology and immunology in a very short ...
Zhu et al. (2018) performed CRISPR-based screening to identify factors that mediate the silencing of unintegrated retroviral DNA. ...
doi:10.3390/v13071373
pmid:34372578
pmcid:PMC8310348
fatcat:jyzoodbtbrhplpp77mqgbxvcca
Targeted redesign of suramin analogs for novel antimicrobial lead development
[article]
2021
bioRxiv
pre-print
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Although some suramin analogs have been developed against specific targets, only limited structure activity relationship (SAR) studies were performed, and virtual screening has yet to be used to identify ...
From this platform, we developed a framework for structure- and docking-guided elaboration of suramin analog scaffolds using virtual screening of suramin and heparin analogs against a panel of diverse ...
This result indicates that virtual screening-based using suramin or heparin analogs can identify ligands with greater selectivity for diverse protein targets compared to using either suramin or heparin ...
doi:10.1101/2021.05.17.444489
fatcat:nkwzgrf7abdkpfkkeyn63mf75y
Systematic review on role of structure based drug design (SBDD) in the identification of anti-viral leads against SARS-Cov-2
2021
Current Research in Pharmacology and Drug Discovery
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The discovery of FDA approved human immunodeficiency virus type 1 (HIV-1) inhibitors represent the foremost success of SBDD. ...
This systematic review provides an overview of the novel coronavirus, its pathology of replication, role of structure based drug design, available drug targets and recent advances in in-silico drug discovery ...
NGB, SR, GG and AS are thankful to Indian Institute of Technology ( Banaras Hindu University) Varanasi for providing teaching assistantships to them. ...
doi:10.1016/j.crphar.2021.100026
pmid:34870145
pmcid:PMC8120892
fatcat:r3men6gzhng4jm5cpgooidavve
Perspectives towards antiviral drug discovery against Ebola virus
2018
Journal of Medical Virology
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This review summarizes the recent therapeutic advances and ongoing research progress from research and development to clinical trials in the development of small-molecule antiviral drugs, small-interference ...
With mortality rates up to 90%, it is nowadays one of the most deadly infectious diseases. ...
., (220) have described the physical properties of the HIV-1 capsid protein using all-atom MD simulations. ...
doi:10.1002/jmv.25357
pmid:30431654
pmcid:PMC7166701
fatcat:c7syd5rirvcplf3dyhcf7y6psq
PHOMOARCHERIN B AS A NOVEL HIV-1 REVERSE TRANSCRIPTASE RNASE H ACTIVITY INHIBITOR; CONCLUSIONS FROM COMPREHENSIVE COMPUTATIONAL ANALYSIS
2021
Zenodo
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Afterwards, a library of around 94.000 small molecule inhibitors was investigated and virtual screening was performed against the RNase domain of the reverse transcriptase to identify potential hits. ...
In this study, genomic analysis was performed on 98 HIV-1 genomes to determine the most coherent target, which could be utilized for termination of the viral replication and the reverse transcriptase enzyme ...
Molecular docking based virtual screening The experimentally determined X-ray diffraction structure of HIV-1 RT with PDB ID 3IG1 was retrieved from the Research Collaboratory for Structural Bioinformatics ...
doi:10.5281/zenodo.5150348
fatcat:a5melfvc3besrcze6gqcw4nyee
Virtual screening, ADME/Tox predictions and the drug repurposing concept for future use of old drugs against the COVID-19
2020
Life Sciences
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Therefore, in order to identify potential inhibitors for Mpro, we used virtual screening approaches based with the structure of the enzyme and two compounds libraries, targeted to SARS-CoV-2, containing ...
These structural data are extremely important for in silico design and development of compounds as well, being possible to quick and effectively identify potential inhibitors addressed to such enzyme's ...
Fig. 1 . 1 Workflow with the mains steps of the methodological procedure performed in the virtual screening. L.I.d.S. Hage-Melim, et al. ...
doi:10.1016/j.lfs.2020.117963
pmid:32535080
pmcid:PMC7289103
fatcat:rjqz2vuz6rbztmldhetgcgnjoi
BioExcel-2 Deliverable D3.3 – Use Case Progress Report
2020
Zenodo
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With regards to COVID-19, core applications and workflow tools were rapidly adapted to perform large-scale mutational and free energy analyses to elucidate the evolutionary and structural relationships ...
targets. ...
Computational screening of avGFP mutants based on thermal-stability and Stokesshift The automated workflow was implemented to set up solution structure models for four well-known GFP mutants: S65T, F64L ...
doi:10.5281/zenodo.5511684
fatcat:civldhbeljctpkcdtay7dvkds4
High-throughput RNA interference screens integrative analysis: Towards a comprehensive understanding of the virus-host interplay
2013
World Journal of Virology
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High-throughput RNA interference screens integrative analysis: Towards a comprehensive understanding of the virus-host interplay. ...
Figure 1 A 1 Figure 1 A schematic workflow for the analysis of high-throughput RNA interference screens to identify host cell regulators of viral life cycle.
Amberkar S et al . ...
in a simple workflow for the analysis of HT-RNAi screens aimed at identifying key host regulators of viral life cycles (Figure 1 ). ...
doi:10.5501/wjv.v2.i2.18
pmid:24175227
pmcid:PMC3785050
fatcat:jpltfxygnrekvhigej6phqobyu
Functional genomic and high-content screening for target discovery and deconvolution
2012
Expert Opinion on Drug Discovery
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Thus, although new targets are identified, caution should be applied toward interpretation of screening data in isolation. ...
Introduction-Functional genomic screens apply knowledge gained from the sequencing of the human genome toward rapid methods of identifying genes involved in cellular function based on a specific phenotype ...
Figure 1 . 1 Venn diagrams representing the overlaps between HIV-1 screening datasets (A) The overlaps between four published RNAi screens identifying HIV host factors are small. ...
doi:10.1517/17460441.2012.711311
pmid:22860749
pmcid:PMC3954969
fatcat:3gk7e5f7ynezpoj37ewh46sf2a
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