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Items: 33

1.

Discovery of Orally Active Inhibitors of Brahma Homolog (BRM)/SMARCA2 ATPase Activity for the Treatment of Brahma Related Gene 1 (BRG1)/SMARCA4-Mutant Cancers.

Papillon JPN, Nakajima K, Adair CD, Hempel J, Jouk AO, Karki RG, Mathieu S, Möbitz H, Ntaganda R, Smith T, Visser M, Hill SE, Hurtado FK, Chenail G, Bhang HC, Bric A, Xiang K, Bushold G, Gilbert T, Vattay A, Dooley J, Costa EA, Park I, Li A, Farley D, Lounkine E, Yue QK, Xie X, Zhu X, Kulathila R, King D, Hu T, Vulic K, Cantwell J, Luu C, Jagani Z.

J Med Chem. 2018 Oct 31. doi: 10.1021/acs.jmedchem.8b01318. [Epub ahead of print]

PMID:
30339381
2.

Reverse translation of adverse event reports paves the way for de-risking preclinical off-targets.

Maciejewski M, Lounkine E, Whitebread S, Farmer P, DuMouchel W, Shoichet BK, Urban L.

Elife. 2017 Aug 8;6. pii: e25818. doi: 10.7554/eLife.25818.

3.

Dark chemical matter as a promising starting point for drug lead discovery.

Wassermann AM, Lounkine E, Hoepfner D, Le Goff G, King FJ, Studer C, Peltier JM, Grippo ML, Prindle V, Tao J, Schuffenhauer A, Wallace IM, Chen S, Krastel P, Cobos-Correa A, Parker CN, Davies JW, Glick M.

Nat Chem Biol. 2015 Dec;11(12):958-66. doi: 10.1038/nchembio.1936. Epub 2015 Oct 19.

PMID:
26479441
4.

Experimental design strategy: weak reinforcement leads to increased hit rates and enhanced chemical diversity.

Maciejewski M, Wassermann AM, Glick M, Lounkine E.

J Chem Inf Model. 2015 May 26;55(5):956-62. doi: 10.1021/acs.jcim.5b00054. Epub 2015 May 14.

PMID:
25915687
5.

The opportunities of mining historical and collective data in drug discovery.

Wassermann AM, Lounkine E, Davies JW, Glick M, Camargo LM.

Drug Discov Today. 2015 Apr;20(4):422-34. doi: 10.1016/j.drudis.2014.11.004. Epub 2014 Nov 18. Review.

PMID:
25463034
6.

Many approved drugs have bioactive analogs with different target annotations.

Hu Y, Lounkine E, Bajorath J.

AAPS J. 2014 Jul;16(4):847-59. doi: 10.1208/s12248-014-9621-8. Epub 2014 May 29.

7.

A screening pattern recognition method finds new and divergent targets for drugs and natural products.

Wassermann AM, Lounkine E, Urban L, Whitebread S, Chen S, Hughes K, Guo H, Kutlina E, Fekete A, Klumpp M, Glick M.

ACS Chem Biol. 2014 Jul 18;9(7):1622-31. doi: 10.1021/cb5001839. Epub 2014 Jun 2.

PMID:
24802392
8.

Efficient search of chemical space: navigating from fragments to structurally diverse chemotypes.

Wassermann AM, Kutchukian PS, Lounkine E, Luethi T, Hamon J, Bocker MT, Malik HA, Cowan-Jacob SW, Glick M.

J Med Chem. 2013 Nov 14;56(21):8879-91. doi: 10.1021/jm401309q. Epub 2013 Oct 31.

PMID:
24117015
9.

Bioturbo similarity searching: combining chemical and biological similarity to discover structurally diverse bioactive molecules.

Wassermann AM, Lounkine E, Glick M.

J Chem Inf Model. 2013 Mar 25;53(3):692-703. doi: 10.1021/ci300607r. Epub 2013 Mar 5.

PMID:
23461561
10.

Biodiversity of small molecules--a new perspective in screening set selection.

Petrone PM, Wassermann AM, Lounkine E, Kutchukian P, Simms B, Jenkins J, Selzer P, Glick M.

Drug Discov Today. 2013 Jul;18(13-14):674-80. doi: 10.1016/j.drudis.2013.02.005. Epub 2013 Feb 20.

PMID:
23454345
11.

Large-scale prediction and testing of drug activity on side-effect targets.

Lounkine E, Keiser MJ, Whitebread S, Mikhailov D, Hamon J, Jenkins JL, Lavan P, Weber E, Doak AK, Côté S, Shoichet BK, Urban L.

Nature. 2012 Jun 10;486(7403):361-7. doi: 10.1038/nature11159.

12.

Identifying mechanism-of-action targets for drugs and probes.

Gregori-Puigjané E, Setola V, Hert J, Crews BA, Irwin JJ, Lounkine E, Marnett L, Roth BL, Shoichet BK.

Proc Natl Acad Sci U S A. 2012 Jul 10;109(28):11178-83. doi: 10.1073/pnas.1204524109. Epub 2012 Jun 18.

13.

Rethinking molecular similarity: comparing compounds on the basis of biological activity.

Petrone PM, Simms B, Nigsch F, Lounkine E, Kutchukian P, Cornett A, Deng Z, Davies JW, Jenkins JL, Glick M.

ACS Chem Biol. 2012 Aug 17;7(8):1399-409. doi: 10.1021/cb3001028. Epub 2012 May 31.

PMID:
22594495
14.

Chemotography for multi-target SAR analysis in the context of biological pathways.

Lounkine E, Kutchukian P, Petrone P, Davies JW, Glick M.

Bioorg Med Chem. 2012 Sep 15;20(18):5416-27. doi: 10.1016/j.bmc.2012.02.034. Epub 2012 Feb 20.

PMID:
22405595
15.

Activity-aware clustering of high throughput screening data and elucidation of orthogonal structure-activity relationships.

Lounkine E, Nigsch F, Jenkins JL, Glick M.

J Chem Inf Model. 2011 Dec 27;51(12):3158-68. doi: 10.1021/ci2004994. Epub 2011 Dec 7.

PMID:
22098146
16.

Computational methods for early predictive safety assessment from biological and chemical data.

Nigsch F, Lounkine E, McCarren P, Cornett B, Glick M, Azzaoui K, Urban L, Marc P, Müller A, Hahne F, Heard DJ, Jenkins JL.

Expert Opin Drug Metab Toxicol. 2011 Dec;7(12):1497-511. doi: 10.1517/17425255.2011.632632. Epub 2011 Nov 4. Review.

PMID:
22050465
17.

Molecular test systems for computational selectivity studies and systematic analysis of compound selectivity profiles.

Stumpfe D, Lounkine E, Bajorath J.

Methods Mol Biol. 2011;672:503-15. doi: 10.1007/978-1-60761-839-3_20.

PMID:
20838982
18.

Data structures and computational tools for the extraction of SAR information from large compound sets.

Wawer M, Lounkine E, Wassermann AM, Bajorath J.

Drug Discov Today. 2010 Aug;15(15-16):630-9. doi: 10.1016/j.drudis.2010.06.004. Epub 2010 Jun 12. Review.

PMID:
20547243
19.

SARANEA: a freely available program to mine structure-activity and structure-selectivity relationship information in compound data sets.

Lounkine E, Wawer M, Wassermann AM, Bajorath J.

J Chem Inf Model. 2010 Jan;50(1):68-78. doi: 10.1021/ci900416a.

PMID:
20053000
20.

Systematic analysis of public domain compound potency data identifies selective molecular scaffolds across druggable target families.

Hu Y, Wassermann AM, Lounkine E, Bajorath J.

J Med Chem. 2010 Jan 28;53(2):752-8. doi: 10.1021/jm9014229.

PMID:
20000355
21.

Molecular Formal Concept Analysis for compound selectivity profiling in biologically annotated databases.

Lounkine E, Stumpfe D, Bajorath J.

J Chem Inf Model. 2009 Jun;49(6):1359-68. doi: 10.1021/ci900095v.

PMID:
19537827
22.

Filtering and counting of extended connectivity fingerprint features maximizes compound recall and the structural diversity of hits.

Hu Y, Lounkine E, Bajorath J.

Chem Biol Drug Des. 2009 Jul;74(1):92-8. doi: 10.1111/j.1747-0285.2009.00830.x.

PMID:
19519749
23.

Relevance of feature combinations for similarity searching using general or activity class-directed molecular fingerprints.

Lounkine E, Hu Y, Batista J, Bajorath J.

J Chem Inf Model. 2009 Mar;49(3):561-70. doi: 10.1021/ci800377n.

PMID:
19434896
24.

Fragment formal concept analysis accurately classifies compounds with closely related biological activities.

Krüger F, Lounkine E, Bajorath J.

ChemMedChem. 2009 Jul;4(7):1174-81. doi: 10.1002/cmdc.200900035.

PMID:
19384901
25.
26.

Methods for computer-aided chemical biology. Part 4: selectivity searching for ion channel ligands and mapping of molecular fragments as selectivity markers.

Ahmed HE, Geppert H, Stumpfe D, Lounkine E, Bajorath J.

Chem Biol Drug Des. 2009 Mar;73(3):273-82. doi: 10.1111/j.1747-0285.2009.00784.x.

PMID:
19207462
27.

RelACCS-FP: a structural minimalist approach to fingerprint design.

Hu Y, Lounkine E, Batista J, Bajorath J.

Chem Biol Drug Des. 2008 Nov;72(5):341-9. doi: 10.1111/j.1747-0285.2008.00723.x.

PMID:
19012570
28.

Topological fragment index for the analysis of molecular substructures and their topological environment in active compounds.

Lounkine E, Bajorath J.

J Chem Inf Model. 2009 Feb;49(2):162-8. doi: 10.1021/ci8002599.

PMID:
19007294
29.

Similarity searching using fingerprints of molecular fragments involved in protein-ligand interactions.

Tan L, Lounkine E, Bajorath J.

J Chem Inf Model. 2008 Dec;48(12):2308-12. doi: 10.1021/ci800322y.

PMID:
19007112
30.

Random molecular fragment methods in computational medicinal chemistry.

Lounkine E, Batista J, Bajorath J.

Curr Med Chem. 2008;15(21):2108-21. Review.

PMID:
18781938
31.

Formal concept analysis for the identification of molecular fragment combinations specific for active and highly potent compounds.

Lounkine E, Auer J, Bajorath J.

J Med Chem. 2008 Sep 11;51(17):5342-8. doi: 10.1021/jm800515r. Epub 2008 Aug 13.

PMID:
18698757
32.

Core trees and consensus fragment sequences for molecular representation and similarity analysis.

Lounkine E, Bajorath J.

J Chem Inf Model. 2008 Jun;48(6):1161-6. doi: 10.1021/ci800020s. Epub 2008 May 21.

PMID:
18491888
33.

Mapping of activity-specific fragment pathways isolated from random fragment populations reveals the formation of coherent molecular cores.

Lounkine E, Batista J, Bajorath J.

J Chem Inf Model. 2007 Nov-Dec;47(6):2133-9. Epub 2007 Oct 16.

PMID:
17939652

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