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Konvalinková D, Dolníček F, Hovorková M, Červený J, Kundrát O, Pelantová H, Petrásková L, Cvačka J, Faizulina M, Varghese B, Kovaříček P, Křen V, Lhoták P, Bojarová P. Glycocalix[4]arenes and their affinity to a library of galectins: the linker matters. Org Biomol Chem 2023; 21:1294-1302. [PMID: 36647793 DOI: 10.1039/d2ob02235d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Galectins are lectins that bind β-galactosides. They are involved in important extra- and intracellular biological processes such as apoptosis, and regulation of the immune system or the cell cycle. High-affinity ligands of galectins may introduce new therapeutic approaches or become new tools for biomedical research. One way of increasing the low affinity of β-galactoside ligands to galectins is their multivalent presentation, e.g., using calixarenes. We report on the synthesis of glycocalix[4]arenes in cone, partial cone, 1,2-alternate, and 1,3-alternate conformations carrying a lactosyl ligand on three different linkers. The affinity of the prepared compounds to a library of human galectins was determined using competitive ELISA assay and biolayer interferometry. Structure-affinity relationships regarding the influence of the linker and the core structure were formulated. Substantial differences were found between various linker lengths and the position of the triazole unit. The formation of supramolecular clusters was detected by atomic force microscopy. The present work gives a systematic insight into prospective galectin ligands based on the calix[4]arene core.
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Affiliation(s)
- Dorota Konvalinková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Prague 4, Czech Republic.
| | - František Dolníček
- Department of Organic Chemistry, University of Chemistry and Technology Prague, Technická 5, CZ-16628 Praha 6, Czech Republic.
| | - Michaela Hovorková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Prague 4, Czech Republic. .,Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, CZ-12843 Prague 2, Czech Republic
| | - Jakub Červený
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Prague 4, Czech Republic. .,Department of Analytical Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843 Prague 2, Czech Republic
| | - Ondřej Kundrát
- Department of Organic Chemistry, University of Chemistry and Technology Prague, Technická 5, CZ-16628 Praha 6, Czech Republic.
| | - Helena Pelantová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Prague 4, Czech Republic.
| | - Lucie Petrásková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Prague 4, Czech Republic.
| | - Josef Cvačka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, CZ-166 10 Prague 6, Czech Republic
| | - Margarita Faizulina
- Department of Organic Chemistry, University of Chemistry and Technology Prague, Technická 5, CZ-16628 Praha 6, Czech Republic.
| | - Beena Varghese
- Department of Organic Chemistry, University of Chemistry and Technology Prague, Technická 5, CZ-16628 Praha 6, Czech Republic.
| | - Petr Kovaříček
- Department of Organic Chemistry, University of Chemistry and Technology Prague, Technická 5, CZ-16628 Praha 6, Czech Republic.
| | - Vladimír Křen
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Prague 4, Czech Republic.
| | - Pavel Lhoták
- Department of Organic Chemistry, University of Chemistry and Technology Prague, Technická 5, CZ-16628 Praha 6, Czech Republic.
| | - Pavla Bojarová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Prague 4, Czech Republic. .,Department of Health Care Disciplines and Population Protection, Faculty of Biomedical Engineering, Czech Technical University in Prague, nám. Sítná 3105, CZ-272 01 Kladno, Czech Republic
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Rastogi V, Yadav P, Porwal M, Sur S, Verma A. Dendrimer as nanocarrier for drug delivery and drug targeting therapeutics: a fundamental to advanced systematic review. INT J POLYM MATER PO 2022. [DOI: 10.1080/00914037.2022.2158334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Vaibhav Rastogi
- Teerthanker Mahaveer College of Pharmacy, Teerthanker Mahaveer University, Moradabad, India
| | - Pragya Yadav
- Department of Pharmaceutics, Amity Institute of Pharmacy, Amity University, Noida, India
| | - Mayur Porwal
- Teerthanker Mahaveer College of Pharmacy, Teerthanker Mahaveer University, Moradabad, India
| | - Souvik Sur
- Research and Development Center, Teerthanker Mahaveer University, Moradabad, India
| | - Anurag Verma
- Teerthanker Mahaveer College of Pharmacy, Teerthanker Mahaveer University, Moradabad, India
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Siva Shanmugam NR, Jino Blessy J, Veluraja K, Gromiha MM. Prediction of protein-carbohydrate complex binding affinity using structural features. Brief Bioinform 2020; 22:6032626. [PMID: 33313775 DOI: 10.1093/bib/bbaa319] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/28/2020] [Accepted: 10/19/2020] [Indexed: 01/03/2023] Open
Abstract
Protein-carbohydrate interactions play a major role in several cellular and biological processes. Elucidating the factors influencing the binding affinity of protein-carbohydrate complexes and predicting their free energy of binding provide deep insights for understanding the recognition mechanism. In this work, we have collected the experimental binding affinity data for a set of 389 protein-carbohydrate complexes and derived several structure-based features such as contact potentials, interaction energy, number of binding residues and contacts between different types of atoms. Our analysis on the relationship between binding affinity and structural features revealed that the important factors depend on the type of the complex based on number of carbohydrate and protein chains. Specifically, binding site residues, accessible surface area, interactions between various atoms and energy contributions are important to understand the binding affinity. Further, we have developed multiple regression equations for predicting the binding affinity of protein-carbohydrate complexes belonging to six categories of protein-carbohydrate complexes. Our method showed an average correlation and mean absolute error of 0.731 and 1.149 kcal/mol, respectively, between experimental and predicted binding affinities on a jackknife test. We have developed a web server PCA-Pred, Protein-Carbohydrate Affinity Predictor, for predicting the binding affinity of protein-carbohydrate complexes. The web server is freely accessible at https://web.iitm.ac.in/bioinfo2/pcapred/. The web server is implemented using HTML and Python and supports recent versions of major browsers such as Chrome, Firefox, IE10 and Opera.
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Affiliation(s)
| | | | - K Veluraja
- Indian Institute of Science, Bangalore, India
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