QTAIM and NCI analysis of intermolecular interactions in steroid ligands binding a cytochrome P450 enzyme – Beyond the most obvious interactions
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Vasaitis, 2011, CYP17 inhibitors for prostate cancer therapy, J. Steroid Biochem. Mol. Biol., 125, 23, 10.1016/j.jsbmb.2010.11.005
Hille, 2009, Novel CYP17 inhibitors: synthesis, biological evaluation, structure–activity relationships and modelling of methoxy- and hydroxy-substituted methyleneimidazolyl biphenyls, Eur. J. Med. Chem., 44, 2765, 10.1016/j.ejmech.2009.01.002
Auchus, 2004, The backdoor pathway to dihydrotestosterone, Trends Endocrinol. Metab., 15, 432, 10.1016/j.tem.2004.09.004
Attard, 2008, Phase I clinical trial of a selective inhibitor of CYP17, abiraterone acetate, confirms that castration-resistant prostate cancer commonly remains hormone driven, J. Clin. Oncol., 26, 4563, 10.1200/JCO.2007.15.9749
Attard, 2009, Selective inhibition of CYP17 with abiraterone acetate is highly active in the treatment of castration-resistant prostate cancer, J. Clin. Oncol., 27, 3742, 10.1200/JCO.2008.20.0642
Reid, 2010, Significant and sustained antitumor activity in post-docetaxel, castration-resistant prostate cancer with the CYP17 inhibitor abiraterone acetate, J. Clin. Oncol., 28, 1489, 10.1200/JCO.2009.24.6819
Ryan, 2010, Phase I clinical trial of the CYP17 inhibitor abiraterone acetate demonstrating clinical activity in patients with castration-resistant prostate cancer who received prior ketoconazole therapy, J. Clin. Oncol., 28, 1481, 10.1200/JCO.2009.24.1281
Fizazi, 2012, Abiraterone acetate for treatment of metastatic castration-resistant prostate cancer: final overall survival analysis of the COU-AA-301 randomised, double-blind, placebo-controlled phase 3 study, Lancet Oncol., 13, 983, 10.1016/S1470-2045(12)70379-0
Jiao, 2009, Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential, J. Comput. Chem., 30, 1701, 10.1002/jcc.21268
Jorgensen, 2004, The many roles of computation in drug discovery, Science, 303, 1813, 10.1126/science.1096361
Kollman, 2000, Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models, Acc. Chem. Res., 33, 889, 10.1021/ar000033j
Jagusch, 2008, Synthesis, biological evaluation and molecular modelling studies of methyleneimidazole substituted biaryls as inhibitors of human 17α-hydroxylase-17,20-lyase (CYP17). Part I: Heterocyclic modifications of the core structure, Bioorganic, Med. Chem., 16, 1992
Pinto-Bazurco Mendieta, 2008, Synthesis, biological evaluation, and molecular modeling of abiraterone analogues: Novel CYP17 inhibitors for the treatment of prostate cancer, J. Med. Chem., 51, 5009, 10.1021/jm800355c
Haider, 2010, Molecular modeling on inhibitor complexes and active-site dynamics of cytochrome P450 C17, a target for prostate cancer therapy, J. Mol. Biol., 400, 1078, 10.1016/j.jmb.2010.05.069
C.F. Matta, From Atoms in Amino Acids to the Genetic Code and Protein Stability, and Backwards, In: Quantum Biochem. Wiley-VCH, pp. 423–472.
Latosińska, 2014, Quantum-chemical insight into structure-reactivity relationship in 4,5,6,7-tetrahalogeno-1 H -benzimidazoles: a combined X-ray, DSC, DFT/QTAIM, hirshfeld surface-based, and molecular docking approach, J. Phys. Chem. A, 118, 2089, 10.1021/jp411547z
Šafář, 2012, Combined chemical, biological and theoretical DFT-QTAIM study of potent glycosidase inhibitors based on quaternary indolizinium salts, Eur. J. Org. Chem., 5498, 10.1002/ejoc.201200431
Astani, 2016, A theoretical study on the characteristics of the intermolecular interactions in the active site of human androsterone sulphotransferase: DFT calculations of NQR and NMR parameters and QTAIM analysis, J. Mol. Graph. Model., 68, 14, 10.1016/j.jmgm.2016.06.002
N. Sukumar, C.M. Breneman, QTAIM in Drug Discovery and Protein Modeling, In: Quantum Theory Atoms Mol. From Solid State to DNA Drug Des. Wiley-VCH Verlag GmbH & Co. KGaA, pp. 471–498.
Vega-Hissi, 2015, Molecular insight into the interaction mechanisms of amino-2H-imidazole derivatives with BACE1 protease: a QM/MM and QTAIM study, Int. J. Quantum Chem., 115, 389, 10.1002/qua.24854
Contreras-García, 2011, NCIPLOT: a program for plotting noncovalent interaction regions, J. Chem. Theory Comput., 7, 625, 10.1021/ct100641a
Wang, 2015, How mutations affecting the ligand-receptor interactions: a combined MD and QM/MM calculation on CYP2E1 and its two mutants, Chem. Res. Chin. Univ., 31, 1029, 10.1007/s40242-015-5071-9
Cerón-Carrasco, 2013, New insights on the molecular recognition of imidacloprid with Aplysia californica AChBP: a computational study, J. Phys. Chem. B, 117, 3944, 10.1021/jp310242n
Fang, 2013, Toward a deeper understanding of enzyme reactions using the coupled ELF/NCI analysis: Application to DNA repair enzymes, J. Chem. Theory Comput., 9, 2156, 10.1021/ct400130b
González, 2016, Unravelling protein-DNA interactions at molecular level: a DFT and NCI study, J. Chem. Theory Comput., 12, 523, 10.1021/acs.jctc.5b00330
Devore, 2012, Structures of cytochrome P450 17A1 with prostate cancer drugs abiraterone and TOK-001, Nature, 482, 116, 10.1038/nature10743
Scott, 1999, The GROMOS biomolecular simulation program package, J. Phys. Chem. A, 103, 3596, 10.1021/jp984217f
Uranga, 2012, Can the protonation state of histidine residues be determined from molecular dynamics simulations?, Comput. Theor. Chem., 1000, 75, 10.1016/j.comptc.2012.09.025
Kim, 2013, Effects of histidine protonation and rotameric states on virtual screening of M. tuberculosis RmlC, J. Comput. Aided Mol. Des., 27, 235, 10.1007/s10822-013-9643-9
Van Der Spoel, 2005, GROMACS: fast, flexible, and free, J. Comput. Chem., 26, 1701, 10.1002/jcc.20291
Berendsen, 1987, The missing term in effective pair potentials, J. Phys. Chem., 91, 6269, 10.1021/j100308a038
Toukan, 1985, Molecular-dynamics study of atomic motions in water, Phys. Rev. B, 31, 2643, 10.1103/PhysRevB.31.2643
Hess, 1997, LINCS: a linear constraint solver for molecular simulations, J. Comput. Chem., 18, 1463, 10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
Essmann, 1995, A smooth particle mesh Ewald method, J. Chem. Phys., 103, 8577, 10.1063/1.470117
Berendsen, 1984, Molecular dynamics with coupling to an external bath, J. Chem. Phys., 81, 3684, 10.1063/1.448118
J. Rupert G. Miller, Beyond ANOVA Basics of Applied Statistics, Wiley, United States of America.
H. Motulsky, Graphpad Prism.
van Aalten, 1996, PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules, J. Comput. Aided Mol. Des., 10, 255, 10.1007/BF00355047
Trabuco, 2009, Molecular dynamics flexible fitting: a practical guide to combine cryo-electron microscopy and X-ray crystallography, Methods, 49, 174, 10.1016/j.ymeth.2009.04.005
Humphrey, 1996, VMD: visual molecular dynamics, J. Mol. Graph., 14, 33, 10.1016/0263-7855(96)00018-5
Yuan, 2005, Prediction of protein B-factor profiles, Proteins Struct. Funct. Genet., 58, 905, 10.1002/prot.20375
Trott, 2010, Software news and update AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading, J. Comput. Chem., 31, 455
Gasteiger, 1980, Iterative partial equalization of orbital electronegativity-a rapid access to atomic charges, Tetrahedron, 36, 3219, 10.1016/0040-4020(80)80168-2
Morris, 2009, Software news and updates AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility, J. Comput. Chem., 30, 2785, 10.1002/jcc.21256
Dapprich, 1999, A new ONIOM implementation in Gaussian98. Part I. The calculation of energies, gradients, vibrational frequencies and electric field derivatives, J. Mol. Struct. THEOCHEM., 461–462, 1, 10.1016/S0166-1280(98)00475-8
Becke, 1993, A new mixing of Hartree-Fock and local density-functional theories, J. Chem. Phys., 98, 1372, 10.1063/1.464304
Becke, 1993, Density-functional thermochemistry. 3. The role of exact exchange, J. Chem. Phys., 98, 5648, 10.1063/1.464913
Lee, 1988, Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density, Phys. Rev. B, 37, 785, 10.1103/PhysRevB.37.785
McLean, 1980, Contracted Gaussian basis sets for molecular calculations. I. Second row atoms, Z=11–18, J. Chem. Phys., 72, 5639, 10.1063/1.438980
Dunning, 1970, Gaussian basis functions for use in molecular calculations. I. Contraction of (9s5p) atomic basis sets for the first-row atoms, J. Chem. Phys., 53, 2823, 10.1063/1.1674408
Cornell, 1995, A second generation force field for the simulation of proteins, nucleic acids, and organic molecules, J. Am. Chem. Soc., 117, 5179, 10.1021/ja00124a002
H.B.S.M. J. Frisch G. E. Scuseria, M.A. Robb, J.R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G.A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H.P. Hratchian, A.F. Izmaylov, J. Bloino, G. Zheng, J.L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fuk, Gaussian 09. Revision A.01.
Degtyarenko, 2006, Structure and dynamics of dioxygen bound to cobalt and iron heme, Biophys. J., 91, 2024, 10.1529/biophysj.106.083048
Ghosh, 1998, First-principles quantum chemical studies of porphyrins, Acc. Chem. Res., 31, 189, 10.1021/ar950033x
Rovira, 1998, Oxygen binding to iron–porphyrin: a density functional study using both LSD and LSD+GC schemes, Int. J. Quantum Chem., 70, 387, 10.1002/(SICI)1097-461X(1998)70:2<387::AID-QUA16>3.0.CO;2-9
Jensen, 2005, Comparison of chemical properties of iron, cobalt, and nickel porphyrins, corrins, and hydrocorphins, J. Porphyr. Phthalocya., 9, 581, 10.1142/S1088424605000691
Liao, 2002, Electronic structure and bonding in unligated and ligated Fe[sup II] porphyrins, J. Chem. Phys., 116, 3635, 10.1063/1.1447902
Pauling, 1936, The magnetic properties and structure of the hemochromogens and related substances, Proc. Natl. Acad. Sci. U.S.A., 22, 159, 10.1073/pnas.22.3.159
Coryell, 1937, The magnetic properties and structure of Ferrihemoglobin (Methemoglobin) and some of its compounds, J. Am. Chem. Soc., 59, 633, 10.1021/ja01283a012
F. Biegler-König, J. Schönbohm, AIM2000.
Tian Lu, MultiWFN.
Lu, 2012, Multiwfn: a multifunctional wavefunction analyzer, J. Comput. Chem., 33, 580, 10.1002/jcc.22885
R. Courant, D. Hilbert, Methods of Mathematical Physics, Interscience Publishers Inc., New York.
Srebrenik, 1975, Rayleigh principle for a subspace of a quantum system, Int. J. Quantum Chem., 9, 375, 10.1002/qua.560090847
R.F.W. Bader, Atoms in Molecules a Quantum Theory, Oxford, Oxford.
Shahbazian, 2011, Letter to the Editor: the mathematical soundness and the physical content of the subsystem variational procedure of the QTAIM, Int. J. Quantum Chem., 111, 4497, 10.1002/qua.22977
Nasertayoob, 2009, Revisiting the foundations of the quantum theory of atoms in molecules: toward a rigorous definition of topological atoms, Int. J. Quantum Chem., 109, 726, 10.1002/qua.21864
Nasertayoob, 2008, Revisiting the foundations of quantum theory of atoms in molecules (QTAIM): the variational procedure and the zero-flux conditions, Int. J. Quantum Chem., 108, 1477, 10.1002/qua.21665
Cassam-Chenaï, 2001, Some fundamental problems with zero flux partitioning of electron densities, Theor. Chem. Acc. Theory Comput. Model (Theor. Chim. Acta), 105, 213
Hirschfelder, 1960, Classical and quantum mechanical hypervirial theorems, J. Chem. Phys., 33, 10.1063/1.1731427
Bader, 1985, Atoms in molecules, Acc. Chem. Res., 18, 9, 10.1021/ar00109a003
Rozenberg, 2014, The hydrogen bond – practice and QTAIM theory, RSC Adv., 4, 26928, 10.1039/C4RA03889D
Matta, 2003, Hydrogen-hydrogen bonding: a stabilizing interaction in molecules and crystals, Chem. Eur. J., 9, 1940, 10.1002/chem.200204626
Monteiro, 2014, Hydrogen-hydrogen bonds in highly branched alkanes and in alkane complexes: A DFT, ab initio, QTAIM, and ELF study, J. Phys. Chem. A, 118, 1730, 10.1021/jp500131z
Wu, 2013, Noncovalent interaction analysis in fluctuating environments, J. Chem. Theory Comput., 9, 2226, 10.1021/ct4001087
Johnson, 2010, Revealing non-covalent interactions, J. Am. Chem. Soc., 132, 6498, 10.1021/ja100936w
Firme, 2009, Relation between bond order and delocalization index of QTAIM, Chem. Phys. Lett., 468, 129, 10.1016/j.cplett.2008.12.004
