Maqbool A. Siddiqui

Synthesis of Conformationally Restricted Carbocyclic Nucleosides: The Role of the O(4′)‐Atom in the Key Hydration Step of Adenosine Deaminase

Conformationally restricted carbocyclic nucleosides with either a northern(N)-type conformation, i.e., N-type 2′-deoxy-methanocarba-adenosine 8 ((N)MCdAdo), or a southern(S)-type conformation, i.e.S-type 2′-deoxy-methanocarba-adenosine 9, ((S)MCdAdo), were used as substrates for adenosine deaminase (ADA) to assess the enzymes preference for a fixed conformation relative to the flexible conformation represented by the carbocyclic nucleoside aristeromycin (10). Further comparison between the rates of deamination of these compounds with those of the two natural substrates adenosine (Ado; 1) and 2′-deoxyadenosine (dAdo; 2), as well as with that of the conformationally locked nucleoside LNA-Ado (11), which, like the natural substrates, has a furanose O(4′) atom, helped differentiate between the roles of the O(4′) anomeric effect and sugar conformation in controlling the rates of deamination by ADA. Differences in rates of deamination as large as 10000 can be attributed to the combined effect of the O(4′) atom and the enzymes preference for an N-type conformation. The hypothesis proposed is that ADAs preference for N-type substrates is not arbitrary; it is rather the direct consequence of the conformationally dependent O(4′) anomeric effect, which is more efficient in N-type conformers in promoting the formation of a covalent hydrate at the active site of the enzyme. The formation of a covalent hydrate at the active site of ADA precedes deamination. A new and efficient synthesis of the important carbobicyclic template 14a, a useful intermediate for the synthesis of (N)MCdAdo (8) and other conformationally restricted nucleosides, is also reported.

Synthesis, Conformational Analysis, and Biological Activity of a Rigid Carbocyclic Analogue of 2′-Deoxy Aristeromycin Built on a Bicyclo[3.1.0]hexane Template #

Abstract A new chiral synthesis of the pseudosugar synthon (1R,2S,4R,5S)-1-[(benzyloxy)methyl]-2-tert-butyloxy-4-hydroxybicyclo[3.1.0]hexane (12) is reported. This compound was used as a template for the construction of carbocyclic nucleoside 4, a conformationally rigid analogue of 2′-deoxyaristeromycin. The X-ray structure and 1H NMR analysis confirmed the exclusive North [2′-exo (2E)] conformation of 4 which is vastly different from that of other non-rigid carbocyclic nucleosides. Compound 4 showed good in vitro antiviral activity against human cytomegalovirus and EBV with minimal cytotoxicity. #This manuscript is dedicated to Professor Yoshihisa Mizuno on the occasion of his 75th birthday.

A diastereoselective synthesis of (S,S)-α-fluoro-2,2-dimethyl-1,3-dioxolane-4-propanoic acid methyl ester, a key intermediate for the preparation of anti-HIV effective fluorodideoxynucleosides

(S,S)-α-fluoro-2,2-dimethyl-1,3-dioxolane-4-propanoic acid methyl ester (10), a key intermediate for the preparation of anti-HIV active 9-(2,3-dideoxy-2-fluoro-β-D-threo-pentofuranosyl)adenine (1, FddA) and 1-(2,3-dideoxy-2-fluoro-β-D-threo-pentofuranosyl)cytosine (2, FddC) was prepared via the diastereoselective fluorination of the chiral imide enolate obtained from 8 with N-fluorobenzenesulfonimide. The overall yield of 10 from the readily available 1,2:5,6-di-O-isopropylidene-D-mannitol was 25% (de 93%).

Conformational Analysis of Nucleosides Constructed on a Bicyclo[3.1.0]hexane Template. Structure-Antiviral Activity Analysis for the Northern and Southern Hemispheres of the Pseudorotational Cycle

Abstract A conformational analysis of carbocyclic nucleosides built on a rigid bicyclo[3.1.0]hexane template (1–4, Northern and 5–8 Southern) showed that the Northern conformation prefers an anti glycosyl torsion angle whereas the Southern conformation favors the syn range. Antiviral activity was mostly associated with the Northern conformers.

A new synthetic approach to the clinically useful, anti-HIV-active nucleoside, 9-(2,3-dideoxy-2-fluoro-β-D-threo-pentofuranosyl)adenine (β-FddA). Introduction of a 2′-β-fluoro substituent via inversion of a readily obtainable 2′-α-fluoro isomer

A convenient route to the anti-HIV active compound, 9-(2,3-dideoxy-2-fluoro-β-D-threo-pentofuranosyl)adenine (1, β-FddA) started with the facile introduction of fluorine at C2′ from the α-side of protected 9-(β-D-arabinofuranosyl)adenine (ara-A). Inversion of the stereochemistry at C2′ was accomplished via a stable vinyl intermediate (6), which underwent stereoselective reduction of the double bond to give the desired 2′-F-threo isomer with the opposite β-fluoro stereochemistry.

The “β-Fluorine Effect” in the Non-Metal Hydride Radical Deoxygenation of Fluorine-Containing Nucleoside Xanthates

Abstract An alternative method to conduct a Barton-McCombie deoxygenation in nucleosides is described. The utility of the procedure is limited to structures with an electronegative substituent, particularly fluorine, in the β-position relative to the radical center. The process is radical in nature and triggered by peroxides. The abstraction of hydrogen from the solvent is favorably influenced by the presence of a β-fluorine.

4′-C-Methyl-2′-Deoxyadenosine and 4′-C-Ethyl-2′-Deoxyadenosine Inhibit HIV-1 Replication

ABSTRACT It is important to develop new anti-HIV drugs that are effective against the existing drug-resistant mutants. Because the excision mechanism is an important pathway for resistance to nucleoside analogs, we are preparing analogs that retain a 3′-OH and can be extended after they are incorporated by the viral reverse transcriptase. We show that 4′-C-alkyl-deoxyadenosine (4′-C-alkyl-dA) compounds can be phosphorylated in cultured cells and can inhibit the replication of HIV-1 vectors: 4′-C-methyl- and 4′-C-ethyl-dA show both efficacy and selectivity against HIV-1. The compounds are also effective against viruses that replicate using reverse transcriptases (RTs) that carry nucleoside reverse transcriptase inhibitor resistance mutations, with the exception of the M184V mutant. Analysis of viral DNA synthesis in infected cells showed that viral DNA synthesis is blocked by the incorporation of either 4′-C-methyl- or 4′-C-ethyl-2′-deoxyadenosine. In vitro experiments with purified HIV-1 RT showed that 4′-C-methyl-2′-dATP can compete with dATP and that incorporation of the analog causes pausing in DNA synthesis. The 4′-C-ethyl compound also competes with dATP and shows a differential ability to block DNA synthesis on RNA and DNA templates. Experiments that measure the ability of the compounds to block DNA synthesis in infected cells suggest that this differential block to DNA synthesis also occurs in infected cells.

LESSONS FROM THE PSEUDOROTATIONAL CYCLE : CONFORMATIONALLY RIGID AZT CARBOCYCLIC NUCLEOSIDES AND THEIR INTERACTION WITH REVERSE TRANSCRIPTASE

Abstract Two conformationally locked carba-AZT nucleoside 5′-triphosphates built on a rigid bicyclo[3.1.0]hexane template showed exclusive Northern (2E) and Southern (3E) conformations, respectively. Inhibition of reverse transcriptase (RT) occurred selectively with the Northern carba-AZX triphosphate.

Contrasting Behavior of Conformationally Locked Carbocyclic Nucleosides of Adenosine and Cytidine as Substrates for Deaminases

In addition to the already known differences between adenosine deaminase (ADA) and cytidine deaminase (CDA) in terms of their tertiary structure, the sphere of Zn+2 coordination, and their reverse stereochemical preference, we present evidence that the enzymes also differ significantly in terms of the North/South conformational preferences for their substrates and the extent to which the lack of the O(4′) oxygen affects the kinetics of the enzymatic deamination of carbocyclic substrates. The carbocyclic nucleoside substrates used in this study have either a flexible cyclopentane ring or a rigid bicyclo[3.1.0]hexane scaffold.

Chemistry and Anti-HIV Activity of 2′-β-Fluoro-2′,3′-dideoxyguanosine

Abstract The 2′-β-fluoro analogue of 2′,3′-dideoxyguanosine has been prepared by two synthetic routes. This compound and two analogues have anti-HIV activity in at least two of three host cell systems used (ATH8, CEM, PBL). These compounds, as well as their ddGuo parents, have been characterized with regard to their acid-stabilities, octanol-water partition coefficients, and enzyme substrate properties for adenosine deaminase and purine nucleoside phosphorylase. F-ddGuo analogues are less potent but more stable than their non-fluorinated parent compounds.