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Leherte L, Vercauteren DP. Smoothed Gaussian molecular fields: an evaluation of molecular alignment problems. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1259-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Zhang J, Yang W, Piquemal JP, Ren P. Modeling Structural Coordination and Ligand Binding in Zinc Proteins with a Polarizable Potential. J Chem Theory Comput 2012; 8:1314-1324. [PMID: 22754403 PMCID: PMC3383645 DOI: 10.1021/ct200812y] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
As the second most abundant cation in human body, zinc is vital for the structures and functions of many proteins. Zinc-containing matrix metalloproteinases (MMPs) have been widely investigated as potential drug targets in a range of diseases ranging from cardiovascular disorders to cancers. However, it remains a challenge in theoretical studies to treat zinc in proteins with classical mechanics. In this study, we examined Zn(2+) coordination with organic compounds and protein side chains using a polarizable atomic multipole based electrostatic model. We find that polarization effect plays a determining role in Zn(2+) coordination geometry in both matrix metalloproteinase (MMP) complexes and in zinc-finger proteins. In addition, the relative binding free energies of selected inhibitors binding with MMP13 have been estimated and compared with experimental results. While not directly interacting with the small molecule inhibitors, the permanent and polarizing field of Zn(2+) exerts a strong influence on the relative affinities of the ligands. The simulation results also reveal the polarization effect on binding is ligand dependent and thus difficult to be incorporated into fixed-charge models implicitly.
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Affiliation(s)
- Jiajing Zhang
- Department of Biomedical Engineering, The University of Texas at Austin, TX 78712
| | - Wei Yang
- The Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306
| | - Jean-Philip Piquemal
- UPMC Univ. Paris 06, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
- CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, TX 78712
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Specific interactions and binding energies between thermolysin and potent inhibitors: Molecular simulations based on ab initio molecular orbital method. J Mol Graph Model 2012; 33:1-11. [DOI: 10.1016/j.jmgm.2011.10.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Revised: 10/18/2011] [Accepted: 10/18/2011] [Indexed: 11/19/2022]
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Dedachi K, Hirakawa T, Fujita S, Khan MTH, Sylte I, Kurita N. Specific interactions and binding free energies between thermolysin and dipeptides: Molecular simulations combined with Ab initio molecular orbital and classical vibrational analysis. J Comput Chem 2011; 32:3047-57. [DOI: 10.1002/jcc.21887] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Revised: 06/18/2011] [Accepted: 06/18/2011] [Indexed: 11/11/2022]
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Roux C, Bhatt F, Foret J, de Courcy B, Gresh N, Piquemal JP, Jeffery CJ, Salmon L. The reaction mechanism of type I phosphomannose isomerases: new information from inhibition and polarizable molecular mechanics studies. Proteins 2011; 79:203-20. [PMID: 21058398 DOI: 10.1002/prot.22873] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Type I phosphomannose isomerases (PMIs) are zinc-dependent metalloenzymes involved in the reversible isomerization of D-mannose 6-phosphate (M6P) and D-fructose 6-phosphate (F6P). 5-Phospho-D-arabinonohydroxamic acid (5PAH), an inhibitor endowed with nanomolar affinity for yeast (Type I) and Pseudomonas aeruginosa (Type II) PMIs (Roux et al., Biochemistry 2004; 43:2926-2934), strongly inhibits human (Type I) PMI (for which we report an improved expression and purification procedure), as well as Escherichia coli (Type I) PMI. Its K(i) value of 41 nM for human PMI is the lowest value ever reported for an inhibitor of PMI. 5-Phospho-D-arabinonhydrazide, a neutral analogue of the reaction intermediate 1,2-cis-enediol, is about 15 times less efficient at inhibiting both enzymes, in accord with the anionic nature of the postulated high-energy reaction intermediate. Using the polarizable molecular mechanics, sum of interactions between fragments ab initio computed (SIBFA) procedure, computed structures of the complexes between Candida albicans (Type I) PMI and the cyclic substrate β-D-mannopyranose 6-phosphate (β-M6P) and between the enzyme and the high-energy intermediate analogue inhibitor 5PAH are reported. Their analysis allows us to identify clearly the nature of each individual active site amino acid and to formulate a hypothesis for the overall mechanism of the reaction catalyzed by Type I PMIs, that is, the ring-opening and isomerization steps, respectively. Following enzyme-catalyzed ring-opening of β-M6P by zinc-coordinated water and Gln111 ligands, Lys136 is identified as the probable catalytic base involved in proton transfer between the two carbon atoms C1 and C2 of the substrate D-mannose 6-phosphate.
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Affiliation(s)
- Céline Roux
- Laboratoire de Chimie Bioorganique et Bioinorganique, ICMMO, Univ Paris-Sud, UMR 8182, Orsay F-91405, France
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Synthesis and evaluation of non-hydrolyzable D-mannose 6-phosphate surrogates reveal 6-deoxy-6-dicarboxymethyl-D-mannose as a new strong inhibitor of phosphomannose isomerases. Bioorg Med Chem 2009; 17:7100-7. [PMID: 19783448 DOI: 10.1016/j.bmc.2009.09.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2009] [Revised: 08/28/2009] [Accepted: 09/03/2009] [Indexed: 11/23/2022]
Abstract
Non-hydrolyzable d-mannose 6-phosphate analogues in which the phosphate group was replaced by a phosphonomethyl, a dicarboxymethyl, or a carboxymethyl group were synthesized and kinetically evaluated as substrate analogues acting as potential inhibitors of type I phosphomannose isomerases (PMIs) from Saccharomyces cerevisiae and Escherichia coli. While 6-deoxy-6-phosphonomethyl-d-mannose and 6-deoxy-6-carboxymethyl-D-mannose did not inhibit the enzymes significantly, 6-deoxy-6-dicarboxymethyl-D-mannose appeared as a new strong competitive inhibitor of both S. cerevisiae and E. coli PMIs with K(m)/K(i) ratios of 28 and 8, respectively. We thus report the first malonate-based inhibitor of an aldose-ketose isomerase to date. Phosphonomethyl mimics of the 1,2-cis-enediolate high-energy intermediate postulated for the isomerization reaction catalyzed by PMIs were also synthesized but behave as poor inhibitors of PMIs. A polarizable molecular mechanics (SIBFA) study was performed on the complexes of d-mannose 6-phosphate and two of its analogues with PMI from Candida albicans, an enzyme involved in yeast infection homologous to S. cerevisiae and E. coli PMIs. It shows that effective binding to the catalytic site occurs with retention of the Zn(II)-bound water molecule. Thus the binding of the hydroxyl group on C1 of the ligand to Zn(II) should be water-mediated. The kinetic study reported here also suggests the dianionic character of the phosphate surrogate as a likely essential parameter for strong binding of the inhibitor to the enzyme active site.
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Dedachi K, Khan MTH, Sylte I, Kurita N. A combined simulation with ab initio MO and classical vibrational analysis on the specific interactions between thermolysin and dipeptide ligands. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.08.036] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Gresh N, Cisneros GA, Darden TA, Piquemal JP. Anisotropic, Polarizable Molecular Mechanics Studies of Inter- and Intramolecular Interactions and Ligand-Macromolecule Complexes. A Bottom-Up Strategy. J Chem Theory Comput 2007; 3:1960-1986. [PMID: 18978934 PMCID: PMC2367138 DOI: 10.1021/ct700134r] [Citation(s) in RCA: 279] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
We present an overview of the SIBFA polarizable molecular mechanics procedure, which is formulated and calibrated on the basis of quantum chemistry (QC). It embodies nonclassical effects such as electrostatic penetration, exchange-polarization, and charge transfer. We address the issues of anisotropy, nonadditivity, and transferability by performing parallel QC computations on multimolecular complexes. These encompass multiply H-bonded complexes and polycoordinated complexes of divalent cations. Recent applications to the docking of inhibitors to Zn-metalloproteins are presented next, namely metallo-beta-lactamase, phosphomannoisomerase, and the nucleocapsid of the HIV-1 retrovirus. Finally, toward third-generation intermolecular potentials based on density fitting, we present the development of a novel methodology, the Gaussian electrostatic model (GEM), which relies on ab initio-derived fragment electron densities to compute the components of the total interaction energy. As GEM offers the possibility of a continuous electrostatic model going from distributed multipoles to densities, it allows an inclusion of short-range quantum effects in the molecular mechanics energies. The perspectives of an integrated SIBFA/GEM/QM procedure are discussed.
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Affiliation(s)
- Nohad Gresh
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université René-Descartes, 45, rue des Saints-Pères, 75006 Paris, France, Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, and Laboratoire de Chimie Théorique, Université Pierre-et-Marie-Curie, UMR 7616 CNRS, case courrier 137, 4, place Jussieu, 75252 Paris, France
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Roux C, Gresh N, Perera LE, Piquemal JP, Salmon L. Binding of 5-phospho-D-arabinonohydroxamate and 5-phospho-D-arabinonate inhibitors to zinc phosphomannose isomerase from Candida albicans studied by polarizable molecular mechanics and quantum mechanics. J Comput Chem 2007; 28:938-57. [PMID: 17253648 DOI: 10.1002/jcc.20586] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Type I phosphomannose isomerase (PMI) is a Zn-dependent metalloenzyme involved in the isomerization of D-fructose 6-phosphate to D-mannose 6-phosphate. One of our laboratories has recently designed and synthesized 5-phospho-D-arabinonohydroxamate (5PAH), an inhibitor endowed with a nanomolar affinity for PMI (Roux et al., Biochemistry 2004, 43, 2926). By contrast, the 5-phospho-D-arabinonate (5PAA), in which the hydroxamate moiety is replaced by a carboxylate one, is devoid of inhibitory potency. Subsequent biochemical studies showed that in its PMI complex, 5PAH binds Zn(II) through its hydroxamate moiety rather than through its phosphate. These results have stimulated the present theoretical investigation in which we resort to the SIBFA polarizable molecular mechanics procedure to unravel the structural and energetical aspects of 5PAH and 5PAA binding to a 164-residue model of PMI. Consistent with the experimental results, our theoretical studies indicate that the complexation of PMI by 5PAH is much more favorable than by 5PAA, and that in the 5PAH complex, Zn(II) ligation by hydroxamate is much more favorable than by phosphate. Validations by parallel quantum-chemical computations on model of the recognition site extracted from the PMI-inhibitor complexes, and totaling up to 140 atoms, showed the values of the SIBFA intermolecular interaction energies in such models to be able to reproduce the quantum-chemistry ones with relative errors < 3%. On the basis of the PMI-5PAH SIBFA energy-minimized structure, we report the first hypothesis of a detailed view of the active site of the zinc PMI complexed to the high-energy intermediate analogue inhibitor, which allows us to identify active site residues likely involved in the proton transfer between the two adjacent carbons of the substrates.
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Affiliation(s)
- Celine Roux
- Laboratoire de Chimie Bioorganique et Bioinorganique, CNRS-UMR 8182, Institut de Chimie Moléculaire et des Matériaux d'Orsay, Bâtiment 420, Université Paris-Sud XI, 15 rue Georges Clémenceau, 91405 Orsay, France
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Gresh N, Piquemal JP, Krauss M. Representation of Zn(II) complexes in polarizable molecular mechanics. Further refinements of the electrostatic and short-range contributions. Comparisons with parallel ab initio computations. J Comput Chem 2005; 26:1113-30. [PMID: 15934064 DOI: 10.1002/jcc.20244] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We present refinements of the SIBFA molecular mechanics procedure to represent the intermolecular interaction energies of Zn(II). The two first-order contributions, electrostatic (E(MTP)), and short-range repulsion (E(rep)), are refined following the recent developments due to Piquemal et al. (Piquemal et al. J Phys Chem A 2003, 107, 9800; and Piquemal et al., submitted). Thus, E(MTP) is augmented with a penetration component, E(pen), which accounts for the effects of reduction in electronic density of a given molecular fragment sensed by another interacting fragment upon mutual overlap. E(pen) is fit in a limited number of selected Zn(II)-mono-ligated complexes so that the sum of E(MTP) and E(pen) reproduces the Coulomb contribution E(c) from an ab initio Hartree-Fock energy decomposition procedure. Denoting by S, the overlap matrix between localized orbitals on the interacting monomers, and by R, the distance between their centroids, E(rep) is expressed by a S(2)/R term now augmented with an S(2)/R(2) one. It is calibrated in selected monoligated Zn(II) complexes to fit the corresponding exchange repulsion E(exch) from ab initio energy decomposition, and no longer as previously the difference between (E(c) + E(exch)) and E(MTP). Along with the reformulation of the first-order contributions, a limited recalibration of the second-order contributions was carried out. As in our original formulation (Gresh, J Comput Chem 1995, 16, 856), the Zn(II) parameters for each energy contribution were calibrated to reproduce the radial behavior of its ab initio HF counterpart in monoligated complexes with N, O, and S ligands. The SIBFA procedure was subsequently validated by comparisons with parallel ab initio computations on several Zn(II) polyligated complexes, including binuclear Zn(II) complexes as in models for the Gal4 and beta-lactamase metalloproteins. The largest relative error with respect to the RVS computations is 3%, and the ordering in relative energies of competing structures reproduced even though the absolute numerical values of the ab initio interaction energies can be as large as 1220 kcal/mol. A term-to-term identification of the SIBFA contributions to their ab initio counterparts remained possible even for the largest sized complexes.
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Affiliation(s)
- Nohad Gresh
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, FRE 2718 CNRS, IFR Biomédicale, 45, Rue des Saints-Pères, 75006, Paris, France.
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Plocki S, Aoun D, Ahamada-Himidi A, Tavarès-Camarinha F, Dong CZ, Massicot F, Huet J, Adolphe-Pierre S, Chau F, Godfroid JJ, Gresh N, Ombetta JE, Heymans F. Molecular Modeling, Design, and Synthesis of Less Lipophilic Derivatives of 3-(4-Tetradecyloxybenzyl)-4H-1,2,4-oxadiazol-5-one (PMS1062) Specific for Group II Enzyme. European J Org Chem 2005. [DOI: 10.1002/ejoc.200400541] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Gresh N, Shi GB. Conformation-dependent intermolecular interaction energies of the triphosphate anion with divalent metal cations. Application to the ATP-binding site of a binuclear bacterial enzyme. A parallel quantum chemical and polarizable molecular mechanics investigation. J Comput Chem 2004; 25:160-8. [PMID: 14648615 DOI: 10.1002/jcc.10312] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We have explored the conformation-dependent interaction energy of the triphosphate moiety, a key constituent of ATP and GTP, with a closed-shell divalent cation, Zn2+, used as a probe. This was done using the SIBFA polarizable molecular mechanics procedure. We have resorted to a previously developed approach in which triphosphate is built out from its elementary constitutive fragments, and the intramolecular, interfragment, interaction energies are computed simultaneously with their intermolecular interactions with the divalent cation. This approach has enabled reproduction of the values of the intermolecular interaction energies from ab initio quantum-chemistry with relative errors <3%. It was extended to the complex of a nonhydrolyzable analog of ATP with the active site of a bacterial enzyme having two Mg2+ cations as cofactors. We obtained following energy-minimization a very close overlap of the ATP analog over its position from X-ray crystallography. For models of the ATP analog-enzyme complex encompassing up to 169 atoms, the values of the SIBFA interaction energies were found to match their DFT counterparts with relative errors of <2%.
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Affiliation(s)
- Nohad Gresh
- Laboratoire de Pharmacochimie Moléculaire et Structurale, FRE 2463 CNRS, U266 INSERM, Université René-Descartes, 4, Avenue de l'Observatoire, 75006, Paris, France.
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Ledecq M, Lebon F, Durant F, Giessner-Prettre C, Marquez A, Gresh N. Modeling of Copper(II) Complexes with the SIBFA Polarizable Molecular Mechanics Procedure. Application to a New Class of HIV-1 Protease Inhibitors. J Phys Chem B 2003. [DOI: 10.1021/jp0354604] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marie Ledecq
- Facultés Universitaires Notre-Dame de la Paix, Laboratoire de Chimie Moléculaire Structurale, 61 rue de Bruxelles, 5000 Namur, Belgium, Laboratoire de Chimie Théorique, UMR7615, Université Pierre & Marie Curie, 4, place Jussieu, 75252 Paris, France, Departamento de Qimica Fisica, Facultad de Qimica, Universitad de Sevilla, E-41012 Sevilla, Spain, and Laboratoire de Pharmacochimie Moléculaire et Structurale, FRE 2463 CNRS, U266 INSERM, Université Rene Descartes, 4, avenue de l'Observatoire, 75006 Paris,
| | - Florence Lebon
- Facultés Universitaires Notre-Dame de la Paix, Laboratoire de Chimie Moléculaire Structurale, 61 rue de Bruxelles, 5000 Namur, Belgium, Laboratoire de Chimie Théorique, UMR7615, Université Pierre & Marie Curie, 4, place Jussieu, 75252 Paris, France, Departamento de Qimica Fisica, Facultad de Qimica, Universitad de Sevilla, E-41012 Sevilla, Spain, and Laboratoire de Pharmacochimie Moléculaire et Structurale, FRE 2463 CNRS, U266 INSERM, Université Rene Descartes, 4, avenue de l'Observatoire, 75006 Paris,
| | - François Durant
- Facultés Universitaires Notre-Dame de la Paix, Laboratoire de Chimie Moléculaire Structurale, 61 rue de Bruxelles, 5000 Namur, Belgium, Laboratoire de Chimie Théorique, UMR7615, Université Pierre & Marie Curie, 4, place Jussieu, 75252 Paris, France, Departamento de Qimica Fisica, Facultad de Qimica, Universitad de Sevilla, E-41012 Sevilla, Spain, and Laboratoire de Pharmacochimie Moléculaire et Structurale, FRE 2463 CNRS, U266 INSERM, Université Rene Descartes, 4, avenue de l'Observatoire, 75006 Paris,
| | - Claude Giessner-Prettre
- Facultés Universitaires Notre-Dame de la Paix, Laboratoire de Chimie Moléculaire Structurale, 61 rue de Bruxelles, 5000 Namur, Belgium, Laboratoire de Chimie Théorique, UMR7615, Université Pierre & Marie Curie, 4, place Jussieu, 75252 Paris, France, Departamento de Qimica Fisica, Facultad de Qimica, Universitad de Sevilla, E-41012 Sevilla, Spain, and Laboratoire de Pharmacochimie Moléculaire et Structurale, FRE 2463 CNRS, U266 INSERM, Université Rene Descartes, 4, avenue de l'Observatoire, 75006 Paris,
| | - Antonio Marquez
- Facultés Universitaires Notre-Dame de la Paix, Laboratoire de Chimie Moléculaire Structurale, 61 rue de Bruxelles, 5000 Namur, Belgium, Laboratoire de Chimie Théorique, UMR7615, Université Pierre & Marie Curie, 4, place Jussieu, 75252 Paris, France, Departamento de Qimica Fisica, Facultad de Qimica, Universitad de Sevilla, E-41012 Sevilla, Spain, and Laboratoire de Pharmacochimie Moléculaire et Structurale, FRE 2463 CNRS, U266 INSERM, Université Rene Descartes, 4, avenue de l'Observatoire, 75006 Paris,
| | - Nohad Gresh
- Facultés Universitaires Notre-Dame de la Paix, Laboratoire de Chimie Moléculaire Structurale, 61 rue de Bruxelles, 5000 Namur, Belgium, Laboratoire de Chimie Théorique, UMR7615, Université Pierre & Marie Curie, 4, place Jussieu, 75252 Paris, France, Departamento de Qimica Fisica, Facultad de Qimica, Universitad de Sevilla, E-41012 Sevilla, Spain, and Laboratoire de Pharmacochimie Moléculaire et Structurale, FRE 2463 CNRS, U266 INSERM, Université Rene Descartes, 4, avenue de l'Observatoire, 75006 Paris,
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Dardenne LE, Werneck AS, de Oliveira Neto M, Bisch PM. Electrostatic properties in the catalytic site of papain: A possible regulatory mechanism for the reactivity of the ion pair. Proteins 2003; 52:236-53. [PMID: 12833547 DOI: 10.1002/prot.10368] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We present an analysis of the electrostatic properties in the catalytic site of papain (EC 3.4.22.2), an archetype enzyme of the C1 cysteine proteinase family, and we investigate their possible role in the formation, stabilization and regulation of the Cys25((-))...His159((+)) catalytic ion pair. The electrostatic properties were computed using a reassociation method based in multicentered multipolar expansions obtained from ab initio quantum calculations of overlapping protein fragments. Solvent effects were introduced by coupling the use of multicentered multipolar expansions to two continuum boundary element methods to solve the Poisson and the linearized Poisson-Boltzmann equations. The electrostatic profile found in the proton transfer region of papain showed that this enzyme has a well-defined electrostatic environment to favor the formation and stabilization of the catalytic ion pair. The papain catalytic site electrostatic profile can be considered as an electrostatic fingerprint of the papain family with the following characteristics: (i) the presence of a net electric field highly aligned in the (Cys25)-SG-->(His159)-ND1 direction; (ii) the electrostatic profile has a saddle-point character; (iii) it is basically a local environmental effect. Furthermore, our analysis describes a possible regulatory mechanism (the E(SG-->ND1) attenuation effect) controlling the ion pair reactivity and permits to infer the Asp57 acidic residue as the most probable candidate to act as the electrostatic modulator.
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Affiliation(s)
- Laurent E Dardenne
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro-UFRJ, CCS, Bloco G, Ilha do Fundão, 21949-900 Rio de Janeiro, RJ, Brazil
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Gresh N, Šponer JE, Špačková N, Leszczynski J, Šponer J. Theoretical Study of Binding of Hydrated Zn(II) and Mg(II) Cations to 5‘-Guanosine Monophosphate. Toward Polarizable Molecular Mechanics for DNA and RNA. J Phys Chem B 2003. [DOI: 10.1021/jp022659s] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Nohad Gresh
- Laboratoire de Pharmacochimie Moléculaire et Structurale, FRE 2463 CNRS, U266 INSERM, Faculté de Pharmacie de Paris, Université René-Descartes, 4, Avenue de l'Observatoire, 75006 Paris, France, Institute of Biophysics, Academy of Sciences of the Czech Republic, National Center for Biomolecular Research, Kralovopolská 135, 612 65 Brno, Czech Republic, Department of Chemistry, Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and J
| | - Judit E. Šponer
- Laboratoire de Pharmacochimie Moléculaire et Structurale, FRE 2463 CNRS, U266 INSERM, Faculté de Pharmacie de Paris, Université René-Descartes, 4, Avenue de l'Observatoire, 75006 Paris, France, Institute of Biophysics, Academy of Sciences of the Czech Republic, National Center for Biomolecular Research, Kralovopolská 135, 612 65 Brno, Czech Republic, Department of Chemistry, Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and J
| | - Nad'a Špačková
- Laboratoire de Pharmacochimie Moléculaire et Structurale, FRE 2463 CNRS, U266 INSERM, Faculté de Pharmacie de Paris, Université René-Descartes, 4, Avenue de l'Observatoire, 75006 Paris, France, Institute of Biophysics, Academy of Sciences of the Czech Republic, National Center for Biomolecular Research, Kralovopolská 135, 612 65 Brno, Czech Republic, Department of Chemistry, Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and J
| | - Jerzy Leszczynski
- Laboratoire de Pharmacochimie Moléculaire et Structurale, FRE 2463 CNRS, U266 INSERM, Faculté de Pharmacie de Paris, Université René-Descartes, 4, Avenue de l'Observatoire, 75006 Paris, France, Institute of Biophysics, Academy of Sciences of the Czech Republic, National Center for Biomolecular Research, Kralovopolská 135, 612 65 Brno, Czech Republic, Department of Chemistry, Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and J
| | - Jiři Šponer
- Laboratoire de Pharmacochimie Moléculaire et Structurale, FRE 2463 CNRS, U266 INSERM, Faculté de Pharmacie de Paris, Université René-Descartes, 4, Avenue de l'Observatoire, 75006 Paris, France, Institute of Biophysics, Academy of Sciences of the Czech Republic, National Center for Biomolecular Research, Kralovopolská 135, 612 65 Brno, Czech Republic, Department of Chemistry, Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and J
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Gresh N, Derreumaux P. Generating Conformations for Two Zinc-Binding Sites of HIV-1 Nucleocapsid Protein from Random Conformations by a Hierarchical Procedure and Polarizable Force Field. J Phys Chem B 2003. [DOI: 10.1021/jp022527z] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nohad Gresh
- Laboratoire de Pharmacochimie Moléculaire, CNRS FRE 2463 4, Avenue de l'Observatoire, 75006 Paris, France, and Information Génétique et Structurale, CNRS-UMR 1889, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Philippe Derreumaux
- Laboratoire de Pharmacochimie Moléculaire, CNRS FRE 2463 4, Avenue de l'Observatoire, 75006 Paris, France, and Information Génétique et Structurale, CNRS-UMR 1889, 31 Chemin Joseph Aiguier, 13402 Marseille, France
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Antony J, Gresh N, Olsen L, Hemmingsen L, Schofield CJ, Bauer R. Binding of D- and L-captopril inhibitors to metallo-beta-lactamase studied by polarizable molecular mechanics and quantum mechanics. J Comput Chem 2002; 23:1281-96. [PMID: 12210153 DOI: 10.1002/jcc.10111] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The bacterial Zn2+ metallo-beta-lactamase from B. fragilis is a zinc-enzyme with two potential metal ion binding sites. It cleaves the lactam ring of antibiotics, thus contributing to the acquired resistance of bacteria against antibiotics. The present study bears on the binuclear form of the enzyme. We compare several possible binding modes of captopril, a mercaptocarboxamide inhibitor of several zinc-metalloenzymes. Two diastereoisomers of captopril were considered, with either a D- or an L-proline residue. We have used the polarizable molecular mechanics procedure SIBFA (Sum of Interactions Between Fragments ab initio computed). Two beta-lactamase models were considered, encompassing 104 and 188 residues, respectively. The energy balances included the inter and intramolecular interaction energies as well as the contribution from solvation computed using a continuum reaction field procedure. The thiolate ion of the inhibitor is binding to both metal ions, expelling the bridging solvent molecule from the uncomplexed enzyme. Different competing binding modes of captopril were considered, either where the inhibitor binds in a monodentate mode to the zinc cations only with its thiolate ion, or in bidentate modes involving additional zinc binding by its carboxylate or ketone carbonyl groups. The additional coordination by the inhibitor's carboxylate or carbonyl group always occurs at the zinc ion, which is bound by a histidine, a cysteine, and an aspartate side chain. For both diastereomers, the energy balances favor monodentate binding of captopril via S-. The preference over bidentate binding is small. The interaction energies were recomputed in model sites restricted to captopril, the Zn2+ cations, and their coordinating end side chains from beta-lactamase (98 atoms). The interaction energies and their ranking among competing arrangements were consistent with those computed by ab initio HF and DFT procedures.
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Affiliation(s)
- Jens Antony
- Department of Mathematics and Physics, The Royal Veterinary and Agricultural University, DK-1871 Frederiksberg C, Denmark
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Gresh N, Policar C, Giessner-Prettre C. Modeling Copper(I) Complexes: SIBFA Molecular Mechanics versus ab Initio Energetics and Geometrical Arrangements. J Phys Chem A 2002. [DOI: 10.1021/jp0106146] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- N. Gresh
- Equipe de Pharmacochimie Moléculaire et Cellulaire, UMR 8638, Université René Descartes, 4, avenue de l'Observatoire, 75270 Paris Cedex 06, France, Laboratoire de Chimie Bioorganique et Bioinorganique, FRE 2127, Bâtiment 420, Université de Paris Sud, 91405 Orsay, Cedex, France, and Laboratoire de Chimie Théorique, UMR 7616, Université P. & M. Curie, Case Courrier 137, 4, place Jussieu, 75252 Paris Cedex 05, France
| | - C. Policar
- Equipe de Pharmacochimie Moléculaire et Cellulaire, UMR 8638, Université René Descartes, 4, avenue de l'Observatoire, 75270 Paris Cedex 06, France, Laboratoire de Chimie Bioorganique et Bioinorganique, FRE 2127, Bâtiment 420, Université de Paris Sud, 91405 Orsay, Cedex, France, and Laboratoire de Chimie Théorique, UMR 7616, Université P. & M. Curie, Case Courrier 137, 4, place Jussieu, 75252 Paris Cedex 05, France
| | - C. Giessner-Prettre
- Equipe de Pharmacochimie Moléculaire et Cellulaire, UMR 8638, Université René Descartes, 4, avenue de l'Observatoire, 75270 Paris Cedex 06, France, Laboratoire de Chimie Bioorganique et Bioinorganique, FRE 2127, Bâtiment 420, Université de Paris Sud, 91405 Orsay, Cedex, France, and Laboratoire de Chimie Théorique, UMR 7616, Université P. & M. Curie, Case Courrier 137, 4, place Jussieu, 75252 Paris Cedex 05, France
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Abstract
Standard force fields used in biomolecular computing describe electrostatic interactions in terms of fixed, usually atom-centered, charges. Real physical systems, however, polarize substantially when placed in a high-dielectric medium such as water--or even when a strongly charged system approaches a neutral body in the gas phase. Such polarization strongly affects the geometry and energetics of molecular recognition. First introduced more than 20 years ago, polarizable force fields seek to account for appropriate variations in charge distribution with dielectric environment. Over the past five years, an accelerated pace of development of such force fields has taken place on systems ranging from liquid water to metalloenzymes. Noteworthy progress has been made in better understanding the capabilities and limitations of polarizable models for water and in the formulation and utilization of complete specifically parameterized polarizable force fields for peptides and proteins.
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Affiliation(s)
- T A Halgren
- Schrödinger Inc, 1 Exchange Place, Suite 604, Jersey City, NJ 07302, USA.
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21
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Dardenne LE, Werneck AS, Oliveira Neto M, Bisch PM. Reassociation of fragments using multicentered multipolar expansions: peptide junction treatments to investigate electrostatic properties of proteins. J Comput Chem 2001. [DOI: 10.1002/jcc.1037] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Guo H, Gresh N, Roques BP, Salahub DR. Many-Body Effects in Systems of Peptide Hydrogen-Bonded Networks and Their Contributions to Ligand Binding: A Comparison of the Performances of DFT and Polarizable Molecular Mechanics. J Phys Chem B 2000. [DOI: 10.1021/jp0012247] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hong Guo
- Centre de Recherche en Calcul Appliqué, Bureau 400, 5160, Boulevard Décarie, Montréal, Quebec H3X 2H9, Canada; Département de Pharmacochimie Moléculaire et Structurale, INSERM U266, CNRS UMR 8600, UFR des Sciences Pharmaceutiques and Biologiques, 4, Avenue de l'Observatoire, 75270 Paris Cedex 06, France; and Département de Chimie, Université de Montréal, C.P. 6128, succursale A, Montréal, Québec, Canada, and Steacie Institute for Molecular Sciences, National Research Council, 100 Sussex Drive, Ottawa,
| | - Nohad Gresh
- Centre de Recherche en Calcul Appliqué, Bureau 400, 5160, Boulevard Décarie, Montréal, Quebec H3X 2H9, Canada; Département de Pharmacochimie Moléculaire et Structurale, INSERM U266, CNRS UMR 8600, UFR des Sciences Pharmaceutiques and Biologiques, 4, Avenue de l'Observatoire, 75270 Paris Cedex 06, France; and Département de Chimie, Université de Montréal, C.P. 6128, succursale A, Montréal, Québec, Canada, and Steacie Institute for Molecular Sciences, National Research Council, 100 Sussex Drive, Ottawa,
| | - Bernard P. Roques
- Centre de Recherche en Calcul Appliqué, Bureau 400, 5160, Boulevard Décarie, Montréal, Quebec H3X 2H9, Canada; Département de Pharmacochimie Moléculaire et Structurale, INSERM U266, CNRS UMR 8600, UFR des Sciences Pharmaceutiques and Biologiques, 4, Avenue de l'Observatoire, 75270 Paris Cedex 06, France; and Département de Chimie, Université de Montréal, C.P. 6128, succursale A, Montréal, Québec, Canada, and Steacie Institute for Molecular Sciences, National Research Council, 100 Sussex Drive, Ottawa,
| | - Dennis R. Salahub
- Centre de Recherche en Calcul Appliqué, Bureau 400, 5160, Boulevard Décarie, Montréal, Quebec H3X 2H9, Canada; Département de Pharmacochimie Moléculaire et Structurale, INSERM U266, CNRS UMR 8600, UFR des Sciences Pharmaceutiques and Biologiques, 4, Avenue de l'Observatoire, 75270 Paris Cedex 06, France; and Département de Chimie, Université de Montréal, C.P. 6128, succursale A, Montréal, Québec, Canada, and Steacie Institute for Molecular Sciences, National Research Council, 100 Sussex Drive, Ottawa,
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Terp GE, Christensen IT, Jørgensen FS. Structural differences of matrix metalloproteinases. Homology modeling and energy minimization of enzyme-substrate complexes. J Biomol Struct Dyn 2000; 17:933-46. [PMID: 10949161 DOI: 10.1080/07391102.2000.10506582] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Matrix metalloproteinases are extracellular enzymes taking part in the remodeling of extracellular matrix. The structures of the catalytic domain of MMP1, MMP3, MMP7 and MMP8 are known, but structures of enzymes belonging to this family still remain to be determined. A general approach to the homology modeling of matrix metalloproteinases, exemplified by the modeling of MMP2, MMP9, MMP12 and MMP14 is described. The models were refined using an energy minimization procedure developed for matrix metalloproteinases. This procedure includes incorporation of parameters for zinc and calcium ions in the AMBER 4.1 force field, applying a non-bonded approach and a full ion charge representation. Energy minimization of the apoenzymes yielded structures with distorted active sites, while reliable three-dimensional structures of the enzymes containing a substrate in active site were obtained. The structural differences between the eight enzyme-substrate complexes were studied with particular emphasis on the active site, and possible sites for obtaining selectivity among the MMP's are discussed. Differences in the P1' pocket are well-documented and have been extensively exploited in inhibitor design. The present work indicates that selectivity could be further improved by considering the P2 pocket as well.
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Affiliation(s)
- G E Terp
- Royal Danish School of Pharmacy, Department of Medicinal Chemistry, Copenhagen, Denmark
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Tiraboschi G, Gresh N, Giessner-Prettre C, Pedersen LG, Deerfield DW. Parallelab initio and molecular mechanics investigation of polycoordinated Zn(II) complexes with model hard and soft ligands: Variations of binding energy and of its components with number and charges of ligands. J Comput Chem 2000. [DOI: 10.1002/1096-987x(200009)21:12<1011::aid-jcc1>3.0.co;2-b] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Gresh N, Šponer J. Complexes of Pentahydrated Zn2+ with Guanine, Adenine, and the Guanine−Cytosine and Adenine−Thymine Base Pairs. Structures and Energies Characterized by Polarizable Molecular Mechanics and ab Initio Calculations. J Phys Chem B 1999. [DOI: 10.1021/jp9921351] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nohad Gresh
- Unité de Pharmacochimie Moléculaire et Structurale, U266 INSERM, UMR 8600 CNRS, U.F.R. des Sciences Pharmaceutiques et Biologiques, 4, avenue de l'Observatoire, 75270 Paris Cedex 06, France
| | - Jırí Šponer
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, and Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
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Tiraboschi G, Roques BP, Gresh N. Joint quantum chemical and polarizable molecular mechanics investigation of formate complexes with penta- and hexahydrated Zn2+: Comparison between energetics of model bidentate, monodentate, and through-water Zn2+ binding modes and evaluation of nonadditivity effects. J Comput Chem 1999. [DOI: 10.1002/(sici)1096-987x(199910)20:13<1379::aid-jcc5>3.0.co;2-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Dumas F, Fressigné C, Langlet J, Giessner-Prettre C. Theoretical Investigations of the Influence of Pressure on the Selectivity of the Michael Addition of Diphenylmethaneamine to Stereogenic Crotonates. J Org Chem 1999; 64:4725-4732. [PMID: 11674545 DOI: 10.1021/jo9825308] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
SIBFA (sum of interactions between fragments ab initio computed) molecular mechanics systematics has been modified to take into account the effect of pressure on intra- and intermolecular energies. The van der Waals radii are related to the pressure, using Bridgman results on the variation of crystal volume, on one hand, and the relation between the volume of an atom and its van der Waals radius on the other. This procedure produces a decrease of the volume of the systems considered. The modified systematics is used for the study of the conformation at 1 atm and 15 kbar of two stereogenic crotonates and of the complexes formed by these two molecules with the diphenylmethaneamine and the three solvent molecules present in the experiment. The results obtained show that in the case of NMECC 1a the diastereoselectivity induced by high pressure and by the presence of methanol proceeds from an important stabilization of the pro-R reactive complex in which the crotonate has a stacked-transoid conformation. This stabilization is mainly due to intermolecular interactions. In the case of the second crotonate considered, NMCC 1b, our results indicate that pressure induces a stabilization of the pro-R and pro-S complexes having the axial conformation for which the reaction exhibits little diastereoselectivity in qualitative agreement with experimental data. This study tends to show that it is possible to account theoretically for the influence of pressure on molecular conformation and/or complex structure, using a molecular mechanics method that is able to take into account the variation of volumes of the different entities present in the system studied.
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Affiliation(s)
- F. Dumas
- Laboratoire de Chimie Théorique, UMR 7616 CNRS, Université P. & M. Curie, Case Courrier 137, 4, place Jussieu, 75252 Paris Cedex 05, France, and Centre Régional Universitaire de Spectroscopie UPRESA 6014 CNRS, IRCOF, Université de Rouen, 76821 Mont St Aignan Cedex, France
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Gresh N, Tiraboschi G, Salahub DR. Conformational properties of a model alanyl dipeptide and of alanine-derived oligopeptides: Effects of solvation in water and in organic solvents—A combined SIBFA/continuum reaction field, ab initio self-consistent field, and density functional theory investigation. Biopolymers 1998. [DOI: 10.1002/(sici)1097-0282(199805)45:6<405::aid-bip1>3.0.co;2-t] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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29
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Garmer DR, Gresh N, Roques BP. Modeling of inhibitor–metalloenzyme interactions and selectivity using molecular mechanics grounded in quantum chemistry. Proteins 1998. [DOI: 10.1002/(sici)1097-0134(19980401)31:1<42::aid-prot5>3.0.co;2-j] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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30
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Gresh N. Model, Multiply Hydrogen-Bonded Water Oligomers (N = 3−20). How Closely Can a Separable, ab Initio-Grounded Molecular Mechanics Procedure Reproduce the Results of Supermolecule Quantum Chemical Computations? J Phys Chem A 1997. [DOI: 10.1021/jp9713423] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nohad Gresh
- Département de Pharmacochimie Moléculaire et Structurale, URA D1500 CNRS, U266 INSERM, UFR des Sciences Pharmaceutiques et Biologiques, 4 Avenue de l'Observatoire, 75270 Paris, Cedex 06, France
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