Jerome De Ruyck | Université des Sciences et Technologies de Lille (Lille-1) (original) (raw)

Papers by Jerome De Ruyck

Acta crystallographica. Section F, Structural biology communications, 2014

Type-2 isopentenyl diphosphate isomerase (IDI-2) is a key flavoprotein involved in the biosynthes... more Type-2 isopentenyl diphosphate isomerase (IDI-2) is a key flavoprotein involved in the biosynthesis of isoprenoids. Since fully reduced flavin mononucleotide (FMNH2) is needed for activity, it was decided to crystallize the enzyme under anaerobic conditions in order to understand how this reduced cofactor binds within the active site and interacts with the substrate isopentenyl diphosphate (IPP). In this study, the protein was expressed and purified under aerobic conditions and then reduced and crystallized under anaerobic conditions. Crystals grown by the sitting-drop vapour-diffusion method and then soaked with IPP diffracted to 2.1 Å resolution and belonged to the hexagonal space group P6322, with unit-cell parameters a = b = 133.3, c = 172.9 Å.

Journal of Medicinal Chemistry, 2005

The synthesis and enzyme inhibitor properties of reversible type B monoamine oxidase inhibitors a... more The synthesis and enzyme inhibitor properties of reversible type B monoamine oxidase inhibitors are described. These compounds belong to the 5H-indeno[1,2-c]pyridazine family and possess a hydrophobic benzyloxy or 4,4,4-trifluorobutoxy side chain which, in contrast to a previous assignment, has been unambiguously located at C(8) of the heterocyclic moiety. Investigation of the regioisomeric structures establishes that substitution of the 5H-indeno[1,2-c]pyridazin-5-one core at C(7) vs C(8) dramatically influences the MAO-inhibiting properties of these compounds.

Acta crystallographica Section B, Structural science, crystal engineering and materials, 2015

Heme oxygenase-1 (HO-1) inhibition is associated with antitumor activity. Imidazole-based analogu... more Heme oxygenase-1 (HO-1) inhibition is associated with antitumor activity. Imidazole-based analogues show effective and selective inhibitory potency of HO-1. In this work, five single-crystal structures of four imidazole-based compounds are presented, with an in-depth structural analysis. In order to study the influence of the conformation of the ligands on binding to protein, conformational data from crystallography are compared with quantum mechanics analysis and molecular docking studies. Molecular docking of imidazole-based analogues in the active site of HO-1 is in good agreement with the experimental structures. Inhibitors interact with the heme cofactor and a hydrophobic pocket (Met34, Phe37, Val50, Leu147 and Phe214) in the HO-1 binding site. An alternate binding mode can be hypothesized for some inhibitors in the series.

Journal of Biological Chemistry, 2015

The two-component sensory transduction system BvgAS controls the virulence regulon of the whoopin... more The two-component sensory transduction system BvgAS controls the virulence regulon of the whooping-cough agent Bordetella pertussis. The periplasmic moiety of the homo-dimeric sensor-kinase BvgS is composed of four bilobed Venus flytrap (VFT) perception domains followed by α helices that extend into the cytoplasmic membrane. In the virulent phase, the default state of B. pertussis, the cytoplasmic enzymatic moiety of BvgS acts as kinase by autophosphorylating and transferring the phosphoryl group to the response regulator BvgA. In laboratory conditions, BvgS shifts to phosphatase activity in response to modulators, notably nicotinate ions. Here, we characterized the effects of nicotinate and related modulators on the BvgS periplasmic moiety by using site-directed mutagenesis, and in silico and biophysical approaches. Modulators bind with low affinity to BvgS in the VFT2 cavity. Electron paramagnetic resonance shows that their binding globally affects the conformation and dynamics of the periplasmic moiety. Specific amino acid substitutions designed to slacken interactions within and between the VFT lobes prevent BvgS from responding to nicotinate, showing that BvgS shifts from kinase to phosphatase activity in response to this modulator via a tense transition state that involves a large periplasmic structural block. We propose that this transition enables the transmembrane helices to adopt a distinct conformation that sets the cytoplasmic enzymatic moiety in the phosphatase mode. The bona fide, in vivo VFT ligands that remain to be identified are likely to trigger similar effects on the transmembrane and cytoplasmic moieties. This mechanism may be relevant to the other VFT-containing sensor-kinases homologous to BvgS.

Current enzyme inhibition, 2011

Isoprenoid compounds constitute an immensely diverse group of acyclic, monocyclic and polycyclic ... more Isoprenoid compounds constitute an immensely diverse group of acyclic, monocyclic and polycyclic compounds that play important roles in all living organisms. Despite the diversity of their structures, this plethora of natural products arises from only two 5-carbon precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). This review will discuss the enzymes in the mevalonate (MVA) and methylerythritol phosphate (MEP) biosynthetic pathways leading to IPP and DMAPP with a particular focus on MEP synthase (DXR) and IPP isomerase (IDI), which are potential targets for the development of antibiotic compounds. DXR is the second enzyme in the MEP pathway and the only one for which inhibitors with antimicrobial activity at pharmaceutically relevant concentrations are known. All of the published DXR inhibitors are fosmidomycin analogues, except for a few bisphosphonates with moderate inhibitory activity. These far, there are no other candidates that target DXR. IDI was...

ChemBioChem, 2014

Isopentenyl diphosphate isomerase (IDI) is a key enzyme in the isoprenoid biosynthetic pathway an... more Isopentenyl diphosphate isomerase (IDI) is a key enzyme in the isoprenoid biosynthetic pathway and is required for all organisms that synthesize isoprenoid metabolites from mevalonate. Type 1 IDI (IDI-1) is a metalloprotein that is found in eukaryotes, whereas the type 2 isoform (IDI-2) is a flavoenzyme found in bacteria that is completely absent from human. IDI-2 from the pathogenic bacterium Streptococcus pneumoniae was recombinantly expressed in Escherichia coli. Steady-state kinetic studies of the enzyme indicated that FMNH2 (KM =0.3 μM) bound before isopentenyl diphosphate (KM =40 μM) in an ordered binding mechanism. An X-ray crystal structure at 1.4 Å resolution was obtained for the holoenzyme in the closed conformation with a reduced flavin cofactor and two sulfate ions in the active site. These results helped to further approach the enzymatic mechanism of IDI-2 and, thus, open new possibilities for the rational design of antibacterial compounds against sequence-similar and structure-related pathogens such as Enterococcus faecalis or Staphylococcus aureus.

The Journal of Physical Chemistry C, 2014

ABSTRACT The origin and the nature of the first hyperpolarizability of collagen has been unravele... more ABSTRACT The origin and the nature of the first hyperpolarizability of collagen has been unraveled by performing first-principles calculations on the PPG10 compound, a molecular model for the collagen triple helix structure, and on its building blocks. The first hyperpolarizability of the triple helix originates from the amide groups. Owing to the rigidity of the structure and of the proline units, the β-tensor components parallel to the helical axis add to each other, whereas the perpendicular components cancel each other, which result in a dipolar first hyperpolarizability and a depolarization ratio close to 9. The calculations have also shown that the resulting β values cannot be viewed as the simple sum of the amide group contributions. Indeed, for a given chain, the β per amino acid increases with the size of the chain, whereas the β of the triple helix is smaller than three times the β of a single chain. The calculations, performed at different levels of approximation, demonstrated also the reliability of the ONIOM scheme when combining high and low layers described with different basis sets and the weak impact of electron correlation.

The Journal of Physical Chemistry B, 2010

Using the SIBFA polarizable molecular mechanics procedure, we analyze the binding energy of a bim... more Using the SIBFA polarizable molecular mechanics procedure, we analyze the binding energy of a bimetallic Mg(II)/Zn(II) enzyme, isopentenyl diphosphate isomerase, to an inhibitor built up of a trianionic diphosphate and of a cationic ethyldimethylammonium (EDMA) moiety. The analyses are performed on the protein recognition site, which totals 13 residues, as well as on some "mutants" in which one selected residue is removed at a time. They are also carried out for the individual recognition sites, namely, EDMA, Mg(II), and Zn(II). Comparisons are done with ab initio quantum chemistry (QC) results on all considered sites, with different basis sets and at different levels of correlation. The SIBFA computations reproduce the evolutions of the QC interaction energies in the recognition site and its "mutants". For such sites, small (<2-3%) relative errors are found after the BSSE correction is done. Such close agreements can conceal, however, some shortcomings found in the individual binding sites, which QC energy decomposition analyses can identify. Figure 1. Representation of (a) the three-dimensional structure of IDI and (b) the molecular structure of the NIPP inhibitor.

Proteins: Structure, Function, and Bioinformatics, 2007

In the first step of this study, type 2 isopentenyl diphosphate isomerase (IDI2) from Pyrococcus ... more In the first step of this study, type 2 isopentenyl diphosphate isomerase (IDI2) from Pyrococcus furiosus (pf-IDI2), a hyperthermophilic microorganism, was cloned and overexpressed in E. coli. After purification, hyperthermophilic behavior of this protein was approached by means of enzymatic assays and thermal denaturation studies. Compared with the mesophilic Streptococcus pneumoniae IDI2, which unfolds and looses activity above 50 degrees C, pf-IDI2 is still folded and active at 80 degrees C. Molecular modeling was applied, in a parallel step, to understand the molecular basis of thermal stability. Comparison of IDI2 from S. pneumoniae, T. thermophilus, and P. furiosus suggested that additional charged residues present in the hyperthermophilic enzyme might contribute to its higher thermal stability. This could increase the number of salt bridges between monomers of IDI2 in P. furiosus enzyme and, hence, decrease flexibility of loops or N-terminal segment, thereby enhancing its thermal stability.

Journal of Medicinal Chemistry, 2005

The synthesis and enzyme inhibitor properties of reversible type B monoamine oxidase inhibitors a... more The synthesis and enzyme inhibitor properties of reversible type B monoamine oxidase inhibitors are described. These compounds belong to the 5H-indeno[1,2-c]pyridazine family and possess a hydrophobic benzyloxy or 4,4,4-trifluorobutoxy side chain which, in contrast to a previous assignment, has been unambiguously located at C(8) of the heterocyclic moiety. Investigation of the regioisomeric structures establishes that substitution of the 5H-indeno[1,2-c]pyridazin-5-one core at C(7) vs C(8) dramatically influences the MAO-inhibiting properties of these compounds.

Journal of Biological Chemistry, 2006

Isopentenyl-diphosphate (IPP):dimethylallyl diphosphate isomerase is a key enzyme in the biosynth... more Isopentenyl-diphosphate (IPP):dimethylallyl diphosphate isomerase is a key enzyme in the biosynthesis of isoprenoids. The mechanism of the isomerization reaction involves protonation of the unactivated carbon-carbon double bond in the substrate, but identity of the acidic moiety providing the proton is still not clear. Multiple sequence alignments and geometrical features observed in crystal structures of complexes with IPP isomerase suggest that Tyr-104 could play an important role during catalysis. A series of mutants was constructed by directed mutagenesis and characterized by enzymology. Crystallographic and thermal denaturation data for Y104A and Y104F mutants were obtained. Those data demonstrate the importance of residue Tyr-104 for proper folding of Escherichia coli type I IPP isomerase.

Current Protein & Peptide Science, 2008

Biosynthesis of the universal terpenoid precursors, isopentenyl diphosphate (IPP) and dimethylall... more Biosynthesis of the universal terpenoid precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), from three acetyl CoA moieties through mevalonate was studied extensively in the 1950s. For several decades, the mevalonate paradigm reigned supreme and a mevalonate origin was attributed to a growing number of natural products, in many cases erroneously. Besides this biosynthetic pathway, the existence of a second one leading to IPP and DMAPP through 1-deoxy-D-xylulose 5-phosphate and 2C-methyl-D-erythritol 4-phosphate was discovered more recently in plants and some eubacteria. This pathway is widely distributed in the bacterial kingdom including major human pathogens, such as Mycobacterium tuberculosis or Helicobacter pylori and is also essential in the malaria vector Plasmodium falciparum. During the last few years, the genes, enzymes, intermediates and mechanisms of the biosynthetic route have been elucidated by a combination of methods including comparative genomics, enzymology, advanced NMR technology and crystallography. The present crystallographic review of enzymes involved in isoprenoid biosynthesis will be useful for understanding the various catalytic mechanisms and could potentially help for structure-based drug design.

Chemical Physics Letters, 2007

The spectrophotometric evaluation of NAD(P) dehydrogenase enzymatic activity is very popular as t... more The spectrophotometric evaluation of NAD(P) dehydrogenase enzymatic activity is very popular as the reduced form (NAD(P)H) absorbs at 340nm, while the aromatic oxidised form does not. In this joint theoretical and experimental investigation, we identify the chromophoric unit of both the NAD(P)+ and NAD(P)H forms. Rather than a modification of size or shape of the frontier orbitals, the sharp variation

Biochemistry, 2008

The N-terminal region is stabilized in the crystal structure of Thermus thermophilus type 2 isope... more The N-terminal region is stabilized in the crystal structure of Thermus thermophilus type 2 isopentenyl diphosphate isomerase in complex with inorganic pyrophosphate, providing new insights about the active site and the catalytic mechanism of the enzyme. The PP i moiety is located near the conserved residues, H10, R97, H152, Q157, E158, and W219, and the flavin cofactor. The putative active site of isopentenyl diphosphate isomerase 2 provides interactions for stabilizing a carbocationic intermediate similar to those that stabilize the intermediate in the well-established protonationdeprotonation mechanism of isopentenyl diphosphate isomerase 1.

Acta Crystallographica Section F Structural Biology and Crystallization Communications, 2008

Type 1 isopentenyl diphosphate isomerase (IDI-1) has been crystallized in a new crystal form. Aft... more Type 1 isopentenyl diphosphate isomerase (IDI-1) has been crystallized in a new crystal form. After data collection from small thin needle-shaped crystals, a new monoclinic form of the studied protein was identified. In this article, the three crystal forms of IDI-1 (orthorhombic, monoclinic and trigonal) are compared.

Acta Crystallographica Section E Structure Reports Online, 2005

Acta Crystallographica Section E Structure Reports Online, 2006

Type 1 isopentenyl diphosphate isomerase has been crystallized in a new crystal form.

Chembiochem : a European journal of chemical biology, Jan 4, 2016

Recently, we extended the anti-adhesive concept showing that potent FimH antagonists can block th... more Recently, we extended the anti-adhesive concept showing that potent FimH antagonists can block the attachment of adherent-invasive E. coli (AIEC) colonizing the intestinal mucosa of patients with Crohn's disease (CD). In this work, we designed a small library of analogs of heptylmannoside (HM), a previously identified nanomolar FimH inhibitor, but displaying poor in vivo anti-adhesive effects. The anomeric oxygen atom was replaced by a sulfur or a methylene group to prevent hydrolysis by intestinal glycosidases, and chemical groups were attached at the end of the alkyl tail. Importantly, a lead compound was shown to reduce AIEC levels in the feces, colonic and ileal mucosa after oral administration in a transgenic mouse model of CD. The compound showed a preferable low bioavailability suggesting the possibility of setting up an innovative antiadhesive therapy for CD patients in which AIEC play a key role, with the water-soluble and non-cytotoxic FimH, antagonists developed here.

Acta crystallographica. Section F, Structural biology communications, 2014

Type-2 isopentenyl diphosphate isomerase (IDI-2) is a key flavoprotein involved in the biosynthes... more Type-2 isopentenyl diphosphate isomerase (IDI-2) is a key flavoprotein involved in the biosynthesis of isoprenoids. Since fully reduced flavin mononucleotide (FMNH2) is needed for activity, it was decided to crystallize the enzyme under anaerobic conditions in order to understand how this reduced cofactor binds within the active site and interacts with the substrate isopentenyl diphosphate (IPP). In this study, the protein was expressed and purified under aerobic conditions and then reduced and crystallized under anaerobic conditions. Crystals grown by the sitting-drop vapour-diffusion method and then soaked with IPP diffracted to 2.1 Å resolution and belonged to the hexagonal space group P6322, with unit-cell parameters a = b = 133.3, c = 172.9 Å.

Journal of Medicinal Chemistry, 2005

The synthesis and enzyme inhibitor properties of reversible type B monoamine oxidase inhibitors a... more The synthesis and enzyme inhibitor properties of reversible type B monoamine oxidase inhibitors are described. These compounds belong to the 5H-indeno[1,2-c]pyridazine family and possess a hydrophobic benzyloxy or 4,4,4-trifluorobutoxy side chain which, in contrast to a previous assignment, has been unambiguously located at C(8) of the heterocyclic moiety. Investigation of the regioisomeric structures establishes that substitution of the 5H-indeno[1,2-c]pyridazin-5-one core at C(7) vs C(8) dramatically influences the MAO-inhibiting properties of these compounds.

Acta crystallographica Section B, Structural science, crystal engineering and materials, 2015

Heme oxygenase-1 (HO-1) inhibition is associated with antitumor activity. Imidazole-based analogu... more Heme oxygenase-1 (HO-1) inhibition is associated with antitumor activity. Imidazole-based analogues show effective and selective inhibitory potency of HO-1. In this work, five single-crystal structures of four imidazole-based compounds are presented, with an in-depth structural analysis. In order to study the influence of the conformation of the ligands on binding to protein, conformational data from crystallography are compared with quantum mechanics analysis and molecular docking studies. Molecular docking of imidazole-based analogues in the active site of HO-1 is in good agreement with the experimental structures. Inhibitors interact with the heme cofactor and a hydrophobic pocket (Met34, Phe37, Val50, Leu147 and Phe214) in the HO-1 binding site. An alternate binding mode can be hypothesized for some inhibitors in the series.

Journal of Biological Chemistry, 2015

The two-component sensory transduction system BvgAS controls the virulence regulon of the whoopin... more The two-component sensory transduction system BvgAS controls the virulence regulon of the whooping-cough agent Bordetella pertussis. The periplasmic moiety of the homo-dimeric sensor-kinase BvgS is composed of four bilobed Venus flytrap (VFT) perception domains followed by α helices that extend into the cytoplasmic membrane. In the virulent phase, the default state of B. pertussis, the cytoplasmic enzymatic moiety of BvgS acts as kinase by autophosphorylating and transferring the phosphoryl group to the response regulator BvgA. In laboratory conditions, BvgS shifts to phosphatase activity in response to modulators, notably nicotinate ions. Here, we characterized the effects of nicotinate and related modulators on the BvgS periplasmic moiety by using site-directed mutagenesis, and in silico and biophysical approaches. Modulators bind with low affinity to BvgS in the VFT2 cavity. Electron paramagnetic resonance shows that their binding globally affects the conformation and dynamics of the periplasmic moiety. Specific amino acid substitutions designed to slacken interactions within and between the VFT lobes prevent BvgS from responding to nicotinate, showing that BvgS shifts from kinase to phosphatase activity in response to this modulator via a tense transition state that involves a large periplasmic structural block. We propose that this transition enables the transmembrane helices to adopt a distinct conformation that sets the cytoplasmic enzymatic moiety in the phosphatase mode. The bona fide, in vivo VFT ligands that remain to be identified are likely to trigger similar effects on the transmembrane and cytoplasmic moieties. This mechanism may be relevant to the other VFT-containing sensor-kinases homologous to BvgS.

Current enzyme inhibition, 2011

Isoprenoid compounds constitute an immensely diverse group of acyclic, monocyclic and polycyclic ... more Isoprenoid compounds constitute an immensely diverse group of acyclic, monocyclic and polycyclic compounds that play important roles in all living organisms. Despite the diversity of their structures, this plethora of natural products arises from only two 5-carbon precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). This review will discuss the enzymes in the mevalonate (MVA) and methylerythritol phosphate (MEP) biosynthetic pathways leading to IPP and DMAPP with a particular focus on MEP synthase (DXR) and IPP isomerase (IDI), which are potential targets for the development of antibiotic compounds. DXR is the second enzyme in the MEP pathway and the only one for which inhibitors with antimicrobial activity at pharmaceutically relevant concentrations are known. All of the published DXR inhibitors are fosmidomycin analogues, except for a few bisphosphonates with moderate inhibitory activity. These far, there are no other candidates that target DXR. IDI was...

ChemBioChem, 2014

Isopentenyl diphosphate isomerase (IDI) is a key enzyme in the isoprenoid biosynthetic pathway an... more Isopentenyl diphosphate isomerase (IDI) is a key enzyme in the isoprenoid biosynthetic pathway and is required for all organisms that synthesize isoprenoid metabolites from mevalonate. Type 1 IDI (IDI-1) is a metalloprotein that is found in eukaryotes, whereas the type 2 isoform (IDI-2) is a flavoenzyme found in bacteria that is completely absent from human. IDI-2 from the pathogenic bacterium Streptococcus pneumoniae was recombinantly expressed in Escherichia coli. Steady-state kinetic studies of the enzyme indicated that FMNH2 (KM =0.3 μM) bound before isopentenyl diphosphate (KM =40 μM) in an ordered binding mechanism. An X-ray crystal structure at 1.4 Å resolution was obtained for the holoenzyme in the closed conformation with a reduced flavin cofactor and two sulfate ions in the active site. These results helped to further approach the enzymatic mechanism of IDI-2 and, thus, open new possibilities for the rational design of antibacterial compounds against sequence-similar and structure-related pathogens such as Enterococcus faecalis or Staphylococcus aureus.

The Journal of Physical Chemistry C, 2014

ABSTRACT The origin and the nature of the first hyperpolarizability of collagen has been unravele... more ABSTRACT The origin and the nature of the first hyperpolarizability of collagen has been unraveled by performing first-principles calculations on the PPG10 compound, a molecular model for the collagen triple helix structure, and on its building blocks. The first hyperpolarizability of the triple helix originates from the amide groups. Owing to the rigidity of the structure and of the proline units, the β-tensor components parallel to the helical axis add to each other, whereas the perpendicular components cancel each other, which result in a dipolar first hyperpolarizability and a depolarization ratio close to 9. The calculations have also shown that the resulting β values cannot be viewed as the simple sum of the amide group contributions. Indeed, for a given chain, the β per amino acid increases with the size of the chain, whereas the β of the triple helix is smaller than three times the β of a single chain. The calculations, performed at different levels of approximation, demonstrated also the reliability of the ONIOM scheme when combining high and low layers described with different basis sets and the weak impact of electron correlation.

The Journal of Physical Chemistry B, 2010

Using the SIBFA polarizable molecular mechanics procedure, we analyze the binding energy of a bim... more Using the SIBFA polarizable molecular mechanics procedure, we analyze the binding energy of a bimetallic Mg(II)/Zn(II) enzyme, isopentenyl diphosphate isomerase, to an inhibitor built up of a trianionic diphosphate and of a cationic ethyldimethylammonium (EDMA) moiety. The analyses are performed on the protein recognition site, which totals 13 residues, as well as on some "mutants" in which one selected residue is removed at a time. They are also carried out for the individual recognition sites, namely, EDMA, Mg(II), and Zn(II). Comparisons are done with ab initio quantum chemistry (QC) results on all considered sites, with different basis sets and at different levels of correlation. The SIBFA computations reproduce the evolutions of the QC interaction energies in the recognition site and its "mutants". For such sites, small (<2-3%) relative errors are found after the BSSE correction is done. Such close agreements can conceal, however, some shortcomings found in the individual binding sites, which QC energy decomposition analyses can identify. Figure 1. Representation of (a) the three-dimensional structure of IDI and (b) the molecular structure of the NIPP inhibitor.

Proteins: Structure, Function, and Bioinformatics, 2007

In the first step of this study, type 2 isopentenyl diphosphate isomerase (IDI2) from Pyrococcus ... more In the first step of this study, type 2 isopentenyl diphosphate isomerase (IDI2) from Pyrococcus furiosus (pf-IDI2), a hyperthermophilic microorganism, was cloned and overexpressed in E. coli. After purification, hyperthermophilic behavior of this protein was approached by means of enzymatic assays and thermal denaturation studies. Compared with the mesophilic Streptococcus pneumoniae IDI2, which unfolds and looses activity above 50 degrees C, pf-IDI2 is still folded and active at 80 degrees C. Molecular modeling was applied, in a parallel step, to understand the molecular basis of thermal stability. Comparison of IDI2 from S. pneumoniae, T. thermophilus, and P. furiosus suggested that additional charged residues present in the hyperthermophilic enzyme might contribute to its higher thermal stability. This could increase the number of salt bridges between monomers of IDI2 in P. furiosus enzyme and, hence, decrease flexibility of loops or N-terminal segment, thereby enhancing its thermal stability.

Journal of Medicinal Chemistry, 2005

The synthesis and enzyme inhibitor properties of reversible type B monoamine oxidase inhibitors a... more The synthesis and enzyme inhibitor properties of reversible type B monoamine oxidase inhibitors are described. These compounds belong to the 5H-indeno[1,2-c]pyridazine family and possess a hydrophobic benzyloxy or 4,4,4-trifluorobutoxy side chain which, in contrast to a previous assignment, has been unambiguously located at C(8) of the heterocyclic moiety. Investigation of the regioisomeric structures establishes that substitution of the 5H-indeno[1,2-c]pyridazin-5-one core at C(7) vs C(8) dramatically influences the MAO-inhibiting properties of these compounds.

Journal of Biological Chemistry, 2006

Isopentenyl-diphosphate (IPP):dimethylallyl diphosphate isomerase is a key enzyme in the biosynth... more Isopentenyl-diphosphate (IPP):dimethylallyl diphosphate isomerase is a key enzyme in the biosynthesis of isoprenoids. The mechanism of the isomerization reaction involves protonation of the unactivated carbon-carbon double bond in the substrate, but identity of the acidic moiety providing the proton is still not clear. Multiple sequence alignments and geometrical features observed in crystal structures of complexes with IPP isomerase suggest that Tyr-104 could play an important role during catalysis. A series of mutants was constructed by directed mutagenesis and characterized by enzymology. Crystallographic and thermal denaturation data for Y104A and Y104F mutants were obtained. Those data demonstrate the importance of residue Tyr-104 for proper folding of Escherichia coli type I IPP isomerase.

Current Protein & Peptide Science, 2008

Biosynthesis of the universal terpenoid precursors, isopentenyl diphosphate (IPP) and dimethylall... more Biosynthesis of the universal terpenoid precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), from three acetyl CoA moieties through mevalonate was studied extensively in the 1950s. For several decades, the mevalonate paradigm reigned supreme and a mevalonate origin was attributed to a growing number of natural products, in many cases erroneously. Besides this biosynthetic pathway, the existence of a second one leading to IPP and DMAPP through 1-deoxy-D-xylulose 5-phosphate and 2C-methyl-D-erythritol 4-phosphate was discovered more recently in plants and some eubacteria. This pathway is widely distributed in the bacterial kingdom including major human pathogens, such as Mycobacterium tuberculosis or Helicobacter pylori and is also essential in the malaria vector Plasmodium falciparum. During the last few years, the genes, enzymes, intermediates and mechanisms of the biosynthetic route have been elucidated by a combination of methods including comparative genomics, enzymology, advanced NMR technology and crystallography. The present crystallographic review of enzymes involved in isoprenoid biosynthesis will be useful for understanding the various catalytic mechanisms and could potentially help for structure-based drug design.

Chemical Physics Letters, 2007

The spectrophotometric evaluation of NAD(P) dehydrogenase enzymatic activity is very popular as t... more The spectrophotometric evaluation of NAD(P) dehydrogenase enzymatic activity is very popular as the reduced form (NAD(P)H) absorbs at 340nm, while the aromatic oxidised form does not. In this joint theoretical and experimental investigation, we identify the chromophoric unit of both the NAD(P)+ and NAD(P)H forms. Rather than a modification of size or shape of the frontier orbitals, the sharp variation

Biochemistry, 2008

The N-terminal region is stabilized in the crystal structure of Thermus thermophilus type 2 isope... more The N-terminal region is stabilized in the crystal structure of Thermus thermophilus type 2 isopentenyl diphosphate isomerase in complex with inorganic pyrophosphate, providing new insights about the active site and the catalytic mechanism of the enzyme. The PP i moiety is located near the conserved residues, H10, R97, H152, Q157, E158, and W219, and the flavin cofactor. The putative active site of isopentenyl diphosphate isomerase 2 provides interactions for stabilizing a carbocationic intermediate similar to those that stabilize the intermediate in the well-established protonationdeprotonation mechanism of isopentenyl diphosphate isomerase 1.

Acta Crystallographica Section F Structural Biology and Crystallization Communications, 2008

Type 1 isopentenyl diphosphate isomerase (IDI-1) has been crystallized in a new crystal form. Aft... more Type 1 isopentenyl diphosphate isomerase (IDI-1) has been crystallized in a new crystal form. After data collection from small thin needle-shaped crystals, a new monoclinic form of the studied protein was identified. In this article, the three crystal forms of IDI-1 (orthorhombic, monoclinic and trigonal) are compared.

Acta Crystallographica Section E Structure Reports Online, 2005

Acta Crystallographica Section E Structure Reports Online, 2006

Type 1 isopentenyl diphosphate isomerase has been crystallized in a new crystal form.

Chembiochem : a European journal of chemical biology, Jan 4, 2016

Recently, we extended the anti-adhesive concept showing that potent FimH antagonists can block th... more Recently, we extended the anti-adhesive concept showing that potent FimH antagonists can block the attachment of adherent-invasive E. coli (AIEC) colonizing the intestinal mucosa of patients with Crohn's disease (CD). In this work, we designed a small library of analogs of heptylmannoside (HM), a previously identified nanomolar FimH inhibitor, but displaying poor in vivo anti-adhesive effects. The anomeric oxygen atom was replaced by a sulfur or a methylene group to prevent hydrolysis by intestinal glycosidases, and chemical groups were attached at the end of the alkyl tail. Importantly, a lead compound was shown to reduce AIEC levels in the feces, colonic and ileal mucosa after oral administration in a transgenic mouse model of CD. The compound showed a preferable low bioavailability suggesting the possibility of setting up an innovative antiadhesive therapy for CD patients in which AIEC play a key role, with the water-soluble and non-cytotoxic FimH, antagonists developed here.