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In Silico Discovery of Aminoacyl-tRNA Synthetase Inhibitors
2014
International Journal of Molecular Sciences
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In this review, we mainly focused on aaRS inhibitor discovery and development using in silico methods including virtual screening and structure-based drug design. ...
These computational methods are relatively fast and cheap, and are proving to be of great benefit for the rational development of more potent aaRS inhibitors and other pharmaceutical agents that may usher ...
Acknowledgments We thank National Science
Conflicts of Interest The authors declare no conflict of interest. ...
doi:10.3390/ijms15011358
pmid:24447926
pmcid:PMC3907873
fatcat:lioemckjtra27ksucnq223g3ya
In silico virtual screening approaches for anti-viral drug discovery
2012
Drug Discovery Today : Technologies
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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 ...
Virtual in silico screening has repeatedly proven to be useful to meet the special challenges of antiviral drug discovery. ...
Talele et al. identified two novel chemotypes as allosteric inhibitors of HCV NS5B through molecular docking of compounds from a commercially available database into the allosteric pocket-1 of NS5 [48 ...
doi:10.1016/j.ddtec.2012.07.009
pmid:24990575
pmcid:PMC7105918
fatcat:jcea6cudwve6jiqf3yb4usn66e
Structure Optimization of Neuraminidase Inhibitors as Potential Anti-Influenza (H1N1Inhibitors) Agents Using QSAR and Molecular Docking Studies
2014
Iranian journal of pharmaceutical research
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Our search for selective inhibitors of neuraminidase has led to the identification of pharmacophoric requirements at various positions around acyl thiourea pharmacophore. ...
The urgent need of neuraminidase inhibitors (NI) has provided an impetus for understanding the structure requisite at molecular level. ...
Kulkarni, Emeritus Professor from Poona College of Pharmacy, Pune, Maharashtra, India for his support and guidance for molecular modeling studies and Dr. A. R. ...
pmid:24734056
pmcid:PMC3985258
fatcat:k3g7xyn75bd4jcrpjlmhga4bym
Application of computational methods for anticancer drug discovery, design, and optimization
2016
Boletín Médico del Hospital Infantil de México
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From hit identification to lead optimization, techniques such as ligand- or structure-based virtual screening are widely used in many discovery efforts. ...
Key principles are illustrated through case studies including specifically successful achievements in the field of anticancer drug design to demonstrate that research advances, with the aid of in silico ...
Structure-based pharmacophore modeling has been extensively used for drug hit discovery and applied in the identification of novel ligands using a database searching approach. 35 Twenty-seven homology ...
doi:10.1016/j.bmhimx.2016.10.006
pmid:29421286
pmcid:PMC7110968
fatcat:3dom2uh5jjg5jarfxcc74d7oxi
Identification of Potential Inhibitors against the Human Influenza A Virus Targeting the CPSF30 and RNA Binding Domains of the NS1 Protein: An E-Pharmacophore approach
2017
Indian Journal of Pharmaceutical Education and Research
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Based on the energyoptimized pharmacophore obtained, the Phase program was used to screen Asinex's MedChem building blocks to find suitable hits with the essential pharmacophore features. ...
Methods: E-pharmacophore models, were generated by docking a fragment library at the active sites of both the domains using GlideXP. ...
ACKNOWLEDGEMENT The authors are thankful to Dr AC Mishra, Former Director and Dr DT Mourya, Director, National Institute of Virology for the facilities provided, encouragement and support. ...
doi:10.5530/ijper.51.1.5
fatcat:pyjo4jcmnvffdajteqggpdao5u
Application of computational methods for anticancer drug discovery, design, and optimization
2016
Boletín Médico Del Hospital Infantil de México (English Edition)
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From hit identification to lead optimization, techniques such as ligand-or structurebased virtual screening are widely used in many discovery efforts. ...
Key principles are illustrated through case studies including specifically successful achievements in the field of anticancer drug design to demonstrate that research advances, with the aid of in silico ...
Structure-based pharmacophore modeling has been extensively used for drug hit discovery and applied in the identification of novel ligands using a database searching approach. 35 Twenty-seven homology ...
doi:10.1016/j.bmhime.2017.11.040
fatcat:qna2hfewqzbrxbwi4fn4muop4m
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. ...
A three dimensional pharmacophore model was generated based on the chemical features using PHASE module of Schrödinger Suite. ...
ACKNOWLEDGEMENT The authors gratefully acknowledge Vellore Institute of Technology, Vellore for the support through Seed Grant for Research. ...
doi:10.5530/ijper.52.3.59
fatcat:o5ksv7gp7fgltj2rp3uecwtehy
Emerging Methods for Ensemble-Based Virtual Screening
2010
Current Topics in Medicinal Chemistry
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or the ranking of virtual screening hits. ...
Ensemble based virtual screening refers to the use of conformational ensembles from crystal structures, NMR studies or molecular dynamics simulations. ...
INTRODUCTION The computational identification of drug leads out of large compound libraries through receptor-based virtual screening (VS) is a well-established method to predict putative inhibitors for ...
doi:10.2174/156802610790232279
pmid:19929833
pmcid:PMC3086266
fatcat:dtupwbrtcvan5buhmq2d3bm4na
Identification of influenza PA-Nter endonuclease inhibitors using pharmacophore- and docking-based virtual screening
2018
Bioorganic & Medicinal Chemistry
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The obtained hypothesis has been fruitfully employed to select three "hit compounds" through an in silico screening campaign on our in-house database of small molecules. ...
Compound 20 proved the most active inhibitor of the endonucleolytic cleavage reaction, with an IC 50 value of 12 μM. ...
Virtual screening Using this pharmacophore model, we performed an in silico screening campaign on our CHIME 1.6 library, which consists of a collection of 1300 small molecules developed and synthesized ...
doi:10.1016/j.bmc.2018.07.046
pmid:30082105
fatcat:3od2tqjmafatxnzmw54ayij7sy
Computational modeling of the bat HKU4 coronavirus 3CLpro inhibitors as a tool for the development of antivirals against the emerging Middle East respiratory syndrome (MERS) coronavirus
2017
Journal of Molecular Recognition
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The best models were used as 3D queries to screen the National Cancer Institute database for novel nonpeptidomimetic 3CL pro inhibitors. ...
We conducted extensive exploration of the pharmacophoric space of a recently identified set of peptidomimetic inhibitors of the bat HKU4-CoV 3CL pro . ...
Both approaches have successfully resulted in the identification of novel potent inhibitors on a wide variety of targets. ...
doi:10.1002/jmr.2644
pmid:28608547
fatcat:pchpizcb4zhypay2cir5dh6lg4
Computational Methods in Drug Discovery
2013
Pharmacological Reviews
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Authorship Contributions Wrote or contributed to the writing of the manuscript: Sliwoski, Kothiwale, Meiler, Lowe. ...
Virtual screening of the binding site with a library of compounds led to the discovery of novel small-molecule inhibitor of H5N1 ). e. Pocket matching. ...
Fig. 18 . 18 (I, A) Novel HIV-1 Integrase inhibitor using ligand-based virtual screening with a pharmacophore model of quinolone 3-carboxylic acid IN inhibitors [from Dayam et al. (2008) ]. ...
doi:10.1124/pr.112.007336
pmid:24381236
pmcid:PMC3880464
fatcat:4dzrdkspkjecnombnchznma2ny
The Role of Molecular Modeling and Bioinformatics in Treating a Pandemic Disease: The Case of COVID-19
2021
The Open COVID Journal
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Some immune-based therapies are also under evaluation, including convalescent plasma, IL-1, IL-6 inhibitors, and interferons. ...
NMR had a minor role and determining the structure of nucleocapsid (N) protein only. ...
ACKNOWLEDGEMENTS The authors thank Fareed Aboul-ela for the critical evaluation of the manuscript's English language. ...
doi:10.2174/2666958702101010216
fatcat:5f3j73jx7ffyjcwgmi2xxvvk7e
Computational screening for potential drug candidates against the SARS-CoV-2 main protease
2020
F1000Research
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Methods: Herein, we performed computational ligand screening of four pharmacophores (OEW, remdesivir, hydroxychloroquine and N3) that are presumed to have positive effects against SARS-CoV-2 Mpro protease ...
Results: We found 40 pharmacophore-like structures of natural compounds from diverse chemical classes that exhibited better affinity of docking as compared to the known ligands. ...
Acknowledgements We would like to thank The OpenEye Science for the OpenEye Software license, which made possible the ligand based virtual screening experiments. ...
doi:10.12688/f1000research.23829.1
pmid:33447372
pmcid:PMC7780344
fatcat:6b4dzbh2fndqrppmbmsf4gogt4
Computational screening for potential drug candidates against the SARS-CoV-2 main protease
2020
F1000Research
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Methods: Herein, we performed computational ligand screening of four pharmacophores (OEW, remdesivir, hydroxychloroquine and N3) that are presumed to have positive effects against SARS-CoV-2 Mpro protease ...
Results: We found 40 pharmacophore-like structures of natural compounds from diverse chemical classes that exhibited better affinity of docking as compared to the known ligands. ...
Acknowledgements We would like to thank The OpenEye Science for the OpenEye Software license, which made possible the ligand based virtual screening experiments. ...
doi:10.12688/f1000research.23829.2
fatcat:uw2jk5cm7rbbvarngttka66mwu
QSAR and its Role in Target-Ligand Interaction
2013
The Open Bioinformatics Journal
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Structure and function of a molecule are related to each other and QSARs (Quantitative Structure-Activity relationships) are based on the criteria that the structure of a molecule must contain the features ...
These types of descriptors are simple to calculate and allow for a relatively fast analysis. 3D-QSAR uses probe-based sampling within a molecular lattice to determine three-dimensional properties of molecules ...
The results obtained provide confidence for the utility of the pharmacophore in the virtual screening of libraries and databases of compounds to discover novel PfDHFR inhibitors [46] . ...
doi:10.2174/1875036201307010063
fatcat:hmsymvtbmrhktmqo4aeq2yuwaa
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