Probing the effect of intermolecular interaction and understanding the electrostatic moments of anacardic acid in the active site of p300 enzyme via DFT and charge density analysis

Journal of Molecular Graphics and Modelling

Volumn 34, Issue , 2012, Pages 57-66

  Devipriya, B ^a   Kumaradhas, P ^a  

^a PERIYAR UNIVERSITY   (India)

Author keywords

Anacardic acid; Dipole moment; Electrostatic potential; Intermolecular interaction; Molecular docking; p300

Indexed keywords

ACID MOLECULES; ACTIVE SITE; BINDING AFFINITIES; CARBOXYL GROUPS; CHARGE DENSITY DISTRIBUTIONS; CHARGE REDISTRIBUTION; CHARGE-DENSITY ANALYSIS; ELECTROSTATIC MOMENTS; ELECTROSTATIC POTENTIAL; ELECTROSTATIC POTENTIALS; ELECTROSTATIC PROPERTIES; GAS-PHASE STRUCTURES; GASPHASE; HF AND DFT; INTERMOLECULAR INTERACTIONS; MOLECULAR DOCKING; P300; QUANTUM CHEMICAL CALCULATIONS;

BINDING ENERGY; CHARGE DENSITY; DIPOLE MOMENT; ELECTROSTATICS; ENZYMES; GASES; MOLECULES; QUANTUM CHEMISTRY;

CONFORMATIONS;

ANACARDIC ACID; CARBOXYL GROUP; PROTEIN P300;

ARTICLE; BINDING AFFINITY; CHARGE DENSITY ANALYSIS; DENSITY FUNCTIONAL THEORY; DIPOLE; ENZYME ACTIVE SITE; MATHEMATICAL ANALYSIS; MOLECULAR DOCKING; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN CONFORMATION; QUANTUM CHEMISTRY; STATIC ELECTRICITY; STRUCTURE ANALYSIS;

ANACARDIC ACIDS; CATALYTIC DOMAIN; COMPUTER SIMULATION; ELECTROCHEMISTRY; HISTONE ACETYLTRANSFERASES; HUMANS; HYDROGEN BONDING; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR CONFORMATION; P300-CBP TRANSCRIPTION FACTORS; PROTEIN BINDING; STATIC ELECTRICITY; THERMODYNAMICS;

EID: 84856501581     PISSN: 10933263     EISSN: 18734243     Source Type: Journal    
DOI: 10.1016/j.jmgm.2011.12.003     Document Type: Article

References (44)

1. Z. Arany, L.E. Huang, R. Eckner, S. Bhattacharya, C. Jiang, M.A. Goldberg, H.F. Bunn, and D.M. Livingston An essential role for p300/CBP in the cellular response to hypoxia Proc. Natl. Acad. Sci. U.S.A. 93 1996 12969 12973 (Pubitemid 26382753)
2. X. Liu, L. Wang, K. Zhao, P.R. Thompson, Y. Hwang, R. Marmorstein, and P.A. Cole The structural basis of protein acetylation by the p300/CBP transcriptional coactivator Nature 451 2008 846 850 (Pubitemid 351253165)
3. E. Kalkhoven CBP and p300: HATs for different occasions Biochem. Pharmacol. 68 2004 1145 1155 (Pubitemid 39094280)
4. L.W. Yuan, and A. Giordano Acetyltransferase machinery conserved in p300/CBP-family proteins Oncogene 21 2002 2253 2260 (Pubitemid 34311379)
5. N. Forster, S. Gallinat, J. Jablonska, S. Weiss, H.P. Elsasser, and W. Lutz p300 protein acetyltranferase activity suppresses systemic lupus erythematosus-like autoimmune disease in mice J. Immunol. 178 2007 6941 6948 (Pubitemid 46847420)
6. G. Sbardella, S. Castellano, C. Vicidomini, D. Rotili, A. Nebbioso, M. Miceli, L. Altuccic, and A. Mai Identification of long chain alkylidenemalonates as novel small molecule modulators of histone acetyltransferases Bioorg. Med. Chem. Lett. 18 2008 2788 2792 (Pubitemid 351608893)
7. L. Wei, N. Jamonnak, J. Choy, Z. Wang, and W. Zheng Differential binding modes of the bromodomains of CREB-binding protein (CBP) and p300 with acetylated MyoD Biochem. Biophys. Res. Commun. 368 2008 279 284
8. K. Mantelingu, B.A. AshokReddy, V. Swaminathan, A. Hari Kishore, N.B. Siddappa, G.V. Pavan Kumar, G. Nagashankar, N. Natesh, S. Roy, P.P. Sadhale, U. Ranga, C. Narayana, and T.K. Kundu Specific inhibition of p300-HAT alters global gene expression and represses HIV replication Chem. Biol. 14 2007 645 657 (Pubitemid 46929090)
9. F.D. Piaz, A. Vassallo, O.C. Rubio, S. Castellano, G. Sbardella, and N.De. Tommasi Chemical biology of histone acetyltransferase natural compounds modulators Mol. Divers. 15 2011 401 416
10. M.W. Rekowski, and A. Giannis Histone acetylation modulation by small molecules: a chemical approach Biochim. Biophys. Acta 1799 2010 760 767
11. Y. Ionov, S.I. Matsui, and J.K. Cowell A role for p300/CREB binding protein genes in promoting cancer progression in colon cancer cell lines with microsatellite instability Proc. Natl. Acad. Sci. U.S.A. 101 2004 1273 1278 (Pubitemid 38182679)
12. K. Ito, C.E. Charron, and I.M. Adlock Impact of protein acetylation in inflammatory lung diseases Pharmacol. Ther. 116 2007 249 265 (Pubitemid 47451510)
13. S.G. Gray, and D.P. Meyts Role of histone and transcription factor acetylation in diabetes pathogenesis Diabetes Metab. Res. Rev. 21 2005 416 433 (Pubitemid 41320653)
14. T. Kakita, K. Hasegawa, T. Morimoto, S. Kaburagi, H. Wada, and S. Sasayama p300 protein as a coactivator of GATA-5 in the transcription of cardiac-restricted atrial natriuretic factor gene J. Biol. Chem. 274 1999 34096 34102 (Pubitemid 129511744)
15. K. Balasubramanyam, V. Swaminathan, R. Anupama, and T.K. Kundu Small molecule modulators of histone acetyltransferase p300 J. Biol. Chem. 278 2003 19134 19140 (Pubitemid 36799302)
16. M. Arif, S.K. Pradhan, G.R. Thanuja, B.M. Vedamurthy, S. Agrawal, D. Dasgupta, and T.K. Kundu Mechanism of p300 specific histone acetyltransferase inhibition by small molecules J. Med. Chem. 52 2009 267 277
17. S.B. Kutluay, J. Doroghazi, M.E. Roemer, and S.J. Triezenberg Curcumin inhibits herpes simplex virus immediate-early gene expression by a mechanism independent of p300/CBP histone acetyltransferase activity Virology 373 2008 239 247
18. I. Kubo, M. Ochi, P.C. Vieira, and S. Komatsu Antitumor agents from the cashew (Anacardium occidentale) apple juice J. Agric. Food. Chem. 41 1993 1012 1015
19. G.M. Morris, R.S. Goodsell, R.S. Halliday, R. Huey, W.E. Hart, R.K. Belew, and A.J. Olson Automated docking using a lamarckian genetic algorithm and empirical binding free energy function J. Comput. Chem. 19 1998 1639 1662 (Pubitemid 128590223)
20. W.L. DeLano PyMol Molecular Graphics System 2002 DeLano Scientific San Carlos, CA, USA
21. S.J. Smith, and B.T. Sutcliffe The development of computational chemistry in the United Kingdom Rev. Comput. Chem. 10 1997 271 316
22. M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, J.A. Montgomery Jr., Vreven, K.N. Kudin, J.C. Burant, J.M. Millam, S.S. Iyengar, J. Tomasi, V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, G.A. Petersson, H. Nakatsuji, M. Hada, M.P. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, M. Klene, X. Li, J.E. Knox, H.P. Hratchian, J.B. Cross, Adamo, J. Jaramillo, R. Gomperts, R.E. Stratmann, O. Yazyev, A.J. Austin, R. Cammi, C. Pomelli, J.W. Ochterski, P.Y. Ayala, Morokuma, G.A. Voth, P. Salvador, J.J. Dannenberg, V.G. Zakrzewski, S. Dapprich, A.D. Daniels, M.C. Strain, O. Farkas, D.K. Malick, A.D. Rabuck, K. Raghavachari, J.B. Foresman, J.V. Ortiz, Q. Cui, A.G. Baboul, S. Clifford, J. Cioslowski, B.B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R.L. Martin, D.J. Fox, T. Keith, M.A. Al-Laham, C.Y. Peng, A. Nanayakkara, M. Challacombe, P.M.W. Gill, B. Johnson, W. Chen, M.W. Wong, C. Gonzalez, and J.A. Pople Gaussian 03, Revision D.1 2005 Gaussian, Inc. Wallingford, CT
23. A.R. Leech Molecular Modelling Principles and Applications 1996 Addison Wesley Longman Essex, England
24. J.K. Labanowski, and J.W. Andzelm Density Functional Methods in Chemistry 1991 Springer New York
25. R.G. Parr, and W. Yang Density Functional Theory of Atoms and Molecules 1989 Oxford New York
26. R.F.W.Bader, Y. Tal, S.G. Anderson, and T.T. Nguyen-Dang Isr. J. Chem. 19 1980 8 29
27. J. Cheeseman, T.A. Keith, and R.F.W. Bader AIMPAC Program Package 1992 McMaster University Hamilton, Ontario
28. T. Koritsanszky, P. Macchi, C. Gatti, L.J. Farrugia, P.R. Mallinson, A. Volkov, T. Richter, XD-2006. A Computer Program Package for Multipole Refinement and Topological Analysis of Charge Densities and Evaluation of Intermolecular Energies from Experimental or Theoretical Structure. Factors, Version 5.33, 2007.
29. T. Koritsanszky, T. Richter, P. Macci, C. Gatti, S. Howard, P.R. Mallinson, L.J. Farrugia, Z.W. Su, and N.K. Hansen X.D. - A Computer Program Package for Multipole Refinement and Analysis of Electron Densities from Diffraction Data 2003 Freie Universitï Berlin
30. C.B. Hubschle, and P. Luger Moliso - a program for colour-mapped iso-surfaces J. Appl. Crystallogr. 39 2006 901 904 (Pubitemid 44786290)
31. K. Mantlingu, A. HariKishore, K. Balasubramanyam, G.V. PavanKumar, M. Altaf, S. Nanjunda Swamy, R. Selvi, C. Das, C. Narayana, K.S. Rangappa, and T.K. Kundu Activation of p300 histone acetyltransferase by small molecules altering enzyme structure: probed by surface-enhanced Raman spectroscopy J. Phys. Chem. B 111 2007 4527 4534 (Pubitemid 46787648)
32. K. Balasubramanyam, R.A. Varier, M. Altaf, V. Swaminathan, N.B. Siddappa, U. Ranga, and T.K. Kundu Curcumin a novel p300/CREB-binding protein-specific inhibitor of acetyltransferase, represses the acetylation of histone/nonhistone proteins and histone acetyltransferase-dependent chromatin transcription J. Biol. Chem. 279 2004 51163 51171 (Pubitemid 40017859)
33. B. Devipriya, A. Renuga Parameswari, G. Rajalakshmi, T. Palvannan, and P. Kumaradhas P. Exploring the Binding affinities of p300 enzyme activators CTPB and CTB using docking method Indian J. Biochem. Biophys. 47 2010 364 369
34. P. Munshi, and T.N. Guru Row Electron density study of 2H-chromene-2-thione Acta Crystallogr. B 58 2002 1011 1017 (Pubitemid 135688534)
35. P. Srinivasan, A. David Stephen, and P. Kumaradhas Effect of gold atom contact in conjugated system of one dimensional octane dithiolate based molecular wire: a theoretical charge density study J. Mol. Struct: Theochem. 910 2009 112 121
36. A. David Stephen, M. Revathi, S.N. Asthana, Rajesh B. Pawar, and P. Kumaradhas Probing the weakest bond and the cleavage of p-chlorobenzaldehyde diperoxide energetic molecule via quantum chemical calculations and theoretical charge density analysis Int. J. Quant. Chem. 111 2011 3741 3754
37. D.E. Hibbs, J.R. Hanrahan, M.B. Hursthouse, D.W. Knight, J. Overgaard, P. Turner, R.O. Piltz, and M.P. Waller Experimental and theoretical charge distribution in (Z)-N-methyl-C-phenylnitrone Org. Biomol. Chem. 1 2003 1034 1040
38. E.J. Yearley, E.A. Zhurova, V.V. Zhurov, and A. Alan Pinkerton Binding of genistein to the estrogen receptor based on an experimental electron density study J. Am. Chem. Soc. 129 2007 15013 15021 (Pubitemid 350237566)
39. P.L.A. Popelier Atom in Molecules an Introduction 1999 Pearson Edition Harlow, UK
40. G.U. Kulkarni, P. Kumaradhas, and C.N.R. Rao Charge density study of the polymorphs of p-nitrophenol Chem. Mater. 10 1998 3498 3505 (Pubitemid 128475283)
41. R.S. Mulliken Electronic population analysis on LCAO-MO molecular wave functions J. Chem. Phys. 23 1955 1833 1841
42. A.E. Reed, R.B. Weinstock, and F.A. Weinhold Natural population analysis J. Chem. Phys. 83 1985 735 747
43. P. Coppens, Y. Abramov, M. Carducci, B. Korjov, I. Novozhilova, C. Alhambra, and M.R. Pressprich Experimental charge densities and intermolecular interactions: electrostatic and topological analysis of dl-histidine J. Am. Chem. Soc. 121 1999 2585 2593 (Pubitemid 29153470)
44. P. Politzer, J.S. Murray, and Z. Peralta-inga Molecular surface electrostatic potentials in relation to noncovalent interactions in biological systems Int. J. Quant. Chem. 85 2001 676 684 (Pubitemid 33105812)