Synthesis and Incorporation of 5″-Amino- and 5′-Mercapto-5′-Deoxy-2′-O-Methyl Nucleosides Into Hammerhead Ribozymes

Abstract

Novel 5′-amino-5′-deoxy-2′-O-methyl uridine, guanosine and adenosine 3′-O-phosphoramidites 5, 11, and 20, as well as protected 5′-mercapto-5′-deoxy-2′-O-methyl uridine 3′-O-phosphoramidite 23 were synthesized from 2′-O-methyl nucleosides. These analogs were incorporated at the 5′-ends of hammerhead ribozymes to evaluate achiral bridging 5′-N- phosphoramidates and 5′-S-phosphorothioates as alternatives for non- bridging phosphorothioates commonly used for end stabilization against nucleases. Oligonucleotide synthesis and deprotection conditions were optimized for better yields of these modified ribozymes.     

Synthesis of Thymidine Derivatives 3′-Modified with a Polar Three-Atom Group as Potential Anti-HIV-1 Agents

Abstract

3′-Modified thymidine analogs, such as 3′-O-[(methylthio)thio-carbonyl]thymidine (4), 3′-O-thiocarbamoylthymidine (7), and N-(3′-deoxy-thymidin-3′-y1)phosphoramidates (9a, b), were synthesized from thymidine derivatives (1), (5), and (8), respectively, as potential anti-human immunodeficiency virus type 1 (HIV-1) agents. No significant activity against HIV-1 was, however, observed with any of these compounds.     

2′-SUBSTITUTED PHOSPHOROTHIOATE CONTAINING OLIGORIBONUCLEOTIDES: AN APPLICATION TO THE SYNTHESIS AND PURIFICATION OF HAMMERHEAD RIBOZYMES

Abstract

A systematic study of the catalytic activity and nuclease stability of selectively modified hammerhead ribozymes has resulted in the identification of a generic motif containing 5 ribose residues and 31 2′- modified sugars (1). This substructure has been further elaborated to include phosphorothioate linkages. Although oligodeoxyribonucleotides containing phosphorothioate linkages have been studied extensively, similarly substituted RNA molecules or ribozymes have not been explored at-length. The synthesis and purification of these ribozymes is discussed (2).     

Polyethylene glycol molecular crowders enhance the catalytic ability of bimolecular bacterial RNase P ribozymes

Abstract

The modular structure of bacterial ribonuclease P (RNase P) ribozymes, which recognize tertiary structures of precursor tRNAs (pre-tRNAs) to cleave their 5′ leader sequence, can be dissected physically into the two structured domain RNAs (S-domain and C-domain). Separately prepared S-domain RNA and C-domain RNA assemble to form bimolecular forms of RNase P ribozymes. We analyzed the effects of polyethylene glycols (PEGs) on pre-tRNA cleavage catalyzed by bimolecular RNase P ribozymes to examine the effects of molecular crowding on the reaction. PEG molecular crowders significantly enhanced the activities of bimolecular RNase P ribozymes, some of which were hardly active without PEGs.     

A Novel Type of Spironucleosides: 2′,5′-O-bis-TBDMS Uridine-3′-spiro-3′-isoxazolidin-5′-one and Its Thymidine Congener

Abstract

TSAO analogues, 2′,5′-O-bis-TBDMS uridine-3′-spiro-3′-isoxazolidin-5′-one (9) and its thymidine congener 10, as well as model spiro sugar derivatives (3 and 4) have been prepared from the corresponding nitrones through a stereospecific tandem nucleophilic attack. Compounds 9 and 10 which are bioisosters of TSAO-U and T respectively but which lack an amino group on the spiro ring, were found inactive against both HIV-1 and HIV-2.

     

Inhibition of HIV-1 Integration by Mono- & Bifunctionalized Triple Helix Forming Oligonucleotides

Abstract

HIV-1 DNA integration is carried out by integrase, a viral protein which binds to specific sequences located on both extremities of the HIV-1 DNA LTR. Inhibition of integration was observed with submicromolar concentrations of mono- or bifunctionalized 11-mer oligonucleotide-intercalators, which were designed to form an alternate strand triple helix with the U5 LTR end containing two adjacent purine tracts on opposite strands 5′-GGAAAATCTCT-3′/3′-CCTTTTAGAGA-5′.     

Inhibitory Effects of 1-Deazaadenosine Analogues on HIV Replication and Adenosine Deaminase

Abstract

A series of 2′,3′-dideoxy-N⁶-(cyclo)alkyl-1-deazaadenosine derivatives were synthesized starting from 2,6-dichloro-1-deazapurine (9). The new nucleosides proved to be good inhibitors of HIV-1 replication, the most active being the 2′,3′-dideoxy-2-chloro-N⁶-cycloctyl-1-deazaadenosine (14h, ED₅₀ = 0.4 μ).     

Synthesis of Tetrazole Oxathiolane Nucleoside Analogues and Their Evaluation as HIV-1 Antiviral Agents

Abstract

The synthesis of The synthesis of 2-hydroxymethyl-5-[N₂-(5′-carboxamido tetrazolyl)]-1,3-oxathiolane (6a and 6b) and 2-hydroxymethyl-5-[N₂-(5′-aminotetrazolyl)]-1,3-oxathiolane (7a and 7b) is described. It involved the preparation of suitable 1,3-oxathiolane precursors via cyclocondensation between benzoyloxyacetaldehyde and 2-mercaptoacetaldehyde di-[2-methoxyethyl] acetal, followed by condensation of adequately substituted tetrazoles using trimethylsilyltriflate or titanium tetrachloride as acid catalysts. In a preliminary in vitro study these new tetrazole oxathiolane nucleoside analogues were found inactive against HIV-1 retrovirus.     

Syntheses of 1-[(2-Hydroxyethoxy)methyl]- and 1-[(1,3-Dihydroxy-2-Propoxy)methyl]- Derivatives of 5-Substituted-2,4-difluorobenzene: Unnatural Acyclo Thymidine Mimics for Evaluation as Anticancer and Antiviral Agents

Abstract

A group of 1-[(2-hydroxyethoxy)methyl]- (12) and 1-[(1,3-dihydroxy-2-propoxy)methyl]- (13) derivatives of 2,4-difluorobenzene possessing a variety of C-5 substituents (R = Me, H, I, NO₂) were designed with the expectation that they may serve as acyclic 5-substituted-2′-deoxyuridine (thymidine) mimics. Compounds 12 and 13 (R = Me, H, I) were inactive as anticancer agents (C₅₀ = 10^?3 to 10^?4 M range), whereas the 5-nitro compounds (12d, 13d) exhibited weak-to-moderate cytotoxicity (CC₅₀ = 10^?5 to 10^?6 M range) against a variety of cancer cell lines. All compounds prepared (12a-d, 13a-d) were inactive as antiviral agents in a broad-spectrum antiviral screen that also included the human immunodeficiency virus (HIV-1 and HIV-2) and herpes simplex virus (HSV-1 and HSV-2).     

Synthesis of 3′-Deoxy-3′-[4-(pyrimidin-1-yl)methyl-1,2,3-triazol-1-yl]thymidine via 1,3-Dipolar Cycloaddition

Abstract

The synthesis of new 3′-deoxy-3′-[4-(pyrimidin-1-yl)methyl-1,2,3-triazol-1-yl]thymidine 6a–f, from 3′-azido-3′-deoxy-5′-O-monomethoxytrityl-thymidine is described. The key step is the 1,3-dipolar cycloaddition between the azido group of the protected AZT 3 and N-1-propargylpyrimidine derivatives 2a–f. All new derivatives 6a–f were evaluated for their inhibitory effects against the replication of HIV-1 (IIIB), HIV-2 (ROD). No marked activity was found.     

Synthesis and Biological Evaluation of a New N4-(N-Formyl Peptide)- 2′,3′-Dideoxy-3′-Thiacytidine as Anti-Hiv Prodrug

Abstract

The synthesis of a new analogue of 2′,3′-dideoxy-3′-thiacytidine 9 covalently linked to an N-formyl methionyl leucyl phenylalanine peptide is described. This new prodrug analogue has been tested on the one hand as activator of human polymorphonuclear leukocytes (an EC₅₀ value of 1.8 10^?5 M was determined from dose-response curve for superoxide production) and on the other hand as inhibitor of the syncitium formation caused by HIV-1 in MT4-cells (IC₅₀ = 8.0± 0.8 μM). In so far as this new prodrug possesses these two biological properties, it represents a useful “chemical-head” capable of targeting specific receptors located on leukocytes membranes.     

5′-Hydrogenphosphonates and 5′-Methylphosphonates of Sugar Modified Pyrimidine Nucleosides as Potential Anti-HIV-1 Agents.1

Abstract

A number of nucleoside 5′-hydrogerphosphonates and nucleoside 5′-methylphosphonates were prepared, to study their ability to inhibit replication of HIV-1. Two compounds, the 5′-hydrogenphosphonate of 3′-azido-3′-deoxythymidine (AZT-HP, IVc) and of 3′-deoxy-3′-fluorothymidine (FLT-HP, IVa), exhibit potent anti-HIV-1 activity with selectivity indices similar to or better than those of their parent nucleosides.     

Preparation and Properties of a New Type of Acyclic,Achiral Nucleoside Analogue

Abstract

Preparation of the nucleoside analogues 1 and incorporation of 1, B = T, in deoxyribooligonucleotides by the phosphoramidite method is described. A two-step deprotection procedure was developed to reduce cleavage of the modified allylic unit. The binding properties of the modified oligonucleotides towards complementary DNA and RNA has been evaluated by T_m measurements showing a ΔT_m of ?2 to ?6.5°C per modification. An oligonucleotide with two modifications at the 3′-end showed considerable resistance towards cleavage by a 3′-exonuclease. No antiviral activity against HIV-1 or HSV-1 was found for 1, B = G or T, or for any of the trihydroxy derivatives 5.     

Structural and Conformational Studies on Deoxyguanosyl-3′,5′-Deoxyadenosine Monophosphate and Its Ethyl Phosphotriester Analogs - Left-Handed Dimers

Abstract

The mode of base-base stacking, the handedness and the sugar(dGpA)phosphate backbone conformation of deoxyguanosyl 3′-5′ deoxyadenosine and its diastereomeric ethyl phosphotriester analogs were studied by ¹H NMR, UV and CD spectroscopy. The results indicate the three dimers are left-handed, while the sugar phosphate backbone is comprised predominantly of C_2′-endo, gg (C_4′-C_5′) and g′g′ (C_5′-O) conformers. The two bases are extensively stacked and interact about 90° along the dyad axes. The extent of base overlap in dGpA is slightly greater than in either ethyl phosphotriester analog. The absolute configurations of the two ethyl phosphotriester diastereoisomers of dGpA can be assigned by one-dimensional and two-dimensional ¹H NMR nuclear Overhauser enhancement experiments.     

Synthesis and Antiviral Evaluation of 3′-Substituted Thymidine Analogues Derived from 3′-Amino-3′-deoxythymidine

Abstract

To assess the structure-activity relationship for antiviral activity, a series of 3′-deoxy-3′-N-functionalized thymidine analogues were synthesized. Several of these thymidine analogues show moderate in vitro activity against HIV-1 and HIV-2.