The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform
Mark Cushman - One of the best experts on this subject based on the ideXlab platform.
-
O-Nucleoside, S-Nucleoside, and N-Nucleoside Probes of Lumazine Synthase and Riboflavin Synthase
The Journal of organic chemistry, 2012Co-Authors: Arindam Talukdar, A. Bacher, Markus Fischer, Boris Illarionov, Yujie Zhao, Mark CushmanAbstract:Lumazine synthase catalyzes the penultimate step in the biosynthesis of riboflavin, while riboflavin synthase catalyzes the last step. O-Nucleoside, S-nucleoside, and N-nucleoside analogues of hypothetical Lumazine biosynthetic intermediates have been synthesized in order to obtain structure and mechanism probes of these two enzymes, as well as inhibitors of potential value as antibiotics. Methods were devised for the selective cleavage of benzyl protecting groups in the presence of other easily reduced functionality by controlled hydrogenolysis over Lindlar catalyst. The deprotection reaction was performed in the presence of other reactive functionality including nitro groups, alkenes, and halogens. The target compounds were tested as inhibitors of Lumazine synthase and riboflavin synthase obtained from a variety of microorganisms. In general, the S-nucleosides and N-nucleosides were more potent than the corresponding O-nucleosides as Lumazine synthase and riboflavin synthase inhibitors, while the C-nucl...
-
structural study and thermodynamic characterization of inhibitor binding to Lumazine synthase from bacillus anthracis
Acta Crystallographica Section D-biological Crystallography, 2010Co-Authors: Ekaterina Morgunova, Adelbert Bacher, Mark Cushman, Markus Fischer, Boris Illarionov, Thota Sambaiah, Sabine Saller, Aleksander Popov, Rudolf LadensteinAbstract:The crystal structure of Lumazine synthase from Bacillus anthracis was solved by molecular replacement and refined to Rcryst = 23.7% (Rfree = 28.4%) at a resolution of 3.5 A. The structure reveals the icosahedral symmetry of the enzyme and specific features of the active site that are unique in comparison with previously determined orthologues. The application of isothermal titration calorimetry in combination with enzyme kinetics showed that three designed pyrimidine derivatives bind to Lumazine synthase with micromolar dissociation constants and competitively inhibit the catalytic reaction. Structure-based modelling suggested the binding modes of the inhibitors in the active site and allowed an estimation of the possible contacts formed upon binding. The results provide a structural framework for the design of antibiotics active against B. anthracis.
-
discovery and development of a small molecule library with Lumazine synthase inhibitory activity
Journal of Organic Chemistry, 2009Co-Authors: Arindam Talukdar, Adelbert Bacher, Markus Fischer, Boris Illarionov, Meghan E Breen, Gunda I Georg, Mark CushmanAbstract:(E)-5-Nitro-6-(2-hydroxystyryl)pyrimidine-2,4(1H,3H)-dione (9) was identified as a novel inhibitor of Schizosaccharomyces pombe Lumazine synthase by high-throughput screening of a 100000 compound library. The K(i) of 9 vs Mycobacterium tuberculosis Lumazine synthase was 95 microM. Compound 9 is a structural analogue of the Lumazine synthase substrate 5-amino-6-(d-ribitylamino)-2,4-(1H,3H)pyrimidinedione (1). This indicates that the ribitylamino side chain of the substrate is not essential for binding to the enzyme. Optimization of the enzyme inhibitory activity through systematic structure modification of the lead compound 9 led to (E)-5-nitro-6-(4-nitrostyryl)pyrimidine-2,4(1H,3H)-dione (26), which has a K(i) of 3.7 microM vs M. tuberculosis Lumazine synthase.
-
15n 31p redor nmr studies of the binding of phosphonate reaction intermediate analogues to saccharomyces cerevisiae Lumazine synthase
Biochemistry, 2008Co-Authors: Robert D Oconnor, Adelbert Bacher, Mark Cushman, Markus Fischer, Ilka Haase, Barbara Poliks, Astrid C Sivertsen, Colby Chiauzzi, Jacob SchaeferAbstract:Lumazine synthase catalyzes the reaction of 5-amino-6-d-ribitylamino-2,4(1H,3H)-pyrimidinedione (1) with (S)-3,4-dihydroxybutanone 4-phosphate (2) to afford 6,7-dimethyl-8-d-ribitylLumazine (3), the immediate biosynthetic precursor of riboflavin. The overall reaction implies a series of intermediates that are incompletely understood. The 15N{31P} REDOR NMR spectra of three metabolically stable phosphonate reaction intermediate analogues complexed to Saccharomyces cerevisiae Lumazine synthase have been obtained at 7 and 12 T. Distances from the phosphorus atoms of the ligands to the side chain nitrogens of Lys92, His97, Arg136, and His148 have been determined. These distances were used in combination with the X-ray crystal coordinates of one of the intermediate analogues complexed with the enzyme in a series of distance-restrained molecular dynamics simulations. The resulting models indicate mobility of the Lys92 side chain, which could facilitate the exchange of inorganic phosphate eliminated from the sub...
-
a new series of n 2 4 dioxo 6 d ribitylamino 1 2 3 4 tetrahydropyrimidin 5 yl oxalamic acid derivatives as inhibitors of Lumazine synthase and riboflavin synthase design synthesis biochemical evaluation crystallography and mechanistic implications
Journal of Organic Chemistry, 2008Co-Authors: Yanlei Zhang, A. Bacher, Markus Fischer, Rudolf Ladenstein, Boris Illarionov, Guangyi Jin, Ekaterina Morgunova, Mark CushmanAbstract:The penultimate step in the biosynthesis of riboflavin is catalyzed by Lumazine synthase. Three metabolically stable analogues of the hypothetical intermediate proposed to arise after phosphate elimination in the Lumazine synthase-catalyzed reaction were synthesized and evaluated as Lumazine synthase inhibitors. All three intermediate analogues were inhibitors of Mycobacterium tuberculosis Lumazine synthase, Bacillus subtilis Lumazine synthase, and Schizosaccharomyces pombe Lumazine synthase, while one of them proved to be an extremely potent inhibitor of Escherichia coli riboflavin synthase with a Ki of 1.3 nM. The crystal structure of M. tuberculosis Lumazine synthase in complex with one of the inhibitors provides a model of the conformation of the intermediate occurring immediately after phosphate elimination, supporting a mechanism in which phosphate elimination occurs before a conformational change of the Schiff base intermediate toward a cyclic structure.
A. Bacher - One of the best experts on this subject based on the ideXlab platform.
-
the Lumazine synthase riboflavin synthase complex shapes and functions of a highly variable enzyme system
FEBS Journal, 2013Co-Authors: Rudolf Ladenstein, A. Bacher, Markus FischerAbstract:The xylene ring of riboflavin (vitamin B2) is assembled from two molecules of 3,4-dihydroxy-2-butanone 4-phosphate by a mechanistically complex process that is jointly catalyzed by Lumazine synthase and riboflavin synthase. In Bacillaceae, these enzymes form a structurally unique complex comprising an icosahedral shell of 60 Lumazine synthase subunits and a core of three riboflavin synthase subunits, whereas many other bacteria have empty Lumazine synthase capsids, fungi, Archaea and some eubacteria have pentameric Lumazine synthases, and the riboflavin synthases of Archaea are paralogs of Lumazine synthase. The structures of the molecular ensembles have been studied in considerable detail by X-ray crystallography, X-ray small-angle scattering and electron microscopy. However, certain mechanistic aspects remain unknown. Surprisingly, the quaternary structure of the icosahedral β subunit capsids undergoes drastic changes, resulting in formation of large, quasi-spherical capsids; this process is modulated by sequence mutations. The occurrence of large shells consisting of 180 or more Lumazine synthase subunits has recently generated interest for protein engineering topics, particularly the construction of encapsulation systems.
-
O-Nucleoside, S-Nucleoside, and N-Nucleoside Probes of Lumazine Synthase and Riboflavin Synthase
The Journal of organic chemistry, 2012Co-Authors: Arindam Talukdar, A. Bacher, Markus Fischer, Boris Illarionov, Yujie Zhao, Mark CushmanAbstract:Lumazine synthase catalyzes the penultimate step in the biosynthesis of riboflavin, while riboflavin synthase catalyzes the last step. O-Nucleoside, S-nucleoside, and N-nucleoside analogues of hypothetical Lumazine biosynthetic intermediates have been synthesized in order to obtain structure and mechanism probes of these two enzymes, as well as inhibitors of potential value as antibiotics. Methods were devised for the selective cleavage of benzyl protecting groups in the presence of other easily reduced functionality by controlled hydrogenolysis over Lindlar catalyst. The deprotection reaction was performed in the presence of other reactive functionality including nitro groups, alkenes, and halogens. The target compounds were tested as inhibitors of Lumazine synthase and riboflavin synthase obtained from a variety of microorganisms. In general, the S-nucleosides and N-nucleosides were more potent than the corresponding O-nucleosides as Lumazine synthase and riboflavin synthase inhibitors, while the C-nucl...
-
a new series of n 2 4 dioxo 6 d ribitylamino 1 2 3 4 tetrahydropyrimidin 5 yl oxalamic acid derivatives as inhibitors of Lumazine synthase and riboflavin synthase design synthesis biochemical evaluation crystallography and mechanistic implications
Journal of Organic Chemistry, 2008Co-Authors: Yanlei Zhang, A. Bacher, Markus Fischer, Rudolf Ladenstein, Boris Illarionov, Guangyi Jin, Ekaterina Morgunova, Mark CushmanAbstract:The penultimate step in the biosynthesis of riboflavin is catalyzed by Lumazine synthase. Three metabolically stable analogues of the hypothetical intermediate proposed to arise after phosphate elimination in the Lumazine synthase-catalyzed reaction were synthesized and evaluated as Lumazine synthase inhibitors. All three intermediate analogues were inhibitors of Mycobacterium tuberculosis Lumazine synthase, Bacillus subtilis Lumazine synthase, and Schizosaccharomyces pombe Lumazine synthase, while one of them proved to be an extremely potent inhibitor of Escherichia coli riboflavin synthase with a Ki of 1.3 nM. The crystal structure of M. tuberculosis Lumazine synthase in complex with one of the inhibitors provides a model of the conformation of the intermediate occurring immediately after phosphate elimination, supporting a mechanism in which phosphate elimination occurs before a conformational change of the Schiff base intermediate toward a cyclic structure.
-
synthesis and enzyme inhibitory activity of the s nucleoside analogue of the ribitylaminopyrimidine substrate of Lumazine synthase and product of riboflavin synthase
Journal of Organic Chemistry, 2007Co-Authors: Arindam Talukdar, Markus Fischer, A. Bacher, Boris Illarionov, Mark CushmanAbstract:Lumazine synthase and riboflavin synthase catalyze the last two steps in the biosynthesis of riboflavin. To obtain structural and mechanistic probes of these two enzymes, as well as inhibitors of potential value as antibiotics, a sulfur analogue of the pyrimidine substrate of the Lumazine synthase-catalyzed reaction and product of the riboflavin synthase-catalyzed reaction was designed. Facile syntheses of the S-nucleoside 5-amino-6-(d-ribitylthio)pyrimidine-2,4(1H,3H)-dione hydrochloride (15) and its nitro precursor 5-nitro-6-(d-ribitylthio)pyrimidine-2,4(1H,3H)-dione (14) are described. These compounds were tested against Lumazine synthase and riboflavin synthase obtained from a variety of microorganisms. Compounds 14 and 15 were found to be inhibitors of both riboflavin synthase and Lumazine synthase. Compound 14 is an inhibitor of Bacillus subtilis Lumazine synthase (Ki 26 μM), Schizosaccharomyces pombe Lumazine synthase (Ki 2.0 μM), Mycobacterium tuberculosis Lumazine synthase (Ki 11 μM), Escherichia...
-
design synthesis and biochemical evaluation of 1 5 6 7 tetrahydro 6 7 dioxo 9 d ribitylaminoLumazines bearing alkyl phosphate substituents as inhibitors of Lumazine synthase and riboflavin synthase
ChemInform, 2005Co-Authors: Mark Cushman, Markus Fischer, Rudolf Ladenstein, Boris Illarionov, Guangyi Jin, A. BacherAbstract:The last two steps in the biosynthesis of riboflavin, an essential metabolite that is involved in electron transport, are catalyzed by Lumazine synthase and riboflavin synthase. To obtain structural probes and inhibitors of these two enzymes, two ribitylLumazinediones bearing alkyl phosphate substituents were synthesized. The synthesis involved the generation of the ribityl side chain, the phosphate side chain, and the Lumazine system in protected form, followed by the simultaneous removal of three different types of protecting groups. The products were designed as intermediate analogue inhibitors of Lumazine synthase that would bind to its phosphate-binding site as well as its Lumazine binding site. Both compounds were found to be effective inhibitors of Bacillus subtilis Lumazine synthase as well as Escherichia coli riboflavin synthase. Molecular modeling of the binding of one of the two compounds provided a structural explanation for how these compounds are able to effectively inhibit both enzymes. In ...
Markus Fischer - One of the best experts on this subject based on the ideXlab platform.
-
One Protein, Two Chromophores: Comparative Spectroscopic Characterization of 6,7-Dimethyl-8-ribitylLumazine and Riboflavin Bound to Lumazine Protein
2014Co-Authors: Bernd Paulus, Adelbert Bacher, Markus Fischer, Boris Illarionov, Sylwia Kacprzak, Stefan Weber, Daniel Nohr, Guillaume Roellinger, Erik SchleicherAbstract:We investigated the Lumazine protein from Photobacterium leiognathi in complex with its biologically active cofactor, 6,7-dimethyl-8-ribitylLumazine, at different redox states and compared the results with samples containing a riboflavin cofactor. Using anaerobic photoreduction, we were able to record optical absorption kinetics from both cofactors in similar protein environments. It could be demonstrated that the protein is able to stabilize a neutral riboLumazine radical with ∼35% yield. The riboLumazine radical state was further investigated by W-band continuous-wave EPR and X-band pulsed ENDOR spectroscopy. Here, both the principal values of the g-tensor and an almost complete mapping of the proton hyperfine couplings (hfcs) could be obtained. Remarkably, the g-tensor’s principal components are similar to those of the respective riboflavin-containing protein; however, the proton hfcs show noticeable differences. Comparing time-resolved optical absorption and fluorescence data from riboLumazine-containing samples, solely fluorescence but no signs of any intermediate radical or a triplet state could be identified. This is in contrast to Lumazine protein samples containing the riboflavin cofactor, for which a high yield of the photogenerated triplet state and some excited flavin radical could be detected using time-resolved spectroscopy. These results clearly demonstrate that riboLumazine is a redox-active molecule and could, in principle, be employed as a cofactor in other enzymatic reactions
-
the Lumazine synthase riboflavin synthase complex shapes and functions of a highly variable enzyme system
FEBS Journal, 2013Co-Authors: Rudolf Ladenstein, A. Bacher, Markus FischerAbstract:The xylene ring of riboflavin (vitamin B2) is assembled from two molecules of 3,4-dihydroxy-2-butanone 4-phosphate by a mechanistically complex process that is jointly catalyzed by Lumazine synthase and riboflavin synthase. In Bacillaceae, these enzymes form a structurally unique complex comprising an icosahedral shell of 60 Lumazine synthase subunits and a core of three riboflavin synthase subunits, whereas many other bacteria have empty Lumazine synthase capsids, fungi, Archaea and some eubacteria have pentameric Lumazine synthases, and the riboflavin synthases of Archaea are paralogs of Lumazine synthase. The structures of the molecular ensembles have been studied in considerable detail by X-ray crystallography, X-ray small-angle scattering and electron microscopy. However, certain mechanistic aspects remain unknown. Surprisingly, the quaternary structure of the icosahedral β subunit capsids undergoes drastic changes, resulting in formation of large, quasi-spherical capsids; this process is modulated by sequence mutations. The occurrence of large shells consisting of 180 or more Lumazine synthase subunits has recently generated interest for protein engineering topics, particularly the construction of encapsulation systems.
-
O-Nucleoside, S-Nucleoside, and N-Nucleoside Probes of Lumazine Synthase and Riboflavin Synthase
The Journal of organic chemistry, 2012Co-Authors: Arindam Talukdar, A. Bacher, Markus Fischer, Boris Illarionov, Yujie Zhao, Mark CushmanAbstract:Lumazine synthase catalyzes the penultimate step in the biosynthesis of riboflavin, while riboflavin synthase catalyzes the last step. O-Nucleoside, S-nucleoside, and N-nucleoside analogues of hypothetical Lumazine biosynthetic intermediates have been synthesized in order to obtain structure and mechanism probes of these two enzymes, as well as inhibitors of potential value as antibiotics. Methods were devised for the selective cleavage of benzyl protecting groups in the presence of other easily reduced functionality by controlled hydrogenolysis over Lindlar catalyst. The deprotection reaction was performed in the presence of other reactive functionality including nitro groups, alkenes, and halogens. The target compounds were tested as inhibitors of Lumazine synthase and riboflavin synthase obtained from a variety of microorganisms. In general, the S-nucleosides and N-nucleosides were more potent than the corresponding O-nucleosides as Lumazine synthase and riboflavin synthase inhibitors, while the C-nucl...
-
structural study and thermodynamic characterization of inhibitor binding to Lumazine synthase from bacillus anthracis
Acta Crystallographica Section D-biological Crystallography, 2010Co-Authors: Ekaterina Morgunova, Adelbert Bacher, Mark Cushman, Markus Fischer, Boris Illarionov, Thota Sambaiah, Sabine Saller, Aleksander Popov, Rudolf LadensteinAbstract:The crystal structure of Lumazine synthase from Bacillus anthracis was solved by molecular replacement and refined to Rcryst = 23.7% (Rfree = 28.4%) at a resolution of 3.5 A. The structure reveals the icosahedral symmetry of the enzyme and specific features of the active site that are unique in comparison with previously determined orthologues. The application of isothermal titration calorimetry in combination with enzyme kinetics showed that three designed pyrimidine derivatives bind to Lumazine synthase with micromolar dissociation constants and competitively inhibit the catalytic reaction. Structure-based modelling suggested the binding modes of the inhibitors in the active site and allowed an estimation of the possible contacts formed upon binding. The results provide a structural framework for the design of antibiotics active against B. anthracis.
-
virtual screening selection and development of a benzindolone structural scaffold for inhibition of Lumazine synthase
Bioorganic & Medicinal Chemistry, 2010Co-Authors: Arindam Talukdar, Adelbert Bacher, Markus Fischer, Winfried Meining, Boris Illarionov, Ekaterina Morgunova, Jianxin Duan, Nicolas Foloppe, Lennart Nilsson, Rudolf LadensteinAbstract:Abstract Virtual screening of a library of commercially available compounds versus the structure of Mycobacterium tuberculosis Lumazine synthase identified 2-(2-oxo-1,2-dihydrobenzo[cd]indole-6-sulfonamido)acetic acid (9) as a possible lead compound. Compound 9 proved to be an effective inhibitor of M. tuberculosis Lumazine synthase with a Ki of 70 μM. Lead optimization through replacement of the carboxymethylsulfonamide sidechain with sulfonamides substituted with alkyl phosphates led to a four-carbon phosphate 38 that displayed a moderate increase in enzyme inhibitory activity (Ki 38 μM). Molecular modeling based on known Lumazine synthase/inhibitor crystal structures suggests that the main forces stabilizing the present benzindolone/enzyme complexes involve π–π stacking interactions with Trp27 and hydrogen bonding of the phosphates with Arg128, the backbone nitrogens of Gly85 and Gln86, and the side chain hydroxyl of Thr87.
Adelbert Bacher - One of the best experts on this subject based on the ideXlab platform.
-
One Protein, Two Chromophores: Comparative Spectroscopic Characterization of 6,7-Dimethyl-8-ribitylLumazine and Riboflavin Bound to Lumazine Protein
2014Co-Authors: Bernd Paulus, Adelbert Bacher, Markus Fischer, Boris Illarionov, Sylwia Kacprzak, Stefan Weber, Daniel Nohr, Guillaume Roellinger, Erik SchleicherAbstract:We investigated the Lumazine protein from Photobacterium leiognathi in complex with its biologically active cofactor, 6,7-dimethyl-8-ribitylLumazine, at different redox states and compared the results with samples containing a riboflavin cofactor. Using anaerobic photoreduction, we were able to record optical absorption kinetics from both cofactors in similar protein environments. It could be demonstrated that the protein is able to stabilize a neutral riboLumazine radical with ∼35% yield. The riboLumazine radical state was further investigated by W-band continuous-wave EPR and X-band pulsed ENDOR spectroscopy. Here, both the principal values of the g-tensor and an almost complete mapping of the proton hyperfine couplings (hfcs) could be obtained. Remarkably, the g-tensor’s principal components are similar to those of the respective riboflavin-containing protein; however, the proton hfcs show noticeable differences. Comparing time-resolved optical absorption and fluorescence data from riboLumazine-containing samples, solely fluorescence but no signs of any intermediate radical or a triplet state could be identified. This is in contrast to Lumazine protein samples containing the riboflavin cofactor, for which a high yield of the photogenerated triplet state and some excited flavin radical could be detected using time-resolved spectroscopy. These results clearly demonstrate that riboLumazine is a redox-active molecule and could, in principle, be employed as a cofactor in other enzymatic reactions
-
vibrational spectra of the ground and the singlet excited ππ state of 6 7 dimethyl 8 ribitylLumazine
Journal of Physical Chemistry B, 2011Co-Authors: Wolfgang J Schreier, Igor Pugliesi, Florian O Koller, Tobias E Schrader, Wolfgang Zinth, Markus Braun, Sylwia Kacprzak, Stefan Weber, Werner Romischmargl, Adelbert BacherAbstract:6,7-Dimethyl-8-ribitylLumazine serves as fluorophore in Lumazine proteins (LumP) of luminescent bacteria. The molecule exhibits several characteristic vibrational absorption bands between 1300 and 1750 cm−1 in its electronic ground state. The IR-absorption pattern of the singlet excited ππ* state was monitored via ultrafast infrared spectroscopy after photoexcitation at 404 nm. The comparison of experimentally observed band shifts for a number of isotopologues allows for a clear assignment of several absorption bands—most importantly the two carbonyl bands. This assignment is confirmed by normal-mode calculations by means of either density functional theory (DFT) calculations for the ground state or the configuration interaction singles (CIS) method for the excited singlet state. A good agreement between experiment and calculation is obtained for models including explicitly a first solvation shell. The results provide a basis for further investigations of Lumazine protein and demonstrate the necessity of ...
-
structural study and thermodynamic characterization of inhibitor binding to Lumazine synthase from bacillus anthracis
Acta Crystallographica Section D-biological Crystallography, 2010Co-Authors: Ekaterina Morgunova, Adelbert Bacher, Mark Cushman, Markus Fischer, Boris Illarionov, Thota Sambaiah, Sabine Saller, Aleksander Popov, Rudolf LadensteinAbstract:The crystal structure of Lumazine synthase from Bacillus anthracis was solved by molecular replacement and refined to Rcryst = 23.7% (Rfree = 28.4%) at a resolution of 3.5 A. The structure reveals the icosahedral symmetry of the enzyme and specific features of the active site that are unique in comparison with previously determined orthologues. The application of isothermal titration calorimetry in combination with enzyme kinetics showed that three designed pyrimidine derivatives bind to Lumazine synthase with micromolar dissociation constants and competitively inhibit the catalytic reaction. Structure-based modelling suggested the binding modes of the inhibitors in the active site and allowed an estimation of the possible contacts formed upon binding. The results provide a structural framework for the design of antibiotics active against B. anthracis.
-
virtual screening selection and development of a benzindolone structural scaffold for inhibition of Lumazine synthase
Bioorganic & Medicinal Chemistry, 2010Co-Authors: Arindam Talukdar, Adelbert Bacher, Markus Fischer, Winfried Meining, Boris Illarionov, Ekaterina Morgunova, Jianxin Duan, Nicolas Foloppe, Lennart Nilsson, Rudolf LadensteinAbstract:Abstract Virtual screening of a library of commercially available compounds versus the structure of Mycobacterium tuberculosis Lumazine synthase identified 2-(2-oxo-1,2-dihydrobenzo[cd]indole-6-sulfonamido)acetic acid (9) as a possible lead compound. Compound 9 proved to be an effective inhibitor of M. tuberculosis Lumazine synthase with a Ki of 70 μM. Lead optimization through replacement of the carboxymethylsulfonamide sidechain with sulfonamides substituted with alkyl phosphates led to a four-carbon phosphate 38 that displayed a moderate increase in enzyme inhibitory activity (Ki 38 μM). Molecular modeling based on known Lumazine synthase/inhibitor crystal structures suggests that the main forces stabilizing the present benzindolone/enzyme complexes involve π–π stacking interactions with Trp27 and hydrogen bonding of the phosphates with Arg128, the backbone nitrogens of Gly85 and Gln86, and the side chain hydroxyl of Thr87.
-
discovery and development of a small molecule library with Lumazine synthase inhibitory activity
Journal of Organic Chemistry, 2009Co-Authors: Arindam Talukdar, Adelbert Bacher, Markus Fischer, Boris Illarionov, Meghan E Breen, Gunda I Georg, Mark CushmanAbstract:(E)-5-Nitro-6-(2-hydroxystyryl)pyrimidine-2,4(1H,3H)-dione (9) was identified as a novel inhibitor of Schizosaccharomyces pombe Lumazine synthase by high-throughput screening of a 100000 compound library. The K(i) of 9 vs Mycobacterium tuberculosis Lumazine synthase was 95 microM. Compound 9 is a structural analogue of the Lumazine synthase substrate 5-amino-6-(d-ribitylamino)-2,4-(1H,3H)pyrimidinedione (1). This indicates that the ribitylamino side chain of the substrate is not essential for binding to the enzyme. Optimization of the enzyme inhibitory activity through systematic structure modification of the lead compound 9 led to (E)-5-nitro-6-(4-nitrostyryl)pyrimidine-2,4(1H,3H)-dione (26), which has a K(i) of 3.7 microM vs M. tuberculosis Lumazine synthase.
Rudolf Ladenstein - One of the best experts on this subject based on the ideXlab platform.
-
the Lumazine synthase riboflavin synthase complex shapes and functions of a highly variable enzyme system
FEBS Journal, 2013Co-Authors: Rudolf Ladenstein, A. Bacher, Markus FischerAbstract:The xylene ring of riboflavin (vitamin B2) is assembled from two molecules of 3,4-dihydroxy-2-butanone 4-phosphate by a mechanistically complex process that is jointly catalyzed by Lumazine synthase and riboflavin synthase. In Bacillaceae, these enzymes form a structurally unique complex comprising an icosahedral shell of 60 Lumazine synthase subunits and a core of three riboflavin synthase subunits, whereas many other bacteria have empty Lumazine synthase capsids, fungi, Archaea and some eubacteria have pentameric Lumazine synthases, and the riboflavin synthases of Archaea are paralogs of Lumazine synthase. The structures of the molecular ensembles have been studied in considerable detail by X-ray crystallography, X-ray small-angle scattering and electron microscopy. However, certain mechanistic aspects remain unknown. Surprisingly, the quaternary structure of the icosahedral β subunit capsids undergoes drastic changes, resulting in formation of large, quasi-spherical capsids; this process is modulated by sequence mutations. The occurrence of large shells consisting of 180 or more Lumazine synthase subunits has recently generated interest for protein engineering topics, particularly the construction of encapsulation systems.
-
structural study and thermodynamic characterization of inhibitor binding to Lumazine synthase from bacillus anthracis
Acta Crystallographica Section D-biological Crystallography, 2010Co-Authors: Ekaterina Morgunova, Adelbert Bacher, Mark Cushman, Markus Fischer, Boris Illarionov, Thota Sambaiah, Sabine Saller, Aleksander Popov, Rudolf LadensteinAbstract:The crystal structure of Lumazine synthase from Bacillus anthracis was solved by molecular replacement and refined to Rcryst = 23.7% (Rfree = 28.4%) at a resolution of 3.5 A. The structure reveals the icosahedral symmetry of the enzyme and specific features of the active site that are unique in comparison with previously determined orthologues. The application of isothermal titration calorimetry in combination with enzyme kinetics showed that three designed pyrimidine derivatives bind to Lumazine synthase with micromolar dissociation constants and competitively inhibit the catalytic reaction. Structure-based modelling suggested the binding modes of the inhibitors in the active site and allowed an estimation of the possible contacts formed upon binding. The results provide a structural framework for the design of antibiotics active against B. anthracis.
-
virtual screening selection and development of a benzindolone structural scaffold for inhibition of Lumazine synthase
Bioorganic & Medicinal Chemistry, 2010Co-Authors: Arindam Talukdar, Adelbert Bacher, Markus Fischer, Winfried Meining, Boris Illarionov, Ekaterina Morgunova, Jianxin Duan, Nicolas Foloppe, Lennart Nilsson, Rudolf LadensteinAbstract:Abstract Virtual screening of a library of commercially available compounds versus the structure of Mycobacterium tuberculosis Lumazine synthase identified 2-(2-oxo-1,2-dihydrobenzo[cd]indole-6-sulfonamido)acetic acid (9) as a possible lead compound. Compound 9 proved to be an effective inhibitor of M. tuberculosis Lumazine synthase with a Ki of 70 μM. Lead optimization through replacement of the carboxymethylsulfonamide sidechain with sulfonamides substituted with alkyl phosphates led to a four-carbon phosphate 38 that displayed a moderate increase in enzyme inhibitory activity (Ki 38 μM). Molecular modeling based on known Lumazine synthase/inhibitor crystal structures suggests that the main forces stabilizing the present benzindolone/enzyme complexes involve π–π stacking interactions with Trp27 and hydrogen bonding of the phosphates with Arg128, the backbone nitrogens of Gly85 and Gln86, and the side chain hydroxyl of Thr87.
-
a new series of n 2 4 dioxo 6 d ribitylamino 1 2 3 4 tetrahydropyrimidin 5 yl oxalamic acid derivatives as inhibitors of Lumazine synthase and riboflavin synthase design synthesis biochemical evaluation crystallography and mechanistic implications
Journal of Organic Chemistry, 2008Co-Authors: Yanlei Zhang, A. Bacher, Markus Fischer, Rudolf Ladenstein, Boris Illarionov, Guangyi Jin, Ekaterina Morgunova, Mark CushmanAbstract:The penultimate step in the biosynthesis of riboflavin is catalyzed by Lumazine synthase. Three metabolically stable analogues of the hypothetical intermediate proposed to arise after phosphate elimination in the Lumazine synthase-catalyzed reaction were synthesized and evaluated as Lumazine synthase inhibitors. All three intermediate analogues were inhibitors of Mycobacterium tuberculosis Lumazine synthase, Bacillus subtilis Lumazine synthase, and Schizosaccharomyces pombe Lumazine synthase, while one of them proved to be an extremely potent inhibitor of Escherichia coli riboflavin synthase with a Ki of 1.3 nM. The crystal structure of M. tuberculosis Lumazine synthase in complex with one of the inhibitors provides a model of the conformation of the intermediate occurring immediately after phosphate elimination, supporting a mechanism in which phosphate elimination occurs before a conformational change of the Schiff base intermediate toward a cyclic structure.
-
Lumazine Synthase from Candida Albicans as an Anti- Fungal Target Enzyme: Structural and Biochemical Basis for Drug Design.
Journal of Biological Chemistry, 2007Co-Authors: Ekaterina Morgunova, Adelbert Bacher, Mark Cushman, Markus Fischer, Ilka Haase, Sabine Saller, Rudolf LadensteinAbstract:Abstract Lumazine synthase is an enzyme involved in riboflavin biosynthesis in many plants and microorganisms, including numerous human pathogens. The fact that the enzymes of the riboflavin biosynthesis pathway are not present in the human or animal host makes them potential targets for anti-infective agents. The crystal structure of Lumazine synthase from Candida albicans was solved by molecular replacement and refined at 2.5-A resolution. The results of crystallographic investigations and sedimentation equilibrium experiments clearly indicated the presence of pentameric assemblies of the enzyme either in crystals or in solution. Isothermal titration calorimetry measurements of the binding reactions of four different inhibitors revealed high affinity for all four compounds with binding constants in the micromolar range. Structural comparison with previously determined structures of the enzyme·ligand complexes of other orthologue allowed modeling of the binding of four different inhibitors into the active site of Lumazine synthase from Candida albicans.
