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Papis M, Colombo S, Spanu D, Recchia S, Nava D, Foschi F, Broggini G, Loro C. Diastereoselective Palladaelectro-Catalyzed Construction of Bromomethyl Morpholines as Key Step To Access Morpholino Homonucleosides. Org Lett 2024. [PMID: 39037909 DOI: 10.1021/acs.orglett.4c01790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
A synthetic protocol for the preparation of a new class of morpholino homonucleosides in enantiopure form starting from readily available 1,2-aminoalcohols or glycidol has been developed. Key intermediates of the synthetic sequence are 2-bromomethyl morpholines, diastereoselectively achieved from the corresponding alkenols by palladaelectro-catalyzed alkoxybromination of unactivated alkenes. The so obtained bromo derivatives are in turn susceptible to functionalization with nucleic bases for easy access to morpholino homonucleosides.
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Affiliation(s)
- Marta Papis
- Dipartimento di Scienza e Alta Tecnologia, Università degli Studi dell'Insubria, Via Valleggio 9, 22100, Como, Italy
| | - Sara Colombo
- Dipartimento di Scienza e Alta Tecnologia, Università degli Studi dell'Insubria, Via Valleggio 9, 22100, Como, Italy
| | - Davide Spanu
- Dipartimento di Scienza e Alta Tecnologia, Università degli Studi dell'Insubria, Via Valleggio 9, 22100, Como, Italy
| | - Sandro Recchia
- Dipartimento di Scienza e Alta Tecnologia, Università degli Studi dell'Insubria, Via Valleggio 9, 22100, Como, Italy
| | - Donatella Nava
- DISFARM, Sezione di Chimica Generale e Organica "A. Marchesini", Università degli Studi di Milano, Via Venezian 21, 20133, Milano, Italy
| | - Francesca Foschi
- Dipartimento di Scienza e Alta Tecnologia, Università degli Studi dell'Insubria, Via Valleggio 9, 22100, Como, Italy
| | - Gianluigi Broggini
- Dipartimento di Scienza e Alta Tecnologia, Università degli Studi dell'Insubria, Via Valleggio 9, 22100, Como, Italy
| | - Camilla Loro
- Dipartimento di Scienza e Alta Tecnologia, Università degli Studi dell'Insubria, Via Valleggio 9, 22100, Como, Italy
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2
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Sivakrishna B, Shukla M, Santra MK, Pal S. Design, synthesis and cytotoxic evaluation of truncated 3'-deoxy- 3', 3' difluororibofuranosyl pyrimidine nucleosides. Carbohydr Res 2020; 497:108113. [PMID: 32858257 DOI: 10.1016/j.carres.2020.108113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 07/28/2020] [Accepted: 07/28/2020] [Indexed: 02/05/2023]
Abstract
Truncated 3'-deoxy- 3', 3' difluororibofuranosyl pyrimidine nucleoside derivatives were synthesized from d-ribose via β-apioribo pyrimidine nucleoside intermediates 11a-c. The synthetic approach signifies that truncation at C3' position of apioribose ring of 13a-c by oxidative cleavage of diols with Pb(OAc)4 and followed by fluorination with DAST as key steps. Cytotoxic evaluation of synthesized truncated nucleoside derivatives 16a-c and 19a-c were tested against MCF7 and MDA-MB-231 breast cancer cell lines. However, only 19a was shown minimal growth suppression activity on MDA-MB-231 cancer cell lines.
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Affiliation(s)
- Balija Sivakrishna
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Argul, Odisha, 752050, India
| | - Meenakshi Shukla
- Cancer Biology Laboratory, National Centre for Cell Science, Ganeshkhind Road, Pune, Maharashtra, 411007, India
| | - Manas Kumar Santra
- Cancer Biology Laboratory, National Centre for Cell Science, Ganeshkhind Road, Pune, Maharashtra, 411007, India.
| | - Shantanu Pal
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Argul, Odisha, 752050, India.
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3
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Comparison of Protein N-Homocysteinylation in Rat Plasma under Elevated Homocysteine Using a Specific Chemical Labeling Method. Molecules 2016; 21:molecules21091195. [PMID: 27617989 PMCID: PMC5292613 DOI: 10.3390/molecules21091195] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 09/02/2016] [Accepted: 09/05/2016] [Indexed: 11/30/2022] Open
Abstract
Elevated blood concentrations of homocysteine have been well established as a risk factor for cardiovascular diseases and neuropsychiatric diseases, yet the etiologic relationship of homocysteine to these disorders remains poorly understood. Protein N-homocysteinylation has been hypothesized as a contributing factor; however, it has not been examined globally owing to the lack of suitable detection methods. We recently developed a selective chemical method to label N-homocysteinylated proteins with a biotin-aldehyde tag followed by Western blotting analysis, which was further optimized in this study. We then investigated the variation of protein N-homocysteinylation in plasma from rats on a vitamin B12 deficient diet. Elevated “total homocysteine” concentrations were determined in rats with a vitamin B12 deficient diet. Correspondingly, overall levels of plasma protein N-homocysteinylation displayed an increased trend, and furthermore, more pronounced and statistically significant changes (e.g., 1.8-fold, p-value: 0.03) were observed for some individual protein bands. Our results suggest that, as expected, a general metabolic correlation exists between “total homocysteine” and N-homocysteinylation, although other factors are involved in homocysteine/homocysteine thiolactone metabolism, such as the transsulfuration of homocysteine by cystathionine β-synthase or the hydrolysis of homocysteine thiolactone by paraoxonase 1 (PON1), may play more significant or direct roles in determining the level of N-homocysteinylation.
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4
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Mildly acidic conditions eliminate deamidation artifact during proteolysis: digestion with endoprotease Glu-C at pH 4.5. Amino Acids 2016; 48:1059-1067. [PMID: 26748652 DOI: 10.1007/s00726-015-2166-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 12/25/2015] [Indexed: 10/22/2022]
Abstract
Common yet often overlooked, deamidation of peptidyl asparagine (Asn or N) generates aspartic acid (Asp or D) or isoaspartic acid (isoAsp or isoD). Being a spontaneous, non-enzymatic protein post-translational modification, deamidation artifact can be easily introduced during sample preparation, especially proteolysis where higher-order structures are removed. This artifact not only complicates the analysis of bona fide deamidation but also affects a wide range of chemical and enzymatic processes; for instance, the newly generated Asp and isoAsp residues may block or introduce new proteolytic sites, and also convert one Asn peptide into multiple species that affect quantification. While the neutral to mildly basic conditions for common proteolysis favor deamidation, mildly acidic conditions markedly slow down the process. Unlike other commonly used endoproteases, Glu-C remains active under mildly acid conditions. As such, as demonstrated herein, deamidation artifact during proteolysis was effectively eliminated by simply performing Glu-C digestion at pH 4.5 in ammonium acetate, a volatile buffer that is compatible with mass spectrometry. Moreover, nearly identical sequence specificity was observed at both pH's (8.0 for ammonium bicarbonate), rendering Glu-C as effective at pH 4.5. In summary, this method is generally applicable for protein analysis as it requires minimal sample preparation and uses the readily available Glu-C protease.
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5
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Duclos RI, Cleary DC, Catcott KC, Zhou ZS. Synthesis and characterization of Se-adenosyl-L-selenohomocysteine selenoxide. J Sulphur Chem 2014; 36:135-144. [PMID: 26005494 DOI: 10.1080/17415993.2014.979173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Selenium is an essential micronutrient in humans due to the important roles of the selenocysteine-containing selenoproteins. Organoselenium metabolites are generally found to be substrates for the biochemical pathways of their sulfur analogs, and the redox chemistry of selenomethionine and some other metabolites have been previously reported. We now report the first synthesis and characterization of Se-adenosylselenohomocysteine selenoxide (SeAHO) prepared via hydrogen peroxide oxidation of Se-adenosylselenohomocysteine (SeAH). The selenoxide SeAHO, in contrast to its corresponding sulfoxide S-adenosylhomocysteine (SAHO), can form hydrate, has an electrostatic interaction between the α-amino acid moiety and the highly polar selenoxide functional group, and readily oxidizes glutathione (GSH) and cysteine thiols.
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Affiliation(s)
- Richard I Duclos
- Department of Pharmaceutical Sciences, 140 The Fenway Bldg., Room 206, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115-5000, Tel: +1 617 373 3163
| | - Dillon C Cleary
- Department of Chemistry and Chemical Biology, Hurtig Hall, Room 102, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115-5000, Tel: +1 617 373 2800
| | - Kalli C Catcott
- Department of Chemistry and Chemical Biology, Hurtig Hall, Room 102, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115-5000, Tel: +1 617 373 2800
| | - Zhaohui Sunny Zhou
- Department of Chemistry and Chemical Biology, Hurtig Hall, Room 102, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115-5000, Tel: +1 617 373 2800
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Sharma V, Chitranshi N, Agarwal AK. Significance and biological importance of pyrimidine in the microbial world. INTERNATIONAL JOURNAL OF MEDICINAL CHEMISTRY 2014; 2014:202784. [PMID: 25383216 PMCID: PMC4207407 DOI: 10.1155/2014/202784] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Revised: 01/13/2014] [Accepted: 01/14/2014] [Indexed: 11/20/2022]
Abstract
Microbes are unique creatures that adapt to varying lifestyles and environment resistance in extreme or adverse conditions. The genetic architecture of microbe may bear a significant signature not only in the sequences position, but also in the lifestyle to which it is adapted. It becomes a challenge for the society to find new chemical entities which can treat microbial infections. The present review aims to focus on account of important chemical moiety, that is, pyrimidine and its various derivatives as antimicrobial agents. In the current studies we represent more than 200 pyrimidines as antimicrobial agents with different mono-, di-, tri-, and tetrasubstituted classes along with in vitro antimicrobial activities of pyrimidines derivatives which can facilitate the development of more potent and effective antimicrobial agents.
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Affiliation(s)
- Vinita Sharma
- School of Pharmacy, Lloyd Institute of Management & Technology, Plot. No. 11, Knowledge Park II, Greater Noida, Uttar Pradesh 201306, India
| | - Nitin Chitranshi
- Bioinformatics Centre, Biotech Park, Sector G, Jankipuram, Lucknow, Uttar Pradesh 226021, India
- Gautam Buddh Technical University, IET Campus, Sitapur Road, Lucknow, Uttar Pradesh 226021, India
| | - Ajay Kumar Agarwal
- Department of Pharmaceutical Sciences, University Institute of Pharmaceutical Sciences, Kurukshetra University, Kurukshetra, Haryana 136119, India
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7
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Zimmermann SC, Sadler JM, O’Daniel PI, Kim NT, Seley-Radtke KL. "Reverse" carbocyclic fleximers: synthesis of a new class of adenosine deaminase inhibitors. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2013; 32:137-54. [PMID: 23473101 PMCID: PMC3712750 DOI: 10.1080/15257770.2013.771187] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
A series of flexible carbocyclic pyrimidine nucleosides has been designed and synthesized. In contrast to previously reported "fleximers" from our laboratory, these analogues have the connectivity of the heterocyclic base system "reversed", where the pyrimidine ring is attached to the sugar moiety, rather than the five membered imidazole ring. As was previously seen with the ribose fleximers, their inherent flexibility should allow them to adjust to enzyme binding site mutations, as well as increase the affinity for atypical enzymes. Preliminary biological screening has revealed surprising inhibition of adenosine deaminase, despite their lack of resemblance to adenosine.
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Affiliation(s)
- Sarah C. Zimmermann
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore, Maryland
| | - Joshua M. Sadler
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore, Maryland
| | - Peter I. O’Daniel
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana
| | - Nathaniel T. Kim
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore, Maryland
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8
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Synthesis and biological evaluation of a series of thieno-expanded tricyclic purine 2'-deoxy nucleoside analogues. Bioorg Med Chem 2012; 20:3009-15. [PMID: 22464686 DOI: 10.1016/j.bmc.2012.03.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Revised: 02/23/2012] [Accepted: 03/01/2012] [Indexed: 11/22/2022]
Abstract
Introducing structural diversity into the nucleoside scaffold for use as potential chemotherapeutics has long been considered an important approach to drug design. In that regard, we have designed and synthesized a number of innovative 2'-deoxy expanded nucleosides where a heteroaromatic thiophene spacer ring has been inserted in between the imidazole and pyrimidine ring systems of the natural purine scaffold. The synthetic efforts towards realizing the expanded 2'-deoxy-guanosine and -adenosine tricyclic analogues as well as the preliminary biological results are presented herein.
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9
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Park YH, Choi WJ, Tipnis AS, Lee KM, Jeong LS. Truncated fluorocyclopentenyl pyrimidines as S-adenosylhomocysteine hydrolase inhibitors. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2010; 28:601-13. [PMID: 20183604 DOI: 10.1080/15257770903054316] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
On the basis of inhibitory activity of truncated cyclopentenyl cytosine against S-adenosylhomocysteine hydrolase (SAH), its fluorocyclopentenyl pyrimidine derivatives were efficiently synthesized from D-ribose via electrophilic fluorination as a key step. The final nucleosides were evaluated for SAH inhibitory activity, among which the uracil derivative 9 showed significant inhibitory activity (IC(50) = 8.53 microM). They were also evaluated for cytotoxic effects in several human cancer cell lines such as fibro sarcoma, stomach cancer, leukemia, and colon cancer, but they did not show any cytotoxic effects up to 100 microM, indicating that 4'-hydroxymethyl groups are essential for the anticancer activity.
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Affiliation(s)
- Yeon Hee Park
- Department of Bioinspired Science and Division of Life and Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, Korea
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10
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Seley-Radtke KL, Sunkara NK. Carbocyclic thymidine analogues for use as potential therapeutic agents. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2010; 28:633-41. [PMID: 20183606 DOI: 10.1080/15257770903091920] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The discovery of azidothymidine's (AZT) activity against human immunodeficiency virus (HIV) provided strong rationale for the design of additional thymidine analogues. One drawback of many nucleoside analogues is the toxicity that often arises due to phosphorylation by cellular kinases. In order to overcome this problem, a number of truncated nucleosides lacking the 4'-hydroxymethyl group have been synthesized. In that regard, the synthesis and preliminary biological results for two truncated carbocyclic thymidine analogues are presented herein.
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Affiliation(s)
- Katherine L Seley-Radtke
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, Maryland, USA.
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11
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Szakonyi Z, Fülöp F. Carbocyclic nucleosides from enantiomeric, α-pinane-based aminodiols. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.tetasy.2010.04.054] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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12
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Zheng F, Fu L, Wang R, Qing FL. Synthesis and conformational analysis ofd-2′-deoxy-2′,2′-difluoro-4′-dihydro-4′-thionucleosides. Org Biomol Chem 2010; 8:163-70. [DOI: 10.1039/b914679b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Feng Zheng
- Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 354 Fenglin Lu, Shanghai 200032, China
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13
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Synthetic strategies toward carbocyclic purine-pyrimidine hybrid nucleosides. Bioorg Med Chem 2009; 17:5520-5. [PMID: 19592260 DOI: 10.1016/j.bmc.2009.06.039] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2009] [Revised: 06/13/2009] [Accepted: 06/16/2009] [Indexed: 11/20/2022]
Abstract
The blending of key structural features from the purine and pyrimidine nucleobase scaffolds gives rise to a new class of hybrid nucleosides. The purine-pyrimidine hybrid nucleosides can be viewed as either N-3 ribosylated purines or 5,6-disubstituted pyrimidines, thus recognition by both purine- and pyrimidine-metabolizing enzymes is possible. Given the increasing reports of the development of resistance in many enzymatic systems, a drug that could be recognized by more than one enzyme could prove highly advantageous in overcoming resistance mechanisms related to binding site mutations. In that regard, the design, synthesis and results of preliminary biological activity for a series of carbocyclic uracil derivatives with either a fused imidazole or thiazole ring are presented herein.
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14
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Broggi J, Kumamoto H, Berteina-Raboin S, Nolan SP, Agrofoglio LA. Click Azide-Alkyne Cycloaddition for the Synthesis of D-(-)-1,4-Disubstituted Triazolo-Carbanucleosides. European J Org Chem 2009. [DOI: 10.1002/ejoc.200801124] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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15
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Reddy MCM, Kuppan G, Shetty ND, Owen JL, Ioerger TR, Sacchettini JC. Crystal structures of Mycobacterium tuberculosis S-adenosyl-L-homocysteine hydrolase in ternary complex with substrate and inhibitors. Protein Sci 2008; 17:2134-44. [PMID: 18815415 DOI: 10.1110/ps.038125.108] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
S-adenosylhomocysteine hydrolase (SAHH) is a ubiquitous enzyme that plays a central role in methylation-based processes by maintaining the intracellular balance between S-adenosylhomocysteine (SAH) and S-adenosylmethionine. We report the first prokaryotic crystal structure of SAHH, from Mycobacterium tuberculosis (Mtb), in complex with adenosine (ADO) and nicotinamide adenine dinucleotide. Structures of complexes with three inhibitors are also reported: 3'-keto aristeromycin (ARI), 2-fluoroadenosine, and 3-deazaadenosine. The ARI complex is the first reported structure of SAHH complexed with this inhibitor, and confirms the oxidation of the 3' hydroxyl to a planar keto group, consistent with its prediction as a mechanism-based inhibitor. We demonstrate the in vivo enzyme inhibition activity of the three inhibitors and also show that 2-fluoradenosine has bactericidal activity. While most of the residues lining the ADO-binding pocket are identical between Mtb and human SAHH, less is known about the binding mode of the homocysteine (HCY) appendage of the full substrate. We report the 2.0 A resolution structure of the complex of SAHH cocrystallized with SAH. The most striking change in the structure is that binding of HCY forces a rotation of His363 around the backbone to flip out of contact with the 5' hydroxyl of the ADO and opens access to a nearby channel that leads to the surface. This complex suggests that His363 acts as a switch that opens up to permit binding of substrate, then closes down after release of the cleaved HCY. Differences in the entrance to this access channel between human and Mtb SAHH are identified.
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Affiliation(s)
- Manchi C M Reddy
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128, USA
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16
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Wnuk SF, Sacasa PR, Lewandowska E, Andrei D, Cai S, Borchardt RT. Synthesis of 5'-functionalized nucleosides: S-Adenosylhomocysteine analogues with the carbon-5' and sulfur atoms replaced by a vinyl or halovinyl unit. Bioorg Med Chem 2008; 16:5424-33. [PMID: 18457953 PMCID: PMC2443866 DOI: 10.1016/j.bmc.2008.04.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2007] [Revised: 04/05/2008] [Accepted: 04/09/2008] [Indexed: 11/17/2022]
Abstract
Adenosine and uridine analogues functionalized with alkenyl or fluoroalkenyl chain at C5' were prepared employing cross-metathesis, Negishi couplings, and Wittig reactions. Metathesis of the protected 5'-deoxy-5'-methyleneadenosine or uridine analogues with six-carbon amino acids (homoallylglycines) in the presence of Grubbs catalysts gave nucleoside analogues with the C5'-C6' double bond. Alternatively, the Pd-catalyzed cross-coupling between the protected 5'-deoxy-5'-(iodomethylene) nucleosides and suitable alkylzinc bromides also provided analogues with alkenyl unit. Stereoselective Pd-catalyzed monoalkylation of 5'-(bromofluoromethylene)-5'-deoxyadenosine with alkylzinc bromides afforded adenosylhomocysteine analogues with a 6'-(fluoro)vinyl motif. The vinylic adenine nucleosides produced time-dependent inactivation of the S-adenosyl-l-homocysteine hydrolases.
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Affiliation(s)
- Stanislaw F Wnuk
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
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