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In silico virtual screening approaches for anti-viral drug discovery

Manuela S. Murgueitio, Marcel Bermudez, Jérémie Mortier, Gerhard Wolber
2012 Drug Discovery Today : Technologies  
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

Shentian Zhuang, Bruce E. Torbett
2021 Viruses  
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

Yogy Simanjuntak, Kira Schamoni-Kast, Alice Grün, Charlotte Uetrecht, Pietro Scaturro
2021 Viruses  
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

Dimitrios Vlachakis, Georgia Tsiliki, Athanasia Pavlopoulou, Maria G. Roubelakis, Spyridon Champeris Tsaniras, Sophia Kossida
2013 Evolutionary Bioinformatics  
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

Dongrong Yi, Quanjie Li, Lili Pang, Yujia Wang, Yongxin Zhang, Zhaojun Duan, Chen Liang, Shan Cen
2020 Frontiers in Microbiology  
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

Rohini Kanagavelu, Shinny Sunny, Preethi Balasundaram, Ramanathan Karuppasamy, Shanthi Veerappapillai
2018 Indian Journal of Pharmaceutical Education and Research  
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

Sergey Brezgin, Anastasiya Kostyusheva, Ekaterina Bayurova, Elena Volchkova, Vladimir Gegechkori, Ilya Gordeychuk, Dieter Glebe, Dmitry Kostyushev, Vladimir Chulanov
2021 Viruses  
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]

Debayan Dey, Suryanarayanarao Ramakumar, Graeme L Conn
2021 bioRxiv   pre-print
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

Nilesh Gajanan Bajad, Swetha Rayala, Gopichand Gutti, Anjali Sharma, Meenakshi Singh, Ashok Kumar, Sushil Kumar Singh
2021 Current Research in Pharmacology and Drug Discovery  
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

Muhammad Usman Mirza, Michiel Vanmeert, Amjad Ali, Kanzal Iman, Matheus Froeyen, Muhammad Idrees
2018 Journal of Medical Virology  
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


Naeem Abdul Ghafoor, Omur Baysal, Baris Ethem Suzek, Ragip Soner Silme
2021 Zenodo  
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

Lorane Izabel da Silva Hage-Melim, Leonardo Bruno Federico, Nayana Keyla Seabra de Oliveira, Viviane Cristina Cardoso Francisco, Lenir Cabral Correa, Henrique Barros de Lima, Suzane Quintana Gomes, Mariana Pegrucci Barcelos, Isaque Antônio Galindo Francischini, Carlos Henrique Tomich de Paula da Silva
2020 Life Sciences  
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

Arno Proeme, Alessandra Villa, Zuzana Jandova, Alexandre Bonvin, Vytautas Gapsys, Adam Hospital, Yvonne Westermaier, Gerrit Groenhof, Dmitry Morozon, Vaibhav Modi, Emiliano Ippolilit
2020 Zenodo  
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

Sandeep Amberkar
2013 World Journal of Virology  
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

Susanne Heynen-Genel, Lars Pache, Sumit K Chanda, Jonathan Rosen
2012 Expert Opinion on Drug Discovery  
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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