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Articles

A computational analysis of the binding free energies of apoptosis signal-regulating kinase 1 inhibitors from different chemotypes

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Pages 1558-1568 | Received 18 Nov 2020, Accepted 19 Apr 2021, Published online: 12 May 2021

References

  • Pan J, Chang Q, Wang X, et al. Reactive oxygen species-activated Akt/ASK1/p38 signaling pathway in nickel compound-induced apoptosis in BEAS 2B cells. Chem Res Toxicol. 2010;23:568–577.
  • Sano R, Reed JC. ER stress-induced cell death mechanisms. Biochim Biophys Acta. 2013;1833:3460–3470.
  • Sumbayev V. LPS-induced Toll-like receptor 4 signalling triggers cross-talk of apoptosis signal-regulating kinase 1 (ASK1) and HIF-1alpha protein. FEBS Lett. 2008;582:319–326.
  • Rastogi S, Rizwani W, Joshi B, et al. TNF-α response of vascular endothelial and vascular smooth muscle cells involve differential utilization of ASK1 kinase and p73. Cell Death Differ. 2012;19:274–283.
  • Song J, Park KA, Lee WT, et al. Apoptosis signal regulating kinase 1 (ASK1): potential as a therapeutic target for Alzheimer’s disease. Int J Mol Sci. 2014;15:2119–2129.
  • Lee KW, Woo JM, Im JY, et al. Apoptosis signal-regulating kinase 1 modulates the phenotype of α-synuclein transgenic mice. Neurobiol Aging. 2015;36:519–526.
  • Toyama K, Koibuchi N, Uekawa K, et al. Apoptosis signal-regulating kinase 1 is a novel target molecule for cognitive impairment induced by chronic cerebral hypoperfusion. Arterioscler Thromb Vasc Biol. 2014;34:616–625.
  • Nakamura T, Kataoka K, Fukuda M, et al. Critical role of apoptosis signal-regulating kinase 1 in aldosterone/salt-induced cardiac inflammation and fibrosis. Hypertension. 2009;54:544–551.
  • Guo X, Harada C, Namekata K, et al. Regulation of the severity of neuroinflammation and demyelination by TLR-ASK1-p38 pathway. EMBO Mol Med. 2010;2:504–515.
  • Mnich SJ, Blanner PM, Hu LG, et al. Critical role for apoptosis signal-regulating kinase 1 in the development of inflammatory K/BxN serum-induced arthritis. Int Immunopharmacol. 2010;10:1170–1176.
  • Yamaguchi K, Takeda K, Kadowaki H, et al. Involvement of ASK1-p38 pathway in the pathogenesis of diabetes triggered by pancreatic β cell exhaustion. Biochim Biophys Acta. 2013;1830:3656–3663.
  • Iriyama T, Takeda K, Nakamura H, et al. ASK1 and ASK2 differentially regulate the counteracting roles of apoptosis and inflammation in tumorigenesis. EMBO J. 2009;28:843–853.
  • Hayakawa Y, Hirata Y, Nakagawa H, et al. Apoptosis signal-regulating kinase 1 and cyclin D1 compose a positive feedback loop contributing to tumor growth in gastric cancer. Proc Natl Acad USA. 2011;108:780–785.
  • Brys R, Gibson K, Poljak T, et al. Chapter three – discovery and development of ASK1 inhibitors. Prog Med Chem. 2020;59:101–179.
  • Volynets GP, Bdzhola VG, Kukharenko OP, et al. Protein kinase ASK1 as potential therapeutic target. Biopolym Cell. 2009;25:169–180.
  • Okamoto M, Saito N, Kojima H, et al. Identification of novel ASK1 inhibitors using virtual screening. Bioorg Med Chem. 2011;19:486–489.
  • Terao Y, Suzuki H, Yoshikawa M, et al. Design and biological evaluation of imidazo[1,2-a]pyridines as novel and potent ASK1 inhibitors. Bioorg Med Chem Lett. 2012;22:7326–7329.
  • Singh O, Shillings A, Craggs P, et al. Crystal structures of ASK1-inhibitor complexes provide a platform for structure-based drug design. Protein Sci. 2013;22:1071–1077.
  • Volynets GP, Bdzhola VG, Kukharenko OP, et al. Identification of low-molecular inhibitors of proteinase ASK1. Ukr Biokhim Zh. 2010;82:41–50.
  • Volynets GP, Chekanov MO, Synyugin AR, et al. Identification of 3H-naphtho[1,2,3-de]quinoline-2,7-diones as inhibitors of apoptosis signal-regulating kinase 1 (ASK1). J Med Chem. 2011;54:2680–2686.
  • Volynets GP, Bdzhola VG, Golub AG, et al. Rational design of apoptosis signal-regulating kinase 1 inhibitors: discovering novel structural scaffold. Eur J Med Chem. 2013;61:104–115.
  • Starosyla SA, Volynets GP, Lukashov SS, et al. Identification of apoptosis signal-regulating kinase 1 (ASK1) inhibitors among the derivatives of benzothiazol-2-yl-3-hydroxy-5-phenyl-1,5-dihydro-pyrrol-2-one. Bioorg Med Chem. 2015;23:2489–2497.
  • Tesch GH, Ma FY, Han Y, et al. ASK1 inhibitor halts progression of diabetic nephropathy in Nos3-deficient mice. Diabetes. 2015;64:3903–3913.
  • Zheng S, Long L, Li Y, et al. A novel ASK inhibitor AGI-1067 inhibits TLR-4-mediated activation of ASK1 by preventing dissociation of thioredoxin from ASK1. Cardiovasc Pharm Open Access. 2015;4(132).
  • Wang Y, Hou S, Tong Y, et al. Discovery of potent apoptosis signal-regulating kinase 1 inhibitors via integrated computational strategy and biological evaluation. J Biomol Struct Dyn. 2020;38:4385–4396.
  • Monastyrskyi A, Bayle S, Quereda V, et al. Discovery of 2-arylquinazoline derivatives as a new class of ASK1 inhibitors. Bioorg Med Chem Lett. 2018;28:400–404.
  • Lanier M, Pickens J, Bigi SV, et al. Structure-based design of ASK1 inhibitors as potential agents for heart failure. ACS Med Chem Lett. 2017;8:316–320.
  • Gibson TS, Johnson B, Fanjul A, et al. Structure-based drug design of novel ASK1 inhibitors using an integrated lead optimization strategy. Bioorg Med Chem Lett. 2017;27:1709–1713.
  • Lovering F, Morgan P, Allais C, et al. Rational approach to highly potent and selective apoptosis signal-regulating kinase 1 (ASK1) inhibitors. Eur J Med Chem. 2018;145:606–621.
  • Himmelbauer MK, Xin Z, Jones JH, et al. Rational design and optimization of a novel class of macrocyclic apoptosis signal-regulating kinase 1 inhibitors. J Med Chem. 2019;62:10740–10756.
  • Xin Z, Himmelbauer MK, Jones JH, et al. Discovery of CNS-penetrant apoptosis signal-regulating kinase 1 (ASK1) inhibitors. ACS Med Chem Lett. 2020;11:485–490.
  • Zhang S, Huang C, Lyu X, et al. Discovery of a 2-pyridinyl urea-containing compound YD57 as a potent inhibitor of apoptosis signal-regulating kinase 1 (ASK1). Eur J Med Chem. 2020;195:112277.
  • Doudou S, Sharma R, Henchman RH, et al. Inhibitors of PIM-1 kinase: a computational analysis of the binding free energies of a range of imidazo[1,2-b]pyridazines. J Chem Inf Model. 2010;50:368–379.
  • Lan NT, Vu KB, Ngoc MKD, et al. Prediction of AChE-ligand affinity using the umbrella sampling simulation. J Mol Graph Model. 2019;93:107441.
  • Ngo ST, Vu KB, Bui LM, et al. Effective estimation of ligand-binding affinity using biased sampling method. ACS Omega. 2019;4:3887–3893.
  • Wu C, Chen X, Chen D, et al. Insight into ponatinib resistance mechanisms in rhabdomyosarcoma caused by the mutations in FGFR4 tyrosine kinase using molecular modeling strategies. Int J Biol Macromol. 2019;135:294–302.
  • Zhang Z, Xu Y, Wu J, et al. Exploration of the selective binding mechanism of protein kinase aurora A selectivity via a comprehensive molecular modeling study. PeerJ. 2019;7:e7832.
  • Bamborough P, Brown M, Christopher J, et al. Selectivity of kinase inhibitor fragments. J Med Chem. 2011;54:5131–5143.
  • Berendsen HJC, van der Spoel D, van Brunen R. GROMACS: A message-passing parallel molecular dynamics implementation. Comp Phys Comm. 1995;91:43–56.
  • van der Spoel D, Lindahl E, Hess B, et al. GROMACS: fast, flexible and free. J Comput Chem. 2005;26:1701–1718.
  • Hess B, Kutzner C, van de Spoel D, et al. GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput. 2008;4:435–447.
  • Oostenbrink C, Villa A, Mark AE, et al. A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6: the GROMOS force-field parameter sets 53A5 and 53A6. J Comput Chem. 2004;25:1656–1676.
  • Hockney RW, Goel SP, Eastwood J. Quiet high resolution computer models of a plasma. J Comput Phys. 1974;14:148–158.
  • Darden T, York D, Pedersen L. Particle mesh Ewald: an N log(N) method for Ewald sums in large systems. J Chem Phys. 1993;98:10089–10092.
  • Essmann U, Perera L, Berkowitz ML, et al. A smooth particle mesh Ewald method. J Chem Phys. 1995;103:8577–8593.
  • Hub JS, de Groot BL, van der Spoel D. G_wham – a free weighted histogram analysis implementation including robust error and autocorrelation estimates. J Chem Theory Comput. 2010;6:3713–3720.
  • Schüttelkopf AW, van Aalten MF. PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. Acta Cryst. 2004;D60:1355–1363.
  • Berendsen HJC, Postma JPM, van Gunsteren WF, et al. Interaction models for water in relation to protein hydration. In: B Pullman, editor. Intermolecular forces. Boston (MA): D. Reidel Publishing Company; 1981. p. 331–342.
  • Bjelkmar P, Larsson P, Cuendet MA, et al. Implementation of the CHARMM force field in GROMACS: analysis of protein stability effects from correction maps, virtual interaction sites, and water models. J Chem Theory Comput. 2010;6:459–466.
  • Jorgensen WL, Chandrasekhar J, Madura JD. Comparison of simple potential functions for simulating liquid water. J Chem Phys. 1983;79:926–935.
  • Lemkul JA, Bevan DR. Assessing the stability of Alzheimer’s amyloid protofibrils using molecular dynamics. J Phys Chem B. 2010;114:1652–1660.

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