UNM HSC School of Medicine

Division of Biocomputing

 

Dr. Tudor I. Oprea

Professor Biochemistry and Molecular Biology (BMB)

University of New Mexico School of Medicine, Albuquerque, New Mexico, United States

Born: 1965, Timisoara, Romania

Email: toprea_at_salud_dot_unm_dot_edu

Institution web page: http://hsc.unm.edu/som/
 

Company web page:www.sunsetmolecular.com
 

Interests: Drug Discovery, Drug Informatics, Cheminformatics, Machine Learning and QSAR, Lead and Probe Identification

Details:

Active research interest in drug discovery, with focus on drug informatics, cheminformatics, virtual screening and drug informatics. Special focus on supporting high throughput flow cytometry, cancer biology, systems chemical biology and target informatics.

Prior work experience includes: Cytochrome P450 (and aromatase), G-protein coupled receptors (and beta-adrenoceptors), Scoring Functions, Lead-like space, Chemical Space Navigation (ChemGPS).
Chair of the Cheminformatics and QSAR society, http://www.qsar.org/ .
Recipient of the 2002 Hansch Award from the QSAR and Modelling Society. http://www.qsar.org/news/oprea.htm
Member of Editorial board for ChemMedChem, J Mol Graph Model, J. Chem. Info Model and QSAR Combi Sci.
Scientific advisory board member to ChemDiv

Talks:
• August 29, 2002 at UNM on Strategies for Virtual Screening and Chemical Space Navigation
• October 2003 at UNM on Cytochrome P450s in Metabolism and Disease
• May 2004 on Informatics - the Key to Preclinical Drug Discovery
• June 2004 on Integrated High-Throughput Virtual and Experimental Screening: An Academic Approach
• September 2004 on Mining Large Chemical Spaces in Lead and Drug Discovery
• September 12 2004 on Understanding the Chemistry: Biology Interface
• April 22 2005 on Virtual Screening Technologies at UNM: An Overview
 

Selected Pictures of New Mexico Click here
 

Text Book publications:
• T.I. Oprea (Editor). Chemoinformatics in Drug Discovery. Wiley-VCH, New York, 2005 (January). ISBN: 3-527-30753-2.
 

Selected publications:

•S.M. Young, C.G. Bologa, D. Fara, Bj.K. Bryant, J.J. Strouse, J.B. Arterburn, R.D. Ye, T.I. Oprea, E.R. Prossnitz, L.A. Sklar, B.S. Edwards. Duplex high-throughput flow cytometry screen identifies two novel formylpeptide receptor family probes. Cytometry 75A:253-263, 2009

•J. Rosén, J. Gottfries, S. Muresan, A. Backlund, T.I. Oprea. Novel Chemical Space Exploration via Natural Products. J. Med. Chem., 52: 1953–1962, 2009

•M. Dennis, R. Burai, C. Ramesh, W. Petrie, S. Alcon, T. Nayak, C. Bologa, A. Leitão, E. Brailoiu, E. Deliu, N.S. Dun, L.A. Sklar, H. Hathaway, J.B. Arterburn, T.I. Oprea, E.R. Prossnitz. In vivo Effects of a GPR30 Antagonist. Nature Chem. Biol., 5:421-427, 2009

•S.L. Dun, G.C. Brailoiu, X. Gao, E. Brailoiu, J.B. Arterburn, E.R. Prossnitz, T.I. Oprea, N.S. Dun. Expression of estrogen receptor GPR30 in the rat spinal cord and in autonomic and sensory ganglia. J. Neurosci. Res., 87:1610-1619, 2009

•T.I. Oprea, C.G. Bologa, S. Boyer, R.F. Curpan, R.C. Glen, A.L. Hopkins, C.A. Lipinski, G.R. Marshall, Y.C. Martin, L. Ostopovici-Halip, G. Rishton, B.K. Shoichet, O. Ursu, R.J. Vaz, C.L. Waller, H. Waldmann, L.A. Sklar. A crowdsourcing evaluation of the NIH chemical probes. Nature Chem. Biol., 5:441-447, 2009

•R.F. Freitas, T.I. Oprea, C.A. Montanari. 2D QSAR and similarity studies on cruzain inhibitors aimed at improving selectivity over cathepsin L. Bioorganic Med. Chem., 16:838-853, 2008

•Q. Li, F.S. Jorgensen, T.I. Oprea, S. Brunak, O. Taboureau. hERG Classification Model Based on a Combination of Support Vector Machine Method and GRIND Descriptors. Mol. Pharmaceutics, 5:117-127, 2008

•E.R. Prossnitz, J.B. Arterburn, H.O. Smith, T.I. Oprea, L.A. Sklar, HJ. Hathaway. Estrogen signaling through the transmembrane G protein–coupled receptor GPR30. Annu. Rev. Physiol., 70:165–190, 2008

•E.R. Prossnitz, L.A. Sklar, T.I. Oprea, J.B. Arterburn. GPR30: a novel therapeutic target in estrogen-related disease. Trends Pharmacol. Sci., 29:116–123, 2008

•E.R. Prossnitz, T.I. Oprea, L.A. Sklar, J.B. Arterburn. The ins and outs of GPR30: A transmembrane estrogen receptor. J. Steroid Biochem. Mol. Biol. 109:350-353, 2008

•S.S. Winter, D.M. Lovato, H.M. Khawaja, B.S. Edwards, I.D. Steele, S.M. Young, T.I. Oprea, L.A. Sklar, R.S. Larson. High-Throughput Screening for daunorubicin-mediated drug resistance identifies mometasone furoate as a novel ABCB1-reversal agent. J. Biomol. Screening, 13:185-193, 2008

•J. Hert, M.J. Keiser, J.J. Irwin, T.I. Oprea, B.K. Shoichet. Quantifying the relationships among drug classes. J. Chem. Info. Model. 48: 755 - 765, 2008

•I.D. Ivnitski-Steele, R.S. Larson, D.M. Lovato, H.M. Khawaja, S.S. Winter, T.I. Oprea, L.A. Sklar, B.S. Edwards. High-Throughput Flow Cytometry to Detect Selective Inhibitors of ABCB1, ABCC1, and ABCG2 Transporters. Assay Drug Dev. Technol., 6:255-262, 2008

•W.M. Brown, A. Sasson, D.R. Bellew, L.A. Hunsaker, S. Martin, A. Leitão, L.M. Deck, D.L. Vander Jagt, T.I. Oprea. Efficient Calculation of Molecular Properties from Simulation Using Kernel Molecular Dynamics. J.Chem. Inf. Model. 48:1626-1637, 2008

•L. Zhang, H. Zhu, T.I. Oprea, A. Golbraikh, A. Tropsha. QSAR modeling of the blood-brain barrier permeability for diverse organic compounds. Pharm. Research 25:1902 - 1914, 2008

•S.N. Pollock, E.A. Coutsias, M.J. Wester, T.I. Oprea. Scaffold Topologies. 1. Exhaustive enumeration up to eight rings. J. Chem. Info. Model. 48:1304 - 1310, 2008

•M.J. Wester, S.N. Pollock, E.A. Coutsias, T.K. Allu, S. Muresan, T.I. Oprea . Scaffold Topologies. 2. Analysis of chemical databases. J. Chem. Info. Model. 48:1311 - 1324, 2008

•A.C. Good, T.I. Oprea. Optimization of CAMD Techniques 3. Virtual Screening enrichment studies: A help or hindrance in tool selection? J. Comput. Aided Mol. Des. 22:169–178, 2008

•D. Hristozov, T.I. Oprea, J. Gasteiger. Ligand-Based Virtual Screening by Novelty Detection with Self-Organizing Maps. J. Chem. Inf. Model. , 47:2044-2062, 2007

•E.A. Ariazi, A. Leitão, T.I. Oprea, B. Chen, T. Louis, A.M. Bertucci, C.G. Sharma, S.D. Gill, H.R. Kim, H.A. Shupp, J.R. Pyle, A. Madrack, A.L. Donato, D. Cheng, J.R. Paige, V.C. Jordan. Exemestane's 17-hydroxylated metabolite exerts biological effects as an androgen. Mol. Cancer Therapeutics, 6:2817-2827, 2007

•T.I. Oprea, A. Tropsha, J.-L. Faulon, M.D. Rintoul. Systems chemical biology. Nature Chem. Biol. , 3, 447-450, 2007

•L. Albanito, A. Madeo, R. Lappano, A. Vivacqua, V. Rago, A. Carpino, T.I. Oprea, E.R. Prossnitz, A.M. Musti, S. Andò, M. Maggiolin. G Protein–Coupled Receptor 30 (GPR30) Mediates Gene Expression Changes and Growth Response to 17ß-Estradiol and Selective GPR30 Ligand G-1 in Ovarian Cancer Cells. Cancer Res., 67:1859-1866, 2007

•T.I. Oprea, T.K. Allu, D.C. Fara, R.F. Rad, L. Ostopovici, C.G. Bologa. Lead-like, drug-like or ‘‘Pub-like’’: how different are they? J. Comput. Aided Mol. Des., 21:113–119, 2007

•Hristozov D, Oprea TI, Gasteiger J.  Ligand-Based Virtual Screening by Novelty Detection with Self-Organizing Maps. J. Chem. Inf. Model. 47, 2044-2062, 2007.

•Oprea TI, Tropsha A, Faulon J-L, Rintoul MD. Systems chemical biology. Nature Chem. Biol.,  3, 447-450, 2007.

•Edwards BS, Young SM, Saunders MJ, Bologa C, Oprea TI, Ye RD, Prossnitz ER, Graves SW, Sklar LA.  High-throughput flow cytometry for drug discovery.  Expert Opin. Drug Discov. 2, 685-696, 2007.

•Paunescu V, Deak E, Herman D, Siska IR, Tanasie G, Bunu C, Anghel S, Tatu CA, Oprea TI, Henschler R, Ruester B, Bistrian R, Seifried E.  In vitro differentiation of human mesenchymal stem cells to epithelial lineage.  J. Cell. Mol. Medicine, 11, 502-508, 2007.

•Olah M, Rad R, Ostopovici L, Bora A, Hadaruga N, Hadaruga D, Moldovan R, Fulias A, Mracec M, Oprea TI.  WOMBAT and WOMBAT-PK: Bioactivity Databases for Lead and Drug Discovery. In Chemical Biology: From Small Molecules to Systems Biology and Drug Design, Schreiber SL, Kapoor TM, Wess G (Eds.), Wiley-VCH, pp 760-786, 2007.

•Exemestane's 17-hydroxylated metabolite exerts biological effects as an androgen
Eric A. Ariazi, Andrei Leitao, Tudor I. Oprea, Bin Chen, Teresa Louis, Anne Marie Bertucci, Catherine G.N. Sharma, Shaun D. Gill, Helen R. Kim, Heather A. Shupp, Jennifer R. Pyle, Alexis Madrack, Anne L. Donato, Dong Cheng, James R. Paige, and V. Craig Jordan
Mol Cancer Ther 2007 6: 2817-2827Published Online First November 7, 2007. doi: 10.1158/1535-7163.MCT-07-0312

•Eugen Brailoiu, Siok L Dun, G Cristina Brailoiu, Keisuke Mizuo, Larry A Sklar, Tudor I Oprea, Eric R Prossnitz and Nae J Dun   Distribution and characterization of estrogen receptor G protein-coupled receptor in the rat central nervous system   Journal of Endocrinology 193: 311-321 (2007).

• Scott W. Burchiel, Todd A. Thompson, Fredine T. Lauer, Tudor I. Oprea Activation of dioxin response element (DRE)-associated genes by benzo(a)pyrene 3,6-quinone and benzo(a)pyrene 1,6-quinone in MCF-10A human mammary epithelial cells Toxicology and Applied Pharmacology 221 (2007) 203–214

•Tudor I Oprea and Alexander Tropsha   Cheminformatics and drug discovery   Drug Discovery Today: Technologies 3 (4): 355-356 (2006).

•Tudor I Oprea and Alexander Tropsha   Target, chemical and bioactivity databases - integration is key   Drug Discovery Today: Technologies 3 (4): 357-365 (2006).

•Dan C Fara, Tudor I Oprea, Eric R Prossnitz, Cristian G Bologa, Bruce S Edwards and Larry A Sklar   Integration of virtual and physical screening   Drug Discovery Today: Technologies 2 (4): 377-385 (2006).

• Tudor I. Oprea, Tharun Kumar Allu, Dan C. Fara, Ramona F. Rad, Lili Ostopovici & Cristian G. Bologa Lead-like, Drug-like or "Pub-like": how different are they?  J. Comp. Aid. Mol. Design 21: 113-119, 2007.

• T.I. Oprea, A Tropsha. Target, chemical and bioactivity databases - integration is key. Drug Discov Today Technol. 2006, 3:357-365

• D.C. Fara, T.I. Oprea, E.R. Prossnitz, C.G. Bologa, B.S. Edwards, L.A. Sklar. Integration of virtual and physical screening. Drug Discov Today Technol. 2006, 3:377-385

• Bruce S Edwards, Susan M Young, Tudor I Oprea, Cristian G Bologa, Eric R Prossnitz & Larry A Sklar Biomolecular screening of formylpeptide receptor ligands with a sensitive, quantitative, high-throughput flow cytometry platform Protocol Online 2006.

• Cristian G Bologa, Chetana M Revankar, Susan M Young, Bruce S Edwards, Jeffrey B Arterburn, Alexander S Kiselyov, Matthew A Parker, Sergey E Tkachenko, Nikolay P Savchuck, Larry A Sklar, Tudor I Oprea and Eric R Prossnitz Virtual and biomolecular screening converge on a selective agonist for GPR30 Nature Chemical Biology 2:207-212, 2006.

• David G. Lloyd, Georgia Golfis, Andrew J. S. Knox, Darren Fayne, Mary J. Meegan and Tudor I. Oprea Oncology exploration: charting cancer medicinal chemistry space  DDT 11, Number 3/4, 2006.

• Cristian Bologa, Tharun Kumar Allu, Marius Olah, Michael A. Kappler & Tudor I. Oprea Descriptor collision and confusion: Toward the design of descriptors to mask chemical structures  J. Comp. Aid. Mol. Design, 19: 625-635, 2005.

• Igor V. Tetko, Ruben Abagyan & Tudor I. Oprea Surrogate data – a secure way to share corporate data J. Comp. Aid. Mol. Design, 19: 749-764, 2005.

• Bruce S. Edwards, Cristian Bologa, Susan M. Young, Konstantin V. Balakin, Eric R. Prossnitz, Nikolay P. Savchuck, Larry A. Sklar, and Tudor I. Oprea. Integration of Virtual Screening with High-Throughput Flow Cytometry to Identify Novel Small Molecule Formylpeptide Receptor Antagonists  Mol Pharmacol 68:1301–1310, 2005.

• Ludovic Kurunczi,Edward Seclaman,Tudor I. Oprea,Luminita Crisan and Zeno Simon . MTD-PLS: A PLS Variant of the Minimal Topologic Difference Method. III. Mapping Interactions between Estradiol Derivatives and the Alpha Estrogenic Receptor J. Chem. Inf. Model  45; 1275-1281 2005.

• Tharun Kumar Allu, Tudor I. Oprea Rapid Evaluation of Synthetic and Molecular Complexity for in Silico Chemistry  J. Chem. Inf. Model  45(5); 1237-1243 2005.

• Richard S. Larson, Terry Davis, Cristian Bologa, Gloria Semenuk, Sreejith Vijayan, Yu Li, Tudor Oprea, Alexandre Chigaev, Tione Buranda, Carston R. Wagner and Larry A. Sklar Dissociation of I Domain and Global Conformational Changes in LFA-1: Refinement of Small Molecule-I Domain Structure-Activity Relationships.Biochemistry 44, 4322-4331, 2005.

•  Tudor I. Oprea, Cristian G. Bologa, Bruce S. Edwards, Eric R. Prossnitz and Larry A. Sklar Post–High-Throughput Screening Analysis: An Empirical Compound Prioritization Scheme. Journal of Biomolecular Screening 10(5), 2005.

• Susan M. Young, Cristian Bologa, Eric R. Prossnitz, Tudor I. Oprea Larry A. Sklar and Bruce S. Edwards High-Throughput Screening with HyperCyt® Flow Cytometry to Detect SmallMolecule Formylpeptide Receptor Ligands. Journal of Biomolecular Screening 10(4), 2005.

• Marius Olah, Cristian Bologa and Tudor I. OpreaAn automated PLS search for biologically relevant QSAR descriptors. J. Comput.-Aided Mol. Design 18:437-449, 2004

• Marius M. Olah, Cristian G. Bologa and Tudor I. OpreaStrategies for Compound Selection. Current Drug Discovery Technologies 1:211-220, 2004

• Bruce S Edwards, Tudor Oprea, Eric R Prossnitz and Larry A Sklar Flow cytometry for high-throughput, high-content screening. Current Opinion in Chemical Biology 8:392-398, 2004

• Tudor I. Oprea and Hans Matter Integrating virtual screening in lead discovery. Current Opinion in Chemical Biology 8:349-358, 2004

• Tudor Oprea Next-generation therapeutics. Current Opinion in Chemical Biology 8:347-348, 2004

• Mike M. Hann and Tudor I. Oprea Pursuing the leadlikeness concept in pharmaceutical research. Current Opinion in Chemical Biology 8:255-263, 2004

• I. Zamora, T.I. Oprea, G. Cruciani, M. Pastor, A.L. Ungell. Surface descriptors for protein ligand affinity prediction. J.Med. Chem. 46, pp 25-33, 2003.

• TI Oprea. Current trends in lead discovery: Are we looking for the appropriate properties?J. Comput.-Aided Mol. Design, 16, pp 325-334, 2002.

•T.I. Oprea. On the information content of 2D and 3D descriptors for QSAR. J. Braz. Chem. Soc., 13, pp 811-815, 2002

• L. Kurunczi, M. Olah, T. I. Oprea, C. Bologa, Z. Simon. MTD-PLS: A PLS-Based Variant of the MTD Method. 2. Mapping Ligand-Receptor Interactions. Enzymatic Acetic Acid Esters Hydrolysis. Journal of Chemical Information and Computer Science, 42, pp. 841-846, 2002.

• Tudor I Oprea. Chemical space navigation in lead discovery. Current Opinion in Chemical Biology, 6, pp. 384-389, 2002.

• Oprea, Tudor I.; Zamora, Ismael; Ungell, Anna-Lena. Pharmacokinetically Based Mapping Device for Chemical Space Navigation. Journal of Combinatorial Chemistry, 4, pp. 258-266, 2002.

• Oprea, Tudor I. . Virtual Screening in Lead Discovery: A Viewpoint. Molecules, 7(1), pp. 51-62, 2002.

• Zamora, Ismael; Oprea, Tudor I.; Ungell, Anna-Lena. Prediction of oral drug permeability. Rational Approaches to Drug Design, Proceedings of the 13th European Symposium on Quantitative Structure-Activity Relationships, pp. 271-280, 2001.

• Oprea, Tudor I.; Gottfries, Johan. ChemGPS: A chemical space navigation tool. In Hoeltje, Hans-Dieter; Sippl, Wolfgang (eds.), Rational Approaches to Drug Design, Proceedings of the 13th European Symposium on Quantitative Structure-Activity Relationships, pp. 437-446. Prous Science, Barcelona, Spain, 2001.

• Oprea, Tudor I.; Gottfries, Johan. . Chemography: The Art of Navigating in Chemical Space. . Journal of Combinatorial Chemistry, 3(2), pp. 157-166, 2001.

• Olsson, Thomas; Oprea, Tudor I. . Cheminformatics: a tool for decision-makers in drug discovery. . Curr. Opin. Drug Discovery Dev. , 4(3), pp. 308-313, 2001.

• Oprea, Tudor I.; Davis, Andrew M.; Teague, Simon J.; Leeson, Paul D. . Is There a Difference between Leads and Drugs? A Historical Perspective. . Journal of Chemical Information and Computer Sciences, 41(5), pp. 1308-1315, 2001.

• Nilsson, Jonas W.; Thorstensson, Fredrik; Kvarnstroem, Ingemar; Oprea, Tudor I.; Samuelsson, Bertil; Nilsson, Ingemar. . Solid-phase synthesis of libraries generated from a 4-phenyl-2-carboxy-piperazine scaffold. . Journal of Combinatorial Chemistry, 3(6), pp. 546-553, 2001.

• Oprea, Tudor I.; Kurunczi, Ludovic; Olah, Marius; Simon, Zeno. MTD-PLS: a PLS-based variant of the MTD method. A 3D-QSAR analysis of receptor affinities for a series of halogenated dibenzoxin and biphenyl derivatives. . SAR QSAR Environ. Res. , 12(1-2), pp. 75-92, 2001.

• Oprea, Tudor I. . Rapid estimation of hydrophobicity for virtual combinatorial library analysis. . SAR and QSAR in Environmental Research, 12(1-2), pp. 129-141, 2001.

• Oprea, Tudor I. . Property distribution of drug-related chemical databases. . J. Comput. -Aided Mol. Des. , 14(3), pp. 251-264, 2000.

• Oprea, T. I.; Gottfries, J.; Sherbukhin, V.; Svensson, P.; Kuhler, T. C. . Chemical information management in drug discovery: optimizing the computational and combinatorial chemistry interfaces. . J. Mol. Graphics Modell. , 18(4/5), pp. 512-524, 2000.

• Mracec, Maria; Oprea, Tudor I.; Mracec, Mircea. Correlation between experimental electron affinities for aromatic derivatives and the values calculated with semiempirical MO methods. . Revue Roumaine de Chimie, 45(10), pp. 949-954, 2000.

• Teague, Simon J.; Davis, Andrew M.; Leeson, Paul D.; Oprea, Tudor I. . The design of leadlike combinatorial libraries. . Angew. Chem., Int. Ed. , 38(24), pp. 3743-3748, 1999.

• Oprea, T. I.; Gottfries, J. . Toward minimalistic modeling of oral drug absorption. . Journal of Molecular Graphics & Modelling, 17(5/6), pp. 261-274, 1999.

• Oprea, Tudor I.; Marshall, Garland R. Receptor-based prediction of binding affinities. . Perspect. Drug Discovery Des. , 9-11, pp. 35-61, 1998.

• Sulea, Traian; Kurunczi, Ludovic; Oprea, Tudor I.; Simon, Zeno. . MTD-ADJ: a multiconformational minimal topologic difference for determining bioactive conformers using adjusted biological activities. . J. Comput. -Aided Mol. Des. , 12(2), pp. 133-146, 1998.

• Oprea, Tudor Ionel; Kurunczi, Ludovic; Timofei, Simona. QSAR studies of disperse azo dyes. Towards the negation of the pharmacophore theory of dye-fiber interaction?. Dyes Pigm. , 33(1), pp. 41-64, 1997.

• Sulea, Traian; Oprea, Tudor Ionel; Muresan, Sorel; Chan, Shek Ling. A different method for steric field evaluation in CoMFA improves model robustness. . J. Chem. Inf. Comput. Sci. , 37(6), pp. 1162-1170, 1997.

• Oprea, Tudor I.; Hummer, Gerhard; Garcia, Angel E. . Identification of a functional water channel in cytochrome P450 enzymes. . Proc. Natl. Acad. Sci. U. S. A. , 94(6), pp. 2133-2138, 1997.

• Head, Richard D.; Smythe, Mark L.; Oprea, Tudor I.; Waller, Chris L.; Green, Stuart M.; Marshall, Garland R. VALIDATE: A New Method for the Receptor-Based Prediction of Binding Affinities of Novel Ligands. . J. Am. Chem. Soc. , 118(16), pp. 3959-3969, 1996.

• Oprea, Tudor I.; Garcia, Angel E. . Three-dimensional quantitative structure-activity relationships of steroid aromatase inhibitors. . J. Comput. -Aided Mol. Des. , 10(3), pp. 186-200, 1996.

• Waller, Chris L.; Oprea, Tudor I.; Chae, Kun; Park, Hee-Kyoung; Korach, Kenneth S.; Laws, Susan C.; Wiese, Thomas E.; Kelce, William R.; Gray, L. Earl Jr. Ligand-Based Identification of Environmental Estrogens. . Chem. Res. Toxicol. , 9(8), pp. 1240-1248, 1996.

• Tung, C. -S.; Oprea, T. I.; Hummer, G.; Garcia, A. E. . Three-dimensional model of a selective theophylline-binding RNA molecule. . J. Mol. Recognit. , 9(4), pp. 275-286, 1996.