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Kodr D, Kužmová E, Pohl R, Kraus T, Hocek M. Lipid-linked nucleoside triphosphates for enzymatic synthesis of hydrophobic oligonucleotides with enhanced membrane anchoring efficiency. Chem Sci 2023; 14:4059-4069. [PMID: 37063801 PMCID: PMC10094435 DOI: 10.1039/d2sc06718h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 03/19/2023] [Indexed: 03/22/2023] Open
Abstract
We designed and synthesized a series of 2'-deoxyribonucleoside triphosphates (dNTPs) bearing various lipid moieties. Fatty acid- and cholesterol-modified dNTPs proved to be substrates for KOD XL DNA polymerase in primer extension reactions. They were also mutually compatible for simultaneous multiple incorporations into the DNA strand. The methodology of enzymatic synthesis opened a pathway to diverse structurally unique lipid-ON probes containing one or more lipid units. We studied interactions of such probes with the plasma membranes of live cells. Employing a rational design, we found a series of lipid-ONs with enhanced membrane anchoring efficiency. The in-membrane stability of multiply modified ONs was superior to that of commonly studied ON analogues, in which a single cholesterol molecule is typically tethered to the thread end. Notably, some of the probes were detected at the cell surface even after 24 h upon removal of the probe solution. Such an effect was general to several studied cell lines.
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Affiliation(s)
- David Kodr
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences Flemingovo namesti 2 CZ-16610 Prague 6 Czech Republic
| | - Erika Kužmová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences Flemingovo namesti 2 CZ-16610 Prague 6 Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences Flemingovo namesti 2 CZ-16610 Prague 6 Czech Republic
| | - Tomáš Kraus
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences Flemingovo namesti 2 CZ-16610 Prague 6 Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences Flemingovo namesti 2 CZ-16610 Prague 6 Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University in Prague Hlavova 8 Prague-2 12843 Czech Republic
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Periyasami G, Kamalraj S, Padmanaban R, Yeswanth Kumar S, Stalin A, Arumugam N, Suresh Kumar R, Rahaman M, Durairaju P, Alrehaili A, Aldalbahi A. Glucosamine-6-phosphate synthase inhibiting C3-β-cholesterol tethered spiro heterocyclic conjugates: Synthesis and their insight of DFT and docking study. Bioorg Chem 2019; 88:102920. [PMID: 30991194 DOI: 10.1016/j.bioorg.2019.102920] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 03/27/2019] [Accepted: 04/09/2019] [Indexed: 11/16/2022]
Abstract
A series of novel covalent cholesterol-spiro pyrrolidine/pyrrolizidine heterocyclic hybrids possessing biologically active oxindole, indanedione, and acenaphthylene-1-one have been synthesized by the reaction of C3-β-cholesteroalacrylate with heterocyclic di- and tri-ketones. All the sixteen compounds were obtained as a single isomer in good yield through a stereo- and regio- selective 1,3-dipolar cycloaddition methodology. Stereochemistry of the spiranic cycloadducts has been established by spectroscopic analysis and the regioselectivity outcome of the spiro adducts has been accomplished by DFT calculations at B3LYP/6-31G (d,p) level study. In vitro antibacterial activity of the newly synthesized cycloadducts were evaluated against highly pathogenic Gram-positive and Gram-negative bacteria and the most active compounds 5a, 13, and 14 underwent automated in silico molecular docking analysis in order to validate their effective orientation as a inhibitors bound in the active site of glucosamine-6-phosphate synthase (1XFF) enzyme by employing AutoDock Tools.
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Affiliation(s)
- Govindasami Periyasami
- Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia; Department of Organic Chemistry, University of Madras, Guindy Campus, Chennai, India.
| | - Subban Kamalraj
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India; Centre for Advanced Studies in Botany & Centre for Herbal Sciences, University of Madras, Guindy Campus, Chennai 600 025, Tamil Nadu, India
| | - Ramanathan Padmanaban
- Department of Chemistry, School of Physical, Chemical & Applied Sciences, Pondicherry University, Puducherry, India
| | - Santhakumar Yeswanth Kumar
- Department of Chemistry, School of Physical, Chemical & Applied Sciences, Pondicherry University, Puducherry, India
| | - Antony Stalin
- Division of Bioinformatics, Entomology Research Institute, Loyola College, Chennai 600 034, Tamil Nadu, India; Centre for Advanced Studies in Botany & Centre for Herbal Sciences, University of Madras, Guindy Campus, Chennai 600 025, Tamil Nadu, India
| | - Natarajan Arumugam
- Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Raju Suresh Kumar
- Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mostafizur Rahaman
- Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Periyan Durairaju
- Department of Chemistry, Thiruvalluar Government Arts College, Periyar University, Raispuram, India
| | - Abdulaziz Alrehaili
- Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Ali Aldalbahi
- Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia.
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Albuquerque HMT, Santos CMM, Silva AMS. Cholesterol-Based Compounds: Recent Advances in Synthesis and Applications. Molecules 2018; 24:E116. [PMID: 30597999 PMCID: PMC6337470 DOI: 10.3390/molecules24010116] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 12/22/2018] [Accepted: 12/24/2018] [Indexed: 01/31/2023] Open
Abstract
This review reports on the latest developments (since 2014) in the chemistry of cholesterol and its applications in different research fields. These applications range from drug delivery or bioimaging applications to cholesterol-based liquid crystals and gelators. A brief overview of the most recent synthetic procedures to obtain new cholesterol derivatives is also provided, as well as the latest anticancer, antimicrobial, and antioxidant new cholesterol-based derivatives. This review discusses not only the synthetic details of the preparation of new cholesterol derivatives or conjugates, but also gives a short summary concerning the specific application of such compounds.
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Affiliation(s)
- Hélio M T Albuquerque
- QOPNA & LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal.
| | - Clementina M M Santos
- QOPNA & LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal.
- Centro de Investigação de Montanha (CIMO) Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal.
| | - Artur M S Silva
- QOPNA & LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal.
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