1
|
Argueta-Gonzalez H, Swenson CS, Skowron KJ, Heemstra JM. Elucidating Sequence-Assembly Relationships for Bilingual PNA Biopolymers. ACS OMEGA 2023; 8:37442-37450. [PMID: 37841192 PMCID: PMC10569013 DOI: 10.1021/acsomega.3c05528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/12/2023] [Indexed: 10/17/2023]
Abstract
Nucleic acids and proteins possess encoded "languages" that can be used for information storage or to direct function. However, each biopolymer is limited to encoding its respective "language." Using a peptide nucleic acid (PNA) scaffold, nucleobase and amino acid residues can be installed on a singular backbone, enabling a single biopolymer to encode both languages. Our laboratory previously reported the development of a "bilingual" PNA biopolymer that incorporates a sequence-specific nucleic acid code interspersed with hydrophobic (alanine) and hydrophilic (lysine) amino acid residues at defined positions to produce amphiphilic character. We observed the amphiphilic amino acid residues directing the biopolymer to undergo self-assembly into micelle-like structures, while the nucleic acid recognition was harnessed for disassembly. Herein, we report a series of bilingual PNA sequences having amino acid residues with varying lengths, functional group charges, hydrophobicities, and spacings to elucidate the effect of these parameters on micelle assembly and nucleic acid recognition. Negative charges in the hydrophilic block or increased bulkiness of the hydrophobic side chains led to assembly into similarly sized micelles; however, the negative charge additionally led to increased critical micelle concentration. Upon PNA sequence truncation to decrease the spacing between side chains, the biopolymers remained capable of self-assembling but formed smaller structures. Characterization of disassembly revealed that each variant retained sequence recognition capabilities and stimuli-responsive disassembly. Together, these data show that the amino acid and nucleic acid sequences of amphiphilic bilingual biopolymers can be customized to finely tune the assembly and disassembly properties, which has implications for applications such as the encapsulation and delivery of cargo for therapeutics.
Collapse
Affiliation(s)
| | - Colin S. Swenson
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Kornelia J. Skowron
- Department
of Chemistry, Washington University in St.
Louis, St. Louis, Missouri 63130, United
States
| | - Jennifer M. Heemstra
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| |
Collapse
|
2
|
Klejch T, Keough DT, King G, Doleželová E, Česnek M, Buděšínský M, Zíková A, Janeba Z, Guddat LW, Hocková D. Stereo-Defined Acyclic Nucleoside Phosphonates are Selective and Potent Inhibitors of Parasite 6-Oxopurine Phosphoribosyltransferases. J Med Chem 2022; 65:4030-4057. [PMID: 35175749 DOI: 10.1021/acs.jmedchem.1c01881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pathogens such as Plasmodium and Trypanosoma spp. are unable to synthesize purine nucleobases. They rely on the salvage of these purines and their nucleosides from the host cell to synthesize the purine nucleotides required for DNA/RNA production. The key enzymes in this pathway are purine phosphoribosyltransferases (PRTs). Here, we synthesized 16 novel acyclic nucleoside phosphonates, 12 with a chiral center at C-2', and eight bearing a second chiral center at C-6'. Of these, bisphosphonate (S,S)-48 is the most potent inhibitor of the Plasmodium falciparum and P. vivax 6-oxopurine PRTs and the most potent inhibitor of two Trypanosoma brucei (Tbr) 6-oxopurine PRTs yet discovered, with Ki values as low as 2 nM. Crystal structures of (S,S)-48 in complex with human and Tbr 6-oxopurine PRTs show that the inhibitor binds to the enzymes in different conformations, providing an explanation for its potency and selectivity (i.e., 35-fold in favor of the parasite enzymes).
Collapse
Affiliation(s)
- Tomáš Klejch
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 6 CZ-16000, Czech Republic
| | - Dianne T Keough
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Australia
| | - Gordon King
- The Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane 4072, Australia
| | - Eva Doleželová
- Institute of Parasitology, Biology Centre ASCR, České Budějovice 37005, Czech Republic
| | - Michal Česnek
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 6 CZ-16000, Czech Republic
| | - Miloš Buděšínský
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 6 CZ-16000, Czech Republic
| | - Alena Zíková
- Institute of Parasitology, Biology Centre ASCR, České Budějovice 37005, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice 37005, Czech Republic
| | - Zlatko Janeba
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 6 CZ-16000, Czech Republic
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Australia
| | - Dana Hocková
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 6 CZ-16000, Czech Republic
| |
Collapse
|
3
|
Shaikh AY, Björkling F, Nielsen PE, Franzyk H. Optimized Synthesis of Fmoc/Boc‐Protected PNA Monomers and their Assembly into PNA Oligomers. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ashif Y. Shaikh
- Center for Peptide-based Antibiotics, Department of Drug Design and Pharmacology Faculty of Heath and Medical Sciences University of Copenhagen Jagtvej 162 2100 Copenhagen Denmark
| | - Fredrik Björkling
- Center for Peptide-based Antibiotics, Department of Drug Design and Pharmacology Faculty of Heath and Medical Sciences University of Copenhagen Jagtvej 162 2100 Copenhagen Denmark
| | - Peter E. Nielsen
- Center for Peptide-based Antibiotics, Department of Cellular and Molecular Medicine, The Panum Institute, Faculty of Heath and Medical Sciences University of Copenhagen Blegdamsvej 3 2200 Copenhagen Denmark
| | - Henrik Franzyk
- Center for Peptide-based Antibiotics, Department of Drug Design and Pharmacology Faculty of Heath and Medical Sciences University of Copenhagen Jagtvej 162 2100 Copenhagen Denmark
| |
Collapse
|
4
|
Fmoc-Based Assembly of PNA Oligomers: Manual and Microwave-Assisted Automated Synthesis. Methods Mol Biol 2021; 2105:1-16. [PMID: 32088861 DOI: 10.1007/978-1-0716-0243-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Exploration of PNA-peptide conjugates as potential antisense antibiotics necessitates a fast and efficient synthesis protocols for amounts that facilitate determination of structure-activity relationships and in vivo studies in animal infection models. Fmoc/Boc-protected PNA monomers are here used for assembly of oligomers by optimized protocols involving either a manual synthesis method at room temperature or automated microwave-assisted coupling of monomers on a peptide synthesizer.
Collapse
|
5
|
Gupta MK, Madhanagopal BR, Ganesh KN. Peptide Nucleic Acid with Double Face: Homothymine–Homocytosine Bimodal Cα-PNA (bm-Cα-PNA) Forms a Double Duplex of the bm-PNA2:DNA Triplex. J Org Chem 2020; 86:414-428. [DOI: 10.1021/acs.joc.0c02158] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Manoj Kumar Gupta
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, India
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road, Tirupati 517507, India
| | - Bharath Raj Madhanagopal
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road, Tirupati 517507, India
| | - Krishna N. Ganesh
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, India
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road, Tirupati 517507, India
| |
Collapse
|
6
|
Cheviet T, Wein S, Bourchenin G, Lagacherie M, Périgaud C, Cerdan R, Peyrottes S. β-Hydroxy- and β-Aminophosphonate Acyclonucleosides as Potent Inhibitors of Plasmodium falciparum Growth. J Med Chem 2020; 63:8069-8087. [PMID: 32687714 DOI: 10.1021/acs.jmedchem.0c00131] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Malaria is an infectious disease caused by a parasite of the genus Plasmodium, and the emergence of parasites resistant to all current antimalarial drugs highlights the urgency of having new classes of molecules. We developed an effective method for the synthesis of a series of β-modified acyclonucleoside phosphonate (ANP) derivatives, using commercially available and inexpensive materials (i.e., aspartic acid and purine heterocycles). Their biological evaluation in cell culture experiments and SAR revealed that the compounds' effectiveness depends on the presence of a hydroxyl group, the chain length (four carbons), and the nature of the nucleobase (guanine). The most active derivative inhibits the growth of Plasmodium falciparum in vitro in the nanomolar range (IC50 = 74 nM) with high selectivity index (SI > 1350). This compound also showed remarkable in vivo activity in P. berghei-infected mice (ED50 ∼ 0.5 mg/kg) when administered by the ip route and is, although less efficient, still active via the oral route. It is the first ANP derivative with such potent antimalarial activity and therefore has considerable potential for development as a new antimalarial drug.
Collapse
Affiliation(s)
- Thomas Cheviet
- Team Nucleosides & Phosphorylated Effectors, Institute for Biomolecules Max Mousseron (IBMM), UMR 5247 UM-CNRS-ENSCM, Université de Montpellier, Place E. Bataillon, cc 1704, 34095 Montpellier, France
| | - Sharon Wein
- Laboratory of Pathogen Host Interactions (LPHI), UMR 5235 UM-CNRS, Université de Montpellier, Place E. Bataillon, 34095 Montpellier, France
| | - Gabriel Bourchenin
- Team Nucleosides & Phosphorylated Effectors, Institute for Biomolecules Max Mousseron (IBMM), UMR 5247 UM-CNRS-ENSCM, Université de Montpellier, Place E. Bataillon, cc 1704, 34095 Montpellier, France
| | - Manon Lagacherie
- Team Nucleosides & Phosphorylated Effectors, Institute for Biomolecules Max Mousseron (IBMM), UMR 5247 UM-CNRS-ENSCM, Université de Montpellier, Place E. Bataillon, cc 1704, 34095 Montpellier, France
| | - Christian Périgaud
- Team Nucleosides & Phosphorylated Effectors, Institute for Biomolecules Max Mousseron (IBMM), UMR 5247 UM-CNRS-ENSCM, Université de Montpellier, Place E. Bataillon, cc 1704, 34095 Montpellier, France
| | - Rachel Cerdan
- Laboratory of Pathogen Host Interactions (LPHI), UMR 5235 UM-CNRS, Université de Montpellier, Place E. Bataillon, 34095 Montpellier, France
| | - Suzanne Peyrottes
- Team Nucleosides & Phosphorylated Effectors, Institute for Biomolecules Max Mousseron (IBMM), UMR 5247 UM-CNRS-ENSCM, Université de Montpellier, Place E. Bataillon, cc 1704, 34095 Montpellier, France
| |
Collapse
|
7
|
Bhingardeve P, Madhanagopal BR, Naick H, Jain P, Manoharan M, Ganesh K. Receptor-Specific Delivery of Peptide Nucleic Acids Conjugated to Three Sequentially Linked N-Acetyl Galactosamine Moieties into Hepatocytes. J Org Chem 2020; 85:8812-8824. [PMID: 32529829 DOI: 10.1021/acs.joc.0c00601] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Peptide nucleic acids (PNAs) are DNA analogs that bind with high affinity to DNA and RNA in a sequence-specific manner but have poor cell permeability, limiting use as therapeutic agents. The work described here is motivated by recent reports of efficient gene silencing specifically in hepatocytes by small interfering RNAs conjugated to triantennary N-acetyl galactosamine (GalNAc), the ligand recognized by the asialoglycoprotein receptor (ASGPR). PNAs conjugated to either triantennary GalNAc at the N-terminus (the branched architecture) or monomeric GalNAc moieties anchored at Cγ of three consecutive PNA monomers of N-(2-aminoethyl)glycine (aeg) scaffolds (the sequential architecture) were synthesized on the solid phase. These formed duplexes with complementary DNA and RNA as shown by UV and circular dichroism spectroscopy. The fluorescently labeled analogs of GalNAc-conjugated PNAs were internalized by HepG2 cells that express the ASGPR but were not taken up by HEK-293 cells that lack this receptor. The sequential conjugate was internalized about 13-fold more efficiently than the branched conjugate into HepG2 cells, as demonstrated by confocal microscopy. The results presented here highlight the potential significance of the architecture of GalNAc conjugation for efficient uptake by target liver cells and indicate that GalNAc-conjugated PNAs have possible therapeutic applications.
Collapse
Affiliation(s)
- Pramod Bhingardeve
- Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
| | - Bharath Raj Madhanagopal
- Indian Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road, Tirupati 517507, Andhra Pradesh, India
| | - Hemanth Naick
- Indian Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road, Tirupati 517507, Andhra Pradesh, India
| | - Prashant Jain
- Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
| | - Muthiah Manoharan
- Alnylam Pharmaceuticals, Cambridge, Massachusetts 02142, United States
| | - Krishna Ganesh
- Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India.,Indian Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road, Tirupati 517507, Andhra Pradesh, India
| |
Collapse
|
8
|
Pyrimethamine conjugated histone deacetylase inhibitors: Design, synthesis and evidence for triple negative breast cancer selective cytotoxicity. Bioorg Med Chem 2020; 28:115345. [DOI: 10.1016/j.bmc.2020.115345] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 01/12/2020] [Accepted: 01/22/2020] [Indexed: 12/25/2022]
|
9
|
Swenson CS, Velusamy A, Argueta-Gonzalez HS, Heemstra JM. Bilingual Peptide Nucleic Acids: Encoding the Languages of Nucleic Acids and Proteins in a Single Self-Assembling Biopolymer. J Am Chem Soc 2019; 141:19038-19047. [PMID: 31711285 DOI: 10.1021/jacs.9b09146] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Nucleic acids and proteins are the fundamental biopolymers that support all life on Earth. Nucleic acids store large amounts of information in nucleobase sequences while peptides and proteins utilize diverse amino acid functional groups to adopt complex structures and perform wide-ranging activities. Although nature has evolved machinery to read the nucleic acid code and translate it into amino acid code, the extant biopolymers are restricted to encoding amino acid or nucleotide sequences separately, limiting their potential applications in medicine and biotechnology. Here we describe the design, synthesis, and stimuli-responsive assembly behavior of a bilingual biopolymer that integrates both amino acid and nucleobase sequences into a single peptide nucleic acid (PNA) scaffold to enable tunable storage and retrieval of tertiary structural behavior and programmable molecular recognition capabilities. Incorporation of a defined sequence of amino acid side-chains along the PNA backbone yields amphiphiles having a "protein code" that directs self-assembly into micellar architectures in aqueous conditions. However, these amphiphiles also carry a "nucleotide code" such that subsequent introduction of a complementary RNA strand induces a sequence-specific disruption of assemblies through hybridization. Together, these properties establish bilingual PNA as a powerful biopolymer that combines two information systems to harness structural responsiveness and sequence recognition. The PNA scaffold and our synthetic system are highly generalizable, enabling fabrication of a wide array of user-defined peptide and nucleotide sequence combinations for diverse future biomedical and nanotechnology applications.
Collapse
Affiliation(s)
- Colin S Swenson
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Arventh Velusamy
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | | | - Jennifer M Heemstra
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| |
Collapse
|
10
|
Baek K, Noblett AD, Ren P, Suggs LJ. Design and Characterization of Nucleopeptides for Hydrogel Self-Assembly. ACS APPLIED BIO MATERIALS 2019; 2:2812-2821. [DOI: 10.1021/acsabm.9b00229] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Kiheon Baek
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Alexander D. Noblett
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Laura J. Suggs
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| |
Collapse
|
11
|
Boháčová S, Ludvíková L, Poštová Slavětínská L, Vaníková Z, Klán P, Hocek M. Protected 5-(hydroxymethyl)uracil nucleotides bearing visible-light photocleavable groups as building blocks for polymerase synthesis of photocaged DNA. Org Biomol Chem 2019; 16:1527-1535. [PMID: 29431832 DOI: 10.1039/c8ob00160j] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nucleosides, nucleotides and 2'-deoxyribonucleoside triphosphates (dNTPs) containing 5-(hydroxymethyl)uracil protected with photocleavable groups (2-nitrobenzyl-, 6-nitropiperonyl or 9-anthrylmethyl) were prepared and tested as building blocks for the polymerase synthesis of photocaged oligonucleotides and DNA. Photodeprotection (photorelease) reactions were studied in detail on model nucleoside monophosphates and their photoreaction quantum yields were determined. Photocaged dNTPs were then tested and used as substrates for DNA polymerases in primer extension or PCR. DNA probes containing photocaged or free 5-hydroxymethylU in the recognition sequence of restriction endonucleases were prepared and used for the study of photorelease of caged DNA by UV or visible light at different wavelengths. The nitropiperonyl-protected nucleotide was found to be a superior building block because the corresponding dNTP is a good substrate for DNA polymerases, and the protecting group is efficiently cleavable by irradiation by UV or visible light (up to 425 nm).
Collapse
Affiliation(s)
- Soňa Boháčová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic.
| | | | | | | | | | | |
Collapse
|
12
|
Hansen AM, Bonke G, Hogendorf WFJ, Björkling F, Nielsen J, Kongstad KT, Zabicka D, Tomczak M, Urbas M, Nielsen PE, Franzyk H. Microwave-assisted solid-phase synthesis of antisense acpP peptide nucleic acid-peptide conjugates active against colistin- and tigecycline-resistant E. coli and K. pneumoniae. Eur J Med Chem 2019; 168:134-145. [PMID: 30807888 DOI: 10.1016/j.ejmech.2019.02.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 02/05/2019] [Accepted: 02/07/2019] [Indexed: 11/26/2022]
Abstract
Recent discovery of potent antibacterial antisense PNA-peptide conjugates encouraged development of a fast and efficient synthesis protocol that facilitates structure-activity studies. The use of an Fmoc/Boc protection scheme for both PNA monomers and amino acid building blocks in combination with microwave-assisted solid-phase synthesis proved to be a convenient procedure for continuous assembly of antisense PNA-peptide conjugates. A validated antisense PNA oligomer (CTCATACTCT; targeting mRNA of the acpP gene) was linked to N-terminally modified drosocin (i.e., RXR-PRPYSPRPTSHPRPIRV; X = aminohexanoic acid) or to a truncated Pip1 peptide (i.e., RXRRXR-IKILFQNRRMKWKK; X = aminohexanoic acid), and determination of the antibacterial effects of the resulting conjugates allowed assessment of the influence of different linkers as well as differences between the L- and D-forms of the peptides. The drosocin-derived compound without a linker moiety exhibited highest antibacterial activity against both wild-type Escherichia coli and Klebsiella pneumoniae (MICs in the range 2-4 μg/mL ∼ 0.3-0.7 μM), while analogues displaying an ethylene glycol (eg1) moiety or a polar maleimide linker also possessed activity toward wild-type K. pneumoniae (MICs of 4-8 μg/mL ∼ 0.6-1.3 μM). Against two colistin-resistant E. coli strains the linker-deficient compound proved most potent (with MICs in the range 2-4 μg/mL ∼ 0.3-0.7 μM). The truncated all-L Pip1 peptide had moderate inherent activity against E. coli, and this was unaltered or reduced upon conjugation to the antisense PNA oligomer. By contrast, this peptide was 8-fold less potent against K. pneumoniae, but in this case some PNA-peptide conjugates exhibited potent antisense activity (MICs of 2-8 μg/mL ∼ 0.3-1.2 μM). Most interestingly, the antibacterial activity of the D-form peptide itself was 2- to 16-fold higher than that of the L-form, even for the colistin- and tigecycline-resistant E. coli strains (MIC of 1-2 μg/mL ∼ 0.25-0.5 μM). Low activity was found for conjugates with a two-mismatch PNA sequence corroborating an antisense mode of action. Conjugates containing a D-form peptide were also significantly less active. In conclusion, we have designed and synthesized antisense PNA-drosocin conjugates with potent antibacterial activity against colistin- and tigecycline-resistant E. coli and K. pneumonia without concomitant hemolytic properties. In addition, a truncated D-form of Pip1 was identified as a peptide exhibiting potent activity against both wild-type and multidrug-resistant E. coli, P. aeruginosa, and A. baumannii (MICs within the range 1-4 μg/mL ∼ 0.25-1 μM) as well as toward wild-type Staphylococcus aureus (MIC of 2-4 μg/mL ∼ 0.5-1.0 μM).
Collapse
Affiliation(s)
- Anna Mette Hansen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100, Denmark
| | - Gitte Bonke
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100, Denmark
| | - Wouter Frederik Johan Hogendorf
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100, Denmark
| | - Fredrik Björkling
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100, Denmark
| | - John Nielsen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100, Denmark
| | - Kenneth T Kongstad
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100, Denmark
| | - Dorota Zabicka
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, ul. Chełmska 30/34, 00-725, Warsaw, Poland
| | - Magdalena Tomczak
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, ul. Chełmska 30/34, 00-725, Warsaw, Poland
| | - Malgorzata Urbas
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, ul. Chełmska 30/34, 00-725, Warsaw, Poland
| | - Peter E Nielsen
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2100, Denmark
| | - Henrik Franzyk
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100, Denmark.
| |
Collapse
|
13
|
Zheng H, Saha M, Appella DH. Synthesis of Fmoc-Protected ( S, S)- trans-Cyclopentane Diamine Monomers Enables the Preparation and Study of Conformationally Restricted Peptide Nucleic Acids. Org Lett 2018; 20:7637-7640. [PMID: 30460846 DOI: 10.1021/acs.orglett.8b03374] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
An efficient synthesis of Fmoc-protected ( S, S)- trans-cyclopentane PNA ( tcypPNA) monomers starting from mono-Boc-protected ( S, S)-1,2-cyclopentanediamine is reported. A general synthetic strategy was developed so that tcypPNA monomers with each nucleobase can be made in sufficient quantity and purity for use in solid-phase peptide synthesis (SPPS). The newly synthesized monomers were then successfully incorporated into 10-residue PNA oligomers using standard Fmoc chemistry for SPPS. The different tcypPNAs allow different positions in the sequence to be conformationally constrained with ( S, S)- trans-cyclopentane to determine the effects on binding to complementary DNA.
Collapse
Affiliation(s)
- Hongchao Zheng
- Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry (LBC), National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) , National Institutes of Health , 8 Center Drive, Room 404 , Bethesda , Maryland 20892 , United States
| | - Mrinmoy Saha
- Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry (LBC), National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) , National Institutes of Health , 8 Center Drive, Room 404 , Bethesda , Maryland 20892 , United States
| | - Daniel H Appella
- Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry (LBC), National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) , National Institutes of Health , 8 Center Drive, Room 404 , Bethesda , Maryland 20892 , United States
| |
Collapse
|
14
|
Malamgari SR, Manikandan P, Ramani P, Katta VR. Synthesis of Peptide Nucleic Acid Monomers via N
-Alkylation of Nosyl-protected Amino Acids with N
-Boc Bromoethyl Amine. ChemistrySelect 2018. [DOI: 10.1002/slct.201800202] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sudhakar Reddy Malamgari
- Dhanvanthri Lab; Department of Sciences; Amrita School of Engineering; Coimbatore, Amrita Vishwa Vidyapeetham India
- Department of Medicinal Chemistry; GVK Biosciences Pvt. Ltd, IDA Mallapur, Hyderabad,; 500076 T.S. India
| | - Priyadharshini Manikandan
- Dhanvanthri Lab; Department of Sciences; Amrita School of Engineering; Coimbatore, Amrita Vishwa Vidyapeetham India
| | - Prasanna Ramani
- Dhanvanthri Lab; Department of Sciences; Amrita School of Engineering; Coimbatore, Amrita Vishwa Vidyapeetham India
| | - Vishweshwar Rao Katta
- Department of Medicinal Chemistry; GVK Biosciences Pvt. Ltd, IDA Mallapur, Hyderabad,; 500076 T.S. India
| |
Collapse
|
15
|
Dhamodharan V, Nomura Y, Dwidar M, Yokobayashi Y. Optochemical control of gene expression by photocaged guanine and riboswitches. Chem Commun (Camb) 2018; 54:6181-6183. [DOI: 10.1039/c8cc02290a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A photocaged guanine was synthesized to optically control gene expression in cells using synthetic riboswitches.
Collapse
Affiliation(s)
- V. Dhamodharan
- Nucleic Acid Chemistry and Engineering Unit
- Okinawa Institute of Science and Technology Graduate University
- Onna
- Okinawa
- Japan
| | - Yoko Nomura
- Nucleic Acid Chemistry and Engineering Unit
- Okinawa Institute of Science and Technology Graduate University
- Onna
- Okinawa
- Japan
| | - Mohammed Dwidar
- Nucleic Acid Chemistry and Engineering Unit
- Okinawa Institute of Science and Technology Graduate University
- Onna
- Okinawa
- Japan
| | - Yohei Yokobayashi
- Nucleic Acid Chemistry and Engineering Unit
- Okinawa Institute of Science and Technology Graduate University
- Onna
- Okinawa
- Japan
| |
Collapse
|
16
|
Chen Z, Cox BD, Garnier-Amblard EC, McBrayer TR, Coats SJ, Schinazi RF, Amblard F. Synthesis and anti-HCV activity of a series of β-d-2'-deoxy-2'-dibromo nucleosides and their corresponding phosphoramidate prodrugs. Bioorg Med Chem Lett 2017; 27:5296-5299. [PMID: 29066308 DOI: 10.1016/j.bmcl.2017.10.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 10/10/2017] [Accepted: 10/11/2017] [Indexed: 12/17/2022]
Abstract
Several β-d-2'-deoxy-2'-substituted nucleoside analogs have displayed potent and selective anti-HCV activities and some of them have reached human clinical trials. In that regard, we report herein the synthesis of a series of 2'-deoxy,2'-dibromo substituted U, C, G and A nucleosides 10a-d and their corresponding phosphoramidate prodrugs 13a-d. The synthesized nucleosides 10a-d and prodrugs 13a-d were evaluated for their inhibitory activity against HCV as well as cellular toxicity. The results showed that the most potent compound was prodrug 13a, which exhibited micromolar inhibitory activity (EC50 = 1.5 ± 0.8 µM) with no observed toxicity. In addition, molecular modeling and free energy perturbation calculations for the 5'-triphosphate formed from 13a and related 2'-modified nucleotides are discussed.
Collapse
Affiliation(s)
- Zhe Chen
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University, School of Medicine, Atlanta, GA 30322, United States
| | - Bryan D Cox
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University, School of Medicine, Atlanta, GA 30322, United States
| | | | | | | | - Raymond F Schinazi
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University, School of Medicine, Atlanta, GA 30322, United States.
| | - Franck Amblard
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University, School of Medicine, Atlanta, GA 30322, United States.
| |
Collapse
|
17
|
Zhou S, Mahmoud S, Liu P, Zhou L, Ehteshami M, Bassit L, Tao S, Domaoal RA, Sari O, Schutter CD, Amiralaei S, Khalil A, Ollinger Russell O, McBrayer T, Whitaker T, Abou-Taleb N, Amblard F, Coats SJ, Schinazi RF. 2'-Chloro,2'-fluoro Ribonucleotide Prodrugs with Potent Pan-genotypic Activity against Hepatitis C Virus Replication in Culture. J Med Chem 2017; 60:5424-5437. [PMID: 28595015 DOI: 10.1021/acs.jmedchem.7b00067] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pan-genotypic nucleoside HCV inhibitors display a high genetic barrier to drug resistance and are the preferred direct-acting agents to achieve complete sustained virologic response in humans. Herein, we report, the discovery of a β-d-2'-Cl,2'-F-uridine phosphoramidate nucleotide 16, as a nontoxic pan-genotypic anti-HCV agent. Phosphoramidate 16 in its 5'-triphosphate form specifically inhibited HCV NS5B polymerase with no marked inhibition of human polymerases and cellular mitochondrial RNA polymerase. Studies on the intracellular half-life of phosphoramidate 16-TP in live cells demonstrated favorable half-life of 11.6 h, suggesting once-a-day dosing. Stability in human blood and favorable metabolism in human intestinal microsomes and liver microsomes make phosphoramidate 16 a prospective candidate for further studies to establish its potential value as a new anti-HCV agent.
Collapse
Affiliation(s)
- Shaoman Zhou
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine , Atlanta, Georgia 30307, United States
| | - Sawsan Mahmoud
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine , Atlanta, Georgia 30307, United States.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Helwan University , Helwan, Egypt
| | - Peng Liu
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine , Atlanta, Georgia 30307, United States
| | - Longhu Zhou
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine , Atlanta, Georgia 30307, United States
| | - Maryam Ehteshami
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine , Atlanta, Georgia 30307, United States
| | - Leda Bassit
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine , Atlanta, Georgia 30307, United States
| | - Sijia Tao
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine , Atlanta, Georgia 30307, United States
| | - Robert A Domaoal
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine , Atlanta, Georgia 30307, United States
| | - Ozkan Sari
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine , Atlanta, Georgia 30307, United States
| | - Coralie De Schutter
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine , Atlanta, Georgia 30307, United States
| | - Sheida Amiralaei
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine , Atlanta, Georgia 30307, United States
| | - Ahmed Khalil
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine , Atlanta, Georgia 30307, United States
| | - Olivia Ollinger Russell
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine , Atlanta, Georgia 30307, United States
| | - Tamara McBrayer
- Cocrystal Pharma, Inc., Tucker, Georgia 30084, United States
| | - Tony Whitaker
- Cocrystal Pharma, Inc., Tucker, Georgia 30084, United States
| | - Nageh Abou-Taleb
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Helwan University , Helwan, Egypt
| | - Franck Amblard
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine , Atlanta, Georgia 30307, United States
| | - Steven J Coats
- Cocrystal Pharma, Inc., Tucker, Georgia 30084, United States
| | - Raymond F Schinazi
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine , Atlanta, Georgia 30307, United States
| |
Collapse
|
18
|
Sugiyama T, Hasegawa G, Niikura C, Kuwata K, Imamura Y, Demizu Y, Kurihara M, Kittaka A. PNA monomers fully compatible with standard Fmoc-based solid-phase synthesis of pseudocomplementary PNA. Bioorg Med Chem Lett 2017; 27:3337-3341. [PMID: 28610975 DOI: 10.1016/j.bmcl.2017.06.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 05/31/2017] [Accepted: 06/02/2017] [Indexed: 11/18/2022]
Abstract
Here we report the synthesis of new PNA monomers for pseudocomplementary PNA (pcPNA) that are fully compatible with standard Fmoc chemistry. The thiocarbonyl group of the 2-thiouracil (sU) monomer was protected with the 4-methoxy-2-methybenzyl group (MMPM), while the exocyclic amino groups of diaminopurine (D) were protected with Boc groups. The newly synthesized monomers were incorporated into a 10-mer PNA oligomer using standard Fmoc chemistry for solid-phase synthesis. Oligomerization proceeded smoothly and the HPLC and MALDI-TOF MS analyses indicated that there was no remaining MMPM on the sU nucleobase. The new PNA monomers reported here would facilitate a wide range of applications, such as antigene PNAs and DNA nanotechnologies.
Collapse
Affiliation(s)
- Toru Sugiyama
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan.
| | - Genki Hasegawa
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan
| | - Chie Niikura
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
| | - Yasutada Imamura
- Faculty of Engineering, Kogakuin University, 2665-1 Nakano, Hachioji, Tokyo 192-0015, Japan
| | - Yosuke Demizu
- Division of Organic Chemistry, National Institute of Health Sciences, Ministry of Health and Welfare, Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
| | - Masaaki Kurihara
- School of Pharmacy, International University of Health and Welfare, 2600-1, Kitakanemaru, Ohtawara, Tochigi 324-8501, Japan
| | - Atsushi Kittaka
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan.
| |
Collapse
|
19
|
Sari O, Bassit L, Gavegnano C, McBrayer TR, McCormick L, Cox B, Coats SJ, Amblard F, Schinazi RF. Synthesis and antiviral evaluation of 2',2',3',3'-tetrafluoro nucleoside analogs. Tetrahedron Lett 2017; 58:642-644. [PMID: 28163339 PMCID: PMC5289701 DOI: 10.1016/j.tetlet.2017.01.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Herein, we report the synthesis of novel 2',2',3',3'-tetrafluorinated nucleoside analogs along with their phosphoramidate prodrugs. A tetrafluoro ribose moiety was coupled with different Boc/benzoyl-protected nucleobases under Mitsunobu conditions. After deprotection, tetrafluorinated nucleosides 13b, 14b, 20b-22b were reacted with phenyl-(isopropoxy-L-alaninyl)-phosphorochloridate to afford corresponding monophosphate prodrugs 24b-28b. All synthesized compounds were evaluated against several DNA and RNA viruses including HIV, HBV, HCV, Ebola and Zika viruses.
Collapse
Affiliation(s)
- Ozkan Sari
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Leda Bassit
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Christina Gavegnano
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | | | - Louise McCormick
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Bryan Cox
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Steven J Coats
- Cocrystal Pharma, Inc., 1860 Montreal Road, Tucker, GA 30084, USA
| | - Franck Amblard
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Raymond F Schinazi
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| |
Collapse
|
20
|
Chevrier F, Chamas Z, Lequeux T, Pfund E, Andrei G, Snoeck R, Roy V, Agrofoglio LA. Synthesis of 5,5-difluoro-5-phosphono-pent-2-en-1-yl nucleosides as potential antiviral agents. RSC Adv 2017. [DOI: 10.1039/c7ra05153k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A series of hitherto unknown acyclic 5,5-difluoro-5-phosphono-pent-2-en-1-yl-pyrimidines, -purines and -(1,2,4)-triazolo-3-carboxamide were successfully synthesized from (E)-1-bromo-5-diethoxyphosphoryl-5,5-difluoro-pent-2-ene in a stereoselective manner.
Collapse
Affiliation(s)
- F. Chevrier
- Université d'Orléans et CNRS
- ICOA
- UMR 7311
- Orléans
- France
| | - Z. Chamas
- Université d'Orléans et CNRS
- ICOA
- UMR 7311
- Orléans
- France
| | - T. Lequeux
- Laboratoire de Chimie Moléculaire et Thio-organique
- ENSICAEN
- UNICAEN
- UMR
- CNRS 6507
| | - E. Pfund
- Laboratoire de Chimie Moléculaire et Thio-organique
- ENSICAEN
- UNICAEN
- UMR
- CNRS 6507
| | - G. Andrei
- REGA Institute for Medical Research
- KU Leuven
- Leuven
- Belgium
| | - R. Snoeck
- REGA Institute for Medical Research
- KU Leuven
- Leuven
- Belgium
| | - V. Roy
- Université d'Orléans et CNRS
- ICOA
- UMR 7311
- Orléans
- France
| | | |
Collapse
|
21
|
Mercurio ME, Tomassi S, Gaglione M, Russo R, Chambery A, Lama S, Stiuso P, Cosconati S, Novellino E, Di Maro S, Messere A. Switchable Protecting Strategy for Solid Phase Synthesis of DNA and RNA Interacting Nucleopeptides. J Org Chem 2016; 81:11612-11625. [DOI: 10.1021/acs.joc.6b01829] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Maria Emilia Mercurio
- Department
of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
| | - Stefano Tomassi
- Department
of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
| | - Maria Gaglione
- Department
of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
| | - Rosita Russo
- Department
of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
| | - Angela Chambery
- Department
of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
| | - Stefania Lama
- Department
of Biochemistry, Biophysics and General Pathology, Second University of Naples, Via De Crecchio 7, 80127 Napoli, Italy
| | - Paola Stiuso
- Department
of Biochemistry, Biophysics and General Pathology, Second University of Naples, Via De Crecchio 7, 80127 Napoli, Italy
| | - Sandro Cosconati
- Department
of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
| | - Ettore Novellino
- Department
of Pharmacy, University of Naples “Federico II”, Via D. Montesano
49, 80131 Napoli, Italy
| | - Salvatore Di Maro
- Department
of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
| | - Anna Messere
- Department
of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
| |
Collapse
|
22
|
Yao D, Lin Z, Wu J. Near-Infrared Fluorogenic Probes with Polarity-Sensitive Emission for in Vivo Imaging of an Ovarian Cancer Biomarker. ACS APPLIED MATERIALS & INTERFACES 2016; 8:5847-5856. [PMID: 26910257 DOI: 10.1021/acsami.5b11826] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Lysophosphatidic acid (LPA, cutoff values ≥ 1.5 μM) is an effective biomarker for early stage ovarian cancer. The development of selective probes for LPA detection is therefore critical for early clinical diagnosis. Although current methods have been developed for the detection of LPA in solution, they cannot be used for tracking LPA in vivo. Here, we report a near-infrared (NIR) fluorescent probe that can selectively respond to LPA based on polarity-sensitive emission at a very low detection limit of 0.5 μM in situ. This probe exhibits a marked increase of fluorescence at 720 nm upon binding to LPA, allowing the direct visualization of LPA in vitro and in vivo without interference from other biomolecules. Moreover, the probe containing two arginine-glycine-aspartic acid units can be efficiently taken up by cancer cells based on an αvβ3 integrin receptor targeting mechanism. It also exhibits excellent biocompatibility and high pH stability in live cells and in vivo. Confocal laser scanning microscopy and flow cytometric imaging of SKOV-3 cells have confirmed that our probe can be used to image LPA in live cells. In particular, its NIR turn-on fluorescence can be used to effectively monitor LPA imaging in a SKOV-3 tumor-bearing mouse model. Our probe may pave the way for the detection of cancer-related biomarkers and even for early stage cancer diagnosis.
Collapse
Affiliation(s)
- Defan Yao
- Key Laboratory for Advanced Materials & Institute of Fine Chemicals, East China University of Science and Technology , Shanghai 200237, China
| | - Zhi Lin
- College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, China
| | - Junchen Wu
- Key Laboratory for Advanced Materials & Institute of Fine Chemicals, East China University of Science and Technology , Shanghai 200237, China
| |
Collapse
|
23
|
Chakraborty K, Dasgupta S, Pathak T. Carboxylated acyclonucleosides: synthesis and RNase A inhibition. Molecules 2015; 20:5924-41. [PMID: 25854756 PMCID: PMC6272279 DOI: 10.3390/molecules20045924] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 03/20/2015] [Accepted: 03/20/2015] [Indexed: 11/17/2022] Open
Abstract
Strategically designed carboxylated acyclonucleosides have been probed as a new class of RNase A inhibitors. Several experimental and theoretical studies have been performed to compile relevant qualitative and quantitative information regarding the nature and extent of inhibition. The inhibition constant (Ki) values were determined using a UV-based kinetics experiment. The changes in the secondary structure of the enzyme upon binding with the inhibitors were obtained from circular dichroism studies. The binding constants for enzyme-inhibitor interactions were determined with the help of fluorescence spectroscopy. Docking studies were performed to reveal the possible binding sites of the inhibitors within the enzyme. The cytosine analogues were found to possess better inhibitory properties in comparison to the corresponding uracil derivatives. An increment in the number of carboxylic acid groups (-COOH) in the inhibitor backbone was found to result in better inhibition.
Collapse
Affiliation(s)
- Kaustav Chakraborty
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
| | - Swagata Dasgupta
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
| | - Tanmaya Pathak
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
| |
Collapse
|
24
|
Musumeci D, Irace C, Santamaria R, Milano D, Tecilla P, Montesarchio D. Guanine-based amphiphiles: synthesis, ion transport properties and biological activity. Bioorg Med Chem 2015; 23:1149-56. [DOI: 10.1016/j.bmc.2014.12.055] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 12/18/2014] [Accepted: 12/22/2014] [Indexed: 12/17/2022]
|
25
|
Liu GJ, Zhang XT, Xing GW. A general method for N-glycosylation of nucleobases promoted by (p-Tol)2SO/Tf2O with thioglycoside as donor. Chem Commun (Camb) 2015; 51:12803-6. [DOI: 10.1039/c5cc03617h] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
35 nucleosides were synthesized by coupling thioglycosides with pyrimidines and purines under the preactivation of (p-Tol)2SO/Tf2O in high yields and with β-stereoselectivities.
Collapse
Affiliation(s)
- Guang-jian Liu
- Department of Chemistry
- Beijing Normal University
- Beijing 100875
- China
| | - Xiao-tai Zhang
- Department of Chemistry
- Beijing Normal University
- Beijing 100875
- China
| | - Guo-wen Xing
- Department of Chemistry
- Beijing Normal University
- Beijing 100875
- China
| |
Collapse
|
26
|
Bessières M, De Schutter C, Roy V, Agofoglio LA. Olefin cross-metathesis for the synthesis of alkenyl acyclonucleoside phosphonates. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2014; 59:14.11.1-17. [PMID: 25501590 DOI: 10.1002/0471142700.nc1411s59] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The detailed synthetic protocol for the straightforward, efficient synthesis of various alkenyl acyclonucleosides, including challenging trisubstituted alkenyl acyclonucleoside phosphonates, is described. The key step of those syntheses is an olefin cross-metathesis reaction between two olefins selected based on their reactivity using well-defined ruthenium alkylidene catalysts.
Collapse
|
27
|
Ball RJ, Green PS, Gale N, Langley GJ, Brown T. Peptide nucleic acid probes with charged photocleavable mass markers: Towards PNA-based MALDI-TOF MS genetic analysis. ARTIFICIAL DNA, PNA & XNA 2014; 1:27-35. [PMID: 21687524 DOI: 10.4161/adna.1.1.12199] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2010] [Revised: 04/06/2010] [Accepted: 04/30/2010] [Indexed: 01/18/2023]
Abstract
Halogen-labelled peptide organic acid (HPOA) monomers have been synthesised and incorporated into sequence-specific peptide nucleic acid (PNA) probes. Three different types of probe have been prepared; the unmodified PNA probe, the PNA probe with a mass marker, and the PNA probe with photocleavable mass marker. All three types of probe have been used in model studies to develop a mass spectrometry-based hybridisation assay for detection of point mutations in DNA.
Collapse
Affiliation(s)
- Rachel J Ball
- School of Chemistry; University of Southampton; Southampton, UK
| | | | | | | | | |
Collapse
|
28
|
Kim K, Punna V, Karri P, Krishnamurthy R. Synthesis of phosphoramidites of isoGNA, an isomer of glycerol nucleic acid. Beilstein J Org Chem 2014; 10:2131-8. [PMID: 25246971 PMCID: PMC4168771 DOI: 10.3762/bjoc.10.220] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 08/15/2014] [Indexed: 12/22/2022] Open
Abstract
IsoGNA, an isomer of glycerol nucleic acid GNA, is a flexible (acyclic) nucleic acid with bases directly attached to its linear backbone. IsoGNA exhibits (limited) base-pairing properties which are unique compared to other known flexible nucleic acids. Herein, we report on the details of the preparation of isoGNA phosphoramidites and an alternative route for the synthesis of the adenine derivative. The synthetic improvements described here enable an easy access to isoGNA and allows for the further exploration of this structural unit in oligonucleotide chemistry thereby spurring investigations of its usefulness and applicability.
Collapse
Affiliation(s)
- Keunsoo Kim
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Venkateshwarlu Punna
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Phaneendrasai Karri
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Ramanarayanan Krishnamurthy
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Rd, La Jolla, CA 92037, USA
| |
Collapse
|
29
|
Huang YC, Cao C, Tan XL, Li X, Liu L. Facile solid-phase synthesis of PNA–peptide conjugates using pNZ-protected PNA monomers. Org Chem Front 2014. [DOI: 10.1039/c4qo00217b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
30
|
Bessières M, Roy V, Agrofoglio LA. A convenient, highly selective and eco-friendly N-Boc protection of pyrimidines under microwave irradiation. RSC Adv 2014. [DOI: 10.1039/c4ra13033b] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A novel and practical microwave-assisted, highly selective N3-Boc protection of pyrimidine nucleobases in eco-friendly DEM/EtOH solvent, under mild conditions and moderate to high yield is described.
Collapse
Affiliation(s)
| | - Vincent Roy
- ICOA UMR CNRS 7311
- Université d'Orléans
- Orléans, France
| | | |
Collapse
|
31
|
Abstract
As microRNA silencing processes are mediated by the protein Argonaute 2 and for target RNA binding only a short sequence at the microRNA's 5' end (seed region) is crucial, we report a novel inhibitor class: the microRNA-specific Argonaute 2 protein inhibitors that not only block this short recognition sequence but also bind to the protein's active site. We developed a model for rational drug design, enabling the identification of Argonaute 2 active site binders and their linkage with a peptide nucleic acid sequence (PNA), which addresses the microRNA of interest. The designed inhibitors targeting microRNA-122, a hepatitis C virus drug target, had an IC50 of 100 nM, 10-fold more active than the simple PNA sequence (IC50 of 1 μM), giving evidence that the strategy has potential. Due to their lower molecular weight, these inhibitors may show better pharmacokinetic properties than reported oligonucleotide inhibitors, enabling them for potential therapeutic use.
Collapse
Affiliation(s)
- Marco F. Schmidt
- University Chemical Laboratory, University of Cambridge, Lensfield Road, CB2 1EW Cambridge,
United Kingdom
| | - Oliver Korb
- Cambridge Crystallographic Data Centre (CCDC), 12 Union Road, CB2 1EZ Cambridge,
United Kingdom
| | - Chris Abell
- University Chemical Laboratory, University of Cambridge, Lensfield Road, CB2 1EW Cambridge,
United Kingdom
| |
Collapse
|
32
|
|
33
|
Hamada M, Roy V, McBrayer TR, Whitaker T, Urbina-Blanco C, Nolan SP, Balzarini J, Snoeck R, Andrei G, Schinazi RF, Agrofoglio LA. Synthesis and broad spectrum antiviral evaluation of bis(POM) prodrugs of novel acyclic nucleosides. Eur J Med Chem 2013; 67:398-408. [PMID: 23911854 PMCID: PMC7111275 DOI: 10.1016/j.ejmech.2013.06.053] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 06/14/2013] [Accepted: 06/20/2013] [Indexed: 11/10/2022]
Abstract
A series of seventeen hitherto unknown ANP analogs bearing the (E)-but-2-enyl aliphatic side chain and modified heterocyclic base such as cytosine and 5-fluorocytosine, 2-pyrazinecarboxamide, 1,2,4-triazole-3-carboxamide or 4-substituted-1,2,3-triazoles were prepared in a straight approach through an olefin acyclic cross metathesis as key synthetic step. All novel compounds were evaluated for their antiviral activities against a large number of DNA and RNA viruses including herpes simplex virus type 1 and 2, varicella zoster virus, feline herpes virus, human cytomegalovirus, hepatitis C virus (HCV), HIV-1 and HIV-2. Among these molecules, only compound 31 showed activity against human cytomegalovirus in HEL cell cultures with at EC50 of ∼10 μM. Compounds 8a, 13, 14, and 24 demonstrated pronounced anti-HCV activity without significant cytotoxicity at 100 μM. The synthesis of new acyclonucleoside phosphonates is proposed. Challenging olefin acyclic cross metathesis is the key synthetic step. CuAAC reaction under microwave activation led to substituted-1,2,3-triazoles. Compounds exhibited pronounced anti-HCV activity. Compounds were also evaluated on a wide panel of other viral strains.
Collapse
Affiliation(s)
- Manabu Hamada
- Institut de Chimie Organique et Analytique, UMR 7311 CNRS, Université d'Orléans, 45067 Orléans, France
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Huang R, Xie C, Huang L, Liu J. Copper-catalyzed N-alkoxyalkylation of nucleobases involving direct functionalization of sp3 C–H bonds adjacent to oxygen atoms. Tetrahedron 2013. [DOI: 10.1016/j.tet.2012.11.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
35
|
Kramer RA, Bleicher KH, Wennemers H. Design and Synthesis of Nucleoproline Amino Acids for the Straightforward Preparation of Chiral and Conformationally Constrained Nucleopeptides. Helv Chim Acta 2012. [DOI: 10.1002/hlca.201200557] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
36
|
Li X, Du X, Gao Y, Shi J, Kuang Y, Xu B. Supramolecular hydrogels formed by the conjugates of nucleobases, Arg-Gly-Asp (RGD) peptides, and glucosamine. SOFT MATTER 2012; 8:7402-7407. [PMID: 22844343 PMCID: PMC3403830 DOI: 10.1039/c2sm25725d] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Here we report the generation of a novel class of supramolecular hydrogelators based on the integration of nucleobase, Arg-Gly-Asp (RGD) peptides, and glucosamine in a single molecule. These novel small molecule hydrogelators self-assemble in water to form stable supramolecular nanofibers/hydrogels and exhibit useful biostability. This approach provides a new opportunity for systematic exploration of the self-assembly of small biomolecules by varying any individual segment to generate a large array of supramolecular hydrogels for biological functions and for biomedical applications.
Collapse
Affiliation(s)
- Xinming Li
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454 USA, Fax: 781-736-2516. Tel: 781-736-5201
| | - Xuewen Du
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454 USA, Fax: 781-736-2516. Tel: 781-736-5201
| | - Yuan Gao
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454 USA, Fax: 781-736-2516. Tel: 781-736-5201
| | - Junfeng Shi
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454 USA, Fax: 781-736-2516. Tel: 781-736-5201
| | - Yi Kuang
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454 USA, Fax: 781-736-2516. Tel: 781-736-5201
| | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454 USA, Fax: 781-736-2516. Tel: 781-736-5201
| |
Collapse
|
37
|
Feagin TA, Shah NI, Heemstra JM. Convenient and scalable synthesis of fmoc-protected Peptide nucleic Acid backbone. J Nucleic Acids 2012; 2012:354549. [PMID: 22848796 PMCID: PMC3400375 DOI: 10.1155/2012/354549] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 06/11/2012] [Indexed: 11/17/2022] Open
Abstract
The peptide nucleic acid backbone Fmoc-AEG-OBn has been synthesized via a scalable and cost-effective route. Ethylenediamine is mono-Boc protected, then alkylated with benzyl bromoacetate. The Boc group is removed and replaced with an Fmoc group. The synthesis was performed starting with 50 g of Boc anhydride to give 31 g of product in 32% overall yield. The Fmoc-protected PNA backbone is a key intermediate in the synthesis of nucleobase-modified PNA monomers. Thus, improved access to this molecule is anticipated to facilitate future investigations into the chemical properties and applications of nucleobase-modified PNA.
Collapse
Affiliation(s)
- Trevor A. Feagin
- Department of Chemistry and the Center for Cell & Genome Science, University of Utah, Salt Lake City, UT 84112, USA
| | - Nirmal I. Shah
- Department of Chemistry and the Center for Cell & Genome Science, University of Utah, Salt Lake City, UT 84112, USA
| | - Jennifer M. Heemstra
- Department of Chemistry and the Center for Cell & Genome Science, University of Utah, Salt Lake City, UT 84112, USA
| |
Collapse
|
38
|
Bollinger M, Manzenrieder F, Kolb R, Bochen A, Neubauer S, Marinelli L, Limongelli V, Novellino E, Moessmer G, Pell R, Lindner W, Fanous J, Hoffman A, Kessler H. Tailoring of integrin ligands: probing the charge capability of the metal ion-dependent adhesion site. J Med Chem 2012; 55:871-82. [PMID: 22185640 DOI: 10.1021/jm2013826] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Intervention in integrin-mediated cell adhesion and integrin signaling pathways is an ongoing area of research in medicinal chemistry and drug development. One key element in integrin-ligand interaction is the coordination of the bivalent cation at the metal ion-dependent adhesion site (MIDAS) by a carboxylic acid function, a consistent feature of all integrin ligands. With the exception of the recently discovered hydroxamic acids, all bioisosteric attempts to replace the carboxylic acid of integrin ligands failed. We report that phosphinates as well as monomethyl phosphonates represent excellent isosters, when introduced into integrin antagonists for the platelet integrin αIIbβ3. The novel inhibitors exhibit in vitro and ex vivo activities in the low nanomolar range. Steric and charge requirements of the MIDAS region were unraveled, thus paving the way for an in silico prediction of ligand activity and in turn the rational design of the next generation of integrin antagonists.
Collapse
Affiliation(s)
- Markus Bollinger
- Institute for Advanced Study and Center of Integrated Protein Science, Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Browne EC, Langford SJ, Abbott BM. Peptide Nucleic Acid Monomers: A Convenient and Efficient Synthetic Approach to Fmoc/Boc Monomers. Aust J Chem 2012. [DOI: 10.1071/ch11471] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A convenient and cost-effective method for the synthesis of Fmoc/Boc-protected peptide nucleic acid monomers is described. The Fmoc/Boc strategy was developed in order to eliminate the solubility issues during peptide nucleic acid solid-phase synthesis, in particular that of the cytosine monomer, that occurred when using the commercialized Bhoc chemistry approach.
Collapse
|
40
|
St Amant AH, Hudson RHE. Synthesis and oligomerization of Fmoc/Boc-protected PNA monomers of 2,6-diaminopurine, 2-aminopurine and thymine. Org Biomol Chem 2011; 10:876-81. [PMID: 22159214 DOI: 10.1039/c1ob06582c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A Boc-protecting group strategy for Fmoc-based PNA (peptide nucleic acid) oligomerization has been developed for thymine, 2,6-diaminopurine (DAP) and 2-aminopurine (2AP). The monomers may be used interchangeably with standard Fmoc PNA monomers. The DAP monomer was incorporated into a PNA and was found to selectively bind to T (ΔT(m)≥ +6 °C) in a complementary DNA strand. The 2AP monomer showed excellent discrimination of T (ΔT(m)≥ +12 °C) over the other nucleobases. 2AP also acted as a fluorescent probe of the PNA:DNA duplexes and displayed fluorescence quenching dependent on the opposite base.
Collapse
Affiliation(s)
- André H St Amant
- Department of Chemistry, University of Western Ontario, London, Canada
| | | |
Collapse
|
41
|
Li X, Kuang Y, Shi J, Gao Y, Lin HC, Xu B. Multifunctional, biocompatible supramolecular hydrogelators consist only of nucleobase, amino acid, and glycoside. J Am Chem Soc 2011; 133:17513-8. [PMID: 21928792 PMCID: PMC3238097 DOI: 10.1021/ja208456k] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The integration of nucleobase, amino acid, and glycoside into a single molecule results in a novel class of supramolecular hydrogelators, which not only exhibit biocompatibility and biostability but also facilitate the entry of nucleic acids into cytosol and nuclei of cells. This work illustrates a simple way to generate an unprecedented molecular architecture from the basic biological building blocks for the development of sophisticated soft nanomaterials, including supramolecular hydrogels.
Collapse
Affiliation(s)
- Xinming Li
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA
| | - Yi Kuang
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA
| | - Junfeng Shi
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA
| | - Yuan Gao
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA
| | - Hsin-Chieh Lin
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA
| | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA
| |
Collapse
|
42
|
Li X, Kuang Y, Lin HC, Gao Y, Shi J, Xu B. Supramolecular nanofibers and hydrogels of nucleopeptides. Angew Chem Int Ed Engl 2011; 50:9365-9. [PMID: 21948432 PMCID: PMC3251214 DOI: 10.1002/anie.201103641] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 07/19/2011] [Indexed: 02/03/2023]
Affiliation(s)
| | | | | | | | | | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA, Fax: (+) 01-781-736-5201
| |
Collapse
|
43
|
Ngamwiriyawong P, Vilaivan T. Synthesis and nucleic acids binding properties of diastereomeric aminoethylprolyl peptide nucleic acids (aepPNA). NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2011; 30:97-112. [PMID: 21360408 DOI: 10.1080/15257770.2010.547839] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
A general synthetic method for Fmoc-protected monomers of all four diastereomeric aminoethyl peptide nucleic acid (aepPNA) has been developed. The key reaction is the coupling of nucleobase-modified proline derivatives and Fmoc-protected aminoacetaldehyde by reductive alkylation. Oligomerization of the aepPNAs up to 10mer was achieved by Fmoc-solid phase peptide synthesis methodology. Preliminary binding studies of these aepPNA oligomers with nucleic acids suggested that the "cis-" homothymine aepPNA decamers with (2'R,4'R) and (2'S,4'S) configurations can bind, albeit with slow kinetics, to their complementary RNA [poly(adenylic acid)] but not to the complementary DNA [poly(deoxyadenylic acid)]. On the other hand, the trans homothymine aepPNA decamers with (2'R,4'S) and (2'S,4'R) configurations failed to form stable hybrid with poly(adenylic acid) and poly(deoxyadenylic acid). No hybrid formation could be observed between a mixed-base (2'R,4'R)-aepPNA decamer with DNA and RNA in both antiparallel and parallel orientations.
Collapse
Affiliation(s)
- Patcharee Ngamwiriyawong
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | | |
Collapse
|
44
|
Li X, Kuang Y, Lin HC, Gao Y, Shi J, Xu B. Supramolecular Nanofibers and Hydrogels of Nucleopeptides. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201103641] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
|
45
|
Zhang Q, Sun J, Zhu Y, Zhang F, Yu B. An Efficient Approach to the Synthesis of Nucleosides: Gold(I)-Catalyzed N-Glycosylation of Pyrimidines and Purines with Glycosyl ortho-Alkynyl Benzoates. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201100514] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
46
|
Zhang Q, Sun J, Zhu Y, Zhang F, Yu B. An Efficient Approach to the Synthesis of Nucleosides: Gold(I)-Catalyzed N-Glycosylation of Pyrimidines and Purines with Glycosyl ortho-Alkynyl Benzoates. Angew Chem Int Ed Engl 2011; 50:4933-6. [DOI: 10.1002/anie.201100514] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Indexed: 01/08/2023]
|
47
|
Groebke–Blackburn–Bienaymé multicomponent reaction in scaffold-modification of adenine, guanine, and cytosine: synthesis of aminoimidazole-condensed nucleobases. Tetrahedron Lett 2011. [DOI: 10.1016/j.tetlet.2010.10.143] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|