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Nandhini KP, Noki S, Brasil E, Albericio F, de la Torre BG. A safety-catch protecting group strategy compatible with Boc-chemistry for the synthesis of peptide nucleic acids (PNAs). Org Biomol Chem 2023; 21:8125-8135. [PMID: 37772422 DOI: 10.1039/d3ob01348k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
Peptide Nucleic Acids (PNAs) are an intriguing class of synthetic biomolecules with great potential in medicine. Although PNAs could be considered analogs of oligonucleotides, their synthesis is more like that of peptides. In both cases, a Solid-Phase Synthesis (SPS) approach is used. Herein, the advantage using Boc as a temporal protecting group has been demonstrated to be more favored than Fmoc. In this context, a new PNA SPS strategy has been developed based on a safety-catch protecting group scheme for the exocyclic nitrogen of the side-chain bases and the linker. Sulfinyl (sulfoxide)-containing moieties are fully stable to the trifluoroacetic acid (TFA) used to remove the Boc group, but they can be reduced to the corresponding sulfide derivatives, which are labile in the presence of TFA. The efficiency of this novel synthetic strategy has been demonstrated in the synthesis of the PNA pentamer H-PNA(TATCT)-βAla-OH.
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Affiliation(s)
- K P Nandhini
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa.
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Westville, Durban 4000, South Africa.
| | - Sikabwe Noki
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa.
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Westville, Durban 4000, South Africa.
| | - Edikarlos Brasil
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Westville, Durban 4000, South Africa.
| | - Fernando Albericio
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Westville, Durban 4000, South Africa.
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, and Department of Organic Chemistry, University of Barcelona, Martí i Franqués 1-11, 08028 Barcelona, Spain
| | - Beatriz G de la Torre
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa.
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Del Bene A, D'Aniello A, Tomassi S, Merlino F, Mazzarella V, Russo R, Chambery A, Cosconati S, Di Maro S, Messere A. Ultrasound-assisted Peptide Nucleic Acids synthesis (US-PNAS). ULTRASONICS SONOCHEMISTRY 2023; 95:106360. [PMID: 36913782 PMCID: PMC10024050 DOI: 10.1016/j.ultsonch.2023.106360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/23/2023] [Accepted: 03/03/2023] [Indexed: 06/18/2023]
Abstract
Herein, we developed an innovative and easily accessible solid-phase synthetic protocol for Peptide Nucleic Acid (PNA) oligomers by systematically investigating the ultrasonication effects in all steps of the PNA synthesis (US-PNAS). When compared with standard protocols, the application of the so-obtained US-PNAS approach succeeded in improving the crude product purities and the isolated yields of different PNA, including small or medium-sized oligomers (5-mer and 9-mer), complex purine-rich sequences (like a 5-mer Guanine homoligomer and the telomeric sequence TEL-13) and longer oligomers (such as the 18-mer anti-IVS2-654 PNA and the 23-mer anti-mRNA 155 PNA). Noteworthy, our ultrasound-assisted strategy is compatible with the commercially available PNA monomers and well-established coupling reagents and only requires the use of an ultrasonic bath, which is a simple equipment generally available in most synthetic laboratories.
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Affiliation(s)
- Alessandra Del Bene
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy
| | - Antonia D'Aniello
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy
| | - Stefano Tomassi
- Department of Pharmacy, University of Naples "Federico II", 80131 Naples, Italy
| | - Francesco Merlino
- Department of Pharmacy, University of Naples "Federico II", 80131 Naples, Italy
| | - Vincenzo Mazzarella
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy
| | - Rosita Russo
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy
| | - Angela Chambery
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy
| | - Sandro Cosconati
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy
| | - Salvatore Di Maro
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy.
| | - Anna Messere
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy.
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3
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Sayer JR, Walldén K, Koss H, Allan H, Daviter T, Gane PJ, Waksman G, Tabor AB. Design, synthesis, and evaluation of peptide-imidazo[1,2-a]pyrazine bioconjugates as potential bivalent inhibitors of the VirB11 ATPase HP0525. J Pept Sci 2021; 27:e3353. [PMID: 34142414 DOI: 10.1002/psc.3353] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 11/07/2022]
Abstract
Helicobacter pylori (H. pylori) infections have been implicated in the development of gastric ulcers and various cancers: however, the success of current therapies is compromised by rising antibiotic resistance. The virulence and pathogenicity of H. pylori is mediated by the type IV secretion system (T4SS), a multiprotein macromolecular nanomachine that transfers toxic bacterial factors and plasmid DNA between bacterial cells, thus contributing to the spread of antibiotic resistance. A key component of the T4SS is the VirB11 ATPase HP0525, which is a hexameric protein assembly. We have previously reported the design and synthesis of a series of novel 8-amino imidazo[1,2-a]pyrazine derivatives as inhibitors of HP0525. In order to improve their selectivity, and potentially develop these compounds as tools for probing the assembly of the HP0525 hexamer, we have explored the design and synthesis of potential bivalent inhibitors. We used the structural details of the subunit-subunit interactions within the HP0525 hexamer to design peptide recognition moieties of the subunit interface. Different methods (cross metathesis, click chemistry, and cysteine-malemide) for bioconjugation to selected 8-amino imidazo[1,2-a]pyrazines were explored, as well as peptides spanning larger or smaller regions of the interface. The IC50 values of the resulting linker-8-amino imidazo[1,2-a]pyrazine derivatives, and the bivalent inhibitors, were related to docking studies with the HP0525 crystal structure and to molecular dynamics simulations of the peptide recognition moieties.
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Affiliation(s)
- James R Sayer
- Department of Chemistry, UCL, London, UK.,MedPharm Ltd, Guildford, UK
| | - Karin Walldén
- Institute of Structural and Molecular Biology, UCL, London, UK.,Department Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Hans Koss
- Department of Chemistry, UCL, London, UK.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA
| | | | - Tina Daviter
- Department of Biological Sciences, ISMB Biophysics Centre, London, UK.,The Institute of Cancer Research, London, UK
| | - Paul J Gane
- Wolfson Institute for Biomedical Research, UCL, London, UK.,Abcam, Cambridge, UK
| | - Gabriel Waksman
- Institute of Structural and Molecular Biology, UCL, London, UK
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Tailhades J, Takizawa H, Gait MJ, Wellings DA, Wade JD, Aoki Y, Shabanpoor F. Solid-Phase Synthesis of Difficult Purine-Rich PNAs through Selective Hmb Incorporation: Application to the Total Synthesis of Cell Penetrating Peptide-PNAs. Front Chem 2017; 5:81. [PMID: 29094037 PMCID: PMC5651559 DOI: 10.3389/fchem.2017.00081] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 09/29/2017] [Indexed: 12/27/2022] Open
Abstract
Antisense oligonucleotide (ASO)-based drug development is gaining significant momentum following the recent FDA approval of Eteplirsen (an ASO based on phosphorodiamidate morpholino) and Spinraza (2′-O-methoxyethyl-phosphorothioate) in late 2016. Their attractiveness is mainly due to the backbone modifications which have improved the in vivo characteristics of oligonucleotide drugs. Another class of ASO, based on peptide nucleic acid (PNA) chemistry, is also gaining popularity as a platform for development of gene-specific therapy for various disorders. However, the chemical synthesis of long PNAs, which are more target-specific, remains an ongoing challenge. Most of the reported methodology for the solid-phase synthesis of PNA suffer from poor coupling efficiency which limits production to short PNA sequences of less than 15 residues. Here, we have studied the effect of backbone modifications with Hmb (2-hydroxy-4-methoxybenzyl) and Dmb (2,4-dimethoxybenzyl) to ameliorate difficult couplings and reduce “on-resin” aggregation. We firstly synthesized a library of PNA dimers incorporating either Hmb or Dmb and identified that Hmb is superior to Dmb in terms of its ease of removal. Subsequently, we used Hmb backbone modification to synthesize a 22-mer purine-rich PNA, targeting dystrophin RNA splicing, which could not be synthesized by standard coupling methodology. Hmb backbone modification allowed this difficult PNA to be synthesized as well as to be continued to include a cell-penetrating peptide on the same solid support. This approach provides a novel and straightforward strategy for facile solid-phase synthesis of difficult purine-rich PNA sequences.
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Affiliation(s)
- Julien Tailhades
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Hotake Takizawa
- Department of Molecular Therapy, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Michael J Gait
- Laboratory of Molecular Biology, Medical Research Council, Cambridge, United Kingdom
| | | | - John D Wade
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, Australia.,School of Chemistry, University of Melbourne, Parkville, VIC, Australia
| | - Yoshitsugu Aoki
- Department of Molecular Therapy, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Fazel Shabanpoor
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, Australia.,School of Chemistry, University of Melbourne, Parkville, VIC, Australia
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Qiao W, Kalachikov S, Liu Y, Levicky R. Charge-neutral morpholino microarrays for nucleic acid analysis. Anal Biochem 2012; 434:207-14. [PMID: 23246344 DOI: 10.1016/j.ab.2012.12.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2012] [Revised: 11/21/2012] [Accepted: 12/03/2012] [Indexed: 12/14/2022]
Abstract
A principal challenge in microarray experiments is to facilitate hybridization between probe strands on the array with complementary target strands from solution while suppressing any competing interactions that the probes and targets may experience. Synthetic DNA analogs, whose hybridization to targets can exhibit qualitatively different dependence on experimental conditions than for nucleic acid probes, open up an attractive alternative for improving selectivity of array hybridization. Morpholinos (MOs), a class of uncharged DNA analogs, are investigated as microarray probes instead of DNA. MO microarrays were fabricated by contact printing of amino-modified probes onto aldehyde slides. In addition to covalent immobilization, MOs were found to efficiently immobilize through physical adsorption; such physically adsorbed probes could be removed by post-printing washes with surfactant solutions. Hybridization of double-stranded DNA targets to MO microarrays revealed a hybridization maximum at intermediate ionic strengths. The decline in hybridization at lower ionic strengths was attributed to an electrostatic barrier accumulated from hybridized DNA targets, whereas at higher ionic strengths it was attributed to stabilization of target secondary structure in solution. These trends, which illustrate ionic strength tuning of forming on-array relative to solution secondary structure, were supported by a stability analysis of MO/DNA and DNA/DNA duplexes in solution.
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Affiliation(s)
- Wanqiong Qiao
- Department of Chemical and Biomolecular Engineering, Polytechnic Institute of New York University, Brooklyn, NY 11201, USA
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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.
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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
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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.
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Affiliation(s)
- André H St Amant
- Department of Chemistry, University of Western Ontario, London, Canada
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9
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Watanabe A, Kiyota N, Yamasaki T, Tanda K, Miyagoe T, Sakamoto M, Otsuka M. Design and stereoselective synthesis of four peptide nucleic acid monomers with cyclic structures in backbone. J Heterocycl Chem 2011. [DOI: 10.1002/jhet.627] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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10
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Roviello GN, Benedetti E, Pedone C, Bucci EM. Nucleobase-containing peptides: an overview of their characteristic features and applications. Amino Acids 2010; 39:45-57. [PMID: 20349320 DOI: 10.1007/s00726-010-0567-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2010] [Accepted: 03/11/2010] [Indexed: 11/26/2022]
Abstract
Reports on nucleobase-containing chiral peptides (both natural and artificial) and achiral pseudopeptides are reviewed. Their synthesis, structural features, DNA and RNA-binding ability, as well as some other interesting applications which make them promising diagnostic/therapeutic agents of great importance in many areas of biology and therapy are taken into critical consideration.
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Affiliation(s)
- Giovanni N Roviello
- Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Via Mezzocannone 16, 80134, Naples, Italy
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11
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Tercero N, Wang K, Gong P, Levicky R. Morpholino monolayers: preparation and label-free DNA analysis by surface hybridization. J Am Chem Soc 2009; 131:4953-61. [PMID: 19296583 PMCID: PMC2730437 DOI: 10.1021/ja810051q] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Surface hybridization, a reaction in which nucleic acid molecules in solution react with nucleic acid partners immobilized on a surface, is widely practiced in life science research. In these applications the immobilized partner, or "probe", is typically single-stranded DNA. Because DNA is strongly charged, high salt conditions are required to enable binding between analyte nucleic acids ("targets") in solution and the DNA probes. High salt, however, compromises prospects for label-free monitoring or control of the hybridization reaction through surface electric fields; it also stabilizes secondary structure in target species that can interfere with probe-target recognition. In this work, initial steps toward addressing these challenges are taken by introducing morpholinos, a class of uncharged DNA analogues, for surface-hybridization applications. Monolayers of morpholino probes on gold supports can be fabricated with methods similar to those employed with DNA and are shown to hybridize efficiently and sequence-specifically with target strands. Hybridization-induced changes in the interfacial charge organization are analyzed with electrochemical methods and compared for morpholino and DNA probe monolayers. Molecular mechanisms connecting surface hybridization state to the interfacial capacitance are identified and interpreted through comparison to numerical Poisson-Boltzmann calculations. Interestingly, positive as well as negative capacitive responses (contrast inversion) to hybridization are possible, depending on surface populations of mobile ions as controlled by the applied potential. Quantitative comparison of surface capacitance with target coverage (targets/area) reveals a nearly linear relationship and demonstrates sensitivities (limits of quantification) in the picogram per square millimeter range.
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Affiliation(s)
- Napoleon Tercero
- Dept. of Chemical & Biological Engineering, Polytechnic Institute of New York University, Brooklyn, NY 11201
- Dept. of Chemical Engineering, Columbia University, New York, NY 10027
| | - Kang Wang
- Dept. of Chemical & Biological Engineering, Polytechnic Institute of New York University, Brooklyn, NY 11201
| | - Ping Gong
- Dept. of Chemical Engineering, Columbia University, New York, NY 10027
| | - Rastislav Levicky
- Dept. of Chemical & Biological Engineering, Polytechnic Institute of New York University, Brooklyn, NY 11201
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Roviello G, Musumeci D, Pedone C, Bucci EM. Synthesis, characterization and hybridization studies of an alternate nucleo-epsilon/gamma-peptide: complexes formation with natural nucleic acids. Amino Acids 2008; 38:103-11. [PMID: 19067107 DOI: 10.1007/s00726-008-0214-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2008] [Accepted: 11/12/2008] [Indexed: 10/21/2022]
Abstract
In order to develop new oligodeoxyribonucleotide (ODN) analogs to be used in biotechnological applications, we report here the synthesis, characterization and nucleic acid binding studies of novel nucleopeptides, that we called epsilon-lys/gamma-dabPNAs, containing a backbone of alternated L-diaminobutyric acid and L-lysine moieties. Exploring the hybridization properties of the new ODN analog, we found, by circular dichroism and UV spectroscopies, that a homothymine epsilon-lys/gamma-dabPNA hexamer binds both DNA and RNA of complementary sequence. Furthermore, human serum stability assays on the alternate nucleopeptide evidenced a noteworthy degradation resistance. These results encourage us to deepen the knowledge of this analog, in order to evaluate its possible use in antigene/antisense or diagnostic applications.
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Affiliation(s)
- Giovanni Roviello
- Istituto di Biostrutture e Bioimmagini-CNR, Via Mezzocannone 16, 80134, Napoli, Italy
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