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Trachy-Bourget MC, Beaulieu C, Li Z, Besterman J, Delorme D (2001) Design and synthesis
of a novel class of histone deacetylase inhibitors. Bioorg Med Chem Lett 11(21):2847–2850
38. Remiszewski SW, Sambucetti LC, Atadja P, Bair KW, Cornell WD, Green MA, Howell KL,
Jung M, Kwon P, Trogani N, Walker H (2002) Inhibitors of human histone deacetylase:
synthesis and enzyme and cellular activity of straight chain hydroxamates. J Med Chem 45
(4):753–757
39. Mai A, Massa S, Ragno R, Cerbara I, Jesacher F, Loidl P, Brosch G (2003) 3-(4-aroyl-1-methyl1H-2-pyrrolyl)-N-hydroxy-2-alkylamides as a new class of synthetic histone deacetylase inhibitors. 1. Design, synthesis, biological evaluation, and binding mode studies performed through
three different docking procedures. J Med Chem 46(4):512–524. https://doi.org/10.1021/
jm021070e
40. Park H, Lee S (2004) Homology modeling, force field design, and free energy simulation
studies to optimize the activities of histone deacetylase inhibitors. J Comput Aided Mol Des 18
(6):375–388
41. Wang DF, 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. https://doi.org/10.
1021/jm0505011
42. Kim HM, Hong SH, Kim MS, Lee CW, Kang JS, Lee K, Park SK, Han JW, Lee HY, Choi Y,
Kwon HJ, Han G (2007) Modification of cap group in delta-lactam-based histone deacetylase
(HDAC) inhibitors. Bioorg Med Chem Lett 17(22):6234–6238. https://doi.org/10.1016/j.
bmcl.2007.09.034
43. Moradei OM, Mallais TC, Frechette S, Paquin I, Tessier PE, Leit SM, Fournel M, Bonfils C,
Trachy-Bourget MC, Liu J, Yan TP, Lu AH, Rahil J, Wang J, Lefebvre S, Li Z, Vaisburg AF,
Besterman JM (2007) Novel aminophenyl benzamide-type histone deacetylase inhibitors with
enhanced potency and selectivity. J Med Chem 50(23):5543–5546. https://doi.org/10.1021/
jm701079h
44. Mukherjee P, Pradhan A, Shah F, Tekwani BL, Avery MA (2008) Structural insights into the
Plasmodium falciparum histone deacetylase 1 (PfHDAC-1): a novel target for the development of antimalarial therapy. Bioorg Med Chem 16(9):5254–5265. https://doi.org/10.1016/j.
bmc.2008.03.005
45. Schafer S, Saunders L, Eliseeva E, Velena A, Jung M, Schwienhorst A, Strasser A,
Dickmanns A, Ficner R, Schlimme S, Sippl W, Verdin E, Jung M (2008) Phenylalaninecontaining hydroxamic acids as selective inhibitors of class IIb histone deacetylases (HDACs).
Bioorg Med Chem 16(4):2011–2033. https://doi.org/10.1016/j.bmc.2007.10.092
46. Weerasinghe SV, Estiu G, Wiest O, Pflum MK (2008) Residues in the 11 A channel of histone
deacetylase 1 promote catalytic activity: implications for designing isoform-selective histone
deacetylase inhibitors. J Med Chem 51(18):5542–5551. https://doi.org/10.1021/jm800081j
47. Witter DJ, Harrington P, Wilson KJ, Chenard M, Fleming JC, Haines B, Kral AM, Secrist JP,
Miller TA (2008) Optimization of biaryl selective HDAC1&2 inhibitors (SHI-1:2). Bioorg
Med Chem Lett 18(2):726–731. https://doi.org/10.1016/j.bmcl.2007.11.047
48. Yan C, Xiu Z, Li X, Li S, Hao C, Teng H (2008) Comparative molecular dynamics simulations
of histone deacetylase-like protein: binding modes and free energy analysis to hydroxamic
acid inhibitors. Proteins 73(1):134–149. https://doi.org/10.1002/prot.22047
49. Krishna S, Kumar V, Siddiqi MI (2016) Recent advances in computer-assisted structure-based
identification and design of histone deacetylases inhibitors. Curr Top Med Chem 16
(9):934–947
50. Price S, Bordogna W, Bull RJ, Clark DE, Crackett PH, Dyke HJ, Gill M, Harris NV, Gorski J,
Lloyd J, Lockey PM, Mullett J, Roach AG, Roussel F, White AB (2007) Identification and
optimisation of a series of substituted 5-(1H-pyrazol-3-yl)-thiophene-2-hydroxamic acids as
478
D. Robaa et al.
(18):8635–8642. https://doi.org/10.1016/j.bmc.2008.08.003
37. Lavoie R, Bouchain G, Frechette S, Woo SH, Abou-Khalil E, Leit S, Fournel M, Yan PT,
Trachy-Bourget MC, Beaulieu C, Li Z, Besterman J, Delorme D (2001) Design and synthesis
of a novel class of histone deacetylase inhibitors. Bioorg Med Chem Lett 11(21):2847–2850
38. Remiszewski SW, Sambucetti LC, Atadja P, Bair KW, Cornell WD, Green MA, Howell KL,
Jung M, Kwon P, Trogani N, Walker H (2002) Inhibitors of human histone deacetylase:
synthesis and enzyme and cellular activity of straight chain hydroxamates. J Med Chem 45
(4):753–757
39. Mai A, Massa S, Ragno R, Cerbara I, Jesacher F, Loidl P, Brosch G (2003) 3-(4-aroyl-1-methyl1H-2-pyrrolyl)-N-hydroxy-2-alkylamides as a new class of synthetic histone deacetylase inhibitors. 1. Design, synthesis, biological evaluation, and binding mode studies performed through
three different docking procedures. J Med Chem 46(4):512–524. https://doi.org/10.1021/
jm021070e
40. Park H, Lee S (2004) Homology modeling, force field design, and free energy simulation
studies to optimize the activities of histone deacetylase inhibitors. J Comput Aided Mol Des 18
(6):375–388
41. Wang DF, 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. https://doi.org/10.
1021/jm0505011
42. Kim HM, Hong SH, Kim MS, Lee CW, Kang JS, Lee K, Park SK, Han JW, Lee HY, Choi Y,
Kwon HJ, Han G (2007) Modification of cap group in delta-lactam-based histone deacetylase
(HDAC) inhibitors. Bioorg Med Chem Lett 17(22):6234–6238. https://doi.org/10.1016/j.
bmcl.2007.09.034
43. Moradei OM, Mallais TC, Frechette S, Paquin I, Tessier PE, Leit SM, Fournel M, Bonfils C,
Trachy-Bourget MC, Liu J, Yan TP, Lu AH, Rahil J, Wang J, Lefebvre S, Li Z, Vaisburg AF,
Besterman JM (2007) Novel aminophenyl benzamide-type histone deacetylase inhibitors with
enhanced potency and selectivity. J Med Chem 50(23):5543–5546. https://doi.org/10.1021/
jm701079h
44. Mukherjee P, Pradhan A, Shah F, Tekwani BL, Avery MA (2008) Structural insights into the
Plasmodium falciparum histone deacetylase 1 (PfHDAC-1): a novel target for the development of antimalarial therapy. Bioorg Med Chem 16(9):5254–5265. https://doi.org/10.1016/j.
bmc.2008.03.005
45. Schafer S, Saunders L, Eliseeva E, Velena A, Jung M, Schwienhorst A, Strasser A,
Dickmanns A, Ficner R, Schlimme S, Sippl W, Verdin E, Jung M (2008) Phenylalaninecontaining hydroxamic acids as selective inhibitors of class IIb histone deacetylases (HDACs).
Bioorg Med Chem 16(4):2011–2033. https://doi.org/10.1016/j.bmc.2007.10.092
46. Weerasinghe SV, Estiu G, Wiest O, Pflum MK (2008) Residues in the 11 A channel of histone
deacetylase 1 promote catalytic activity: implications for designing isoform-selective histone
deacetylase inhibitors. J Med Chem 51(18):5542–5551. https://doi.org/10.1021/jm800081j
47. Witter DJ, Harrington P, Wilson KJ, Chenard M, Fleming JC, Haines B, Kral AM, Secrist JP,
Miller TA (2008) Optimization of biaryl selective HDAC1&2 inhibitors (SHI-1:2). Bioorg
Med Chem Lett 18(2):726–731. https://doi.org/10.1016/j.bmcl.2007.11.047
48. Yan C, Xiu Z, Li X, Li S, Hao C, Teng H (2008) Comparative molecular dynamics simulations
of histone deacetylase-like protein: binding modes and free energy analysis to hydroxamic
acid inhibitors. Proteins 73(1):134–149. https://doi.org/10.1002/prot.22047
49. Krishna S, Kumar V, Siddiqi MI (2016) Recent advances in computer-assisted structure-based
identification and design of histone deacetylases inhibitors. Curr Top Med Chem 16
(9):934–947
50. Price S, Bordogna W, Bull RJ, Clark DE, Crackett PH, Dyke HJ, Gill M, Harris NV, Gorski J,
Lloyd J, Lockey PM, Mullett J, Roach AG, Roussel F, White AB (2007) Identification and
optimisation of a series of substituted 5-(1H-pyrazol-3-yl)-thiophene-2-hydroxamic acids as
478
D. Robaa et al.