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Sample records for murd s1-int s1-ext

  1. MurD enzymes: some recent developments.

    Science.gov (United States)

    Šink, Roman; Barreteau, Hélène; Patin, Delphine; Mengin-Lecreulx, Dominique; Gobec, Stanislav; Blanot, Didier

    2013-12-01

    The synthesis of the peptide stem of bacterial peptidoglycan involves four enzymes, the Mur ligases (MurC, D, E and F). Among them, MurD is responsible for the ATP-dependent addition of d-glutamic acid to UDP-MurNAc-l-Ala, a reaction which involves acyl-phosphate and tetrahedral intermediates. Like most enzymes of peptidoglycan biosynthesis, MurD constitutes an attractive target for the design and synthesis of new antibacterial agents. Escherichia coli MurD has been the first Mur ligase for which the tridimensional (3D) structure was solved. Thereafter, several co-crystal structures with different ligands or inhibitors were released. In the present review, we will deal with work performed on substrate specificity, reaction mechanism and 3D structure of E. coli MurD. Then, a part of the review will be devoted to recent work on MurD orthologs from species other than E. coli and to cellular organization of Mur ligases and in vivo regulation of the MurD activity. Finally, we will review the different classes of MurD inhibitors that have been designed and assayed to date with the hope of obtaining new antibacterial compounds.

  2. Virtual screening for potential inhibitors of bacterial MurC and MurD ligases.

    Science.gov (United States)

    Tomašić, Tihomir; Kovač, Andreja; Klebe, Gerhard; Blanot, Didier; Gobec, Stanislav; Kikelj, Danijel; Mašič, Lucija Peterlin

    2012-03-01

    Mur ligases are bacterial enzymes involved in the cytoplasmic steps of peptidoglycan biosynthesis and are viable targets for antibacterial drug discovery. We have performed virtual screening for potential ATP-competitive inhibitors targeting MurC and MurD ligases, using a protocol of consecutive hierarchical filters. Selected compounds were evaluated for inhibition of MurC and MurD ligases, and weak inhibitors possessing dual inhibitory activity have been identified. These compounds represent new scaffolds for further optimisation towards multiple Mur ligase inhibitors with improved inhibitory potency.

  3. Inhibitor design strategy based on an enzyme structural flexibility: a case of bacterial MurD ligase.

    Science.gov (United States)

    Perdih, Andrej; Hrast, Martina; Barreteau, Hélène; Gobec, Stanislav; Wolber, Gerhard; Solmajer, Tom

    2014-05-27

    Increasing bacterial resistance to available antibiotics stimulated the discovery of novel efficacious antibacterial agents. The biosynthesis of the bacterial peptidoglycan, where the MurD enzyme is involved in the intracellular phase of the UDP-MurNAc-pentapeptide formation, represents a collection of highly selective targets for novel antibacterial drug design. In our previous computational studies, the C-terminal domain motion of the MurD ligase was investigated using Targeted Molecular Dynamic (TMD) simulation and the Off-Path Simulation (OPS) technique. In this study, we present a drug design strategy using multiple protein structures for the identification of novel MurD ligase inhibitors. Our main focus was the ATP-binding site of the MurD enzyme. In the first stage, three MurD protein conformations were selected based on the obtained OPS/TMD data as the initial criterion. Subsequently, a two-stage virtual screening approach was utilized combining derived structure-based pharmacophores with molecular docking calculations. Selected compounds were then assayed in the established enzyme binding assays, and compound 3 from the aminothiazole class was discovered to act as a dual MurC/MurD inhibitor in the micomolar range. A steady-state kinetic study was performed on the MurD enzyme to provide further information about the mechanistic aspects of its inhibition. In the final stage, all used conformations of the MurD enzyme with compound 3 were simulated in classical molecular dynamics (MD) simulations providing atomistic insights of the experimental results. Overall, the study depicts several challenges that need to be addressed when trying to hit a flexible moving target such as the presently studied bacterial MurD enzyme and show the possibilities of how computational tools can be proficiently used at all stages of the drug discovery process.

  4. Synthesis and biological evaluation of N-acylhydrazones as inhibitors of MurC and MurD ligases.

    Science.gov (United States)

    Sink, Roman; Kovac, Andreja; Tomasić, Tihomir; Rupnik, Veronika; Boniface, Audrey; Bostock, Julieanne; Chopra, Ian; Blanot, Didier; Masic, Lucija Peterlin; Gobec, Stanislav; Zega, Anamarija

    2008-09-01

    The Mur ligases have an essential role in the intracellular biosynthesis of bacterial peptidoglycan, and they represent attractive targets for the design of novel antibacterials. A series of compounds with an N-acylhydrazone scaffold were synthesized and screened for inhibition of the MurC and MurD enzymes from Escherichia coli. Compounds with micromolar inhibitory activities against both MurC and MurD were identified, and some of them also showed antibacterial activity.

  5. Crystallographic Study of Peptidoglycan Biosynthesis Enzyme MurD: Domain Movement Revisited.

    Directory of Open Access Journals (Sweden)

    Roman Šink

    Full Text Available The biosynthetic pathway of peptidoglycan, an essential component of bacterial cell wall, is a well-recognized target for antibiotic development. Peptidoglycan precursors are synthesized in the bacterial cytosol by various enzymes including the ATP-hydrolyzing Mur ligases, which catalyze the stepwise addition of amino acids to a UDP-MurNAc precursor to yield UDP-MurNAc-pentapeptide. MurD catalyzes the addition of D-glutamic acid to UDP-MurNAc-L-Ala in the presence of ATP; structural and biochemical studies have suggested the binding of the substrates with an ordered kinetic mechanism in which ligand binding inevitably closes the active site. In this work, we challenge this assumption by reporting the crystal structures of intermediate forms of MurD either in the absence of ligands or in the presence of small molecules. A detailed analysis provides insight into the events that lead to the closure of MurD and reveals that minor structural modifications contribute to major overall conformation alterations. These novel insights will be instrumental in the development of new potential antibiotics designed to target the peptidoglycan biosynthetic pathway.

  6. In-Silico Testing Of Nutraceutical Against The Murd Enzymes From Mycobacterium Tuberculosis

    Directory of Open Access Journals (Sweden)

    Mohammad Teimouri

    2015-08-01

    Full Text Available In spite of availability of moderately protective vaccine and antibiotics new antibacterial agents are urgently needed to decrease the global incidence of Mycobacterium tuberculosis infections. Mur family is an important target for the development of new drugs as they are involved in the biosynthesis of bacterial cell wall. MurC-MurF ligases catalyze a series of irreversible steps in the biosynthesis of peptidoglycan precursor i.e. MurD catalyzes the ligation of D-glutamate to the nucleotide precursor UMA. Here we developed a homology model of MurD from M. Tuberculosis and was validated by using rampage Errat and ProSA online servers. Different nutraceuticals were tested and reported for their activity. Among the 14 nutraceuticals Diosgenin Xanthohumol Capsaicin 1-acetoxychavicol acetate and 6-Gingerol have best docking score. The best of all was Diosgenin with the docking score -14.22988 Xanthohumol with -13.923555 Capsaicin with -12.880404 1-acetoxychavicol acetate with -12.573502 and 6-Gingerol -12.349156 which will play a guiding role in the experimental design and development of mycobacterium tuberculosis MurD

  7. The EIR-programmes for computing the gross heat output of solar collectors (MURD and ETA)

    International Nuclear Information System (INIS)

    Widder, F.

    1980-11-01

    For the computation of the gross heat output of solar collectors by means of meteo data and characteristic collector parameters two programs were developed: MURD for the determination of the ''mean usable radiation density'' and ETA for the calculation of the collector efficiency i.e. relative values of gross heat output. The main features of these programs are described and detailed instructions for the use of them are given. Results of some cases for the meteo-situation of Zurich airport are given. (Auth.)

  8. New 5-benzylidenethiazolidin-4-one inhibitors of bacterial MurD ligase: design, synthesis, crystal structures, and biological evaluation.

    Science.gov (United States)

    Zidar, Nace; Tomašić, Tihomir; Šink, Roman; Kovač, Andreja; Patin, Delphine; Blanot, Didier; Contreras-Martel, Carlos; Dessen, Andréa; Premru, Manica Müller; Zega, Anamarija; Gobec, Stanislav; Mašič, Lucija Peterlin; Kikelj, Danijel

    2011-11-01

    Mur ligases (MurC-MurF), a group of bacterial enzymes that catalyze four consecutive steps in the formation of cytoplasmic peptidoglycan precursor, are becoming increasingly adopted as targets in antibacterial drug design. Based on the crystal structure of MurD cocrystallized with thiazolidine-2,4-dione inhibitor I, we have designed, synthesized, and evaluated a series of improved glutamic acid containing 5-benzylidenerhodanine and 5-benzylidenethiazolidine-2,4-dione inhibitors of MurD with IC(50) values up to 28 μM. Inhibitor 37, with an IC(50) of 34 μM, displays a weak antibacterial activity against S. aureus ATCC 29213 and E. faecalis ATCC 29212 with minimal inhibitory concentrations of 128 μg/mL. High-resolution crystal structures of MurD in complex with two new inhibitors (compounds 23 and 51) reveal details of their binding modes within the active site and provide valuable information for further structure-based optimization. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

  9. Homology modeling, molecular dynamics and inhibitor binding study on MurD ligase of Mycobacterium tuberculosis.

    Science.gov (United States)

    Arvind, Akanksha; Kumar, Vivek; Saravanan, Parameswaran; Mohan, C Gopi

    2012-09-01

    The cell wall of mycobacterium offers well validated targets which can be exploited for discovery of new lead compounds. MurC-MurF ligases catalyze a series of irreversible steps in the biosynthesis of peptidoglycan precursor, i.e. MurD catalyzes the ligation of D-glutamate to the nucleotide precursor UMA. The three dimensional structure of Mtb-MurD is not known and was predicted by us for the first time using comparative homology modeling technique. The accuracy and stability of the predicted Mtb-MurD structure was validated using Procheck and molecular dynamics simulation. Key interactions in Mtb-MurD were studied using docking analysis of available transition state inhibitors of E.coli-MurD. The docking analysis revealed that analogues of both L and D forms of glutamic acid have similar interaction profiles with Mtb-MurD. Further, residues His192, Arg382, Ser463, and Tyr470 are proposed to be important for inhibitor-(Mtb-MurD) interactions. We also identified few pharmacophoric features essential for Mtb-MurD ligase inhibitory activity and which can further been utilized for the discovery of putative antitubercular chemotherapy.

  10. Discovery of new inhibitors of the bacterial peptidoglycan biosynthesis enzymes MurD and MurF by structure-based virtual screening.

    Science.gov (United States)

    Turk, Samo; Kovac, Andreja; Boniface, Audrey; Bostock, Julieanne M; Chopra, Ian; Blanot, Didier; Gobec, Stanislav

    2009-03-01

    The ATP-dependent Mur ligases (MurC, MurD, MurE and MurF) successively add L-Ala, D-Glu, meso-A(2)pm or L-Lys, and D-Ala-D-Ala to the nucleotide precursor UDP-MurNAc, and they represent promising targets for antibacterial drug discovery. We have used the molecular docking programme eHiTS for the virtual screening of 1990 compounds from the National Cancer Institute 'Diversity Set' on MurD and MurF. The 50 top-scoring compounds from screening on each enzyme were selected for experimental biochemical evaluation. Our approach of virtual screening and subsequent in vitro biochemical evaluation of the best ranked compounds has provided four novel MurD inhibitors (best IC(50)=10 microM) and one novel MurF inhibitor (IC(50)=63 microM).

  11. Formation of adenosine 5'-tetraphosphate from the acyl phosphate intermediate: a difference between the MurC and MurD synthetases of Escherichia coli.

    Science.gov (United States)

    Bouhss, A; Dementin, S; van Heijenoort, J; Parquet, C; Blanot, D

    1999-06-18

    The mechanism of the Mur synthetases of peptidoglycan biosynthesis is thought to involve in each case the successive formation of an acyl phosphate and a tetrahedral intermediate. The existence of the acyl phosphates for the MurC and MurD enzymes from Escherichia coli was firmly established by their in situ reduction by sodium borohydride followed by acid hydrolysis, yielding the corresponding amino alcohols. Furthermore, it was found that MurD, but not MurC, catalyses the synthesis of adenosine 5'-tetraphosphate from the acyl phosphate, thereby substantiating its existence and pointing out a difference between the two enzymes.

  12. Design and Synthesis of Novel N-Benzylidenesulfonohydrazide Inhibitors of MurC and MurD as Potential Antibacterial Agents

    Directory of Open Access Journals (Sweden)

    Aleš Obreza

    2008-01-01

    Full Text Available A series of novel N-benzylidenesulfonohydrazide compounds were designedand synthesized as inhibitors of UDP-N-acetylmuramic acid:L-alanine ligase (MurC andUDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase (MurD from E. coli, involved inthe biosynthesis of bacterial cell-walls. Some compounds possessed inhibitory activityagainst both enzymes with IC50 values as low as 30 μM. In addition, a new, one-potsynthesis of amidobenzaldehydes is reported.

  13. Design and synthesis of novel N-benzylidenesulfonohydrazide inhibitors of MurC and MurD as potential antibacterial agents.

    Science.gov (United States)

    Frlan, Rok; Kovac, Andreja; Blanot, Didier; Gobec, Stanislav; Pecar, Slavko; Obreza, Ales

    2008-01-11

    A series of novel N-benzylidenesulfonohydrazide compounds were designed and synthesized as inhibitors of UDP-N-acetylmuramic acid: L-alanine ligase (MurC) and UDP-N-acetylmuramoyl-L-alanine: D-glutamate ligase (MurD) from E. coli, involved in the biosynthesis of bacterial cell-walls. Some compounds possessed inhibitory activity against both enzymes with IC(50) values as low as 30 microM. In addition, a new, one-pot synthesis of amidobenzaldehydes is reported.

  14. Ulgumerelaineid "murdes" / Jan Kaus

    Index Scriptorium Estoniae

    Kaus, Jan, 1971-

    2006-01-01

    22. dets. teatris NO99 toimunud ühekordsest aktsioonist "Ulgumerelainetel" S. Mrozheki "Ulgumerel" järgi (lavastaja Tiit Ojasoo). Pärast aktsiooni toimus publiku ja lava vahel arutelu, millest võttis osa Jan Kaus. Teater palus, et ta jätkaks saalis alustatud sõnavõtuga, mida ta kirja teel ka tegi

  15. Helsingi saab eestlaste disainitud pingid / Raivo Murde

    Index Scriptorium Estoniae

    Murde, Raivo

    2010-01-01

    Eesti ettevõtte Frog Industrial Designi kaubamärgi Extery pingid "Klaar" võitsid Helsingi avaliku ruumi mööblikonkursi. Tooteseeria autoriteks on Martin Pärn, Edina Dufala-Pärn, Sven Sõrmus ja Pent Talvet disainibüroost Iseasi. Žürii valis Exteri toodangust välja ka teisi linnaruumis kasutatavaid elemente. Eestlaste disainitud linnamööbel on eksponeeritud Helsingi sisustusmessil Habitare

  16. Riikide murd(u)mine Euroopas : Kosovo / Ahto Lobjakas

    Index Scriptorium Estoniae

    Lobjakas, Ahto, 1970-

    2008-01-01

    Kosovo iseseisvumine kui pretsedent võib saada innustuseks nii separistidele kui ka vähem autonoomsetele vähemustele, sest kinnitab, et territoriaalse terviklikkuse printsiip ei pruugi olla murdumatu

  17. The most ambitious innovation project in Estonia / Raivo Murde

    Index Scriptorium Estoniae

    Murde, Raivo

    2010-01-01

    Tänavu jaanuaris EAS-ile esitatud 14 tehnoloogia arenduskeskuse loomise taotlusest valiti välja kaheksa arenduskeskust, keda toetatakse Euroopa Regionaalarengu Fondi rahadest enam kui 900 miljoni krooniga, arenduskeskustega liitunud ettevõtted investeerivad keskustesse ligi 400 miljonit krooni

  18. Eesti tudengid disainisid päästjatele erivarustuse / Raivo Murde

    Index Scriptorium Estoniae

    Murde, Raivo

    2010-01-01

    Eesti Kunstiakadeemia tootedisaini tudengid mõtlesid välja erivarustuse maavärina ja üleujutuste piirkonnas töötavatele päästjatele, aga ka kannatanutele. Projekti juhendaja: Heikki Zoova. Vesti disainisid Klaarika Sinimeri, Kertu Rattasepp ja Merle Visak. Viljandi ettevõte Galvi-Linda on valmis neid tooteid tootma

  19. Investigations on pollutant reduction in iron murd from the Schlema-Alberoda and Poehla pits

    International Nuclear Information System (INIS)

    Knappik, R.; Fleischer, K.; Meyer, J.

    1998-01-01

    By examplary investigations with two typical iron muds from the Schlema-Alberoda and Poehla pits it was examined whether a reducing agent in flushing water is able to contribute to changes in flushing water quality by dissolution of muds. Two closed circuit apparatuses are used, in which soluted sodium dithionite as reducing agent was added periodically and the reaction progress was monitored by in-situ-measuring of redox potential and pH as well as by sampling. The experiments were planned as to apply the results for worst-case assessment. Two very different typs of mining muds regarding to their mobilizing behavior were detected. The reaction consists of the following steps: consumption of oxygen in solution, mobilization of Fe and Mn, increasing reduction of Fe(III) to Fe(II) in the solid phase. The extent of concentration change of Fe(II), Mn, As, U and other components in flushing water at conditioning as well as depending on geochemical milieu (number of reduction steps) was discussed. On experimental conditions a complete dissolution of all iron compounds is impossible even at excess of reducing agent. On the base of estimed substance potential and reaction turn-over this results may be transferred to conditions in the mines. A partial dissolution at optimal hydrodynamic conditions does not result in mobilization of pollutants (uranium, radium, arsene) but in formation of Fe(II) and Mn(II), the extent depending on potential of mud and reducing agent. The redox buffer range will not be exceeded. (orig.)

  20. In Studio Vinum / Lylian Meister

    Index Scriptorium Estoniae

    Meister, Lylian, 1966-

    2007-01-01

    Vinoteek ja keldrirestoran In Studio Vinum Tallinnas Suur-Karja tänavas. Sisekujunduse autor sisearhitekt Marit Murd. Sommeljee Imre Uussaare disainitud on vinoteegi seinu kattev veiniriiulite süsteem. 4 värv. vaadet

  1. Za raznoobrazije protiv stereotipov

    Index Scriptorium Estoniae

    2007-01-01

    Üleeuroopalise plakativõistluse "Breaking Stereotypes" (Murdes stereotüüpe) paremate tööde näitus Narva Keskraamatukogus. Konkursi võitis poola üliõpilase Aleksandra Woldanska plakat "Together"

  2. Omavalitsusjuhid Riigikontrolli urgitsemist ei karda / Erik Kalda

    Index Scriptorium Estoniae

    Kalda, Erik, 1969-

    2005-01-01

    Ilmunud ka: Severnoje 18. märts lk. 1,4. Poberezhje Iisaku vallavanem Avo Kiir, Kohtla-Järve linnapea Jevgeni Solovjov, Narva linnavolikogu esimees Mihhail Stalnuhhin, Jõhvi linnapea Aavo Keerme, Ida-Viru omavalitsuste liidu tegevdirektor Urve Erikson ja Sillamäe volikogu esimees Valdek Murd kommenteerivad valitsuses heakskiidu leidnud Riigikontrolli volituste laiendamist

  3. Welcome to Estonia märk on kaotanud oma sära / Kadi Heinsalu

    Index Scriptorium Estoniae

    Heinsalu, Kadi, 1966-

    2004-01-01

    Ettevõtluse Arendamise Sihtasutus loodab parandada Welcome to Estonia märgi mainet. Märki kasutavad ettevõtjad ei näe märgist olulist kasu toodete müügil. Kommenteerivad Evelin Int-Lambot, Leena Murd ja Olaf Merisalu

  4. Sinikael jätab jälgi / Tristan Priimägi

    Index Scriptorium Estoniae

    Priimägi, Tristan, 1976-

    2002-01-01

    Mängufilm "Agent Sinikael" : stsenaristid Marko Raat ja Andres Maimik : režissöör Marko Raat : operaator Arko Okk : helilooja Janek Murd : kunstnikud Margus Tammik ja Jaana Jüris : nimiosas Mait Malmsten : produtsendid Peeter Urbla ja Veiko Õunapuu : Exitfilm ja Suhkur Film, 2002. Lisatud Marko Raati filmograafia lk. 103

  5. Raat värbab oma filmi heliloojaks Jimi Tenorit / Tiit Tuumalu

    Index Scriptorium Estoniae

    Tuumalu, Tiit, 1971-

    2001-01-01

    Marko Raat soovib oma uue mängufilmi "Agent Sinikael" soundtracki loomisel kasutada soome rahvusvaheliselt tuntud muusiku Jimi Tenori teeneid. Lisaks on muusika loomisse haaratud Janek Murd ning ansamblid JMKE ja Velikije Luki. Filmi tootjaks on Suhkurfilm koostöös Exitfilmi ja Taani kuulsa firmaga Zentropa

  6. Võigas ja seletamatu tsirkus : kaasaja ja alateadvuse pained "Agent Sinikaelas" / Sven Vabar

    Index Scriptorium Estoniae

    Vabar, Sven

    2002-01-01

    Mängufilm "Agent Sinikael" : stsenaristid Marko Raat ja Andres Maimik : režissöör Marko Raat : operaator Arko Okk : helilooja Janek Murd : kunstnikud Margus Tammik ja Jaana Jüris : nimiosas Mait Malmsten : produtsendid Peeter Urbla ja Veiko Õunapuu : Exitfilm ja Suhkur Film, 2002

  7. Raamatukogus on üleval plakatinäitus

    Index Scriptorium Estoniae

    2007-01-01

    Üleeuroopalise plakativõistluse "Breaking Stereotypes" (Murdes stereotüüpe) paremate tööde näitus Viljandi linnaraamatukogus. Konkursi võitis poola üliõpilase Aleksandra Woldanska plakat "Together". Eestist osales võistlusel kümme tööd

  8. Kodavere keelest ja selle hoidjatest / Vaike Käosaar

    Index Scriptorium Estoniae

    Käosaar, Vaike, 1948-

    2008-01-01

    Kodavere murrakust. Sisaldab Heino Õunapi ja Ella Viirmaa murdetekste. Ilmunud on Kodavere murdes kogumikud: Õlemä elon : lugusid Kodavere murrakus. - Ranna [Jõgevamaa] : Sääritsa Küla Seltsing, 2006 ; Põlvess põlve. - [Kodavere (Jõgevamaa)] : E. Treial, 2007

  9. Arno Rossman: "Paksu nahata põled poliitikas kiiresti läbi" / Arno Rossman ; interv. Erik Gamzejev

    Index Scriptorium Estoniae

    Rossman, Arno, 1954-

    2006-01-01

    Ilmunud ka: Severnoje Poberezhje Ilmunud ka: Severnoje Poberezhje : Subbota 4. nov. lk. 3. Keskkonnaministri nõunik oma tööst ning tulevastest parlamendivalimistest. Lisa: Arno Rossman. Arvamust avaldavad Ida-Virumaa omavalitsuste liidu tegevdirektor Urve Erikson ja Ida-Viru spordiliidu esimees Valdek Murd

  10. Micro reflectance difference techniques: Optical probes for surface exploration

    Energy Technology Data Exchange (ETDEWEB)

    Lastras-Martinez, L.F.; Del Pozo-Zamudio, O.; Herrera-Jasso, R.; Ulloa-Castillo, N.A.; Balderas-Navarro, R.E.; Ortega-Gallegos, J.; Lastras-Martinez, A. [Instituto de Investigacion en Comunicacion Optica, Universidad Autonoma de San Luis Potosi, Alvaro Obregon 64, 78000 San Luis Potosi, S.L.P. (Mexico)

    2012-06-15

    Micro reflectance difference spectroscopy ({mu}-RDS) is a promising tool for the in-situ and ex-situ characterization of semiconductors surfaces and interfaces. We discuss and compare two different approaches used to measure {mu}-RD spectra. One is based on a charge-coupled device (CCD) camera, while the other uses a laser and a XY translation stage. To show the performance of these systems, we have measured surface optical anisotropies of GaSb(001) sample on which anisotropic strains have been generated by preferential mechanical polishing along [110] and [1 anti 10] directions. The spectrometers are complementary and the selection of one of them depends on the sample to be investigated and on experimental conditions. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  11. Uudised : Rubik 3001. Akordionipätid ja muu folk

    Index Scriptorium Estoniae

    2005-01-01

    Koostöös Erkki Tero ja Tristan Priimäega annab artistinime Rubik 3001 kandev Janek Murd 10. märtsil välja esimese singli "Miru mir" mais-juunis ilmuvalt uuelt albumilt (kolme looga singel ilmub värskel Raadio Kosmos netileheküljel www.3pead.com). Aprillis ilmub ka kolme looga singel "My Mind Is Going". Üritusest sarjast MAAjaILM 11. märtsil Tartu Vanemuises

  12. Eesti jäämurdekontseptsioon / Carol Kirss, Tarmo Kõuts

    Index Scriptorium Estoniae

    Kirss, Carol

    2005-01-01

    Autorite arvates on Eestis olemas risk, et sadamad jäävad külmadel talvedel piisava jäämurdevõimsuse juures blokeerituks. Võimalikest jäämurdekontseptsioonidest Eestis. Diagrammid: Kaubavedu Eesti sadamate kaudu; Eesti sadamate laevakülastused. Tabelid: Talvesadmate osatähtsus; Jäämurdjate optimaalse arvu selgitamine; Soome ja Liivi lahe erinevate jäämurdesüsteemide versioonide maksumus

  13. MreB and MurG as scaffolds for the cytoplasmic steps of peptidoglycan biosynthesis.

    Science.gov (United States)

    Favini-Stabile, Sandy; Contreras-Martel, Carlos; Thielens, Nicole; Dessen, Andréa

    2013-12-01

    Peptidoglycan is a major determinant of cell shape in bacteria, and its biosynthesis involves the concerted action of cytoplasmic, membrane-associated and periplasmic enzymes. Within the cytoplasm, Mur enzymes catalyse the first steps leading to peptidoglycan precursor biosynthesis, and have been suggested as being part of a multicomponent complex that could also involve the transglycosylase MurG and the cytoskeletal protein MreB. In order to initialize the characterization of a potential Mur interaction network, we purified MurD, MurE, MurF, MurG and MreB from Thermotoga maritima and characterized their interactions using membrane blotting and surface plasmon resonance. MurD, MurE and MurF all recognize MurG and MreB, but not each other, while the two latter proteins interact. In addition, we solved the crystal structures of MurD, MurE and MurF, which indicate that their C-termini display high conformational flexibilities. The differences in Mur conformations could be important parameters for the stability of an intracytoplasmic murein biosynthesis complex. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

  14. The cell wall and cell division gene cluster in the Mra operon of Pseudomonas aeruginosa: cloning, production, and purification of active enzymes.

    Science.gov (United States)

    Azzolina, B A; Yuan, X; Anderson, M S; El-Sherbeini, M

    2001-04-01

    We have cloned the Pseudomonas aeruginosa cell wall biosynthesis and cell division gene cluster that corresponds to the mra operon in the 2-min region of the Escherichia coli chromosome. The organization of the two chromosomal regions in P. aeruginosa and E. coli is remarkably similar with the following gene order: pbp3/pbpB, murE, murF, mraY, murD, ftsW, murG, murC, ddlB, ftsQ, ftsA, ftsZ, and envA/LpxC. All of the above P. aeruginosa genes are transcribed from the same strand of DNA with very small, if any, intragenic regions, indicating that these genes may constitute a single operon. All five amino acid ligases, MurC, MurD, MurE, MurF, and DdlB, in addition to MurG and MraY were cloned in expression vectors. The four recombinant P. aeruginosa Mur ligases, MurC, MurD, MurE, and MurF were overproduced in E. coli and purified as active enzymes. Copyright 2001 Academic Press.

  15. Furan-based benzene mono- and dicarboxylic acid derivatives as multiple inhibitors of the bacterial Mur ligases (MurC-MurF): experimental and computational characterization

    Science.gov (United States)

    Perdih, Andrej; Hrast, Martina; Pureber, Kaja; Barreteau, Hélène; Grdadolnik, Simona Golič; Kocjan, Darko; Gobec, Stanislav; Solmajer, Tom; Wolber, Gerhard

    2015-06-01

    Bacterial resistance to the available antibiotic agents underlines an urgent need for the discovery of novel antibacterial agents. Members of the bacterial Mur ligase family MurC-MurF involved in the intracellular stages of the bacterial peptidoglycan biosynthesis have recently emerged as a collection of attractive targets for novel antibacterial drug design. In this study, we have first extended the knowledge of the class of furan-based benzene-1,3-dicarboxylic acid derivatives by first showing a multiple MurC-MurF ligase inhibition for representatives of the extended series of this class. Steady-state kinetics studies on the MurD enzyme were performed for compound 1, suggesting a competitive inhibition with respect to ATP. To the best of our knowledge, compound 1 represents the first ATP-competitive MurD inhibitor reported to date with concurrent multiple inhibition of all four Mur ligases (MurC-MurF). Subsequent molecular dynamic (MD) simulations coupled with interaction energy calculations were performed for two alternative in silico models of compound 1 in the UMA/ d-Glu- and ATP-binding sites of MurD, identifying binding in the ATP-binding site as energetically more favorable in comparison to the UMA/ d-Glu-binding site, which was in agreement with steady-state kinetic data. In the final stage, based on the obtained MD data novel furan-based benzene monocarboxylic acid derivatives 8- 11, exhibiting multiple Mur ligase (MurC-MurF) inhibition with predominantly superior ligase inhibition over the original series, were discovered and for compound 10 it was shown to possess promising antibacterial activity against S. aureus. These compounds represent novel leads that could by further optimization pave the way to novel antibacterial agents.

  16. Design, Synthesis and in vitro Biochemical Activity of Novel Amino Acid Sulfonohydrazide Inhibitors of MurC.

    Science.gov (United States)

    Frlan, Rok; Kovač, Andreja; Blanot, Didier; Gobec, Stanislav; Pečar, Slavko; Obreza, Aleš

    2011-06-01

    Mur ligases are essential enzymes involved in the cytoplasmic steps of peptidoglycan synthesis which remain attractive, yet unexploited targets. In order to develop new antibacterial agents, we have designed a series of new MurC and MurD inhibitors bearing amino acid sulfonohydrazide moiety. The L-Leu series of this class displayed the highest enzyme inhibition with IC50 in the concentration range between 100 and 500 µM, with L-Thr, L-Pro and L-Ala derivatives being inactive. The most promising compound of the series also expressed weak antibacterial activity against S. aureus with MIC = 128 µg/mL.

  17. Characterisation of ATP-dependent Mur ligases involved in the biogenesis of cell wall peptidoglycan in Mycobacterium tuberculosis.

    Science.gov (United States)

    Munshi, Tulika; Gupta, Antima; Evangelopoulos, Dimitrios; Guzman, Juan David; Gibbons, Simon; Keep, Nicholas H; Bhakta, Sanjib

    2013-01-01

    ATP-dependent Mur ligases (Mur synthetases) play essential roles in the biosynthesis of cell wall peptidoglycan (PG) as they catalyze the ligation of key amino acid residues to the stem peptide at the expense of ATP hydrolysis, thus representing potential targets for antibacterial drug discovery. In this study we characterized the division/cell wall (dcw) operon and identified a promoter driving the co-transcription of mur synthetases along with key cell division genes such as ftsQ and ftsW. Furthermore, we have extended our previous investigations of MurE to MurC, MurD and MurF synthetases from Mycobacterium tuberculosis. Functional analyses of the pure recombinant enzymes revealed that the presence of divalent cations is an absolute requirement for their activities. We also observed that higher concentrations of ATP and UDP-sugar substrates were inhibitory for the activities of all Mur synthetases suggesting stringent control of the cytoplasmic steps of the peptidoglycan biosynthetic pathway. In line with the previous findings on the regulation of mycobacterial MurD and corynebacterial MurC synthetases via phosphorylation, we found that all of the Mur synthetases interacted with the Ser/Thr protein kinases, PknA and PknB. In addition, we critically analyzed the interaction network of all of the Mur synthetases with proteins involved in cell division and cell wall PG biosynthesis to re-evaluate the importance of these key enzymes as novel therapeutic targets in anti-tubercular drug discovery.

  18. Chemogenomics profiling of drug targets of peptidoglycan biosynthesis pathway in Leptospira interrogans by virtual screening approaches.

    Science.gov (United States)

    Bhattacharjee, Biplab; Simon, Rose Mary; Gangadharaiah, Chaithra; Karunakar, Prashantha

    2013-06-28

    Leptospirosis is a worldwide zoonosis of global concern caused by Leptospira interrogans. The availability of ligand libraries has facilitated the search for novel drug targets using chemogenomics approaches, compared with the traditional method of drug discovery, which is time consuming and yields few leads with little intracellular information for guiding target selection. Recent subtractive genomics studies have revealed the putative drug targets in peptidoglycan biosynthesis pathways in Leptospira interrogans. Aligand library for the murD ligase enzyme in the peptidoglycan pathway has also been identified. Our approach in this research involves screening of the pre-existing ligand library of murD with related protein family members in the putative drug target assembly in the peptidoglycan biosynthesis pathway. A chemogenomics approach has been implemented here, which involves screening of known ligands of a protein family having analogous domain architecture for identification of leads for existing druggable protein family members. By means of this approach, one murC and one murF inhibitor were identified, providing a platform for developing an antileptospirosis drug targeting the peptidoglycan biosynthesis pathway. Given that the peptidoglycan biosynthesis pathway is exclusive to bacteria, the in silico identified mur ligase inhibitors are expected to be broad-spectrum Gram-negative inhibitors if synthesized and tested in in vitro and in vivo assays.

  19. Eesti linnu juhivad keskeas mehed

    Index Scriptorium Estoniae

    1999-01-01

    Eesti omavalitsusjuhtide tutvustus - I. Eesmaa, E. Tamm, J. Tamkivi, P. Jalakas, A. Heinvee, M. Tilga, A. Õun, K. Kaugija, M. Mettus, T. Asi, M. Lepik, U. Heinla, A. Pajula, R. Amos, M. Kadak, T. Loog, L. Mägi, R. Siim, T. Kõiv, A. Taimla, A. Tisler, I. Eesalu, P. Aru, T. Juul, V. Tõemets, L. Meltsa, J. Lillsoo, zh. Botvinkina, G. Bõstrov, H. Vinkman, A. Kaskla, R. Heina, T. Laimets, K. Aun, M. Jürisson, M. Moll, J. Aab, A. Pärna, T. Tamm, P. Urman, V. Nellis, I. Müür, M. Jaago, J. Jalakas, U. Tamm, A. Tamme, A. Lumi, V. Mäesepp, P. Kostromin, K. Pajula, M. Ein, R. Kirsel, M. Mälberg, O. Tuvik, V. Murd, T. Kuusmik, V. Kruzman, A. Keerme, A. Kiir, M. Kärbo, R. Annik, T. Pruul, A. Anderson, T. Järveoja, T. Hilpus, R. Fjodorov, T. Jõgi, T. Anton

  20. The biology of Mur ligases as an antibacterial target.

    Science.gov (United States)

    Kouidmi, Imène; Levesque, Roger C; Paradis-Bleau, Catherine

    2014-10-01

    With antibiotic resistance mechanisms increasing in diversity and spreading among bacterial pathogens, the development of new classes of antibacterial agents against judiciously chosen targets is a high-priority task. The biochemical pathway for peptidoglycan biosynthesis is one of the best sources of antibacterial targets. Within this pathway are the Mur ligases, described in this review as highly suitable targets for the development of new classes of antibacterial agents. The amide ligases MurC, MurD, MurE and MurF function with the same catalytic mechanism and share conserved amino acid regions and structural features that can conceivably be exploited for the design of inhibitors that simultaneously target more than one enzyme. This would provide multi-target antibacterial weapons with minimized likelihood of target-mediated resistance development. © 2014 John Wiley & Sons Ltd.

  1. Spatially localized motion aftereffect disappears faster from awareness when selectively attended to according to its direction.

    Science.gov (United States)

    Murd, Carolina; Bachmann, Talis

    2011-05-25

    In searching for the target-afterimage patch among spatially separate alternatives of color-afterimages the target fades from awareness before its competitors (Bachmann, T., & Murd, C. (2010). Covert spatial attention in search for the location of a color-afterimage patch speeds up its decay from awareness: Introducing a method useful for the study of neural correlates of visual awareness. Vision Research 50, 1048-1053). In an analogous study presented here we show that a similar effect is obtained when a target spatial location specified according to the direction of motion aftereffect within it is searched by covert top-down attention. The adverse effect of selective attention on the duration of awareness of sensory qualiae known earlier to be present for color and periodic spatial contrast is extended also to sensory channels carrying motion information. Copyright © 2011 Elsevier Ltd. All rights reserved.

  2. Multi-targeted therapy for leprosy: insilico strategy to overcome multi drug resistance and to improve therapeutic efficacy.

    Science.gov (United States)

    Anusuya, Shanmugam; Natarajan, Jeyakumar

    2012-12-01

    Leprosy remains a major public health problem, since single and multi-drug resistance has been reported worldwide over the last two decades. In the present study, we report the novel multi-targeted therapy for leprosy to overcome multi drug resistance and to improve therapeutic efficacy. If multiple enzymes of an essential metabolic pathway of a bacterium were targeted, then the therapy would become more effective and can prevent the occurrence of drug resistance. The MurC, MurD, MurE and MurF enzymes of peptidoglycan biosynthetic pathway were selected for multi targeted therapy. The conserved or class specific active site residues important for function or stability were predicted using evolutionary trace analysis and site directed mutagenesis studies. Ten such residues which were present in at least any three of the four Mur enzymes (MurC, MurD, MurE and MurF) were identified. Among the ten residues G125, K126, T127 and G293 (numbered based on their position in MurC) were found to be conserved in all the four Mur enzymes of the entire bacterial kingdom. In addition K143, T144, T166, G168, H234 and Y329 (numbered based on their position in MurE) were significant in binding substrates and/co-factors needed for the functional events in any three of the Mur enzymes. These are the probable residues for designing newer anti-leprosy drugs in an attempt to reduce drug resistance. Copyright © 2012 Elsevier B.V. All rights reserved.

  3. Purification and biochemical characterization of Mur ligases from Staphylococcus aureus.

    Science.gov (United States)

    Patin, Delphine; Boniface, Audrey; Kovač, Andreja; Hervé, Mireille; Dementin, Sébastien; Barreteau, Hélène; Mengin-Lecreulx, Dominique; Blanot, Didier

    2010-12-01

    The Mur ligases (MurC, MurD, MurE and MurF) catalyze the stepwise synthesis of the UDP-N-acetylmuramoyl-pentapeptide precursor of peptidoglycan. The murC, murD, murE and murF genes from Staphylococcus aureus, a major pathogen, were cloned and the corresponding proteins were overproduced in Escherichia coli and purified as His(6)-tagged forms. Their biochemical properties were investigated and compared to those of the E. coli enzymes. Staphylococcal MurC accepted L-Ala, L-Ser and Gly as substrates, as the E. coli enzyme does, with a strong preference for L-Ala. S. aureus MurE was very specific for L-lysine and in particular did not accept meso-diaminopimelic acid as a substrate. This mirrors the E. coli MurE specificity, for which meso-diaminopimelic acid is the preferred substrate and L-lysine a very poor one. S. aureus MurF appeared less specific and accepted both forms (L-lysine and meso-diaminopimelic acid) of UDP-MurNAc-tripeptide, as the E. coli MurF does. The inverse and strict substrate specificities of the two MurE orthologues is thus responsible for the presence of exclusively meso-diaminopimelic acid and L-lysine at the third position of the peptide in the peptidoglycans of E. coli and S. aureus, respectively. The specific activities of the four Mur ligases were also determined in crude extracts of S. aureus and compared to cell requirements for peptidoglycan biosynthesis. Copyright © 2010 Elsevier Masson SAS. All rights reserved.

  4. Benzene-1,3-dicarboxylic acid 2,5-dimethylpyrrole derivatives as multiple inhibitors of bacterial Mur ligases (MurC-MurF).

    Science.gov (United States)

    Perdih, Andrej; Hrast, Martina; Barreteau, Hélène; Gobec, Stanislav; Wolber, Gerhard; Solmajer, Tom

    2014-08-01

    Enzymes catalyzing the biosynthesis of bacterial peptidoglycan represent traditionally a collection of highly selective targets for novel antibacterial drug design. Four members of the bacterial Mur ligase family-MurC, MurD, MurE and MurF-are involved in the intracellular steps of peptidoglycan biosynthesis, catalyzing the synthesis of the peptide moiety of the Park's nucleotide. In our previous virtual screening campaign, a chemical class of benzene-1,3-dicarboxylic acid 2,5-dimethylpyrrole derivatives exhibiting dual MurD/MurE inhibition properties was discovered. In the present study we further investigated this class of compounds by performing inhibition assays on all four Mur ligases (MurC-MurF). Furthermore, molecular dynamics (MD) simulation studies of one of the initially discovered compound 1 were performed to explore its geometry as well as its energetic behavior based on the Linear Interaction Energy (LIE) method. Further in silico virtual screening (VS) experiments based on the parent active compound 1 were conducted to optimize the discovered series. Selected hits were assayed against all Escherichia coli MurC-MurF enzymes in biochemical inhibition assays and molecules 10-14 containing benzene-1,3-dicarboxylic acid 2,5-dimethylpyrrole coupled with five member-ring rhodanine moiety were found to be multiple inhibitors of the whole MurC-MurF cascade of bacterial enzymes in the micromolar range. Steady-state kinetics studies suggested this class to act as competitive inhibitors of the MurD enzyme towards d-Glu. These compounds represent novel valuable starting point in the development of novel antibacterial agents. Copyright © 2014 Elsevier Ltd. All rights reserved.

  5. Characterisation of ATP-dependent Mur ligases involved in the biogenesis of cell wall peptidoglycan in Mycobacterium tuberculosis.

    Directory of Open Access Journals (Sweden)

    Tulika Munshi

    Full Text Available ATP-dependent Mur ligases (Mur synthetases play essential roles in the biosynthesis of cell wall peptidoglycan (PG as they catalyze the ligation of key amino acid residues to the stem peptide at the expense of ATP hydrolysis, thus representing potential targets for antibacterial drug discovery. In this study we characterized the division/cell wall (dcw operon and identified a promoter driving the co-transcription of mur synthetases along with key cell division genes such as ftsQ and ftsW. Furthermore, we have extended our previous investigations of MurE to MurC, MurD and MurF synthetases from Mycobacterium tuberculosis. Functional analyses of the pure recombinant enzymes revealed that the presence of divalent cations is an absolute requirement for their activities. We also observed that higher concentrations of ATP and UDP-sugar substrates were inhibitory for the activities of all Mur synthetases suggesting stringent control of the cytoplasmic steps of the peptidoglycan biosynthetic pathway. In line with the previous findings on the regulation of mycobacterial MurD and corynebacterial MurC synthetases via phosphorylation, we found that all of the Mur synthetases interacted with the Ser/Thr protein kinases, PknA and PknB. In addition, we critically analyzed the interaction network of all of the Mur synthetases with proteins involved in cell division and cell wall PG biosynthesis to re-evaluate the importance of these key enzymes as novel therapeutic targets in anti-tubercular drug discovery.

  6. VADJA KIRJAVIISIST JA SÕNALOOMEST

    Directory of Open Access Journals (Sweden)

    Enn Ernits

    2010-01-01

    Full Text Available Võimalikult efektiivse kirjakeele loomiseks tuleb lahendada järgmised põhiprobleemid: 1 valida sobiv(ad murdetaust(ad, 2 kehtestada keele normid, 3 luua kirjaviis ning 4 kohaldada keel vastavaks tänapäeva kultuuri- ja ühiskonnanõuetele (Tauli 1968: 19. Nimetatud küsimuste lahendamisel võib lähtuda nii keelekorralduse üldpõhimõtetest kui ka teiste läänemeresoome keelte (eesti, soome, võru ja vepsa kirjakeele korraldamise kogemustest. Pisikeele probleeme on tänapäeval soovitatav lahendada võimalikult paindlikult. Siinkirjutaja eelistab võtta vadja kirjakeele põhjaks Kattila murde, kuid ei välista teistegi murrete kasutamist. Vähemalt esialgu tuleks kirjakeelt normeerida nii vähe kui võimalik. Soovitatav on tarvitada maksimaalselt foneemilist kirja, milles oleksid c, č, š, ž; õ, ä, ö, ü; ď, ń, ŕ, ź, ť. Sandhi tuleks jätta tähistamata. Keelt on vaja rikastada tänapäevaste mõistetega, kusjuures sõnavara saab luua nii oma ressursside kui ka naaberkeelte leksika varal. Omasõnu luuakse põhiliselt liitmise ja sufiksite abil tuletamise teel, näiteks čehsi-škoulu ’keskkool’, nimezikko ’nimekiri, nimestik’ (< nimi ’nimi’.

  7. VERBA DICENDI, SENTIENDI ET SCIENDI JA NEID SISALDAVAD KONSTRUKTSIOONID 17. SAJANDI JA 18. SAJANDI ALGUSE KIRJAKEELES

    Directory of Open Access Journals (Sweden)

    Kristiina Ross

    2010-01-01

    Full Text Available Eesti kirjakeele morfosüntaksi kujunemisel mängisid olulist osa 16.–18. sajandi vaimulikud tõlked, mille loomise käigus kohandati seni suulisena funktsioneerinud rahvakeel kirjalike kristlike tekstide nõuetele. Artiklis vaadeldakse ühe väikese morfosüntaktilise rühma arenguid sel perioodil. Analüüsitakse konstruktsioone, milles ütlemist, tajumist ja teadmist väljendavaid verbe laiendab infiniitne vorm. Kirjeldatakse niisuguseid konstruktsioone rahvalaulukeeles, eeskujukeeltes ja varases kirjakeeles ning jõutakse järeldusele, et vastavad rahvakeelsed mallid võeti kirjakeeles suhteliselt vara kasutusele tänu sellele, et eeskujukeeled pakkusid nende rakendamiseks soodsaid võimalusi. 17. sajandi alguse põhjaeesti kirjakeeles tarvitati neis konstruktsioonides läbisegi partitsiipi ja infinitiivi, sest eri murded pakkusidki eri võimalusi (tüdruk kuulis poissi laulVAT /laulMA. Partitsiipsete konstruktsioonide kirjakeelne kasutus põhjaeesti tekstides erines alguses rahvakeelsest ning selles võib oletada klassikaliste keelte eeskuju. 17. sajandi lõpus loobuti põhjaeesti kirjakeeles infinitiivsetest konstruktsioonidest partitsiipsete kasuks. Niisuguses valikus võib näha lõunaeesti mõju, aga ka soovi vältida võimalikke germanisme, millega infinitiivseid konstruktsioone võidi siduda.

  8. Homology modeling and docking analyses of M. leprae Mur ligases reveals the common binding residues for structure based drug designing to eradicate leprosy.

    Science.gov (United States)

    Shanmugam, Anusuya; Natarajan, Jeyakumar

    2012-06-01

    Multi drug resistance capacity for Mycobacterium leprae (MDR-Mle) demands the profound need for developing new anti-leprosy drugs. Since most of the drugs target a single enzyme, mutation in the active site renders the antibiotic ineffective. However, structural and mechanistic information on essential bacterial enzymes in a pathway could lead to the development of antibiotics that targets multiple enzymes. Peptidoglycan is an important component of the cell wall of M. leprae. The biosynthesis of bacterial peptidoglycan represents important targets for the development of new antibacterial drugs. Biosynthesis of peptidoglycan is a multi-step process that involves four key Mur ligase enzymes: MurC (EC:6.3.2.8), MurD (EC:6.3.2.9), MurE (EC:6.3.2.13) and MurF (EC:6.3.2.10). Hence in our work, we modeled the three-dimensional structure of the above Mur ligases using homology modeling method and analyzed its common binding features. The residues playing an important role in the catalytic activity of each of the Mur enzymes were predicted by docking these Mur ligases with their substrates and ATP. The conserved sequence motifs significant for ATP binding were predicted as the probable residues for structure based drug designing. Overall, the study was successful in listing significant and common binding residues of Mur enzymes in peptidoglycan pathway for multi targeted therapy.

  9. Structural and functional features of enzymes of Mycobacterium tuberculosis peptidoglycan biosynthesis as targets for drug development.

    Science.gov (United States)

    Moraes, Gleiciane Leal; Gomes, Guelber Cardoso; Monteiro de Sousa, Paulo Robson; Alves, Cláudio Nahum; Govender, Thavendran; Kruger, Hendrik G; Maguire, Glenn E M; Lamichhane, Gyanu; Lameira, Jerônimo

    2015-03-01

    Tuberculosis (TB) is the second leading cause of human mortality from infectious diseases worldwide. The WHO reported 1.3 million deaths and 8.6 million new cases of TB in 2012. Mycobacterium tuberculosis (M. tuberculosis), the infectious bacteria that causes TB, is encapsulated by a thick and robust cell wall. The innermost segment of the cell wall is comprised of peptidoglycan, a layer that is required for survival and growth of the pathogen. Enzymes that catalyse biosynthesis of the peptidoglycan are essential and are therefore attractive targets for discovery of novel antibiotics as humans lack similar enzymes making it possible to selectively target bacteria only. In this paper, we have reviewed the structures and functions of enzymes GlmS, GlmM, GlmU, MurA, MurB, MurC, MurD, MurE and MurF from M. tuberculosis that are involved in peptidoglycan biosynthesis. In addition, we report homology modelled 3D structures of those key enzymes from M. tuberculosis of which the structures are still unknown. We demonstrated that natural substrates can be successfully docked into the active sites of the GlmS and GlmU respectively. It is therefore expected that the models and the data provided herein will facilitate translational research to develop new drugs to treat TB. Copyright © 2015. Published by Elsevier Ltd.

  10. Characterization and chromosomal organization of the murD-murC-ftsQ region of Corynebacterium glutamicum ATCC 13869.

    Science.gov (United States)

    Ramos, Angelina; Honrubia, Maria P; Vega, Daniel; Ayala, Juan A; Bouhss, Ahmed; Mengin-Lecreulx, Dominique; Gil, José A

    2004-04-01

    The sequence of a 4.6-kb region of DNA from Corynebacterium glutamicum ATCC 13869 lying upstream from the ftsQ-ftsZ region has been determined. The region contains four genes with high similarity to the murD, ftsW, murG, and murC genes from different microorganisms. The products of these mur genes probably catalyse several steps in the formation of the precursors for peptidoglycan synthesis in C. glutamicum, whereas ftsW might play also a role in the stabilisation of the FtsZ ring during cell division. The murC gene product was purified to near homogeneity and its UDP-N-acetylmuramate: L-alanine adding activity was demonstrated. Northern analysis indicated that ftsW, murG and ftsQ are poorly expressed in C. glutamicum whereas murC and ftsZ are expressed at higher levels at the beginning of the exponential phase. Dicistronic (ftsQ-ftsZ) and monocistronic (murC and ftsZ) transcripts can be detected using specific probes and are in agreement with the lack of transcriptional terminators in the partially analysed dcw cluster. Disruption experiments performed in C. glutamicum using internal fragments of the ftsW, murG and murC genes allowed us to conclude that FtsW, MurG, and MurC are essential gene products in C. glutamicum.

  11. Structure and function of the first full-length murein peptide ligase (Mpl cell wall recycling protein.

    Directory of Open Access Journals (Sweden)

    Debanu Das

    2011-03-01

    Full Text Available Bacterial cell walls contain peptidoglycan, an essential polymer made by enzymes in the Mur pathway. These proteins are specific to bacteria, which make them targets for drug discovery. MurC, MurD, MurE and MurF catalyze the synthesis of the peptidoglycan precursor UDP-N-acetylmuramoyl-L-alanyl-γ-D-glutamyl-meso-diaminopimelyl-D-alanyl-D-alanine by the sequential addition of amino acids onto UDP-N-acetylmuramic acid (UDP-MurNAc. MurC-F enzymes have been extensively studied by biochemistry and X-ray crystallography. In gram-negative bacteria, ∼30-60% of the bacterial cell wall is recycled during each generation. Part of this recycling process involves the murein peptide ligase (Mpl, which attaches the breakdown product, the tripeptide L-alanyl-γ-D-glutamyl-meso-diaminopimelate, to UDP-MurNAc. We present the crystal structure at 1.65 Å resolution of a full-length Mpl from the permafrost bacterium Psychrobacter arcticus 273-4 (PaMpl. Although the Mpl structure has similarities to Mur enzymes, it has unique sequence and structure features that are likely related to its role in cell wall recycling, a function that differentiates it from the MurC-F enzymes. We have analyzed the sequence-structure relationships that are unique to Mpl proteins and compared them to MurC-F ligases. We have also characterized the biochemical properties of this enzyme (optimal temperature, pH and magnesium binding profiles and kinetic parameters. Although the structure does not contain any bound substrates, we have identified ∼30 residues that are likely to be important for recognition of the tripeptide and UDP-MurNAc substrates, as well as features that are unique to Psychrobacter Mpl proteins. These results provide the basis for future mutational studies for more extensive function characterization of the Mpl sequence-structure relationships.

  12. Novel drug targets in cell wall biosynthesis exploited by gene disruption in Pseudomonas aeruginosa.

    Science.gov (United States)

    Elamin, Ayssar A; Steinicke, Susanne; Oehlmann, Wulf; Braun, Yvonne; Wanas, Hanaa; Shuralev, Eduard A; Huck, Carmen; Maringer, Marko; Rohde, Manfred; Singh, Mahavir

    2017-01-01

    For clinicians, Pseudomonas aeruginosa is a nightmare pathogen that is one of the top three causes of opportunistic human infections. Therapy of P. aeruginosa infections is complicated due to its natural high intrinsic resistance to antibiotics. Active efflux and decreased uptake of drugs due to cell wall/membrane permeability appear to be important issues in the acquired antibiotic tolerance mechanisms. Bacterial cell wall biosynthesis enzymes have been shown to be essential for pathogenicity of Gram-negative bacteria. However, the role of these targets in virulence has not been identified in P. aeruginosa. Here, we report knockout (k.o) mutants of six cell wall biosynthesis targets (murA, PA4450; murD, PA4414; murF, PA4416; ppiB, PA1793; rmlA, PA5163; waaA, PA4988) in P. aeruginosa PAO1, and characterized these in order to find out whether these genes and their products contribute to pathogenicity and virulence of P. aeruginosa. Except waaA k.o, deletion of cell wall biosynthesis targets significantly reduced growth rate in minimal medium compared to the parent strain. The k.o mutants showed exciting changes in cell morphology and colonial architectures. Remarkably, ΔmurF cells became grossly enlarged. Moreover, the mutants were also attenuated in vivo in a mouse infection model except ΔmurF and ΔwaaA and proved to be more sensitive to macrophage-mediated killing than the wild-type strain. Interestingly, the deletion of the murA gene resulted in loss of virulence activity in mice, and the virulence was restored in a plant model by unknown mechanism. This study demonstrates that cell wall targets contribute significantly to intracellular survival, in vivo growth, and pathogenesis of P. aeruginosa. In conclusion, these findings establish a link between cell wall targets and virulence of P. aeruginosa and thus may lead to development of novel drugs for the treatment of P. aeruginosa infection.

  13. Structure and function of the first full-length murein peptide ligase (Mpl) cell wall recycling protein.

    Science.gov (United States)

    Das, Debanu; Hervé, Mireille; Feuerhelm, Julie; Farr, Carol L; Chiu, Hsiu-Ju; Elsliger, Marc-André; Knuth, Mark W; Klock, Heath E; Miller, Mitchell D; Godzik, Adam; Lesley, Scott A; Deacon, Ashley M; Mengin-Lecreulx, Dominique; Wilson, Ian A

    2011-03-18

    Bacterial cell walls contain peptidoglycan, an essential polymer made by enzymes in the Mur pathway. These proteins are specific to bacteria, which make them targets for drug discovery. MurC, MurD, MurE and MurF catalyze the synthesis of the peptidoglycan precursor UDP-N-acetylmuramoyl-L-alanyl-γ-D-glutamyl-meso-diaminopimelyl-D-alanyl-D-alanine by the sequential addition of amino acids onto UDP-N-acetylmuramic acid (UDP-MurNAc). MurC-F enzymes have been extensively studied by biochemistry and X-ray crystallography. In gram-negative bacteria, ∼30-60% of the bacterial cell wall is recycled during each generation. Part of this recycling process involves the murein peptide ligase (Mpl), which attaches the breakdown product, the tripeptide L-alanyl-γ-D-glutamyl-meso-diaminopimelate, to UDP-MurNAc. We present the crystal structure at 1.65 Å resolution of a full-length Mpl from the permafrost bacterium Psychrobacter arcticus 273-4 (PaMpl). Although the Mpl structure has similarities to Mur enzymes, it has unique sequence and structure features that are likely related to its role in cell wall recycling, a function that differentiates it from the MurC-F enzymes. We have analyzed the sequence-structure relationships that are unique to Mpl proteins and compared them to MurC-F ligases. We have also characterized the biochemical properties of this enzyme (optimal temperature, pH and magnesium binding profiles and kinetic parameters). Although the structure does not contain any bound substrates, we have identified ∼30 residues that are likely to be important for recognition of the tripeptide and UDP-MurNAc substrates, as well as features that are unique to Psychrobacter Mpl proteins. These results provide the basis for future mutational studies for more extensive function characterization of the Mpl sequence-structure relationships.

  14. Identification of Ideal Multi-targeting Bioactive Compounds Against Mur Ligases of Enterobacter aerogenes and Its Binding Mechanism in Comparison with Chemical Inhibitors.

    Science.gov (United States)

    Chakkyarath, Vijina; Natarajan, Jeyakumar

    2017-10-31

    Enterobacter aerogenes have been reported as important opportunistic and multi-resistant bacterial pathogens for humans during the last three decades in hospital wards. The emergence of drug-resistant E. aerogenes demands the need for developing new drugs. Peptidoglycan is an important component of the cell wall of bacteria and the peptidoglycan biochemical pathway is considered as the best source of antibacterial targets. Within this pathway, four Mur ligases MurC, MurD, MurE, and MurF are responsible for the successive additions of L-alanine and suitable targets for developing novel antibacterial drugs. As an inference from this fact, we modeled the three-dimensional structure of above Mur ligases using best template structures available in PDB and analyzed its common binding features. Structural refinement and energy minimization of the predicted Mur ligases models is also being done using molecular dynamics studies. The models of Mur ligases were further investigated for in silico docking studies using bioactive plant compounds from the literature. Interestingly, these results indicate that four plant compounds Isojuripidine, Atroviolacegenin, Porrigenin B, and Nummularogenin showing better docking results in terms of binding energy and number of hydrogen bonds. All these four compounds are spirostan-based compounds with differences in side chains and the amino acid such as ASN, LYS, THR, HIS, ARG (polar) and PHE, GLY, VAL, ALA, MET (non-polar) playing active role in binding site of all four Mur ligases. Overall, in the predicted model, the four plant compounds with its binding features could pave way to design novel multi-targeted antibacterial plant-based bioactive compounds specific to Mur ligases for the treatment of Enterobacter infections.

  15. Contribution of the Pmra Promoter to Expression of Genes in the Escherichia coli mra Cluster of Cell Envelope Biosynthesis and Cell Division Genes

    Science.gov (United States)

    Mengin-Lecreulx, Dominique; Ayala, Juan; Bouhss, Ahmed; van Heijenoort, Jean; Parquet, Claudine; Hara, Hiroshi

    1998-01-01

    Recently, a promoter for the essential gene ftsI, which encodes penicillin-binding protein 3 of Escherichia coli, was precisely localized 1.9 kb upstream from this gene, at the beginning of the mra cluster of cell division and cell envelope biosynthesis genes (H. Hara, S. Yasuda, K. Horiuchi, and J. T. Park, J. Bacteriol. 179:5802–5811, 1997). Disruption of this promoter (Pmra) on the chromosome and its replacement by the lac promoter (Pmra::Plac) led to isopropyl-β-d-thiogalactopyranoside (IPTG)-dependent cells that lysed in the absence of inducer, a defect which was complemented only when the whole region from Pmra to ftsW, the fifth gene downstream from ftsI, was provided in trans on a plasmid. In the present work, the levels of various proteins involved in peptidoglycan synthesis and cell division were precisely determined in cells in which Pmra::Plac promoter expression was repressed or fully induced. It was confirmed that the Pmra promoter is required for expression of the first nine genes of the mra cluster: mraZ (orfC), mraW (orfB), ftsL (mraR), ftsI, murE, murF, mraY, murD, and ftsW. Interestingly, three- to sixfold-decreased levels of MurG and MurC enzymes were observed in uninduced Pmra::Plac cells. This was correlated with an accumulation of the nucleotide precursors UDP–N-acetylglucosamine and UDP–N-acetylmuramic acid, substrates of these enzymes, and with a depletion of the pool of UDP–N-acetylmuramyl pentapeptide, resulting in decreased cell wall peptidoglycan synthesis. Moreover, the expression of ftsZ, the penultimate gene from this cluster, was significantly reduced when Pmra expression was repressed. It was concluded that the transcription of the genes located downstream from ftsW in the mra cluster, from murG to ftsZ, is also mainly (but not exclusively) dependent on the Pmra promoter. PMID:9721276

  16. Invariant amino acids in the Mur peptide synthetases of bacterial peptidoglycan synthesis and their modification by site-directed mutagenesis in the UDP-MurNAc:L-alanine ligase from Escherichia coli.

    Science.gov (United States)

    Bouhss, A; Mengin-Lecreulx, D; Blanot, D; van Heijenoort, J; Parquet, C

    1997-09-30

    The comparison of the amino acid sequences of 20 cytoplasmic peptidoglycan synthetases (MurC, MurD, MurE, MurF, and Mpl) from various bacterial organisms has allowed us to detect common invariants: seven amino acids and the ATP-binding consensus sequence GXXGKT/S all at the same position in the alignment. The Mur synthetases thus appeared as a well-defined class of closely functionally related proteins. The conservation of a constant backbone length between certain invariants suggested common structural motifs. Among the other enzymes catalyzing a peptide bond formation driven by ATP hydrolysis to ADP and Pi, only folylpoly-gamma-l-glutamate synthetases presented the same common conserved amino acid residues, except for the most N-terminal invariant D50. Site-directed mutageneses were carried out to replace the K130, E174, H199, N293, N296, R327, and D351 residues by alanine in the MurC protein from Escherichia coli taken as model. For this purpose, plasmid pAM1005 was used as template, MurC being highly overproduced in this genetic setting. Analysis of the Vmax values of the mutated proteins suggested that residues K130, E174, and D351 are essential for the catalytic process whereas residues H199, N293, N296, and R327 were not. Mutations K130A, H199A, N293A, N296A, and R327A led to important variations of the Km values for one or more substrates, thereby indicating that these residues are involved in the structure of the active site and suggesting that the binding order of the substrates could be ATP, UDP-MurNAc, and alanine. The various mutated murC plasmids were tested for their effects on the growth, cell morphology, and peptidoglycan cell content of a murC thermosensitive strain at 42 degrees C. The observed effects (complementation, altered morphology, and reduced peptidoglycan content) paralleled more or less the decreased values of the MurC activity of each mutant.