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Molecular Designing of Small-Molecule Inhibitors for Apoptosis Regulation

Chapter
Part of the Current Human Cell Research and Applications book series (CHCRA)

Abstract

Apoptosis is a distinctive mode of programmed cell death, which is involved in organ life cycle in multicellular organism. Dysregulation of apoptotic processes has been implicated in a wide variety of diseases, such as cancer, neurodegenerative disorders, and ischemic injury. To date, many kinds of key proteins in apoptotic processes have been identified and targeted for therapeutic strategies. Several effective small molecules have been designed to modulate the key regulatory proteins, such as Bcl-2, XIAP, MDM2, and caspases. This chapter reviews the current development of small-molecule inhibitors targeting apoptosis regulatory proteins, and as an example, our structure-based approaches for the designing of caspase-3-specific inhibitors will be described.

Keywords

Apoptosis Protein-protein interactions Structure-based drug design Small molecules 

References

  1. 1.
    Lockshin RA, Williams CM. Programmed cell death—I. Cytology of degeneration in the intersegmental muscles of the pernyi silkmoth. J Insect Physiol. 1965;11:123–33.CrossRefPubMedGoogle Scholar
  2. 2.
    Kerr JF, Wyllie AH, Currie AR. Apoptosis: a basic biological phenomenon with wide-ranging implications in tissue kinetics. Br J Cancer. 1972;26(4):239–57.CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Häcker G. The morphology of apoptosis. Cell Tissue Res. 2000;301(1):5–17.CrossRefPubMedGoogle Scholar
  4. 4.
    Toné S, Sugimoto K, Tanda K, et al. Three distinct stages of apoptotic nuclear condensation revealed by time-lapse imaging, biochemical and electron microscopy analysis of cell-free apoptosis. Exp Cell Res. 2007;313(16):3635–44.CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Wyllie AH. Glucocorticoid-induced thymocyte apoptosis is associated with endogenous endonuclease activation. Nature. 1980;284(5756):555–6.CrossRefPubMedGoogle Scholar
  6. 6.
    Kannan K, Jain SK. Oxidative stress and apoptosis. Pathophysiology. 2000;7(3):153–63.CrossRefPubMedGoogle Scholar
  7. 7.
    Takasawa R, Nakamura H, Mori T, et al. Differential apoptotic pathways in human keratinocyte HaCaT cells exposed to UVB and UVC. Apoptosis. 2005;10(5):1121–30.CrossRefPubMedGoogle Scholar
  8. 8.
    Roulston A, Marcellus RC, Branton PE. Viruses and apoptosis. Annu Rev Microbiol. 1999;53:577–628.CrossRefPubMedGoogle Scholar
  9. 9.
    Fadeel B, Orrenius S, Zhivotovsky B. Apoptosis in human disease: a new skin for the old ceremony? Biochem Biophys Res Commun. 1999;266(3):699–717.CrossRefPubMedGoogle Scholar
  10. 10.
    Kim TW, Pettingell WH, Jung YK, et al. Alternative cleavage of Alzheimer-associated presenilins during apoptosis by a caspase-3 family protease. Science. 1997;277(5324):373–6.CrossRefPubMedGoogle Scholar
  11. 11.
    Guicciardi ME, Gores GJ. Apoptosis: a mechanism of acute and chronic liver injury. Gut. 2005;54(7):1024–33.CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Barreyro FJ, Holod S, Finocchietto PV, et al. The pan-caspase inhibitor Emricasan (IDN-6556) decreases liver injury and fibrosis in a murine model of non-alcoholic steatohepatitis. Liver Int. 2015;35(3):953–66.CrossRefPubMedGoogle Scholar
  13. 13.
    McIlwain DR, Berger T, Mak TW. Caspase functions in cell death and disease. Cold Spring Harb Perspect Biol. 2013;5(4):a008656.CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Baskin-Bey ES, Washburn K, Feng S, et al. Clinical trial of the pan-caspase inhibitor, IDN-6556, in human liver preservation injury. Am J Transplant. 2007;7(1):218–25.CrossRefPubMedGoogle Scholar
  15. 15.
    Plati J, Bucur O, Khosravi-Far R. Dysregulation of apoptotic signaling in cancer: molecular mechanisms and therapeutic opportunities. J Cell Biochem. 2008;104(4):1124–49.CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Birchall MA, Winterford CM, Allan DJ, et al. Apoptosis in normal epithelium, premalignant and malignant lesions of the oropharynx and oral cavity: a preliminary study. Eur J Cancer B Oral Oncol. 1995;31B(6):380–3.CrossRefPubMedGoogle Scholar
  17. 17.
    Weinstein RS, Manolagas SC. Apoptosis and osteoporosis. Am J Med. 2000;108(2):153–64.CrossRefPubMedGoogle Scholar
  18. 18.
    Fulda S. Tumor resistance to apoptosis. Int J Cancer. 2009;124(3):511–5.CrossRefPubMedGoogle Scholar
  19. 19.
    Hassan M, Watari H, AbuAlmaaty A, et al. Apoptosis and molecular targeting therapy in cancer. Biomed Res Int. 2014;2014:150845.PubMedPubMedCentralGoogle Scholar
  20. 20.
    Deveraux QL, Reed JC. IAP family proteins—suppressors of apoptosis. Genes Dev. 1999;13(3):239–52.CrossRefPubMedGoogle Scholar
  21. 21.
    Scott FL, Denault J-B, Riedl SJ, et al. XIAP inhibits caspase-3 and -7 using two binding sites: evolutionarily conserved mechanism of IAPs. EMBO J. 2005;24(3):645–55.CrossRefPubMedPubMedCentralGoogle Scholar
  22. 22.
    Shiozaki EN, Chai J, Rigotti DJ, et al. Mechanism of XIAP-mediated inhibition of caspase-9. Mol Cell. 2003;11(2):519–27.CrossRefPubMedGoogle Scholar
  23. 23.
    Cai Q, Sun H, Peng Y, et al. A potent and orally active antagonist of multiple inhibitor of apoptosis proteins (IAPs) (SM-406/AT-406) in clinical development for cancer treatment. J Med Chem. 2011;54(8):2714–26.CrossRefPubMedPubMedCentralGoogle Scholar
  24. 24.
    Wu G, Chai J, Suber TL, et al. Structural basis of IAP recognition by Smac/DIABLO. Nature. 2000;408(6815):1008–12.CrossRefPubMedGoogle Scholar
  25. 25.
    Kvansakul M, Hinds MG. Structural biology of the Bcl-2 family and its mimicry by viral proteins. Cell Death Dis. 2013;4:e909.CrossRefPubMedPubMedCentralGoogle Scholar
  26. 26.
    Kussie PH, Gorina S, Marechal V, et al. Structure of the MDM2 oncoprotein bound to the p53 tumor suppressor transactivation domain. Science. 1996;274(5289):948–53.CrossRefPubMedGoogle Scholar
  27. 27.
    Wei Y, Fox T, Chambers SP, et al. The structures of caspases-1, −3, −7 and −8 reveal the basis for substrate and inhibitor selectivity. Chem Biol. 2000;7(6):423–32.CrossRefPubMedGoogle Scholar
  28. 28.
    Elmore S. Apoptosis: a review of programmed cell death. Toxicol Pathol. 2007;35(4):495–516.CrossRefPubMedPubMedCentralGoogle Scholar
  29. 29.
    Micheau O, Tschopp J. Induction of TNF receptor I-mediated apoptosis via two sequential signaling complexes. Cell. 2003;114(2):181–90.CrossRefPubMedGoogle Scholar
  30. 30.
    Waring P, Müllbacher A. Cell death induced by the Fas/Fas ligand pathway and its role in pathology. Immunol Cell Biol. 1999;77(4):312–7.CrossRefPubMedGoogle Scholar
  31. 31.
    Schneider P, Thome M, Burns K, et al. TRAIL receptors 1 (DR4) and 2 (DR5) signal FADD-dependent apoptosis and activate NF-kappaB. Immunity. 1997;7(6):831–6.CrossRefPubMedGoogle Scholar
  32. 32.
    Walczak H. Death receptor-ligand systems in cancer, cell death, and inflammation. Cold Spring Harb Perspect Biol. 2013;5(5):a008698.CrossRefPubMedPubMedCentralGoogle Scholar
  33. 33.
    Chang DW, Xing Z, Capacio VL, et al. Interdimer processing mechanism of procaspase-8 activation. EMBO J. 2003;22(16):4132–42.CrossRefPubMedPubMedCentralGoogle Scholar
  34. 34.
    Stennicke HR, Jürgensmeier JM, Shin H, et al. Pro-caspase-3 is a major physiologic target of caspase-8. J Biol Chem. 1998;273(42):27084–90.CrossRefPubMedGoogle Scholar
  35. 35.
    Enari M, Sakahira H, Yokoyama H, et al. A caspase-activated DNase that degrades DNA during apoptosis, and its inhibitor ICAD. Nature. 1998;391(6662):43–50.CrossRefPubMedGoogle Scholar
  36. 36.
    Los M, Mozoluk M, Ferrari D, et al. Activation and caspase-mediated inhibition of PARP: a molecular switch between fibroblast necrosis and apoptosis in death receptor signaling. Mol Biol Cell. 2002;13(3):978–88.CrossRefPubMedPubMedCentralGoogle Scholar
  37. 37.
    Sahara S, Aoto M, Eguchi Y, et al. Acinus is a caspase-3-activated protein required for apoptotic chromatin condensation. Nature. 1999;401(6749):168–73.CrossRefPubMedGoogle Scholar
  38. 38.
    Wolf BB, Schuler M, Echeverri F, et al. Caspase-3 is the primary activator of apoptotic DNA fragmentation via DNA fragmentation factor-45/inhibitor of caspase-activated DNase inactivation. J Biol Chem. 1999;274(43):30651–6.CrossRefPubMedGoogle Scholar
  39. 39.
    Li H, Zhu H, CJ X, et al. Cleavage of BID by caspase 8 mediates the mitochondrial damage in the Fas pathway of apoptosis. Cell. 1998;94(4):491–501.CrossRefPubMedGoogle Scholar
  40. 40.
    Bellail AC, Qi L, Mulligan P, et al. TRAIL agonists on clinical trials for cancer therapy: the promises and the challenges. Rev Recent Clin Trials. 2009;4(1):34–41.CrossRefPubMedGoogle Scholar
  41. 41.
    Wang G, Wang X, Yu H, et al. Small-molecule activation of the TRAIL receptor DR5 in human cancer cells. Nat Chem Biol. 2013;9(2):84–9.CrossRefPubMedGoogle Scholar
  42. 42.
    Saelens X, Festjens N, Vande Walle L, et al. Toxic proteins released from mitochondria in cell death. Oncogene. 2004;23(16):2861–74.CrossRefPubMedGoogle Scholar
  43. 43.
    Cain K, Bratton SB, Cohen GM. The Apaf-1 apoptosome: a large caspase-activating complex. Biochimie. 2002;84(2–3):203–14.CrossRefPubMedGoogle Scholar
  44. 44.
    Tsujimoto Y. Role of Bcl-2 family proteins in apoptosis: apoptosomes or mitochondria? Genes Cells. 1998;3(11):697–707.CrossRefPubMedGoogle Scholar
  45. 45.
    Shamas-Din A, Kale J, Leber B, et al. Mechanisms of action of Bcl-2 family proteins. Cold Spring Harb Perspect Biol. 2013;5(4):a008714.CrossRefPubMedPubMedCentralGoogle Scholar
  46. 46.
    Yip KW, Reed JC. Bcl-2 family proteins and cancer. Oncogene. 2008;27(50):6398–406.CrossRefPubMedGoogle Scholar
  47. 47.
    Ding J, Zhang Z, Roberts GJ, et al. Bcl-2 and Bax interact via the BH1-3 groove-BH3 motif interface and a novel interface involving the BH4 motif. J Biol Chem. 2010;285(37):28749–63.CrossRefPubMedPubMedCentralGoogle Scholar
  48. 48.
    Lessene G, Czabotar PE, Colman PM. BCL-2 family antagonists for cancer therapy. Nat Rev Drug Discov. 2008;7(12):989–1000.CrossRefPubMedGoogle Scholar
  49. 49.
    Liu Z, Sun C, Olejniczak ET, et al. Structural basis for binding of Smac/DIABLO to the XIAP BIR3 domain. Nature. 2000;408(6815):1004–8.CrossRefPubMedGoogle Scholar
  50. 50.
    Gyrd-Hansen M, Meier P. IAPs: from caspase inhibitors to modulators of NF-kappaB, inflammation and cancer. Nat Rev Cancer. 2010;10(8):561–74.CrossRefPubMedGoogle Scholar
  51. 51.
    Moll UM, Petrenko O. The MDM2-p53 interaction. Mol Cancer Res. 2003;1(14):1001–8.PubMedGoogle Scholar
  52. 52.
    Zhao Y, Aguilar A, Bernard D, et al. Small-molecule inhibitors of the MDM2-p53 protein-protein interaction (MDM2 inhibitors) in clinical trials for cancer treatment. J Med Chem. 2015;58(3):1038–52.CrossRefPubMedGoogle Scholar
  53. 53.
    Shangary S, Johnson DE. Peptides derived from BH3 domains of Bcl-2 family members: a comparative analysis of inhibition of Bcl-2, Bcl-xL and Bax oligomerization, induction of cytochrome c release, and activation of cell death. Biochemistry. 2002;41(30):9485–95.CrossRefPubMedGoogle Scholar
  54. 54.
    Petros AM, Nettesheim DG, Wang Y, et al. Rationale for Bcl-xL/Bad peptide complex formation from structure, mutagenesis, and biophysical studies. Protein Sci. 2000;9(12):2528–34.CrossRefPubMedPubMedCentralGoogle Scholar
  55. 55.
    Yin H, Lee GI, Sedey KA, et al. Terphenyl-based Bak BH3 alpha-helical proteomimetics as low-molecular-weight antagonists of Bcl-xL. J Am Chem Soc. 2005;127(29):10191–6.CrossRefPubMedGoogle Scholar
  56. 56.
    Cao X, Yap JL, Newell-Rogers MK, et al. The novel BH3 α-helix mimetic JY-1-106 induces apoptosis in a subset of cancer cells (lung cancer, colon cancer and mesothelioma) by disrupting Bcl-xL and Mcl-1 protein-protein interactions with Bak. Mol Cancer. 2013;12(1):42.CrossRefPubMedPubMedCentralGoogle Scholar
  57. 57.
    Wang Z, Song T, Feng Y, et al. Bcl-2/MDM2 dual inhibitors based on universal pyramid-like α-helical mimetics. J Med Chem. 2016;59(7):3152–62.CrossRefPubMedGoogle Scholar
  58. 58.
    Petros AM, Dinges J, Augeri DJ, et al. Discovery of a potent inhibitor of the antiapoptotic protein Bcl-xL from NMR and parallel synthesis. J Med Chem. 2006;49(2):656–63.CrossRefPubMedGoogle Scholar
  59. 59.
    Oltersdorf T, Elmore SW, Shoemaker AR, et al. An inhibitor of Bcl-2 family proteins induces regression of solid tumours. Nature. 2005;435(7042):677–81.CrossRefPubMedGoogle Scholar
  60. 60.
    Wei Y, Fan T, Yu M. Inhibitor of apoptosis proteins and apoptosis. Acta Biochim Biophys Sin Shanghai. 2008;40(4):278–88.CrossRefPubMedGoogle Scholar
  61. 61.
    Shiraki K, Sugimoto K, Yamanaka Y, et al. Overexpression of X-linked inhibitor of apoptosis in human hepatocellular carcinoma. Int J Mol Med. 2003;12(5):705–8.PubMedGoogle Scholar
  62. 62.
    Sharma SK, Straub C, Zawel L. Development of peptidomimetics targeting IAPs. Int J Pept Res Ther. 2006;12(1):21–32.CrossRefPubMedPubMedCentralGoogle Scholar
  63. 63.
    Flygare JA, Beresini M, Budha N, et al. Discovery of a potent small-molecule antagonist of inhibitor of apoptosis (IAP) proteins and clinical candidate for the treatment of cancer (GDC-0152). J Med Chem. 2012;55(9):4101–13.CrossRefPubMedPubMedCentralGoogle Scholar
  64. 64.
    Brunckhorst MK, Lerner D, Wang S, et al. AT-406, an orally active antagonist of multiple inhibitor of apoptosis proteins, inhibits progression of human ovarian cancer. Cancer Biol Ther. 2012;13(9):804–11.CrossRefPubMedPubMedCentralGoogle Scholar
  65. 65.
    Varfolomeev E, Blankenship JW, Wayson SM, et al. IAP antagonists induce autoubiquitination of c-IAPs, NF-κB activation, and TNFα-dependent apoptosis. Cell. 2007;131(4):669–81.CrossRefPubMedGoogle Scholar
  66. 66.
    Eschenburg G, Eggert A, Schramm A, et al. Smac mimetic LBW242 sensitizes XIAP-overexpressing neuroblastoma cells for TNF-α-independent apoptosis. Cancer Res. 2012;72(10):2645–56.CrossRefPubMedGoogle Scholar
  67. 67.
    Benetatos CA, Mitsuuchi Y, Burns JM, et al. Birinapant (TL32711), a bivalent SMAC mimetic, targets TRAF2-associated cIAPs, abrogates TNF-induced NF-κB activation, and is active in patient-derived xenograft models. Mol Cancer Ther. 2014;13(4):867–79.CrossRefPubMedGoogle Scholar
  68. 68.
    Seigal BA, Connors WH, Fraley A, et al. The discovery of macrocyclic XIAP antagonists from a DNA-programmed chemistry library, and their optimization to give lead compounds with in vivo antitumor activity. J Med Chem. 2015;58(6):2855–61.CrossRefPubMedGoogle Scholar
  69. 69.
    Bieging KT, Mello SS, Attardi LD. Unravelling mechanisms of p53-mediated tumour suppression. Nat Rev Cancer. 2014;14(5):359–70.CrossRefPubMedPubMedCentralGoogle Scholar
  70. 70.
    Vogelstein B, Lane D, Levine AJ. Surfing the p53 network. Nature. 2000;408(6810):307–10.CrossRefPubMedGoogle Scholar
  71. 71.
    Vassilev LT, BT V, Graves B, et al. In vivo activation of the p53 pathway by small-molecule antagonists of MDM2. Science. 2004;303(5659):844–8.CrossRefPubMedGoogle Scholar
  72. 72.
    Shangary S, Wang S. Small-molecule inhibitors of the MDM2-p53 protein-protein interaction to reactivate p53 function: a novel approach for cancer therapy. Annu Rev Pharmacol Toxicol. 2009;49:223–41.CrossRefPubMedPubMedCentralGoogle Scholar
  73. 73.
    Vu B, Wovkulich P, Pizzolato G, et al. Discovery of RG7112: a small-molecule MDM2 inhibitor in clinical development. ACS Med Chem Lett. 2013;4(5):466–9.CrossRefPubMedPubMedCentralGoogle Scholar
  74. 74.
    Ding Q, Zhang Z, Liu J-J, et al. Discovery of RG7388, a potent and selective p53–MDM2 inhibitor in clinical development. J Med Chem. 2013;56(14):5979–83.CrossRefPubMedGoogle Scholar
  75. 75.
    Wade M, Wang YV, Wahl GM. The p53 orchestra: Mdm2 and Mdmx set the tone. Trends Cell Biol. 2010;20(5):299–309.CrossRefPubMedPubMedCentralGoogle Scholar
  76. 76.
    Shangary S, Qin D, McEachern D, et al. Temporal activation of p53 by a specific MDM2 inhibitor is selectively toxic to tumors and leads to complete tumor growth inhibition. Proc Natl Acad Sci U S A. 2008;105(10):3933–8.CrossRefPubMedPubMedCentralGoogle Scholar
  77. 77.
    Reed D, Shen Y, Shelat AA, et al. Identification and characterization of the first small molecule inhibitor of MDMX. J Biol Chem. 2010;285(14):10786–9.CrossRefPubMedPubMedCentralGoogle Scholar
  78. 78.
    Bista M, Smithson D, Pecak A, et al. On the mechanism of action of SJ-172550 in inhibiting the interaction of MDM4 and p53. PLoS One. 2012;7(6):e37518.CrossRefPubMedPubMedCentralGoogle Scholar
  79. 79.
    Graves B, Thompson T, Xia M, et al. Activation of the p53 pathway by small-molecule-induced MDM2 and MDMX dimerization. Proc Natl Acad Sci U S A. 2012;109(29):11788–93.CrossRefPubMedPubMedCentralGoogle Scholar
  80. 80.
    Rotonda J, Nicholson DW, Fazil KM, et al. The three-dimensional structure of apopain/CPP32, a key mediator of apoptosis. Nat Struct Biol. 1996;3(7):619–25.CrossRefPubMedGoogle Scholar
  81. 81.
    Lazebnik YA, Kaufmann SH, Desnoyers S, et al. Cleavage of poly(ADP-ribose) polymerase by a proteinase with properties like ICE. Nature. 1994;371(6495):346–7.CrossRefPubMedGoogle Scholar
  82. 82.
    Garcia-Calvo M, Peterson EP, Leiting B, et al. Inhibition of human caspases by peptide-based and macromolecular inhibitors. J Biol Chem. 1998;273(49):32608–13.CrossRefPubMedGoogle Scholar
  83. 83.
    Yoshimori A, Takasawa R, Tanuma S. A novel method for evaluation and screening of caspase inhibitory peptides by the amino acid positional fitness score. BMC Pharmacol. 2004;4:7.CrossRefPubMedPubMedCentralGoogle Scholar
  84. 84.
    Morris GM, Goodsell DS, Haliday RS, et al. Automated docking using a lamarckian genetic algorithm and an empirical binding free energy function. J Comp Chem. 1998;19(14):1639–62.CrossRefGoogle Scholar
  85. 85.
    Na S, Chuang TH, Cunningham A, et al. D4-GDI, a substrate of CPP32, is proteolyzed during Fas-induced apoptosis. J Biol Chem. 1996;271(19):11209–13.CrossRefPubMedGoogle Scholar
  86. 86.
    Yoshimori A, Sakai J, Sunaga S, et al. Structural and functional definition of the specificity of a novel caspase-3 inhibitor, Ac-DNLD-CHO. BMC Pharmacol. 2007;7:8.CrossRefPubMedPubMedCentralGoogle Scholar
  87. 87.
    Sakai J, Yoshimori A, Nose Y, et al. Structure-based discovery of a novel non-peptidic small molecular inhibitor of caspase-3. Bioorg Med Chem. 2008;16(9):4854–9.CrossRefPubMedGoogle Scholar

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© Springer Nature Singapore Pte Ltd. 2018

Authors and Affiliations

  1. 1.Institute for Theoretical Medicine, Inc.YokohamaJapan
  2. 2.Department of Biochemistry, Faculty of Pharmaceutical SciencesTokyo University of ScienceChibaJapan

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