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

Márquez, Víctor E.; Russ, Pamela; Alonso, Randolph; Siddiqui, M. Arshad; Hernández, Susana; George, Clifford; Nicklaus, Marc C.; Dai, Fang; Ford, Harry

doi:10.1002/(sici)1522-2675(19991215)82:12<2119::aid-hlca2119>3.0.co;2-y

Cited by 74 publications

(76 citation statements)

References 17 publications

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“…The activity of ADA is affected by the structural determinants of its substrates. While we have previously demonstrated (Marquez and colleagues) that this enzyme efficiently deaminates nucleoside analogs in the north conformation (43)(44)(45)(46), the kinetic analysis of ADA that we report here shows that the presence of a substituent at the 2 position of the adenine base makes these derivatives poor substrates for ADA. These results agree with previous studies reporting that 2-halo-substituted compounds are not efficiently deaminated by ADA (29,(31)(32)(33).…”

Section: Discussionmentioning

confidence: 99%

“…In contrast, host cell kinases appear to prefer the sugar ring in the south conformation; compounds that favor the north conformation are generally phosphorylated inefficiently (41,42). Sugar ring conformation has also been reported to play an important role in ADA recognition; the enzyme has been reported to deaminate nucleosides biased toward the north conformation up to 65-fold faster than those biased toward the south conformation (43)(44)(45)(46). Additionally, 2-fluoro-2=-deoxyadenosine (FdA) analogs are somewhat resistant to ADA-mediated catabolism due to the electron withdrawing properties of the 2-fluoro group (47,48), and we have previously reported that EFdA is poorly deaminated by ADA because of the 2-fluoro group (21).…”

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confidence: 99%

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Effects of Substitutions at the 4′ and 2 Positions on the Bioactivity of 4′-Ethynyl-2-Fluoro-2′-Deoxyadenosine

Kirby

Michailidis

Fetterly

et al. 2013

Antimicrob Agents Chemother

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i Nucleos(t)ide reverse transcriptase inhibitors (NRTIs) form the backbone of most anti-HIV therapies. We have shown that 4=-ethynyl-2-fluoro-2=-deoxyadenosine (EFdA) is a highly effective NRTI; however, the reasons for the potent antiviral activity of EFdA are not well understood. Here, we use a combination of structural, computational, and biochemical approaches to examine how substitutions in the sugar or adenine rings affect the incorporation of dA-based NRTIs like EFdA into DNA by HIV RT and their susceptibility to deamination by adenosine deaminase (ADA). Nuclear magnetic resonance (NMR) spectroscopy studies of 4=-substituted NRTIs show that ethynyl or cyano groups stabilize the sugar ring in the C-2=-exo/C-3=-endo (north) conformation. Steady-state kinetic analysis of the incorporation of 4=-substituted NRTIs by RT reveals a correlation between the north conformation of the NRTI sugar ring and efficiency of incorporation into the nascent DNA strand. Structural analysis and the kinetics of deamination by ADA demonstrate that 4=-ethynyl and cyano substitutions decrease the susceptibility of adenosinebased compounds to ADA through steric interactions at the active site. However, the major determinant for decreased susceptibility to ADA is the 2-halo substitution, which alters the pK a of N1 on the adenine base. These results provide insight into how NRTI structural attributes affect their antiviral activities through their interactions with the RT and ADA active sites. There are 10 nucleos(t)ide reverse transcriptase inhibitors (NRTIs) that are currently approved for the treatment of human immunodeficiency virus type 1 (HIV-1) infections (1-5). Several more nucleoside analog drugs are approved or being studied for the treatment of viruses, such as herpes simplex virus (HSV), hepatitis C virus (HCV), and hepatitis B virus (HBV), or as anticancer agents (6-10). NRTIs are among the most effective anti-HIV drugs. All approved anti-HIV NRTIs lack a 3=-hydroxyl moiety and, thus, act as chain terminators following their incorporation by the viral reverse transcriptase (RT) into the nascent DNA chain. However, the absence of a 3=-OH, while essential for the inhibition of DNA synthesis, also imparts detrimental properties to these inhibitors, including reduced intracellular phosphorylation to the active triphosphate form and reduced RT binding affinity (11). Prolonged exposure to NRTI-based treatments causes mitochondrial toxicity (12-14) and leads to the development of NRTI resistance mutations (15-18), giving rise to complications in the treatment of HIV-infected patients.Ideally, an NRTI should have a strong binding affinity for the RT target, a high barrier for the development of resistance, and low toxicity. We have reported that a series of 4=-substituted nucleosides in which the 3=-OH is retained has exceptional inhibitory activity against HIV-1 RT (19). Among these compounds, 4=-ethynyl-2-fluoro-2=-deoxyadenosine (EFdA) is a highly active RT inhibitor that prevents translocation of the nucleic acid from the n...

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Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

Effects of Substitutions at the 4′ and 2 Positions on the Bioactivity of 4′-Ethynyl-2-Fluoro-2′-Deoxyadenosine

Kirby

Michailidis

Fetterly

et al. 2013

Antimicrob Agents Chemother

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“…[26,27] In contrast, studies in our laboratory with carbocyclic nucleosides have revealed that the sugar moiety in ADA seems to play a significant role in catalysis by providing effective electronic communication between the O(4’) and the base through the anomeric effect and also by providing electron-withdrawing activation. [28]…”

Section: Introductionmentioning

confidence: 99%

“…Therefore, the loss of this interaction resulting from the replacement of the furanose ring of adenosine or 2’-deoxyadenosine with a cyclopentane ring —as in the fermentation product aristeromycin ( 3 )— also helps explains the significant drop in the deamination rate of 3 to 0.58% the rate of adenosine. [28] Obviously the absence of the O(4’) oxygen abolishes the stereoelectronic interplay between the purine ring and the ribofuranosyl moiety, impacting negatively on the propensity of the base to form a covalent hydrate. [29] It has been clearly demonstrated by Chattopadhyaya and coworkers that the electronic properties of the aglycon are effectively transmitted to the pentofuranose moiety through the anomeric effect.…”

Section: Introductionmentioning

confidence: 99%

“…[28] Significantly, despite this considerable drop in activity, the enzyme still showed a 100-fold preference for North -dAdo ( 4 ) over South -dAdo ( 5 ), and the former compound was in turn preferred by nearly 2-fold over the flexible aristeromycin ( 3 ). Based on these findings we postulated that the preference of ADA for North -dAdo resulted principally from the correct equatorial disposition of the 3’-OH engaged in effective hydrogen bonding with Asp16, as observed in the crystal structure.…”

Section: Introductionmentioning

confidence: 99%

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

Márquez

Schroeder

Ludek

et al. 2009

Nucleosides, Nucleotides & Nucleic Acids

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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.

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Synthesis of a North‐Methanocarba‐Thymidine (N‐MCT) Analog

Thompson

Márquez

2012

CP Nucleic Acid Chemistry

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A detailed protocol for the synthesis of North-methanocarba-thymidine (N-MCT), a potent antiviral nucleoside with a restricted bicyclo[3.1.0]hexane pseudosugar conformation, is presented. The process is described in two parts. The first basic protocol deals with the synthesis of the carbobicyclic pseudosugar precursor that can be utilized in the syntheses of other bicyclo[3.1.0]hexane nucleosides with natural and non-natural nucleobases. The second basic protocol describes the specific construction of the thymine base in a linear fashion from the carbobicyclic intermediate.

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

Cited by 74 publications

References 17 publications

Effects of Substitutions at the 4′ and 2 Positions on the Bioactivity of 4′-Ethynyl-2-Fluoro-2′-Deoxyadenosine

Effects of Substitutions at the 4′ and 2 Positions on the Bioactivity of 4′-Ethynyl-2-Fluoro-2′-Deoxyadenosine

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

Synthesis of a North‐Methanocarba‐Thymidine (N‐MCT) Analog

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