101
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Luo L, Wang XC, Ngo HH, Guo W. Thermodynamic entropy of organic oxidation in the water environment: experimental evaluation compared to semi-empirical calculation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:21350-21359. [PMID: 27502459 DOI: 10.1007/s11356-016-7324-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 07/25/2016] [Indexed: 06/06/2023]
Abstract
Residual organic matters in the secondary effluent are usually less biodegradable in terms of the total organic carbon content, and when discharged into a receiving water body, their further decomposition most likely mainly occurs due to chemical oxidation. Using this scenario, a semi-empirical method was previously developed to calculate the thermodynamic entropy of organic oxidation to quantitatively evaluate the impact of organic discharge on the water environment. In this study, the relationship between the entropy increase (ΔSC) and excess organic mass (ΔTOC) was experimentally verified via combustion heat measurement using typical organic chemicals and mixtures. For individual organic chemicals, a linear relationship was detected between ΔSC and ΔTOC with the same proportionality coefficient, 54.0 kJ/g, determined in the previous semi-empirical relationship. For the organic mixtures, a linear relationship was also identified; however, the proportionality coefficient was 69.2 kJ/g, indicating an approximately 28 % increase in the oxidation heat required to decompose the same organic mass. This increase in energy can likely be attributed to the synergistic effects of hydrogen bonding, hydrophobic interactions, π-π interactions, and van der Waals interactions between functional groups of different organic compounds. Intermolecular interactions may result in 17-32 % more dissociation energy for organic mixtures compared to the organic components' chemical structures. Because organics discharged into a water body are always a mixture of organic compounds, the proportionality coefficient obtained using organic mixtures should be adopted to modify the previously proposed semi-empirical equation.
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Affiliation(s)
- Li Luo
- International Science & Technology Cooperation Center for Urban Alternative Water Resources Development, Key Lab of Northwest Water Resource, Environment and Ecology, Ministry of Education, Xi'an University of Architecture and Technology, Xi'an, 710055, China
| | - Xiaochang C Wang
- International Science & Technology Cooperation Center for Urban Alternative Water Resources Development, Key Lab of Northwest Water Resource, Environment and Ecology, Ministry of Education, Xi'an University of Architecture and Technology, Xi'an, 710055, China.
| | - Huu Hao Ngo
- School of Civil and Environmental Engineering, Faculty of Engineering and Information Technology, University of Technology, Broadway, Sydney, NSW, 2007, Australia
| | - Wenshan Guo
- School of Civil and Environmental Engineering, Faculty of Engineering and Information Technology, University of Technology, Broadway, Sydney, NSW, 2007, Australia
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102
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Chung MK, White PS, Lee SJ, Gagné MR, Waters ML. Investigation of a Catenane with a Responsive Noncovalent Network: Mimicking Long-Range Responses in Proteins. J Am Chem Soc 2016; 138:13344-13352. [PMID: 27631725 PMCID: PMC5553285 DOI: 10.1021/jacs.6b07833] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report a functional synthetic model for studying the noncovalent networks (NCNs) required for complex protein functions. The model [2]-catenane is self-assembled from dipeptide building blocks and contains an extensive network of hydrogen bonds and aromatic interactions. Perturbations to the catenane cause compensating changes in the NCNs structure and dynamics, resulting in long-distance changes reminiscent of a protein. Key findings include the notion that NCNs require regions of negative cooperativity, or "frustrated" noncovalent interactions, as a source of potential energy for driving the response. We refer to this potential energy as latent free energy and describe a mechanistic and energetic model for responsive systems.
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Affiliation(s)
| | | | - Stephen J. Lee
- U.S. Army Research Office, P.O. Box 12211, Research Triangle Park, North Carolina 27709, United States
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103
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Piazza M, Dieckmann T, Guillemette JG. Structural Studies of a Complex Between Endothelial Nitric Oxide Synthase and Calmodulin at Physiological Calcium Concentration. Biochemistry 2016; 55:5962-5971. [DOI: 10.1021/acs.biochem.6b00821] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michael Piazza
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Thorsten Dieckmann
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - J. Guy Guillemette
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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104
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Pera-Titus M. Direct inference of site strength in basic solids upon CO2 adsorption: enthalpy-entropy compensation effects. Phys Chem Chem Phys 2016; 18:22548-56. [PMID: 27468818 DOI: 10.1039/c6cp03941c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The adsorption of CO2 coupled to calorimetry is a state-of-the-art technique for characterizing the basic properties of solids. In this paper, we show that the differential heat and entropy curves measured upon CO2 adsorption on a basic solid can be reasonably estimated from a single CO2 isotherm with no need for any independent heat (calorimetric) measurement. Our method relies on two important observations: (1) formulation of generalized F-H-TS thermodynamic isotherms, the former (F) being directly generated from the raw CO2 isotherms, and (2) the presence of unexpected enthalpy-entropy compensation effects upon CO2 adsorption linking the integral enthalpy and entropy of adsorption until saturation for different solids. Our thermodynamic method has been validated using a broad library of basic solids with variable site strength and heterogeneity. Finally, a new scale of basicity is proposed using the parameters fitted from the thermodynamic isotherm (free energy basis) as descriptors of basic strength. This method opens an avenue to the inference of site strength of basic solids without the need for expensive calorimeters.
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Affiliation(s)
- M Pera-Titus
- Eco-Efficient Products and Processes Laboratory (E2P2L), UMI 3464 CNRS-Solvay, 3966 Jin Du Road, Xin Zhuang Ind. Zone, 201108 Shanghai, China.
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105
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Ligand binding cooperativity: Bioisosteric replacement of CO with SO2 among thrombin inhibitors. Bioorg Med Chem Lett 2016; 26:3850-4. [DOI: 10.1016/j.bmcl.2016.07.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 07/07/2016] [Accepted: 07/08/2016] [Indexed: 01/22/2023]
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106
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Abstract
On the basis of many literature measurements, a critical overview is given on essential noncovalent interactions in synthetic supramolecular complexes, accompanied by analyses with selected proteins. The methods, which can be applied to derive binding increments for single noncovalent interactions, start with the evaluation of consistency and additivity with a sufficiently large number of different host-guest complexes by applying linear free energy relations. Other strategies involve the use of double mutant cycles, of molecular balances, of dynamic combinatorial libraries, and of crystal structures. Promises and limitations of these strategies are discussed. Most of the analyses stem from solution studies, but a few also from gas phase. The empirically derived interactions are then presented on the basis of selected complexes with respect to ion pairing, hydrogen bonding, electrostatic contributions, halogen bonding, π-π-stacking, dispersive forces, cation-π and anion-π interactions, and contributions from the hydrophobic effect. Cooperativity in host-guest complexes as well as in self-assembly, and entropy factors are briefly highlighted. Tables with typical values for single noncovalent free energies and polarity parameters are in the Supporting Information.
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Affiliation(s)
- Frank Biedermann
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT) , Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Hans-Jörg Schneider
- FR Organische Chemie der Universität des Saarlandes , D-66041 Saarbrücken, Germany
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107
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Praveen C, Ananth DB. Design, synthesis and cytotoxicity of pyrano[4,3-b]indol-1(5H)-ones: A hybrid pharmacophore approach via gold catalyzed cyclization. Bioorg Med Chem Lett 2016; 26:2507-2512. [DOI: 10.1016/j.bmcl.2016.03.087] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 03/16/2016] [Accepted: 03/25/2016] [Indexed: 01/29/2023]
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108
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Taimoory SM, Dudding T. An Evolving Insight into Chiral H-Bond Catalyzed Aza-Henry Reactions: A Cooperative Role for Noncovalent Attractive Interactions Unveiled by Density Functional Theory. J Org Chem 2016; 81:3286-95. [PMID: 27008440 DOI: 10.1021/acs.joc.6b00248] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The role of cooperative effects arising from noncovalent attractive interactions as a vital factor governing stereoinduction in chiral H-bond catalyzed aza-Henry reactions is reported. Supporting this finding were density functional theory (DFT) calculations which revealed a shape and size dependency existed between the catalyst and substrates that when matched lead to high enantioselectivity, as reflected by favorable activation parameters. Associated with optimal catalyst and substrate pairing were a closed catalytic binding pocket and a synclinal orientation of the substrates that reinforced favorable stereoelectronic effects and dispersive type forces. Meanwhile, unfavorable steric interactions were found to be a dominant effect controlling diastereoselection.
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Affiliation(s)
| | - Travis Dudding
- Brock University , 1812 Sir Isaac Brock Way, St. Catharines, ON, L2S 3A1 Canada
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109
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JEYAVEERAN JC, PRAVEEN CHANDRASEKAR, ARUN Y, PRINCE AAM, PERUMAL PT. Flexible synthesis of isomeric pyranoindolones and evaluation of cytotoxicity towards HeLa cells. J CHEM SCI 2016. [DOI: 10.1007/s12039-016-1070-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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110
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Shokri A, Wang XB, Wang Y, O’Doherty GA, Kass SR. Flexible Acyclic Polyol-Chloride Anion Complexes and Their Characterization by Photoelectron Spectroscopy and Variable Temperature Binding Constant Determinations. J Phys Chem A 2016; 120:1661-8. [DOI: 10.1021/acs.jpca.5b12286] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alireza Shokri
- Department
of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Xue-Bin Wang
- Physical
Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, MS K8-88, Richland, Washington 99352, United States
| | - Yanping Wang
- Department
of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - George A. O’Doherty
- Department
of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Steven R. Kass
- Department
of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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111
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Miles JA, Yeo DJ, Rowell P, Rodriguez-Marin S, Pask CM, Warriner SL, Edwards TA, Wilson AJ. Hydrocarbon constrained peptides - understanding preorganisation and binding affinity. Chem Sci 2016; 7:3694-3702. [PMID: 28970875 PMCID: PMC5618334 DOI: 10.1039/c5sc04048e] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 02/15/2016] [Indexed: 12/19/2022] Open
Abstract
The development of constrained peptides represents an emerging strategy to generate peptide based probes and hits for drug-discovery that address challenging protein-protein interactions (PPIs). In this manuscript we report on the use of a novel α-alkenylglycine derived amino acid to synthesise hydrocarbon constrained BH3-family sequences (BIM and BID). Our biophysical and structural analyses illustrate that whilst the introduction of the constraint increases the population of the bioactive α-helical conformation of the peptide in solution, it does not enhance the inhibitory potency against pro-apoptotic Bcl-xL and Mcl-1 PPIs. SPR analyses indicate binding occurs via an induced fit mechanism whilst X-ray analyses illustrate none of the key interactions between the helix and protein are disturbed. The behaviour derives from enthalpy-entropy compensation which may be considered in terms of the ground state energies of the unbound constrained and unconstrained peptides; this has implications for the design of preorganised peptides to target protein-protein interactions.
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Affiliation(s)
- Jennifer A Miles
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre for Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK .
| | - David J Yeo
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre for Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK .
| | - Philip Rowell
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,School of Molecular and Cellular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - Silvia Rodriguez-Marin
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre for Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK .
| | - Christopher M Pask
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK .
| | - Stuart L Warriner
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre for Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK .
| | - Thomas A Edwards
- Astbury Centre for Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,School of Molecular and Cellular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - Andrew J Wilson
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre for Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK .
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112
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Nübel C, Appel B, Hospach I, Mai M, Krasteva N, Nelles G, Petruschka L, Müller S. Challenges and Opportunities in the Development of Aptamers for TNFα. Appl Biochem Biotechnol 2016; 179:398-414. [PMID: 26922730 DOI: 10.1007/s12010-016-2002-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 01/27/2016] [Indexed: 11/24/2022]
Abstract
RNA aptamers for tumor necrosis factor-alpha (TNFα), for which functionality was demonstrated in L929 cells, show only little affinity for the protein in vitro. Detailed investigation of the aptamer-protein interaction by surface plasmon resonance and quartz crystal microbalance analysis revealed that affinity is not the only crucial parameter for efficacy and functionality of those aptamers. Instead, the sensitive equilibrium of the monomeric and homotrimeric form of soluble TNFα decides on aptamer binding. Our results show that the field of application and the source of TNFα have to be carefully defined before selection of aptamer sequences.
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Affiliation(s)
- Claudia Nübel
- Institut für Biochemie, Ernst-Moritz-Arndt Universität Greifswald, Greifswald, Germany
| | - Bettina Appel
- Institut für Biochemie, Ernst-Moritz-Arndt Universität Greifswald, Greifswald, Germany
| | - Ingeborg Hospach
- Materials Science Laboratory, Sony Deutschland GmbH, Stuttgart, Germany.,Institute of Electronics and Sensor Materials, Technical University Freiberg, Freiberg, Germany
| | - Michaela Mai
- Materials Science Laboratory, Sony Deutschland GmbH, Stuttgart, Germany
| | - Nadejda Krasteva
- Materials Science Laboratory, Sony Deutschland GmbH, Stuttgart, Germany
| | - Gabriele Nelles
- Materials Science Laboratory, Sony Deutschland GmbH, Stuttgart, Germany
| | - Lothar Petruschka
- Interfakultäres Institut für Genetik und funktionelle Genomforschung, Ernst-Moritz-Arndt Universität Greifswald, Greifswald, Germany
| | - Sabine Müller
- Institut für Biochemie, Ernst-Moritz-Arndt Universität Greifswald, Greifswald, Germany.
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113
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Riskowski RA, Armstrong RE, Greenbaum NL, Strouse GF. Triangulating Nucleic Acid Conformations Using Multicolor Surface Energy Transfer. ACS NANO 2016; 10:1926-1938. [PMID: 26795549 DOI: 10.1021/acsnano.5b05764] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Optical ruler methods employing multiple fluorescent labels offer great potential for correlating distances among several sites, but are generally limited to interlabel distances under 10 nm and suffer from complications due to spectral overlap. Here we demonstrate a multicolor surface energy transfer (McSET) technique able to triangulate multiple points on a biopolymer, allowing for analysis of global structure in complex biomolecules. McSET couples the competitive energy transfer pathways of Förster Resonance Energy Transfer (FRET) with gold-nanoparticle mediated Surface Energy Transfer (SET) in order to correlate systematically labeled points on the structure at distances greater than 10 nm and with reduced spectral overlap. To demonstrate the McSET method, the structures of a linear B-DNA and a more complex folded RNA ribozyme were analyzed within the McSET mathematical framework. The improved multicolor optical ruler method takes advantage of the broad spectral range and distances achievable when using a gold nanoparticle as the lowest energy acceptor. The ability to report distance information simultaneously across multiple length scales, short-range (10-50 Å), mid-range (50-150 Å), and long-range (150-350 Å), distinguishes this approach from other multicolor energy transfer methods.
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Affiliation(s)
- Ryan A Riskowski
- Molecular Biophysics Program, Florida State University , Tallahassee, Florida 32306, United States
| | - Rachel E Armstrong
- Department of Chemistry and Biochemistry, Florida State University , Tallahassee, Florida 32306, United States
| | - Nancy L Greenbaum
- Department of Chemistry and Biochemistry, Hunter College and The Graduate Center of the City University of New York , New York, New York 10065, United States
| | - Geoffrey F Strouse
- Molecular Biophysics Program, Florida State University , Tallahassee, Florida 32306, United States
- Department of Chemistry and Biochemistry, Florida State University , Tallahassee, Florida 32306, United States
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114
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Affiliation(s)
- A. Subha Mahadevi
- Centre for Molecular Modelling, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, India 500607
| | - G. Narahari Sastry
- Centre for Molecular Modelling, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, India 500607
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115
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Fuenzalida JP, Nareddy PK, Moreno-Villoslada I, Moerschbacher BM, Swamy MJ, Pan S, Ostermeier M, Goycoolea FM. On the role of alginate structure in complexing with lysozyme and application for enzyme delivery. Food Hydrocoll 2016. [DOI: 10.1016/j.foodhyd.2015.04.017] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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116
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Gunasekara RW, Zhao Y. Enhancing binding affinity and selectivity through preorganization and cooperative enhancement of the receptor. Chem Commun (Camb) 2016; 52:4345-8. [DOI: 10.1039/c5cc10405j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
When direct host–guest binding interactions are weakened by unfavorable solvent competition, guest-triggered intrareceptor interactions could be used to augment the binding.
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Affiliation(s)
| | - Yan Zhao
- Department of Chemistry
- Iowa State University
- Ames
- USA
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117
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Zhang Z, Ma N, Xuan X. An unusual CC⋯CO interaction in (Z)-3-[(4-halogenphenyl)amino]-2-cyanoprop-2-enoates. NEW J CHEM 2016. [DOI: 10.1039/c5nj01814e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
An unusual CC⋯CO interaction has been discovered in (Z)-3-[(4-halogenphenyl)amino]-2-cyanoprop-2-enoates and rationalized by the density functional theory calculations.
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Affiliation(s)
- Zhenfeng Zhang
- School of Chemistry and Chemical Engineering
- Henan Normal University
- Xinxiang 453007
- P. R. China
| | - Nana Ma
- School of Chemistry and Chemical Engineering
- Henan Normal University
- Xinxiang 453007
- P. R. China
| | - Xiaopeng Xuan
- School of Chemistry and Chemical Engineering
- Henan Normal University
- Xinxiang 453007
- P. R. China
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118
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Abstract
It is shown that the conformational energy ΔGC required for the formation of a suitable cavity or cleft for ligand binding in absence of an effector E is the essential factor for the efficiency of synthetic allosteric systems with positive cooperativity.
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119
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Chang HY, Huang CW, Chen YF, Chen SY, Sheng YJ, Tsao HK. Assembly of Lock-and-Key Colloids Mediated by Polymeric Depletant. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:13085-13093. [PMID: 26566068 DOI: 10.1021/acs.langmuir.5b02527] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Polymer-mediated lock-and-key assembly via depletion attraction is purely a shape-recognition process without any molecular bonding. Since the depletion attraction relates to osmotic pressure and excluded volume, the binding tendency in a dispersion of lock-and-key colloids can be controlled by adjusting the characteristics of polymeric depletants. In this work, dissipative particle dynamics accounting for explicit solvents, polymers, and multiple lock-key pairs are performed to investigate the influences of the polymer concentration, chain length, solvent quality, and chain stiffness. As the polymer concentration associated with osmotic pressure is increased, the binding free energy (E(b)) between a lock-key pair rises linearly and the binding fraction (θ(LK)) in the dispersion grows sigmoidally. Moreover, the increases in the chain length, solvent quality, and chain stiffness lead to the expansion of the polymer size associated with excluded volume and thus both E(b) and θ(LK) rise accordingly. However, E(b) and θ(LK) grow to be insensitive to the chain length for long enough polymer coils but still can be enhanced if the polymer becomes rod-like. As the solvent quality is varied, θ(LK) can be dramatically altered, although the radius of gyration of polymers is slightly changed.
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Affiliation(s)
- Hung-Yu Chang
- Department of Chemical Engineering, National Taiwan University , Taipei, Taiwan 106, R.O.C
| | - Chang-Wei Huang
- Department of Chemical Engineering, National Taiwan University , Taipei, Taiwan 106, R.O.C
| | - Yen-Fu Chen
- Department of Chemical Engineering, National Taiwan University , Taipei, Taiwan 106, R.O.C
| | - Shyh-Yun Chen
- Department of Chemical Engineering, National Taiwan University , Taipei, Taiwan 106, R.O.C
| | - Yu-Jane Sheng
- Department of Chemical Engineering, National Taiwan University , Taipei, Taiwan 106, R.O.C
| | - Heng-Kwong Tsao
- Department of Chemical and Materials Engineering, Department of Physics, National Central University , Jhongli, Taiwan 320, R.O.C
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120
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Bordiga S, Lamberti C, Bonino F, Travert A, Thibault-Starzyk F. Probing zeolites by vibrational spectroscopies. Chem Soc Rev 2015; 44:7262-341. [PMID: 26435467 DOI: 10.1039/c5cs00396b] [Citation(s) in RCA: 188] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This review addresses the most relevant aspects of vibrational spectroscopies (IR, Raman and INS) applied to zeolites and zeotype materials. Surface Brønsted and Lewis acidity and surface basicity are treated in detail. The role of probe molecules and the relevance of tuning both the proton affinity and the steric hindrance of the probe to fully understand and map the complex site population present inside microporous materials are critically discussed. A detailed description of the methods needed to precisely determine the IR absorption coefficients is given, making IR a quantitative technique. The thermodynamic parameters of the adsorption process that can be extracted from a variable-temperature IR study are described. Finally, cutting-edge space- and time-resolved experiments are reviewed. All aspects are discussed by reporting relevant examples. When available, the theoretical literature related to the reviewed experimental results is reported to support the interpretation of the vibrational spectra on an atomic level.
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Affiliation(s)
- Silvia Bordiga
- Department of Chemistry, NIS and INSTM Reference Centers, University of Torino, Via Quarello 15, I-10135 Torino, Italy
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121
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Zhang Y, Huang Y, Zhang J, Zhu L, Chen K, Hao J. Two unprecedented aromatic guanidines supramolecular chains self-assembled by hydrogen bonding interaction. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2015.05.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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122
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Teilum K, Olsen JG, Kragelund BB. Globular and disordered-the non-identical twins in protein-protein interactions. Front Mol Biosci 2015. [PMID: 26217672 PMCID: PMC4496568 DOI: 10.3389/fmolb.2015.00040] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In biology proteins from different structural classes interact across and within classes in ways that are optimized to achieve balanced functional outputs. The interactions between intrinsically disordered proteins (IDPs) and other proteins rely on changes in flexibility and this is seen as a strong determinant for their function. This has fostered the notion that IDP's bind with low affinity but high specificity. Here we have analyzed available detailed thermodynamic data for protein-protein interactions to put to the test if the thermodynamic profiles of IDP interactions differ from those of other protein-protein interactions. We find that ordered proteins and the disordered ones act as non-identical twins operating by similar principles but where the disordered proteins complexes are on average less stable by 2.5 kcal mol(-1).
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Affiliation(s)
- Kaare Teilum
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen Copenhagen, Denmark
| | - Johan G Olsen
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen Copenhagen, Denmark
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen Copenhagen, Denmark
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123
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Wang S, Ding XH, Li YH, Huang W. Effects of strong hydrogen bonds and weak intermolecular interactions on supramolecular assemblies of 4-fluorobenzylamine. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2015.02.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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124
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Xu JF, Chen L, Zhang X. How to Make Weak Noncovalent Interactions Stronger. Chemistry 2015; 21:11938-46. [DOI: 10.1002/chem.201500568] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Indexed: 12/20/2022]
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125
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Li Y, Cheng M, Hao J, Wang C, Jia G, Li C. Terpyridine-Cu(ii) targeting human telomeric DNA to produce highly stereospecific G-quadruplex DNA metalloenzyme. Chem Sci 2015; 6:5578-5585. [PMID: 29861895 PMCID: PMC5949855 DOI: 10.1039/c5sc01381j] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 06/23/2015] [Indexed: 11/21/2022] Open
Abstract
The cofactors commonly involved in natural enzymes have provided the inspiration for numerous advances in the creation of artificial metalloenzymes. Nevertheless, to design an appropriate cofactor for a given biomolecular scaffold or vice versa remains a challenge in developing efficient catalysts in biochemistry. Herein, we extend the idea of G-quadruplex-targeting anticancer drug design to construct a G-quadruplex DNA metalloenzyme. We found that a series of terpyridine-Cu(ii) complexes (CuLn) can serve as excellent cofactors to dock with human telemetric G-quadruplex DNA. The resulting G-quadruplex DNA metalloenzyme utilising CuL1 catalyzes an enantioselective Diels-Alder reaction with enantioselectivity of >99% enantiomeric excess and about 73-fold rate acceleration compared to CuL1 alone. The terpyridine-Cu(ii) complex cofactors demonstrate dual functions, both as an active site to perform catalysis and as a structural regulator to promote the folding of human telemetric G-quadruplex DNA towards excellent catalysts.
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Affiliation(s)
- Yinghao Li
- State Key Laboratory of Catalysis , Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian 116023 , China . ; .,University of Chinese Academy of Sciences , No. 19A Yuquan Road , Beijing , 100049 , China
| | - Mingpan Cheng
- State Key Laboratory of Catalysis , Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian 116023 , China . ; .,University of Chinese Academy of Sciences , No. 19A Yuquan Road , Beijing , 100049 , China
| | - Jingya Hao
- State Key Laboratory of Catalysis , Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian 116023 , China . ; .,University of Chinese Academy of Sciences , No. 19A Yuquan Road , Beijing , 100049 , China
| | - Changhao Wang
- State Key Laboratory of Catalysis , Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian 116023 , China . ;
| | - Guoqing Jia
- State Key Laboratory of Catalysis , Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian 116023 , China . ;
| | - Can Li
- State Key Laboratory of Catalysis , Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian 116023 , China . ;
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126
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Yang RCK, Huang JTB, Chen YL, Hung CC, Liao M, Yao WC, Chen CH, Liou CC, Waring MJ, Sheh L. Enthalpy-driven nuclease-like activity and mechanism of peptide-chlorambucil conjugates. Org Biomol Chem 2015; 12:4890-904. [PMID: 24874710 DOI: 10.1039/c4ob00123k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the results of attaching the anticancer drug chlorambucil (CLB) to two high-affinity DNA binding peptides: Met-Hyp-Arg-Lys-(Py)4-Lys-Arg-NH2 (HyM-10) and Gln-Hyp-Arg-Lys-(Py)4-Lys-Arg-NH2 (HyQ-10). These CLB-peptide conjugates cleave DNA very effectively and sequence-selectively without the use of chemicals, heat, or UV irradiation. Polyacrylamide gel electrophoresis identifies the sites where CLB-HyM-10 and CLB-HyQ-10 attack a complementary pair of 5'-(32)P-labeled duplexes derived from pBR322 in the absence of piperidine or other chemical additives. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) has confirmed the preferential cleavage sites as well as a novel stepwise cleavage mechanism of sequence-selective DNA cleavage. Resembling restriction endonucleases, the CLB-peptide conjugates appear to be capable of producing double strand DNA breaks. Circular dichroism studies show that CLB-HyM-10 and CLB-HyQ-10 induce significant local conformational changes in DNA via the minor groove, possibly with dimeric binding stoichiometry. The energetic basis of DNA binding by these conjugates has been investigated by isothermal titration calorimetry, revealing that the binding of both the peptides and their CLB conjugates is overwhelmingly enthalpy-driven. The maintenance of a conserved negative binding free energy in DNA-conjugate interactions is a crucial feature of the universal enthalpy-entropy compensation phenomenon. The strongly enthalpy-driven binding of CLB-peptide conjugates to preferred loci in DNA furnishes the required proximity effect to generate the observed nuclease-like sequence-selective cleavage.
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Affiliation(s)
- Robin C K Yang
- Department of Chemistry and Life Science Center, Tunghai Christian University, Taichung, Taiwan 407, Republic of China.
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127
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Niu S, Ruotolo BT. Collisional unfolding of multiprotein complexes reveals cooperative stabilization upon ligand binding. Protein Sci 2015; 24:1272-81. [PMID: 25970849 DOI: 10.1002/pro.2699] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Revised: 04/13/2015] [Accepted: 04/29/2015] [Indexed: 12/19/2022]
Abstract
Cooperative binding mechanisms are a common feature in biology, enabling a diverse range of protein-based molecular machines to regulate activities ranging from oxygen uptake to cellular membrane transport. Much, however, is not known about such cooperative binding mechanisms, including how such events typically add to the overall stability of such protein systems. Measurements of such cooperative stabilization events are challenging, as they require the separation and resolution of individual protein complex bound states within a mixture of potential stoichiometries to individually assess protein stabilities. Here, we report ion mobility-mass spectrometry results for the concanavalin A tetramer bound to a range of polysaccharide ligands. We use collision induced unfolding, a relatively new methodology that functions as a gas-phase analog of calorimetry experiments in solution, to individually assess the stabilities of concanavalin A bound states. By comparing the differences in activation voltage required to unfold different concanavalin A-ligand stoichiometries, we find evidence suggesting a cooperative stabilization of concanavalin A occurs upon binding most carbohydrate ligands. We critically evaluate this observation by assessing a broad range of ligands, evaluating the unfolding properties of multiple protein charge states, and by comparing our gas-phase results with those obtained from calorimetry experiments carried out in solution.
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Affiliation(s)
- Shuai Niu
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109
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128
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Chen S, Itoh Y, Masuda T, Shimizu S, Zhao J, Ma J, Nakamura S, Okuro K, Noguchi H, Uosaki K, Aida T. Ionic interactions. Subnanoscale hydrophobic modulation of salt bridges in aqueous media. Science 2015; 348:555-9. [PMID: 25931555 DOI: 10.1126/science.aaa7532] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Polar interactions such as electrostatic forces and hydrogen bonds play an essential role in biological molecular recognition. On a protein surface, polar interactions occur mostly in a hydrophobic environment because nonpolar amino acid residues cover ~75% of the protein surface. We report that ionic interactions on a hydrophobic surface are modulated by their subnanoscale distance to the surface. We developed a series of ionic head groups-appended self-assembled monolayers with C2, C6, C8, and C12 space-filling alkyl chains, which capture a dendritic guest via the formation of multiple salt bridges. The guest release upon protonolysis is progressively suppressed when its distance from the background hydrophobe changes from 1.2 (C2) to 0.2 (C12) nanometers, with an increase in salt bridge strength of ~3.9 kilocalories per mole.
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Affiliation(s)
- Shuo Chen
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yoshimitsu Itoh
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
| | - Takuya Masuda
- Global Research Center for Environment and Energy based on Nanomaterials Science (GREEN), National Institute for Materials Science (NIMS), Tsukuba 305-0044, Japan
| | - Seishi Shimizu
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
| | - Jun Zhao
- Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, P. R. China
| | - Jing Ma
- Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, P. R. China
| | - Shugo Nakamura
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kou Okuro
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Hidenori Noguchi
- Global Research Center for Environment and Energy based on Nanomaterials Science (GREEN), National Institute for Materials Science (NIMS), Tsukuba 305-0044, Japan. International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science (NIMS), Tsukuba 305-0044, Japan. Graduate School of Chemical Science and Engineering, Hokkaido University, Sapporo 060-0810, Japan
| | - Kohei Uosaki
- Global Research Center for Environment and Energy based on Nanomaterials Science (GREEN), National Institute for Materials Science (NIMS), Tsukuba 305-0044, Japan. International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science (NIMS), Tsukuba 305-0044, Japan. Graduate School of Chemical Science and Engineering, Hokkaido University, Sapporo 060-0810, Japan
| | - Takuzo Aida
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan. RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
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129
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Fong CW. Binding energies of tyrosine kinase inhibitors: Error assessment of computational methods for imatinib and nilotinib binding. Comput Biol Chem 2015; 58:40-54. [PMID: 26025598 DOI: 10.1016/j.compbiolchem.2015.05.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 05/09/2015] [Accepted: 05/13/2015] [Indexed: 11/30/2022]
Abstract
The binding energies of imatinib and nilotinib to tyrosine kinase have been determined by quantum mechanical (QM) computations, and compared with literature binding energy studies using molecular mechanics (MM). The potential errors in the computational methods include these critical factors. Errors in X-ray structures such as structural distortions and steric clashes give unrealistically high van der Waals energies, and erroneous binding energies.MM optimization gives a very different configuration to the QM optimization for nilotinib, whereas the imatinib ion gives similar configurations. Solvation energies are a major component of the overall binding energy. The QM based solvent model (PCM/SMD) gives different values from those used in the implicit PBSA solvent MM models. A major error in inhibitor—kinase binding lies in the non-polar solvation terms. Solvent transfer free energies and the required empirical solvent accessible surface area factors for nilotinib and imatinib ion to give the transfer free energies have been reverse calculated. These values differ from those used in the MM PBSA studies.An intertwined desolvation—conformational binding selectivity process is a balance of thermodynamic desolvation and intramolecular conformational kinetic control.The configurational entropies (TΔS) are minor error sources.
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130
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Said AM, Hangauer DG. Binding cooperativity between a ligand carbonyl group and a hydrophobic side chain can be enhanced by additional H-bonds in a distance dependent manner: A case study with thrombin inhibitors. Eur J Med Chem 2015; 96:405-24. [DOI: 10.1016/j.ejmech.2015.03.059] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 03/21/2015] [Accepted: 03/25/2015] [Indexed: 01/07/2023]
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131
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Chong Y, Kleinhammes A, Tang P, Xu Y, Wu Y. Dominant Alcohol-Protein Interaction via Hydration-Enabled Enthalpy-Driven Binding Mechanism. J Phys Chem B 2015; 119:5367-75. [PMID: 25856773 DOI: 10.1021/acs.jpcb.5b00378] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Water plays an important role in weak associations of small drug molecules with proteins. Intense focus has been on binding-induced structural changes in the water network surrounding protein binding sites, especially their contributions to binding thermodynamics. However, water is also tightly coupled to protein conformations and dynamics, and so far little is known about the influence of water-protein interactions on ligand binding. Alcohols are a type of low-affinity drugs, and it remains unclear how water affects alcohol-protein interactions. Here, we present alcohol adsorption isotherms under controlled protein hydration using in situ NMR detection. As functions of hydration level, Gibbs free energy, enthalpy, and entropy of binding were determined from the temperature dependence of isotherms. Two types of alcohol binding were found. The dominant type is low-affinity nonspecific binding, which is strongly dependent on temperature and the level of hydration. At low hydration levels, this nonspecific binding only occurs above a threshold of alcohol vapor pressure. An increased hydration level reduces this threshold, with it finally disappearing at a hydration level of h ≈ 0.2 (g water/g protein), gradually shifting alcohol binding from an entropy-driven to an enthalpy-driven process. Water at charged and polar groups on the protein surface was found to be particularly important in enabling this binding. Although further increase in hydration has smaller effects on the changes of binding enthalpy and entropy, it results in a significant negative change in Gibbs free energy due to unmatched enthalpy-entropy compensation. These results show the crucial role of water-protein interplay in alcohol binding.
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Affiliation(s)
- Yuan Chong
- †Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27599-3255, United States
| | - Alfred Kleinhammes
- †Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27599-3255, United States
| | | | | | - Yue Wu
- †Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27599-3255, United States
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132
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Yang Y, Zhang L, Guo M, Sun J, Matsukawa S, Xie J, Wei D. Novel α-L-arabinofuranosidase from Cellulomonas fimi ATCC 484 and its substrate-specificity analysis with the aid of computer. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:3725-33. [PMID: 25797391 DOI: 10.1021/jf5059683] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
In the process of gene mining for novel α-L-arabinofuranosidases (AFs), the gene Celf_3321 from Cellulomonas fimi ATCC 484 encodes an AF, termed as AbfCelf, with potent activity, 19.4 U/mg under the optimum condition, pH 6.0 and 40 °C. AbfCelf can hydrolyze α-1,5-linked oligosaccharides, sugar beet arabinan, linear 1,5-α-arabinan, and wheat flour arabinoxylan, which is partly different from some previously well-characterized GH 51 AFs. The traditional substrate-specificity analysis for AFs is labor-consuming and money costing, because the substrates include over 30 kinds of various 4-nitrophenol (PNP)-glycosides, oligosaccharides, and polysaccharides. Hence, a preliminary structure and mechanism based method was applied for substrate-specificity analysis. The binding energy (ΔG, kcal/mol) obtained by docking suggested the reaction possibility and coincided with the experimental results. AbfA crystal 1QW9 was used to test the rationality of docking method in simulating the interaction between enzyme and substrate, as well the credibility of the substrate-specificity analysis method in silico.
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Affiliation(s)
- Ying Yang
- †State Key Laboratory of Bioreactor Engineering, Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Lujia Zhang
- †State Key Laboratory of Bioreactor Engineering, Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Mingrong Guo
- †State Key Laboratory of Bioreactor Engineering, Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Jiaqi Sun
- †State Key Laboratory of Bioreactor Engineering, Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Shingo Matsukawa
- §Department of Food Science and Technology, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
| | - Jingli Xie
- †State Key Laboratory of Bioreactor Engineering, Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, People's Republic of China
- ‡Shanghai Collaborative Innovation Center for Biomanufacturing, Shanghai 200237, People's Republic of China
| | - Dongzhi Wei
- †State Key Laboratory of Bioreactor Engineering, Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, People's Republic of China
- ‡Shanghai Collaborative Innovation Center for Biomanufacturing, Shanghai 200237, People's Republic of China
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133
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Piazza M, Guillemette JG, Dieckmann T. Dynamics of nitric oxide synthase-calmodulin interactions at physiological calcium concentrations. Biochemistry 2015; 54:1989-2000. [PMID: 25751535 DOI: 10.1021/bi501353s] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The intracellular Ca²⁺ concentration is an important regulator of many cellular functions. The small acidic protein calmodulin (CaM) serves as a Ca²⁺ sensor and control element for many enzymes. Nitric oxide synthase (NOS) is one of the proteins that is activated by CaM and plays a major role in a number of key physiological and pathological processes. Previous studies have shown CaM to act like a switch that causes a conformational change in NOS to allow for the electron transfer between the reductase and oxygenase domains through a process that is thought to be highly dynamic. We have analyzed the structure and dynamics of complexes formed by peptides based on inducible NOS (iNOS) and endothelial NOS (eNOS) with CaM at Ca²⁺ concentrations that mimic the physiological basal (17 and 100 nM) and elevated levels (225 nM) found in mammalian cells using fluorescence techniques and nuclear magnetic resonance spectroscopy. The results show the CaM-NOS complexes have similar structures at physiological and fully saturated Ca²⁺ levels; however, their dynamics are remarkably different. At 225 nM Ca²⁺, the CaM-NOS complexes show overall an increase in backbone dynamics, when compared to the dynamics of the complexes at saturating Ca²⁺ concentrations. Specifically, the N-lobe of CaM in the CaM-iNOS complex displays a lower internal mobility (higher S²) and higher exchange protection compared to those of the CaM-eNOS complex. In contrast, the C-lobe of CaM in the CaM-eNOS complex is less dynamic. These results illustrate that structures of CaM-NOS complexes determined at saturated Ca²⁺ concentrations cannot provide a complete picture because the differences in intramolecular dynamics become visible only at physiological Ca²⁺ levels.
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Affiliation(s)
- Michael Piazza
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - J Guy Guillemette
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Thorsten Dieckmann
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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134
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Kawai H. Hydrindacenes as Versatile Supramolecular Scaffolds. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2015. [DOI: 10.1246/bcsj.20140313] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Hidetoshi Kawai
- Department of Chemistry, Faculty of Science, Tokyo University of Science
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135
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Gunasekara RW, Zhao Y. Rationally Designed Cooperatively Enhanced Receptors To Magnify Host–Guest Binding in Water. J Am Chem Soc 2015; 137:843-9. [DOI: 10.1021/ja510823h] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Roshan W. Gunasekara
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, United States
| | - Yan Zhao
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, United States
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136
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Experimental confirmation of ground state isotopic isomerization from OC⋯HI to OC⋯ID. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2014.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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137
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Zafar A, Ahmad S, Naseem I. Insight into the structural stability of coumestrol with human estrogen receptor α and β subtypes: a combined approach involving docking and molecular dynamics simulation studies. RSC Adv 2015. [DOI: 10.1039/c5ra14745j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Structural stability of coumestrol with human estrogen receptor α and β subtypes.
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Affiliation(s)
- Atif Zafar
- Department of Biochemistry
- Faculty of Life Sciences
- Aligarh Muslim University
- Aligarh 202002
- India
| | - Sabahuddin Ahmad
- Department of Computer Science
- Faculty of Natural Sciences
- New Delhi 110025
- India
| | - Imrana Naseem
- Department of Biochemistry
- Faculty of Life Sciences
- Aligarh Muslim University
- Aligarh 202002
- India
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138
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Hitaoka S, Chuman H, Yoshizawa K. A QSAR study on the inhibition mechanism of matrix metalloproteinase-12 by arylsulfone analogs based on molecular orbital calculations. Org Biomol Chem 2015; 13:793-806. [DOI: 10.1039/c4ob01843e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The inhibition mechanism of matrix metalloproteinase-12 by arylsulfone analogs is revealed using a comprehensive computational approach including docking simulations, molecular orbital calculations, and QSAR.
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Affiliation(s)
- Seiji Hitaoka
- Institute for Materials Chemistry and Engineering and International Research Center for Molecular System
- Kyushu University
- Fukuoka 819-0395
- Japan
| | - Hiroshi Chuman
- Institute of Health Biosciences
- The University of Tokushima Graduate School
- Tokushima 770-8505
- Japan
| | - Kazunari Yoshizawa
- Institute for Materials Chemistry and Engineering and International Research Center for Molecular System
- Kyushu University
- Fukuoka 819-0395
- Japan
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139
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Insight into the effect of inhibitor resistant S130G mutant on physico-chemical properties of SHV type beta-lactamase: a molecular dynamics study. PLoS One 2014; 9:e112456. [PMID: 25479359 PMCID: PMC4257546 DOI: 10.1371/journal.pone.0112456] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Accepted: 10/14/2014] [Indexed: 11/29/2022] Open
Abstract
Bacterial resistance is a serious threat to human health. The production of β-lactamase, which inactivates β-lactams is most common cause of resistance to the β-lactam antibiotics. The Class A enzymes are most frequently encountered among the four β-lactamases in the clinic isolates. Mutations in class A β-lactamases play a crucial role in substrate and inhibitor specificity. SHV and TEM type are known to be most common class A β-lactamases. In the present study, we have analyzed the effect of inhibitor resistant S130G point mutation of SHV type Class-A β-lactamase using molecular dynamics and other in silico approaches. Our study involved the use of different in silico methods to investigate the affect of S130G point mutation on the major physico-chemical properties of SHV type class A β-lactamase. We have used molecular dynamics approach to compare the dynamic behaviour of native and S130G mutant form of SHV β-lactamase by analyzing different properties like root mean square deviation (RMSD), H-bond, Radius of gyration (Rg) and RMS fluctuation of mutation. The results clearly suggest notable loss in the stability of S130G mutant that may further lead to decrease in substrate specificity of SHV. Molecular docking further indicates that S130G mutation decreases the binding affinity of all the three inhibitors in clinical practice.
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140
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Bardelang D, Casano G, Poulhès F, Karoui H, Filippini J, Rockenbauer A, Rosas R, Monnier V, Siri D, Gaudel-Siri A, Ouari O, Tordo P. Spin Exchange Monitoring of the Strong Positive Homotropic Allosteric Binding of a Tetraradical by a Synthetic Receptor in Water. J Am Chem Soc 2014; 136:17570-7. [DOI: 10.1021/ja509586k] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- David Bardelang
- Aix-Marseille Université, CNRS, Institut de Chimie Radicalaire, UMR 7273, 13397 Marseille, France
| | - Gilles Casano
- Aix-Marseille Université, CNRS, Institut de Chimie Radicalaire, UMR 7273, 13397 Marseille, France
| | - Florent Poulhès
- Aix-Marseille Université, CNRS, Institut de Chimie Radicalaire, UMR 7273, 13397 Marseille, France
| | - Hakim Karoui
- Aix-Marseille Université, CNRS, Institut de Chimie Radicalaire, UMR 7273, 13397 Marseille, France
| | - Jessica Filippini
- Aix-Marseille Université, CNRS, Institut de Chimie Radicalaire, UMR 7273, 13397 Marseille, France
| | - Antal Rockenbauer
- Department of Physics, Budapest University of Technology and Economics and MTA-BME Condensed Matter Research Group, Budafoki ut 8, 1111 Budapest, Hungary
| | - Roselyne Rosas
- Aix-Marseille Université, CNRS, Spectropole, FR 1739, 13013 Marseille, France
| | - Valérie Monnier
- Aix-Marseille Université, CNRS, Spectropole, FR 1739, 13013 Marseille, France
| | - Didier Siri
- Aix-Marseille Université, CNRS, Institut de Chimie Radicalaire, UMR 7273, 13397 Marseille, France
| | - Anouk Gaudel-Siri
- Aix-Marseille Université, CNRS, Institut de Chimie Radicalaire, UMR 7273, 13397 Marseille, France
| | - Olivier Ouari
- Aix-Marseille Université, CNRS, Institut de Chimie Radicalaire, UMR 7273, 13397 Marseille, France
| | - Paul Tordo
- Aix-Marseille Université, CNRS, Institut de Chimie Radicalaire, UMR 7273, 13397 Marseille, France
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141
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Charisiadis P, Tsiafoulis CG, Tzakos AG, Gerothanassis IP. Dynamic changes in composition of extracts of natural products as monitored by in situ NMR. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2014; 52:764-768. [PMID: 25139153 DOI: 10.1002/mrc.4128] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 07/24/2014] [Accepted: 07/27/2014] [Indexed: 06/03/2023]
Abstract
The direct in situ NMR observation and quantification, based on the aldehyde -CH chemical shift region, of the inter-conversion of secoiridoid derivatives due to temperature and solvent effects is demonstrated in complex extracts of natural products without prior isolation of the individual components. The equilibrium between the aldehyde hydrate form and the dialdehyde form of the oleuropein aglycon of an olive leaf aqueous extract in D(2)O was shown to be temperature dependent. The resulting thermodynamic values of the Van't Hoff plot with ΔH(o) = -26.34 ± 1.00 kJ mol(-1) and TΔS° (298 K) = -24.70 ± 1.00 kJ mol(-1) demonstrate a significant entropy term which nearly compensates the effect of enthalpy at room temperature. The equilibrium between the two diastereomeric hemiacetal forms and the dialdehyde form of the oleuropein 6-O-β-d-glucopyranoside aglycon of an olive leaf aqueous extract in CD(3) OD was also shown to be strongly temperature dependent again because of the significant entropy term (TΔS° (298 K) = -26.50 ± 1.39 kJ mol(-1)) compared with that of the enthalpy term (ΔH(o) = -36.64 ± 1.46 kJ mol(-1)). This is the first demonstration of the significant role of the entropy parameter in determining the equilibrium of chemical transformations in complex mixtures of natural products due to solvent and temperature effects.
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Affiliation(s)
- Pantelis Charisiadis
- Section of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, Ioannina, GR-45110, Greece
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142
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Singh RK, Suzuki T, Mandal T, Balsubramanian N, Haldar M, Mueller DJ, Strode JA, Cook G, Mallik S, Srivastava DK. Thermodynamics of binding of structurally similar ligands to histone deacetylase 8 sheds light on challenges in the rational design of potent and isozyme-selective inhibitors of the enzyme. Biochemistry 2014; 53:7445-58. [PMID: 25407689 PMCID: PMC4263425 DOI: 10.1021/bi500711x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
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Among the different histone deacetylase
(HDAC) isozymes, HDAC8
is the most highly malleable enzyme, and it exhibits the potential
to accommodate structurally diverse ligands (albeit with moderate
binding affinities) in its active site pocket. To probe the molecular
basis of this feature, we performed detailed thermodynamic studies
of the binding of structurally similar ligands, which differed with
respect to the “cap”, “linker”, and “metal-binding”
regions of the suberoylanilide hydroxamic acid (SAHA) pharmacophore,
to HDAC8. The experimental data revealed that although the enthalpic
(ΔH°) and entropic (ΔS°) changes for the binding of individual SAHA analogues to HDAC8
were substantially different, their binding free energies (ΔG°) were markedly similar, conforming to a strong enthalpy–entropy
compensation effect. This effect was further observed in the temperature-dependent
thermodynamics of binding of all SAHA analogues to the enzyme. Notably,
in contrast to other metalloenzymes, our isothermal titration calorimetry
experiments (performed in different buffers of varying ionization
enthalpies) suggest that depending on the ligand, its zinc-binding
group may or may not be deprotonated upon the binding to HDAC8. Furthermore,
the heat capacity changes (ΔCp°) associated with the ligand binding
to HDAC8 markedly differed from one SAHA analogue to the other, and
such features could primarily be rationalized in light of the dynamic
flexibility in the enzyme structure in conjunction with the reorganization
of the active site resident water molecules. Arguments are presented
that although the binding thermodynamic features described above would
facilitate identification of weak to moderately tight-binding HDAC8
inhibitors (by a high-throughput and/or virtual screening of libraries
of small molecules), they would pose major challenges for the structure-based
rational design of highly potent and isozyme-selective inhibitors
of human HDAC8.
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Affiliation(s)
- Raushan K Singh
- Department of Chemistry and Biochemistry, North Dakota State University , Fargo, North Dakota 58102, United States
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143
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Rakipov IT, Varfolomeev MA, Kirgizov AY, Solomonov BN. Thermochemistry of dissolution, solvation, and hydrogen bonding of anilines in proton-acceptor organic solvents at 298.15 K. RUSS J GEN CHEM+ 2014. [DOI: 10.1134/s1070363214090059] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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144
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Machan CW, Chabolla SA, Yin J, Gilson MK, Tezcan FA, Kubiak CP. Supramolecular Assembly Promotes the Electrocatalytic Reduction of Carbon Dioxide by Re(I) Bipyridine Catalysts at a Lower Overpotential. J Am Chem Soc 2014; 136:14598-607. [DOI: 10.1021/ja5085282] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Charles W. Machan
- Department
of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Steven A. Chabolla
- Department
of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Jian Yin
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California-San Diego, 9500 Gilman Drive, La Jolla, California 92093-0736, United States
| | - Michael K. Gilson
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California-San Diego, 9500 Gilman Drive, La Jolla, California 92093-0736, United States
| | - F. Akif Tezcan
- Department
of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Clifford P. Kubiak
- Department
of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
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145
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Facile surface functionalization of multiwalled carbon nanotubes by soft dielectric barrier discharge plasma: Generate compatible interface for lipase immobilization. Biochem Eng J 2014. [DOI: 10.1016/j.bej.2014.05.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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146
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Gupta N, Goyal M, Wu CH, Wu GY. The Molecular and Structural Basis of HBV-resistance to Nucleos(t)ide Analogs. J Clin Transl Hepatol 2014; 2:202-11. [PMID: 26357626 PMCID: PMC4548360 DOI: 10.14218/jcth.2014.00021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 07/26/2014] [Accepted: 07/27/2014] [Indexed: 02/06/2023] Open
Abstract
Infection with hepatitis B virus (HBV) is a worldwide health problem. Chronic hepatitis B can lead to fibrosis, liver cirrhosis, and hepatocellular carcinoma (HCC). Management of the latter two conditions often requires liver transplantation. Treatment with conventional interferon or pegylated interferon alpha can clear the virus, but the rates are very low. The likelihood, however, of viral resistance to interferon is minimal. The main problems with this therapy are the frequency and severity of side effects. In contrast, nucleos(t)ide analogs (NAs) have significantly lower side effects, but require long term treatment as sustained virological response rates are extremely low. However, long term treatment with NAs increases the risk for the development of anti-viral drug resistance. Only by understanding the molecular basis of resistance and using agents with multiple sites of action can drugs be designed to optimally prevent the occurrence of HBV antiviral resistance.
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Affiliation(s)
- Nidhi Gupta
- Department of Medicine, Division of Gastroenterology-Hepatology, University of Connecticut Heath Center, Farmington, USA
| | - Milky Goyal
- Department of Microbiology, College of Basic Sciences and Humanities, Punjab Agriculture University, Ludhiana, Punjab, India
| | - Catherine H. Wu
- Department of Medicine, Division of Gastroenterology-Hepatology, University of Connecticut Heath Center, Farmington, USA
| | - George Y. Wu
- Department of Medicine, Division of Gastroenterology-Hepatology, University of Connecticut Heath Center, Farmington, USA
- Correspondence to: George Y. Wu, Department of Medicine, Division of Gastroenterology-Hepatology, University of Connecticut Health Center, Farmington, CT 06030, USA. Tel: +1-800-535-6232. E-mail:
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147
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A B3LYP and MP2(full) theoretical investigation into cooperativity effects, aromaticity and thermodynamic properties in the Na(+)⋯benzonitrile⋯H2O ternary complex. J Mol Model 2014; 20:2341. [PMID: 25005001 DOI: 10.1007/s00894-014-2341-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Accepted: 06/08/2014] [Indexed: 10/25/2022]
Abstract
The cooperativity effects between H-bonding and Na(+)⋯π or Na(+)⋯σ interactions in Na(+)⋯benzonitrile⋯H2O complexes were investigated using the B3LYP and MP2(full) methods with 6-311++G(2d,p) and aug-cc-pVTZ basis sets. The thermodynamic cooperativity and the influence of this cooperativity on aromaticity was evaluated by nucleus-independent chemical shifts (NICS). The results showed that the influence of the Na(+)⋯σ or Na(+)⋯π interaction on the hydrogen bond is more pronounced than that of the latter on the former. The cooperativity effect appeared in the Na(+)⋯σ interaction complex while the anti-cooperativity effect tended to be in the Na(+)⋯π system. The change in enthalpy is the major factor driving cooperativity. Thermodynamic cooperativity is not in accordance with the cooperativity effect evaluated by the change of interaction energy. The ring aromaticity of is weakened while the bond dissociation energy (BDE) of the C-CN bond increases upon ternary complex formation. The cooperativity effect (E coop) correlates with R c (NICS(1)ternary/NICS(1)binary) and ΔΔδ (Δδ ternary - Δδ binary) involving the ring and C ≡ N bond, as well as R BDE(C-CN) [BDE(C-CN)ternary/BDE(C-CN)binary], respectively. AIM (atoms in molecules) analysis confirms the existence of cooperativity.
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148
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Structure, mechanism, and enantioselectivity shifting of lipase LipK107 with a simple way. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1183-92. [DOI: 10.1016/j.bbapap.2014.02.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 02/16/2014] [Accepted: 02/24/2014] [Indexed: 11/18/2022]
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149
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Zhao C, Li P, Smith MD, Pellechia PJ, Shimizu KD. Experimental Study of the Cooperativity of CH−π Interactions. Org Lett 2014; 16:3520-3. [DOI: 10.1021/ol5014729] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Chen Zhao
- Department
of Chemistry and
Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Ping Li
- Department
of Chemistry and
Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Mark D. Smith
- Department
of Chemistry and
Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Perry J. Pellechia
- Department
of Chemistry and
Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Ken D. Shimizu
- Department
of Chemistry and
Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
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150
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Affiliation(s)
- Alan C. Gibbs
- Janssen Pharmaceutical Research and Development, LLC, Welsh and McKean Road, Spring House, Pennsylvania 19477-0776, United States
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