Theoretical studies on the binding of rhenium(I) complexes to inducible nitric oxide synthase

Journal of Molecular Graphics and Modelling

Volumn 45, Issue , 2013, Pages 13-25

  Oliveira, Bruno L ^a   Moreira, Irina S ^b   Fernandes, Pedro A ^b   Ramos, Maria J ^b   Santos, Isabel ^a   Correia, João D G ^a  

^a INSTITUTO TECNOLÓGICO E NUCLEAR   (Portugal)

^b Campus Universitário de Santiago   (Portugal)

Author keywords

Docking; Free energy perturbation calculations; Molecular dynamics; Nitric oxide synthase; Rhenium; Technetium

Indexed keywords

FREE ENERGY PERTURBATION; INDUCIBLE NITRIC OXIDE SYNTHASE; MOLECULAR DOCKING; MOLECULAR DYNAMICS SIMULATIONS; NITRIC-OXIDE SYNTHASE; RELATIVE BINDING ENERGIES; RHENIUM COMPLEXES; THEORETICAL STUDY;

AMINO ACIDS; CARBON; DOCKING; FREE ENERGY; MOLECULAR DYNAMICS; NITRIC OXIDE; NITROGEN OXIDES; ORGANOMETALLICS; POSITIVE IONS; RHENIUM; TECHNETIUM;

RHENIUM COMPOUNDS;

INDUCIBLE NITRIC OXIDE SYNTHASE; RHENIUM COMPLEX;

ARTICLE; BINDING AFFINITY; CONJUGATE; MOLECULAR DOCKING; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; PRIORITY JOURNAL; RADIOENZYMATIC ASSAY; STATIC ELECTRICITY; THEORETICAL STUDY;

DOCKING; FREE ENERGY PERTURBATION CALCULATIONS; MOLECULAR DYNAMICS; NITRIC OXIDE SYNTHASE; RHENIUM; TECHNETIUM;

CATALYTIC DOMAIN; ENZYME INHIBITORS; HYDROGEN BONDING; ISOENZYMES; LIGANDS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MOLECULAR DOCKING SIMULATION; MOLECULAR DYNAMICS SIMULATION; NITRIC OXIDE SYNTHASE TYPE II; PROTEIN BINDING; RHENIUM; THERMODYNAMICS;

EID: 84884558273     PISSN: 10933263     EISSN: 18734243     Source Type: Journal    
DOI: 10.1016/j.jmgm.2013.07.007     Document Type: Article

References (80)

1. W.K. Alderton, and R.G. Knowles Nitric oxide synthases: structure, function and inhibition Biochemistry Journal 357 2001 593 615 (Pubitemid 32735142)
2. U. Grädler, T. Fuchß, W.-R. Ulrich, R. Boer, A. Strub, and C. Hesslinger Novel nanomolar imidazo[4,5-b]pyridines as selective nitric oxide synthase (iNOS) inhibitors: SAR and structural insights Bioorganic & Medicinal Chemistry Letters 21 2011 4228 4232
3. P. Vallance, and J. Leiper Blocking NO synthesis: how, where and why Nature Reviews Drug Discovery 1 2002 939 950 (Pubitemid 37361600)
4. B.L. Oliveira, P.D. Raposinho, F. Mendes, I.C. Santos, I. Santos, and A. Ferreira Targeting nitric oxide synthase with 99mTc/Re-tricarbonyl complexes containing pendant guanidino or isothiourea moieties Journal of Organometallic Chemistry 696 2011 1057 1065
5. B.L. Oliveira, P.D. Raposinho, F. Mendes, FigueiraS F.V., I. Santos, and A.N. Ferreira Re and Tc tricarbonyl complexes: from the suppression of NO biosynthesis in macrophages to in vivo targeting of inducible nitric oxide synthase Bioconjugate Chemistry 21 2010 2168 2172
6. B.L. Oliveira, J.D.G. Correia, P.D. Raposinho, I. Santos, A. Ferreira, and C. Cordeiro Re and 99mTc organometallic complexes containing pendant l-arginine derivatives as potential probes of inducible nitric oxide synthase Dalton Transactions 15 2009 2 62
7. A.C. Wallace, R.A. Laskowski, and J.M. Thornton LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions Protein Engineering 8 1995 127 134
8. B.R. Crane, A.S. Arvai, S. Ghosh, E.D. Getzoff, D.J. Stuehr, and J.A. Tainer Structures of the Nω-hydroxy-l-arginine complex of inducible nitric oxide synthase oxygenase dimer with active and inactive pterins Biochemistry 39 2000 4608 4621 (Pubitemid 30225324)
9. B.R. Crane, A.S. Arvai, D.K. Ghosh, C. Wu, E.D. Getzoff, and D.J. Stuehr Structure of nitric oxide synthase oxygenase dimer with pterin and substrate Science 279 1998 2121 2126 (Pubitemid 28196359)
10. R. Fedorov, E. Hartmann, D.K. Ghosh, and I. Schlichting Structural basis for the specificity of the nitric-oxide synthase inhibitors W1400 and Nω-propyl-l-Arg for the inducible and neuronal isoforms Journal of Biological Chemistry 278 2003 45818 45825 (Pubitemid 37432727)
11. E. Ann Hallinan, S.W. Kramer, S.C. Houdek, W.M. Moore, G.M. Jerome, and D.P. Spangler 4-Fluorinated l-lysine analogs as selective i-NOS inhibitors: methodology for introducing fluorine into the lysine side chain Organic and Biomolecular Chemistry 1 2003 3527 3534
12. E.D. Garcin, A.S. Arvai, R.J. Rosenfeld, M.D. Kroeger, B.R. Crane, and G. Andersson Anchored plasticity opens doors for selective inhibitor design in nitric oxide synthase Nature Chemical Biology 4 2008 700 707
13. B. Oliveira, I. Moreira, P. Fernandes, M. Ramos, I. Santos, and J.G. Correia Insights into the structural determinants for selective inhibition of nitric oxide synthase isoforms Journal of Molecular Modeling 19 2012 1537 1551
14. F. Xue, J. Huang, H. Ji, J. Fang, H. Li, and P. Martasek Structure-based design, synthesis, and biological evaluation of lipophilic-tailed monocationic inhibitors of neuronal nitric oxide synthase Bioorganic & Medicinal Chemistry 18 2010 6526 6537
15. C. Maccallini, A. Patruno, N. Besker, J. Isabella, A. Ammazzalorso, and B. de Filippis Synthesis, biological evaluation, and docking studies of N-substituted acetamidines as selective inhibitors of inducible nitric oxide synthase Journal of Medicinal Chemistry 52 2009 1481 1485
16. S.M. Francis, A. Mittal, M. Sharma, and P. Bharatam Design of benzene-1,2-diamines as selective inducible nitric oxide synthase inhibitors: a combined de novo design and docking analysis Journal of Molecular Modeling 14 2008 215 224
17. V. Aparna, G. Desiraju, and B. Gopalakrishnan Insights into ligand selectivity in nitric oxide synthase isoforms: a molecular dynamics study Journal of Molecular Graphics and Modelling 26 2007 457 470 (Pubitemid 47337194)
18. B.R. Crane, R.J. Rosenfeld, A.S. Arvai, D.K. Ghosh, S. Ghosh, and J.A. Tainer N-terminal domain swapping and metal ion binding in nitric oxide synthase dimerization EMBO Journal 18 1999 6271 6281 (Pubitemid 29533231)
19. S.A. Jackson, S. Sahni, L. Lee, Y. Luo, T.R. Nieduzak, and G. Liang Design, synthesis and characterization of a novel class of coumarin-based inhibitors of inducible nitric oxide synthase Bioorganic and Medicinal Chemistry 13 2005 2723 2739 (Pubitemid 40387483)
20. R.J. Rosenfeld, E.D. Garcin, K. Panda, G. Andersson, A. Åberg, and A.V. Wallace Conformational changes in nitric oxide synthases induced by chlorzoxazone and nitroindazoles: crystallographic and computational analyses of inhibitor potency Biochemistry 41 2002 13915 13925 (Pubitemid 35364865)
21. VolArea João Ribeiro, Group of Computational BioChemistry, Faculty of Sciences of the University of Porto, Porto, Portugal 2013 http://www.compbiochem.org/Software/Volarea/Home.html
22. G. Steinkellner, R. Rader, G. Thallinger, C. Kratky, and K. Gruber VASCo: computation and visualization of annotated protein surface contacts BMC Bioinformatics 10 2009 32
23. C.-E.A. Chang, W. Chen, and M.K. Gilson Ligand configurational entropy and protein binding Proceedings of the National Academy of Sciences 104 2007 1534 1539 (Pubitemid 46214625)
24. D.L. Mobley, and K.A. Dill Binding of small-molecule ligands to proteins: what you see is not always what you get Structure 17 2009 489 498
25. C. Gao, M.-S. Park, and H.A. Stern Accounting for ligand conformational restriction in calculations of protein-ligand binding affinities Biophysical Journal 98 2010 901 910
26. E. Perola, and P.S. Charifson Conformational analysis of drug-like molecules bound to proteins: an extensive study of ligand reorganization upon binding Journal of Medicinal Chemistry 47 2004 2499 2510 (Pubitemid 38580088)
27. C. Diehl, O. Engström, T. Delaine, M. Håkansson, S. Genheden, and K. Modig Protein flexibility and conformational entropy in ligand design targeting the carbohydrate recognition domain of galectin-3 Journal of the American Chemical Society 132 2010 14577 14589
28. J.C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, and E. Villa Scalable molecular dynamics with NAMD Journal of Computational Chemistry 26 2005 1781 1802 (Pubitemid 43078511)
29. W. Humphrey, A. Dalke, and K.V.M.D. Schulten Visual molecular dynamics Journal of Molecular Graphics 14 1996 33 38
30. M.A.S. Perez, P.A. Fernandes, and M.J. Ramos Substrate recognition in HIV-1 protease: a computational study Journal of Physical Chemistry B 114 2010 2525 2532
31. D.A. Pearlman A comparison of alternative approaches to free energy calculations Journal of Physical Chemistry 98 1994 1487 1493
32. J. Hénin, C. Harrison, and C. Chipot A Tutorial for Alchemical FEP in NAMD vol. 2011 2010
33. J. Gasteiger, and M. Marsili Iterative partial equalization of orbital electronegativity - a rapid access to atomic charges Tetrahedron 36 1980 3219 3228
34. G.M. Morris, D.S. Goodsell, R.S. Halliday, R. Huey, W.E. Hart, and R.K. Belew Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function Journal of Computational Chemistry 19 1998 1639 1662 (Pubitemid 128590223)
35. G.M. Morris, R. Huey, W. Lindstrom, M.F. Sanner, R.K. Belew, and D.S. Goodsell AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility Journal of Computational Chemistry 30 2009 2785 2791
36. J. Shelley, A. Cholleti, L. Frye, J. Greenwood, M. Timlin, and M. Uchimaya Epik: a software program for pKa prediction and protonation state generation for drug-like molecules Journal of Computer-Aided Molecular Design 21 2007 681 691
37. E. Palma, J.D.G. Correia, B.L. Oliveira, L. Gano, I.C. Santos, and I. Santos 99mTc(CO)3-labeled pamidronate and alendronate for bone imaging Dalton Transactions 40 2011 2787 2796
38. T. Ziegler Approximate density functional theory as a practical tool in molecular energetics and dynamics Chemical Reviews 91 1991 651 667
39. A.D. Becke Density-functional thermochemistry. III. The role of exact exchange Journal of Chemical Physics 98 1993 5648 5652
40. S.F. Sousa, P.A. Fernandes, and M.J. Ramos General performance of density functionals Journal of Physical Chemistry A 111 2007 10439 10452 (Pubitemid 350046111)
41. C. Lee, W. Yang, and R.G. Parr Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density Physical Review B 37 1988 785
42. K. Vanommeslaeghe, E. Hatcher, C. Acharya, S. Kundu, S. Zhong, and J. Shim CHARMM general force field: a force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields Journal of Computational Chemistry 31 2010 671 690
43. X. Li, X. Liu, Z. Wu, and H. Zhang DFT/TDDFT studies on the electronic structures and spectral properties of rhenium(I) pyridinybenzoimidazole complexes Journal of Physical Chemistry A 112 2008 11190 11197
44. C.I. Bayly, P. Cieplak, W. Cornell, and P.A. Kollman A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model Journal of Physical Chemistry 97 1993 10269 10280
45. W.D. Cornell, P. Cieplak, C.I. Bayly, and P.A. Kollmann Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation Journal of the American Chemical Society 115 1993 9620 9631
46. M. Connolly Analytical molecular surface calculation Journal of Applied Crystallography 16 1983 548 558
47. D. Andrae, U. Häußermann, M. Dolg, H. Stoll, and H. Preuß Energy-adjusted ab initio pseudopotentials for the second and third row transition elements Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) 77 1990 123 141
48. T.H. Dunning Jr., and P.J. Hay Modern Theoretical Chemistry vol. 3 1976 Plenum New York 1 28
49. M. Dolg, H. Stoll, and H. Preuss Energy-adjusted ab initio pseudopotentials for the first row transition elements Journal of Chemical Physics 86 1987 866 873
50. F.-Y. Dupradeau, A. Pigache, T. Zaffran, C. Savineau, R. Lelong, and N. Grivel The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building Physical Chemistry Chemical Physics 12 2010 7821 7839
51. F.-Y. Dupradeau, C. Cézard, R. Lelong, É. Stanislawiak, J. Pêcher, and J.C. Delepine R.E.DD.B.: a database for RESP and ESP atomic charges, and force field libraries Nucleic Acids Research 36 2008 D360 D367
52. E. Vanquelef, S. Simon, G. Marquant, E. Garcia, G. Klimerak, and J.C. Delepine R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments Nucleic Acids Research 39 2011 W511 W517
53. K. Vanommeslaeghe, and A.D. MacKerell Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing Journal of Chemical Information and Modeling 52 2012 3144 3154
54. K. Vanommeslaeghe, E.P. Raman, and A.D. MacKerell Automation of the CHARMM General Force Field (CGenFF) II: assignment of bonded parameters and partial atomic charges Journal of Chemical Information and Modeling 52 2012 3155 3168
55. D.E. Reichert, and M.J. Welch Applications of molecular mechanics to metal-based imaging agents Coordination Chemistry Reviews 212 2001 111 131
56. P. Wolohan, and D.E. Reichert CoMSIA and docking study of rhenium based estrogen receptor ligand analogs Steroids 72 2007 247 260 (Pubitemid 46273506)
57. M. Stichelberger, D. Desbouis, V. Spiwok, L. Scapozza, P.A. Schubiger, and R. Schibli Synthesis, in vitro and in silico assessment of organometallic rhenium(I) and technetium(I) thymidine complexes Journal of Organometallic Chemistry 692 2007 1255 1264 (Pubitemid 46209171)
58. Desbouis, D. Struthers, H. Spiwok, V. Küster, T. Schibli, and R. Synthesis In vitro, and in silico evaluation of organometallic technetium and rhenium thymidine complexes with retained substrate activity toward human thymidine kinase type 1 Journal of Medicinal Chemistry 51 2008 6689 6698
59. S. James, K.P. Maresca, D.G. Allis, J.F. Valliant, W. Eckelman, and J.W. Babich Extension of the single amino acid chelate concept (SAAC) to bifunctional biotin analogues for complexation of the M(CO)3 + 1 core (M = Tc and Re): syntheses, characterization, biotinidase stability, and avidin binding Bioconjugate Chemistry 17 2006 579 589 (Pubitemid 43841387)
60. S.C. Hoops, K.W. Anderson, and K.M. Merz Force field design for metalloproteins Journal of the American Chemical Society 113 1991 8262 8270
61. M.B. Peters, Y. Yang, B. Wang, L.S. Füsti-Molnár, M.N. Weaver, and K.M. Merz Structural survey of zinc-containing proteins and development of the zinc AMBER force field (ZAFF) Journal of Chemical Theory and Computation 6 2010 2935 2947
62. S. Sousa, P. Fernandes, and M. Ramos Effective tailor-made force field parameterization of the several Zn coordination environments in the puzzling FTase enzyme: opening the door to the full understanding of its elusive catalytic mechanism Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) 117 2007 171 181 (Pubitemid 44791252)
63. P.-O. Norrby, and P. Brandt Deriving force field parameters for coordination complexes Coordination Chemistry Reviews 212 2001 79 109
64. A.D. MacKerell, D. Bashford, R.L. Bellott Dunbrack, J.D. Evanseck, and M.J. Field All-atom empirical potential for molecular modeling and dynamics studies of proteins Journal of Physical Chemistry B 102 1998 3586 3616 (Pubitemid 128576688)
65. K.-B. Cho, E. Derat, and S. Shaik Compound I of nitric oxide synthase: the active site protonation state Journal of the American Chemical Society 129 2007 3182 3188 (Pubitemid 46449351)
66. T.J. Dolinsky, J.E. Nielsen, J.A. McCammon, and N.A. Baker PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations Nucleic Acids Research 32 2004 W665 W667
67. T.J. Dolinsky, P. Czodrowski, H. Li, J.E. Nielsen, J.H. Jensen, and G. Klebe PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations Nucleic Acids Research 35 2007 W522 W525
68. H. Li, A.D. Robertson, and J.H. Jensen Very fast empirical prediction and rationalization of protein pKa values Proteins: structure, function, and bioinformatics 61 2005 704 721 (Pubitemid 41753142)
69. U. Essmann, L. Perera, M.L. Berkowitz, T. Darden, H. Lee, and L.G. Pedersen A smooth particle mesh Ewald method Journal of chemical physics 103 1995 8577 8593
70. W.G. Hoover Canonical dynamics: equilibrium phase-space distributions Physical Review A 31 1985 1695
71. S.E. Feller, Y. Zhang, R.W. Pastor, and B.R. Brooks Constant pressure molecular dynamics simulation: the Langevin piston method Journal of Chemical Physics 103 1995 4613 4621
72. S. Nosé A molecular dynamics method for simulations in the canonical ensemble Molecular Physics: An International Journal at the Interface Between Chemistry and Physics 100 2002 191 198
73. G.S. Grest, and K. Kremer Molecular dynamics simulation for polymers in the presence of a heat bath Physical Review A 33 1986 3628
74. W.L. DeLano The PyMOL Molecular Graphics System 2002 DeLano Scientific San Carlos, CA, USA
75. M. Bhandarkar, R. Brunner, C. Chipot, A. Dalke, and S. Dixit NAMD User's Guide, Version 2.6b1., Theoretical Biophysics Group 2005 University of Illinois and Beckman Institute Urbana, IL
76. J.W. Pitera, and W.F. van Gunsteren A comparison of non-bonded scaling approaches for free energy calculations Molecular Simulation 28 2002 45 65 (Pubitemid 44115177)
77. C. Chipot, and D.A. Pearlman Free energy calculations. The long and winding gilded road Molecular Simulation 28 2002 1 12 (Pubitemid 44121112)
78. A. Pohorille, C. Jarzynski, and C. Chipot Good practices in free-energy calculations Journal of Physical Chemistry B 114 2010 10235 10253
79. M. Zacharias, T.P. Straatsma, and J.A. McCammon Separation shifted scaling, a new scaling method for Lennard-Jones interactions in thermodynamic integration The Journal of Chemical Physics 100 1994 9025 9031
80. T.C. Beutler, A.E. Mark, R.C. van Schaik, P.R. Gerber, and W.F. van Gunsteren Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations Chemical Physics Letters 222 1994 529 539