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Liang Z, Li QX. π-Cation Interactions in Molecular Recognition: Perspectives on Pharmaceuticals and Pesticides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:3315-3323. [PMID: 29522678 PMCID: PMC7357627 DOI: 10.1021/acs.jafc.8b00758] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The π-cation interaction that differs from the cation-π interaction is a valuable concept in molecular design of pharmaceuticals and pesticides. In this Perspective we present an up-to-date review (from 1995 to 2017) on bioactive molecules involving π-cation interactions with the recognition site, and categorize into systems of inhibitor-enzyme, ligand-receptor, ligand-transporter, and hapten-antibody. The concept of π-cation interactions offers use of π systems in a small molecule to enhance the binding affinity, specificity, selectivity, lipophilicity, bioavailability, and metabolic stability, which are physiochemical features desired for drugs and pesticides.
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Affiliation(s)
| | - Qing X. Li
- Corresponding Author: . Fax: (808) 965-3542
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Dong JX, Xie X, Hu DW, Chen SC, He YS, Beier RC, Shen YD, Sun YM, Xu ZL, Wang H, Yang JY. Codon modification for the DNA sequence of a single-chain Fv antibody against clenbuterol and expression in Pichia pastoris. Appl Microbiol Biotechnol 2013; 98:3679-89. [PMID: 24190495 DOI: 10.1007/s00253-013-5324-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 10/08/2013] [Accepted: 10/09/2013] [Indexed: 10/26/2022]
Abstract
The expression efficiency was improved for the recombinant single-chain variable fragment (scFv) against clenbuterol (CBL) obtained from mouse and expressed in the methylotrophic yeast Pichia pastoris GS115, by redesigning and synthesizing the DNA sequence encoding for CBL-scFv based on the codon bias of P. pastoris. The codons encoding 124 amino acids were optimized, in which a total of 156 nucleotides were changed, and the G+C ratio was simultaneously decreased from 53 to 47.2 %. Under the optimized expression conditions, the yield of the recombinant CBL-scFv (41 kDa) antibodies was 0.223 g L⁻¹ in shake culture. Compared to the non-optimized control, the expression level of the optimized recombinant CBL-scFv based on preferred codons in P. pastoris demonstrated a 2.35-fold higher yield. Furthermore, the recombinant CBL-scFv was purified by Ni-NTA column chromatography, and the purity was 95 %. The purified CBL-scFv showed good CBL recognition by a competitive indirect enzyme-linked immunoassay. The average concentration required for 50 % inhibition of binding and the limit of detection for the assay were 5.82 and 0.77 ng mL⁻¹, respectively.
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Affiliation(s)
- Jie-Xian Dong
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou, Guangdong Province, 510642, People's Republic of China
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Van Dorst B, Mehta J, Rouah-Martin E, Blust R, Robbens J. Phage display as a method for discovering cellular targets of small molecules. Methods 2012; 58:56-61. [PMID: 22819857 DOI: 10.1016/j.ymeth.2012.07.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2011] [Accepted: 07/11/2012] [Indexed: 12/12/2022] Open
Abstract
Phage display can be used for the discovery of cellular targets of small molecules in order to unravel their mechanism of action, which is important in the drug discovery field to assess biological effects of drugs at the molecular level and to investigate pharmacokinetic characteristics of drugs in clinical use. The potential of phage display in the drug discovery field is shown by a lot of successful cellular target identifications of drug-like small molecules in the last decade. More recently, phage display was also introduced in environmental science to predict risks of small molecules, like nickel, 17β estradiol and bisphenol A on both environmental and human health, wherefore knowledge about the mechanism of action and cellular targets is essential. This paper discusses some important aspects of the phage display approach for the discovery of cellular targets of small molecules. The different phage display libraries and immobilization strategies used for the discovery of cellular target of small molecules are described. In general, the phage display approach is very useful in drug discovery and environmental science as a fast and cost-effective in vitro tool to determine cellular targets of small molecules, which increases our understanding of the mechanisms of action of small molecules.
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Affiliation(s)
- Bieke Van Dorst
- University Antwerp, Department of Biology, Laboratory for Ecophysiology, Biochemistry and Toxicology, Groenenborgerlaan 171, B-2020 Antwerp, Belgium.
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Zhu X, Kriegel AM, Boustany CA, Blake DA. Single-Chain Variable Fragment (scFv) Antibodies Optimized for Environmental Analysis of Uranium. Anal Chem 2011; 83:3717-24. [DOI: 10.1021/ac200159x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Xiaoxia Zhu
- Department of Biochemistry, Tulane University School of Medicine, New Orleans, Louisiana 70112, United States
| | - Alison M. Kriegel
- Department of Biochemistry, Tulane University School of Medicine, New Orleans, Louisiana 70112, United States
| | - Christopher A. Boustany
- Department of Biochemistry, Tulane University School of Medicine, New Orleans, Louisiana 70112, United States
| | - Diane A. Blake
- Department of Biochemistry, Tulane University School of Medicine, New Orleans, Louisiana 70112, United States
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Inui H, Takehara A, Doi F, Nishi K, Takai M, Miyake S, Ohkawa H. A scFv antibody-based immunoaffinity chromatography column for clean-up of bisphenol A-contaminated water samples. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2009; 57:353-358. [PMID: 19102649 DOI: 10.1021/jf802781t] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
This is a report on the development of immunoaffinity chromatography using a column of silica gel with an immobilized single-chain variable fragment (scFv) antibody specific to bisphenol A (BPA) for cleanup of BPA-contaminated water samples. The BBA-2187 scFv antibody specific to BPA was purified from the periplasmic fractions of the recombinant Escherichia coli. After a sample of BPA-contaminated river water was applied to the immunoaffinity column, the background signal intensity observed in high-performance liquid chromatography (HPLC) analysis of the eluates was markedly lower than that observed in HPLC analysis of the eluates from an Oasis HLB cartridge treated with the same sample. The immunoaffinity column efficiently concentrated BPA from actual river water samples with different matrices. Our results demonstrate that the immunoaffinity column with immobilized BBA-2187 scFv antibody is efficient for the cleanup of BPA-contaminated water samples from different sources.
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Affiliation(s)
- Hideyuki Inui
- Research Center for Environmental Genomics and Graduate School of Science and Technology, Kobe University, Rokkodaicho, Nada-ku, Kobe, Hyogo, Japan
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Kim HJ, González-Techera A, González-Sapienza GG, Ahn KC, Gee SJ, Hammock BD. Phage-borne peptidomimetics accelerate the development of polyclonal antibody-based heterologous immunoassays for the detection of pesticide metabolites. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2008; 42:2047-2053. [PMID: 18409635 DOI: 10.1021/es702219a] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Competitive immunoassays for the detection of small analytes, such as pesticides and their metabolites, use haptens that compete with the target compounds for binding to the antibody. This competing hapten can be either the same as the immunizing hapten (homologous assay) or structurally modified mimics of the immunizing hapten (heterologous assay). Polyclonal antibody-based heterologous immunoassays have shown superior sensitivities to homologous ones, butthe synthesis of heterologous haptens may be time-consuming, requiring expertise in synthetic chemistry. In this work we demonstrate that phage display peptide libraries can be used as a source of phage-borne peptidomimetics to facilitate the development of sensitive heterologous assays. Different strategies for the isolation of these peptides were explored using two metabolites of pyrethroid insecticides. The sensitivities of the best competitive phage heterologous enzyme-linked immunosorbent assays were 13 fold and 100 fold better than the homologous assay, for the glycine conjugate of trans-3-(2,2-dichlorovinyl)-2,2-dimethylcyclopropane-1-carboxylic acid and 3-phenoxybenzoic acid, respectively. The phage particles were highly versatile as tracer reagents, allowing the use of enzymatic, chemiluminescent, or immuno-polymerase chain reaction detection. The data presented here shows a new systematic procedure that enables the fast generation of several competing haptens for the rapid development of sensitive heterologous immunoassays.
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Affiliation(s)
- Hee-Joo Kim
- Department ofEntomology and UCD Cancer Research Center, University of California, Davis, California 95616, USA
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Zhao J, Li G, Yi GX, Wang BM, Deng AX, Nan TG, Li ZH, Li QX. Comparison between conventional indirect competitive enzyme-linked immunosorbent assay (icELISA) and simplified icELISA for small molecules. Anal Chim Acta 2006; 571:79-85. [PMID: 17723423 DOI: 10.1016/j.aca.2006.04.060] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2005] [Revised: 02/21/2006] [Accepted: 04/24/2006] [Indexed: 11/18/2022]
Abstract
A simplified indirect competitive enzyme-linked immunosorbent assay (icELISA) for small molecules was established by modifying the procedure of conventional icELISA. The key change was that the analyte, antibody, and enzyme-labeled second antibody in the simplified icELISA were added in one step, whereas in conventional icELISA these reagents were added in two separate steps. Three small chemicals, namely zeatin riboside, glycyrrhetinic acid, and chlorimuron-ethyl, were used to verify the new assay format and compare the results obtained from conventional icELISA and simplified icELISA. The results indicated that, under optimized conditions, the new assay offered several advantages over the conventional icELISA, which are simpler, less time consuming and higher sensitive although it requires more amount of reagents. The assay sensitivity (IC50) was improved for 1.2-1.4-fold. Four licorice roots samples were analyzed by conventional icELISA and simplified icELISA, as well as liquid chromatography (LC). There was no significant difference among the content obtained from the three methods for each sample. The correlation between data obtained from conventional icELISA and simplified icELISA analyses was 0.9888. The results suggest that the simplified icELISA be useful for high throughput screening of small molecules.
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Affiliation(s)
- Jing Zhao
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100094, China
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Pellequer JL, Chen SWW, Keum YS, Karu AE, Li QX, Roberts VA. Structural basis for preferential binding of non-ortho-substituted polychlorinated biphenyls by the monoclonal antibody S2B1. J Mol Recognit 2005; 18:282-94. [PMID: 15880452 DOI: 10.1002/jmr.740] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Polychlorinated biphenyls (PCBs) are a family of 209 isomers (congeners) with a wide range of toxic effects. In structural terms, they are of two types: those with and those without chlorines at the ortho positions (2, 2', 6 and 6'). Only 20 congeners have no ortho chlorines. Three of these are bound by the aryl hydrocarbon receptor and are one to four orders of magnitude more toxic than all others. A monoclonal antibody, S2B1, and its recombinant Fab have high selectivity and nanomolar binding affinities for two of the most toxic non-ortho-chlorinated PCBs, 3,4,3',4'-tetrachlorobiphenyl and 3,4,3',4',5'-pentachlorobiphenyl. To investigate the basis for these properties, we built a three-dimensional structure model of the S2B1 variable fragment (Fv) based on the high-resolution crystallographic structures of antibodies 48G7 and N1G9. Two plausible conformations for the complementarity-determining region (CDR) H3 loop led to two putative PCB-binding pockets with very different shapes (models A and B). Docking studies using molecular mechanics and potentials of mean force (PMF) indicated that model B was most consistent with the selectivity observed for S2B1 in competition ELISAs. The binding site in model B had a deep, narrow pocket between V(L) and V(H), with a slight constriction at the top that opened into a wider pocket between CDRs H1 and H3 on the antibody surface. This binding site resembles those of esterolytic antibodies that bind haptens with phenyl rings. One phenyl ring of the PCB fits into the deep pocket, and the other ring is bound in the shallower one. The bound PCB is surrounded by the side chains of TyrL91, TyrL96 and TrpH98, and it has a pi-cation interaction with ArgL46. The tight fit of the binding pocket around the ortho positions of the bound PCBs indicates that steric hindrance of ortho chlorines in the binding site, rather than induced conformational change of the PCBs, is responsible for the selectivity of S2B1.
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Affiliation(s)
- Jean-Luc Pellequer
- Département d'Ingenierie et d'Etudes des Proteines, Service de Biochimie Post-Génomique et Toxicologie Nucléaire, Commissariat à L'Energie Atomique, Centre de Marcoule, BP17171, 30207 Bagnols Sur Cèze, France.
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Development and characterization of new monoclonal antibodies specific for coplanar polychlorinated biphenyls. Anal Chim Acta 2004. [DOI: 10.1016/j.aca.2004.04.038] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Churchill RL, Sheedy C, Yau KY, Hall J. Evolution of antibodies for environmental monitoring: from mice to plants. Anal Chim Acta 2002. [DOI: 10.1016/s0003-2670(02)00093-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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