1
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Cui J, Fan Y, Lian D, Wang S, Wang M, Du Y, Li Y, Li L. Interaction of narcissoside with α-amylase from Bacillus subtilis and Porcine pancreatic by multi-spectral analysis and molecular dynamics simulation. LUMINESCENCE 2023. [PMID: 38038156 DOI: 10.1002/bio.4637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 09/23/2023] [Accepted: 11/11/2023] [Indexed: 12/02/2023]
Abstract
In this work, interaction mechanism of narcissoside with two α-amylase from Bacillus subtilis (BSA) and Porcine pancreatic (PPA) are comparatively studied by multi-spectral analysis, molecular docking and molecular dynamics simulation. The results prove that narcissoside can statically quench fluorescence of BSA/PPA. Two complexes are mainly formed by hydrogen bond and van der Waals force. With the increase of temperature, the two complexes formed by narcissoside and two enzymes become unstable. At the same experimental temperature, the binding force of narcissoside to PPA is higher than that of BSA. The binding of narcissoside to PPA/BSA increases the hydrophobicity of microenvironment. Moreover, the secondary structure of PPA/BSA is mainly changed by decreasing the α-helix. The optimal binding modes of narcissoside with BSA/PPA are predicted by molecular docking, and the stability of the two complexes is evaluated by molecular dynamics simulations.
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Affiliation(s)
- Jingjing Cui
- The College of Chemistry, Changchun Normal University, Changchun, China
| | - Yangyang Fan
- The College of Chemistry, Changchun Normal University, Changchun, China
| | - Di Lian
- The College of Chemistry, Changchun Normal University, Changchun, China
| | - Suqing Wang
- The College of Chemistry, Changchun Normal University, Changchun, China
| | - Meizi Wang
- The College of Chemistry, Changchun Normal University, Changchun, China
| | - Yutong Du
- The College of Chemistry, Changchun Normal University, Changchun, China
| | - Yuan Li
- The College of Chemistry, Changchun Normal University, Changchun, China
| | - Li Li
- The College of Chemistry, Changchun Normal University, Changchun, China
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2
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A Simulation Model for the Non-Electrogenic Uniport Carrier-Assisted Transport of Ions across Lipid Membranes. MEMBRANES 2022; 12:membranes12030292. [PMID: 35323767 PMCID: PMC8955484 DOI: 10.3390/membranes12030292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 02/24/2022] [Accepted: 03/01/2022] [Indexed: 12/10/2022]
Abstract
Impressive work has been completed in recent decades on the transmembrane anion transport capability of small synthetic transporters from many different structural classes. However, very few predicting models have been proposed for the fast screening of compound libraries before spending time and resources on the laboratory bench for their synthesis. In this work, a new approach is presented which aims at describing the transport process by taking all the steps into explicit consideration, and includes all possible experiment-derived parameters. The algorithm is able to simulate the macroscopic experiments performed with lipid vesicles to assess the ion-transport ability of the synthetic transporters following a non-electrogenic uniport mechanism. While keeping calculation time affordable, the final goal is the curve-fitting of real experimental data—so, to obtain both an analysis and a predictive tool. The role and the relative weight of the different parameters is discussed and the agreement with the literature is shown by using the simulations of a virtual benchmark case. The fitting of real experimental curves is also shown for two transporters of different structural type.
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3
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Jagleniec D, Wilczek M, Romański J. Tripodal, Squaramide-Based Ion Pair Receptor for Effective Extraction of Sulfate Salt. Molecules 2021; 26:2751. [PMID: 34067071 PMCID: PMC8125518 DOI: 10.3390/molecules26092751] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/01/2021] [Accepted: 05/05/2021] [Indexed: 11/20/2022] Open
Abstract
Combining three features-the high affinity of squaramides toward anions, cooperation in ion pair binding and preorganization of the binding domains in the tripodal platform-led to the effective receptor 2. The lack of at least one of these key elements in the structures of reference receptors 3 and 4 caused a lower affinity towards ion pairs. Receptor 2 was found to form an intramolecular network in wet chloroform, which changed into inorganic-organic associates after contact with ions and allowed salts to be extracted from an aqueous to an organic phase. The disparity in the binding mode of 2 with sulfates and with other monovalent anions led to the selective extraction of extremely hydrated sulfate anions in the presence of more lipophilic salts, thus overcoming the Hofmeister series.
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Affiliation(s)
| | | | - Jan Romański
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland; (D.J.); (M.W.)
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4
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Nunes RS, Vila-Viçosa D, Costa PJ. Halogen Bonding: An Underestimated Player in Membrane–Ligand Interactions. J Am Chem Soc 2021; 143:4253-4267. [DOI: 10.1021/jacs.0c12470] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Rafael Santana Nunes
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
- Centro de Química Estrutural, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Diogo Vila-Viçosa
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
| | - Paulo J. Costa
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
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5
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Li B, Hong S, Zhang X, Xiong C, Zhao G, Yang Q, Liu H. Understanding Interfacial Mechanics and Mechanisms of Exfoliation and Stabilization of Graphene Using Urea/Glycerol Solvents. ADVANCED THEORY AND SIMULATIONS 2019. [DOI: 10.1002/adts.201900155] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Bei Li
- School of Materials Science and EngineeringWuhan University of Technology Wuhan 430070 China
- Research Center for Materials Genome EngineeringWuhan University of Technology Wuhan 430070 China
| | - Shibo Hong
- School of Materials Science and EngineeringWuhan University of Technology Wuhan 430070 China
- Research Center for Materials Genome EngineeringWuhan University of Technology Wuhan 430070 China
| | - Xu Zhang
- School of Materials Science and EngineeringWuhan University of Technology Wuhan 430070 China
- Research Center for Materials Genome EngineeringWuhan University of Technology Wuhan 430070 China
| | - Chuanxi Xiong
- School of Materials Science and EngineeringWuhan University of Technology Wuhan 430070 China
| | - Guanghui Zhao
- Research Center for Materials Genome EngineeringWuhan University of Technology Wuhan 430070 China
- School of Computer Science and TechnologyWuhan University of Technology Wuhan 430070 China
| | - Quanling Yang
- School of Materials Science and EngineeringWuhan University of Technology Wuhan 430070 China
| | - Hanxing Liu
- Research Center for Materials Genome EngineeringWuhan University of Technology Wuhan 430070 China
- International School of Materials Science and EngineeringWuhan University of Technology Wuhan 430070 China
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6
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Marques I, Costa PMR, Q. Miranda M, Busschaert N, Howe ENW, Clarke HJ, Haynes CJE, Kirby IL, Rodilla AM, Pérez-Tomás R, Gale PA, Félix V. Full elucidation of the transmembrane anion transport mechanism of squaramides using in silico investigations. Phys Chem Chem Phys 2018; 20:20796-20811. [DOI: 10.1039/c8cp02576b] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The anion carrier mechanism promoted by squaramide-based molecules has been elucidated by molecular dynamics and chloride efflux studies.
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Affiliation(s)
- Igor Marques
- Department of Chemistry
- CICECO – Aveiro Institute of Materials
- University of Aveiro
- Aveiro
- Portugal
| | - Pedro M. R. Costa
- Department of Chemistry
- CICECO – Aveiro Institute of Materials
- University of Aveiro
- Aveiro
- Portugal
| | - Margarida Q. Miranda
- Department of Chemistry
- CICECO – Aveiro Institute of Materials
- University of Aveiro
- Aveiro
- Portugal
| | | | - Ethan N. W. Howe
- Chemistry
- University of Southampton
- Southampton
- UK
- School of Chemistry
| | | | | | | | - Ananda M. Rodilla
- University of Barcelona
- Faculty of Medicine
- Dept. Pathology and Experimental Therapeutics
- CCBRG
- Barcelona
| | - Ricardo Pérez-Tomás
- University of Barcelona
- Faculty of Medicine
- Dept. Pathology and Experimental Therapeutics
- CCBRG
- Barcelona
| | - Philip A. Gale
- Chemistry
- University of Southampton
- Southampton
- UK
- School of Chemistry
| | - Vítor Félix
- Department of Chemistry
- CICECO – Aveiro Institute of Materials
- University of Aveiro
- Aveiro
- Portugal
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7
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Li Z, Yu XH, Chen Y, Yuan DQ, Chen WH. Synthesis, Anion Recognition, and Transmembrane Anionophoric Activity of Tripodal Diaminocholoyl Conjugates. J Org Chem 2017; 82:13368-13375. [DOI: 10.1021/acs.joc.7b02447] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Zhi Li
- Guangdong
Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical
Sciences, Southern Medical University, Guangzhou 510515, P.R. China
| | - Xi-Hui Yu
- Guangdong
Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical
Sciences, Southern Medical University, Guangzhou 510515, P.R. China
| | - Yun Chen
- Guangdong
Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical
Sciences, Southern Medical University, Guangzhou 510515, P.R. China
| | - De-Qi Yuan
- Faculty
of Pharmaceutical Sciences, Kobe Gakuin University, Minatojima 1-1-3, Chuo-ku, Kobe 650-8586, Japan
| | - Wen-Hua Chen
- Guangdong
Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical
Sciences, Southern Medical University, Guangzhou 510515, P.R. China
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8
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Remarkable hexafunctional anion receptor with operational urea-based inner cleft and thiourea-based outer cleft: Novel design with high-efficiency for sulfate binding. Sci Rep 2017; 7:6032. [PMID: 28729544 PMCID: PMC5519707 DOI: 10.1038/s41598-017-05831-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 06/05/2017] [Indexed: 01/15/2023] Open
Abstract
The recognition of anions by designed receptors has attracted much attention in recent days. In particular, the selective binding of sulfate with artificial receptors is important because of its relevance to many biological and environmental applications. However, the development of organized molecular receptors with high-efficiency for sulfate binding still remains a significant challenge. We report a novel para-phenylene-bridged hexafunctional tripodal receptor that contains a urea-based inner cleft and a thiourea-based outer cleft, providing perfect sites for step-wise binding of two anions within a single cavity. The new receptor was synthesized in a three-step process, and was investigated for its anion binding properties by 1H NMR titrations, 2D NOESY experiments and computational studies. As indicated by solution binding studies, the receptor selectively binds sulfate over other oxoanions, forming a 1:2 stoichiometric complex that is stabilized via strong H-bonding interactions. High-level DFT calculations reveal that the receptor, owing to the enhanced H-bonding ability of thiourea groups, initially encapsulates one sulfate in its thiourea-based outer cleft, followed by a second encapsulation in its urea-based inner cleft. Such a functionalized receptor with the unique combination of urea-based cleft and thiourea-based cleft in a single receptor has not been reported previously.
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9
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Cai XJ, Li Z, Chen WH. Tripodal squaramide conjugates as highly effective transmembrane anion transporters. Bioorg Med Chem Lett 2017; 27:1999-2002. [DOI: 10.1016/j.bmcl.2017.03.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 02/18/2017] [Accepted: 03/06/2017] [Indexed: 11/17/2022]
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10
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Nunes R, Costa PJ. Ion-Pair Halogen Bonds in 2-Halo-Functionalized Imidazolium Chloride Receptors: Substituent and Solvent Effects. Chem Asian J 2017; 12:586-594. [PMID: 28052536 DOI: 10.1002/asia.201601690] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 01/02/2017] [Indexed: 01/14/2023]
Abstract
The interaction of 2-halo-functionalized imidazolium derivatives (n-X+ ; X=Cl, Br, I) with a chloride anion through ion-pair halogen bonds (n-X⋅Cl) was studied by means of DFT and ab initio calculations. A method benchmark was performed on 2-bromo-1H-imidazol-3-ium in association with chloride (1-Br⋅Cl); MP2 yielded the best results when compared with CCSD(T) calculations. The interaction energies (ΔE) in the gas phase are high and, although the electrostatic interaction is strong owing to the ion-pair nature of the system, large X⋅⋅⋅Cl- Wiberg bond orders and contributions from charge transfer (nCl- →σ*C-X) are obtained. These values drop considerably in chloroform and water; this shows that solvent plays a role in modulating the interaction and that gas-phase calculations are particularly unrealistic for experimental applications. The introduction of electron-withdrawing groups in the 4,5-positions of the imidazolium (e.g., -NO2 , -F) increases the halogen-bond strength in both the gas phase and solvent, including water. The effect of the substituents on the 1,3-positions (N-H groups) also depends on the solvent. The variation of ΔE can be predicted through a two-parameter linear regression that optimizes the weights of charge-transfer and electrostatic interactions, which are different in vacuum and in solvent (chloroform and water). These results could be used in the rational design of efficient chloride receptors based on halogen bonds that work in solution, in particular, in an aqueous environment.
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Affiliation(s)
- Rafael Nunes
- Centro de Química e Bioquímica, DQB, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Paulo J Costa
- Centro de Química e Bioquímica, DQB, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
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11
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Yang Y, Wu X, Busschaert N, Furuta H, Gale PA. Dissecting the chloride–nitrate anion transport assay. Chem Commun (Camb) 2017; 53:9230-9233. [DOI: 10.1039/c7cc04912a] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The chloride/nitrate selectivity of anion transporters in both binding and membrane transport is examined revealing the limitations of chloride–nitrate anion exchange assay.
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Affiliation(s)
- Yufeng Yang
- Chemistry
- University of Southampton
- Southampton
- UK
- Department of Chemistry and Biochemistry
| | - Xin Wu
- School of Chemistry
- The University of Sydney
- Australia
| | | | - Hiroyuki Furuta
- Department of Chemistry and Biochemistry
- Kyushu University
- Fukuoka
- Japan
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12
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Edwards SJ, Marques I, Dias CM, Tromans RA, Lees NR, Félix V, Valkenier H, Davis AP. Tilting and Tumbling in Transmembrane Anion Carriers: Activity Tuning through n-Alkyl Substitution. Chemistry 2016; 22:2004-2011. [PMID: 26748870 PMCID: PMC5064602 DOI: 10.1002/chem.201504057] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Indexed: 11/07/2022]
Abstract
Anion transport by synthetic carriers (anionophores) holds promise for medical applications, especially the treatment of cystic fibrosis. Among the factors which determine carrier activity, the size and disposition of alkyl groups is proving remarkably important. Herein we describe a series of dithioureidodecalin anionophores, in which alkyl substituents on one face are varied from C0 to C10 in two-carbon steps. Activities increase then decrease as the chain length grows, peaking quite sharply at C6 . Molecular dynamics simulations showed the transporter chloride complexes releasing chloride as they approach the membrane-aqueous interface. The free transporter then stays at the interface, adopting an orientation that depends on the alkyl substituent. If chloride release is prevented, the complex is positioned similarly. Longer chains tilt the binding site away from the interface, potentially freeing the transporter or complex to move through the membrane. However, chains which are too long can also slow transport by inhibiting movement, and especially reorientation, within the phospholipid bilayer.
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Affiliation(s)
- Sophie J Edwards
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Igor Marques
- Departamento de Química, iBiMED and CICECO, Universidade de Aveiro, 3810-193, Aveiro, Portugal
| | - Christopher M Dias
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Robert A Tromans
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Nicholas R Lees
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Vítor Félix
- Departamento de Química, iBiMED and CICECO, Universidade de Aveiro, 3810-193, Aveiro, Portugal.
| | - Hennie Valkenier
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Anthony P Davis
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
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13
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Khansari ME, Johnson CR, Basaran I, Nafis A, Wang J, Leszczynski J, Hossain MA. Synthesis and anion binding studies of tris(3-aminopropyl)amine-based tripodal urea and thiourea receptors: Proton transfer-induced selectivity for hydrogen sulfate over sulfate. RSC Adv 2015; 5:17606-17614. [PMID: 28184300 PMCID: PMC5295472 DOI: 10.1039/c5ra01315a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Tris(3-aminopropyl)amine-based tripodal urea and thiourea receptors, tris([(4-cyanophenyl)amino]propyl)urea (L1) and tris([(4-cyanophenyl)amino]propyl)thiourea (L2), have been synthesized and their anion binding properties have been investigated for halides and oxoanions. As investigated by 1H NMR titrations, each receptor binds an anion with a 1:1 stoichiometry via hydrogen-bonding interactions (NH⋯anion), showing the binding trend in the order of F- > H2PO4- > HCO3- > HSO4- > CH3COO- > SO42- > Cl- > Br- > I in DMSO-d6 . The interactions of the receptors were further studied by 2D NOESY, showing the loss of NOESY contacts of two NH resonances for the complexes of F-, H2PO4-, HCO3-, HSO4- or CH3COO- due to the strong NH⋯anion interactions. The observed higher binding affinity for HSO4- than SO42- is attributed to the proton transfer from HSO4- to the central nitrogen of L1 or L2 which was also supported by the DFT calculations, leading to the secondary acid-base interactions. The thiourea receptor L2 has a general trend to show a higher affinity for an anion as compared to the urea receptor L1 for the corresponding anion in DMSO-d6 . In addition, the compound L2 has been exploited for its extraction properties for fluoride in water using a liquid-liquid extraction technique, and the results indicate that the receptor effectively extracts fluoride from water showing ca. 99% efficiency (based on L2).
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Affiliation(s)
- Maryam Emami Khansari
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS 39217, USA
| | - Corey R Johnson
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS 39217, USA
| | - Ismet Basaran
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS 39217, USA; Department of Chemistry, Balikesir University, 10145, Balikesir, Turkey
| | - Aemal Nafis
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS 39217, USA
| | - Jing Wang
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS 39217, USA
| | - Jerzy Leszczynski
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS 39217, USA
| | - Md Alamgir Hossain
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS 39217, USA
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14
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Li Z, Deng LQ, Chen JX, Zhou CQ, Chen WH. Does lipophilicity affect the effectiveness of a transmembrane anion transporter? Insight from squaramido-functionalized bis(choloyl) conjugates. Org Biomol Chem 2015; 13:11761-9. [DOI: 10.1039/c5ob01920f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Lipophilicity was found to have little effect on the effectiveness of squaramido-functionalized bis(choloyl) conjugates.
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Affiliation(s)
- Zhi Li
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Li-Qun Deng
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Jin-Xiang Chen
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Chun-Qiong Zhou
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Wen-Hua Chen
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
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