101
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Cai YH, Guo Y, Li Z, Wu D, Li X, Zhang H, Yang J, Lu H, Sun Z, Luo HB, Yin S, Wu Y. Discovery and modelling studies of natural ingredients from Gaultheria yunnanensis (FRANCH.) against phosphodiesterase-4. Eur J Med Chem 2015; 114:134-40. [PMID: 26978121 DOI: 10.1016/j.ejmech.2015.12.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Revised: 11/30/2015] [Accepted: 12/01/2015] [Indexed: 01/07/2023]
Abstract
Phosphodiesterase-4 (PDE4) is an anti-inflammatory target for treatment of asthma and chronic obstructive pulmonary disease (COPD). Here, we report the isolation and characterization of 13 compounds (G1-G13) by bioassay-guided fractionation of the ethyl acetate extraction of Gaultheria yunnanensis (FRANCH.), one of which pentacyclic triterpene (G1) has never been reported. Four of them (G1, G2, G4, and G5) inhibit PDE4 with the IC50 values < 20 μM and G1 is the most potent ingredient with an IC50 of 245 nM and moderate selectivity over other PDE families. Molecular dynamics simulations suggest that G1 forms a hydrogen bond with Asn362, in addition to the hydrogen bond with Gln369 and π-π interactions with Phe372, which are commonly observed in the binding of most PDE4 inhibitors. The calculated binding free energies for the interactions of PDE4-G1 and PDE4-G2 are -19.4 and -18.8 kcal/mol, in consistence with the bioassay that G1 and G2 have IC50 of 245 nM and 542 nM, respectively. The modelling results of these active compounds may aid the rational design of novel PDE4 inhibitors as anti-inflammatory agents.
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Affiliation(s)
- Ying-Hong Cai
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China
| | - Yanqiong Guo
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China
| | - Zhe Li
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China
| | - Deyang Wu
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China
| | - Xiruo Li
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China
| | - Heng Zhang
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China
| | - Junjie Yang
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China
| | - Heng Lu
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China
| | - Zhaowei Sun
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China
| | - Hai-Bin Luo
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China
| | - Sheng Yin
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China.
| | - Yinuo Wu
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China.
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102
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Rayón VM, Valdés H, Díaz N, Suárez D. Monoligand Zn(II) Complexes: Ab Initio Benchmark Calculations and Comparison with Density Functional Theory Methodologies. J Chem Theory Comput 2015; 4:243-56. [PMID: 26620656 DOI: 10.1021/ct700229e] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A systematic theoretical study on several models of Zn(II) complexes has been carried out employing both ab initio correlated wave function and density functional methods. The performance of five different functionals namely PW91, PBE, B3LYP, MPWLYP1M, and TPSS in the prediction of metal-ligand bond distances, binding energies, and proton affinities has been assessed comparing the results to those obtained with the MP2 and CCSD(T) wave function methodologies. Several basis sets ranging from double-ζ up to quintuple-ζ quality have been used, including the recently developed all-electron correlation consistent basis sets for zinc. It is shown that all the tested functionals overestimate both the metal-ligand bond distances and the binding energies, being that the B3LYP and TPSS functionals are the ones that perform the best. An analysis of the metal-ligand interaction energy shows that induction and charge-transfer effects play a prominent role in the bonding of these systems, even for those complexes with the less polarizable ligands. This finding highlights the importance of a correct description of the polarization of the monomers' charge densities by any theoretical method which aims to be applied to the study of Zn(II) complexes.
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Affiliation(s)
- Víctor M Rayón
- Departamento de Química Física y Química Inorgánica, Facultad de Ciencias, Universidad de Valladolid, 47005 Valladolid, Spain, Center for Biomolecules and Complex Molecular Systems, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 16610 Prague 6, Czech Republic, and Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, 33007 Oviedo, Spain
| | - Haydee Valdés
- Departamento de Química Física y Química Inorgánica, Facultad de Ciencias, Universidad de Valladolid, 47005 Valladolid, Spain, Center for Biomolecules and Complex Molecular Systems, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 16610 Prague 6, Czech Republic, and Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, 33007 Oviedo, Spain
| | - Natalia Díaz
- Departamento de Química Física y Química Inorgánica, Facultad de Ciencias, Universidad de Valladolid, 47005 Valladolid, Spain, Center for Biomolecules and Complex Molecular Systems, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 16610 Prague 6, Czech Republic, and Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, 33007 Oviedo, Spain
| | - Dimas Suárez
- Departamento de Química Física y Química Inorgánica, Facultad de Ciencias, Universidad de Valladolid, 47005 Valladolid, Spain, Center for Biomolecules and Complex Molecular Systems, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 16610 Prague 6, Czech Republic, and Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, 33007 Oviedo, Spain
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103
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Sjøli S, Nuti E, Camodeca C, Bilto I, Rossello A, Winberg JO, Sylte I, Adekoya OA. Synthesis, experimental evaluation and molecular modelling of hydroxamate derivatives as zinc metalloproteinase inhibitors. Eur J Med Chem 2015; 108:141-153. [PMID: 26638045 DOI: 10.1016/j.ejmech.2015.11.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 11/09/2015] [Accepted: 11/13/2015] [Indexed: 10/22/2022]
Abstract
Enzymes of the M4 family of zinc-metalloproteinases are virulence factors secreted from gram-positive or gram-negative bacteria, and putative drug targets in the treatment of bacterial infections. In order to have a therapeutic value such inhibitors should not interfere with endogenous zinc-metalloproteinases. In the present study we have synthesised a series of hydroxamate derivatives and validated the compounds as inhibitors of the M4 enzymes thermolysin and pseudolysin, and the endogenous metalloproteinases ADAM-17, MMP-2 and MMP-9 using experimental binding studies and molecular modelling. In general, the compounds are stronger inhibitors of the MMPs than of the M4 enzymes, however, an interesting exception is LM2. The compounds bound stronger to pseudolysin than to thermolysin, and the molecular modelling studies showed that occupation of the S2(') subpocket by an aromatic group is favourable for strong interactions with pseudolysin.
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Affiliation(s)
- Stian Sjøli
- Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, NO-9037 Tromsø, Norway
| | - Elisa Nuti
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Caterina Camodeca
- Division of Immunology, Transplants and Infectious Diseases, San Raffaele Scientific Institute, Milan, Italy
| | - Irina Bilto
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, NO-9037 Tromsø, Norway
| | - Armando Rossello
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Jan-Olof Winberg
- Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, NO-9037 Tromsø, Norway
| | - Ingebrigt Sylte
- Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, NO-9037 Tromsø, Norway.
| | - Olayiwola A Adekoya
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, NO-9037 Tromsø, Norway
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104
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Fadouloglou VE, Stavrakoudis A, Bouriotis V, Kokkinidis M, Glykos NM. Molecular Dynamics Simulations of BcZBP, A Deacetylase from Bacillus cereus: Active Site Loops Determine Substrate Accessibility and Specificity. J Chem Theory Comput 2015; 5:3299-311. [PMID: 26602510 DOI: 10.1021/ct9002338] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BcZBP is an LmbE-like, homohexameric, zinc-dependent deacetylase from the opportunistic pathogen Bacillus cereus with three, thus far uncharacterized, homologues in B. anthracis. Although its specific substrate is still unknown, the enzyme has been shown to preferentially deacetylate N-acetylglucosamine and diacetylchitobiose via an active site based on a zinc-binding motif of the type HXDDXnH. In the crystal structure, the active site is located at a deep and partially blocked cleft formed at the interface between monomers related by the molecular 3-fold axis, although the major, in structural terms, building block of the enzyme is not the trimer, but the intertwined dimer. Here, we report results from a 50 ns molecular dynamics simulation of BcZBP in explicit solvent with full electrostatics and show that (i) the view of the intertwined dimer as the major structural and functional building block of this class of hexameric enzymes is possibly an oversimplification of the rather complex dynamics observed in the simulation, (ii) the most mobile (with respect to their atomic fluctuations) parts of the structure coincide with three surface loops surrounding the active site, and (iii) these mobile loops define the active site's accessibility, and may be implicated in the determination of the enzyme's specificity.
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Affiliation(s)
- Vasiliki E Fadouloglou
- Department of Molecular Biology and Genetics, Democritus University of Thrace, University campus, GR-68100, Alexandroupolis, Greece, Department of Biology, University of Crete, PO Box 2208, GR-71409, Heraklion, Crete, Greece, Department of Economics, University of Ioannina, GR-45110, Ioannina, Greece, and Institute of Molecular Biology and Biotechnology (IMBB), PO Box 1527, GR-71110, Heraklion, Crete, Greece
| | - Athanassios Stavrakoudis
- Department of Molecular Biology and Genetics, Democritus University of Thrace, University campus, GR-68100, Alexandroupolis, Greece, Department of Biology, University of Crete, PO Box 2208, GR-71409, Heraklion, Crete, Greece, Department of Economics, University of Ioannina, GR-45110, Ioannina, Greece, and Institute of Molecular Biology and Biotechnology (IMBB), PO Box 1527, GR-71110, Heraklion, Crete, Greece
| | - Vassilis Bouriotis
- Department of Molecular Biology and Genetics, Democritus University of Thrace, University campus, GR-68100, Alexandroupolis, Greece, Department of Biology, University of Crete, PO Box 2208, GR-71409, Heraklion, Crete, Greece, Department of Economics, University of Ioannina, GR-45110, Ioannina, Greece, and Institute of Molecular Biology and Biotechnology (IMBB), PO Box 1527, GR-71110, Heraklion, Crete, Greece
| | - Michael Kokkinidis
- Department of Molecular Biology and Genetics, Democritus University of Thrace, University campus, GR-68100, Alexandroupolis, Greece, Department of Biology, University of Crete, PO Box 2208, GR-71409, Heraklion, Crete, Greece, Department of Economics, University of Ioannina, GR-45110, Ioannina, Greece, and Institute of Molecular Biology and Biotechnology (IMBB), PO Box 1527, GR-71110, Heraklion, Crete, Greece
| | - Nicholas M Glykos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, University campus, GR-68100, Alexandroupolis, Greece, Department of Biology, University of Crete, PO Box 2208, GR-71409, Heraklion, Crete, Greece, Department of Economics, University of Ioannina, GR-45110, Ioannina, Greece, and Institute of Molecular Biology and Biotechnology (IMBB), PO Box 1527, GR-71110, Heraklion, Crete, Greece
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105
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Gong W, Wu R, Zhang Y. Thiol versus hydroxamate as zinc binding group in HDAC inhibition: An ab initio QM/MM molecular dynamics study. J Comput Chem 2015; 36:2228-35. [PMID: 26452222 DOI: 10.1002/jcc.24203] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 07/17/2015] [Accepted: 08/30/2015] [Indexed: 12/21/2022]
Abstract
Zinc-dependent histone deacetylases (HDACs) play a critical role in transcriptional repression and gene silencing, and are among the most attractive targets for the development of new therapeutics against cancer and various other diseases. Two HDAC inhibitors have been approved by FDA as anti-cancer drugs: one is SAHA whose hydroxamate is directly bound to zinc, the other is FK228 whose active form may use thiol as the zinc binding group. In spite of extensive studies, it remains to be ambiguous regarding how thiol and hydroxamate are bound to the zinc active site of HDACs. In this work, our computational approaches center on Born-Oppenheimer ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics with umbrella sampling, which allow for modeling of the zinc active site with reasonable accuracy while properly including dynamics and effects of protein environment. Meanwhile, an improved short-long effective function (SLEF2) to describe non-bonded interactions between zinc and other atoms has been employed in initial MM equilibrations. Our ab initio QM/MM MD simulations have confirmed that hydroxamate is neutral when it is bound to HDAC8, and found that thiol is deprotonated when directly bound to zinc in the HDAC active site. By comparing thiol and hydroxamate, our results elucidated the differences in their binding environment in the HDAC active sites, and emphasized the importance of the linker design to achieve more specific binding toward class IIa HDACs.
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Affiliation(s)
- Wenjing Gong
- Department of Chemistry, New York University, New York, New York, 10003
| | - Ruibo Wu
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, New York, 10003.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, 200062, China
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106
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Elucidating the Role of Residue 67 in IMP-Type Metallo-β-Lactamase Evolution. Antimicrob Agents Chemother 2015; 59:7299-307. [PMID: 26369960 DOI: 10.1128/aac.01651-15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 09/06/2015] [Indexed: 02/07/2023] Open
Abstract
Antibiotic resistance in bacteria is ever changing and adapting, as once-novel β-lactam antibiotics are losing their efficacy, primarily due to the production of β-lactamases. Metallo-β-lactamases (MBLs) efficiently inactivate a broad range of β-lactam antibiotics, including carbapenems, and are often coexpressed with other antibacterial resistance factors. The rapid dissemination of MBLs and lack of novel antibacterials pose an imminent threat to global health. In an effort to better counter these resistance-conferring β-lactamases, an investigation of their natural evolution and resulting substrate specificity was employed. In this study, we elucidated the effects of different amino acid substitutions at position 67 in IMP-type MBLs on the ability to hydrolyze and confer resistance to a range of β-lactam antibiotics. Wild-type β-lactamases IMP-1 and IMP-10 and mutants IMP-1-V67A and IMP-1-V67I were characterized biophysically and biochemically, and MICs for Escherichia coli cells expressing these enzymes were determined. We found that all variants exhibited catalytic efficiencies (kcat/Km) equal to or higher than that of IMP-1 against all tested β-lactams except penicillins, against which IMP-1 and IMP-1-V67I showed the highest kcat/Km values. The substrate-specific effects of the different amino acid substitutions at position 67 are discussed in light of their side chain structures and possible interactions with the substrates. Docking calculations were employed to investigate interactions between different side chains and an inhibitor used as a β-lactam surrogate. The differences in binding affinities determined experimentally and computationally seem to be governed by hydrophobic interactions between residue 67 and the inhibitor and, by inference, the β-lactam substrates.
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107
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Huang YMM, Huber G, McCammon JA. Electrostatic steering enhances the rate of cAMP binding to phosphodiesterase: Brownian dynamics modeling. Protein Sci 2015; 24:1884-9. [PMID: 26346301 DOI: 10.1002/pro.2794] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 08/20/2015] [Accepted: 08/24/2015] [Indexed: 01/18/2023]
Abstract
Signaling in cells often involves co-localization of the signaling molecules. Most experimental evidence has shown that intracellular compartmentalization restricts the range of action of the second messenger, 3'-5'-cyclic adenosine monophosphate (cAMP), which is degraded by phosphodiesterases (PDEs). The objective of this study is to understand the details of molecular encounter that may play a role in efficient operation of the cAMP signaling apparatus. The results from electrostatic potential calculations and Brownian dynamics simulations suggest that positive potential of the active site from PDE enhances capture of diffusing cAMP molecules. This electrostatic steering between cAMP and the active site of a PDE plays a major role in the enzyme-substrate encounter, an effect that may be of significance in sequestering cAMP released from a nearby binding site or in attracting more freely diffusing cAMP molecules.
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Affiliation(s)
- Yu-ming M Huang
- Department of Pharmacology, University of California, San Diego, La Jolla, California, 92093
| | - Gary Huber
- Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California, 92093
| | - J Andrew McCammon
- Department of Pharmacology, University of California, San Diego, La Jolla, California, 92093.,Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California, 92093.,Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, 92093
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108
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Panteva MT, GiambaȈsu GM, York DM. Comparison of structural, thermodynamic, kinetic and mass transport properties of Mg(2+) ion models commonly used in biomolecular simulations. J Comput Chem 2015; 36:970-82. [PMID: 25736394 PMCID: PMC4409555 DOI: 10.1002/jcc.23881] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 01/17/2015] [Accepted: 02/08/2015] [Indexed: 01/09/2023]
Abstract
The prevalence of Mg(2+) ions in biology and their essential role in nucleic acid structure and function has motivated the development of various Mg(2+) ion models for use in molecular simulations. Currently, the most widely used models in biomolecular simulations represent a nonbonded metal ion as an ion-centered point charge surrounded by a nonelectrostatic pairwise potential that takes into account dispersion interactions and exchange effects that give rise to the ion's excluded volume. One strategy toward developing improved models for biomolecular simulations is to first identify a Mg(2+) model that is consistent with the simulation force fields that closely reproduces a range of properties in aqueous solution, and then, in a second step, balance the ion-water and ion-solute interactions by tuning parameters in a pairwise fashion where necessary. The present work addresses the first step in which we compare 17 different nonbonded single-site Mg(2+) ion models with respect to their ability to simultaneously reproduce structural, thermodynamic, kinetic and mass transport properties in aqueous solution. None of the models based on a 12-6 nonelectrostatic nonbonded potential was able to reproduce the experimental radial distribution function, solvation free energy, exchange barrier and diffusion constant. The models based on a 12-6-4 potential offered improvement, and one model in particular, in conjunction with the SPC/E water model, performed exceptionally well for all properties. The results reported here establish useful benchmark calculations for Mg(2+) ion models that provide insight into the origin of the behavior in aqueous solution, and may aid in the development of next-generation models that target specific binding sites in biomolecules.
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Affiliation(s)
- Maria T. Panteva
- Center for Integrative Proteomics Research, BioMaPS Institute and Department of Chemistry & Chemical Biology, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ 08854-8076, USA
| | - George M. GiambaȈsu
- Center for Integrative Proteomics Research, BioMaPS Institute and Department of Chemistry & Chemical Biology, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ 08854-8076, USA
| | - Darrin M. York
- Center for Integrative Proteomics Research, BioMaPS Institute and Department of Chemistry & Chemical Biology, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ 08854-8076, USA
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109
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Li P, Song LF, Merz KM. Systematic Parameterization of Monovalent Ions Employing the Nonbonded Model. J Chem Theory Comput 2015; 11:1645-57. [PMID: 26574374 DOI: 10.1021/ct500918t] [Citation(s) in RCA: 256] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Monovalent ions play fundamental roles in many biological processes in organisms. Modeling these ions in molecular simulations continues to be a challenging problem. The 12-6 Lennard-Jones (LJ) nonbonded model is widely used to model monovalent ions in classical molecular dynamics simulations. A lot of parameterization efforts have been reported for these ions with a number of experimental end points. However, some reported parameter sets do not have a good balance between the two Lennard-Jones parameters (the van der Waals (VDW) radius and potential well depth), which affects their transferability. In the present work, via the use of a noble gas curve we fitted in former work (J. Chem. Theory Comput. 2013, 9, 2733), we reoptimized the 12-6 LJ parameters for 15 monovalent ions (11 positive and 4 negative ions) for three extensively used water models (TIP3P, SPC/E, and TIP4P(EW)). Since the 12-6 LJ nonbonded model performs poorly in some instances for these ions, we have also parameterized the 12-6-4 LJ-type nonbonded model (J. Chem. Theory Comput. 2014, 10, 289) using the same three water models. The three derived parameter sets focused on reproducing the hydration free energies (the HFE set) and the ion-oxygen distance (the IOD set) using the 12-6 LJ nonbonded model and the 12-6-4 LJ-type nonbonded model (the 12-6-4 set) overall give improved results. In particular, the final parameter sets showed better agreement with quantum mechanically calculated VDW radii and improved transferability to ion-pair solutions when compared to previous parameter sets.
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Affiliation(s)
- Pengfei Li
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan 48824-1322, United States
| | - Lin Frank Song
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan 48824-1322, United States
| | - Kenneth M Merz
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan 48824-1322, United States
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110
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Dyakonova ES, Koval VV, Lomzov AA, Ishchenko AA, Fedorova OS. The role of His-83 of yeast apurinic/apyrimidinic endonuclease Apn1 in catalytic incision of abasic sites in DNA. Biochim Biophys Acta Gen Subj 2015; 1850:1297-309. [PMID: 25766873 DOI: 10.1016/j.bbagen.2015.03.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 02/16/2015] [Accepted: 03/04/2015] [Indexed: 10/23/2022]
Abstract
BACKGROUND The apurinic/apyrimidinic (AP) endonuclease Apn1 from Saccharomyces cerevisiae is a key enzyme involved in the base excision repair (BER) at the cleavage stage of abasic sites (AP sites) in DNA. The crystal structure of Apn1 from S. cerevisiae is unresolved. Based on its high amino acid homology to Escherichia coli Endo IV, His-83 is believed to coordinate one of three Zn2+ ions in Apn1's active site similar to His-69 in Endo IV. Substituting His-83 with Ala is proposed to decrease the AP endonuclease activity of Apn1 owing to weak coordination of Zn2+ ions involved in enzymatic catalysis. METHODS The kinetics of recognition, binding, and incision of DNA substrates with the H83A Apn1 mutant was investigated. The stopped-flow method detecting fluorescence intensity changes of 2-aminopurine (2-aPu) was used to monitor the conformational dynamics of DNA at pre-steady-state conditions. RESULTS We found substituting His-83 with Ala influenced catalytic complex formation and further incision of the damaged DNA strand. The H83A Apn1 catalysis depends not only on the location of the mismatch relative to the abasic site in DNA, but also on the nature of damage. CONCLUSIONS We consider His-83 properly coordinates the active site Zn2+ ion playing a crucial role in catalytic incision stage. Our data prove suppressed enzymatic activity of H83A Apn1 results from the reduced number of active site Zn2+ ions. GENERAL SIGNIFICANCE Our study provides insights into mechanistic specialty of AP site repair by yeast AP endonuclease Apn1 of Endo IV family, which members are not found in mammals, but are present in many microorganisms. The results will provide useful guidelines for design of new anti-fungal and anti-malarial agents.
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Affiliation(s)
- Elena S Dyakonova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk, 630090, Russian Federation
| | - Vladimir V Koval
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk, 630090, Russian Federation; Novosibirsk State University, Pirogov St., 2, Novosibirsk, 630090, Russian Federation
| | - Alexander A Lomzov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk, 630090, Russian Federation; Novosibirsk State University, Pirogov St., 2, Novosibirsk, 630090, Russian Federation
| | - Alexander A Ishchenko
- Groupe «Réparation de l'ADN», Université Paris-Sud XI, UMR8200 CNRS, Institut Gustave Roussy, Villejuif Cedex F-94805, France
| | - Olga S Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk, 630090, Russian Federation; Novosibirsk State University, Pirogov St., 2, Novosibirsk, 630090, Russian Federation.
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111
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Li W, Wang J, Zhang J, Wang W. Molecular simulations of metal-coupled protein folding. Curr Opin Struct Biol 2015; 30:25-31. [DOI: 10.1016/j.sbi.2014.11.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 11/24/2014] [Accepted: 11/24/2014] [Indexed: 01/22/2023]
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112
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Joh NH, Wang T, Bhate MP, Acharya R, Wu Y, Grabe M, Hong M, Grigoryan G, DeGrado WF. De novo design of a transmembrane Zn²⁺-transporting four-helix bundle. Science 2015; 346:1520-4. [PMID: 25525248 DOI: 10.1126/science.1261172] [Citation(s) in RCA: 225] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The design of functional membrane proteins from first principles represents a grand challenge in chemistry and structural biology. Here, we report the design of a membrane-spanning, four-helical bundle that transports first-row transition metal ions Zn(2+) and Co(2+), but not Ca(2+), across membranes. The conduction path was designed to contain two di-metal binding sites that bind with negative cooperativity. X-ray crystallography and solid-state and solution nuclear magnetic resonance indicate that the overall helical bundle is formed from two tightly interacting pairs of helices, which form individual domains that interact weakly along a more dynamic interface. Vesicle flux experiments show that as Zn(2+) ions diffuse down their concentration gradients, protons are antiported. These experiments illustrate the feasibility of designing membrane proteins with predefined structural and dynamic properties.
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Affiliation(s)
- Nathan H Joh
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Tuo Wang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Manasi P Bhate
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Rudresh Acharya
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, Odisha, India
| | - Yibing Wu
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Michael Grabe
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Gevorg Grigoryan
- Department of Computer Science and Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA.
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA.
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113
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Wang B, Opron K, Burton ZF, Cukier RI, Feig M. Five checkpoints maintaining the fidelity of transcription by RNA polymerases in structural and energetic details. Nucleic Acids Res 2014; 43:1133-46. [PMID: 25550432 PMCID: PMC4333413 DOI: 10.1093/nar/gku1370] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Transcriptional fidelity, which prevents the misincorporation of incorrect nucleoside monophosphates in RNA, is essential for life. Results from molecular dynamics (MD) simulations of eukaryotic RNA polymerase (RNAP) II and bacterial RNAP with experimental data suggest that fidelity may involve as many as five checkpoints. Using MD simulations, the effects of different active site NTPs in both open and closed trigger loop (TL) structures of RNAPs are compared. Unfavorable initial binding of mismatched substrates in the active site with an open TL is proposed to be the first fidelity checkpoint. The leaving of an incorrect substrate is much easier than a correct one energetically from the umbrella sampling simulations. Then, the closing motion of the TL, required for catalysis, is hindered by the presence of mismatched NTPs. Mismatched NTPs also lead to conformational changes in the active site, which perturb the coordination of magnesium ions and likely affect the ability to proceed with catalysis. This step appears to be the most important checkpoint for deoxy-NTP discrimination. Finally, structural perturbations in the template DNA and the nascent RNA in the presence of mismatches likely hinder nucleotide addition and provide the structural foundation for backtracking followed by removing erroneously incorporated nucleotides during proofreading.
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Affiliation(s)
- Beibei Wang
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Kristopher Opron
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Zachary F Burton
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Robert I Cukier
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Michael Feig
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
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114
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Li Z, Wu Y, Feng LJ, Wu R, Luo HB. Ab Initio QM/MM Study Shows a Highly Dissociated SN2 Hydrolysis Mechanism for the cGMP-Specific Phosphodiesterase-5. J Chem Theory Comput 2014; 10:5448-57. [DOI: 10.1021/ct500761d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Zhe Li
- School of Pharmaceutical
Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Yinuo Wu
- School of Pharmaceutical
Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Ling-Jun Feng
- School of Pharmaceutical
Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Ruibo Wu
- School of Pharmaceutical
Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Hai-Bin Luo
- School of Pharmaceutical
Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
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115
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Chaskar P, Zoete V, Röhrig UF. Toward On-The-Fly Quantum Mechanical/Molecular Mechanical (QM/MM) Docking: Development and Benchmark of a Scoring Function. J Chem Inf Model 2014; 54:3137-52. [DOI: 10.1021/ci5004152] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Prasad Chaskar
- Swiss Institute of Bioinformatics, Molecular Modeling Group,
Quartier Sorge, Bâtiment
Génopode, CH-1015 Lausanne, Switzerland
| | - Vincent Zoete
- Swiss Institute of Bioinformatics, Molecular Modeling Group,
Quartier Sorge, Bâtiment
Génopode, CH-1015 Lausanne, Switzerland
| | - Ute F. Röhrig
- Swiss Institute of Bioinformatics, Molecular Modeling Group,
Quartier Sorge, Bâtiment
Génopode, CH-1015 Lausanne, Switzerland
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116
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Li Z, Lu X, Feng LJ, Gu Y, Li X, Wu Y, Luo HB. Molecular dynamics-based discovery of novel phosphodiesterase-9A inhibitors with non-pyrazolopyrimidinone scaffolds. MOLECULAR BIOSYSTEMS 2014; 11:115-25. [PMID: 25328054 DOI: 10.1039/c4mb00389f] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Phosphodiesterase-9A (PDE9A) is a promising therapeutic target for the treatment of diabetes and Alzheimer's disease (AD). The Pfizer PDE9A inhibitor PF-04447943 has completed Phase II clinical trials in subjects with mild to moderate AD in 2013. However, most of the reported PDE9A inhibitors share the same scaffold as pyrazolopyrimidinone, which lacks structural diversity and is unfavorable for the development of novel PDE9A inhibitors. In the present study, a combinatorial method including pharmacophores, molecular docking, molecular dynamics simulations, binding free energy calculations, and bioassay was used to discover novel PDE9A inhibitors with new scaffolds rather than pyrazolopyrimidinones from the SPECS database containing about 200,000 compounds. As a result, 15 hits out of 29 molecules (a hit rate of 52%) with five novel scaffolds were identified to be PDE9A inhibitors with inhibitory affinities no more than 50 μM to enrich the structural diversity, different from the pyrazolopyrimidinone-derived family. The high hit ratio of 52% for this virtual screening method indicated that the combinatorial method is a good compromise between computational cost and accuracy. Binding pattern analyses indicate that those hits with non-pyrazolopyrimidinone scaffolds can bind the same active site pocket of PDE9A as classical PDE9A inhibitors. In addition, structural modification of compound AG-690/40135604 (IC50=8.0 μM) led to a new one, 16, with an improved inhibitory affinity of 2.1 μM as expected. The five novel scaffolds discovered in the present study can be used for the rational design of PDE9A inhibitors with higher affinities.
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Affiliation(s)
- Zhe Li
- School of Pharmaceutical Sciences, SunYat-Sen University, Guangzhou 510006, P. R. China.
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117
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Adekoya OA, Sjøli S, Wuxiuer Y, Bilto I, Marques SM, Santos MA, Nuti E, Cercignani G, Rossello A, Winberg JO, Sylte I. Inhibition of pseudolysin and thermolysin by hydroxamate-based MMP inhibitors. Eur J Med Chem 2014; 89:340-8. [PMID: 25462250 DOI: 10.1016/j.ejmech.2014.10.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 09/30/2014] [Accepted: 10/04/2014] [Indexed: 11/24/2022]
Abstract
In the present study, we have investigated the inhibition of thermolysin and pseudolysin by a series of compounds previously identified as matrix metalloproteinase (MMP) inhibitors using experimental binding studies and theoretical calculations. The experimental studies showed that some of the compounds were able to inhibit thermolysin and pseudolysin in the low μM range. The studies revealed that, in general, the compounds bound in the order MMPs > pseudolysin > thermolysin, and the strongest pseudolysin and thermolysin binders were compounds 8-12. Furthermore, compounds 8 and 9 were unique in that they bound much stronger to the two bacterial enzymes than to the MMPs. The docking calculations suggested that the phenyl group of the strongest binders (compounds 8 and 9) occupy the S2(')-subpocket, while a second ring system occupy the S1-subpocket in both thermolysin and pseudolysin. When the compounds possess two ring systems, the largest and most electron rich ring system seems to occupy the S1-subpocket.
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Affiliation(s)
- Olayiwola A Adekoya
- Department of Pharmacy, Faculty of Health Sciences, UiT - The Arctic University of Norway, NO-9037 Tromsø, Norway.
| | - Stian Sjøli
- Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, NO-9037 Tromsø, Norway
| | - Yimingjiang Wuxiuer
- Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, NO-9037 Tromsø, Norway
| | - Irina Bilto
- Department of Pharmacy, Faculty of Health Sciences, UiT - The Arctic University of Norway, NO-9037 Tromsø, Norway
| | - Sérgio M Marques
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal
| | - M Amélia Santos
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal
| | - Elisa Nuti
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Giovanni Cercignani
- Dipartimento di Biologia, Unità di Biochimica, Università di Pisa, Via San Zeno 51, 56127 Pisa, Italy
| | - Armando Rossello
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Jan-Olof Winberg
- Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, NO-9037 Tromsø, Norway
| | - Ingebrigt Sylte
- Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, NO-9037 Tromsø, Norway.
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118
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Lahiri S, Panja A, Dasgupta D. Association of a Zn(2+) containing metallo β-lactamase with the anticancer antibiotic mithramycin. J Inorg Biochem 2014; 142:75-83. [PMID: 25450021 DOI: 10.1016/j.jinorgbio.2014.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Revised: 10/03/2014] [Accepted: 10/03/2014] [Indexed: 12/13/2022]
Abstract
Pathogenic bacteria that are resistant to β-lactam antibiotics mostly utilize serine β-lactamases to degrade the antibiotics. Current studies have shown that different subclasses of metallo β-lactamases (E[MBL]) are involved in the defense mechanism of drug resistant bacteria. Here we report that the Zn(2+) containing subclass B1 E[MBL] from Bacillus cereus binds to a naturally occurring anti-cancer drug mithramycin (MTR). Spectroscopic (CD and fluorescence) and isothermal titration calorimetry studies show that MTR forms a high affinity complex with the Zn(2+) ion containing E[MBL]. Abolished interaction of MTR with apo E[MBL] suggests that the formation of this high affinity complex occurs due to the potential of MTR to bind bivalent metal ions like Zn(2+). Furthermore, CD spectroscopy, dynamic light scattering and differential scanning calorimetry studies indicate that the strong association with sub-micromolar dissociation constant leads to an alteration in the enzyme conformation at both secondary and tertiary structural levels. The enzyme activity decreases as a consequence to this conformational disruption arising from the formation of a ternary complex involving MTR, catalytic Zn(2+) and the enzyme. Our results suggest that the naturally occurring antibiotic MTR, a generic drug, has the potential as an E[MBL] inhibitor.
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Affiliation(s)
- Shibojyoti Lahiri
- Biophysics Division, Saha Institute of Nuclear Physics, 1/AF Sector-1, Bidhannagar, Kolkata 700064, India.
| | - Amrita Panja
- Biophysics Division, Saha Institute of Nuclear Physics, 1/AF Sector-1, Bidhannagar, Kolkata 700064, India
| | - Dipak Dasgupta
- Biophysics Division, Saha Institute of Nuclear Physics, 1/AF Sector-1, Bidhannagar, Kolkata 700064, India.
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119
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Wang H, Geng L, Chen BZ, Ji M. Computational study on the molecular mechanisms of drug resistance of Narlaprevir due to V36M, R155K, V36M+R155K, T54A, and A156T mutations of HCV NS3/4A protease. Biochem Cell Biol 2014; 92:357-69. [DOI: 10.1139/bcb-2014-0039] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Narlaprevir is a novel NS3/4A protease inhibitor of hepatitis C virus (HCV), and it has been tested in a phase II clinical trial recently. However, distinct drug-resistance of Narlaprevir has been discovered. In our study, the molecular mechanisms of drug-resistance of Narlaprevir due to the mutations V36M, R155K, V36M+R155K, T54A, and A156T of NS3/4A protease have been investigated by molecular dynamics (MD) simulations, free energy calculations, and free energy decomposition analysis. The predicted binding free energies of Narlaprevir towards the wild-type and five mutants show that the mutations V36M, R155K, and T54A lead to low-level drug resistance and the mutations V36M+R155K and A156T lead to high-level drug resistance, which is consistent with the experimental data. The analysis of the individual energy terms indicates that the van der Waals contribution is important for distinguishing the binding affinities of these six complexes. These findings again show that the combination of different molecular modeling techniques is an efficient way to interpret the molecular mechanism of drug-resistance. Our work mainly elaborates the molecular mechanism of drug-resistance of Narlaprevir and further provides valuable information for developing novel, safer, and more potent HCV antiviral drugs in the near future.
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Affiliation(s)
- Huiqun Wang
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Yuquan Road 19A, 100049 Beijing, P.R. China
| | - Lingling Geng
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Yuquan Road 19A, 100049 Beijing, P.R. China
| | - Bo-Zhen Chen
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Yuquan Road 19A, 100049 Beijing, P.R. China
| | - Mingjuan Ji
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Yuquan Road 19A, 100049 Beijing, P.R. China
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120
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Abstract
Nicotinamidase (Pnc1) is a member of Zn-dependent amidohydrolases that hydrolyzes nicotinamide (NAM) to nicotinic acid (NA), which is a key step in the salvage pathway of NAD(+) biosynthesis. In this paper, the catalytic mechanism of Pnc1 has been investigated by using a combined quantum-mechanical/molecular-mechanical (QM/MM) approach based on the recently obtained crystal structure of Pnc1. The reaction pathway, the detail of each elementary step, the energetics of the whole catalytic cycle, and the roles of key residues and Zn-binding site are illuminated. Our calculation results indicate that the catalytic water molecule comes from the bulk solvent, which is then deprotonated by residue D8. D8 functions as a proton transfer station between C167 and NAM, while the activated C167 serves as the nucleophile. The residue K122 only plays a role in stabilizing intermediates and transition states. The oxyanion hole formed by the amide backbone nitrogen atoms of A163 and C167 has the function to stabilize the hydroxyl anion of nicotinamide. The Zn-binding site rather than a single Zn(2+) ion acts as a Lewis acid to influence the reaction. Two elementary steps, the activation of C167 in the deamination process and the decomposition of catalytic water in the hydrolysis process, correspond to the large energy barriers of 25.7 and 28.1 kcal mol(-1), respectively, meaning that both of them contribute a lot to the overall reaction barrier. Our results may provide useful information for the design of novel and efficient Pnc1 inhibitors and related biocatalytic applications.
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Affiliation(s)
- Xiang Sheng
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
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121
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Yoshimori A, Oyama T, Takahashi S, Abe H, Kamiya T, Abe T, Tanuma SI. Structure-activity relationships of the thujaplicins for inhibition of human tyrosinase. Bioorg Med Chem 2014; 22:6193-200. [PMID: 25288494 DOI: 10.1016/j.bmc.2014.08.027] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 08/20/2014] [Accepted: 08/21/2014] [Indexed: 11/19/2022]
Abstract
Tyrosinase inhibitors have become increasingly critical agents in cosmetic, agricultural, and medicinal products. Although a large number of tyrosinase inhibitors have been reported, almost all the inhibitors were unfortunately evaluated by using commercial available mushroom tyrosinase. Here, we examined the inhibitory effects of three isomers of thujaplicin (α, β, and γ) on human tyrosinase and analyzed their binding modes using homology model and docking studies. As the results, γ-thujaplicin was found to strongly inhibit human tyrosinase with the IC50 of 1.15 μM, extremely superior to a well-known tyrosinase inhibitor kojic acid (IC50 = 571.17 μM). MM-GB/SA binding free energy decomposition analyses suggested that the potent inhibitory activity of γ-thujaplicin may be due to the interactions with His367, Ile368, and Val377 (hot spot amino acid residues) in human tyrosinase. Furthermore, the binding mode of α-thujaplicin indicated that Val377 and Ser380 may cause van der Waals clashes with the isopropyl group of α-thujaplicin. These results provide a novel structural insight into the hot spot of human tyrosinase for the specific binding of γ-thujaplicin and a way to optimize not only thujaplicins but also other lead compounds as specific inhibitors for human tyrosinase in a rational manner.
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Affiliation(s)
- Atsushi Yoshimori
- Institute for Theoretical Medicine, Inc., 4259-3 Nagatsuda-cho, Midori-ku, Yokohama 226-8510, Japan
| | - Takahiro Oyama
- Hinoki Shinyaku Co., Ltd, 9-6 Nibancho, Chiyoda-ku, Tokyo 102-0084, Japan
| | - Satoshi Takahashi
- Institute for Theoretical Medicine, Inc., 4259-3 Nagatsuda-cho, Midori-ku, Yokohama 226-8510, Japan
| | - Hideaki Abe
- Hinoki Shinyaku Co., Ltd, 9-6 Nibancho, Chiyoda-ku, Tokyo 102-0084, Japan
| | - Takanori Kamiya
- Hinoki Shinyaku Co., Ltd, 9-6 Nibancho, Chiyoda-ku, Tokyo 102-0084, Japan
| | - Takehiko Abe
- Hinoki Shinyaku Co., Ltd, 9-6 Nibancho, Chiyoda-ku, Tokyo 102-0084, Japan
| | - Sei-ichi Tanuma
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki Noda, Chiba 278-8510, Japan; Genome and Drug Research Center, Tokyo University of Science, 2641 Yamazaki Noda, Chiba 278-8510, Japan.
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122
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Lu X, Gaus M, Elstner M, Cui Q. Parametrization of DFTB3/3OB for magnesium and zinc for chemical and biological applications. J Phys Chem B 2014; 119:1062-82. [PMID: 25178644 PMCID: PMC4306495 DOI: 10.1021/jp506557r] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
We report the parametrization of
the approximate density functional
theory, DFTB3, for magnesium and zinc for chemical and biological
applications. The parametrization strategy follows that established
in previous work that parametrized several key main group elements
(O, N, C, H, P, and S). This 3OB set of parameters can thus be used
to study many chemical and biochemical systems. The parameters are
benchmarked using both gas-phase and condensed-phase systems. The
gas-phase results are compared to DFT (mostly B3LYP), ab initio (MP2 and G3B3), and PM6, as well as to a previous DFTB parametrization
(MIO). The results indicate that DFTB3/3OB is particularly successful
at predicting structures, including rather complex dinuclear metalloenzyme
active sites, while being semiquantitative (with a typical mean absolute
deviation (MAD) of ∼3–5 kcal/mol) for energetics. Single-point
calculations with high-level quantum mechanics (QM) methods generally
lead to very satisfying (a typical MAD of ∼1 kcal/mol) energetic
properties. DFTB3/MM simulations for solution and two enzyme systems
also lead to encouraging structural and energetic properties in comparison
to available experimental data. The remaining limitations of DFTB3,
such as the treatment of interaction between metal ions and highly
charged/polarizable ligands, are also discussed.
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Affiliation(s)
- Xiya Lu
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
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123
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Li P, Song LF, Merz KM. Parameterization of highly charged metal ions using the 12-6-4 LJ-type nonbonded model in explicit water. J Phys Chem B 2014; 119:883-95. [PMID: 25145273 PMCID: PMC4306492 DOI: 10.1021/jp505875v] [Citation(s) in RCA: 210] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
Highly charged metal ions act as
catalytic centers and structural
elements in a broad range of chemical complexes. The nonbonded model
for metal ions is extensively used in molecular simulations due to
its simple form, computational speed, and transferability. We have
proposed and parametrized a 12-6-4 LJ (Lennard-Jones)-type nonbonded
model for divalent metal ions in previous work, which showed a marked
improvement over the 12-6 LJ nonbonded model. In the present study,
by treating the experimental hydration free energies and ion–oxygen
distances of the first solvation shell as targets for our parametrization,
we evaluated 12-6 LJ parameters for 18 M(III) and 6 M(IV) metal ions
for three widely used water models (TIP3P, SPC/E, and TIP4PEW). As expected, the interaction energy underestimation of the 12-6
LJ nonbonded model increases dramatically for the highly charged metal
ions. We then parametrized the 12-6-4 LJ-type nonbonded model for
these metal ions with the three water models. The final parameters
reproduced the target values with good accuracy, which is consistent
with our previous experience using this potential. Finally, tests
were performed on a protein system, and the obtained results validate
the transferability of these nonbonded model parameters.
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Affiliation(s)
- Pengfei Li
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Michigan State University , 578 S. Shaw Lane, East Lansing, Michigan 48824-1322, United States
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124
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Zhou ZG, Yao QZ, Lei D, Zhang QQ, Zhang J. Investigations on the mechanisms of interactions between matrix metalloproteinase 9 and its flavonoid inhibitors using a combination of molecular docking, hybrid quantum mechanical/molecular mechanical calculations, and molecular dynamics simulations. CAN J CHEM 2014. [DOI: 10.1139/cjc-2014-0180] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Many experimental studies have found that flavonoids can inhibit the activities of matrix metalloproteinases (MMPs), but the relevant mechanisms are still unclear. In this paper, the interaction mechanisms of MMP-9 with its five flavonoid inhibitors are investigated using a combination of molecular docking, hybrid quantum mechanical and molecular mechanical (QM/MM) calculations, and molecular dynamics simulations. The molecular dynamics simulation results show a good linear correlation between the calculated binding free energies of QM/MM−Poisson–Boltzmann surface area (PBSA) and the experimental −log(EC50) regarding the studied five flavonoids on MMP-9 inhibition in explicit solvent. It is found that compared with the MM−PBSA method, the QM/MM−PBSA method can obviously improve the accuracy for the calculated binding free energies. The predicted binding modes of the five flavonoid−MMP-9 complexes reveal that the different hydrogen bond networks can form besides producing the Zn−O coordination bonds, which can reasonably explain previous experimental results. The agreement between our calculated results and the previous experimental facts indicates that the force field parameters used here are effective and reliable for investigating the systems of flavonoid−MMP-9 interactions, and thus, these simulations and analyses could be reproduced for the other related systems involving protein−ligand interactions. This paper may be helpful for designing the new MMP-9 inhibitors having higher biological activities by carrying out the structural modifications of flavonoid molecules.
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Affiliation(s)
- Zhi-Guang Zhou
- School of Pharmacy, China Pharmaceutical University, Nanjing 210009, People’s Republic of China
| | - Qi-Zheng Yao
- School of Pharmacy, China Pharmaceutical University, Nanjing 210009, People’s Republic of China
| | - Dong Lei
- School of Pharmacy, China Pharmaceutical University, Nanjing 210009, People’s Republic of China
| | - Qing-Qing Zhang
- School of Pharmacy, China Pharmaceutical University, Nanjing 210009, People’s Republic of China
| | - Ji Zhang
- Department of Physical Chemistry, China Pharmaceutical University, Nanjing 210009, People’s Republic of China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, People’s Republic of China
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125
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Santos-Martins D, Forli S, Ramos MJ, Olson AJ. AutoDock4(Zn): an improved AutoDock force field for small-molecule docking to zinc metalloproteins. J Chem Inf Model 2014; 54:2371-9. [PMID: 24931227 PMCID: PMC4144784 DOI: 10.1021/ci500209e] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Indexed: 12/14/2022]
Abstract
Zinc is present in a wide variety of proteins and is important in the metabolism of most organisms. Zinc metalloenzymes are therapeutically relevant targets in diseases such as cancer, heart disease, bacterial infection, and Alzheimer's disease. In most cases a drug molecule targeting such enzymes establishes an interaction that coordinates with the zinc ion. Thus, accurate prediction of the interaction of ligands with zinc is an important aspect of computational docking and virtual screening against zinc containing proteins. We have extended the AutoDock force field to include a specialized potential describing the interactions of zinc-coordinating ligands. This potential describes both the energetic and geometric components of the interaction. The new force field, named AutoDock4Zn, was calibrated on a data set of 292 crystal complexes containing zinc. Redocking experiments show that the force field provides significant improvement in performance in both free energy of binding estimation as well as in root-mean-square deviation from the crystal structure pose. The new force field has been implemented in AutoDock without modification to the source code.
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Affiliation(s)
- Diogo Santos-Martins
- Department of Integrative Structural and Computational
Biology, The Scripps Research Institute, La Jolla, California 92037, United States
- REQUIMTE, Departamento
de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Stefano Forli
- Department of Integrative Structural and Computational
Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Maria João Ramos
- REQUIMTE, Departamento
de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Arthur J. Olson
- Department of Integrative Structural and Computational
Biology, The Scripps Research Institute, La Jolla, California 92037, United States
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126
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Sheng X, Liu Y. QM/MM Study of the Reaction Mechanism of the Carboxyl Transferase Domain of Pyruvate Carboxylase from Staphylococcus aureus. Biochemistry 2014; 53:4455-66. [DOI: 10.1021/bi500020r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xiang Sheng
- School
of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Yongjun Liu
- School
of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
- Northwest
Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810001, China
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127
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Duarte F, Bauer P, Barrozo A, Amrein BA, Purg M, Aqvist J, Kamerlin SCL. Force field independent metal parameters using a nonbonded dummy model. J Phys Chem B 2014; 118:4351-62. [PMID: 24670003 PMCID: PMC4180081 DOI: 10.1021/jp501737x] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
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The cationic dummy atom approach
provides a powerful nonbonded
description for a range of alkaline-earth and transition-metal centers,
capturing both structural and electrostatic effects. In this work
we refine existing literature parameters for octahedrally coordinated
Mn2+, Zn2+, Mg2+, and Ca2+, as well as providing new parameters for Ni2+, Co2+, and Fe2+. In all the cases, we are able to reproduce
both M2+–O distances and experimental solvation
free energies, which has not been achieved to date for transition
metals using any other model. The parameters have also been tested
using two different water models and show consistent performance.
Therefore, our parameters are easily transferable to any force field
that describes nonbonded interactions using Coulomb and Lennard-Jones
potentials. Finally, we demonstrate the stability of our parameters
in both the human and Escherichia coli variants of
the enzyme glyoxalase I as showcase systems, as both enzymes are active
with a range of transition metals. The parameters presented in this
work provide a valuable resource for the molecular simulation community,
as they extend the range of metal ions that can be studied using classical
approaches, while also providing a starting point for subsequent parametrization
of new metal centers.
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Affiliation(s)
- Fernanda Duarte
- Department of Cell and Molecular Biology, Uppsala University , BMC Box 596, S-751 24 Uppsala, Sweden
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128
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Khrenova MG, Nemukhin AV, Savitsky AP. Computational characterization of ketone-ketal transformations at the active site of matrix metalloproteinases. J Phys Chem B 2014; 118:4345-50. [PMID: 24684684 DOI: 10.1021/jp501674b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We modeled the first steps of hydrolysis reactions of a natural oligopeptide substrate of matrix metalloproteinase MMP-2 as well as of a substrate analogue. In the latter, the scissile amide group is substituted by a ketomethylene group which can be transformed to the ketal group upon binding of this compound to the enzyme active site. According to our quantum mechanical-molecular mechanical (QM/MM) calculations, the reaction of the ketone-ketal transformation proceeds with a low energy barrier (3.4 kcal/mol) and a high equilibrium constant (10(4)). The reaction product with the ketal group formed directly at the active site of the enzyme works as an inhibitor that chelates the zinc ion. On the other hand, the oligopeptide mimetic retains molecular groups responsible for binding of this compound to the enzyme active site. This example illustrates a strategy to design MMP inhibitors in situ by using data on binding specificity of substrates to a particular type of MMP and details of the reaction mechanism.
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Affiliation(s)
- Maria G Khrenova
- A.N. Bach Institute of Biochemistry, Russian Academy of Sciences , Leninsky prospect, 33, Moscow 119071, Russian Federation
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129
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Wang B, Predeus AV, Burton ZF, Feig M. Energetic and structural details of the trigger-loop closing transition in RNA polymerase II. Biophys J 2014; 105:767-75. [PMID: 23931324 DOI: 10.1016/j.bpj.2013.05.060] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 05/26/2013] [Accepted: 05/29/2013] [Indexed: 10/26/2022] Open
Abstract
An evolutionarily conserved element in RNA polymerase II, the trigger loop (TL), has been suggested to play an important role in the elongation rate, fidelity of selection of the matched nucleoside triphosphate (NTP), catalysis of transcription elongation, and translocation in both eukaryotes and prokaryotes. In response to NTP binding, the TL undergoes large conformational changes to switch between distinct open and closed states to tighten the active site and avail catalysis. A computational strategy for characterizing the conformational transition pathway is presented to bridge the open and closed states of the TL. Information from a large number of independent all-atom molecular dynamics trajectories from Hamiltonian replica exchange and targeted molecular dynamics simulations is gathered together to assemble a connectivity map of the conformational transition. The results show that with a cognate NTP, TL closing should be a spontaneous process. One major intermediate state is identified along the conformational transition pathway, and the key structural features are characterized. The complete pathway from the open TL to the closed TL provides a clear picture of the TL closing.
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Affiliation(s)
- Beibei Wang
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, USA
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130
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131
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Li P, Merz KM. Taking into Account the Ion-induced Dipole Interaction in the Nonbonded Model of Ions. J Chem Theory Comput 2014; 10:289-297. [PMID: 24659926 PMCID: PMC3960013 DOI: 10.1021/ct400751u] [Citation(s) in RCA: 255] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Metal ions exist in almost half of the proteins in the protein databank and they serve as structural, electron-transfer and catalytic elements in the metabolic processes of organisms. Molecular Dynamics (MD) simulation is a powerful tool that provides information about biomolecular systems at the atomic level. Coupled with the growth in computing power, algorithms like the Particle Mesh Ewald (PME) method have become the accepted standard when dealing with long-range interactions in MD simulations. The nonbonded model of metal ions consists of an electrostatic plus 12-6 Lennard Jones (LJ) potential and is used largely because of its speed relative to more accurate models. In previous work we found that ideal parameters do not exist that reproduce several experimental properties for M(II) ions simultaneously using the nonbonded model coupled with the PME method due to the underestimation of metal ion-ligand interactions. Via a consideration of the nature of the nonbonded model, we proposed that the observed error largely arises from overlooking charge-induced dipole interactions. The electrostatic plus 12-6 LJ potential model works reasonably well for neutral systems but does struggle with more highly charged systems. In the present work we designed and parameterized a new nonbonded model for metal ions by adding a 1/r4 term to the 12-6 model. We call it the 12-6-4 LJ-type nonbonded model due to its mathematical construction. Parameters were determined for 16 +2 metal ions for the TIP3P, SPC/E and TIP4PEW water models. The final parameters reproduce the experimental hydration free energies (HFE), ion-oxygen distances (IOD) in the first solvation shell and coordination numbers (CN) accurately for the metal ions investigated. Preliminary tests on MgCl2 at different concentrations in aqueous solution and Mg2+--nucleic acid systems show reasonable results suggesting that the present parameters can work in mixed systems. The 12-6-4 LJ-type nonbonded model is readily adopted into standard force fields like AMBER, CHARMM and OPLS-AA with only a modest computational overhead. The new nonbonded model doesn't consider charge-transfer effects explicitly and, hence, may not suitable for the simulation of systems where charge-transfer effects play a decisive role.
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Affiliation(s)
- Pengfei Li
- 2328 New Physics Building, PO Box 118435, University of Florida, Gainesville, Florida 32611-8435, And Department of Chemistry, Michigan State University, East Lansing, Michigan 48824
| | - Kenneth M. Merz
- 2328 New Physics Building, PO Box 118435, University of Florida, Gainesville, Florida 32611-8435, And Department of Chemistry, Michigan State University, East Lansing, Michigan 48824
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132
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Ranaghan KE, Hung JE, Bartlett GJ, Mooibroek TJ, Harvey JN, Woolfson DN, van der Donk WA, Mulholland AJ. A catalytic role for methionine revealed by a combination of computation and experiments on phosphite dehydrogenase. Chem Sci 2014. [DOI: 10.1039/c3sc53009d] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Novel role for methionine in enzyme catalysis.
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Affiliation(s)
- Kara E. Ranaghan
- Centre for Computational Chemistry
- School of Chemistry
- University of Bristol
- Bristol, UK
- School of Chemistry
| | - John E. Hung
- Department of Chemistry and The Howard Hughes Medical Institute
- University of Illinois at Urbana-Champaign
- Urbana, USA
| | | | | | - Jeremy N. Harvey
- Centre for Computational Chemistry
- School of Chemistry
- University of Bristol
- Bristol, UK
- School of Chemistry
| | - Derek N. Woolfson
- School of Chemistry
- University of Bristol
- Bristol, UK
- School of Biochemistry
- Medical Sciences
| | - Wilfred A. van der Donk
- Department of Chemistry and The Howard Hughes Medical Institute
- University of Illinois at Urbana-Champaign
- Urbana, USA
| | - Adrian J. Mulholland
- Centre for Computational Chemistry
- School of Chemistry
- University of Bristol
- Bristol, UK
- School of Chemistry
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133
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Huang YY, Li Z, Cai YH, Feng LJ, Wu Y, Li X, Luo HB. The Molecular Basis for the Selectivity of Tadalafil toward Phosphodiesterase 5 and 6: A Modeling Study. J Chem Inf Model 2013; 53:3044-53. [DOI: 10.1021/ci400458z] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Yi-You Huang
- School of Pharmaceutical
Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Zhe Li
- School of Pharmaceutical
Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Ying-Hong Cai
- School of Pharmaceutical
Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Ling-Jun Feng
- School of Pharmaceutical
Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Yinuo Wu
- School of Pharmaceutical
Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Xingshu Li
- School of Pharmaceutical
Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Hai-Bin Luo
- School of Pharmaceutical
Sciences, Sun Yat-Sen University, Guangzhou 510006, China
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134
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Cichero E, D'Ursi P, Moscatelli M, Bruno O, Orro A, Rotolo C, Milanesi L, Fossa P. Homology Modeling, Docking Studies and Molecular Dynamic Simulations Using Graphical Processing Unit Architecture to Probe the Type-11 Phosphodiesterase Catalytic Site: A Computational Approach for the Rational Design of Selective Inhibitors. Chem Biol Drug Des 2013; 82:718-31. [DOI: 10.1111/cbdd.12193] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 06/14/2013] [Accepted: 07/09/2013] [Indexed: 01/21/2023]
Affiliation(s)
- Elena Cichero
- Dipartimento di Farmacia; Sezione di Chimica del Farmaco e del Prodotto Cosmetico; Università degli Studi di Genova; Viale Benedetto XV 3 16132 Genova Italy
| | - Pasqualina D'Ursi
- Institute for Biomedical Technologies-National Research Council (ITB-CNR); Via Fratelli Cervi 93 20090 Segrate (MI) Italy
| | - Marco Moscatelli
- Institute for Biomedical Technologies-National Research Council (ITB-CNR); Via Fratelli Cervi 93 20090 Segrate (MI) Italy
- University of Milano-Bicocca; DISAT; Piazza della Scienza 1 20126 Milan Italy
| | - Olga Bruno
- Dipartimento di Farmacia; Sezione di Chimica del Farmaco e del Prodotto Cosmetico; Università degli Studi di Genova; Viale Benedetto XV 3 16132 Genova Italy
| | - Alessandro Orro
- Institute for Biomedical Technologies-National Research Council (ITB-CNR); Via Fratelli Cervi 93 20090 Segrate (MI) Italy
| | - Chiara Rotolo
- Dipartimento di Farmacia; Sezione di Chimica del Farmaco e del Prodotto Cosmetico; Università degli Studi di Genova; Viale Benedetto XV 3 16132 Genova Italy
| | - Luciano Milanesi
- Institute for Biomedical Technologies-National Research Council (ITB-CNR); Via Fratelli Cervi 93 20090 Segrate (MI) Italy
| | - Paola Fossa
- Dipartimento di Farmacia; Sezione di Chimica del Farmaco e del Prodotto Cosmetico; Università degli Studi di Genova; Viale Benedetto XV 3 16132 Genova Italy
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135
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Jiang N, Kuznetsov A, Nocek JM, Hoffman BM, Crane BR, Hu X, Beratan DN. Distance-independent charge recombination kinetics in cytochrome c-cytochrome c peroxidase complexes: compensating changes in the electronic coupling and reorganization energies. J Phys Chem B 2013; 117:9129-41. [PMID: 23895339 PMCID: PMC3809023 DOI: 10.1021/jp401551t] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Charge recombination rate constants vary no more than 3-fold for interprotein ET in the Zn-substituted wild type (WT) cytochrome c peroxidase (CcP):cytochrome c (Cc) complex and in complexes with four mutants of the Cc protein (i.e., F82S, F82W, F82Y, and F82I), despite large differences in the ET distance. Theoretical analysis indicates that charge recombination for all complexes involves a combination of tunneling and hopping via Trp191. For three of the five structures (WT and F82S(W)), the protein favors hopping more than that in the other two structures that have longer heme → ZnP distances (F82Y(I)). Experimentally observed biexponential ET kinetics is explained by the complex locking in alternative coupling pathways, where the acceptor hole state is either primarily localized on ZnP (slow phase) or on Trp191 (fast phase). The large conformational differences between the CcP:Cc interface for the F82Y(I) mutants compared to that the WT and F82S(W) complexes are predicted to change the reorganization energies for the CcP:Cc ET reactions because of changes in solvent exposure and interprotein ET distances. Since the recombination reaction is likely to occur in the inverted Marcus regime, an increased reorganization energy compensates the decreased role for hopping recombination (and the longer transfer distance) in the F82Y(I) mutants. Taken together, coupling pathway and reorganization energy effects for the five protein complexes explain the observed insensitivity of recombination kinetics to donor-acceptor distance and docking pose and also reveals how hopping through aromatic residues can accelerate long-range ET.
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Affiliation(s)
- Nan Jiang
- Department of Chemistry, Duke University, Durham, NC 27708
| | | | - Judith M. Nocek
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Brian M. Hoffman
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Brian R. Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
| | - Xiangqian Hu
- Department of Chemistry, Duke University, Durham, NC 27708
| | - David N. Beratan
- Department of Chemistry, Duke University, Durham, NC 27708
- Department of Biochemistry, Duke University, Durham, NC 27708
- Department of Physics, Duke University, Durham, NC 27708
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136
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Biochemical characterization of IMP-30, a metallo-β-lactamase with enhanced activity toward ceftazidime. Antimicrob Agents Chemother 2013; 57:5122-6. [PMID: 23836186 DOI: 10.1128/aac.02341-12] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
IMP-type enzymes constitute a clinically important family of metallo-β-lactamases that has grown dramatically in the past decade to its current 45 known members. Here, we report the biochemical characterization of IMP-30 in comparison to IMP-1, from which it deviates by a single E59K mutation. Kinetics, MIC assays, docking, and molecular dynamics simulations support a scenario in which Lys59 interacts with the ceftazidime R1 group, resulting in increased water access and enhanced turnover and MIC of ceftazidime.
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137
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Di Micco S, Chini MG, Terracciano S, Bruno I, Riccio R, Bifulco G. Structural basis for the design and synthesis of selective HDAC inhibitors. Bioorg Med Chem 2013; 21:3795-807. [DOI: 10.1016/j.bmc.2013.04.036] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 04/09/2013] [Accepted: 04/10/2013] [Indexed: 10/26/2022]
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138
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Xue W, Ban Y, Liu H, Yao X. Computational study on the drug resistance mechanism against HCV NS3/4A protease inhibitors vaniprevir and MK-5172 by the combination use of molecular dynamics simulation, residue interaction network, and substrate envelope analysis. J Chem Inf Model 2013; 54:621-33. [PMID: 23745769 DOI: 10.1021/ci400060j] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Hepatitis C virus (HCV) NS3/4A protease is an important and attractive target for anti-HCV drug development and discovery. Vaniprevir (phase III clinical trials) and MK-5172 (phase II clinical trials) are two potent antiviral compounds that target NS3/4A protease. However, the emergence of resistance to these two inhibitors reduced the effectiveness of vaniprevir and MK-5172 against viral replication. Among the drug resistance mutations, three single-site mutations at residues Arg155, Ala156, and Asp168 in NS3/4A protease are especially important due to their resistance to nearly all inhibitors in clinical development. A detailed understanding of drug resistance mechanism to vaniprevir and MK-5172 is therefore very crucial for the design of novel potent agents targeting viral variants. In this work, molecular dynamics (MD) simulation, binding free energy calculation, free energy decomposition, residue interaction network (RIN), and substrate envelope analysis were used to study the detailed drug resistance mechanism of the three mutants R155K, A156T, and D168A to vaniprevir and MK-5172. MD simulation was used to investigate the binding mode for these two inhibitors to wild-type and resistant mutants of HCV NS3/4A protease. Binding free energy calculation and free energy decomposition analysis reveal that drug resistance mutations reduced the interactions between the active site residues and substituent in the P2 to P4 linker of vaniprevir and MK-5172. Furthermore, RIN and substrate envelope analysis indicate that the studied mutations of the residues are located outside the substrate (4B5A) binding site and selectively decrease the affinity of inhibitors but not the activity of the enzyme and consequently help NS3/4A protease escape from the effect of the inhibitors without influencing the affinity of substrate binding. These findings can provide useful information for understanding the drug resistance mechanism against vaniprevir and MK-5172. The results can also provide some potential clues for further design of novel inhibitors that are less susceptible to drug resistance.
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Affiliation(s)
- Weiwei Xue
- State Key Laboratory of Applied Organic Chemistry, Department of Chemistry, Lanzhou University , Lanzhou 730000, China
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139
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Li P, Roberts BP, Chakravorty DK, Merz KM. Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent. J Chem Theory Comput 2013; 9:2733-2748. [PMID: 23914143 PMCID: PMC3728907 DOI: 10.1021/ct400146w] [Citation(s) in RCA: 459] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Metal ions play significant roles in biological systems. Accurate molecular dynamics (MD) simulations on these systems require a validated set of parameters. Although there are more detailed ways to model metal ions, the nonbonded model, which employs a 12-6 Lennard-Jones (LJ) term plus an electrostatic potential is still widely used in MD simulations today due to its simple form. However, LJ parameters have limited transferability due to different combining rules, various water models and diverse simulation methods. Recently, simulations employing a Particle Mesh Ewald (PME) treatment for long-range electrostatics have become more and more popular owing to their speed and accuracy. In the present work we have systematically designed LJ parameters for 24 +2 metal (M(II)) cations to reproduce different experimental properties appropriate for the Lorentz-Berthelot combining rules and PME simulations. We began by testing the transferability of currently available M(II) ion LJ parameters. The results showed that there are differences between simulations employing Ewald summation with other simulation methods and that it was necessary to design new parameters specific for PME based simulations. Employing the thermodynamic integration (TI) method and performing periodic boundary MD simulations employing PME, allowed for the systematic investigation of the LJ parameter space. Hydration free energies (HFEs), the ion-oxygen distance in the first solvation shell (IOD) and coordination numbers (CNs) were obtained for various combinations of the parameters of the LJ potential for four widely used water models (TIP3P, SPC/E, TIP4P and TIP4PEW). Results showed that the three simulated properties were highly correlated. Meanwhile, M(II) ions with the same parameters in different water models produce remarkably different HFEs but similar structural properties. It is difficult to reproduce various experimental values simultaneously because the nonbonded model underestimates the interaction between the metal ions and water molecules at short range. Moreover, the extent of underestimation increases successively for the TIP3P, SPC/E, TIP4PEW and TIP4P water models. Nonetheless, we fitted a curve to describe the relationship between ε (the well depth) and radius (Rmin/2) from experimental data on noble gases to facilitate the generation of the best possible compromise models. Hence, by targeting different experimental values, we developed three sets of parameters for M(II) cations for three different water models (TIP3P, SPC/E and TIP4PEW). These parameters we feel represent the best possible compromise that can be achieved using the nonbonded model for the ions in combination with simple water models. From a computational uncertainty analysis we estimate that the uncertainty in our computed HFEs is on the order of ±1kcal/mol. Further improvements will require more advanced non-bonded models likely with inclusion of polarization.
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Affiliation(s)
- Pengfei Li
- 2328 New Physics Building, PO Box 118435, University of Florida, Gainesville, Florida 32611-8435, Phone: 352-392-6973, Fax: 352-392-8722
| | - Benjamin P. Roberts
- 2328 New Physics Building, PO Box 118435, University of Florida, Gainesville, Florida 32611-8435, Phone: 352-392-6973, Fax: 352-392-8722
| | - Dhruva K. Chakravorty
- 2328 New Physics Building, PO Box 118435, University of Florida, Gainesville, Florida 32611-8435, Phone: 352-392-6973, Fax: 352-392-8722
| | - Kenneth M. Merz
- 2328 New Physics Building, PO Box 118435, University of Florida, Gainesville, Florida 32611-8435, Phone: 352-392-6973, Fax: 352-392-8722
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140
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Neves RPP, Sousa SF, Fernandes PA, Ramos MJ. Parameters for Molecular Dynamics Simulations of Manganese-Containing Metalloproteins. J Chem Theory Comput 2013; 9:2718-32. [DOI: 10.1021/ct400055v] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Rui P. P. Neves
- REQUIMTE,
Departamento de Química e Bioquímica,
Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Sérgio F. Sousa
- REQUIMTE,
Departamento de Química e Bioquímica,
Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Pedro A. Fernandes
- REQUIMTE,
Departamento de Química e Bioquímica,
Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Maria J. Ramos
- REQUIMTE,
Departamento de Química e Bioquímica,
Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
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141
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Huang YD, Shuai JW. Induced Dipoles Incorporated into All-Atom Zn Protein Simulations with Multiscale Modeling. J Phys Chem B 2013; 117:6138-48. [DOI: 10.1021/jp4021933] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Yan-Dong Huang
- Department of Physics
and Institute
of Theoretical Physics and Astrophysics, Xiamen University, Xiamen 361005, China
| | - Jian-Wei Shuai
- Department of Physics
and Institute
of Theoretical Physics and Astrophysics, Xiamen University, Xiamen 361005, China
- Fujian Provincial Key Laboratory
of Theoretical and Computational Chemistry, Xiamen University, Xiamen 361005, China
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142
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Carvalho ATP, Teixeira AFS, Ramos MJ. Parameters for molecular dynamics simulations of iron-sulfur proteins. J Comput Chem 2013; 34:1540-8. [PMID: 23609049 DOI: 10.1002/jcc.23287] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 03/01/2013] [Accepted: 03/05/2013] [Indexed: 11/06/2022]
Abstract
Iron-sulfur proteins involved in electron transfer reactions have finely tuned redox potentials, which allow them to be highly efficient and specific. Factors such as metal center solvent exposure, interaction with charged residues, or hydrogen bonds between the ligand residues and amide backbone groups have all been pointed out to cause such specific redox potentials. Here, we derived parameters compatible with the AMBER force field for the metal centers of iron-sulfur proteins and applied them in the molecular dynamics simulations of three iron-sulfur proteins. We used density-functional theory (DFT) calculations and Seminario's method for the parameterization. Parameter validation was obtained by matching structures and normal frequencies at the quantum mechanics and molecular mechanics levels of theory. Having guaranteed a correct representation of the protein coordination spheres, the amide H-bonds and the water exposure to the ligands were analyzed. Our results for the pattern of interactions with the metal centers are consistent to those obtained by nuclear magnetic resonance spectroscopy (NMR) experiments and DFT calculations, allowing the application of molecular dynamics to the study of those proteins.
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Affiliation(s)
- Alexandra T P Carvalho
- Institut de Química Computacional and Departament de Química, Universitat de Girona, Girona 17071, Spain.
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143
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Li Z, Cai YH, Cheng YK, Lu X, Shao YX, Li X, Liu M, Liu P, Luo HB. Identification of Novel Phosphodiesterase-4D Inhibitors Prescreened by Molecular Dynamics-Augmented Modeling and Validated by Bioassay. J Chem Inf Model 2013; 53:972-81. [DOI: 10.1021/ci400063s] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Zhe Li
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China
| | - Ying-Hong Cai
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China
| | - Yuen-Kit Cheng
- Department of Chemistry, Hong Kong Baptist University, Kowloon, Hong Kong
| | - Xiao Lu
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China
| | - Yong-Xian Shao
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China
| | - Xingshu Li
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China
| | - Ming Liu
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China
| | - Peiqing Liu
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China
| | - Hai-Bin Luo
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, PR China
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144
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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.
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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
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145
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Kalyaanamoorthy S, Chen YPP. Energy based pharmacophore mapping of HDAC inhibitors against class I HDAC enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:317-28. [DOI: 10.1016/j.bbapap.2012.08.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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146
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Xue W, Jin X, Ning L, Wang M, Liu H, Yao X. Exploring the Molecular Mechanism of Cross-Resistance to HIV-1 Integrase Strand Transfer Inhibitors by Molecular Dynamics Simulation and Residue Interaction Network Analysis. J Chem Inf Model 2012; 53:210-22. [DOI: 10.1021/ci300541c] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Weiwei Xue
- State
Key Laboratory of Applied Organic Chemistry, Department of Chemistry, ‡School of Pharmacy, and §Key Lab of Preclinical
Study for New Drugs of Gansu Province, Lanzhou University, Lanzhou 730000, China
| | - Xiaojie Jin
- State
Key Laboratory of Applied Organic Chemistry, Department of Chemistry, ‡School of Pharmacy, and §Key Lab of Preclinical
Study for New Drugs of Gansu Province, Lanzhou University, Lanzhou 730000, China
| | - Lulu Ning
- State
Key Laboratory of Applied Organic Chemistry, Department of Chemistry, ‡School of Pharmacy, and §Key Lab of Preclinical
Study for New Drugs of Gansu Province, Lanzhou University, Lanzhou 730000, China
| | - Meixia Wang
- State
Key Laboratory of Applied Organic Chemistry, Department of Chemistry, ‡School of Pharmacy, and §Key Lab of Preclinical
Study for New Drugs of Gansu Province, Lanzhou University, Lanzhou 730000, China
| | - Huanxiang Liu
- State
Key Laboratory of Applied Organic Chemistry, Department of Chemistry, ‡School of Pharmacy, and §Key Lab of Preclinical
Study for New Drugs of Gansu Province, Lanzhou University, Lanzhou 730000, China
| | - Xiaojun Yao
- State
Key Laboratory of Applied Organic Chemistry, Department of Chemistry, ‡School of Pharmacy, and §Key Lab of Preclinical
Study for New Drugs of Gansu Province, Lanzhou University, Lanzhou 730000, China
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147
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Computational insights into the selectivity mechanism of APP-IP over matrix metalloproteinases. J Comput Aided Mol Des 2012; 26:1327-42. [PMID: 23224743 DOI: 10.1007/s10822-012-9617-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 11/06/2012] [Indexed: 12/20/2022]
Abstract
In this work, selectivity mechanism of APP-IP inhibitor (β-amyloid precursor protein-derived inhibitory peptide) over matrix metalloproteinases (MMPs including MMP-2, MMP-7, MMP-9 and MMP-14) was investigated by molecular modeling methods. Among MMPs, MMP-2 is the most favorable one for APP-IP interacting based on our calculations. The predicted binding affinities can give a good explanation of the activity difference of inhibitor APP-IP. In Comparison with MMP-2/APP-IP complex, the side chain of Tyr214(MMP-7) makes the binding pocket so shallow that the whole side chain of Tyr3(APP-IP) can not be fully embraced, thus unfavorable for the N-terminal of APP-IP binding to MMP-7. The poor selectivity of APP-IP toward MMP-9 is mainly related with the decrease of interaction between the APP-IP C-terminal and MMP-9 due to the bulky side chains of Pro193 and Gln199, which is in agreement with experiment. The mutations at residues P193A and Q199G of MMP-9 alternate the binding pattern of the C-terminal of APP-IP by forming two new hydrogen bonds and hydrophobic interactions with MMP-9. The mutants favor the binding affinity of MMP-9 largely. For MMP-14/APP-IP, the large steric effect of Phe204(MMP-14) and the weak contributions of the polar residues Asn231(MMP-14) and Thr190(MMP-14) could explain why MMP-14 is non-selective for APP-IP interacting. Here, the molecular modeling methods were successfully employed to explore the selective inhibitor of MMPs, and our work gives valuable information for future rational design of selective peptide inhibitors toward individual MMP.
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148
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Marcial BL, Sousa SF, Barbosa IL, Dos Santos HF, Ramos MJ. Chemically Modified Tetracyclines as Inhibitors of MMP-2 Matrix Metalloproteinase: A Molecular and Structural Study. J Phys Chem B 2012; 116:13644-54. [DOI: 10.1021/jp3079748] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bruna L. Marcial
- REQUIMTE, Departamento
de Química
e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007, Porto,
Portugal
- Núcleo
de Estudos em
Química Computacional (NEQC), Departamento de Química
− ICE, Universidade Federal de Juiz de Fora, Juiz de Fora, MG, 36036-330, Brazil
| | - Sergio F. Sousa
- REQUIMTE, Departamento
de Química
e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007, Porto,
Portugal
| | - Ingrid L. Barbosa
- Núcleo
de Estudos em
Química Computacional (NEQC), Departamento de Química
− ICE, Universidade Federal de Juiz de Fora, Juiz de Fora, MG, 36036-330, Brazil
| | - Helio F. Dos Santos
- Núcleo
de Estudos em
Química Computacional (NEQC), Departamento de Química
− ICE, Universidade Federal de Juiz de Fora, Juiz de Fora, MG, 36036-330, Brazil
| | - Maria J. Ramos
- REQUIMTE, Departamento
de Química
e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007, Porto,
Portugal
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149
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Bernadat G, Supuran CT, Iorga BI. Carbonic anhydrase binding site parameterization in OPLS-AA force field. Bioorg Med Chem 2012. [PMID: 23182217 DOI: 10.1016/j.bmc.2012.10.040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The parameterization of carbonic anhydrase binding site in OPLS-AA force field was performed using quantum chemistry calculations. Both OH2 and OH(-) forms of the binding site were considered, showing important differences in terms of atomic partial charges. Three different parameterization protocols were used, and the results obtained highlighted the importance of including an extended binding site in the charge calculation. The force field parameters were subsequently validated using standard molecular dynamics simulations. The results presented in this work should greatly facilitate the use of molecular dynamics simulations for studying the carbonic anhydrase, and more generally, the metallo-enzymes.
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Affiliation(s)
- Guillaume Bernadat
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Labex LERMIT, Centre de Recherche de Gif, 1 Avenue de la Terrasse, F-91198 Gif-sur-Yvette, France
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150
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HUANG DAWEI, LI XIAOHUI, XIU ZHILONG. MOLECULAR MODELING OF THE INTERACTIONS BETWEEN HISTONE DEACETYLASE 8 AND INHIBITORS. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2012. [DOI: 10.1142/s0219633612500617] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Inhibitors of histone deacetylases (HDACs) have become an attractive class of anticancer agent. To understand the interaction between HDAC8 and inhibitors, including "pan-" inhibitors that inhibit many HDACs isoforms and selective inhibitors with no linker domain, docking and molecular dynamics simulation were conducted. Docking results showed the presence of π-π interactions between "linkerless" inhibitors and the aromatic amino acid residues of HDAC8 in the active site. Binding between HDAC8 and inhibitors was also stabilized by hydrogen bond and hydrophobic interaction. In molecular dynamics simulations, the zinc ion was shown to coordinate one more atom of HDAC8-"linkerless" inhibitor complexes than HDAC8-"pan-" inhibitor complexes. Persistent hydrogen bonds also existed between Tyr306 of HDAC8 and some inhibitors. When inhibitors with large cap groups bound to the active pocket of HDAC8, Phe152 and Met274 shifted from their initial positions and the entrance of the active pocket became more open, resulting in the formation of sub-pocket. Hydrophobic interactions contributed most favorably to the binding free energy between HDAC8 and inhibitors. Lys33, Asp178, Asp267, Tyr306 and Leu308 of HDAC8 were favorable for binding with all inhibitors.
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Affiliation(s)
- DAWEI HUANG
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, P. R. China
| | - XIAOHUI LI
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, P. R. China
| | - ZHILONG XIU
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, P. R. China
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