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Nie K, Zhang J, Xu H, Ren K, Yu C, Zhang Q, Li F, Yang Q. Reverse design of haptens based on antigen spatial conformation to prepare anti-capsaicinoids&gingerols antibodies for monitoring of gutter cooking oil. Food Chem X 2024; 22:101273. [PMID: 38524780 PMCID: PMC10957407 DOI: 10.1016/j.fochx.2024.101273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/24/2024] [Accepted: 03/06/2024] [Indexed: 03/26/2024] Open
Abstract
Rapid simultaneous detection of multi-component adulteration markers can improve the accuracy of identification of gutter cooking oil in edible oil, which is made possible by broad-spectrum antibody (bs-mAb). This study used capsaicinoids (CPCs) and gingerol derivatives (GDs) as adulteration markers, and two broad-spectrum haptens (bs-haptens) were designed and synthesized based on a reverse design strategy of molecular docking. Electrostatic potential (ESP) and monoclonal antibodies (mAbs) preparation verified the strategy's feasibility. To further investigate the recognition mechanism, five other reported antigens and mAbs were also used. Finally, the optimal combination (Hapten 5-OVA/1-F12) and key functional groups (f-groups) were determined. The half maximal inhibitory concentration (IC50) for CPCs-GDs was between 88.13 and 499.16 ng/mL. Meanwhile, a preliminary lateral flow immunoassay (LFIA) study made practical monitoring possible. The study provided a theoretical basis for the virtual screening of bs-haptens and simultaneous immunoassay of multiple exogenous markers to monitor gutter oil rapidly and accurately.
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Affiliation(s)
- Kunying Nie
- School of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo 255049, Shandong Province, China
- Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo 255049, Shandong Province, China
- Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo 255049, Shandong Province, China
| | - Jiali Zhang
- School of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo 255049, Shandong Province, China
- Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo 255049, Shandong Province, China
- Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo 255049, Shandong Province, China
| | - Haitao Xu
- School of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo 255049, Shandong Province, China
- Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo 255049, Shandong Province, China
- Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo 255049, Shandong Province, China
| | - Keyun Ren
- School of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo 255049, Shandong Province, China
- Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo 255049, Shandong Province, China
- Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo 255049, Shandong Province, China
| | - Chunlei Yu
- School of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo 255049, Shandong Province, China
- Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo 255049, Shandong Province, China
- Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo 255049, Shandong Province, China
| | - Qi Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Key Laboratory of Detection for Mycotoxins, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
- Laboratory of Risk Assessment for Oil-seeds Products, Wuhan, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Falan Li
- School of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo 255049, Shandong Province, China
- Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo 255049, Shandong Province, China
- Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo 255049, Shandong Province, China
| | - Qingqing Yang
- School of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo 255049, Shandong Province, China
- Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo 255049, Shandong Province, China
- Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo 255049, Shandong Province, China
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Mohammed AF, Othman SA, Abou-Ghadir OF, Kotb AA, Mostafa YA, El-Mokhtar MA, Abdu-Allah HHM. Design, synthesis, biological evaluation and docking study of some new aryl and heteroaryl thiomannosides as FimH antagonists. Bioorg Chem 2024; 145:107258. [PMID: 38447463 DOI: 10.1016/j.bioorg.2024.107258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 03/08/2024]
Abstract
FimH is a mannose-recognizing lectin that is expressed by Escherichia coli guiding its ability to adhere and infect cells. It is involved in pathogenesis of urinary tract infections and Chron's disease. Several X-ray structure-guided ligand design studies were extensively utilized in the discovery and optimization of small molecule aryl mannoside FimH antagonists. These antagonists retain key specific interactions of the mannose scaffolds with the FimH carbohydrate recognition domains. Thiomannosides are attractive and stable scaffolds, and this work reports the synthesis of some of their new aryl and heteroaryl derivatives as FimH antagonists. FimH-competitive binding assays as well as biofilm inhibition of the new compounds (24-32) were determined in comparison with the reference n-heptyl α-d-mannopyranoside (HM). The affinity among these compounds was found to be governed by the structure of the aryl and heteroarylf aglycones. Two compounds 31 and 32 revealed higher activity than HM. Molecular docking and total hydrophobic to topological polar surface area ratio calculations attributed to explain the obtained biological results. Finally, the SAR study suggested that introducing an aryl or heteroaryl aglycone of sufficient hydrophobicity and of proper orientation within the tyrosine binding site considerably enhance binding affinity. The potent and synthetically feasible FimH antagonists described herein hold potential as leads for the development of sensors for detection of E. coli and treatment of its diseases.
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Affiliation(s)
- Anber F Mohammed
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
| | - Shimaa A Othman
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
| | - Ola F Abou-Ghadir
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
| | - Ahmed A Kotb
- Department of Microbiology and Immunology, Faculty of Pharmacy, Assiut University, Assiut, 71526, Egypt
| | - Yaser A Mostafa
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
| | - Mohamed A El-Mokhtar
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut 71515, Egypt
| | - Hajjaj H M Abdu-Allah
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt.
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Shi Y, Zhang X, Yang Y, Cai T, Peng C, Wu L, Zhou L, Han J, Ma M, Zhu W, Xu Z. D3CARP: a comprehensive platform with multiple-conformation based docking, ligand similarity search and deep learning approaches for target prediction and virtual screening. Comput Biol Med 2023; 164:107283. [PMID: 37536095 DOI: 10.1016/j.compbiomed.2023.107283] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/15/2023] [Accepted: 07/28/2023] [Indexed: 08/05/2023]
Abstract
Resource- and time-consuming biological experiments are unavoidable in traditional drug discovery, which have directly driven the evolution of various computational algorithms and tools for drug-target interaction (DTI) prediction. For improving the prediction reliability, a comprehensive platform is highly expected as some previously reported webservers are small in scale, single-method, or even out of service. In this study, we integrated the multiple-conformation based docking, 2D/3D ligand similarity search and deep learning approaches to construct a comprehensive webserver, namely D3CARP, for target prediction and virtual screening. Specifically, 9352 conformations with positive control of 1970 targets were used for molecular docking, and approximately 2 million target-ligand pairs were used for 2D/3D ligand similarity search and deep learning. Besides, the positive compounds were added as references, and related diseases of therapeutic targets were annotated for further disease-based DTI study. The accuracies of the molecular docking and deep learning approaches were 0.44 and 0.89, respectively. And the average accuracy of five ligand similarity searches was 0.94. The strengths of D3CARP encompass the support for multiple computational methods, ensemble docking, utilization of positive controls as references, cross-validation of predicted outcomes, diverse disease types, and broad applicability in drug discovery. The D3CARP is freely accessible at https://www.d3pharma.com/D3CARP/index.php.
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Affiliation(s)
- Yulong Shi
- State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinben Zhang
- State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yanqing Yang
- State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tingting Cai
- State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Cheng Peng
- State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Leyun Wu
- State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liping Zhou
- State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiaxin Han
- State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Minfei Ma
- State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiliang Zhu
- State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Zhijian Xu
- State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China.
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Prescher H, Schweizer A, Frank M, Kuhfeldt E, Ring J, Nitschke L. Targeting Human CD22/Siglec-2 with Dimeric Sialosides as Novel Oligosaccharide Mimetics. J Med Chem 2022; 65:10588-10610. [PMID: 35881556 DOI: 10.1021/acs.jmedchem.2c00765] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Significant interest in the development of high-affinity ligands for Siglecs exists due to the various therapeutically relevant functions of these proteins. Here, we report a new strategy to develop and design Siglec ligands as disialyl-oligosaccharide mimetics exemplified on Siglec-2 (CD22). We report insights into development of dimeric ligands with high affinity and avidity to cell surface-expressed CD22, assay development, tool compounds, structure activity relationships, and biological data on calcium flux regulation in B-cells. The binding modes of selected ligands have been modeled based on state-of-the-art molecular dynamics simulations on the microsecond timescale, providing detailed views on ligand binding and opening a new perspective on drug design efforts for Siglecs. High-avidity dimeric ligands containing a linker opening the way towards bispecifics are presented as well.
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Affiliation(s)
| | - Astrid Schweizer
- Chair of Genetics, Department of Biology, University of Erlangen, 91058 Erlangen, Germany
| | - Martin Frank
- Biognos AB, Generatorsgatan 1, 40274 Göteborg, Sweden
| | | | - Julia Ring
- Chair of Genetics, Department of Biology, University of Erlangen, 91058 Erlangen, Germany
| | - Lars Nitschke
- Chair of Genetics, Department of Biology, University of Erlangen, 91058 Erlangen, Germany
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de Andrade P, Ahmadipour S, Field RA. Anomeric 1,2,3-triazole-linked sialic acid derivatives show selective inhibition towards a bacterial neuraminidase over a trypanosome trans-sialidase. Beilstein J Org Chem 2022; 18:208-216. [PMID: 35280952 PMCID: PMC8895027 DOI: 10.3762/bjoc.18.24] [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: 11/08/2021] [Accepted: 02/02/2022] [Indexed: 11/25/2022] Open
Abstract
Sialic acid is the natural substrate for sialidases and its chemical modification has been a useful approach to generate potent and selective inhibitors. Aiming at advancing the discovery of selective Trypanosoma cruzi trans-sialidase (TcTS) inhibitors, we have synthesised a small series of anomeric 1,2,3-triazole-linked sialic acid derivatives in good yields and high purity via copper-catalysed azide–alkyne cycloaddition (CuAAC, click chemistry) and evaluated their activity towards TcTS and neuraminidase. Surprisingly, the compounds showed practically no TcTS inhibition, whereas ca. 70% inhibition was observed for neuraminidase in relation to the analogues bearing hydrophobic substituents and ca. 5% for more polar substituents. These results suggest that polarity changes are less tolerated by neuraminidase due to the big difference in impact of hydrophobicity upon inhibition, thus indicating a simple approach to differentiate both enzymes. Moreover, such selectivity might be reasoned based on a possible steric hindrance caused by a bulky hydrophobic loop that sits over the TcTS active site and may prevent the hydrophobic inhibitors from binding. The present study is a step forward in exploiting subtle structural differences in sialidases that need to be addressed in order to achieve selective inhibition.
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Affiliation(s)
- Peterson de Andrade
- Manchester Institute of Biotechnology and Department of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Sanaz Ahmadipour
- Manchester Institute of Biotechnology and Department of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
- Iceni Glycoscience Ltd, Norwich Research Park NR4 7GJ, UK
| | - Robert A Field
- Manchester Institute of Biotechnology and Department of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
- Iceni Glycoscience Ltd, Norwich Research Park NR4 7GJ, UK
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