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Research Informatics

Group Site: 
toronto
Group Leader: 

Matthieu Schapira

Group Info

Research Areas

The primary activity of the group is to apply computational chemistry tools, target-based rational, and medicinal chemistry thinking to support the development of chemical probes, with particular focus on epigenetics related targets. The team also manages the wealth of biological and chemical data generated at SGC-Toronto, and offers expertise and solutions to Information Technology related matters.


Group Members
Matthieu Schapira

Matthieu holds a M.Sc degree in chemistry from the National Superior Chemistry School, Nancy, France, and a Ph.D in biochemistry from Ecole Normale Superieure, Paris. After graduating in 1995, he completed a couple post-docs in protein crystallography and computational chemistry at New York University Medical Center. In 2000, he joined Molsoft, a San-Diego based biotech, as senior research scientist. In 2003, he moved to Lyon, France, to lead structure-based drug design at Aptanomics/Imaxio, a drug discovery start-up. In 2007, he joined the SGC as head of research informatics. Matthieu holds an Associate Professor cross-appointment with the Department of Pharmacology and Toxicology at University of Toronto, and an adjunct Associate Professor position with the Department of Pharmacology at New York University.

Emily Denton

Emily is an undergraduate student at the University of Toronto studying Computer Science and Cognitive Science with a focus in artificial intelligence. She is interested in learning and inference in both biological and artificial neural systems as well as applications of machine learning and, more broadly AI in general, to a variety of domains. This latter interest, as well as her desire to learn about and work in an exciting and highly relevant field has helped lead her to a position as a co-op student at the SGC.

Lihua Liu

Lihua received her Master's degree in computer science from State University of New York at Stony Brook in 2003. She then worked for SUNY at Stony Brook and Cold Spring Harbor Laboratory as application developer. Lihua joined SGC in 2007 as Informatics Programmer.

Kong Nguyen

Kong received his PhD from University of Berne in Switzerland with Prof. Jean-Louis Reymond in 2009. He then moved to University of California San Francisco for a postdoc with Prof. Brian Shoichet and Prof. John Irwin. Currently he is a postdoc fellow in the Research Informatics group at SGC Toronto. Kong enjoys doing molecular docking, computational biology and chemoinformatics.

Publications
  • Arrowsmith CH, Bountra C, Fish PV, Lee K, Schapira M - Nat Rev Drug Discov. 2012 Apr 13 - Epigenetic protein families: a new frontier for drug discovery pubmed

  • Santiago C, Nguyen K, Schapira M - J Comput Aided Mol Des. 2011;(12):1171-8 - Druggability of methyl-lysine binding sites pubmed
     
  • Schapira M - Handb Exp Pharmacol. 2011;(206):225-40 - Structural biology of human metal-dependent histone deacetylases pubmed
     
  • Schapira M - Current Chemical Genomics 2011;(5):85:94 - Structural chemistry of human SET domain protein methyltransferases pubmed
     
  • Artz JD, Wernimont AK, Allali-Hassani A, Zhao Y, Amani M, Lin YH, Senisterra G, Wasney GA, Fedorov O, King O, Roos A, Lunin VV, Qiu W, Finerty P Jr, Hutchinson A, Chau I, von Delft F, Mackenzie F, Lew J, Kozieradzki I, Vedadi M, Schapira M, Zhang C, Shokat K, Heightman T, Hui R - BMC Genomics. 2011 Sep 30;12(1):478 - The Cryptosporidium parvum kinome pubmed
     
  • Wallach I, Jaitly N, Nguyen K, Schapira M, Lilien RH - J Chem Inf Model. 2011 Aug 22;51(8):1817-30 - Normalizing molecular docking rankings using virtually generated decoys pubmed
     
  • Campagna-Slater V, Mok MW, Nguyen KT, Feher M, Najmanovich R, Schapira M - J Chem Inf Model. 2011 Mar 28;51(3):612-23 - Structural chemistry of the histone methyltransferases cofactor binding site pubmed
     
  • Yap DB, Chu J, Berg T, Schapira M, Cheng SW, Moradian A, Morin RD, Mungall AJ, Meissner B, Boyle M, Marquez VE, Marra MA, Gascoyne RD, Humphries RK, Arrowsmith CH, Morin GB, Aparicio SA - Blood. 2011 Feb 24;117(8):2451-9 - Somatic mutations at EZH2 Y641 act dominantly through a mechanism of selectively altered PRC2 catalytic activity, to increase H3K27 trimethylation pubmed
     
  • Turgeon Z, Jørgensen R, Visschedyk D, Edwards PR, Legree S, McGregor C, Fieldhouse RJ, Mangroo D, Schapira M, Merrill AR - Antimicrob Agents Chemother. 2011 Mar;55(3):983-91 - Newly Discovered and Characterized Antivirulence Compounds inhibit Bacterial Mono-ADP-ribosyltransferase Toxins pubmed
     
  • Artz JD, Wernimont AK, Dunford JE, Schapira M, Dong A, Zhao Y, Lew J, Russell RG, Ebetino FH, Oppermann U, Hui R - J Biol Chem. 2011 Feb 4;286(5):3315-22 - Molecular characterization of a novel geranylgeranyl pyrophosphate synthase from Plasmodium parasites pubmed
     
  • Kaustov L, Quyang H, Amaya M, Lemak A, Nady N, Duan S, Wasney G, Li Z, Vedadi M, Schapira M, Min J, Arrowsmith CH - J Biol Chem. 2011 Jan 7;286(1):521-9 - Recognition and specificity determinants of the human Cbx chromodomains pubmed
     
  • Wang M, Mok MW, Harper H, Lee WH, Min J, Knapp S, Oppermann U, Marsden B, Schapira M - Bioinformatics. 2010 Oct 15;26(20):2629-30 - Structural Genomics of Histone Tail Recognitionpubmed
     
  • Campagna-Slater V, Schapira M. - Molecular Informatics 2010, 29:322-331 - Finding inspiration in the Protein Data Bank to chemically antagonize readers of the histone code journal
     
  • Zhao R, Leung E, Schapira M, Houry WA - PLoS One. 2010 Apr 1;5(4):e9934 - Tamoxifen enhances the Hsp90 molecular chaperone ATPase activity pubmed
     
  • Schapira M - Burger's Medicinal Chemistry, Drug Discovery and Development, 2010 - Structural genomics, its application in Chemistry, Biology, Medicine, and Drug Discovery book chapter
     
  • Campagna-Slater V, Arrowsmith AG, Zhao Y, Schapira M. - J Chem Inf Model. 2010 Feb; 50:358-367. - Pharmacophore screening of the Protein Data Bank for specific binding site chemistrypubmed - (in top 10 list of most accessed JCIM articles, first and second quarters 2010)
     
  • Wu H, Min J, Lunin VL, Antoshenko T, Dombrovski L, Zeng H, Allali-Hassani A, Campagna-Slater V, Vedadi M, Arrowsmith CH, Plotnikov AN, Schapira M. - PLoS One. 2010 Jan 11;5(1):e8570 - Structural biology of human H3K9 Methyltransferases pubmed
     
  • Campagna-Slater V, Schapira M. - J Chem Inf Model. 2009 Sep;49(9):2082-91 - Evaluation of virtual screening as a tool for chemical genetic applications pubmed - faculty of 1000
     
  • Allali-Hassani A, Wasney GA, Chau I, Hong BS, Senisterra G, Loppnau P, Shi Z, Moult J, Edwards AM, Arrowsmith CH, Park HW, Schapira M, Vedadi M. - Biochem J. 2009 Oct 23;424(1):15-26 - A survey of proteins encoded by non-synonymous SNPs reveals a significant fraction with altered stability and activity pubmed
     
  • Guo Y, Nady N, Qi C, Allali-Hassani A, Zhu H, Pan P, Adams-Cioaba MA, Amaya MF, Dong A, Vedadi M, Schapira M, Read RJ, Arrowsmith CH, Min J. - Nucleic Acids Res. 2009 Apr;37(7):2204-10 - Methylation-state-specific recognition of histones by the MBT repeat protein L3MBTL2 pubmed
     
  • Qiu W, Wernimont A, Tang K, Taylor S, Lunin V, Schapira M, Fentress S, Hui R, Sibley LD. - EMBO J. 2009 Apr 8;28(7):969-79 - Novel structural and regulatory features of rhoptry secretory kinases in Toxoplasma gondii pubmed
     
  • Poondra RR, Kumar NN, Bijian K, Prakesch M, Campagna-Slater V, Reayi A, Reddy PT, Choudhry A, Barnes ML, Leek DM, Daroszewska M, Lougheed C, Xu B, Schapira M, Alaoui-Jamali MA, Arya P. - J Comb Chem. 2009 Jan 15 - Discovery of Indoline-Based, Natural-Product-like Compounds as Probes of Focal Adhesion Kinase Signaling Pathways pubmed
     
  • Huang X, Finerty P Jr, Walker JR, Butler-Cole C, Vedadi M, Schapira M, Parker SA, Turk BE, Thompson DA, Dhe-Paganon S. - J Struct Biol. 2009 Feb;165(2):88-96 - Structural insights into the inhibited states of the Mer receptor tyrosine kinase pubmed
     
  • Prakesch M, Bijian K, Campagna-Slater V, Quevillon S, Joseph R, Wei CQ, Sesmilo E, Reayi A, Poondra RR, Schapira M, Alaoui-Jamali M, Arya P. - Bioorg Med Chem. 2008 Nov 1;16(21):9596-602 - Building skeletally diverse architectures on the Indoline Scaffold: the discovery of a chemical probe of focal adhesion kinase signaling networks pubmed
     
  • Schuetz A, Min J, Allali-Hassani A, Schapira M, Shuen M, Loppnau P, Mazitschek R, Kwiatkowski NP, Lewis TA, Maglathin RL, McLean TH, Bochkarev A, Plotnikov AN, Vedadi M, Arrowsmith CH. - J Biol Chem. 2008 Apr 25;283(17):11355-63 - Human HDAC7 harbors a class IIa HDAC-specific zinc binding motif and cryptic deacetylase activity pubmed
     
  • Weigelt J, McBroom-Cerajewski LD, Schapira M, Zhao Y, Arrowmsmith CH. - Curr Opin Chem Biol. 2008 Feb;12(1):32-9 - Structural genomics and drug discovery: all in the family pubmed
     
  • Pamonsinlapatham P, Hadj-Slimane R, Schapira M, Samson J, Mathieu AL, Dufour S, Garbay C, Colas P - PLoS ONE. 2008 Aug 6;3(8):e2902 - A RasGAP SH3 peptide aptamer inhibits RasGAP-Aurora interaction and induces caspase-independent tumor cell death pubmed
     
  • Das S, Schapira M, Tomic-Canic M, Goyanka R, Cardozo T, Samuels HH. - Mol Endocrinol. 2007 Nov;21(11):2672-86 - Farnesyl Pyrophosphate is a Novel Transcriptional Activator for a Subset of Nuclear Hormone Receptors pubmed
     
  • Abed N, Bickle M, Mari B, Schapira M, Sanjuan-España R, Robbe Sermesant K, Moncorgé O, Mouradian-Garcia S, Barbry P, Rudkin BB, Fauvarque MO, Michaud-Soret I, Colas P - Mol Cell Proteomics. 2007 Dec;6(12):2110-21 - A comparative analysis of perturbations caused by a gene knock-out, a dominant negative allele, and a set of peptide aptamers pubmed
     
  • Schapira M, Lamigeon C, Gutmann M, Barthelaix A, Hugo N, Colas P. - EP06290821.5 (2006) - Anti-proliferative compounds deriving from a 3-aryl-coumarine or 3-aryl-quinolin-2-one and uses thereof.
     
  • Yeoun Y-J, Sackett DL, Schapira M, Walsh, Min J, Pannell LK, Chang YT - Bioorg. & Med. Chem 2006 Feb 15;14(4):1169-75. - Identification of 12Cys on tubulin as the binding site of tubulyzinepubmed
     
  • Samuels H, Abagyan R, Schapira M, Totrov M, Raaka B, Wilson S, Fan L, Zhou Z - WO2004103289 - EP20040752150 (2004) - Diverse thyroid hormone receptor antagonists and uses thereof
     
  • Anglister J, Sharon M, Schapira M, Zolla-Pazner S, Rosen O - WO2004069863 - EP20040708239 (2004) - Constrained HIV V3 loop as immunogens and receptor antagonists
     
  • Schapira M, Das S, Raaka B, Fan L, Totrov M, Wilson SR, Abagyan RA, Samuels HH - Proc Natl Acad Sci U S A. 2003; 100(12):7354-9 - Discovery of Diverse Thyroid Hormone Receptor Antagonists by High-Throughput Docking pubmed
     
  • Schapira M, Abagyan R, Totrov M - J Med Chem. 2003; 46(14):3045-59 - Nuclear Hormone Receptor Targeted Virtual Screening pubmed
     
  • Min G, Zhou G, Schapira M, Sun TT, Kong XP - J Cell Sci. 2003 Oct 15;116(Pt 20):4087-94 - Structural basis of urothelial permeability barrier function as revealed by Cryo-EM studies of the 16 nm uroplakin particle pubmed
     
  • Oxelmark E, Knoblauch R, Arnal S, Su LF, Schapira M, Garabedian MJ - J Biol Chem. 2003 Sep 19;278(38):36547-55 - Genetic dissection of p23, an Hsp90 cochaperone, reveals a distinct surface involved in estrogen receptor signaling pubmed
     
  • Schapira M. - Curr. Canc. Drug Targ 2002;2(3):243:256 - Pharmacogenomics Opportunities in Nuclear Receptor Targeted Cancer Therapy pubmed
     
  • Diwa AA, Jiang X, Schapira M, Belasco JG. - Mol Microbiol. 2002 Nov;46(4):959-69 - Two distinct regions on the surface of an RNA-binding domain are crucial for RNase E function pubmed
     
  • Schapira M, Abagyan R, Totrov M - BMC Struct Biol. 2002;2(1):1-9 - Structural model of nicotinic acetylcholine receptor isotypes bound to acetylcholine and nicotine pubmed
     
  • Harding HP, Novoa I, Zhang Y, Zeng H, Wek R, Schapira M, and Ron D - Molecular Cell 2000 Nov 17; 6:1099-1108 - Regulated translational initiation controls stress-induced gene expression in mammalian cells pubmed
     
  • Schapira M, Raaka B, Samuels HH, and Abagyan R - Proc Natl Acad Sci U S A. 2000 97(3):1008-13 Rational design of novel nuclear receptor antagonists pubmed
     
  • Schapira M, Abagyan R, Totrov M - Prediction of the binding energy for small molecules, peptides and proteins - Journal of Molecular Recognition, 1999; 12(3):177-190 pubmed
     
  • Hegde RS, Wang A-F, Kim, S-S and Schapira M - Journal of Molecular Biology, 1998, 276:797-808 - Subunit rearrangement accompanies sequence-specific DNA binding by the bovine papillomavirus-1 E2 protein pubmed
Contact

matthieu [dot] schapira[at]utoronto [dot] ca

416-978-3092

Alumni

A Big Thanks and Farewell to previous group members!

  • Veronica Cheung, Undergraduate Student [2007]
  • Michael De Guzman, Undergraduate Student [2008]
  • Andrew Arrowsmith, Undergraduate Student [2008-2009]
  • Valerie Campagna-Slater, Post-doctoral Fellow [2008-2010]
  • Yong Zhao, Research Associate [2007-2010]
  • Angela Mok, Undergraduate Student [2009-2010]
  • Seacy Zhen, Undergraduate Student [2009 -2010]
  • Sabrina Mota, Visiting Scientist [2010]
  • Alex Ignatchenko, Informatics Developer, Database Administrator [2008-2010]
  •  Cavin Santiago, Undergraduate Student [2010 -2011]
  • Salar Sayyad, Undergraduate Student [2010 -2011]