1
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Llamosí A, Szymański MP, Szumna A. Molecular vessels from preorganised natural building blocks. Chem Soc Rev 2024; 53:4434-4462. [PMID: 38497833 DOI: 10.1039/d3cs00801k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Supramolecular vessels emerged as tools to mimic and better understand compartmentalisation, a central aspect of living matter. However, many more applications that go beyond those initial goals have been documented in recent years, including new sensory systems, artificial transmembrane transporters, catalysis, and targeted drug or gene delivery. Peptides, carbohydrates, nucleobases, and steroids bear great potential as building blocks for the construction of supramolecular vessels, possessing complexity that is still difficult to attain with synthetic methods - they are rich in functional groups and well-defined stereogenic centers, ready for noncovalent interactions and further functions. One of the options to tame the functional and dynamic complexity of natural building blocks is to place them at spatially designed positions using synthetic scaffolds. In this review, we summarise the historical and recent advances in the construction of molecular-sized vessels by the strategy that couples synthetic predictability and durability of various scaffolds (cyclodextrins, porphyrins, crown ethers, calix[n]arenes, resorcin[n]arenes, pillar[n]arenes, cyclotriveratrylenes, coordination frameworks and multivalent high-symmetry molecules) with functionality originating from natural building blocks to obtain nanocontainers, cages, capsules, cavitands, carcerands or coordination cages by covalent chemistry, self-assembly, or dynamic covalent chemistry with the ultimate goal to apply them in sensing, transport, or catalysis.
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Affiliation(s)
- Arturo Llamosí
- Institute of Organic Chemistry, Polish academy of Sciences, Kasprzaka 44/52, Warsaw 01-224, Poland.
| | - Marek P Szymański
- Institute of Organic Chemistry, Polish academy of Sciences, Kasprzaka 44/52, Warsaw 01-224, Poland.
| | - Agnieszka Szumna
- Institute of Organic Chemistry, Polish academy of Sciences, Kasprzaka 44/52, Warsaw 01-224, Poland.
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2
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Tan KXY, Shigenobu S. In vivo interference of pea aphid endosymbiont Buchnera groEL gene by synthetic peptide nucleic acids. Sci Rep 2024; 14:5378. [PMID: 38438424 PMCID: PMC10912616 DOI: 10.1038/s41598-024-55179-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 02/21/2024] [Indexed: 03/06/2024] Open
Abstract
The unculturable nature of intracellular obligate symbionts presents a significant challenge for elucidating gene functionality, necessitating the development of gene manipulation techniques. One of the best-studied obligate symbioses is that between aphids and the bacterial endosymbiont Buchnera aphidicola. Given the extensive genome reduction observed in Buchnera, the remaining genes are crucial for understanding the host-symbiont relationship, but a lack of tools for manipulating gene function in the endosymbiont has significantly impeded the exploration of the molecular mechanisms underlying this mutualism. In this study, we introduced a novel gene manipulation technique employing synthetic single-stranded peptide nucleic acids (PNAs). We targeted the critical Buchnera groEL using specially designed antisense PNAs conjugated to an arginine-rich cell-penetrating peptide (CPP). Within 24 h of PNA administration via microinjection, we observed a significant reduction in groEL expression and Buchnera cell count. Notably, the interference of groEL led to profound morphological malformations in Buchnera, indicative of impaired cellular integrity. The gene knockdown technique developed in this study, involving the microinjection of CPP-conjugated antisense PNAs, provides a potent approach for in vivo gene manipulation of unculturable intracellular symbionts, offering valuable insights into their biology and interactions with hosts.
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Affiliation(s)
- Kathrine Xin Yee Tan
- Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), 38 Nishigonaka, Myodaiji, Okazaki, Aichi, 444-8585, Japan
- Laboratory of Evolutionary Genomics, National Institute for Basic Biology, 38 Nishigonaka Myodaiji, Okazaki, Aichi, 444-8585, Japan
| | - Shuji Shigenobu
- Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), 38 Nishigonaka, Myodaiji, Okazaki, Aichi, 444-8585, Japan.
- Laboratory of Evolutionary Genomics, National Institute for Basic Biology, 38 Nishigonaka Myodaiji, Okazaki, Aichi, 444-8585, Japan.
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3
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Eskandari S, Rezayof A, Asghari SM, Hashemizadeh S. Neurobiochemical characteristics of arginine-rich peptides explain their potential therapeutic efficacy in neurodegenerative diseases. Neuropeptides 2023; 101:102356. [PMID: 37390744 DOI: 10.1016/j.npep.2023.102356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/02/2023]
Abstract
Neurodegenerative diseases, including Alzheimer̕ s disease (AD), Parkinson̕ s disease (PD), Huntington̕ s disease (HD), and Amyotrophic Lateral Sclerosis (ALS) require special attention to find new potential treatment methods. This review aims to summarize the current knowledge of the relationship between the biochemical properties of arginine-rich peptides (ARPs) and their neuroprotective effects to deal with the harmful effects of risk factors. It seems that ARPs have portrayed a promising and fantastic landscape for treating neurodegeneration-associated disorders. With multimodal mechanisms of action, ARPs play various unprecedented roles, including as the novel delivery platforms for entering the central nervous system (CNS), the potent antagonists for calcium influx, the invader molecules for targeting mitochondria, and the protein stabilizers. Interestingly, these peptides inhibit the proteolytic enzymes and block protein aggregation to induce pro-survival signaling pathways. ARPs also serve as the scavengers of toxic molecules and the reducers of oxidative stress agents. They also have anti-inflammatory, antimicrobial, and anti-cancer properties. Moreover, by providing an efficient nucleic acid delivery system, ARPs can play an essential role in developing various fields, including gene vaccines, gene therapy, gene editing, and imaging. ARP agents and ARP/cargo therapeutics can be raised as an emergent class of neurotherapeutics for neurodegeneration. Part of the aim of this review is to present recent advances in treating neurodegenerative diseases using ARPs as an emerging and powerful therapeutic tool. The applications and progress of ARPs-based nucleic acid delivery systems have also been discussed to highlight their usefulness as a broad-acting class of drugs.
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Affiliation(s)
- Sedigheh Eskandari
- Department of Animal Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran; Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Ameneh Rezayof
- Department of Animal Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran.
| | - S Mohsen Asghari
- Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran.
| | - Shiva Hashemizadeh
- School of Cognitive Sciences, Institute for Research in Fundamental Sciences, IPM, Tehran, Iran
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4
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Podlaski F, Cornwell S, Wong K, McKittrick B, Kim JH, Jung D, Jeon Y, Jung KB, Tolias P, Windsor WT. Peptide Nucleic Acids Containing Cationic/Amino-Alkyl Modified Bases Promote Enhanced Hybridization Kinetics and Thermodynamics with Single-Strand DNA. ACS OMEGA 2023; 8:33426-33436. [PMID: 37744819 PMCID: PMC10515352 DOI: 10.1021/acsomega.3c03184] [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: 05/08/2023] [Accepted: 08/18/2023] [Indexed: 09/26/2023]
Abstract
Peptide nucleic acids (PNAs) are antisense molecules with excellent polynucleotide hybridization properties; they are resistant to nuclease degradation but often have poor cell permeability leading to moderate cellular activity and limited clinical results. The addition of cationic substitutions (positive charges) to PNA molecules greatly increases cell permeability. In this report, we describe the synthesis and polynucleotide hybridization properties of a novel cationic/amino-alkyl nucleotide base-modified PNA (OPNA). This study was designed to quantitate the effect the cationic/amino-alkyl nucleotide base modification had on the kinetic and thermodynamic properties of OPNA-DNA hybridization using surface plasmon resonance and UV thermal melt studies. Kinetic studies reveal a favorable 10-30 fold increase in affinity for a single cationic modification on the base of an adenine, cytosine, or guanidine OPNA sequence compared to the nonmodified PNA strand. The increase in affinity is correlated directly with a favorable decrease in the dissociation rate constant and increase in the association rate constant. Introducing additional amino-alkyl base modifications further favors a decrease in the dissociation rate (3-10-fold per amino-alkyl). The thermodynamics driving the OPNA hybridization is promoted by an additional favorable -80 kJ/mol enthalpy of binding for a single amino-alkyl modification compared to the PNA strand. This increase in enthalpy is consistent with an ion-ion interaction with the DNA strand. These kinetic and thermodynamic hybridization studies reveal for the first time that this type of cationic/amino-alkyl base-modified PNA has favorable hybridization properties suitable for development as an antisense oligomer.
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Affiliation(s)
- Frank Podlaski
- Department
of Chemistry and Chemical Biology, Stevens
Institute of Technology, 1 Castle Point Terrace, Hoboken, New Jersey 07030, United States
| | - Stephen Cornwell
- Department
of Chemistry and Chemical Biology, Stevens
Institute of Technology, 1 Castle Point Terrace, Hoboken, New Jersey 07030, United States
| | - Kenny Wong
- Department
of Chemistry and Chemical Biology, Stevens
Institute of Technology, 1 Castle Point Terrace, Hoboken, New Jersey 07030, United States
| | - Brian McKittrick
- Department
of Global Sciences & Strategy, OliPass
Corporation, Yongin, Gyeonggi 17015, Republic of Korea
| | - Jae-Hun Kim
- Department
of Monomer Research, OliPass Corporation, Suwon, Gyeonggi 16229, Republic
of Korea
| | - Daram Jung
- Department
of Oligo Sciences, OliPass Corporation, Yongin, Gyeonggi 17015, Republic
of Korea
| | - Yeasel Jeon
- Department
of Oligo Sciences, OliPass Corporation, Yongin, Gyeonggi 17015, Republic
of Korea
| | - Kwang-Bok Jung
- Department
of Monomer Manufacture, OliPass Corporation, Suwon, Gyeonggi 16229, Republic
of Korea
| | - Peter Tolias
- Department
of Biology, School of Natural and Behavioral Sciences, Brooklyn College, CUNY, Brooklyn, New York 11210, United States
| | - William T. Windsor
- Department
of Chemistry and Chemical Biology, Stevens
Institute of Technology, 1 Castle Point Terrace, Hoboken, New Jersey 07030, United States
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5
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Gasparello J, Papi C, Zurlo M, Volpi S, Gambari R, Corradini R, Casnati A, Sansone F, Finotti A. Cationic Calix[4]arene Vectors to Efficiently Deliver AntimiRNA Peptide Nucleic Acids (PNAs) and miRNA Mimics. Pharmaceutics 2023; 15:2121. [PMID: 37631335 PMCID: PMC10460053 DOI: 10.3390/pharmaceutics15082121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 08/03/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
One of the most appealing approaches for regulating gene expression, named the "microRNA therapeutic" method, is based on the regulation of the activity of microRNAs (miRNAs), the intracellular levels of which are dysregulated in many diseases, including cancer. This can be achieved by miRNA inhibition with antimiRNA molecules in the case of overexpressed microRNAs, or by using miRNA-mimics to restore downregulated microRNAs that are associated with the target disease. The development of new efficient, low-toxic, and targeted vectors of such molecules represents a key topic in the field of the pharmacological modulation of microRNAs. We compared the delivery efficiency of a small library of cationic calix[4]arene vectors complexed with fluorescent antimiRNA molecules (Peptide Nucleic Acids, PNAs), pre-miRNA (microRNA precursors), and mature microRNAs, in glioma- and colon-cancer cellular models. The transfection was assayed by cytofluorimetry, cell imaging assays, and RT-qPCR. The calix[4]arene-based vectors were shown to be powerful tools to facilitate the uptake of both neutral (PNAs) and negatively charged (pre-miRNAs and mature microRNAs) molecules showing low toxicity in transfected cells and ability to compete with commercially available vectors in terms of delivery efficiency. These results could be of great interest to validate microRNA therapeutics approaches for future application in personalized treatment and precision medicine.
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Affiliation(s)
- Jessica Gasparello
- Section of Biochemistry and Molecular Biology, Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy; (J.G.); (C.P.); (M.Z.); (R.G.)
| | - Chiara Papi
- Section of Biochemistry and Molecular Biology, Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy; (J.G.); (C.P.); (M.Z.); (R.G.)
| | - Matteo Zurlo
- Section of Biochemistry and Molecular Biology, Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy; (J.G.); (C.P.); (M.Z.); (R.G.)
| | - Stefano Volpi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (S.V.); (R.C.); (A.C.)
| | - Roberto Gambari
- Section of Biochemistry and Molecular Biology, Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy; (J.G.); (C.P.); (M.Z.); (R.G.)
| | - Roberto Corradini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (S.V.); (R.C.); (A.C.)
| | - Alessandro Casnati
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (S.V.); (R.C.); (A.C.)
| | - Francesco Sansone
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (S.V.); (R.C.); (A.C.)
| | - Alessia Finotti
- Section of Biochemistry and Molecular Biology, Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy; (J.G.); (C.P.); (M.Z.); (R.G.)
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6
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Zheng H, Clausse V, Amarasekara H, Mazur SJ, Botos I, Appella DH. Variation of Tetrahydrofurans in Thyclotides Enhances Oligonucleotide Binding and Cellular Uptake of Peptide Nucleic Acids. JACS AU 2023; 3:1952-1964. [PMID: 37502163 PMCID: PMC10369417 DOI: 10.1021/jacsau.3c00198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/15/2023] [Accepted: 06/16/2023] [Indexed: 07/29/2023]
Abstract
Selective incorporation of conformational constraints into thyclotides can be used to modulate their binding to complementary oligonucleotides, increase polarity, and optimize uptake into HCT116 cells without assistance from moieties known to promote cell uptake. The X-ray structure and biophysical studies of a thyclotide-DNA duplex reveal that incorporation of tetrahydrofurans into an aegPNA backbone promotes a helical conformation that enhances binding to complementary DNA and RNA. Selective incorporation of tetrahydrofurans into the aegPNA backbone allows polarity to be increased incrementally so that uptake into HCT116 cells can be optimized. The enhanced binding, polarity, and cellular uptake properties of thyclotides were used to demonstrate effective inhibition of microRNA-21 in HCT116 cells.
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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
| | - Victor Clausse
- 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
| | - Harsha Amarasekara
- 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
| | - Sharlyn J. Mazur
- Laboratory
of Cell Biology, National Cancer Institute,
National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20892, United States
| | - Istvan Botos
- Laboratory
of Molecular Biology, National Institute
of Diabetes and Digestive and Kidney Diseases, National Institutes
of Health, Department of Health and Human Services, 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
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7
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Deka Dey A, Yousefiasl S, Kumar A, Dabbagh Moghaddam F, Rahimmanesh I, Samandari M, Jamwal S, Maleki A, Mohammadi A, Rabiee N, Cláudia Paiva‐Santos A, Tamayol A, Sharifi E, Makvandi P. miRNA-encapsulated abiotic materials and biovectors for cutaneous and oral wound healing: Biogenesis, mechanisms, and delivery nanocarriers. Bioeng Transl Med 2023; 8:e10343. [PMID: 36684081 PMCID: PMC9842058 DOI: 10.1002/btm2.10343] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/21/2022] [Accepted: 04/23/2022] [Indexed: 01/25/2023] Open
Abstract
MicroRNAs (miRNAs) as therapeutic agents have attracted increasing interest in the past decade owing to their significant effectiveness in treating a wide array of ailments. These polymerases II-derived noncoding RNAs act through post-transcriptional controlling of different proteins and their allied pathways. Like other areas of medicine, researchers have utilized miRNAs for managing acute and chronic wounds. The increase in the number of patients suffering from either under-healing or over-healing wound demonstrates the limited efficacy of the current wound healing strategies and dictates the demands for simpler approaches with greater efficacy. Various miRNA can be designed to induce pathway beneficial for wound healing. However, the proper design of miRNA and its delivery system for wound healing applications are still challenging due to their limited stability and intracellular delivery. Therefore, new miRNAs are required to be identified and their delivery strategy needs to be optimized. In this review, we discuss the diverse roles of miRNAs in various stages of wound healing and provide an insight on the most recent findings in the nanotechnology and biomaterials field, which might offer opportunities for the development of new strategies for this chronic condition. We also highlight the advances in biomaterials and delivery systems, emphasizing their challenges and resolutions for miRNA-based wound healing. We further review various biovectors (e.g., adenovirus and lentivirus) and abiotic materials such as organic and inorganic nanomaterials, along with dendrimers and scaffolds, as the delivery systems for miRNA-based wound healing. Finally, challenges and opportunities for translation of miRNA-based strategies into clinical applications are discussed.
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Affiliation(s)
| | - Satar Yousefiasl
- School of DentistryHamadan University of Medical SciencesHamadanIran
| | - Arun Kumar
- Chitkara College of PharmacyChitkara UniversityPunjabIndia
| | - Farnaz Dabbagh Moghaddam
- Department of Biology, Science and Research BranchIslamic Azad UniversityTehranIran
- Institute for Photonics and Nanotechnologies, National Research Council, Via Fosso del Cavaliere, 100RomeItaly
| | - Ilnaz Rahimmanesh
- Applied Physiology Research CenterCardiovascular Research Institute, Isfahan University of Medical SciencesIsfahanIran
| | | | - Sumit Jamwal
- Department of Psychiatry, Yale School of MedicineYale UniversityNew HavenConnecticutUSA
| | - Aziz Maleki
- Department of Pharmaceutical Nanotechnology, School of PharmacyZanjan University of Medical SciencesZanjanIran
- Zanjan Pharmaceutical Nanotechnology Research Center (ZPNRC)Zanjan University of Medical SciencesZanjanIran
- Cancer Research CentreShahid Beheshti University of Medical SciencesTehranIran
| | | | - Navid Rabiee
- Department of PhysicsSharif University of TechnologyTehranIran
- School of EngineeringMacquarie UniversitySydneyNew South WalesAustralia
| | - Ana Cláudia Paiva‐Santos
- Department of Pharmaceutical TechnologyFaculty of Pharmacy of the University of Coimbra, University of CoimbraCoimbraPortugal
- LAQV, REQUIMTE, Department of Pharmaceutical TechnologyFaculty of Pharmacy of the University of Coimbra, University of CoimbraCoimbraPortugal
| | - Ali Tamayol
- Department of Biomedical EngineeringUniversity of ConnecticutFarmingtonConnecticutUSA
| | - Esmaeel Sharifi
- Department of Tissue Engineering and Biomaterials, School of Advanced Medical Sciences and TechnologiesHamadan University of Medical SciencesHamadanIran
| | - Pooyan Makvandi
- Istituto Italiano di Tecnologia, Centre for Materials InterfacesPontederaItaly
- School of Chemistry, Damghan UniversityDamghanIran
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8
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Ivanov GS, Tribulovich VG, Pestov NB, David TI, Amoah AS, Korneenko TV, Barlev NA. Artificial genetic polymers against human pathologies. Biol Direct 2022; 17:39. [PMID: 36474260 PMCID: PMC9727881 DOI: 10.1186/s13062-022-00353-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
Originally discovered by Nielsen in 1991, peptide nucleic acids and other artificial genetic polymers have gained a lot of interest from the scientific community. Due to their unique biophysical features these artificial hybrid polymers are now being employed in various areas of theranostics (therapy and diagnostics). The current review provides an overview of their structure, principles of rational design, and biophysical features as well as highlights the areas of their successful implementation in biology and biomedicine. Finally, the review discusses the areas of improvement that would allow their use as a new class of therapeutics in the future.
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Affiliation(s)
- Gleb S Ivanov
- Institute of Cytology, Tikhoretsky Ave 4, Saint Petersburg, Russia, 194064
- St. Petersburg State Technological Institute (Technical University), Saint Petersburg, Russia, 190013
| | - Vyacheslav G Tribulovich
- St. Petersburg State Technological Institute (Technical University), Saint Petersburg, Russia, 190013
| | - Nikolay B Pestov
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products, Moscow, Russia, 108819
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia, 141701
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia, 117997
- Institute of Biomedical Chemistry, Moscow, Russia, 119121б
| | - Temitope I David
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia, 141701
| | - Abdul-Saleem Amoah
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia, 141701
| | - Tatyana V Korneenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia, 117997
| | - Nikolai A Barlev
- Institute of Cytology, Tikhoretsky Ave 4, Saint Petersburg, Russia, 194064.
- Institute of Biomedical Chemistry, Moscow, Russia, 119121б.
- School of Medicine, Nazarbayev University, 010000, Astana, Kazakhstan.
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9
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Ma L, Gilani A, Yi Q, Tang L. MicroRNAs as Mediators of Adipose Thermogenesis and Potential Therapeutic Targets for Obesity. BIOLOGY 2022; 11:1657. [PMID: 36421371 PMCID: PMC9687157 DOI: 10.3390/biology11111657] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 07/30/2023]
Abstract
Obesity is a growing health problem worldwide, associated with an increased risk of multiple chronic diseases. The thermogenic activity of brown adipose tissue (BAT) correlates with leanness in adults. Understanding the mechanisms behind BAT activation and the process of white fat "browning" has important implications for developing new treatments to combat obesity. MicroRNAs (miRNAs) are small transcriptional regulators that control gene expression in various tissues, including adipose tissue. Recent studies show that miRNAs are involved in adipogenesis and adipose tissue thermogenesis. In this review, we discuss recent advances in the role of miRNAs in adipocyte thermogenesis and obesity. The potential for miRNA-based therapies for obesity and recommendations for future research are highlighted, which may help provide new targets for treating obesity and obesity-related diseases.
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Affiliation(s)
- Lunkun Ma
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Ankit Gilani
- Weill Center for Metabolic Health, Cardiovascular Research Institute, Division of Cardiology, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Qian Yi
- Department of Physiology, School of Basic Medical Science, Southwest Medical University, Luzhou 646099, China
| | - Liling Tang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
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10
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Rodik RV, Cherenok SO, Postupalenko VY, Oncul S, Brusianska V, Borysko P, Kalchenko VI, Mely Y, Klymchenko AS. Anionic amphiphilic calixarenes for peptide assembly and delivery. J Colloid Interface Sci 2022; 624:270-278. [PMID: 35660896 DOI: 10.1016/j.jcis.2022.05.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 05/14/2022] [Accepted: 05/19/2022] [Indexed: 10/18/2022]
Abstract
Shape-persistent macrocycles enable superior control on molecular self-assembly, allowing the preparation of well-defined nanostructures with new functions. Here, we report on anionic amphiphilic calixarenes of conic shape and their self-assembly behavior in aqueous media for application in intracellular delivery of peptides. Newly synthesized calixarenes bearing four phosphonate groups and two or four long alkyl chains were found to form micelles of ∼ 10 nm diameter, in contrast to an analogue with short alkyl chains. These amphiphilic calixarenes are able to complex model (oligo-lysine) and biologically relevant (HIV-1 nucleocapsid peptide) cationic peptides into small nanoparticles (20-40 nm). By contrast, a control anionic calixarene with short alkyl chains fails to form small nanoparticles with peptides, highlighting the importance of micellar assembly of amphiphilic calixarenes for peptide complexation. Cellular studies reveal that anionic amphiphilic calixarenes exhibit low cytotoxicity and enable internalization of fluorescently labelled peptides into live cells. These findings suggest anionic amphiphilic macrocycles as promising building blocks for the preparation of peptide delivery vehicles.
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Affiliation(s)
- Roman V Rodik
- Institute of Organic Chemistry, National Academy of Science of Ukraine, 02660 Kyiv, Ukraine.
| | - Sergiy O Cherenok
- Institute of Organic Chemistry, National Academy of Science of Ukraine, 02660 Kyiv, Ukraine
| | - Viktoriia Y Postupalenko
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74, Route du Rhin, 67401 ILLKIRCH Cedex, France
| | - Sule Oncul
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74, Route du Rhin, 67401 ILLKIRCH Cedex, France; İstanbul Medeniyet Üniversitesi, Istanbul, Turkey
| | | | - Petro Borysko
- Enamine Ltd, Chervonotkatska 78, 02094 Kyiv, Ukraine
| | - Vitaly I Kalchenko
- Institute of Organic Chemistry, National Academy of Science of Ukraine, 02660 Kyiv, Ukraine
| | - Yves Mely
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74, Route du Rhin, 67401 ILLKIRCH Cedex, France
| | - Andrey S Klymchenko
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74, Route du Rhin, 67401 ILLKIRCH Cedex, France.
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11
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Clausse V, Zheng H, Amarasekara H, Kruhlak M, Appella DH. Thyclotides, tetrahydrofuran-modified peptide nucleic acids that efficiently penetrate cells and inhibit microRNA-21. Nucleic Acids Res 2022; 50:10839-10856. [PMID: 36215040 DOI: 10.1093/nar/gkac864] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 09/14/2022] [Accepted: 09/26/2022] [Indexed: 11/12/2022] Open
Abstract
Peptide nucleic acids (PNAs) are promising therapeutic molecules for gene modulation; however, they suffer from poor cell uptake. Delivery of PNAs into cells requires conjugation of the PNA to another large molecule, typically a cell-penetrating peptide or nanoparticle. In this study, we describe a new PNA-based molecule with cyclic tetrahydrofuran (THF) backbone modifications that in some cases considerably improve cell uptake. We refer to these THF-PNA oligomers as thyclotides. With THF groups at every position of the oligomer, the cell uptake of thyclotides targeted to miR-21 is enhanced compared with the corresponding unmodified PNA based on an aminoethylglycine backbone. An optimized thyclotide can efficiently enter cells without the use of cell-penetrating peptides, bind miR-21, its designated microRNA target, decrease expression of miR-21 and increase expression of three downstream targets (PTEN, Cdc25a and KRIT1). Using a plasmid with the PTEN-3'UTR coupled with luciferase, we further confirmed that a miR-21-targeted thyclotide prevents miR-21 from binding to its target RNA. Additionally, the thyclotide shows no cytotoxicity when administered at 200 times its active concentration. We propose that thyclotides be further explored as therapeutic candidates to modulate miRNA levels.
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Affiliation(s)
- Victor Clausse
- Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hongchao Zheng
- Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Harsha Amarasekara
- Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael Kruhlak
- Microscopy Core Facility, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel H Appella
- Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
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12
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Terracciano M, Fontana F, Falanga AP, D'Errico S, Torrieri G, Greco F, Tramontano C, Rea I, Piccialli G, De Stefano L, Oliviero G, Santos HA, Borbone N. Development of Surface Chemical Strategies for Synthesizing Redox-Responsive Diatomite Nanoparticles as a Green Platform for On-Demand Intracellular Release of an Antisense Peptide Nucleic Acid Anticancer Agent. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2204732. [PMID: 36089668 DOI: 10.1002/smll.202204732] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Indexed: 06/15/2023]
Abstract
Redox-responsive silica drug delivery systems are synthesized by aeco-friendly diatomite source to achieve on-demand release of peptide nucleic acid (PNA) in tumor reducing microenvironment, aiming to inhibit the immune checkpoint programmed cell death 1 receptor/programmed cell death receptor ligand 1 (PD-1/PD-L1) in cancer cells. The nanoparticles (NPs) are coated with polyethylene glycol chains as gatekeepers to improve their physicochemical properties and control drug release through the cleavable disulfide bonds (S-S) in a reductive environment. This study describes different chemical conditions to achieve the highest NPs' surface functionalization yield, exploring both multistep and one-pot chemical functionalization strategies. The best formulation is used for covalent PNA conjugation via the S-S bond reaching a loading degree of 306 ± 25 µg PNA mg-1 DNPs . These systems are used for in vitro studies to evaluate the kinetic release, biocompatibility, cellular uptake, and activity on different cancer cells expressing high levels of PD-L1. The obtained results prove the safety of the NPs up to 200 µg mL-1 and their advantage for controlling and enhancing the PNA intracellular release as well as antitumor activity. Moreover, the downregulation of PD-L1 observed only with MDA-MB-231 cancer cells paves the way for targeted immunotherapy.
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Affiliation(s)
- Monica Terracciano
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, Naples, 80131, Italy
| | - Flavia Fontana
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Viikinkaari 9, Helsinki, FI-00014, Finland
| | - Andrea Patrizia Falanga
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, Naples, 80131, Italy
| | - Stefano D'Errico
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, Naples, 80131, Italy
| | - Giulia Torrieri
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Viikinkaari 9, Helsinki, FI-00014, Finland
| | - Francesca Greco
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, Naples, 80131, Italy
| | - Chiara Tramontano
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, Naples, 80131, Italy
| | - Ilaria Rea
- Institute of Applied Sciences and Intelligent Systems, Unit of Naples, National Research Council, via P. Castellino 111, Naples, 80131, Italy
| | - Gennaro Piccialli
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, Naples, 80131, Italy
| | - Luca De Stefano
- Institute of Applied Sciences and Intelligent Systems, Unit of Naples, National Research Council, via P. Castellino 111, Naples, 80131, Italy
| | - Giorgia Oliviero
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, via S. Pansini 5, Naples, 80131, Italy
| | - Hélder A Santos
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Viikinkaari 9, Helsinki, FI-00014, Finland
- Department of Biomedical Engineering, W.J. Kolff Institute for Biomedical Engineering and Materials Science, University Medical Center Groningen, University of Groningen, Ant. Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Nicola Borbone
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, Naples, 80131, Italy
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13
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Jain CK, Srivastava P, Pandey AK, Singh N, Kumar RS. miRNA therapeutics in precision oncology: a natural premium to nurture. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2022; 3:511-532. [PMID: 36071981 PMCID: PMC9446160 DOI: 10.37349/etat.2022.00098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/02/2022] [Indexed: 11/22/2022] Open
Abstract
The dynamic spectrum of microRNA (miRNA) has grown significantly over the years with its identification and exploration in cancer therapeutics and is currently identified as an important resource for innovative strategies due to its functional behavior for gene regulation and modulation of complex biological networks. The progression of cancer is the consequence of uncontrolled, nonsynchronous procedural faults in the biological system. Diversified and variable cellular response of cancerous cells has always raised challenges in effective cancer therapy. miRNAs, a class of non-coding RNAs (ncRNAs), are the natural genetic gift, responsible to preserve the homeostasis of cell to nurture. The unprecedented significance of endogenous miRNAs has exhibited promising therapeutic potential in cancer therapeutics. Currently, miRNA mimic miR-34, and an antimiR aimed against miR-122 has entered the clinical trials for cancer treatments. This review, highlights the recent breakthroughs, challenges, clinical trials, and advanced delivery vehicles in the administration of miRNA therapies for precision oncology.
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Affiliation(s)
- Chakresh Kumar Jain
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida 201307, India
| | - Poornima Srivastava
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida 201307, India
| | - Amit Kumar Pandey
- Amity Institute of Biotechnology, Amity University Haryana, Panchgaon, Manesar, Haryana 122413, India
| | - Nisha Singh
- Department of Bioinformatics, Gujarat Biotechnology University, Gandhinagar, GIFT city 382355, India
| | - R Suresh Kumar
- Molecular Genetics Lab, Molecular Biology Group, National Institute of Cancer Prevention and Research (ICMR), Noida 201307, India
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14
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Zare M, Pemmada R, Madhavan M, Shailaja A, Ramakrishna S, Kandiyil SP, Donahue JM, Thomas V. Encapsulation of miRNA and siRNA into Nanomaterials for Cancer Therapeutics. Pharmaceutics 2022; 14:pharmaceutics14081620. [PMID: 36015246 PMCID: PMC9416290 DOI: 10.3390/pharmaceutics14081620] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/21/2022] [Accepted: 07/28/2022] [Indexed: 01/22/2023] Open
Abstract
Globally, cancer is amongst the most deadly diseases due to the low efficiency of the conventional and obsolete chemotherapeutic methodologies and their many downsides. The poor aqueous solubility of most anticancer medications and their low biocompatibility make them ineligible candidates for the design of delivery systems. A significant drawback associated with chemotherapy is that there are no advanced solutions to multidrug resistance, which poses a major obstacle in cancer management. Since RNA interference (RNAi) can repress the expression of genes, it is viewed as a novel tool for advanced drug delivery. this is being explored as a promising drug targeting strategy for the treatment of multiple diseases, including cancer. However, there are many obstructions that hinder the clinical uses of siRNA drugs due to their low permeation into cells, off-target impacts, and possible unwanted immune responses under physiological circumstances. Thus, in this article, we review the design measures for siRNA conveyance frameworks and potential siRNA and miRNA drug delivery systems for malignant growth treatment, including the use of liposomes, dendrimers, and micelle-based nanovectors and functional polymer-drug delivery systems. This article sums up the advancements and challenges in the use of nanocarriers for siRNA delivery and remarkably centers around the most critical modification strategies for nanocarriers to build multifunctional siRNA and miRNA delivery vectors. In short, we hope this review will throw light on the dark areas of RNA interference, which will further open novel research arenas in the development of RNAi drugs for cancer.
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Affiliation(s)
- Mina Zare
- Center for Nanotechnology and Sustainability, Department of Mechanical Engineering, National University of Singapore, Singapore 117581, Singapore; (M.Z.); (S.R.)
- Department of Food and Nutrition, University of Helsinki, 00014 Helsinki, Finland
| | - Rakesh Pemmada
- Departments of Materials Science and Engineering, Biomedical Engineering, University of Alabama at Birmingham (UAB), Birmingham, AL 35294, USA;
| | - Maya Madhavan
- Department of Biochemistry, Government College for Women, Thiruvananthapuram 695014, India
- Correspondence: (M.M.); (V.T.)
| | - Aswathy Shailaja
- Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA;
| | - Seeram Ramakrishna
- Center for Nanotechnology and Sustainability, Department of Mechanical Engineering, National University of Singapore, Singapore 117581, Singapore; (M.Z.); (S.R.)
| | | | - James M. Donahue
- School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA;
| | - Vinoy Thomas
- Departments of Materials Science and Engineering, Biomedical Engineering, University of Alabama at Birmingham (UAB), Birmingham, AL 35294, USA;
- Center for Nanoscale Materials and Biointegration (CNMB), Center for Clinical and Translational Science (CCTS), University of Alabama at Birmingham (UAB), Birmingham, AL 35294, USA
- Correspondence: (M.M.); (V.T.)
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15
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Economos NG, Quijano E, Carufe KEW, Perera J, Glazer P. Antispacer peptide nucleic acids for sequence-specific CRISPR-Cas9 modulation. Nucleic Acids Res 2022; 50:e59. [PMID: 35235944 PMCID: PMC9177974 DOI: 10.1093/nar/gkac095] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 01/22/2022] [Accepted: 02/22/2022] [Indexed: 12/14/2022] Open
Abstract
Despite the rapid and broad implementation of CRISPR-Cas9-based technologies, convenient tools to modulate dose, timing, and precision remain limited. Building on methods using synthetic peptide nucleic acids (PNAs) to bind RNA with unusually high affinity, we describe guide RNA (gRNA) spacer-targeted, or 'antispacer', PNAs as a tool to modulate Cas9 binding and activity in cells in a sequence-specific manner. We demonstrate that PNAs rapidly and efficiently target complexed gRNA spacer sequences at low doses and without design restriction for sequence-selective Cas9 inhibition. We further show that short PAM-proximal antispacer PNAs achieve potent cleavage inhibition (over 2000-fold reduction) and that PAM-distal PNAs modify gRNA affinity to promote on-target specificity. Finally, we apply antispacer PNAs for temporal regulation of two dCas9-fusion systems. These results present a novel rational approach to nucleoprotein engineering and describe a rapidly implementable antisense platform for CRISPR-Cas9 modulation to improve spatiotemporal versatility and safety across applications.
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Affiliation(s)
- Nicholas G Economos
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06520 USA
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520 USA
| | - Elias Quijano
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06520 USA
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520 USA
| | - Kelly E W Carufe
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06520 USA
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520 USA
| | - J Dinithi R Perera
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06520 USA
| | - Peter M Glazer
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06520 USA
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520 USA
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16
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Gorai A, Chaudhuri R, Mukhopadhyay TK, Datta A, Dash J. Thiazole Containing PNA Mimic Regulates c-MYC Gene Expression through DNA G-Quadruplex. Bioconjug Chem 2022; 33:1145-1155. [PMID: 35537180 DOI: 10.1021/acs.bioconjchem.2c00075] [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
Peptide nucleic acids (PNAs), besides hybridizing to complementary DNA and RNAs, bind and stabilize DNA secondary structures. Herein, we illustrate the design and synthesis of PNA-like scaffolds by incorporating five-membered thiazole rings as modified bases instead of nucleobases and their subsequent effects on gene regulation by biophysical and in vitro assays. A thiazole-modified PNA trimer selectively recognizes c-MYC G-quadruplex (G4) DNA over other G4s and duplex DNA. It displays a high stabilization potential for the c-MYC G4 DNA and shows remarkable fluorescence enhancement with the c-MYC G4. It is flexible enough to bind at 5' and 3' ends as well as in the groove region of c-MYC G4. Furthermore, the PNA trimer easily permeates the cellular membrane and suppresses c-MYC mRNA expression in HeLa cells by targeting the promoter G4. This study illuminates modified PNAs as flexible molecular tools for selective targeting of noncanonical nucleic acids and modulating gene function.
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Affiliation(s)
- Ananta Gorai
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
| | - Ritapa Chaudhuri
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
| | - Titas Kumar Mukhopadhyay
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
| | - Ayan Datta
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
| | - Jyotirmayee Dash
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
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17
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The emerging role of bacterial regulatory RNAs in disease. Trends Microbiol 2022; 30:959-972. [DOI: 10.1016/j.tim.2022.03.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 03/02/2022] [Accepted: 03/09/2022] [Indexed: 02/02/2023]
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18
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Todkari I, Gupta MK, Ganesh KN. Silver soldering of PNA:DNA duplexes: assembly of a triple duplex from bimodal PNAs with all-C on one face. Chem Commun (Camb) 2022; 58:4083-4086. [PMID: 35266467 DOI: 10.1039/d1cc07297h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA:bm-PNA duplexes endowed with all-C on either the t-amide or triazole face and mixed base sequence on the other face can be welded with silver ions through C:Ag+:C connects to give triple duplexes in one complex. The interplay of WC and Ag+-mediated duplexes leads to synergistic stability effects on both duplexes and the complex.
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Affiliation(s)
- Iranna Todkari
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, Maharashtra, India.
| | - Manoj Kumar Gupta
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, Maharashtra, India. .,Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road Road, Tirupati, 517507, Andhra Pradesh, India
| | - Krishna N Ganesh
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, Maharashtra, India. .,Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road Road, Tirupati, 517507, Andhra Pradesh, India
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19
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Exner RM, Paisey SJ, Redman JE, Pascu SI. Explorations into Peptide Nucleic Acid Contrast Agents as Emerging Scaffolds for Breakthrough Solutions in Medical Imaging and Diagnosis. ACS OMEGA 2021; 6:28455-28462. [PMID: 34746541 PMCID: PMC8569549 DOI: 10.1021/acsomega.1c03994] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/23/2021] [Indexed: 05/11/2023]
Abstract
Peptide nucleic acids (PNAs, nucleic acid analogues with a peptide backbone rather than a phosphoribosyl backbone) have emerged as promising chemical agents in antigene or antisense therapeutics, as splicing modulators or in gene editing. Their main benefits, compared to DNA or RNA agents, are their biochemical stability and the lack of negative charges throughout the backbone, leading to negligible electrostatic interaction with the strand with which they are hybridizing. As a result, hybridization of PNA strands with DNA or RNA strands leads to higher binding energies and melting temperatures. A lack of natural transporters, however, necessitates the formation of PNA-containing chimeras or the formulation of nanoparticular cell delivery methods. Here, we set out to explore the progress made in using imaging agents based on PNAs in diagnostic applications and highlight selected developments and challenges.
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Affiliation(s)
- Rüdiger M. Exner
- Department
of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
| | - Stephen J. Paisey
- Wales
Research & Diagnostic Positron Emission Tomography Imaging Centre
(PETIC), School of Medicine, Cardiff University,
University Hospital of Wales, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - James E. Redman
- School
of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
| | - Sofia I. Pascu
- Department
of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
- Centre
for Sustainable and Circular Technologies, 1 South, University of Bath, Claverton Down, Bath BA2
7AY, United Kingdom
- Centre
for Therapeutic Innovation, 3 West 2.03, University of Bath, Claverton Down, Bath BA2
7AY, United Kingdom
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20
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Papukashvili D, Rcheulishvili N, Liu C, Xie F, Tyagi D, He Y, Wang PG. Perspectives on miRNAs Targeting DKK1 for Developing Hair Regeneration Therapy. Cells 2021; 10:2957. [PMID: 34831180 PMCID: PMC8616136 DOI: 10.3390/cells10112957] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 02/08/2023] Open
Abstract
Androgenetic alopecia (AGA) remains an unsolved problem for the well-being of humankind, although multiple important involvements in hair growth have been discovered. Up until now, there is no ideal therapy in clinical practice in terms of efficacy and safety. Ultimately, there is a strong need for developing a feasible remedy for preventing and treating AGA. The Wnt/β-catenin signaling pathway is critical in hair restoration. Thus, AGA treatment via modulating this pathway is rational, although challenging. Dickkopf-related protein 1 (DKK1) is distinctly identified as an inhibitor of canonical Wnt/β-catenin signaling. Thus, in order to stimulate the Wnt/β-catenin signaling pathway, inhibition of DKK1 is greatly demanding. Studying DKK1-targeting microRNAs (miRNAs) involved in the Wnt/β-catenin signaling pathway may lay the groundwork for the promotion of hair growth. Bearing in mind that DKK1 inhibition in the balding scalp of AGA certainly makes sense, this review sheds light on the perspectives of miRNA-mediated hair growth for treating AGA via regulating DKK1 and, eventually, modulating Wnt/β-catenin signaling. Consequently, certain miRNAs regulating the Wnt/β-catenin signaling pathway via DKK1 inhibition might represent attractive candidates for further studies focusing on promoting hair growth and AGA therapy.
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Affiliation(s)
| | | | | | | | | | - Yunjiao He
- School of Medicine, Southern University of Science and Technology, Shenzhen 518000, China; (D.P.); (N.R.); (C.L.); (F.X.); (D.T.)
| | - Peng George Wang
- School of Medicine, Southern University of Science and Technology, Shenzhen 518000, China; (D.P.); (N.R.); (C.L.); (F.X.); (D.T.)
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21
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Antipin IS, Alfimov MV, Arslanov VV, Burilov VA, Vatsadze SZ, Voloshin YZ, Volcho KP, Gorbatchuk VV, Gorbunova YG, Gromov SP, Dudkin SV, Zaitsev SY, Zakharova LY, Ziganshin MA, Zolotukhina AV, Kalinina MA, Karakhanov EA, Kashapov RR, Koifman OI, Konovalov AI, Korenev VS, Maksimov AL, Mamardashvili NZ, Mamardashvili GM, Martynov AG, Mustafina AR, Nugmanov RI, Ovsyannikov AS, Padnya PL, Potapov AS, Selektor SL, Sokolov MN, Solovieva SE, Stoikov II, Stuzhin PA, Suslov EV, Ushakov EN, Fedin VP, Fedorenko SV, Fedorova OA, Fedorov YV, Chvalun SN, Tsivadze AY, Shtykov SN, Shurpik DN, Shcherbina MA, Yakimova LS. Functional supramolecular systems: design and applications. RUSSIAN CHEMICAL REVIEWS 2021. [DOI: 10.1070/rcr5011] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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22
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Bhingardeve P, Jain P, Ganesh KN. Molecular Assembly of Triplex of Duplexes from Homothyminyl-Homocytosinyl Cγ( S/ R)-Bimodal Peptide Nucleic Acids with dA 8/dG 6 and the Cell Permeability of Bimodal Peptide Nucleic Acids. ACS OMEGA 2021; 6:19757-19770. [PMID: 34368563 PMCID: PMC8340421 DOI: 10.1021/acsomega.1c02451] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 07/05/2021] [Indexed: 05/08/2023]
Abstract
Peptide nucleic acids (PNAs) are analogues of DNA with a neutral acyclic polyamide backbone containing nucleobases attached through a t-amide link on repeating units of aminoethylglycine (aeg). They bind to complementary DNA or RNA in a sequence-specific manner to form duplexes with higher stablity than DNA:DNA and DNA:RNA hybrids. We have recently explored a new type of PNA termed bimodal PNA (bm-PNA) designed with two nucleobases per aeg repeating unit of PNA oligomer and attached at Cα or Cγ of each aeg unit through a spacer sidechain. We demonstrated that Cγ-bimodal PNA oligomers with mixed nucleobase sequences bind concurrently two different complementary DNAs, forming double duplexes, one from each t-amide and Cγ face, sharing a common PNA backbone. In such bm-PNA:DNA ternary complexes, the two duplexes show higher thermal stability than individual duplexes. Herein, we show that Cγ(S/R)-bimodal PNAs with homothymines (T8) on a t-amide face and homocytosine (C6) on a Cγ-face form a conjoined pentameric complex consisting of a triplex (bm-PNA-T8)2:dA8 and two duplexes of bm-PNA-C6:dG6. The pentameric complex [dG6:Cγ(S/R)-bm-PNA:dA8:Cγ(S/R)-bm-PNA:dG6] exhibits higher thermal stability than the individual triplex and duplex, with Cγ(S)-bm-PNA complexes being more stable than Cγ(R)-bm-PNA complexes. The conjoined duplexes of Cγ-bimodal PNAs can be used to generate novel higher-order assemblies with DNA and RNA. The Cγ(S/R)-bimodal PNAs are shown to enter MCF7 and NIH 3T3 cells and exhibit low toxicity to cells.
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Affiliation(s)
- Pramod Bhingardeve
- Indian
Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, India
| | - Prashant Jain
- Indian
Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, India
| | - Krishna N. Ganesh
- Indian
Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, India
- Indian
Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road, Mangalam, Tirupati 517507, India
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23
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Liang X, Liu M, Komiyama M. Recognition of Target Site in Various Forms of DNA and RNA by Peptide Nucleic Acid (PNA): From Fundamentals to Practical Applications. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210086] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, P. R. China
| | - Mengqin Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
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24
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Finotti A, Gasparello J, Casnati A, Corradini R, Gambari R, Sansone F. Delivery of Peptide Nucleic Acids Using an Argininocalix[4]arene as Vector. Methods Mol Biol 2021; 2211:123-143. [PMID: 33336275 DOI: 10.1007/978-1-0716-0943-9_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The importance of peptide nucleic acids (PNAs) for alteration of gene expression is nowadays firmly established. PNAs are characterized by a pseudo-peptide backbone composed of N-(2-aminoethyl)glycine units and have been found to be excellent candidates for antisense and antigene therapies. Recently, PNAs have been demonstrated to alter the action of microRNAs and thus can be considered very important tools for miRNA therapeutics. In fact, the pharmacological modulation of microRNA activity appears to be a very interesting approach in the development of new types of drugs. Among the limits of PNAs in applied molecular biology, the delivery to target cells and tissues is of key importance. The aim of this chapter is to describe methods for the efficient delivery of unmodified PNAs designed to target microRNAs involved in cancer, using as model system miR-221-3p and human glioma cells as in vitro experimental cellular system. The methods employed to deliver PNAs targeting miR-221-3p here presented are based on a macrocyclic multivalent tetraargininocalix[4]arene used as non-covalent vector for anti-miR-221-3p PNAs. High delivery efficiency, low cytotoxicity, maintenance of the PNA biological activity, and easy preparation makes this vector a candidate for a universal delivery system for this class of nucleic acid analogs.
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Affiliation(s)
- Alessia Finotti
- Section of Biochemistry and Molecular Biology, Department of Life Sciences and Biotechnology, Ferrara University, Ferrara, Italy.
| | - Jessica Gasparello
- Section of Biochemistry and Molecular Biology, Department of Life Sciences and Biotechnology, Ferrara University, Ferrara, Italy
| | - Alessandro Casnati
- Department of Chemistry, Life Sciences and Environmental Sustainability, Parma University, Parma, Italy
| | - Roberto Corradini
- Department of Chemistry, Life Sciences and Environmental Sustainability, Parma University, Parma, Italy
| | - Roberto Gambari
- Section of Biochemistry and Molecular Biology, Department of Life Sciences and Biotechnology, Ferrara University, Ferrara, Italy.,Interuniversity Consortium for Biotechnology, Trieste University, Trieste, Italy
| | - Francesco Sansone
- Department of Chemistry, Life Sciences and Environmental Sustainability, Parma University, Parma, Italy.
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25
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Dasgupta I, Chatterjee A. Recent Advances in miRNA Delivery Systems. Methods Protoc 2021; 4:mps4010010. [PMID: 33498244 PMCID: PMC7839010 DOI: 10.3390/mps4010010] [Citation(s) in RCA: 127] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 12/27/2022] Open
Abstract
MicroRNAs (miRNAs) represent a family of short non-coding regulatory RNA molecules that are produced in a tissue and time-specific manner to orchestrate gene expression post-transcription. MiRNAs hybridize to target mRNA(s) to induce translation repression or mRNA degradation. Functional studies have demonstrated that miRNAs are engaged in virtually every physiological process and, consequently, miRNA dysregulations have been linked to multiple human pathologies. Thus, miRNA mimics and anti-miRNAs that restore miRNA expression or downregulate aberrantly expressed miRNAs, respectively, are highly sought-after therapeutic strategies for effective manipulation of miRNA levels. In this regard, carrier vehicles that facilitate proficient and safe delivery of miRNA-based therapeutics are fundamental to the clinical success of these pharmaceuticals. Here, we highlight the strengths and weaknesses of current state-of-the-art viral and non-viral miRNA delivery systems and provide perspective on how these tools can be exploited to improve the outcomes of miRNA-based therapeutics.
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Affiliation(s)
- Ishani Dasgupta
- Horae Gene Therapy Center, Department of Pediatrics, University of Massachusetts Medical School, Worcester, MA 01605, USA;
| | - Anushila Chatterjee
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Correspondence:
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26
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Morbioli I, Casnati A, Esko JD, Tor Y, Sansone F. Calixarene-decorated liposomes for intracellular cargo delivery. Org Biomol Chem 2021; 19:6598-6602. [PMID: 34268550 DOI: 10.1039/d1ob01055g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Amphiphilic calix[4]arenes, functionalized with guanidinium groups, are used to decorate the outer surface of liposomes and significantly improve the cellular uptake of a cargo compared to plain liposomes. The improved uptake is elicited and mediated by the interaction between the cationic polar heads of the macrocycle units embedded in the liposome bilayer and anionic heparan-sulfate proteoglycans surrounding the exterior of cells.
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Affiliation(s)
- Ilaria Morbioli
- Department of Chemistry, Life Sciences and Environmental Sustainability, Università degli Studi di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy.
| | - Alessandro Casnati
- Department of Chemistry, Life Sciences and Environmental Sustainability, Università degli Studi di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy.
| | - Jeffrey D Esko
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA.
| | - Francesco Sansone
- Department of Chemistry, Life Sciences and Environmental Sustainability, Università degli Studi di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy.
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27
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Hadidi K, Bellucci MC, Dall'Angelo S, Leeson-Payne A, Rochford JJ, Esko JD, Tor Y, Volonterio A. Guanidinoneomycin-maleimide molecular transporter: synthesis, chemistry and cellular uptake. Org Biomol Chem 2021; 19:6513-6520. [PMID: 34254106 DOI: 10.1039/d1ob01101d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Guanidinoglycosides are a class of non-cytotoxic molecular transporters capable of delivering high molecular weight bioactive cargos into cells at low nanomolar concentrations. Efficient bioconjugation with guanidinoglycosides has been previously demonstrated by utilizing a guanidinoneomycin decorated with a reactive but also unstable N-hydroxysuccinimmide ester-containing linker. Herein we report the synthesis, chemistry, and application of a new, stable guanidinoneomycin derivative armed with a highly specific maleimide moiety which allows for thiol-maleimide click chemistry, a highly popular bioconjugation strategy, widening the field of application of these intriguing and useful delivery vehicles.
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Affiliation(s)
- Kaivin Hadidi
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA.
| | - Maria Cristina Bellucci
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, via Celoria 2, 20133 Milano, Italy
| | - Sergio Dall'Angelo
- Institute of Medical Sciences, University of Aberdeen, AB25 2ZD Aberdeen, UK
| | - Alasdair Leeson-Payne
- The Rowett Institute and Aberdeen Cardiovascular and Diabetes Centre, University of Aberdeen, Aberdeen AB25 2ZD, UK
| | - Justin J Rochford
- The Rowett Institute and Aberdeen Cardiovascular and Diabetes Centre, University of Aberdeen, Aberdeen AB25 2ZD, UK
| | - Jeffery D Esko
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA.
| | - Alessandro Volonterio
- Department of Chemistry, Material and Chemical Engineer "Giulio Natta", Politecnico di Milano, via Mancinelli 7, 20131 Milano, Italy.
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28
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Gasparello J, Finotti A, Gambari R. Tackling the COVID-19 "cytokine storm" with microRNA mimics directly targeting the 3'UTR of pro-inflammatory mRNAs. Med Hypotheses 2021; 146:110415. [PMID: 33422363 PMCID: PMC7685948 DOI: 10.1016/j.mehy.2020.110415] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 11/22/2020] [Indexed: 12/17/2022]
Abstract
COVID-19 is characterized by two major clinical phases, the SARS-CoV-2 infection of target cells and tissues, and a deep inflammatory state, known as "cytokine storm", caused by activation of pro-inflammatory genes, such as NF-kB, STAT-3, IL-6, IL-8, IL-1ß. Among possible anti-inflammatory agents, the "microRNA targeting" should be carefully considered, since it is well known that microRNAs are deeply involved in the expression of cytokines, chemokines and growth factors. The working general hypothesis is that targeting the microRNA network might be important for the development of therapeutic approaches to counteract the COVID-19 induction of inflammatory response. This hypothesis is based on several publications demonstrating the use of miRNA mimics for inhibitory effects on the production of proteins characterizing the COVID-19 "cytokine storm".
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Affiliation(s)
- Jessica Gasparello
- Department of Life Sciences and Biotechnology, University of Ferrara, Italy
| | - Alessia Finotti
- Department of Life Sciences and Biotechnology, University of Ferrara, Italy
| | - Roberto Gambari
- Department of Life Sciences and Biotechnology, University of Ferrara, Italy; Center for Innovative Therapies in Cystic Fibrosis, University of Ferrara, Italy.
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Volpi S, Cancelli U, Neri M, Corradini R. Multifunctional Delivery Systems for Peptide Nucleic Acids. Pharmaceuticals (Basel) 2020; 14:14. [PMID: 33375595 PMCID: PMC7823687 DOI: 10.3390/ph14010014] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/21/2020] [Accepted: 12/23/2020] [Indexed: 02/07/2023] Open
Abstract
The number of applications of peptide nucleic acids (PNAs)-oligonucleotide analogs with a polyamide backbone-is continuously increasing in both in vitro and cellular systems and, parallel to this, delivery systems able to bring PNAs to their targets have been developed. This review is intended to give to the readers an overview on the available carriers for these oligonucleotide mimics, with a particular emphasis on newly developed multi-component- and multifunctional vehicles which boosted PNA research in recent years. The following approaches will be discussed: (a) conjugation with carrier molecules and peptides; (b) liposome formulations; (c) polymer nanoparticles; (d) inorganic porous nanoparticles; (e) carbon based nanocarriers; and (f) self-assembled and supramolecular systems. New therapeutic strategies enabled by the combination of PNA and proper delivery systems are discussed.
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Affiliation(s)
| | | | | | - Roberto Corradini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (S.V.); (U.C.); (M.N.)
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30
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Rivero-Barbarroja G, Benito JM, Ortiz Mellet C, García Fernández JM. Cyclodextrin-Based Functional Glyconanomaterials. NANOMATERIALS (BASEL, SWITZERLAND) 2020; 10:E2517. [PMID: 33333914 PMCID: PMC7765426 DOI: 10.3390/nano10122517] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/11/2020] [Accepted: 12/12/2020] [Indexed: 12/29/2022]
Abstract
Cyclodextrins (CDs) have long occupied a prominent position in most pharmaceutical laboratories as "off-the-shelve" tools to manipulate the pharmacokinetics of a broad range of active principles, due to their unique combination of biocompatibility and inclusion abilities. The development of precision chemical methods for their selective functionalization, in combination with "click" multiconjugation procedures, have further leveraged the nanoscaffold nature of these oligosaccharides, creating a direct link between the glyco and the nano worlds. CDs have greatly contributed to understand and exploit the interactions between multivalent glycodisplays and carbohydrate-binding proteins (lectins) and to improve the drug-loading and functional properties of nanomaterials through host-guest strategies. The whole range of capabilities can be enabled through self-assembly, template-assisted assembly or covalent connection of CD/glycan building blocks. This review discusses the advancements made in this field during the last decade and the amazing variety of functional glyconanomaterials empowered by the versatility of the CD component.
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Affiliation(s)
- Gonzalo Rivero-Barbarroja
- Department of Organic Chemistry, Faculty of Chemistry, University of Seville, 41012 Seville, Spain; (G.R.-B.); (C.O.M.)
| | - Juan Manuel Benito
- Instituto de Investigaciones Químicas (IIQ), CSIC, Universidad de Sevilla, 41092 Sevilla, Spain;
| | - Carmen Ortiz Mellet
- Department of Organic Chemistry, Faculty of Chemistry, University of Seville, 41012 Seville, Spain; (G.R.-B.); (C.O.M.)
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31
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Oguz M, Kalay E, Akocak S, Nocentini A, Lolak N, Boga M, Yilmaz M, Supuran CT. Synthesis of calix[4]azacrown substituted sulphonamides with antioxidant, acetylcholinesterase, butyrylcholinesterase, tyrosinase and carbonic anhydrase inhibitory action. J Enzyme Inhib Med Chem 2020; 35:1215-1223. [PMID: 32401067 PMCID: PMC7269057 DOI: 10.1080/14756366.2020.1765166] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 04/29/2020] [Accepted: 04/30/2020] [Indexed: 02/07/2023] Open
Abstract
A series of novel calix[4]azacrown substituted sulphonamide Schiff bases was synthesised by the reaction of calix[4]azacrown aldehydes with different substituted primary and secondary sulphonamides. The obtained novel compounds were investigated as inhibitors of six human (h) isoforms of carbonic anhydrases (CA, EC 4.2.1.1). Their antioxidant profile was assayed by various bioanalytical methods. The calix[4]azacrown substituted sulphonamide Schiff bases were also investigated as inhibitors of acetylcholinesterase (AChE), butyrylcholinesterase (BChE) and tyrosinase enzymes, associated with several diseases such as Alzheimer, Parkinson, and pigmentation disorders. The new sulphonamides showed low to moderate inhibition against hCAs, AChE, BChE, and tyrosinase enzymes. However, some of them possessed relevant antioxidant activity, comparable with standard antioxidants used in the study.
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Affiliation(s)
- Mehmet Oguz
- Department of Chemistry, University of Selcuk, Konya, Turkey
- Department of Advanced Material and Nanotechnology, Selcuk University, Konya, Turkey
| | - Erbay Kalay
- Kars Vocational School, Kafkas University, Kars, Turkey
| | - Suleyman Akocak
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Adiyaman University, Adiyaman, Turkey
| | - Alessio Nocentini
- NEUROFARBA Department, Sezione di Scienze Farmaceutiche, Università degli Studi di Firenze, Florence, Italy
| | - Nebih Lolak
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Adiyaman University, Adiyaman, Turkey
| | - Mehmet Boga
- Department of Analytical Chemistry, Faculty of Pharmacy, Dicle University, Diyarbakir, Turkey
| | - Mustafa Yilmaz
- Department of Chemistry, University of Selcuk, Konya, Turkey
| | - Claudiu T. Supuran
- NEUROFARBA Department, Sezione di Scienze Farmaceutiche, Università degli Studi di Firenze, Florence, Italy
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32
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Hashemi A, Gorji-Bahri G. MicroRNA: Promising Roles in Cancer Therapy. Curr Pharm Biotechnol 2020; 21:1186-1203. [PMID: 32310047 DOI: 10.2174/1389201021666200420101613] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 03/17/2020] [Accepted: 03/31/2020] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRNA) are small non-coding RNAs that act as one of the main regulators of gene expression. They are involved in maintaining a proper balance of diverse processes, including differentiation, proliferation, and cell death in normal cells. Cancer biology can also be affected by these molecules by modulating the expression of oncogenes or tumor suppressor genes. Thus, miRNA based anticancer therapy is currently being developed either alone or in combination with chemotherapy agents used in cancer management, aiming at promoting tumor regression and increasing cure rate. Access to large quantities of RNA agents can facilitate RNA research and development. In addition to currently used in vitro methods, fermentation-based approaches have recently been developed, which can cost-effectively produce biological RNA agents with proper folding needed for the development of RNA-based therapeutics. Nevertheless, a major challenge in translating preclinical studies to clinical for miRNA-based cancer therapy is the efficient delivery of these agents to target cells. Targeting miRNAs/anti-miRNAs using antibodies and/or peptides can minimize cellular and systemic toxicity. Here, we provide a brief review of miRNA in the following aspects: biogenesis and mechanism of action of miRNAs, the role of miRNAs in cancer as tumor suppressors or oncogenes, the potential of using miRNAs as novel and promising therapeutics, miRNA-mediated chemo-sensitization, and currently utilized methods for the in vitro and in vivo production of RNA agents. Finally, an update on the viral and non-viral delivery systems is addressed.
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Affiliation(s)
- Atieh Hashemi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Gilar Gorji-Bahri
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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33
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Neva T, Carbajo-Gordillo AI, Benito JM, Lana H, Marcelo G, Ortiz Mellet C, Tros de Ilarduya C, Mendicuti F, García Fernández JM. Tuning the Topological Landscape of DNA-Cyclodextrin Nanocomplexes by Molecular Design. Chemistry 2020; 26:15259-15269. [PMID: 32710799 DOI: 10.1002/chem.202002951] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Indexed: 12/25/2022]
Abstract
Original molecular vectors that ensure broad flexibility to tune the shape and surface properties of plasmid DNA (pDNA) condensates are reported herein. The prototypic design involves a cyclodextrin (CD) platform bearing a polycationic cluster at the primary face and a doubly linked aromatic module bridging two consecutive monosaccharide units at the secondary face that behaves as a topology-encoding element. Subtle differences at the molecular level then translate into disparate morphologies at the nanoscale, including rods, worms, toroids, globules, ellipsoids, and spheroids. In vitro evaluation of the transfection capabilities revealed marked selectivity differences as a function of nanocomplex morphology. Remarkably high transfection efficiencies were associated with ellipsoidal or spherical shapes with a lamellar internal arrangement of pDNA chains and CD bilayers. Computational studies support that the stability of such supramolecular edifices is directly related to the tendency of the molecular vector to form noncovalent dimers upon DNA templating. Because the stability of the dimers depends on the protonation state of the polycationic clusters, the coaggregates display pH responsiveness, which facilitates endosomal escape and timely DNA release, a key step in successful transfection. The results provide a versatile strategy for the construction of fully synthetic and perfectly monodisperse nonviral gene delivery systems uniquely suited for optimization schemes.
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Affiliation(s)
- Tania Neva
- Institute for Chemical Research, IIQ, CSIC-Univ. Sevilla, C/ Américo Vespucio 49, 41092, Sevilla, Spain
| | - Ana I Carbajo-Gordillo
- Institute for Chemical Research, IIQ, CSIC-Univ. Sevilla, C/ Américo Vespucio 49, 41092, Sevilla, Spain
| | - Juan M Benito
- Institute for Chemical Research, IIQ, CSIC-Univ. Sevilla, C/ Américo Vespucio 49, 41092, Sevilla, Spain
| | - Hugo Lana
- Department of Pharmaceutical Technology and Chemistry, School of Pharmacy and Nutrition, University of Navarra, 31080, Pamplona, Spain
| | - Gema Marcelo
- Department of Analytical Chemistry, Physical Chemistry and Chemical Engineering, Instituto de Investigación Química, "Andrés M. del Rio" (IQAR), University of Alcalá, Campus Universitario Ctra. Madrid-Barcelona, Km 33.600, 28871, Alcalá de Henares, Spain
| | - Carmen Ortiz Mellet
- Department of Organic Chemistry, Faculty of Chemistry, University of Sevilla, C/ Prof García González 1, 41012, Sevilla, Spain
| | - Conchita Tros de Ilarduya
- Department of Pharmaceutical Technology and Chemistry, School of Pharmacy and Nutrition, University of Navarra, 31080, Pamplona, Spain
| | - Francisco Mendicuti
- Department of Analytical Chemistry, Physical Chemistry and Chemical Engineering, Instituto de Investigación Química, "Andrés M. del Rio" (IQAR), University of Alcalá, Campus Universitario Ctra. Madrid-Barcelona, Km 33.600, 28871, Alcalá de Henares, Spain
| | - José M García Fernández
- Institute for Chemical Research, IIQ, CSIC-Univ. Sevilla, C/ Américo Vespucio 49, 41092, Sevilla, Spain
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34
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Bhingardeve P, Madhanagopal BR, Ganesh KN. Cγ( S/ R)-Bimodal Peptide Nucleic Acids (Cγ- bm-PNA) Form Coupled Double Duplexes by Synchronous Binding to Two Complementary DNA Strands. J Org Chem 2020; 85:13680-13693. [PMID: 32985197 DOI: 10.1021/acs.joc.0c01853] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Peptide nucleic acids (PNAs) are linear equivalents of DNA with a neutral acyclic polyamide backbone that has nucleobases attached via tert-amide link on repeating units of aminoethylglycine. They bind complementary DNA or RNA with sequence specificity to form hybrids that are more stable than the corresponding DNA/RNA self-duplexes. A new type of PNA termed bimodal PNA [Cγ(S/R)-bm-PNA] is designed to have a second nucleobase attached via amide spacer to a side chain at Cγ on the repeating aeg units of PNA oligomer. Cγ-bimodal PNA oligomers that have two nucleobases per aeg unit are demonstrated to concurrently bind two different complementary DNAs, to form duplexes from both tert-amide side and Cγ side. In such PNA:DNA ternary complexes, the two duplexes share a common PNA backbone. The ternary DNA 1:Cγ(S/R)-bm-PNA:DNA 2 complexes exhibit better thermal stability than the isolated duplexes, and the Cγ(S)-bm-PNA duplexes are more stable than Cγ(R)-bm-PNA duplexes. Bimodal PNAs are first examples of PNA analogues that can form DNA2:PNA:DNA1 double duplexes via recognition through natural bases. The conjoined duplexes of Cγ-bimodal PNAs can be used to generate novel higher-level assemblies.
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Affiliation(s)
- Pramod Bhingardeve
- Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Bharath Raj Madhanagopal
- Indian Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road, Mangalam, Tirupati 517507, India
| | - Krishna N Ganesh
- Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pune 411008, India.,Indian Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road, Mangalam, Tirupati 517507, India
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35
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Patel R, Sarma S, Shukla A, Parmar P, Goswami D, Saraf M. Walking through the wonder years of artificial DNA: peptide nucleic acid. Mol Biol Rep 2020; 47:8113-8131. [PMID: 32990905 DOI: 10.1007/s11033-020-05819-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 09/04/2020] [Indexed: 11/26/2022]
Abstract
Peptide Nucleic Acid (PNA) serves as an artificial functional analog of DNA. Being immune to enzymatic degradation and possessing strong affinity towards DNA and RNA, it is an ideal candidate for many medical and biotechnological applications that are of antisense and antigene in nature. PNAs are anticipated to have its application in DNA and RNA detection as well as quantification, to serve as antibacterial and antiviral agents, and silencing gene for developing anticancer strategies. Although, their restricted entry in both eukaryotic and prokaryotic cells limit their applications. In addition, aggregation of PNA in storage containers reduces the quality and quantity of functional PNA that makes it inadequate for their mass production and storage. To overcome these limitations, researchers have modified PNA either by the addition of diverse functional groups at various loci on its backbone, or by synthesizing chimeras with other moieties associated with various delivery agents that aids their entry into the cell. Here, this review article summarizes few of the structural modifications that are performed with PNA, methods used to improve their cellular uptake and shedding light on the applications of PNA in various prospects in biological sciences.
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Affiliation(s)
- Rohit Patel
- Department of Microbiology and Biotechnology, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Sameera Sarma
- Department of Microbiology and Biotechnology, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Arpit Shukla
- Department of Microbiology and Biotechnology, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Paritosh Parmar
- Department of Microbiology and Biotechnology, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Dweipayan Goswami
- Department of Microbiology and Biotechnology, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Meenu Saraf
- Department of Microbiology and Biotechnology, Gujarat University, Ahmedabad, Gujarat, 380009, India.
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36
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Gupta MK, Madhanagopal BR, Datta D, Ganesh KN. Structural Design and Synthesis of Bimodal PNA That Simultaneously Binds Two Complementary DNAs To Form Fused Double Duplexes. Org Lett 2020; 22:5255-5260. [PMID: 32551691 DOI: 10.1021/acs.orglett.0c01950] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Bimodal PNAs are new PNA constructs designed to bind two different cDNA sequences synchronously to form double duplexes. They are synthesized on solid phase using sequential coupling and click reaction to introduce a second base in each monomer at Cα via alkyltriazole linker. The ternary bimodal PNA:DNA complexes show stability higher than that of individual duplexes. Bimodal PNAs are appropriate to create higher-order fused nucleic acid assemblies.
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Affiliation(s)
- Manoj Kumar Gupta
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, India
| | - Bharath Raj Madhanagopal
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road, Tirupati 517507, India
| | - Dhrubajyoti Datta
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, 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
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37
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Baldini L, Casnati A, Sansone F. Multivalent and Multifunctional Calixarenes in Bionanotechnology. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000255] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Laura Baldini
- Department of Chemistry Life Sciences and Environmental Sustainability University of Parma Parco Area delle Scienze, 17/a 43124 Parma Italy
| | - Alessandro Casnati
- Department of Chemistry Life Sciences and Environmental Sustainability University of Parma Parco Area delle Scienze, 17/a 43124 Parma Italy
| | - Francesco Sansone
- Department of Chemistry Life Sciences and Environmental Sustainability University of Parma Parco Area delle Scienze, 17/a 43124 Parma Italy
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Segal M, Slack FJ. Challenges identifying efficacious miRNA therapeutics for cancer. Expert Opin Drug Discov 2020; 15:987-992. [PMID: 32421364 DOI: 10.1080/17460441.2020.1765770] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Meirav Segal
- HMS Initiative for RNA Medicine, Department of Pathology, Beth, Israel Deaconess Medical Center/Harvard Medical School , Boston, MA, USA
| | - Frank J Slack
- HMS Initiative for RNA Medicine, Department of Pathology, Beth, Israel Deaconess Medical Center/Harvard Medical School , Boston, MA, USA
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Muangkaew P, Vilaivan T. Modulation of DNA and RNA by PNA. Bioorg Med Chem Lett 2020; 30:127064. [PMID: 32147357 DOI: 10.1016/j.bmcl.2020.127064] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 02/22/2020] [Accepted: 02/24/2020] [Indexed: 02/08/2023]
Abstract
Peptide nucleic acid (PNA), a synthetic DNA mimic that is devoid of the (deoxy)ribose-phosphate backbone yet still perfectly retains the ability to recognize natural nucleic acids in a sequence-specific fashion, can be employed as a tool to modulate gene expressions via several different mechanisms. The unique strength of PNA compared to other oligonucleotide analogs is its ability to bind to nucleic acid targets with secondary structures such as double-stranded and quadruplex DNA as well as RNA. This digest aims to introduce general readers to the advancement in the area of modulation of DNA/RNA functions by PNA, its current status and future research opportunities, with emphasis on recent progress in new targeting modes of structured DNA/RNA by PNA and PNA-mediated gene editing.
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Affiliation(s)
- Penthip Muangkaew
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand.
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Galli V, Sadhu KK, Masi D, Saarbach J, Roux A, Winssinger N. Caprin‐1 Promotes Cellular Uptake of Nucleic Acids with Backbone and Sequence Discrimination. Helv Chim Acta 2019. [DOI: 10.1002/hlca.201900255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Valentina Galli
- School of Chemistry and BiochemistryFaculty of Science and National Centre of Competence in Research (NCCR) Chemical BiologyUniversity of Geneva CH-1211 Geneva Switzerland
| | - Kalyan K. Sadhu
- School of Chemistry and BiochemistryFaculty of Science and National Centre of Competence in Research (NCCR) Chemical BiologyUniversity of Geneva CH-1211 Geneva Switzerland
| | - Daniela Masi
- School of Chemistry and BiochemistryFaculty of Science and National Centre of Competence in Research (NCCR) Chemical BiologyUniversity of Geneva CH-1211 Geneva Switzerland
| | - Jacques Saarbach
- School of Chemistry and BiochemistryFaculty of Science and National Centre of Competence in Research (NCCR) Chemical BiologyUniversity of Geneva CH-1211 Geneva Switzerland
| | - Aurélien Roux
- School of Chemistry and BiochemistryFaculty of Science and National Centre of Competence in Research (NCCR) Chemical BiologyUniversity of Geneva CH-1211 Geneva Switzerland
| | - Nicolas Winssinger
- School of Chemistry and BiochemistryFaculty of Science and National Centre of Competence in Research (NCCR) Chemical BiologyUniversity of Geneva CH-1211 Geneva Switzerland
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Salvio R, Volpi S, Folcarelli T, Casnati A, Cacciapaglia R. A calix[4]arene with acylguanidine units as an efficient catalyst for phosphodiester bond cleavage in RNA and DNA model compounds. Org Biomol Chem 2019; 17:7482-7492. [DOI: 10.1039/c9ob01141b] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Conjugated carbonyl units in a calixarene scaffold provide the right amount of flexibility for catalysis with a minimum entropic cost.
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Affiliation(s)
- Riccardo Salvio
- Dipartimento di Scienze e Tecnologie Chimiche
- Università “Tor Vergata”
- I-00133 Roma
- Italy
- ISB - CNR Sezione Meccanismi di Reazione
| | - Stefano Volpi
- Dipartimento di Scienze Chimiche
- della Vita e della Sostenibilità Ambientale
- Università degli Studi di Parma
- 43124 Parma
- Italy
| | | | - Alessandro Casnati
- Dipartimento di Scienze Chimiche
- della Vita e della Sostenibilità Ambientale
- Università degli Studi di Parma
- 43124 Parma
- Italy
| | - Roberta Cacciapaglia
- ISB - CNR Sezione Meccanismi di Reazione
- Università La Sapienza
- 00185 Roma
- Italy
- Dipartimento di Chimica
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