Skip to main content

Designing of Selective and Brain-Penetrant HDAC Inhibitors for Effective Therapy Against Neurological Disorders

  • Chapter
  • First Online:
Histone Deacetylase Inhibitors — Epidrugs for Neurological Disorders
  • 282 Accesses

Abstract

Aberrant activity of all the 18 HDACs does not form the etiology of neuronal disorders. Certain HDACs have strong implications in these disorders, while others are not at all involved. Thus therapeutic intervention against neurological disorders demands selective rather than pan-targeting. In addition to selectivity, these inhibitors should have high brain penetrance to achieve the desired therapeutic effect. This chapter discusses the different computational and medicinal chemistry approaches for designing selective HDAC inhibitors. Further, the chapter also gives bird’s eye view on image-guided approach for identifying the brain-penetrant HDACi.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Aparoy P, Reddy KK, Reddanna P (2012) Structure and ligand based drug design strategies in the development of novel 5- LOX inhibitors. Curr Med Chem 19(22):3763–3778

    Article  CAS  Google Scholar 

  • Bates SE, Rosing DR, Fojo T, Piekarz RL (2006) Challenges of evaluating the cardiac effects of anticancer agents. Clin Cancer Res 12(13):3871–3874

    Article  CAS  Google Scholar 

  • Bhuiyan MP, Kato T, Okauchi T, Nishino N, Maeda S, Nishino TG, Yoshida M (2006) Chlamydocin analogs bearing carbonyl group as possible ligand toward zinc atom in histone deacetylases. Bioorg Med Chem 14(10):3438–3446

    Article  CAS  Google Scholar 

  • Bieliauskas AV, Pflum MKH (2008) Isoform-selective histone deacetylase inhibitors. Chem Soc Rev 37(7):1402–1413

    Article  CAS  Google Scholar 

  • Boutillier AL, Trinh E, Loeffler JP (2003) Selective E2F-dependent gene transcription is controlled by histone deacetylase activity during neuronal apoptosis. J Neurochem 84(4):814–828

    Article  CAS  Google Scholar 

  • Castellano JF, Fletcher BR, Patzke H, Long JM, Sewal A, Kim DH, Kelley-Bell B, Rapp PR (2014) Reassessing the effects of histone deacetylase inhibitors on hippocampal memory and cognitive aging. Hippocampus 24(8):1006–1016

    Article  CAS  Google Scholar 

  • Di Micco S, Chini MG, Terracciano S, Bruno I, Riccio R, Bifulco G (2013) Structural basis for the design and synthesis of selective HDAC inhibitors. Bioorg Med Chem 21(13):3795–3807

    Article  Google Scholar 

  • Durham B (2012) Novel histone deacetylase (HDAC) inhibitors with improved selectivity for HDAC2 and 3 protect against neural cell death. Biosci Horiz 5:hzs003

    Article  CAS  Google Scholar 

  • Fass DM, Reis SA, Ghosh B, Hennig KM, Joseph NF, Zhao WN, Nieland TJ, Guan JS, Kuhnle CE, Tang W, Barker DD, Mazitschek R, Schreiber SL, Tsai LH, Haggarty SJ (2013) Crebinostat: a novel cognitive enhancer that inhibits histone deacetylase activity and modulates chromatin-mediated neuroplasticity. Neuropharmacology 64:81–96

    Article  CAS  Google Scholar 

  • Ganai SA (2015) Strategy for enhancing the therapeutic efficacy of histone deacetylase inhibitor dacinostat: the novel paradigm to tackle monotonous cancer chemoresistance. Arch Pharm Res 19(10):015–0673

    Google Scholar 

  • Ganai SA (2016) Novel approaches towards designing of isoform-selective inhibitors against class II histone deacetylases: the acute requirement for targetted anticancer therapy. Curr Top Med Chem 16(22):2441–2452

    Article  CAS  Google Scholar 

  • Ganai SA (2017) Designing isoform-selective inhibitors against classical HDACs for effective anticancer therapy: insight and perspectives from in silico. Curr Drug Targets 12(81013):EPUB-81013

    Google Scholar 

  • Ganai SA, Shanmugam K, Mahadevan V (2015) Energy-optimised pharmacophore approach to identify potential hotspots during inhibition of Class II HDAC isoforms. J Biomol Struct Dyn 33(2):374–387

    Article  CAS  Google Scholar 

  • Ganai SA, Ramadoss M, Mahadevan V (2016) Histone deacetylase (HDAC) inhibitors – emerging roles in neuronal memory, learning, synaptic plasticity and neural regeneration. Curr Neuropharmacol 14(1):55–71

    Article  CAS  Google Scholar 

  • Ghosh B, Zhao W-N, Reis SA, Patnaik D, Fass DM, Tsai L-H, Mazitschek R, Haggarty SJ (2016) Dissecting structure-activity-relationships of crebinostat: brain penetrant HDAC inhibitors for neuroepigenetic regulation. Bioorg Med Chem Lett 26(4):1265–1271

    Article  CAS  Google Scholar 

  • Haggarty SJ, Koeller KM, Wong JC, Grozinger CM, Schreiber SL (2003) Domain-selective small-molecule inhibitor of histone deacetylase 6 (HDAC6)-mediated tubulin deacetylation. Proc Natl Acad Sci 100(8):4389–4394

    Article  CAS  Google Scholar 

  • Hung CL, Chen CC (2014) Computational approaches for drug discovery. Drug Dev Res 75(6):412–418

    Article  CAS  Google Scholar 

  • Jarpe M, Golonzhka O, Jones S (2017) A highly brain penetrant hdac1,2 inhibitor (rcy-1305) improves cognitive function in mouse models of Alzheimer’s disease. Alzheimers Dement 13(7):P1243

    Article  Google Scholar 

  • Kalyaanamoorthy S, Chen YP (2013) Energy based pharmacophore mapping of HDAC inhibitors against class I HDAC enzymes. Biochim Biophys Acta 1:317–328

    Article  Google Scholar 

  • KrennHrubec K, Marshall BL, Hedglin M, Verdin E, Ulrich SM (2007) Design and evaluation of ‘Linkerless’ hydroxamic acids as selective HDAC8 inhibitors. Bioorg Med Chem Lett 17(10):2874–2878

    Article  CAS  Google Scholar 

  • Luthi-Carter R, Taylor DM, Pallos J, Lambert E, Amore A, Parker A, Moffitt H, Smith DL, Runne H, Gokce O, Kuhn A, Xiang Z, Maxwell MM, Reeves SA, Bates GP, Neri C, Thompson LM, Marsh JL, Kazantsev AG (2010) SIRT2 inhibition achieves neuroprotection by decreasing sterol biosynthesis. Proc Natl Acad Sci U S A 107(17):7927–7932

    Article  CAS  Google Scholar 

  • Mai A, Massa S, Pezzi R, Simeoni S, Rotili D, Nebbioso A, Scognamiglio A, Altucci L, Loidl P, Brosch G (2005) Class II (IIa)-selective histone deacetylase inhibitors. 1. Synthesis and biological evaluation of novel (aryloxopropenyl)pyrrolyl hydroxyamides. J Med Chem 48(9):3344–3353

    Article  CAS  Google Scholar 

  • Natarajan P, Priyadarshini V, Pradhan D, Manne M, Swargam S, Kanipakam H, Bhuma V, Amineni U (2016) E-pharmacophore-based virtual screening to identify GSK-3beta inhibitors. J Recept Signal Transduct Res 36(5):445–458

    Article  CAS  Google Scholar 

  • Noureen N, Rashid H, Kalsoom S (2010) Identification of type-specific anticancer histone deacetylase inhibitors: road to success. Cancer Chemother Pharmacol 66(4):625–633

    Article  CAS  Google Scholar 

  • Saha RN, Pahan K (2006) HATs and HDACs in neurodegeneration: a tale of disconcerted acetylation homeostasis. Cell Death Differ 13(4):539–550

    Article  CAS  Google Scholar 

  • Salam NK, Nuti R, Sherman W (2009) Novel method for generating structure-based pharmacophores using energetic analysis. J Chem Inf Model 49(10):2356–2368

    Article  CAS  Google Scholar 

  • Schroeder FA, Lewis MC, Fass DM, Wagner FF, Zhang YL, Hennig KM, Gale J, Zhao WN, Reis S, Barker DD, Berry-Scott E, Kim SW, Clore EL, Hooker JM, Holson EB, Haggarty SJ, Petryshen TL (2013) A selective HDAC 1/2 inhibitor modulates chromatin and gene expression in brain and alters mouse behavior in two mood-related tests. PLoS One 8(8):e71323

    Article  CAS  Google Scholar 

  • Schroeder FA, Wang C, Van de Bittner GC, Neelamegam R, Takakura WR, Karunakaran A, Wey HY, Reis SA, Gale J, Zhang YL, Holson EB, Haggarty SJ, Hooker JM (2014) PET imaging demonstrates histone deacetylase target engagement and clarifies brain penetrance of known and novel small molecule inhibitors in rat. ACS Chem Neurosci 5(10):1055–1062

    Article  CAS  Google Scholar 

  • Seo YJ, Kang Y, Muench L, Reid A, Caesar S, Jean L, Wagner F, Holson E, Haggarty SJ, Weiss P, King P, Carter P, Volkow ND, Fowler JS, Hooker JM, Kim SW (2014) Image-guided synthesis reveals potent blood-brain barrier permeable histone deacetylase inhibitors. ACS Chem Neurosci 5(7):588–596

    Article  CAS  Google Scholar 

  • Shah MH, Binkley P, Chan K, Xiao J, Arbogast D, Collamore M, Farra Y, Young D, Grever M (2006) Cardiotoxicity of histone deacetylase inhibitor depsipeptide in patients with metastatic neuroendocrine tumors. Clin Cancer Res 12(13):3997–4003

    Article  CAS  Google Scholar 

  • Somoza JR, Skene RJ, Katz BA, Mol C, Ho JD, Jennings AJ, Luong C, Arvai A, Buggy JJ, Chi E, Tang J, Sang BC, Verner E, Wynands R, Leahy EM, Dougan DR, Snell G, Navre M, Knuth MW, Swanson RV, McRee DE, Tari LW (2004) Structural snapshots of human HDAC8 provide insights into the class I histone deacetylases. Structure 12(7):1325–1334

    Article  CAS  Google Scholar 

  • Suzuki T, Kouketsu A, Itoh Y, Hisakawa S, Maeda S, Yoshida M, Nakagawa H, Miyata N (2006) Highly potent and selective histone deacetylase 6 inhibitors designed based on a small-molecular substrate. J Med Chem 49(16):4809–4812

    Article  CAS  Google Scholar 

  • Taylor DM, Balabadra U, Xiang Z, Woodman B, Meade S, Amore A, Maxwell MM, Reeves S, Bates GP, Luthi-Carter R, Lowden PAS, Kazantsev AG (2011) A brain-permeable small molecule reduces neuronal cholesterol by inhibiting activity of Sirtuin 2 deacetylase. ACS Chem Biol 6(6):540–546

    Article  CAS  Google Scholar 

  • Thangapandian S, John S, Lee Y, Kim S, Lee KW (2011) Dynamic structure-based pharmacophore model development: a new and effective addition in the histone deacetylase 8 (HDAC8) inhibitor discovery. Int J Mol Sci 12(12):9440–9462

    Article  CAS  Google Scholar 

  • Verlinde CLMJ, Hol WGJ (1994) Structure-based drug design: progress, results and challenges. Structure 2(7):577–587

    Article  CAS  Google Scholar 

  • Wagner FF, Zhang YL, Fass DM, Joseph N, Gale JP, Weïwer M, McCarren P, Fisher SL, Kaya T, Zhao WN, Reis SA, Hennig KM, Thomas M, Lemercier BC, Lewis MC, Guan JS, Moyer MP, Scolnick E, Haggarty SJ, Tsai LH, Holson EB (2015) Kinetically selective inhibitors of histone deacetylase 2 (HDAC2) as cognition enhancers. Chem Sci 6(1):804–815

    Article  CAS  Google Scholar 

  • Wang D-F, Helquist P, Wiech NL, Wiest O (2005) Toward selective histone deacetylase inhibitor design: homology modeling, docking studies, and molecular dynamics simulations of human class I histone deacetylases. J Med Chem 48(22):6936–6947

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Nature Singapore Pte Ltd.

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Ganai, S.A. (2019). Designing of Selective and Brain-Penetrant HDAC Inhibitors for Effective Therapy Against Neurological Disorders. In: Histone Deacetylase Inhibitors — Epidrugs for Neurological Disorders. Springer, Singapore. https://doi.org/10.1007/978-981-13-8019-8_8

Download citation

Publish with us

Policies and ethics