1bmq Citations

Peptide based interleukin-1 beta converting enzyme (ICE) inhibitors: synthesis, structure activity relationships and crystallographic study of the ICE-inhibitor complex.

Chem Pharm Bull (Tokyo) 47 11-21 (1999)
Cited: 34 times
EuropePMC logo PMID: 9987822

Abstract

Based on the X-ray structure of the complex of Ac-Tyr-Val-Ala-Asp-H (L-709049) and interleukin-1 beta converting enzyme (ICE), we synthesized compounds which were derived from 2-NapCO-Val-Pro-Asp-CH2OPh (1) to obtain a potent inhibitor in the cell assay. Among these compounds, (3S)-N-methanesulfonyl-3-[[1-[N-(2-naphthoyl)-L-valyl]-L-prolyl]amino]- 4-oxobutanamide (27c) showed high potency not only in the enzyme assay but also cell assay with IC50 values of 38 nM and 0.23 microM, respectively. Compound 27c, with a c log P value of 1.76, had a more hydrophilic character compared with 1. Compound 27c also dose dependently inhibited LPS-primed ATP-induced IL-1 beta release in mice. The crystal structure of the complex of compound 27c and ICE revealed that compound 27c had further interactions with ICE in the naphthoyl group at the P4 position and in the methyl group of the methanesulfonamidecarbonyl group at the P1 position, compared with L-709049. To our knowledge, compound 27c is the first example that shows a strong inhibitory activity without the carboxyl group at the P1 position.

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  3. Interaction preferences across protein-protein interfaces of obligatory and non-obligatory components are different. De S, Krishnadev O, Srinivasan N, Rekha N. BMC Struct Biol 5 15 (2005)
  4. A highly potent and selective caspase 1 inhibitor that utilizes a key 3-cyanopropanoic acid moiety. Boxer MB, Quinn AM, Shen M, Jadhav A, Leister W, Simeonov A, Auld DS, Thomas CJ. ChemMedChem 5 730-738 (2010)
  5. Statistical analysis of physical-chemical properties and prediction of protein-protein interfaces. Negi SS, Braun W. J Mol Model 13 1157-1167 (2007)
  6. Berkeleyones and related meroterpenes from a deep water acid mine waste fungus that inhibit the production of interleukin 1-β from induced inflammasomes. Stierle DB, Stierle AA, Patacini B, McIntyre K, Girtsman T, Bolstad E. J Nat Prod 74 2273-2277 (2011)
  7. Identification of protein-ligand binding sites by the level-set variational implicit-solvent approach. Guo Z, Li B, Cheng LT, Zhou S, McCammon JA, Che J. J Chem Theory Comput 11 753-765 (2015)
  8. Truly Target-Focused Pharmacophore Modeling: A Novel Tool for Mapping Intermolecular Surfaces. Mortier J, Dhakal P, Volkamer A. Molecules 23 E1959 (2018)
  9. Predicting Protein-Protein Interaction Sites Using Sequence Descriptors and Site Propensity of Neighboring Amino Acids. Kuo TH, Li KB. Int J Mol Sci 17 E1788 (2016)
  10. An integrative approach to develop computational pipeline for drug-target interaction network analysis. Bansal A, Srivastava PA, Singh TR. Sci Rep 8 10238 (2018)
  11. How fullerene derivatives (FDs) act on therapeutically important targets associated with diabetic diseases. Fjodorova N, Novič M, Venko K, Drgan V, Rasulev B, Türker Saçan M, Sağ Erdem S, Tugcu G, Toropova AP, Toropov AA. Comput Struct Biotechnol J 20 913-924 (2022)
  12. Exploring functionally related enzymes using radially distributed properties of active sites around the reacting points of bound ligands. Ueno K, Mineta K, Ito K, Endo T. BMC Struct Biol 12 5 (2012)
  13. CARDIO-PRED: an in silico tool for predicting cardiovascular-disorder associated proteins. Jain P, Thukral N, Gahlot LK, Hasija Y. Syst Synth Biol 9 55-66 (2015)
  14. Enhancing Ezetimibe Anticancer Activity Through Development of Drug Nano-Micelles Formulations: A Promising Strategy Supported by Molecular Docking. Ahmed TA, Ali EMM, Omar AM, Almehmady AM, El-Say KM. Int J Nanomedicine 18 6689-6703 (2023)


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  1. The protein structures that shape caspase activity, specificity, activation and inhibition. Fuentes-Prior P, Salvesen GS. Biochem J 384 201-232 (2004)
  2. Apoptosis-based therapies and drug targets. Fischer U, Schulze-Osthoff K. Cell Death Differ 12 Suppl 1 942-961 (2005)
  3. Small molecular anti-cytokine agents. Wagner G, Laufer S. Med Res Rev 26 1-62 (2006)
  4. Small Molecule Active Site Directed Tools for Studying Human Caspases. Poreba M, Szalek A, Kasperkiewicz P, Rut W, Salvesen GS, Drag M. Chem Rev 115 12546-12629 (2015)
  5. Caspase 8: igniting the death machine. Salvesen GS. Structure 7 R225-9 (1999)

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  1. Discovery of an allosteric site in the caspases. Hardy JA, Lam J, Nguyen JT, O'Brien T, Wells JA. Proc Natl Acad Sci U S A 101 12461-12466 (2004)
  2. Crystal structures of a ligand-free and malonate-bound human caspase-1: implications for the mechanism of substrate binding. Romanowski MJ, Scheer JM, O'Brien T, McDowell RS. Structure 12 1361-1371 (2004)
  3. Highly conserved caspase and Bcl-2 homologues from the sea anemone Aiptasia pallida: lower metazoans as models for the study of apoptosis evolution. Dunn SR, Phillips WS, Spatafora JW, Green DR, Weis VM. J Mol Evol 63 95-107 (2006)
  4. Protective effect of gedunin on TLR-mediated inflammation by modulation of inflammasome activation and cytokine production: Evidence of a multitarget compound. Borges PV, Moret KH, Raghavendra NM, Maramaldo Costa TE, Monteiro AP, Carneiro AB, Pacheco P, Temerozo JR, Bou-Habib DC, das Graças Henriques M, Penido C. Pharmacol Res 115 65-77 (2017)
  5. The structure-function relationship in the clostripain family of peptidases. Labrou NE, Rigden DJ. Eur J Biochem 271 983-992 (2004)
  6. Reaction mechanism of caspases: insights from QM/MM Car-Parrinello simulations. Sulpizi M, Laio A, VandeVondele J, Cattaneo A, Rothlisberger U, Carloni P. Proteins 52 212-224 (2003)
  7. Tethering identifies fragment that yields potent inhibitors of human caspase-1. Fahr BT, O'Brien T, Pham P, Waal ND, Baskaran S, Raimundo BC, Lam JW, Sopko MM, Purkey HE, Romanowski MJ. Bioorg Med Chem Lett 16 559-562 (2006)
  8. Molecular dynamics studies of caspase-3. Sulpizi M, Rothlisberger U, Carloni P. Biophys J 84 2207-2215 (2003)
  9. Structure-based design of nonpeptide inhibitors of interleukin-1beta converting enzyme (ICE, caspase-1). Shahripour AB, Plummer MS, Lunney EA, Albrecht HP, Hays SJ, Kostlan CR, Sawyer TK, Walker NP, Brady KD, Allen HJ, Talanian RV, Wong WW, Humblet C. Bioorg Med Chem 10 31-40 (2002)
  10. An assessment of protein-ligand binding site polarizability. Nayeem A, Krystek S, Stouch T. Biopolymers 70 201-211 (2003)
  11. Carboxylate isosteres for caspase inhibitors: the acylsulfonamide case revisited. Adriaenssens Y, Jiménez Fernández D, Vande Walle L, Elvas F, Joossens J, Lambeir A, Augustyns K, Lamkanfi M, Van der Veken P. Org Biomol Chem 15 7456-7473 (2017)
  12. Development of cell death-based method for the selectivity screening of caspase-1 inhibitors. Chopra P, Gupta S, Dastidar SG, Ray A. Cytotechnology 60 77 (2009)
  13. Structure-based combinatorial library design: discovery of non-peptidic inhibitors of caspases 3 and 8. Head MS, Ryan MD, Lee D, Feng Y, Janson CA, Concha NO, Keller PM, deWolf WE. J Comput Aided Mol Des 15 1105-1117 (2001)
  14. Intermolecular relaxation has little effect on intra-peptide exchange-transferred NOE intensities. Zabell AP, Post CB. J Biomol NMR 22 303-315 (2002)
  15. Bibliography Laser literature watch. J Clin Laser Med Surg 17 275-277 (1999)