1
|
Madern JM, Kim RQ, Misra M, Dikic I, Zhang Y, Ovaa H, Codée JDC, Filippov DV, van der Heden van Noort GJ. Synthesis of Stable NAD + Mimics as Inhibitors for the Legionella pneumophila Phosphoribosyl Ubiquitylating Enzyme SdeC. Chembiochem 2020; 21:2903-2907. [PMID: 32421893 PMCID: PMC7687180 DOI: 10.1002/cbic.202000230] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/15/2020] [Indexed: 12/14/2022]
Abstract
Stable NAD+ analogues carrying single atom substitutions in either the furanose ring or the nicotinamide part have proven their value as inhibitors for NAD+ -consuming enzymes. To investigate the potential of such compounds to inhibit the adenosine diphosphate ribosyl (ADPr) transferase activity of the Legionella SdeC enzyme, we prepared three NAD+ analogues, namely carbanicotinamide adenosine dinucleotide (c-NAD+ ), thionicotinamide adenosine dinucleotide (S-NAD+ ) and benzamide adenosine dinucleotide (BAD). We optimized the chemical synthesis of thionicotinamide riboside and for the first time used an enzymatic approach to convert all three ribosides into the corresponding NAD+ mimics. We thus expanded the known scope of substrates for the NRK1/NMNAT1 enzyme combination by turning all three modified ribosides into NAD+ analogues in a scalable manner. We then compared the three NAD+ mimics side-by-side in a single assay for enzyme inhibition on Legionella effector enzyme SdeC. The class of SidE enzymes to which SdeC belongs was recently identified to be important in bacterial virulence, and we found SdeC to be inhibited by S-NAD+ and BAD with IC50 values of 28 and 39 μM, respectively.
Collapse
Affiliation(s)
- Jerre M. Madern
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Robbert Q. Kim
- Oncode Institute and Department of Cell and Chemical BiologyLeiden University Medical CentreEinthovenweg 202333 ZCLeidenThe Netherlands
| | - Mohit Misra
- Institute of Biochemistry IIGoethe University Faculty of MedicineTheodor-Stern-Kai 760590Frankfurt am MainGermany
- Buchmann Institute for Molecular Life SciencesGoethe University Frankfurt, Riedberg CampusMax-von-Laue-Strasse 1560438Frankfurt amMainGermany
| | - Ivan Dikic
- Institute of Biochemistry IIGoethe University Faculty of MedicineTheodor-Stern-Kai 760590Frankfurt am MainGermany
- Buchmann Institute for Molecular Life SciencesGoethe University Frankfurt, Riedberg CampusMax-von-Laue-Strasse 1560438Frankfurt amMainGermany
| | - Yong Zhang
- Department of Pharmacology and Pharmaceutical SciencesSchool of PharmacyUniversity of Southern California1985 Zonal AvenueLos AngelesCA 90089USA
| | - Huib Ovaa
- Oncode Institute and Department of Cell and Chemical BiologyLeiden University Medical CentreEinthovenweg 202333 ZCLeidenThe Netherlands
| | - Jeroen D. C. Codée
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Dmitri V. Filippov
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | | |
Collapse
|
2
|
Zachos I, Nowak C, Sieber V. Biomimetic cofactors and methods for their recycling. Curr Opin Chem Biol 2018; 49:59-66. [PMID: 30336443 DOI: 10.1016/j.cbpa.2018.10.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 09/30/2018] [Accepted: 10/02/2018] [Indexed: 12/19/2022]
Abstract
Nicotinamide cofactor biomimetics (NCBs) belong to a class of compounds that, as the name suggests, mimic the structures and functions of natural nicotinamide cofactors, namely nicotinamide adenine dinucleotide and nicotinamide adenine dinucleotide phosphate and their corresponding reduced forms. The first set of NCBs was discovered in the 1930s; these were initially used to study the chemical properties of this class of cofactors as well as understand nicotinamide binding of oxidoreductases. Since then, various NCBs, enzymes, and recycling systems have evolved and lately, new NCBs have been developed and used to run biocatalytic reactions.
Collapse
Affiliation(s)
- Ioannis Zachos
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, 94315 Straubing, Germany
| | - Claudia Nowak
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, 94315 Straubing, Germany; Current address: Dr. Ebeling & Assoc. GmbH, Hamburg, Germany
| | - Volker Sieber
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, 94315 Straubing, Germany; Catalysis Research Center, Technical University of Munich, Garching, Germany; Fraunhofer Institute of InterfacialBiotechnology (IGB), Bio-, Electro- and Chemo Catalysis (BioCat) Branch, Straubing, Germany; School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Qld, Australia.
| |
Collapse
|
3
|
Abstract
The sirtuins form a superfamily of evolutionarily conserved NAD+-dependent protein N-ϵ-acyl-lysine (AcK) deacylases with roles in a variety of key cellular processes. Sirtuins have a broadly conserved overall structure with a catalytic site formed by a hydrophobic channel between the NAD+-binding Rossmann fold domain and a smaller Zn2+-binding domain. Schistosomes express five members of the sirtuin family and generic sirtuin inhibitors induce apoptosis and death in schistosome larvae, the disruption of adult worm pairs, inhibition of egg laying and damage to the male and female worm reproductive systems. Sirtuins in schistosomes and other parasitic flatworms present structural differences from their human orthologues that should allow the development of selective inhibitors that can be developed as drug leads.
Collapse
|
4
|
Probing the catalytic mechanism of bovine CD38/NAD+ glycohydrolase by site directed mutagenesis of key active site residues. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1317-31. [PMID: 24721563 DOI: 10.1016/j.bbapap.2014.03.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 03/28/2014] [Accepted: 03/31/2014] [Indexed: 01/14/2023]
Abstract
Bovine CD38/NAD(+) glycohydrolase catalyzes the hydrolysis of NAD(+) to nicotinamide and ADP-ribose and the formation of cyclic ADP-ribose via a stepwise reaction mechanism. Our recent crystallographic study of its Michaelis complex and covalently-trapped intermediates provided insights into the modalities of substrate binding and the molecular mechanism of bCD38. The aim of the present work was to determine the precise role of key conserved active site residues (Trp118, Glu138, Asp147, Trp181 and Glu218) by focusing mainly on the cleavage of the nicotinamide-ribosyl bond. We analyzed the kinetic parameters of mutants of these residues which reside within the bCD38 subdomain in the vicinity of the scissile bond of bound NAD(+). To address the reaction mechanism we also performed chemical rescue experiments with neutral (methanol) and ionic (azide, formate) nucleophiles. The crucial role of Glu218, which orients the substrate for cleavage by interacting with the N-ribosyl 2'-OH group of NAD(+), was highlighted. This contribution to catalysis accounts for almost half of the reaction energy barrier. Other contributions can be ascribed notably to Glu138 and Asp147 via ground-state destabilization and desolvation in the vicinity of the scissile bond. Key interactions with Trp118 and Trp181 were also proven to stabilize the ribooxocarbenium ion-like transition state. Altogether we propose that, as an alternative to a covalent acylal reaction intermediate with Glu218, catalysis by bCD38 proceeds through the formation of a discrete and transient ribooxocarbenium intermediate which is stabilized within the active site mostly by electrostatic interactions.
Collapse
|
5
|
Paul CE, Arends IWCE, Hollmann F. Is Simpler Better? Synthetic Nicotinamide Cofactor Analogues for Redox Chemistry. ACS Catal 2014. [DOI: 10.1021/cs4011056] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Caroline E. Paul
- Department of Biotechnology, Delft University of Technology, Julianalaan
136, 2628BL Delft, The Netherlands
| | - Isabel W. C. E. Arends
- Department of Biotechnology, Delft University of Technology, Julianalaan
136, 2628BL Delft, The Netherlands
| | - Frank Hollmann
- Department of Biotechnology, Delft University of Technology, Julianalaan
136, 2628BL Delft, The Netherlands
| |
Collapse
|
6
|
Szczepankiewicz BG, Dai H, Koppetsch KJ, Qian D, Jiang F, Mao C, Perni RB. Synthesis of carba-NAD and the structures of its ternary complexes with SIRT3 and SIRT5. J Org Chem 2012; 77:7319-29. [PMID: 22849721 DOI: 10.1021/jo301067e] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Carba-NAD is a synthetic compound identical to NAD except for one substitution, where an oxygen atom adjacent to the anomeric linkage bearing nicotinamide is replaced with a methylene group. Because it is inert in nicotinamide displacement reactions, carba-NAD is an unreactive substrate analogue for NAD-consuming enzymes. SIRT3 and SIRT5 are NAD-consuming enzymes that are potential therapeutic targets for the treatment of metabolic diseases and cancers. We report an improved carba-NAD synthesis, including a pyrophosphate coupling method that proceeds in approximately 60% yield. We also disclose the X-ray crystal structures of the ternary complexes of SIRT3 and SIRT5 bound to a peptide substrate and carba-NAD. These X-ray crystal structures provide critical snapshots of the mechanism by which human sirtuins function as protein deacylation catalysts.
Collapse
|
7
|
von Ketteler A, Herten DP, Petrich W. Fluorescence properties of carba nicotinamide adenine dinucleotide for glucose sensing. Chemphyschem 2012; 13:1302-6. [PMID: 22337358 DOI: 10.1002/cphc.201100921] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Revised: 01/16/2012] [Indexed: 11/11/2022]
Abstract
Carba nicotinamide adenine dinucleotide (cNAD) may serve as a stable cofactor for the enzyme-based detection of glucose. Many characteristics of cNAD and its reduced form cNADH resemble those of NAD and NADH, respectively. The fluorescence lifetimes of cNADH are determined to be 0.32(2) ns and 0.66(3) ns compared to 0.28(2) ns and 0.60(3) ns for NADH, and the temperature dependence of these lifetimes hints towards identical processes for quenching. The maximum emission occurs at 464 nm for both cNADH and NADH and absorbance maxima are found at 360 nm and 340 nm, respectively. In contrast to previous suggestions the respective maximum extinction coefficient of cNADH equals that of NADH and amounts to 6.2(2) mM(-1) cm(-1). When changing from NADH to cNADH we observe a ~50% increase in quantum efficiency, which--together with the larger excitation wavelength and the higher stability--should make cNAD a well suited alternative as coenzyme for robust glucose detection.
Collapse
Affiliation(s)
- Alexa von Ketteler
- Kirchhoff Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69210 Heidelberg, Germany.
| | | | | |
Collapse
|
8
|
Cen Y. Sirtuins inhibitors: the approach to affinity and selectivity. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1804:1635-44. [PMID: 19931429 DOI: 10.1016/j.bbapap.2009.11.010] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2009] [Revised: 11/07/2009] [Accepted: 11/10/2009] [Indexed: 10/20/2022]
Abstract
Accumulating evidence has indicated the importance of sirtuins (class III histone deacetylases) in various biological processes. Their potential roles in metabolic and neurodegenerative diseases have encouraged scientists to seek potent and selective sirtuin inhibitors to investigate their biological functions with a view to eventual new therapeutic treatments. This article surveys current knowledge of sirtuin inhibitors including those discovered via high-throughput screening (HST) or via mechanism-based drug design from synthetic or natural sources. Their inhibitory affinity, selectivities, and possible inhibition mechanisms are discussed.
Collapse
Affiliation(s)
- Yana Cen
- Department of Pharmacology, Weill Medical College of Cornell University, New York, NY 10065, USA.
| |
Collapse
|
9
|
Sanders BD, Zhao K, Slama JT, Marmorstein R. Structural basis for nicotinamide inhibition and base exchange in Sir2 enzymes. Mol Cell 2007; 25:463-72. [PMID: 17289592 PMCID: PMC2693224 DOI: 10.1016/j.molcel.2006.12.022] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2006] [Revised: 10/13/2006] [Accepted: 12/27/2006] [Indexed: 11/19/2022]
Abstract
The Sir2 family of proteins consists of broadly conserved NAD(+)-dependent deacetylases that are implicated in diverse biological processes, including DNA regulation, metabolism, and longevity. Sir2 proteins are regulated in part by the cellular concentrations of a noncompetitive inhibitor, nicotinamide, that reacts with a Sir2 reaction intermediate via a base-exchange reaction to reform NAD(+) at the expense of deacetylation. To gain a mechanistic understanding of nicotinamide inhibition in Sir2 enzymes, we captured the structure of nicotinamide bound to a Sir2 homolog, yeast Hst2, in complex with its acetyl-lysine 16 histone H4 substrate and a reaction intermediate analog, ADP-HPD. Together with related biochemical studies and structures, we identify a nicotinamide inhibition and base-exchange site that is distinct from the so-called "C pocket" binding site for the nicotinamide group of NAD(+). These results provide insights into the Sir2 mechanism of nicotinamide inhibition and have important implications for the development of Sir2-specific effectors.
Collapse
Affiliation(s)
- Brandi D. Sanders
- The Wistar Institute, University of Pennsylvania, Philadelphia, PA, 19104 USA
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104 USA
| | - Kehao Zhao
- The Wistar Institute, University of Pennsylvania, Philadelphia, PA, 19104 USA
| | - James T. Slama
- Department of Medicinal and Biological Chemistry, College of Pharmacy, University of Toledo, OH, 43606 USA
| | - Ronen Marmorstein
- The Wistar Institute, University of Pennsylvania, Philadelphia, PA, 19104 USA
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104 USA
- Correspondence: e-mail:
| |
Collapse
|
10
|
Zhao K, Harshaw R, Chai X, Marmorstein R. Structural basis for nicotinamide cleavage and ADP-ribose transfer by NAD(+)-dependent Sir2 histone/protein deacetylases. Proc Natl Acad Sci U S A 2004; 101:8563-8. [PMID: 15150415 PMCID: PMC423234 DOI: 10.1073/pnas.0401057101] [Citation(s) in RCA: 136] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sir2 enzymes are broadly conserved from bacteria to humans and have been implicated to play roles in gene silencing, DNA repair, genome stability, longevity, metabolism, and cell physiology. These enzymes bind NAD(+) and acetyllysine within protein targets and generate lysine, 2'-O-acetyl-ADP-ribose, and nicotinamide products. To provide structural insights into the chemistry catalyzed by Sir2 proteins we report the high-resolution ternary structure of yeast Hst2 (homologue of Sir two 2) with an acetyllysine histone H4 peptide and a nonhydrolyzable NAD(+) analogue, carba-NAD(+), as well as an analogous ternary complex with a reaction intermediate analog formed immediately after nicotinamide hydrolysis, ADP-ribose. The ternary complex with carba-NAD(+) reveals that the nicotinamide group makes stabilizing interactions within a binding pocket harboring conserved Sir2 residues. Moreover, an asparagine residue, N116, strictly conserved within Sir2 proteins and shown to be essential for nicotinamide exchange, is in position to stabilize the oxocarbenium intermediate that has been proposed to proceed the hydrolysis of nicotinamide. A comparison of this structure with the ADP-ribose ternary complex and a previously reported ternary complex with the 2'-O-acetyl-ADP-ribose reaction product reveals that the ribose ring of the cofactor and the highly conserved beta1-alpha2 loop of the protein undergo significant structural rearrangements to facilitate the ordered NAD(+) reactions of nicotinamide cleavage and ADP-ribose transfer to acetate. Together, these studies provide insights into the chemistry of NAD(+) cleavage and acetylation by Sir2 proteins and have implications for the design of Sir2-specific regulatory molecules.
Collapse
Affiliation(s)
- Kehao Zhao
- The Wistar Institute, Department of Biochemistry and Biophysics, School of Medicine, and Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | | | | | | |
Collapse
|
11
|
Rusche LN, Kirchmaier AL, Rine J. The establishment, inheritance, and function of silenced chromatin in Saccharomyces cerevisiae. Annu Rev Biochem 2003; 72:481-516. [PMID: 12676793 DOI: 10.1146/annurev.biochem.72.121801.161547] [Citation(s) in RCA: 586] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genomes are organized into active regions known as euchromatin and inactive regions known as heterochromatin, or silenced chromatin. This review describes contemporary knowledge and models for how silenced chromatin in Saccharomyces cerevisiae forms, functions, and is inherited. In S. cerevisiae, Sir proteins are the key structural components of silenced chromatin. Sir proteins interact first with silencers, which dictate which regions are silenced, and then with histone tails in nucleosomes as the Sir proteins spread from silencers along chromosomes. Importantly, the spreading of silenced chromatin requires the histone deacetylase activity of Sir2p. This requirement leads to a general model for the spreading and inheritance of silenced chromatin or other special chromatin states. Such chromatin domains are marked by modifications of the nucleosomes or DNA, and this mark is able to recruit an enzyme that makes further marks. Thus, among different organisms, multiple forms of repressive chromatin can be formed using similar strategies but completely different proteins. We also describe emerging evidence that mutations that cause global changes in the modification of histones can alter the balance between euchromatin and silenced chromatin within a cell.
Collapse
Affiliation(s)
- Laura N Rusche
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California 94720-3202, USA.
| | | | | |
Collapse
|
12
|
Landry J, Slama JT, Sternglanz R. Role of NAD(+) in the deacetylase activity of the SIR2-like proteins. Biochem Biophys Res Commun 2000; 278:685-90. [PMID: 11095969 DOI: 10.1006/bbrc.2000.3854] [Citation(s) in RCA: 200] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this report we describe the role of NAD(+) in the deacetylation reaction catalyzed by the SIR2 family of enzymes. We first show that the products of the reaction detected by HPLC analysis are ADP-ribose, nicotinamide, and a deacetylated peptide substrate. These products are in a 1:1:1 molar ratio, indicating that deacetylation involves the hydrolysis of one NAD(+) to ADP-ribose and nicotinamide for each acetyl group removed. Three results suggest that deacetylation requires an enzyme-ADP-ribose intermediate. First, the enzyme can promote an NAD(+) if nicotinamide exchange reaction that depends on an acetylated substrate. Second, a non-hydrolyzable NAD(+) analog is a competitive inhibitor of the enzyme, and, third, nicotinamide shows product inhibition of deacetylase activity.
Collapse
Affiliation(s)
- J Landry
- Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, New York, 11794-5215, USA
| | | | | |
Collapse
|
13
|
Wall KA, Klis M, Kornet J, Coyle D, Amé JC, Jacobson MK, Slama JT. Inhibition of the intrinsic NAD+ glycohydrolase activity of CD38 by carbocyclic NAD analogues. Biochem J 1998; 335 ( Pt 3):631-6. [PMID: 9794804 PMCID: PMC1219825 DOI: 10.1042/bj3350631] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Carba-NAD and pseudocarba-NAD are carbocyclic analogues of NAD+ in which a 2,3-dihydroxycyclopentane methanol replaces the beta-d-ribonucleotide ring of the nicotinamide riboside moiety of NAD+ [Slama and Simmons (1988) Biochemistry 27, 183-193]. These carbocyclic NAD+ analogues, related to each other as diastereomers, have been tested as inhibitors of the intrinsic NAD+ glycohydrolase activity of human CD38, dog spleen NAD+ glycohydrolase, mouse CD38 and Aplysia californica cADP-ribose synthetase. Pseudocarba-NAD, the carbocyclic dinucleotide in which l-2,3-dihydroxycyclopentane methanol replaces the d-ribose of the nicotinamide riboside moiety of NAD+, was found to be the more potent inhibitor. Pseudocarba-NAD was shown to inhibit the intrinsic NAD+ glycohydrolase activity of human CD38 competitively, with Ki=148 microM determined for the recombinant extracellular protein domain and Ki=180 microM determined for the native protein expressed as a cell-surface enzyme on cultured Jurkat cells. Pseudocarba-NAD was shown to be a non-competitive inhibitor of the purified dog spleen NAD+ glycohydrolase, with Kis=47 miroM and Kii=198 microM. Neither pseudocarba-NAD nor carba-NAD inhibited mouse CD38 or Aplysia californica cADP-ribose synthetase significantly at concentrations up to 1 mM. The results underscore significant species differences in the sensitivity of these enzymes to inhibition, and indicate that pseudocarba-NAD will be useful as an inhibitor of the enzymic activity of human but not mouse CD38 in studies using cultured cells.
Collapse
Affiliation(s)
- K A Wall
- Department of Medicinal and Biological Chemistry, College of Pharmacy, University of Toledo, Toledo, OH 43606, USA
| | | | | | | | | | | | | |
Collapse
|
14
|
Ruf A, Rolli V, de Murcia G, Schulz GE. The mechanism of the elongation and branching reaction of poly(ADP-ribose) polymerase as derived from crystal structures and mutagenesis. J Mol Biol 1998; 278:57-65. [PMID: 9571033 DOI: 10.1006/jmbi.1998.1673] [Citation(s) in RCA: 124] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The binding site for the acceptor substrate poly(ADP-ribose) in the elongation reaction of the ADP-ribosyl transferase poly(ADP-ribose) polymerase (PARP) was detected by cocrystallizing the enzyme with an NAD+ analogue. The site was confirmed by mutagenesis studies. In conjunction with the binding site of the donor NAD+, the bound acceptor reveals the geometry of the elongation reaction. It shows in particular that the strictly conserved glutamate residue of all ADP-ribosylating enzymes (Glu988 of PARP) facilitates the reaction by polarizing both, donor and acceptor. Moreover, the binding properties of the acceptor site suggest a mechanism for the branching reaction, that also explains the dual specificity of this transferase for elongation and branching, which is unique among polymer-forming enzymes.
Collapse
Affiliation(s)
- A Ruf
- Institut für Organische Chemie und Biochemie, Albertstr. 21, Freiburg im Breisgau, D-79104, Germany
| | | | | | | |
Collapse
|
15
|
Sethi JK, Empson RM, Galione A. Nicotinamide inhibits cyclic ADP-ribose-mediated calcium signalling in sea urchin eggs. Biochem J 1996; 319 ( Pt 2):613-7. [PMID: 8912702 PMCID: PMC1217811 DOI: 10.1042/bj3190613] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Cyclic ADP ribose (cADPR) is a potent Ca(2+)-releasing agent, and putative second messenger, the endogenous levels of which are tightly regulated by synthetic (ADP-ribosyl cyclases) and degradative (cADPR hydrolase) enzymes. These enzymes have been characterized in a number of mammalian and invertebrate tissues and their activities are often found on a single polypeptide. beta-NAD+, cGMP and nitric oxide (NO) have been reported to mobilize Ca2+ in the sea urchin egg via the cADPR-mediated pathway. We now report that in sea urchin egg homogenates, nicotinamide inhibits the Ca(2+)-mobilizing action of beta-NAD+, cGMP and NO, but has no effect on cADPR-induced Ca2+ release. Moreover, nicotinamide inhibits cGMP-induced regenerative Ca2+ waves in the intact sea urchin egg. By successfully separating the cADPR-metabolizing machinery from that which releases Ca2+, we have shown that nicotinamide inhibits cADPR-mediated Ca2+ signalling at the level of cADPR generation. Importantly, nicotinamide had no effect upon the hydrolysis of cADPR, and its selective action on cyclase activity was supported by its inhibition of purified Aplysia ADP-ribosyl cyclase, which does not exhibit detectable hydrolytic activity. The action of nicotinamide in blocking Ca2+ release by beta-NAD+, cGMP and NO strongly suggests that these agents act as modulators of cADPR synthesis rather than to sensitize calcium release channels to cADPR.
Collapse
Affiliation(s)
- J K Sethi
- University Department of Pharmacology, Oxford University, U.K
| | | | | |
Collapse
|
16
|
|
17
|
Calvani F, Macchia M, Rossello A, Gismondo M, Drago L, Fassina M, Cisternino M, Domiano P. Synthesis and antiviral activity of dihydroxycyclohexyl pyrimidine and purine carbocyclic nucleosides. Bioorg Med Chem Lett 1995. [DOI: 10.1016/0960-894x(95)00439-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
18
|
Griffin RJ, Curtin NJ, Newell DR, Golding BT, Durkacz BW, Calvert AH. The role of inhibitors of poly(ADP-ribose) polymerase as resistance-modifying agents in cancer therapy. Biochimie 1995; 77:408-22. [PMID: 7578423 DOI: 10.1016/0300-9084(96)88154-5] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Poly(ADP-ribose) polymerase (PARP) plays an important role in a number of cellular processes including DNA repair. Since poly(ADP-ribosyl)ation occurs in response to radiation- or drug-induced DNA damage, inhibitors of the enzyme may enhance the antitumour activity of radiotherapy or cytotoxic drug treatment. In this review the development of PARP inhibitors is discussed, and structure-activity relationships amongst inhibitors of the enzyme are presented. Studies to date regarding the in vitro and in vivo activity of PARP inhibitors, as resistance modifying agents in cancer therapy, are also overviewed.
Collapse
Affiliation(s)
- R J Griffin
- Department of Chemistry, University of Newcastle, Newcastle upon Tyne, UK
| | | | | | | | | | | |
Collapse
|
19
|
Abstract
The pyridine nucleotides have important non-redox activities as cellular effectors and metabolic regulators [1-3]. The enzyme-catalyzed cleavage of the nicotinamide-ribosyl bond of NAD+ and the attendant delivery of the ADPRibosyl moiety to acceptors is central to these many diverse biological activities. Included are the medically important NAD-dependent toxins associated with cholera, diphtheria, pertussis, and related diseases [4]; the reversible ADPRibosylation-mediated biological regulatory systems [5,6]; the synthesis of poly(ADPRibose) in response to DNA damage or cellular division [7]; and the synthesis of cyclic ADPRibose as part of an independent, calcium-mediated regulatory system [8]. As will be presented in this chapter, all evidence points to both the chemical and enzyme-catalyzed cleavage of the nicotinamide-ribosyl bond being dissociative in character via an oxocarbenium intermediate.
Collapse
Affiliation(s)
- N J Oppenheimer
- Department of Pharmaceutical Chemistry, University of California, San Francisco 94143-0446
| |
Collapse
|
20
|
Pankiewicz KW, Ciszewski LA, Ptak AT. Synthesis of 2,2′-Anhydro-2-Hydroxy- and 6,2′-Anhydro-6-Hydroxy-1-β-D-Arabindfuranosylnicotinamide as Conformationally Restricted Nicotinamide Nucleoside Analogs1. ACTA ACUST UNITED AC 1991. [DOI: 10.1080/07328319108047066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
21
|
|
22
|
Slama JT, Simmons AM. Synthesis and properties of photoaffinity labels for the pyridine dinucleotide binding site of NAD glycohydrolase. Biochemistry 1991; 30:2527-34. [PMID: 1848099 DOI: 10.1021/bi00223a033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Two new photoactive analogues of oxidized nicotinamide adenine dinucleotide (NAD+) which are resistant to cleavage by NAD glycohydrolase were synthesized and characterized. The beta-D-ribonucleotide ring of the nicotinamide riboside moiety of NAD+ was replaced with a 2,3-dihydroxycyclopentane ring forming a carbocyclic dinucleotide analogue. Photoreactivity was achieved by the incorporation of an azido group at the 8-position of the adenosyl ring. The previously published synthesis of carbocyclic pyridine dinucleotide analogues [Slama, J. T., & Simmons, A. M. (1988) Biochemistry 27, 183] was modified by resolving the carbocyclic 1-aminoribose analogues and producing optically pure (+)-(1S)- or (-)-(1R)-4 beta-amino-2 alpha,3 alpha-dihydroxy-1 beta-cyclopentanemethanol. Each of these was converted to the corresponding carbocyclic nicotinamide 5'-nucleotide analogue and coupled with 8-azidoadenosine 5'-monophosphate. Two photoactive and isomeric NAD+ analogues were thus prepared. 8-Azidoadenosyl carba-NAD is the analogue in which D-dihydroxycyclopentane is substituted for the D-ribose of the nicotinamide nucleoside moiety. 8-Azido-adenosyl pseudocarba-NAD contains the L-carbocycle in place of the D-ribotide ring. 8-Azidoadenosyl carba-NAD was shown to inhibit the NAD glycohydrolase from Bungarus fasciatus venom competitively with an inhibitor dissociation constant of 187 microM. 8-Azidoadenosyl pseudocarba-NAD was shown to inhibit the same enzyme competitively with a Ki of 73 microM. The superior NADase inhibitor, 8-azidoadenosyl pseudocarba-NAD, was characterized kinetically and shown to fulfill the criteria required of a specific active site directed photoaffinity probe. Irradiation of mixtures of the photoprobe and NAD glycohydrolase with short-wave ultraviolet light resulted in the rapid and irreversible loss of enzyme activity.(ABSTRACT TRUNCATED AT 250 WORDS)
Collapse
Affiliation(s)
- J T Slama
- Department of Biochemistry, University of Texas Health Science Center, San Antonio 78284-7760
| | | |
Collapse
|