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Repurposing of FDA approved ring systems through bi-directional target-ring system dual screening

Surendra Kumar, Cheongyun Jang, Lalita Subedi, Sun Yeou Kim, Mi-hyun Kim
2020 Scientific Reports  
The TR screening suggested RAR β and cyproheptadine as the best pair of target and ring system to escape a saddle point.  ...  As a complementary approach to the drawbacks, ring systems of approved drugs (instead of clinical drugs) can be optimized and used for repurposing purposes.  ...  Acknowledgements This study was supported by the Basic Science Research Program of the National Research Foundation of Korea (NRF), which is funded by the Ministry of Education, Science and Technology  ... 
doi:10.1038/s41598-020-78077-9 pmid:33273509 fatcat:bov57mlk75d2bkralfhepqebje

Online structure-based screening of purchasable approved drugs and natural compounds: retrospective examples of drug repositioning on cancer targets

Nathalie Lagarde, Julien Rey, Aram Gyulkhandanyan, Pierre Tufféry, Maria A. Miteva, Bruno O. Villoutreix
2018 OncoTarget  
Drug discovery is a long and difficult process that benefits from the integration of virtual screening methods in experimental screening campaigns such as to generate testable hypotheses, accelerate and  ...  structure-based virtual screening studies.  ...  ACKNOWLEDGMENTS We thank the Inserm Institute and the University Paris Diderot for continuous supports. CONFLICTS OF INTEREST The authors declare no conflicts of interest.  ... 
doi:10.18632/oncotarget.25966 pmid:30190791 pmcid:PMC6122352 fatcat:l76txsj4f5ghtmihxgu7upau7q

Pharmmaker: Pharmacophore modeling and hit identification based on druggability simulations

Ji Young Lee, James M. Krieger, Hongchun Li, Ivet Bahar
2019 Protein Science  
hits by virtual screening of libraries of compounds, has been lacking.  ...  An important consecutive step is to analyze the trajectories to construct pharmacophore models (PMs) to use for virtual screening of libraries of small molecules.  ...  A specific target conformation is important in order to have accurate binding scores in virtual screening, for example, probe position and affinity are dependent on the side chains' rotameric states as  ... 
doi:10.1002/pro.3732 pmid:31576621 pmcid:PMC6933858 fatcat:rbyg3mtshnar5plmf3gbehiufu

Mapping the Azolog Space Enables the Optical Control of New Biological Targets

Johannes Morstein, Mahendra Awale, Jean-Louis Reymond, Dirk Trauner
2019 ACS Central Science  
Here, we systematically assess the space of molecules amenable to azologization from databases of bioactive molecules (DrugBank, PDB, CHEMBL) and the Cambridge Structural Database.  ...  Our analysis suggests that a very large number of bioactive ligands (>40 000) is amenable to azologization and that many new biological targets could be addressed with photopharmacology.  ...  Analysis of PDB Ligands and CSD Structures.  ... 
doi:10.1021/acscentsci.8b00881 pmid:31041380 pmcid:PMC6487453 fatcat:dusg7yengzgtlpxcwivbbmzqfi

Reverse Screening Methods to Search for the Protein Targets of Chemopreventive Compounds

Hongbin Huang, Guigui Zhang, Yuquan Zhou, Chenru Lin, Suling Chen, Yutong Lin, Shangkang Mai, Zunnan Huang
2018 Frontiers in Chemistry  
Here, we conducted a systematic analysis and multilevel classification of the computational programs, online services and compound libraries available for shape screening, pharmacophore screening and reverse  ...  ligands and receptor crystal structures, such as ChEMBL, BindingDB, and the Protein Data Bank (PDB), are available for use in these computational methods.  ...  Shape Screening Shape-screening services have a wide range of applications.  ... 
doi:10.3389/fchem.2018.00138 pmid:29868550 pmcid:PMC5954125 fatcat:g3j74fnqf5e23ptnr3zxm3c4y4

PSnpBind: a database of mutated binding site protein–ligand complexes constructed using a multithreaded virtual screening workflow

Ammar Ammar, Rachel Cavill, Chris Evelo, Egon Willighagen
2022 Journal of Cheminformatics  
In this work, we present PSnpBind: A large database of 0.6 million mutated binding site protein–ligand complexes constructed using a multithreaded virtual screening workflow.  ...  Having a large database of protein–ligand complexes covering a wide range of binding pocket mutations and a large small molecules' landscape is of great importance for several types of studies.  ...  SBDD includes structure-based virtual screening (SBVS) or molecular docking, followed by Molecular Dynamics [58] .  ... 
doi:10.1186/s13321-021-00573-5 pmid:35227289 pmcid:PMC8886843 fatcat:mac7atc7kzb4hk7lbimzzkd5z4

Virtual screening web servers: designing chemical probes and drug candidates in the cyberspace

2020 Briefings in Bioinformatics  
This article provides an overview of internet resources enabling and supporting chemical biology and early drug discovery with a main emphasis on web servers dedicated to virtual ligand screening and small-molecule  ...  This survey first introduces some key concepts and then presents recent and easily accessible virtual screening and related target-fishing tools as well as briefly discusses case studies enabled by some  ...  all the protein side chains), and on the application of a robotics-inspired algorithm to explore the conformational space [234] .  ... 
doi:10.1093/bib/bbaa034 pmid:32187356 pmcid:PMC7986591 fatcat:mq3csvzjkfekhpjfti2wmyipxi

Scaffold Hopping and Bioisosteric Replacements Based on Binding Site Alignments

Samo Lešnik, Janez Konc, Dušanka Janežič
2016 Croatica Chemica Acta  
Bioisosteric replacements and scaffold hopping play an important role in modern drug discovery and design, as they enable the change of either a core scaffold or substitutes in a drug structure, thereby  ...  The new molecule containing bioisosteric replacements was evaluated virtually using AutoDock Vina; a similar score for the original and the compound with replacements was obtained, suggesting that the  ...  This work was supported by Grants P1-0002 and J1-6743 of the Ministry of Higher Education, Science and Technology of Slovenia and Slovenian Research Agency.  ... 
doi:10.5562/cca2993 fatcat:zkwft5vo7nfxtmhftan7cxcg4y

Compound Activity Prediction Using Models of Binding Pockets or Ligand Properties in 3D

Irina Kufareva, Yu-Chen Chen, Andrey V. Ilatovskiy, Ruben Abagyan
2012 Current Topics in Medicinal Chemistry  
Family-wide benchmarking of the models highlights strengths of both approaches and helps identify their inherent bottlenecks and challenges.  ...  Transient interactions of endogenous and exogenous small molecules with flexible binding sites in proteins or macromolecular assemblies play a critical role in all biological processes.  ...  Acknowledgments Number of seeds reflects the amount of chemical information used in the model generation. Curr Top Med Chem. Author manuscript; available in PMC 2014 July 07.  ... 
doi:10.2174/156802612804547335 pmid:23116466 pmcid:PMC4085113 fatcat:cxm5b724djdgjnqf7vnaelbe5e

Virtual Screening in Search for a Chemical Probe for Angiotensin-Converting Enzyme 2 (ACE2)

Iryna O. Kravets, Dmytro V. Dudenko, Alexander E. Pashenko, Tatiana A. Borisova, Ganna M. Tolstanova, Sergey V. Ryabukhin, Dmitriy M. Volochnyuk
2021 Molecules  
The efficacy of elaborated roadmaps is demonstrated through the cost-effective molecular docking of 1.4 billion compounds. Savings of up to 10-fold in CPU time are demonstrated.  ...  We propose promising workflows for working with huge compound collections, thereby enabling us to discover optimized protocols for virtual screening management.  ...  Acknowledgments: The authors thank Enamine Ltd. for access to "Enamine Stock Compound Collection" and "Enamine REAL database", Andrey A.  ... 
doi:10.3390/molecules26247584 pmid:34946667 pmcid:PMC8707431 fatcat:arlb5zl2gfc73mt3rbtbkd7b44

Exploring protein hotspots by optimized fragment pharmacophores

Dávid Bajusz, Warren S. Wade, Grzegorz Satała, Andrzej J. Bojarski, Janez Ilaš, Jessica Ebner, Florian Grebien, Henrietta Papp, Ferenc Jakab, Alice Douangamath, Daren Fearon, Frank von Delft (+7 others)
2021 Nature Communications  
Biochemical screening against a set of GPCRs and proteases retrieves compounds containing an average of 70% of known pharmacophores for these targets.  ...  The efficiency of this approach is demonstrated with a pilot library of 96 fragment-sized compounds (SpotXplorer0) that is validated on popular target classes and emerging drug targets.  ...  Acknowledgements The authors thank the COVID Moonshot collaboration, particularly Anthony Aimon and Tamás  ... 
doi:10.1038/s41467-021-23443-y pmid:34045440 pmcid:PMC8159961 fatcat:vzfatvi7szeknd7m6k2xu55x7u

Recent Advances in In Silico Target Fishing

Salvatore Galati, Miriana Di Stefano, Elisa Martinelli, Giulio Poli, Tiziano Tuccinardi
2021 Molecules  
Moreover, the possibility to use it in combination with docking and virtual screening studies, as well as the increasing number of web-based tools that have been recently developed, make target fishing  ...  In silico target fishing, whose aim is to identify possible protein targets for a query molecule, is an emerging approach used in drug discovery due its wide variety of applications.  ...  , considering alternative conformations of specific residues side chains [71, 72] .  ... 
doi:10.3390/molecules26175124 pmid:34500568 fatcat:jmz5qvhosjcg7jyey4rzbpuvce

ProSelection: A Novel Algorithm to Select Proper Protein Structure Subsets for in Silico Target Identification and Drug Discovery Research

Nanyi Wang, Lirong Wang, Xiang-Qun Xie
2017 Journal of Chemical Information and Modeling  
Application of docking in modeling varies from single lead compound optimization to large-scale virtual screening.  ...  Molecular docking is widely applied to computer-aided drug design and has become relatively mature in the recent decades.  ...  Acknowledgments The project is supported by funding to Xie laboratory from the NIH NIDA (P30 DA035778A1) and DOD (W81XWH-16-1-0490).  ... 
doi:10.1021/acs.jcim.7b00277 pmid:29016123 pmcid:PMC5836547 fatcat:2gorfzhb5ffb7oiffay46wbita

Historeceptomic Fingerprints for Drug-Like Compounds

Evgeny Shmelkov, Arsen Grigoryan, James Swetnam, Junyang Xin, Doreen Tivon, Sergey V. Shmelkov, Timothy Cardozo
2015 Frontiers in Physiology  
We thank the Visiting Faculty for Exacycle program for support of the work of JS and Daniel Belov, Chris van Arsdale, David Konerding and Daniel Meredith of Google Inc. for technical assistance.  ...  ACKNOWLEDGMENTS We thank Ruben Abagyan, Maxim Totrov, Yuval Kluger, Fabio Parisi and Francesco Strini for helpful discussions.  ...  Improved polypharmacological profiles of a drug can be identified only by a more comprehensive analysis of drug-target interactions on a proteome-wide scale (Xie et al., 2012) .  ... 
doi:10.3389/fphys.2015.00371 pmid:26733872 pmcid:PMC4683199 fatcat:tvaqv7xn65fzfgwcbvg2pfjsye

Large-Scale Chemical Similarity Networks for Target Profiling of Compounds Identified in Cell-Based Chemical Screens

Yu-Chen Lo, Silvia Senese, Chien-Ming Li, Qiyang Hu, Yong Huang, Robert Damoiseaux, Jorge Z. Torres, Christos A. Ouzounis
2015 PLoS Computational Biology  
of bioactive compounds from a wide range of chemical screens.  ...  We further coupled CSNAP to a mitotic database and successfully determined the major mitotic drug targets of a diverse compound set identified in a cell-based chemical screen.  ...  Acknowledgments We thank members of the Torres lab and Tom Holton at the UCLA Molecular Biology Institute for helpful discussions. Author Contributions  ... 
doi:10.1371/journal.pcbi.1004153 pmid:25826798 pmcid:PMC4380459 fatcat:dqurgzm2yrc6xckoxdtzktcnxm
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