[go: up one dir, main page]
More Web Proxy on the site http://driver.im/ Skip to main content

Advertisement

Springer Nature Link
Log in

Exploring the inhibitory activity of valproic acid against the HDAC family using an MMGBSA approach

  • Published:
Journal of Computer-Aided Molecular Design Aims and scope Submit manuscript

Abstract

Valproic acid (VPA) is a compound currently used in clinical practice for the treatment of epilepsy as well as bipolar and mood disorders. VPA targets histone deacetylases (HDACs), which participate in the removal of acetyl groups from lysine in several proteins, regulating a wide variety of functions within the organism. An imbalance or malfunction of these enzymes is associated with the development and progression of several diseases, such as cancer and neurodegenerative diseases. HDACs are divided into four classes, but VPA only targets Class I (HDAC1–3 and 8) and Class IIa (HDAC4–5, 7 and 9) HDACs; however, structural and energetic information regarding the manner by which VPA inhibits these HDACs is lacking. Here, the structural and energetic features that determine this recognition were studied using molecular docking and molecular dynamics (MD) simulation. It was found that VPA reaches the catalytic site in HDAC1–3 and 7, whereas in HDAC6, VPA only reaches the catalytic tunnel. In HDAC4, VPA was bound adjacent to L1 and L2, a zone that participates in corepressor binding, and in HDAC8, VPA was bound to the hydrophobic active site channel (HASC), in line with previous reports.

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

Access this article

Log in via an institution

Subscribe and save

Springer+ Basic
£29.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price includes VAT (United Kingdom)

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Scheme 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8

Similar content being viewed by others

References

  1. Philp A, Rowland T, Perez-Schindler J, Schenk S (2014) Understanding the acetylome: translating targeted proteomics into meaningful physiology. Am J Physiol Cell Physiol 307:C763–C773

    CAS  PubMed  PubMed Central  Google Scholar 

  2. Peserico A, Simone C (2011) Physical and functional HAT/HDAC interplay regulates protein acetylation balance. J Biomed Biotechnol 2011:371832

    PubMed  Google Scholar 

  3. Wu X, Oh MH, Schwarz EM, Larue CT, Sivaguru M, Imai BS, Yau PM, Ort DR, Huber SC (2011) Lysine acetylation is a widespread protein modification for diverse proteins in Arabidopsis. Plant Physiol 155:1769–1778

    CAS  PubMed  PubMed Central  Google Scholar 

  4. Perchey RT, Tonini L, Tosolini M, Fournie JJ, Lopez F, Besson A, Pont F (2019) PTMselect: optimization of protein modifications discovery by mass spectrometry. Sci Rep 9:4181

    PubMed  PubMed Central  Google Scholar 

  5. Seto E, Yoshida M (2014) Erasers of histone acetylation: the histone deacetylase enzymes. Cold Spring Harb Perspect Biol 6:a018713

    PubMed  PubMed Central  Google Scholar 

  6. Yao YL, Yang WM (2011) Beyond histone and deacetylase: an overview of cytoplasmic histone deacetylases and their nonhistone substrates. J Biomed Biotechnol 2011:146493

    PubMed  Google Scholar 

  7. Glozak MA, Sengupta N, Zhang X, Seto E (2005) Acetylation and deacetylation of non-histone proteins. Gene 363:15–23

    CAS  PubMed  Google Scholar 

  8. Parbin S, Kar S, Shilpi A, Sengupta D, Deb M, Rath SK, Patra SK (2014) Histone deacetylases: a saga of perturbed acetylation homeostasis in cancer. J Histochem Cytochem 62:11–33

    PubMed  PubMed Central  Google Scholar 

  9. Eckschlager T, Plch J, Stiborova M, Hrabeta J (2017) Histone deacetylase inhibitors as anticancer drugs. Int J Mol Sci. https://doi.org/10.3390/ijms18071414

    Article  PubMed  PubMed Central  Google Scholar 

  10. Frey RR, Wada CK, Garland RB, Curtin ML, Michaelides MR, Li J, Pease LJ, Glaser KB, Marcotte PA, Bouska JJ, Murphy SS, Davidsen SK (2002) Trifluoromethyl ketones as inhibitors of histone deacetylase. Bioorg Med Chem Lett 12:3443–3447

    CAS  PubMed  Google Scholar 

  11. Lobera M, Madauss KP, Pohlhaus DT, Wright QG, Trocha M, Schmidt DR, Baloglu E, Trump RP, Head MS, Hofmann GA, Murray-Thompson M, Schwartz B, Chakravorty S, Wu Z, Mander PK, Kruidenier L, Reid RA, Burkhart W, Turunen BJ, Rong JX, Wagner C, Moyer MB, Wells C, Hong X, Moore JT, Williams JD, Soler D, Ghosh S, Nolan MA (2013) Selective class IIa histone deacetylase inhibition via a nonchelating zinc-binding group. Nat Chem Biol 9:319–325

    CAS  PubMed  Google Scholar 

  12. Yang F, Zhao N, Ge D, Chen Y (2019) Next-generation of selective histone deacetylase inhibitors. RSC Adv 9(34):19571–19583

    CAS  PubMed  PubMed Central  Google Scholar 

  13. Bartolini G, Orlandi M, Ammar K, Magrini E, Ferreri AM, Rocchi P (2003) Effect of a new derivative of retinoic acid on proliferation and differentiation in human neuroblastoma cells. Anticancer Res 23:1495–1499

    CAS  PubMed  Google Scholar 

  14. Kwiecinska P, Wrobel A, Tauboll E, Gregoraszczuk EL (2014) Valproic acid, but not levetiracetam, selectively decreases HDAC7 and HDAC2 expression in human ovarian cancer cells. Toxicol Lett 224:225–232

    CAS  PubMed  Google Scholar 

  15. Chuang DM, Leng Y, Marinova Z, Kim HJ, Chiu CT (2009) Multiple roles of HDAC inhibition in neurodegenerative conditions. Trends Neurosci 32:591–601

    CAS  PubMed  PubMed Central  Google Scholar 

  16. Brodie SA, Brandes JC (2014) Could valproic acid be an effective anticancer agent? The evidence so far, Expert review of anticancer therapy. Expert Rev Anticancer Ther 14:1097–1100

    CAS  PubMed  PubMed Central  Google Scholar 

  17. Duenas-Gonzalez A, Candelaria M, Perez-Plascencia C, Perez-Cardenas E, de la Cruz-Hernandez E, Herrera LA (2008) Valproic acid as epigenetic cancer drug: preclinical, clinical and transcriptional effects on solid tumors. Cancer Treat Rev 34:206–222

    CAS  PubMed  Google Scholar 

  18. Mohseni J, Zabidi-Hussin ZA, Sasongko TH (2013) Histone deacetylase inhibitors as potential treatment for spinal muscular atrophy. Genet Mol Biol 36:299–307

    CAS  PubMed  PubMed Central  Google Scholar 

  19. Elbadawi MA, Awadalla MK, Hamid MM, Mohamed MA, Awad TA (2015) Valproic acid as a potential inhibitor of Plasmodium falciparum histone deacetylase 1 (PfHDAC1): an in silico approach. Int J Mol Sci 16:3915–3931

    PubMed  PubMed Central  Google Scholar 

  20. Azzi A, Cosseau C, Grunau C (2009) Schistosoma mansoni: developmental arrest of miracidia treated with histone deacetylase inhibitors. Exp Parasitol 121:288–291

    CAS  PubMed  Google Scholar 

  21. Phiel CJ, Zhang F, Huang EY, Guenther MG, Lazar MA, Klein PS (2001) Histone deacetylase is a direct target of valproic acid, a potent anticonvulsant, mood stabilizer, and teratogen. J Biol Chem 276:36734–36741

    CAS  PubMed  Google Scholar 

  22. Gottlicher M, Minucci S, Zhu P, Kramer OH, Schimpf A, Giavara S, Sleeman JP, Lo Coco F, Nervi C, Pelicci PG, Heinzel T (2001) Valproic acid defines a novel class of HDAC inhibitors inducing differentiation of transformed cells. EMBO J 20:6969–6978

    CAS  PubMed  PubMed Central  Google Scholar 

  23. Gurvich N, Tsygankova OM, Meinkoth JL, Klein PS (2004) Histone deacetylase is a target of valproic acid-mediated cellular differentiation. Cancer Res 64:1079–1086

    CAS  PubMed  Google Scholar 

  24. Annemieke JM, Ruijter DE, van Gennip AH, Caron HN, Kemp S, van Kuilenburg AB (2003) Histone deacetylases characterization of the classical HDAC family. Biochem J 370:737–749

    Google Scholar 

  25. Bermudez-Lugo JA, Perez-Gonzalez O, Rosales-Hernandez MC, Ilizaliturri-Flores I, Trujillo-Ferrara J, Correa-Basurto J (2012) Exploration of the valproic acid binding site on histone deacetylase 8 using docking and molecular dynamic simulations. J Mol Model 18:2301–2310

    CAS  PubMed  Google Scholar 

  26. Göttlicher M, Minucci S, Zhu P, Krämer OH, Schimpf A, Giavara S, Sleeman JP, Coco FL, Nervi C, Pelicci PG, Heinzel T (2001) Valproic acid defines a novel class of HDAC inhibitors inducing differentiation of transformed cells. J EMBO 20:6969–6978

    Google Scholar 

  27. Ganai SA, Abdullah E, Rashid R, Altaf M (2017) Combinatorial in silico strategy towards identifying potential hotspots during inhibition of structurally identical HDAC1 and HDAC2 enzymes for effective chemotherapy against neurological disorders. Front Mol Neurosci 10:357

    PubMed  PubMed Central  Google Scholar 

  28. Sixto-Lopez Y, Bello M, Correa-Basurto J (2018) Structural and energetic basis for the inhibitory selectivity of both catalytic domains of dimeric HDAC6. J Biomol Struct Dyn. https://doi.org/10.1080/07391102.2018.1557560

    Article  PubMed  Google Scholar 

  29. Lloyd KA (2013) A scientific review: mechanisms of valproate-mediated teratogenesis. Biosci Horiz 6:hzt003

    CAS  Google Scholar 

  30. Dennington R, Keith T, Millam J (2009) GaussView. Semichem Inc., Shawnee Mission, KS, p 2009

    Google Scholar 

  31. Frisch MJT, GW Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA, Nakatsuji H, Caricato M, Li X, Hratchian HP, Izmaylov AF, Bloino J, Zheng G, Sonnenberg JL, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Montgomery JA, Jr, Peralta JE, Ogliaro F, Bearpark M, Heyd JJ, Brothers E, Kudin KN, Staroverov VN, Kobayashi R, Normand J, Raghavachari K, Rendell A, Burant JC, Iyengar SS, Tomasi J, Cossi M, Rega N, Millam JM, Klene M, Knox JE, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Martin RL, Morokuma K, Zakrzewski VG, Voth GA, Salvador P, Dannenberg JJ, Dapprich S, Daniels AD, Farkas Ö, Foresman JB, Ortiz JV, Cioslowski J, Fox DJ (2009) Gaussian Gaussian Inc.

  32. Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ (2009) AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem 30(16):2785–2791

    CAS  PubMed  PubMed Central  Google Scholar 

  33. Gasteiger J, Marsili M (1980) Iterative partial equalization of orbital electronegativity—a rapid access to atomic charges. Tetrahedron 36:3219–3228

    CAS  Google Scholar 

  34. Arts J, King P, Marien A, Floren W, Belien A, Janssen L, Pilatte I, Roux B, Decrane L, Gilissen R, Hickson I, Vreys V, Cox E, Bol K, Talloen W, Goris I, Andries L, Du Jardin M, Janicot M, Page M, van Emelen K, Angibaud P (2009) JNJ-26481585, a novel "second-generation" oral histone deacetylase inhibitor, shows broad-spectrum preclinical antitumoral activity. Clin Cancer Res 15:6841–6851

    CAS  PubMed  Google Scholar 

  35. Lauffer BE, Mintzer R, Fong R, Mukund S, Tam C, Zilberleyb I, Flicke B, Ritscher A, Fedorowicz G, Vallero R, Ortwine DF, Gunzner J, Modrusan Z, Neumann L, Koth CM, Lupardus PJ, Kaminker JS, Heise CE, Steiner P (2013) Histone deacetylase (HDAC) inhibitor kinetic rate constants correlate with cellular histone acetylation but not transcription and cell viability. J Biol Chem 288:26926–26943

    CAS  PubMed  PubMed Central  Google Scholar 

  36. Malvaez M, McQuown SC, Rogge GA, Astarabadi M, Jacques V, Carreiro S, Rusche JR, Wood MA (2013) HDAC3-selective inhibitor enhances extinction of cocaine-seeking behavior in a persistent manner. Proc Natl Acad Sci USA 110:2647–2652

    CAS  PubMed  PubMed Central  Google Scholar 

  37. Bottomley MJ, Lo Surdo P, Di Giovine P, Cirillo A, Scarpelli R, Ferrigno F, Jones P, Neddermann P, De Francesco R, Steinkuhler C, Gallinari P, Carfi A (2008) Structural and functional analysis of the human HDAC4 catalytic domain reveals a regulatory structural zinc-binding domain. J Biol Chem 283:26694–26704

    CAS  PubMed  PubMed Central  Google Scholar 

  38. Burli RW, Luckhurst CA, Aziz O, Matthews KL, Yates D, Lyons KA, Beconi M, McAllister G, Breccia P, Stott AJ, Penrose SD, Wall M, Lamers M, Leonard P, Muller I, Richardson CM, Jarvis R, Stones L, Hughes S, Wishart G, Haughan AF, O'Connell C, Mead T, McNeil H, Vann J, Mangette J, Maillard M, Beaumont V, Munoz-Sanjuan I, Dominguez C (2013) Design, synthesis, and biological evaluation of potent and selective class IIa histone deacetylase (HDAC) inhibitors as a potential therapy for Huntington's disease. J Med Chem 56:9934–9954

    CAS  PubMed  Google Scholar 

  39. Hai Y, Christianson DW (2016) Histone deacetylase 6 structure and molecular basis of catalysis and inhibition. Nat Chem Biol 12:741–747

    CAS  PubMed  PubMed Central  Google Scholar 

  40. Dowling DP, Gantt SL, Gattis SG, Fierke CA, Christianson DW (2008) Structural studies of human histone deacetylase 8 and its site-specific variants complexed with substrate and inhibitors. Biochemistry 47:13554–13563

    CAS  PubMed  Google Scholar 

  41. Santos-Martins D, Forli S, Ramos MJ, Olson AJ (2014) AutoDock4(Zn): an improved AutoDock force field for small-molecule docking to zinc metalloproteins. J Chem Inf Model 54:2371–2379

    CAS  PubMed  PubMed Central  Google Scholar 

  42. Singh UC, Kollman PA (1984) An approach to computing electrostatic charges for molecules. J Comput Chem 5:129–145

    CAS  Google Scholar 

  43. Biovia DS (2017) Discovery studio. In: Biovia DS (ed), Dassault Systèmes, San Diego

  44. DeLano (2002) The PyMOL molecular graphics system. In: L. Schrödinger (ed)

  45. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF Chimera–a visualization system for exploratory research and analysis. J Comput Chem 25:1605–1612

    CAS  PubMed  Google Scholar 

  46. Cole JC, Murray CW, Nissink JW, Taylor RD, Taylor R (2005) Comparing protein-ligand docking programs is difficult. Proteins 60:325–332

    CAS  PubMed  Google Scholar 

  47. Case DA, Brozell SR, Cerutti DS, Cheatham TE, Cruzeiro VWD, Darden TA, Duke RE, Ghoreishi D, Gohlke H, Goetz AW, Greene D, Harris R, Homeyer N, Izadi S, Kovalenko A, Lee TS, LeGrand S, Li P, Lin C, Liu J, Luchko T, Luo R, Mermelstein DJ, Merz KM, Miao Y, Monard NHG, Omelyan I, Onufriev A, Pan F, Qi R, Roe DR, Roitberg A, Sagui C, Schott-Verdugo S, Shen J, Simmerling CL, Smith J, Swails J, Walker RC, Wang J, Wei H, Wolf RM, Wu X, Xiao L, Y. DM, K. PA, AMBER (2018) University of California, San Francisco, 2018

  48. Duan Y, Wu C, Chowdhury S, Lee MC, Xiong G, Zhang W, Yang R, Cieplak P, Luo R, Lee T, Caldwell J, Wang J, Kollman P (2003) A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J Comput Chem 24:1999–2012

    CAS  PubMed  Google Scholar 

  49. Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA (2004) Development and testing of a general amber force field. J Comput Chem 25:1157–1174

    CAS  PubMed  Google Scholar 

  50. Peters MB, Yang Y, Wang B, Fusti-Molnar L, Weaver MN, Merz KM Jr (2010) Structural survey of zinc containing proteins and the development of the zinc AMBER force field (ZAFF). J Chem Theor Comput 6:2935–2947

    CAS  Google Scholar 

  51. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926–935

    CAS  Google Scholar 

  52. Darden T, York D, Pedersen L (1993) Particle Mesh Ewald-an N.Log(N) method for Ewald sums in large systems. J Chem Phys 98:10089–10092

    CAS  Google Scholar 

  53. van Gunsteren WF, Berendsen HJC (1977) Algorithms for macromolecular dynamics and constraint dynamics. Mol Phys 34:1311–1327

    Google Scholar 

  54. Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81:3684–3690

    CAS  Google Scholar 

  55. Amadei A, Linssen AB, Berendsen HJ (1993) Essential dynamics of proteins. Proteins 17:412–425

    CAS  PubMed  Google Scholar 

  56. Miller BR, McGee TD, Swails JM, Homeyer N, Gohlke H, Roitberg AE (2012) MMPBSA.py: an efficient program for end-state free energy calculations. J Chem Theory Comput 8:3314–3321

    CAS  PubMed  Google Scholar 

  57. Gohlke H, Kiel C, Case DAJ (2003) Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes. Mol Biol 330:891–913

    CAS  Google Scholar 

  58. Onufriev A, Bashford D, Case DA (2004) Exploring protein native states and large-scale conformational changes with a modified generalized born model. Proteins 55:383–394

    CAS  PubMed  Google Scholar 

  59. Bello M, Mendieta-Wejebe JE, Correa-Basurto J (2014) Structural and energetic analysis to provide insight residues of CYP2C9, 2C11 and 2E1 involved in valproic acid dehydrogenation selectivity. Biochem Pharmacol 90(2):145–158

    CAS  PubMed  Google Scholar 

  60. Sixto-López Y, Bello M, Correa-Basurto J (2018) Insights into structural features of HDAC1 and its selectivity inhibition elucidated by Molecular dynamic simulation and Molecular Docking, J Biomol Struct Dyn 1–64

  61. Choubey SK, Jeyaraman J (2016) A mechanistic approach to explore novel HDAC1 inhibitor using pharmacophore modeling, 3D- QSAR analysis, molecular docking, density functional and molecular dynamics simulation study. J Mol Graph Model 70:54–69

    CAS  PubMed  Google Scholar 

  62. Methot JL, Chakravarty PK, Chenard M, Close J, Cruz JC, Dahlberg WK, Fleming J, Hamblett CL, Hamill JE, Harrington P, Harsch A, Heidebrecht R, Hughes B, Jung J, Kenific CM, Kral AM, Meinke PT, Middleton RE, Ozerova N, Sloman DL, Stanton MG, Szewczak AA, Tyagarajan S, Witter DJ, Secrist JP, Miller TA (2008) Exploration of the internal cavity of histone deacetylase (HDAC) with selective HDAC1/HDAC2 inhibitors (SHI-1:2). Bioorg Med Chem Lett 18:973–978

    CAS  PubMed  Google Scholar 

  63. Lu A, Luo H, Shi M, Wu G, Yuan Y, Liu J, Tang F (2011) Design, synthesis and docking studies on benzamide derivatives as histone deacetylase inhibitors. Bioorg Med Chem Lett 21:4924–4927

    CAS  PubMed  Google Scholar 

  64. Abdizadeh T, Kalani MR, Abnous K, Tayarani-Najaran Z, Khashyarmanesh BZ, Abdizadeh R, Ghodsi R, Hadizadeh F (2017) Design, synthesis and biological evaluation of novel coumarin-based benzamides as potent histone deacetylase inhibitors and anticancer agents. Eur J Med Chem 132:42–62

    CAS  PubMed  Google Scholar 

  65. Khan N, Jeffers M, Kumar S, Hackett C, Boldog F, Khramtsov N, Qian X, Mills E, Berghs SC, Carey N, Finn PW, Collins LS, Tumber A, Ritchie JW, Jensen PB, Lichenstein HS, Sehested M (2008) Determination of the class and isoform selectivity of small-molecule histone deacetylase inhibitors. Biochem J 409:581–589

    CAS  PubMed  Google Scholar 

  66. Miyake Y, Keusch JJ, Wang L, Saito M, Hess D, Wang X, Melancon BJ, Helquist P, Gut H, Matthias P (2016) Structural insights into HDAC6 tubulin deacetylation and its selective inhibition. Nat Chem Biol 12:748–754

    CAS  PubMed  Google Scholar 

  67. Bora-Tatar G, Dayangac-Erden D, Demir AS, Dalkara S, Yelekci K, Erdem-Yurter H (2009) Molecular modifications on carboxylic acid derivatives as potent histone deacetylase inhibitors: Activity and docking studies. Bioorg Med Chem 17:5219–5228

    CAS  PubMed  Google Scholar 

  68. Ortore G, Di Colo F, Martinelli A (2009) Docking of hydroxamic acids into HDAC1 and HDAC8: a rationalization of activity trends and selectivities. J Chem Inf Model 49:2774–2785

    CAS  PubMed  Google Scholar 

  69. Wambua MK, Nalawansha DA, Negmeldin AT, Pflum MK (2014) Mutagenesis studies of the 14 A internal cavity of histone deacetylase 1: insights toward the acetate-escape hypothesis and selective inhibitor design. J Med Chem 57:642–650

    CAS  PubMed  PubMed Central  Google Scholar 

  70. Wang DF, Wiest O, Helquist P, Lan-Hargest HY, Wiech NL (2004) On the function of the 14 A long internal cavity of histone deacetylase-like protein: implications for the design of histone deacetylase inhibitors. J Med Chem 47:3409–3417

    CAS  PubMed  Google Scholar 

  71. Wang D (2009) Computational studies on the histone deacetylases and the design of selective histone deacetylase inhibitors. Curr Top Med Chem 9:241–256

    CAS  PubMed  PubMed Central  Google Scholar 

  72. Hudson GM, Watson PJ, Fairall L, Jamieson AG, Schwabe JW (2015) Insights into the recruitment of class IIa histone deacetylases (HDACs) to the SMRT/NCoR transcriptional repression complex. J Biol Chem 290:18237–18244

    CAS  PubMed  PubMed Central  Google Scholar 

  73. Yuan Y, Hu Z, Bao M, Sun R, Long X, Long L, Li J, Wu C, Bao J (2018) Screening of novel histone deacetylase 7 inhibitors through molecular docking followed by a combination of molecular dynamics simulations and ligand-based approach, J Biomol Struct Dyn 1–30

  74. Gotfryd K, Skladchikova G, Lepekhin EA, Berezin V, Bock E, Walmod PS (2010) Cell type-specific anti-cancer properties of valproic acid: independent effects on HDAC activity and Erk1/2 phosphorylation. BMC Cancer 10:383

    PubMed  PubMed Central  Google Scholar 

  75. Khan S, Jena G, Tikoo K, Kumar V (2015) Valproate attenuates the proteinuria, podocyte and renal injury by facilitating autophagy and inactivation of NF-kappaB/iNOS signaling in diabetic rat. Biochimie 110:1–16

    CAS  PubMed  Google Scholar 

  76. Kee HJ, Bae EH, Park S, Lee KE, Suh SH, Kim SW, Jeong MH (2013) HDAC inhibition suppresses cardiac hypertrophy and fibrosis in DOCA-salt hypertensive rats via regulation of HDAC6/HDAC8 enzyme activity. Kidney Blood Press Res 37:229–239

    CAS  PubMed  Google Scholar 

  77. Mannaerts I, Nuytten NR, Rogiers V, Vanderkerken K, van Grunsven LA, Geerts A (2010) Chronic administration of valproic acid inhibits activation of mouse hepatic stellate cells in vitro and in vivo. Hepatology 51:603–614

    CAS  PubMed  Google Scholar 

  78. Leng Y, Wang J, Wang Z, Liao HM, Wei M, Leeds P, Chuang DM (2016) Valproic acid and other HDAC inhibitors upregulate FGF21 gene expression and promote process elongation in glia by inhibiting HDAC2 and 3. Int J Neuropsychopharmacol. https://doi.org/10.1093/ijnp/pyw035

    Article  PubMed  PubMed Central  Google Scholar 

  79. Duan HY, Zhou KY, Wang T, Zhang Y, Li YF, Hua YM, Wang C (2018) Disruption of planar cell polarity pathway attributable to valproic acid-induced congenital heart disease through Hdac3 participation in mice. Chin Med J 131:2080–2088

    PubMed  PubMed Central  Google Scholar 

  80. Sixto-Lopez Y, Bello M, Rodriguez-Fonseca RA, Rosales-Hernandez MC, Martinez-Archundia M, Gomez-Vidal JA, Correa-Basurto J (2017) Searching the conformational complexity and binding properties of HDAC6 through docking and molecular dynamic simulations. J Biomol Struct Dyn 35:2794–2814

    CAS  PubMed  Google Scholar 

  81. Uba AI, Yelekci K (2018) Identification of potential isoform-selective histone deacetylase inhibitors for cancer therapy: a combined approach of structure-based virtual screening. ADMET prediction and molecular dynamics simulation assay, J Biomol Struct Dyn 36:3231–3245

    CAS  PubMed  Google Scholar 

  82. Haider S, Joseph CG, Neidle S, Fierke CA, Fuchter MJ (2011) On the function of the internal cavity of histone deacetylase protein 8: R37 is a crucial residue for catalysis. Bioorg Med Chem Lett 21:2129–2132

    CAS  PubMed  PubMed Central  Google Scholar 

  83. Leus NG, van der Wouden PE, van den Bosch T, Hooghiemstra WT, Ourailidou ME, Kistemaker LE, Bischoff R, Gosens R, Haisma HJ, Dekker FJ (2016) HDAC 3-selective inhibitor RGFP966 demonstrates anti-inflammatory properties in RAW 264*7 macrophages and mouse precision-cut lung slices by attenuating NF-kappaB p65 transcriptional activity. Biochem Pharmacol 108:58–74

    CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

The work was supported by grants from CONACYT (CB-A1-S-21278) and SIP/IPN (20201015).

Author information

Authors and Affiliations

  1. Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos de La Escuela Superior de Medicina, Instituto Politécnico Nacional, México, Plan de San Luis Y Diaz Mirón S/N, Col. Casco de Santo Tomas, CP: 11340, Mexico City, Mexico

    Yudibeth Sixto-López, Martiniano Bello & José Correa-Basurto

Authors
  1. Yudibeth Sixto-López
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Martiniano Bello
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. José Correa-Basurto
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Martiniano Bello.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary file1 (DOCX 5274 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Sixto-López, Y., Bello, M. & Correa-Basurto, J. Exploring the inhibitory activity of valproic acid against the HDAC family using an MMGBSA approach. J Comput Aided Mol Des 34, 857–878 (2020). https://doi.org/10.1007/s10822-020-00304-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10822-020-00304-2

Keywords

Search

Navigation