1
|
Wagh AA, Kumar VA, Ravindranathan S, Fernandes M. Unlike RNA-TBA (rTBA), iso-rTBA, the 2'-5'-linked RNA-thrombin-binding aptamer, is a functional equivalent of TBA. Chem Commun (Camb) 2023; 59:1461-1464. [PMID: 36651344 DOI: 10.1039/d2cc05718b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
An antiparallel, functional RNA G-quadruplex of the 2'-5'-linked thrombin-binding aptamer (iso-rTBA) is reported for the first time. It can inhibit clotting and is remarkably stable to nuclease-degradation, besides having high thermal stability. It is thus, a superior candidate to TBA, rTBA or isoTBA, for further development as an anticoagulant.
Collapse
Affiliation(s)
- Atish A Wagh
- Organic Chemistry Division, CSIR-National Chemical Laboratory (CSIR-NCL), Pune 411008, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Vaijayanti A Kumar
- Organic Chemistry Division, CSIR-National Chemical Laboratory (CSIR-NCL), Pune 411008, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sapna Ravindranathan
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.,Central NMR Facility, CSIR-National Chemical Laboratory (CSIR-NCL), Pune 411008, India
| | - Moneesha Fernandes
- Organic Chemistry Division, CSIR-National Chemical Laboratory (CSIR-NCL), Pune 411008, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| |
Collapse
|
2
|
Riccardi C, Napolitano E, Platella C, Musumeci D, Montesarchio D. G-quadruplex-based aptamers targeting human thrombin: Discovery, chemical modifications and antithrombotic effects. Pharmacol Ther 2020; 217:107649. [PMID: 32777331 DOI: 10.1016/j.pharmthera.2020.107649] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 07/29/2020] [Indexed: 02/07/2023]
Abstract
First studies on thrombin-inhibiting DNA aptamers were reported in 1992, and since then a large number of anticoagulant aptamers has been discovered. TBA - also named HD1, a 15-mer G-quadruplex (G4)-forming oligonucleotide - is the best characterized thrombin binding aptamer, able to specifically recognize the protein exosite I, thus inhibiting the conversion of soluble fibrinogen into insoluble fibrin strands. Unmodified nucleic acid-based aptamers, in general, and TBA in particular, exhibit limited pharmacokinetic properties and are rapidly degraded in vivo by nucleases. In order to improve the biological performance of aptamers, a widely investigated strategy is the introduction of chemical modifications in their backbone at the level of the nucleobases, sugar moieties or phosphodiester linkages. Besides TBA, also other thrombin binding aptamers, able to adopt a well-defined G4 structure, e.g. mixed duplex/quadruplex sequences, as well as homo- and hetero-bivalent constructs, have been identified and optimized. Considering the growing need of new efficient anticoagulant agents associated with the strong therapeutic potential of these thrombin inhibitors, the research on thrombin binding aptamers is still a very hot and intriguing field. Herein, we comprehensively described the state-of-the-art knowledge on the DNA-based aptamers targeting thrombin, especially focusing on the optimized analogues obtained by chemically modifying the oligonucleotide backbone, and their biological performances in therapeutic applications.
Collapse
Affiliation(s)
- Claudia Riccardi
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; Department of Advanced Medical and Surgical Sciences, 2(nd) Division of Neurology, Center for Rare Diseases and InterUniversity Center for Research in Neurosciences, University of Campania Luigi Vanvitelli, via Sergio Pansini, 5, I-80131 Naples, Italy.
| | - Ettore Napolitano
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy.
| | - Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy.
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; Institute of Biostructures and Bioimages, CNR, via Mezzocannone 16, I-80134 Naples, Italy.
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy.
| |
Collapse
|
3
|
Sochacka E, Szczepanowski RH, Cypryk M, Sobczak M, Janicka M, Kraszewska K, Bartos P, Chwialkowska A, Nawrot B. 2-Thiouracil deprived of thiocarbonyl function preferentially base pairs with guanine rather than adenine in RNA and DNA duplexes. Nucleic Acids Res 2015; 43:2499-512. [PMID: 25690900 PMCID: PMC4357714 DOI: 10.1093/nar/gkv109] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 01/30/2015] [Accepted: 02/02/2015] [Indexed: 12/12/2022] Open
Abstract
2-Thiouracil-containing nucleosides are essential modified units of natural and synthetic nucleic acids. In particular, the 5-substituted-2-thiouridines (S2Us) present in tRNA play an important role in tuning the translation process through codon-anticodon interactions. The enhanced thermodynamic stability of S2U-containing RNA duplexes and the preferred S2U-A versus S2U-G base pairing are appreciated characteristics of S2U-modified molecular probes. Recently, we have demonstrated that 2-thiouridine (alone or within an RNA chain) is predominantly transformed under oxidative stress conditions to 4-pyrimidinone riboside (H2U) and not to uridine. Due to the important biological functions and various biotechnological applications for sulfur-containing nucleic acids, we compared the thermodynamic stabilities of duplexes containing desulfured products with those of 2-thiouracil-modified RNA and DNA duplexes. Differential scanning calorimetry experiments and theoretical calculations demonstrate that upon 2-thiouracil desulfuration to 4-pyrimidinone, the preferred base pairing of S2U with adenosine is lost, with preferred base pairing with guanosine observed instead. Therefore, biological processes and in vitro assays in which oxidative desulfuration of 2-thiouracil-containing components occurs may be altered. Moreover, we propose that the H2U-G base pair is a suitable model for investigation of the preferred recognition of 3'-G-ending versus A-ending codons by tRNA wobble nucleosides, which may adopt a 4-pyrimidinone-type structural motif.
Collapse
Affiliation(s)
- Elzbieta Sochacka
- Institute of Organic Chemistry, Technical University of Lodz, Zeromskiego 116, 90-924 Lodz, Poland
| | - Roman H Szczepanowski
- International Institute of Molecular and Cell Biology, Ks. J. Trojdena 4, 02-109 Warsaw, Poland
| | - Marek Cypryk
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Milena Sobczak
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Magdalena Janicka
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Karina Kraszewska
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Paulina Bartos
- Institute of Organic Chemistry, Technical University of Lodz, Zeromskiego 116, 90-924 Lodz, Poland
| | - Anna Chwialkowska
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Barbara Nawrot
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| |
Collapse
|
4
|
Aher MN, Erande ND, Fernandes M, Kumar VA. Unimolecular antiparallel G-quadruplex folding topology of 2′–5′-isoTBA sequences remains unaltered by loop composition. Org Biomol Chem 2015; 13:11696-703. [DOI: 10.1039/c5ob01923k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Unlike 3′–5′-linked TBA, the 2′–5′-linked isoTBA formed only unimolecular antiparallel G-quadruplexes independent of loop length.
Collapse
Affiliation(s)
- Manisha N. Aher
- Organic Chemistry Division
- CSIR-National Chemical Laboratory
- Pune 411008
- India
| | - Namrata D. Erande
- Organic Chemistry Division
- CSIR-National Chemical Laboratory
- Pune 411008
- India
| | - Moneesha Fernandes
- Organic Chemistry Division
- CSIR-National Chemical Laboratory
- Pune 411008
- India
| | | |
Collapse
|
5
|
Gambari R. Peptide nucleic acids: a review on recent patents and technology transfer. Expert Opin Ther Pat 2014; 24:267-94. [PMID: 24405414 DOI: 10.1517/13543776.2014.863874] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
INTRODUCTION DNA/RNA-based drugs are considered of major interest in molecular diagnosis and nonviral gene therapy. In this field, peptide nucleic acids (PNAs, DNA analogs in which the sugar-phosphate backbone is replaced by N-(2-aminoethyl)glycine units or similar building blocks) have been demonstrated to be excellent candidates as diagnostic reagents and biodrugs. AREAS COVERED Recent (2002 - 2013) patents based on studies on development of PNA analogs, delivery systems for PNAs, applications of PNAs in molecular diagnosis, and use of PNA for innovative therapeutic protocols. EXPERT OPINION PNAs are unique reagents in molecular diagnosis and have been proven to be very active and specific for alteration of gene expression, despite the fact that solubility and uptake by target cells can be limiting factors. Accordingly, patents on PNAs have taken in great consideration delivery strategies. PNAs have been proven stable and effective in vivo, despite the fact that possible long-term toxicity should be considered. For possible clinical applications, the use of PNA molecules in combination with drugs already employed in therapy has been suggested. Considering the patents available and the results on in vivo testing on animal models, we expect in the near future relevant PNA-based clinical trials.
Collapse
Affiliation(s)
- Roberto Gambari
- University of Ferrara, Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section , Via Fossato di Mortara n.74, 44100 Ferrara , Italy +39 532 974443 ; +39 532 974500 ;
| |
Collapse
|
6
|
Gunjal AD, Fernandes M, Erande N, Rajamohanan PR, Kumar VA. Functional isoDNA aptamers: modified thrombin binding aptamers with a 2'-5'-linked sugar-phosphate backbone (isoTBA). Chem Commun (Camb) 2013; 50:605-7. [PMID: 24281045 DOI: 10.1039/c3cc47569g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The regioisomeric 3'-deoxy-2'-5'-linked thrombin binding DNA aptamers (isoTBAs) were chemically synthesized and their ability to form unimolecular anti-parallel G-quadruplexes in the presence of K(+) ions was evaluated. These modified sequences retain the function of the native thrombin binding aptamer (TBA), exhibit better stability against exonuclease and are capable of slowing down the process of blood clotting.
Collapse
Affiliation(s)
- Anita D Gunjal
- Organic Chemistry Division, CSIR-National Chemical Laboratory, Dr Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India.
| | | | | | | | | |
Collapse
|
7
|
Plevnik M, Cevec M, Plavec J. NMR structure of 2'-O-(2-methoxyethyl) modified and C5-methylated RNA dodecamer duplex. Biochimie 2013; 95:2385-91. [PMID: 24012551 DOI: 10.1016/j.biochi.2013.08.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 08/26/2013] [Indexed: 10/26/2022]
Abstract
The solution-state structure of 2'-O-(2-methoxyethly) substituted dodecamer r(*CG*CGAA*U*U*CG*C)d(G), 2'-MOE RNA, with all cytosines and uracils methylated at the C5-position has been determined by NMR spectroscopy. The chemical modifications were used to improve the oligonucleotide's drug-like properties. The 2'-MOE group drives pseudorotational equilibrium of the ribofuranose moiety to the N-type conformation and supposedly results in structural preorganization leading to high affinity of a modified oligonucleotide towards its complementary biological target, improved pharmacokinetic and toxicological properties. The high melting temperature of the antiparallel duplex structure adopted by 2'-MOE RNA was explained through the formation of a stable A-form RNA consistent with effective base-pairing and stacking interactions. The comparison of the solution-state structure with the crystal structure of a non-methylated analogue shows an increase in the stacking at the base pair steps for the C5-methylated 2'-MOE RNA duplex. The MOE substituents adopt a well-defined structure in the minor groove with the predominant gauche conformations around the ethylene bond.
Collapse
Affiliation(s)
- Miha Plevnik
- Krka, d.d., Šmarješka cesta 6, 8501 Novo mesto, Slovenia
| | | | | |
Collapse
|
8
|
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
|
9
|
Erande N, Gunjal AD, Fernandes M, Kumar VA. Probing the furanose conformation in the 2′–5′strand of isoDNA : RNA duplexes by freezing the nucleoside conformations. Chem Commun (Camb) 2011; 47:4007-9. [DOI: 10.1039/c0cc05402j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
|
10
|
Podbevsek P, Allerson CR, Bhat B, Plavec J. Solution-state structure of a fully alternately 2'-F/2'-OMe modified 42-nt dimeric siRNA construct. Nucleic Acids Res 2010; 38:7298-307. [PMID: 20624819 PMCID: PMC2978378 DOI: 10.1093/nar/gkq621] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
A high-resolution solution structure of a stable 42-nt RNA dimeric construct has been derived based on a high number of NMR observables including nuclear overhauser effects (NOEs), J-coupling constants and residual dipolar couplings (RDCs), which were all obtained with isotopically unlabeled molecules. Two 21-nt siRNA that efficiently hybridize consist of ribose units that were alternately substituted by 2′-fluoro or 2′-methoxy groups. Structure calculations utilized a set of H-F RDC values for all 21 2′-fluoro modified nucleotides under conditions of weak alignment achieved by Pf1 phages. A completely 2′-F/2′-OMe modified dimeric RNA construct adopts an antiparallel double-helical structure consisting of 19 Watson–Crick base pairs with additional 3′ UU overhangs and a 5′ phosphate group on the antisense strand. NMR data suggest that the stability of individual base pairs is not uniform throughout the construct. While most of the double helical segment exhibits well dispersed imino resonances, the last three base pairs either display uncharacteristic chemical shifts of imino protons or absence of imino resonances even at lower temperatures. Accessibility of imino protons to solvent exchange suggests a difference in stability of duplex ends, which might be of importance for incorporation of the guide siRNA strand into a RISC.
Collapse
Affiliation(s)
- Peter Podbevsek
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | | | | | | |
Collapse
|
11
|
Horowitz ED, Lilavivat S, Holladay BW, Germann MW, Hud NV. Solution structure and thermodynamics of 2',5' RNA intercalation. J Am Chem Soc 2009; 131:5831-8. [PMID: 19309071 DOI: 10.1021/ja810068e] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
As a means to explore the influence of the nucleic acid backbone on the intercalative binding of ligands to DNA and RNA, we have determined the solution structure of a proflavine-bound 2',5'-linked octamer duplex with the sequence GCCGCGGC. This structure represents the first NMR structure of an intercalated RNA duplex, of either backbone structural isomer. By comparison with X-ray crystal structures, we have identified similarities and differences between intercalated 3',5' and 2',5'-linked RNA duplexes. First, the two forms of RNA have different sugar pucker geometries at the intercalated nucleotide steps, yet have the same interphosphate distances. Second, as in intercalated 3',5' RNA, the phosphate backbone angle zeta at the 2',5' RNA intercalation site prefers to be in the trans conformation, whereas unintercalated 2',5' and 3',5' RNA prefer the -gauche conformation. These observations provide new insights regarding the transitions required for intercalation of a phosphodiester-ribose backbone and suggest a possible contribution of the backbone to the origin of the nearest-neighbor exclusion principle. Thermodynamic studies presented for intercalation of both structural RNA isomers also reveal a surprising sensitivity of intercalator binding enthalpy and entropy to the details of RNA backbone structure.
Collapse
Affiliation(s)
- Eric D Horowitz
- Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, School of Chemistry and Biochemistry, Atlanta, Georgia 30332-0400, USA
| | | | | | | | | |
Collapse
|
12
|
Plevnik M, Gdaniec Z, Plavec J. Solution structure of a modified 2',5'-linked RNA hairpin involved in an equilibrium with duplex. Nucleic Acids Res 2005; 33:1749-59. [PMID: 15788747 PMCID: PMC1069515 DOI: 10.1093/nar/gki318] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The isomerization of phosphodiester functionality of nucleic acids from 3′,5′- to a less common 2′,5′-linkage influences the complex interplay of stereoelectronic effects that drive pseudorotational equilibrium of sugar rings and thus affect the conformational propensities for compact or more extended structures. The present study highlights the subtle balance of non-covalent forces at play in structural equilibrium of 2′,5′-linked RNA analogue, 3′-O-(2-methoxyethyl) substituted dodecamer *CG*CGAA*U*U*CG*CG, 3′-MOE-2′,5′-RNA, where all cytosines and uracils are methylated at C5. The NMR and UV spectroscopic studies have shown that 3′-MOE-2′,5′-RNA adopts both hairpin and duplex secondary structures, which are involved in a dynamic exchange that is slow on the NMR timescale and exhibits strand and salt concentration as well as pH dependence. Unusual effect of pH over a narrow physiological range is observed for imino proton resonances with exchange broadening observed at lower pH and relatively sharp lines observed at higher pH. The solution structure of 3′-MOE-2′,5′-RNA hairpin displays a unique and well-defined loop, which is stabilized by Watson–Crick A5·*U8 base pair and by n → π* stacking interactions of O4′ lone-pair electrons of A6 and *U8 with aromatic rings of A5 and *U7, respectively. In contrast, the stem region of 3′-MOE-2′,5′-RNA hairpin is more flexible. Our data highlight the important feature of backbone modifications that can have pronounced effects on interstrand association of nucleic acids.
Collapse
Affiliation(s)
| | - Zofia Gdaniec
- Institute of Bioorganic Chemistry, Polish Academy of SciencesNoskowskiego 12/14, 61-704 Poznan, Poland
| | - Janez Plavec
- To whom correspondence should be addressed. Tel: +386 1 47 60 353; Fax: +386 1 47 60 300;
| |
Collapse
|
13
|
Aboul-Fadl T, Agrawal VK, Buckheit RW, Broom AD. An unusual "senseless" 2',5'-oligoribonucleotide with potent anti-HIV activity. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2004; 23:545-54. [PMID: 15113022 DOI: 10.1081/ncn-120030713] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
A new 32-mer 2',5'-oligoribonucleotide of 1-methyl-6-thioinosinic acid (10) has been synthesized. The design of this unique oligoribonucleotide is based on the reported HIV inhibitory activities of both 2',5'-oligonucleotides and the 3',5'-oligoribonucleotides containing the 1-methyl-6-mercaptopurine base. Tm and CD studies of 10 revealed that it has no organized secondary structure, presumably due to the rigidity of the molecule. The synthesized oligomer, 10, showed a potent inhibitory effect on HIV-1RF and significantly inhibited HIV-1 reverse transcriptase.
Collapse
Affiliation(s)
- Tarek Aboul-Fadl
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
| | | | | | | |
Collapse
|