Publications & References -

Regulatory T cells suppress the formation of potent KLRK1 and IL-7R expressing effector CD8 T cells by limiting IL-2
Tsyklauri O, Chadimova T, Niederlova V, Kovarova J, Michalik J, Malatova I, Janusova S, Ivashchenko O, Rossez H, Drobek A, Vecerova H
The SUMOylation inhibitor subasumstat potentiates rituximab activity by IFN1-dependent macrophage and NK cell stimulation
Nakamura A, Grossman S, Song K, Xega K, Zhang Y, Cvet D, Berger A, Shapiro G, Huszar D.
Comparison of four in vitro cytotoxicity assays for assessing the potency of CD3-bispecific antibodies redirecting T cells to kill tumor target cells
Jun Guan, Charlie Kang, Alejandro Amador Arjona, Ricardo Macarron, Patrick Mayes and Yao-Bin Liu2
Discovering cell-active BCL6 inhibitors: effectively combining biochemical HTS with multiple biophysical techniques, X-ray crystallography and cell-based assays
Olivier A. Pierrat, Manjuan Liu, Gavin W. Collie, Kartika Shetty, Matthew J. Rodrigues, Yann-Vaï Le Bihan, Emma A. Gunnell, P. Craig McAndrew, Mark Stubbs, Martin G. Rowlands, Norhakim Yahya, Erald Shehu, Rachel Talbot, Lisa Pickard, Benjamin R. Bellenie, Kwai-Ming J. Cheung, Ludovic Drouin, Paolo Innocenti, Hannah Woodward, Owen A. Davis, Matthew G. Lloyd, Ana Varela, Rosemary Huckvale, Fabio Broccatelli, …Rob L. M. van Montfort
The Identification of Potent, Selective, and Brain Penetrant PI5P4Kγ Inhibitors as In Vivo-Ready Tool Molecules
Timothy P. C. Rooney, Gregory G. Aldred, Helen K. Boffey, Henriëtte M. G. Willems, Simon Edwards, Stephen J. Chawner, Duncan E. Scott, Christopher Green, David Winpenny, John Skidmore, Jonathan H. Clarke, and Stephen P. Andrews
Inhibition of Bitter Taste from Oral Tenofovir Alafenamide.
Schwiebert E, Wang Y, Xi R, Choma K, Streiff J, Flammer LJ, Rivers N, Ozdener MH, Margolskee RF, Christensen CM, Rawson NE, Jiang P, Breslin PAS. Inhibition of Bitter Taste from Oral Tenofovir Alafenamide. Mol Pharmacol. 2021 May;99(5):319-327.
Small-molecule allosteric activators of PDE4 long form cyclic AMP phosphodiesterases.
Omar F, Findlay JE, Carfray G, Allcock RW, Jiang Z, Moore C, Muir AL, Lannoy M, Fertig BA, Mai D, Day JP, Bolger G, Baillie GS, Schwiebert E, Klussmann E, Pyne NJ, Ong ACM, Bowers K, Adam JM, Adams DR, Houslay MD, Henderson DJP. Small-molecule allosteric activators of PDE4 long form cyclic AMP phosphodiesterases. Proc Natl Acad Sci U S A. 2019 Jul 2;116(27):13320-13329.
The Engineered CD80 Variant Fusion Therapeutic Davoceticept Combines Checkpoint Antagonism with Conditional CD28 Costimulation for Anti-Tumor Immunity
Mark F. Maurer, Katherine E. Lewis, Joseph L. Kuijper, Dan Ardourel, Chelsea J. Gudgeon, Siddarth Chandrasekaran, Sherri L., et al.
Development of Selective Phosphatidylinositol 5‑Phosphate 4‑Kinase γ Inhibitors with a Non-ATP-competitive, Allosteric Binding Mode
Helen K. Boffey, Timothy P. C. Rooney, Henriette M. G. Willems, Simon Edwards, Christopher Green, Tina Howard, Derek Ogg, Tamara Romero, Duncan E. Scott, David Winpenny, James Duce, John Skidmore, Jonathan H. Clarke, and Stephen P. Andrews
The First WHO International Standard for Harmonizing the Biological Activity of Bevacizumab
Haiyan Jia, Parvathy Harikumar, Eleanor Atkinson, Peter Rigsby, and Meenu Wadhwa
The First WHO International Standard for Harmonizing the Biological Activity of Bevacizumab
Biomolecules, 2021;11:1610.
Use of a rapid human primary cell-based disease screening model to compare next generation products to combustible cigarettes.
Simms L, Mason E, Berg EL, Yu F, Rudd K, Czekala L, Trelles Sticken E, Brinster O, Wieczorek R, Stevenson M, Walele T.
Use of a rapid human primary cell-based disease screening model to compare next generation products to combustible cigarettes.
Current Research in Toxicology. 2021;2:309-321.
Expanding the drug discovery space with predicted metabolite–target interactions.
Nuzzo A, Saha S, Berg E, Jayawickreme C, Tocker J, Brown JR. Expanding the drug discovery space with predicted metabolite–target interactions. Commun Biol. 2021;4:288.
Investigating Molecular Mechanisms of Immunotoxicity and the Utility of ToxCast for Immunotoxicity Screening of Chemicals Added to Food.
Naidenko OV, Andrews DQ, Temkin AM, Stoiber T, Uche UI, Evans S, Perrone-Gray S. Investigating Molecular Mechanisms of Immunotoxicity and the Utility of ToxCast for Immunotoxicity Screening of Chemicals Added to Food. Int J Environ Res Public Health. 2021;18(7):3332.
ILB® resolves inflammatory scarring and promotes functional tissue repair.
Hill LJ, Botfield HF, Begum G, Qureshi O, Vigneswara V, Masood I, Barnes NM, Bruce L, Logan A. ILB® resolves inflammatory scarring and promotes functional tissue repair. NPJ Regen Med. 2021;6:3.
The future of phenotypic drug discovery.
Berg EL. The future of phenotypic drug discovery. Cell Chemical Biology. 2021;28(3):424-430.
Chapter 2: Development and Validation of Disease Assays for Phenotypic Screening.
Berg EL, Denker SP, O’Mahony A. Chapter 2: Development and Validation of Disease Assays for Phenotypic Screening. In: Phenotypic Drug Discovery.; 2020:20-36.
C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-ones: Studies towards the identification of potent, cell penetrant Jumonji C domain containing histone lysine demethylase 4 subfamily (KDM4) inhibitors, compound profiling in cell-based target engagement assays
Yann-Vaï Le Bihana, Rachel M.Lanigana, et al. Eur J of Med. Chem. 2019 Sept 1 (177): 316-337. doi.org/10.1016/j.ejmech.2019.05.041
Tapinarof Is a Natural AhR Agonist that Resolves Skin Inflammation in Mice and Humans.
Smith SH, Jayawickreme C, Rickard DJ, Nicodeme E, Bui T, Simmons C, Coquery CM, Neil J, Pryor WM, Mayhew D, Rajpal DK, Creech K, Furst S, Lee J, Wu D, Rastinejad F, Willson TM, Viviani F, Morris DC, Moore JT, Cote-Sierra J. Tapinarof Is a Natural AhR Agonist that Resolves Skin Inflammation in Mice and Humans. J Invest Dermatol. 2017;137(10):2110-2119.
A Next-Generation Risk Assessment Case Study for Coumarin in Cosmetic Products.
Baltazar MT, Cable S, Carmichael PL, Cubberley R, Cull T, Delagrange M, Dent MP, Hatherell S, Houghton J, Kukic P, Li H, Lee M-Y, Malcomber S, Middleton AM, Moxon TE, Nathanail AV, Nicol B, Pendlington R, Reynolds G, Reynolds J, White A, Westmoreland C. A Next-Generation Risk Assessment Case Study for Coumarin in Cosmetic Products. Toxicol Sci. 2020;176(1):236-252.
Btk inhibition treats TLR7/IFN driven murine lupus.
Bender AT, Pereira A, Fu K, Samy E, Wu Y, Liu-Bujalski L, Caldwell R, Chen Y-Y, Tian H, Morandi F, Head J, Koehler U, Genest M, Okitsu SL, Xu D, Grenningloh R. Btk inhibition treats TLR7/IFN driven murine lupus. Clinical Immunology. 2016;164:65-77.

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A Pharmacochaperone-Based High-Throughput Screening Assay for the Discovery of Chemical Probes of Orphan Receptors.
Morfa CJ, Bassoni D, Szabo A, McAnally D, Sharir H, Hood BL, Vasile S, Wehrman T, Lamerdin J, Smith LH. Assay Drug Dev Technol. 2018 Sep 22.
Measurement of β-Arrestin Recruitment for GPCR Targets.
Wang T, Li Z, Cvijic ME, Krause C, Zhang L, Sum CS. Measurement of β-Arrestin Recruitment for GPCR Targets. Assay Guidance Manual [Internet]. 2017 Nov 20.
Orphan GPR61, GPR62 and GPR135 receptors and the melatonin MT2 receptor reciprocally modulate their signaling functions
Oishi A, Karamitri A, Gerbier R, Lahuna O, Ahmad R, Jockers R. Orphan GPR61, GPR62 and GPR135 receptors and the melatonin MT2 receptor reciprocally modulate their signaling functions. Scientific Reports. 2017;7:8990
Alternatively spliced mu opioid receptor C termini impact the diverse actions of morphine.
Xu J, Lu Z, Narayan A, Le Rouzic VP, Xu M, Hunkele A, Brown TG, Hoefer WF, Rossi GC, Rice RC, Martínez-Rivera A, Rajadhyaksha AM, Cartegni L, Bassoni DL, Pasternak GW, Pan YX. Alternatively spliced mu opioid receptor C termini impact the diverse actions of morphine. J Clin Invest. 2017 Apr 3;127(4):1561-1573. PMID:28319053.
Distinct conformations of GPCR-β-arrestin complexes mediate desensitization, signaling, and endocytosis.
Cahill TJ 3rd, Thomsen AR, Tarrasch JT, Plouffe B, Nguyen AH, Yang F, Huang LY, Kahsai AW, Bassoni DL, Gavino BJ, Lamerdin JE, Triest S, Shukla AK, Berger B, Little J 4th, Antar A, Blanc A, Qu CX, Chen X, Kawakami K, Inoue A, Aoki J, Steyaert J, Sun JP, Bouvier M, Skiniotis G, Lefkowitz RJ. Distinct conformations of GPCR-β-arrestin complexes mediate desensitization, signaling, and endocytosis. Proc Natl Acad Sci U S A. 2017 Mar 7;114(10):2562-2567. PMID:28223524.
Allosteric "beta-blocker" isolated from a DNA-encoded small molecule library.
Ahn S, Kahsai AW, Pani B, Wang QT, Zhao S, Wall AL, Strachan RT, Staus DP, Wingler LM, Sun LD, Sinnaeve J, Choi M, Cho T, Xu TT, Hansen GM, Burnett MB, Lamerdin JE, Bassoni DL, Gavino BJ, Husemoen G, Olsen EK, Franch T, Costanzi S, Chen X, Lefkowitz RJ. Allosteric "beta-blocker" isolated from a DNA-encoded small molecule library. Proc Natl Acad Sci U S A. 2017 Feb 14;114(7):1708-1713. PMID:28130548.
New Screening Strategy and Analysis for Identification of Allosteric Modulators for GLP-1 Receptor Using GLP-1(9-36)amide.
Nakane A, Gotoh Y, Ichihara J, Nagata H. New Screening Strategy and Analysis for Identification of Allosteric Modulators for GLP-1 Receptor Using GLP-1(9-36)amide. Anal Biochem. 2015 Sep 2. pii: S0003-2697(15)00412-1. PMID:26341912
Identification of resolvin D2 receptor mediating resolution of infections and organ protection.
Chiang N, Dalli J, Colas RA, Serhan CN. Identification of resolvin D2 receptor mediating resolution of infections and organ protection. J Exp Med. 2015 Jul 27;212(8):1203-17. PMID:26195725
Navigating CYP1A induction and arylhydrocarbon receptor agonism in drug discovery. A case history with S1P1 agonists.
Taylor SJ, Demont EH, Gray J, Deeks N, Patel A, Nguyen D, Taylor M, Hood S, Watson R, Bit RA, McClure F, Ashall H, Witherington J. Navigating CYP1A induction and arylhydrocarbon receptor agonism in drug discovery. A case history with S1P1 agonists. J Med Chem. 2015 Oct 1. PMID:26393276
Ligand-Based Discovery of a New Scaffold for Allosteric Modulation of the mu-Opioid Receptor.
Bisignano P, Burford NT, Shang Y, Marlow B, Livingston K, Fenton AM, Rockwell K, Budenholzer L, Traynor JR, Gerritz SW, Alt A, Filizola M. Ligand-Based Discovery of a New Scaffold for Allosteric Modulation of the mu-Opioid Receptor. J Chem Inf Model. 2015 Sep 28;55(9):1836-43. PMID:26347990
In vitro pharmacological characterization of vorapaxar, a novel platelet thrombin receptor antagonist.
Hawes BE, Zhai Y, Hesk D, Wirth M, Wei H, Chintala M, Seiffert D. In vitro pharmacological characterization of vorapaxar, a novel platelet thrombin receptor antagonist. Eur J Pharmacol. 2015 Sep 5;762:221-8. PMID:26022529
Re-Designing of Existing Pharmaceuticals for Environmental Biodegradability: A tiered approach with β-Blocker Propranolol as an example.
Rastogi T, Leder C, Kümmerer K. Re-Designing of Existing Pharmaceuticals for Environmental Biodegradability: A tiered approach with β-Blocker Propranolol as an example. Environ Sci Technol. 2015 Oct 6;49(19):11756-63. PMID:26291878
The novel, orally available and peripherally restricted selective cannabinoid CB2 -receptor agonist LEI-101 prevents cisplatin-induced nephrotoxicity.
Mukhopadhyay P, Baggelaar M, Erdelyi K, Cao Z, Cinar R, Fezza F, Ignatowska-Jankowska B, Wilkerson J, van Gils N, Hansen T, Ruben M, Soethoudt M, Heitman L, Kunos G, Maccarrone M, Lichtman A, Pacher P, van der Stelt M. The novel, orally available and peripherally restricted selective cannabinoid CB2 -receptor agonist LEI-101 prevents cisplatin-induced nephrotoxicity. Br J Pharmacol. 2015 Sep 23. PMID:26398481
In vitro pharmacological characterization of vorapaxar, a novel platelet thrombin receptor antagonist.
Hawes BE, Zhai Y, Hesk D, Wirth M, Wei H, Chintala M, Seiffert D. In vitro pharmacological characterization of vorapaxar, a novel platelet thrombin receptor antagonist. Eur J Pharmacol. 2015 Sep 5;762:221-8. PMID:26022529
The orexin 1 receptor modulates kappa opioid receptor function via a JNK-dependent mechanism.
Robinson, JD., and McDonald, PH. The orexin 1 receptor modulates kappa opioid receptor function via a JNK-dependent mechanism. Cellular Signaling. 27(7):1449-56. PMID:25857454
Discovery, Synthesis and Molecular Pharmacology of Selective Positive Allosteric Modulators of the δ-Opioid Receptor.
Burford NT, Livingston K, Canals M, Ryan M, Budenholzer L, Han Y, Shang Y, Herbst JJ, O'Connell J, Banks M, Zhang L, Filizola M, Bassoni D, Wehrman TS, Christopoulos A, Traynor JR, Gerritz SW, Alt A. Discovery, Synthesis and Molecular Pharmacology of Selective Positive Allosteric Modulators of the δ-Opioid Receptor. J Med Chem. 58(10):4220-9. PMID:25901762
A novel insulinotropic mechanism of whole grain-derived γ-oryzanol via the suppression of local dopamine D2 receptor signaling in mouse islet.
Kozuka C, Sunagawa S, Ueda R, Higa M, Ohshiro Y, Tanaka H, Shimizu-Okabe C, Takayama C, Matsushita M, Tsutsui M, Ishiuchi S, Nakata M, Yada T, Miyazaki JI, Oyadomari S, Shimabukuro M, Masuzaki H. A novel insulinotropic mechanism of whole grain-derived γ-oryzanol via the suppression of local dopamine D2 receptor signaling in mouse islet. Br J Pharmacol. 2015 Jul 3. PMID:26140534
Identification of the first surrogate agonists for the G protein-coupled receptor GPR132.
Shehata MA, Christensen HB, Isberg V, Pedersen D, Bender A, Bräuner-Osborne H and Gloriam D. Identification of the first surrogate agonists for the G protein-coupled receptor GPR132. RSC Adv., 2015,5, 48551-48557.
Novel Human Cytomegalovirus Viral Chemokines, vCXCL-1s, Display Functional Selectivity for Neutrophil Signaling and Function.
Heo J, Dogra P, Masi TJ, Pitt EA, de Kruijf P, Smit MJ, Sparer TE. Novel Human Cytomegalovirus Viral Chemokines, vCXCL-1s, Display Functional Selectivity for Neutrophil Signaling and Function. J Immunol. 195(1):227-36. PMID:25987741
Boronic acid-containing CXCR1/2 antagonists: Optimization of metabolic stability, in vivo evaluation, and a proposed receptor binding model.
Maedaa DY, Pecka AM, Schulera AD, Quinnb MT, Kirpotinab LN, Wicombc WN, Autend RL, Gundlae R, Zebalaa JA. Boronic acid-containing CXCR1/2 antagonists: Optimization of metabolic stability, in vivo evaluation, and a proposed receptor binding model. Bioorg & Med Chem Let. 25(11):2280-4. PMID:25933594

Displaying results 1-20 (of 187)

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Discovering cell-active BCL6 inhibitors: effectively combining biochemical HTS with multiple biophysical techniques, X-ray crystallography and cell-based assays
Olivier A. Pierrat, Manjuan Liu, Gavin W. Collie, Kartika Shetty, Matthew J. Rodrigues, Yann-Vaï Le Bihan, Emma A. Gunnell, P. Craig McAndrew, Mark Stubbs, Martin G. Rowlands, Norhakim Yahya, Erald Shehu, Rachel Talbot, Lisa Pickard, Benjamin R. Bellenie, Kwai-Ming J. Cheung, Ludovic Drouin, Paolo Innocenti, Hannah Woodward, Owen A. Davis, Matthew G. Lloyd, Ana Varela, Rosemary Huckvale, Fabio Broccatelli, …Rob L. M. van Montfort
C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-ones: Studies towards the identification of potent, cell penetrant Jumonji C domain containing histone lysine demethylase 4 subfamily (KDM4) inhibitors, compound profiling in cell-based target engagement assays
Yann-Vaï Le Bihana, Rachel M.Lanigana, et al. Eur J of Med. Chem. 2019 Sept 1 (177): 316-337. doi.org/10.1016/j.ejmech.2019.05.041
A Potent, Selective and Cell-Active Allosteric Inhibitor of Protein Arginine Methyltransferase 3 (PRMT3)
Kaniskan HÜ1, Szewczyk MM, Yu Z, Eram MS, Yang X, Schmidt K, Luo X, Dai M, He F, Zang I, Lin Y,Kennedy S, Li F, Dobrovetsky E, Dong A, Smil D, Min SJ, Landon M, Lin-Jones J, Huang XP, Roth BL,Schapira M, Atadja P, Barsyte-Lovejoy D, Arrowsmith CH, Brown PJ, Zhao K, Jin J, Vedadi M. A Potent, Selective and Cell-Active Allosteric Inhibitor of Protein Arginine Methyltransferase 3 (PRMT3). Angew Chem Int Ed Engl. 2015 Apr 20;54(17):5166-70. doi: 10.1002/anie.201412154. Epub 2015 Feb 27. PMID:25728001
Cell-based protein stabilization assays for the detection of interactions between small-molecule inhibitors and BRD4.
Schulze J, Moosmayer D, Weiske J, Fernández-Montalván A, Herbst C, Jung M, Haendler B, Bader B. Cell-based protein stabilization assays for the detection of interactions between small-molecule inhibitors and BRD4. J Biomol Screen. 2015 Feb;20(2):180-9. doi: 10.1177/1087057114552398. Epub 2014 Sep 29. PMID:25266565

The Identification of Potent, Selective, and Brain Penetrant PI5P4Kγ Inhibitors as In Vivo-Ready Tool Molecules
Timothy P. C. Rooney, Gregory G. Aldred, Helen K. Boffey, Henriëtte M. G. Willems, Simon Edwards, Stephen J. Chawner, Duncan E. Scott, Christopher Green, David Winpenny, John Skidmore, Jonathan H. Clarke, and Stephen P. Andrews
Development of Selective Phosphatidylinositol 5‑Phosphate 4‑Kinase γ Inhibitors with a Non-ATP-competitive, Allosteric Binding Mode
Helen K. Boffey, Timothy P. C. Rooney, Henriette M. G. Willems, Simon Edwards, Christopher Green, Tina Howard, Derek Ogg, Tamara Romero, Duncan E. Scott, David Winpenny, James Duce, John Skidmore, Jonathan H. Clarke, and Stephen P. Andrews
A cellular target engagement assay for the characterization of SHP2 (PTPN11) phosphatase inhibitors
Celeste Romero , Lester J. Lambert , Douglas J. Sheffler , Laurent J.S. De Backer , Dhanya RaveendraPanickar , Maria Celeridad , Stefan Grotegut , Socorro Rodiles , John Holleran , Eduard Sergienko , Elena B. Pasquale3 , Nicholas D. P. Cosford , and Lutz Tautz. A cellular target engagement assay for the characterization of SHP2 (PTPN11) phosphatase inhibitors
Sorafenib activity and disposition in liver cancer does not depend on organic cation transporter 1 (OCT1).
Chen M, Neul C, Schaeffeler E, Frisch F, Winter S, Schwab M, Koepsell H, Hu S, Laufer S, Baker SD, Sparreboom A, Nies AT. Clin Pharmacol Ther. 2019 Jul 27
Activation of TrkB with TAM-163 results in opposite effects on body weight in rodents and non-human primates.
Perreault M, Feng G, Will S, Gareski T, Kubasiak D, Marquette K, Vugmeyster Y, Unger TJ, Jones J, Qadri A, Hahm S, Sun Y, Rohde CM, Zwijnenberg R, Paulsen J, Gimeno RE. Activation of TrkB with TAM-163 results in opposite effects on body weight in rodents and non-human primates. PLoS One. 2013 May 20;8(5):e62616. PMID:23700410
Development of Three Orthogonal Assays Suitable for the Identification and Qualification of PIKfyve Inhibitors.
Fogarty K, Kashem M, Bauer A, Bernardino A, Brennan D, Cook B, Farrow N, Molinaro T, Nelson R. Development of Three Orthogonal Assays Suitable for the Identification and Qualification of PIKfyve Inhibitors. Assay Drug Dev Technol. 2017 Jul;15(5):210-219. PMID:28723271
A High-Throughput Dose-Response Cellular Thermal Shift Assay for Rapid Screening of Drug Target Engagement in Living Cells, Exemplified Using SMYD3 and IDO1
McNulty DE, Bonnette WG, Qi H, Wang L, Ho TF, Waszkiewicz A, Kallal LA, Nagarajan RP, Stern M, Quinn AM, Creasy CL, Su DS, Graves AP, Annan RS, Sweitzer SM, Holbert MA. A High-Throughput Dose-Response Cellular Thermal Shift Assay for Rapid Screening of Drug Target Engagement in Living Cells, Exemplified Using SMYD1 and IDO1. SLAS Discov. 2017 Sep;1:2472555217732014. PMID:28957646
Structural characterization of nonactive site, TrkA-selective kinase inhibitors
Su HP1, Rickert K2, Burlein C3, Narayan K3, Bukhtiyarova M3, Hurzy DM4, Stump CA4, Zhang X4, Reid J4, Krasowska-Zoladek A5, Tummala S2, Shipman JM2, Kornienko M2, Lemaire PA3, Krosky D2, Heller A3, Achab A6, Chamberlin C6, Saradjian P6, Sauvagnat B6, Yang X6, Ziebell MR6, Nickbarg E6, Sanders JM4, Bilodeau MT4, Carroll SS3, Lumb KJ2, Soisson SM4, Henze DA5, Cooke AJ4. Structural characterization of nonactive site, TrkA-selective kinase inhibitors. Proc Natl Acad Sci U S A. 2017 Jan 17; 114 (3): E297-E306.
Multiplex quantitative assays indicate a need for reevaluating reported small-molecule TrkB agonists
Boltaev U1,2, Meyer Y1, Tolibzoda F1,2, Jacques T1, Gassaway M1,2, Xu Q3, Wagner F3, Zhang YL3, Palmer M3, Holson E3, Sames D4,2.. Multiplex quantitative assays indicate a need for reevaluating reported small-molecule TrkB agonists. Sci Signal. 2017 Aug 22; 10 (493).
Design, synthesis and SAR of substituted indoles as selective TrkA inhibitors.
Hurzy DM1, Henze DA2, Cabalu TD3, Narayan K4, Heller A5, Cooke AJ6. Design, synthesis and SAR of substituted indoles as selective TrkA inhibitors. Bioorg Med Chem Lett. 2017 Jun 15; 27 (12): 2695-2701.
Small-Molecule Target Engagement in Cells.
Schürmann M, Janning P, Ziegler S, Waldmann H. Small-Molecule Target Engagement in Cells. Cell Chem Biol. 2016 Apr 21;23(4):435-41. doi:10.1016/j.chembiol.2016.03.008. Epub 2016 Mar 31. PMID:27049669
Examining Ligand-Based Stabilization of Proteins in Cells with MEK1 Kinase Inhibitors.
Auld DS, Davis CA, Jimenez M, Knight S, Orme JP. Examining Ligand-Based Stabilization of Proteins in Cells with MEK1 Kinase Inhibitors. Assay Drug Dev Technol. 2015 Jun;13(5):266-76. PMID:26107610
Discovery of MINC1, a GTPase-Activating Protein Small Molecule Inhibitor, Targeting MgcRacGAP
van Adrichem AJ, Fagerholm A, Turunen L, Lehto A, Saarela J, Koskinen A, Repasky GA, Wennerberg K. Discovery of MINC1, a GTPase-Activating Protein Small Molecule Inhibitor, Targeting MgcRacGAP. Comb Chem High Throughput Screen. 2015;18(1):3-17. PMID:25479424
The Use of TrkA-PathHunter Assay in High-Throughput Screening to identify Compounds That Affect Nerve Growth Factor Signaling.
Forsell P, Almqvist H, Hillertz P, Akerud T, Otrocka M, Eisele L, Sun K, Andersson H, Trivedi S, Wollberg AR, Dekker N, Rottici D, Sandberg K. The Use of TrkA-PathHunter Assay in High-Throughput Screening to Identify Compounds That Affect Nerve Growth Factor Signaling. J Biomol Screen. 2013 Mar 4. PMID:19940259
Development of a Highly Selective c-Src Kinase Inhibitor
Kristoffer R. Brandvold, Michael E. Steffey, Christel C. Fox, and Matthew B. Soellner. Development of a Highly Selective c-Src Kinase Inhibitor. ACS Chem Biol. 2012 Aug 17;7(8):1393-8. Epub 2012 Jun 4. PMID:22594480
Comprehensive analysis of kinase inhibitor selectivity
Mindy I Davis, Jeremy P Hunt, Sanna Herrgard, Pietro Ciceri, Lisa M Wodicka, Gabriel Pallares, Michael Hocker, Daniel K Treiber & Patrick P Zarrinkar. Comprehensive analysis of kinase inhibitor selectivity. Nat Biotechnol. 2011 Oct 30;29(11):1046-51. doi: 10.1038/nbt.1990.. PMID:22037378
Trends in kinase selectivity: insights for target class-focused library screening.
Posy SL, Hermsmeier MA, Vaccaro W, Ott KH, Todderud G, Lippy JS, Trainor GL, Loughney DA, Johnson SR.. Trends in kinase selectivity: insights for target class-focused library screening.. J Med Chem. 2011 Jan 13;54(1):54-66. Epub 2010 Dec 3.. PMID:21128601
Why do kinase inhibitors cause cardiotoxicity and what can be done about it?
Cheng H, Force T.. Why do kinase inhibitors cause cardiotoxicity and what can be done about it?. Prog Cardiovasc Dis. 2010 Sep-Oct;53(2):114-20.. PMID:20728698
Small-molecule kinase inhibitors provide insight into Mps1 cell cycle function.
Kwiatkowski N, Jelluma N, Filippakopoulos P, Soundararajan M, Manak MS, Kwon M, Choi HG, Sim T, Deveraux QL, Rottmann S, Pellman D, Shah JV, Kops GJ, Knapp S, Gray NS.. Small-molecule kinase inhibitors provide insight into Mps1 cell cycle function.. Nat Chem Biol. 2010 May;6(5):359-68. Epub 2010 Apr 11.. PMID:20383151
Synthesis and structure-activity relationships of 1,2,3,4-tetrahydropyrido[2,3-b]pyrazines as potent and selective inhibitors of the anaplastic lymphoma kinase.
Milkiewicz KL, Weinberg LR, Albom MS, Angeles TS, Cheng M, Ghose AK, Roemmele RC, Theroff JP, Underiner TL, Zificsak CA, Dorsey BD.. Synthesis and structure-activity relationships of 1,2,3,4-tetrahydropyrido[2,3-b]pyrazines as potent and selective inhibitors of the anaplastic lymphoma kinase.. Bioorg Med Chem. 2010 Jun 15;18(12):4351-62. Epub 2010 Apr 29.. PMID:20483621

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Discovery of Benzimidazole Oxazolidinediones as Novel and Selective Nonsteroidal Mineralocorticoid Receptor Antagonists
Christine Yang, Jaume Balsells, Hong D. Chu, Jason M. Cox, Alejandro Crespo, Xiuying Ma, Lisa Contino, Patricia Brown, Sheng Gao, Beata Zamlynny, Judyann Wiltsie, Joseph Clemas, JeanMarie Lisnock, Jack Gibson, Gaochao Zhou, Margarita Garcia-Calvo, Thomas J. Bateman, Vincent Tong, Ling Xu, Martin Crook, Peter Sinclair, Hong C. Shen. Discovery of Benzimidazole Oxazolidinediones as Novel and Selective Nonsteroidal Mineralocorticoid Receptor Antagonists. ACS Med. Chem. Lett., 2015, 6 (4), pp 461–465. 10.1021/acsmedchemlett.5b00010
Discovery of a novel isoxazoline derivative of prednisolone endowed with a robust anti-inflammatory profile and suitable for topical pulmonary administration.
Ghidini E, Capelli AM, Carnini C, Cenacchi V, Marchini G, Virdis A, Italia A, Facchinetti F. Discovery of a novel isoxazoline derivative of prednisolone endowed with a robust anti-inflammatory profile and suitable for topical pulmonary administration. Steroids. 2015 Mar;95:88-95. doi: 10.1016/j.steroids.2014.12.016. Epub 2014 Dec 31. PMID:25556984
The translational efficacy of a nonsteroidal progesterone receptor antagonist, 4-[3-cyclopropyl-1-(mesylmethyl)-5-methyl-1H-pyrazol-4-yl]oxy,-2,6-dimethylbenzonitrile (PF-02413873), on endometrial growth in macaque and human.
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Acute inhibition of 11beta-hydroxysteroid dehydrogenase type-1 improves memory in rodent models of cognition.
Mohler EG, Browman KE, Roderwald VA, Cronin EA, Markosyan S, Scott Bitner R, Strakhova MI, Drescher KU, Hornberger W, Rohde JJ, Brune ME, Jacobson PB, Rueter LE.. Acute inhibition of 11beta-hydroxysteroid dehydrogenase type-1 improves memory in rodent models of cognition.. J Neurosci. 2011 Apr 6;31(14):5406-13.. PMID:21471376
Resveratrol modulates the expression of PTGS2 and cellular proliferation in the normal rat endometrium in an AKT-dependent manner.
Singh M, Parent S, Leblanc V, Asselin E.. Resveratrol modulates the expression of PTGS2 and cellular proliferation in the normal rat endometrium in an AKT-dependent manner.. Biol Reprod. 2011 May;84(5):1045-52. Epub 2011 Jan 19.. PMID:21248286
Cleavage of zearalenone by Trichosporon mycotoxinivorans to a novel nonestrogenic metabolite.
Vekiru E, Hametner C, Mitterbauer R, Rechthaler J, Adam G, Schatzmayr G, Krska R, Schuhmacher R.. Cleavage of zearalenone by Trichosporon mycotoxinivorans to a novel nonestrogenic metabolite.. Appl Environ Microbiol. 2010 Apr;76(7):2353-9. Epub 2010 Jan 29.. PMID:20118365
Expression of Human Nuclear Receptors in Plants for the Discovery of Plant-Derived Ligands.
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Active participation of cellular chaperone Hsp90 in regulating the function of rotavirus nonstructural protein 3 (NSP3).
Dutta D, Chattopadhyay S, Bagchi P, Halder UC, Nandi S, Mukherjee A, Kobayashi N, Taniguchi K, Chawla-Sarkar M.. Active participation of cellular chaperone Hsp90 in regulating the function of rotavirus nonstructural protein 3 (NSP3).. J Biol Chem. 2011 Jun 3;286(22):20065-77. Epub 2011 Apr 13.. PMID:21489987
Beta-Galactosidase enzyme fragment complementation for the measurement of Wnt/beta-catenin signaling
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Inhibition of Bitter Taste from Oral Tenofovir Alafenamide.
Schwiebert E, Wang Y, Xi R, Choma K, Streiff J, Flammer LJ, Rivers N, Ozdener MH, Margolskee RF, Christensen CM, Rawson NE, Jiang P, Breslin PAS. Inhibition of Bitter Taste from Oral Tenofovir Alafenamide. Mol Pharmacol. 2021 May;99(5):319-327.
Small-molecule allosteric activators of PDE4 long form cyclic AMP phosphodiesterases.
Omar F, Findlay JE, Carfray G, Allcock RW, Jiang Z, Moore C, Muir AL, Lannoy M, Fertig BA, Mai D, Day JP, Bolger G, Baillie GS, Schwiebert E, Klussmann E, Pyne NJ, Ong ACM, Bowers K, Adam JM, Adams DR, Houslay MD, Henderson DJP. Small-molecule allosteric activators of PDE4 long form cyclic AMP phosphodiesterases. Proc Natl Acad Sci U S A. 2019 Jul 2;116(27):13320-13329.
Use of a rapid human primary cell-based disease screening model to compare next generation products to combustible cigarettes.
Simms L, Mason E, Berg EL, Yu F, Rudd K, Czekala L, Trelles Sticken E, Brinster O, Wieczorek R, Stevenson M, Walele T.
Use of a rapid human primary cell-based disease screening model to compare next generation products to combustible cigarettes.
Current Research in Toxicology. 2021;2:309-321.
Expanding the drug discovery space with predicted metabolite–target interactions.
Nuzzo A, Saha S, Berg E, Jayawickreme C, Tocker J, Brown JR. Expanding the drug discovery space with predicted metabolite–target interactions. Commun Biol. 2021;4:288.
Investigating Molecular Mechanisms of Immunotoxicity and the Utility of ToxCast for Immunotoxicity Screening of Chemicals Added to Food.
Naidenko OV, Andrews DQ, Temkin AM, Stoiber T, Uche UI, Evans S, Perrone-Gray S. Investigating Molecular Mechanisms of Immunotoxicity and the Utility of ToxCast for Immunotoxicity Screening of Chemicals Added to Food. Int J Environ Res Public Health. 2021;18(7):3332.
ILB® resolves inflammatory scarring and promotes functional tissue repair.
Hill LJ, Botfield HF, Begum G, Qureshi O, Vigneswara V, Masood I, Barnes NM, Bruce L, Logan A. ILB® resolves inflammatory scarring and promotes functional tissue repair. NPJ Regen Med. 2021;6:3.
The future of phenotypic drug discovery.
Berg EL. The future of phenotypic drug discovery. Cell Chemical Biology. 2021;28(3):424-430.
Chapter 2: Development and Validation of Disease Assays for Phenotypic Screening.
Berg EL, Denker SP, O’Mahony A. Chapter 2: Development and Validation of Disease Assays for Phenotypic Screening. In: Phenotypic Drug Discovery.; 2020:20-36.
Tapinarof Is a Natural AhR Agonist that Resolves Skin Inflammation in Mice and Humans.
Smith SH, Jayawickreme C, Rickard DJ, Nicodeme E, Bui T, Simmons C, Coquery CM, Neil J, Pryor WM, Mayhew D, Rajpal DK, Creech K, Furst S, Lee J, Wu D, Rastinejad F, Willson TM, Viviani F, Morris DC, Moore JT, Cote-Sierra J. Tapinarof Is a Natural AhR Agonist that Resolves Skin Inflammation in Mice and Humans. J Invest Dermatol. 2017;137(10):2110-2119.
A Next-Generation Risk Assessment Case Study for Coumarin in Cosmetic Products.
Baltazar MT, Cable S, Carmichael PL, Cubberley R, Cull T, Delagrange M, Dent MP, Hatherell S, Houghton J, Kukic P, Li H, Lee M-Y, Malcomber S, Middleton AM, Moxon TE, Nathanail AV, Nicol B, Pendlington R, Reynolds G, Reynolds J, White A, Westmoreland C. A Next-Generation Risk Assessment Case Study for Coumarin in Cosmetic Products. Toxicol Sci. 2020;176(1):236-252.
Btk inhibition treats TLR7/IFN driven murine lupus.
Bender AT, Pereira A, Fu K, Samy E, Wu Y, Liu-Bujalski L, Caldwell R, Chen Y-Y, Tian H, Morandi F, Head J, Koehler U, Genest M, Okitsu SL, Xu D, Grenningloh R. Btk inhibition treats TLR7/IFN driven murine lupus. Clinical Immunology. 2016;164:65-77.
Development of a Topical Treatment for Psoriasis Targeting RORγ: From Bench to Skin.
Smith SH, Peredo CE, Takeda Y, Bui T, Neil J, Rickard D, Millerman E, Therrien J-P, Nicodeme E, Brusq J-M, Birault V, Viviani F, Hofland H, Jetten AM, Cote-Sierra J. Development of a Topical Treatment for Psoriasis Targeting RORγ: From Bench to Skin. PLOS ONE. 2016;11(2):e0147979.
Targeting JAK2 reduces GVHD and xenograft rejection through regulation of T cell differentiation.
Betts BC, Bastian D, Iamsawat S, Nguyen H, Heinrichs JL, Wu Y, Daenthanasanmak A, Veerapathran A, O’Mahony A, Walton K, Reff J, Horna P, Sagatys EM, Lee MC, Singer J, Chang Y-J, Liu C, Pidala J, Anasetti C, Yu X-Z. Targeting JAK2 reduces GVHD and xenograft rejection through regulation of T cell differentiation. PNAS. 2018;115(7):1582-1587.
The activities of drug inactive ingredients on biological targets.
Pottel J, Armstrong D, Zou L, Fekete A, Huang X-P, Torosyan H, Bednarczyk D, Whitebread S, Bhhatarai B, Liang G, Jin H, Ghaemi SN, Slocum S, Lukacs KV, Irwin JJ, Berg EL, Giacomini KM, Roth BL, Shoichet BK, Urban L. The activities of drug inactive ingredients on biological targets. Science. 2020;369(6502):403-413.
Application of a phenotypic drug discovery strategy to identify biological and chemical starting points for inhibition of TSLP production in lung epithelial cells.
Orellana A, García-González V, López R, Pascual-Guiral S, Lozoya E, Díaz J, Casals D, Barrena A, Paris S, Andrés M, Segarra V, Vilella D, Malhotra R, Eastwood P, Planagumà A, Miralpeix M, Nueda A. Application of a phenotypic drug discovery strategy to identify biological and chemical starting points for inhibition of TSLP production in lung epithelial cells. PLOS ONE. 2018;13(1):e0189247.
Pharmacological Profile of the Novel Antiepileptic Drug Candidate Padsevonil: Interactions with Synaptic Vesicle 2 Proteins and the GABAA Receptor.
Wood M, Daniels V, Provins L, Wolff C, Kaminski RM, Gillard M. Pharmacological Profile of the Novel Antiepileptic Drug Candidate Padsevonil: Interactions with Synaptic Vesicle 2 Proteins and the GABAA Receptor. J Pharmacol Exp Ther. 2020;372(1):1-10.
Human Cell-Based in vitro Phenotypic Profiling for Drug Safety-Related Attrition.
Berg EL. Human Cell-Based in vitro Phenotypic Profiling for Drug Safety-Related Attrition. Front Big Data. 2019;2. doi:10.3389/fdata.2019.00047.
Comparative phenotypic profiling of the JAK2 inhibitors ruxolitinib, fedratinib, momelotinib, and pacritinib reveals distinct mechanistic signatures.
Singer JW, Al-Fayoumi S, Taylor J, Velichko S, O’Mahony A. Comparative phenotypic profiling of the JAK2 inhibitors ruxolitinib, fedratinib, momelotinib, and pacritinib reveals distinct mechanistic signatures. PLOS ONE. 2019;14(9):e0222944.
Efficacy and Pharmacodynamic Modeling of the BTK Inhibitor Evobrutinib in Autoimmune Disease Models.
Haselmayer P, Camps M, Liu-Bujalski L, Nguyen N, Morandi F, Head J, O’Mahony A, Zimmerli SC, Bruns L, Bender AT, Schroeder P, Grenningloh R. Efficacy and Pharmacodynamic Modeling of the BTK Inhibitor Evobrutinib in Autoimmune Disease Models. The Journal of Immunology. 2019 Apr 15; ji1800583.
Advancing nonclinical innovation and safety in pharmaceutical testing.
Baker EJ, Beck NA, Berg EL, Clayton-Jeter HD, Chandrasekera PC, Curley JL, Donzanti BA, Ewart LC, Gunther JM, Kenna JG, LeCluyse EL, Liebman MN, Pugh CL, Watkins PB, Sullivan KM. Advancing nonclinical innovation and safety in pharmaceutical testing. Drug Discovery Today. 2019;24(2):624–628.
Rational discovery of dual-action multi-target kinase inhibitor for precision anti-cancer therapy using structural systems pharmacology.
Xie L, Lim H, He D, Qiu Y, Krawczuk P, Sun X. Rational discovery of dual-action multi-target kinase inhibitor for precision anti-cancer therapy using structural systems pharmacology. bioRxiv. 2018 Nov 7 [accessed 2019 Mar 21]:465054.
Predictive gene signatures determine tumor sensitivity to MDM2 inhibition.
Ishizawa J, Nakamaru K, Seki T, Tazaki K, Kojima K, Chachad D, Zhao R, Heese L, Ma W, Ma MCJ, DiNardo C, Pierce S, Patel KP, Tse A, Davis RE, Rao A, Andreeff M. Predictive gene signatures determine tumor sensitivity to MDM2 inhibition. Cancer Research. 2018;78(10):2721–2731.
Small-molecule activators of protein phosphatase 2A for the treatment of castration-resistant prostate cancer.
McClinch K, Avelar RA, Callejas D, Izadmehr S, Wiredja D, Perl A, Sangodkar J, Kastrinsky DB, Schlatzer D, Cooper M, Kiselar J, Stachnik A, Yao S, Hoon D, McQuaid D, Zaware N, Gong Y, Brautigan DL, Plymate SR, Sprenger CCT, Oh WK, Levine AC, Kirschenbaum A, Sfakianos JP, Sears R, DiFeo A, Ioannou Y, Ohlmeyer M, Narla G, Galsky MD. Small-molecule activators of protein phosphatase 2A for the treatment of castration-resistant prostate cancer. Cancer Research. 2018;78(8):2065–2080.
Assessing bioactivity-exposure profiles of fruit and vegetable extracts in the BioMAP profiling system.
Wetmore BA, Clewell RA, Cholewa B, Parks B, Pendse SN, Black MB, Mansouri K, Haider S, Berg EL, Judson RS, Houck KA, Martin M, Clewell HJ 3rd, Andersen ME, Thomas RS, McMullen PD. Assessing bioactivity-exposure profiles of fruit and vegetable extracts in the BioMAP profiling system. Toxicology in Vitro. 2019;54:41–57.
Mechanism of action of the third generation benzopyrans and evaluation of their broad anti-cancer activity in vitro and in vivo.
Stevenson AJ, Ager EI, Proctor MA, Škalamera D, Heaton A, Brown D, Gabrielli BG. Mechanism of action of the third generation benzopyrans and evaluation of their broad anti-cancer activity in vitro and in vivo. Scientific Reports. 2018;8(1).
Efficacy of the highly selective focal adhesion kinase inhibitor BI 853520 in adenocarcinoma xenograft models is linked to a mesenchymal tumor phenotype.
Hirt UA, Waizenegger IC, Schweifer N, Haslinger C, Gerlach D, Braunger J, Weyer-Czernilofsky U, Stadtmüller H, Sapountzis I, Bader G, Zoephel A, Bister B, Baum A, Quant J, Kraut N, Garin-Chesa P, Adolf GR. Efficacy of the highly selective focal adhesion kinase inhibitor BI 853520 in adenocarcinoma xenograft models is linked to a mesenchymal tumor phenotype. Oncogenesis. 2018;7(2):21.
Mebendazole stimulates CD14+ myeloid cells to enhance T-cell activation and tumour cell killing.
Rubin J, Mansoori S, Blom K, Berglund M, Lenhammar L, Andersson C, Loskog A, Fryknäs M, Nygren P, Larsson R. Mebendazole stimulates CD14+ myeloid cells to enhance T-cell activation and tumour cell killing. Oncotarget. 2018;9(56):30805-30813.
Discriminating phenotypic signatures identified for tocilizumab, adalimumab, and tofacitinib monotherapy and their combinations with methotrexate.
O’Mahony A, John MR, Cho H, Hashizume M, Choy EH. Discriminating phenotypic signatures identified for tocilizumab, adalimumab, and tofacitinib monotherapy and their combinations with methotrexate. Journal of Translational Medicine. 2018;16(156).
Small molecule inhibitors and CRISPR/Cas9 mutagenesis demonstrate that SMYD2 and SMYD3 activity are dispensable for autonomous cancer cell proliferation.
Thomenius MJ, Totman J, Harvey D, Mitchell LH, Riera TV, Cosmopoulos K, Grassian AR, Klaus C, Foley M, Admirand EA, Jahic H, Majer C, Wigle T, Jacques SL, Gureasko J, Brach D, Lingaraj T, West K, Smith S, Rioux N, Waters NJ, Tang C, Raimondi A, Munchhof M, Mills JE, Ribich S, Porter Scott M, Kuntz KW, Janzen WP, Moyer M, Smith JJ, Chesworth R, Copeland RA, Boriack-Sjodin PA. Small molecule inhibitors and CRISPR/Cas9 mutagenesis demonstrate that SMYD2 and SMYD3 activity are dispensable for autonomous cancer cell proliferation. PLOS ONE. 2018;13(6):e0197372.
Anti-tumor efficacy of a novel CLK inhibitor via targeting RNA splicing and MYC-dependent vulnerability.
Iwai K, Yaguchi M, Nishimura K, Yamamoto Y, Tamura T, Nakata D, Dairiki R, Kawakita Y, Mizojiri R, Ito Y, Asano M, Maezaki H, Nakayama Y, Kaishima M, Hayashi K, Teratani M, Miyakawa S, Iwatani M, Miyamoto M, Klein MG, Lane W, Snell G, Tjhen R, He X, Pulukuri S, Nomura T. Anti-tumor efficacy of a novel CLK inhibitor via targeting RNA splicing and MYC-dependent vulnerability. EMBO Molecular Medicine. 2018;10(6).
Mechanisms of skin toxicity associated with metabotropic glutamate receptor 5 negative allosteric modulators.
Shah F, Stepan AF, O’Mahony A, Velichko S, Folias AE, Houle C, Shaffer CL, Marcek J, Whritenour J, Stanton R, Berg EL. Mechanisms of skin toxicity associated with metabotropic glutamate receptor 5 negative allosteric modulators. Cell Chemical Biology. 2017;24(7):858–869.e5.
Phenotypic chemical biology for predicting safety and efficacy.
Berg EL. Phenotypic chemical biology for predicting safety and efficacy. Drug Discovery Today: Technologies. 2017;23:53–60.
Empirical drug discovery: a view from the proteome.
Lee JA, Carragher NO, Berg EL. Empirical drug discovery: a view from the proteome. Drug Discovery Today: Technologies. 2017;23:1–5.
Identification of a chemical probe for family VIII bromodomains through optimization of a fragment hit.
Gerstenberger BS, Trzupek JD, Tallant C, Fedorov O, Filippakopoulos P, Brennan PE, Fedele V, Martin S, Picaud S, Rogers C, Parikh M, Taylor A, Samas B, O’Mahony A, Berg EL, Pallares G, Torrey AD, Treiber DK, Samardjiev IJ, Nasipak BT, Padilla-Benavides T, Wu Q, Imbalzano AN, Nickerson JA, Bunnage ME, Müller S, Knapp S, Owen DR. Identification of a chemical probe for family VIII bromodomains through optimization of a fragment hit. Journal of medicinal chemistry. 2016;59(10):4800–4811.
CBP30, a selective CBP/p300 bromodomain inhibitor, suppresses human Th17 responses.
Hammitzsch A, Tallant C, Fedorov O, O’Mahony A, Brennan PE, Hay DA, Martinez FO, Al-Mossawi MH, de Wit J, Vecellio M, Wells C, Wordsworth P, Müller S, Knapp S, Bowness P. CBP30, a selective CBP/p300 bromodomain inhibitor, suppresses human Th17 responses. PNAS. 2015;112(34):10768–10773.
DMF, but not other fumarates, inhibits NF-κB activity in vitro in an Nrf2-independent manner.
Gillard GO, Collette B, Anderson J, Chao J, Scannevin RH, Huss DJ, Fontenot JD. DMF, but not other fumarates, inhibits NF-κB activity in vitro in an Nrf2-independent manner. Journal of Neuroimmunology. 2015;283:74–85.
Elucidating mechanisms of toxicity using phenotypic data from primary human cell systems—a chemical biology approach for thrombosis-related side effects.
Berg EL, Polokoff MA, O’Mahony A, Nguyen D, Li X. Elucidating mechanisms of toxicity using phenotypic data from primary human cell systems—a chemical biology approach for thrombosis-related side effects. International Journal of Molecular Sciences. 2015;16(1):1008–1029.
Targeting interleukin-2-inducible T-cell kinase (ITK) and resting lymphocyte kinase (RLK) using a novel covalent inhibitor PRN694.
Zhong Y, Dong S, Strattan E, Ren L, Butchar JP, Thornton K, Mishra A, Porcu P, Bradshaw JM, Bisconte A, Owens TD, Verner E, Brameld KA, Funk JO, Hill RJ, Johnson AJ, Dubovsky JA. Targeting interleukin-2-inducible T-cell kinase (ITK) and resting lymphocyte kinase (RLK) using a novel covalent inhibitor PRN694. Journal of Biological Chemistry. 2015;290(10):5960–5978.
Complex Primary Human Cell Systems for Drug Discovery. In: Human-based Systems for Translational Research.
Berg EL, O’Mahony A. Complex Primary Human Cell Systems for Drug Discovery. In: Human-based Systems for Translational Research. The Royal Society of Chemistry; 2014; p.88–109. Chapter 5; Edited by Robert Coleman.
Phenotypic screening of the ToxCast chemical library to classify toxic and therapeutic mechanisms.
Kleinstreuer NC, Yang J, Berg EL, Knudsen TB, Richard AM, Martin MT, Reif DM, Judson RS, Polokoff M, Dix DJ, Kavlock RJ, Houck KA. Phenotypic screening of the ToxCast chemical library to classify toxic and therapeutic mechanisms. Nature Biotechnology. 2014;32(6):583–591.
Characterization of novel PI3Kδ inhibitors as potential therapeutics for SLE and lupus nephritis in pre-clinical studies.
Haselmayer P, Camps M, Muzerelle M, El Bawab S, Waltzinger C, Bruns L, Abla N, Polokoff MA, Jond-Necand C, Gaudet M, Benoit A, Bertschy Meier D, Martin C, Gretener D, Lombardi MS, Grenningloh R, Ladel C, Petersen JS, Gaillard P, Ji H. Characterization of novel PI3Kδ inhibitors as potential therapeutics for SLE and lupus nephritis in pre-clinical studies. Frontiers in Immunology. 2014;5:233.
Consideration of the cellular microenvironment: physiologically relevant co-culture systems in drug discovery.
Berg EL, Hsu Y-C, Lee JA. Consideration of the cellular microenvironment: physiologically relevant co-culture systems in drug discovery. Advanced Drug Delivery Reviews. 2014;69–70:190–204.
Dual kinase-bromodomain inhibitors for rationally designed polypharmacology.
Ciceri P, Müller S, O’Mahony A, Fedorov O, Filippakopoulos P, Hunt JP, Lasater EA, Pallares G, Picaud S, Wells C, Martin S, Wodicka LM, Shah NP, Treiber DK, Knapp S. Dual kinase-bromodomain inhibitors for rationally designed polypharmacology. Nature Chemical Biology. 2014;10(4):305–312.
Building predictive models for mechanism-of-action classification from phenotypic assay data sets.
Berg EL, Yang J, Polokoff MA. Building predictive models for mechanism-of-action classification from phenotypic assay data sets. Journal of Biomolecular Screening. 2013;18(10):1260–1269.
Regulation of IL-17A production is distinct from IL-17F in a primary human cell co-culture model of T cell-mediated B cell activation.
Melton AC, Melrose J, Alajoki L, Privat S, Cho H, Brown N, Plavec AM, Nguyen D, Johnston ED, Yang J, Polokoff MA, Plavec I, Berg EL, O’Mahony A. Regulation of IL-17A production is distinct from IL-17F in a primary human cell co-culture model of T cell-mediated B cell activation. PLOS ONE. 2013;8(3):e58966.
A selective inhibitor reveals PI3Kγ dependence of T(H)17 cell differentiation.
Bergamini G, Bell K, Shimamura S, Werner T, Cansfield A, Müller K, Perrin J, Rau C, Ellard K, Hopf C, Doce C, Leggate D, Mangano R, Mathieson T, O'Mahony A, Plavec I, Rharbaoui F, Reinhard F, Savitski MM, Ramsden N, Hirsch E, Drewes G, Rausch O, Bantscheff M, Neubauer G. A selective inhibitor reveals PI3Kγ dependence of T(H)17 cell differentiation. Nature Chemical Biology. 2012;8(6):576–582.
A novel framework for predicting in vivo toxicities from in vitro data using optimal methods for dense and sparse matrix reordering and logistic regression.
DiMaggio PA, Subramani A, Judson RS, Floudas CA. A novel framework for predicting in vivo toxicities from in vitro data using optimal methods for dense and sparse matrix reordering and logistic regression. Toxicological Sciences. 2010;118(1):251–265.
Discovery of dual inhibitors of the immune cell PI3Ks p110δ and p110γ: a prototype for new anti-inflammatory drugs.
Williams O, Houseman BT, Kunkel EJ, Aizenstein B, Hoffman R, Knight ZA, Shokat KM. Discovery of dual inhibitors of the immune cell PI3Ks p110δ and p110γ: a prototype for new anti-inflammatory drugs. Chemistry & Biology. 2010;17(2):123–134.
Chemical target and pathway toxicity mechanisms defined in primary human cell systems.
Berg EL, Yang J, Melrose J, Nguyen D, Privat S, Rosler E, Kunkel EJ, Ekins S. Chemical target and pathway toxicity mechanisms defined in primary human cell systems. Journal of Pharmacological and Toxicological Methods. 2010;61(1):3–15.
Profiling bioactivity of the ToxCast chemical library using BioMAP primary human cell systems.
Houck KA, Dix DJ, Judson RS, Kavlock RJ, Yang J, Berg EL. Profiling bioactivity of the ToxCast chemical library using BioMAP primary human cell systems. Journal of Biomolecular Screening. 2009;14(9):1054–1066.
Characterization of compound mechanisms and secondary activities by BioMAP analysis.
Berg EL, Kunkel EJ, Hytopoulos E, Plavec I. Characterization of compound mechanisms and secondary activities by BioMAP analysis. Journal of Pharmacological and Toxicological Methods. 2006;53(1):67–74.
Biological complexity and drug discovery: a practical systems biology approach.
Berg EL, Kunkel EJ, Hytopoulos E. Biological complexity and drug discovery: a practical systems biology approach. Systems Biology. 2005;152(4):201–206.
Can cell systems biology rescue drug discovery?
Butcher EC. Can cell systems biology rescue drug discovery? Nature Reviews Drug Discovery. 2005; 4(6):461–467.
Rapid structure-activity and selectivity analysis of kinase inhibitors by BioMAP analysis in complex human primary cell-based models.
Kunkel EJ, Plavec I, Nguyen D, Melrose J, Rosler ES, Kao LT, Wang Y, Hytopoulos E, Bishop AC, Bateman R, Shokat KM, Butcher EC, Berg EL. Rapid structure-activity and selectivity analysis of kinase inhibitors by BioMAP analysis in complex human primary cell-based models. Assay and Drug Development Technologies. 2004;2(4):431–441.
An integrative biology approach for analysis of drug action in models of human vascular inflammation.
Kunkel EJ, Dea M, Ebens A, Hytopoulos E, Melrose J, Nguyen D, Ota KS, Plavec I, Wang Y, Watson SR, Butcher EC, Berg EL. An integrative biology approach for analysis of drug action in models of human vascular inflammation. FASEB Journal. 2004;18(11):1279–1281.

Cross-site and cross-platform variability of automated patch clamp assessments of drug effects on human cardiac currents in recombinant cells.
Kramer J, Himmel HM, Lindqvist A, Stoelzle-Feix S, Chaudhary KW, Li D, Bohme GA, Bridgland-Taylor M, Hebeisen S, Fan J, Renganathan M, Imredy J, Humphries E, Brinkwirth N, Strassmaier T, Ohtsuki A, Danker T, Vanoye C, Polonchuk L, Fermini B, Beck Pierson J, Gintant G. Cross-site and cross-platform variability of automated patch clamp assessments of drug effects on human cardiac currents in recombinant cells. Scientific Reports. 2020 Mar 27;10(1):5627
A systematic strategy for estimating hERG block potency and its implications in a new cardiac safety paradigm.
Ridder BJ, Leishman DJ, Bridgland-Taylor M, Samieegohar M, Han X, Wu WW, Randolph A, Tran P, Sheng J, Danker T, Lindqvist A, Konrad D, Hebeisen S, Polonchuk L, Gissinger E, Renganathan M, Koci B, Wei H, Fan J, Levesque P, Kwagh J, Imredy J, Zhai J, Rogers M, Humphries E, Kirby R, Stoelzle-Feix S, Brinkwirth N, Rotordam MG, Becker N, Friis S, Rapedius M, Goetze TA, Strassmaier T, Okeyo G, Kramer J, Kuryshev Y, Wu C, Himmel H, Mirams GR, Strauss DG, Bardenet R, Li Z. A systematic strategy for estimating hERG block potency and its implications in a new cardiac safety paradigm. Toxicol Appl Pharmacol. May 1;394. 2020

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