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ZINCPharmer: pharmacophore search of the ZINC database

D. R. Koes, C. J. Camacho
2012 Nucleic Acids Research  
ZINCPharmer (http://zincpharmer.csb.pitt.edu) is an online interface for searching the purchasable compounds of the ZINC database using the Pharmer pharmacophore search technology.  ...  The results can be immediately viewed, or the aligned structures may be downloaded for off-line analysis. ZINCPharmer enables the rapid and interactive search of purchasable chemical space.  ...  ACKNOWLEDGEMENTS The ZINC database is incorporated into ZINCPharmer by permission. We thank NIH for supporting this resource.  ... 
doi:10.1093/nar/gks378 pmid:22553363 pmcid:PMC3394271 fatcat:hui7siifgrdofelktb3g7jop74

A Teach-Discover-Treat Application of ZincPharmer: An Online Interactive Pharmacophore Modeling and Virtual Screening Tool

David Ryan Koes, Nicolas A. Pabon, Xiaoyi Deng, Margaret A. Phillips, Carlos J. Camacho, Robert W Sobol
2015 PLoS ONE  
Facilitated by ZincPharmer, an open access online interactive pharmacophore search of the ZINC database, the experience resulted in the development of a novel classification scheme that successfully predicted  ...  Pose prediction of compound 6. Receptor structure and binding site residues of 3I65 are shown in blue. Compound 6 is shown in magenta sticks. (a) Compound 6 aligned to the pharmacophore of Fig 1.  ...  We would also like to thank the students of the University of Pittsburgh TECBio REU and the UPCI Summer Academy. Author Contributions  ... 
doi:10.1371/journal.pone.0134697 pmid:26258606 pmcid:PMC4530941 fatcat:kae35r6vu5avlaaqdspdnawviy

Pharmacophore and ligand-guided screening of antibacterial leads targeting antibiotic resistance factor in Gram-negative bacteria [article]

Abi Sofyan Ghifari
2018 arXiv   pre-print
A total of 8166 hit molecules obtained from ZincPharmer pharmacophore-based screening and PubMed ligand similarity search were further examined through individual two-step semi-flexible docking simulation  ...  In this study, a combination of pharmacophore- and ligand-based approach has been employed to explore novel potent EptA inhibitors among millions of commercially-available compounds and approved drugs.  ...  and their support towards the publication of this study.  ... 
arXiv:1803.04661v1 fatcat:fwbblyt7svblhktmaltiadqaoy

DISCOVERY OF NOVEL GLUCOKINASE ACTIVATORS THROUGH STRUCTURE-BASED PHARMACOPHORE MODELING, VIRTUAL SCREENING AND MOLECULAR DOCKING APPROACHES

2021 International Journal of Biology Pharmacy and Allied Sciences  
In this study, structure-based Pharmacophore model was generated; virtual screening was performed using Asinex and Zinc database library compounds.  ...  The prevalence of Diabetes mellitus has been increasing day-by-day. Available drug therapies are associated with some side-effects.  ...  Virtual Screening of Asinex and ZincPharmer databases The generated Pharmacophore model was then copied to screening perspective of Ligand Scout software.  ... 
doi:10.31032/ijbpas/2021/10.10.1048 fatcat:auefvgkwtfgpxeziekfnmd3g74

Repurposing Hydroxychloroquine as a Model Drug for the Prediction of Potential SARS-CoV-2 Inhibitor

K. K. Igwe, O. V. Ikpeazu, F. J. Amaku, I. E. Otuokere
2020 European Journal of Engineering Research and Science  
To exhaustively assess the benefit of hydroxychloroquine in the search for SARS-CoV-2 cure, this paper repositioned hydroxychloroquine as a model for virtual screening on the ZINC database.  ...  The binding scores of the top five ligands were higher than that of the reference molecule.  ...  Pharmacophore-based virtual screening and database preparation The pharmacophoric features of hydroxychloroquine were used as a reference model to search the ZINC database for hit ligands with similar  ... 
doi:10.24018/ejers.2020.5.9.2056 fatcat:4xbyhjqbgfhk5cbtspws3uhb2y

Pharmacophore and Virtual Screening of JAK3 inhibitors
English

Murugesan Rajeswari, Natchimuthu Santhi, Vembu Bhuvaneswari
2014 Bioinformation  
The statistically significant pharmacophore hypothesis of AAHR.92 with r 2 value of 0.942 was used as 3D query to search against 3D database namely Zincpharmer.  ...  In this study, about 116 JAK3 inhibitors were collected from the literature and were used to build four-point pharmacophore model using Phase (Schrodinger module).  ...  Methodology: Dataset Virtual screening Virtual screening was carried out using ZincPharmer (zincpharmer.csb.pitt.edu ) which uses the pharmacophore to efficiently search the ZINC database of fixed conformers  ... 
doi:10.6026/97320630010157 pmid:24748756 pmcid:PMC3974243 fatcat:7x3mau5i75fjbhqwex4ae4ociq

Structure based pharmacophore modeling, virtual screening, molecular docking and ADMET approaches for identification of natural anti-cancer agents targeting XIAP protein

Firoz A Dain Md Opo, Mohammed M Rahman, Foysal Ahammad, Istiak Ahmed, Mohiuddin Ahmed Bhuiyan, Abdullah M Asiri
2021 Scientific Reports  
Overexpression of the protein decreased the apoptosis process in the cell and resulting development of cancer.  ...  To identify natural compound, a structure-based pharmacophore model to the protein active site cavity was generated following by virtual screening, molecular docking and molecular dynamics (MD) simulation  ...  Acknowledgements This project was funded by the National Plan for Science, Technology and Innovation (MAARIFAH) -King Abdulaziz City for Science and Technology -the Kingdom of Saudi Arabia -award number  ... 
doi:10.1038/s41598-021-83626-x pmid:33603068 pmcid:PMC7892887 fatcat:5bf4yfdntnfmdnn6i4mon2b32a

PocketQuery: protein-protein interaction inhibitor starting points from protein-protein interaction structure

D. R. Koes, C. J. Camacho
2012 Nucleic Acids Research  
PocketQuery rapidly focuses attention on the key interacting residues of an interaction using a 'druggability' score that provides an estimate of how likely the chemical mimicry of a cluster of interface  ...  PocketQuery (http://pocketquery.csb.pitt.edu) is a web interface for exploring the properties of protein-protein interaction (PPI) interfaces with a focus on the discovery of promising starting points  ...  ZINCPharmer is a general interactive pharmacophore search technology for the ZINC database (34) . ZINCPharmer is routinely updated to search the most recent set of purchasable compounds from ZINC.  ... 
doi:10.1093/nar/gks336 pmid:22523085 pmcid:PMC3394328 fatcat:xgatl54cavahxor2k6avjzceau

An Integrated Computational Approach for Plant-Based Protein Tyrosine Phosphatase Non-Receptor Type 1 Inhibitors

Shabana Bibi, Katsumi Sakata
2017 Current Computer - Aided Drug Design  
A common feature pharmacophore model was generated. Pharmacophore-based screening of plant-derived compounds of the ZINC database was conducted using ZINCpharmer.  ...  The present study proposes a pipeline for the development of effective and plant-derived anti-diabetic drugs that may be safer and better tolerated.  ...  Both authors had a significant role in the conceptualization and writing of this manuscript.  ... 
doi:10.2174/1573409913666170406145607 pmid:28382867 pmcid:PMC5744427 fatcat:zinxeyf6sbdg3c3kbltyfcmdu4

Ligand-Based Pharmacophore Modeling, Molecular Docking, and Molecular Dynamic Studies of Dual Tyrosine Kinase Inhibitor of EGFR and VEGFR2

Frangky Sangande, Elin Julianti, Daryono Hadi Tjahjono
2020 International Journal of Molecular Sciences  
Firstly, the ligand-based pharmacophore model for each target was setup to screen of ZINC database of purchasable compounds.  ...  The hit compounds obtained by pharmacophore screening were then further screened by molecular docking studies.  ...  The previously obtained pharmacophore model of EGFR was submitted to ZINCPharmer, to search hits from the ZINC database of "purchasable compounds" consist of 22,723,923 compounds [32] .  ... 
doi:10.3390/ijms21207779 pmid:33096664 fatcat:nsdpiron5vcghecrvrogtovnxm

Identification of novel inhibitors for TNFα, TNFR1 and TNFα-TNFR1 complex using pharmacophore-based approaches

Madhu Sudhana Saddala, Hu Huang
2019 Journal of Translational Medicine  
TNFα-TNF receptor-1 (TNFR1) signaling contributes to the pathological processes of these disorders.  ...  The current study is focused on finding novel small molecules that can directly bind to TNFα and/or TNFR1, preventing the interaction between TNFα or TNFR1, and regulating downstream signaling pathways  ...  Acknowledgements The authors would like to acknowledge Dr. Anton Lennikov (University of Missouri, Columbia, Missouri, USA) for his insightful discussion, and Ms.  ... 
doi:10.1186/s12967-019-1965-5 pmid:31266509 pmcid:PMC6604280 fatcat:a5asttnmxng7dfmsxwf4gxigea

Finding inhibitors for PCSK9 using computational methods

Rida Zainab, Afshan Kaleem, Michał B. Ponczek, Roheena Abdullah, Mehwish Iqtedar, Daniel C. Hoessli, Emilio Gallicchio
2021 PLoS ONE  
Selected models were later screened against the ZINC database using ZINCPHARMER to define potential drug candidates that were docked with the target protein to understand their interactions.  ...  To start with, reported ACE inhibitors were incorporated into pharmacophore designing using PharmaGist to produce pharmacophore models.  ...  Acknowledgments The authors would like to thank the editor and the anonymous reviewers, whose comments helped improve the quality of the final manuscript.  ... 
doi:10.1371/journal.pone.0255523 pmid:34351937 pmcid:PMC8341581 fatcat:ppgabimibrca7njlbuokclxacq

Virtual Screening and Statistical Analysis in the Design of New Caffeine Analogues Molecules with Potential Epithelial Anticancer Activity

Josivan da Silva Costa, Karina da Silva Lopes Costa, Josiane Viana Cruz, Ryan da Silva Ramos, Luciane Barros Silva, Davi Do Socorro Barros Brasil, Carlos Henrique Tomich de Paula da Silva, Cleydson Breno Rodrigues dos Santos, Williams Jorge da Cruz Macedo
2018 Current pharmaceutical design  
The generated pharmacophore was used to select 350 molecules available at the ZINCpharmer server, followed by reduction to 24 molecules, after selection using the Tanimoto index, yielding 10 molecules  ...  For this, a training set of 21 molecules was used for pharmacophore perception procedures.  ...  ACKNOWLEDGEMENTS We acknowledge the support provided by the PROPESP/UFPA.  ... 
doi:10.2174/1381612823666170711112510 pmid:28699538 pmcid:PMC5944109 fatcat:zsmj3evwxzeotjzglugwsiwcu4

Pharmacophore feature-based virtual screening for finding potent GSK-3 inhibitors using molecular docking and dynamics simulations

Navneet Chauhan, Anuradha Gajjar, Syed Hussain Basha
2016 Bioinformation  
In the present study, we performed pharmacophore feature-based virtual screening for identifying potent targetspecific GSK-3 inhibitors.  ...  These findings are expected to play a crucial role in the binding of target-specific GSK-3 inhibitors.  ...  Chauhan gratefully acknowledges the Head, Department of Pharmaceutical Chemistry, Saraswati Institute of Pharmaceutical Sciences, Gandhinagar, India, for providing necessary facilities required to execute  ... 
doi:10.6026/97320630012391 pmid:28293069 pmcid:PMC5320924 fatcat:nlrzocasyfeq7gi6gcgycxfjae

Identification and Validation of a Potent Dual Inhibitor of the P. falciparum M1 and M17 Aminopeptidases Using Virtual Screening

Chiara Ruggeri, Nyssa Drinkwater, Komagal Kannan Sivaraman, Rebecca S. Bamert, Sheena McGowan, Alessandro Paiardini, Juan Carlos Pizarro
2015 PLoS ONE  
Starting from the ZINC database of purchasable compounds, sequential 3D-pharmacophore and molecular docking steps were applied to filter the virtual 'hits'.  ...  To this end, we undertook a virtual screen of the ZINC database of purchasable subsets (~18 millions of compounds) [17, 18] and used successive 3D-pharmacophore and molecular docking to filter the virtual  ...  Acknowledgments We thank the Australian Synchrotron for beam time (MXCAP 8208) and technical assistance. Author Contributions  ... 
doi:10.1371/journal.pone.0138957 pmid:26406322 pmcid:PMC4583420 fatcat:5m4khtw3jrd3rodj4vpnmt3aai
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