Natural Product-like Scaffolds for Molecular Dissection of Macromolecular Interactions and New Therapeutic Applications



In this postgenomics era, small molecule-mediated molecular dissection of protein–protein interactions is a highly desired task, which promises to fulfill the development of novel therapeutic approaches in biomedical research. However, chemical probes which demonstrate bioactivity over a broad chemical space have been an important limiting factor for this achievement. As such, scientists have been exploring natural products which exhibit highly diverse chemical structures capable of fulfilling this void. Emerging areas of research, such as diversity-oriented synthesis, aim to generate complex and diverse natural product-like compounds capable of modulating these macromolecular interactions. Current strategies reviewed in this chapter include different methods utilized for novel molecule identification, as well as various techniques which provide tools for chemical optimization, leading to molecules with increased biological significance.


T98G Cell Chemical Space Focal Adhesion Complex Macromolecular Interaction Focal Adhesion Kinase Tyrosine 


  1. 1.
    Berg T. Modulation of protein-protein interactions with small organic molecules. Angew Chem Int Ed Engl. 2003;42(22):2462–81.Google Scholar
  2. 2.
    Boger DL, Desharnais J, Capps K. Solution-phase combinatorial libraries: modulating cellular signaling by targeting protein-protein or protein-DNA interactions. Angew Chem Int Ed Engl. 2003;42(35):4138–76.Google Scholar
  3. 3.
    Cochran AG. Antagonists of protein-protein interactions. Chem Biol. 2000;7(4):R85–94.Google Scholar
  4. 4.
    Cochran AG. Protein-protein interfaces: mimics and inhibitors. Curr Opin Chem Biol. 2001;5(6):654–9.Google Scholar
  5. 5.
    Pagliaro L, Felding J, Audouze K, et al. Emerging classes of protein-protein interaction inhibitors and new tools for their development. Curr Opin Chem Biol. 2004;8(4):442–9.Google Scholar
  6. 6.
    Reayi A, Arya P. Natural product-like chemical space: search for chemical dissectors of macromolecular interactions. Curr Opin Chem Biol. 2005;9(3):240–7.Google Scholar
  7. 7.
    Schwalbe H, Wess G. Molecules as modulators: systems biology challenges chemistry. Chembiochem. 2004;5(10):1311–13.Google Scholar
  8. 8.
    Wess G, Urmann M, Sickenberger B. Medicinal chemistry: challenges and opportunities. Angew Chem Int Ed Engl. 2001;40(18):3341–50.Google Scholar
  9. 9.
    Austin CP. The completed human genome: implications for chemical biology. Curr Opin Chem Biol. 2003;7(4):511–15.Google Scholar
  10. 10.
    Crews CM. Deciphering isozyme function: exploring cell biology with chemistry in the post-genomic era. Chem Biol. 1996;3(12):961–5.Google Scholar
  11. 11.
    Crews CM, Mohan R. Small-molecule inhibitors of the cell cycle. Curr Opin Chem Biol. 2000;4(1):47–53.PubMedGoogle Scholar
  12. 12.
    Crews CM, Shotwell JB. Small-molecule inhibitors of the cell cycle: an overview. Prog Cell Cycle Res. 2003;5:125–33.Google Scholar
  13. 13.
    Gura T. A chemistry set for life. Nature 2000;407(6802):282–4.Google Scholar
  14. 14.
    Mayer TU. Chemical genetics: tailoring tools for cell biology. Trends Cell Biol. 2003;13(5):270–7.Google Scholar
  15. 15.
    Peterson JR, Mitchison TJ. Small molecules, big impact: a history of chemical inhibitors and the cytoskeleton. Chem Biol. 2002;9(12):1275–85.Google Scholar
  16. 16.
    Schreiber SL. Chemical genetics resulting from a passion for synthetic organic chemistry. Bioorg Med Chem. 1998;6(8):1127–52.Google Scholar
  17. 17.
    Stockwell BR. Frontiers in chemical genetics. Trends Biotechnol. 2000;18(11):449–55.Google Scholar
  18. 18.
    Stockwell BR. Chemical genetics: ligand-based discovery of gene function. Nat Rev. 2000;1(2):116–25.Google Scholar
  19. 19.
    Strausberg RL, Schreiber SL. From knowing to controlling: a path from genomics to drugs using small molecule probes. Science 2003;300(5617):294–5.Google Scholar
  20. 20.
    Austin CP, Brady LS, Insel TR, Collins FS. NIH molecular libraries initiative. Science 2004;306(5699):1138–9.Google Scholar
  21. 21.
    Arkin M. Protein-protein interactions and cancer: small molecules going in for the kill. Curr Opin Chem Biol. 2005;9(3):317–24.Google Scholar
  22. 22.
    Arkin MR, Wells JA. Small-molecule inhibitors of protein-protein interactions: progressing towards the dream. Nat Rev Drug Discov. 2004;3(4):301–17.Google Scholar
  23. 23.
    Schaller MD, Borgman CA, Cobb BS, Vines RR, Reynolds AB, Parsons JT. pp125FAK a structurally distinctive protein-tyrosine kinase associated with focal adhesions. Proc Natl Acad Sci USA 1992;89(11):5192–6.Google Scholar
  24. 24.
    Han DC, Guan JL. Association of focal adhesion kinase with Grb7 and its role in cell migration. J Biol Chem. 1999;274(34):24425–30.Google Scholar
  25. 25.
    Reiske HR, Kao SC, Cary LA, Guan JL, Lai JF, Chen HC. Requirement of phosphatidylinositol 3-kinase in focal adhesion kinase-promoted cell migration. J Biol Chem. 1999;274(18):12361–6.Google Scholar
  26. 26.
    Schaller MD, Hildebrand JD, Shannon JD, Fox JW, Vines RR, Parsons JT. Autophosphorylation of the focal adhesion kinase, pp125FAK, directs SH2-dependent binding of pp60src. Mol Cell Biol. 1994;14(3):1680–8.Google Scholar
  27. 27.
    Zhang X, Chattopadhyay A, Ji QS, et al. Focal adhesion kinase promotes phospholipase C-gamma1 activity. Proc Natl Acad Sci USA 1999;96(16):9021–6.Google Scholar
  28. 28.
    Schlaepfer DD, Hanks SK, Hunter T, van der Geer P. Integrin-mediated signal transduction linked to Ras pathway by GRB2 binding to focal adhesion kinase. Nature 1994;372(6508):786–91.Google Scholar
  29. 29.
    Hildebrand JD, Taylor JM, Parsons JT. An SH3 domain-containing GTPase-activating protein for Rho and Cdc42 associates with focal adhesion kinase. Mol Cell Biol. 1996;16(6):3169–78.Google Scholar
  30. 30.
    Polte TR, Hanks SK. Interaction between focal adhesion kinase and Crk-associated tyrosine kinase substrate p130Cas. Proc Natl Acad Sci USA 1995;92(23):10678–82.Google Scholar
  31. 31.
    Schlaepfer DD, Broome MA, Hunter T. Fibronectin-stimulated signaling from a focal adhesion kinase-c-Src complex: involvement of the Grb2, p130cas, and Nck adaptor proteins. Mol Cell Biol. 1997;17(3):1702–13.Google Scholar
  32. 32.
    Oktay M, Wary KK, Dans M, Birge RB, Giancotti FG. Integrin-mediated activation of focal adhesion kinase is required for signaling to Jun NH2-terminal kinase and progression through the G1 phase of the cell cycle. J Cell Biol. 1999;145(7):1461–9.Google Scholar
  33. 33.
    Schlaepfer DD, Hunter T. Focal adhesion kinase overexpression enhances ras-dependent integrin signaling to ERK2/mitogen-activated protein kinase through interactions with and activation of c-Src. J Biol Chem. 1997;272(20):13189–95.Google Scholar
  34. 34.
    King WG, Mattaliano MD, Chan TO, Tsichlis PN, Brugge JS. Phosphatidylinositol 3-kinase is required for integrin-stimulated AKT and Raf-1/mitogen-activated protein kinase pathway activation. Mol Cell Biol. 1997;17(8):4406–18.Google Scholar
  35. 35.
    Ilic D, Furuta Y, Kanazawa S, et al. Reduced cell motility and enhanced focal adhesion contact formation in cells from FAK-deficient mice. Nature 1995;377(6549):539–44.Google Scholar
  36. 36.
    Frisch SM, Vuori K, Ruoslahti E, Chan-Hui PY. Control of adhesion-dependent cell survival by focal adhesion kinase. J Cell Biol. 1996;134(3):793–9.Google Scholar
  37. 37.
    Sieg DJ, Hauck CR, Schlaepfer DD. Required role of focal adhesion kinase (FAK) for integrin-stimulated cell migration. J Cell Sci. 1999;112(Pt 16):2677–91.Google Scholar
  38. 38.
    Schlaepfer DD, Mitra SK, Ilic D. Control of motile and invasive cell phenotypes by focal adhesion kinase. Biochim Biophys Acta. 2004;1692(2–3):77–102.PubMedGoogle Scholar
  39. 39.
    Schmitz KJ, Grabellus F, Callies R, et al. High expression of focal adhesion kinase (p125FAK) in node-negative breast cancer is related to overexpression of HER-2/neu and activated Akt kinase but does not predict outcome. Breast Cancer Res. 2005;7(2):R194–203.Google Scholar
  40. 40.
    van Nimwegen MJ, Verkoeijen S, van Buren L, Burg D, van de Water B. Requirement for focal adhesion kinase in the early phase of mammary adenocarcinoma lung metastasis formation. Cancer Res. 2005;65(11):4698–706.Google Scholar
  41. 41.
    Slamon DJ, Clark GM, Wong SG, Levin WJ, Ullrich A, McGuire WL. Human breast cancer: correlation of relapse and survival with amplification of the HER-2/neu oncogene. Science 1987;235(4785):177–82.Google Scholar
  42. 42.
    Benlimame N, He Q, Jie S, et al. FAK signaling is critical for ErbB-2/ErbB-3 receptor cooperation for oncogenic transformation and invasion. J Cell Biol. 2005;171(3):505–16.Google Scholar
  43. 43.
    Lu Z, Jiang G, Blume-Jensen P, Hunter T. Epidermal growth factor-induced tumor cell invasion and metastasis initiated by dephosphorylation and downregulation of focal adhesion kinase. Mol Cell Biol. 2001;21(12):4016–31.Google Scholar
  44. 44.
    Sieg DJ, Hauck CR, Ilic D, et al. FAK integrates growth-factor and integrin signals to promote cell migration. Nat Cell Biol. 2000;2(5):249–56.Google Scholar
  45. 45.
    Vadlamudi RK, Sahin AA, Adam L, Wang RA, Kumar R. Heregulin and HER2 signaling selectively activates c-Src phosphorylation at tyrosine 215. FEBS Lett. 2003;543(1–3):76–80.PubMedGoogle Scholar
  46. 46.
    Sonoda Y, Watanabe S, Matsumoto Y, Aizu-Yokota E, Kasahara T. FAK is the upstream signal protein of the phosphatidylinositol 3-kinase-Akt survival pathway in hydrogen peroxide-induced apoptosis of a human glioblastoma cell line. J Biol Chem. 1999;274(15):10566–70.Google Scholar
  47. 47.
    Sakurai S, Sonoda Y, Koguchi E, Shinoura N, Hamada H, Kasahara T. Mutated focal adhesion kinase induces apoptosis in a human glioma cell line, T98G. Biochem Biophys Res Commun. 2002;293(1):174–81.Google Scholar
  48. 48.
    Ling J, Liu Z, Wang D, Gladson CL. Malignant astrocytoma cell attachment and migration to various matrix proteins is differentially sensitive to phosphoinositide 3-OH kinase inhibitors. J Cell Biochem. 1999;73(4):533–44.Google Scholar
  49. 49.
    Thamilselvan V, Craig DH, Basson MD. FAK association with multiple signal proteins mediates pressure-induced colon cancer cell adhesion via a Src-dependent PI3K/Akt pathway. Faseb J. 2007;21(8):1730–41.Google Scholar
  50. 50.
    Sumitomo M, Shen R, Walburg M, et al. Neutral endopeptidase inhibits prostate cancer cell migration by blocking focal adhesion kinase signaling. J Clin Invest. 2000;106(11):1399–407.Google Scholar
  51. 51.
    Pylayeva Y, Gillen KM, Gerald W, Beggs HE, Reichardt LF, Giancotti FG. Ras- and PI3K-dependent breast tumorigenesis in mice and humans requires focal adhesion kinase signaling. J Clin Invest. 2009;119(2):252–66.Google Scholar
  52. 52.
    Golubovskaya VM, Finch R, Cance WG. Direct interaction of the N-terminal domain of focal adhesion kinase with the N-terminal transactivation domain of p53. J Biol Chem. 2005;280(26):25008–21.Google Scholar
  53. 53.
    Yamamoto D, Sonoda Y, Hasegawa M, Funakoshi-Tago M, Aizu-Yokota E, Kasahara T. FAK overexpression upregulates cyclin D3 and enhances cell proliferation via the PKC and PI3-kinase-Akt pathways. Cell Signal 2003;15(6):575–83.Google Scholar
  54. 54.
    Cary LA, Han DC, Polte TR, Hanks SK, Guan JL. Identification of p130Cas as a mediator of focal adhesion kinase-promoted cell migration. J Cell Biol. 1998;140(1):211–21.Google Scholar
  55. 55.
    Tomar A, Lim ST, Lim Y, Schlaepfer DD. A FAK-p120RasGAP-p190RhoGAP complex regulates polarity in migrating cells. J Cell Sci. 2009;122(Pt 11):1852–62.Google Scholar
  56. 56.
    Kurenova E, Xu LH, Yang X, et al. Focal adhesion kinase suppresses apoptosis by binding to the death domain of receptor-interacting protein. Mol Cell Biol. 2004;24(10):4361–71.Google Scholar
  57. 57.
    Lightfoot HM Jr, Lark A, Livasy CA, et al. Upregulation of focal adhesion kinase (FAK) expression in ductal carcinoma in situ (DCIS) is an early event in breast tumorigenesis. Breast Cancer Res Treat. 2004;88(2):109–16.Google Scholar
  58. 58.
    Lark AL, Livasy CA, Dressler L, et al. High focal adhesion kinase expression in invasive breast carcinomas is associated with an aggressive phenotype. Mod Pathol. 2005;18(10):1289–94.Google Scholar
  59. 59.
    Felding-Habermann B, O'Toole TE, Smith JW, et al. Integrin activation controls metastasis in human breast cancer. Proc Natl Acad Sci USA 2001;98(4):1853–8.Google Scholar
  60. 60.
    Diaz LK, Cristofanilli M, Zhou X, et al. Beta4 integrin subunit gene expression correlates with tumor size and nuclear grade in early breast cancer. Mod Pathol. 2005;18(9):1165–75.Google Scholar
  61. 61.
    Takayama S, Ishii S, Ikeda T, Masamura S, Doi M, Kitajima M. The relationship between bone metastasis from human breast cancer and integrin alpha(v)beta3 expression. Anticancer Res. 2005;25(1A):79–83.PubMedGoogle Scholar
  62. 62.
    Jordan A, Hadfield JA, Lawrence NJ, McGown AT. Tubulin as a target for anticancer drugs: agents which interact with the mitotic spindle. Med Res Rev. 1998;18(4):259–96.Google Scholar
  63. 63.
    Choi J, Chen J, Schreiber SL, Clardy J. Structure of the FKBP12-rapamycin complex interacting with the binding domain of human FRAP. Science 1996;273(5272):239–42.Google Scholar
  64. 64.
    Duncan SJ, Gruschow S, Williams DH, et al. Isolation and structure elucidation of Chlorofusin, a novel p53-MDM2 antagonist from a Fusarium sp. J Am Chem Soc. 2001;123(4):554–60.Google Scholar
  65. 65.
    Lain S. Protecting p53 from degradation. Biochem Soc Trans. 2003;31(2):482–5.Google Scholar
  66. 66.
    Woods YL, Lane DP. Exploiting the p53 pathway for cancer diagnosis and therapy. Hematol J. 2003;4(4):233–47.Google Scholar
  67. 67.
    Haupt Y, Maya R, Kazaz A, Oren M. Mdm2 promotes the rapid degradation of p53. Nature 1997;387(6630):296–9.Google Scholar
  68. 68.
    Kubbutat MH, Jones SN, Vousden KH. Regulation of p53 stability by Mdm2. Nature 1997;387(6630):299–303.PubMedGoogle Scholar
  69. 69.
    Xirodimas DP, Saville MK, Bourdon JC, Hay RT, Lane DP. Mdm2-mediated NEDD8 conjugation of p53 inhibits its transcriptional activity. Cell 2004;118(1):83–97.PubMedGoogle Scholar
  70. 70.
    Ho Y, Gruhler A, Heilbut A, et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 2002;415(6868):180–3.Google Scholar
  71. 71.
    Figeys D, McBroom LD, Moran MF. Mass spectrometry for the study of protein-protein interactions. Methods 2001;24(3):230–9.Google Scholar
  72. 72.
    Gavin AC, Bosche M, Krause R, et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 2002;415(6868):141–7.Google Scholar
  73. 73.
    Bouwmeester T, Bauch A, Ruffner H, et al. A physical and functional map of the human TNF-alpha/NF-kappa B signal transduction pathway. Nat Cell Biol. 2004;6(2):97–105.PubMedGoogle Scholar
  74. 74.
    Boute N, Jockers R, Issad T. The use of resonance energy transfer in high-throughput screening: BRET versus FRET. Trends Pharmacol Sci. 2002;23(8):351–4.Google Scholar
  75. 75.
    Iuchi S, Hoffner G, Verbeke P, Djian P, Green H. Oligomeric and polymeric aggregates formed by proteins containing expanded polyglutamine. Proc Natl Acad Sci USA 2003;100(5):2409–14.Google Scholar
  76. 76.
    Gentz R, Chen CH, Rosen CA. Bioassay for trans-activation using purified human immunodeficiency virus tat-encoded protein: trans-activation requires mRNA synthesis. Proc Natl Acad Sci USA 1989;86(3):821–4.Google Scholar
  77. 77.
    Rigaut G, Shevchenko A, Rutz B, Wilm M, Mann M, Seraphin B. A generic protein purification method for protein complex characterization and proteome exploration. Nat Biotechnol. 1999;17(10):1030–2.Google Scholar
  78. 78.
    Einhauer A, Jungbauer A. The FLAG peptide, a versatile fusion tag for the purification of recombinant proteins. J Biochem Biophys Methods 2001;49(1–3):455–65.Google Scholar
  79. 79.
    Schweitzer B, Predki P, Snyder M. Microarrays to characterize protein interactions on a whole-proteome scale. Proteomics 2003;3(11):2190–9.Google Scholar
  80. 80.
    MacBeath G, Schreiber SL. Printing proteins as microarrays for high-throughput function determination. Science 2000;289(5485):1760–3.Google Scholar
  81. 81.
    Zhu H, Bilgin M, Bangham R, et al. Global analysis of protein activities using proteome chips. Science 2001;293(5537):2101–5.Google Scholar
  82. 82.
    Vegas AJ, Fuller JH, Koehler AN. Small-molecule microarrays as tools in ligand discovery. Chem Soc Rev. 2008;37(7):1385–94.Google Scholar
  83. 83.
    Erlanson DA, McDowell RS, O'Brien T. Fragment-based drug discovery. J Med Chem. 2004;47(14):3463–82.Google Scholar
  84. 84.
    Shuker SB, Hajduk PJ, Meadows RP, Fesik SW. Discovering high-affinity ligands for proteins: SAR by NMR. Science 1996;274(5292):1531–4.Google Scholar
  85. 85.
    Denisov AY, Kozlov G, Gravel M, Sprules T, Braun PE, Gehring K. 1H, 13C and 15 N resonance assignments of the catalytic domain of the goldfish RICH protein. J Biomol NMR 2006;36 Suppl 1:75.Google Scholar
  86. 86.
    Pollock JR, Swenson RP, Stockman BJ. 1H and 15 N NMR resonance assignments and solution secondary structure of oxidized Desulfovibrio desulfuricans flavodoxin. J Biomol NMR 1996;7(3):225–35.Google Scholar
  87. 87.
    Stockman BJ, Farley KA, Angwin DT. Screening of compound libraries for protein binding using flow-injection nuclear magnetic resonance spectroscopy. Methods Enzymol. 2001;338:230–46.Google Scholar
  88. 88.
    Prakesch M, Denisov AY, Naim M, Gehring K, Arya P. The discovery of small molecule chemical probes of Bcl-X(L) and Mcl-1. Bioorg Med Chem. 2008;16(15):7443–9.Google Scholar
  89. 89.
    Szczepankiewicz BG, Liu G, Hajduk PJ, et al. Discovery of a potent, selective protein tyrosine phosphatase 1B inhibitor using a linked-fragment strategy. J Am Chem Soc. 2003;125(14):4087–96.Google Scholar
  90. 90.
    Liu G, Xin Z, Pei Z, et al. Fragment screening and assembly: a highly efficient approach to a selective and cell active protein tyrosine phosphatase 1B inhibitor. J Med Chem. 2003;46(20):4232–5.Google Scholar
  91. 91.
    Congreve MS, Davis DJ, Devine L, et al. Detection of ligands from a dynamic combinatorial library by X-ray crystallography. Angew Chem Intl Ed Engl. 2003;42(37):4479–82.Google Scholar
  92. 92.
    Arya P, Baek M. Natural-product-like chiral derivatives by solid-phase synthesis. Curr Opin Chem Biol 2001;5(3):292–301.PubMedGoogle Scholar
  93. 93.
    Arya P, Chou DT, Baek MG. Diversity-based Organic Synthesis in the Era of Genomics and Proteomics NRC publication no. 43843. David Thomas is a senior colleague and mentor. Angew Chem Intl Ed Engl. 2001;40(2):339–46.Google Scholar
  94. 94.
    Arya P, Joseph R, Chou DT. Toward high-throughput synthesis of complex natural product-like compounds in the genomics and proteomics age. Chem Biol. 2002;9(2):145–56.Google Scholar
  95. 95.
    Arya P, Joseph R, Gan Z, Rakic B. Exploring new chemical space by stereocontrolled diversity-oriented synthesis. Chem Biol. 2005;12(2):163–80.Google Scholar
  96. 96.
    Ganesan A. Natural products as a hunting ground for combinatorial chemistry. Curr Opin Biotechnol. 2004;15(6):584–90.Google Scholar
  97. 97.
    Thiagalingam S, Cheng KH, Lee HJ, Mineva N, Thiagalingam A, Ponte JF. Histone deacetylases: unique players in shaping the epigenetic histone code. Ann NY Acad Sci. 2003;983:84–100.PubMedGoogle Scholar
  98. 98.
    Marks P, Rifkind RA, Richon VM, Breslow R, Miller T, Kelly WK. Histone deacetylases and cancer: causes and therapies. Nat Rev Cancer 2001;1(3):194–202.PubMedGoogle Scholar
  99. 99.
    Marks PA. Discovery and development of SAHA as an anticancer agent. Oncogene 2007;26(9):1351–6.Google Scholar
  100. 100.
    Dolle RE, Le Bourdonnec B, Goodman AJ, Morales GA, Salvino JM, Zhang W. Comprehensive survey of chemical libraries for drug discovery and chemical biology: 2006. J Comb Chem. 2007;9(6):855–902.Google Scholar
  101. 101.
    Dolle RE, Le Bourdonnec B, Goodman AJ, Morales GA, Thomas CJ, Zhang W. Comprehensive survey of chemical libraries for drug discovery and chemical biology: 2007. J Comb Chem. 2008;10(6):753–802.Google Scholar
  102. 102.
    Dolle RE, Le Bourdonnec B, Morales GA, Moriarty KJ, Salvino JM. Comprehensive survey of combinatorial library synthesis: 2005. J Comb Chem. 2006;8(5):597–635.Google Scholar
  103. 103.
    Geysen HM, Schoenen F, Wagner D, Wagner R. Combinatorial compound libraries for drug discovery: an ongoing challenge. Nat Rev Drug Discov. 2003;2(3):222–30.Google Scholar
  104. 104.
    Hall DG, Manku S, Wang F. Solution- and solid-phase strategies for the design, synthesis, and screening of libraries based on natural product templates: a comprehensive survey. J Comb Chem. 2001;3(2):125–50.Google Scholar

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© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  1. 1.Departments of Medicine and OncologySegal Comprehensive Cancer Center, Lady Davis Institute for Medical Research, The Sir Mortimer B. Davis Jewish General Hospital, McGill UniversityMontrealCanada
  2. 2.Steacie Institute for MolecularSciences National Research Council of CanadaOttawaCanada

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