Computer-aided Molecular Design of Compounds Targeting Histone Modifying Enzymes

Computational and Structural Biotechnology Journal

Volumn 13, Issue , 2015, Pages 358-365

  Andreoli, Federico ^a   Del Rio, Alberto ^a,b  

^a UNIVERSITY OF BOLOGNA   (Italy)

^b CNR   (Italy)

Author keywords

Computer aided molecular design; Drug design; Drug discovery; Epigenetics; Histone; Post translational modifications

Indexed keywords

CURCUMIN; ENZYME; GENISTEIN; HISTONE; HISTONE DEACETYLASE; ISOTHIOCYANIC ACID DERIVATIVE; RESVERATROL; SULFORAPHANE; THIOBARBITURIC ACID DERIVATIVE; TURMERIC;

ADENOSINE DIPHOSPHATE RIBOSYLATION; BIOTINYLATION; CHROMATIN ASSEMBLY AND DISASSEMBLY; COMPUTATIONAL FLUID DYNAMICS; COMPUTER AIDED DESIGN; DEACETYLATION; DRUG DESIGN; ENZYME GLYCOSYLATION; EPIGENETICS; HISTONE ACETYLATION; HISTONE CODE; HISTONE DEMETHYLATION; HISTONE METHYLATION; HISTONE MODIFICATION; HUMAN; MOLECULAR DYNAMICS; MOLECULAR MODEL; PALMITOYLATION; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; PROTEIN DEPHOSPHORYLATION; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING; REVIEW; SUMOYLATION; UBIQUITINATION;

EID: 84940203251     PISSN: None     EISSN: 20010370     Source Type: Journal    
DOI: 10.1016/j.csbj.2015.04.007     Document Type: Review

References (164)

1. F. Cavallo, C. De Giovanni, P. Nanni, G. Forni, and P.-L. Lollini The immune hallmarks of cancer Cell 60 2011 319 326
2. G.L. Semenza A return to cancer metabolism J Mol Med (Berl) 89 2011 203 204
3. H.-C. Tsai, and S.B. Baylin Cancer epigenetics: linking basic biology to clinical medicine Cell Res 21 2011 502 517
4. C. Martin, and Y. Zhang Mechanisms of epigenetic inheritance Curr Opin Cell Biol 19 2007 266 272
5. M.A. Dawson, T. Kouzarides, and B.J.P. Huntly Targeting epigenetic readers in cancer N Engl J Med 367 2012 647 657
6. T.E. Fandy Development of DNA methyltransferase inhibitors for the treatment of neoplastic diseases Curr Med Chem 16 2009 2075 2085
7. M. Kulis, and M. Esteller DNA methylation and cancer Adv Genet 70 2010 27 56
8. B. Brueckner, D. Kuck, and F. Lyko DNA methyltransferase inhibitors for cancer therapy Cancer J 13 2007 17 22
9. F. De Santa, I. Iosue, A. Del Rio, and F. Fazi microRNA biogenesis pathway as therapeutic target for human disease and cancer Curr Pharm Des 19 2013 745 764
10. M. Fabbri, and G.A. Calin Epigenetics and miRNAs in human cancer 1st ed. 2010 Elsevier Inc. [vol. 70]
11. H. Ling, M. Fabbri, and G.A. Calin MicroRNAs and other non-coding RNAs as targets for anticancer drug development Nat Rev Drug Discov 12 2013 847 865
12. Z. Herceg, and T. Ushijima Introduction: epigenetics and cancer 1st ed. 2010 Elsevier Inc. [vol. 70]
13. S.B. Baylin The molecular basis of cancer 2008 Elsevier [vol. 2]
14. P.A. Jones, and S.B. Baylin The epigenomics of cancer Cell 128 2007 683 692
15. T. Kouzarides Chromatin modifications and their function Cell 128 2007 693 705
16. T.K. Kelly, D.D. De Carvalho, and P.A. Jones Epigenetic modifications as therapeutic targets Nat Biotechnol 28 2010 1069 1078
17. F. Andreoli, and A. Del Rio Physicochemical modifications of histones and their impact on epigenomics Drug Discov Today 19 2014 1372 1379
18. F. Andreoli, A.J.M. Barbosa, M.D. Parenti, and A. Del Rio Modulation of epigenetic targets for anticancer therapy: clinicopathological relevance, structural data and drug discovery perspectives Curr Pharm Des 19 2013 578 613
19. S. Henikoff, and A. Shilatifard Histone modification: cause or cog? Trends Genet 27 2011 389 396
20. T. Suganuma, and J.L. Workman Crosstalk among histone modifications Cell 135 2008 604 607
21. M.N. Cruickshank, P. Besant, and D. Ulgiati The impact of histone post-translational modifications on developmental gene regulation Amino Acids 39 2010 1087 1105
22. W. Sippl, and M. Jung Epigenetic targets in drug discovery 2009
23. P. Chi, C.D. Allis, and G.G. Wang Covalent histone modifications - miswritten, misinterpreted and mis-erased in human cancers Nat Rev Cancer 10 2010 457 469
24. H. Santos-Rosa, and C. Caldas Chromatin modifier enzymes, the histone code and cancer Eur J Cancer 41 2005 2381 2402
25. A.J. Bannister, and T. Kouzarides Regulation of chromatin by histone modifications Cell Res 21 2011 381 395
26. S. Golbabapour, M.A. Abdulla, and M. Hajrezaei A concise review on epigenetic regulation: insight into molecular mechanisms Int J Mol Sci 12 2011 8661 8694
27. M. Rius, and F. Lyko Epigenetic cancer therapy: rationales, targets and drugs Oncogene 31 2012 4257 4265
28. R.A. Copeland, E.J. Olhava, and M.P. Scott Targeting epigenetic enzymes for drug discovery Curr Opin Chem Biol 14 2010 505 510
29. D. Dhanak Cracking the code: the promise of epigenetics ACS Med Chem Lett 3 2012 521 523
30. J.D. Best, and N. Carey Epigenetic therapies for non-oncology indications Drug Discov Today 15 2010 1008 1014
31. J.D. Best, and N. Carey Epigenetic opportunities and challenges in cancer Drug Discov Today 15 2010 65 70
32. L. Ellis, P.W. Atadja, and R.W. Johnstone Epigenetics in cancer: targeting chromatin modifications Mol Cancer Ther 8 2009 1409 1420
33. L. Altucci, and S. Minucci Epigenetic therapies in haematological malignancies: searching for true targets Eur J Cancer 45 2009 1137 1145
34. M. Herranz, and M. Esteller New therapeutic targets in cancer: the epigenetic connection Clin Transl Oncol 8 2006 242 249
35. J.S. Graham, S.B. Kaye, and R. Brown The promises and pitfalls of epigenetic therapies in solid tumours Eur J Cancer 45 2009 1129 1136
36. M. Rodríguez-Paredes, and M. Esteller Cancer epigenetics reaches mainstream oncology Nat Med 17 2011 330 339
37. S.M. Meeran, A. Ahmed, and T.O. Tollefsbol Epigenetic targets of bioactive dietary components for cancer prevention and therapy Clin Epigenetics 1 2010 101 116
38. M. Ljungman Targeting the DNA damage response in cancer Chem Rev 109 2009 2929 2950
39. B. Claes, I. Buysschaert, and D. Lambrechts Pharmaco-epigenomics: discovering therapeutic approaches and biomarkers for cancer therapy Heredity (Edinb) 105 2010 152 160
40. R.M. Pollock, and V.M. Richon Epigenetic approaches to cancer therapy Drug Discov Today Ther Strateg 6 2009 71 79
41. A. Spannhoff, W. Sippl, and M. Jung Cancer treatment of the future: inhibitors of histone methyltransferases Int J Biochem Cell Biol 41 2009 4 11
42. A. Sala, and D.F.V. Corona Epigenetics: more than genetics Fly (Austin) 2 2008 165 168
43. M. Lohrum, H.G. Stunnenberg, and C. Logie The new frontier in cancer research: deciphering cancer epigenetics Int J Biochem Cell Biol 39 2007 1450 1461
44. A.G. Inche, and N.B. La Thangue Chromatin control and cancer-drug discovery: realizing the promise Drug Discov Today 11 2006 97 109
45. M. Albert, and K. Helin Histone methyltransferases in cancer Semin Cell Dev Biol 21 2010 209 220
46. R.A. Copeland, M.E. Solomon, and V.M. Richon Protein methyltransferases as a target class for drug discovery Nat Rev Drug Discov 8 2009 724 732
47. T.D. Heightman Chemical biology of lysine demethylases Curr Chem Genomics 5 2011 62 71
48. G. Natoli, G. Testa, and F. De Santa The future therapeutic potential of histone demethylases: a critical analysis Curr Opin Drug Discov Devel 12 2009 607 615
49. B. Lohse, J.L. Kristensen, L.H. Kristensen, K. Agger, K. Helin, M. Gajhede, and et al. Inhibitors of histone demethylases Bioorg Med Chem 19 2011 3625 3636
50. H. Huang, B.R. Sabari, B.A. Garcia, C.D. Allis, and Y. Zhao SnapShot: histone modifications Cell 159 2014 458-458.e1
51. T. Jenuwein, and C.D. Allis Translating the histone code Science 293 2001 1074 1080
52. A.J. Bannister, and T. Kouzarides Reversing histone methylation Nature 436 2005 1103 1106
53. S. Karberg Switching on epigenetic therapy Cell 139 2009 1029 1031
54. C.A. Hamm, and F.F. Costa The impact of epigenomics on future drug design and New therapies Drug Discov Today 16 2011 626 635
55. L. Adwan, and N.H. Zawia Epigenetics: a novel therapeutic approach for the treatment of Alzheimer's disease Pharmacol Ther 139 2013 41 50
56. G. Drewes Future strategies in epigenetic drug discovery Drug Discov Today Ther Strateg 9 2012 e121 e127
57. C.H. Arrowsmith, C. Bountra, P.V. Fish, K. Lee, and M. Schapira Epigenetic protein families: a new frontier for drug discovery Nat Rev Drug Discov 11 2012 384 400
58. E.L. Greer, and Y. Shi Histone methylation: a dynamic mark in health, disease and inheritance Nat Rev Genet 13 2012 343 357
59. K. Tatton-Brown, and N. Rahman The NSD1 and EZH2 overgrowth genes, similarities and differences Am J Med Genet C Semin Med Genet 163C 2013 86 91
60. E.M. Jobe, A.L. McQuate, and X. Zhao Crosstalk among epigenetic pathways regulates neurogenesis Front Neurosci 6 2012 59
61. R. Fujiki, W. Hashiba, H. Sekine, A. Yokoyama, T. Chikanishi, S. Ito, and et al. GlcNAcylation of histone H2B facilitates its monoubiquitination Nature 480 2011 557 560
62. Z. Wang, C. Zang, J.A. Rosenfeld, D.E. Schones, A. Barski, S. Cuddapah, and et al. Combinatorial patterns of histone acetylations and methylations in the human genome Nat Genet 40 2008 897 903
63. H. Denis, R. Deplus, P. Putmans, M. Yamada, R. Métivier, and F. Fuks Functional connection between deimination and deacetylation of histones Mol Cell Biol 29 2009 4982 4993
64. P.M. Lombardi, K.E. Cole, D.P. Dowling, and D.W. Christianson Structure, mechanism, and inhibition of histone deacetylases and related metalloenzymes Curr Opin Struct Biol 21 2011 735 743
65. A. Peserico, and C. Simone Physical and functional HAT/HDAC interplay regulates protein acetylation balance J Biomed Biotechnol 2011 2011 371832
66. S. Bruzzone, M.D. Parenti, A. Grozio, A. Ballestrero, I. Bauer, A. Del Rio, and et al. Rejuvenating sirtuins: the rise of a new family of cancer drug targets Curr Pharm Des 19 2013 614 623
67. M. Roth, and W.Y. Chen Sorting out functions of sirtuins in cancer Oncogene 26 2013 1 12
68. S. Libert, K. Pointer, E.L. Bell, A. Das, D.E. Cohen, J.M. Asara, and et al. SIRT1 activates MAO-A in the brain to mediate anxiety and exploratory drive Cell 147 2011 1459 1472
69. T. Finkel, C.-X. Deng, and R. Mostoslavsky Recent progress in the biology and physiology of sirtuins Nature 460 2009 587 591
70. M.D. Parenti, S. Bruzzone, A. Nencioni, and A. Del Rio Selectivity hot-spots of sirtuin catalytic cores, Mol Biosyst 2015 10.1039/C5MB00205B
71. B.J. Morris Seven sirtuins for seven deadly diseases of aging Free Radic Biol Med 56 2013 133 171
72. S.C. Hodawadekar, and R. Marmorstein Chemistry of acetyl transfer by histone modifying enzymes: structure, mechanism and implications for effector design Oncogene 26 2007 5528 5540
73. R.A. Stein Epigenetic therapies - a new direction in clinical medicine Int J Clin Pract 68 2014 802 811
74. R.A. Copeland Protein methyltransferase inhibitors as personalized cancer therapeutics Drug Discov Today Ther Strateg 9 2012 e83 e90
75. N. Martinet, B.Y. Michel, P. Bertrand, and R. Benhida Small molecules DNA methyltransferases inhibitors MedChemComm 3 2011 263
76. K. Nimura, K. Ura, and Y. Kaneda Histone methyltransferases: regulation of transcription and contribution to human disease J Mol Med (Berl) 88 2010 1213 1220
77. F.I. Daniel, K. Cherubini, L.S. Yurgel, M.A.Z. de Figueiredo, and F.G. Salum The role of epigenetic transcription repression and DNA methyltransferases in cancer Cancer 117 2011 677 687
78. K.J. Ferrari, and D. Pasini Regulation and Function of DNA and Histone Methylations Curr Pharm Des 19 2013 719 733
79. A. Piunti, and D. Pasini Epigenetic factors in cancer development: polycomb group proteins Future Oncol 7 2011 57 75
80. J. Yoo, and J.L. Medina-Franco Discovery and optimization of inhibitors of DNA methyltransferase as novel drugs for cancer therapy 2011
81. W.A. Burgers, F. Fuks, and T. Kouzarides DNA methyltransferases get connected to chromatin Trends Genet 18 2002 275 277
82. Y. Shi, F. Lan, C. Matson, P. Mulligan, J.R. Whetstine, P.A. Cole, and et al. Histone demethylation mediated by the nuclear amine oxidase homolog LSD1 Cell 119 2004 941 953
83. S.M. Kooistra, and K. Helin Molecular mechanisms and potential functions of histone demethylases Nat Rev Mol Cell Biol 13 2012 297 311
84. V.M. Weake, and J.L. Workman Histone ubiquitination: triggering gene activity Mol Cell 29 2008 653 663
85. J. Kim, M. Guermah, R.K. McGinty, J.-S. Lee, Z. Tang, T.A. Milne, and et al. RAD6-mediated transcription-coupled H2B ubiquitylation directly stimulates H3K4 methylation in human cells Cell 137 2009 459 471
86. J.-S. Lee, A. Shukla, J. Schneider, S.K. Swanson, M.P. Washburn, L. Florens, and et al. Histone crosstalk between H2B monoubiquitination and H3 methylation mediated by COMPASS Cell 131 2007 1084 1096
87. D. Stoleru, Y. Peng, J. Agosto, and M. Rosbash Coupled oscillators control morning and evening locomotor behaviour of drosophila Nature 431 2004 862 868
88. S. Messner, and M.O. Hottiger Histone ADP-ribosylation in DNA repair, replication and transcription Trends Cell Biol 21 2011 534 542
89. V. Cepeda, M.A. Fuertes, J. Castilla, C. Alonso, C. Quevedo, M. Soto, and et al. Poly(ADP-ribose) polymerase-1 (PARP-1) inhibitors in cancer chemotherapy Recent Pat Anticancer Drug Discov 1 2006 39 53
90. P. Jagtap, and C. Szabó Poly(ADP-ribose) polymerase and the therapeutic effects of its inhibitors Nat Rev Drug Discov 4 2005 421 440
91. D. Quénet, R. El Ramy, V. Schreiber, and F. Dantzer The role of poly(ADP-ribosyl)ation in epigenetic events Int J Biochem Cell Biol 41 2009 60 65
92. A. Hakmé, H.-K. Wong, F. Dantzer, and V. Schreiber The expanding field of poly(ADP-ribosyl)ation reactions. "Protein modifications: beyond the usual suspects" review series EMBO Rep 9 2008 1094 1100
93. F. Mendes, M. Groessl, A.A. Nazarov, Y.O. Tsybin, G. Sava, I. Santos, and et al. Metal-based inhibition of poly(ADP-ribose) polymerase - the guardian angel of DNA J Med Chem 54 2011 2196 2206
94. M. Rouleau, A. Patel, M.J. Hendzel, S.H. Kaufmann, and G.G. Poirier PARP inhibition: PARP1 and beyond Nat Rev Cancer 10 2010 293 301
95. S. Laing, M. Unger, F. Koch-Nolte, and F. Haag ADP-ribosylation of arginine Amino Acids 41 2011 257 269
96. M.O. Hottiger, P.O. Hassa, B. Lüscher, H. Schüler, and F. Koch-Nolte Toward a unified nomenclature for mammalian ADP-ribosyltransferases Trends Biochem Sci 35 2010 208 219
97. J.A. Hanover Epigenetics gets sweeter: O-GlcNAc joins the "histone code" Chem Biol 17 2010 1272 1274
98. J.A. Hanover, M.W. Krause, and D.C. Love Post-translational modifications: bittersweet memories: linking metabolism to epigenetics through O-GlcNAcylation Nat Rev Mol Cell Biol 13 2012 312 321
99. K. Sakabe, Z. Wang, and G.W. Hart Beta-N-acetylglucosamine (O-GlcNAc) is part of the histone code Proc Natl Acad Sci U S A 107 2010 19915 19920
100. S. Zhang, K. Roche, H.-P. Nasheuer, and N.F. Lowndes Modification of histones by sugar B-N-acetylglucosamine (GlcNAc) occurs on multiple residues, including histone H3 serine 10, and is cell cycle-regulated J Biol Chem 286 2011 37483 37495
101. W. Ahmad, K. Shabbiri, N. Nazar, S. Nazar, S. Qaiser, and M.A. Shabbir Mughal Human linker histones: interplay between phosphorylation and O-B-GlcNAc to mediate chromatin structural modifications Cell Div 6 2011 15
102. C. Anzilotti, F. Pratesi, C. Tommasi, and P. Migliorini Peptidylarginine deiminase 4 and citrullination in health and disease Autoimmun Rev 9 2010 158 160
103. K. Kobza, G. Camporeale, B. Rueckert, A. Kueh, J.B. Griffin, G. Sarath, and et al. K4, K9 and K18 in human histone H3 are targets for biotinylation by biotinidase FEBS J 272 2005 4249 4259
104. G. Camporeale, E.E. Shubert, G. Sarath, R. Cerny, and J. Zempleni K8 and K12 are biotinylated in human histone H4 Eur J Biochem 271 2004 2257 2263
105. L. Tong, and J.M. Denu Function and metabolism of sirtuin metabolite O-acetyl-ADP-ribose Biochim Biophys Acta 1804 2010 1617 1625
106. A. Barski, S. Cuddapah, K. Cui, T.-Y. Roh, D.E. Schones, Z. Wang, and et al. High-resolution profiling of histone methylations in the human genome Cell 129 2007 823 837
107. P.J. Hurd, A.J. Bannister, K. Halls, M.A. Dawson, M. Vermeulen, J.V. Olsen, and et al. Phosphorylation of histone H3 Thr-45 is linked to apoptosis J Biol Chem 284 2009 16575 16583
108. J. Cieśla, T. Frączyk, and W. Rode Phosphorylation of basic amino acid residues in proteins: important but easily missed Acta Biochim Pol 58 2011 137 148
109. Y. Wang, J. Wysocka, J. Sayegh, Y.-H. Lee, J.R. Perlin, L. Leonelli, and et al. Human PAD4 regulates histone arginine methylation levels via demethylimination Science 306 2004 279 283
110. S. Messner, M. Altmeyer, H. Zhao, A. Pozivil, B. Roschitzki, P. Gehrig, and et al. PARP1 ADP-ribosylates lysine residues of the core histone tails Nucleic Acids Res 38 2010 6350 6362
111. P.O. Hassa, S.S. Haenni, M. Elser, and M.O. Hottiger Nuclear ADP-ribosylation reactions in mammalian cells: where are we today and where are we going? Microbiol Mol Biol Rev 70 2006 789 829
112. N. Kothapalli, G. Camporeale, A. Kueh, Y.C. Chew, A.M. Oommen, J.B. Griffin, and et al. Biological functions of biotinylated histones J Nutr Biochem 16 2005 446 448
113. V. Dehennaut, D. Leprince, and T. Lefebvre O-GlcNAcylation, an epigenetic mark Focus on the histone code, TET family proteins, and Polycomb group proteins, Front Endocrinol 5 2014 1 7
114. T.T. Talele, S.A. Khedkar, and A.C. Rigby Successful applications of computer aided drug discovery: moving drugs from concept to the clinic Curr Top Med Chem 10 2010 127 141
115. J.H. Van Drie Computer-aided drug design: the next 20 years J Comput Aided Mol Des 21 2007 591 601
116. D.W. Borhani, and D.E. Shaw The future of molecular dynamics simulations in drug discovery J Comput Aided Mol Des 26 2012 15 26
117. A.J. Moura Barbosa, and A. Del Rio Freely accessible databases of commercial compounds for high-throughput virtual screenings Curr Top Med Chem 12 2012 866 877
118. A. Del Rio, A.J.M. Barbosa, F. Caporuscio, and G.F. Mangiatordi CoCoCo: a free suite of multiconformational chemical databases for high-throughput virtual screening purposes Mol Biosyst 6 2010 2122 2128
119. A. Del Rio, A.J.M. Barbosa, and F. Caporuscio Use of large multiconformational databases with structure-based pharmacophore models for fast screening of commercial compound collections J Cheminform 3 2011 P27
120. W.P. Janzen, T.J. Wigle, J. Jin, and S.V. Frye Epigenetics: tools and technologies Drug Discov Today Technol 7 2010 e59 e65
121. P. Jones Development of second generation epigenetic agents MedChemComm 3 2012 135
122. A. Mai Targeting epigenetics in drug discovery ChemMedChem 9 2014 415 417
123. S. Masciarelli, R. Quaranta, I. Iosue, G. Colotti, F. Padula, G. Varchi, and et al. A small-molecule targeting the MicroRNA binding domain of argonaute 2 improves the retinoic acid differentiation response of the acute promyelocytic leukemia cell line NB4 ACS Chem Biol 9 2014 1674 1679
124. M.F. Schmidt Drug target miRNAs: chances and challenges Trends Biotechnol 32 2014 578 585
125. M. Malumbres miRNAs and cancer: an epigenetics view Mol Aspects Med 34 2013 863 874
126. W. Sippl, and M. Jung Epigenetic drug discovery special issue Bioorg Med Chem 19 2009 3603 3604
127. R. Heinke, L. Carlino, S. Kannan, M. Jung, and W. Sippl Computer- and structure-based lead design for epigenetic targets Bioorg Med Chem 19 2011 3605 3615
128. J.L. Medina-Franco, and T. Caulfield Advances in the computational development of DNA methyltransferase inhibitors Drug Discov Today 16 2011 418 425
129. J. Yoo, and J.L. Medina-Franco Inhibitors of DNA methyltransferases: insights from computational studies Curr Med Chem 2012 37 40
130. L. Zhang, X. Wang, X. Li, and W. Xu Discovery of a series of small molecules as potent histone deacetylase inhibitors J Enzyme Inhib Med Chem 29 2014 333 337
131. S. Kalyaanamoorthy, and Y.-P.P. Chen A steered molecular dynamics mediated hit discovery for histone deacetylases Phys Chem Chem Phys 16 2014 3777 3791
132. S. Kalyaanamoorthy, and Y.-P.P. Chen Energy based pharmacophore mapping of HDAC inhibitors against class I HDAC enzymes Biochim Biophys Acta Proteins Proteomics 1834 2013 317 328
133. L. Zhao, Y. Xiang, J. Song, and Z. Zhang A novel two-step QSAR modeling work flow to predict selectivity and activity of HDAC inhibitors Bioorg Med Chem Lett 23 2013 929 933
134. S. Thangapandian, T. Sundarapandian, S. John, J. Shalini, S. Sakkiah, S. Sugunadevi, and et al. Docking-enabled pharmacophore model for histone deacetylase 8 inhibitors and its application in anti-cancer drug discovery J Mol Graph Model 29 2010 382 395
135. S.B. Nair, M.K. Teli, H. Pradeep, and G.K. Rajanikant Computational identification of novel histone deacetylase inhibitors by docking based QSAR Comput Biol Med 42 2012 697 705
136. H. Tang, X.S. Wang, X.-P. Huang, B.L. Roth, K.V. Butler, A.P. Kozikowski, and et al. Novel inhibitors of human histone deacetylase (HDAC) identified by QSAR modeling of known inhibitors, virtual screening, and experimental validation J Chem Inf Model 49 2009 461 476
137. Y. Chen, H. Li, W. Tang, C. Zhu, Y. Jiang, J. Zou, and et al. 3D-QSAR studies of HDACs inhibitors using pharmacophore-based alignment Eur J Med Chem 44 2009 2868 2876
138. S. Vadivelan, B.N. Sinha, G. Rambabu, K. Boppana, and S.A.R.P. Jagarlapudi Pharmacophore modeling and virtual screening studies to design some potential histone deacetylase inhibitors as new leads J Mol Graph Model 26 2008 935 946
139. H. Park, S. Kim, Y.E. Kim, and S.-J. Lim A structure-based virtual screening approach toward the discovery of histone deacetylase inhibitors: identification of promising zinc-chelating groups ChemMedChem 5 2010 591 597
140. S. Kannan, J. Melesina, A. Hauser, A. Chakrabarti, T. Heimburg, K. Schmidtkunz, and et al. Discovery of inhibitors of Schistosoma mansoni HDAC8 by combining homology modeling J Chem Inf Model 54 2014 3005 3019
141. F.-Q. Zeng, S.-M. Peng, L. Li, L.-B. Mu, Z.-H. Zhang, Z.-Y. Zhang, and et al. Structure-based identification of drug-like inhibitors of p300 histone acetyltransferase Acta Pharm Sin 48 2013 700 708
142. E.M. Bowers, G. Yan, C. Mukherjee, A. Orry, L. Wang, M.A. Holbert, and et al. Virtual ligand screening of the p300/CBP histone acetyltransferase: identification of a selective small molecule inhibitor Chem Biol 17 2010 471 482
143. M. Tortorici, M.T. Borrello, M. Tardugno, L.R. Chiarelli, S. Pilotto, G. Ciossani, and et al. Protein recognition by short peptide reversible inhibitors of the chromatin-modifying LSD1/CoREST lysine demethylase ACS Chem Biol 8 2013 1677 1682
144. J.C. Robertson, N.C. Hurley, M. Tortorici, G. Ciossani, M.T. Borrello, N.A. Vellore, and et al. Expanding the druggable space of the LSD1/CoREST epigenetic target: new potential binding regions for drug-like molecules, peptides, protein partners, and chromatin PLoS Comput Biol 9 2013 e1003158
145. D. Ogasawara, Y. Itoh, H. Tsumoto, T. Kakizawa, K. Mino, K. Fukuhara, and et al. Lysine-specific demethylase 1-selective inactivators: protein-targeted drug delivery mechanism Angew Chem Int Ed 52 2013 8620 8624
146. Y. Itoh, D. Ogasawara, Y. Ota, T. Mizukami, and T. Suzuki Synthesis, LSD1 inhibitory activity, and LSD1 binding model of optically pure lysine-PCPA conjugates Comput Struct Biotechnol J 9 2014 e201402002
147. M.L. Schmitt, K.I. Ladwein, L. Carlino, J. Schulz-Fincke, D. Willmann, E. Metzger, and et al. Heterogeneous antibody-based activity assay for lysine specific demethylase 1 (LSD1) on a histone peptide substrate J Biomol Screen 19 2014 973 978
148. V.K. Pulla, M. Alvala, D.S. Sriram, S. Viswanadha, D. Sriram, and P. Yogeeswari Structure-based drug design of small molecule SIRT1 modulators to treat cancer and metabolic disorders J Mol Graph Model 52 2014 46 56
149. U. Uciechowska, J. Schemies, R.C. Neugebauer, E.-M. Huda, M.L. Schmitt, R. Meier, and et al. Thiobarbiturates as sirtuin inhibitors: virtual screening, free-energy calculations, and biological testing ChemMedChem 3 2008 1965 1976
150. M.D. Parenti, A. Grozio, I. Bauer, L. Galeno, P. Damonte, E. Millo, and et al. Discovery of novel and selective SIRT6 inhibitors J Med Chem 57 2014 4796 4804
151. R. Heinke, A. Spannhoff, R. Meier, P. Trojer, I. Bauer, M. Jung, W. Sippl, and et al. Virtual screening and biological characterization of novel histone arginine methyltransferase PRMT1 inhibitors ChemMedChem 4 2009 69 77
152. N. Deschamps, C.A. Simões-Pires, P.-A. Carrupt, and A. Nurisso How the flexibility of human histone deacetylases influences ligand binding: an overview Drug Discov Today 2015 1 7
153. N.A. Vellore, and R. Baron Epigenetic molecular recognition: a biomolecular modeling perspective ChemMedChem 9 2014 484 494
154. T. Ran, Z. Zhang, K. Liu, Y. Lu, H. Li, J. Xu, and et al. Insight into the key interactions of bromodomain inhibitors based on molecular docking, interaction fingerprinting, molecular dynamics and binding free energy calculation Mol BioSyst 11 2015 1295 1304
155. K. Chen, X. Zhang, Y.-D. Wu, and O. Wiest Inhibition and mechanism of HDAC8 revisited J Am Chem Soc 2014 1 8
156. J. Pottel, E. Therrien, J.L. Gleason, and N. Moitessier Docking ligands into flexible and solvated macromolecules. 6. Development and application to the docking of HDACs and other zinc metalloenzymes inhibitors J Chem Inf Model 54 2014 254 265
157. K. Chen, L. Xu, and O. Wiest Computational exploration of zinc binding groups for HDAC inhibition J Org Chem 78 2013 5051 5055
158. J. Smadbeck, M.B. Peterson, B.M. Zee, S. Garapaty, A. Mago, C. Lee, and et al. De novo peptide design and experimental validation of histone methyltransferase inhibitors PLoS One 9 2014
159. J. Lötsch, G. Schneider, D. Reker, M.J. Parnham, P. Schneider, G. Geisslinger, and et al. Common non-epigenetic drugs as epigenetic modulators Trends Mol Med 19 2013 742 753
160. K.S. vel Szic, M.N. Ndlovu, G. Haegeman, and W. Vanden Berghe Nature or nurture: let food Be your epigenetic medicine in chronic inflammatory disorders Biochem Pharmacol 80 2010 1816 1832
161. P. Rajendran, D.E. Williams, E. Ho, and R.H. Dashwood Metabolism as a key to histone deacetylase inhibition Crit Rev Biochem Mol Biol 46 2011 181 199
162. C. Gerhäuser Cancer cell metabolism, epigenetics and the potential influence of dietary components - a perspective Biomed Res 23 2012 1 21
163. S.I. Khan, P. Aumsuwan, I.A. Khan, L.A. Walker, and A.K. Dasmahapatra Epigenetic events associated with breast cancer and their prevention by dietary components targeting the epigenome Chem Res Toxicol 25 2012 61 73
164. M. Nyström Diet and epigenetics in colon cancer World J Gastroenterol 15 2009 257