1
|
Tolba MM, Jabbar A, Afzal S, Mahmoud M, Zulfiqar F, El-Soudany I, Samir S, Wadan AHS, Ellakwa TE, Ellakwa DES. A promising RNA nanotechnology in clinical therapeutics: a future perspective narrative review. Future Sci OA 2023; 9:FSO883. [PMID: 37621841 PMCID: PMC10445585 DOI: 10.2144/fsoa-2023-0067] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 07/03/2023] [Indexed: 08/26/2023] Open
Abstract
Nanotechnology is the use of materials that have unique nanoscale properties. In recent years, nanotechnologies have shown promising results for human health, especially in cancer treatment. The self-assembly characteristic of RNA is a powerful bottom-up approach to the design and creation of nanostructures through interdisciplinary biological, chemical and physical techniques. The use of RNA nanotechnology in therapeutics is about to be realized. This review discusses different kinds of nano-based drug delivery systems and their characteristic features.
Collapse
Affiliation(s)
- Mahmoud M Tolba
- Pharmaceutical Division, Ministry of health & population, Faiyum, Egypt
| | - Abdul Jabbar
- Department of Veterinary Medicine, Faculty of Veterinary Science, University of Veterinary & Animal Sciences, Lahore Punjab, Pakistan
| | - Sadia Afzal
- Department of Botany, Faculty of Life Science, Women University Multan
| | | | - Farheen Zulfiqar
- Department of Food Science & Human Nutrition, University of Veterinary & Animal Sciences Lahore Punjab Pakistan
| | - Ingy El-Soudany
- Microbiology & Immunology Department, Faculty of Pharmacy, Pharos University in Alexandria, Alexandria, Egypt
| | - Salma Samir
- Genetics & Genetic engineering Department, Faculty of Agriculture, Benha University
| | | | - Takwa E Ellakwa
- Physical Chemistry, Faculty of Pharmacy, Egyptian Russian University, Egypt
| | - Doha El-Sayed Ellakwa
- Department of Biochemistry & Molecular Biology, Faculty of Pharmacy for Girls, Al-Azhar University, Cairo, Egypt
- Department of Biochemistry, Faculty of Pharmacy, Sinai University, Kantra Branch, Ismailia, Egypt
| |
Collapse
|
2
|
Bafleh WS, Abdulsamad HMR, Al-Qaraghuli SM, El Khatib RY, Elbahrawi RT, Abdukadir AM, Alsawae SM, Dimassi Z, Hamdan H, Kashir J. Applications of advances in mRNA-based platforms as therapeutics and diagnostics in reproductive technologies. Front Cell Dev Biol 2023; 11:1198848. [PMID: 37305677 PMCID: PMC10250609 DOI: 10.3389/fcell.2023.1198848] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/18/2023] [Indexed: 06/13/2023] Open
Abstract
The recent COVID-19 pandemic led to many drastic changes in not only society, law, economics, but also in science and medicine, marking for the first time when drug regulatory authorities cleared for use mRNA-based vaccines in the fight against this outbreak. However, while indeed representing a novel application of such technology in the context of vaccination medicine, introducing RNA into cells to produce resultant molecules (proteins, antibodies, etc.) is not a novel principle. It has been common practice to introduce/inject mRNA into oocytes and embryos to inhibit, induce, and identify several factors in a research context, while such aspects have also been proposed as potential therapeutic and diagnostic applications to combat infertility in humans. Herein, we describe key areas where mRNA-based platforms have thus far represented potential areas of clinical applications, describing the advantages and limitations of such applications. Finally, we also discuss how recent advances in mRNA-based platforms, driven by the recent pandemic, may stand to benefit the treatment of infertility in humans. We also present brief future directions as to how we could utilise recent and current advancements to enhance RNA therapeutics within reproductive biology, specifically with relation to oocyte and embryo delivery.
Collapse
Affiliation(s)
- Wjdan S. Bafleh
- Department of Physiology and Immunology, College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Haia M. R. Abdulsamad
- Department of Physiology and Immunology, College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Sally M. Al-Qaraghuli
- Department of Physiology and Immunology, College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Riwa Y. El Khatib
- Department of Physiology and Immunology, College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Rawdah Taha Elbahrawi
- Department of Physiology and Immunology, College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Azhar Mohamud Abdukadir
- Department of Physiology and Immunology, College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, United Arab Emirates
| | | | - Zakia Dimassi
- Department of Pediatrics, College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Hamdan Hamdan
- Department of Physiology and Immunology, College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, United Arab Emirates
- Healthcare Engineering Innovation Center (HEIC), Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Junaid Kashir
- Department of Biology, College of Arts and Science, Khalifa University, Abu Dhabi, United Arab Emirates
- Department of Comparative Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| |
Collapse
|
3
|
Jurado S, Illa O, Álvarez-Larena A, Pannecouque C, Busqué F, Alibés R. Conformationally Locked Carbocyclic Nucleosides Built on a 4'-Hydroxymethyl-3'-hydroxybicyclo[4.1.0]heptane Template. Stereoselective Synthesis and Antiviral Activity. J Org Chem 2022; 87:15166-15177. [PMID: 36300902 PMCID: PMC9680032 DOI: 10.1021/acs.joc.2c01661] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Two new families of enantiomerically pure carbocyclic nucleoside analogues based on a cyclohexane moiety with five chiral centers and a fused cyclopropyl ring have been synthesized. A highly regio- and stereoselective synthetic approach for the modular construction of the functionalized bicyclo[4.1.0]heptyl azide intermediate 6 has been established. Key steps to achieve this asymmetric synthesis involved highly diastereoselective allylic oxidation and hydroboration reactions. The first family of compounds, 1a,b and 2, presents different natural nucleobases, whereas the second one 3a-e bears functionalized 1,2,3-triazoles. These derivatives have been tested as antiviral agents, and compound 3d has shown to display moderate activity against coxsackie B4 virus.
Collapse
Affiliation(s)
- Sergio Jurado
- Departament
de Química, Universitat Autònoma
de Barcelona, Bellaterra, Barcelona 08193, Spain
| | - Ona Illa
- Departament
de Química, Universitat Autònoma
de Barcelona, Bellaterra, Barcelona 08193, Spain
| | - Angel Álvarez-Larena
- Servei
de Difracció de Raigs X, Universitat
Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
| | - Christophe Pannecouque
- Department
of Microbiology and Immunology, Laboratory of Virology and Chemotherapy,
Rega Institute for Medical Research, KU
Leuven, Herestraat 49, Leuven B-3000, Belgium
| | - Félix Busqué
- Departament
de Química, Universitat Autònoma
de Barcelona, Bellaterra, Barcelona 08193, Spain,
| | - Ramon Alibés
- Departament
de Química, Universitat Autònoma
de Barcelona, Bellaterra, Barcelona 08193, Spain,
| |
Collapse
|
4
|
Kusaka S, Yamamoto K, Shinohara M, Minato Y, Ichikawa S. Design, synthesis and conformation-activity relationship analysis of LNA/BNA-type 5'-O-aminoribosyluridine as MraY inhibitors. Bioorg Med Chem 2022; 65:116744. [PMID: 35500521 DOI: 10.1016/j.bmc.2022.116744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/03/2022] [Accepted: 04/05/2022] [Indexed: 11/02/2022]
Abstract
It is important to understand and control the biologically active conformation in medicinal chemistry. Muraymycins and caprazamycins, which are strong inhibitors of MraY, are promising antibacterial agents with a novel mode of action. Focusing on a sugar puckering and a dihedral angle ϕ of the uridine moiety of these natural products, LNA/BNA-type 5'-O-aminoribosyluridine analogues, whose puckering of the ribose moiety are completely restricted to the N-type, were designed and synthesized as simplified MraY inhibitors. Their conformation-activity relationship was further investigated in details. The conformation-activity relationship analysis investigated in this study could be a general guideline for simplification and rational drug design of MraY inhibitory nucleoside natural products.
Collapse
Affiliation(s)
- Shintaro Kusaka
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Kazuki Yamamoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Motoko Shinohara
- Department of Microbiology, Fujita Health University School of Medicine, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Yusuke Minato
- Department of Microbiology, Fujita Health University School of Medicine, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Satoshi Ichikawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan; Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan; Global Station for Biosurfaces and Drug Discovery, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan.
| |
Collapse
|
5
|
Pal S, Chandra G, Patel S, Singh S. Fluorinated Nucleosides: Synthesis, Modulation in Conformation and Therapeutic Application. CHEM REC 2022; 22:e202100335. [PMID: 35253973 DOI: 10.1002/tcr.202100335] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/22/2022] [Indexed: 12/17/2022]
Abstract
Over the last twenty years, fluorination on nucleoside has established itself as the most promising tool to use to get biologically active compounds that could sustain the clinical trial by affecting the pharmacodynamics and pharmacokinetic properties. Due to fluorine's inherent unique properties and its judicious introduction into the molecule, makes the corresponding nucleoside metabolically very stable, lipophilic, and opens a new site of intermolecular binding. Fluorination on various nucleosides has been extensively studied as a result, a series of fluorinated nucleosides come up for different therapeutic uses which are either approved by the FDA or under the advanced stage of the clinical trial. Here in this review, we are summarizing the latest development in the chemistry of fluorination on nucleoside that led to varieties of new analogs like carbocyclic, acyclic, and conformationally biased nucleoside and their biological properties, the influence of fluorine on conformation, oligonucleotide stability, and their use in therapeutics.
Collapse
Affiliation(s)
- Shantanu Pal
- School of Basic Sciences, Indian Institute of Technology, Bhubaneswar Argul, Odisha, India, 752050
| | - Girish Chandra
- Department of Chemistry, School of Physical and Chemical Sciences, Central University of South Bihar, SH-7, Gaya Panchanpur Road, Gaya, Bihar, India, 824236
| | - Samridhi Patel
- Department of Chemistry, School of Physical and Chemical Sciences, Central University of South Bihar, SH-7, Gaya Panchanpur Road, Gaya, Bihar, India, 824236
| | - Sakshi Singh
- School of Basic Sciences, Indian Institute of Technology, Bhubaneswar Argul, Odisha, India, 752050
| |
Collapse
|
6
|
Couturier S, Peyrottes S, Périgaud C. 2’‐Derivatisation of 3’‐
C‐
Methyl Pyrimidine Nucleosides. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sarah Couturier
- UMR 5247 CNRS Université Montpellier, ENSCM Institut des Biomolécules Max Mousseron (IBMM) Campus Triolet case courrier 1705, Place E. Bataillon 34095 Montpellier France
| | - Suzanne Peyrottes
- UMR 5247 CNRS Université Montpellier, ENSCM Institut des Biomolécules Max Mousseron (IBMM) Campus Triolet case courrier 1705, Place E. Bataillon 34095 Montpellier France
| | - Christian Périgaud
- UMR 5247 CNRS Université Montpellier, ENSCM Institut des Biomolécules Max Mousseron (IBMM) Campus Triolet case courrier 1705, Place E. Bataillon 34095 Montpellier France
| |
Collapse
|
7
|
Candito DA, Ye Y, Quiroz RV, Reutershan MH, Witter D, Gadamsetty SB, Li H, Saurí J, Schneider SE, Lam YH, Palte RL. Development of a Flexible and Robust Synthesis of Tetrahydrofuro[3,4- b]furan Nucleoside Analogues. J Org Chem 2021; 86:5142-5151. [PMID: 33755465 DOI: 10.1021/acs.joc.0c02969] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In the context of a PRMT5 inhibitor program, we describe our efforts to develop a flexible and robust strategy to access tetrahydrofuro[3,4-b]furan nucleoside analogues. Ultimately, it was found that a Wolfe type carboetherification from an alkenol derived from d-glucofuranose diacetonide was capable of furnishing the B-ring and installing the desired heteroaryl group in a single step. Using this approach, key intermediate 1.3-A was delivered on a gram scale in a 62% yield and 9.1:1 dr in favor of the desired S-isomer. After deprotection of 1.3-A, a late-stage glycosylation was performed under Mitsunobu conditions to install the pyrrolopyrimidine base. This provided serviceable yields of nucleoside analogues in the range of 31-48% yield. Compound 1.1-C was profiled in biochemical and cellular assays and was demonstrated to be a potent and cellularly active PRMT5 inhibitor, with a PRMT5-MEP50 biochemical IC50 of 0.8 nM, a MCF-7 target engagement EC50 of 3 nM, and a Z138 cell proliferation EC50 of 15 nM. This work sets the stage for the development of new inhibitors of PRMT5 and novel nucleoside chemical matter for alternate drug discovery programs.
Collapse
Affiliation(s)
- David A Candito
- Process Research and Development, Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Yingchun Ye
- Discovery Chemistry, Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Ryan V Quiroz
- Discovery Chemistry, Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Michael H Reutershan
- Discovery Chemistry, Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - David Witter
- Discovery Chemistry, Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Surendra B Gadamsetty
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Hongming Li
- External Capabilities, Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Josep Saurí
- Analytical Enabling Technologies, Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Sebastian E Schneider
- Computational and Structural Chemistry, Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Yu-Hong Lam
- Computational and Structural Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Rachel L Palte
- Computational and Structural Chemistry, Merck & Co., Inc., Boston, Massachusetts 02115, United States
| |
Collapse
|
8
|
Rungta P, Kumar M, Mangla P, Kumar S, Prasad AK. Chemo-enzymatic access to C-4′-hydroxyl-tetrahydrofurano-spironucleosides. NEW J CHEM 2021. [DOI: 10.1039/d0nj03253k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The biocatalytic synthesis of C-4′-hydroxyl-tetrahydrofurano-spironucleosides where the tetrahydrofuranospirocyclic ring at C-4′ position locks the furanose ring of nucleosides in the NE-conformation (C4′-exo).
Collapse
Affiliation(s)
- Pallavi Rungta
- Bioorganic Laboratory
- Department of Chemistry
- University of Delhi
- Delhi
- India
| | - Manish Kumar
- Bioorganic Laboratory
- Department of Chemistry
- University of Delhi
- Delhi
- India
| | - Priyanka Mangla
- Bioorganic Laboratory
- Department of Chemistry
- University of Delhi
- Delhi
- India
| | - Sandeep Kumar
- Bioorganic Laboratory
- Department of Chemistry
- University of Delhi
- Delhi
- India
| | - Ashok K. Prasad
- Bioorganic Laboratory
- Department of Chemistry
- University of Delhi
- Delhi
- India
| |
Collapse
|
9
|
Zheng Q, Tang S, Xiong DC, Li Q, Ye XS. Carbocyclic Ring Closure of Aryl C-Glycosides Promoted by Fluoroboric Acid. J Org Chem 2020; 85:9339-9346. [PMID: 32567318 DOI: 10.1021/acs.joc.0c00784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A novel transformation from rhamnose-type C-glycosides to 2-cyclopentenones is described. With the promotion of fluoroboric acid, C-glycosides underwent ring opening and subsequent Nazarov cyclization to afford 2-cyclopentenones in good to excellent yields. The solvent and the concentration of acid are crucial to the yield of this transformation.
Collapse
Affiliation(s)
- Qiannan Zheng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Shengbiao Tang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - De-Cai Xiong
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Qin Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Xin-Shan Ye
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| |
Collapse
|
10
|
Aher MN, Erande ND, Kumar VA, Fernandes M, Gonnade RG. Influence of fluorine substitution on the molecular conformation of 3'-deoxy-3'-fluoro-5-methyluridine. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2020; 76:346-352. [PMID: 32229715 DOI: 10.1107/s2053229620003083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 03/04/2020] [Indexed: 11/10/2022]
Abstract
Fluorine substitutions on the furanose ring of nucleosides are known to strongly influence the conformational properties of oligonucleotides. In order to assess the effect of fluorine on the conformation of 3'-deoxy-3'-fluoro-5-methyluridine (RTF), C10H13FN2O5, we studied its stereochemistry in the crystalline state using X-ray crystallography. The compound crystallizes in the chiral orthorhombic space group P212121 and contains two symmetry-independent molecules (A and B) in the asymmetric unit. The furanose ring in molecules A and B adopts conformations between envelope (2E, 2'-endo, P = 162°) and twisted (2T3, 2'-endo and 3'exo, P = 180°), with pseudorotation phase angles (P) of 164.3 and 170.2°, respectively. The maximum puckering amplitudes, νmax, for molecules A and B are 38.8 and 36.1°, respectively. In contrast, for 5-methyluridine (RTOH), the value of P is 21.2°, which is between the 3E (3'-endo, P = 18.0°) and 3T4 (3'-endo and 4'-exo, P = 36°) conformations. The value of νmax for RTOH is 41.29°. Molecules A and B of RTF generate respective helical assemblies across the crystallographic 21-screw axis through classical N-H...O aand O-H...O hydrogen bonds supplemented by C-H...O contacts. Adjacent parallel helices of both molecules are linked to each other via O-H...O and O...π interactions.
Collapse
Affiliation(s)
- Manisha N Aher
- Organic Chemistry Division, CSIR-National Chemical Laboratory, Pune 411 008, India
| | - Namrata D Erande
- National Centre for Cell Science, SPPU University Campus, Pune 411 007, India
| | - Vaijayanti A Kumar
- Organic Chemistry Division, CSIR-National Chemical Laboratory, Pune 411 008, India
| | - Moneesha Fernandes
- Organic Chemistry Division, CSIR-National Chemical Laboratory, Pune 411 008, India
| | - Rajesh G Gonnade
- Academy of Scientific and Innovative Research (AcSIR), Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201002, India
| |
Collapse
|
11
|
Calabrese C, Uriarte I, Insausti A, Vallejo-López M, Basterretxea FJ, Cochrane SA, Davis BG, Corzana F, Cocinero EJ. Observation of the Unbiased Conformers of Putative DNA-Scaffold Ribosugars. ACS CENTRAL SCIENCE 2020; 6:293-303. [PMID: 32123748 PMCID: PMC7047431 DOI: 10.1021/acscentsci.9b01277] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Indexed: 06/10/2023]
Abstract
The constitution, configuration, and flexibility of the core sugars of DNA molecules alter their function in diverse roles. Conformational itineraries of the ribofuranosides (fs) have long been known to finely determine rates of processing, yet we also know that, strikingly, semifunctional DNAs containing pyranosides (ps) or other configurations can be created, suggesting sufficient but incompletely understood plasticity. The multiple conformers involved in such processes are necessarily influenced by context and environment: solvent, hosts, ligands. Notably, however, to date the unbiased, "naked" conformers have not been experimentally determined. Here, the inherent conformational biases of DNA scaffold deoxyribosides in unsolvated and solvated forms have now been defined using gas-phase microwave and solution-phase NMR spectroscopies coupled with computational analyses and exploitation of critical differences between natural-abundance isotopologues. Serial determination of precise, individual spectra for conformers of these 25 isotopologues in alpha (α-d) and beta (β-d); pyrano (p) and furano (f) methyl 2-deoxy-d-ribosides gave not only unprecedented atomic-level resolution structures of associated conformers but also their quantitative populations. Together these experiments revealed that typical 2E and 3E conformations of the sugar found in complex DNA structures are not inherently populated. Moreover, while both OH-5' and OH-3' are constrained by intramolecular hydrogen bonding in the unnatural αf scaffold, OH-3' is "born free" in the "naked" lowest lying energy conformer of natural βf. Consequently, upon solvation, unnatural αf is strikingly less perturbable (retaining 2T1 conformation in vacuo and water) than natural βf. Unnatural αp and βp ribosides also display low conformational perturbability. These first experimental data on inherent, unbiased conformers therefore suggest that it is the background of conformational flexibility of βf that may have led to its emergence out of multiple possibilities as the sugar scaffold for "life's code" and suggest a mechanism by which the resulting freedom of OH-3' (and hence accessibility as a nucleophile) in βf may drive preferential processing and complex structure formation, such as replicative propagation of DNA from 5'-to-3'.
Collapse
Affiliation(s)
- Camilla Calabrese
- Departamento
de Química Física, Facultad de Ciencia y
Tecnología, Universidad del
País Vasco (UPV/EHU), Campus de Leioa, Ap. 644, 48080 Bilbao, Spain
- Instituto
Biofisika (CSIC, UPV/EHU), 48080 Bilbao, Spain
| | - Iciar Uriarte
- Departamento
de Química Física, Facultad de Ciencia y
Tecnología, Universidad del
País Vasco (UPV/EHU), Campus de Leioa, Ap. 644, 48080 Bilbao, Spain
- Instituto
Biofisika (CSIC, UPV/EHU), 48080 Bilbao, Spain
| | - Aran Insausti
- Departamento
de Química Física, Facultad de Ciencia y
Tecnología, Universidad del
País Vasco (UPV/EHU), Campus de Leioa, Ap. 644, 48080 Bilbao, Spain
- Instituto
Biofisika (CSIC, UPV/EHU), 48080 Bilbao, Spain
| | - Montserrat Vallejo-López
- Departamento
de Química Física, Facultad de Ciencia y
Tecnología, Universidad del
País Vasco (UPV/EHU), Campus de Leioa, Ap. 644, 48080 Bilbao, Spain
| | - Francisco J. Basterretxea
- Departamento
de Química Física, Facultad de Ciencia y
Tecnología, Universidad del
País Vasco (UPV/EHU), Campus de Leioa, Ap. 644, 48080 Bilbao, Spain
| | - Stephen A. Cochrane
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Benjamin G. Davis
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, United Kingdom
- The
Rosalind Franklin Institute, Oxfordshire, OX11 0FA, United Kingdom
| | - Francisco Corzana
- Departamento
de Química, Centro de Investigación en Síntesis
Química, Universidad de La
Rioja, 26006 Logroño, Spain
| | - Emilio J. Cocinero
- Departamento
de Química Física, Facultad de Ciencia y
Tecnología, Universidad del
País Vasco (UPV/EHU), Campus de Leioa, Ap. 644, 48080 Bilbao, Spain
- Instituto
Biofisika (CSIC, UPV/EHU), 48080 Bilbao, Spain
| |
Collapse
|
12
|
Fujisaka A, Hari Y, Takuma H, Rahman SMA, Yoshikawa H, Pang J, Imanishi T, Obika S. Effective syntheses of 2',4'-BNA NC monomers bearing adenine, guanine, thymine, and 5-methylcytosine, and the properties of oligonucleotides fully modified with 2',4'-BNA NC. Bioorg Med Chem 2019; 27:1728-1741. [PMID: 30862430 DOI: 10.1016/j.bmc.2019.02.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 02/15/2019] [Accepted: 02/16/2019] [Indexed: 12/11/2022]
Abstract
We efficiently synthesized 2'-O,4'-C-aminomethylene-bridged nucleic acid (2',4'-BNANC) monomers bearing the four nucleobases, guanine, adenine, thymine, and 5-methylcytosine and incorporated these monomers into oligonucleotides. Initially, we carried out the transglycosylation reaction on several 2'-O-substituted 5-methyluridines to evaluate the effects of 2'-substitutions on this reaction. Under the optimized conditions, purine nucleobases were successfully introduced, and 2',4'-BNANC monomers bearing adenine or guanine were obtained over several steps. In addition, the improved synthesis of the 2',4'-BNANC monomers bearing thymine or 5-methylcytosine was also achieved. The obtained 2',4'-BNANC monomers were subsequently incorporated into oligonucleotides and the duplex-forming abilities of the modified oligonucleotides were investigated. Duplexes containing 2',4'-BNANC monomers in both or either strands were found to possess excellent thermal stabilities.
Collapse
Affiliation(s)
- Aki Fujisaka
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; Faculty of Pharmacy, Osaka Ohtani University, Nishikiori-Kita 3-11-1, Tondabayashi, Osaka 584-8540, Japan
| | - Yoshiyuki Hari
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima 770-8514, Japan
| | - Hiroko Takuma
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - S M Abdur Rahman
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; Department of Clinical Pharmacy & Pharmacology, Faculty of Pharmacy, University of Dhaka, Dhaka 1000, Bangladesh
| | - Haruhisa Yoshikawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; BNA Inc, 7-7-20 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Juanjuan Pang
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takeshi Imanishi
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; BNA Inc, 7-7-20 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| |
Collapse
|
13
|
Iannazzo L, Fonvielle M, Braud E, Hřebabecký H, Procházková E, Nencka R, Mathé C, Arthur M, Etheve-Quelquejeu M. Synthesis of tRNA analogues containing a terminal ribose locked in the South conformation to study tRNA-dependent enzymes. Org Biomol Chem 2019; 16:1903-1911. [PMID: 29484333 DOI: 10.1039/c8ob00019k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report here the synthetic route of two constrained dinucleotides and the determination of the sugar puckering by NMR analyses of the starting nucleosides. Enzymatic ligation to microhelix-RNAs provide access to tRNA analogues containing a 3' terminal A76 locked in South conformation. Biological evaluation of our tRNA analogues has been performed using amino-acyl tRNA-dependent transferase FemXWv, which mediates non-ribosomal incorporation of amino acids into the bacterial cell wall. We have shown that our tRNA analogues inhibited the aminoacyl transfer reaction catalyzed by FemXWv with IC50s of 10 and 8 μM. These results indicate that FemXWv displays a moderate preference for tRNAs containing a terminal A76 locked in the South conformation and that a South to North switch in the conformation of the terminal ribose might contribute to the release of the uncharged tRNAAla product of the aminoacyl transfer reaction catalyzed by FemXwv.
Collapse
Affiliation(s)
- Laura Iannazzo
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, UMR 8601, Paris, F-75005, France
| | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Rana N, Kumar M, Singh A, Maity J, Shukla P, Prasad AK. Synthesis of novel 3'-azido-3'-deoxy-α-L-ribo configured nucleosides: A comparative study between chemical and chemo-enzymatic methodologies. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2018; 37:217-231. [PMID: 29723115 DOI: 10.1080/15257770.2018.1460476] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Syntheses of novel 3'-azido-3'-deoxy-2'-O,4'-C-methylene-α-L-ribofuranosyl nucleosides have been carried out from 3'-azido-3'-deoxy-4'-C-hydroxymethyl-β-D-xylofuranosyl nucleosides following both chemical and chemo-enzymatic methodologies. The precursor nucleoside in turn was synthesized from a common glycosyl donor 4-C-acetoxymethyl-1,2,5-tri-O-acetyl-3-azido-3-deoxy-α,β-D-xylofuranose, which was obtained by the acetolysis of 4-C-acetoxymethyl-5-O-acetyl-3-azido-3-deoxy-1,2-O-isopropylidene-α-D-xylofuranose in 96% yield. It has been observed that a chemo-enzymatic pathway for the synthesis of targeted nucleosides is much more efficient than a chemical pathway, leading to the improvement in yield for the synthesis of 3'-azido-3'-deoxy-α-L-ribofuranosyl thymine and uracil from 49 to 89% and 55 to 93%, respectively.
Collapse
Affiliation(s)
- Neha Rana
- a Bioorganic Laboratory, Department of Chemistry , University of Delhi , Delhi , India
| | - Manish Kumar
- a Bioorganic Laboratory, Department of Chemistry , University of Delhi , Delhi , India
| | - Ankita Singh
- a Bioorganic Laboratory, Department of Chemistry , University of Delhi , Delhi , India
| | - Jyotirmoy Maity
- a Bioorganic Laboratory, Department of Chemistry , University of Delhi , Delhi , India
| | - Poonam Shukla
- a Bioorganic Laboratory, Department of Chemistry , University of Delhi , Delhi , India
| | - Ashok K Prasad
- a Bioorganic Laboratory, Department of Chemistry , University of Delhi , Delhi , India
| |
Collapse
|
15
|
Chaudhary V, Jangra S, Yadav NR. Nanotechnology based approaches for detection and delivery of microRNA in healthcare and crop protection. J Nanobiotechnology 2018; 16:40. [PMID: 29653577 PMCID: PMC5897953 DOI: 10.1186/s12951-018-0368-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 04/07/2018] [Indexed: 12/31/2022] Open
Abstract
Nanobiotechnology has the potential to revolutionize diverse sectors including medicine, agriculture, food, textile and pharmaceuticals. Disease diagnostics, therapeutics and crop protection strategies are fast emerging using nanomaterials preferably nanobiomaterials. It has potential for development of novel nanobiomolecules which offer several advantages over conventional treatment methods. RNA nanoparticles with many unique features are promising candidates in disease treatment. The miRNAs are involved in many biochemical and developmental pathways and their regulation in plants and animals. These appear to be a powerful tool for controlling various pathological diseases in human, plants and animals, however there are challenges associated with miRNA based nanotechnology. Several advancements made in the field of miRNA therapeutics make it an attractive approach, but a lot more has to be explored in nanotechnology assisted miRNA therapy. The miRNA based technologies can be employed for detection and combating crop diseases as well. Despite these potential advantages, nanobiotechnology applications in the agricultural sector are still in its infancy and have not yet made its mark in comparison with healthcare sector. The review provides a platform to discuss nature, role and use of miRNAs in nanobiotechnology applications.
Collapse
Affiliation(s)
- Vrantika Chaudhary
- Department of Molecular Biology, Biotechnology and Bioinformatics, CCS Haryana Agricultural University, Hisar, 125004 India
| | - Sumit Jangra
- Department of Molecular Biology, Biotechnology and Bioinformatics, CCS Haryana Agricultural University, Hisar, 125004 India
| | - Neelam R. Yadav
- Department of Molecular Biology, Biotechnology and Bioinformatics, CCS Haryana Agricultural University, Hisar, 125004 India
| |
Collapse
|
16
|
Hřebabecký H, Dračínský M, Procházková E, Šála M, Mackman R, Nencka R. Control of α/β Anomer Formation by a 2',5' Bridge: Toward Nucleoside Derivatives Locked in the South Conformation. J Org Chem 2017; 82:11337-11347. [PMID: 28972760 DOI: 10.1021/acs.joc.7b01000] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We describe a novel stereoselective synthesis of nucleoside derivatives with the ribose ring locked in the South conformation by a bridge between C2' and C5'. Despite the intrinsic constraints of the bicyclic structure, we demonstrate that their synthesis can be achieved by ring closing metathesis of readily accessible precursors. The obtained ribose derivatives are, however, very poor substrates for further installation of the nucleobases, and even simple nucleophiles, such as azido or cyano anions, react with unexpected stereo- or regioselectivity under standard glycosylation conditions. Here we explain this behavior by employing density functional theory (DFT) computations and devise an alternative approach resulting in isomers with the desired orientation of the nucleobase.
Collapse
Affiliation(s)
- Hubert Hřebabecký
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , v.v.i, Gilead Sciences & IOCB Research Centre, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , v.v.i, Gilead Sciences & IOCB Research Centre, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Eliška Procházková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , v.v.i, Gilead Sciences & IOCB Research Centre, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Michal Šála
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , v.v.i, Gilead Sciences & IOCB Research Centre, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Richard Mackman
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Radim Nencka
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , v.v.i, Gilead Sciences & IOCB Research Centre, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| |
Collapse
|
17
|
Abstract
Focusing on the recent literature (since 2000), this review outlines the main synthetic approaches for the preparation of 5'-mono-, 5'-di-, and 5'-triphosphorylated nucleosides, also known as nucleotides, as well as several derivatives, namely, cyclic nucleotides and dinucleotides, dinucleoside 5',5'-polyphosphates, sugar nucleotides, and nucleolipids. Endogenous nucleotides and their analogues can be obtained enzymatically, which is often restricted to natural substrates, or chemically. In chemical synthesis, protected or unprotected nucleosides can be used as the starting material, depending on the nature of the reagents selected from P(III) or P(V) species. Both solution-phase and solid-support syntheses have been developed and are reported here. Although a considerable amount of research has been conducted in this field, further work is required because chemists are still faced with the challenge of developing a universal methodology that is compatible with a large variety of nucleoside analogues.
Collapse
Affiliation(s)
- Béatrice Roy
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier, ENSCM , Campus Triolet, cc 1705, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Anaïs Depaix
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier, ENSCM , Campus Triolet, cc 1705, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Christian Périgaud
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier, ENSCM , Campus Triolet, cc 1705, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Suzanne Peyrottes
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier, ENSCM , Campus Triolet, cc 1705, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| |
Collapse
|
18
|
Affiliation(s)
- Sophie Racine
- Ecole polytechnique fédérale de Lausanne; Institut des sciences et ingénierie chimiques; SB ISIC LCSO, EPFL CH-1015 Lausanne Switzerland
| | - Jérémy Vuilleumier
- Ecole polytechnique fédérale de Lausanne; Institut des sciences et ingénierie chimiques; SB ISIC LCSO, EPFL CH-1015 Lausanne Switzerland
| | - Jérôme Waser
- Ecole polytechnique fédérale de Lausanne; Institut des sciences et ingénierie chimiques; SB ISIC LCSO, EPFL CH-1015 Lausanne Switzerland
| |
Collapse
|
19
|
Shu D, Li H, Shu Y, Xiong G, Carson WE, Haque F, Xu R, Guo P. Systemic Delivery of Anti-miRNA for Suppression of Triple Negative Breast Cancer Utilizing RNA Nanotechnology. ACS NANO 2015; 9:9731-40. [PMID: 26387848 PMCID: PMC4723066 DOI: 10.1021/acsnano.5b02471] [Citation(s) in RCA: 189] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 09/05/2015] [Indexed: 05/20/2023]
Abstract
MicroRNAs play important roles in regulating the gene expression and life cycle of cancer cells. In particular, miR-21, an oncogenic miRNA is a major player involved in tumor initiation, progression, invasion and metastasis in several cancers, including triple negative breast cancer (TNBC). However, delivery of therapeutic miRNA or anti-miRNA specifically into cancer cells in vivo without collateral damage to healthy cells remains challenging. We report here the application of RNA nanotechnology for specific and efficient delivery of anti-miR-21 to block the growth of TNBC in orthotopic mouse models. The 15 nm therapeutic RNA nanoparticles contains the 58-nucleotide (nt) phi29 pRNA-3WJ as a core, a 8-nt sequence complementary to the seed region of miR-21, and a 39-nt epidermal growth factor receptor (EGFR) targeting aptamer for internalizing RNA nanoparticles into cancer cells via receptor mediated endocytosis. The RNase resistant and thermodynamically stable RNA nanoparticles remained intact after systemic injection into mice and strongly bound to tumors with little or no accumulation in healthy organs 8 h postinjection, and subsequently repressed tumor growth at low doses. The observed specific cancer targeting and tumor regression is a result of several key attributes of RNA nanoparticles: anionic charge which disallows nonspecific passage across negatively charged cell membrane; "active" targeting using RNA aptamers which increases the homing of RNA nanoparticles to cancer cells; nanoscale size and shape which avoids rapid renal clearance and engulfment by lung macrophages and liver Kupffer cells; favorable biodistribution profiles with little accumulation in healthy organs, which minimizes nonspecific side effects; and favorable pharmacokinetic profiles with extended in vivo half-life. The results demonstrate the clinical potentials of RNA nanotechnology based platform to deliver miRNA based therapeutics for cancer treatment.
Collapse
Affiliation(s)
- Dan Shu
- Nanobiotechnology Center, Markey Cancer Center, Department of Pharmaceutical Sciences, Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, Kentucky 40536, United States
- Address correspondence to ,
| | - Hui Li
- Nanobiotechnology Center, Markey Cancer Center, Department of Pharmaceutical Sciences, Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Yi Shu
- Nanobiotechnology Center, Markey Cancer Center, Department of Pharmaceutical Sciences, Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Gaofeng Xiong
- Nanobiotechnology Center, Markey Cancer Center, Department of Pharmaceutical Sciences, Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, Kentucky 40536, United States
| | - William E. Carson
- OSU Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Farzin Haque
- Nanobiotechnology Center, Markey Cancer Center, Department of Pharmaceutical Sciences, Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Ren Xu
- Nanobiotechnology Center, Markey Cancer Center, Department of Pharmaceutical Sciences, Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Peixuan Guo
- Nanobiotechnology Center, Markey Cancer Center, Department of Pharmaceutical Sciences, Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, Kentucky 40536, United States
- Address correspondence to ,
| |
Collapse
|
20
|
Fakhfakh K, Marais O, Cheng XBJ, Castañeda JR, Hughesman CB, Haynes C. Molecular thermodynamics of LNA:LNA base pairs and the hyperstabilizing effect of 5′-proximal LNA:DNA base pairs. AIChE J 2015. [DOI: 10.1002/aic.14916] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Kareem Fakhfakh
- Michael Smith Laboratories, University of British Columbia; Vancouver BC Canada
- Dept. of Chemical and Biological Engineering; University of British Columbia; Vancouver BC Canada
| | - Olivia Marais
- Dept. of Chemical and Biological Engineering; University of British Columbia; Vancouver BC Canada
| | - Xin Bo Justin Cheng
- Dept. of Chemical and Biological Engineering; University of British Columbia; Vancouver BC Canada
| | - Jorge Real Castañeda
- Dept. of Chemical and Biological Engineering; University of British Columbia; Vancouver BC Canada
| | - Curtis B. Hughesman
- Michael Smith Laboratories, University of British Columbia; Vancouver BC Canada
| | - Charles Haynes
- Michael Smith Laboratories, University of British Columbia; Vancouver BC Canada
- Dept. of Chemical and Biological Engineering; University of British Columbia; Vancouver BC Canada
- RES'EAU Water Research Network, Dept. of Chemical and Biological Engineering; University of British Columbia; Vancouver BC Canada
| |
Collapse
|
21
|
Conformational restriction: an effective tactic in 'follow-on'-based drug discovery. Future Med Chem 2015; 6:885-901. [PMID: 24962281 DOI: 10.4155/fmc.14.50] [Citation(s) in RCA: 154] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The conformational restriction (rigidification) of a flexible ligand has often been a commonly used strategy in drug design, as it can minimize the entropic loss associated with the ligand adopting a preferred conformation for binding, which leads to enhanced potency for a given physiological target, improved selectivity for isoforms and reduced the possibility of drug metabolism. Therefore, the application of conformational restriction strategy is a core aspect of drug discovery and development that is widely practiced by medicinal chemists either deliberately or subliminally. The present review will highlight current representative examples and a brief overview on the rational design of conformationally restricted agents as well as discuss its advantages over the flexible counterparts.
Collapse
|
22
|
Panda A, Das S, Pal S. Highly regio- and diastereoselective, acidic clay supported intramolecular nitrile oxide–alkene cycloaddition on d-ribose derived nitriles: an efficient synthetic route to isoxazoline fused five and six membered carbocycles. Carbohydr Res 2014; 398:13-8. [DOI: 10.1016/j.carres.2014.06.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 06/02/2014] [Accepted: 06/06/2014] [Indexed: 12/19/2022]
|
23
|
Zaed AM, Grafton MW, Ahmad S, Sutherland A. Asymmetric synthesis of cis-aminocyclopentenols, building blocks for medicinal chemistry. J Org Chem 2014; 79:1511-5. [PMID: 24386912 DOI: 10.1021/jo402712r] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A highly efficient one-pot multistep process involving an asymmetric Pd(II)-catalyzed Overman rearrangement and a Ru(II)-catalyzed ring-closing metathesis reaction has been developed for the preparation of (R)- or (S)-aminocyclopenta-2-enes. The rapid strategy employed and the relatively mild conditions of the one-pot process allowed the multigram synthesis of the carbocycles in high enantiomeric excess (92% ee). The synthetic utility of these compounds was demonstrated by the stereoselective incorporation of hydroxyl groups, generating cis-4- and cis-5-aminocyclopenta-2-en-1-ols, important building blocks for medicinal chemistry.
Collapse
|
24
|
3′-Amino-5′-carboxymethyl-3′,5′-dideoxy nucleosides for the synthesis of fully amide-linked RNA mimics. Tetrahedron 2014. [DOI: 10.1016/j.tet.2014.06.119] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
25
|
Kaci M, Uttaro JP, Lefort V, Mathé C, El Amri C, Périgaud C. Synthesis of {[5-(adenin-9-yl)-2-furyl]methoxy}methyl phosphonic acid and evaluations against human adenylate kinases. Bioorg Med Chem Lett 2014; 24:4227-30. [DOI: 10.1016/j.bmcl.2014.07.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 07/11/2014] [Accepted: 07/12/2014] [Indexed: 01/29/2023]
|
26
|
Synthesis of (Carbo)nucleoside Analogues by [3+2] Annulation of Aminocyclopropanes. Angew Chem Int Ed Engl 2014; 53:8484-7. [DOI: 10.1002/anie.201404832] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Indexed: 11/07/2022]
|
27
|
Racine S, de Nanteuil F, Serrano E, Waser J. Synthesis of (Carbo)nucleoside Analogues by [3+2] Annulation of Aminocyclopropanes. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201404832] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
28
|
Nguyen HV, Sallustrau A, Balzarini J, Bedford MR, Eden JC, Georgousi N, Hodges NJ, Kedge J, Mehellou Y, Tselepis C, Tucker JHR. Organometallic nucleoside analogues with ferrocenyl linker groups: synthesis and cancer cell line studies. J Med Chem 2014; 57:5817-22. [PMID: 24905419 DOI: 10.1021/jm500246h] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Examples of organometallic compounds as nucleoside analogues are rare within the field of medicinal bioorganometallic chemistry. We report on the synthesis and properties of two chiral ferrocene derivatives containing a nucleobase and a hydroxyalkyl group. These so-called ferronucleosides show promising anticancer activity, with cytostatic studies on five different cancer cell lines indicating that both functional groups are required for optimal activity.
Collapse
Affiliation(s)
- Huy V Nguyen
- School of Chemistry, ‡School of Cancer Sciences, College of Medical and Dental Sciences, §School of Biosciences, College of Life and Environmental Sciences, and ∥School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham , Edgbaston, Birmingham, B15 2TT, U.K
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Synthesis and Anti-HIV Activity of Triazolo-Fused, Medium-Sized Cyclic Nucleoside Analogs Prepared by an IntramolecularHuisgen1,3-Dipolar Cycloaddition. Helv Chim Acta 2014. [DOI: 10.1002/hlca.201300289] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
30
|
Shu Y, Pi F, Sharma A, Rajabi M, Haque F, Shu D, Leggas M, Evers BM, Guo P. Stable RNA nanoparticles as potential new generation drugs for cancer therapy. Adv Drug Deliv Rev 2014; 66:74-89. [PMID: 24270010 DOI: 10.1016/j.addr.2013.11.006] [Citation(s) in RCA: 181] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 10/11/2013] [Accepted: 11/13/2013] [Indexed: 12/13/2022]
Abstract
Human genome sequencing revealed that only ~1.5% of the DNA sequence coded for proteins. More and more evidence has uncovered that a substantial part of the 98.5% so-called "junk" DNAs actually code for noncoding RNAs. Two milestones, chemical drugs and protein drugs, have already appeared in the history of drug development, and it is expected that the third milestone in drug development will be RNA drugs or drugs that target RNA. This review focuses on the development of RNA therapeutics for potential cancer treatment by applying RNA nanotechnology. A therapeutic RNA nanoparticle is unique in that its scaffold, ligand, and therapeutic component can all be composed of RNA. The special physicochemical properties lend to the delivery of siRNA, miRNA, ribozymes, or riboswitches; imaging using fluogenenic RNA; and targeting using RNA aptamers. With recent advances in solving the chemical, enzymatic, and thermodynamic stability issues, RNA nanoparticles have been found to be advantageous for in vivo applications due to their uniform nano-scale size, precise stoichiometry, polyvalent nature, low immunogenicity, low toxicity, and target specificity. In vivo animal studies have revealed that RNA nanoparticles can specifically target tumors with favorable pharmacokinetic and pharmacodynamic parameters without unwanted accumulation in normal organs. This review summarizes the key studies that have led to the detailed understanding of RNA nanoparticle formation as well as chemical and thermodynamic stability issue. The methods for RNA nanoparticle construction, and the current challenges in the clinical application of RNA nanotechnology, such as endosome trapping and production costs, are also discussed.
Collapse
Affiliation(s)
- Yi Shu
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Fengmei Pi
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Ashwani Sharma
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Mehdi Rajabi
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Farzin Haque
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Dan Shu
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Markos Leggas
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - B Mark Evers
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Peixuan Guo
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA.
| |
Collapse
|
31
|
New carbocyclic nucleoside analogues with a bicyclo[2.2.1]heptane fragment as sugar moiety; Synthesis, X-ray crystallography and anticancer activity. Bioorg Med Chem 2014; 22:513-22. [DOI: 10.1016/j.bmc.2013.10.056] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 10/23/2013] [Accepted: 10/31/2013] [Indexed: 11/15/2022]
|
32
|
Hervé G, Sartori G, Enderlin G, Mackenzie G, Len C. Palladium-catalyzed Suzuki reaction in aqueous solvents applied to unprotected nucleosides and nucleotides. RSC Adv 2014. [DOI: 10.1039/c3ra47911k] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Nucleoside analogues have attracted much attention due to their potential biological activities.
Collapse
Affiliation(s)
- Gwénaëlle Hervé
- Transformations Intégrées de la Matière Renouvelable
- UTC-ESCOM
- Centre de Recherche Royallieu
- F-60200 Compiègne, France
| | - Guillaume Sartori
- Transformations Intégrées de la Matière Renouvelable
- UTC-ESCOM
- Centre de Recherche Royallieu
- F-60200 Compiègne, France
| | - Gérald Enderlin
- Transformations Intégrées de la Matière Renouvelable
- UTC-ESCOM
- Centre de Recherche Royallieu
- F-60200 Compiègne, France
| | | | - Christophe Len
- Transformations Intégrées de la Matière Renouvelable
- UTC-ESCOM
- Centre de Recherche Royallieu
- F-60200 Compiègne, France
| |
Collapse
|
33
|
Qiu M, Khisamutdinov E, Zhao Z, Pan C, Choi JW, Leontis NB, Guo P. RNA nanotechnology for computer design and in vivo computation. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2013; 371:20120310. [PMID: 24000362 PMCID: PMC3758167 DOI: 10.1098/rsta.2012.0310] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Molecular-scale computing has been explored since 1989 owing to the foreseeable limitation of Moore's law for silicon-based computation devices. With the potential of massive parallelism, low energy consumption and capability of working in vivo, molecular-scale computing promises a new computational paradigm. Inspired by the concepts from the electronic computer, DNA computing has realized basic Boolean functions and has progressed into multi-layered circuits. Recently, RNA nanotechnology has emerged as an alternative approach. Owing to the newly discovered thermodynamic stability of a special RNA motif (Shu et al. 2011 Nat. Nanotechnol. 6, 658-667 (doi:10.1038/nnano.2011.105)), RNA nanoparticles are emerging as another promising medium for nanodevice and nanomedicine as well as molecular-scale computing. Like DNA, RNA sequences can be designed to form desired secondary structures in a straightforward manner, but RNA is structurally more versatile and more thermodynamically stable owing to its non-canonical base-pairing, tertiary interactions and base-stacking property. A 90-nucleotide RNA can exhibit 4⁹⁰ nanostructures, and its loops and tertiary architecture can serve as a mounting dovetail that eliminates the need for external linking dowels. Its enzymatic and fluorogenic activity creates diversity in computational design. Varieties of small RNA can work cooperatively, synergistically or antagonistically to carry out computational logic circuits. The riboswitch and enzymatic ribozyme activities and its special in vivo attributes offer a great potential for in vivo computation. Unique features in transcription, termination, self-assembly, self-processing and acid resistance enable in vivo production of RNA nanoparticles that harbour various regulators for intracellular manipulation. With all these advantages, RNA computation is promising, but it is still in its infancy. Many challenges still exist. Collaborations between RNA nanotechnologists and computer scientists are necessary to advance this nascent technology.
Collapse
Affiliation(s)
- Meikang Qiu
- Department of Computer Engineering, San Jose State University, San Jose, CA 95192, USA
| | - Emil Khisamutdinov
- Department of Pharmaceutical Science, University of Kentucky, Lexington, KY 40506, USA
| | - Zhengyi Zhao
- Department of Pharmaceutical Science, University of Kentucky, Lexington, KY 40506, USA
| | - Cheryl Pan
- Department of Electrical and Computer Engineering, University of Kentucky, Lexington, KY 40506, USA
| | - Jeong-Woo Choi
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul 121-742, Korea
| | - Neocles B. Leontis
- Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Peixuan Guo
- Department of Pharmaceutical Science, University of Kentucky, Lexington, KY 40506, USA
| |
Collapse
|
34
|
Guo P, Haque F, Hallahan B, Reif R, Li H. Uniqueness, advantages, challenges, solutions, and perspectives in therapeutics applying RNA nanotechnology. Nucleic Acid Ther 2012; 22:226-45. [PMID: 22913595 DOI: 10.1089/nat.2012.0350] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The field of RNA nanotechnology is rapidly emerging. RNA can be manipulated with the simplicity characteristic of DNA to produce nanoparticles with a diversity of quaternary structures by self-assembly. Additionally RNA is tremendously versatile in its function and some RNA molecules display catalytic activities much like proteins. Thus, RNA has the advantage of both worlds. However, the instability of RNA has made many scientists flinch away from RNA nanotechnology. Other concerns that have deterred the progress of RNA therapeutics include the induction of interferons, stimulation of cytokines, and activation of other immune systems, as well as short pharmacokinetic profiles in vivo. This review will provide some solutions and perspectives on the chemical and thermodynamic stability, in vivo half-life and biodistribution, yield and production cost, in vivo toxicity and side effect, specific delivery and targeting, as well as endosomal trapping and escape.
Collapse
Affiliation(s)
- Peixuan Guo
- Nanobiotechnology Center, Markey Cancer Center and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40536, USA.
| | | | | | | | | |
Collapse
|
35
|
Erande N, Gunjal AD, Fernandes M, Gonnade R, Kumar VA. Synthesis and structural studies of S-type/N-type-locked/frozen nucleoside analogues and their incorporation in RNA-selective, nuclease resistant 2'-5' linked oligonucleotides. Org Biomol Chem 2012; 11:746-57. [PMID: 23223853 DOI: 10.1039/c2ob26762d] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
2'-endo locked or frozen (S-type)/3'-endo locked or frozen (N-type) nucleoside analogues were synthesized. Conformational analysis based on (3)J(HH) and NOE measurements is presented which is further confirmed by X-ray crystal structural studies. 2'-5'isoDNA oligonucleotides (ON) were synthesized using these modified nucleoside analogues and UV-T(m) studies of the resultant 2'-5'isoDNA : RNA duplexes reflect the site- and sequence-dependent effects and confirm that the S-type sugar conformations were preferred over the N-type sugar geometry in such duplexes.
Collapse
Affiliation(s)
- Namrata Erande
- Organic Chemistry Division, CSIR-National Chemical Laboratory, Homi Bhabha Road, Pune 411008, India
| | | | | | | | | |
Collapse
|
36
|
Taha HA, Richards MR, Lowary TL. Conformational Analysis of Furanoside-Containing Mono- and Oligosaccharides. Chem Rev 2012; 113:1851-76. [DOI: 10.1021/cr300249c] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Hashem A. Taha
- Alberta Glycomics Centre and Department of Chemistry, Gunning−Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2
| | - Michele R. Richards
- Alberta Glycomics Centre and Department of Chemistry, Gunning−Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2
| | - Todd L. Lowary
- Alberta Glycomics Centre and Department of Chemistry, Gunning−Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2
| |
Collapse
|
37
|
Guo P, Haque F, Hallahan B, Reif R, Li H. Uniqueness, advantages, challenges, solutions, and perspectives in therapeutics applying RNA nanotechnology. Nucleic Acid Ther 2012. [PMID: 22913595 DOI: 10.1201/b15152-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023] Open
Abstract
The field of RNA nanotechnology is rapidly emerging. RNA can be manipulated with the simplicity characteristic of DNA to produce nanoparticles with a diversity of quaternary structures by self-assembly. Additionally RNA is tremendously versatile in its function and some RNA molecules display catalytic activities much like proteins. Thus, RNA has the advantage of both worlds. However, the instability of RNA has made many scientists flinch away from RNA nanotechnology. Other concerns that have deterred the progress of RNA therapeutics include the induction of interferons, stimulation of cytokines, and activation of other immune systems, as well as short pharmacokinetic profiles in vivo. This review will provide some solutions and perspectives on the chemical and thermodynamic stability, in vivo half-life and biodistribution, yield and production cost, in vivo toxicity and side effect, specific delivery and targeting, as well as endosomal trapping and escape.
Collapse
Affiliation(s)
- Peixuan Guo
- Nanobiotechnology Center, Markey Cancer Center and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40536, USA.
| | | | | | | | | |
Collapse
|
38
|
Zhou C, Chattopadhyaya J. Intramolecular free-radical cyclization reactions on pentose sugars for the synthesis of carba-LNA and carba-ENA and the application of their modified oligonucleotides as potential RNA targeted therapeutics. Chem Rev 2012; 112:3808-32. [PMID: 22530946 DOI: 10.1021/cr100306q] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Chuanzheng Zhou
- Chemical Biology Program, Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Sweden
| | | |
Collapse
|
39
|
Figueras A, Miralles-Llumà R, Flores R, Rustullet A, Busqué F, Figueredo M, Font J, Alibés R, Maréchal JD. Synthesis, Anti-HIV Activity Studies, and in silico Rationalization of Cyclobutane-Fused Nucleosides. ChemMedChem 2012; 7:1044-56. [DOI: 10.1002/cmdc.201200059] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Indexed: 12/22/2022]
|
40
|
Pallan PS, Marquez VE, Egli M. The conformationally constrained N-methanocarba-dT analogue adopts an unexpected C4'-exo sugar pucker in the structure of a DNA hairpin. Biochemistry 2012; 51:2639-41. [PMID: 22409313 DOI: 10.1021/bi300215k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Incorporation of a bicyclo[3.1.0]hexane scaffold into the nucleoside sugar was devised to lock the embedded cyclopentane ring in conformations that mimic the furanose North and South sugar puckers. To analyze the effects of North-methanocarba-2'-deoxythymidine (N-MCdT) on the B-form DNA, we crystallized d(CGCGAA[mcTmcT]CGCG) with two N-MCdTs. Instead of a duplex, the 12mer forms a tetraloop hairpin, whereby loop N-MCdTs adopt the C4'-exo pucker (NE; P = 50°). Thus, the bicyclic framework does not limit the pucker to the anticipated C2'-exo range (NNW; P = -18°).
Collapse
Affiliation(s)
- Pradeep S Pallan
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232, United States
| | | | | |
Collapse
|
41
|
Savion M, Memeo MG, Bovio B, Grazioso G, Legnani L, Quadrelli P. Synthesis and molecular modeling of novel dihydroxycyclopentane-carbonitrile nor-nucleosides by bromonitrile oxide 1,3-dipolar cycloaddition. Tetrahedron 2012. [DOI: 10.1016/j.tet.2011.12.086] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
42
|
Mukherjee S, Mandal SB, Bhattacharjya A. Carbohydrate nitrone and nitrile oxide cycloaddition approach to chiral sulfur heterocycles and nucleosides. RSC Adv 2012. [DOI: 10.1039/c2ra20689g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
|
43
|
Shelton JR, Cutler CE, Oliveira M, Balzarini J, Peterson MA. Synthesis, SAR, and preliminary mechanistic evaluation of novel antiproliferative N6,5′-bis-ureido- and 5′-carbamoyl-N6-ureidoadenosine derivatives. Bioorg Med Chem 2012; 20:1008-19. [DOI: 10.1016/j.bmc.2011.11.043] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Revised: 11/19/2011] [Accepted: 11/19/2011] [Indexed: 01/26/2023]
|
44
|
Hatton W, Hunault J, Egorov M, Len C, Pipelier M, Blot V, Silvestre V, Fargeas V, Ané A, McBrayer T, Detorio M, Cho JH, Bourgougnon N, Dubreuil D, Schinazi RF, Lebreton J. Synthesis and Biological Evaluation of 4'- C,3'- O-Propylene-Linked Bicyclic Nucleosides. European J Org Chem 2011; 2011:7390-7399. [PMID: 34566488 DOI: 10.1002/ejoc.201100859] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
A set of pyrimidine nucleosides fused with a 4'-C,3'-O-propylene bridge was successfully synthesised in 12 steps from 1,2:5,6-di-O-isopropylidene-α-d-glucofuranose, an inexpensive starting material, based on a ring-closing metathesis (RCM) reaction followed by Vorbrüggen-type nucleobase coupling. Antiviral and cytotoxicity activities of the targeted modified nucleosides, as well as their phosphoramidate prodrugs, are described.
Collapse
Affiliation(s)
- Wilfried Hatton
- Université de Nantes, CNRS, Laboratoire CEISAM-UMR 6230, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - Julie Hunault
- Université de Nantes, CNRS, Laboratoire CEISAM-UMR 6230, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - Maxim Egorov
- Université de Nantes, CNRS, Laboratoire CEISAM-UMR 6230, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - Christophe Len
- Université de Technologie de Compiègne, Ecole Supérieure de Chimie Organique Minérale, EA 4297, Transformations Intégrées de la Matière Renouvelable, 1 allée du Réseau Jean-Marie Buckmaster, 60200 Compiègne, France
| | - Muriel Pipelier
- Université de Nantes, CNRS, Laboratoire CEISAM-UMR 6230, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - Virginie Blot
- Université de Nantes, CNRS, Laboratoire CEISAM-UMR 6230, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - Virginie Silvestre
- Université de Nantes, CNRS, Laboratoire CEISAM-UMR 6230, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - Valérie Fargeas
- Université de Nantes, CNRS, Laboratoire CEISAM-UMR 6230, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - Adjou Ané
- Laboratoire de Chimie Organique, UFR SSMT, Université de Cocody 22, BP 582, Abidjan 22, Cote d'Ivoire
| | - Tami McBrayer
- Center for AIDS Research, Department of Pediatrics, Emory University School of Medicine/Veterans Affair Medical Center, Decatur, Georgia 30033, USA
| | - Mervi Detorio
- Center for AIDS Research, Department of Pediatrics, Emory University School of Medicine/Veterans Affair Medical Center, Decatur, Georgia 30033, USA
| | - Jong-Hyun Cho
- Center for AIDS Research, Department of Pediatrics, Emory University School of Medicine/Veterans Affair Medical Center, Decatur, Georgia 30033, USA
| | - Nathalie Bourgougnon
- Université de Bretagne-Sud Laboratoire de Biotechnologie et Chimie Marines, Campus de Tohannic, 56017 Vannes, France
| | - Didier Dubreuil
- Université de Nantes, CNRS, Laboratoire CEISAM-UMR 6230, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - Raymond F Schinazi
- Center for AIDS Research, Department of Pediatrics, Emory University School of Medicine/Veterans Affair Medical Center, Decatur, Georgia 30033, USA
| | - Jacques Lebreton
- Université de Nantes, CNRS, Laboratoire CEISAM-UMR 6230, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| |
Collapse
|
45
|
Pryde DC, Middleton DS, Stephenson PT, Wainwright P, Maddaford A, Zhang X, Leese D, Glen R, Hart J, Forrest N, Guyot T. Practical synthetic routes to carbon-substituted nucleosides. Tetrahedron Lett 2011. [DOI: 10.1016/j.tetlet.2011.09.074] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
46
|
Abstract
Numerous chemically modified oligonucleotides have been developed so far and show their own unique chemical properties and pharmacodynamic/pharmacokinetic characteristics. Among all non-natural nucleotides, to the best of our knowledge, only five chemistries are currently being tested in clinical trials: phosphorothioate, 2´-O-methyl RNA, 2´-O-methoxyethyl RNA, 2´,4´-bridged nucleic acid/locked nucleic acid and the phosphorodiamidate morpholino oligomer. Since phosphorothioate modification can improve the pharmacokinetics of oligonucleotides, this modification is currently used in combination with all other modifications except phosphorodiamidate morpholino oligomer. For the treatment of metabolic, cardiovascular, cancer and other systemic diseases, the phosphorothioate class of drugs is obviously helpful, while superior efficacies can be observed in phosphorodiamidate morpholino oligomer compared to other classes of oligonucleotides for the treatment of Duchenne muscular dystrophy. Which properties of antisense molecules are actually essential for clinical applications? In this article, we provide an overview of the medicinal chemistry of existing non-natural antisense molecules, as well as their clinical applications, to discuss which properties of antisense oligonuculeotides affect therapeutic potency.
Collapse
|
47
|
Nicolaou KC, Ellery SP, Rivas F, Saye K, Rogers E, Workinger TJ, Schallenberger M, Tawatao R, Montero A, Hessell A, Romesberg F, Carson D, Burton D. Synthesis and biological evaluation of 2',4'- and 3',4'-bridged nucleoside analogues. Bioorg Med Chem 2011; 19:5648-69. [PMID: 21840722 PMCID: PMC3348725 DOI: 10.1016/j.bmc.2011.07.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Revised: 07/12/2011] [Accepted: 07/13/2011] [Indexed: 10/18/2022]
Abstract
Most nucleosides in solution typically exist in equilibrium between two major sugar pucker forms, N-type and S-type, but bridged nucleosides can be locked into one of these conformations depending on their specific structure. While many groups have researched these bridged nucleosides for the purpose of determining their binding affinity for antisense applications, we opted to look into the potential for biological activity within these conformationally-locked structures. A small library of 2',4'- and 3',4'-bridged nucleoside analogues was synthesized, including a novel 3',4'-carbocyclic bridged system. The synthesized compounds were tested for antibacterial, antitumor, and antiviral activities, leading to the identification of nucleosides possessing such biological activities. To the best of our knowledge, these biologically active compounds represent the first example of 2',4'-bridged nucleosides to demonstrate such properties. The most potent compound, nucleoside 33, exhibited significant antiviral activity against pseudoviruses SF162 (IC(50)=7.0 μM) and HxB2 (IC(50)=2.4 μM). These findings render bridged nucleosides as credible leads for drug discovery in the anti-HIV area of research.
Collapse
Affiliation(s)
- K C Nicolaou
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Flores R, Rustullet A, Alibés R, Álvarez-Larena A, de March P, Figueredo M, Font J. Synthesis of Purine Nucleosides Built on a 3-Oxabicyclo[3.2.0]heptane Scaffold. J Org Chem 2011; 76:5369-83. [DOI: 10.1021/jo200775x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Ramon Flores
- Departament de Quı́mica and ‡Unitat de Crystal·lografia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Albert Rustullet
- Departament de Quı́mica and ‡Unitat de Crystal·lografia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Ramon Alibés
- Departament de Quı́mica and ‡Unitat de Crystal·lografia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Angel Álvarez-Larena
- Departament de Quı́mica and ‡Unitat de Crystal·lografia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Pedro de March
- Departament de Quı́mica and ‡Unitat de Crystal·lografia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Marta Figueredo
- Departament de Quı́mica and ‡Unitat de Crystal·lografia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Josep Font
- Departament de Quı́mica and ‡Unitat de Crystal·lografia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| |
Collapse
|
49
|
Bonache MC, Cordeiro A, Quesada E, Vanstreels E, Daelemans D, Camarasa MJ, Balzarini J, San-Félix A. Selective inhibition of Human Immunodeficiency Virus type 1 (HIV-1) by a novel family of tricyclic nucleosides. Antiviral Res 2011; 92:37-44. [PMID: 21600933 DOI: 10.1016/j.antiviral.2011.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Revised: 04/27/2011] [Accepted: 05/05/2011] [Indexed: 10/18/2022]
Abstract
Nucleoside 1, with an unusual tricyclic carbohydrate moiety, specifically inhibits HIV-1 replication while being inactive against HIV-2 or other (retro) viruses. In an attempt to increase the inhibitory efficacy against HIV-1, and to further explore the structural features required for anti-HIV-1 activity, different types of modifications have been carried out on this prototype compound. These include substitution of the ethoxy group at the C-4″ position by alkoxy groups of different length, branching, conformational freedom or functionalization. In addition, the 4″-ethoxy group has been removed or substituted by other functional groups. The role of the tert-butyldimethylsilyl (TBDMS) group at the 2' position has also been studied by preparing the corresponding 2'-deprotected derivative or by replacing it by other silyl (tert-hexyldimethylsilyl) or acyl (acetyl) moieties. Finally, the thymine of the prototype compound has been replaced by N-3-methylthymine, uracil or thiophenyl. Some of these compounds were endowed with a 6- to 7-fold higher selectivity than the prototype 1. The tricyclic nucleosides here described represent a novel type of selective anti HIV-1 inhibitors, targeted at the HIV-1-encoded reverse transcriptase.
Collapse
Affiliation(s)
- María-Cruz Bonache
- Instituto de Química Médica (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | | | | | | | | | | | | | | |
Collapse
|
50
|
Shukla GC, Haque F, Tor Y, Wilhelmsson LM, Toulmé JJ, Isambert H, Guo P, Rossi JJ, Tenenbaum SA, Shapiro BA. A boost for the emerging field of RNA nanotechnology. ACS NANO 2011; 5:3405-18. [PMID: 21604810 PMCID: PMC3102291 DOI: 10.1021/nn200989r] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
This Nano Focus article highlights recent advances in RNA nanotechnology as presented at the First International Conference of RNA Nanotechnology and Therapeutics, which took place in Cleveland, OH, USA (October 23-25, 2010) ( http://www.eng.uc.edu/nanomedicine/RNA2010/ ), chaired by Peixuan Guo and co-chaired by David Rueda and Scott Tenenbaum. The conference was the first of its kind to bring together more than 30 invited speakers in the frontier of RNA nanotechnology from France, Sweden, South Korea, China, and throughout the United States to discuss RNA nanotechnology and its applications. It provided a platform for researchers from academia, government, and the pharmaceutical industry to share existing knowledge, vision, technology, and challenges in the field and promoted collaborations among researchers interested in advancing this emerging scientific discipline. The meeting covered a range of topics, including biophysical and single-molecule approaches for characterization of RNA nanostructures; structure studies on RNA nanoparticles by chemical or biochemical approaches, computation, prediction, and modeling of RNA nanoparticle structures; methods for the assembly of RNA nanoparticles; chemistry for RNA synthesis, conjugation, and labeling; and application of RNA nanoparticles in therapeutics. A special invited talk on the well-established principles of DNA nanotechnology was arranged to provide models for RNA nanotechnology. An Administrator from National Institutes of Health (NIH) National Cancer Institute (NCI) Alliance for Nanotechnology in Cancer discussed the current nanocancer research directions and future funding opportunities at NCI. As indicated by the feedback received from the invited speakers and the meeting participants, this meeting was extremely successful, exciting, and informative, covering many groundbreaking findings, pioneering ideas, and novel discoveries.
Collapse
Affiliation(s)
- Girish C. Shukla
- Center for Gene Regulation in Health and Disease, Department of Biological Sciences, Cleveland State University, Cleveland, Ohio 44115, United States
| | - Farzin Haque
- Nanobiomedical Center, College of Engineering and Applied Science, and College of Medicine, University of Cincinnati, Cincinnati, Ohio 45267, United States
| | - Yitzhak Tor
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - L. Marcus Wilhelmsson
- Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, Kemivägen 10, SE-412 96 Göteborg, Sweden
| | - Jean-Jacques Toulmé
- Université Bordeaux Segalen, INSERM U869, Bâtiment 3A 1er étage, 33076 Bordeaux Cedex, France
| | - Hervé Isambert
- Institut Curie, Research Division, CNRS UMR 168, 11 rue P. & M. Curie, 75005 Paris, France
| | - Peixuan Guo
- Nanobiomedical Center, College of Engineering and Applied Science, and College of Medicine, University of Cincinnati, Cincinnati, Ohio 45267, United States
| | - John J. Rossi
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, California 91010, United States
| | - Scott A. Tenenbaum
- College of Nanoscale Science & Engineering, University at Albany-SUNY, Albany, New York 12203, United States
| | - Bruce A. Shapiro
- Center for Cancer Research Nanobiology Program, National Cancer Institute at Frederick, Frederick, Maryland 21702, United States
| |
Collapse
|