96
Views
1
CrossRef citations to date
0
Altmetric
Original Research

The TwistDock workflow for evaluation of bivalent Smac mimetics targeting XIAP

, , , , &
Pages 1373-1388 | Published online: 26 Apr 2019

References

  • Scott FL, Denault JB, Riedl SJ, Shin H, Renatus M, Salvesen GS. XIAP inhibits caspase-3 and -7 using two binding sites: evolutionarily conserved mechanism of IAPs. Embo J. 2005;24(3):645–655. doi:10.1038/sj.emboj.760054415650747
  • Du C, Fang M, Li Y, Li L, Wang X. Smac, a mitochondrial protein that promotes cytochrome c-dependent caspase activation by eliminating IAP inhibition. Cell. 2000;102(1):33–42.10929711
  • Chai JJ, Shiozaki E, Srinivasula SM, et al. Structural basis of caspase-7 inhibition by XIAP. Cell. 2001;104(5):769–780.11257230
  • Verhagen AM, Ekert PG, Pakusch M, et al. Identification of DIABLO, a mammalian protein that promotes apoptosis by binding to and antagonizing IAP proteins. Cell. 2000;102(1):43–53.10929712
  • Chai JJ, Du CY, Wu JW, Kyin S, Wang XD, Shi YG. Structural and biochemical basis of apoptotic activation by Smac/DIABLO. Nature. 2000;406(6798):855–862. doi:10.1038/3502251410972280
  • Huang YH, Rich RL, Myszka DG, Wu H. Requirement of both the second and third BIR domains for the relief of X-linked inhibitor of apoptosis protein (XIAP)-mediated caspase inhibition by Smac. J Biol Chem. 2003;278(49):49517–49522. doi:10.1074/jbc.M31006120014512414
  • Lowe SW, Lin AW. Apoptosis in cancer. Carcinogenesis. 2000;21(3):485–495.10688869
  • Benetatos CA, Mitsuuchi Y, Burns JM, et al. Birinapant (TL32711), a bivalent SMAC mimetic, targets TRAF2-associated cIAPs, abrogates TNF-induced NF-kB activation, and is active in patient-derived xenograft models. Mol Cancer Ther. 2014;13(4):867–879. doi:10.1158/1535-7163.MCT-13-079824563541
  • Chessari G, Buck IM, Day JEH, et al. Fragment-based drug discovery targeting inhibitor of apoptosis proteins: discovery of a non-alanine lead series with dual activity against cIAP1 and XIAP. J Med Chem. 2015;58(16):6574–6588. doi:10.1021/acs.jmedchem.5b0070626218264
  • Gao Z, Tian Y, Wang J, et al. A dimeric Smac/diablo peptide directly relieves caspase-3 inhibition by XIAP. Dynamic and cooperative regulation of XIAP by Smac/Diablo. J Biol Chem. 2007;282(42):30718–30727. doi:10.1074/jbc.M70525820017724022
  • Hird AW, Aquila BM, Hennessy EJ, Vasbinder MM, Yang B. Small molecule inhibitor of apoptosis proteins antagonists: a patent review. Expert Opin Ther Pat. 2015;25(7):755–774. doi:10.1517/13543776.2015.104192225980951
  • Lecis D, Mastrangelo E, Belvisi L, et al. Dimeric Smac mimetics/IAP inhibitors as in vivo-active pro-apoptotic agents. Part II: structural and biological characterization. Bioorg Med Chem. 2012;20(22):6709–6723. doi:10.1016/j.bmc.2012.09.04123062821
  • Li L, Thomas RM, Suzuki H, De Brabander JK, Wang XD, Harran PG. A small molecule Smac mimic potentiates TRAIL- and TNF alpha-mediated cell death. Science. 2004;305(5689):1471–1474. doi:10.1126/science.109823115353805
  • Lu J, Rong S, Sun H, et al. A potent and highly efficacious bivalent Smac mimetic APG-1387 in Phase I clinical development. Eur J Cancer. 2014;50(50):89. doi:10.1016/S0959-8049(14)70394-6
  • Nikolovska-Coleska Z, Meagher JL, Jiang S, et al. Interaction of a cyclic, bivalent Smac mimetic with the X-linked inhibitor of apoptosis protein. Biochemistry-Us. 2008;47(37):9811–9824. doi:10.1021/bi800785y
  • 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):2855–2861. doi:10.1021/jm501892g25695766
  • Sun HY, Nikolovska-Coleska Z, Lu JF, et al. Design, synthesis, and characterization of a potent, nonpeptide, cell-permeable, bivalent smac mimetic that concurrently targets both the BIR2 and BIR3 domains in XIAP. J Am Chem Soc. 2007;129(49):15279–15294. doi:10.1021/ja074725f17999504
  • Fulda S, Vucic D. Targeting IAP proteins for therapeutic intervention in cancer. Nat Rev Drug Discov. 2012;11(2):109–124. doi:10.1038/nrd362722293567
  • Wang SM. Design of small-molecule smac mimetics as IAP antagonists. Curr Top Microbiol. 2011;348:89–113.
  • Speer KF, Cosimini CL, Splan KE. Characterization of a heterodimeric Smac-based peptide that features sequences specific to both the BIR2 and BIR3 domains of the X-linked inhibitor of apoptosis protein. Biopolymers. 2012;98(2):122–130. doi:10.1002/bip.2173222020922
  • Tamm I, Kornblau SM, Segall H, et al. Expression and prognostic significance of IAP-family genes in human cancers and myeloid leukemias. Clin Cancer Res. 2000;6(5):1796–1803.10815900
  • Salvesen GS, Duckett CS. IAP proteins: blocking the road to death’s door. Nat Rev Mol Cell Bio. 2002;3(6):401–410. doi:10.1038/nrm83012042762
  • Reubold TF, Eschenburg S. A molecular view on signal transduction by the apoptosome. Cell Signal. 2012;24(7):1420–1425. doi:10.1016/j.cellsig.2012.03.00722446004
  • Crowder RN, El-Deiry WS. Caspase-8 regulation of TRAIL-mediated cell death. Exp Oncol. 2012;34(3):160–164.23070000
  • Cohen GM. Caspases: the executioners of apoptosis. Biochem J. 1997;326(Pt 1):1–16.9337844
  • Obexer P, Ausserlechner MJ. X-linked inhibitor of apoptosis protein – a critical death resistance regulator and therapeutic target for personalized cancer therapy. Front Oncol. 2014;4:197. doi:10.3389/fonc.2014.0019725120954
  • Lukacs C, Belunis C, Crowther R, et al. The structure of XIAP BIR2: understanding the selectivity of the BIR domains. Acta Crystallogr D. 2013;69:1717–1725. doi:10.1107/S090744491301628423999295
  • Peng YF, Sun HY, Lu JF, et al. Bivalent Smac mimetics with a diazabicyclic core as highly potent antagonists of XIAP and cIAP1/2 and novel anticancer agents. J Med Chem. 2012;55(1):106–114. doi:10.1021/jm201072x22148838
  • Sun H, Liu L, Lu J, et al. Potent bivalent Smac mimetics: effect of the linker on binding to inhibitor of apoptosis proteins (IAPs) and anticancer activity. J Med Chem. 2011;54(9):3306–3318. doi:10.1021/jm101651b21462933
  • Condon SM, Mitsuuchi Y, Deng YJ, et al. Birinapant, a Smac-Mimetic with improved tolerability for the treatment of solid tumors and hematological malignancies. J Med Chem. 2014;57(9):3666–3677. doi:10.1021/jm500176w24684347
  • Krishnamurthy VM, Estroff LA, Whitesides GM. Multivalency in ligand design In: Jahnke W and  Erlanson DA, editors. Fragment-Based Approaches in Drug Discovery. Weinheim: Wiley-VCH Verlag GmbH & Co. KGaA; 2006:11–53.
  • Cossu F, Milani M, Vachette P, et al. Structural insight into inhibitor of apoptosis proteins recognition by a potent divalent Smac-mimetic. PLoS One. 2012;7(11). doi:10.1371/journal.pone.0049527.
  • Zhang H, Xi W, Hansmann UH, Wei Y. Fibril–barrel transitions in cylindrin amyloids. J Chem Theory Comput. 2017;13(8):3936–3944. doi:10.1021/acs.jctc.7b0038328671829
  • Wu G, Chai JJ, Suber TL, et al. Structural basis of IAP recognition by Smac/DIABLO. Nature. 2000;408(6815):1008–1012. doi:10.1038/3505001211140638
  • Weininger D. SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules. J Chem Inf Comput Sci. 1988;28(1):31–35.
  • Blaney JM, Dixon JS. Distance geometry in molecular modeling In: Lipkowitz KB, Boyd DB, editors. Reviews in Computational Chemistry, Volume 5. New York: VCH Publishers, Inc.; 2007:299–335.
  • Landrum G and Penzotti J.RDKit: Open-Source Cheminformatics Software [Computer Program]. Available from: http://www.rdkit.org/. Accessed December 12, 2014.
  • Halgren TA. Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94. J Comput Chem. 1996;17(5–6):490–519. doi:10.1002/(SICI)1096-987X(199604)17:5/6<>1.0.CO;2-C
  • Selleck Chemicals. AT-406 (SM-406, ARRY-334543). Available from: http://www.selleckchem.com/products/at-406.html. Accessed 1120, 2013.
  • Trott O, Olson AJ. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem. 2010;31(2):455–461. doi:10.1002/jcc.2133419499576
  • Wang JM, Wolf RM, Caldwell JW, Kollman PA, Case DA. Development and testing of a general amber force field. J Comput Chem. 2004;25(9):1157–1174. doi:10.1002/jcc.2003515116359
  • Case DA, Babin V, Berryman JT, et al. AMBER 14 [Computer Program] San Francisco: University of California; 2014.
  • Pang YP, Xu K, Yazal JE, Prendergas FG. Successful molecular dynamics simulation of the zinc-bound farnesyltransferase using the cationic dummy atom approach. Protein Sci. 2000;9(10):1857–1865.11106157
  • Phillips JC, Braun R, Wang W, et al. Scalable molecular dynamics with NAMD. J Comput Chem. 2005;26(16):1781–1802. doi:10.1002/jcc.2028916222654
  • Heyer LJ, Kruglyak S, Yooseph S. Exploring expression data: identification and analysis of coexpressed genes. Genome Res. 1999;9(11):1106–1115.10568750
  • Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J Mol Graph Model. 1996;14(1):33–38. doi:10.1016/0263-7855(96)00018-5
  • Miller BR, McGee TD, Swails JM, Homeyer N, Gohlke H, Roitberg AE. MMPBSA.py: an efficient program for end-state free energy calculations. J Chem Theory Comput. 2012;8(9):3314–3321. doi:10.1021/ct300418h26605738
  • Weiser J, Shenkin PS, Still WC. Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO). J Comput Chem. 1999;20(2):217–230. doi:10.1002/(ISSN)1096-987X
  • Roux B. The calculation of the potential of mean force using computer simulations. Comput Phys Commun. 1995;91(1–3):275–282. doi:10.1016/0010-4655(95)00053-I
  • Lemieux C. Preface In: Monte Carlo and Quasi-Monte Carlo Sampling. Springer Series in Statistics Vol. 2009 New York: Springer Science+Business Media, LLC; 2009:vii.
  • Cossu F, Milani M, Mastrangelo E, et al. Structural basis for bivalent smac-mimetics recognition in the IAP protein family. J Mol Biol. 2009;392(3):630–644. doi:10.1016/j.jmb.2009.04.03319393243
  • Splan KE, Allen JE, McLendon GL. Biochemical basis for enhanced binding of peptide dimers to X-linked inhibitor of apoptosis protein. Biochemistry-Us. 2007;46(42):11938–11944. doi:10.1021/bi061938t
  • Jahromi AH, Fu Y, Miller KA, et al. Developing bivalent ligands to target CUG triplet repeats, the causative agent of myotonic dystrophy type 1. J Med Chem. 2013;56(23):9471–9481. doi:10.1021/jm400794z24188018
  • Joce C, White R, Stockley PG, Warriner S, Turnbull WB, Nelson A. Design, synthesis and in vitro evaluation of novel bivalent S-adenosylmethionine analogues. Bioorg Med Chem Lett. 2012;22(1):278–284. doi:10.1016/j.bmcl.2011.11.01722137339
  • Shan M, Bujotzek A, Abendroth F, et al. Conformational analysis of bivalent estrogen receptor ligands: from intramolecular to intermolecular binding. Chembiochem. 2011;12(17):2587–2598. doi:10.1002/cbic.20110052922025425
  • Sheng R, Sun H, Liu L, et al. A potent bivalent Smac Mimetic (SM-1200) achieving rapid, complete, and durable tumor regression in mice. J Med Chem. 2013;56(10):3969–3979. doi:10.1021/jm400216d23651223
  • Silke J, Vaux DL. IAP gene deletion and conditional knockout models. Semin Cell Dev Biol. 2015;39:97–105. doi:10.1016/j.semcdb.2014.12.00425545814
  • Zhang A, Liu ZL, Kan Y. Receptor dimerization – rationale for the design of bivalent ligands. Curr Top Med Chem. 2007;7(4):343–345.17305575