In silico study of the inhibition of DNA polymerase by a novel catalpol derivative

Journal of Molecular Modeling

Volumn 17, Issue 10, 2011, Pages 2717-2723

  Martin, Osvaldo A ^a   Garro, Hugo A ^a   Kurina Sanz, Marcela B ^a   Pungitore, Carlos Rodolfo ^a   Tonn, Carlos E ^a  

^a UNIVERSIDAD NACIONAL DE SAN LUIS   (Argentina)

Author keywords

Catalpol; Docking; Iridoid; Molecular dynamics; Taq DNA polymerase

Indexed keywords

6,10,2',6' TETRAACETYL O CATALPOL; CATALPOL; TAQ POLYMERASE; UNCLASSIFIED DRUG;

BINDING AFFINITY; BINDING SITE; CHEMICAL STRUCTURE; ENZYME CONFORMATION; ENZYME INHIBITION; MOLECULAR DOCKING; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; REVIEW; THERMUS AQUATICUS;

DNA-DIRECTED DNA POLYMERASE; ENZYME INHIBITORS; IRIDOID GLUCOSIDES; LIGANDS; MOLECULAR DYNAMICS SIMULATION; PROTEIN BINDING; PROTEIN CONFORMATION; SOLUTIONS;

THERMUS AQUATICUS;

EID: 80255140512     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-010-0938-7     Document Type: Review

References (25)

1. Newman DJ, Cragg GM, Snader KM (2003) Natural products as sources of new drugs over the period 1981-2002. J Nat Prod 66:1022-1037 (Pubitemid 36909859)
2. El-Naggar LJ, Beal JL (1980) Iridoids: a review. J Nat Prod 43:649-707
3. Gotor V, Alfonso I, García-Urdiales E (2008) Asymmetric organic synthesis with enzymes. Weinheim, Wiley VCH
4. Bornscheuer UT, Kazlauskas RJ (2005) Hydrolases in organic synthesis, 2nd edn. Wiley-VCH, Weinheim
5. CR Pungitore MJ Ayub M García EJ Borkowski ME Sosa G Ciuffo CE Tonn 2004 Iridoids as allelochemicals and DNA polymerase inhibitors J Nat Prod 67 357 361 10.1021/np030238b 1:CAS:528:DC%2BD2cXosFOmtQ%3D%3D (Pubitemid 38405695)
6. Pungitore CR (2008) Natural products as inhibitors of DNA related enzymes: a review. Curr Enz Inhib 4:194-215
7. CR Pungitore LG León C García VS Martín CE Tonn JM Padrón 2007 Novel antiproliferative analogs of the Taq DNA polymerase inhibitor catalpol Bioorg Med Chem Lett 17 1332 1335 10.1016/j.bmcl.2006.11.086 1:CAS:528:DC%2BD2sXhvVyjtr0%3D (Pubitemid 46240834)
8. Garro HA (2008) Undergraduate thesis. Universidad Nacional de San Luis, San Luis
9. Allouche A (2010) What is Gabedit? http://gabedit.sourceforge.net/, accessed 21 June 2009
10. Stewart JJ (2010) MOPAC 2009. http://openmopac.net/, accessed 21 June 2009
11. JJ Stewart 2007 Optimization of parameters for semiempirical methods V: modification of NDDO approximations and application to 70 elements J Mol Model 13 1173 1213 10.1007/s00894-007-0233-4 1:CAS:528:DC%2BD2sXhtlequr7N (Pubitemid 47629446)
12. D Van der Spoel E Lindahl B Hess G Groenhof AE Mark HJ Berendsen 2005 GROMACS: fast, flexible, and free J Comput Chem 26 1701 1718 10.1002/jcc.20291 (Pubitemid 43076182)
13. Hess B, Kutzner C, van der Spoel D, Lindahl E (2008) GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theor Comput 4:435-447
14. Schüttelkopf AW, van Aalten DM (2004) PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr D 60:1355-1363 (Pubitemid 41079731)
15. U Essmann L Perera ML Berkowitz T Darden H Lee LG Pedersen 1995 A smooth particle mesh Ewald method J Chem Phys 103 8577 8593 10.1063/1.470117 1:CAS:528:DyaK2MXptlehtrw%3D
16. E Krieger T Darden SB Nabuurs A Finkelstein G Vriend 2004 Making optimal use of empirical energy functions: force-field parameterization in crystal space Proteins 57 678 683 10.1002/prot.20251 1:CAS:528:DC%2BD2cXhtVaqtLrE (Pubitemid 39626989)
17. Y Duan C Wu S Chowdhury MC Lee G Xiong W Zhang 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 10.1002/jcc.10349 1:CAS:528:DC%2BD3sXovVygsbc%3D
18. Vasilef I (2009) QtiPlot: data analysis and scientific visualization. http://soft.proindependent.com/qtiplot.html, accessed 21 June 2009
19. GM Morris DS Goodsell RS Halliday R Huey WE Hart RK Belew 1998 Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function J Comput Chem 19 1639 1662 10.1002/(SICI)1096-987X(19981115)19: 14<1639::AID-JCC10>3.0.CO;2-B 1:CAS:528:DyaK1cXntFemur4%3D (Pubitemid 128590223)
20. DS Goodsell GM Morris AJ Olson 1996 Automated docking of flexible ligands: applications of AutoDock J Mol Recognit 9 1 5 10.1002/(SICI)1099- 1352(199601)9:1<1::AID-JMR241>3.0.CO;2-6 1:CAS:528:DyaK28Xis1SqtrY%3D (Pubitemid 126565462)
21. HM Berman 2000 The Protein Data Bank Nucleic Acids Res 28 235 242 10.1093/nar/28.1.235 1:CAS:528:DC%2BD3cXhvVKjt7w%3D (Pubitemid 30047768)
22. Y Li S Korolev G Waksman 1998 Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation EMBO J 17 7514 7525 10.1093/emboj/17.24.7514 1:CAS:528:DyaK1MXksVGnsQ%3D%3D (Pubitemid 29002718)
23. C Hetényi D van Der Spoel 2002 Efficient docking of peptides to proteins without prior knowledge of the binding site Protein Sci 11 1729 1737 10.1110/ps.0202302 (Pubitemid 34663553)
24. Golosov AA, Warren JJ, Beese LS, Karplus M (2010) The mechanism of the translocation step in DNA replication by DNA polymerase I: a computer simulation analysis. Structure 18:83-93
25. Schrödinger L (2010) The PyMOL molecular graphics system, v.1.2r1. http://www.pymol.org/, accessed 21 June 2009