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Martínez-Montero S, Rajwanshi VK, Pandey RK, De Costa NTS, Hong J, Beigelman L, Gryaznov SM, Pourshahian S. New Oligonucleotide 2'-O-Alkyl N3'→P5' (Thio)-Phosphoramidates as Potent Antisense Agents: Physicochemical Properties and Biological Activity. Nucleic Acid Ther 2023; 33:319-328. [PMID: 37638793 DOI: 10.1089/nat.2023.0014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023] Open
Abstract
We describe here the design, synthesis, physicochemical properties, and hepatitis B antiviral activity of new 2'-O-alkyl ribonucleotide N3'→P5' phosphoramidate (2'-O-alkyl-NPO) and (thio)-phosphoramidite (2'-O-alkyl-NPS) oligonucleotide analogs. Oligonucleotides with different 2'-O-alkyl modifications such as 2'-O-methyl, -O-ethyl, -O-allyl, and -O-methoxyethyl combined with 3'-amino sugar-phosphate backbone were synthesized and evaluated. These molecules form stable duplexes with complementary DNA and RNA strands. They show an increase in duplex melting temperatures of up to 2.5°C and 4°C per linkage, respectively, compared to unmodified DNA. The results agree with predominantly C3'-endo sugar pucker conformation. Moreover, 2'-O-alkyl phosphoramidites demonstrate higher hydrolytic stability at pH 5.5 than 2'-deoxy NPOs. In addition, the relative lipophilicity of the 2'-O-alkyl-NPO and NPS oligonucleotides is higher than that of their 3'-O- counterparts. The 2'-O-alkyl-NPS oligonucleotides were evaluated as antisense (ASO) compounds in vitro and in vivo using Hepatitis B virus as a model system. Subcutaneous delivery of GalNAc conjugated 2'-O-MOE-NPS gapmers demonstrated higher activity than the 3'-O-containing 2'-O-MOE counterpart. The properties of 2'-O-alkyl-NPS constructs make them attractive candidates as ASO suitable for further evaluation and development.
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Affiliation(s)
- Saúl Martínez-Montero
- Janssen Pharmaceutical Companies of Johnson and Johnson, South San Francisco, California, USA
| | - Vivek K Rajwanshi
- Janssen Pharmaceutical Companies of Johnson and Johnson, South San Francisco, California, USA
| | - Rajendra K Pandey
- Janssen Pharmaceutical Companies of Johnson and Johnson, South San Francisco, California, USA
| | - N Tilani S De Costa
- Janssen Pharmaceutical Companies of Johnson and Johnson, South San Francisco, California, USA
| | - Jin Hong
- Janssen Pharmaceutical Companies of Johnson and Johnson, South San Francisco, California, USA
| | - Leonid Beigelman
- Janssen Pharmaceutical Companies of Johnson and Johnson, South San Francisco, California, USA
| | - Sergei M Gryaznov
- Janssen Pharmaceutical Companies of Johnson and Johnson, South San Francisco, California, USA
| | - Soheil Pourshahian
- Janssen Pharmaceutical Companies of Johnson and Johnson, South San Francisco, California, USA
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2
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Malek-Adamian E, Fakhoury J, Arnold AE, Martínez-Montero S, Shoichet MS, Damha MJ. Effect of Sugar 2',4'-Modifications on Gene Silencing Activity of siRNA Duplexes. Nucleic Acid Ther 2019; 29:187-194. [PMID: 31084536 PMCID: PMC6686699 DOI: 10.1089/nat.2019.0792] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
In this study, we explore the effect of a library of 2′-, 4′-, and 2′,4′-modified uridine nucleosides and their impact on silencing firefly luciferase and on down-regulated in renal cell carcinoma (DRR) gene targets. The modifications studied were 2′-F-ribose, 2′-F-arabinose, 2′-OMe-ribose, 2′-F,4′-OMe-ribose, 2′-F,4′-OMe-arabinose, and 2′-OMe,4′-F-ribose. We found that 2′,4′-modifications are well tolerated within A-form RNA duplexes, leading to virtually no change in melting temperature as assessed by UV thermal melting. The impact of the dual (2′,4′) modification was assessed by comparing gene silencing ability to 2′- or 4′- (singly) modified siRNA counterparts. siRNAs with (2′,4′)-modified overhangs generally outperformed the native siRNA as well as siRNAs with a 2′- or 4′-modified overhang, suggesting that 2′,4′-modified nucleotides interact favorably with Argonaute protein's PAZ domain. Among the most active siRNAs were those with 2′-F,4′-OMe-ribose or 2′-F,4′-OMe-arabinose at the overhangs. When modifications were placed at both overhangs and internal positions, a duplex with the 2′-F (internal) and 2′-F,4′-OMe (overhang) combination was found to be the most potent, followed by the duplex with 2′-OMe (internal) and 2′,4′-diOMe (overhang) modifications. Given the nuclease resistance exhibited by 2′,4′-modified siRNAs, particularly when the modification is placed at or near the overhangs, these findings may allow the creation of superior siRNAs for therapy.
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Affiliation(s)
| | - Johans Fakhoury
- 1Department of Chemistry, McGill University, Montreal, Canada
| | - Amy E Arnold
- 2Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | | | - Molly S Shoichet
- 2Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada.,3Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Canada.,4Department of Chemistry, University of Toronto, Toronto, Canada
| | - Masad J Damha
- 1Department of Chemistry, McGill University, Montreal, Canada
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3
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Malek-Adamian E, Patrascu MB, Jana SK, Martínez-Montero S, Moitessier N, Damha MJ. Adjusting the Structure of 2'-Modified Nucleosides and Oligonucleotides via C4'-α-F or C4'-α-OMe Substitution: Synthesis and Conformational Analysis. J Org Chem 2018; 83:9839-9849. [PMID: 29963864 DOI: 10.1021/acs.joc.8b01329] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We report the first syntheses of three nucleoside analogues, namely, 2',4'-diOMe-rU, 2'-OMe,4'-F-rU, and 2'-F,4'-OMe-araU, via stereoselective introduction of fluorine or methoxy functionalities at the C4'-α-position of a 4',5'-olefinic intermediate. Conformational analyses of these nucleosides and comparison to other previously reported 2',4'-disubstituted nucleoside analogues make it possible to evaluate the effect of fluorine and methoxy substitution on the sugar pucker, as assessed by NMR, X-ray diffraction, and computational methods. We found that C4'-α-F/OMe substituents reinforce the C3'-endo ( north) conformation of 2'-OMe-rU. Furthermore, the predominant C2'-endo ( south/ east) conformation of 2'-F-araU switches to C3'-endo upon introduction of these substituents at C4'. The nucleoside analogues were incorporated into DNA and RNA oligonucleotides via standard phosphoramidite chemistry, and their effects on the thermal stability of homo- and heteroduplexes were assessed via UV thermal melting experiments. We found that 4'-substituents can modulate the binding affinity of the parent 2'-modified oligomers, inducing a mildly destabilizing or stabilizing effect depending on the duplex type. This study expands the spectrum of oligonucleotide modifications available for rational design of oligonucleotide therapeutics.
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Affiliation(s)
- Elise Malek-Adamian
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec , Canada H3A 0B8
| | - Mihai Burai Patrascu
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec , Canada H3A 0B8
| | - Sunit Kumar Jana
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec , Canada H3A 0B8
| | - Saúl Martínez-Montero
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec , Canada H3A 0B8
| | - Nicolas Moitessier
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec , Canada H3A 0B8
| | - Masad J Damha
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec , Canada H3A 0B8
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4
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Arnold AE, Malek-Adamian E, Le PU, Meng A, Martínez-Montero S, Petrecca K, Damha MJ, Shoichet MS. Antibody-Antisense Oligonucleotide Conjugate Downregulates a Key Gene in Glioblastoma Stem Cells. Mol Ther Nucleic Acids 2018; 11:518-527. [PMID: 29858087 PMCID: PMC5992475 DOI: 10.1016/j.omtn.2018.04.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 03/29/2018] [Accepted: 04/13/2018] [Indexed: 12/17/2022]
Abstract
Glioblastoma stem cells (GSCs) are invasive, treatment-resistant brain cancer cells that express downregulated in renal cell carcinoma (DRR), also called FAM107A, a genetic driver of GSC invasion. We developed antibody-antisense oligonucleotide (AON) conjugates to target and reduce DRR/FAM107A expression. Specifically, we used antibodies against antigens expressed on the GSCs, such as CD44 and EphA2, conjugated to chemically modified AONs against DRR/FAM107A, which were designed as chimeras of DNA and 2'-deoxy-2'-fluoro-beta-D-arabinonucleic acid (FANA) for increased nuclease stability and mRNA affinity. We demonstrate that these therapeutic conjugates successfully internalize, accumulate, and reduce DRR/FAM107A expression in patient-derived GSCs. This is the first example of an antibody-antisense strategy against cancer stem cells.
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Affiliation(s)
- Amy E Arnold
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Elise Malek-Adamian
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| | - Phuong U Le
- Department of Neurology and Neurosurgery, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, Canada
| | - Anika Meng
- Division of Engineering Science, University of Toronto, 35 St. George Street, Toronto, ON M5S 1A4, Canada
| | - Saúl Martínez-Montero
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| | - Kevin Petrecca
- Department of Neurology and Neurosurgery, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, Canada
| | - Masad J Damha
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada.
| | - Molly S Shoichet
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada; Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5, Canada; Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON M5S 3G9, Canada.
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5
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Malek-Adamian E, Guenther DC, Matsuda S, Martínez-Montero S, Zlatev I, Harp J, Burai Patrascu M, Foster DJ, Fakhoury J, Perkins L, Moitessier N, Manoharan RM, Taneja N, Bisbe A, Charisse K, Maier M, Rajeev KG, Egli M, Manoharan M, Damha MJ. 4'-C-Methoxy-2'-deoxy-2'-fluoro Modified Ribonucleotides Improve Metabolic Stability and Elicit Efficient RNAi-Mediated Gene Silencing. J Am Chem Soc 2017; 139:14542-14555. [PMID: 28937776 DOI: 10.1021/jacs.7b07582] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We designed novel 4'-modified 2'-deoxy-2'-fluorouridine (2'-F U) analogues with the aim to improve nuclease resistance and potency of therapeutic siRNAs by introducing 4'-C-methoxy (4'-OMe) as the alpha (C4'α) or beta (C4'β) epimers. The C4'α epimer was synthesized by a stereoselective route in six steps; however, both α and β epimers could be obtained by a nonstereoselective approach starting from 2'-F U. 1H NMR analysis and computational investigation of the α-epimer revealed that the 4'-OMe imparts a conformational bias toward the North-East sugar pucker, due to intramolecular hydrogen bonding and hyperconjugation effects. The α-epimer generally conceded similar thermal stability as unmodified nucleotides, whereas the β-epimer led to significant destabilization. Both 4'-OMe epimers conferred increased nuclease resistance, which can be explained by the close proximity between 4'-OMe substituent and the vicinal 5'- and 3'-phosphate group, as seen in the X-ray crystal structure of modified RNA. siRNAs containing several C4'α-epimer monomers in the sense or antisense strands triggered RNAi-mediated gene silencing with efficiencies comparable to that of 2'-F U.
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Affiliation(s)
- Elise Malek-Adamian
- Department of Chemistry, McGill University , 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Dale C Guenther
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Shigeo Matsuda
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Saúl Martínez-Montero
- Department of Chemistry, McGill University , 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Ivan Zlatev
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Joel Harp
- Department of Biochemistry, School of Medicine, Vanderbilt University , Nashville, Tennessee 37232, United States
| | - Mihai Burai Patrascu
- Department of Chemistry, McGill University , 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Donald J Foster
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Johans Fakhoury
- Department of Chemistry, McGill University , 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Lydia Perkins
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Nicolas Moitessier
- Department of Chemistry, McGill University , 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Rajar M Manoharan
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Nate Taneja
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Anna Bisbe
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Klaus Charisse
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Martin Maier
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | | | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University , Nashville, Tennessee 37232, United States
| | - Muthiah Manoharan
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Masad J Damha
- Department of Chemistry, McGill University , 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
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6
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Abbas YM, Laudenbach BT, Martínez-Montero S, Cencic R, Habjan M, Pichlmair A, Damha MJ, Pelletier J, Nagar B. Structure of human IFIT1 with capped RNA reveals adaptable mRNA binding and mechanisms for sensing N1 and N2 ribose 2'-O methylations. Proc Natl Acad Sci U S A 2017; 114:E2106-E2115. [PMID: 28251928 PMCID: PMC5358387 DOI: 10.1073/pnas.1612444114] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
IFIT1 (IFN-induced protein with tetratricopeptide repeats-1) is an effector of the host innate immune antiviral response that prevents propagation of virus infection by selectively inhibiting translation of viral mRNA. It relies on its ability to compete with the translation initiation factor eIF4F to specifically recognize foreign capped mRNAs, while remaining inactive against host mRNAs marked by ribose 2'-O methylation at the first cap-proximal nucleotide (N1). We report here several crystal structures of RNA-bound human IFIT1, including a 1.6-Å complex with capped RNA. IFIT1 forms a water-filled, positively charged RNA-binding tunnel with a separate hydrophobic extension that unexpectedly engages the cap in multiple conformations (syn and anti) giving rise to a relatively plastic and nonspecific mode of binding, in stark contrast to eIF4E. Cap-proximal nucleotides encircled by the tunnel provide affinity to compete with eIF4F while allowing IFIT1 to select against N1 methylated mRNA. Gel-shift binding assays confirm that N1 methylation interferes with IFIT1 binding, but in an RNA-dependent manner, whereas translation assays reveal that N1 methylation alone is not sufficient to prevent mRNA recognition at high IFIT1 concentrations. Structural and functional analysis show that 2'-O methylation at N2, another abundant mRNA modification, is also detrimental for RNA binding, thus revealing a potentially synergistic role for it in self- versus nonself-mRNA discernment. Finally, structure-guided mutational analysis confirms the importance of RNA binding for IFIT1 restriction of a human coronavirus mutant lacking viral N1 methylation. Our structural and biochemical analysis sheds new light on the molecular basis for IFIT1 translational inhibition of capped viral RNA.
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Affiliation(s)
- Yazan M Abbas
- Department of Biochemistry and Groupe de Recherche Axe sur la Structure des Proteines, McGill University, Montreal, QC, Canada H3G 0B1
| | | | | | - Regina Cencic
- Department of Biochemistry, McGill University, Montreal, QC, Canada H3G 1Y6
| | - Matthias Habjan
- Innate Immunity Laboratory, Max-Planck Institute of Biochemistry, 82152 Martinsried/Munich, Germany
| | - Andreas Pichlmair
- Innate Immunity Laboratory, Max-Planck Institute of Biochemistry, 82152 Martinsried/Munich, Germany
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, QC, Canada H3A 0B8
| | - Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal, QC, Canada H3G 1Y6
- The Rosalind and Morris Goodman Cancer Research Center, Montreal, QC, Canada H3A 1A3
- Department of Oncology, McGill University, Montreal, QC, Canada H3G 1Y6
| | - Bhushan Nagar
- Department of Biochemistry and Groupe de Recherche Axe sur la Structure des Proteines, McGill University, Montreal, QC, Canada H3G 0B1;
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7
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Moroz E, Lee SH, Yamada K, Halloy F, Martínez-Montero S, Jahns H, Hall J, Damha MJ, Castagner B, Leroux JC. Carrier-free Gene Silencing by Amphiphilic Nucleic Acid Conjugates in Differentiated Intestinal Cells. Mol Ther Nucleic Acids 2016; 5:e364. [PMID: 27648924 PMCID: PMC5056993 DOI: 10.1038/mtna.2016.69] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 07/20/2016] [Indexed: 12/14/2022]
Abstract
Nucleic acid therapy can be beneficial for the local treatment of gastrointestinal diseases that currently lack appropriate treatments. Indeed, several oligonucleotides (ONs) are currently progressing through clinical trials as potential treatments for inflammatory bowel diseases. However, due to low uptake of carrier-free ONs by mucosal cells, strategies aimed at increasing the potency of orally administered ONs would be highly desirable. In this work, we explored the silencing properties of chemically modified and highly resistant ONs derivatized with hydrophobic alkyl chain on intestinal epithelial cells. We screened a set of lipid-ON conjugates for the silencing of model Bcl-2 mRNA and selected 2'-deoxy-2'-fluoro-arabinonucleic acid modified ON bearing docosanoyl moiety (L-FANA) as the most potent candidate with lowest toxicity. The efficacy of L-FANA conjugate was preserved in simulated intestinal fluids and in the inverted transfection setup. Importantly, L-FANA conjugate was able to downregulate target gene expression at both mRNA and protein levels in a difficult-to-transfect polarized epithelial cell monolayer in the absence of delivery devices and membrane disturbing agents. These findings indicate that lipid-ON conjugates could be promising therapeutics for the treatment of intestinal diseases as well as a valuable tool for the discovery of new therapeutic targets.
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Affiliation(s)
- Elena Moroz
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland
| | - Soo Hyeon Lee
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland
| | - Ken Yamada
- Department of Chemistry, McGill University, Montreal, Canada
| | - François Halloy
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland
| | | | - Hartmut Jahns
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland
| | - Jonathan Hall
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, Canada
| | - Bastien Castagner
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland.,Department of Pharmacology & Therapeutics, McGill University, Montreal, Canada
| | - Jean-Christophe Leroux
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland
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8
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Habibian M, Martínez-Montero S, Portella G, Chua Z, Bohle DS, Orozco M, Damha MJ. Seven-Membered Ring Nucleoside Analogues: Stereoselective Synthesis and Studies on Their Conformational Properties. Org Lett 2015; 17:5416-9. [PMID: 26492193 DOI: 10.1021/acs.orglett.5b02769] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Maryam Habibian
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A
0B8, Canada
| | - Saúl Martínez-Montero
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A
0B8, Canada
| | - Guillem Portella
- Chemistry
Department, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Zhijie Chua
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A
0B8, Canada
| | - D. Scott Bohle
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A
0B8, Canada
| | - Modesto Orozco
- Joint
BSC-CRG-IRB Programme on Computational Biology, Institute for Research in Biomedicine, Baldiri i Reixac 19, 08028 Barcelona, Spain
- Departament
de Bioquímica i Biologia Molecular, Facultat de Biologia, Universitat de Barcelona, Avgda Diagonal 643, 08028 Barcelona, Spain
| | - Masad J. Damha
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A
0B8, Canada
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9
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Martínez-Montero S, Deleavey GF, Martín-Pintado N, Fakhoury JF, González C, Damha MJ. Locked 2'-Deoxy-2',4'-Difluororibo Modified Nucleic Acids: Thermal Stability, Structural Studies, and siRNA Activity. ACS Chem Biol 2015; 10:2016-23. [PMID: 26053215 DOI: 10.1021/acschembio.5b00218] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
2'-Deoxy-2',4'-difluorouridine (2',4'-diF-rU) was readily incorporated into DNA and RNA oligonucleotides via standard solid phase synthesis protocols. NMR and thermal denaturation (Tm) data of duplexes was consistent with the 2',4'-diF-rU nucleotides adopting a rigid North (RNA-like) sugar conformation, as previously observed for the nucleoside monomer. The impact of this modification on Tm is neutral when incorporated within RNA:RNA duplexes, mildly destabilizing when located in the RNA strand of a DNA:RNA duplex, and highly destabilizing when inserted in the DNA strand of DNA:RNA and DNA:DNA duplexes. Molecular dynamics calculations suggest that the destabilization effect in DNA:DNA and DNA:RNA duplexes is the result of structural distortions created by A/B junctions within the helical structures. Quantum mechanics calculations suggest that the "neutral" effect imparted to A-form duplexes is caused by alterations in charge distribution that compensate the stabilizing effect expected for a pure North-puckered furanose sugar. 2',4'-diF-RNA modified siRNAs were able to trigger RNA interference with excellent efficiency. Of note, incorporation of a few 2',4'-diF-rU residues in the middle of the guide (antisense) strand afforded siRNAs that were more potent than the corresponding siRNAs containing LNA and 2'-F-ANA modifications, and as active as the 2'-F-RNA modified siRNAs.
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Affiliation(s)
- Saúl Martínez-Montero
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8
| | - Glen F. Deleavey
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8
| | - Nerea Martín-Pintado
- Instituto de Química Física Rocasolano, CSIC, C/. Serrano 119, 28006 Madrid, Spain
| | - Johans F. Fakhoury
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8
| | - Carlos González
- Instituto de Química Física Rocasolano, CSIC, C/. Serrano 119, 28006 Madrid, Spain
| | - Masad J. Damha
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8
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10
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Yamada K, Wahba AS, Bernatchez JA, Ilina T, Martínez-Montero S, Habibian M, Deleavey GF, Götte M, Parniak MA, Damha MJ. Nucleotide Sugar Pucker Preference Mitigates Excision by HIV-1 RT. ACS Chem Biol 2015; 10:2024-33. [PMID: 26131619 DOI: 10.1021/acschembio.5b00263] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of DNA primers containing nucleotides with various sugar pucker conformations at the 3'-terminus were chemically synthesized by solid-phase synthesis. The ability of wild-type (WT) HIV-1 reverse transcriptase (RT) and AZT-resistant (AZTr) RT to excise the 3'-terminal nucleotide was assessed. Nucleosides with a preference for the North conformation were more refractory to excision by both WT-RT and AZTr-RT. We found that DNA primers that contain North puckered-nucleotides at the 3'-terminus can also affect the translocation status of the RT/template/primer complex, which provides an underlying mechanism to avoid being excised. Together, these results point to a correlation between the sugar conformation of the 3'-terminal nucleotide, the precise position of HIV-1 RT on its nucleic acid substrate, and, in turn, its catalytic function. Nucleotide sugar conformation is therefore an important parameter in defining the susceptibility to RT-catalyzed phosphorolytic excision.
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Affiliation(s)
- Ken Yamada
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Alexander S. Wahba
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Jean A. Bernatchez
- Department
of Biochemistry, McGill University, 3655 Sir William Osler Promenade, Montreal, Quebec H3G1Y6, Canada
| | - Tatiana Ilina
- Department
of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, 450 Technology Drive, Pittsburgh, Pennsylvania 15219-3143, United States
| | - Saúl Martínez-Montero
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Maryam Habibian
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Glen F. Deleavey
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Matthias Götte
- Department
of Biochemistry, McGill University, 3655 Sir William Osler Promenade, Montreal, Quebec H3G1Y6, Canada
- Department
of Microbiology and Immunology, McGill University, 3775 University, Montreal, Quebec H3A 2B4, Canada
| | - Michael A. Parniak
- Department
of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, 450 Technology Drive, Pittsburgh, Pennsylvania 15219-3143, United States
| | - Masad J. Damha
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
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11
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Martínez-Montero S, Deleavey GF, Dierker-Viik A, Lindovska P, Ilina T, Portella G, Orozco M, Parniak MA, González C, Damha MJ. Synthesis and properties of 2'-deoxy-2',4'-difluoroarabinose-modified nucleic acids. J Org Chem 2015; 80:3083-91. [PMID: 25723361 PMCID: PMC4484724 DOI: 10.1021/jo502948t] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We report the synthesis, thermal stability, and RNase H substrate activity of 2'-deoxy-2',4'-difluoroarabino-modified nucleic acids. 2'-Deoxy-2',4'-difluoroarabinouridine (2,'4'-diF-araU) was prepared in a stereoselective way in six steps from 2'-deoxy-2'-fluoroarabinouridine (2'-F-araU). NMR analysis and quantum mechanical calculations at the nucleoside level reveal that introduction of 4'-fluorine introduces a strong bias toward the North conformation, despite the presence of the 2'-βF, which generally steers the sugar pucker toward the South/East conformation. Incorporation of the novel monomer into DNA results on a neutral to slightly stabilizing thermal effect on DNA-RNA hybrids. Insertion of 2',4'-diF-araU nucleotides in the DNA strand of a DNA-RNA hybrid decreases the rate of both human and HIV reverse transcriptase-associated RNase H-mediated cleavage of the complement RNA strand compared to that for an all-DNA strand or a DNA strand containing the corresponding 2'-F-araU nucleotide units, consistent with the notion that a 4'-fluorine in 2'-F-araU switches the preferred sugar conformation from DNA-like (South/East) to RNA-like (North).
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Affiliation(s)
- Saúl Martínez-Montero
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| | - Glen F. Deleavey
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| | - Arden Dierker-Viik
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| | - Petra Lindovska
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| | - Tatiana Ilina
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, 450 Technology Drive, Pittsburgh, Pennsylvania 15219-3143, United States
| | - Guillem Portella
- Joint IRB–BSC program on Computational Biology, Institute for Research in Biomedicine, Barcelona Supercomputing Center, and Department of Biochemistry, University of Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Modesto Orozco
- Joint IRB–BSC program on Computational Biology, Institute for Research in Biomedicine, Barcelona Supercomputing Center, and Department of Biochemistry, University of Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Michael A. Parniak
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, 450 Technology Drive, Pittsburgh, Pennsylvania 15219-3143, United States
| | - Carlos González
- Instituto de Química Física Rocasolano, CSIC, C/Serrano 119, 28006 Madrid, Spain
| | - Masad J. Damha
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
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12
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Abou Assi H, Martínez-Montero S, Dixit DM, Chua Z, Bohle DS, Damha MJ. Synthesis, Structure, and Conformational Analysis of Nucleoside Analogues Comprising Six-Membered 1,3-Oxathiane Sugar Rings. European J Org Chem 2015. [DOI: 10.1002/ejoc.201403642] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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13
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Martínez-Montero S, Deleavey GF, Kulkarni A, Martín-Pintado N, Lindovska P, Thomson M, González C, Götte M, Damha MJ. Rigid 2',4'-difluororibonucleosides: synthesis, conformational analysis, and incorporation into nascent RNA by HCV polymerase. J Org Chem 2014; 79:5627-35. [PMID: 24873952 DOI: 10.1021/jo500794v] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We report on the synthesis and conformational properties of 2'-deoxy-2',4'-difluorouridine (2',4'-diF-rU) and cytidine (2',4'-diF-rC) nucleosides. NMR analysis and quantum mechanical calculations show that the strong stereoelectronic effects induced by the two fluorines essentially "lock" the conformation of the sugar in the North region of the pseudorotational cycle. Our studies also demonstrate that NS5B HCV RNA polymerase was able to accommodate 2',4'-diF-rU 5'-triphosphate (2',4'-diF-rUTP) and to link the monophosphate to the RNA primer strand. 2',4'-diF-rUTP inhibited RNA synthesis in dinucleotide-primed reactions, although with relatively high half-maximal inhibitory concentrations (IC50 > 50 μM). 2',4'-diF-rU/C represents rare examples of "locked" ribonucleoside mimics that lack a bicyclic ring structure.
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Affiliation(s)
- Saúl Martínez-Montero
- Department of Chemistry, McGill University , 801 Sherbrooke Street West, Montreal, QC Canada H3A 0B8
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14
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Martínez-Montero S, Fernández S, Sanghvi YS, Theodorakis EA, Detorio MA, McBrayer TR, Whitaker T, Schinazi RF, Gotor V, Ferrero M. Synthesis, evaluation of anti-HIV-1 and anti-HCV activity of novel 2',3'-dideoxy-2',2'-difluoro-4'-azanucleosides. Bioorg Med Chem 2012; 20:6885-93. [PMID: 23085031 DOI: 10.1016/j.bmc.2012.09.026] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 09/11/2012] [Accepted: 09/13/2012] [Indexed: 10/27/2022]
Abstract
A series of 2',3'-dideoxy-2',2'-difluoro-4'-azanucleosides of both pyrimidine and purine nucleobases were synthesized in an efficient manner starting from commercially available L-pyroglutamic acid via glycosylation of difluorinated pyrrolidine derivative 15. Several 4'-azanucleosides were prepared as a separable mixture of α- and β-anomers. The 6-chloropurine analogue was obtained as a mixture of N(7) and N(9) regioisomers and their structures were identified based on NOESY and HMBC spectral data. Among the 4'-azanucleosides tested as HIV-1 inhibitors in primary human lymphocytes, four compounds showed modest activity and the 5-fluorouracil analogue (18d) was found to be the most active compound (EC(50)=36.9μM) in this series. None of the compounds synthesized in this study demonstrated anti-HCV activity.
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Affiliation(s)
- Saúl Martínez-Montero
- Departamento de Química Orgánica e Inorgánica and Instituto Universitario de Biotecnología de Asturias, Universidad de Oviedo, Oviedo (Asturias), Spain
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15
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Martínez-Montero S, Fernández S, Sanghvi YS, Gotor V, Ferrero M. CAL-B-Catalyzed Acylation of Nucleosides and Role of the Sugar Conformation: An Improved Understanding of the Enzyme-Substrate Recognition. European J Org Chem 2012. [DOI: 10.1002/ejoc.201200609] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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16
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Martínez-Montero S, Fernández S, Sanghvi YS, Gotor V, Ferrero M. An expedient biocatalytic procedure for abasic site precursors useful in oligonucleotide synthesis. Org Biomol Chem 2011; 9:5960-6. [PMID: 21748181 DOI: 10.1039/c1ob05739a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Preparation of abasic site precursors through a divergent chemoenzymatic synthesis has been accomplished. Several biocatalysts and acylating agents were studied furnishing a practical and scalable green method useful for industrial applications. Highly regioselective acylation and deacylation reactions with 1,2-dideoxy-D-ribose are described resulting in excellent yield. A fast, atom-efficient and convenient synthesis of 3-, and 5-O-DMTr-1,2-dideoxyribose 17 and 19 has been achieved. These compounds are useful precursors for the preparation of phosphoramidites required for the assembly of oligonucleotides containing the tetrahydrofuran abasic lesions.
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Affiliation(s)
- Saúl Martínez-Montero
- Departamento de Química Orgánica e Inorgánica and Instituto Universitario de Biotecnología de Asturias, Universidad de Oviedo, 33006, Oviedo, Asturias, Spain
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17
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Martínez-Montero S, Fernández S, Sanghvi YS, Gotor V, Ferrero M. Enzymatic Parallel Kinetic Resolution of Mixtures of d/l 2′-Deoxy and Ribonucleosides: An Approach for the Isolation of β-l-Nucleosides. J Org Chem 2010; 75:6605-13. [DOI: 10.1021/jo101368z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Saúl Martínez-Montero
- Departamento de Química Orgánica e Inorgánica and Instituto Universitario de Biotecnología de Asturias, Universidad de Oviedo, 33006-Oviedo (Asturias), Spain
| | - Susana Fernández
- Departamento de Química Orgánica e Inorgánica and Instituto Universitario de Biotecnología de Asturias, Universidad de Oviedo, 33006-Oviedo (Asturias), Spain
| | - Yogesh S. Sanghvi
- Rasayan Inc., 2802 Crystal Ridge Road, Encinitas, California 92024-6615
| | - Vicente Gotor
- Departamento de Química Orgánica e Inorgánica and Instituto Universitario de Biotecnología de Asturias, Universidad de Oviedo, 33006-Oviedo (Asturias), Spain
| | - Miguel Ferrero
- Departamento de Química Orgánica e Inorgánica and Instituto Universitario de Biotecnología de Asturias, Universidad de Oviedo, 33006-Oviedo (Asturias), Spain
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18
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Rodríguez-Pérez T, Fernández S, Martínez-Montero S, González-García T, Sanghvi YS, Gotor V, Ferrero M. Chemoenzymatic Synthesis of 3′-O-Acetal-Protected 2′-Deoxynucleosides as Building Blocks for Nucleic Acid Chemistry. European J Org Chem 2010. [DOI: 10.1002/ejoc.200901428] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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19
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Martínez-Montero S, Fernández S, Rodríguez-Pérez T, Sanghvi YS, Wen K, Gotor V, Ferrero M. Improved Synthesis and Isolation of 2′-O-Methyladenosine: Effective and Scalable Enzymatic Separation of 2′/3′-O-Methyladenosine Regioisomers. European J Org Chem 2009. [DOI: 10.1002/ejoc.200900348] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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