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Caradec T, Anoz-Carbonell E, Petrov R, Billamboz M, Antraygues K, Cantrelle FX, Boll E, Beury D, Hot D, Drobecq H, Trivelli X, Hartkoorn RC. A Novel Natural Siderophore Antibiotic Conjugate Reveals a Chemical Approach to Macromolecule Coupling. ACS Cent Sci 2023; 9:2138-2149. [PMID: 38033789 PMCID: PMC10683483 DOI: 10.1021/acscentsci.3c00965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/13/2023] [Accepted: 10/13/2023] [Indexed: 12/02/2023]
Abstract
Inspired by natural sideromycins, the conjugation of antibiotics to siderophores is an attractive strategy to facilitate "Trojan horse" delivery of antibiotics into bacteria. Genome analysis of a soil bacterium, Dactylosporangium fulvum, found a "hybrid" biosynthetic gene cluster responsible for the production of both an antibiotic, pyridomycin, and a novel chlorocatechol-containing siderophore named chlorodactyloferrin. While both of these natural products were synthesized independently, analysis of the culture supernatant also identified a conjugate of both molecules. We then found that the addition of ferric iron to purified chlorodactyloferrin and pyridomycin instigated their conjugation, leading to the formation of a covalent bond between the siderophore-catechol and the pyridomycin-pyridine groups. Using model reactants, this iron-based reaction was found to proceed through a Michael-type addition reaction, where ferric iron oxidizes the siderophore-catechol group into its quinone form, which is then attacked by the antibiotic pyridyl-nitrogen to form the catechol-pyridinium linkage. These findings prompted us to explore if other "cargo" molecules could be attached to chlorodactyloferrin in a similar manner, and this was indeed confirmed with a pyridine-substituted TAMRA fluorophore as well as with pyridine-substituted penicillin, rifampicin, and norfloxacin antibiotic analogues. The resultant biomimetic conjugates were demonstrated to effectively enter a number of bacteria, with TAMRA-chlorodactyloferrin conjugates causing fluorescent labeling of the bacteria, and with penicillin and rifampicin conjugates eliciting antibiotic activity. These findings open up new opportunities for the design and facile synthesis of a novel class of biomimetic siderophore conjugates with antibiotic activity.
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Affiliation(s)
- Thibault Caradec
- Université
Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019 - UMR 9017 - CIIL - Center for Infection and
Immunity of Lille, F-59000 Lille, France
| | - Ernesto Anoz-Carbonell
- Université
Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019 - UMR 9017 - CIIL - Center for Infection and
Immunity of Lille, F-59000 Lille, France
| | - Ravil Petrov
- Université
Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019 - UMR 9017 - CIIL - Center for Infection and
Immunity of Lille, F-59000 Lille, France
| | - Muriel Billamboz
- Université
Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related
Diseases, F-59000 Lille, France
- JUNIA,
Health and Environment, Laboratory of Sustainable
Chemistry and Health, F-59000 Lille, France
| | - Kevin Antraygues
- Université
Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Francois-Xavier Cantrelle
- Université
Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related
Diseases, F-59000 Lille, France
- CNRS, EMR9002
BSI Integrative Structural Biology, 59000 Lille, France
| | - Emmanuelle Boll
- Université
Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related
Diseases, F-59000 Lille, France
- CNRS, EMR9002
BSI Integrative Structural Biology, 59000 Lille, France
| | - Delphine Beury
- Université
Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR2014 - US41 - PLBS-Plateformes Lilloises de Biologie
& Santé, F-59000 Lille, France
| | - David Hot
- Université
Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR2014 - US41 - PLBS-Plateformes Lilloises de Biologie
& Santé, F-59000 Lille, France
| | - Herve Drobecq
- Université
Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019 - UMR 9017 - CIIL - Center for Infection and
Immunity of Lille, F-59000 Lille, France
| | - Xavier Trivelli
- Université
Lille, CNRS, INRAE, Centrale Lille, Université d’Artois, FR 2638 - IMEC - Institut Michel-Eugène Chevreul, 59000 Lille, France
| | - Ruben C. Hartkoorn
- Université
Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019 - UMR 9017 - CIIL - Center for Infection and
Immunity of Lille, F-59000 Lille, France
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2
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Pacheco-Garcia JL, Anoz-Carbonell E, Loginov DS, Vankova P, Salido E, Man P, Medina M, Palomino-Morales R, Pey AL. Different phenotypic outcome due to site-specific phosphorylation in the cancer-associated NQO1 enzyme studied by phosphomimetic mutations. Arch Biochem Biophys 2022; 729:109392. [PMID: 36096178 DOI: 10.1016/j.abb.2022.109392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 08/29/2022] [Accepted: 08/31/2022] [Indexed: 11/02/2022]
Abstract
Protein phosphorylation is a common phenomenon in human flavoproteins although the functional consequences of this site-specific modification are largely unknown. Here, we evaluated the effects of site-specific phosphorylation (using phosphomimetic mutations at sites S40, S82 and T128) on multiple functional aspects as well as in the structural stability of the antioxidant and disease-associated human flavoprotein NQO1 using biophysical and biochemical methods. In vitro biophysical studies revealed effects of phosphorylation at different sites such as decreased binding affinity for FAD and structural stability of its binding site (S82), conformational stability (S40 and S82) and reduced catalytic efficiency and functional cooperativity (T128). Local stability measurements by H/D exchange in different ligation states provided structural insight into these effects. Transfection of eukaryotic cells showed that phosphorylation at sites S40 and S82 may reduce steady-levels of NQO1 protein by enhanced proteasome-induced degradation. We show that site-specific phosphorylation of human NQO1 may cause pleiotropic and counterintuitive effects on this multifunctional protein with potential implications for its relationships with human disease. Our approach allows to establish relationships between site-specific phosphorylation, functional and structural stability effects in vitro and inside cells paving the way for more detailed analyses of phosphorylation at the flavoproteome scale.
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Affiliation(s)
- Juan Luis Pacheco-Garcia
- Departamento de Química Física, Universidad de Granada, Av. Fuentenueva s/n, 18071, Granada, Spain
| | - Ernesto Anoz-Carbonell
- Departamento de Bioquímica y Biología Molecular y Cellular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) (GBsC-CSIC Joint Unit), Universidad de Zaragoza, 50009, Zaragoza, Spain
| | - Dmitry S Loginov
- Institute of Microbiology - BioCeV, Academy of Sciences of the Czech Republic, Prumyslova 595, Vestec, 252 50, Czech Republic
| | - Pavla Vankova
- Institute of Biotechnology - BioCeV, Academy of Sciences of the Czech Republic, Prumyslova 595, Vestec, 252 50, Czech Republic
| | - Eduardo Salido
- Center for Rare Diseases (CIBERER), Hospital Universitario de Canarias, Universidad de la Laguna, 38320, Tenerife, Spain
| | - Petr Man
- Institute of Microbiology - BioCeV, Academy of Sciences of the Czech Republic, Prumyslova 595, Vestec, 252 50, Czech Republic
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Cellular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) (GBsC-CSIC Joint Unit), Universidad de Zaragoza, 50009, Zaragoza, Spain
| | - Rogelio Palomino-Morales
- Department of Biochemistry and Molecular Biology I, Faculty of Sciences and Biomedical Research Center (CIBM), University of Granada, Granada, Spain
| | - Angel L Pey
- Departamento de Química Física, Unidad de Excelencia en Química Aplicada a Biomedicina y Medioambiente e Instituto de Biotecnología, Universidad de Granada, Av. Fuentenueva s/n, 18071, Granada, Spain.
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3
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Pacheco-Garcia JL, Loginov DS, Anoz-Carbonell E, Vankova P, Palomino-Morales R, Salido E, Man P, Medina M, Naganathan AN, Pey AL. Allosteric Communication in the Multifunctional and Redox NQO1 Protein Studied by Cavity-Making Mutations. Antioxidants (Basel) 2022; 11:antiox11061110. [PMID: 35740007 PMCID: PMC9219786 DOI: 10.3390/antiox11061110] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/28/2022] [Accepted: 05/30/2022] [Indexed: 02/01/2023] Open
Abstract
Allosterism is a common phenomenon in protein biochemistry that allows rapid regulation of protein stability; dynamics and function. However, the mechanisms by which allosterism occurs (by mutations or post-translational modifications (PTMs)) may be complex, particularly due to long-range propagation of the perturbation across protein structures. In this work, we have investigated allosteric communication in the multifunctional, cancer-related and antioxidant protein NQO1 by mutating several fully buried leucine residues (L7, L10 and L30) to smaller residues (V, A and G) at sites in the N-terminal domain. In almost all cases, mutated residues were not close to the FAD or the active site. Mutations L→G strongly compromised conformational stability and solubility, and L30A and L30V also notably decreased solubility. The mutation L10A, closer to the FAD binding site, severely decreased FAD binding affinity (≈20 fold vs. WT) through long-range and context-dependent effects. Using a combination of experimental and computational analyses, we show that most of the effects are found in the apo state of the protein, in contrast to other common polymorphisms and PTMs previously characterized in NQO1. The integrated study presented here is a first step towards a detailed structural–functional mapping of the mutational landscape of NQO1, a multifunctional and redox signaling protein of high biomedical relevance.
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Affiliation(s)
- Juan Luis Pacheco-Garcia
- Departamento de Química Física, Universidad de Granada, Av. Fuentenueva s/n, 18071 Granada, Spain
- Correspondence: (J.L.P.-G.); (A.L.P.); Tel.: +34-958243173 (A.L.P.)
| | - Dmitry S. Loginov
- Institute of Microbiology—BioCeV, Academy of Sciences of the Czech Republic, Prumyslova 595, 252 50 Vestec, Czech Republic; (D.S.L.); (P.M.)
| | - Ernesto Anoz-Carbonell
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) (GBsC-CSIC Joint Unit), Universidad de Zaragoza, 50009 Zaragoza, Spain; (E.A.-C.); (M.M.)
| | - Pavla Vankova
- Institute of Biotechnology—BioCeV, Academy of Sciences of the Czech Republic, Prumyslova 595, 252 50 Vestec, Czech Republic;
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 128 43 Prague, Czech Republic
| | - Rogelio Palomino-Morales
- Departamento de Bioquímica y Biología Molecular I, Facultad de Ciencias y Centro de Investigaciones Biomédicas (CIBM), Universidad de Granada, 18016 Granada, Spain;
| | - Eduardo Salido
- Center for Rare Diseases (CIBERER), Hospital Universitario de Canarias, Universidad de la Laguna, 38320 Tenerife, Spain;
| | - Petr Man
- Institute of Microbiology—BioCeV, Academy of Sciences of the Czech Republic, Prumyslova 595, 252 50 Vestec, Czech Republic; (D.S.L.); (P.M.)
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) (GBsC-CSIC Joint Unit), Universidad de Zaragoza, 50009 Zaragoza, Spain; (E.A.-C.); (M.M.)
| | - Athi N. Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras (IITM), Chennai 600036, India;
| | - Angel L. Pey
- Departamento de Química Física, Unidad de Excelencia en Química Aplicada a Biomedicina y Medioambiente e Instituto de Biotecnología, Universidad de Granada, Av. Fuentenueva s/n, 18071 Granada, Spain
- Correspondence: (J.L.P.-G.); (A.L.P.); Tel.: +34-958243173 (A.L.P.)
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4
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Moreno A, Taleb V, Sebastián M, Anoz-Carbonell E, Martínez-Júlvez M, Medina M. Cofactors and pathogens: Flavin mononucleotide and flavin adenine dinucleotide (FAD) biosynthesis by the FAD synthase from Brucella ovis. IUBMB Life 2021; 74:655-671. [PMID: 34813144 PMCID: PMC9299109 DOI: 10.1002/iub.2576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/14/2021] [Accepted: 10/26/2021] [Indexed: 02/02/2023]
Abstract
The biosynthesis of the flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), cofactors used by 2% of proteins, occurs through the sequential action of two ubiquitous activities: a riboflavinkinase (RFK) that phosphorylates the riboflavin (RF) precursor to FMN, and a FMN:adenylyltransferase (FMNAT) that transforms FMN into FAD. In most mammals two different monofunctional enzymes have each of these activities, but in prokaryotes a single bifunctional enzyme, FAD synthase (FADS), holds them. Differential structural and functional traits for RFK and FMNAT catalysis between bacteria and mammals, as well as within the few bacterial FADSs so far characterized, has envisaged the potentiality of FADSs from pathogens as targets for the development of species‐specific inhibitors. Here, we particularly characterize the FADS from the ovine pathogen Brucella ovis (BoFADS), causative agent of brucellosis. We show that BoFADS has RFK activity independently of the media redox status, but its FMNAT activity (in both forward and reverse senses) only occurs under strong reducing conditions. Moreover, kinetics for flavin and adenine nucleotides binding to the RFK site show that BoFADS binds preferentially the substrates of the RFK reaction over the products and that the adenine nucleotide must bind prior to flavin entrapment. These results, together with multiple sequence alignments and phylogenetic analysis, point to variability in the less conserved regions as contributing to the species‐specific features in prokaryotic FADSs, including those from pathogens, that allow them to adopt alternative strategies in FMN and FAD biosynthesis and overall flavin homeostasis.
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Affiliation(s)
- Andrea Moreno
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos, BIFI (GBsC-CSIC Joint Unit), Universidad de Zaragoza, Zaragoza, Spain.,Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida, Venezuela
| | - Victor Taleb
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos, BIFI (GBsC-CSIC Joint Unit), Universidad de Zaragoza, Zaragoza, Spain
| | - María Sebastián
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos, BIFI (GBsC-CSIC Joint Unit), Universidad de Zaragoza, Zaragoza, Spain
| | - Ernesto Anoz-Carbonell
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos, BIFI (GBsC-CSIC Joint Unit), Universidad de Zaragoza, Zaragoza, Spain
| | - Marta Martínez-Júlvez
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos, BIFI (GBsC-CSIC Joint Unit), Universidad de Zaragoza, Zaragoza, Spain
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos, BIFI (GBsC-CSIC Joint Unit), Universidad de Zaragoza, Zaragoza, Spain
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5
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Pacheco-Garcia JL, Anoz-Carbonell E, Vankova P, Kannan A, Palomino-Morales R, Mesa-Torres N, Salido E, Man P, Medina M, Naganathan AN, Pey AL. Structural basis of the pleiotropic and specific phenotypic consequences of missense mutations in the multifunctional NAD(P)H:quinone oxidoreductase 1 and their pharmacological rescue. Redox Biol 2021; 46:102112. [PMID: 34537677 PMCID: PMC8455868 DOI: 10.1016/j.redox.2021.102112] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/21/2021] [Accepted: 08/17/2021] [Indexed: 10/31/2022] Open
Abstract
The multifunctional nature of human flavoproteins is critically linked to their ability to populate multiple conformational states. Ligand binding, post-translational modifications and disease-associated mutations can reshape this functional landscape, although the structure-function relationships of these effects are not well understood. Herein, we characterized the structural and functional consequences of two mutations (the cancer-associated P187S and the phosphomimetic S82D) on different ligation states which are relevant to flavin binding, intracellular stability and catalysis of the disease-associated NQO1 flavoprotein. We found that these mutations affected the stability locally and their effects propagated differently through the protein structure depending both on the nature of the mutation and the ligand bound, showing directional preference from the mutated site and leading to specific phenotypic manifestations in different functional traits (FAD binding, catalysis and inhibition, intracellular stability and pharmacological response to ligands). Our study thus supports that pleitropic effects of disease-causing mutations and phosphorylation events on human flavoproteins may be caused by long-range structural propagation of stability effects to different functional sites that depend on the ligation-state and site-specific perturbations. Our approach can be of general application to investigate these pleiotropic effects at the flavoproteome scale in the absence of high-resolution structural models.
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Affiliation(s)
- Juan Luis Pacheco-Garcia
- Departamento de Química Física, Universidad de Granada, Av. Fuentenueva s/n, 18071, Granada, Spain
| | - Ernesto Anoz-Carbonell
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and Joint Unit), Universidad de Zaragoza, 50009, Zaragoza, Spain
| | - Pavla Vankova
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4, 142 20, Czech Republic; Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, Prague 2, 128 43, Czech Republic
| | - Adithi Kannan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras (IITM), Chennai, 600036, India
| | - Rogelio Palomino-Morales
- Departmento de Bioquímica y Biología Molecular I, Facultad de Ciencias y Centro de Investigaciones Biomédicas (CIBM), Universidad de Granada, Granada, Spain
| | - Noel Mesa-Torres
- Departamento de Química Física, Universidad de Granada, Av. Fuentenueva s/n, 18071, Granada, Spain
| | - Eduardo Salido
- Center for Rare Diseases (CIBERER), Hospital Universitario de Canarias, Universidad de la Laguna, 38320, Tenerife, Spain
| | - Petr Man
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4, 142 20, Czech Republic
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and Joint Unit), Universidad de Zaragoza, 50009, Zaragoza, Spain
| | - Athi N Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras (IITM), Chennai, 600036, India
| | - Angel L Pey
- Departamento de Química Física, Unidad de Excelencia en Química Aplicada a Biomedicina y Medioambiente e Instituto de Biotecnología, Universidad de Granada, Av. Fuentenueva s/n, 18071, Granada, Spain.
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6
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Salillas S, Galano-Frutos JJ, Mahía A, Maity R, Conde-Giménez M, Anoz-Carbonell E, Berlamont H, Velazquez-Campoy A, Touati E, Mamat U, Schaible UE, Gálvez JA, Díaz-de-Villegas MD, Haesebrouck F, Aínsa JA, Sancho J. Selective Targeting of Human and Animal Pathogens of the Helicobacter Genus by Flavodoxin Inhibitors: Efficacy, Synergy, Resistance and Mechanistic Studies. Int J Mol Sci 2021; 22:ijms221810137. [PMID: 34576300 PMCID: PMC8467567 DOI: 10.3390/ijms221810137] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 02/08/2023] Open
Abstract
Antimicrobial resistant (AMR) bacteria constitute a global health concern. Helicobacter pylori is a Gram-negative bacterium that infects about half of the human population and is a major cause of peptic ulcer disease and gastric cancer. Increasing resistance to triple and quadruple H. pylori eradication therapies poses great challenges and urges the development of novel, ideally narrow spectrum, antimicrobials targeting H. pylori. Here, we describe the antimicrobial spectrum of a family of nitrobenzoxadiazol-based antimicrobials initially discovered as inhibitors of flavodoxin: an essential H. pylori protein. Two groups of inhibitors are described. One group is formed by narrow-spectrum compounds, highly specific for H. pylori, but ineffective against enterohepatic Helicobacter species and other Gram-negative or Gram-positive bacteria. The second group includes extended-spectrum antimicrobials additionally targeting Gram-positive bacteria, the Gram-negative Campylobacter jejuni, and most Helicobacter species, but not affecting other Gram-negative pathogens. To identify the binding site of the inhibitors in the flavodoxin structure, several H. pylori-flavodoxin variants have been engineered and tested using isothermal titration calorimetry. An initial study of the inhibitors capacity to generate resistances and of their synergism with antimicrobials commonly used in H. pylori eradication therapies is described. The narrow-spectrum inhibitors, which are expected to affect the microbiota less dramatically than current antimicrobial drugs, offer an opportunity to develop new and specific H. pylori eradication combinations to deal with AMR in H. pylori. On the other hand, the extended-spectrum inhibitors constitute a new family of promising antimicrobials, with a potential use against AMR Gram-positive bacterial pathogens.
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Affiliation(s)
- Sandra Salillas
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, 50018 Zaragoza, Spain; (S.S.); (J.J.G.-F.); (A.M.); (R.M.); (M.C.-G.); (E.A.-C.); (A.V.-C.); (J.A.A.)
- Departamento de Bioquímica y Biología Molecular y Celular, Faculty of Science, University of Zaragoza, 50009 Zaragoza, Spain
- Aragon Health Research Institute (IIS Aragón), 50009 Zaragoza, Spain
| | - Juan José Galano-Frutos
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, 50018 Zaragoza, Spain; (S.S.); (J.J.G.-F.); (A.M.); (R.M.); (M.C.-G.); (E.A.-C.); (A.V.-C.); (J.A.A.)
- Departamento de Bioquímica y Biología Molecular y Celular, Faculty of Science, University of Zaragoza, 50009 Zaragoza, Spain
- Aragon Health Research Institute (IIS Aragón), 50009 Zaragoza, Spain
| | - Alejandro Mahía
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, 50018 Zaragoza, Spain; (S.S.); (J.J.G.-F.); (A.M.); (R.M.); (M.C.-G.); (E.A.-C.); (A.V.-C.); (J.A.A.)
- Departamento de Bioquímica y Biología Molecular y Celular, Faculty of Science, University of Zaragoza, 50009 Zaragoza, Spain
- Aragon Health Research Institute (IIS Aragón), 50009 Zaragoza, Spain
| | - Ritwik Maity
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, 50018 Zaragoza, Spain; (S.S.); (J.J.G.-F.); (A.M.); (R.M.); (M.C.-G.); (E.A.-C.); (A.V.-C.); (J.A.A.)
- Departamento de Bioquímica y Biología Molecular y Celular, Faculty of Science, University of Zaragoza, 50009 Zaragoza, Spain
- Aragon Health Research Institute (IIS Aragón), 50009 Zaragoza, Spain
| | - María Conde-Giménez
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, 50018 Zaragoza, Spain; (S.S.); (J.J.G.-F.); (A.M.); (R.M.); (M.C.-G.); (E.A.-C.); (A.V.-C.); (J.A.A.)
- Departamento de Bioquímica y Biología Molecular y Celular, Faculty of Science, University of Zaragoza, 50009 Zaragoza, Spain
- Aragon Health Research Institute (IIS Aragón), 50009 Zaragoza, Spain
| | - Ernesto Anoz-Carbonell
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, 50018 Zaragoza, Spain; (S.S.); (J.J.G.-F.); (A.M.); (R.M.); (M.C.-G.); (E.A.-C.); (A.V.-C.); (J.A.A.)
- Departamento de Bioquímica y Biología Molecular y Celular, Faculty of Science, University of Zaragoza, 50009 Zaragoza, Spain
- Departamento de Microbiología, Pediatría, Radiología y Salud Pública, Faculty of Medicine, University of Zaragoza, 50009 Zaragoza, Spain
| | - Helena Berlamont
- Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B9820 Merelbeke, Belgium; (H.B.); (F.H.)
| | - Adrian Velazquez-Campoy
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, 50018 Zaragoza, Spain; (S.S.); (J.J.G.-F.); (A.M.); (R.M.); (M.C.-G.); (E.A.-C.); (A.V.-C.); (J.A.A.)
- Departamento de Bioquímica y Biología Molecular y Celular, Faculty of Science, University of Zaragoza, 50009 Zaragoza, Spain
- Aragon Health Research Institute (IIS Aragón), 50009 Zaragoza, Spain
- ARAID Foundation, Government of Aragon, 50018 Zaragoza, Spain
- CIBER de Enfermedades Hepáticas y Digestivas CIBERehd, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Eliette Touati
- Unit of Helicobacter Pathogenesis, CNRS UMR2001, Department of Microbiology, Institut Pasteur, 25-28 Rue du Dr. Roux, 75724 Paris, France;
| | - Uwe Mamat
- Cellular Microbiology, Program Area Infections, Research Center Borstel, Leibniz Lung Center, 23845 Borstel, Germany; (U.M.); (U.E.S.)
| | - Ulrich E. Schaible
- Cellular Microbiology, Program Area Infections, Research Center Borstel, Leibniz Lung Center, 23845 Borstel, Germany; (U.M.); (U.E.S.)
| | - José A. Gálvez
- Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), CSIC—Departamento de Química Orgánica, Faculty of Science, University of Zaragoza, 50009 Zaragoza, Spain; (J.A.G.); (M.D.D.-d.-V.)
| | - María D. Díaz-de-Villegas
- Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), CSIC—Departamento de Química Orgánica, Faculty of Science, University of Zaragoza, 50009 Zaragoza, Spain; (J.A.G.); (M.D.D.-d.-V.)
| | - Freddy Haesebrouck
- Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B9820 Merelbeke, Belgium; (H.B.); (F.H.)
| | - José A. Aínsa
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, 50018 Zaragoza, Spain; (S.S.); (J.J.G.-F.); (A.M.); (R.M.); (M.C.-G.); (E.A.-C.); (A.V.-C.); (J.A.A.)
- Aragon Health Research Institute (IIS Aragón), 50009 Zaragoza, Spain
- Departamento de Microbiología, Pediatría, Radiología y Salud Pública, Faculty of Medicine, University of Zaragoza, 50009 Zaragoza, Spain
- CIBER de Enfermedades Respiratorias—CIBERES, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Javier Sancho
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, 50018 Zaragoza, Spain; (S.S.); (J.J.G.-F.); (A.M.); (R.M.); (M.C.-G.); (E.A.-C.); (A.V.-C.); (J.A.A.)
- Departamento de Bioquímica y Biología Molecular y Celular, Faculty of Science, University of Zaragoza, 50009 Zaragoza, Spain
- Aragon Health Research Institute (IIS Aragón), 50009 Zaragoza, Spain
- Correspondence:
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7
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Anoz-Carbonell E, Timson DJ, Pey AL, Medina M. The Catalytic Cycle of the Antioxidant and Cancer-Associated Human NQO1 Enzyme: Hydride Transfer, Conformational Dynamics and Functional Cooperativity. Antioxidants (Basel) 2020; 9:E772. [PMID: 32825392 PMCID: PMC7554937 DOI: 10.3390/antiox9090772] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/11/2020] [Accepted: 08/18/2020] [Indexed: 12/11/2022] Open
Abstract
Human NQO1 [NAD(H):quinone oxidoreductase 1] is a multi-functional and stress-inducible dimeric protein involved in the antioxidant defense, the activation of cancer prodrugs and the stabilization of oncosuppressors. Despite its roles in human diseases, such as cancer and neurological disorders, a detailed characterization of its enzymatic cycle is still lacking. In this work, we provide a comprehensive analysis of the NQO1 catalytic cycle using rapid mixing techniques, including multiwavelength and spectral deconvolution studies, kinetic modeling and temperature-dependent kinetic isotope effects (KIEs). Our results systematically support the existence of two pathways for hydride transfer throughout the NQO1 catalytic cycle, likely reflecting that the two active sites in the dimer catalyze two-electron reduction with different rates, consistent with the cooperative binding of inhibitors such as dicoumarol. This negative cooperativity in NQO1 redox activity represents a sort of half-of-sites activity. Analysis of KIEs and their temperature dependence also show significantly different contributions from quantum tunneling, structural dynamics and reorganizations to catalysis at the two active sites. Our work will improve our understanding of the effects of cancer-associated single amino acid variants and post-translational modifications in this protein of high relevance in cancer progression and treatment.
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Affiliation(s)
- Ernesto Anoz-Carbonell
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, 50009 Zaragoza, Spain;
| | - David J. Timson
- School of Pharmacy and Biomolecular Sciences, The University of Brighton, Brighton BN2 4GJ, UK;
| | - Angel L. Pey
- Departamento de Química Física, Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, 50009 Zaragoza, Spain;
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8
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Lans I, Anoz-Carbonell E, Palacio-Rodríguez K, Aínsa JA, Medina M, Cossio P. In silico discovery and biological validation of ligands of FAD synthase, a promising new antimicrobial target. PLoS Comput Biol 2020; 16:e1007898. [PMID: 32797038 PMCID: PMC7449411 DOI: 10.1371/journal.pcbi.1007898] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 08/26/2020] [Accepted: 07/09/2020] [Indexed: 01/06/2023] Open
Abstract
New treatments for diseases caused by antimicrobial-resistant microorganisms can be developed by identifying unexplored therapeutic targets and by designing efficient drug screening protocols. In this study, we have screened a library of compounds to find ligands for the flavin-adenine dinucleotide synthase (FADS) -a potential target for drug design against tuberculosis and pneumonia- by implementing a new and efficient virtual screening protocol. The protocol has been developed for the in silico search of ligands of unexplored therapeutic targets, for which limited information about ligands or ligand-receptor structures is available. It implements an integrative funnel-like strategy with filtering layers that increase in computational accuracy. The protocol starts with a pharmacophore-based virtual screening strategy that uses ligand-free receptor conformations from molecular dynamics (MD) simulations. Then, it performs a molecular docking stage using several docking programs and an exponential consensus ranking strategy. The last filter, samples the conformations of compounds bound to the target using MD simulations. The MD conformations are scored using several traditional scoring functions in combination with a newly-proposed score that takes into account the fluctuations of the molecule with a Morse-based potential. The protocol was optimized and validated using a compound library with known ligands of the Corynebacterium ammoniagenes FADS. Then, it was used to find new FADS ligands from a compound library of 14,000 molecules. A small set of 17 in silico filtered molecules were tested experimentally. We identified five inhibitors of the activity of the flavin adenylyl transferase module of the FADS, and some of them were able to inhibit growth of three bacterial species: C. ammoniagenes, Mycobacterium tuberculosis, and Streptococcus pneumoniae, where the last two are human pathogens. Overall, the results show that the integrative VS protocol is a cost-effective solution for the discovery of ligands of unexplored therapeutic targets.
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Affiliation(s)
- Isaias Lans
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia UdeA, Medellin, Colombia
| | - Ernesto Anoz-Carbonell
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos (Unidades Asociadas BIFI-IQFR y CBsC-CSIC), Universidad de Zaragoza, Spain
- Grupo de Genética de Micobacterias, Departamento de Microbiología, Pediatría, Radiología y Salud Pública. Facultad de Medicina, Universidad de Zaragoza, Zaragoza, Spain
| | - Karen Palacio-Rodríguez
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia UdeA, Medellin, Colombia
| | - José Antonio Aínsa
- Instituto de Biocomputación y Física de Sistemas Complejos (Unidades Asociadas BIFI-IQFR y CBsC-CSIC), Universidad de Zaragoza, Spain
- Grupo de Genética de Micobacterias, Departamento de Microbiología, Pediatría, Radiología y Salud Pública. Facultad de Medicina, Universidad de Zaragoza, Zaragoza, Spain
- CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Spain
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos (Unidades Asociadas BIFI-IQFR y CBsC-CSIC), Universidad de Zaragoza, Spain
| | - Pilar Cossio
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia UdeA, Medellin, Colombia
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt, Germany
- * E-mail:
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9
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Anoz-Carbonell E, Rivero M, Polo V, Velázquez-Campoy A, Medina M. Human riboflavin kinase: Species-specific traits in the biosynthesis of the FMN cofactor. FASEB J 2020; 34:10871-10886. [PMID: 32649804 DOI: 10.1096/fj.202000566r] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 05/26/2020] [Accepted: 06/05/2020] [Indexed: 11/11/2022]
Abstract
Human riboflavin kinase (HsRFK) catalyzes vitamin B2 (riboflavin) phosphorylation to flavin mononucleotide (FMN), obligatory step in flavin cofactor synthesis. HsRFK expression is related to protection from oxidative stress, amyloid-β toxicity, and some malignant cancers progression. Its downregulation alters expression profiles of clock-controlled metabolic-genes and destroys flavins protection on stroke treatments, while its activity reduction links to protein-energy malnutrition and thyroid hormones decrease. We explored specific features of the mechanisms underlying the regulation of HsRFK activity, showing that both reaction products regulate it through competitive inhibition. Fast-kinetic studies show that despite HsRFK binds faster and preferably the reaction substrates, the complex holding both products is kinetically most stable. An intricate ligand binding landscape with all combinations of substrates/products competing with the catalytic complex and exhibiting moderate cooperativity is also presented. These data might contribute to better understanding the molecular bases of pathologies coursing with aberrant HsRFK availability, and envisage that interaction with its client-apoproteins might favor FMN release. Finally, HsRFK parameters differ from those of the so far evaluated bacterial counterparts, reinforcing the idea of species-specific mechanisms in RFK catalysis. These observations support HsRFK as potential therapeutic target because of its key functions, while also envisage bacterial RFK modules as potential antimicrobial targets.
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Affiliation(s)
- Ernesto Anoz-Carbonell
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain
| | - Maribel Rivero
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
| | - Victor Polo
- Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain.,Departamento de Química Física, Universidad de Zaragoza, Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain.,Fundación ARAID, Diputación General de Aragón, Zaragoza, Spain.,Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain.,Biomedical Research Networking Centre for Liver and Digestive Diseases (CIBERehd), Madrid, Spain
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain
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Leone P, Galluccio M, Quarta S, Anoz-Carbonell E, Medina M, Indiveri C, Barile M. Mutation of Aspartate 238 in FAD Synthase Isoform 6 Increases the Specific Activity by Weakening the FAD Binding. Int J Mol Sci 2019; 20:ijms20246203. [PMID: 31835305 PMCID: PMC6941110 DOI: 10.3390/ijms20246203] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/04/2019] [Accepted: 12/06/2019] [Indexed: 02/07/2023] Open
Abstract
FAD synthase (FADS, or FMN:ATP adenylyl transferase) coded by the FLAD1 gene is the last enzyme in the pathway of FAD synthesis. The mitochondrial isoform 1 and the cytosolic isoform 2 are characterized by the following two domains: the C-terminal PAPS domain (FADSy) performing FAD synthesis and pyrophosphorolysis; the N-terminal molybdopterin-binding domain (FADHy) performing a Co++/K+-dependent FAD hydrolysis. Mutations in FLAD1 gene are responsible for riboflavin responsive and non-responsive multiple acyl-CoA dehydrogenases and combined respiratory chain deficiency. In patients harboring frameshift mutations, a shorter isoform (hFADS6) containing the sole FADSy domain is produced representing an emergency protein. With the aim to ameliorate its function we planned to obtain an engineered more efficient hFADS6. Thus, the D238A mutant, resembling the D181A FMNAT “supermutant” of C. glabrata, was overproduced and purified. Kinetic analysis of this enzyme highlighted a general increase of Km, while the kcat was two-fold higher than that of WT. The data suggest that the FAD synthesis rate can be increased. Additional modifications could be performed to further improve the synthesis of FAD. These results correlate with previous data produced in our laboratory, and point towards the following proposals (i) FAD release is the rate limiting step of the catalytic cycle and (ii) ATP and FMN binding sites are synergistically connected.
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Affiliation(s)
- Piero Leone
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, via Orabona 4–, 70126 Bari, Italy; (P.L.); (S.Q.)
- Department of Biology, Ecology and Earth Sciences (DiBEST), Unit of Biochemistry and Molecular Biotechnology, University of Calabria, via P. Bucci 4c, 87036 Arcavacata di Rende, Italy; (M.G.); (C.I.)
| | - Michele Galluccio
- Department of Biology, Ecology and Earth Sciences (DiBEST), Unit of Biochemistry and Molecular Biotechnology, University of Calabria, via P. Bucci 4c, 87036 Arcavacata di Rende, Italy; (M.G.); (C.I.)
| | - Stefano Quarta
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, via Orabona 4–, 70126 Bari, Italy; (P.L.); (S.Q.)
| | - Ernesto Anoz-Carbonell
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, 50009 Zaragoza, Spain; (E.A.-C.); (M.M.)
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, 50009 Zaragoza, Spain; (E.A.-C.); (M.M.)
| | - Cesare Indiveri
- Department of Biology, Ecology and Earth Sciences (DiBEST), Unit of Biochemistry and Molecular Biotechnology, University of Calabria, via P. Bucci 4c, 87036 Arcavacata di Rende, Italy; (M.G.); (C.I.)
| | - Maria Barile
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, via Orabona 4–, 70126 Bari, Italy; (P.L.); (S.Q.)
- Correspondence:
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11
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Pérez-Amigot D, Taleb V, Boneta S, Anoz-Carbonell E, Sebastián M, Velázquez-Campoy A, Polo V, Martínez-Júlvez M, Medina M. Towards the competent conformation for catalysis in the ferredoxin-NADP + reductase from the Brucella ovis pathogen. Biochim Biophys Acta Bioenerg 2019; 1860:148058. [PMID: 31394095 DOI: 10.1016/j.bbabio.2019.148058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 07/19/2019] [Accepted: 08/02/2019] [Indexed: 02/02/2023]
Abstract
Brucella ovis encodes a bacterial subclass 1 ferredoxin-NADP(H) reductase (BoFPR) that, by similarity with other FPRs, is expected either to deliver electrons from NADPH to the redox-based metabolism and/or to oxidize NADPH to regulate the soxRS regulon that protects bacteria against oxidative damage. Such potential roles for the pathogen survival under infection conditions make of interest to understand and to act on the BoFPR mechanism. Here, we investigate the NADP+/H interaction and NADPH oxidation by hydride transfer (HT) to BoFPR. Crystal structures of BoFPR in free and in complex with NADP+ hardly differ. The latter shows binding of the NADP+ adenosine moiety, while its redox-reactive nicotinamide protrudes towards the solvent. Nonetheless, pre-steady-state kinetics show formation of a charge-transfer complex (CTC-1) prior to the hydride transfer, as well as conversion of CTC-1 into a second charge-transfer complex (CTC-2) concomitantly with the HT event. Thus, during catalysis nicotinamide and flavin reacting rings stack. Kinetic data also identify the HT itself as the rate limiting step in the reduction of BoFPR by NADPH, as well as product release limiting the overall reaction. Using all-atom molecular dynamics simulations with a thermal effect approach we are able to visualise a potential transient catalytically competent interaction of the reacting rings. Simulations indicate that the architecture of the FAD folded conformation in BoFPR might be key in catalysis, pointing to its adenine as an element to orient the reactive atoms in conformations competent for HT.
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Affiliation(s)
- Daniel Pérez-Amigot
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - Víctor Taleb
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - Sergio Boneta
- Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain; Departamento de Química Física, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Ernesto Anoz-Carbonell
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - María Sebastián
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain; Aragon Institute for Health Research (IIS-Aragon), Zaragoza 50009, Spain; Biomedical Research Networking Center in Digestive and Hepatic Diseases (CIBERehd), Madrid, Spain; Fundacion ARAID, Government of Aragon, Zaragoza 50018, Spain
| | - Víctor Polo
- Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain; Departamento de Química Física, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Marta Martínez-Júlvez
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain.
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain.
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12
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Sanz-García F, Anoz-Carbonell E, Pérez-Herrán E, Martín C, Lucía A, Rodrigues L, Aínsa JA. Mycobacterial Aminoglycoside Acetyltransferases: A Little of Drug Resistance, and a Lot of Other Roles. Front Microbiol 2019; 10:46. [PMID: 30761098 PMCID: PMC6363676 DOI: 10.3389/fmicb.2019.00046] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 01/11/2019] [Indexed: 12/11/2022] Open
Abstract
Aminoglycoside acetyltransferases are important determinants of resistance to aminoglycoside antibiotics in most bacterial genera. In mycobacteria, however, aminoglycoside acetyltransferases contribute only partially to aminoglycoside susceptibility since they are related with low level resistance to these antibiotics (while high level aminoglycoside resistance is due to mutations in the ribosome). Instead, aminoglycoside acetyltransferases contribute to other bacterial functions, and this can explain its widespread presence along species of genus Mycobacterium. This review is focused on two mycobacterial aminoglycoside acetyltransferase enzymes. First, the aminoglycoside 2'-N-acetyltransferase [AAC(2')], which was identified as a determinant of weak aminoglycoside resistance in M. fortuitum, and later found to be widespread in most mycobacterial species; AAC(2') enzymes have been associated with resistance to cell wall degradative enzymes, and bactericidal mode of action of aminoglycosides. Second, the Eis aminoglycoside acetyltransferase, which was identified originally as a virulence determinant in M. tuberculosis (enhanced intracellular survival); Eis protein in fact controls production of pro-inflammatory cytokines and other pathways. The relation of Eis with aminoglycoside susceptibility was found after the years, and reaches clinical significance only in M. tuberculosis isolates resistant to the second-line drug kanamycin. Given the role of AAC(2') and Eis proteins in mycobacterial biology, inhibitory molecules have been identified, more abundantly in case of Eis. In conclusion, AAC(2') and Eis have evolved from a marginal role as potential drug resistance mechanisms into a promising future as drug targets.
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Affiliation(s)
- Fernando Sanz-García
- Departamento de Microbiología, Facultad de Medicina - Instituto Universitario de Investigación de Biocomputación y Física de Sistemas Complejos, Instituto de Investigación Sanitaria Aragón, Universidad de Zaragoza, Zaragoza, Spain
| | - Ernesto Anoz-Carbonell
- Departamento de Microbiología, Facultad de Medicina - Instituto Universitario de Investigación de Biocomputación y Física de Sistemas Complejos, Instituto de Investigación Sanitaria Aragón, Universidad de Zaragoza, Zaragoza, Spain.,Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias - Instituto Universitario de Investigación de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Zaragoza, Spain
| | - Esther Pérez-Herrán
- Departamento de Microbiología, Facultad de Medicina - Instituto Universitario de Investigación de Biocomputación y Física de Sistemas Complejos, Instituto de Investigación Sanitaria Aragón, Universidad de Zaragoza, Zaragoza, Spain
| | - Carlos Martín
- Departamento de Microbiología, Facultad de Medicina - Instituto Universitario de Investigación de Biocomputación y Física de Sistemas Complejos, Instituto de Investigación Sanitaria Aragón, Universidad de Zaragoza, Zaragoza, Spain.,Centro de Investigación Biomédica en Red Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Ainhoa Lucía
- Departamento de Microbiología, Facultad de Medicina - Instituto Universitario de Investigación de Biocomputación y Física de Sistemas Complejos, Instituto de Investigación Sanitaria Aragón, Universidad de Zaragoza, Zaragoza, Spain.,Centro de Investigación Biomédica en Red Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Liliana Rodrigues
- Departamento de Microbiología, Facultad de Medicina - Instituto Universitario de Investigación de Biocomputación y Física de Sistemas Complejos, Instituto de Investigación Sanitaria Aragón, Universidad de Zaragoza, Zaragoza, Spain.,Centro de Investigación Biomédica en Red Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.,Fundación Agencia Aragonesa para la Investigación y el Desarrollo, Zaragoza, Spain
| | - José A Aínsa
- Departamento de Microbiología, Facultad de Medicina - Instituto Universitario de Investigación de Biocomputación y Física de Sistemas Complejos, Instituto de Investigación Sanitaria Aragón, Universidad de Zaragoza, Zaragoza, Spain.,Centro de Investigación Biomédica en Red Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
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Sebastián M, Anoz-Carbonell E, Gracia B, Cossio P, Aínsa JA, Lans I, Medina M. Discovery of antimicrobial compounds targeting bacterial type FAD synthetases. J Enzyme Inhib Med Chem 2017; 33:241-254. [PMID: 29258359 PMCID: PMC7012052 DOI: 10.1080/14756366.2017.1411910] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The increase of bacterial strains resistant to most of the available antibiotics shows a need to explore novel antibacterial targets to discover antimicrobial drugs. Bifunctional bacterial FAD synthetases (FADSs) synthesise the flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD). These cofactors act in vital processes as part of flavoproteins, making FADS an essential enzyme. Bacterial FADSs are potential antibacterial targets because of differences to mammalian enzymes, particularly at the FAD producing site. We have optimised an activity-based high throughput screening assay targeting Corynebacterium ammoniagenes FADS (CaFADS) that identifies inhibitors of its different activities. We selected the three best high-performing inhibitors of the FMN:adenylyltransferase activity (FMNAT) and studied their inhibition mechanisms and binding properties. The specificity of the CaFADS hits was evaluated by studying also their effect on the Streptococcus pneumoniae FADS activities, envisaging differences that can be used to discover species-specific antibacterial drugs. The antimicrobial effect of these compounds was also evaluated on C. ammoniagenes, S. pneumoniae, and Mycobacterium tuberculosis cultures, finding hits with favourable antimicrobial properties.
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Affiliation(s)
- María Sebastián
- a Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias , Universidad de Zaragoza , Zaragoza , Spain.,b Institute of Biocomputation and Physics of Complex Systems (BIFI-IQFR and CBsC-CSIC Joint Units) , Universidad de Zaragoza , Zaragoza , Spain
| | - Ernesto Anoz-Carbonell
- a Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias , Universidad de Zaragoza , Zaragoza , Spain.,b Institute of Biocomputation and Physics of Complex Systems (BIFI-IQFR and CBsC-CSIC Joint Units) , Universidad de Zaragoza , Zaragoza , Spain.,c Grupo de Genética de Micobacterias, Departamento de Microbiología, Medicina Preventiva y Salud Pública. Facultad de Medicina , Universidad de Zaragoza , Zaragoza , Spain
| | - Begoña Gracia
- c Grupo de Genética de Micobacterias, Departamento de Microbiología, Medicina Preventiva y Salud Pública. Facultad de Medicina , Universidad de Zaragoza , Zaragoza , Spain.,d CIBER Enfermedades Respiratorias (CIBERES) , Instituto de Salud Carlos III , Madrid , Spain
| | - Pilar Cossio
- e Department of Theoretical Biophysics , Max Planck Institute of Biophysics , Frankfurt , Germany.,f Biophysics of Tropical Diseases, Max Planck Tandem Group , University of Antioquia , Medellín , Colombia
| | - José Antonio Aínsa
- b Institute of Biocomputation and Physics of Complex Systems (BIFI-IQFR and CBsC-CSIC Joint Units) , Universidad de Zaragoza , Zaragoza , Spain.,c Grupo de Genética de Micobacterias, Departamento de Microbiología, Medicina Preventiva y Salud Pública. Facultad de Medicina , Universidad de Zaragoza , Zaragoza , Spain.,d CIBER Enfermedades Respiratorias (CIBERES) , Instituto de Salud Carlos III , Madrid , Spain
| | - Isaías Lans
- f Biophysics of Tropical Diseases, Max Planck Tandem Group , University of Antioquia , Medellín , Colombia
| | - Milagros Medina
- a Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias , Universidad de Zaragoza , Zaragoza , Spain.,b Institute of Biocomputation and Physics of Complex Systems (BIFI-IQFR and CBsC-CSIC Joint Units) , Universidad de Zaragoza , Zaragoza , Spain
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