Binding of pyrazole-based inhibitors to Mycobacterium tuberculosis pantothenate synthetase: Docking and MM-GB(PB)SA analysis

Molecular BioSystems

Volumn 10, Issue 2, 2014, Pages 223-239

  Ntie Kang, Fidele ^a,b,c   Kannan, Srinivasaraghavan ^c,d   Wichapong, Kanin ^c   Owono Owono, Luc C ^a,e   Sippl, Wolfgang ^c   Megnassan, Eugene ^f  

^a UNIVERSITY OF DOUALA   (Cameroon)

^b UNIVERSITY OF BUEA   (Cameroon)

^c MARTIN LUTHER UNIVERSITY HALLE WITTENBERG   (Germany)

^d Agency for Science   (Singapore)

^e UNIVERSITY OF YAOUNDÉ I   (Cameroon)

^f UNIVERSITÉ NANGUI ABROGOUA   (Côte d’Ivoire)

Author keywords

[No Author keywords available]

Indexed keywords

5 TERT BUTYL N PYRAZOL 4 YL 4,5,6,7 TETRAHYDROBENZO(D)ISOXAZOLE 3 CARBOXAMIDE; 5-TERT-BUTYL-N-PYRAZOL-4-YL-4,5,6,7-TETRAHYDROBENZO(D)ISOXAZOLE-3-CARBOXAMIDE; BACTERIAL PROTEIN; ENZYME INHIBITOR; ISOXAZOLE DERIVATIVE; PANTOTHENATE SYNTHETASE; PEPTIDE SYNTHASE; PYRAZOLE DERIVATIVE;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; DRUG ANTAGONISM; DRUG EFFECT; ENZYME ACTIVE SITE; ENZYMOLOGY; GENETICS; HUMAN; METABOLISM; MOLECULAR DOCKING; MOLECULAR DYNAMICS; MYCOBACTERIUM TUBERCULOSIS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN TERTIARY STRUCTURE; STRUCTURE ACTIVITY RELATION;

BACTERIAL PROTEINS; CATALYTIC DOMAIN; ENZYME INHIBITORS; HUMANS; ISOXAZOLES; MODELS, MOLECULAR; MOLECULAR DOCKING SIMULATION; MOLECULAR DYNAMICS SIMULATION; MYCOBACTERIUM TUBERCULOSIS; PEPTIDE SYNTHASES; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; PYRAZOLES; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 84891461640     PISSN: 1742206X     EISSN: 17422051     Source Type: Journal    
DOI: 10.1039/c3mb70449a     Document Type: Article

References (66)

1. I. Smith Mycobacterium tuberculosis pathogenesis and molecular determinants of virulence Clin. Microbiol. Rev. 2003 16 463 496
2. S. Nwaka A. Hudson Innovative lead discovery strategies for tropical diseases Nat. Rev. Drug Discovery 2006 5 941 955
3. K. Sharma P. Chopra Y. Singh Recent advances towards identification of new drug targets for Mycobacteriun tuberculosis Expert Opin. Ther. Targets 2004 8 79 93
4. 5) biosynthesis pathway in higher plants Plant J. 2004 37 61 72
5. S. M. Hingley-Wilson V. Sambandamurthy W. R. Jacobs Jr Survival perspectives from the world's most successful pathogen, Mycobacterium tuberculosis Nat. Immunol. 2003 4 949 955
6. R. Zheng J. S. Blanchard Steady-state and pre-steady-state kinetic analysis of Mycobacterium tuberculosis pantothenate synthetase Biochemistry 2001 40 12904 12912
7. K. L. Tuck S. A. Saldanha L. M. Birch A. G. Smith C. Abell The design and synthesis of inhibitors of pantothenate synthetase Org. Biomol. Chem. 2006 4 3598 3610
8. S. Velaparthi M. Brunsteiner R. Uddin B. Wan S. G. Franzblau P. A. Petukhov 5-tert-Butyl-N-pyrazol-4-yl-4,5,6,7-tetrahydrobenzo[d]isoxazole-3- carboxamide derivatives as novel potent inhibitors of Mycobacterium tuberculosis pantothenate synthetase: initiating a quest for new antitubercular drugs J. Med. Chem. 2008 51 1999 2002
9. E. L. White K. Southworth L. Ross S. Cooley R. B. Gill M. I. Sosa A. Manouvakhova L. Rasmussen C. Goulding D. Eisenberg T. M. Fletcher III A novel inhibitor of Mycobacterium tuberculosis pantothenate synthetase J. Biomol. Screening 2007 12 100 105
10. A. Ciulli D. E. Scott M. Ando F. Reyes S. A. Saldanha K. L. Tuck D. Y. Chirgadze T. L. Blundell C. Abell Inhibition of Mycobacterium tuberculosis pantothenate synthetase by analogues of the reaction intermediate ChemBioChem 2008 9 2606 2611
11. R. Zheng T. K. Dam C. F. Brewer J. S. Blanchard Active site residues in Mycobacterium tuberculosis pantothenate synthetase required in the formation and stabilization of the adenylate intermediate Biochemistry 2004 43 7171 7178
12. A. W. Hung H. L. Silvestre S. Wen A. Ciulli T. L. Blundell C. Abell Application of fragment growing and fragment linking to the discovery of inhibitors of Mycobacterium tuberculosis pantothenate synthetase Angew. Chem., Int. Ed. 2009 48 8452 8546
13. D. E. Scott G. J. Dawes M. Ando C. Abell A. Ciulli A fragment-based approach to probing adenosine recognition sites by using dynamic combinatorial chemistry ChemBioChem 2009 10 2772 2779
14. P. Sledz H. L. Silvestre A. W. Hung A. Ciulli T. L. Blundell C. Abell Application to inhibitor discovery against Mycobacterium tuberculosis pantothenate synthetase J. Am. Chem. Soc. 2010 132 4544 4545
15. Y. Yang P. Gao Y. Liu X. Ji M. Gan Y. Guan H. Hao Z. Li C. Xiao A discovery of novel Mycobacterium tuberculosis pantothenate synthetase inhibitors based on the molecular mechanism of actinomycin D inhibition Bioorg. Med. Chem. Lett. 2011 21 3943 3946
16. A. Spannhoff R. Heinke I. Bauer P. Trojer E. Metzger R. Gust R. Schüle G. Brosch W. Sippl M. Jung Target-based approach to inhibitors of histone arginine methyltransferases J. Med. Chem. 2007 50 10 2319 2325
17. A. Kumar M. I. Siddiqi S. Miertus New molecular scaffolds for the design of Mycobacterium tuberculosis type II dehydroquinase inhibitors identified using ligand and receptor based virtual screening J. Mol. Model. 2010 16 693 712
18. R. Heinke A. Spannhoff R. Meier P. Trojer I. Bauer M. Jung W. Sippl Virtual screening and biological characterization of novel histone arginine methyltransferase PRMT1 inhibitors ChemMedChem 2009 4 1 69 77
19. W. Sippl Development of biologically active compounds by combining 3D QSAR and structure-based design methods J. Comput.-Aided Mol. Des. 2002 16 11 825 830
20. Molecular Operating Environment Software, Chemical Computing Group Inc., Montreal, 2010
21. T. A. Halgren Merck molecular forcefield J. Comput. Chem. 1996 17 490 641
22. S. Wang D. Eisenberg Crystal structure of the pantothenate synthetase from Mycobacterium tuberculosis, snapshots of the enzyme in action Biochemistry 2006 45 1554 1561
23. S. Wang D. Eisenberg Crystal structures of a pantothenate synthetase from M. tuberculosis and its complexes with substrates and a reaction intermediate Protein Sci. 2003 12 1097 1108
24. H. M. Berman J. Westbrook Z. Feng G. G. Gilliland T. N. Bhat H. Weissig I. N. Shindyalov P. E. Bourne The protein databank Nucleic Acids Res. 2000 28 1 235 242
25. Schrödinger: Maestro, version 9.2, LLC, New York, NY, 2011
26. D. Shivakumar J. Williams Y. Wu W. Damm J. Shelley W. Sherman Prediction of absolute solvation free energies using molecular dynamics free energy perturbation and the OPLS force field J. Chem. Theory Comput. 2010 6 1509 1519
27. W. L. Jorgensen D. S. Maxwell J. Tirado-Rives Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids J. Am. Chem. Soc. 1996 118 45 11225 11236
28. W. L. Jorgensen J. Tirado-Rives The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin J. Am. Chem. Soc. 1988 110 6 1657 1666
29. G. Jones P. Willet R. C. Glen Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation J. Mol. Biol. 1995 245 43 53
30. C. A. Baxter C. W. Murray D. E. Clark D. R. Westhead M. D. Eldridge Flexible docking using Tabu search and an empirical estimate of binding affinity Proteins: Struct., Funct., Genet. 1998 33 367 382
31. M. D. Eldridge C. W. Murray T. R. Auton G. V. Paolini R. P. Mee Empirical scoring functions: I. The development of fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes J. Comput.-Aided Mol. Des. 1997 11 425 445
32. G. Jones P. Willet R. C. Glen A. R. Leach R. Taylor Development and validation of genetic algorithm for flexible docking J. Mol. Biol. 1997 3 727 748
33. M. L. Verdonk G. Chessari J. C. Cole M. J. Hartshom C. W. Murray J. W. Nissink R. D. Taylor R. Taylor Modeling water molecules in protein-ligand docking using GOLD J. Med. Chem. 2005 48 6504 6515
34. Schrödinger: Glide, version 5.5, LLC, New York, NY, 2009
35. Schrödinger Suite 2011 Induced Fit Docking protocol, Glide version 5.7, Schrödinger, LLC, New York, NY, 2011
36. Schrödinger: Prime version 3.0, LLC, New York, NY, 2011
37. W. Sherman T. Day M. P. Jacobson R. A. Friesner R. Farid Novel procedure for modeling ligand/receptor induced fit effects J. Med. Chem. 2006 49 534 553
38. W. Sherman H. S. Beard R. Farid Use of an induced fit receptor structure in virtual screening Chem. Biol. Drug Des. 2006 67 83 84
39. G. Wolber T. Langer LigandScout: 3D-Pharmacophores derived from protein-bound ligands and their use as virtual screening filters J. Chem. Inf. Model. 2005 45 1 160 169
40. M. L. Verdonk V. Berdini M. J. Hartshom W. T. Mooij C. W. Murray R. D. Taylor P. Watson Virtual screening using protein-ligand docking: avoiding artificial enrichment J. Chem. Inf. Model. 2004 44 3 793 806
41. O. F. Güner and D. R. Henry, Pharmacophore perception, development, and use in drug design, IUL Biotechnology Series, in Metric for analyzing hit lists and pharmacophores, ed., O. F. Güner, International University Line, La Jolla, CA, 2000, pp. 191-212
42. O. F. Güner, M. Waldman, R. D. Hoffmann and J. H. Kim, Pharmacophore perception, development, and use in drug design, IUL Biotechnology Series, in Strategies for database mining and pharmacophore development, ed., O. F. Güner, International University Line, La Jolla, 1st edn, 2000, pp. 213-236
43. T. Langer and R. D. Hoffmann, Pharmacophores and pharmacophore searches, WILEY-VCH, Weinheim, 2006, pp. 338-340
44. AMBER 11, University of California, San Francisco, CA, 2010
45. J. Wang R. M. Wolf J. W. Caldwell P. A. Kollman D. A. Case Development and testing of a general amber forcefield J. Comput. Chem. 2004 25 1157 1174
46. J. Wang P. Cieplak P. A. Kollman How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules J. Comput. Chem. 2000 21 1049 1074
47. A. Jakalian D. B. Jack C. I. Bayly Fast, efficient generation of high quality atomic charges. AM1-BCC model: Parameterization and validation J. Comput. Chem. 2002 23 1623 1641
48. J. P. Ryckaert G. Ciccotti H. J. C. Berendsen Numerical integration of the cartesian equations of motions of a system with constraints: Molecular dynamics of n-alkanes J. Comput. Phys. 1977 23 327 341
49. D. M. York T. A. Darden L. G. Pederson The effect of long-range electrostatic interactions in simulations of macromolecular crystals: a comparison of the Ewald and truncated list methods J. Chem. Phys. 1993 99 8345 8348
50. T. Darden L. Perera L. Li L. Pedersen New tricks for modelers from the crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic acid simulations Structure 1999 7 R55 R60
51. U. Essmann L. Perera M. L. Berkowitz T. Darden H. Lee L. G. Pedersen A smooth particle mesh Ewald method J. Chem. Phys. 1995 103 8577 8593
52. C. Sagui T. A. Darden Molecular dynamics simulations of biomolecules: long range electrostatic effects Annu. Rev. Biophys. Biomol. Struct. 1999 28 155 179
53. C.-H. Yi J.-Z. Chen S.-H. Shi G.-D. Hu Q.-G. Zhang A computational analysis of pyrazole-based inhibitors binding to Hsp90 using molecular dynamics simulation and the MM-GBSA method Mol. Simul. 2010 36 454 460
54. P. A. Kollman I. Massova C. Reyes B. Kuhn S. Huo L. Chong M. Lee T. Lee Y. Duan W. Wang O. Donini P. Cieplak J. Scrinivasan D. A. Case T. E. Cheatham III Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models Acc. Chem. Res. 2000 33 889 897
55. W. C. Still A. Tempczyk R. C. Hawley T. Hendrickson Semianalytical treatment of solvation for molecular mechanics and dynamics J. Chem. Phys. 1990 115 6127 6129
56. V. Tsui D. A. Case Theory and application of the generalized Born solvation model in macromolecular simulations Biopolymers 2001 56 275 291
57. J. Weiser P. S. Wenkin W. C. Still Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO) J. Comput. Chem. 1999 20 217 230
58. W. L. DeLano, The PyMOL Molecular Graphics System, DeLano Scientific, San Carlos, CA, USA, 2002, http://www.pymol.org
59. P. Markt, Pharmacophore models for virtual screening, in Virtual Screening, ed., C. Sotriffer, Wiley-VCH, 2011, pp. 115-152
60. K. Wichapong M. Lawson S. Pianwanit S. Kokpol W. Sippl Postprocessing of protein-ligand docking poses using linear response MM-PB/SA: application to Wee1 kinase inhibitors J. Chem. Inf. Model. 2010 50 9 1574 1588
61. E. Muzzioli A. Del Rio G. Rastelli Assessing protein kinase selectivity with molecular dynamics and mm-pbsa binding free energy calculations Chem. Biol. Drug Des. 2011 78 2 252 259
62. F. Ntie-Kang J. A. Mbah L. M. Mbaze L. L. Lifongo M. Scharfe J. Ngo Hanna F. Cho-Ngwa P. Amoa Onguéné L. C. Owono Owono E. Megnassan W. Sippl S. M. N. Efange CamMedNP: Building the Cameroonian 3D structural natural products database for virtual screening BMC Complementary Altern. Med. 2013 13 88
63. F. Ntie-Kang L. L. Lifongo L. M. Mbaze N. Ekwelle L. C. Owono Owono E. Megnassan P. N. Judson W. Sippl S. M. N. Efange Cameroonian medicinal plants: a bioactivity versus ethnobotanical survey and chemotaxonomic classification BMC Complementary Altern. Med. 2013 13 147
64. F. Ntie-Kang P. Amoa Onguéné M. Scharfe L. C. Owono Owono E. Megnassan L. M. Mbaze W. Sippl S. M. N. Efange ConMedNP: A natural product library from Central African medicinal plants for drug discovery RSC Adv. 2013 10.1039/c3ra43754j
65. D. Zofou F. Ntie-Kang W. Sippl S. M. N. Efange Bioactive natural products derived from the Central African flora against neglected tropical diseases and HIV Nat. Prod. Rep. 2013 30 1098 1120
66. F. Ntie-Kang D. Zofou S. B. Babiaka R. Meudom L. L. Lifongo J. A. Mbah M. Scharfe L. M. Mbaze W. Sippl S. M. N. Efange AfroDb: A select highly potent and diverse natural product library from African medicinal plants PLoS One 2013 8 10 e78085