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Pidugu LS, Bright H, Lin WJ, Majumdar C, Van Ostrand RP, David SS, Pozharski E, Drohat AC. Structural Insights into the Mechanism of Base Excision by MBD4. J Mol Biol 2021; 433:167097. [PMID: 34107280 PMCID: PMC8286355 DOI: 10.1016/j.jmb.2021.167097] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/24/2021] [Accepted: 06/01/2021] [Indexed: 11/28/2022]
Abstract
DNA glycosylases remove damaged or modified nucleobases by cleaving the N-glycosyl bond and the correct nucleotide is restored through subsequent base excision repair. In addition to excising threatening lesions, DNA glycosylases contribute to epigenetic regulation by mediating DNA demethylation and perform other important functions. However, the catalytic mechanism remains poorly defined for many glycosylases, including MBD4 (methyl-CpG binding domain IV), a member of the helix-hairpin-helix (HhH) superfamily. MBD4 excises thymine from G·T mispairs, suppressing mutations caused by deamination of 5-methylcytosine, and it removes uracil and modified uracils (e.g., 5-hydroxymethyluracil) mispaired with guanine. To investigate the mechanism of MBD4 we solved high-resolution structures of enzyme-DNA complexes at three stages of catalysis. Using a non-cleavable substrate analog, 2'-deoxy-pseudouridine, we determined the first structure of an enzyme-substrate complex for wild-type MBD4, which confirms interactions that mediate lesion recognition and suggests that a catalytic Asp, highly conserved in HhH enzymes, binds the putative nucleophilic water molecule and stabilizes the transition state. Observation that mutating the Asp (to Gly) reduces activity by 2700-fold indicates an important role in catalysis, but probably not one as the nucleophile in a double-displacement reaction, as previously suggested. Consistent with direct-displacement hydrolysis, a structure of the enzyme-product complex indicates a reaction leading to inversion of configuration. A structure with DNA containing 1-azadeoxyribose models a potential oxacarbenium-ion intermediate and suggests the Asp could facilitate migration of the electrophile towards the nucleophilic water. Finally, the structures provide detailed snapshots of the HhH motif, informing how these ubiquitous metal-binding elements mediate DNA binding.
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Affiliation(s)
- Lakshmi S Pidugu
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Hilary Bright
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Wen-Jen Lin
- Department of Chemistry, University of California Davis, Davis, CA 95616, USA
| | - Chandrima Majumdar
- Department of Chemistry, University of California Davis, Davis, CA 95616, USA
| | | | - Sheila S David
- Department of Chemistry, University of California Davis, Davis, CA 95616, USA
| | - Edwin Pozharski
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Center for Biomolecular Therapeutics, Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA.
| | - Alexander C Drohat
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
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2
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Ishihara H, Huang J, Mochizuki T, Hatano M, Ishihara K. Enantio- and Diastereoselective Carbonyl-Ene Cyclization–Acetalization Tandem Reaction Catalyzed by Tris(pentafluorophenyl)borane-Assisted Chiral Phosphoric Acids. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01242] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Hideyuki Ishihara
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8603, Japan
| | - Jianhao Huang
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8603, Japan
| | - Takuya Mochizuki
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8603, Japan
| | - Manabu Hatano
- Graduate School of Pharmaceutical Sciences, Kobe Pharmaceutical University, 4-19-1, Motoyamakita-machi, Higashinada, Kobe 658-8558, Japan
| | - Kazuaki Ishihara
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8603, Japan
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3
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Russelburg LP, O’Shea Murray VL, Demir M, Knutsen KR, Sehgal SL, Cao S, David SS, Horvath MP. Structural Basis for Finding OG Lesions and Avoiding Undamaged G by the DNA Glycosylase MutY. ACS Chem Biol 2020; 15:93-102. [PMID: 31829624 DOI: 10.1021/acschembio.9b00639] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The adenine glycosylase MutY selectively initiates repair of OG:A lesions and, by comparison, avoids G:A mispairs. The ability to distinguish these closely related substrates relies on the C-terminal domain of MutY, which structurally resembles MutT. To understand the mechanism for substrate specificity, we crystallized MutY in complex with DNA containing G across from the high-affinity azaribose transition state analogue. Our structure shows that G is accommodated by the OG site and highlights the role of a serine residue in OG versus G discrimination. The functional significance of Ser308 and its neighboring residues was evaluated by mutational analysis, revealing the critical importance of a β loop in the C-terminal domain for mutation suppression in cells, and biochemical performance in vitro. This loop comprising residues Phe307, Ser308, and His309 (Geobacillus stearothermophilus sequence positions) is conserved in MutY but absent in MutT and other DNA repair enzymes and may therefore serve as a MutY-specific target exploitable by chemical biological probes.
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Affiliation(s)
- L. Peyton Russelburg
- School of Biological Sciences, University of Utah, 257 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Valerie L. O’Shea Murray
- Department of Chemistry, University of California, Davis, California 95616, United States
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Merve Demir
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Kyle R. Knutsen
- School of Biological Sciences, University of Utah, 257 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Sonia L. Sehgal
- School of Biological Sciences, University of Utah, 257 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Sheng Cao
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Sheila S. David
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Martin P. Horvath
- School of Biological Sciences, University of Utah, 257 South 1400 East, Salt Lake City, Utah 84112, United States
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4
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Evans GB, Schramm VL, Tyler PC. The transition to magic bullets - transition state analogue drug design. MEDCHEMCOMM 2018; 9:1983-1993. [PMID: 30627387 PMCID: PMC6295874 DOI: 10.1039/c8md00372f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 08/24/2018] [Indexed: 12/17/2022]
Abstract
In the absence of industry partnerships, most academic groups lack the infrastructure to rationally design and build drugs via methods used in industry. Instead, academia needs to work smarter using mechanism-based design. Working smarter can mean the development of new drug discovery paradigms and then demonstrating their utility and reproducibility to industry. The collaboration between Vern Schramm's group at the Albert Einstein College of Medicine, USA and Peter Tyler at the Ferrier Research Institute at The Victoria University of Wellington, NZ has refined a drug discovery process called transition state analogue design. This process has been applied to several biomedically relevant nucleoside processing enzymes. In 2017, Mundesine®, conceived using transition state analogue design, received market approval for the treatment of peripheral T-cell lymphoma in Japan. This short review looks at a brief history of transition state analogue design, the fundamentals behind the development of this process, and the success of enzyme inhibitors produced using this drug design methodology.
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Affiliation(s)
- Gary B Evans
- The Ferrier Research Institute , Victoria University of Wellington , 69 Gracefield Rd , Lower Hutt , 5010 , New Zealand . ; Tel: +64 4 463 0048
- The Maurice Wilkins Centre for Molecular Biodiscovery , The University of Auckland , Auckland , New Zealand
| | - Vern L Schramm
- Department of Biochemistry , Albert Einstein College of Medicine , Bronx , NY 10461 , USA
| | - Peter C Tyler
- The Ferrier Research Institute , Victoria University of Wellington , 69 Gracefield Rd , Lower Hutt , 5010 , New Zealand . ; Tel: +64 4 463 0048
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5
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Andrés C, González I, Nieto J, Rosón CD. Lewis acid mediated diastereoselective keto-ene cyclization on chiral perhydro-1,3-benzoxazines: synthesis of enantiopure cis-3,4-disubstituted 3-hydroxypyrrolidines. Tetrahedron 2009. [DOI: 10.1016/j.tet.2009.09.091] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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6
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Rubinson EH, Metz AH, O'Quin J, Eichman BF. A new protein architecture for processing alkylation damaged DNA: the crystal structure of DNA glycosylase AlkD. J Mol Biol 2008; 381:13-23. [PMID: 18585735 PMCID: PMC3763988 DOI: 10.1016/j.jmb.2008.05.078] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2008] [Revised: 05/28/2008] [Accepted: 05/29/2008] [Indexed: 01/02/2023]
Abstract
DNA glycosylases safeguard the genome by locating and excising chemically modified bases from DNA. AlkD is a recently discovered bacterial DNA glycosylase that removes positively charged methylpurines from DNA, and was predicted to adopt a protein fold distinct from from those of other DNA repair proteins. The crystal structure of Bacillus cereus AlkD presented here shows that the protein is composed exclusively of helical HEAT-like repeats, which form a solenoid perfectly shaped to accommodate a DNA duplex on the concave surface. Structural analysis of the variant HEAT repeats in AlkD provides a rationale for how this protein scaffolding motif has been modified to bind DNA. We report 7mG excision and DNA binding activities of AlkD mutants, along with a comparison of alkylpurine DNA glycosylase structures. Together, these data provide important insight into the requirements for alkylation repair within DNA and suggest that AlkD utilizes a novel strategy to manipulate DNA in its search for alkylpurine bases.
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Affiliation(s)
- Emily H. Rubinson
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Audrey H. Metz
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Jami O'Quin
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Brandt F. Eichman
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
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7
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Clinch K, Evans GB, Furneaux RH, Lenz DH, Mason JM, Mee SPH, Tyler PC, Wilcox SJ. A practical synthesis of (3R,4R)-N-tert-butoxycarbonyl-4-hydroxymethylpyrrolidin-3-ol. Org Biomol Chem 2007; 5:2800-2. [PMID: 17700848 DOI: 10.1039/b708796a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The title compound (+)-, required for production of transition state analogue inhibitors of enzymes involved in T-cell-dependent disorders, was synthesized in five steps. A 1,3-dipolar cycloaddition of the nitrone formed from formaldehyde and N-benzylhydroxylamine to diethyl maleate gave the racemic cis-isoxazolidine (+/-)-. Reduction of the N-O bond of this compound gave pyrrolidone (+/-)- in excellent yield. A very efficient enzymic resolution of this racemic product led to the title enantiomer (+)-. This route employs only one chromatographic purification.
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Affiliation(s)
- Keith Clinch
- Carbohydrate Chemistry Team, Industrial Research Ltd, P.O. Box 31310, Lower Hutt, New Zealand
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8
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Faigl F, Thurner A, Farkas F, Battancs M, Poppe L. Synthesis and enantioselective rearrangement of (Z)-4-triphenylmethoxy-2,3-epoxybutan-1-ol enantiomers. Chirality 2007; 19:197-202. [PMID: 17192839 DOI: 10.1002/chir.20361] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Efficient enzyme catalyzed kinetic resolutions of a synthetically useful chiral building block, (Z)-4-triphenylmethoxy-2,3-epoxybutan-1-ol, are reported. The highest selectivities were achieved by Lipozyme TL IM and Amano Lipase PS enzymes in the presence of vinyl acetate. Enantiomeric enrichment of the optically active acetate isomer was accomplished by selective crystallization of the racemic part of the enantiomeric mixture. Enzyme catalyzed hydrolysis of the acetate also provided an optically pure epoxybutanol derivative. O-Benzylation of (+)-(Z)-1-hydroxy-4-triphenylmethoxy-2,3-epoxybutane followed by super base promoted diastereo- and enantio-selective rearrangement resulted in (+)-(2R,3R,1'R)-3-[1-hydroxy-2-(triphenylmethoxy)ethyl]-2-phenyloxetane in >98% ee and de. Configurations of the new optically active products were determined by chemical correlation.
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Affiliation(s)
- Ferenc Faigl
- Department of Organic Chemical Technology, Budapest University of Technology and Economics, H-1111 Budapest, Budafoki út 8., Hungary.
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9
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Clinch K, Evans GB, Fleet GWJ, Furneaux RH, Johnson SW, Lenz DH, Mee SPH, Rands PR, Schramm VL, Taylor Ringia EA, Tyler PC. Syntheses and bio-activities of the l-enantiomers of two potent transition state analogue inhibitors of purine nucleoside phosphorylases. Org Biomol Chem 2006; 4:1131-9. [PMID: 16525558 DOI: 10.1039/b517883e] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
(1R)-1-(9-Deazahypoxanthin-9-yl)-1,4-dideoxy-1,4-imino-L-ribitol [(+)-5] and (3S,4S)-1-[(9-deazahypoxanthin-9-yl)methyl]-4-(hydroxymethyl)pyrrolidin-3-ol [(-)-6] are the L-enantiomers of immucillin-H (D-ImmH) and DADMe-immucillin-H (D-DADMe-ImmH), respectively, these D-isomers being high affinity transition state analogue inhibitors of purine nucleoside phosphorylases (PNPases) developed as potential pharmaceuticals against diseases involving irregular activation of T-cells. The C-nucleoside hydrochloride D-ImmH [(-)-5) x HCl], now "Fodosine" is in phase II clinical trials as an anti-T-cell leukaemia agent, while D-DADMe-ImmH is a second generation inhibitor with extreme binding to the target enzyme and has entered the clinic for phase I testing as an anti-psoriasis drug. Since the enantiomers of some pharmaceuticals have revealed surprising biological activities, the L-nucleoside analogues (+)-5 x HCl and (-)-6, respectively, of D-ImmH and D-DADMe-ImmH, were prepared and their PNPase binding properties were studied. For the synthesis of compound (-)-6 suitable enzyme-based routes to the enantiomerically pure starting material (3S,4S)-4-(hydroxymethyl)pyrrolidin-3-ol [(-)-6] and its enantiomer were developed. The L-enantiomers (+)-5 x HCl and (-)-6 bind to the PNPases approximately 5- to 600-times less well than do the D-compounds, but nevertheless remain powerful inhibitors with nanomolar dissociation constants.
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Affiliation(s)
- Keith Clinch
- Carbohydrate Chemistry Team, Industrial Research Limited, P.O. Box 31310, Lower Hutt, New Zealand.
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10
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Hillaert U, Van Calenbergh S. Synthesis of a Versatile (S)-3-(Hydroxymethyl)butane-1,2,4-triol Building Block and its Application for the Stereoselective Synthesis of N-Homoceramides. Org Lett 2005; 7:5769-72. [PMID: 16354062 DOI: 10.1021/ol052335x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[structures: see text] A versatile (S)-3-(hydroxymethyl)butane-1,2,4-triol building block has been synthesized starting from D-isoascorbic acid, a common food preservative. The key transformation in this approach was the introduction of branching through a high yield and fully regioselective epoxide opening. This flexible synthon has been elaborated to a new class of (dihydro-)N-homo(phyto)ceramides.
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Affiliation(s)
- Ulrik Hillaert
- Laboratory for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University, Harelbekestraat 72, B-9000 Ghent, Belgium
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11
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Moffat D, Nichols CJ, Riley DA, Simpkins NS. The synthesis of bioactive indolocarbazoles related to K-252a. Org Biomol Chem 2005; 3:2953-75. [PMID: 16186927 DOI: 10.1039/b506444a] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A range of functionalised indolocarbazoles, related to the natural product K-252a, have been prepared, starting from a readily available bridged cyclopentene. Sequences of transformations, involving initial hydroboration-oxidation to give a ketone, or by dihydroxylation and cyclic sulfate formation, enable the preparation of diverse indolocarbazole products. Issues of imide nitrogen protection for the indolocarbazole, and opportunities for asymmetric desymmetrisation of key intermediates were also explored. A novel chiral lithium amide base mediated transformation of a cyclic sulfate intermediate gave the anticipated ketone product in up to 87% ee. A number of compounds, in the form of unprotected imide substituted indolocarbazoles, were screened for biological activity and were found to be potent inhibitors of a number of kinase enzymes.
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Affiliation(s)
- David Moffat
- Celltech Therapeutics Ltd, 216 Bath Road, Slough, SL1 4EN, UK
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12
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An efficient stereoselective synthesis of (3S,4R)-4-(hydroxymethyl)pyrrolidin-3-ol from (S)-diethylmalate. Tetrahedron Lett 2005. [DOI: 10.1016/j.tetlet.2005.03.077] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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13
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Kotian PL, Lin TH, El-Kattan Y, Chand P. A Practical Large-Scale Synthesis of (3R,4R)-4-(Hydroxymethyl)pyrrolidin-3-ol via Asymmetric 1,3-Dipolar Cycloaddition. Org Process Res Dev 2005. [DOI: 10.1021/op049768k] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pravin L. Kotian
- Department of Medicinal Chemistry, BioCryst Pharmaceuticals, Inc., 2190 Parkway Lake Drive, Birmingham, Alabama 35244, U.S.A
| | - Tsu-Hsing Lin
- Department of Medicinal Chemistry, BioCryst Pharmaceuticals, Inc., 2190 Parkway Lake Drive, Birmingham, Alabama 35244, U.S.A
| | - Yahya El-Kattan
- Department of Medicinal Chemistry, BioCryst Pharmaceuticals, Inc., 2190 Parkway Lake Drive, Birmingham, Alabama 35244, U.S.A
| | - Pooran Chand
- Department of Medicinal Chemistry, BioCryst Pharmaceuticals, Inc., 2190 Parkway Lake Drive, Birmingham, Alabama 35244, U.S.A
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14
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Jiang YL, Cao C, Stivers JT, Song F, Ichikawa Y. The merits of bipartite transition-state mimics for inhibition of uracil DNA glycosylase. Bioorg Chem 2005; 32:244-62. [PMID: 15210339 DOI: 10.1016/j.bioorg.2004.03.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2004] [Indexed: 10/26/2022]
Abstract
The glycosidic bond hydrolysis reaction of the enzyme uracil DNA glycosylase (UDG) occurs by a two-step mechanism involving complete bond breakage to the uracil anion leaving group in the first step, formation of a discrete glycosyl cation-uracil anion intermediate, followed by water attack in a second transition-state leading to the enzyme-bound products of uracil and abasic DNA. We have synthesized and determined the binding affinities of unimolecular mimics of the substrate and first transition-state (TS1) in which the uracil base is covalently attached to the sugar, and in addition, bimolecular mimics of the second addition transition state (TS2) in which the base and sugar are detached. We find that the bipartite mimics of TS2 are superior to the TS1 mimics. These results indicate that bipartite TS2 inhibitors could be useful for inhibition of glycosylases that proceed by stepwise reaction mechanisms.
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Affiliation(s)
- Yu Lin Jiang
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205-2185, USA
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15
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Chiral 3-hydroxypyrrolidin-2-ones from a Baylis–Hillman adduct: convergent, stereoselective synthesis of a glycosidase inhibitor. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/j.tetasy.2004.08.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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16
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Ciaccio JA, Smrtka M, Maio WA, Rucando D. Synthesis of β-hydroxy nitriles and 1,3-amino alcohols from epoxides using acetone cyanohydrin as a LiCN precursor. Tetrahedron Lett 2004. [DOI: 10.1016/j.tetlet.2004.08.039] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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17
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Stivers JT, Jiang YL. A mechanistic perspective on the chemistry of DNA repair glycosylases. Chem Rev 2003; 103:2729-59. [PMID: 12848584 DOI: 10.1021/cr010219b] [Citation(s) in RCA: 374] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- James T Stivers
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205, USA.
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18
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Jiang YL, Ichikawa Y, Song F, Stivers JT. Powering DNA repair through substrate electrostatic interactions. Biochemistry 2003; 42:1922-9. [PMID: 12590578 DOI: 10.1021/bi027014x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The reaction catalyzed by the DNA repair enzyme uracil DNA glycosylase (UDG) proceeds through an unprecedented stepwise mechanism involving a positively charged oxacarbenium ion sugar and uracil anion leaving group. Here we use a novel approach to evaluate the catalytic contribution of electrostatic interactions between four essential phosphodiester groups of the DNA substrate and the cationic transition state. Our strategy was to substitute each of these phosphate groups with an uncharged (R)- or (S)-methylphosphonate linkage (MeP). We then compared the damaging effects of these methylphosphonate substitutions on catalysis with their damaging effects on binding of a cationic 1-azadeoxyribose (1-aza-dR(+)) oxacarbenium ion analogue to the UDG-uracil anion binary complex. A plot of log k(cat)/K(m) for the series of MeP-substituted substrates against log K(D) for binding of the 1-aza-dR(+) inhibitors gives a linear correlation of unit slope, confirming that the electronic features of the transition state resemble that of the 1-aza-dR(+), and that the anionic backbone of DNA is used in transition state stabilization. We estimate that all of the combined phosphodiester interactions with the substrate contribute 6-8 kcal/mol toward lowering the activation barrier, a stabilization that is significant compared to the 16 kcal/mol catalytic power of UDG. However, unlike groups of the enzyme that selectively stabilize the charged transition state by an estimated 7 kcal/mol, these phosphodiester groups also interact strongly in the ground state. To our knowledge, these results provide the first experimental evidence for electrostatic stabilization of a charged enzymatic transition state and intermediate using the anionic backbone of DNA.
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Affiliation(s)
- Yu Lin Jiang
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205-2185, USA
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19
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Bonini C, Righi G. A critical outlook and comparison of enantioselective oxidation methodologies of olefins. Tetrahedron 2002. [DOI: 10.1016/s0040-4020(02)00440-4] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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20
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Jiang YL, Drohat AC, Ichikawa Y, Stivers JT. Probing the limits of electrostatic catalysis by uracil DNA glycosylase using transition state mimicry and mutagenesis. J Biol Chem 2002; 277:15385-92. [PMID: 11859082 DOI: 10.1074/jbc.m200634200] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The DNA repair enzyme uracil DNA glycosylase (UDG) hydrolyzes the glycosidic bond of deoxyuridine in DNA by a remarkable mechanism involving formation of a positively charged oxacarbenium ion-uracil anion intermediate. We have proposed that the positively charged intermediate is stabilized by being sandwiched between the combined negative charges of the anionic uracil leaving group and a conserved aspartate residue that are located on opposite faces of the sugar ring. Here we establish that a duplex DNA oligonucleotide containing a cationic 1-aza-deoxyribose (I) oxacarbenium ion mimic is a potent inhibitor of UDG that binds tightly to the enzyme-uracil anion (EU(-)) product complex (K(D) of EU(-) = 110 pm). The tight binding of I to the EU(-) complex results from its extremely slow off rate (k(off) = 0.0008 s(-1)), which is 25,000-fold slower than substrate analogue DNA. Removal of Asp(64) and His(187), which are involved in stabilization of the cationic sugar and the anionic uracil leaving group, respectively, specifically weakens binding of I to the UDG-uracil complex by 154,000-fold, without significantly affecting substrate or product binding. These results suggest that electrostatic effects can effectively stabilize such an intermediate by at least -7 kcal/mol, without leading to anticatalytic stabilization of the substrate and products.
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Affiliation(s)
- Yu Lin Jiang
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205-2185, USA
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21
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Lillelund VH, Jensen HH, Liang X, Bols M. Recent developments of transition-state analogue glycosidase inhibitors of non-natural product origin. Chem Rev 2002; 102:515-53. [PMID: 11841253 DOI: 10.1021/cr000433k] [Citation(s) in RCA: 614] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Vinni H Lillelund
- Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
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Hollis T, Lau A, Ellenberger T. Crystallizing thoughts about DNA base excision repair. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2002; 68:305-14. [PMID: 11554308 DOI: 10.1016/s0079-6603(01)68109-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Chemically damaged bases are removed from DNA by glycosylases that locate the damage and cleave the bond between the modified base and the deoxyribose sugar of the DNA backbone. The detection of damaged bases in DNA poses two problems: (1) The aberrant bases are mostly buried within the double helix, and (2) a wide variety of chemically different modifications must be efficiently recognized and removed. The human alkyladenine glycosylase (AAG) and Escherichia coli Alka DNA glycosylases excise many different types of alkylated bases from DNA. Crystal structures of these enzymes show how substrate bases are exposed to the enzyme active site and they suggest mechanisms of catalytic specificity. Both enzymes bend DNA and flip substrate bases out of the double helix and into the enzyme active site for cleavage. Although AAG and AlkA have very different overall folds, some common features of their substrate-binding sites suggest related strategies for the selective recognition of a chemically diverse group of alkylated substrates.
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Affiliation(s)
- T Hollis
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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23
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Thurner A, Faigl F, Tőke L, Mordini A, Valacchi M, Reginato G, Czira G. Useful base promoted elaborations of oxiranyl ethers. Tetrahedron 2001. [DOI: 10.1016/s0040-4020(01)00790-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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24
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Synthesis of enantiomerically pure 4-substituted pyrrolidin-3-ols via asymmetric 1,3-dipolar cycloaddition. ACTA ACUST UNITED AC 2001. [DOI: 10.1016/s0957-4166(01)00367-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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25
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Tanaka KS, Chen XY, Ichikawa Y, Tyler PC, Furneaux RH, Schramm VL. Ricin A-chain inhibitors resembling the oxacarbenium ion transition state. Biochemistry 2001; 40:6845-51. [PMID: 11389598 DOI: 10.1021/bi010499p] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ricin toxin A-chain (RTA) is expressed by the castor bean plant and is among the most potent mammalian toxins. Upon activation in the cytosol, RTA depurinates a single adenine from position 4324 of rat 28S ribosomal RNA, causing inactivation of ribosomes by preventing the binding of elongation factors. Kinetic isotope effect studies have established that RTA operates via a D(N)*A(N) mechanism involving an oxacarbenium ion intermediate with bound adenine [Chen, X.-Y., Berti, P. J., and Schramm, V. L. (2000) J. Am. Chem. Soc. 122, 1609-1617]. On the basis of this information, stem-loop RNA molecules were chemically synthesized, incorporating structural features of the oxacarbenium ion-like transition state. A 10-base RNA stem-loop incorporating (1S)-1-(9-deazaadenin-9-yl)-1,4-dideoxy-1,4-imino-D-ribitol at the depurination site binds four times better (0.57 microM) than the 10-base RNA stem-loop with adenosine at the depurination site (2.2 microM). A 10-base RNA stem-loop with 1,2-dideoxyribitol [(2R,3S)-2-(hydroxymethyl)-3-hydroxytetrahydrofuran] at the depurination site binds with a Kd of 3.2 microM and tightens to 0.75 microM in the presence of 9-deazaadenine. A similar RNA stem-loop with 1,4-dideoxy-1,4-imino-D-ribitol at the depurination site binds with a K(d) of 1.3 microM and improves to 0.65 micro;M with 9-deazaadenine added. When (3S,4R)-4-hydroxy-3-(hydroxymethyl)pyrrolidine was incorporated at the depurination site of a 14-base RNA stem-loop, the Kd was 0.48 microM. Addition of 9-deazaadenine tightens the binding to 0.10 microM whereas added adenine increases the affinity to 12 nM. The results of this study are consistent with the unusual dissociative D(N)*A(N) mechanism determined for RTA. Knowledge of this intermediate has led to the design and synthesis of the highest affinity inhibitor reported for the catalytic site of RTA.
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Affiliation(s)
- K S Tanaka
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA
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26
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Kim YJ, Kaiser DA, Pollard TD, Ichikawa Y. Synthesis of (3R)-carboxy pyrrolidine (a beta-proline analogue) and its oligomer. Bioorg Med Chem Lett 2000; 10:2417-9. [PMID: 11078191 DOI: 10.1016/s0960-894x(00)00486-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A decamer of a beta-amino acid analogue of L-proline, (3R)-carboxy pyrrolidine (beta-proline), was synthesized from a readily available (R)-glycidol. It was found to possess a rigid secondary structure, as evidenced by its CD spectrum. The beta-proline decamer, however, failed to bind to profilin, whereas the corresponding alpha-L-proline decamer bound tightly to this protein.
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Affiliation(s)
- Y J Kim
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA
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Hollis T, Lau A, Ellenberger T. Structural studies of human alkyladenine glycosylase and E. coli 3-methyladenine glycosylase. Mutat Res 2000; 460:201-10. [PMID: 10946229 DOI: 10.1016/s0921-8777(00)00027-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Human alkyladenine glycosylase (AAG) and Escherichia coli 3-methyladenine glycosylase (AlkA) are base excision repair glycosylases that recognize and excise a variety of alkylated bases from DNA. The crystal structures of these enzymes have provided insight into their substrate specificity and mechanisms of catalysis. Both enzymes utilize DNA bending and base-flipping mechanisms to expose and bind substrate bases. Crystal structures of AAG complexed to DNA suggest that the enzyme selects substrate bases through a combination of hydrogen bonding and the steric constraints of the active site, and that the enzyme activates a water molecule for an in-line backside attack of the N-glycosylic bond. In contrast to AAG, the structure of the AlkA-DNA complex suggests that AlkA substrate recognition and catalytic specificity are intimately integrated in a S(N)1 type mechanism in which the catalytic Asp238 directly promotes the release of modified bases.
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Affiliation(s)
- T Hollis
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
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28
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Kim YJ, Ichikawa M, Ichikawa Y. Highly selective synthesis of 1-N-iminosugars of the D-glucose and -glucuronic acid types. J Org Chem 2000; 65:2599-602. [PMID: 10789483 DOI: 10.1021/jo9917700] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Y J Kim
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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Hollis T, Ichikawa Y, Ellenberger T. DNA bending and a flip-out mechanism for base excision by the helix-hairpin-helix DNA glycosylase, Escherichia coli AlkA. EMBO J 2000; 19:758-66. [PMID: 10675345 PMCID: PMC305614 DOI: 10.1093/emboj/19.4.758] [Citation(s) in RCA: 180] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The Escherichia coli AlkA protein is a base excision repair glycosylase that removes a variety of alkylated bases from DNA. The 2.5 A crystal structure of AlkA complexed to DNA shows a large distortion in the bound DNA. The enzyme flips a 1-azaribose abasic nucleotide out of DNA and induces a 66 degrees bend in the DNA with a marked widening of the minor groove. The position of the 1-azaribose in the enzyme active site suggests an S(N)1-type mechanism for the glycosylase reaction, in which the essential catalytic Asp238 provides direct assistance for base removal. Catalytic selectivity might result from the enhanced stacking of positively charged, alkylated bases against the aromatic side chain of Trp272 in conjunction with the relative ease of cleaving the weakened glycosylic bond of these modified nucleotides. The structure of the AlkA-DNA complex offers the first glimpse of a helix-hairpin-helix (HhH) glycosylase complexed to DNA. Modeling studies suggest that other HhH glycosylases can bind to DNA in a similar manner.
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Affiliation(s)
- T Hollis
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
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