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Hu Z, Leus IV, Chandar B, Sherborne BS, Avila QP, Rybenkov VV, Zgurskaya HI, Duerfeldt AS. Structure-Uptake Relationship Studies of Oxazolidinones in Gram-Negative ESKAPE Pathogens. J Med Chem 2022; 65:14144-14179. [PMID: 36257060 PMCID: PMC9942527 DOI: 10.1021/acs.jmedchem.2c01349] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The clinical success of linezolid for treating Gram-positive infections paired with the high conservation of bacterial ribosomes predicts that if oxazolidinones were engineered to accumulate in Gram-negative bacteria, then this pharmacological class would find broad utility in eradicating infections. Here, we report an investigative study of a strategically designed library of oxazolidinones to determine the effects of molecular structure on accumulation and biological activity. Escherichia coli, Acinetobacter baumannii, and Pseudomonas aeruginosa strains with varying degrees of compromise (in efflux and outer membrane) were used to identify motifs that hinder permeation across the outer membrane and/or enhance efflux susceptibility broadly and specifically between species. The results illustrate that small changes in molecular structure are enough to overcome the efflux and/or permeation issues of this scaffold. Three oxazolidinone analogues (3e, 8d, and 8o) were identified that exhibit activity against all three pathogens assessed, a biological profile not observed for linezolid.
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Affiliation(s)
- Ziwei Hu
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Inga V Leus
- Department of Chemistry & Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
| | - Brinda Chandar
- Department of Chemistry & Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
| | | | - Quentin P Avila
- Department of Chemistry & Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
| | - Valentin V Rybenkov
- Department of Chemistry & Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
| | - Helen I Zgurskaya
- Department of Chemistry & Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
| | - Adam S Duerfeldt
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55414, United States
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2
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Saini P, Sonika, Singh G, Kaur G, Singh J, Singh H. Robust and Versatile Cu(I) metal frameworks as potential catalysts for azide-alkyne cycloaddition reactions: Review. MOLECULAR CATALYSIS 2021. [DOI: 10.1016/j.mcat.2021.111432] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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3
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Guerrero S, Agüí L, Yáñez-Sedeño P, Pingarrón J. Design of electrochemical immunosensors using electro-click chemistry. Application to the detection of IL-1β cytokine in saliva. Bioelectrochemistry 2020; 133:107484. [DOI: 10.1016/j.bioelechem.2020.107484] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 02/13/2020] [Accepted: 02/13/2020] [Indexed: 12/16/2022]
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4
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Post-synthesis modification of thermo-responsive hydrogels: Hydrazone crosslinking of α-oxoaldehyde obtained from NIPAm-based polymers. Eur Polym J 2019. [DOI: 10.1016/j.eurpolymj.2019.01.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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5
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Martín-Serrano Ortiz Á, Stenström P, Mesa Antunez P, Andrén OCJ, Torres MJ, Montañez MI, Malkoch M. Design of multivalent fluorescent dendritic probes for site-specific labeling of biomolecules. ACTA ACUST UNITED AC 2018. [DOI: 10.1002/pola.29055] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Ángela Martín-Serrano Ortiz
- Research Laboratory and Allergy Unit; IBIMA-Regional University Hospital of Malaga-UMA, Hospital Civil, Plaza del Hospital Civil; Malaga 29009 Spain
- BIONAND-Andalusian Centre for Nanomedicine and Biotechnology, Parque Tecnológico de Andalucía; Malaga 29590 Spain
| | - Patrik Stenström
- Department of Fibre and Polymer Technology, Teknikringen 56-58; KTH Royal Institute of Technology; Stockholm 100 44 Sweden
| | - Pablo Mesa Antunez
- Department of Fibre and Polymer Technology, Teknikringen 56-58; KTH Royal Institute of Technology; Stockholm 100 44 Sweden
| | - Oliver C. J. Andrén
- Department of Fibre and Polymer Technology, Teknikringen 56-58; KTH Royal Institute of Technology; Stockholm 100 44 Sweden
| | - Maria J. Torres
- Research Laboratory and Allergy Unit; IBIMA-Regional University Hospital of Malaga-UMA, Hospital Civil, Plaza del Hospital Civil; Malaga 29009 Spain
- BIONAND-Andalusian Centre for Nanomedicine and Biotechnology, Parque Tecnológico de Andalucía; Malaga 29590 Spain
| | - Maria I. Montañez
- Research Laboratory and Allergy Unit; IBIMA-Regional University Hospital of Malaga-UMA, Hospital Civil, Plaza del Hospital Civil; Malaga 29009 Spain
- BIONAND-Andalusian Centre for Nanomedicine and Biotechnology, Parque Tecnológico de Andalucía; Malaga 29590 Spain
| | - Michael Malkoch
- Department of Fibre and Polymer Technology, Teknikringen 56-58; KTH Royal Institute of Technology; Stockholm 100 44 Sweden
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Jeong S, Park JY, Cha MG, Chang H, Kim YI, Kim HM, Jun BH, Lee DS, Lee YS, Jeong JM, Lee YS, Jeong DH. Highly robust and optimized conjugation of antibodies to nanoparticles using quantitatively validated protocols. NANOSCALE 2017; 9:2548-2555. [PMID: 28150822 DOI: 10.1039/c6nr04683e] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Antibody-conjugated nanoparticles (NPs) have attracted great attention in diagnostic and therapeutic applications due to their high sensitivity and specificity for biotargets, as well as their wide applicability. Unfortunately, these features are significantly affected by antibody conjugation methods in terms of conjugation efficiency, orientation of the target binding site in the antibody, and denaturation during chemical conjugation reactions. Furthermore, the number of conjugated antibodies on each NP and the overall targeting efficacy are critical factors for a quantitative bioassay with antibody-conjugated NPs. Herein, we report a versatile and oriented antibody conjugation method using copper-free click chemistry. Moreover, the number of conjugated antibodies and their binding capacity were quantitatively and experimentally evaluated using fluorescently-labeled antibodies and antigens. The strong binding capability of antibody-conjugated NPs prepared using the copper-free click chemistry-based conjugation strategy was 8 times superior to the binding capability seen following the use of the EDC/NHS-coupling method. Additionally, the versatility of the developed antibody conjugation method was also demonstrated by conjugation of the antibody to three kinds of silica-encapsulated NPs.
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Affiliation(s)
- Sinyoung Jeong
- Department of Chemistry Education, Seoul National University, Seoul 08826, Korea.
| | - Ji Yong Park
- Department of Nuclear Medicine, Seoul National University College of Medicine, Seoul 03080, Korea. and Major in Biomedical Sciences, Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 08826, Korea
| | - Myeong Geun Cha
- Department of Chemistry Education, Seoul National University, Seoul 08826, Korea.
| | - Hyejin Chang
- Department of Chemistry Education, Seoul National University, Seoul 08826, Korea.
| | - Yong-Il Kim
- Department of Nuclear Medicine, Seoul National University College of Medicine, Seoul 03080, Korea.
| | - Hyung-Mo Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Korea
| | - Bong-Hyun Jun
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Korea
| | - Dong Soo Lee
- Department of Nuclear Medicine, Seoul National University College of Medicine, Seoul 03080, Korea. and Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, and College of Medicine or College of Pharmacy, Seoul National University, Seoul 08826, Korea
| | - Yoon-Sik Lee
- School of Chemical and Biological Engineering, Seoul National University, Seoul 08826, Korea
| | - Jae Min Jeong
- Department of Nuclear Medicine, Seoul National University College of Medicine, Seoul 03080, Korea.
| | - Yun-Sang Lee
- Department of Nuclear Medicine, Seoul National University College of Medicine, Seoul 03080, Korea. and Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, and College of Medicine or College of Pharmacy, Seoul National University, Seoul 08826, Korea
| | - Dae Hong Jeong
- Department of Chemistry Education, Seoul National University, Seoul 08826, Korea.
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7
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A covalent and cleavable antibody-DNA conjugation strategy for sensitive protein detection via immuno-PCR. Sci Rep 2016; 6:22675. [PMID: 26947912 PMCID: PMC4780193 DOI: 10.1038/srep22675] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 02/17/2016] [Indexed: 12/28/2022] Open
Abstract
Immuno-PCR combines specific antibody-based protein detection with the sensitivity of PCR-based quantification through the use of antibody-DNA conjugates. The production of such conjugates depends on the availability of quick and efficient conjugation strategies for the two biomolecules. Here, we present an approach to produce cleavable antibody-DNA conjugates, employing the fast kinetics of the inverse electron-demand Diels-Alder reaction between tetrazine and trans-cyclooctene (TCO). Our strategy consists of three steps. First, antibodies are functionalized with chemically cleavable NHS-s-s-tetrazine. Subsequently, double-stranded DNA is functionalized with TCO by enzymatic addition of N3-dATP and coupling to trans-Cyclooctene-PEG12-Dibenzocyclooctyne (TCO-PEG12-DBCO). Finally, conjugates are quickly and efficiently obtained by mixing the functionalized antibodies and dsDNA at low molar ratios of 1:2. In addition, introduction of a chemically cleavable disulphide linker facilitates release and sensitive detection of the dsDNA after immuno-staining. We show specific and sensitive protein detection in immuno-PCR for human epidermal stem cell markers, ITGA6 and ITGB1, and the differentiation marker Transglutaminase 1 (TGM1). We anticipate that the production of chemically cleavable antibody-DNA conjugates will provide a solid basis for the development of multiplexed immuno-PCR experiments and immuno-sequencing methodologies.
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Sánchez-Tirado E, González-Cortés A, Yáñez-Sedeño P, Pingarrón JM. Carbon nanotubes functionalized by click chemistry as scaffolds for the preparation of electrochemical immunosensors. Application to the determination of TGF-beta 1 cytokine. Analyst 2016; 141:5730-5737. [DOI: 10.1039/c6an00941g] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The first electrochemical immunosensor for TGF-β1 cytokine in human serum based on carbon nanotubes functionalized by click chemistry is reported.
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Affiliation(s)
- E. Sánchez-Tirado
- Department of Analytical Chemistry
- Faculty of Chemistry
- University Complutense of Madrid
- 28040-Madrid
- Spain
| | - A. González-Cortés
- Department of Analytical Chemistry
- Faculty of Chemistry
- University Complutense of Madrid
- 28040-Madrid
- Spain
| | - P. Yáñez-Sedeño
- Department of Analytical Chemistry
- Faculty of Chemistry
- University Complutense of Madrid
- 28040-Madrid
- Spain
| | - J. M. Pingarrón
- Department of Analytical Chemistry
- Faculty of Chemistry
- University Complutense of Madrid
- 28040-Madrid
- Spain
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9
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Perols A, Arcos Famme M, Eriksson Karlström A. Site-Specific Antibody Labeling by Covalent Photoconjugation of Z Domains Functionalized for Alkyne-Azide Cycloaddition Reactions. Chembiochem 2015; 16:2522-9. [DOI: 10.1002/cbic.201500300] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Indexed: 12/23/2022]
Affiliation(s)
- Anna Perols
- KTH Royal School of Technology; School of Biotechnology; Division of Protein Technology; AlbaNova University Centre; 10691 Stockholm Sweden
| | - Melina Arcos Famme
- KTH Royal School of Technology; School of Biotechnology; Division of Protein Technology; AlbaNova University Centre; 10691 Stockholm Sweden
| | - Amelie Eriksson Karlström
- KTH Royal School of Technology; School of Biotechnology; Division of Protein Technology; AlbaNova University Centre; 10691 Stockholm Sweden
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10
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Berg R, Straub BF. Advancements in the mechanistic understanding of the copper-catalyzed azide-alkyne cycloaddition. Beilstein J Org Chem 2013; 9:2715-50. [PMID: 24367437 PMCID: PMC3869285 DOI: 10.3762/bjoc.9.308] [Citation(s) in RCA: 169] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 10/30/2013] [Indexed: 12/21/2022] Open
Abstract
The copper-catalyzed azide-alkyne cycloaddition (CuAAC) is one of the most broadly applicable and easy-to-handle reactions in the arsenal of organic chemistry. However, the mechanistic understanding of this reaction has lagged behind the plethora of its applications for a long time. As reagent mixtures of copper salts and additives are commonly used in CuAAC reactions, the structure of the catalytically active species itself has remained subject to speculation, which can be attributed to the multifaceted aggregation chemistry of copper(I) alkyne and acetylide complexes. Following an introductory section on common catalyst systems in CuAAC reactions, this review will highlight experimental and computational studies from early proposals to very recent and more sophisticated investigations, which deliver more detailed insights into the CuAAC's catalytic cycle and the species involved. As diverging mechanistic views are presented in articles, books and online resources, we intend to present the research efforts in this field during the past decade and finally give an up-to-date picture of the currently accepted dinuclear mechanism of CuAAC. Additionally, we hope to inspire research efforts on the development of molecularly defined copper(I) catalysts with defined structural characteristics, whose main advantage in contrast to the regularly used precatalyst reagent mixtures is twofold: on the one hand, the characteristics of molecularly defined, well soluble catalysts can be tuned according to the particular requirements of the experiment; on the other hand, the understanding of the CuAAC reaction mechanism can be further advanced by kinetic studies and the isolation and characterization of key intermediates.
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Affiliation(s)
- Regina Berg
- Organisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Bernd F Straub
- Organisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
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Lim CW, Le HT, Han JH, Kim DH, Jang JG, Kim TW. New Water-soluble Alkynylating Agent for Cell Surface Protein: Sulfosuccinimidyl 4-Pentynoate. B KOREAN CHEM SOC 2013. [DOI: 10.5012/bkcs.2013.34.6.1895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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