1
|
Naseem-Khan S, Lagardère L, Narth C, Cisneros GA, Ren P, Gresh N, Piquemal JP. Development of the Quantum-Inspired SIBFA Many-Body Polarizable Force Field: Enabling Condensed-Phase Molecular Dynamics Simulations. J Chem Theory Comput 2022; 18:3607-3621. [PMID: 35575306 PMCID: PMC10851344 DOI: 10.1021/acs.jctc.2c00029] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We present the extension of the Sum of Interactions Between Fragments Ab initio Computed (SIBFA) many-body polarizable force field to condensed-phase molecular dynamics (MD) simulations. The quantum-inspired SIBFA procedure is grounded on simplified integrals obtained from localized molecular orbital theory and achieves full separability of its intermolecular potential. It embodies long-range multipolar electrostatics (up to quadrupole) coupled to a short-range penetration correction (up to charge-quadrupole), exchange repulsion, many-body polarization, many-body charge transfer/delocalization, exchange dispersion, and dispersion (up to C10). This enables the reproduction of all energy contributions of ab initio symmetry-adapted perturbation theory (SAPT(DFT)) gas-phase reference computations. The SIBFA approach has been integrated within the Tinker-HP massively parallel MD package. To do so, all SIBFA energy gradients have been derived and the approach has been extended to enable periodic boundary conditions simulations using smooth particle mesh Ewald. This novel implementation also notably includes a computationally tractable simplification of the many-body charge transfer/delocalization contribution. As a proof of concept, we perform a first computational experiment defining a water model fitted on a limited set of SAPT(DFT) data. SIBFA is shown to enable a satisfactory reproduction of both gas-phase energetic contributions and condensed-phase properties highlighting the importance of its physically motivated functional form.
Collapse
Affiliation(s)
- Sehr Naseem-Khan
- LCT, UMR 7616 CNRS, Sorbonne Université, 75005 Paris, France
- Department of Chemistry, University of North Texas, Denton, Texas 76201, United States
| | - Louis Lagardère
- LCT, UMR 7616 CNRS, Sorbonne Université, 75005 Paris, France
- IP2CT, FR 2622, CNRS, Sorbonne Université, 75005 Paris, France
| | | | - G Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, Texas 76201, United States
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Nohad Gresh
- LCT, UMR 7616 CNRS, Sorbonne Université, 75005 Paris, France
| | - Jean-Philip Piquemal
- LCT, UMR 7616 CNRS, Sorbonne Université, 75005 Paris, France
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
- Institut Universitaire de France, 75005 Paris, France
| |
Collapse
|
2
|
Enzyme Inhibitors: The Best Strategy to Tackle Superbug NDM-1 and Its Variants. Int J Mol Sci 2021; 23:ijms23010197. [PMID: 35008622 PMCID: PMC8745225 DOI: 10.3390/ijms23010197] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 12/20/2021] [Accepted: 12/23/2021] [Indexed: 01/06/2023] Open
Abstract
Multidrug bacterial resistance endangers clinically effective antimicrobial therapy and continues to cause major public health problems, which have been upgraded to unprecedented levels in recent years, worldwide. β-Lactam antibiotics have become an important weapon to fight against pathogen infections due to their broad spectrum. Unfortunately, the emergence of antibiotic resistance genes (ARGs) has severely astricted the application of β-lactam antibiotics. Of these, New Delhi metallo-β-lactamase-1 (NDM-1) represents the most disturbing development due to its substrate promiscuity, the appearance of variants, and transferability. Given the clinical correlation of β-lactam antibiotics and NDM-1-mediated resistance, the discovery, and development of combination drugs, including NDM-1 inhibitors, for NDM-1 bacterial infections, seems particularly attractive and urgent. This review summarizes the research related to the development and optimization of effective NDM-1 inhibitors. The detailed generalization of crystal structure, enzyme activity center and catalytic mechanism, variants and global distribution, mechanism of action of existing inhibitors, and the development of scaffolds provides a reference for finding potential clinically effective NDM-1 inhibitors against drug-resistant bacteria.
Collapse
|
3
|
Kwapien K, Gavara L, Docquier J, Berthomieu D, Hernandez J, Gresh N. Intermolecular interactions of the extended recognition site of
VIM
‐2
metallo‐β‐lactamase
with 1,2,4‐triazole‐3‐thione inhibitors. Validations of a polarizable molecular mechanics potential by ab initio
QC. J Comput Chem 2020; 42:86-106. [DOI: 10.1002/jcc.26437] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Karolina Kwapien
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques Université de Paris UMR 8601 Paris France
- Laboratoire de Chimie Théorique Paris France
- Institut Charles Gerhardt, UMR 5253, CNRS, Université de Montpellier, ENSCM Montpellier France
| | - Laurent Gavara
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS, Université de Montpellier, ENSCM, Faculté de Pharmacie Montpellier France
| | | | - Dorothée Berthomieu
- Institut Charles Gerhardt, UMR 5253, CNRS, Université de Montpellier, ENSCM Montpellier France
| | - Jean‐François Hernandez
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS, Université de Montpellier, ENSCM, Faculté de Pharmacie Montpellier France
| | - Nohad Gresh
- Laboratoire de Chimie Théorique Paris France
| |
Collapse
|
4
|
Grimme S, Bannwarth C, Caldeweyher E, Pisarek J, Hansen A. A general intermolecular force field based on tight-binding quantum chemical calculations. J Chem Phys 2017; 147:161708. [DOI: 10.1063/1.4991798] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstr. 4, D-53115 Bonn,
Germany
| | - Christoph Bannwarth
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstr. 4, D-53115 Bonn,
Germany
| | - Eike Caldeweyher
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstr. 4, D-53115 Bonn,
Germany
| | - Jana Pisarek
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstr. 4, D-53115 Bonn,
Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstr. 4, D-53115 Bonn,
Germany
| |
Collapse
|
5
|
Kwapien K, Damergi M, Nader S, El Khoury L, Hobaika Z, Maroun RG, Piquemal JP, Gavara L, Berthomieu D, Hernandez JF, Gresh N. Calibration of 1,2,4-Triazole-3-Thione, an Original Zn-Binding Group of Metallo-β-Lactamase Inhibitors. Validation of a Polarizable MM/MD Potential by Quantum Chemistry. J Phys Chem B 2017; 121:6295-6312. [DOI: 10.1021/acs.jpcb.7b01053] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Karolina Kwapien
- Chemistry
and Biology, Nucléo(s)tides and Immunology for Therapy (CBNIT),
UMR 8601, CNRS, UFR Biomédicale, Paris, France
- Institut Charles-Gerhardt, MACS, UMR 5253 CNRS-ENSCM-UM, 8 rue de l’Ecole Normale, 34296 Montpellier Cedex 5, France
| | - Mirna Damergi
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC, UMR7616 CNRS, Paris, France
- Centre
d’Analyses et de Recherche, UR EGFEM, LSIM, Faculté
des Sciences, Saint Joseph University of Beirut, BP 11-514, Riad El Solh, Beirut 1116-2050, Lebanon
| | - Serge Nader
- Chemistry
and Biology, Nucléo(s)tides and Immunology for Therapy (CBNIT),
UMR 8601, CNRS, UFR Biomédicale, Paris, France
- Centre
d’Analyses et de Recherche, UR EGFEM, LSIM, Faculté
des Sciences, Saint Joseph University of Beirut, BP 11-514, Riad El Solh, Beirut 1116-2050, Lebanon
| | - Léa El Khoury
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC, UMR7616 CNRS, Paris, France
- Centre
d’Analyses et de Recherche, UR EGFEM, LSIM, Faculté
des Sciences, Saint Joseph University of Beirut, BP 11-514, Riad El Solh, Beirut 1116-2050, Lebanon
| | - Zeina Hobaika
- Centre
d’Analyses et de Recherche, UR EGFEM, LSIM, Faculté
des Sciences, Saint Joseph University of Beirut, BP 11-514, Riad El Solh, Beirut 1116-2050, Lebanon
| | - Richard G. Maroun
- Centre
d’Analyses et de Recherche, UR EGFEM, LSIM, Faculté
des Sciences, Saint Joseph University of Beirut, BP 11-514, Riad El Solh, Beirut 1116-2050, Lebanon
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC, UMR7616 CNRS, Paris, France
- Institut Universitaire de France, Paris Cedex 05, 75231, France
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Laurent Gavara
- Institut des Biomolécules Max Mousseron,
UMR 5247 CNRS, Faculté de Pharmacie, Université de Montpellier, ENSCM, 15 avenue Charles Flahault, 34093 Montpellier, France
| | - Dorothée Berthomieu
- Institut Charles-Gerhardt, MACS, UMR 5253 CNRS-ENSCM-UM, 8 rue de l’Ecole Normale, 34296 Montpellier Cedex 5, France
| | - Jean-François Hernandez
- Institut des Biomolécules Max Mousseron,
UMR 5247 CNRS, Faculté de Pharmacie, Université de Montpellier, ENSCM, 15 avenue Charles Flahault, 34093 Montpellier, France
| | - Nohad Gresh
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC, UMR7616 CNRS, Paris, France
| |
Collapse
|
6
|
Abstract
Metal ions play significant roles in numerous fields including chemistry, geochemistry, biochemistry, and materials science. With computational tools increasingly becoming important in chemical research, methods have emerged to effectively face the challenge of modeling metal ions in the gas, aqueous, and solid phases. Herein, we review both quantum and classical modeling strategies for metal ion-containing systems that have been developed over the past few decades. This Review focuses on classical metal ion modeling based on unpolarized models (including the nonbonded, bonded, cationic dummy atom, and combined models), polarizable models (e.g., the fluctuating charge, Drude oscillator, and the induced dipole models), the angular overlap model, and valence bond-based models. Quantum mechanical studies of metal ion-containing systems at the semiempirical, ab initio, and density functional levels of theory are reviewed as well with a particular focus on how these methods inform classical modeling efforts. Finally, conclusions and future prospects and directions are offered that will further enhance the classical modeling of metal ion-containing systems.
Collapse
Affiliation(s)
| | - Kenneth M. Merz
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute of Cyber-Enabled Research, Michigan State University, East Lansing, Michigan 48824, United States
| |
Collapse
|
7
|
Wang H, Yang W. Determining polarizable force fields with electrostatic potentials from quantum mechanical linear response theory. J Chem Phys 2017; 144:224107. [PMID: 27305996 DOI: 10.1063/1.4953558] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We developed a new method to calculate the atomic polarizabilities by fitting to the electrostatic potentials (ESPs) obtained from quantum mechanical (QM) calculations within the linear response theory. This parallels the conventional approach of fitting atomic charges based on electrostatic potentials from the electron density. Our ESP fitting is combined with the induced dipole model under the perturbation of uniform external electric fields of all orientations. QM calculations for the linear response to the external electric fields are used as input, fully consistent with the induced dipole model, which itself is a linear response model. The orientation of the uniform external electric fields is integrated in all directions. The integration of orientation and QM linear response calculations together makes the fitting results independent of the orientations and magnitudes of the uniform external electric fields applied. Another advantage of our method is that QM calculation is only needed once, in contrast to the conventional approach, where many QM calculations are needed for many different applied electric fields. The molecular polarizabilities obtained from our method show comparable accuracy with those from fitting directly to the experimental or theoretical molecular polarizabilities. Since ESP is directly fitted, atomic polarizabilities obtained from our method are expected to reproduce the electrostatic interactions better. Our method was used to calculate both transferable atomic polarizabilities for polarizable molecular mechanics' force fields and nontransferable molecule-specific atomic polarizabilities.
Collapse
Affiliation(s)
- Hao Wang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - Weitao Yang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| |
Collapse
|
8
|
Gresh N, Perahia D, de Courcy B, Foret J, Roux C, El-Khoury L, Piquemal JP, Salmon L. Complexes of a Zn-metalloenzyme binding site with hydroxamate-containing ligands. A case for detailed benchmarkings of polarizable molecular mechanics/dynamics potentials when the experimental binding structure is unknown. J Comput Chem 2016; 37:2770-2782. [DOI: 10.1002/jcc.24503] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 08/31/2016] [Accepted: 09/04/2016] [Indexed: 12/15/2022]
Affiliation(s)
- Nohad Gresh
- Laboratoire de Chimie Théorique; Sorbonne Universités; UPMC, UMR 7616 CNRS Paris France
- Chemistry and Biology, Nucleo(s)tides and Immunology for Therapy (CBNIT); UMR 8601 CNRS, UFR Biomédicale; Paris France
| | - David Perahia
- Laboratoire de Biologie et Pharmacologie Appliquées (LBPA), UMR 8113; Ecole Normale Supérieure Cachan France
| | - Benoit de Courcy
- Laboratoire de Chimie Théorique; Sorbonne Universités; UPMC, UMR 7616 CNRS Paris France
- Chemistry and Biology, Nucleo(s)tides and Immunology for Therapy (CBNIT); UMR 8601 CNRS, UFR Biomédicale; Paris France
| | - Johanna Foret
- Laboratoire de Chimie Bioorganique et Bioinorganique; Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), Univ Paris-Saclay, Univ Paris-Sud, UMR 8182 CNRS; rue du Doyen Georges Poitou Orsay F-91405 France
| | - Céline Roux
- Laboratoire de Chimie Bioorganique et Bioinorganique; Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), Univ Paris-Saclay, Univ Paris-Sud, UMR 8182 CNRS; rue du Doyen Georges Poitou Orsay F-91405 France
| | - Lea El-Khoury
- Laboratoire de Chimie Théorique; Sorbonne Universités; UPMC, UMR 7616 CNRS Paris France
- Centre d'Analyses et de Recherche; UR EGFEM, LSIM, Faculté de Sciences, Saint Joseph University of Beirut; BP 11-514, Riad El Solh Beirut 1116-2050 Lebanon
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique; Sorbonne Universités; UPMC, UMR 7616 CNRS Paris France
- Department of Biomolecular Engineering; The University of Texas at Austin; Texas 78712
| | - Laurent Salmon
- Laboratoire de Chimie Bioorganique et Bioinorganique; Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), Univ Paris-Saclay, Univ Paris-Sud, UMR 8182 CNRS; rue du Doyen Georges Poitou Orsay F-91405 France
| |
Collapse
|
9
|
Shi Y, Ren P, Schnieders M, Piquemal JP. Polarizable Force Fields for Biomolecular Modeling. REVIEWS IN COMPUTATIONAL CHEMISTRY 2015. [DOI: 10.1002/9781118889886.ch2] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
10
|
Conformational analysis of a polyconjugated protein-binding ligand by joint quantum chemistry and polarizable molecular mechanics. Addressing the issues of anisotropy, conjugation, polarization, and multipole transferability. J Mol Model 2014; 20:2472. [PMID: 25367040 DOI: 10.1007/s00894-014-2472-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 09/21/2014] [Indexed: 01/13/2023]
Abstract
We investigate the conformational properties of a potent inhibitor of neuropilin-1, a protein involved in cancer processes and macular degeneration. This inhibitor consists of four aromatic/conjugated fragments: a benzimidazole, a methylbenzene, a carboxythiourea, and a benzene-linker dioxane, and these fragments are all linked together by conjugated bonds. The calculations use the SIBFA polarizable molecular mechanics procedure. Prior to docking simulations, it is essential to ensure that variations in the ligand conformational energy upon rotations around its six main-chain torsional bonds are correctly represented (as compared to high-level ab initio quantum chemistry, QC). This is done in two successive calibration stages and one validation stage. In the latter, the minima identified following independent stepwise variations of each of the six main-chain torsion angles are used as starting points for energy minimization of all the torsion angles simultaneously. Single-point QC calculations of the minimized structures are then done to compare their relative energies ΔE conf to the SIBFA ones. We compare three different methods of deriving the multipoles and polarizabilities of the central, most critical moiety of the inhibitor: carboxythiourea (CTU). The representation that gives the best agreement with QC is the one that includes the effects of the mutual polarization energy E pol between the amide and thioamide moieties. This again highlights the critical role of this contribution. The implications and perspectives of these findings are discussed.
Collapse
|
11
|
Gresh N, El Hage K, Perahia D, Piquemal JP, Berthomieu C, Berthomieu D. Polarizable molecular mechanics studies of Cu(I)/Zn(II) superoxide dismutase: Bimetallic binding site and structured waters. J Comput Chem 2014; 35:2096-106. [DOI: 10.1002/jcc.23724] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 08/09/2014] [Accepted: 08/12/2014] [Indexed: 11/11/2022]
Affiliation(s)
- Nohad Gresh
- Chemistry and Biology, Nucleo(s)tides and Immunology for Therapy (CBNIT); UMR 8601 CNRS, UFR Biomédicale Paris France
| | - Krystel El Hage
- Chemistry and Biology, Nucleo(s)tides and Immunology for Therapy (CBNIT); UMR 8601 CNRS, UFR Biomédicale Paris France
- Unité de Biochimie, Université Saint-Joseph; Beirut Lebanon
| | - David Perahia
- Laboratoire de Biologie et Pharmacologie Appliquée (LBPA); UMR 8113, Ecole Normale Supérieure France
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, Sorbonne Universités; UPMC, UMR7616 CNRS Paris France
| | - Catherine Berthomieu
- CEA, DSV, IBEB, Laboratoire des Interactions Protéine-Métal; Saint-Paul-lez-Durance France
- CNRS, UMR Biologie Végétale et Microbiologie Environnementale; Saint-Paul-lez-Durance France
| | - Dorothée Berthomieu
- Institut Charles Gerhardt, UMR 5253, CNRS-UM2-UM1-ENSCM; 8 rue de l'Ecole Normale 34296 Montpellier Cedex 5 France
| |
Collapse
|
12
|
Jones A, Crain J, Cipcigan F, Sokhan V, Modani M, Martyna G. Electronically coarse-grained molecular dynamics using quantum Drude oscillators. Mol Phys 2013. [DOI: 10.1080/00268976.2013.843032] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
13
|
Zhu T, Xiao X, Ji C, Zhang JZH. A New Quantum Calibrated Force Field for Zinc-Protein Complex. J Chem Theory Comput 2013; 9:1788-98. [PMID: 26587635 DOI: 10.1021/ct301091z] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A quantum calibrated polarizable-charge transfer force field (QPCT) has been proposed to accurately describe the interaction dynamics of zinc-protein complexes. The parameters of the QPCT force field were calibrated by quantum chemistry calculation and capture the polarization and charge transfer effect. QPCTs are validated by molecular dynamic simulation of the hydration shell of the zinc ion, five proteins containing the most common zinc-binding sites (ZnCys2His2, ZnCys3His1, ZnCys4, Zn2Cys6), as well as protein-ligand binding energy in zinc protein MMP3. The calculated results show excellent agreement with the experimental measurement and with results from QM/MM simulation, demonstrating that QPCT is accurate enough to maintain the correct structural integrity of the zinc binding pocket and provide accurate interaction dynamics of the zinc-residue complex. The current approach can also be extended to the study of interaction dynamics of other metal-containing proteins by recalibrating the corresponding parameters to the specific complexes.
Collapse
Affiliation(s)
- Tong Zhu
- Center for Laser and Computational Biophysics, State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Xudong Xiao
- Center for Laser and Computational Biophysics, State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China.,Institute of Theoretical and Computational Science, Institutes for Advanced Interdisciplinary Research, East China Normal University, Shanghai 200062, China
| | - Changge Ji
- Center for Laser and Computational Biophysics, State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China.,Institute of Theoretical and Computational Science, Institutes for Advanced Interdisciplinary Research, East China Normal University, Shanghai 200062, China
| | - John Z H Zhang
- Center for Laser and Computational Biophysics, State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China.,Institute of Theoretical and Computational Science, Institutes for Advanced Interdisciplinary Research, East China Normal University, Shanghai 200062, China.,Department of Chemistry, New York University, New York, New York 10003, United States
| |
Collapse
|
14
|
Hage KE, Piquemal JP, Hobaika Z, Maroun RG, Gresh N. Could an anisotropic molecular mechanics/dynamics potential account for sigma hole effects in the complexes of halogenated compounds? J Comput Chem 2013; 34:1125-35. [DOI: 10.1002/jcc.23242] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 12/28/2012] [Accepted: 01/12/2013] [Indexed: 02/02/2023]
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
Li YL, Mei Y, Zhang DW, Xie DQ, Zhang JZH. Structure and dynamics of a dizinc metalloprotein: effect of charge transfer and polarization. J Phys Chem B 2011; 115:10154-62. [PMID: 21766867 DOI: 10.1021/jp203505v] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Structures and dynamics of a recently designed dizinc metalloprotein (DFsc) (J. Mol. Biol. 2003, 334, 1101) are studied by molecular dynamics simulation using a dynamically adapted polarized force field derived from fragment quantum calculation for protein in solvent. To properly describe the effect of charge transfer and polarization in the present approach, quantum chemistry calculation of the zinc-binding group is periodically performed (on-the-fly) to update the atomic charges of the zinc-binding group during the MD simulation. Comparison of the present result with those obtained from simulations under standard AMBER force field reveals that charge transfer and polarization are critical to maintaining the correct asymmetric metal coordination in the DFsc. Detailed analysis of the result also shows that dynamic fluctuation of the zinc-binding group facilitates solvent interaction with the zinc ions. In particular, the dynamic fluctuation of the zinc-zinc distance is shown to be an important feature of the catalytic function of the di-ion zinc-binding group. Our study demonstrates that the dynamically adapted polarization approach is computationally practical and can be used to study other metalloprotein systems.
Collapse
Affiliation(s)
- Yong L Li
- Key Laboratory of Mesoscopic Chemistry of MOE, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | | | | | | | | |
Collapse
|
17
|
Gresh N, de Courcy B, Piquemal JP, Foret J, Courtiol-Legourd S, Salmon L. Polarizable Water Networks in Ligand–Metalloprotein Recognition. Impact on the Relative Complexation Energies of Zn-Dependent Phosphomannose Isomerase with d-Mannose 6-Phosphate Surrogates. J Phys Chem B 2011; 115:8304-16. [DOI: 10.1021/jp2024654] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nohad Gresh
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR8601 CNRS, Univ Paris Descartes, UFR Biomédicale, Faculté de Médecine de Paris, F-75006, Paris, France
| | - Benoit de Courcy
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR8601 CNRS, Univ Paris Descartes, UFR Biomédicale, Faculté de Médecine de Paris, F-75006, Paris, France
- Laboratoire de Chimie Théorique, UPMC Univ Paris 06, UMR7616, F-75252, Paris, France
- Laboratoire de Chimie Théorique, CNRS, UMR7616, F-75252, Paris, France
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, UPMC Univ Paris 06, UMR7616, F-75252, Paris, France
- Laboratoire de Chimie Théorique, CNRS, UMR7616, F-75252, Paris, France
| | - Johanna Foret
- Laboratoire de Chimie Bioorganique et Bioinorganique, Univ Paris-Sud, ICMMO, UMR8182, F-91405, Orsay, France
- Laboratoire de Chimie Bioorganique et Bioinorganique, CNRS, ICMMO, UMR8182, F-91405, Orsay, France
| | - Stéphanie Courtiol-Legourd
- Laboratoire de Chimie Bioorganique et Bioinorganique, Univ Paris-Sud, ICMMO, UMR8182, F-91405, Orsay, France
- Laboratoire de Chimie Bioorganique et Bioinorganique, CNRS, ICMMO, UMR8182, F-91405, Orsay, France
| | - Laurent Salmon
- Laboratoire de Chimie Bioorganique et Bioinorganique, Univ Paris-Sud, ICMMO, UMR8182, F-91405, Orsay, France
- Laboratoire de Chimie Bioorganique et Bioinorganique, CNRS, ICMMO, UMR8182, F-91405, Orsay, France
| |
Collapse
|
18
|
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.
Collapse
Affiliation(s)
- Céline Roux
- Laboratoire de Chimie Bioorganique et Bioinorganique, ICMMO, Univ Paris-Sud, UMR 8182, Orsay F-91405, France
| | | | | | | | | | | | | | | |
Collapse
|
19
|
Yamaguchi Y, Imamura K, Sasao A, Murakami E, Arakawa Y, Kurosaki H. Metal preference of Zn(ii) and Co(ii) for the dinuclear metal binding site of IMP-1 metallo-β-lactamase and spectroscopic properties of Co(ii)-substituted IMP-1 with mercaptoacetic acid. MEDCHEMCOMM 2011. [DOI: 10.1039/c1md00062d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
20
|
Devereux M, van Severen MC, Parisel O, Piquemal JP, Gresh N. Role of Cation Polarization in holo- and hemi-Directed [Pb(H2O)n]2+ Complexes and Development of a Pb2+ Polarizable Force Field. J Chem Theory Comput 2010; 7:138-47. [DOI: 10.1021/ct1004005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Mike Devereux
- Université Paris Descartes, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, UFR Biomédicale, 45 rue des Saints-Pères, 75270 Paris Cedex06, France; UPMC, Université Paris 06, UMR 7616, Laboratoire de Chimie Théorique, Case Courrier 137, 4 Place Jussieu, F-75005 Paris, France; and CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005 Paris, France
| | - Marie-Céline van Severen
- Université Paris Descartes, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, UFR Biomédicale, 45 rue des Saints-Pères, 75270 Paris Cedex06, France; UPMC, Université Paris 06, UMR 7616, Laboratoire de Chimie Théorique, Case Courrier 137, 4 Place Jussieu, F-75005 Paris, France; and CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005 Paris, France
| | - Olivier Parisel
- Université Paris Descartes, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, UFR Biomédicale, 45 rue des Saints-Pères, 75270 Paris Cedex06, France; UPMC, Université Paris 06, UMR 7616, Laboratoire de Chimie Théorique, Case Courrier 137, 4 Place Jussieu, F-75005 Paris, France; and CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005 Paris, France
| | - Jean-Philip Piquemal
- Université Paris Descartes, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, UFR Biomédicale, 45 rue des Saints-Pères, 75270 Paris Cedex06, France; UPMC, Université Paris 06, UMR 7616, Laboratoire de Chimie Théorique, Case Courrier 137, 4 Place Jussieu, F-75005 Paris, France; and CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005 Paris, France
| | - Nohad Gresh
- Université Paris Descartes, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, UFR Biomédicale, 45 rue des Saints-Pères, 75270 Paris Cedex06, France; UPMC, Université Paris 06, UMR 7616, Laboratoire de Chimie Théorique, Case Courrier 137, 4 Place Jussieu, F-75005 Paris, France; and CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005 Paris, France
| |
Collapse
|
21
|
Bebrone C, Lassaux P, Vercheval L, Sohier JS, Jehaes A, Sauvage E, Galleni M. Current challenges in antimicrobial chemotherapy: focus on ß-lactamase inhibition. Drugs 2010; 70:651-79. [PMID: 20394454 DOI: 10.2165/11318430-000000000-00000] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The use of the three classical beta-lactamase inhibitors (clavulanic acid, tazobactam and sulbactam) in combination with beta-lactam antibacterials is currently the most successful strategy to combat beta-lactamase-mediated resistance. However, these inhibitors are efficient in inactivating only class A beta-lactamases and the efficiency of the inhibitor/antibacterial combination can be compromised by several mechanisms, such as the production of naturally resistant class B or class D enzymes, the hyperproduction of AmpC or even the production of evolved inhibitor-resistant class A enzymes. Thus, there is an urgent need for the development of novel inhibitors. For serine active enzymes (classes A, C and D), derivatives of the beta-lactam ring such as 6-beta-halogenopenicillanates, beta-lactam sulfones, penems and oxapenems, monobactams or trinems seem to be potential starting points to design efficient molecules (such as AM-112 and LK-157). Moreover, a promising non-beta-lactam molecule, NXL-104, is now under clinical development. In contrast, an ideal inhibitor of metallo-beta-lactamases (class B) remains to be found, despite the huge number of potential molecules already described (biphenyl tetrazoles, cysteinyl peptides, mercaptocarboxylates, succinic acid derivatives, etc.). The search for such an inhibitor is complicated by the absence of a covalent intermediate in their catalytic mechanisms and the fact that beta-lactam derivatives often behave as substrates rather than as inhibitors. Currently, the most promising broad-spectrum inhibitors of class B enzymes are molecules presenting chelating groups (thiols, carboxylates, etc.) combined with an aromatic group. This review describes all the types of molecules already tested as potential beta-lactamase inhibitors and thus constitutes an update of the current status in beta-lactamase inhibitor discovery.
Collapse
Affiliation(s)
- Carine Bebrone
- Biological Macromolecules, Centre for Protein Engineering, University of Liège, Liège, Belgium.
| | | | | | | | | | | | | |
Collapse
|
22
|
Wu JC, Piquemal JP, Chaudret R, Reinhardt P, Ren P. Polarizable molecular dynamics simulation of Zn(II) in water using the AMOEBA force field. J Chem Theory Comput 2010; 6:2059-2070. [PMID: 21116445 DOI: 10.1021/ct100091j] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The hydration free energy, structure, and dynamics of the zinc divalent cation are studied using a polarizable force field in molecular dynamics simulations. Parameters for the Zn(2+) are derived from gas-phase ab initio calculation of Zn(2+)-water dimer. The Thole-based dipole polarization is adjusted based on the Constrained Space Orbital Variations (CSOV) calculation while the Symmetry Adapted Perturbation Theory (SAPT) approach is also discussed. The vdW parameters of Zn(2+) have been obtained by comparing the AMOEBA Zn(2+)-water dimerization energy with results from several theory levels and basis sets over a range of distances. Molecular dynamics simulations of Zn(2+) solvation in bulk water are subsequently performed with the polarizable force field. The calculated first-shell water coordination number, water residence time and free energy of hydration are consistent with experimental and previous theoretical values. The study is supplemented with extensive Reduced Variational Space (RVS) and Electron Localization Function (ELF) computations in order to unravel the nature of the bonding in Zn(2+)(H(2)O)(n) (n=1,6) complexes and to analyze the charge transfer contribution to the complexes. Results show that the importance of charge transfer decreases as the size of Zn-water cluster grows due to anticooperativity and to changes in the nature of the metal-ligand bonds. Induction could be dominated by polarization when the system approaches condensed-phase and the covelant effects are eliminated from the Zn(II)-water interaction. To construct an "effective" classical polarizable potential for Zn(2+) in bulk water, one should therefore avoid over-fitting to the ab initio charge transfer energy of Zn(2+)-water dimer. Indeed, in order to avoid overestimation of condensed-phase many-body effects, which is crucial to the transferability of polarizable molecular dynamics, charge transfer should not be included within the classical polarization contribution and should preferably be either incorporated in to the pairwise van der Waals contribution or treated explicitly.
Collapse
Affiliation(s)
- Johnny C Wu
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas 78712-1062, USA
| | | | | | | | | |
Collapse
|
23
|
Gresh N, Audiffren N, Piquemal JP, de Ruyck J, Ledecq M, Wouters J. Analysis of the Interactions Taking Place in the Recognition Site of a Bimetallic Mg(II)−Zn(II) Enzyme, Isopentenyl Diphosphate Isomerase. A Parallel Quantum-Chemical and Polarizable Molecular Mechanics Study. J Phys Chem B 2010; 114:4884-95. [DOI: 10.1021/jp907629k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Nohad Gresh
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université Paris Descartes, 45 rue des Saints-Pères, 75006 Paris, France, Centre Informatique National de l’Enseignement Supérieur, 950, rue de Saint Priest, 34097 Montpellier, France, Laboratoire de Chimie Théorique, Centre National de la Recherche Scientifique, UMR 7616, Université Pierre et Marie Curie, 4 place Jussieu, 75252 Paris Cedex 05, France, and Laboratoire de Chimie Biologique Structurale, FUNDP, 61 Rue de
| | - Nicole Audiffren
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université Paris Descartes, 45 rue des Saints-Pères, 75006 Paris, France, Centre Informatique National de l’Enseignement Supérieur, 950, rue de Saint Priest, 34097 Montpellier, France, Laboratoire de Chimie Théorique, Centre National de la Recherche Scientifique, UMR 7616, Université Pierre et Marie Curie, 4 place Jussieu, 75252 Paris Cedex 05, France, and Laboratoire de Chimie Biologique Structurale, FUNDP, 61 Rue de
| | - Jean-Philip Piquemal
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université Paris Descartes, 45 rue des Saints-Pères, 75006 Paris, France, Centre Informatique National de l’Enseignement Supérieur, 950, rue de Saint Priest, 34097 Montpellier, France, Laboratoire de Chimie Théorique, Centre National de la Recherche Scientifique, UMR 7616, Université Pierre et Marie Curie, 4 place Jussieu, 75252 Paris Cedex 05, France, and Laboratoire de Chimie Biologique Structurale, FUNDP, 61 Rue de
| | - Jerome de Ruyck
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université Paris Descartes, 45 rue des Saints-Pères, 75006 Paris, France, Centre Informatique National de l’Enseignement Supérieur, 950, rue de Saint Priest, 34097 Montpellier, France, Laboratoire de Chimie Théorique, Centre National de la Recherche Scientifique, UMR 7616, Université Pierre et Marie Curie, 4 place Jussieu, 75252 Paris Cedex 05, France, and Laboratoire de Chimie Biologique Structurale, FUNDP, 61 Rue de
| | - Marie Ledecq
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université Paris Descartes, 45 rue des Saints-Pères, 75006 Paris, France, Centre Informatique National de l’Enseignement Supérieur, 950, rue de Saint Priest, 34097 Montpellier, France, Laboratoire de Chimie Théorique, Centre National de la Recherche Scientifique, UMR 7616, Université Pierre et Marie Curie, 4 place Jussieu, 75252 Paris Cedex 05, France, and Laboratoire de Chimie Biologique Structurale, FUNDP, 61 Rue de
| | - Johan Wouters
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université Paris Descartes, 45 rue des Saints-Pères, 75006 Paris, France, Centre Informatique National de l’Enseignement Supérieur, 950, rue de Saint Priest, 34097 Montpellier, France, Laboratoire de Chimie Théorique, Centre National de la Recherche Scientifique, UMR 7616, Université Pierre et Marie Curie, 4 place Jussieu, 75252 Paris Cedex 05, France, and Laboratoire de Chimie Biologique Structurale, FUNDP, 61 Rue de
| |
Collapse
|
24
|
de Courcy B, Piquemal JP, Garbay C, Gresh N. Polarizable Water Molecules in Ligand−Macromolecule Recognition. Impact on the Relative Affinities of Competing Pyrrolopyrimidine Inhibitors for FAK Kinase. J Am Chem Soc 2010; 132:3312-20. [DOI: 10.1021/ja9059156] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Benoit de Courcy
- Université Paris Descartes, Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, 45 rue des Saints-Pères, 75270 Paris Cedex 06, France, UPMC Université Paris 06, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005 Paris, France, and CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005 Paris, France
| | - Jean-Philip Piquemal
- Université Paris Descartes, Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, 45 rue des Saints-Pères, 75270 Paris Cedex 06, France, UPMC Université Paris 06, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005 Paris, France, and CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005 Paris, France
| | - Christiane Garbay
- Université Paris Descartes, Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, 45 rue des Saints-Pères, 75270 Paris Cedex 06, France, UPMC Université Paris 06, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005 Paris, France, and CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005 Paris, France
| | - Nohad Gresh
- Université Paris Descartes, Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, 45 rue des Saints-Pères, 75270 Paris Cedex 06, France, UPMC Université Paris 06, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005 Paris, France, and CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005 Paris, France
| |
Collapse
|
25
|
Söderhjelm P, Aquilante F, Ryde U. Calculation of protein-ligand interaction energies by a fragmentation approach combining high-level quantum chemistry with classical many-body effects. J Phys Chem B 2009; 113:11085-94. [PMID: 19618955 DOI: 10.1021/jp810551h] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We have developed a method to estimate accurate interaction energies between a full protein and a bound ligand. It is based on the recently proposed PMISP (polarizable multipole interaction with supermolecular pairs) method (Soderhjelm, P.; Ryde, U. J. Phys. Chem. A 2009, 113, 617), which treats electrostatic interaction by multipoles up to quadrupoles, induction by anisotropic polarizabilities, and nonclassical interactions by explicit quantum mechanical (QM) calculations, using a fragmentation approach. For a whole protein, electrostatics and induction are treated the same way, but for the nonclassical interactions, a Lennard-Jones term from a standard molecular mechanics (MM) force field (e.g., Amber) is used outside a certain distance from the ligand (4-7 A). This QM/MM variant of the PMISP method is carefully tested by varying this distance. Several approximations related to the classical interactions are also evaluated. It is found that one can speed up the calculation by using density functional theory to compute multipoles and polarizabilities but that a proper treatment of polarization is important. As a demonstration of the method, the interaction energies of two ligands bound to avidin are calculated at the MP2/aug-cc-pVTZ level, with an expected relative error of 1-2%.
Collapse
Affiliation(s)
- Pär Söderhjelm
- Department of Theoretical Chemistry, Lund University, Chemical Center, SE-22100 Lund, Sweden.
| | | | | |
Collapse
|
26
|
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.
Collapse
|
27
|
Illingworth CJ, Domene C. Many-body effects and simulations of potassium channels. Proc Math Phys Eng Sci 2009. [DOI: 10.1098/rspa.2009.0014] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The electronic polarizability of an ion or a molecule is a measure of the relative tendency of its electron cloud to be distorted from its normal shape by an electric field. On the molecular scale, in a condensed phase, any species sits in an electric field due to its neighbours, and the resulting polarization is an important contribution to the total interaction energy. Electrostatic interactions are crucial for determining the majority of chemical–physical properties of the system and electronic polarization is a fundamental component of these interactions. Thus, polarization effects should be taken into account if accurate descriptions are desired. In classical computer simulations, the forces required to drive the system are typically based on interatomic interaction potentials derived in part from electronic structure calculations or from experimental data. Owing to the difficulties in including polarization effects in classical force fields, most of them are based just on pairwise additive interaction potentials. At present, major efforts are underway to develop polarizable interaction potentials for biomolecular simulations. In this review, various ways of introducing explicit polarizability into biomolecular models and force fields are reviewed, and the progress that might be achieved in applying such methods to study potassium channels is described.
Collapse
Affiliation(s)
- Christopher J. Illingworth
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of OxfordOxford OX1 3QZ, UK
| | - Carmen Domene
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of OxfordOxford OX1 3QZ, UK
| |
Collapse
|
28
|
Oelschlaeger P. Outsmarting metallo-β-lactamases by mimicking their natural evolution. J Inorg Biochem 2008; 102:2043-51. [DOI: 10.1016/j.jinorgbio.2008.05.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2008] [Revised: 05/20/2008] [Accepted: 05/21/2008] [Indexed: 11/25/2022]
|
29
|
de Courcy B, Piquemal JP, Gresh N. Energy Analysis of Zn Polycoordination in a Metalloprotein Environment and of the Role of a Neighboring Aromatic Residue. What Is the Impact of Polarization? J Chem Theory Comput 2008; 4:1659-68. [DOI: 10.1021/ct800200j] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Benoit de Courcy
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université Paris Descartes, 45, rue des Saints-Pères, 75006 Paris, France UPMC Univ Paris 06, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France, and CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
| | - Jean-Philip Piquemal
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université Paris Descartes, 45, rue des Saints-Pères, 75006 Paris, France UPMC Univ Paris 06, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France, and CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
| | - Nohad Gresh
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université Paris Descartes, 45, rue des Saints-Pères, 75006 Paris, France UPMC Univ Paris 06, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France, and CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
| |
Collapse
|
30
|
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: 281] [Impact Index Per Article: 16.5] [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.
Collapse
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
| | | | | | | |
Collapse
|
31
|
Estiu G, Suárez D, Merz KM. Quantum mechanical and molecular dynamics simulations of ureases and Zn beta-lactamases. J Comput Chem 2007; 27:1240-62. [PMID: 16773613 DOI: 10.1002/jcc.20411] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Herein we briefly review theoretical contributions that have increased our understanding of the structure and function of metallo-beta-lactamases and ureases. Both are bimetallic metalloenzymes, with the former containing two zinc ions and the latter containing two nickel ions. We describe the use of several different methodologies, including quantum chemical calculations, molecular dynamic simulations, as well as mixed QM/MM approaches and how they have impacted our understanding of the structure and function of metallo-beta-lactamases and ureases.
Collapse
Affiliation(s)
- Guillermina Estiu
- Department of Chemistry, Quantum Theory Project, University of Florida, 2328 New Physics Building, P.O. Box 118435, Gainesville, Florida 32611-8435, USA
| | | | | |
Collapse
|
32
|
Piquemal JP, Cisneros GA, Reinhardt P, Gresh N, Darden TA. Towards a force field based on density fitting. J Chem Phys 2007; 124:104101. [PMID: 16542062 PMCID: PMC2080832 DOI: 10.1063/1.2173256] [Citation(s) in RCA: 165] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Total intermolecular interaction energies are determined with a first version of the Gaussian electrostatic model (GEM-0), a force field based on a density fitting approach using s-type Gaussian functions. The total interaction energy is computed in the spirit of the sum of interacting fragment ab initio (SIBFA) force field by separately evaluating each one of its components: electrostatic (Coulomb), exchange repulsion, polarization, and charge transfer intermolecular interaction energies, in order to reproduce reference constrained space orbital variation (CSOV) energy decomposition calculations at the B3LYP/aug-cc-pVTZ level. The use of an auxiliary basis set restricted to spherical Gaussian functions facilitates the rotation of the fitted densities of rigid fragments and enables a fast and accurate density fitting evaluation of Coulomb and exchange-repulsion energy, the latter using the overlap model introduced by Wheatley and Price [Mol. Phys. 69, 50718 (1990)]. The SIBFA energy scheme for polarization and charge transfer has been implemented using the electric fields and electrostatic potentials generated by the fitted densities. GEM-0 has been tested on ten stationary points of the water dimer potential energy surface and on three water clusters (n = 16,20,64). The results show very good agreement with density functional theory calculations, reproducing the individual CSOV energy contributions for a given interaction as well as the B3LYP total interaction energies with errors below kBT at room temperature. Preliminary results for Coulomb and exchange-repulsion energies of metal cation complexes and coupled cluster singles doubles electron densities are discussed.
Collapse
Affiliation(s)
- Jean-Philip Piquemal
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA.
| | | | | | | | | |
Collapse
|
33
|
Piquemal JP, Chelli R, Procacci P, Gresh N. Key Role of the Polarization Anisotropy of Water in Modeling Classical Polarizable Force Fields. J Phys Chem A 2007; 111:8170-6. [PMID: 17665882 DOI: 10.1021/jp072687g] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We have evaluated the extent to which classical polarizable force fields, based either on the chemical potential equalization principle or on distributed polarizabilities in the framework of the Sum of Interactions Between Fragments Ab initio computed (SIBFA), can reproduce the ab initio polarization energy and the dipole moment of three distinct water oligomers: bifurcated chains, transverse hydrogen-bonded chains, and longitudinal hydrogen-bonded chains of helical shape. To analyze the many-body polarization effect, chains of different size, i.e., from 2 to 12 water monomers, have been considered. Although the dipole moment is a well-defined quantity in both classical polarizable models and quantum mechanical methods, polarization energy can be defined unequivocally only in the former type of approaches. In this study we have used the Kitaura-Morokuma (KM) procedure. Although the KM approach is on the one hand known to overestimate the polarization energy for strongly interacting molecules, on the other hand it can account for the many-body polarization effectively, whereas some other procedures do not. Our data show that, if off-centered lone pair polarizabilities are explicitly represented, classical polarizable force fields can afford a close agreement with the ab initio results, both in terms of polarization energy and in terms of dipole moment.
Collapse
Affiliation(s)
- Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, Université Pierre et Marie Curie (Paris VI), case 137, 4 place Jussieu, 75252 Paris Cedex 05, France.
| | | | | | | |
Collapse
|
34
|
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.
Collapse
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
| | | | | | | | | |
Collapse
|
35
|
Piquemal JP, Chevreau H, Gresh N. Toward a Separate Reproduction of the Contributions to the Hartree−Fock and DFT Intermolecular Interaction Energies by Polarizable Molecular Mechanics with the SIBFA Potential. J Chem Theory Comput 2007; 3:824-37. [DOI: 10.1021/ct7000182] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, UMR 7616, Université P. & M. Curie, Case courrier 137, 4, place Jussieu, F. 75252 Paris, Cedex 05, France, and Laboratoire de Pharmacochimie Moléculaire et Structurale, U648 INSERM, IFR Biomédicale, 45, Rue des Saints-Pères, 75006, Paris, France
| | - Hilaire Chevreau
- Laboratoire de Chimie Théorique, UMR 7616, Université P. & M. Curie, Case courrier 137, 4, place Jussieu, F. 75252 Paris, Cedex 05, France, and Laboratoire de Pharmacochimie Moléculaire et Structurale, U648 INSERM, IFR Biomédicale, 45, Rue des Saints-Pères, 75006, Paris, France
| | - Nohad Gresh
- Laboratoire de Chimie Théorique, UMR 7616, Université P. & M. Curie, Case courrier 137, 4, place Jussieu, F. 75252 Paris, Cedex 05, France, and Laboratoire de Pharmacochimie Moléculaire et Structurale, U648 INSERM, IFR Biomédicale, 45, Rue des Saints-Pères, 75006, Paris, France
| |
Collapse
|
36
|
Leroux V, Gresh N, Liu WQ, Garbay C, Maigret B. Role of water molecules for binding inhibitors in the SH2 domain of Grb2: A molecular dynamics study. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.theochem.2006.11.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
37
|
Costello AL, Sharma NP, Yang KW, Crowder MW, Tierney DL. X-ray absorption spectroscopy of the zinc-binding sites in the class B2 metallo-beta-lactamase ImiS from Aeromonas veronii bv. sobria. Biochemistry 2007; 45:13650-8. [PMID: 17087519 DOI: 10.1021/bi061547e] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
X-ray absorption spectroscopy was used to investigate the metal-binding sites of ImiS from Aeromonas veronii bv. sobria in catalytically active (1-Zn), product-inhibited (1-Zn plus imipenem), and inactive (2-Zn) forms. The first equivalent of zinc(II) was found to bind to the consensus Zn(2) site. The reaction of 1-Zn ImiS with imipenem leads to a product-bound species, coordinated to Zn via a carboxylate group. The inhibitory binding site of ImiS was examined by a comparison of wild-type ImiS with 1 and 2 equiv of bound zinc. 2-Zn ImiS extended X-ray absorption fine structure data support a binding site that is distant from the active site and contains both one sulfur donor and one histidine ligand. On the basis of the amino acid sequence of ImiS and the crystal structure of CphA [Garau et al. (2005) J. Mol. Biol. 345, 785-795], we propose that the inhibitory binding site is formed by M146, found on the B2-distinct alpha3 helix, and H118, a canonical Zn(1) ligand, proposed to help activate the nucleophilic water. The mutation of M146 to isoleucine abolishes metal inhibition. This is the first characterization of ImiS with the native metal Zn and establishes, for the first time, the location of the inhibitory metal site.
Collapse
Affiliation(s)
- Alison L Costello
- Department of Chemistry, University of New Mexico, Albuquerque, New Mexico 87131-0001, USA
| | | | | | | | | |
Collapse
|
38
|
Dal Peraro M, Spiegel K, Lamoureux G, De Vivo M, DeGrado WF, Klein ML. Modeling the charge distribution at metal sites in proteins for molecular dynamics simulations. J Struct Biol 2006; 157:444-53. [PMID: 17188512 DOI: 10.1016/j.jsb.2006.10.019] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2006] [Revised: 10/19/2006] [Accepted: 10/19/2006] [Indexed: 10/24/2022]
Abstract
Almost half of the proteome of living organisms is constituted of metalloproteins. Unfortunately, the ability of the current generation of molecular dynamics pairwise-additive forcefields to properly describe metal pockets is severely lacking due to the intrinsic difficulty of handling polarization and charge transfer contributions. In order to improve the description of metalloproteins, a simple reparameterization strategy is proposed herein that does not involve artificial constraints. Specifically, a non-bonded quantum mechanical-based model is used to capture the mean polarization and charge transfer contributions to the interatomic forces within the metal site. The present approach is demonstrated to provide enough accuracy to maintain the integrity of the metal pocket for a variety of metalloproteins during extended (multi-nanosecond) molecular dynamics simulations. The method enables the sampling of small conformational changes and the relaxation of local frustrations in NMR structures.
Collapse
Affiliation(s)
- M Dal Peraro
- Center for Molecular Modeling and Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104-6323, USA.
| | | | | | | | | | | |
Collapse
|
39
|
Piquemal JP, Perera L, Cisneros GA, Ren P, Pedersen LG, Darden TA. Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure. J Chem Phys 2006; 125:054511. [PMID: 16942230 DOI: 10.1063/1.2234774] [Citation(s) in RCA: 163] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Molecular dynamics simulations were performed using a modified amoeba force field to determine hydration and dynamical properties of the divalent cations Ca2+ and Mg2+. The extension of amoeba to divalent cations required the introduction of a cation specific parametrization. To accomplish this, the Thole polarization damping model parametrization was modified based on the ab initio polarization energy computed by a constrained space orbital variation energy decomposition scheme. Excellent agreement has been found with condensed phase experimental results using parameters derived from gas phase ab initio calculations. Additionally, we have observed that the coordination of the calcium cation is influenced by the size of the periodic water box, a recurrent issue in first principles molecular dynamics studies.
Collapse
Affiliation(s)
- Jean-Philip Piquemal
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA.
| | | | | | | | | | | |
Collapse
|
40
|
Oliveira FG, Sant'Anna CMR, Caffarena ER, Dardenne LE, Barreiro EJ. Molecular docking study and development of an empirical binding free energy model for phosphodiesterase 4 inhibitors. Bioorg Med Chem 2006; 14:6001-11. [PMID: 16843671 DOI: 10.1016/j.bmc.2006.05.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2005] [Revised: 05/10/2006] [Accepted: 05/10/2006] [Indexed: 10/24/2022]
Abstract
In the present work, several computational methodologies were combined to develop a model for the prediction of PDE4B inhibitors' activity. The adequacy of applying the ligand docking approach, keeping the enzyme rigid, to the study of a series of PDE4 inhibitors was confirmed by a previous molecular dynamics analysis of the complete enzyme. An exhaustive docking procedure was performed to identify the most probable binding modes of the ligands to the enzyme, including the active site metal ions and the surrounding structural water molecules. The enzyme-inhibitor interaction enthalpies, refined by using the semiempirical molecular orbital approach, were combined with calculated solvation free energies and entropy considerations in an empirical free energy model that enabled the calculation of binding free energies that correlated very well with experimentally derived binding free energies. Our results indicate that both the inclusion of the structural water molecules close to the ions in the binding site and the use of a free energy model with a quadratic dependency on the ligand free energy of solvation are important aspects to be considered for molecular docking investigations involving the PDE4 enzyme family.
Collapse
Affiliation(s)
- Fernanda G Oliveira
- LASSBio, Laboratório de Avaliação e Síntese de Substãncias Bioativas, Faculdade de Farmácia and Instituto de Química, Universidade Federal do Rio de Janeiro, PO Box 68006, Rio de Janeiro, RJ 21944-910, Brazil
| | | | | | | | | |
Collapse
|