Nucleic Acid Related Compounds. 91. Biomimetic Reactions Are in Harmony with Loss of 2‘-Substituents as Free Radicals (Not Anions) during Mechanism-Based Inactivation of Ribonucleotide Reductases. Differential Interactions of Azide, Halogen, and Alkylthio Groups with Tributylstannane and Triphenylsilane<sup>1</sup>

Robins, Morris J.; Wnuk, Stanislaw F.; Hernández-Thirring, and Amelia E.; Samano, Mirna C.

doi:10.1021/ja962117m

Cited by 22 publications

(35 citation statements)

References 59 publications

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“…Generation of the closed-shell ketone intermediate 3 in step 3 now only requires reshuffling of the hydrogen bonding network of the active site. That the substituent connected to the C29 carbon atom is cleaved homolytically has previously not been assumed to be relevant for the natural substrates of RNR enzymes, but represents the default pathway in model reactions performed in apolar solvents on substrates carrying a C29 leaving group, such as thiol (Pereira et al, 2005), phenylsulfinyl (Robins et al, 1999), or halides (Robins et al, 1996). For disulfide substituents in the C29 position, experimental and computational studies are suggestive of homolytic cleavage, even in the enzyme-catalyzed reaction (Covè s et al, 1996;Pereira et al, 2005).…”

Section: Bereitgestellt Von | Universitaetsbibliothek Der Lmu Muenchenmentioning

confidence: 99%

Spectroscopic and theoretical approaches for studying radical reactions in class I ribonucleotide reductase

Bennati

Lendzian²,

Schmittel³

et al. 2005

Biological Chemistry

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Ribonucleotide reductases (RNRs) catalyze the production of deoxyribonucleotides, which are essential for DNA synthesis and repair in all organisms. The three currently known classes of RNRs are postulated to utilize a similar mechanism for ribonucleotide reduction via a transient thiyl radical, but they differ in the way this radical is generated. Class I RNR, found in all eukaryotic organisms and in some eubacteria and viruses, employs a diferric iron center and a stable tyrosyl radical in a second protein subunit, R2, to drive thiyl radical generation near the substrate binding site in subunit R1. From extensive experimental and theoretical research during the last decades, a general mechanistic model for class I RNR has emerged, showing three major mechanistic steps: generation of the tyrosyl radical by the diiron center in subunit R2, radical transfer to generate the proposed thiyl radical near the substrate bound in subunit R1, and finally catalytic reduction of the bound ribonucleotide. Amino acid-or substrate-derived radicals are involved in all three major reactions. This article summarizes the present mechanistic picture of class I RNR and highlights experimental and theoretical approaches that have contributed to our current understanding of this important class of radical enzymes.

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Section: Bereitgestellt Von | Universitaetsbibliothek Der Lmu Muenchenmentioning

confidence: 99%

Spectroscopic and theoretical approaches for studying radical reactions in class I ribonucleotide reductase

Bennati

Lendzian²,

Schmittel³

et al. 2005

Biological Chemistry

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“…The latter nucleosides displayed the same behavior with azide (instead of chlorine) in the 2'position, although in the former the azide was reduced to amine. [46] The substrate analogue 2'-chloro-2'-deoxy-6'-O-nitrohomouridine also eliminated radical chlorine under similar conditions, to give 2-(2-hydroxyethyl)-3(2H)-furanone, an analogue of 5.…”

Section: Introductionmentioning

confidence: 96%

Theoretical Studies on the Mode of Inhibition of Ribonucleotide Reductase by 2′‐Substituted Substrate Analogues

Fernandes

Ramos

2003

Chemistry A European J

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Several 2'-substituted-2'-deoxyribonucleotides are potent time-dependent inactivators of the enzyme ribonucleotide reductase (RNR), which function by destructing its essential tyrosil radical and/or by performing covalent addition to the enzyme. The former leads to inhibition of the R2 dimer of RNR and the latter to inhibition of the R1 dimer. Efforts to elucidate the mechanism of inhibition have been undertaken in the last decades, and a general mechanistic scheme has emerged. Accordingly, two alternative pathways lead either to the inhibition of R1 or R2, for which the 2'-chloro-2'-deoxynucleotides serve as the model for the inhibition of R1 and the 2'-azido-2'-deoxynucleotides the model for the inhibition of R2. However, the underlying reason for the different behavior of the inhibitors has remained unknown until now. Moreover, a fundamental mechanistic alternative has been proposed, based on results from biomimetic reactions, in which the 2'-substituents would be eliminated as radicals, and not as anions, as previously assumed. This would lead to further reactions not predicted by the existing mechanistic scheme. To gain a better understanding we have performed high-level theoretical calculations on the active site of RNR. Results from this work support the general Stubbe's paradigm, although some changes to that mechanism are necessary. In addition, a rational explanation of the factors that determine which of the dimers (R1 or R2) will be inactivated is provided for the first time. It has been demonstrated also that the 2'-substituents are indeed eliminated as anions, and not as radicals. Biomimetic experiments have led to different results because they lack a basic group capable of deprotonating the 3'-HO group of the substrate. It has been found here that the chemical character of the leaving group (radical or anionic) can be manipulated by controlling the protonation state of the 3'-HO group.

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“…34 Treatment with Hg salts was also unsuccessful for S -detritylation, 34 but treatment of 7 with TFA in the presence of Et 3 SiH 35 cleanly removed the S -trityl group affording 8 (79%). It is noteworthy that the azido group was not affected 36 by Et 3 SiH employed in the S -detritylation step, although reduction of an azido group to a primary amino group by the more reactive radical-based reducing agent (Me 3 Si) 3 SiH is known. 22 Compound 8 is prone to oxidation to the disulfide and/or cleavage of the cysteinate ester bond at the 2′ position during silica gel column purification.…”

Section: Resultsmentioning

confidence: 99%

Investigation of reactions postulated to occur during inhibition of ribonucleotide reductases by 2′-azido-2′-deoxynucleotides

et al. 2012

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Model 3′-azido-3′-deoxynucleosides with thiol or vicinal dithiol substituents at C2′ or C5′ were synthesized to study reactions postulated to occur during inhibition of ribonucleotide reductases by 2′-azido-2′-deoxynucleotides. Esterification of 5′-(tert-butyldiphenylsilyl)-3′-azido-3′-deoxyadenosine and 3′-azido-3′-deoxythymidine (AZT) with 2,3-S-isopropylidene-2,3-dimercaptopropanoic acid or N-Boc-S-trityl-L-cysteine and deprotection gave 3′-azido-3′-deoxy-2′-O-(2,3-dimercaptopropanoyl or cysteinyl)adenosine and the 3′-azido-3′-deoxy-5′-O-(2,3-dimercaptopropanoyl or cysteinyl)thymidine analogs. Density functional calculations predicted that intramolecular reactions between generated thiyl radicals and an azido group on such model compounds would be exothermic by 33.6-41.2 kcal/mol and have low energy barriers of 10.4-13.5 kcal/mol. Reduction of the azido group occurred to give 3′-amino-3′-deoxythymidine, which was postulated to occur with thiyl radicals generated by treatment of 3′-azido-3′-deoxy-5′-O-(2,3-dimercaptopropanoyl)thymidine with 2,2′-azobis-(2-methyl-2-propionamidine) dihydrochloride. Gamma radiolysis of N2O-saturated aqueous solutions of AZT and cysteine produced 3′-amino-3′-deoxythymidine and thymine most likely by both radical and ionic processes.

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Cited by 22 publications

References 59 publications

Spectroscopic and theoretical approaches for studying radical reactions in class I ribonucleotide reductase

Spectroscopic and theoretical approaches for studying radical reactions in class I ribonucleotide reductase

Theoretical Studies on the Mode of Inhibition of Ribonucleotide Reductase by 2′‐Substituted Substrate Analogues

Investigation of reactions postulated to occur during inhibition of ribonucleotide reductases by 2′-azido-2′-deoxynucleotides

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