Publications

List of publications per year

CELL_167_1.c1.indd
2017
2016
2015
2014
2013
2012
2011
2010
2009
2008

Additional publications from Chemoinformatics group can be found here.

2017

Return to Top
Cannon DC, Yang JJ, Mathias SL, Ursu O, Mani S, Waller A, Schürer SC, Jensen LJ, Sklar LA, Bologa CG, Oprea TI. TIN-X: Target Importance and Novelty Explorer. Bioinformatics. 2017 Apr 7. doi: 10.1093/bioinformatics/btx200. [Epub ahead of print] PMID: 28398460 .

2016

Return to Top
Whitt JD, Keeton AB, Gary BD, Sklar LA, Sodani K, Chen ZS, Piazza GA. Sulindac sulfide selectively increases sensitivity of ABCC1 expressing tumor cells to doxorubicin and glutathione depletion. J Biomed Res. 2016 Mar;30(2):120-133. doi: 555/JBR.30.20150108. Epub 2015 Nov 20.  PMID: 28276667 PMCID: PMC4820889 .

Nguyen DT, Mathias S, Bologa C, Brunak S, Fernandez N, Gaulton A, Hersey A, Holmes J, Jensen LJ, Karlsson A, Liu G, Ma’ayan A, Mandava G, Mani S, Mehta S, Overington J, Patel J, Rouillard AD, Schürer S, Sheils T, Simeonov A, Sklar LA, Southall N, Ursu O, Vidovic D, Waller A, Yang J, Jadhav A, Oprea TI, Guha R. Pharos: Collating protein information to shed light on the druggable genome. Nucleic Acids Res. 2017 Jan 4;45(D1):D995-D1002. doi: 10.1093/nar/gkw1072. Epub 2016 Nov 29. PMID: 27903890 PMCID: PMC5210555

Ricci JW, Lovato DM, Severns V, Sklar LA, Larson RS. Novel ABCG2 Antagonists Reverse Topotecan-Mediated Chemotherapeutic Resistance in Ovarian Carcinoma Xenografts. Mol Cancer Ther. 2016 Dec;15(12):2853-2862. Epub 2016 Sep 26. PMID: 27671528

Sykes DB, Kfoury YS, Mercier FE, Wawer MJ, Law JM, Haynes MK, Lewis TA, Schajnovitz A, Jain E, Lee D, Meyer H, Pierce KA, Tolliday NJ, Waller A, Ferrara SJ, Eheim AL, Stoeckigt D, Maxcy KL, Cobert JM, Bachand J, Szekely BA, Mukherjee S, Sklar LA, Kotz JD, Clish CB, Sadreyev RI, Clemons PA, Janzer A, Schreiber SL, Scadden DT. Inhibition of Dihydroorotate Dehydrogenase Overcomes Differentiation Blockade in Acute Myeloid Leukemia. Cell. 2016 Sep 22;167(1):171-186.e15. doi: 10.1016/j.cell.2016.08.057. Epub 2016 Sep 15. PMID: 27641501

Holmes AR, Cardno TS, Strouse JJ, Ivnitski-Steele I, Keniya MV, Lackovic K, Monk BC, Sklar LA, Cannon RD. Targeting efflux pumps to overcome antifungal drug resistance. Future Med Chem. 2016 Aug;8(12):1485-501. doi: 10.4155/fmc-2016-0050. Epub 2016 Jul 27. PMID: 27463566

Perez D, Simons PC, Smagley Y, Sklar LA, Chigaev A. A High-Throughput Flow Cytometry Assay for Identification of Inhibitors of 3′,5′-Cyclic Adenosine Monophosphate Efflux. Methods Mol Biol. 2016;1439:227-44. doi: 10.1007/978-1-4939-3673-1_15. PMID: 27316999

Yang JJ, Ursu O, Lipinski CA, Sklar LA, Oprea TI, Bologa CG., Badapple: promiscuity patterns from noisy evidence. J Cheminform. 2016 May 28;8:29. doi: 10.1186/s13321-016-0137-3. eCollection 2016. PMID: 27239230 PMCID: PMC4884375.

Perez DR, Smagley Y, Garcia M, Carter MB, Evangelisti A, Matlawska-Wasowska K, Winter SS, Sklar LA, Chigaev A. Cyclic AMP efflux inhibitors as potential therapeutic agents for leukemia. Oncotarget. 2016 Jun 7;7(23):33960-82. doi: 10.18632/oncotarget.8986. PMID: 27129155 PMCID: PMC5085131.

2015

Return to Top
Oprea TI, Sklar LA, Agola JO, Guo Y, Silberberg M, Roxby J, Vestling A, Romero E, Surviladze Z, Murray-Krezan C, Waller A, Ursu O, Hudson LG, Wandinger-Ness A. Novel Activities of Select NSAID R-Enantiomers against Rac1 and Cdc42 GTPases. PLoS One. 2015 Nov 11;10(11):e0142182. doi: 10.1371/journal.pone.0142182. eCollection 2015. PubMed PMID: 26558612; PubMed Central PMCID: PMC4641600.

Wu Y, Stauffer SR, Stanfield RL, Tapia PH, Ursu O, Fisher GW, Szent-Gyorgyi C, Evangelisti A, Waller A, Strouse JJ, Carter MB, Bologa C, Gouveia K, Poslusney M, Waggoner AS, Lindsley CW, Jarvik JW, Sklar LA. Discovery of Small-Molecule Nonfluorescent Inhibitors of Fluorogen-Fluorogen Activating Protein Binding Pair. J Biomol Screen. 2016 Jan;21(1):74-87. doi: 10.1177/1087057115609145. Epub 2015 Oct 6. PubMed PMID: 26442911.

Bologa CG, Ursu O, Halip L, Curpăn R, Oprea TI. CHEMICAL AND BIOLOGICAL DESCRIPTOR INTEGRATION IMPROVES COMPUTATIONAL MODELING OF IN VIVO RAT TOXICITY. Rev Roum Chim. 2015 Feb-Mar;60(2-3):219-226. PubMed PMID: 26346852; PubMed Central PMCID: PMC4557807.

Hong L, Guo Y, BasuRay S, Agola JO, Romero E, Simpson DS, Schroeder CE, Simons P, Waller A, Garcia M, Carter M, Ursu O, Gouveia K, Golden JE, Aubé J, Wandinger-Ness A, Sklar LA. A Pan-GTPase Inhibitor as a Molecular Probe. PLoS One. 2015 Aug 6;10(8):e0134317. doi: 10.1371/journal.pone.0134317. eCollection 2015. PubMed PMID: 26247207; PubMed Central PMCID: PMC4527730.

Guo Y, Kenney SR, Muller CY, Adams S, Rutledge T, Romero E, Murray-Krezan C, Prekeris R, Sklar LA, Hudson LG, Wandinger-Ness A. R-Ketorolac Targets Cdc42 and Rac1 and Alters Ovarian Cancer Cell Behaviors Critical for Invasion and Metastasis. Mol Cancer Ther. 2015 Oct;14(10):2215-27. doi: 10.1158/1535-7163.MCT-15-0419. Epub 2015 Jul 23. PubMed PMID: 26206334; PubMed Central PMCID: PMC4596774.

Guo Y, Kenney SR, Cook L, Adams SF, Rutledge T, Romero E, Oprea TI, Sklar LA,  Bedrick E, Wiggins CL, Kang H, Lomo L, Muller CY, Wandinger-Ness A, Hudson LG. A Novel Pharmacologic Activity of Ketorolac for Therapeutic Benefit in Ovarian Cancer Patients. Clin Cancer Res. 2015 Nov 15;21(22):5064-72. doi: 10.1158/1078-0432.CCR-15-0461. Epub 2015 Jun 12. PubMed PMID: 26071482; PubMed Central PMCID: PMC4644688.

Schreiber SL, Kotz JD, Li M, Aubé J, Austin CP, Reed JC, Rosen H, White EL, Sklar LA, Lindsley CW, Alexander BR, Bittker JA, Clemons PA, de Souza A, Foley MA, Palmer M, Shamji AF, Wawer MJ, McManus O, Wu M, Zou B, Yu H, Golden JE, Schoenen FJ, Simeonov A, Jadhav A, Jackson MR, Pinkerton AB, Chung TD, Griffin PR, Cravatt BF, Hodder PS, Roush WR, Roberts E, Chung DH, Jonsson CB, Noah JW, Severson WE, Ananthan S, Edwards B, Oprea TI, Conn PJ, Hopkins CR, Wood MR, Stauffer SR, Emmitte KA; NIH Molecular Libraries Project Team. Advancing Biological Understanding and Therapeutics Discovery with Small-Molecule Probes. Cell. 2015 Jun 4;161(6):1252-65. doi: 10.1016/j.cell.2015.05.023. Review. PubMed  PMID: 26046436; PubMed Central PMCID: PMC4564295.

Edwards BS, Sklar LA. Flow Cytometry: Impact on Early Drug Discovery. J Biomol Screen. 2015 Jul;20(6):689-707. doi: 10.1177/1087057115578273. Epub 2015 Mar 24.  Review. PubMed PMID: 25805180; PubMed Central PMCID: PMC4606936.

Agola JO, Sivalingam D, Cimino DF, Simons PC, Buranda T, Sklar LA, Wandinger-Ness A. Quantitative bead-based flow cytometry for assaying Rab7 GTPase interaction with the Rab-interacting lysosomal protein (RILP) effector protein. Methods Mol Biol. 2015;1298:331-54. doi: 10.1007/978-1-4939-2569-8_28. PubMed PMID: 25800855.

Magana M, Ioannidis A, Magiorkinis E, Ursu O, Bologa CG, Chatzipanagiotou S, Hamblin MR, Tegos GP. Therapeutic options and emerging alternatives for multidrug resistant staphylococcal infections. Curr Pharm Des. 2015;21(16):2058-72. Review. PubMed PMID: 25760340.

Hong L, Chavez S, Smagley Y, Chigaev A, Sklar LA. Relationship of light scatter change and Cdc42-regulated actin status. Cytometry B Clin Cytom. 2015 Jan 13. doi: 10.1002/cyto.b.21223. [Epub ahead of print] PubMed PMID: 25641607; PubMed Central PMCID: PMC4500678.

Zhao Z, Haynes MK, Ursu O, Edwards BS, Sklar LA, Zweifach A. A high-throughput phenotypic screen of cytotoxic T lymphocyte lytic granule exocytosis reveals candidate immunosuppressants. J Biomol Screen. 2015 Mar;20(3):359-71. doi: 10.1177/1087057114557620. Epub 2014 Nov 7. PubMed PMID: 25381253; PubMed Central PMCID: PMC4523125.

2014

Return to Top
Chigaev A, Smagley Y, Sklar LA. Carbon monoxide down-regulates α4β1 integrin-specific ligand binding and cell adhesion: a possible mechanism for cell mobilization. BMC Immunol. 2014 Oct 31;15:52. doi: 10.1186/s12865-014-0052-1. PubMed PMID: 25367365; PubMed Central PMCID: PMC4221689.

Bernardo SM, Allen CP, Waller A, Young SM, Oprea T, Sklar LA, Lee SA. An automated high-throughput cell-based multiplexed flow cytometry assay to identify novel compounds to target Candida albicans virulence-related proteins. PLoS One.  2014 Oct 28;9(10):e110354. doi: 10.1371/journal.pone.0110354. eCollection 2014. PubMed PMID: 25350399; PubMed Central PMCID: PMC4211665.

Cordero D, Fullenkamp CR, Pelly RR, Reed KM, Caffo LM, Zahrt AN, Newman M, Komanapalli S, Niemeier EM, Bishop DL, Bruns HA, Haynes MK, Sklar LA, Sammelson RE, McDowell SA. Small Molecule Inhibitors Limit Endothelial Cell Invasion by Staphylococcus aureus. Curr Pharm Biotechnol. 2014;15(8):727-37. PubMed PMID: 25213310; PubMed Central PMCID: PMC4469273.

Tegos GP, Evangelisti AM, Strouse JJ, Ursu O, Bologa C, Sklar LA. A high throughput flow cytometric assay platform targeting transporter inhibition. Drug Discov Today Technol. 2014 Jun;12:e95-103. doi: 10.1016/j.ddtec.2014.03.010. Review. PubMed PMID: 25027381; PubMed Central PMCID: PMC4101541.

Sully EK, Malachowa N, Elmore BO, Alexander SM, Femling JK, Gray BM, DeLeo FR, Otto M, Cheung AL, Edwards BS, Sklar LA, Horswill AR, Hall PR, Gresham HD. Selective chemical inhibition of agr quorum sensing in Staphylococcus aureus promotes host defense with minimal impact on resistance. PLoS Pathog. 2014 Jun 12;10(6):e1004174. doi: 10.1371/journal.ppat.1004174. eCollection 2014 Jun. PubMed PMID: 24945495; PubMed Central PMCID: PMC4055767.

Wu Y, Tapia PH, Jarvik J, Waggoner AS, Sklar LA. Real-time detection of protein trafficking with high-throughput flow cytometry (HTFC) and fluorogen-activating protein (FAP) base biosensor. Curr Protoc Cytom. 2014 Jan 2;67:Unit 9.43.. doi: 10.1002/0471142956.cy0943s67. PubMed PMID: 24510772; PubMed Central PMCID: PMC3961059.

Edwards BS, Gouveia K, Oprea TI, Sklar LA. The University of New Mexico Center for Molecular Discovery. Comb Chem High Throughput Screen. 2014 Mar;17(3):256-65. PubMed PMID: 24409953; PubMed Central PMCID: PMC4476788.

2013

Return to Top
May EE, Leitão A, Tropsha A, Oprea TI. A systems chemical biology study of malate synthase and isocitrate lyase inhibition in Mycobacterium tuberculosis during active and NRP growth. Comput Biol Chem. 2013 Dec;47:167-80. doi: 10.1016/j.compbiolchem.2013.07.002. Epub 2013 Sep 4. PubMed PMID: 24121675; PubMed Central PMCID: PMC4010430.

Chibebe Junior J, Sabino CP, Tan X, Junqueira JC, Wang Y, Fuchs BB, Jorge AO, Tegos GP, Hamblin MR, Mylonakis E. Selective photoinactivation of Candida albicans in the non-vertebrate host infection model Galleria mellonella. BMC Microbiol. 2013 Oct 1;13:217. doi: 10.1186/1471-2180-13-217. PubMed PMID: 24083556; PubMed Central PMCID: PMC3849975.

Bologa CG, Ursu O, Oprea TI, Melançon CE 3rd, Tegos GP. Emerging trends in the discovery of natural product antibacterials. Curr Opin Pharmacol. 2013 Oct;13(5):678-87. doi: 10.1016/j.coph.2013.07.002. Epub 2013 Jul 24. Review. PubMed PMID: 23890825; PubMed Central PMCID: PMC3795984.

Vatansever F, de Melo WC, Avci P, Vecchio D, Sadasivam M, Gupta A, Chandran R, Karimi M, Parizotto NA, Yin R, Tegos GP, Hamblin MR. Antimicrobial strategies centered around reactive oxygen species–bactericidal antibiotics, photodynamic therapy, and beyond. FEMS Microbiol Rev. 2013 Nov;37(6):955-89. doi: 10.1111/1574-6976.12026. Epub 2013 Jul 25. Review. PubMed PMID: 23802986; PubMed Central PMCID: PMC3791156.

Pinilla C, Edwards BS, Appel JR, Yates-Gibbins T, Giulianotti MA, Medina-Franco JL, Young SM, Santos RG, Sklar LA, Houghten RA. Selective agonists and antagonists of formylpeptide receptors: duplex flow cytometry and mixture-based positional scanning libraries. Mol Pharmacol. 2013 Sep;84(3):314-24. doi: 10.1124/mol.113.086595. Epub 2013 Jun 20. PubMed PMID: 23788657; PubMed Central PMCID: PMC3876812.

Santos RG, Appel JR, Giulianotti MA, Edwards BS, Sklar LA, Houghten RA, Pinilla C. The mathematics of a successful deconvolution: a quantitative assessment of mixture-based combinatorial libraries screened against two formylpeptide receptors. Molecules. 2013 May 30;18(6):6408-24. doi: 10.3390/molecules18066408. PubMed PMID: 23722730; PubMed Central PMCID: PMC4106117.

Medina-Franco JL, Edwards BS, Pinilla C, Appel JR, Giulianotti MA, Santos RG, Yongye AB, Sklar LA, Houghten RA. Rapid scanning structure-activity relationships in combinatorial data sets: identification of activity switches. J Chem Inf Model. 2013 Jun 24;53(6):1475-85. doi: 10.1021/ci400192y. Epub 2013 Jun 7. PubMed PMID: 23705689; PubMed Central PMCID: PMC3715655.

Jane Tseng Y, Martin E, G Bologa C, Shelat AA. Cheminformatics aspects of high throughput screening: from robots to models: symposium summary. J Comput Aided Mol Des. 2013 May;27(5):443-53. doi: 10.1007/s10822-013-9646-6. Epub 2013 May 1. PubMed PMID: 23636795; PubMed Central PMCID: PMC4205101.

Strouse JJ, Ivnitski-Steele I, Waller A, Young SM, Perez D, Evangelisti AM, Ursu O, Bologa CG, Carter MB, Salas VM, Tegos G, Larson RS, Oprea TI, Edwards BS, Sklar LA. Fluorescent substrates for flow cytometric evaluation of efflux inhibition in ABCB1, ABCC1, and ABCG2 transporters. Anal Biochem. 2013 Jun 1;437(1):77-87. doi: 10.1016/j.ab.2013.02.018. Epub 2013 Mar 5. PubMed PMID: 23470221; PubMed Central PMCID: PMC3785545.

Chibebe Junior J, Fuchs BB, Sabino CP, Junqueira JC, Jorge AO, Ribeiro MS, Gilmore MS, Rice LB, Tegos GP, Hamblin MR, Mylonakis E. Photodynamic and antibiotic therapy impair the pathogenesis of Enterococcus faecium in a whole animal insect model. PLoS One. 2013;8(2):e55926. doi: 10.1371/journal.pone.0055926. Epub 2013 Feb 14. PubMed PMID: 23457486; PubMed Central PMCID: PMC3573038.

Hong L, Kenney SR, Phillips GK, Simpson D, Schroeder CE, Nöth J, Romero E, Swanson S, Waller A, Strouse JJ, Carter M, Chigaev A, Ursu O, Oprea T, Hjelle B,  Golden JE, Aubé J, Hudson LG, Buranda T, Sklar LA, Wandinger-Ness A. Characterization of a Cdc42 protein inhibitor and its use as a molecular probe. J Biol Chem. 2013 Mar 22;288(12):8531-43. doi: 10.1074/jbc.M112.435941. Epub 2013 Feb 4. Erratum in: J Biol Chem. 2014 Mar 7;289(10):6837. PubMed PMID: 23382385; PubMed Central PMCID: PMC3605667.

Prates RA, Fuchs BB, Mizuno K, Naqvi Q, Kato IT, Ribeiro MS, Mylonakis E, Tegos GP, Hamblin MR. Effect of virulence factors on the photodynamic inactivation of Cryptococcus neoformans. PLoS One. 2013;8(1):e54387. doi: 10.1371/journal.pone.0054387. Epub 2013 Jan 18. PubMed PMID: 23349872; PubMed Central PMCID: PMC3548784.

Wu Y, Tapia PH, Fisher GW, Waggoner AS, Jarvik J, Sklar LA. High-throughput flow cytometry compatible biosensor based on fluorogen activating protein technology. Cytometry A. 2013 Feb;83(2):220-6. doi: 10.1002/cyto.a.22242. Epub 2013 Jan 9. PubMed PMID: 23303704; PubMed Central PMCID: PMC3621705.

Manallack DT, Prankerd RJ, Nassta GC, Ursu O, Oprea TI, Chalmers DK. A chemogenomic analysis of ionization constants–implications for drug discovery. ChemMedChem. 2013 Feb;8(2):242-55. doi: 10.1002/cmdc.201200507. Epub 2013 Jan 9.  PubMed PMID: 23303535; PubMed Central PMCID: PMC3777741.

2012

Return to Top
Florian AE, Lepensky CK, Kwon O, Haynes MK, Sklar LA, Zweifach A. Flow cytometry enables a high-throughput homogeneous fluorescent antibody-binding assay for cytotoxic T cell lytic granule exocytosis. J Biomol Screen. 2013 Apr;18(4):420-9. doi: 10.1177/1087057112466697. Epub 2012 Nov 15. PubMed PMID: 23160568; PubMed Central PMCID: PMC4043149.

Kato IT, Prates RA, Sabino CP, Fuchs BB, Tegos GP, Mylonakis E, Hamblin MR, Ribeiro MS. Antimicrobial photodynamic inactivation inhibits Candida albicans virulence factors and reduces in vivo pathogenicity. Antimicrob Agents Chemother. 2013 Jan;57(1):445-51. doi: 10.1128/AAC.01451-12. Epub 2012 Nov 5. PubMed PMID: 23129051; PubMed Central PMCID: PMC3535901.

Williamson EA, Damiani L, Leitao A, Hu C, Hathaway H, Oprea T, Sklar L, Shaheen M, Bauman J, Wang W, Nickoloff JA, Lee SH, Hromas R. Targeting the transposase domain of the DNA repair component Metnase to enhance chemotherapy. Cancer Res. 2012 Dec 1;72(23):6200-8. doi: 10.1158/0008-5472.CAN-12-0313. Epub 2012 Oct 22. PubMed PMID: 23090115; PubMed Central PMCID: PMC3972061.

Custodi C, Nuti R, Oprea TI, Macchiarulo A. Fitting the complexity of GPCRs modulation into simple hypotheses of ligand design. J Mol Graph Model. 2012 Sep;38:70-81. doi: 10.1016/j.jmgm.2012.07.002. Epub 2012 Jul 20. PubMed PMID: 23079642; PubMed Central PMCID: PMC3508176.

Dai T, Murray CK, Vrahas MS, Baer DG, Tegos GP, Hamblin MR. Ultraviolet C light for Acinetobacter baumannii wound infections in mice: potential use for battlefield wound decontamination? J Trauma Acute Care Surg. 2012 Sep;73(3):661-7. PubMed PMID: 22929495; PubMed Central PMCID: PMC3463377.

Strouse JJ, Ivnitski-Steele I, Khawaja HM, Perez D, Ricci J, Yao T, Weiner WS, Schroeder CE, Simpson DS, Maki BE, Li K, Golden JE, Foutz TD, Waller A, Evangelisti AM, Young SM, Chavez SE, Garcia MJ, Ursu O, Bologa CG, Carter MB, Salas VM, Gouveia K, Tegos GP, Oprea TI, Edwards BS, Aubé J, Larson RS, Sklar LA. A selective ATP-binding cassette subfamily G member 2 efflux inhibitor revealed via high-throughput flow cytometry. J Biomol Screen. 2013 Jan;18(1):26-38. doi: 10.1177/1087057112456875. Epub 2012 Aug 24. PubMed PMID: 22923785; PubMed Central PMCID: PMC3623016.

Thal DM, Homan KT, Chen J, Wu EK, Hinkle PM, Huang ZM, Chuprun JK, Song J, Gao E, Cheung JY, Sklar LA, Koch WJ, Tesmer JJ. Paroxetine is a direct inhibitor  of g protein-coupled receptor kinase 2 and increases myocardial contractility. ACS Chem Biol. 2012 Nov 16;7(11):1830-9. doi: 10.1021/cb3003013. Epub 2012 Aug 21. PubMed PMID: 22882301; PubMed Central PMCID: PMC3500392.

Oprea TI, Mestres J. Drug repurposing: far beyond new targets for old drugs.  AAPS J. 2012 Dec;14(4):759-63. doi: 10.1208/s12248-012-9390-1. Epub 2012 Jul 24.  PubMed PMID: 22826034; PubMed Central PMCID: PMC3475856.

Bologa CG, Oprea TI. Compound collection preparation for virtual screening. Methods Mol Biol. 2012;910:125-43. doi: 10.1007/978-1-61779-965-5_7. PubMed PMID: 22821595.

Polireddy K, Khan MM, Chavan H, Young S, Ma X, Waller A, Garcia M, Perez D, Chavez S, Strouse JJ, Haynes MK, Bologa CG, Oprea TI, Tegos GP, Sklar LA, Krishnamurthy P. A novel flow cytometric HTS assay reveals functional modulators  of ATP binding cassette transporter ABCB6. PLoS One. 2012;7(7):e40005. doi: 10.1371/journal.pone.0040005. Epub 2012 Jul 10. PubMed PMID: 22808084; PubMed Central PMCID: PMC3393737.

Wu Y, Tapia PH, Fisher GW, Simons PC, Strouse JJ, Foutz T, Waggoner AS, Jarvik J, Sklar LA. Discovery of regulators of receptor internalization with high-throughput flow cytometry. Mol Pharmacol. 2012 Oct;82(4):645-57. Epub 2012 Jul 5. PubMed PMID: 22767611; PubMed Central PMCID: PMC3463215.

Dai T, Fuchs BB, Coleman JJ, Prates RA, Astrakas C, St Denis TG, Ribeiro MS,  Mylonakis E, Hamblin MR, Tegos GP. Concepts and principles of photodynamic therapy as an alternative antifungal discovery platform. Front Microbiol. 2012 Apr 10;3:120. doi: 10.3389/fmicb.2012.00120. eCollection 2012. PubMed PMID: 22514547; PubMed Central PMCID: PMC3322354.

Agola JO, Hong L, Surviladze Z, Ursu O, Waller A, Strouse JJ, Simpson DS, Schroeder CE, Oprea TI, Golden JE, Aubé J, Buranda T, Sklar LA, Wandinger-Ness A. A competitive nucleotide binding inhibitor: in vitro characterization of Rab7 GTPase inhibition. ACS Chem Biol. 2012 Jun 15;7(6):1095-108. doi: 10.1021/cb3001099. Epub 2012 Apr 23. PubMed PMID: 22486388; PubMed Central PMCID: PMC3440014.

Edwards BS, Zhu J, Chen J, Carter MB, Thal DM, Tesmer JJ, Graves SW, Sklar LA. Cluster cytometry for high-capacity bioanalysis. Cytometry A. 2012 May;81(5):419-29. doi: 10.1002/cyto.a.22039. Epub 2012 Mar 21. PubMed PMID: 22438314; PubMed Central PMCID: PMC3331957.

2011

Return to Top
Oprea TI, Nielsen SK, Ursu O, Yang JJ, Taboureau O, Mathias SL, Kouskoumvekaki L, Sklar LA, Bologa CG. Associating Drugs, Targets and Clinical Outcomes into an Integrated Network Affords a New Platform for Computer-Aided Drug Repurposing. Mol Inform. 2011 Mar 14;30(2-3):100-111. PubMed PMID: 22287994; PubMed Central PMCID: PMC3266123.

Broccatelli F, Larregieu CA, Cruciani G, Oprea TI, Benet LZ. Improving the prediction of the brain disposition for orally administered drugs using BDDCS. Adv Drug Deliv Rev. 2012 Jan;64(1):95-109. doi: 10.1016/j.addr.2011.12.008. Epub  2011 Dec 21. Review. PubMed PMID: 22261306; PubMed Central PMCID: PMC3496430.

Chen J, Young SM, Allen C, Seeber A, Péli-Gulli MP, Panchaud N, Waller A, Ursu O, Yao T, Golden JE, Strouse JJ, Carter MB, Kang H, Bologa CG, Foutz TD, Edwards BS, Peterson BR, Aubé J, Werner-Washburne M, Loewith RJ, De Virgilio C, Sklar LA. Identification of a small molecule yeast TORC1 inhibitor with a multiplex screen based on flow cytometry. ACS Chem Biol. 2012 Apr 20;7(4):715-22. doi: 10.1021/cb200452r. Epub 2012 Feb 1. PubMed PMID: 22260433; PubMed Central PMCID: PMC3331904.

Vera DM, Haynes MH, Ball AR, Dai T, Astrakas C, Kelso MJ, Hamblin MR, Tegos GP. Strategies to potentiate antimicrobial photoinactivation by overcoming resistant phenotypes. Photochem Photobiol. 2012 May-Jun;88(3):499-511. doi: 10.1111/j.1751-1097.2012.01087.x. Epub 2012 Feb 13. Review. PubMed PMID: 22242675; PubMed Central PMCID: PMC3345078.

Broccatelli F, Cruciani G, Benet LZ, Oprea TI. BDDCS class prediction for new molecular entities. Mol Pharm. 2012 Mar 5;9(3):570-80. doi: 10.1021/mp2004302. Epub 2012 Feb 7. PubMed PMID: 22224483; PubMed Central PMCID: PMC3295927.

Chan CY, Prudom C, Raines SM, Charkhzarrin S, Melman SD, De Haro LP, Allen C, Lee SA, Sklar LA, Parra KJ. Inhibitors of V-ATPase proton transport reveal uncoupling functions of tether linking cytosolic and membrane domains of V0 subunit a (Vph1p). J Biol Chem. 2012 Mar 23;287(13):10236-50. doi: 10.1074/jbc.M111.321133. Epub 2012 Jan 3. PubMed PMID: 22215674; PubMed Central PMCID: PMC3323027.

Oprea TI, Taboureau O, Bologa CG. Of possible cheminformatics futures. J Comput Aided Mol Des. 2012 Jan;26(1):107-12. doi: 10.1007/s10822-011-9535-9. Epub 2011 Dec 30. PubMed PMID: 22207193.

Holmes AR, Keniya MV, Ivnitski-Steele I, Monk BC, Lamping E, Sklar LA, Cannon RD. The monoamine oxidase A inhibitor clorgyline is a broad-spectrum inhibitor of fungal ABC and MFS transporter efflux pump activities which reverses the azole resistance of Candida albicans and Candida glabrata clinical isolates. Antimicrob Agents Chemother. 2012 Mar;56(3):1508-15. doi: 10.1128/AAC.05706-11. Epub 2011 Dec 27. PubMed PMID: 22203607; PubMed Central PMCID: PMC3294898.

Surviladze Z, Young SM, Sklar LA. High-throughput flow cytometry bead-based multiplex assay for identification of Rho GTPase inhibitors. Methods Mol Biol. 2012;827:253-70. doi: 10.1007/978-1-61779-442-1_17. PubMed PMID: 22144280; PubMed Central PMCID: PMC4467469.

Zwartz GJ, Chigaev A, Foutz TD, Edwards B, Sklar LA. A miniature Couette to generate shear for flow cytometry: studying real-time modulation of intracellular calcium in monocytic cells. Cytometry A. 2011 Mar;79(3):233-40. doi: 10.1002/cyto.a.21027. Epub 2011 Feb 10. PubMed PMID: 22045643; PubMed Central PMCID: PMC3584716.

Mestres J, Seifert SA, Oprea TI. Linking pharmacology to clinical reports: cyclobenzaprine and its possible association with serotonin syndrome. Clin Pharmacol Ther. 2011 Nov;90(5):662-5. doi:  0.1038/clpt.2011.177. Epub 2011 Oct 5. PubMed PMID: 21975349; PubMed Central PMCID:  PMC3809033.

St Denis TG, Dai T, Izikson L, Astrakas C, Anderson RR, Hamblin MR, Tegos GP. All you need is light: antimicrobial photoinactivation as an evolving and emerging discovery strategy against infectious disease. Virulence. 2011 Nov-Dec;2(6):509-20. doi: 10.4161/viru.2.6.17889. Epub 2011 Nov 1. Review. PubMed PMID: 21971183; PubMed Central PMCID: PMC3260545.

Chigaev A, Winter SS, Sklar LA. Is prolonged stem cell mobilization detrimental for hematopoiesis? Med Hypotheses. 2011 Dec;77(6):1111-3. doi: 10.1016/j.mehy.2011.09.015. Epub 2011 Oct 2. PubMed PMID: 21963354; PubMed Central PMCID: PMC3210378.

Chen J, Carter MB, Edwards BS, Cai H, Sklar LA. High throughput flow cytometry based yeast two-hybrid array approach for large-scale analysis of protein-protein interactions. Cytometry A. 2012 Jan;81(1):90-8. doi: 10.1002/cyto.a.21144. Epub 2011 Sep 27. PubMed PMID: 21954189; PubMed Central PMCID: PMC3250062.

Dai T, Bil de Arce VJ, Tegos GP, Hamblin MR. Blue dye and red light, a dynamic combination for prophylaxis and treatment of cutaneous Candida albicans infections in mice. Antimicrob Agents Chemother. 2011 Dec;55(12):5710-7. doi: 10.1128/AAC.05404-11. Epub 2011 Sep 19. PubMed PMID: 21930868; PubMed Central PMCID: PMC3232820.

Chigaev A, Sklar LA. Overview: assays for studying integrin-dependent cell adhesion. Methods Mol Biol. 2012;757:3-14. doi: 10.1007/978-1-61779-166-6_1. Review. PubMed PMID: 21909902; PubMed Central PMCID: PMC3805125.

Briansó F, Carrascosa MC, Oprea TI, Mestres J. Cross-pharmacology analysis of G protein-coupled receptors. Curr Top Med Chem. 2011;11(15):1956-63. PubMed PMID: 21851335; PubMed Central PMCID: PMC3717414.

Benet LZ, Broccatelli F, Oprea TI. BDDCS applied to over 900 drugs. AAPS J. 2011 Dec;13(4):519-47. doi: 10.1208/s12248-011-9290-9. Epub 2011 Aug 5. PubMed PMID: 21818695; PubMed Central PMCID: PMC3231854.

Dennis MK, Field AS, Burai R, Ramesh C, Petrie WK, Bologa CG, Oprea TI, Yamaguchi Y, Hayashi S, Sklar LA, Hathaway HJ, Arterburn JB, Prossnitz ER. Identification of a GPER/GPR30 antagonist with improved estrogen receptor counterselectivity. J Steroid Biochem Mol Biol. 2011 Nov;127(3-5):358-66. doi: 10.1016/j.jsbmb.2011.07.002. Epub 2011 Jul 14. PubMed PMID: 21782022; PubMed Central PMCID: PMC3220788.

Simons PC, Young SM, Carter MB, Waller A, Zhai D, Reed JC, Edwards BS, Sklar LA. Simultaneous in vitro molecular screening of protein-peptide interactions by flow cytometry, using six Bcl-2 family proteins as examples. Nat Protoc. 2011 Jun 9;6(7):943-52. doi: 10.1038/nprot.2011.339. PubMed PMID: 21720309; PubMed Central PMCID: PMC3646541.

Ostopovici-Halip L, Curpăn R, Mracec M, Bologa CG. Structural determinants of the alpha2 adrenoceptor subtype selectivity. J Mol Graph Model. 2011 Aug;29(8):1030-8. doi: 10.1016/j.jmgm.2011.04.011. Epub 2011 May 6. PubMed PMID:  21602069; PubMed Central PMCID: PMC3307019.

Chigaev A, Smagley Y, Zhang Y, Waller A, Haynes MK, Amit O, Wang W, Larson RS, Sklar LA. Real-time analysis of the inside-out regulation of lymphocyte function-associated antigen-1 revealed similarities to and differences from very  late antigen-4. J Biol Chem. 2011 Jun 10;286(23):20375-86. doi: 10.1074/jbc.M110.206185. Epub 2011 Apr 22. PubMed PMID: 21515675; PubMed Central  PMCID: PMC3121518.

Fiamegos YC, Kastritis PL, Exarchou V, Han H, Bonvin AM, Vervoort J, Lewis K, Hamblin MR, Tegos GP. Antimicrobial and efflux pump inhibitory activity of caffeoylquinic acids from Artemisia absinthium against gram-positive pathogenic bacteria. PLoS One. 2011 Apr 4;6(4):e18127. doi: 10.1371/journal.pone.0018127. PubMed PMID: 21483731; PubMed Central PMCID: PMC3070693.

Tegos GP, Haynes M, Strouse JJ, Khan MM, Bologa CG, Oprea TI, Sklar LA. Microbial efflux pump inhibition: tactics and strategies. Curr Pharm Des. 2011;17(13):1291-302. Review. PubMed PMID: 21470111; PubMed Central PMCID: PMC3717411.

Evdokimov NM, Van Slambrouck S, Heffeter P, Tu L, Le Calvé B, Lamoral-Theys D, Hooten CJ, Uglinskii PY, Rogelj S, Kiss R, Steelant WF, Berger W, Yang JJ, Bologa CG, Kornienko A, Magedov IV. Structural simplification of bioactive natural products with multicomponent synthesis. 3. Fused uracil-containing heterocycles as novel topoisomerase-targeting agents. J Med Chem. 2011 Apr 14;54(7):2012-21. doi: 10.1021/jm1009428. Epub 2011 Mar 9. PubMed PMID: 21388138; PubMed Central PMCID: PMC3087497.

Broccatelli F, Carosati E, Neri A, Frosini M, Goracci L, Oprea TI, Cruciani G. A novel approach for predicting P-glycoprotein (ABCB1) inhibition using molecular interaction fields. J Med Chem. 2011 Mar 24;54(6):1740-51. doi: 10.1021/jm101421d. Epub 2011 Feb 22. PubMed PMID: 21341745; PubMed Central PMCID: PMC3069647.

Hwang I, Ki D. Receptor-mediated T cell absorption of antigen presenting cell-derived molecules. Front Biosci (Landmark Ed). 2011 Jan 1;16:411-21. Review. PubMed PMID: 21196178; PubMed Central PMCID: PMC3057749.

2010

Return to Top
Chigaev A, Wu Y, Williams DB, Smagley Y, Sklar LA. Discovery of very late antigen-4 (VLA-4, alpha4beta1 integrin) allosteric antagonists. J Biol Chem. 2011 Feb 18;286(7):5455-63. doi: 10.1074/jbc.M110.162636. Epub 2010 Dec 3. PubMed PMID: 21131351; PubMed Central PMCID: PMC3037658.

Buranda T, Wu Y, Sklar LA. Quantum dots for quantitative flow cytometry. Methods Mol Biol. 2011;699:67-84. doi: 10.1007/978-1-61737-950-5_4. PubMed PMID:  21116979; PubMed Central PMCID: PMC4388555.

Saunders MJ, Edwards BS, Zhu J, Sklar LA, Graves SW. Microsphere-based flow cytometry protease assays for use in protease activity detection and high-throughput screening. Curr Protoc Cytom. 2010 Oct;Chapter 13:Unit 13.12.1-17. doi: 10.1002/0471142956.cy1312s54. PubMed PMID: 20938917; PubMed Central PMCID: PMC4486899.

Oprea TI, May EE, Leitão A, Tropsha A. Computational systems chemical biology. Methods Mol Biol. 2011;672:459-88. doi: 10.1007/978-1-60761-839-3_18. Review. PubMed PMID: 20838980; PubMed Central PMCID: PMC3547368.

Ursu O, Oprea TI. Model-free drug-likeness from fragments. J Chem Inf Model.  2010 Aug 23;50(8):1387-94. doi: 10.1021/ci100202p. PubMed PMID: 20726597.

Slack JP, Brockhoff A, Batram C, Menzel S, Sonnabend C, Born S, Galindo MM, Kohl S, Thalmann S, Ostopovici-Halip L, Simons CT, Ungureanu I, Duineveld K, Bologa CG, Behrens M, Furrer S, Oprea TI, Meyerhof W. Modulation of bitter taste  perception by a small molecule hTAS2R antagonist. Curr Biol. 2010 Jun 22;20(12):1104-9. doi: 10.1016/j.cub.2010.04.043. Epub 2010 May 27. PubMed PMID: 20537538; PubMed Central PMCID: PMC2925244.

Nayak TK, Dennis MK, Ramesh C, Burai R, Atcher RW, Sklar LA, Norenberg JP, Hathaway HJ, Arterburn JB, Prossnitz ER. Influence of charge on cell permeability and tumor imaging of GPR30-targeted 111in-labeled nonsteroidal imaging agents. ACS Chem Biol. 2010 Jul 16;5(7):681-90. doi: 10.1021/cb1000636. PubMed PMID: 20486699; PubMed Central PMCID: PMC2912446.

Burai R, Ramesh C, Shorty M, Curpan R, Bologa C, Sklar LA, Oprea T, Prossnitz ER, Arterburn JB. Highly efficient synthesis and characterization of the GPR30-selective agonist G-1 and related tetrahydroquinoline analogs. Org Biomol Chem. 2010 May 7;8(9):2252-9. doi: 10.1039/c001307b. Epub 2010 Mar 16. PubMed PMID: 20401403; PubMed Central PMCID: PMC2913306.

Wetzel S, Wilk W, Chammaa S, Sperl B, Roth AG, Yektaoglu A, Renner S, Berg T, Arenz C, Giannis A, Oprea TI, Rauh D, Kaiser M, Waldmann H. A scaffold-tree-merging strategy for prospective bioactivity annotation of gamma-pyrones. Angew Chem Int Ed Engl. 2010 May 10;49(21):3666-70. doi: 10.1002/anie.200906555. PubMed PMID: 20394088.

Buranda T, Wu Y, Perez D, Jett SD, BonduHawkins V, Ye C, Edwards B, Hall P, Larson RS, Lopez GP, Sklar LA, Hjelle B. Recognition of decay accelerating factor and alpha(v)beta(3) by inactivated hantaviruses: Toward the development of high-throughput screening flow cytometry assays. Anal Biochem. 2010 Jul 15;402(2):151-60. doi: 10.1016/j.ab.2010.03.016. Epub 2010 Apr 2. PubMed PMID: 20363206; PubMed Central PMCID: PMC2905740.

Garcia-Serna R, Ursu O, Oprea TI, Mestres J. iPHACE: integrative navigation in pharmacological space. Bioinformatics. 2010 Apr 1;26(7):985-6. doi: 10.1093/bioinformatics/btq061. Epub 2010 Feb 15. PubMed PMID: 20156991; PubMed Central PMCID: PMC2844997.

Ariazi EA, Brailoiu E, Yerrum S, Shupp HA, Slifker MJ, Cunliffe HE, Black MA, Donato AL, Arterburn JB, Oprea TI, Prossnitz ER, Dun NJ, Jordan VC. The G protein-coupled receptor GPR30 inhibits proliferation of estrogen receptor-positive breast cancer cells. Cancer Res. 2010 Feb 1;70(3):1184-94. doi: 10.1158/0008-5472.CAN-09-3068. Epub 2010 Jan 19. PubMed PMID: 20086172; PubMed Central PMCID: PMC2879282.

Broccatelli F, Carosati E, Cruciani G, Oprea TI. Transporter-mediated Efflux  Influences CNS Side Effects: ABCB1, from Antitarget to Target. Mol Inform. 2010 Jan 12;29(1-2):16-26. PubMed PMID: 22347894; PubMed Central PMCID: PMC3281213.

Ramesh C, Nayak TK, Burai R, Dennis MK, Hathaway HJ, Sklar LA, Prossnitz ER,  Arterburn JB. Synthesis and characterization of iodinated tetrahydroquinolines targeting the G protein-coupled estrogen receptor GPR30. J Med Chem. 2010 Feb 11;53(3):1004-14. doi: 10.1021/jm9011802. PubMed PMID: 20041667; PubMed Central PMCID: PMC2818973.

Saunders MJ, Graves SW, Sklar LA, Oprea TI, Edwards BS. High-throughput multiplex flow cytometry screening for botulinum neurotoxin type a light chain protease inhibitors. Assay Drug Dev Technol. 2010 Feb;8(1):37-46. doi: 10.1089/adt.2009.0219. PubMed PMID: 20035615; PubMed Central PMCID: PMC3096553.

Johnson RM, Allen C, Melman SD, Waller A, Young SM, Sklar LA, Parra KJ. Identification of inhibitors of vacuolar proton-translocating ATPase pumps in yeast by high-throughput screening flow cytometry. Anal Biochem. 2010 Mar 15;398(2):203-11. doi: 10.1016/j.ab.2009.12.020. Epub 2009 Dec 14. PubMed PMID: 20018164; PubMed Central PMCID: PMC2853757.

2009

Return to Top
Surviladze Z, Waller A, Wu Y, Romero E, Edwards BS, Wandinger-Ness A, Sklar LA. Identification of a small GTPase inhibitor using a high-throughput flow cytometry bead-based multiplex assay. J Biomol Screen. 2010 Jan;15(1):10-20. doi: 10.1177/1087057109352240. Epub 2009 Dec 11. PubMed PMID: 20008126; PubMed Central PMCID: PMC3433230.

Arterburn JB, Oprea TI, Prossnitz ER, Edwards BS, Sklar LA. Discovery of selective probes and antagonists for G-protein-coupled receptors FPR/FPRL1 and GPR30. Curr Top Med Chem. 2009;9(13):1227-36. Review. PubMed PMID: 19807662; PubMed Central PMCID: PMC2885834.

Ivnitski-Steele I, Holmes AR, Lamping E, Monk BC, Cannon RD, Sklar LA. Identification of Nile red as a fluorescent substrate of the Candida albicans ATP-binding cassette transporters Cdr1p and Cdr2p and the major facilitator superfamily transporter Mdr1p. Anal Biochem. 2009 Nov 1;394(1):87-91. doi: 10.1016/j.ab.2009.07.001. Epub 2009 Jul 3. PubMed PMID: 19577533; PubMed Central PMCID: PMC2739806.

Wetzel S, Klein K, Renner S, Rauh D, Oprea TI, Mutzel P, Waldmann H. Interactive exploration of chemical space with Scaffold Hunter. Nat Chem Biol. 2009 Aug;5(8):581-3. doi: 10.1038/nchembio.187. Epub 2009 Jun 28. Erratum in: Nat Chem Biol. 2009 Sep;5(9):696. PubMed PMID: 19561620.

Renner S, van Otterlo WA, Dominguez Seoane M, Möcklinghoff S, Hofmann B, Wetzel S, Schuffenhauer A, Ertl P, Oprea TI, Steinhilber D, Brunsveld L, Rauh D,  Waldmann H. Bioactivity-guided mapping and navigation of chemical space. Nat Chem Biol. 2009 Aug;5(8):585-92. doi: 10.1038/nchembio.188. Epub 2009 Jun 28. PubMed PMID: 19561619.

Oprea TI, Bologa CG, Boyer S, Curpan RF, Glen RC, Hopkins AL, Lipinski CA, Marshall GR, Martin YC, Ostopovici-Halip L, Rishton G, Ursu O, Vaz RJ, Waller C,  Waldmann H, Sklar LA. A crowdsourcing evaluation of the NIH chemical probes. Nat  Chem Biol. 2009 Jul;5(7):441-7. doi: 10.1038/nchembio0709-441. Erratum in: Nat Chem Biol. 2009 Aug;5(8):600. PubMed PMID: 19536101; PubMed Central PMCID: PMC3596119.

Haynes MK, Strouse JJ, Waller A, Leitao A, Curpan RF, Bologa C, Oprea TI, Prossnitz ER, Edwards BS, Sklar LA, Thompson TA. Detection of intracellular granularity induction in prostate cancer cell lines by small molecules using the  HyperCyt high-throughput flow cytometry system. J Biomol Screen. 2009 Jul;14(6):596-609. doi: 10.1177/1087057109335671. Epub 2009 May 21. PubMed PMID:  19470718; PubMed Central PMCID: PMC3666167.

Prossnitz ER, Maggiolini M. Mechanisms of estrogen signaling and gene expression via GPR30. Mol Cell Endocrinol. 2009 Sep 24;308(1-2):32-8. doi: 10.1016/j.mce.2009.03.026. Epub 2009 Apr 15. Review. PubMed PMID: 19464786; PubMed Central PMCID: PMC2847286.

Prossnitz ER, Barton M. Signaling, physiological functions and clinical relevance of the G protein-coupled estrogen receptor GPER. Prostaglandins Other Lipid Mediat. 2009 Sep;89(3-4):89-97. doi: 10.1016/j.prostaglandins.2009.05.001.  Epub 2009 May 13. Review. PubMed PMID: 19442754; PubMed Central PMCID: PMC2740807.

Dennis MK, Burai R, Ramesh C, Petrie WK, Alcon SN, Nayak TK, Bologa CG, Leitao A, Brailoiu E, Deliu E, Dun NJ, Sklar LA, Hathaway HJ, Arterburn JB, Oprea TI, Prossnitz ER. In vivo effects of a GPR30 antagonist. Nat Chem Biol. 2009 Jun;5(6):421-7. doi: 10.1038/nchembio.168. PubMed PMID: 19430488; PubMed Central  PMCID: PMC2864230.

Rosén J, Gottfries J, Muresan S, Backlund A, Oprea TI. Novel chemical space  exploration via natural products. J Med Chem. 2009 Apr 9;52(7):1953-62. doi: 10.1021/jm801514w. PubMed PMID: 19265440; PubMed Central PMCID: PMC2696019.

2008

Return to Top
Wester MJ, Pollock SN, Coutsias EA, Allu TK, Muresan S, Oprea TI. Scaffold topologies. 2. Analysis of chemical databases. J Chem Inf Model. 2008 Jul;48(7):1311-24. doi: 10.1021/ci700342h. Epub 2008 Jul 8. PubMed PMID: 18605681; PubMed Central PMCID: PMC2807378.

Pollock SN, Coutsias EA, Wester MJ, Oprea TI. Scaffold topologies. 1. Exhaustive enumeration up to eight rings. J Chem Inf Model. 2008 Jul;48(7):1304-10. doi: 10.1021/ci7003412. Epub 2008 Jul 8. PubMed PMID: 18605680; PubMed Central PMCID: PMC2734505.

University of New Mexico flow cytometry research center