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23 results on '"ANR-14-JAMR-0002,DesInMBL,Structure-guided design of pan inhibitors of metallo-ß-lactamases(2014)"'

1. Structural and Biochemical Features of OXA-517: a Carbapenem and Expanded-Spectrum Cephalosporin Hydrolyzing OXA-48 Variant

Author

Laura Dabos, Joanna E. Raczynska, Pierre Bogaerts, Agustin Zavala, Delphine Girlich, Remy A. Bonnin, Laurent Dortet, Aurélie Peyrat, Pascal Retailleau, Bogdan I. Iorga, Mariusz Jaskólski, Youri Glupczynski, Thierry Naas, UCL - SSS/IREC/MONT - Pôle Mont Godinne, UCL - (MGD) Laboratoire de biologie clinique, Team Resist [Le Kremlin-Bicêtre], Immunologie des maladies virales, auto-immunes, hématologiques et bactériennes (IMVA-HB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, INSERM, UMR_S 999, Laboratoire d’Excellence (LabEx) en Recherche sur le Médicament et l’Innovation Thérapeutique (LERMIT), Université Paris Sud (Paris 11), French National Reference Center for Antibiotic Resistance: Carbapenemase producing Enterobacteriaceae [Le Kremlin-Bicêtre], Institute of Bioorganic Chemistry [Poznań], Polska Akademia Nauk = Polish Academy of Sciences (PAN), CHU UCL Namur, Institut de Chimie des Substances Naturelles (ICSN), Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), ANR-10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010), ANR-14-JAMR-0002,DesInMBL,Structure-guided design of pan inhibitors of metallo-ß-lactamases(2014), and ANR-10-LABX-0033,LERMIT,Research Laboratory on Drugs and Therapeutic Innovation(2010)

Subjects
Pharmacology, antibiotic resistance, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], oxacillinase, cephalosporin, Microbial Sensitivity Tests, extended-spectrum β-lactamase, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Ceftazidime, beta-Lactamases, Cephalosporins, Anti-Bacterial Agents, carbapenem, Infectious Diseases, Carbapenems, hydrolysis, Escherichia coli, Pharmacology (medical), Monobactams
Abstract

International audience; OXA-48-producing Enterobacterales have now widely disseminated throughout the world. Several variants have now been reported, differing by just a few amino-acid substitutions or deletions, mostly in the region of the loop β5-β6. As OXA-48 hydrolyzes carbapenems but lacks significant expanded-spectrum cephalosporin (ESC) hydrolytic activity, ESCs were suggested as a therapeutic option. Here, we have characterized OXA-517, a natural variant of OXA-48- with an Arg214Lys substitution and a deletion of Ile215 and Glu216 in the β5-β6 loop, capable of hydrolyzing at the same time ESC and carbapenems. MICs values of E. coli expressing blaOXA-517 gene revealed reduced susceptibility to carbapenems (similarly to OXA-48) and resistance to ESCs. Steady-state kinetic parameters revealed high catalytic efficiencies for ESCs and carbapenems. The blaOXA-517 gene was located on a ca. 31-kb plasmid identical to the prototypical IncL blaOXA-48-carrying plasmid except for an IS1R-mediated deletion of 30.7-kb in the tra operon. The crystal structure of OXA-517, determined to 1.86 Å resolution, revealed an expanded active site compared to that of OXA-48, which allows for accommodation of the bulky ceftazidime substrate. Our work illustrates the remarkable propensity of OXA-48-like carbapenemases to evolve through mutation/deletion in the β5-β6 loop to extend its hydrolysis profile to encompass most β-lactam substrates.

Published
2023

2. Class C β-Lactamases: Molecular Characteristics

Author

Alain Philippon, Guillaume Arlet, Roger Labia, Bogdan I. Iorga, Université Paris Cité (UPCité), Centre d'Immunologie et des Maladies Infectieuses (CIMI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Universitaire de Biodiversité et Ecologie Microbienne (LUBEM), Université de Brest (UBO), Institut de Chimie des Substances Naturelles (ICSN), Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), ANR-10-LABX-0033,LERMIT,Research Laboratory on Drugs and Therapeutic Innovation(2010), ANR-14-JAMR-0002,DesInMBL,Structure-guided design of pan inhibitors of metallo-ß-lactamases(2014), ANR-20-PAMR-0010,Seq2DiAg,Séquençage du génome entier et intelligence artificielle pour caratériser et diagnostiquer la résistance aux antibiotiques et la capacité d'échapper au traitement(2020), IORGA, Bogdan, Research Laboratory on Drugs and Therapeutic Innovation - - LERMIT2010 - ANR-10-LABX-0033 - LABX - VALID, programmation conjointe européenne sur la résistance antimicrobienne - Structure-guided design of pan inhibitors of metallo-ß-lactamases - - DesInMBL2014 - ANR-14-JAMR-0002 - JPI AMR - VALID, and Séquençage du génome entier et intelligence artificielle pour caratériser et diagnostiquer la résistance aux antibiotiques et la capacité d'échapper au traitement - - Seq2DiAg2020 - ANR-20-PAMR-0010 - PAMR - VALID

Subjects
Microbiology (medical), AmpC β-lactamases, cephalosporinases, General Immunology and Microbiology, Epidemiology, Public Health, Environmental and Occupational Health, Porins, Review, Microbial Sensitivity Tests, ESAC, primary structure, beta-Lactams, phylogeny, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, beta-Lactamases, Anti-Bacterial Agents, Infectious Diseases, Bacterial Proteins, Carbapenems, extended-spectrum, Serine, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology
Abstract

Class C β-lactamases or cephalosporinases can be classified into two functional groups (1, 1e) with considerable molecular variability (≤20% sequence identity). These enzymes are mostly encoded by chromosomal and inducible genes and are widespread among bacteria, including Proteobacteria in particular. Molecular identification is based principally on three catalytic motifs ((64)SXSK, (150)YXN, (315)KTG), but more than 70 conserved amino-acid residues (≥90%) have been identified, many close to these catalytic motifs. Nevertheless, the identification of a tiny, phylogenetically distant cluster (including enzymes from the genera Legionella, Bradyrhizobium, and Parachlamydia) has raised questions about the possible existence of a C2 subclass of β-lactamases, previously identified as serine hydrolases. In a context of the clinical emergence of extended-spectrum AmpC β-lactamases (ESACs), the genetic modifications observed in vivo and in vitro (point mutations, insertions, or deletions) during the evolution of these enzymes have mostly involved the Ω- and H-10/R2-loops, which vary considerably between genera, and, in some cases, the conserved triplet (150)YXN. Furthermore, the conserved deletion of several amino-acid residues in opportunistic pathogenic species of Acinetobacter, such as A. baumannii, A. calcoaceticus, A. pittii and A. nosocomialis (deletion of residues 304–306), and in Hafnia alvei and H. paralvei (deletion of residues 289–290), provides support for the notion of natural ESACs. The emergence of higher levels of resistance to β-lactams, including carbapenems, and to inhibitors such as avibactam is a reality, as the enzymes responsible are subject to complex regulation encompassing several other genes (ampR, ampD, ampG, etc.). Combinations of resistance mechanisms may therefore be at work, including overproduction or change in permeability, with the loss of porins and/or activation of efflux systems.

Published
2022

3. Substrate Specificity of OXA-48 after β5−β6 Loop Replacement

Author

Agustin Zavala, Rémy A. Bonnin, Pascal Retailleau, Thierry Naas, Oliver Beckstein, Bogdan I. Iorga, Laura Dabos, Structure, Dynamique, Fonction Et Expression Des Beta-Lactamases À Large Spectre, Université Paris-Sud - Paris 11 - Faculté de médecine (UP11 UFR Médecine), Université Paris-Sud - Paris 11 (UP11)-Université Paris-Sud - Paris 11 (UP11)-Centre National de Référence de la Résistance aux Antibiotiques (CNR), Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon)-Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), Institut de Chimie des Substances Naturelles (ICSN), Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Department of Physics, Arizona State University (ASU), Arizona State University [Tempe] (ASU), We acknowledge SOLEIL for provision of synchrotron radiation facilities (proposal ID BAG20170782) in using PROXIMA beamlines. This work has benefited from the platform and expertise of the Macromolecular Interactions Measurements Platform of I2BC and from the I2BC crystallization platform, supported by FRISBI ANR-10-INSB-05-01. This work was supported by the Assistance Publique − Hôpitaux de Paris (AP-HP), the University Paris-Sud, the Laboratory of Excellence in Research on Medication and Innovative Therapeutics (LERMIT) supported by a grant from the French National Research Agency [ANR-10-LABX-33], by the Joint Programming Initiative on Antimicrobial Resistance (JPIAMR) DesInMBL [ANR-14-JAMR-002], and by DIM Malinf, Ile de France, for L.D.’s Ph.D. fellowship., ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), ANR-14-JAMR-0002,DesInMBL,Structure-guided design of pan inhibitors of metallo-ß-lactamases(2014), and ANR-10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010)

Subjects
0301 basic medicine, Molecular model, Stereochemistry, 030106 microbiology, Crystallography, X-Ray, β5−β6 loop, beta-Lactamases, Substrate Specificity, Carbapenemase, 03 medical and health sciences, Hydrolysis, polycyclic compounds, Enzyme kinetics, expanded-spectrum cephalosporins, chemistry.chemical_classification, oxacillinases, Substrate (chemistry), biochemical phenomena, metabolism, and nutrition, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Cephalosporins, Amino acid, Loop (topology), Kinetics, 030104 developmental biology, Infectious Diseases, Enzyme, Carbapenems, chemistry, bacteria, β5-β6 loop, Function (biology)
Abstract

International audience; OXA-48 carbapenemase has rapidly spread in many countries worldwide with several OXA-48-variants being described, differing by a few amino acid (AA) substitutions or deletions, mostly in the β5-β6 loop. While single AA substitutions have only a minor impact on OXA-48 hydrolytic profiles, others with 4 AA deletions result in loss of carbapenem hydrolysis and gain of expanded-spectrum cephalosporin (ESC) hydrolysis. We have replaced the β5-β6 loop of OXA-48 with that of OXA-18, a clavulanic-acid inhibited oxacillinase capable of hydrolyzing ESCs but not carbapenems. The hybrid enzyme OXA-48Loop18 was able to hydrolyze ESCs and carbapenems (although with a lower kcat), even though the β5-β6 loop was longer and its sequence quite different from that of OXA-48. The kinetic parameters of OXA-48Loop18 were in agreement with the MIC values. X-ray crystallography and molecular modeling suggest that the conformation of the grafted loop allows the binding of bulkier substrates, unlike that of the native loop, expanding the hydrolytic profile. This seems to be due not only to differences in AA sequence, but also to the backbone conformation the loop can adopt. Finally, our results provide further experimental evidence for the role of the β5-β6 loop in substrate selectivity of OXA-48-like enzymes and additional details on the structure-function relationship of β-lactamases, demonstrating how localized changes in these proteins can alter or expand their function, highlighting their plasticity.

Published
2020

4. Azetidinimines as a novel series of non-covalent broad-spectrum inhibitors of β-lactamases with submicromolar activities against carbapenemases KPC-2 (class A), NDM-1 (class B) and OXA-48 (class D)

Author

Mohamed Benchekroun, Saoussen Oueslati, Sandrine Ventre, Kamsana Vijayakumar, Eddy Elisée, Laetitia A. Nguyen, Edithe Selwa, Robert H. Dodd, Linda Tlili, Alain Pruvost, Pascal Retailleau, Thierry Naas, Agustin Zavala, Bogdan I. Iorga, Agathe C. A. D'Hollander, Eugénie Romero, Cynthia Exilie, Kevin Cariou, Corinne Minard, Institut de Chimie des Substances Naturelles (ICSN), Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), AP-HP Hôpital Bicêtre (Le Kremlin-Bicêtre), Immunologie des maladies virales, auto-immunes, hématologiques et bactériennes (IMVA-HB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, Médicaments et Technologies pour la Santé (MTS), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ecologie et Evolution de la Résistance aux Antibiotiques / Ecology and Evolution of Antibiotics Resistance (EERA), Institut Pasteur [Paris] (IP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), This work was supported by the Laboratory of Excellence in Research on Medication and Innovative Therapeutics (LERMIT, grant ANR-10-LABX-33 under the program Investissements d’Avenir ANR-11-IDEX-0003-01), the FCS Campus Paris-Saclay pre-maturation program (project Inhibase), the SATT Paris-Saclay (project CARBAMAT), the JPIAMR transnational project DesInMBL (grant ANR-14-JAMR-0002) and the Région Ile-de-France (DIM Malinf). The authors also thank CNRS, AP-HP, Université Paris-Saclay, and ICSN, for financial support., ANR-10-LABX-0033,LERMIT,Research Laboratory on Drugs and Therapeutic Innovation(2010), ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), ANR-14-JAMR-0002,DesInMBL,Structure-guided design of pan inhibitors of metallo-ß-lactamases(2014), Institut Pasteur [Paris]-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Cariou, Kevin, Research Laboratory on Drugs and Therapeutic Innovation - - LERMIT2010 - ANR-10-LABX-0033 - LABX - VALID, Idex Paris-Saclay - - IPS2011 - ANR-11-IDEX-0003 - IDEX - VALID, and programmation conjointe européenne sur la résistance antimicrobienne - Structure-guided design of pan inhibitors of metallo-ß-lactamases - - DesInMBL2014 - ANR-14-JAMR-0002 - JPI AMR - VALID

Subjects
Imipenem, Non covalent, Antibiotics, [CHIM.THER]Chemical Sciences/Medicinal Chemistry, medicine.disease_cause, 01 natural sciences, Broad spectrum, Catalytic Domain, Drug Discovery, polycyclic compounds, OXA-48, chemistry.chemical_classification, 0303 health sciences, biology, Escherichia coli Proteins, General Medicine, Ynamides, Anti-Bacterial Agents, Molecular Docking Simulation, Microsomes, Liver, beta-Lactamase Inhibitors, medicine.drug, Gram-negative bacteria, Carbapenemase inhibitors, medicine.drug_class, Stereochemistry, Azetidinimines, [CHIM.THER] Chemical Sciences/Medicinal Chemistry, Microbial Sensitivity Tests, NDM-1, beta-Lactamases, Bacterial resistance, KPC-2, Cell Line, Inhibitory Concentration 50, Structure-Activity Relationship, 03 medical and health sciences, Antibiotic resistance, Gram-Negative Bacteria, medicine, Humans, Escherichia coli, Cell Proliferation, 030304 developmental biology, Pharmacology, Binding Sites, 010405 organic chemistry, Organic Chemistry, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, 0104 chemical sciences, Enzyme, chemistry, Azetidines
Abstract

International audience; The occurrence of resistances in Gram negative bacteria is steadily increasing to reach extremely worrying levels and one of the main causes of resistance is the massive spread of very efficient β-lactamases which render most β-lactam antibiotics useless. Herein, we report the development of a series of imino-analogues of β-lactams (namely azetidinimines) as efficient non-covalent inhibitors of β-lactamases. Despite the structural and mechanistic differences between serine-β-lactamases KPC-2 and OXA-48 and metallo-β-lactamase NDM-1, all three enzymes can be inhibited at a submicromolar level by compound 7dfm, which can also repotentiate imipenem against a resistant strain of Escherichia coli expressing NDM-1. We show that 7dfm can efficiently inhibit not only the three main clinically-relevant carbapenemases of Ambler classes A (KPC-2), B (NDM-1) and D (OXA-48) with Ki’s below 0.3 μM, but also the cephalosporinase CMY-2 (class C, 86% inhibition at 10 μM). Our results pave the way for the development of a new structurally original family of non-covalent broad-spectrum inhibitors of β-lactamases.

Published
2021

5. Unravelling ceftazidime/avibactam resistance of KPC-28, a KPC-2 variant lacking carbapenemase activity

Author

Laurent Dortet, Agnès B Jousset, Saoussen Oueslati, Rémy A. Bonnin, Linda Tlili, Thierry Naas, Agustin Zavala, Cynthia Exilie, Sandrine Bernabeu, Bogdan I. Iorga, Structure, Dynamique, Fonction Et Expression Des Beta-Lactamases À Large Spectre, Université Paris-Sud - Paris 11 - Faculté de médecine (UP11 UFR Médecine), Université Paris-Sud - Paris 11 (UP11)-Université Paris-Sud - Paris 11 (UP11)-Centre National de Référence de la Résistance aux Antibiotiques (CNR), Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon)-Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), Institut de Chimie des Substances Naturelles (ICSN), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Centre National de Référence de la Résistance aux Antibiotiques (CNR), Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), AP-HP Hôpital Bicêtre (Le Kremlin-Bicêtre), This work was supported by the Assistance Publique – Hôpitaux de Paris, by a grant from the Université Paris-Sud (EA 7361), and by the LabEx LERMIT with a grant from the French National Research Agency (ANR-10-LABX-33). This work was also funded in part by a grant from the Joint Programming Initiative on Antimicrobial Resistance (ANR-14-JAMR-0002)., ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), and ANR-14-JAMR-0002,DesInMBL,Structure-guided design of pan inhibitors of metallo-ß-lactamases(2014)

Subjects
Microbiology (medical), Imipenem, Carbapenem, Avibactam, Mutagenesis (molecular biology technique), Ceftazidime, Microbial Sensitivity Tests, medicine.disease_cause, beta-Lactamases, Microbiology, Gene product, 03 medical and health sciences, chemistry.chemical_compound, Bacterial Proteins, Escherichia coli, polycyclic compounds, medicine, Pharmacology (medical), Cloning, Molecular, 030304 developmental biology, Pharmacology, 0303 health sciences, 030306 microbiology, Genetic Variation, biochemical phenomena, metabolism, and nutrition, bacterial infections and mycoses, Ceftazidime/avibactam, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Anti-Bacterial Agents, Molecular Docking Simulation, Drug Combinations, Kinetics, Klebsiella pneumoniae, Infectious Diseases, Amino Acid Substitution, chemistry, Mutagenesis, Site-Directed, [SDV.SP.PHARMA]Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, Azabicyclo Compounds, medicine.drug
Abstract

BackgroundKPC-like carbapenemases have spread worldwide with more than 30 variants identified that differ by single or double amino-acid substitutions.ObjectivesTo describe the steady-state kinetic parameters of KPC-28, which differs from KPC-2 by a H274Y substitution and the deletion of two amino acids (Δ242-GT-243).MethodsThe blaKPC-2, blaKPC-3, blaKPC-14 and blaKPC-28 genes were cloned into a pTOPO vector for susceptibility testing or into pET41b for overexpression, purification and subsequent kinetic parameter (Km, kcat) determination. Molecular docking experiments were performed to explore the role of the amino-acid changes in the carbapenemase activity.ResultsSusceptibility testing revealed that Escherichia coli producing KPC-28 displayed MICs that were lower for carbapenems and higher for ceftazidime and ceftazidime/avibactam as compared with KPC-2. The catalytic efficiencies of KPC-28 and KPC-14 for imipenem were 700-fold and 200-fold lower, respectively, than those of KPC-2, suggesting that Δ242-GT-243 in KPC-28 and KPC-14 is responsible for reduced carbapenem hydrolysis. Similarly, the H274Y substitution resulted in KPC-28 in a 50-fold increase in ceftazidime hydrolysis that was strongly reversed by clavulanate.ConclusionsWe have shown that KPC-28 lacks carbapenemase activity, has increased ceftazidime hydrolytic activity and is strongly inhibited by clavulanate. KPC-28-producing E. coli isolates display an avibactam-resistant ESBL profile, which may be wrongly identified by molecular and immunochromatographic assays as the presence of a carbapenemase. Accordingly, confirmation of carbapenem hydrolysis will be mandatory with assays based solely on blaKPC gene or gene product detection.

Published
2019

6. SME-4-producing Serratia marcescens from Argentina belonging to clade 2 of the S. marcescens phylogeny

Author

Marcela Nastro, Angela Famiglietti, Philippe Glaser, Carlos Hernán Rodríguez, Rafael Patiño-Navarrete, Laura Dabos, Thierry Naas, Structure, Dynamique, Fonction Et Expression Des Beta-Lactamases À Large Spectre, Université Paris-Sud - Paris 11 - Faculté de médecine (UP11 UFR Médecine), Université Paris-Sud - Paris 11 (UP11)-Université Paris-Sud - Paris 11 (UP11)-Centre National de Référence de la Résistance aux Antibiotiques (CNR), Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon)-Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), Ecologie et Evolution de la Résistance aux Antibiotiques / Ecology and Evolution of Antibiotics Resistance (EERA), Université Paris-Sud - Paris 11 (UP11)-Institut Pasteur [Paris] (IP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Centre National de la Recherche Scientifique (CNRS), Laboratorio de Bacteriología Clínica [Buenos Aires], Facultad de Farmacia y Bioquímica [Buenos Aires] (FFYB), Universidad de Buenos Aires [Buenos Aires] (UBA)-Universidad de Buenos Aires [Buenos Aires] (UBA), Universidad de Buenos Aires [Buenos Aires] (UBA), AP-HP Hôpital Bicêtre (Le Kremlin-Bicêtre), Centre National de Référence Associé de la Résistance aux Antibiotiques [Hôpital Bicêtre AP-HP] (CNRARA/Service de Microbiologie), This work was supported by the Assistance Publique – Hôpitaux de Paris (AP-HP), the University Paris-Sud, the LabExs Laboratory of Excellence in Research on Medication and Innovative Therapeutics (LERMIT) and Integrative Biology of Emerging Infectious Diseases (IBEID) supported by grants from the French National Research Agency (ANR-10-LABX-33), and by the Joint Programming Initiative on Antimicrobial Resistance (JPIAMR) DesInMBL (ANR-14-JAMR-002), and by DIM Malinf, Ile deFrance, for L. D.’s PhD fellowship., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-14-JAMR-0002,DesInMBL,Structure-guided design of pan inhibitors of metallo-ß-lactamases(2014), Institut Pasteur [Paris]-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Sud Orsay-Centre National de la Recherche Scientifique (CNRS), and Centre National de Référence Associé de la Résistance aux Antibiotiques

Subjects
Male, 0301 basic medicine, Microbiology (medical), Imipenem, Genomic Islands, Genotype, 030106 microbiology, Argentina, Microbial Sensitivity Tests, Genome, beta-Lactamases, Serratia Infections, 03 medical and health sciences, 0302 clinical medicine, Bacterial Proteins, Phylogenetics, Genomic island, medicine, Humans, Pharmacology (medical), 030212 general & internal medicine, Clade, Phylogeny, Serratia marcescens, Pharmacology, Genetics, Whole genome sequencing, Whole Genome Sequencing, biology, Phylogenetic tree, Computational Biology, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Middle Aged, biology.organism_classification, Carbapenem-Resistant Enterobacteriaceae, Infectious Diseases, Genome, Bacterial, medicine.drug
Abstract

Background SME carbapenemases are increasingly reported, especially from North and South America. Here, we describe an SME-4-producing Serratia marcescens (SME-Sm) clinical isolate from Argentina and compare its genome with other SME-Sm and Sm isolates recovered from public databases. Methods Sm isolates were characterized by WGS using Illumina technology, susceptibility testing and MIC determination. Carbapenemase activity was revealed by biochemical tests based on imipenem hydrolysis. A whole-genome phylogeny was estimated for all the Sm isolates retrieved from public databases with kSNP3 and a whole-genome phylogenetic analysis based on non-recombinant core SNPs was inferred for Sm complete genomes and for those encoding any blaSME variants. Results Sm163 was resistant to amoxicillin, temocillin, aztreonam and carbapenems, remaining susceptible to extended-spectrum cephalosporins. WGS analysis of Sm163 revealed a genome of 5139329 bp and a chromosomally encoded blaSME-4 carbapenemase gene located on a genomic island closely related to SmarGI1-1 of Sm N11-02820. Comparison of the Sm genomes revealed that the 14 SME-Sm isolates possess this genomic island inserted at the same loci, that 13/14 belong to clade 1 and that 11/14 form a well-defined subcluster of cluster I of Sm clade 1, while Sm163 belongs to clade 2, suggesting that an SME-encoding genomic island may have been transferred between isolates from different clades. Conclusions To the best of our knowledge this is the first report of an SME-4-encoding Sm from Argentina. The blaSME-4 gene is located on a SmarGI1-1-like genomic island. The genome of Sm163 belongs to clade 2, unlike all the other SME-Sm isolates, which belong to clade 1.

Published
2019

7. Carbapenemase-producing Pseudomonas aeruginosa isolates from Turkey: first report of P. aeruginosa high-risk clones with VIM-5– and IMP-7–type carbapenemases in a tertiary hospital

Author

Banu Bayraktar, Elif Aktaş, Laura Dabos, Gülşah Malkoçoğlu, Nicolas Fortineau, Bogdan I. Iorga, Zuhal Kalaycı Çekin, Thierry Naas, Şişli Etfal Hamidiye Education and Research Hospital, Team Resist [Le Kremlin-Bicêtre], Immunologie des maladies virales, auto-immunes, hématologiques et bactériennes (IMVA-HB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, Ecologie et Evolution de la Résistance aux Antibiotiques / Ecology and Evolution of Antibiotics Resistance (EERA), Institut Pasteur [Paris] (IP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Kocaeli University [Turkey], Institut de Chimie des Substances Naturelles (ICSN), Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), AP-HP Hôpital Bicêtre (Le Kremlin-Bicêtre), This work was supported by the Assistance Publique – Hôpitaux de Paris (AP-HP), the University Paris-Sud, the Laboratory of Excellence in Research on Medication and Innovative Therapeutics (LERMIT) supported by a grant from the French National Research Agency [ANR-10-LABX-33] and by the Joint Programming Initiative on Antimicrobial Resistance (JPIAMR) DesInMBL [ANR-14-JAMR-002], and by DIM Malinf, Ile de France, for LD’s PhD fellowship., ANR-10-LABX-0033,LERMIT,Research Laboratory on Drugs and Therapeutic Innovation(2010), ANR-14-JAMR-0002,DesInMBL,Structure-guided design of pan inhibitors of metallo-ß-lactamases(2014), and Institut Pasteur [Paris]-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Carbapenem, Turkey, Fluoroquinolone resistance, medicine.disease_cause, law.invention, Tertiary Care Centers, 0302 clinical medicine, law, Drug Resistance, Multiple, Bacterial, 030212 general & internal medicine, Polymerase chain reaction, General Medicine, 3. Good health, Anti-Bacterial Agents, Infectious Diseases, Pseudomonas aeruginosa, ST308, medicine.drug, Fluoroquinolones, Plasmids, Microbiology (medical), DNA, Bacterial, Carbapenem resistance, 030106 microbiology, Microbial Sensitivity Tests, Biology, ST357, beta-Lactamases, Microbiology, 03 medical and health sciences, Bacterial Proteins, medicine, Humans, crpP, Pseudomonas Infections, Gene, Whole genome sequencing, Whole Genome Sequencing, Carbapenemase producing, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Multiple drug resistance, Carbapenems, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, VIM-5, [SDV.SP.PHARMA]Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, IMP-7, Genome, Bacterial, Multilocus Sequence Typing
Abstract

International audience; We investigated the presence of carbapenemases in carbapenem-resistant Pseudomonas aeruginosa isolates, which were collected over a 14-month period in a Turkish hospital, with in-depth molecular characterization of carbapenemase-producing isolates. Among 45 study isolates, 2 isolates were identified as carbapenemase producers by both Carba NP and Carbapenem Inactivation Method tests, and only 1 of them gave a positive result in polymerase chain reaction tests for a carbapenemase gene (blaVIM). Whole genome sequencing of the 2 isolates revealed the presence of blaVIM-5 gene in an ST308 isolate, while the other one expressed IMP-7 in an ST357 isolate; both STs are considered high-risk clones. The 2 carbapenemase-producing isolates were multidrug resistant, as they harbored other resistance determinants, including a variant of the recently described plasmid-encoded fluoroquinolone resistance determinant crpP gene, crpP-2. We report for the first time P. aeruginosa high-risk clones carrying VIM-5– and IMP-7–type carbapenemases with multiple resistance determinants in Turkey.

Published
2021

8. Stepwise evolution and convergent recombination underlie the global dissemination of carbapenemase-producing Escherichia coli

Author

Rafael Patiño-Navarrete, Lauraine Gauthier, Julie Takissian, Nicolas Cabanel, Isabelle Rosinski-Chupin, Rémy A. Bonnin, Monzer Hamze, Philippe Glaser, Jean-Yves Madec, Thierry Naas, Ecologie et Evolution de la Résistance aux Antibiotiques / Ecology and Evolution of Antibiotics Resistance (EERA), Université Paris-Sud - Paris 11 (UP11)-Institut Pasteur [Paris] (IP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Centre National de la Recherche Scientifique (CNRS), Centre National de Référence Associé de la Résistance aux Antibiotiques [Hôpital Bicêtre AP-HP] (CNRARA/Service de Microbiologie), AP-HP Hôpital Bicêtre (Le Kremlin-Bicêtre), Hôpital Bicêtre, Université Paris-Sud - Paris 11 (UP11)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Bicêtre, Unité Antibiorésistance et Virulence Bactériennes (AVB), Laboratoire de Lyon [ANSES], Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Université Libanaise, This work was supported by grants from the French National Research Agency (ANR LabEx IBEID and ANR-10-LABX-33), from the Joint Program Initiative on Antimicrobial Resistance (ANR-14-JAMR-0002), and from the European Union’s Horizon 2020 Research and Innovation Program under Grant Agreement No. 773830 (Project ARDIG, EJP One Health), ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-14-JAMR-0002,DesInMBL,Structure-guided design of pan inhibitors of metallo-ß-lactamases(2014), European Project: 773830,H2020-SFS-2017-1,MedVetKlebs (a component of European Joint Programme One Health)(2018), Institut Pasteur [Paris]-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Sud Orsay-Centre National de la Recherche Scientifique (CNRS), Centre National de Référence Associé de la Résistance aux Antibiotiques, Hôpital Bicêtre-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris-Sud - Paris 11 (UP11), Unité Antibiorésistance et Virulence Bactériennes, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), and European Project: 773830,H2020-SFS-2017-1,MedVetKlebs (a component of European Joint Programme One Health EJP)(2018)

Subjects
0301 basic medicine, Penicillin binding proteins, lcsh:Medicine, Multidrug resistance, medicine.disease_cause, Genome, Bacterial evolution, Enteropathogenic Escherichia coli, Shigella, Genetics (clinical), Phylogeny, Genetics, 0303 health sciences, Escherichia coli Proteins, Porin, Multidrug resistance bacteria, Enterobacteriaceae, Phenotype, 3. Good health, Molecular Medicine, Penicillin-binding proteins, Porine, Lineage (genetic), lcsh:QH426-470, Gene Transfer, Horizontal, 030106 microbiology, Porins, Biology, beta-Lactam Resistance, beta-Lactamases, Lateral gene transfers, Evolution, Molecular, 03 medical and health sciences, Bacterial Proteins, Phylogenetics, medicine, Allele, Molecular Biology, Gene, Escherichia coli, 030304 developmental biology, Molecular epidemiology, 030306 microbiology, Research, lcsh:R, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, biology.organism_classification, lcsh:Genetics, 030104 developmental biology, Carbapenems, Mutation, Peptidoglycan Glycosyltransferase
Abstract

Background Carbapenem-resistant Enterobacteriaceae are considered by WHO as “critical” priority pathogens for which novel antibiotics are urgently needed. The dissemination of carbapenemase-producing Escherichia coli (CP-Ec) in the community is a major public health concern. However, the global molecular epidemiology of CP-Ec isolates remains largely unknown as well as factors contributing to the acquisition of carbapenemase genes. Methods We first analyzed the whole-genome sequence and the evolution of the E. coli sequence type (ST) 410 and its disseminated clade expressing the carbapenemase OXA-181. We reconstructed the phylogeny of 19 E. coli ST enriched in CP-Ec and corresponding to a total of 2026 non-redundant isolates. Using the EpiCs software, we determined the significance of the association between specific mutations and the acquisition of a carbapenemase gene and the most probable order of events. The impact of the identified mutations was assessed experimentally by genetic manipulations and phenotypic testing. Results In 13 of the studied STs, acquisition of carbapenemase genes occurred in multidrug-resistant lineages characterized by a combination of mutations in ftsI encoding the penicillin-binding protein 3 and in the porin genes ompC and ompF. Mutated ftsI genes and a specific ompC allele related to that from ST38 inducing reduced susceptibility to diverse β-lactams spread across the species by recombination. We showed that these mutations precede in most cases the acquisition of a carbapenemase gene. The ompC allele from ST38 might have contributed to the selection of CP-Ec disseminated lineages within this ST. On the other hand, in the pandemic ST131 lineage, CP-Ec were not associated with mutations in ompC or ftsI and show no signs of dissemination. Conclusions Lineages of CP-Ec have started to disseminate globally. However, their selection is a multistep process involving mutations, recombination, acquisition of antibiotic resistance genes, and selection by β-lactams from diverse families. This process did not yet occur in the high-risk lineage ST131.

Published
2020

9. A single Proteus mirabilis lineage from human and animal sources: a hidden reservoir of OXA-23 or OXA-58 carbapenemases in Enterobacterales

Author

Pierre Bogaerts, Marisa Haenni, Elodie Couvé-Deacon, Rémy A. Bonnin, Jean-Yves Madec, Olivier Barraud, Lauraine Gauthier, Nicolas Fortineau, Philippe Glaser, Gaelle Cuzon, Laurent Dortet, Agnès B Jousset, Delphine Girlich, Thierry Naas, Youri Glupczynski, Team Resist [Le Kremlin-Bicêtre], Immunologie des maladies virales, auto-immunes, hématologiques et bactériennes (IMVA-HB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, French National Reference Center for Antibiotic Resistance: Carbapenemase producing Enterobacteriaceae [Le Kremlin-Bicêtre], Ecologie et Evolution de la Résistance aux Antibiotiques / Ecology and Evolution of Antibiotics Resistance (EERA), Institut Pasteur [Paris]-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Sud Orsay-Centre National de la Recherche Scientifique (CNRS), Bacteriology-Hygiene unit [Le Kremlin-Bicêtre], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-AP-HP Hôpital Bicêtre (Le Kremlin-Bicêtre), CHU UCL Namur, Unité Antibiorésistance et Virulence Bactériennes, Laboratoire de Lyon [ANSES], Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Anti-infectieux : supports moléculaires des résistances et innovations thérapeutiques (RESINFIT), CHU Limoges-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Génomique, Environnement, Immunité, Santé, Thérapeutique (GEIST), Université de Limoges (UNILIM)-Université de Limoges (UNILIM), This work was partially funded by the University Paris-Sud, France. LD, TN and RAB are members of the Laboratory of Excellence in Research on Medication and Innovative Therapeutics (LERMIT) supported by a grant from the French National Research Agency (ANR-10-LABX-33) and by the Joint Programming Initiative on Antimicrobial Resistance (JPIAMR) DesInMBL [ANR-14-JAMR-002]., We want to thanks Pasteur International Bioressources Networking (PibNet, Paris, France) for providing whole genome sequencing facilities. We would like to thank the Transposon Registry for transposon nomenclature (https://transposon.lstmed.ac.uk/tn-registry). We thank INTEGRALL database for integron and gene cassette nomenclatures., ANR-10-LABX-0033,LERMIT,Research Laboratory on Drugs and Therapeutic Innovation(2010), ANR-14-JAMR-0002,DesInMBL,Structure-guided design of pan inhibitors of metallo-ß-lactamases(2014), Université Paris-Sud - Paris 11 (UP11)-Institut Pasteur [Paris] (IP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Centre National de la Recherche Scientifique (CNRS), Unité Antibiorésistance et Virulence Bactériennes (AVB), Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), UCL - (MGD) Laboratoire de biologie clinique, UCL - SSS/IREC/MONT - Pôle Mont Godinne, Institut Pasteur [Paris] (IP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Sud Orsay-Centre National de la Recherche Scientifique (CNRS), Bodescot, Myriam, Research Laboratory on Drugs and Therapeutic Innovation - - LERMIT2010 - ANR-10-LABX-0033 - LABX - VALID, and programmation conjointe européenne sur la résistance antimicrobienne - Structure-guided design of pan inhibitors of metallo-ß-lactamases - - DesInMBL2014 - ANR-14-JAMR-0002 - JPI AMR - VALID

Subjects
DNA, Bacterial, 0301 basic medicine, clone (Java method), Lineage (genetic), Science, 030106 microbiology, Antimicrobial resistance, beta-Lactamases, Article, 03 medical and health sciences, Plasmid, Bacterial Proteins, Belgium, Recombinase, polycyclic compounds, Animals, Humans, Clinical microbiology, Proteus mirabilis, Gene, Genetics, Multidisciplinary, biology, Phylogenetic tree, integumentary system, [SDV.MHEP.HEG]Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology, Chromosomes, Bacterial, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV.MHEP.HEG] Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology, 030104 developmental biology, Composite transposon, Genes, Bacterial, DNA Transposable Elements, bacteria, Medicine, France, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Plasmids
Abstract

In Enterobacterales, the most common carbapenemases are Ambler’s class A (KPC-like), class B (NDM-, VIM- or IMP-like) or class D (OXA-48-like) enzymes. This study describes the characterization of twenty-four OXA-23 or OXA-58 producing-Proteus mirabilis isolates recovered from human and veterinary samples from France and Belgium. Twenty-two P. mirabilis isolates producing either OXA-23 (n = 21) or OXA-58 (n = 1), collected between 2013 and 2018, as well as 2 reference strains isolated in 1996 and 2015 were fully sequenced. Phylogenetic analysis revealed that 22 of the 24 isolates, including the isolate from 1996, belonged to a single lineage that has disseminated in humans and animals over a long period of time. The blaOXA-23 gene was located on the chromosome and was part of a composite transposon, Tn6703, bracketed by two copies of IS15∆II. Sequencing using Pacbio long read technology of OXA-23-producing P. mirabilis VAC allowed the assembly of a 55.5-kb structure encompassing the blaOXA-23 gene in that isolate. By contrast to the blaOXA-23 genes, the blaOXA-58 gene of P. mirabilis CNR20130297 was identified on a 6-kb plasmid. The acquisition of the blaOXA-58 gene on this plasmid involved XerC-XerD recombinases. Our results suggest that a major clone of OXA-23-producing P. mirabilis is circulating in France and Belgium since 1996.

Published
2020

10. NMR Characterization of the Influence of Zinc(II) Ions on the Structural and Dynamic Behavior of the New Delhi Metallo-β-Lactamase-1 and on the Binding with Flavonols as Inhibitors

Author

Gwladys Rivière, Bogdan I. Iorga, François Giraud, Eric Guittet, Jean-Bernard Créchet, Maud Gayral, Nelly Morellet, Ewen Lescop, Stéphanie Pethe, Saoussen Oueslati, Jean-Christophe Cintrat, Naïma Nhiri, Carine van Heijenoort, Thierry Naas, Eric Jacquet, Institut de Chimie des Substances Naturelles (ICSN), Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Structure, Dynamique, Fonction Et Expression Des Beta-Lactamases À Large Spectre, Université Paris-Sud - Paris 11 - Faculté de médecine (UP11 UFR Médecine), Université Paris-Sud - Paris 11 (UP11)-Université Paris-Sud - Paris 11 (UP11)-Centre National de Référence de la Résistance aux Antibiotiques (CNR), Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon)-Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), Université Paris-Sud - Paris 11 (UP11)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Service de Chimie Bio-Organique et de Marquage (SCBM), Médicaments et Technologies pour la Santé (MTS), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), This work was supported by the Assistance Publique-Les Hôpitaux de Paris (AP-HP), the University Paris-Sud, the Laboratory of Excellence in Research on Medication and Innovative Therapeutics (LERMIT) supported by a grant from the French National Research Agency [ANR-10-LABX-33] and by the Joint Programming Initiative on Antimicrobial Resistance (JPIAMR) DesInMBL [ANR-14-JAMR-002], and the French National Centre for Scientific Research-CNRS. Financial support from the IR-RMN-THC Fr3050 CNRS for conducting the research is gratefully acknowledged., ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), ANR-14-JAMR-0002,DesInMBL,Structure-guided design of pan inhibitors of metallo-ß-lactamases(2014), and Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)

Subjects
Stereochemistry, medicine.drug_class, General Chemical Engineering, Antibiotics, chemistry.chemical_element, Zinc, 01 natural sciences, Metallo β lactamase, Article, 03 medical and health sciences, Flavonols, polycyclic compounds, medicine, QD1-999, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], 010405 organic chemistry, Chemistry, General Chemistry, biochemical phenomena, metabolism, and nutrition, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 0104 chemical sciences, New delhi, geographic locations
Abstract

International audience; New Delhi metallo-β-lactamase-1 (NDM-1) has recently emerged as a global threat because of its ability to confer resistance to all common β-lactam antibiotics. Understanding the molecular basis of β-lactam hydrolysis by NDM is crucial for designing NDM inhibitors or β-lactams resistant to their hydrolysis. In this study, for the first time, NMR was used to study the influence of Zn(II) ions on the dynamic behavior of NDM-1. Our results highlighted that the binding of Zn(II) in the NDM-1 active site induced several structural and dynamic changes on active site loop 2 (ASL2) and L9 loops and on helix α2. We subsequently studied the interaction of several flavonols: morin, quercetin, and myricetin were identified as natural and specific inhibitors of NDM-1. Quercetin conjugates were also synthesized in an attempt to increase the solubility and bioavailability. Our NMR investigations on NDM-1/flavonol interactions highlighted that both Zn(II) ions and the residues of the NDM-1 ASL1, ASL2, and ASL4 loops are involved in the binding of flavonols. This is the first NMR interaction study of NDM-1/inhibitors, and the models generated using HADDOCK will be useful for the rational design of more active inhibitors, directed against NDM-1.

Published
2020

11. Concomitant carriage of KPC-producing and non-KPC-producing Klebsiella pneumoniae ST512 within a single patient

Author

Agnès B Jousset, Rémy A. Bonnin, Nicolas Cabanel, Julie Takissian, Philippe Glaser, Thierry Naas, Delphine Girlich, Laurent Dortet, Liliana Mihaila, Structure, Dynamique, Fonction Et Expression Des Beta-Lactamases À Large Spectre, Université Paris-Sud - Paris 11 - Faculté de médecine (UP11 UFR Médecine), Université Paris-Sud - Paris 11 (UP11)-Université Paris-Sud - Paris 11 (UP11)-Centre National de Référence de la Résistance aux Antibiotiques (CNR), Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon)-Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), AP-HP Hôpital Bicêtre (Le Kremlin-Bicêtre), Ecologie et Evolution de la Résistance aux Antibiotiques / Ecology and Evolution of Antibiotics Resistance (EERA), Institut Pasteur [Paris] (IP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), This work was partially funded by the University Paris-Sud, France. L.D., T.N. and R.A.B. are members of the Laboratory of Excellence in Research on Medication and Innovative Therapeutics (LERMIT) supported by a grant from the French National Research Agency (ANR-10-LABX-33), by the Joint Programming Initiative on Antimicrobial Resistance (JPIAMR) DesInMBL (ANR-14-JAMR-002) and by the European Union’s Horizon 2020 Research and Innovation Program under Grant Agreement No. 773830 (Project MedVetKlebs, One Health EJP)., ANR-10-LABX-0033,LERMIT,Research Laboratory on Drugs and Therapeutic Innovation(2010), ANR-14-JAMR-0002,DesInMBL,Structure-guided design of pan inhibitors of metallo-ß-lactamases(2014), European Project: 773830,H2020-SFS-2017-1,MedVetKlebs (a component of European Joint Programme One Health)(2018), Institut Pasteur [Paris]-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), and European Project: 773830,H2020-SFS-2017-1,MedVetKlebs (a component of European Joint Programme One Health EJP)(2018)

Subjects
Microbiology (medical), Klebsiella pneumoniae, Population, Single-nucleotide polymorphism, Microbial Sensitivity Tests, beta-Lactamases, Microbiology, 03 medical and health sciences, Plasmid, Bacterial Proteins, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Humans, Pharmacology (medical), education, Phylogeny, 030304 developmental biology, Pharmacology, Whole genome sequencing, Molecular Epidemiology, 0303 health sciences, education.field_of_study, Genetic diversity, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], biology, 030306 microbiology, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Anti-Bacterial Agents, Klebsiella Infections, 3. Good health, Infectious Diseases, Carriage, Chromosomal region, Plasmids
Abstract

Background: KPC-producing Klebsiella pneumoniae of clonal group 258 are prominent in healthcare settings in many regions of the world. The blaKPC gene is mostly carried by a multireplicon IncFIIk-IncFI plasmid suspected to be highly compatible and stable in this genetic background. Here, we analysed the genetic diversity of an ST512 K. pneumoniae population in a single patient. Methods: Twelve K. pneumoniae isolates (n = 5 from urine samples and n = 7 from rectal swabs) were recovered from one patient over a 2 month period. Antimicrobial susceptibility testing, plasmid extraction and WGS were performed on all isolates. The first K. pneumoniae isolate, D1, was used as a reference for phylogenetic analysis. Results: Antimicrobial susceptibility testing, plasmid analysis and WGS revealed concomitant carriage of carbapenem-resistant and carbapenem-susceptible K. pneumoniae isolates of ST512, with the absence of the entire blaKPC-carrying plasmid in the susceptible population. Furthermore, 14 other genetic events occurred with- in the genome, including 3 chromosomal deletions (of 71 kb, 33 kb and 11 bp), 2 different insertions of ISKpn26 and 9 SNPs. Interestingly, most of the events occurred in the same chromosomal region that has been deleted independently several times, probably after homologous recombination involving 259 bp repeated sequences. Conclusions: Our study revealed (to the best of our knowledge) the first case of in vivo blaKPC-carrying plasmid curing and a wide within-patient genetic diversity of a single K. pneumoniae ST512 clone over a short period of carriage. This within-patient diversity must be taken into account when characterizing transmission chains using WGS during nosocomial outbreaks., This work was partially funded by the University Paris-Sud, France. L.D., T.N. and R.A.B. are members of the Laboratory of Excellence in Research on Medication and Innovative Therapeutics (LERMIT) supported by a grant from the French National Research Agency (ANR-10-LABX-33), by the Joint Programming Initiative on Antimicrobial Resistance (JPIAMR) DesInMBL (ANR-14-JAMR-002) and by the European Union's Horizon 2020 Research and Innovation Program under Grant Agreement No. 773830 (Project MedVetKlebs, One Health EJP).

Published
2020

12. Prediction of octanol-water partition coefficients for the SAMPL6-logP molecules using molecular dynamics simulations with OPLS-AA, AMBER and CHARMM force fields

Author

Shujie Fan, Bogdan I. Iorga, Oliver Beckstein, Department of Physics, Arizona State University (ASU), Arizona State University [Tempe] (ASU), Institut de Chimie des Substances Naturelles (ICSN), Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Grants from National Institute Of General Medical Sciences of the National Institutes of Health under Awards Number R01GM118772 and R01GM125081.A grant DIM MAL-INF from the Région Ile- de-France., ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), and ANR-14-JAMR-0002,DesInMBL,Structure-guided design of pan inhibitors of metallo-ß-lactamases(2014)

Subjects
Octanol, Octanols, OPLS-AA force field, Entropy, AMBER force field, Thermodynamics, Thermodynamic integration, ligand parametrization, Molecular Dynamics Simulation, octanol-water partition coefficient, 01 natural sciences, Article, Force field (chemistry), Free energy perturbation, chemistry.chemical_compound, Molecular dynamics, solvation free energy, 0103 physical sciences, Drug Discovery, Bennett acceptance ratio, Physical and Theoretical Chemistry, free energy perturbation, Mathematics, 010304 chemical physics, Solvation, Water, molecular dynamics, 0104 chemical sciences, Computer Science Applications, Partition coefficient, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, 010404 medicinal & biomolecular chemistry, Models, Chemical, Solubility, chemistry, 13. Climate action, Solvents, CHARMM force field
Abstract

All-atom molecular dynamics simulations with stratified alchemical free energy calculations were used to predict the octanol-water partition coefficient [Formula: see text] of eleven small molecules as part of the SAMPL6-[Formula: see text] blind prediction challenge using four different force field parametrizations: standard OPLS-AA with transferable charges, OPLS-AA with non-transferable CM1A charges, AMBER/GAFF, and CHARMM/CGenFF. Octanol parameters for OPLS-AA, GAFF and CHARMM were validated by comparing the density as a function of temperature, the chemical potential, and the hydration free energy to experimental values. The partition coefficients were calculated from the solvation free energy for the compounds in water and pure ("dry") octanol or "wet" octanol with 27 mol% water dissolved. Absolute solvation free energies were computed by thermodynamic integration (TI) and the multistate Bennett acceptance ratio with uncorrelated samples from data generated by an established protocol using 5-ns windowed alchemical free energy perturbation (FEP) calculations with the Gromacs molecular dynamics package. Equilibration of sets of FEP simulations was quantified by a new measure of convergence based on the analysis of forward and time-reversed trajectories. The accuracy of the [Formula: see text] predictions was assessed by descriptive statistical measures such as the root mean square error (RMSE) of the data set compared to the experimental values. Discarding the first 1 ns of each 5-ns window as an equilibration phase had a large effect on the GAFF data, where it improved the RMSE by up to 0.8 log units, while the effect for other data sets was smaller or marginally worsened the agreement. Overall, CGenFF gave the best prediction with RMSE 1.2 log units, although for only eight molecules because the current CGenFF workflow for Gromacs does not generate files for certain halogen-containing compounds. Over all eleven compounds, GAFF gave an RMSE of 1.5. The effect of using a mixed water/octanol solvent slightly decreased the accuracy for CGenFF and GAFF and slightly increased it for OPLS-AA. The GAFF and OPLS-AA results displayed a systematic error where molecules were too hydrophobic whereas CGenFF appeared to be more balanced, at least on this small data set.

Published
2020

13. Biochemical and Structural Characterization of OXA-405, an OXA-48 Variant with Extended-Spectrum β-Lactamase Activity

Author

Rémy A. Bonnin, Bogdan I. Iorga, Thierry Naas, Ludovic Marchini, Saoussen Oueslati, Pascal Retailleau, Laurent Dortet, Structure, Dynamique, Fonction Et Expression Des Beta-Lactamases À Large Spectre, Université Paris-Sud - Paris 11 - Faculté de médecine (UP11 UFR Médecine), Université Paris-Sud - Paris 11 (UP11)-Université Paris-Sud - Paris 11 (UP11)-Centre National de Référence de la Résistance aux Antibiotiques (CNR), Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon)-Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), Institut de Chimie des Substances Naturelles (ICSN), Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), and ANR-14-JAMR-0002,DesInMBL,Structure-guided design of pan inhibitors of metallo-ß-lactamases(2014)

Subjects
Microbiology (medical), Carbapenem, crystal structure, antibiotic resistance, Molecular model, Stereochemistry, Microbiology, Article, 03 medical and health sciences, Molecular dynamics, Hydrolysis, carbapenemase, Virology, medicine, polycyclic compounds, Molecule, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], 030304 developmental biology, 0303 health sciences, biology, integumentary system, oxacillinase, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], 030306 microbiology, Chemistry, Active site, biochemical phenomena, metabolism, and nutrition, substrate selectivity, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, OXA-ESBL, 3. Good health, Covalent bond, Docking (molecular), docking, biology.protein, bacteria, beta-lactamase, medicine.drug
Abstract

OXA-48-producing Enterobacterales have now widely disseminated globally. A sign of their extensive spread is the identification of an increasing number of OXA-48 variants. Among them, three are particularly interesting, OXA-163, OXA-247 and OXA-405, since they have lost carbapenem activities and gained expanded-spectrum cephalosporin hydrolytic activity subsequent to a four amino-acid (AA) deletion in the &beta, 5&ndash, &beta, 6 loop. We investigated the mechanisms responsible for substrate specificity of OXA-405. Kinetic parameters confirmed that OXA-405 has a hydrolytic profile compatible with an ESBL (hydrolysis of expanded spectrum cephalosporins and susceptibility to class A inhibitors). Molecular modeling techniques and 3D structure determination show that the overall dimeric structure of OXA-405 is very similar to that of OXA-48, except for the &beta, 6 loop, which is shorter for OXA-405, suggesting that the length of the &beta, 6 loop is critical for substrate specificity. Covalent docking with selected substrates and molecular dynamics simulations evidenced the structural changes induced by substrate binding, as well as the distribution of water molecules in the active site and their role in substrate hydrolysis. All this data may represent the structural basis for the design of new and efficient class D inhibitors.

Published
2020

14. A 4.5-Year Within-Patient Evolution of a Colistin-Resistant Klebsiella pneumoniae Carbapenemase–Producing K. pneumoniae Sequence Type 258

Author

Eric Farfour, Rémy A. Bonnin, Isabelle Rosinski-Chupin, Philippe Glaser, Agnès B Jousset, Laurent Dortet, Delphine Girlich, Hélène Frech, Thierry Naas, Gaelle Cuzon, Nicolas Cabanel, Centre National de Référence Associé de la Résistance aux Antibiotiques, AP-HP Hôpital Bicêtre (Le Kremlin-Bicêtre), Hôpital Bicêtre, Hôpital Bicêtre-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris-Sud - Paris 11 (UP11), Ecologie et Evolution de la Résistance aux Antibiotiques / Ecology and Evolution of Antibiotics Resistance (EERA), Institut Pasteur [Paris]-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Sud Orsay-Centre National de la Recherche Scientifique (CNRS), Structure, Dynamique, Fonction Et Expression Des Beta-Lactamases À Large Spectre, Université Paris-Sud - Paris 11 - Faculté de médecine (UP11 UFR Médecine), Université Paris-Sud - Paris 11 (UP11)-Université Paris-Sud - Paris 11 (UP11)-Centre National de Référence de la Résistance aux Antibiotiques (CNR), Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon)-Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), Université de Bordeaux (UB), CHI Poissy-Saint-Germain, Hôpital Foch [Suresnes], This work was supported by the Assistance Publique–Hôpitaux de Paris, Université Paris Sud (grant number EA 7361), LabEx Laboratoire d’Excellence en Recherche sur le Médicament et l’InnovationThérapeutique, supported by the French National Research Agency (grant number Agence Nationale de la Recherche [ANR]-10-LABX-33), by a project of ANR LabEx Integrative Biology of Emerging Infectious Diseases, and the Joint Program Initiative on Antimicrobial Resistance (grant number ANR-14-JAMR-0002)., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-14-JAMR-0002,DesInMBL,Structure-guided design of pan inhibitors of metallo-ß-lactamases(2014), Centre National de Référence Associé de la Résistance aux Antibiotiques [Hôpital Bicêtre AP-HP] (CNRARA/Service de Microbiologie), Université Paris-Sud - Paris 11 (UP11)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Bicêtre, and Université Paris-Sud - Paris 11 (UP11)-Institut Pasteur [Paris] (IP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Male, 0301 basic medicine, MESH: Fatal Outcome, Klebsiella pneumoniae, MESH: Klebsiella pneumoniae, Respiratory chain, MESH: beta-Lactamases, Bacteremia, Drug resistance, phylogeny, Fatal Outcome, carrier, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, polycyclic compounds, Medicine, MESH: Bacteremia, MESH: Bacterial Proteins, MESH: Microbial Sensitivity Tests, biology, MESH: Polymorphism, Single Nucleotide, within-host evolution, Anti-Bacterial Agents, 3. Good health, MESH: Klebsiella Infections, Infectious Diseases, NGS, Carrier State, MESH: Equipment Contamination, MESH: Carrier State, MESH: Whole Genome Sequencing, medicine.drug, Microbiology (medical), MESH: Mutation, 030106 microbiology, Virulence, Microbial Sensitivity Tests, MESH: Biofilms, Polymorphism, Single Nucleotide, beta-Lactamases, MESH: Endoscopy, MESH: Fimbriae, Bacterial, Microbiology, Evolution, Molecular, 03 medical and health sciences, Antibiotic resistance, Bacterial Proteins, MESH: Anti-Bacterial Agents, Drug Resistance, Bacterial, MESH: Drug Resistance, Bacterial, Humans, MESH: Humans, Whole Genome Sequencing, Colistin, business.industry, Endoscopy, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, MESH: Colistin, biochemical phenomena, metabolism, and nutrition, bacterial infections and mycoses, biology.organism_classification, medicine.disease, MESH: Male, Klebsiella Infections, KPC, Carriage, Biofilms, Fimbriae, Bacterial, Mutation, Equipment Contamination, business
Abstract

International audience; Background. Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae (KPC-Kp) has emerged globally over the last decade as a major nosocomial pathogen that threatens patient care. These highly resistant bacteria are mostly associated with a single Kp clonal group, CG258, but the reasons for its host and hospital adaptation remain largely unknown. Methods. We analyzed the in vivo evolution of a colistin-resistant KPC-Kp CG258 strain that contaminated a patient following an endoscopy and was responsible for a fatal bacteremia 4.5 years later. Whole-genome sequencing was performed on 17 KPC-Kp isolates from this patient; single-nucleotide polymorphisms were analyzed and their implication in antimicrobial resistance and bacterial host adaptation investigated. Results. The patient KPC-Kp strain diversified over 4.5 years at a rate of 7.5 substitutions per genome per year, resulting in broad phenotypic modifications. After 2 years of carriage, all isolates restored susceptibility to colistin. Higher expression of the fimbriae conferred the ability to produce more biofilm, and the isolate responsible for a bacteremia grew in human serum. The convergent mutations occurring in specific pathways, such as the respiratory chain and the cell envelope, revealed a complex long-term adaptation of KPC-Kp. Conclusions. Broad genomic and phenotypic diversification and the parallel selection of pathoadaptive mutations might contribute to long-term carriage and virulence of KPC-Kp CG258 strains and to the dissemination of this clone.

Published
2018

15. LMB-1 producing Citrobacter freundii from Argentina, a novel player in the field of MBLs

Author

Rémy A. Bonnin, Angela Famiglietti, Carlos Vay, Marcela Nastro, Laura Dabos, Carlos Hernán Rodríguez, Laurent Dortet, Bogdan I. Iorga, Thierry Naas, Structure, Dynamique, Fonction Et Expression Des Beta-Lactamases À Large Spectre, Université Paris-Sud - Paris 11 - Faculté de médecine (UP11 UFR Médecine), Université Paris-Sud - Paris 11 (UP11)-Université Paris-Sud - Paris 11 (UP11)-Centre National de Référence de la Résistance aux Antibiotiques (CNR), Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon)-Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), Laboratorio de Bacteriología Clínica [Buenos Aires], Facultad de Farmacia y Bioquímica [Buenos Aires] (FFYB), Universidad de Buenos Aires [Buenos Aires] (UBA)-Universidad de Buenos Aires [Buenos Aires] (UBA), Institut de Chimie des Substances Naturelles (ICSN), Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), and ANR-14-JAMR-0002,DesInMBL,Structure-guided design of pan inhibitors of metallo-ß-lactamases(2014)

Subjects
0301 basic medicine, Microbiology (medical), medicine.drug_class, 030106 microbiology, Cephalosporin, Argentina, Ceftazidime, Aztreonam, Microbial Sensitivity Tests, beta-Lactamases, Microbiology, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Plasmid, Bacterial Proteins, polycyclic compounds, medicine, Escherichia coli, Pharmacology (medical), 030212 general & internal medicine, Gene, Peptide sequence, biology, Whole Genome Sequencing, General Medicine, biochemical phenomena, metabolism, and nutrition, bacterial infections and mycoses, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Enterobacteriaceae, Citrobacter freundii, Infectious Diseases, Carbapenem-Resistant Enterobacteriaceae, chemistry, Genes, Bacterial, medicine.drug
Abstract

Carbapenemase-producing Enterobacterales expressing OXA-48, KPC, NDM, VIM or IMP enzymes are increasingly reported worldwide. We have characterized LMB-1, a novel metallo-β-lactamase (MBL) of Ambler class B3 from Citrobacter freundii 164 (Cf164) clinical isolate from Buenos Aires, Argentina. Cf164 displayed reduced susceptibility to carbapenems but gave inconsistent results with carbapenemase confirmatory tests, indicating the presence of a weak carbapenemase. Analysis of whole-genome sequencing (WGS) of Cf164 using Resfinder revealed four β-lactamase genes coding for CTX-M-8, PER-2, TEM-1 and CMY-150, a novel chromosomally-encoded CMY variant. Kinetic parameters of purified CMY-150 did not reveal any carbapenemase activity. However, CMY-150 conferred higher minimum inhibitory concentrations (MICs) to E. coli for ceftazidime and aztreonam compared with CMY-2. The in-house-developed β-lactamase search software (ResMiner) in WGS data revealed a novel subclass B3 MBL named LMB-1. LMB-1 conferred resistance to penicillins and expanded-spectrum cephalosporins and reduced susceptibility to carbapenems in E. coli. The blaLMB-1 gene was located on a 176-kb IncA/C2 plasmid. LMB-1 shared 99% amino acid sequence identity with the MBL encoded in the chromosome of Rheinheimera pacifica, it's likely progenitor. Despite repeated attempts, LMB-1 could not be purified, thus only specific activities could indicate hydrolysis of carbapenems. Here we report on CMY-150, a novel CMY-2 variant that confers increased ceftazidime and aztreonam MICs to E. coli and the first description of LMB-1 in Argentina. This work underlines the need for several carbapenemase-producing Enterobacteriaceae (CPE) confirmatory tests, as this novel enzyme might have been missed using only one.

Published
2019

16. Performance evaluation of molecular docking and free energy calculations protocols using the D3R Grand Challenge 4 dataset

Author

Bogdan I. Iorga, Ludovic Chaput, Bert L. de Groot, Nawel Mele, Eddy Elisée, Vytautas Gapsys, Edithe Selwa, Institut de Chimie des Substances Naturelles (ICSN), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Max Planck Institute for Biophysical Chemistry (MPI-BPC), Max-Planck-Gesellschaft, Maladies rénales fréquentes et rares : des mécanismes moléculaires à la médecine personnalisée (CoRaKID), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Research reported in this publication was supported by grants ANR-10-LABX-33 (LabEx LERMIT) and ANR-14-JAMR-0002 (JPIAMR) from the French National Research Agency (ANR), by the Région Ile-de-France (DIM Malinf), by the Université Paris- Saclay (Globetalkers 2019) and by European Research Council grant ERC-2012-ADG_20120314 (Grant Agreement 322947)., ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), ANR-14-JAMR-0002,DesInMBL,Structure-guided design of pan inhibitors of metallo-ß-lactamases(2014), European Project: 322947,EC:FP7:ERC,ERC-2012-ADG_20120314,OSAI(2013), IORGA, Bogdan, Idex Paris-Saclay - - IPS2011 - ANR-11-IDEX-0003 - IDEX - VALID, programmation conjointe européenne sur la résistance antimicrobienne - Structure-guided design of pan inhibitors of metallo-ß-lactamases - - DesInMBL2014 - ANR-14-JAMR-0002 - JPI AMR - VALID, Membranous nephropathy : a model for solving organ-specific auto-immunity (OSAI) - OSAI - - EC:FP7:ERC2013-05-01 - 2018-04-30 - 322947 - VALID, Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), and Common and Rare Kidney Diseases = Maladies Rénales Fréquentes et Rares: des Mécanismes Moléculaires à la Médecine Personnalisée (CORAKID)

Subjects
Protein Conformation, Computer science, Entropy, [CHIM.THER] Chemical Sciences/Medicinal Chemistry, [CHIM.THER]Chemical Sciences/Medicinal Chemistry, Crystallography, X-Ray, Ligands, computer.software_genre, 01 natural sciences, Molecular dynamics, Software, 0103 physical sciences, Drug Discovery, Humans, Physical and Theoretical Chemistry, Binding Sites, 010304 chemical physics, business.industry, 0104 chemical sciences, Computer Science Applications, Molecular Docking Simulation, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, 010404 medicinal & biomolecular chemistry, [CHIM.THEO] Chemical Sciences/Theoretical and/or physical chemistry, Workflow, Docking (molecular), Drug Design, Computer-Aided Design, Thermodynamics, Data mining, business, computer, Protein Binding
Abstract

International audience; Using the D3R Grand Challenge 4 dataset containing Beta-secretase 1 (BACE) and Cathepsin S (CatS) inhibitors, we have evaluated the performance of our in-house docking workflow that involves in the first step the selection of the most suitable docking software for the system of interest based on structural and functional information available in public databases, followed by the docking of the dataset to predict the binding modes and ranking of ligands. The macrocyclic nature of the BACE ligands brought additional challenges, which were dealt with by a careful preparation of the three-dimensional input structures for ligands. This provided top-performing predictions for BACE, in contrast with CatS, where the predictions in the absence of guiding constraints provided poor results. These results highlight the importance of previous structural knowledge that is needed for correct predictions on some challenging targets. After the end of the challenge, we also carried out free energy calculations (i.e. in a non-blinded manner) for CatS using the pmx software and several force fields (AMBER, Charmm). Using knowledge-based starting pose construction allowed reaching remarkable accuracy for the CatS free energy estimates. Interestingly, we show that the use of a consensus result, by averaging the results from different force fields, increases the prediction accuracy.

Published
2019

17. Blinded evaluation of cathepsin S inhibitors from the D3RGC3 dataset using molecular docking and free energy calculations

Author

Eddy Elisée, Ludovic Chaput, Bogdan I. Iorga, Edithe Selwa, Institut de Chimie des Substances Naturelles (ICSN), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Des Maladies Rénales Rares aux Maladies Fréquentes, Remodelage et Réparation, Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Région Ile-de-France (Conseil Régional, Île-de-France, DIM Malinf), ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), ANR-14-JAMR-0002,DesInMBL,Structure-guided design of pan inhibitors of metallo-ß-lactamases(2014), IORGA, Bogdan, Idex Paris-Saclay - - IPS2011 - ANR-11-IDEX-0003 - IDEX - VALID, programmation conjointe européenne sur la résistance antimicrobienne - Structure-guided design of pan inhibitors of metallo-ß-lactamases - - DesInMBL2014 - ANR-14-JAMR-0002 - JPI AMR - VALID, and Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Computer science, Protein Data Bank (RCSB PDB), Computational biology, Molecular Dynamics Simulation, Crystallography, X-Ray, Ligands, 01 natural sciences, 03 medical and health sciences, Molecular dynamics, Structure-Activity Relationship, 0103 physical sciences, Drug Discovery, Physical and Theoretical Chemistry, Enzyme Inhibitors, Databases, Protein, ComputingMilieux_MISCELLANEOUS, Binding Sites, 010304 chemical physics, Molecular Structure, chEMBL, Cathepsins, Computer Science Applications, Molecular Docking Simulation, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, [CHIM.THEO] Chemical Sciences/Theoretical and/or physical chemistry, 030104 developmental biology, Docking (molecular), Drug Design, Solvents, Computer-Aided Design, Thermodynamics, BindingDB, PubChem, Protein Binding
Abstract

During the last few years, we have developed a docking protocol involving two steps: (i) the choice of the most appropriate docking software and parameters for the system of interest using structural and functional information available in public databases (PDB, ChEMBL, PubChem Assay, BindingDB, etc.); (ii) the docking of ligand dataset to provide a prediction for the binding modes and ranking of ligands. We applied this protocol to the D3R Grand Challenge 3 dataset containing cathepsin S (CatS) inhibitors. Considering the size and conformational flexibility of ligands, the docking calculations afforded reasonable overall pose predictions, which are however dependent on the specific nature of each ligand. As expected, the correct ranking of docking poses is still challenging. Post-processing of docking poses with molecular dynamics simulations in explicit solvent provided a significantly better prediction, whereas free energy calculations on a subset of compounds brought no significant improvement in the ranking prediction compared with the direct ranking obtained from the scoring function.

Published
2019

18. Transcriptional Landscape of a bla KPC-2 Plasmid and Response to Imipenem Exposure in Escherichia coli TOP10

Author

Agnès B. Jousset, Isabelle Rosinski-Chupin, Julie Takissian, Philippe Glaser, Rémy A. Bonnin, Thierry Naas, Centre National de Référence Associé de la Résistance aux Antibiotiques [Hôpital Bicêtre AP-HP] (CNRARA/Service de Microbiologie), AP-HP Hôpital Bicêtre (Le Kremlin-Bicêtre), Ecologie et Evolution de la Résistance aux Antibiotiques / Ecology and Evolution of Antibiotics Resistance (EERA), Université Paris-Sud - Paris 11 (UP11)-Institut Pasteur [Paris] (IP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Centre National de la Recherche Scientifique (CNRS), Structure, Dynamique, Fonction Et Expression Des Beta-Lactamases À Large Spectre, Université Paris-Sud - Paris 11 - Faculté de médecine (UP11 UFR Médecine), Université Paris-Sud - Paris 11 (UP11)-Université Paris-Sud - Paris 11 (UP11)-Centre National de Référence de la Résistance aux Antibiotiques (CNR), Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon)-Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), This work was supported by the Assistance Publique—Hôpitaux de Paris, by a grant from the Université Paris-Sud (EA7361), by the LabEx LERMIT supported by a grant from the French National Research Agency (ANR-10-LABX-33), and by a project of ANR LabEx IBEID. This work was also funded in part by agrant from Joint Program Initiative on Antimicrobial Resistance(ANR-14-JAMR-0002)., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-14-JAMR-0002,DesInMBL,Structure-guided design of pan inhibitors of metallo-ß-lactamases(2014), Centre National de Référence Associé de la Résistance aux Antibiotiques, and Institut Pasteur [Paris]-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Sud Orsay-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Microbiology (medical), Imipenem, Operon, Klebsiella pneumoniae, 030106 microbiology, lcsh:QR1-502, Biology, medicine.disease_cause, Microbiology, lcsh:Microbiology, Transcriptome, 03 medical and health sciences, carbapenemase, Plasmid, medicine, oxidative-stress, Gene, Escherichia coli, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, 3. Good health, 030104 developmental biology, Regulon, KPC-producing plasmids, RNA-seq, transcriptome, medicine.drug
Abstract

International audience; The diffusion of KPC-2 carbapenemase is closely related to the spread of Klebsiella pneumoniae of the clonal-group 258 and linked to IncFII K plasmids. Little is known about the biology of multi-drug resistant plasmids and the reasons of their successful dissemination. Using E. coli TOP10 strain harboring a multi-replicon IncFII K-IncFIB bla KPC−2-gene carrying plasmid pBIC1a from K. pneumoniae ST-258 clinical isolate BIC-1, we aimed to identify basal gene expression and the effects of imipenem exposure using whole transcriptome approach by RNA sequencing (RNA-Seq). Independently of the antibiotic pressure, most of the plasmid-backbone genes were expressed at low levels. The most expressed pBIC1a genes were involved in antibiotic resistance (bla KPC−2 , bla TEM and aph(3 ′)-I), in plasmid replication and conjugation, or associated to mobile elements. After antibiotic exposure, 34% of E. coli (pBIC1a) genome was differentially expressed. Induction of oxidative stress response was evidenced, with numerous upregulated genes of the SoxRS/OxyR oxydative stress regulons, the Fur regulon (for iron uptake machinery), and IscR regulon (for iron sulfur cluster synthesis). Nine genes carried by pBIC1a were up-regulated, including the murein DD-endopeptidase mepM and the copper resistance operon. Despite the presence of a carbapenemase, we observed a major impact on E. coli (pBIC1a) whole transcriptome after imipenem exposure, but no effect on the level of transcription of antimicrobial resistance genes. We describe adaptive responses of E. coli to imipenem-induced stress, and identified plasmid-encoded genes that could be involved in resistance to stressful environments.

Published
2018

19. Structural and Functional Aspects of Class A Carbapenemases

Author

Thierry Naas, Bogdan I. Iorga, Laurent Dortet, Structure, Dynamique, Fonction Et Expression Des Beta-Lactamases À Large Spectre, Université Paris-Sud - Paris 11 - Faculté de médecine (UP11 UFR Médecine), Université Paris-Sud - Paris 11 (UP11)-Université Paris-Sud - Paris 11 (UP11)-Centre National de Référence de la Résistance aux Antibiotiques (CNR), Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon)-Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), Institut de Chimie des Substances Naturelles (ICSN), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Our laboratories are members of the Laboratory of Excellence in Research on Medication and Innovative Therapeutics (LERMIT) supported by a grant from the French National Research Agency (ANR-10-LABX-33). This work was also funded in part by a grant from Joint Programme Initiative on Antimicrobial Resistance (ANR-14-JAMR- 0002)., ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), and ANR-14-JAMR-0002,DesInMBL,Structure-guided design of pan inhibitors of metallo-ß-lactamases(2014)

Subjects
Models, Molecular, 0301 basic medicine, class A, Protein Conformation, 030106 microbiology, Clinical Biochemistry, Biology, Crystallography, X-Ray, Communicable Diseases, Article, beta-Lactamases, Microbiology, Structure-Activity Relationship, carbapenemase, 03 medical and health sciences, Drug Resistance, Bacterial, Gram-Negative Bacteria, Drug Discovery, Humans, Pharmacology & Pharmacy, crystallography, Monobactams, Biochemical properties, Phylogeny, Pharmacology, Genetics, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], molecular modeling, Hydrolysis, Treatment options, Chromosomes, Bacterial, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Anti-Bacterial Agents, 3. Good health, Molecular Medicine, 1115 Pharmacology And Pharmaceutical Sciences, Mobile genetic elements, mutagenesis, Plasmids
Abstract

International audience; The fight against infectious diseases is probably one of the greatest public health challenges faced by our society, especially with the emergence of carbapenem-resistant gram-negatives that are in some cases pan-drug resistant. Currently,-lactamase-mediated resistance does not spare even the newest and most powerful-lactams (carbapenems), whose activity is challenged by carbapenemases. The worldwide dissemination of carbapenemases in gram-negative organisms threatens to take medicine back into the pre-antibiotic era since the mortality associated with infections caused by these "su-perbugs" is very high, due to limited treatment options. Clinically-relevant carbapenemases belong either to metallo-lactamases (MBLs) of Ambler class B or to serine-lactamases (SBLs) of Ambler class A and D enzymes. Class A car-bapenemases may be chromosomally-encoded (SME, NmcA, SFC-1, BIC-1, PenA, FPH-1, SHV-38), plasmid-encoded (KPC, GES, FRI-1) or both (IMI). The plasmid-encoded enzymes are often associated with mobile elements responsible for their mobilization. These enzymes, even though weakly related in terms of sequence identities, share structural features and a common mechanism of action. They variably hydrolyse penicillins, cephalosporins, monobactams, carbap-enems, and are inhibited by clavulanate and tazobactam. Three-dimensional structures of class A carbapenemases, in the apo form or in complex with substrates/inhibitors, together with site-directed mutagenesis studies, provide essential input for identifying the structural factors and subtle conformational changes that influence the hydrolytic profile and inhibition of these enzymes. Overall, these data represent the building blocks for understanding the structure-function relationships that define the phenotypes of class A carbapenemases and can guide the design of new molecules of therapeutic interest.

Published
2016

20. Beta-lactamase database (BLDB) – structure and function

Author

Agustin Zavala, Thierry Naas, Rémy A. Bonnin, Laurent Dortet, Pascal Retailleau, Bogdan I. Iorga, Maria Laura Dabos, Saoussen Oueslati, Structure, Dynamique, Fonction Et Expression Des Beta-Lactamases À Large Spectre, Université Paris-Sud - Paris 11 - Faculté de médecine (UP11 UFR Médecine), Université Paris-Sud - Paris 11 (UP11)-Université Paris-Sud - Paris 11 (UP11)-Centre National de Référence de la Résistance aux Antibiotiques (CNR), Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon)-Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), Institut de Chimie des Substances Naturelles (ICSN), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), This work was supported by the Laboratory of Excellence in Research on Medication and Innovative Therapeutics (LERMIT) [grant number ANR-10-LABX-33], by the JPIAMR transnational project DesInMBL [grant number ANR-14-JAMR-0002] and by the Région Ile-de-France (DIM Malinf)., ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), and ANR-14-JAMR-0002,DesInMBL,Structure-guided design of pan inhibitors of metallo-ß-lactamases(2014)

Subjects
0301 basic medicine, antibiotic resistance, Subfamily, Protein Conformation, medicine.medical_treatment, 030106 microbiology, Context (language use), Biology, computer.software_genre, beta-Lactamases, hydrolytic profile, Database, 03 medical and health sciences, Drug Discovery, medicine, mutant, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Databases, Protein, Public resource, Pharmacology, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], lcsh:RM1-950, SUPERFAMILY, General Medicine, computer.file_format, Protein Data Bank, Structure and function, lcsh:Therapeutics. Pharmacology, 030104 developmental biology, Beta-lactamase, Original Article, beta-lactamase, computer
Abstract

International audience; Beta-Lactamase Database (BLDB) is a comprehensive, manually curated public resource providing up-to-date structural and functional information focused on this superfamily of enzymes with a great impact on antibiotic resistance. All the enzymes reported and characterised in the literature are presented according to the class (A, B, C and D), family and subfamily to which they belong. All three-dimensional structures of b-lactamases present in the Protein Data Bank are also shown. The characterisation of representative mutants and hydrolytic profiles (kinetics) completes the picture and altogether these four elements constitute the essential foundation for a better understanding of the structure-function relationship within this enzymes family. BLDB can be queried using different protein-and nucleotide-based BLAST searches, which represents a key feature of particular importance in the context of the surveillance of the evolution of the antibiotic resistance. BLDB is available online at http://bldb.eu without any registration and supports all modern browsers.

Published
2017

21. SAMPL6: Calculation of macroscopic pK(a) values from ab initio quantum mechanical free energies

Author

Bogdan I. Iorga, Edithe Selwa, Oliver Beckstein, Ian M. Kenney, Institut de Chimie des Substances Naturelles (ICSN), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Department of Physics, Arizona State University (ASU), Arizona State University [Tempe] (ASU), Grant DIM MAL-INF from the Région Ile-de-FranceNational Institute Of General Medical Sciences of the National Institutes of Health under Award Number R01GM118772, ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), and ANR-14-JAMR-0002,DesInMBL,Structure-guided design of pan inhibitors of metallo-ß-lactamases(2014)

Subjects
0301 basic medicine, Mean squared error, Implicit solvation, Ab initio, Thermodynamics, 01 natural sciences, Quantum chemistry, Article, 03 medical and health sciences, Polarizability, Heterocyclic Compounds, 0103 physical sciences, Drug Discovery, Physical and Theoretical Chemistry, Physics::Chemical Physics, Quantum, Physics, Quantitative Biology::Biomolecules, 010304 chemical physics, Molecular Structure, Solvation, Hydrogen-Ion Concentration, Microstate (statistical mechanics), Computer Science Applications, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, 030104 developmental biology, Models, Chemical, Solvents, Quantum Theory, Databases, Chemical
Abstract

International audience; Macroscopic pKa values were calculated for all compounds in the SAMPL6 blind prediction challenge, based on quantum chemical calculations with a continuum solvation model and a linear correction derived from a small training set. Microscopic pKa values were derived from the gas-phase free energy difference between protonated and deprotonated forms together with the Conductor-like Polarizable Continuum Solvation Model and the experimental solvation free energy of the proton. pH-dependent microstate free energies were obtained from the microscopic pKas with a maximum likelihood estimator and appropriately summed to yield macroscopic pKa values or microstate populations as function of pH. We assessed the accuracy of three approaches to calculate the microscopic pKas: direct use of the quantum mechanical free energy differences and correction of the direct values for short-comings in the QM solvation model with two different linear models that we independently derived from a small training set of 38 compounds with known pKa. The predictions that were corrected with the linear models had much better accuracy [root-mean-square error (RMSE) 2.04 and 1.95 pKa units] than the direct calculation (RMSE 3.74). Statistical measures indicate that some systematic errors remain, likely due to differences in the SAMPL6 data set and the small training set with respect to their interactions with water. Overall, the current approach provides a viable physics-based route to estimate macroscopic pKa values for novel compounds with reasonable accuracy.

Published
2018

22. Genetic and Biochemical Characterization of OXA-519, a Novel OXA-48-Like β-Lactamase

Author

Rémy A. Bonnin, Pierre Bogaerts, Daniel T. Huang, Thierry Naas, Agustin Zavala, Youri Glupczynski, Laura Dabos, Bogdan I. Iorga, Pierre Sacré, UCL - SSS/IREC/MONT - Pôle Mont Godinne, UCL - (MGD) Laboratoire de biologie clinique, Structure, Dynamique, Fonction Et Expression Des Beta-Lactamases À Large Spectre, Université Paris-Sud - Paris 11 - Faculté de médecine (UP11 UFR Médecine), Université Paris-Sud - Paris 11 (UP11)-Université Paris-Sud - Paris 11 (UP11)-Centre National de Référence de la Résistance aux Antibiotiques (CNR), Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon)-Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), CHU Dinant-Godinne UCL Namur [Yvoir, Belgique], Institut de Chimie des Substances Naturelles (ICSN), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), This work was supported by the Assistance Publique-Hôpitaux de Paris (AP-HP), the University Paris-Sud, the Laboratory of Excellence in Research on Medication and Innovative Therapeutics (LERMIT) supported by a grant from the French National Research Agency (grant ANR-10-LABX-33) and by the Joint Programming Initiative on Antimicrobial Resistance (JPIAMR) DesInMBL (grant ANR-14-JAMR-002), and by DIM Malinf, Ile de France, for L.D.’s PhD fellowship., ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), and ANR-14-JAMR-0002,DesInMBL,Structure-guided design of pan inhibitors of metallo-ß-lactamases(2014)

Subjects
0301 basic medicine, Ertapenem, Imipenem, Carbapenem, Klebsiella pneumoniae, 030106 microbiology, Mutant, Microbial Sensitivity Tests, Meropenem, beta-Lactam Resistance, beta-Lactamases, Microbiology, 03 medical and health sciences, chemistry.chemical_compound, Plasmid, Mechanisms of Resistance, medicine, polycyclic compounds, Humans, Pharmacology (medical), Gene, ComputingMilieux_MISCELLANEOUS, Sequence Deletion, Pharmacology, Aged, 80 and over, biology, Base Sequence, Chemistry, Hydrolysis, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, Anti-Bacterial Agents, Klebsiella Infections, Isoenzymes, Mutagenesis, Insertional, Infectious Diseases, Amino Acid Substitution, bacteria, medicine.drug, Plasmids
Abstract

A multidrug-resistant Klebsiella pneumoniae 1210 isolate with reduced carbapenem susceptibility revealed the presence of a novel plasmid-encoded blaOXA-48-like gene, named blaOXA-519 The 60.7-kb plasmid (pOXA-519) was similar to the IncL-OXA-48 prototypical plasmid except for a ca. 2-kb deletion due to an IS1R insertion. OXA-519 differed from OXA-48 by a Val120Leu substitution, which resulted in an overall reduced β-lactam-hydrolysis profile, except those for ertapenem and meropenem, which were increased. Thus, detection of OXA-519 producers using biochemical tests that monitor imipenem hydrolysis will be difficult.

Published
2018

23. Blinded evaluation of farnesoid X receptor (FXR) ligands binding using molecular docking and free energy calculations

Author

Eddy Elisée, Edithe Selwa, Agustin Zavala, Bogdan I. Iorga, Institut de Chimie des Substances Naturelles (ICSN), Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), and ANR-14-JAMR-0002,DesInMBL,Structure-guided design of pan inhibitors of metallo-ß-lactamases(2014)

Subjects
0301 basic medicine, Protein Conformation, Protein Data Bank (RCSB PDB), Receptors, Cytoplasmic and Nuclear, Computational biology, [CHIM.THER]Chemical Sciences/Medicinal Chemistry, Ligands, 01 natural sciences, Molecular Docking Simulation, Force field (chemistry), Small Molecule Libraries, 03 medical and health sciences, Chemical Moiety, Farnesoid X receptor, Drug Discovery, scoring function, Humans, Drug Design Data Resource, Spiro Compounds, Physical and Theoretical Chemistry, Databases, Protein, Simulation, Autodock, Sulfonamides, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Chemistry, Grand Challenge 2 2, Isoxazoles, AutoDock, 0104 chemical sciences, Computer Science Applications, 010404 medicinal & biomolecular chemistry, 030104 developmental biology, Protein–ligand docking, FXR, Docking (molecular), Drug Design, Vina, docking, Thermodynamics, Benzimidazoles, Gold, Software, D3R, [CHIM.CHEM]Chemical Sciences/Cheminformatics, Protein Binding
Abstract

This work was supported by the Laboratory of Excellence in Research on Medication and Innovative Therapeutics (LERMIT) [grant number ANR-10-LABX-33], by the JPIAMR transnational project DesInMBL [grant number ANR-14-JAMR-0002] and by the Région Ile-de-France (DIM Malinf).; International audience; Our participation to the D3R Grand Challenge 2 involved a protocol in two steps, with an initial analysis of the available structural data from the PDB allowing the selection of the most appropriate combination of docking software and scoring function. Subsequent docking calculations showed that the pose prediction can be carried out with a certain precision, but this is dependent on the specific nature of the ligands. The correct ranking of docking poses is still a problem and cannot be successful in the absence of good pose predictions. Our free energy calculations on two different subsets provided contrasted results, which might have the origin in non-optimal force field parameters associated with the sulfonamide chemical moiety.

Published
2018

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