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Systems approaches to polypharmacology and drug discovery

Aislyn D W Boran, Ravi Iyengar
2010 Current opinion in drug discovery & development  
Polypharmacology for complex diseases is likely to involve multiple drugs acting on distinct targets that are part of a network regulating physiological responses.  ...  An important area of integration between systems biology and drug discovery is the concept of polypharmacology: the treatment of diseases by modulating more than one target.  ...  Acknowledgments The authors thank Seth Berger and Sherry Jenkins for help with analyzing the drug target data presented in Figure 2 .  ... 
pmid:20443163 pmcid:PMC3068535 fatcat:6prsqmgdcfghdnqesexm3rdpz4

Structural and Functional View of Polypharmacology [article]

Aurelio Moya Garcia, Tolulope Adeyelu, Natalie L Dawson, Felix A Kruger, Jonathan Lees, John Overington, Christine Orengo, Juan Antonio Garcia Ranea
2016 bioRxiv   pre-print
Protein domains mediate drug-protein interactions and this effect can explain drug polypharmacology.  ...  In this study, we associate polypharmacological drugs with CATH functional families, a type of protein domain and we use the network properties of these druggable protein families to analyse their relationships  ...  We propose that CATH-FunFams are a reasonable annotation level for studying the drug-target interactions of polypharmacological drugs, offering valuable insights into possible drug polypharmacology with  ... 
doi:10.1101/044289 fatcat:6deatkwl2bcufax4g5ds5ydwf4

Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data

Bin Chen, Xiao Dong, Dazhi Jiao, Huijun Wang, Qian Zhu, Ying Ding, David J Wild
2010 BMC Bioinformatics  
Chem2Bio2RDF by aggregating data from multiple chemogenomics repositories that is cross-linked into Bio2RDF and LODD.  ...  We demonstrate the utility of Chem2Bio2RDF in investigating polypharmacology, identification of potential multiple pathway inhibitors, and the association of pathways with adverse drug reactions.  ...  Through integrated and intelligent data mining, this information could provide important insights into the complex functions of biological systems and the actions of chemical compounds or drugs on these  ... 
doi:10.1186/1471-2105-11-255 pmid:20478034 pmcid:PMC2881087 fatcat:zn64ucchfrbllgsxg4dmdgxhja

Polypharmacology and supercomputer-based docking: opportunities and challenges

Sally R. Ellingson, Jeremy C. Smith, Jerome Baudry
2014 Molecular Simulation  
Polypharmacology has the potential to greatly benefit drug repurposing, bringing existing pharmaceuticals on the market to treat different ailments quicker and more affordably than developing new drugs  ...  Polypharmacology, the ability of drugs to interact with multiple targets, is a fundamental concept of interest to the pharmaceutical industry in its efforts to solve the current issues of the rise in the  ...  new insights into drug targets.  ... 
doi:10.1080/08927022.2014.899699 fatcat:p4qlkalpoffbtj6uw67fgjwte4

Chemogenomics knowledgebased polypharmacology analyses of drug abuse related G-protein coupled receptors and their ligands

Xiang-Qun Xie, Lirong Wang, Haibin Liu, Qin Ouyang, Cheng Fang, Weiwei Su
2014 Frontiers in Pharmacology  
To fully explore the molecular interaction networks that underlie DA and to effectively modulate the GPCRs in these networks with small molecules for DA treatment, we built a drug-abuse domain specific  ...  Finally, the polypharmacology effects of GPCRs-targeted medicines for DA treatment were investigated and such effects can be exploited for the development of drugs with polypharmacophore for DA intervention  ...  Authors would also like to acknowledge the collaboration support from the National Natural Science Foundation of China (NSFC21202201) (Qin Ouyang), and from Science and Technological Program for Dongguan's  ... 
doi:10.3389/fphar.2014.00003 pmid:24567719 pmcid:PMC3915241 fatcat:gzm2i2o4vfgltfszll65bwvml4

A simple mathematical approach to the analysis of polypharmacology and polyspecificity data

Gerry Maggiora, Vijay Gokhale
2017 F1000Research  
Moya-García AA, Ranea JA: Insights into polypharmacology from drug-domain associations. Bioinformatics. 2013; 29(16): 1934-1937. PubMed Abstract | Publisher Full Text 42.  ...  Sturm N, Desaphy J, Quinn RJ, et al.: Structural insights into the molecular basis of the ligand promiscuity. J Chem Inf Model. 2012; 52(9): 2410-2421. PubMed Abstract | Publisher Full Text 47.  ...  Martin Vogt, both from Department of Life Science Informatics, B-IT, Rheinische Friedrich-Wilhelms-Universität in Bonn, Germany, for a number of useful comments regarding this work.  ... 
doi:10.12688/f1000research.11517.1 pmid:28690829 pmcid:PMC5482344 fatcat:c3sz3e2m3fhzndkwzyclhjufnm

Drug-target and disease networks: polypharmacology in the post-genomic era

Ali Masoudi-Nejad, Zaynab Mousavian, Joseph H Bozorgmehr
2013 In Silico Pharmacology  
With the growing understanding of complex diseases, the focus of drug discovery has shifted away from the wellaccepted "one target, one drug" model, to a new "multi-target, multi-drug" model, aimed at  ...  An emerging paradigm of polypharmacology in the postgenomic era is that drug, target and disease spaces can be correlated to study the effect of drugs on different spaces and their interrelationships can  ...  Acknowledgement Authors appreciate great help from LBB's members during their course of study.  ... 
doi:10.1186/2193-9616-1-17 pmid:25505661 pmcid:PMC4230718 fatcat:daaturwzxzdsdlkkgefqwsjrom

Curation and Analysis of Multitargeting Agents for Polypharmacological Modeling

A. Srinivas Reddy, Zhi Tan, Shuxing Zhang
2014 Journal of Chemical Information and Modeling  
The present study provides more insight of drug multitargeting and is particularly useful for polypharmacology modeling.  ...  In drug discovery and development, the conventional "single drug, single target" concept has been shifted to "single drug, multiple targets"--a concept coined as polypharmacology.  ...  These data will provide new insights for off-target identification and polypharmacological agent design. A flowchart illustrating the data curation is provided in Figure 1 .  ... 
doi:10.1021/ci500092j pmid:25133604 pmcid:PMC4170814 fatcat:klm7c3onbfe4lfaknexbb5os4e

Structural and Functional View of Polypharmacology

Aurelio Moya-García, Tolulope Adeyelu, Felix A. Kruger, Natalie L. Dawson, Jon G. Lees, John P. Overington, Christine Orengo, Juan A. G. Ranea
2017 Scientific Reports  
Protein domains mediate drug-protein interactions and this principle can guide the design of multitarget drugs i.e. polypharmacology.  ...  association with drug side effects.  ...  Our drug to CATH-FunFams mapping also yields insights into the adverse side effects associated with sunitinib-a receptor tyrosine kinase inhibitor used in the treatment of renal cell carcinoma and other  ... 
doi:10.1038/s41598-017-10012-x pmid:28860623 pmcid:PMC5579063 fatcat:dk2lwyeekbcaxmof2sptw7zedu

PubChem applications in drug discovery: a bibliometric analysis

Tiejun Cheng, Yongmei Pan, Ming Hao, Yanli Wang, Stephen H. Bryant
2014 Drug Discovery Today  
PubChem supports drug discovery in many aspects such as lead identification and optimization, compound-target profiling, polypharmacology studies and unknown chemical identity elucidation.  ...  growing PubChem resource with its public availability offers support and great opportunities for the interrogation of pharmacological mechanisms and the genetic basis of diseases, which are vital for drug  ...  systems to gain insights into drug polypharmacology study that could be helpful to future drug design [18] [19] [20] .  ... 
doi:10.1016/j.drudis.2014.08.008 pmid:25168772 pmcid:PMC4252728 fatcat:ht66r6b2h5bcpjh4m74mhspvjm

Recent Advances in Multi-Task QSAR Modeling for Drug Design

Amit Halder, Mohammad Goodarzi
2015 Pharmaceutical Sciences  
Computer-aided drug design may provide a massive scope to reduce the overall duration as well as the expenditure associated with drug discovery.  ...  However, for several diseases the availability of a data is less and developed models on the available data may not be able to provide detailed insight into structural requirements of the molecules for  ... 
doi:10.15171/ps.2015.33 fatcat:unuyiprghjawplldqerx4db5k4

Artificial intelligence in drug development: clinical pharmacologist perspective

In-Jin Jang
2019 Translational and Clinical Pharmacology  
The AI drug discovery process will have better performance with collaboration with domain experts who have insight into target product profile (TPP) and label driven drug development.  ...  In drug discovery, if AI is properly trained with optimal data, it can provide insight into a new molecule to target, complex metabolic pathways of a compound, and predict toxicity.  ... 
doi:10.12793/tcp.2019.27.3.87 pmid:32055587 pmcid:PMC6989241 fatcat:ygaadmnou5cddanv3vb3maxc3u

ToxEvaluator: an integrated computational platform to aid the interpretation of toxicology study-related findings

D. Pelletier, T. C. Wiegers, A. Enayetallah, C. Kibbey, M. Gosink, P. Koza-Taylor, C. J. Mattingly, M. Lawton
2016 Database: The Journal of Biological Databases and Curation  
The user enters compound and target identifiers, and selects adverse event descriptors from a safety lexicon and mapped MeSH disease terms.  ...  Attempts are frequently made to investigate adverse findings from preclinical toxicology studies in order to better understand underlying toxicity mechanisms.  ...  Functionally, it is involved in the uptake of a number of endogenous (e.g. bilirubin) and small-molecule drugs from the blood into the hepatocytes of the liver.  ... 
doi:10.1093/database/baw062 pmid:27161010 pmcid:PMC4860628 fatcat:vtlf6jn6tnhufe2kffoazmz64i

Data driven polypharmacological drug design for lung cancer: analyses for targeting ALK, MET, and EGFR

Dilip Narayanan, Osman A. B. S. M. Gani, Franz X. E. Gruber, Richard A. Engh
2017 Journal of Cheminformatics  
Both EGFR and ALK represent sources of primary oncogenic lesions, while drug resistance arises from MET amplification and EGFR mutation.  ...  These are not typically encoded into molecular mechanics force fields.  ...  For drug polypharmacology design purposes, it may be advantageous to enhance recognition of correlated sensitivities to ligand variation.  ... 
doi:10.1186/s13321-017-0229-8 pmid:29086093 pmcid:PMC5496928 fatcat:vtxsrhrtavcezms6fjjaeckvhe

Drug repurposing improves disease targeting 11-fold and can be augmented by network module targeting, applied to COVID-19

Inés Rivero-García, Miguel Castresana-Aguirre, Luca Guglielmo, Dimitri Guala, Erik L. L. Sonnhammer
2021 Scientific Reports  
Moreover, our results highlight that drug repurposing is more dependent on target proteins being shared between diseases than on polypharmacological properties of drugs.  ...  drug being increased from 134 to 167 after extending the drug targets with their high confidence first neighbors.  ...  Acknowledgements The project that gave rise to these results received support for a fellowship from Fundación Margit y Folke Pehrzon.  ... 
doi:10.1038/s41598-021-99721-y pmid:34667255 pmcid:PMC8526804 fatcat:qjxumuhilzhxvpgnrzmaprxlsu
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