Sylvie Garneau-tsodikova

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Organization: University of Michigan
Department: Department of Medicinal Chemistry in the College of Pharmacy
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Co-reporter:Todd J. Eckroat, Keith D. Green, Rebecca A. Reed, Joshua J. Bornstein, Sylvie Garneau-Tsodikova
Bioorganic & Medicinal Chemistry 2013 Volume 21(Issue 12) pp:3614-3623
Publication Date(Web):15 June 2013
DOI:10.1016/j.bmc.2013.02.047
Alzheimer’s disease (AD) is a complex neurological disorder with multiple inter-connected factors playing roles in the onset and progression of the disease. One strategy currently being explored for the development of new therapeutics for AD involves linking tacrine, a known acetylcholinesterase (AChE) inhibitor, to another drug to create bifunctional hybrids. The role and influence on activity of the linker moiety in these hybrids remains ill-defined. In this study, three series of 6-chlorotacrine with linkers varying in terminal functional group and length were synthesized, evaluated for AChE inhibition, and compared to tacrine and 6-chlorotacrine–mefenamic acid hybrids. Out of the compounds with terminal amine, methyl, and hydroxyl moieties tested, several highly potent molecules (low nanomolar IC50 values) comprised of linkers with terminal amines were identified. These 6-chlorotacrine with linkers were significantly more potent than tacrine alone and were often more potent than similar 6-chlorotacrine–mefenamic acid hybrids.
Co-reporter:Wenjing Chen, Keith D. Green, Oleg V. Tsodikov, and Sylvie Garneau-Tsodikova
Biochemistry 2012 Volume 51(Issue 24) pp:4959-4967
Publication Date(Web):May 30, 2012
DOI:10.1021/bi3004473
The enhanced intracellular survival (Eis) protein improves the survival of Mycobacterium smegmatis (Msm) in macrophages and functions as the acetyltransferase responsible for kanamycin A resistance, a hallmark of extensively drug-resistant (XDR) tuberculosis, in a large number of Mycobacterium tuberculosis (Mtb) clinical isolates. We recently demonstrated that Eis from Mtb (Eis_Mtb) efficiently multiacetylates a variety of aminoglycoside (AG) antibiotics. Here, to gain insight into the origin of substrate selectivity of AG multiacetylation by Eis, we analyzed AG acetylation by Eis_Msm, investigated its inhibition, and compared these functions to those of Eis_Mtb. Even though for several AGs the multiacetylation properties of Eis_Msm and Eis_Mtb are similar, there are three major differences. (i) Eis_Msm diacetylates apramycin, a conformationally constrained AG, which Eis_Mtb cannot modify. (ii) Eis_Msm triacetylates paromomycin, which can be only diacetylated by Eis_Mtb. (iii) Eis_Msm only monoacetylates hygromycin, a structurally unique AG that is diacetylated by Eis_Mtb. Several nonconserved amino acid residues lining the AG-binding pocket of Eis are likely responsible for these differences between the two Eis homologues. Specifically, we propose that because the AG-binding pocket of Eis_Msm is more open than that of Eis_Mtb, it accommodates apramycin for acetylation in Eis_Msm, but not in Eis_Mtb. We also demonstrate that inhibitors of Eis_Mtb that we recently discovered can inhibit Eis_Msm activity. These observations help define the structural origins of substrate preference among Eis homologues and suggest that Eis_Mtb inhibitors may be applied against all pathogenic mycobacteria to overcome AG resistance caused by Eis upregulation.
Co-reporter:Rachel E. Pricer, Jacob L. Houghton, Keith D. Green, Abdelrahman S. Mayhoub and Sylvie Garneau-Tsodikova  
Molecular BioSystems 2012 vol. 8(Issue 12) pp:3305-3313
Publication Date(Web):09 Oct 2012
DOI:10.1039/C2MB25341K
The Mycobacterium tuberculosis enhanced intracellular survival (Eis_Mtb) protein is a clinically important aminoglycoside (AG) multi-acetylating enzyme. Eis homologues are found in a variety of mycobacterial and non-mycobacterial species. Variation of the residues lining the AG-binding pocket and positions of the loops bearing these residues in the Eis homologues dictates the substrate specificity and, thus, Eis homologues are Nature-made tools for elucidating principles of AG recognition by Eis. Here, we demonstrate that the Eis from Anabaena variabilis (Eis_Ava), the first non-mycobacterial Eis homologue reported, is a multi-acetylating AG-acetyltransferase. Eis_Ava, Eis from Mycobacterium tuberculosis (Eis_Mtb), and Eis from Mycobacterium smegmatis (Eis_Msm) have different structures of their AG-binding pockets. We perform comparative analysis of these differences and investigate how they dictate the substrate and cosubstrate recognition and acetylation of AGs by Eis.
Co-reporter:Olga E. Zolova and Sylvie Garneau-Tsodikova  
MedChemComm 2012 vol. 3(Issue 8) pp:950-955
Publication Date(Web):20 Jun 2012
DOI:10.1039/C2MD20131C
The 3-hydroxyquinaldic acid (3HQA) chromophores of thiocoraline are essential for the biological DNA bisintercalating function of this antitumor agent. The 3HQA units are also proposed to play a critical role in the resistance mechanism of the thiocoraline-producing organism against this natural product. Because of their important functions, there is a great interest in understanding the 3HQA formation from L-Trp. The first proposed committed steps during 3HQA biosynthesis consist of conversion of L-Trp into L-Trp-AMP by the adenylation domain of TioK followed by installation of the activated amino acid onto the thiolation domain of this didomain enzyme. However, testing this series of events has been hindered by the inability to heterologously express soluble TioK. Here, we demonstrated that the MbtH-like protein TioT is required for production and activation of TioK. With soluble functional TioK in hand, we established the amino acid substrate profile and kinetically characterized this enzyme. By site-directed mutagenesis of TioT, we also investigated the significance of three Pro residues that are universally conserved in MbtH-like proteins.
Co-reporter:Ido M. Herzog;Dr. Keith D. Green;Yifat Berkov-Zrihen;Dr. Mark Feldman;Dr. Roee R. Vidavski;Anat Eldar-Boock;Dr. Ronit Satchi-Fainaro;Dr. Avigdor Eldar;Dr. Sylvie Garneau-Tsodikova;Dr. Micha Fridman
Angewandte Chemie International Edition 2012 Volume 51( Issue 23) pp:5652-5656
Publication Date(Web):
DOI:10.1002/anie.201200761
Co-reporter:Ido M. Herzog;Dr. Keith D. Green;Yifat Berkov-Zrihen;Dr. Mark Feldman;Dr. Roee R. Vidavski;Anat Eldar-Boock;Dr. Ronit Satchi-Fainaro;Dr. Avigdor Eldar;Dr. Sylvie Garneau-Tsodikova;Dr. Micha Fridman
Angewandte Chemie International Edition 2012 Volume 51( Issue 23) pp:
Publication Date(Web):
DOI:10.1002/anie.201203240
Co-reporter:Ido M. Herzog;Dr. Keith D. Green;Yifat Berkov-Zrihen;Dr. Mark Feldman;Dr. Roee R. Vidavski;Anat Eldar-Boock;Dr. Ronit Satchi-Fainaro;Dr. Avigdor Eldar;Dr. Sylvie Garneau-Tsodikova;Dr. Micha Fridman
Angewandte Chemie 2012 Volume 124( Issue 23) pp:5750-5754
Publication Date(Web):
DOI:10.1002/ange.201200761
Co-reporter:Ido M. Herzog;Dr. Keith D. Green;Yifat Berkov-Zrihen;Dr. Mark Feldman;Dr. Roee R. Vidavski;Anat Eldar-Boock;Dr. Ronit Satchi-Fainaro;Dr. Avigdor Eldar;Dr. Sylvie Garneau-Tsodikova;Dr. Micha Fridman
Angewandte Chemie 2012 Volume 124( Issue 23) pp:
Publication Date(Web):
DOI:10.1002/ange.201203240
Co-reporter:Dr. Keith D. Green;Wenjing Chen;Dr. Sylvie Garneau-Tsodikova
ChemMedChem 2012 Volume 7( Issue 1) pp:73-77
Publication Date(Web):
DOI:10.1002/cmdc.201100332
Co-reporter:Dr. Keith D. Green;Wenjing Chen;Dr. Sylvie Garneau-Tsodikova
ChemMedChem 2012 Volume 7( Issue 1) pp:
Publication Date(Web):
DOI:10.1002/cmdc.201190063
Co-reporter:Pazit Shaul, Keith D. Green, Roi Rutenberg, Maria Kramer, Yifat Berkov-Zrihen, Elinor Breiner-Goldstein, Sylvie Garneau-Tsodikova and Micha Fridman  
Organic & Biomolecular Chemistry 2011 vol. 9(Issue 11) pp:4057-4063
Publication Date(Web):28 Jan 2011
DOI:10.1039/C0OB01133A
Amongst the many synthetic aminoglycoside analogues that were developed to regain the efficacy of this class of antibiotics against resistant bacterial strains, the 1-N-acylated analogues are the most clinically used. In this study we demonstrate that 6′-N-acylation of the clinically used compound tobramycin and 6′′′-N-acylation of paromomycin result in derivatives resistant to deactivation by 6′-aminoglycoside acetyltransferase (AAC(6′)) which is widely found in aminoglycoside resistant bacteria. When tested against AAC(6′)- or AAC(3)-expressing bacteria as well as pathogenic bacterial strains, some of the analogues demonstrated improved antibacterial activity compared to their parent antibiotics. Improvement of the biological performance of the N-acylated analogues was found to be highly dependent on the specific aminoglycoside and acyl group. Our study indicates that as for 1-N-acylation, 6′- and 6′′′-N-acylation of aminoglycosides offer an additional promising direction in the search for aminoglycosides capable of overcoming infections by resistant bacteria.
Co-reporter:Ahmed S. A. Mady, Olga E. Zolova, María Álvarez San Millán, Germán Villamizar, Fernando de la Calle, Felipe Lombó and Sylvie Garneau-Tsodikova  
Molecular BioSystems 2011 vol. 7(Issue 6) pp:1999-2011
Publication Date(Web):11 Apr 2011
DOI:10.1039/C1MB05044C
An antitumor agent thiocoraline is a thiodepsipeptide marine product derived from two Micromonospora sp. strains that inhibits protein synthesis by binding of its key 3-hydroxyquinaldic acid (3HQA) chromophores to duplex DNA. There are at least two potential pathways via which the 3HQA moiety could be biosynthesized from L-Trp. By biochemical characterization and by preparation of knockouts of an adenylation–thiolation enzyme, TioK, and of two type II thioesterases, TioP and TioQ, found in the thiocoraline biosynthetic gene cluster, we gained valuable insight into the pathway followed for the production of 3HQA.
Co-reporter:Joshua J. Bornstein, Todd J. Eckroat, Jacob L. Houghton, Christopher K. Jones, Keith D. Green and Sylvie Garneau-Tsodikova  
MedChemComm 2011 vol. 2(Issue 5) pp:406-412
Publication Date(Web):09 Mar 2011
DOI:10.1039/C0MD00256A
Alzheimer's disease (AD) is a complex syndrome characterized by the degeneration of the brain and central nervous system that may be caused by an assortment of genetic and environmental factors. Consequently, a conjunctive approach targeting multiple affecters of AD could lead to improved drug candidates for the treatment of AD. A convergent chemical synthetic approach yielded a series of tacrine-mefenamic acid hybrids that were evaluated for their ability to inhibit acetylcholinesterase (AChE). A majority of the compounds tested showed low nanomolar IC50 values, an improvement over the parent compound, tacrine, suggesting that they could be effective in increasing cholinergic function. Additionally, an assay to evaluate the compounds upon exposure to reactive oxygen species was performed, the results of which may suggest a role for the mefenamic acid moiety in the inhibition of AChE. Molecular modeling studies were performed to rationalize the experimental results.
Co-reporter:Wenjing Chen;Tapan Biswas;Vanessa R. Porter;Oleg V. Tsodikov
PNAS 2011 Volume 108 (Issue 24 ) pp:9804-9808
Publication Date(Web):2011-06-14
DOI:10.1073/pnas.1105379108
The emergence of multidrug-resistant and extensively drug-resistant (XDR) tuberculosis (TB) is a serious global threat. Aminoglycoside antibiotics are used as a last resort to treat XDR-TB. Resistance to the aminoglycoside kanamycin is a hallmark of XDR-TB. Here, we reveal the function and structure of the mycobacterial protein Eis responsible for resistance to kanamycin in a significant fraction of kanamycin-resistant Mycobacterium tuberculosis clinical isolates. We demonstrate that Eis has an unprecedented ability to acetylate multiple amines of many aminoglycosides. Structural and mutagenesis studies of Eis indicate that its acetylation mechanism is enabled by a complex tripartite fold that includes two general control non-derepressible 5 (GCN5)-related N-acetyltransferase regions. An intricate negatively charged substrate-binding pocket of Eis is a potential target of new antitubercular drugs expected to overcome aminoglycoside resistance.
Co-reporter:Keith D. Green, Vanessa R. Porter, Yaru Zhang and Sylvie Garneau-Tsodikova
Biochemistry 2010 Volume 49(Issue 29) pp:
Publication Date(Web):June 18, 2010
DOI:10.1021/bi1007996
In eukaryotes, choline acetyltransferase (ChAT) catalyzes the reversible formation of the neurotransmitter acetylcholine from choline and acetyl-CoA. ChAT belongs to a family of CoA-dependent enzymes that also includes the carnitine acyltransferases CrAT, CrOT, and CPTs. In contrast to CrOT and CPTs that are very active toward medium- and long-chain acyl-CoAs, respectively, CrAT and ChAT display activity toward only short-chain acyl-CoAs. We recently demonstrated the substrate and cosubstrate promiscuity of the wild-type human ChAT (hChAT). To extend the flexibility of this enzyme, we have generated a series of single, double, and triple hChAT mutants. Here we report the conversion of hChAT into choline octanoyltransferase (ChOT) and choline palmitoyltransferase (ChPT). The E337 and C550 residues (numbering from hChAT) were previously shown to dictate the acyl-CoA cosubstrate specificity in the carnitine series. Here we identify and demonstrate the importance of C551, in addition to E337 and C550, in contributing to the acyl-CoA specificity of hChAT. We also show that either C550 or C551 needs to be present for the transfer of medium- and long-chain acyl-CoAs by hChAT. By exploring the potential expansion of the tunnel on the substrate side, we demonstrate that residues M84, Y436, and Y552 play a critical role in binding and holding the choline substrate in the ChAT active site.
Co-reporter:Keith D. Green Dr.;Wenjing Chen;Jacob L. Houghton;Micha Fridman Dr. Dr.
ChemBioChem 2010 Volume 11( Issue 1) pp:
Publication Date(Web):
DOI:10.1002/cbic.200990088
Co-reporter:Keith D. Green Dr.;Wenjing Chen;Jacob L. Houghton;Micha Fridman Dr. Dr.
ChemBioChem 2010 Volume 11( Issue 1) pp:119-126
Publication Date(Web):
DOI:10.1002/cbic.200900584

Abstract

Aminoglycosides are broad-spectrum antibiotics commonly used for the treatment of serious bacterial infections. Decades of clinical use have led to the widespread emergence of bacterial resistance to this family of drugs limiting their efficacy in the clinic. Here, we report the development of a methodology that utilizes aminoglycoside acetyltransferases (AACs) and unnatural acyl coenzyme A analogues for the chemoenzymatic generation of N-acylated aminoglycoside analogues. Generation of N-acylated aminoglycosides is followed by a simple qualitative test to assess their potency as potential antibacterials. The studied AACs (AAC(6′)-APH(2′′) and AAC(3)-IV) show diverse substrate promiscuity towards a variety of aminoglycosides as well as acyl coenzyme A derivatives. The enzymes were also used for the sequential generation of homo- and hetero-di-N-acylated aminoglycosides. Following the clinical success of the N-acylated amikacin and arbekacin, our chemoenzymatic approach offers access to regioselectively N-acylated aminoglycosides in quantities that allow testing of the antibacterial potential of the synthetic analogues making it possible to decide which molecules will be worth synthesizing on a larger scale.

Co-reporter:Jacob L. Houghton ;Keith D. Green Dr.;Wenjing Chen  Dr.
ChemBioChem 2010 Volume 11( Issue 7) pp:880-902
Publication Date(Web):
DOI:10.1002/cbic.200900779

Abstract

Although aminoglycosides have been used as antibacterials for decades, their use has been hindered by their inherent toxicity and the resistance that has emerged to these compounds. It seems that such issues have relegated a formerly front-line class of antimicrobials to the proverbial back shelf. However, recent advances have demonstrated that novel aminoglycosides have a potential to overcome resistance as well as to be used to treat HIV-1 and even human genetic disorders, with abrogated toxicity. It is not the end for aminoglycosides, but rather, the challenges faced by researchers have led to ingenuity and a change in how we view this class of compounds, a renaissance.

Co-reporter:Olga E. Zolova;Ahmed S. A. Mady
Biopolymers 2010 Volume 93( Issue 9) pp:777-790
Publication Date(Web):
DOI:10.1002/bip.21489

Abstract

The bisintercalator natural products are a family of nonribosomal peptides possessing a range of biological properties that include antiviral, antibiotic, and anticancer activities. The name bisintercalator is derived from the ability to directly bind to duplex DNA through two planar intercalating moieties. Although 19 members of this family of compounds have been identified over the past 50 years, the biosynthetic genes responsible for the formation of four of these molecules (thiocoraline, SW-163, triostin A, and echinomycin) were identified only recently. This recent progress opens an avenue towards understanding how Nature produces these bisintercalating products and provides the potential to develop and identify novel potent analogous lead compounds for clinical applications. This review discusses the mode of action of bisintercalators and summarizes recent genetic and biochemical insights into their biosynthetic production, analog formation, and possible mechanisms by which resistance to these compounds is achieved by their producing organisms. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 777–790, 2010.

Co-reporter:Thomas J. McQuade, Abbie D. Shallop, Anita Sheoran, James E. DelProposto, Oleg V. Tsodikov, Sylvie Garneau-Tsodikova
Analytical Biochemistry 2009 Volume 386(Issue 2) pp:244-250
Publication Date(Web):15 March 2009
DOI:10.1016/j.ab.2008.12.014
Adenylation domains are critical enzymes that dictate the identity of the amino acid building blocks to be incorporated during nonribosomal peptide (NRP) biosynthesis. NRPs display a wide range of biological activities and are some of the most important drugs currently used in clinics. Traditionally, activity of adenylation domains has been measured by radioactive ATP-[32P]pyrophosphate (PPi) exchange assays. To identify adenylation domains for future combinatorial production of novel NRPs as potential drugs, we report a convenient high-throughput nonradioactive method to measure activity of these enzymes. In our assay, malachite green is used to measure orthophosphate (Pi) concentrations after degradation by inorganic pyrophosphatase of the PPi released during aminoacyl-AMP formation by action of the adenylation domains. The assay is quantitative, accurate, and robust, and it can be performed in 96- and 384-well plate formats. The performance of our assay was tested by using NcpB-A4, one of the seven adenylation domains involved in nostocyclopeptide biosynthesis. The kinetics of pyrophosphate release monitored by this method are much slower than those measured by a traditional ATP-[32P]PPi exchange assay. This observation indicates that the formation of the adenylated amino acid and its release are the rate-limiting steps during the catalytic turnover.
Co-reporter:Keith D. Green Dr.;Micha Fridman Dr. Dr.
ChemBioChem 2009 Volume 10( Issue 13) pp:2191-2194
Publication Date(Web):
DOI:10.1002/cbic.200900309
Co-reporter:Anita Sheoran, Andrew King, Ana Velasco, Jessica M. Pero and Sylvie Garneau-Tsodikova  
Molecular BioSystems 2008 vol. 4(Issue 6) pp:622-628
Publication Date(Web):04 Apr 2008
DOI:10.1039/B801391H
Thiocoraline is a thiodepsipeptide antitumor agent that belongs to the family of bisintercalator natural products that bind duplex DNA through their two planar intercalating moieties. In thiocoraline, the 3-hydroxyquinaldic acid (3HQA) chromophores required for intercalation are derived from L-Trp. We have expressed the Micromonospora sp. ML1 tryptophan 2,3-dioxygenase (TDO) TioF, purified it from E. coli, and confirmed its role in the irreversible oxidation of L-Trp to N-formylkynurenine, the proposed first step during 3HQA biosynthesis. We have established that TioF is a catalyst with broader specificity than other TDOs, but that is less promiscuous than indoleamine 2,3-dioxygenases. TioF was found to display activity with various L-Trp analogs (serotonin, D-Trp, and indole). The TioF reaction products generated during this study will be used as substrates for subsequent analysis of the other enzymes involved in 3HQA biosynthesis.
Co-reporter:Tapan Biswas, Olga E. Zolova, Felipe Lombó, Fernando de la Calle, ... Sylvie Garneau-Tsodikova
Journal of Molecular Biology (26 March 2010) Volume 397(Issue 2) pp:495-507
Publication Date(Web):26 March 2010
DOI:10.1016/j.jmb.2010.01.053
Thiocoraline is a thiodepsipeptide with potent antitumor activity. TioX, a protein with an unidentified function, is encoded by a gene of the thiocoraline biosynthetic gene cluster. The crystal structure of the full-length TioX protein at 2.15 Å resolution reveals that TioX protomer shares an ancient βαβββ fold motif with glyoxalase I and bleomycin resistance protein families, despite a very low sequence homology. Intriguingly, four TioX monomers form a unique 2-fold symmetric tetrameric assembly that is stabilized by four intermolecular disulfide bonds formed cyclically between Cys60 and Cys66 of adjacent monomers. The arrangement of two of the four monomers in the TioX tetramer is analogous to that in dimeric bleomycin resistance proteins. This analogy indicates that this novel higher-order structural scaffold of TioX may have evolved to bind thiocoraline. Our equilibrium titration studies demonstrate the binding of a thiocoraline chromophore analog, quinaldic acid, to TioX, thereby substantiating this model. Furthermore, a strain of Streptomyces albus containing an exogenous thiocoraline gene cluster devoid of functional tioX maintains thiocoraline production, albeit with a lower yield. Taken together, these observations rule out a direct enzymatic function of TioX and suggest that TioX is involved in thiocoraline resistance or secretion.
Co-reporter:Pazit Shaul, Keith D. Green, Roi Rutenberg, Maria Kramer, Yifat Berkov-Zrihen, Elinor Breiner-Goldstein, Sylvie Garneau-Tsodikova and Micha Fridman
Organic & Biomolecular Chemistry 2011 - vol. 9(Issue 11) pp:NaN4063-4063
Publication Date(Web):2011/01/28
DOI:10.1039/C0OB01133A
Amongst the many synthetic aminoglycoside analogues that were developed to regain the efficacy of this class of antibiotics against resistant bacterial strains, the 1-N-acylated analogues are the most clinically used. In this study we demonstrate that 6′-N-acylation of the clinically used compound tobramycin and 6′′′-N-acylation of paromomycin result in derivatives resistant to deactivation by 6′-aminoglycoside acetyltransferase (AAC(6′)) which is widely found in aminoglycoside resistant bacteria. When tested against AAC(6′)- or AAC(3)-expressing bacteria as well as pathogenic bacterial strains, some of the analogues demonstrated improved antibacterial activity compared to their parent antibiotics. Improvement of the biological performance of the N-acylated analogues was found to be highly dependent on the specific aminoglycoside and acyl group. Our study indicates that as for 1-N-acylation, 6′- and 6′′′-N-acylation of aminoglycosides offer an additional promising direction in the search for aminoglycosides capable of overcoming infections by resistant bacteria.
Carbamic acid,[4-(formylamino)butyl]-, 1,1-dimethylethyl ester (9CI)
Pentanoic acid,5-[[bis[[(1,1-dimethylethoxy)carbonyl]amino]methylene]amino]-
Hexanoic acid, 6-(acetylthio)-
OCTANOIC ACID, 8-[(AMINOIMINOMETHYL)AMINO]-
6-Guanidinecaproic acid hydrochloride
5-[(diaminomethylidene)amino]pentanoic acid