First principles calculations of thermodynamics and kinetic parameters and molecular dynamics simulations of acetylcholinesterase reactivators: can mouse data provide new insights into humans?

References

• Akten , E.D. , Cansu , S. and Doruker , P. 2009 . A docking study using atomistic conformers generated via elastic network model for cyclosporin a/cyclophilin a complex . Journal of Biomolecular Structure & Dynamics , 27 : 13 – 25 .
   PubMed Web of Science ®Google Scholar
• Andrianov , A.M. 2009 . Immunophilins and HIV-1 V3 loop for structure-based anti-AIDS drug design . Journal of Biomolecular Structure & Dynamics , 26 : 445 – 454 .
   PubMed Web of Science ®Google Scholar
• Ashani , Y. , Radic , Z. , Tsigelny , I. , Vellom , D.C. , Pickering , N.A. , Quinn , D.M. , … and Taylor , P. 1995 . Amino acid residues controlling reactivation of organophosphonyl conjugates of acetylcholinesterase by mono- and bisquaternary oximes . Journal of Biological Chemistry , 11 : 6370 – 6380 .
   Web of Science ®Google Scholar
• Bairagya , H.R. , Mukhopadhyay , B.P. and Sekar , K. 2009 . An insight to the dynamics of conserved water molecular triad in IMPDH II (Human): Recognition of cofactor and substrate to catalytic Arg 322 . Journal of Biomolecular Structure & Dynamics , 27 : 149 – 158 .
   PubMed Web of Science ®Google Scholar
• Barnard , E.A. 1974 . “ Neuromuscular transmission – enzymatic destruction of acetylcholine ” . In The peripheral nervous system , Edited by: Hubbard , J.I. 30 – 50 . New York , NY : Plenum Press .
   Google Scholar
• Bernard , P.P. , Kireev , D.B. , Pintore , M. , Chrétien , J.R. , Fortier , P.L. and Froment , D. 2000 . A CoMFA study of enantiomeric organophosphorus inhibitors of acetylcholinesteras . Journal of Molecular Modeling , 6 : 618 – 629 .
   Web of Science ®Google Scholar
• Black , R.M. and Harrison , J.M. 1996 . “ The chemistry of organophosphorus chemical warfare agents ” . In The chemistry of organophosphorus compounds , Edited by: Hartley , F.R. Vol. 4 , 120 – 240 . Chichester : Wiley .
   Google Scholar
• Borkar , A. , Ghosh , I. and Bhattacharyya , D. 2010 . Structure and dynamics of double helical DNA in torsion angle hyperspace: A molecular mechanics approach . Journal of Biomolecular Structure & Dynamics , 27 : 695 – 712 .
   PubMed Web of Science ®Google Scholar
• Brooks, B.R., Brooks C.L. III, MacKerell Jr., A.D., Nilsson, L., Petrella, R.J., Roux, B.
   Google Scholar
• Brunger , A.T. 2007 . Version 1.2 of the crystallography and NMR system . Nature Protocols , 2 : 2728 – 2733 .
   PubMed Web of Science ®Google Scholar
• Cambria , M.T. , Di Marino , D. , Falconi , M. , Garavaglia , S. and Cambria , A. 2010 . Docking simulation and competitive experiments validate the interaction between the 2,5-xylidine Inhibitor and Rigidoporus lignosus laccase . Journal of Biomolecular Structure & Dynamics , 27 : 501 – 509 .
   PubMed Web of Science ®Google Scholar
• Chen , C.Y.C. 2009 . Weighted equation and rules – a novel concept for evaluating protein–ligand interaction . Journal of Biomolecular Structure & Dynamics , 27 : 271 – 282 .
   PubMed Web of Science ®Google Scholar
• Chen , C.Y. 2010 . Virtual screening and drug design for PdDe-5 receptor from traditional Chinese medicine database . Journal of Biomolecular Structure & Dynamics , 27 : 627 – 640 .
   PubMed Web of Science ®Google Scholar
• Chen , C.Y. , Chang , Y.H. , Bau , D.T. , Huang , H.J. , Tsai , F.J. , Tsai , C.H. and Chen , C.Y.C. 2009 . Ligand-based dual target drug design for H1N1: Swine flu – a preliminary first study . Journal of Biomolecular Structure & Dynamics , 27 : 171 – 178 .
   PubMed Web of Science ®Google Scholar
• Cordomi , A. and Perez , J.J. 2009 . Structural rearrangements of rhodopsin subunits in a dimer complex: A molecular dynamics simulation study . Journal of Biomolecular Structure & Dynamics , 27 : 127 – 147 .
   PubMed Web of Science ®Google Scholar
• Cornell , W.D. , Cieplak , P. , Bayly , C.I. , Gould , I.R. , Merz , K.M. , Ferguson , D.M. , … and Kollman , P.A. 1995 . A second generation force field for the simulation of proteins, nucleic acids, and organic molecules . Journal of the American Chemical Society , 117 : 5179 – 5197 .
   Web of Science ®Google Scholar
• da Cunha , E.F.F. , Barbosa , E.F. , Oliveira , A.A. and Ramalho , T.C. 2010 . Molecular modeling of mycobacterium tuberculosis DNA gyrase and its molecular docking study with gatifloxacin inhibitors . Journal of Biomolecular Structure & Dynamics , 27 : 619 – 625 .
   PubMed Web of Science ®Google Scholar
• da Cunha , E.F.F. , Ramalho , T.C. , Mancini , D.T. , Fonseca , E.M.B. and Oliveira , A.A. 2010 . New approaches to the development of anti-protozoan drug candidates: A review of patents . Journal of the Brazilian Chemical Society , 21 : 1787 – 1806 .
   Web of Science ®Google Scholar
• Dvir , H. , Silman , I. , Harel , M. , Rosenberry , T.L. and Sussman , J.L. 2010 . Acetylcholinesterase: From 3D structure to function . Chemico-Biological Interactions , 187 : 10 – 22 .
   PubMed Web of Science ®Google Scholar
• Ekström , F.J. , Astot , C. and Pang , Y.P. 2007 . Novel nerve-agent antidote design based on crystallographic and mass spectrometric analyses of tabun-conjugated acetylcholinesterase in complex with antidotes . Clinical Pharmacology and Therapeutics , 82 ( 3 ) : 282 – 293 .
   PubMedGoogle Scholar
• Ekström , F. , Hörnberg , A. , Artursson , E. , Hammarström , L. , Schneider , G. and Pang , Y. 2009 . Structure of HI-6NSarin-Acetylcholinesterase determined by X-ray crystallography and molecular dynamics simulation: Reactivator mechanism and design . PLoS ONE , 4 : e5957
   PubMed Web of Science ®Google Scholar
• Ekström , F.J. , Yuan-Ping , P. , Boman , M. , Artursson , E. , Akfur , C. and Börjegren , S. 2006 . Crystal structures of acetylcholinesterase in complex with HI-6, Ortho-7 and obidoxime: Structural basis for differences in the ability to reactivate tabun conjugates . Biochemical Pharmacology , 72 : 597 – 607 .
   PubMed Web of Science ®Google Scholar
• Frisch, M.J., Trucks, G.W., Schlegel, H.B., Scuseria, G.E., Robb, M.A., Cheeseman, J.R., … Pople, J.A. (2004). Gaussian, Inc. Wallingford, CT.
   Google Scholar
• Gonçalves , A.S. , França , T.C.C. , Figueroa-Villar , J.D. and Pascutti , P.G. 2010 . Conformational analysis of toxogonine, TMB-4 and HI-6 using PM6 and RM1 methods . Journal of the Brazilian Chemical Society , 21 : 179 – 184 .
   Web of Science ®Google Scholar
• Gonçalves , A.S. , França , T.C.C. , Figueroa-Villar , J.D. and Pascutti , P.G. 2011 . Molecular dynamics simulations and QM/MM studies of the reactivation by 2-PAM of tabun inhibited human acethylcolinesterase . Journal of the Brazilian Chemical Society , 22 : 155 – 165 .
   Web of Science ®Google Scholar
• Gonçalves , A.S. , França , T.C.C. , Wilter , A. and Figueroa-Villar , J.D. 2006 . Molecular dynamics of the interaction of pralidoxime and deazapralidoxime with acetylcholinesterase inhibited by the neurotoxic agent tabun . Journal of the Brazilian Chemical Society , 17 : 968 – 975 .
   Web of Science ®Google Scholar
• Guex , N. and Peitsch , M.C. 1997 . Peitsch, swiss-model and Swiss-PdbViewer: An environment for comparative protein modeling . Electrophoresis , 18 : 2714 – 2723 .
   PubMed Web of Science ®Google Scholar
• Guimarães , A.P. , França , T.C.C. , Ramalho , T.C. , Rennó , M.N. , da Cunha , E.F.F. , Matos , K.S. , Mancini , D.T. and Kuča , K. 2011 . Docking studies and effects of syn-anti isomery of oximes derived from pyridine imidazol bicycled systems as potential human acetylcholinesterase reactivators . Journal of Applied Biomedicine , 9 : 163 – 171 .
   Web of Science ®Google Scholar
• Hage-Melim , L.I.D. , da Silva , C.H.T.D. , Semighini , E.P. , Taft , C.A. and Sampaio , S.V. 2009 . Computer-aided drug design of novel PLA2 inhibitor candidates for treatment of snakebite . Journal of Biomolecular Structure & Dynamics , 27 : 27 – 35 .
   PubMed Web of Science ®Google Scholar
• Hehre , W.J. , Deppmeier , B.J. and Klunzinger , P.E. 1999 . PC SPARTAN Pro , Irvine , CA : Wavefunction .
   Google Scholar
• Hess , B. , Kutzner , C. , van der Spoel , D. and Lindahl , E. 2008 . GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation . Journal of Chemical Theory and Computation , 4 : 435 – 447 .
   PubMed Web of Science ®Google Scholar
• Huang , H.J. , Lee , K.J. , Yu , H.W. , Chen , C.Y. , Hsu , C.H. , Chen , H.Y. , Tsai , F.J. and Chen , C.Y.C. 2010 . Structure-based and ligand-based drug design for HER 2 receptor . Journal of Biomolecular Structure & Dynamics , 28 : 23 – 37 .
   PubMed Web of Science ®Google Scholar
• Huang , H.J. , Lee , K.J. , Yu , H.W. , Chen , H.Y. , Tsai , F.J. and Chen , C.Y. 2010 . A novel strategy for designing the selective PPAR agonist by the “sum of activity” model . Journal of Biomolecular Structure & Dynamics , 28 : 187 – 200 .
   PubMed Web of Science ®Google Scholar
• Humphrey , W. , Dalke , A. and Schulte , K. 1996 . VMD – visual molecular dynamics . Journal of Molecular Graphics , 14 : 33 – 38 .
   PubMed Web of Science ®Google Scholar
• Jin , B. , Lee , H.M. and Kim , S.K. 2010 . Conformational analysis of genotoxic benzo[a]pyrene-7,8-dione-duplex DNA adducts using a molecular dynamics method . Journal of Biomolecular Structure & Dynamics , 27 : 457 – 464 .
   PubMed Web of Science ®Google Scholar
• Jorgensen , W.L. 1991 . Rusting of the lock and key model for protein-ligand binding . Science , 254 : 954 – 955 .
   PubMed Web of Science ®Google Scholar
• Jorgensen , W.L. , Chandrasekhar , J. , Madura , J.D. , Impey , R.W. and Klein , M.L. 1983 . Comparison of simple potential functions for simulating liquid water . Journal of Computational Physics , 79 : 926 – 935 .
   Web of Science ®Google Scholar
• Jorgensen , W.L. , Maxwell , D.S. and Tirado-Rives , J. 1996 . Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids . Journal of the American Chemical Society , 118 ( 45 ) : 11225 – 11236 .
   Web of Science ®Google Scholar
• Kahlon , A.K. , Roy , S. and Sharma , A. 2010 . Molecular docking studies to map the binding site of squalene synthase inhibitors on dehydrosqualene synthase of Staphylococcus aureus . Journal of Biomolecular Structure & Dynamics , 28 : 201 – 210 .
   PubMed Web of Science ®Google Scholar
• Kassa , J. , Kuca , K. , Bartosova , L. and Kunesova , G. 2007 . The development of new structural analogues of oximes for the antidotal treatment of poisoning by nerve agents and the comparison of their reactivating and therapeutic efficacy with currently available oximes . Current Organic Chemistry , 11 : 267 – 283 .
   Web of Science ®Google Scholar
• Koradi , R. , Billeter , M. and Wüthrich , K. 1996 . MOLMOL: A program for display and analysis of macromolecular structures . Journal of Molecular Graphics , 14 : 51 – 55 .
   PubMedGoogle Scholar
• Koshy , C. , Parthiban , M. and Sowdhamini , R. 2010 . 100 ns molecular dynamics simulations to study intramolecular conformational changes in bax . Journal of Biomolecular Structure & Dynamics , 28 : 71 – 83 .
   PubMed Web of Science ®Google Scholar
• Kryger , G. , Harel , M. , Giles , K. , Toker , L. , Velan , B. , Lazar , A. , … and Sussman , J.L. 2000 . Structures of recombinant native and E202Q mutant human acetylcholinesterase complexed with the snake-venom toxin fasciculin-II . Acta Crystallographica. Section D, Biological Crystallography , 56 : 1385 – 1394 .
   PubMedGoogle Scholar
• Likhatskaya , G.N. , Solov’eva , T.F. , Novikova , O.D. , Issaeva , M.P. , Gusev , K.V. , Kryzhko , I.B. , … and Nurminski , E.A. 2005 . Homology models of the Yersinia pseudotuberculosis and Yersinia pestis general porins and comparative analysis of their functional and antigenic regions . Journal of Biomolecular Structure & Dynamics , 23 : 113 – 232 .
   PubMedGoogle Scholar
• Maseras , F. and Morokuma , K. 1995 . IMOMM: A new integrated ab initio + molecular mechanics geometry optimization scheme of equilibrium structures and transition states . Journal of Computational Chemistry , 16 : 1170 – 1179 .
   Web of Science ®Google Scholar
• Matos , K.S. , Mancini , D.T. , da Cunha , E.F.F. , Kuča , K. , França , T.C.C. and Ramalho , T.C. 2011 . Molecular aspects of the reactivation process of acetylcholinesterase inhibited by cyclosarin . Journal of the Brazilian Chemical Society , 22 : 1999 – 2004 .
   Web of Science ®Google Scholar
• Mehrnejad , F. and Zarei , M. 2010 . Molecular dynamics simulation study of the interaction of piscidin 1 with DPPC bilayers: Structure–activity relationship . Journal of Biomolecular Structure & Dynamics , 27 : 551 – 559 .
   PubMed Web of Science ®Google Scholar
• Meynier , C. , Guerlesquin , F. and Roche , P. 2009 . Computational studies of human galectin-1: Role of conserved tryptophan residue in stacking interaction with carbohydrate ligands . Journal of Biomolecular Structure & Dynamics , 27 : 49 – 57 .
   PubMed Web of Science ®Google Scholar
• Mohan , S. , Perry , J.J.P. , Poulose , N. , Nair , B.G. and Anilkumar , G. 2009 . Homology modeling of GLUT4, an insulin regulated facilitated glucose transporter and docking studies with ATP and its inhibitors . Journal of Biomolecular Structure & Dynamics , 26 : 455 – 464 .
   PubMed Web of Science ®Google Scholar
• Nemukhim , A.V. , Lushchekina , S.V. , Bochenkova , A.V. , Golubeva , A.A. and Varfolomeev , S.D. 2008 . Characterization of a complete cycle of acetylcholinesterase catalysis by ab initio QM/MM modelin . Journal of Molecular Modeling , 14 : 409 – 416 .
   PubMedGoogle Scholar
• Ordentlich , A. , Barak , D. , Kronman , C. , Ariel , N. , Segall , Y. , Velan , B. and Shafferman , A. 1996 . The architecture of human acetylcholinesterase active center probed by interactions with selected organophosphate inhibitors . Journal of Biological Chemistry , 271 ( 20 ) : 11953 – 11962 .
   PubMed Web of Science ®Google Scholar
• Quinn , D.M. 1987 . Acetylcholinesterase: Enzyme structure, reaction dynamics, and virtual transition states . Chemical Reviews , 87 : 955 – 975 .
   Web of Science ®Google Scholar
• Ramalho , T.C. , Caetano , M.S. , Cunha , E.F.F. , Souza , T.C.S. and Rocha , M.V.J. 2009 . Construction and assessment of reaction models of class I EPSP synthase: Molecular docking and density functional theoretical calculations . Journal of Biomolecular Structure & Dynamics , 27 : 195 – 207 .
   PubMed Web of Science ®Google Scholar
• Ramalho , T.C. , França , T.C.C. , Rennó , M.N. , Guimarães , A.P. , Cunha , E.F.F. and Kuča , K. 2010 . Development of new acetylcholinesterase reactivators: Molecular modeling versus in vitro data . Chemico-Biological Interactions , 185 : 73 – 77 .
   PubMed Web of Science ®Google Scholar
• Ramalho , T.C. and Taft , C.A. 2005 . Thermal and solvent effects on the NMR and UV parameters of some bioreductive drugs . Journal of Chemical Physics , 123 ( 5 ) : 054319
   Google Scholar
• Rieping , W. , Habeck , M. , Bardiaux , B. , Bernard , A. , Malliavin , T.E. and Nilges , M. 2007 . ARIA2: Automated NOE assignment and data integration in NMR structure calculation . Bioinformatics , 23 : 381 – 382 .
   PubMed Web of Science ®Google Scholar
• Roy , S. and Thakur , A.R. 2010 . 20ns Molecular dynamics simulation of the antennapedia homeodomain-DnaA complex: Water interaction and DnaA structure analysis . Journal of Biomolecular Structure & Dynamics , 27 : 443 – 455 .
   PubMed Web of Science ®Google Scholar
• Schwieters , C.D. , Kuszewski , J.J. and Clore , G.M. 2006 . Using Xplor–NIH for NMR molecular structure determination . Progress in Nuclear Magnetic Resonance Spectroscopy , 48 : 47 – 62 .
   Web of Science ®Google Scholar
• Sharadadevi , A. and Nagaraj , R. 2010 . A molecular dynamics study of human defensins HBD-1 and HNP-3 in water . Journal of Biomolecular Structure & Dynamics , 27 : 541 – 550 .
   PubMed Web of Science ®Google Scholar
• Sidell , F.R. , Takafuji , E.T. and Franz , D.R. , eds. 1997 . Medical aspects of chemical and biological warfare-textbook of military medicine , Washington , DC : Office of the Surgeon General, US Army .
   Google Scholar
• Sharma , S. , Sonavane , U.B. and Joshi , R.R. 2010 . Molecular dynamics simulations of cyclohexyl modified peptide nucleic acids (PNA) . Journal of Biomolecular Structure & Dynamics , 27 : 663 – 676 .
   PubMed Web of Science ®Google Scholar
• Sille , J. and Remko , M. 2009 . Computational study of the sulfonylated amino acid hydroxamates binding to the zinc ion within the active site of carbonic anhydrase . Journal of Biomolecular Structure & Dynamics , 26 : 431 – 444 .
   PubMed Web of Science ®Google Scholar
• Somani , S.M. , Solana , R.P. and Dube , S.N. 1992 . “ Toxicology of nerve agents ” . In Chemical warfare agents , Edited by: Somani , S.M. 67 – 123 . San Diego , CA : Academic Press .
   Google Scholar
• Sousa da Silva, A.W., & Vranken, W.F. (BMC Research Notes, in press). ACPYPE – AnteChamber python parser interface. http://www.ccpn.ac.uk/software/ACPYPE-folder.
   Google Scholar
• Steven , S.Z. , Peterson , M.W. , Hamza , A. , Zhan , C.G. , Cerasoli , D.M. and Chang , W.E. 2011 . Computational characterization of how the VX nerve agent binds human serum paraoxonase 1 . Journal of Molecular Modeling , 17 : 97 – 109 .
   PubMedGoogle Scholar
• Tao , Y. , Rao , Z.H. and Liu , S.Q. 2010 . Insight derived from molecular dynamics simulation into substrate-induced changes in protein motions of proteinase K . Journal of Biomolecular Structure & Dynamics , 28 : 143 – 158 .
   PubMed Web of Science ®Google Scholar
• Thomsen , R. and Christensen , M.H. 2006 . MolDock: A new technique for high-accuracy molecular docking . Journal of Medicinal Chemistry , 49 : 3315 – 3321 .
   PubMed Web of Science ®Google Scholar
• Timofeyeva , N.A. , Koval , V.V. , Knorre , D.G. , Zharkov , D.O. , Saparbaev , M.K. , … and Fedorova , O.S. 2009 . Conformational dynamics of human AP endonuclease in base excision and nucleotide incision repair pathways . Journal of Biomolecular Structure & Dynamics , 26 : 637 – 652 .
   PubMed Web of Science ®Google Scholar
• Varughese , J.F. , Chalovich , J.M. and Li , Y. 2010 . Molecular dynamics studies on troponin (TnI-TnT-TnC) complexes: Insight into the regulation of muscle contraction . Journal of Biomolecular Structure & Dynamics , 28 : 159 – 174 .
   PubMed Web of Science ®Google Scholar
• Vranken , W.F. , Boucher , W. , Stevens , T.J. , Fogh , R.H. , Pajon , A. , Llinas , M. , … and Laue , E.D. 2005 . The CCPN data model for NMR spectroscopy: Development of a software pipeline . Proteins: Structure, Function, and Bioinformatics , 59 : 687 – 696 .
   PubMed Web of Science ®Google Scholar
• Walker , R.C. , Crowley , M.F. and Case , D.A. 2008 . The implementation of a fast and accurate QM/MM potential method in amber . Journal of Computational Physics , 29 : 1019 – 1031 .
   Google Scholar
• Wang , J. , Wang , W. , Kollman , P.A. and Case , D.A. 2006 . Automatic atom type and bond type perception in molecular mechanical calculations . Journal of Molecular Graphics and Modelling , 25 : 247 – 260 .
   PubMed Web of Science ®Google Scholar
• Warren , D. 2002 . The PyMOL molecular graphics system , San Carlos , CA : DeLano Scientific .
   Google Scholar
• Wong , L. , Radic , Z. , Brüggemann , R.J.M. , Hosea , N. , Berman , H.A. and Taylor , P. 2000 . Mechanism of oxime reactivation of acetylcholinesterase analyzed by chirality and mutagenesis . Biochemistry , 39 : 5750 – 5757 .
   PubMed Web of Science ®Google Scholar
• Worek , F. , Aurbek , N. , Koller , M. , Becker , C. , Eyer , P. and Thiermann , H. 2007 . Kinetic analysis of reactivation and aging of human acetylcholinesterase inhibited by different phosphoramidates . Biochemical Pharmacology , 73 ( 11 ) : 1807 – 1817 .
   PubMedGoogle Scholar
• Zhang , J.P. 2009 . Studies on the structural stability of rabbit prion probed by molecular dynamics simulations . Journal of Biomolecular Structure & Dynamics , 27 : 159 – 162 .
   PubMed Web of Science ®Google Scholar
• Zhong , L.H. and Xie , J.M. 2009 . Investigation of the effect of glycosylation on human prion protein by molecular dynamics . Journal of Biomolecular Structure & Dynamics , 26 : 525 – 533 .
   PubMed Web of Science ®Google Scholar