Hydroxyl Group Of Adenosine Research Articles

Insights into phosphate cooperativity and influence of substrate modifications on binding and catalysis of hexameric purine nucleoside phosphorylases.

The hexameric purine nucleoside phosphorylase from Bacillus subtilis (BsPNP233) displays great potential to produce nucleoside analogues in industry and can be exploited in the development of new anti-tumor gene therapies. In order to provide structural basis for enzyme and substrates rational optimization, aiming at those applications, the present work shows a thorough and detailed structural description of the binding mode of substrates and nucleoside analogues to the active site of the hexameric BsPNP233. Here we report the crystal structure of BsPNP233 in the apo form and in complex with 11 ligands, including clinically relevant compounds. The crystal structure of six ligands (adenine, 2′deoxyguanosine, aciclovir, ganciclovir, 8-bromoguanosine, 6-chloroguanosine) in complex with a hexameric PNP are presented for the first time. Our data showed that free bases adopt alternative conformations in the BsPNP233 active site and indicated that binding of the co-substrate (2′deoxy)ribose 1-phosphate might contribute for stabilizing the bases in a favorable orientation for catalysis. The BsPNP233-adenosine complex revealed that a hydrogen bond between the 5′ hydroxyl group of adenosine and Arg43* side chain contributes for the ribosyl radical to adopt an unusual C3’-endo conformation. The structures with 6-chloroguanosine and 8-bromoguanosine pointed out that the Cl6 and Br8 substrate modifications seem to be detrimental for catalysis and can be explored in the design of inhibitors for hexameric PNPs from pathogens. Our data also corroborated the competitive inhibition mechanism of hexameric PNPs by tubercidin and suggested that the acyclic nucleoside ganciclovir is a better inhibitor for hexameric PNPs than aciclovir. Furthermore, comparative structural analyses indicated that the replacement of Ser90 by a threonine in the B. cereus hexameric adenosine phosphorylase (Thr91) is responsible for the lack of negative cooperativity of phosphate binding in this enzyme.

Simultaneous and site-directed incorporation of an ester linkage and an azide group into a polypeptide by in vitro translation

A method is presented by which an azide-containing side chain can be introduced into any internal position of a polypeptide chain by in vitro translation. For this, 2'-deoxy-cytidylyl-(3'-->5')-adenosine was acylated on the 3'(2')-hydroxyl group of adenosine with 6-azido-2(S)-hydroxyhexanoic acid (AHHA), an alpha-hydroxy- and epsilon-azide derivative of L-lysine. The acylated dinucleotide was enzymatically ligated with a tRNA transcript to provide chemically stable E. coli suppressor AHHA-tRNA(Cys(CUA)). The esterase 2 gene from Alicyclobacillus acidocaldarius was modified by the amber stop codon (UAG) on position 118. Using AHHA-tRNA(Cys(CUA)) in an E. coli in vitro translation/transcription system, the site-directed introduction of an azide group linked to a backbone ester into the esterase polypeptide was achieved. The yield of the synthesized modified protein reached 80% compared to translation of the native esterase. Subsequently, azide coupling with an alkyne-modified oligodeoxynucleotide demonstrated the feasibility of this approach for conjugation of polypeptides.

Biomimetic monoacylation of diols in water. Lanthanide-promoted reactions of methyl benzoyl phosphate.

The direct monoacylation of diols by acyl phosphate monoesters in water is a biomimetic analogy to the enzymic aminoacylation of tRNA by aminoacyl adenylates. Without catalysis, acyl phosphate monoesters react rapidly with amines but very slowly with water and alcohols. Lanthanide ions dramatically and selectively facilitate the base-catalyzed monoacylation of diols in water by methyl benzoyl phosphate (MBP), a typical acyl phosphate monoester, in neutral solutions where reactive amines are protonated and unreactive. The reaction patterns and reactivity of various diols with MBP in the presence of lanthanides are consistent with a mechanism that involves internal addition from the conjugate base of the bis-bidentate complex of the lanthanide with the diol and MBP. The method is also applicable to reactions of nucleosides as evidenced by the selective monoacylation of the 2'- or 3'-hydroxyl group of adenosine, without reaction of the 5'-hydroxyl group or the 6-amino group. Analogues of adenosine without the diol are unreactive. This suggests that the method will selectively monoacylate the hydroxyl groups at the unique diol in tRNA that forms the 3'-terminus.

Roles for adenosine ribose hydroxyl groups in cyclic adenosine 5'-diphosphate ribose-mediated Ca2+ release.

Cyclic adenosine diphosphate ribose (cADPR) is a naturally occurring and potent Ca2+-mobilizing agent. Structural analogues are currently required as pharmacological tools for the investigation of this topical molecule, but modifications to date have concentrated primarily upon the purine ring. Two novel dehydroxylated analogues of cADPR have now been prepared from chemically synthesized nicotinamide adenine dinucleotide (NAD+) precursors modified in the ribose moiety linked to adenine. ADP-ribosyl cyclase of Aplysia californica catalyzed the conversion of 2'A-deoxy-NAD+ and 3'A-deoxy-NAD+ into the corresponding 2'A-deoxy-cADPR and 3'A-deoxy-cADPR analogues, respectively. These analogues were used to assess the effect of 2'- and 3'-hydroxyl group deletion in the adenosine ribose moiety of cADPR on the Ca2+-releasing potential of cADPR. These compounds were found to have comparatively markedly different activities as agonists for Ca2+ mobilization in sea urchin egg homogenate. 2'A-Deoxy-cADPR is similar to cADPR, whereas 3'A-deoxy-cADPR is at least 100-fold less potent, indicating that the 3'A-hydroxyl group, but not the 2'A-hydroxyl group, is essential for calcium releasing activity. EC50 values recorded were 32 nM, 58 nM, and 5 microM for cADPR, 2'A-deoxy-cADPR, and 3'A-deoxy-cADPR, respectively. Moreover, 200 nM 2'A-deoxy-cADPR was required to desensitize the cADPR-sensitive Ca2+ channel to a subsequent addition of 100 nM cADPR, but 20 microM 3'A-deoxy-cADPR was required to produce the same desensitizing effect. This is in accordance with the 100-fold lower potency exhibited by the latter analogue. To further investigate the importance of the 3'-hydroxyl group, we have also synthesized 3'A-O-methyl-cADPR, in which the 3'-hydroxyl group of adenosine has been methylated and its ability potentially to donate a hydrogen atom in a hydrogen bond has been removed. Although inactive in releasing Ca2+, 3'A-O-methyl-cADPR inhibited cADPR-induced Ca2+ release in a dose-dependent manner with an approximate IC50 value of 5 microM, whereas 3'-O-methyladenosine had no effect. This further supports the requirement of a 3'-OH group for Ca2+ releasing activity. In addition, however, it suggests that this group may not be crucial for ligand-receptor recognition. Thus, replacement of the hydrogen atom of the hydroxyl with a methyl group effects a change of activity from an agonist to an antagonist of cADPR-induced Ca2+ release. Two other analogues with modifications in the 2' and/or 3' positions, 3'-cADPR phosphate and 2',3'-cyclic-cADPR phosphate, were synthesized and tested for their Ca2+-mobilizing activity in sea urchin egg homogenates. Both analogues were inactive with respect to both agonistic and antagonistic activities on the cADPR-sensitive Ca2+ release mechanism. These are the first steps toward a wider structure-activity relationship for cADPR, and this is the first study to implicate a crucial role for the adenosine ribose hydroxyl groups of cADPR in the biological activity of this cyclic nucleotide. Additionally, this is the first report of a cADPR receptor antagonist that is not modified at the 8-position of the purine ring.

High-resolution NMR study of a GdAGA tetranucleotide loop that is an improved substrate for ricin, a cytotoxic plant protein.

Ricin is a cytotoxic plant protein that inactivates ribosomes by hydrolyzing the N-glycosidic bond at position A4324 in eukaryotic 28S rRNA. Recent studies showed that a four-nucleotide loop, GAGA, can function as a minimum substrate for ricin (the first adenosine corresponds to the site of depurination). We previously clarified the solution structure of this loop by NMR spectroscopy [Orita et al. (1993) Nucleic Acids Res. 21, 5670-5678]. To elucidate further details of the structural basis for recognition of its substrate by ricin, we studied the properties of a synthetic dodecanucleotide, r1C2U3C4A5G6dA7G8A9U10G11A12G (6dA12mer), which forms an RNA hairpin structure with a GdAGA loop and in which the site of depurination is changed from adenosine to 2'-deoxyadenosine. The N-glycosidase activity against the GdAGA loop of the A-chain of ricin was 26 times higher than that against the GAGA loop. NMR studies indicated that the overall structure of the GdAGA loop was similar to that of the GAGA loop with the exception of the sugar puckers of 6dA and 7G. Therefore, it appears that the 2'-hydroxyl group of adenosine at the depurination site (6A) does not participate in the recognition by ricin of the substrate. Since the 2'-hydroxyl group can potentially destabilize the developing positive charge of the putative transition state intermediate, an oxycarbonium ion, the electronic effect may explain, at least in part, the faster rate of depurination of the GdAGA loop compared to that of GAGA loop. We also show that the amino group of 7G is essential for substrate recognition the ricin A-chain.

ChemInform Abstract: Synthesis of 2′(3′)-O-(L-Phenylalanyl) and 2′(3′)-O-(D-Phenylalanyl) Cytidylyl(3′-5′)adenosine.

A general route to the synthesis of the 2′(3′)-O-aminoacyl CpA using the 1-ethoxyethyl group for tentative protection of the 2′-hydroxyl group of adenosine, is described.

Synthesis of 2′(3′)-O-(L-Phenylalanyl) and 2′(3′)-O-(D-Phenylalanyl) Cytidylyl(3′-5′)adenosine

Abstract A general route to the synthesis of the 2′(3′)-O-aminoacyl CpA using the 1-ethoxyethyl group for tentative protection of the 2′-hydroxyl group of adenosine, is described.

Inhibition of adenosine and thymidylate kinases by bisubstrate analogs.

Potential bisubstrate analogs, in which the 5'-hydroxyl group of adenosine was joined to the phosphoryl group acceptor by polyphosphoryl bridges of varying length (ApnX, where n is the number of phosphoryl groups and X is the nucleoside moiety of the acceptor), were tested as inhibitors of human liver adenosine kinase and of thymidylate kinase from peripheral blast cells of patients with acute myelocytic leukemia. Adenosine kinase was most strongly inhibited by P1,P4-(diadenosine 5')-tetraphosphate (Kd = 30 nM) and P1,P5-(diadenosine 5')-pentaphosphate (Kd = 73 nM). Thymidylate kinase was most strongly inhibited by P1-(adenosine 5')-P5-(thymidine 5')-pentaphosphate (Kd = 120 nM) and by P1(adenosine 5')-P6-(thymidine 5')-hexaphosphate (Kd = 43 nM). In these enzymes, as in adenylate and thymidylate kinases, strongest inhibition was achieved in compounds containing one or two more phosphoryl groups than the substrates combined. These results support the view that nucleoside and nucleotide kinases mediate direct transfer of phosphoryl groups from ATP to acceptors, rather than acting by a double displacement mechanism.

ChemInform Abstract: SYNTHESIS OF OLIGORIBONUCLEOTIDES USING 4‐METHOXYBENZYL GROUP AS A NEW PROTECTING GROUP OF THE 2′‐HYDROXYL GROUP OF ADENOSINE

Chemischer InformationsdienstVolume 13, Issue 31 Natural Products ChemInform Abstract: SYNTHESIS OF OLIGORIBONUCLEOTIDES USING 4-METHOXYBENZYL GROUP AS A NEW PROTECTING GROUP OF THE 2′-HYDROXYL GROUP OF ADENOSINE H. TAKAKU, H. TAKAKUSearch for more papers by this authorK. KAMAIKE, K. KAMAIKESearch for more papers by this author H. TAKAKU, H. TAKAKUSearch for more papers by this authorK. KAMAIKE, K. KAMAIKESearch for more papers by this author First published: August 3, 1982 https://doi.org/10.1002/chin.198231318AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat No abstract is available for this article. Volume13, Issue31August 3, 1982 RelatedInformation

Substrate specificity of adenosine deaminase—Function of the 5′-hydroxyl group of adenosine

Nucleosides in which the adenine ring has been moved from the 1′ position to the 5′ position are resistant to degradation by the enzyme, adenosine deaminase. This study provides further evidence for the importance of the 5′-hydroxyl group as a structural requirement for significant substrate activity.

Mode of action of nuclease P1 on nucleic acids and its specificity for synthetic phosphodiesters.

Nuclease P1 was found to attack RNA and heat-denatured DNA in endo- and exonucleolytic manners. The evidence was as follows: (1) In the early stage of digestion both mononucleotides and oligonucleotides with various sizes were formed simultaneously with rapid fragmentation of polynucleotides. (2) The relative amount of the monomer was larger than that of any class of oligomers throughout the process of digestion. Nuclease P1 showed a preference for the linkages between 3′-hydroxyl group of adenosine or deoxyadenosine and the 5′-phosphoryl group of the adjacent nucleotides. p-Nitrophenyl ester of 3′-dTMP was hydrolyzed to thymidine and p-nitrophenyl phosphate, while p-nitrophenyl ester of 5′-dTMP was not attacked. It is concluded from these findings that the basic structure required for the substrate of nuclease P1 is a nucleoside 3′-phosphate-containing structure and the enzyme cleaves the diester bond between the phosphate and the 3′-hydroxyl group of the sugar.

The role of the 5'-hydroxyl group of adenosine in determining substrate specificity for adenosine deaminase.

The role of the 5'-hydroxyl group of adenosine in determining substrate specificity for adenosine deaminase.

STUDIES OF NUCLEOSIDES AND NUCLEOTIDES. XXII. PHOSPHORYLATION OF ADENOSINE USING BORATE COMPLEX AS PROTECTING GROUP FOR 2'-AND 3'-HYDROXYL GROUPS.

Phosphorylation of adenosine with morpholino phosphorodichloridate, P1-diphenyl P2-morpholino pyrophosphorochloridate and 2, 6-lupetidyl phosphorodichloridate in the presence of boric acid was performed in DMF solution. It was observed that the ratio of resulting 5'-monophosphate to 2'-+3'-monophosphate was in the range of 2.7∼5.5, which indicated the protection of borate complex on 2'-and 3'-hydroxyl group of adenosine against the attack of the phosphorylating agent.