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C-methyl flavonoid from the leaves of Cleistocalyx conspersipunctatus: α-glucosidase inhibitory, molecular docking simulation and biosynthetic pathway. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2022.103687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Biswas R, Ghosh P, Banerjee T, Ali SM, Singha Deb AK. Interfacial Behavior of Cs +, K +, Na +, and Rb + Extraction in the Presence of Dibenzo-18-Crown-6 from the Nitrobenzene-Water Biphasic System: Experimental, Quantum Chemical, and Molecular Dynamic Studies. ACS OMEGA 2018; 3:1663-1674. [PMID: 31458486 PMCID: PMC6641252 DOI: 10.1021/acsomega.7b01828] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 01/29/2018] [Indexed: 06/10/2023]
Abstract
Extraction of metal ions (i.e., Cs+, K+, Na+, and Rb+) in the presence of ionophore such as dibenzo-18-crown-6 (DB18C6) from the nitrobenzene-water biphasic system is reported by COSMO-RS (conductor-like screening model for real solvents) predictions, molecular dynamics simulation, along with experimental validation. The predicted values of selectivity as obtained for the Na+-DB18C6 complex were 4.571, 4.877, and 4.947 at 298.15, 308.15, and 318.15 K, respectively. This was then confirmed by the experimental distribution coefficient (D) as obtained in the diluent systems along with by varying the metal ion to crown ether ligand (M-L) mole ratios: 10:1 (0.1 M M+ and 0.01 M DB18C6), 1:1 (0.01 M M+ and 0.01 M DB18C6), and 1:10 (0.001 M M+ and 0.01 M DB18C6). The experimentally determined values of D Na (i.e., 0.059, 0.060, and 0.056) were found to be very large as compared to the values of D Cs (i.e., 0.001, 0.010, and 0.024) in the nitrobenzene phase. It indicates an excellent extraction ability of DB18C6 for Na+. The rate of phase separation for the Cs+NO3 - system was slow as compared to other metal ion systems. The binding energies, free energies, and nonbonded interaction energies of the complexed metal ion in solution were calculated with both explicit and implicit solvent models. A higher interaction energy between Na+-DB18C6 complex and nitrobenzene was observed (i.e., -289.92 in the explicit model and -143.12 kcal/mol in the implicit model) when compared with other metal ions (i.e., Cs+, K+, and Rb+).
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Affiliation(s)
- Rima Biswas
- Department
of Chemical Engineering, Indian Institute
of Technology Guwahati, Guwahati, 781039 Assam, India
| | - Pallab Ghosh
- Department
of Chemical Engineering, Indian Institute
of Technology Guwahati, Guwahati, 781039 Assam, India
| | - Tamal Banerjee
- Department
of Chemical Engineering, Indian Institute
of Technology Guwahati, Guwahati, 781039 Assam, India
| | - Sk. Musharaf Ali
- Bhabha
Atomic Research Center, Chemical Engineering
Division, Mumbai, 400085 Maharashtra, India
| | - Ashish Kumar Singha Deb
- Bhabha
Atomic Research Center, Chemical Engineering
Division, Mumbai, 400085 Maharashtra, India
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Biswas R, Malviya A, Banerjee T, Ghosh P, Ali SM. Alkali Metal Ion Partitioning with Calix[4]arene-benzo-crown-6 Ionophore in Acidic Medium: Insights from Experiments, Statistical Mechanical Framework, and Molecular Dynamics Simulations. J Phys Chem B 2018; 122:2102-2112. [DOI: 10.1021/acs.jpcb.7b10632] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rima Biswas
- Department of Chemical
Engineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Abhigyan Malviya
- Department of Chemical
Engineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Tamal Banerjee
- Department of Chemical
Engineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Pallab Ghosh
- Department of Chemical
Engineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Sk. Musharaf Ali
- Chemical Engineering Division, Bhabha Atomic Research Center, Mumbai 400085, India
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Richards LA, Nash A, Willetts A, Entwistle C, de Leeuw NH. Modelling water diffusion in plasticizers: development and optimization of a force field for 2,4-dinitroethylbenzene and 2,4,6-trinitroethylbenzene. RSC Adv 2018; 8:5728-5739. [PMID: 35557986 PMCID: PMC9092615 DOI: 10.1039/c7ra12254c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 01/19/2018] [Indexed: 11/21/2022] Open
Abstract
A classical all-atom force field has been developed for 2,4,6-trinitroethylbenzene and 2,4-dinitroethylbenzene and applied in molecular dynamics simulations of the two pure and two mixed plasticizer systems. Bonding parameters and partial charges were derived through electronic and geometry optimization of the single molecules. The other required parameters were derived from values already available in the literature for generic nitro aromatic compounds, which were adjusted to reproduce to a high level of accuracy the densities of 2,4-dinitroethylbenzene, 2,4,6-trinitroethylbenzene and the energetic plasticizers K10 and R8002. This force field has been applied to both K10 and R8002, which when used as plasticizers form an energetic binder with nitrocellulose. Nitrocellulose decomposes in storage, under varying conditions, but in particular where it may become increasingly dry. Following the derivation of the force field, we have therefore applied it to calculate water diffusion coefficients for each of the different materials at 298 K and 338 K, thereby providing a starting point for understanding water behaviour in a nitrocellulose binder. A classical all-atom force field has been developed for the plasticizer molecules 2,4,6-trinitroethylbenzene and 2,4-dinitroethylbenzene which can be used to investigate properties and energetic output of nitrocellulose-based propellants and binders.![]()
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Affiliation(s)
- Lisa A. Richards
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
| | - Anthony Nash
- Department of Physiology Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, OX1 3QX, UK
| | - Andrew Willetts
- Atomic Weapons Establishment, Aldermaston, Reading, Berkshire, RG7 4PR, UK
| | - Chris Entwistle
- Atomic Weapons Establishment, Aldermaston, Reading, Berkshire, RG7 4PR, UK
| | - Nora H. de Leeuw
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, UK
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Nieto-Draghi C, Fayet G, Creton B, Rozanska X, Rotureau P, de Hemptinne JC, Ungerer P, Rousseau B, Adamo C. A General Guidebook for the Theoretical Prediction of Physicochemical Properties of Chemicals for Regulatory Purposes. Chem Rev 2015; 115:13093-164. [PMID: 26624238 DOI: 10.1021/acs.chemrev.5b00215] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Carlos Nieto-Draghi
- IFP Energies nouvelles , 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France
| | - Guillaume Fayet
- INERIS, Parc Technologique Alata, BP2 , 60550 Verneuil-en-Halatte, France
| | - Benoit Creton
- IFP Energies nouvelles , 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France
| | - Xavier Rozanska
- Materials Design S.A.R.L. , 18, rue de Saisset, 92120 Montrouge, France
| | - Patricia Rotureau
- INERIS, Parc Technologique Alata, BP2 , 60550 Verneuil-en-Halatte, France
| | | | - Philippe Ungerer
- Materials Design S.A.R.L. , 18, rue de Saisset, 92120 Montrouge, France
| | - Bernard Rousseau
- Laboratoire de Chimie-Physique, Université Paris Sud , UMR 8000 CNRS, Bât. 349, 91405 Orsay Cedex, France
| | - Carlo Adamo
- Institut de Recherche Chimie Paris, PSL Research University, CNRS, Chimie Paristech , 11 rue P. et M. Curie, F-75005 Paris, France.,Institut Universitaire de France , 103 Boulevard Saint Michel, F-75005 Paris, France
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Shang L, Zhang S, Yang X, Sun J, Li L, Cui Z, He Q, Guo Y, Sun Y, Yin Z. Biochemical characterization of recombinant Enterovirus 71 3C protease with fluorogenic model peptide substrates and development of a biochemical assay. Antimicrob Agents Chemother 2015; 59:1827-36. [PMID: 25421478 PMCID: PMC4356770 DOI: 10.1128/aac.04698-14] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 11/17/2014] [Indexed: 02/08/2023] Open
Abstract
Enterovirus 71 (EV71), a primary pathogen of hand, foot, and mouth disease (HFMD), affects primarily infants and children. Currently, there are no effective drugs against HFMD. EV71 3C protease performs multiple tasks in the viral replication, which makes it an ideal antiviral target. We synthesized a small set of fluorogenic model peptides derived from cleavage sites of EV71 polyprotein and examined their efficiencies of cleavage by EV71 3C protease. The novel peptide P08 [(2-(N-methylamino)benzoyl) (NMA)-IEALFQGPPK(DNP)FR] was determined to be the most efficiently cleaved by EV71 3C protease, with a kinetic constant kcat/Km of 11.8 ± 0.82 mM(-1) min(-1). Compared with literature reports, P08 gave significant improvement in the signal/background ratio, which makes it an attractive substrate for assay development. A Molecular dynamics simulation study elaborated the interactions between substrate P08 and EV71 3C protease. Arg39, which is located at the bottom of the S2 pocket of EV71 3C protease, may participate in the proteolysis process of substrates. With an aim to evaluate EV71 3C protease inhibitors, a reliable and robust biochemical assay with a Z' factor of 0.87 ± 0.05 was developed. A novel compound (compound 3) (50% inhibitory concentration [IC50] = 1.89 ± 0.25 μM) was discovered using this assay, which effectively suppressed the proliferation of EV 71 (strain Fuyang) in rhabdomyosarcoma (RD) cells with a highly selective index (50% effective concentration [EC50] = 4.54 ± 0.51 μM; 50% cytotoxic concentration [CC50] > 100 μM). This fast and efficient assay for lead discovery and optimization provides an ideal platform for anti-EV71 drug development targeting 3C protease.
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Affiliation(s)
- Luqing Shang
- College of Pharmacy & State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, People's Republic of China Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, People's Republic of China
| | - Shumei Zhang
- College of Pharmacy & State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, People's Republic of China Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, People's Republic of China
| | - Xi Yang
- College of Pharmacy & State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, People's Republic of China Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, People's Republic of China
| | - Jixue Sun
- College of Pharmacy & State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, People's Republic of China
| | - Linfeng Li
- College of Pharmacy & State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, People's Republic of China Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, People's Republic of China
| | - Zhengjie Cui
- College of Pharmacy & State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, People's Republic of China Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, People's Republic of China
| | - Qiuhong He
- High-Throughput Molecular Drug Discovery Center, Tianjin International Joint Academy of Biotechnology & Medicine, Tianjin, People's Republic of China
| | - Yu Guo
- College of Pharmacy & State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, People's Republic of China
| | - Yuna Sun
- National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing, People's Republic of China
| | - Zheng Yin
- College of Pharmacy & State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, People's Republic of China Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, People's Republic of China
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Fukuda I, Kamiya N, Nakamura H. The zero-multipole summation method for estimating electrostatic interactions in molecular dynamics: analysis of the accuracy and application to liquid systems. J Chem Phys 2014; 140:194307. [PMID: 24852538 DOI: 10.1063/1.4875693] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
In the preceding paper [I. Fukuda, J. Chem. Phys. 139, 174107 (2013)], the zero-multipole (ZM) summation method was proposed for efficiently evaluating the electrostatic Coulombic interactions of a classical point charge system. The summation takes a simple pairwise form, but prevents the electrically non-neutral multipole states that may artificially be generated by a simple cutoff truncation, which often causes large energetic noises and significant artifacts. The purpose of this paper is to judge the ability of the ZM method by investigating the accuracy, parameter dependencies, and stability in applications to liquid systems. To conduct this, first, the energy-functional error was divided into three terms and each term was analyzed by a theoretical error-bound estimation. This estimation gave us a clear basis of the discussions on the numerical investigations. It also gave a new viewpoint between the excess energy error and the damping effect by the damping parameter. Second, with the aid of these analyses, the ZM method was evaluated based on molecular dynamics (MD) simulations of two fundamental liquid systems, a molten sodium-chlorine ion system and a pure water molecule system. In the ion system, the energy accuracy, compared with the Ewald summation, was better for a larger value of multipole moment l currently induced until l ≲ 3 on average. This accuracy improvement with increasing l is due to the enhancement of the excess-energy accuracy. However, this improvement is wholly effective in the total accuracy if the theoretical moment l is smaller than or equal to a system intrinsic moment L. The simulation results thus indicate L ∼ 3 in this system, and we observed less accuracy in l = 4. We demonstrated the origins of parameter dependencies appearing in the crossing behavior and the oscillations of the energy error curves. With raising the moment l we observed, smaller values of the damping parameter provided more accurate results and smoother behaviors with respect to cutoff length were obtained. These features can be explained, on the basis of the theoretical error analyses, such that the excess energy accuracy is improved with increasing l and that the total accuracy improvement within l ⩽ L is facilitated by a small damping parameter. Although the accuracy was fundamentally similar to the ion system, the bulk water system exhibited distinguishable quantitative behaviors. A smaller damping parameter was effective in all the practical cutoff distance, and this fact can be interpreted by the reduction of the excess subset. A lower moment was advantageous in the energy accuracy, where l = 1 was slightly superior to l = 2 in this system. However, the method with l = 2 (viz., the zero-quadrupole sum) gave accurate results for the radial distribution function. We confirmed the stability in the numerical integration for MD simulations employing the ZM scheme. This result is supported by the sufficient smoothness of the energy function. Along with the smoothness, the pairwise feature and the allowance of the atom-based cutoff mode on the energy formula lead to the exact zero total-force, ensuring the total-momentum conservations for typical MD equations of motion.
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Affiliation(s)
- Ikuo Fukuda
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Narutoshi Kamiya
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
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Ahmed A, Sandler SI. Hydration Free Energies of Multifunctional Nitroaromatic Compounds. J Chem Theory Comput 2013; 9:2774-85. [DOI: 10.1021/ct3011002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Alauddin Ahmed
- Department
of Chemical and Biomolecular Engineering,
University of Delaware, Newark, Delaware 19716, United States
| | - Stanley I. Sandler
- Department
of Chemical and Biomolecular Engineering,
University of Delaware, Newark, Delaware 19716, United States
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9
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Bellido EP, Seminario JM. Harmonic force field for nitro compounds. J Mol Model 2011; 18:2805-11. [DOI: 10.1007/s00894-011-1273-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2011] [Accepted: 10/06/2011] [Indexed: 11/24/2022]
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Klauda JB, Venable RM, Freites JA, O’Connor JW, Tobias DJ, Mondragon-Ramirez C, Vorobyov I, MacKerell AD, Pastor RW. Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types. J Phys Chem B 2010; 114:7830-43. [PMID: 20496934 PMCID: PMC2922408 DOI: 10.1021/jp101759q] [Citation(s) in RCA: 3106] [Impact Index Per Article: 221.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A significant modification to the additive all-atom CHARMM lipid force field (FF) is developed and applied to phospholipid bilayers with both choline and ethanolamine containing head groups and with both saturated and unsaturated aliphatic chains. Motivated by the current CHARMM lipid FF (C27 and C27r) systematically yielding values of the surface area per lipid that are smaller than experimental estimates and gel-like structures of bilayers well above the gel transition temperature, selected torsional, Lennard-Jones and partial atomic charge parameters were modified by targeting both quantum mechanical (QM) and experimental data. QM calculations ranging from high-level ab initio calculations on small molecules to semiempirical QM studies on a 1,2-dipalmitoyl-sn-phosphatidylcholine (DPPC) bilayer in combination with experimental thermodynamic data were used as target data for parameter optimization. These changes were tested with simulations of pure bilayers at high hydration of the following six lipids: DPPC, 1,2-dimyristoyl-sn-phosphatidylcholine (DMPC), 1,2-dilauroyl-sn-phosphatidylcholine (DLPC), 1-palmitoyl-2-oleoyl-sn-phosphatidylcholine (POPC), 1,2-dioleoyl-sn-phosphatidylcholine (DOPC), and 1-palmitoyl-2-oleoyl-sn-phosphatidylethanolamine (POPE); simulations of a low hydration DOPC bilayer were also performed. Agreement with experimental surface area is on average within 2%, and the density profiles agree well with neutron and X-ray diffraction experiments. NMR deuterium order parameters (S(CD)) are well predicted with the new FF, including proper splitting of the S(CD) for the aliphatic carbon adjacent to the carbonyl for DPPC, POPE, and POPC bilayers. The area compressibility modulus and frequency dependence of (13)C NMR relaxation rates of DPPC and the water distribution of low hydration DOPC bilayers also agree well with experiment. Accordingly, the presented lipid FF, referred to as C36, allows for molecular dynamics simulations to be run in the tensionless ensemble (NPT), and is anticipated to be of utility for simulations of pure lipid systems as well as heterogeneous systems including membrane proteins.
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Affiliation(s)
- Jeffery B. Klauda
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742
| | - Richard M. Venable
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - J. Alfredo Freites
- Department of Chemistry, University of California, Irvine, CA 92697-2025
| | - Joseph W. O’Connor
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742
| | - Douglas J. Tobias
- Department of Chemistry, University of California, Irvine, CA 92697-2025
| | - Carlos Mondragon-Ramirez
- Department of Pharmaceutical Sciences, 20 Penn Street HSF II, University of Maryland, Baltimore, Maryland 21201
| | - Igor Vorobyov
- Department of Pharmaceutical Sciences, 20 Penn Street HSF II, University of Maryland, Baltimore, Maryland 21201
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, 20 Penn Street HSF II, University of Maryland, Baltimore, Maryland 21201
| | - Richard W. Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
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