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Romano K, Hung D. Targeting LPS biosynthesis and transport in gram-negative bacteria in the era of multi-drug resistance. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119407. [PMID: 36543281 PMCID: PMC9922520 DOI: 10.1016/j.bbamcr.2022.119407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 11/09/2022] [Accepted: 11/18/2022] [Indexed: 12/23/2022]
Abstract
Gram-negative bacteria pose a major threat to human health in an era fraught with multi-drug resistant bacterial infections. Despite extensive drug discovery campaigns over the past decades, no new antibiotic target class effective against gram-negative bacteria has become available to patients since the advent of the carbapenems in 1985. Antibiotic discovery efforts against gram-negative bacteria have been hampered by limited intracellular accumulation of xenobiotics, in large part due to the impermeable cell envelope comprising lipopolysaccharide (LPS) in the outer leaflet of the outer membrane, as well as a panoply of efflux pumps. The biosynthesis and transport of LPS are essential to the viability and virulence of most gram-negative bacteria. Thus, both LPS biosynthesis and transport are attractive pathways to target therapeutically. In this review, we summarize the LPS biosynthesis and transport pathways and discuss efforts to find small molecule inhibitors against targets within these pathways.
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Affiliation(s)
- K.P. Romano
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA, USA,The Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
| | - D.T. Hung
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA,Department of Genetics, Harvard Medical School, Boston, MA, USA,Corresponding author at: The Broad Institute of MIT and Harvard, Cambridge, MA, USA. (D.T. Hung)
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2
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Troudi A, Pagès JM, Brunel JM. Chemical Highlights Supporting the Role of Lipid A in Efficient Biological Adaptation of Gram-Negative Bacteria to External Stresses. J Med Chem 2021; 64:1816-1834. [PMID: 33538159 DOI: 10.1021/acs.jmedchem.0c02185] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The outer membrane (OM) of Gram-negative bacteria provides an efficient barrier against external noxious compounds such as antimicrobial agents. Associated with drug target modification, it contributes to the overall failure of chemotherapy. In the complex OM architecture, Lipid A plays an essential role by anchoring the lipopolysaccharide in the membrane and ensuring the spatial organization between lipids, proteins, and sugars. Currently, the targets of almost all antibiotics are intracellularly located and require translocation across membranes. We report herein an integrated view of Lipid A synthesis, membrane assembly, a structure comparison at the molecular structure level of numerous Gram-negative bacterial species, as well as its recent use as a target for original antibacterial molecules. This review paves the way for a new vision of a key membrane component that acts during bacterial adaptation to environmental stresses and for the development of new weapons against microbial resistance to usual antibiotics.
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Affiliation(s)
- Azza Troudi
- UMR-MD1, U1261, Aix Marseille Université, INSERM, SSA, MCT, 13385 Marseille, France.,Laboratory of Microorganisms and Active Biomolecules, Department of Biology, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis 1008, Tunisia
| | - Jean Marie Pagès
- UMR-MD1, U1261, Aix Marseille Université, INSERM, SSA, MCT, 13385 Marseille, France
| | - Jean Michel Brunel
- UMR-MD1, U1261, Aix Marseille Université, INSERM, SSA, MCT, 13385 Marseille, France
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3
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Ma X, Prathapam R, Wartchow C, Chie-Leon B, Ho CM, De Vicente J, Han W, Li M, Lu Y, Ramurthy S, Shia S, Steffek M, Uehara T. Structural and Biological Basis of Small Molecule Inhibition of Escherichia coli LpxD Acyltransferase Essential for Lipopolysaccharide Biosynthesis. ACS Infect Dis 2020; 6:1480-1489. [PMID: 31402665 DOI: 10.1021/acsinfecdis.9b00127] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
LpxD, acyl-ACP-dependent N-acyltransferase, is the third enzyme of lipid A biosynthesis in Gram-negative bacteria. A recent probe-based screen identified several compounds, including 6359-0284 (compound 1), that inhibit the enzymatic activity of Escherichia coli (E. coli) LpxD. Here, we use these inhibitors to chemically validate LpxD as an attractive antibacterial target. We first found that compound 1 was oxidized in solution to the more stable aromatized tetrahydro-pyrazolo-quinolinone compound 1o. From the Escherichia coli strain deficient in efflux, we isolated a mutant that was less susceptible to compound 1o and had an lpxD missense mutation (Gly268Cys), supporting the cellular on-target activity. Using surface plasma resonance, we showed direct binding to E. coli LpxD for compound 1o and other reported LpxD inhibitors in vitro. Furthermore, we determined eight cocrystal structures of E. coli LpxD/inhibitor complexes. These costructures pinpointed the 4'-phosphopantetheine binding site as the common ligand binding hotspot, where hydrogen bonds to Gly269 and/or Gly287 were important for inhibitor binding. In addition, the LpxD/compound 1o costructure rationalized the reduced activity of compound 1o in the LpxDGly268Cys mutant. Moreover, we obtained the LpxD structure in complex with a previously reported LpxA/LpxD dual targeting peptide inhibitor, RJPXD33, providing structural rationale for the unique dual targeting properties of this peptide. Given that the active site residues of LpxD are conserved in multidrug resistant Enterobacteriaceae, this work paves the way for future LpxD drug discovery efforts combating these Gram-negative pathogens.
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Kroeck KG, Sacco MD, Smith EW, Zhang X, Shoun D, Akhtar A, Darch SE, Cohen F, Andrews LD, Knox JE, Chen Y. Discovery of dual-activity small-molecule ligands of Pseudomonas aeruginosa LpxA and LpxD using SPR and X-ray crystallography. Sci Rep 2019; 9:15450. [PMID: 31664082 PMCID: PMC6820557 DOI: 10.1038/s41598-019-51844-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 10/09/2019] [Indexed: 11/09/2022] Open
Abstract
The lipid A biosynthesis pathway is essential in Pseudomonas aeruginosa. LpxA and LpxD are the first and third enzymes in this pathway respectively, and are regarded as promising antibiotic targets. The unique structural similarities between these two enzymes make them suitable targets for dual-binding inhibitors, a characteristic that would decrease the likelihood of mutational resistance and increase cell-based activity. We report the discovery of multiple small molecule ligands that bind to P. aeruginosa LpxA and LpxD, including dual-binding ligands. Binding poses were determined for select compounds by X-ray crystallography. The new structures reveal a previously uncharacterized magnesium ion residing at the core of the LpxD trimer. In addition, ligand binding in the LpxD active site resulted in conformational changes in the distal C-terminal helix-bundle, which forms extensive contacts with acyl carrier protein (ACP) during catalysis. These ligand-dependent conformational changes suggest a potential allosteric influence of reaction intermediates on ACP binding, and vice versa. Taken together, the novel small molecule ligands and their crystal structures provide new chemical scaffolds for ligand discovery targeting lipid A biosynthesis, while revealing structural features of interest for future investigation of LpxD function.
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Affiliation(s)
- Kyle G Kroeck
- Department of Molecular Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, Tampa, Florida, 33612, United States
| | - Michael D Sacco
- Department of Molecular Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, Tampa, Florida, 33612, United States
| | - Emmanuel W Smith
- Department of Molecular Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, Tampa, Florida, 33612, United States
| | - Xiujun Zhang
- Department of Molecular Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, Tampa, Florida, 33612, United States
| | - Daniel Shoun
- Department of Molecular Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, Tampa, Florida, 33612, United States
| | - Afroza Akhtar
- Department of Molecular Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, Tampa, Florida, 33612, United States
| | - Sophie E Darch
- Department of Molecular Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, Tampa, Florida, 33612, United States
| | - Frederick Cohen
- Former employees of ACHAOGEN Inc., 1 Tower Place, Suite 400, South San Francisco, California, 94080, United States
| | - Logan D Andrews
- Former employees of ACHAOGEN Inc., 1 Tower Place, Suite 400, South San Francisco, California, 94080, United States
| | - John E Knox
- Former employees of ACHAOGEN Inc., 1 Tower Place, Suite 400, South San Francisco, California, 94080, United States
| | - Yu Chen
- Department of Molecular Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, Tampa, Florida, 33612, United States.
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5
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González-Bello C. The Inhibition of Lipid A Biosynthesis-The Antidote Against Superbugs? ADVANCED THERAPEUTICS 2018. [DOI: 10.1002/adtp.201800117] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS); Departamento de Química Orgánica; Universidade de Santiago de Compostela; calle Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
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Zhou P, Zhao J. Structure, inhibition, and regulation of essential lipid A enzymes. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1862:1424-1438. [PMID: 27940308 DOI: 10.1016/j.bbalip.2016.11.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 11/28/2016] [Accepted: 11/30/2016] [Indexed: 10/20/2022]
Abstract
The Raetz pathway of lipid A biosynthesis plays a vital role in the survival and fitness of Gram-negative bacteria. Research efforts in the past three decades have identified individual enzymes of the pathway and have provided a mechanistic understanding of the action and regulation of these enzymes at the molecular level. This article reviews the discovery, biochemical and structural characterization, and regulation of the essential lipid A enzymes, as well as continued efforts to develop novel antibiotics against Gram-negative pathogens by targeting lipid A biosynthesis. This article is part of a Special Issue entitled: Bacterial Lipids edited by Russell E. Bishop.
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Affiliation(s)
- Pei Zhou
- Department of Biochemistry, Duke University Medical Center, Research Drive, DUMC 3711, Durham, NC 27710, USA.
| | - Jinshi Zhao
- Department of Biochemistry, Duke University Medical Center, Research Drive, DUMC 3711, Durham, NC 27710, USA
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Smith EW, Zhang X, Behzadi C, Andrews LD, Cohen F, Chen Y. Structures of Pseudomonas aeruginosa LpxA Reveal the Basis for Its Substrate Selectivity. Biochemistry 2015; 54:5937-48. [PMID: 26352800 DOI: 10.1021/acs.biochem.5b00720] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In Gram-negative bacteria, the first step of lipid A biosynthesis is catalyzed by UDP-N-acetylglucosamine acyltransferase (LpxA) through the transfer of a R-3-hydroxyacyl chain from the acyl carrier protein (ACP) to the 3-hydroxyl group of UDP-GlcNAc. Previous studies suggest that LpxA is a critical determinant of the acyl chain length found in lipid A, which varies among species of bacteria. In Escherichia coli and Leptospira interrogans, LpxA prefers to incorporate longer R-3-hydroxyacyl chains (C14 and C12, respectively), whereas in Pseudomonas aeruginosa, the enzyme is selective for R-3-hydroxydecanoyl, a 10-hydrocarbon long acyl chain. We now report three P. aeruginosa LpxA crystal structures: apo protein, substrate complex with UDP-GlcNAc, and product complex with UDP-3-O-(R-3-hydroxydecanoyl)-GlcNAc. A comparison between the apo form and complexes identifies key residues that position UDP-GlcNAc appropriately for catalysis and supports the role of catalytic His121 in activating the UDP-GlcNAc 3-hydroxyl group for nucleophilic attack during the reaction. The product-complex structure, for the first time, offers structural insights into how Met169 serves to constrain the length of the acyl chain and thus functions as the so-called hydrocarbon ruler. Furthermore, compared with ortholog LpxA structures, the purported oxyanion hole, formed by the backbone amide group of Gly139, displays a different conformation in P. aeruginosa LpxA, which suggests flexibility of this structural feature important for catalysis and the potential need for substrate-induced conformational change in catalysis. Taken together, the three structures provide valuable insights into P. aeruginosa LpxA catalysis and substrate specificity as well as templates for future inhibitor discovery.
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Affiliation(s)
- Emmanuel W Smith
- Department of Molecular Medicine, University of South Florida , 12901 Bruce B. Downs Boulevard, Tampa, Florida 33612, United States
| | - XiuJun Zhang
- Department of Molecular Medicine, University of South Florida , 12901 Bruce B. Downs Boulevard, Tampa, Florida 33612, United States
| | - Cyrus Behzadi
- Department of Molecular Medicine, University of South Florida , 12901 Bruce B. Downs Boulevard, Tampa, Florida 33612, United States
| | - Logan D Andrews
- ACHAOGEN Inc. , 7000 Shoreline Court, South San Francisco, California 94080, United States
| | - Frederick Cohen
- ACHAOGEN Inc. , 7000 Shoreline Court, South San Francisco, California 94080, United States
| | - Yu Chen
- Department of Molecular Medicine, University of South Florida , 12901 Bruce B. Downs Boulevard, Tampa, Florida 33612, United States
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Ngo A, Fong KT, Cox DL, Chen X, Fisher AJ. Structures of Bacteroides fragilis uridine 5'-diphosphate-N-acetylglucosamine (UDP-GlcNAc) acyltransferase (BfLpxA). ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:1068-76. [PMID: 25945572 PMCID: PMC4427197 DOI: 10.1107/s1399004715003326] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Accepted: 02/16/2015] [Indexed: 11/11/2022]
Abstract
Uridine 5'-diphosphate-N-acetylglucosamine (UDP-GlcNAc) acyltransferase (LpxA) catalyzes a reversible reaction for adding an O-acyl group to the GlcNAc in UDP-GlcNAc in the first step of lipid A biosynthesis. Lipid A constitutes a major component of lipopolysaccharides, also referred to as endotoxins, which form the outer monolayer of the outer membrane of Gram-negative bacteria. Ligand-free and UDP-GlcNAc-bound crystal structures of LpxA from Bacteroides fragilis NCTC 9343, the most common pathogenic bacteria found in abdominal abscesses, have been determined and are presented here. The enzyme crystallizes in a cubic space group, with the crystallographic threefold axis generating the biological functional homotrimer and with each monomer forming a nine-rung left-handed β-helical (LβH) fold in the N-terminus followed by an α-helical motif in the C-terminus. The structure is highly similar to LpxA from other organisms. Yet, despite sharing a similar LβH structure with LpxAs from Escherichia coli and others, previously unseen calcium ions are observed on the threefold axis in B. fragilis LpxA to help stabilize the trimeric assembly.
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Affiliation(s)
- Alice Ngo
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Kai T. Fong
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Daniel L. Cox
- Department of Physics, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Xi Chen
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Andrew J. Fisher
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA
- Department of Molecular and Cellular Biology, University of California, One Shields Avenue, Davis, CA 95616, USA
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Alshalchi SA, Anderson GG. Expression of the lipopolysaccharide biosynthesis gene lpxD affects biofilm formation of Pseudomonas aeruginosa. Arch Microbiol 2014; 197:135-45. [PMID: 25173672 DOI: 10.1007/s00203-014-1030-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 08/13/2014] [Accepted: 08/15/2014] [Indexed: 12/28/2022]
Abstract
Bacterial biofilms are an important cause of nosocomial infections. Microorganisms such as Pseudomonas aeruginosa colonize biotic and abiotic surfaces leading to chronic infections that are difficult to eradicate. To characterize novel genes involved in biofilm formation, we identified the lpxD gene from a transposon-mutant library of P. aeruginosa. This gene encodes a glucosamine-N acyltransferase, which is important for lipopolysaccharide biosynthesis. Our results showed that a loss-of-expression mutant of lpxD was defective for biofilm formation on biotic and abiotic surfaces. Additionally, this mutant strain exhibited significantly decreased bacterial attachment to cultured airway epithelial cells, as well as increased bacterial cytotoxicity toward airway cells. However, consistent with a defect in lipid A structure, airway cells incubated with the lpxD mutant or with mutant lipid A extracts exhibited decreased IL-8 production and necrosis, respectively. Overall, our data indicate that manipulating lpxD expression may influence P. aeruginosa's ability to establish biofilm infections.
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Affiliation(s)
- Sahar A Alshalchi
- Department of Biology, Indiana University Purdue University Indianapolis, 723 West Michigan Street, SL 320, Indianapolis, IN, 46202, USA
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10
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Abstract
Lipopolysaccharide molecules represent a unique family of glycolipids based on a highly conserved lipid moiety known as lipid A. These molecules are produced by most gram-negative bacteria, in which they play important roles in the integrity of the outer-membrane permeability barrier and participate extensively in host-pathogen interplay. Few bacteria contain lipopolysaccharide molecules composed only of lipid A. In most forms, lipid A is glycosylated by addition of the core oligosaccharide that, in some bacteria, provides an attachment site for a long-chain O-antigenic polysaccharide. The complexity of lipopolysaccharide structures is reflected in the processes used for their biosynthesis and export. Rapid growth and cell division depend on the bacterial cell's capacity to synthesize and export lipopolysaccharide efficiently and in large amounts. We review recent advances in those processes, emphasizing the reactions that are essential for viability.
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Affiliation(s)
- Chris Whitfield
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada;
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Yeom DH, Kim SK, Lee MN, Lee JH. Pleiotropic effects of acyltransferases on various virulence-related phenotypes of Pseudomonas aeruginosa. Genes Cells 2013; 18:682-93. [PMID: 23848169 DOI: 10.1111/gtc.12076] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2013] [Accepted: 04/16/2013] [Indexed: 02/01/2023]
Abstract
Pseudomonas aeruginosa, an opportunistic pathogen causing various infections, expresses various virulence factors under the control of quorum sensing (QS), a cell density-sensing mechanism. Because the major signal molecules of QS are acyl homoserine lactones (acyl-HSLs), acyltransferases, the enzymes that act upon acyl group transfer could affect the QS signaling and QS-related virulence phenotypes. In this study, we overexpressed acyltransferases of P. aeruginosa and screened them for the activity influencing the QS and QS-related virulence phenotypes. Among seven acyltransferases tested in this study, two acyltransferases, PA3984 (apolipoprotein N-acyltransferase) and PA2537 (putative acyltransferase), significantly affected both growth of P. aeruginosa and the activity of LasR, a major QS regulator, when overexpressed. These acyltransferases also reduced virulence and swarming motility of P. aeruginosa. The other acyltransferase, PA3646 (UDP-3-O-[3-hydroxylauroyl] glucosamine N-acyltransferase), reduced the LasR activity, swarming motility, protease production and virulence without any influence on growth. These effects by PA3646 over-expression were caused by less production of QS signal. PA3644 (UDP-N-acetylglucosamine acyltransferase) enhanced biofilm formation and swarming motility with no effect on the growth and QS activity. These results suggest that acyltransferases may be an important factor regulating the cellular activity about virulence-related phenotypes.
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Affiliation(s)
- Doo Hwan Yeom
- Laboratory of Microbiology, Department of Pharmacy, College of Pharmacy, Pusan National University, Research Building 537, San 30, Jangjun-Dong, Geumjung-Gu, Busan 609-735, South Korea
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Badger J, Chie-Leon B, Logan C, Sridhar V, Sankaran B, Zwart PH, Nienaber V. Structure determination of LpxD from the lipopolysaccharide-synthesis pathway of Acinetobacter baumannii. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 69:6-9. [PMID: 23295477 DOI: 10.1107/s1744309112048890] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 11/28/2012] [Indexed: 11/10/2022]
Abstract
Acinetobacter baumannii is a Gram-negative bacterium that is resistant to many currently available antibiotics. The protein LpxD is a component of the biosynthetic pathway for lipopolysaccharides in the outer membrane of this bacterium and is a potential target for new antibacterial agents. This paper describes the structure determination of apo forms of LpxD in space groups P2(1) and P4(3)22. These crystals contained six and three copies of the protein molecule in the asymmetric unit and diffracted to 2.8 and 2.7 Å resolution, respectively. A comparison of the multiple protein copies in the asymmetric units of these crystals reveals a common protein conformation and a conformation in which the relative orientation between the two major domains in the protein is altered.
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Affiliation(s)
- John Badger
- Zenobia Therapeutics Inc., 505 Coast Boulevard South, Suite 111, La Jolla, CA 92037, USA.
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