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Systematic identification of target set-dependent activity cliffs

Huabin Hu, Dagmar Stumpfe, Jürgen Bajorath
2019 Future Science OA  
Generating a knowledge base of new activity cliffs (ACs) defined on the basis of compound set-dependent potency distributions, also taking confirmed inactive compounds into account.  ...  Second-generation ACs will be subjected to systematic structure-activity relationship analysis.  ...  AC: Activity cliff; CPD: Compound; MMP: Matched molecular pair. Extended matched molecular pair-cliff networks (cont.).  ... 
doi:10.4155/fsoa-2018-0089 pmid:30828462 pmcid:PMC6391634 fatcat:wrfzl2mqmbhofi6vedqoxtwawu

Advancing the activity cliff concept

Ye Hu, Dagmar Stumpfe, Jürgen Bajorath
2013 F1000Research  
.: MMP-Cliffs: Systematic Identification of Activity Cliffs on the Basis of Matched Molecular Pairs. J Chem Inf Model. 2012; 52(5): 1138-1145. PubMed Abstract | Publisher Full Text 15.  ...  In addition to studying activity cliffs on the basis of individual compounds series, they can be systematically identified through mining of compound activity data.  ...  Acknowledgements The authors thank Dilyana Dimova for help with data sets.  ... 
doi:10.12688/f1000research.2-199.v1 pmid:24555097 pmcid:PMC3869489 fatcat:zppqvjdhyng6hlhh3urcd4shc4

Prediction of activity cliffs on the basis of images using convolutional neural networks

Javed Iqbal, Martin Vogt, Jürgen Bajorath
2021 Journal of Computer-Aided Molecular Design  
AbstractAn activity cliff (AC) is formed by a pair of structurally similar compounds with a large difference in potency.  ...  Therefore, pairs of structural analogs were extracted from different compound activity classes that formed or did not form ACs.  ...  Acknowledgements J.I. is supported by a PhD fellowship from the German Academic Exchange Service (DAAD) in collaboration with the Higher Education Commission (HEC) of Pakistan.  ... 
doi:10.1007/s10822-021-00380-y pmid:33740200 pmcid:PMC8636405 fatcat:pdt7f4b7gzf5zimol6gifounoy

Comprehensive knowledge base of two- and three-dimensional activity cliffs for medicinal and computational chemistry

Ye Hu, Norbert Furtmann, Dagmar Stumpfe, Jürgen Bajorath
2015 F1000Research  
Activity cliffs are formed by pairs or groups of structurally similar or analogous active compounds with large differences in potency.  ...  Furthermore, we have systematically searched for 2D extensions of 3D-cliffs.  ...  Acknowledgements N.F. was supported by a fellowship from the Jürgen Manchot Foundation, Düsseldorf, Germany.  ... 
doi:10.12688/f1000research.6661.1 fatcat:yrzlzqmntnf2hprysazfgdkdai

Advances in exploring activity cliffs

Dagmar Stumpfe, Huabin Hu, Jürgen Bajorath
2020 Journal of Computer-Aided Molecular Design  
The activity cliff (AC) concept is of comparable relevance for medicinal chemistry and chemoinformatics.  ...  The way in which the molecular similarity and potency difference criteria have been addressed for defining ACs distinguishes between different generations of ACs and mirrors the evolution of the AC concept  ...  However, ACs can be also defined on the basis of threedimensional (3D) structures of protein-ligand complexes, leading to the identification so-called 3D-cliffs [24, 25] .  ... 
doi:10.1007/s10822-020-00315-z pmid:32367387 fatcat:xpaeu7op45amtj6d3rrarllgky

Simplified activity cliff network representations with high interpretability and immediate access to SAR information

Huabin Hu, Jürgen Bajorath
2020 Journal of Computer-Aided Molecular Design  
Activity cliffs (ACs) consist of structurally similar compounds with a large difference in potency against their target.  ...  Accordingly, ACs introduce discontinuity in structure-activity relationships (SARs) and are a prime source of SAR information.  ...  To view a copy of this licence, visit http://creat iveco mmons .org/licen ses/by/4.0/.  ... 
doi:10.1007/s10822-020-00319-9 pmid:32500478 fatcat:h3z7dnlodraajoyfect3ybol2q

Computational method for the identification of third generation activity cliffs

Dagmar Stumpfe, Huabin Hu, Jürgen Bajorath
2020 MethodsX  
Herein, we introduce a computational methodology for AC identification and analysis that includes three novel components: •ACs are identified on the basis of variable target set-dependent potency difference  ...  In medicinal chemistry and chemoinformatics, activity cliffs (ACs) are defined as pairs of structurally similar compounds that are active against the same target but have a large difference in potency.  ...  Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper  ... 
doi:10.1016/j.mex.2020.100793 pmid:31993342 pmcid:PMC6974786 fatcat:6xt4vu7xbbckvhhi5hpwi4hrc4

Advancing the activity cliff concept, part II

Dagmar Stumpfe, Antonio de la Vega de León, Dilyana Dimova, Jürgen Bajorath
2014 F1000Research  
Hu X, Hu Y, Vogt M: MMP-Cliffs: systematic identification of activity cliffs on the basis of matched molecular pairs. J Chem Inf Model. 2012; 52(5): 1138-1145.  ...  We present a follow up contribution to further complement a previous commentary on the activity cliff concept and recent advances in activity cliff research.  ...  Acknowledgements The authors thank Ye Hu for discussions and help with data sets. The recurrent topologies covered many clusters of small to medium size.  ... 
doi:10.12688/f1000research.4057 pmid:24741442 pmcid:PMC3983935 fatcat:shbuo2qvs5eyjdabchdh2jc6j4

Advancing the activity cliff concept, part II

Dagmar Stumpfe, Antonio de la Vega de León, Dilyana Dimova, Jürgen Bajorath
2014 F1000Research  
Hu X, Hu Y, Vogt M: MMP-Cliffs: systematic identification of activity cliffs on the basis of matched molecular pairs. J Chem Inf Model. 2012; 52(5): 1138-1145.  ...  We present a follow up contribution to further complement a previous commentary on the activity cliff concept and recent advances in activity cliff research.  ...  Acknowledgements The authors thank Ye Hu for discussions and help with data sets. The recurrent topologies covered many clusters of small to medium size.  ... 
doi:10.12688/f1000research.3788.1 pmid:24741442 pmcid:PMC3983935 fatcat:tl2a5psj6jed5idpgcroomlmvu

Activity cliffs in drug discovery: Dr Jekyll or Mr Hyde?

Maykel Cruz-Monteagudo, José L. Medina-Franco, Yunierkis Pérez-Castillo, Orazio Nicolotti, M. Natália D.S. Cordeiro, Fernanda Borges
2014 Drug Discovery Today  
Point of view of the current state of the activity cliff phenomenon focusing on the rationale, effects and potential solutions to handle the influence of activity cliffs in drug discovery.  ...  The impact activity cliffs have on drug discovery is double-edged.  ...  cliffs are defined on the basis of the matched molecular pair (MMP) formalism (MMP-cliffs).  ... 
doi:10.1016/j.drudis.2014.02.003 pmid:24560935 fatcat:5dieee6zvjemzkghtlukdhrfbi

Evolving Concept of Activity Cliffs

Dagmar Stumpfe, Huabin Hu, Jürgen Bajorath
2019 ACS Omega  
Activity cliffs (ACs) are generally defined as pairs or groups of structurally similar compounds that are active against the same target but have large differences in potency.  ...  Furthermore, ACs are often perceived differently in medicinal and computational chemistry, depending on whether they are studied on a case-by-case basis or systematically.  ...  from pairs of enantiomers that did not form ACs. 11 Another substructure-based similarity criterion for ACs is provided by the formation of matched molecular pairs (MMPs), 12 i.e., pairs of compounds  ... 
doi:10.1021/acsomega.9b02221 pmid:31528788 pmcid:PMC6740043 fatcat:7lbdx34al5hwrfitfqdsr22nxm

Rapid Scanning Structure–Activity Relationships in Combinatorial Data Sets: Identification of Activity Switches

José L. Medina-Franco, Bruce S. Edwards, Clemencia Pinilla, Jon R. Appel, Marc A. Giulianotti, Radleigh G. Santos, Austin B. Yongye, Larry A. Sklar, Richard A. Houghten
2013 Journal of Chemical Information and Modeling  
Scanning the SAR of data sets using DAD maps allows the visual and quantitative identification of activity switches defined as specific substitutions that have an opposite effect on the activity of the  ...  We present a general approach to describe the structure-activity relationships (SAR) of combinatorial data sets with activity for two biological endpoints with emphasis on the rapid identification of substitutions  ...  We also thank funding from the State of Florida, Executive Office of the Governor's Department of Economic Opportunity.  ... 
doi:10.1021/ci400192y pmid:23705689 pmcid:PMC3715655 fatcat:tttaizqairapdnbyokxueke7h4

Towards a systematic assessment of assay interference: Identification of extensively tested compounds with high assay promiscuity

Erik Gilberg, Dagmar Stumpfe, Jürgen Bajorath
2017 F1000Research  
Hu X, Hu Y, Vogt M, et al.: MMP-Cliffs: systematic identification of activity cliffs on the basis of matched molecular pairs. J Chem Inf Model. 2012; 52(5): 1138-1145.  ...  .: Matched molecular pairs as a medicinal chemistry tool. J Med Chem. 2011; 54(22): 7739-7750.  ...  Matched molecular pairs and series A matched molecular pair (MMP) is a pair of compounds that are only distinguished by a chemical change at a single site 24 , termed a chemical transformation 25 .  ... 
doi:10.12688/f1000research.12370.1 pmid:28928939 pmcid:PMC5596351 fatcat:mfxnbh3jgvhujkfxwm2nmsorhm

Referee report. For: Advancing the activity cliff concept [v1; indexed, http://f1000r.es/1wf]

Gerhard Müller
2013
In addition to studying activity cliffs on the basis of individual compounds series, they can be systematically identified through mining of compound activity data.  ...  Activity cliffs have originally been defined as pairs of structurally similar compounds that are active against the same target but have a large difference in potency.  ...  Acknowledgements The authors thank Dilyana Dimova for help with data sets. the most critical step in activity cliff analysis. Although calculated  ... 
doi:10.5256/f1000research.2463.r1940 fatcat:67fbf24bujbjlmoj6nb7nx3lom

Referee report. For: Comprehensive knowledge base of two- and three-dimensional activity cliffs for medicinal and computational chemistry [v1; indexed, http://f1000r.es/5ir]

Gerhard Müller
2015
Activity cliffs are formed by pairs or groups of structurally similar or analogous active compounds with large differences in potency.  ...  Furthermore, we have systematically searched for 2D extensions of 3D-cliffs.  ...  Acknowledgements N.F. was supported by a fellowship from the Jürgen Manchot Foundation, Düsseldorf, Germany.  ... 
doi:10.5256/f1000research.7155.r9508 fatcat:z7bqjedhu5bq3muj2zrhxqkyv4
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