1
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Niu Z, Lei P, Wang Y, Wang J, Yang J, Zhang J. Small molecule LpxC inhibitors against gram-negative bacteria: Advances and future perspectives. Eur J Med Chem 2023; 253:115326. [PMID: 37023679 DOI: 10.1016/j.ejmech.2023.115326] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/18/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023]
Abstract
Uridine diphosphate-3-O-(hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC) is a metalloenzyme with zinc ions as cofactors and is a key enzyme in the essential structural outer membrane lipid A synthesis commitment step of gram-negative bacteria. As LpxC is extremely homologous among different Gram-negative bacteria, it is conserved in almost all gram-negative bacteria, which makes LpxC a promising target. LpxC inhibitors have been reported extensively in recent years, such as PF-5081090 and CHIR-090 were found to have broad-spectrum antibiotic activity against P. aeruginosa and E. coli. They are mainly classified into hydroxamate inhibitors and non-hydroxamate inhibitors based on their structure, but no LpxC inhibitors have been marketed due to safety and activity issues. This review, therefore, focuses on small molecule inhibitors of LpxC against gram-negative pathogenic bacteria and covers recent advances in LpxC inhibitors, focusing on their structural optimization process, structure-activity relationships, and future directions, with the aim of providing ideas for the development of LpxC inhibitors and clinical research.
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2
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Dewachter L, Brooks AN, Noon K, Cialek C, Clark-ElSayed A, Schalck T, Krishnamurthy N, Versées W, Vranken W, Michiels J. Deep mutational scanning of essential bacterial proteins can guide antibiotic development. Nat Commun 2023; 14:241. [PMID: 36646716 PMCID: PMC9842644 DOI: 10.1038/s41467-023-35940-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 01/09/2023] [Indexed: 01/18/2023] Open
Abstract
Deep mutational scanning is a powerful approach to investigate a wide variety of research questions including protein function and stability. Here, we perform deep mutational scanning on three essential E. coli proteins (FabZ, LpxC and MurA) involved in cell envelope synthesis using high-throughput CRISPR genome editing, and study the effect of the mutations in their original genomic context. We use more than 17,000 variants of the proteins to interrogate protein function and the importance of individual amino acids in supporting viability. Additionally, we exploit these libraries to study resistance development against antimicrobial compounds that target the selected proteins. Among the three proteins studied, MurA seems to be the superior antimicrobial target due to its low mutational flexibility, which decreases the chance of acquiring resistance-conferring mutations that simultaneously preserve MurA function. Additionally, we rank anti-LpxC lead compounds for further development, guided by the number of resistance-conferring mutations against each compound. Our results show that deep mutational scanning studies can be used to guide drug development, which we hope will contribute towards the development of novel antimicrobial therapies.
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Affiliation(s)
- Liselot Dewachter
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium. .,VIB-KU Leuven Center for Microbiology, Leuven, Belgium.
| | | | | | | | | | - Thomas Schalck
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium.,VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | | | - Wim Versées
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,VIB-VUB Center for Structural Biology, Brussels, Belgium
| | - Wim Vranken
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,VIB-VUB Center for Structural Biology, Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels, Belgium
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium. .,VIB-KU Leuven Center for Microbiology, Leuven, Belgium.
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3
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Fan S, Li D, Yan M, Feng X, Lv G, Wu G, Jin Y, Wang Y, Yang Z. The Complex Structure of Protein AaLpxC from Aquifex aeolicus with ACHN-975 Molecule Suggests an Inhibitory Mechanism at Atomic-Level against Gram-Negative Bacteria. Molecules 2021; 26:molecules26051451. [PMID: 33800069 PMCID: PMC7962117 DOI: 10.3390/molecules26051451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 02/28/2021] [Accepted: 03/04/2021] [Indexed: 11/16/2022] Open
Abstract
New drugs with novel antibacterial targets for Gram-negative bacterial pathogens are desperately needed. The protein LpxC is a vital enzyme for the biosynthesis of lipid A, an outer membrane component of Gram-negative bacterial pathogens. The ACHN-975 molecule has high enzymatic inhibitory capacity against the infectious diseases, which are caused by multidrug-resistant bacteria, but clinical research was halted because of its inflammatory response in previous studies. In this work, the structure of the recombinant UDP-3-O-(R-3-hydroxymyristol)-N-acetylglucosamine deacetylase from Aquifex aeolicus in complex with ACHN-975 was determined to a resolution at 1.21 Å. According to the solved complex structure, ACHN-975 was docked into the AaLpxC’s active site, which occupied the site of AaLpxC substrate. Hydroxamate group of ACHN-975 forms five-valenced coordination with resides His74, His226, Asp230, and the long chain part of ACHN-975 containing the rigid alkynyl groups docked in further to interact with the hydrophobic area of AaLpxC. We employed isothermal titration calorimetry for the measurement of affinity between AaLpxC mutants and ACHN-975, and the results manifest the key residues (His74, Thr179, Tyr212, His226, Asp230 and His253) for interaction. The determined AaLpxC crystal structure in complex with ACHN-975 is expected to serve as a guidance and basis for the design and optimization of molecular structures of ACHN-975 analogues to develop novel drug candidates against Gram-negative bacteria.
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Affiliation(s)
- Shuai Fan
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China; (S.F.); (D.L.); (X.F.); (G.L.); (Y.J.)
| | - Danyang Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China; (S.F.); (D.L.); (X.F.); (G.L.); (Y.J.)
| | - Maocai Yan
- School of Pharmacy, Jining Medical University, Rizhao, Shandong 276800, China;
| | - Xiao Feng
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China; (S.F.); (D.L.); (X.F.); (G.L.); (Y.J.)
| | - Guangxin Lv
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China; (S.F.); (D.L.); (X.F.); (G.L.); (Y.J.)
| | - Guangteng Wu
- ArNuXon Pharm-Sci Co., Ltd., Beijing 100085, China;
| | - Yuanyuan Jin
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China; (S.F.); (D.L.); (X.F.); (G.L.); (Y.J.)
| | - Yucheng Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China; (S.F.); (D.L.); (X.F.); (G.L.); (Y.J.)
- Correspondence: (Y.W.); (Z.Y.)
| | - Zhaoyong Yang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China; (S.F.); (D.L.); (X.F.); (G.L.); (Y.J.)
- Correspondence: (Y.W.); (Z.Y.)
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4
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Pasala C, Katari SK, Nalamolu RM, Bitla AR, Amineni U. Hierarchical-Clustering, Scaffold-Mining Exercises and Dynamics Simulations for Effectual Inhibitors Against Lipid-A Biosynthesis of Helicobacter pylori. Cell Mol Bioeng 2019; 12:255-274. [PMID: 31719913 DOI: 10.1007/s12195-019-00572-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Accepted: 04/23/2019] [Indexed: 12/19/2022] Open
Abstract
Introduction Treatment failures of standard regimens and new strains egression are due to the augmented drug resistance conundrum. These confounding factors now became the drug designers spotlight to implement therapeutics against Helicobacter pylori strains and to safeguard infected victims with devoid of adverse drug reactions. Thereby, to navigate the chemical space for medicine, paramount vital drug target opting considerations should be imperative. The study is therefore aimed to develop potent therapeutic variants against an insightful extrapolative, common target LpxC as a follow-up to previous studies. Methods We explored the relationships between existing inhibitors and novel leads at the scaffold level in an appropriate conformational plasticity for lead-optimization campaign. Hierarchical-clustering and shape-based screening against an in-house library of > 21 million compounds resulted in panel of 11,000 compounds. Rigid-receptor docking through virtual screening cascade, quantum-polarized-ligand, induced-fit dockings, post-docking processes and system stability assessments were performed. Results After docking experiments, an enrichment performance unveiled seven ranked actives better binding efficiencies with Zinc-binding potency than substrate and in-actives (decoy-set) with ROC (1.0) and area under accumulation curve (0.90) metrics. Physics-based membrane permeability accompanied ADME/T predictions and long-range dynamic simulations of 250 ns chemical time have depicted good passive diffusion with no toxicity of leads and sustained consistency of lead1-LpxC in the physiological milieu respectively. Conclusions In the study, as these static outcomes obtained from this approach competed with the substrate and existing ligands in binding affinity estimations as well as positively correlated from different aspects of predictions, which could facilitate promiscuous new chemical entities against H. pylori.
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Affiliation(s)
- Chiranjeevi Pasala
- Bioinformatics Centre, Department of Bioinformatics, SVIMS University, Tirupati, 517507 AP India
| | - Sudheer Kumar Katari
- Bioinformatics Centre, Department of Bioinformatics, SVIMS University, Tirupati, 517507 AP India
| | | | - Aparna R Bitla
- Department of Biochemistry, SVIMS University, Tirupati, 517507 AP India
| | - Umamaheswari Amineni
- Bioinformatics Centre, Department of Bioinformatics, SVIMS University, Tirupati, 517507 AP India
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5
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Žalubovskis R, Winum JY. Inhibitors of Selected Bacterial Metalloenzymes. Curr Med Chem 2018; 26:2690-2714. [PMID: 29611472 DOI: 10.2174/0929867325666180403154018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 03/14/2018] [Accepted: 03/19/2018] [Indexed: 12/26/2022]
Abstract
The utilization of bacterial metalloenzymes, especially ones not having mammalian (human) counterparts, has drawn attention to develop novel antibacterial agents to overcome drug resistance and especially multidrug resistance. In this review, we focus on the recent achievements on the development of inhibitors of bacterial enzymes peptide deformylase (PDF), metallo-β-lactamase (MBL), methionine aminopeptidase (MetAP) and UDP-3-O-acyl- N-acetylglucosamine deacetylase (LpxC). The state of the art of the design and investigation of inhibitors of bacterial metalloenzymes is presented, and challenges are outlined and discussed.
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Affiliation(s)
- Raivis Žalubovskis
- Latvian Institute of Organic Synthesis, Riga, Latvia.,Institute of Technology of Organic Chemistry, Faculty of Materials Science and Applied Chemistry, Riga Technical University, Latvia
| | - Jean-Yves Winum
- Institut des Biomolecules Max Mousseron, Universite de Montpellier, France
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6
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Miller MD, Gao N, Ross PL, Olivier NB. Crystal structure of A. aeolicus LpxC with bound product suggests alternate deacetylation mechanism. Proteins 2015; 83:1706-19. [PMID: 26177919 DOI: 10.1002/prot.24856] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 06/08/2015] [Accepted: 07/01/2015] [Indexed: 11/07/2022]
Abstract
UDP-3-O-acyl-N-acetylglucosamine deacetylase (LpxC) is the first committed step to form lipid A, an essential component of the outer membrane of Gram-negative bacteria. As it is essential for the survival of many pathogens, LpxC is an attractive target for antibacterial therapeutics. Herein, we report the product-bound co-crystal structure of LpxC from the acheal Aquifex aeolicus solved to 1.6 Å resolution. We identified interactions by hydroxyl and hydroxymethyl substituents of the product glucosamine ring that may enable new insights to exploit waters in the active site for structure-based design of LpxC inhibitors with novel scaffolds. By using this product structure, we have performed quantum mechanical modeling on the substrate in the active site. Based on our results and published experimental data, we propose a new mechanism that may lead to a better understanding of LpxC catalysis and inhibition.
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Affiliation(s)
- Matthew D Miller
- AstraZeneca R&D Boston, Infection Innovative Medicines Unit, Waltham, Massachusetts, 02451
| | - Ning Gao
- AstraZeneca R&D Boston, Discovery Sciences, Waltham, Massachusetts, 02451
| | - Philip L Ross
- AstraZeneca R&D Boston, Discovery Sciences, Waltham, Massachusetts, 02451
| | - Nelson B Olivier
- AstraZeneca R&D Cambridge-UK, Discovery Sciences, Cambridge, CB4 0FZ, United Kingdom
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7
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Clayton GM, Klein DJ, Rickert KW, Patel SB, Kornienko M, Zugay-Murphy J, Reid JC, Tummala S, Sharma S, Singh SB, Miesel L, Lumb KJ, Soisson SM. Structure of the bacterial deacetylase LpxC bound to the nucleotide reaction product reveals mechanisms of oxyanion stabilization and proton transfer. J Biol Chem 2013; 288:34073-34080. [PMID: 24108127 DOI: 10.1074/jbc.m113.513028] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The emergence of antibiotic-resistant strains of pathogenic bacteria is an increasing threat to global health that underscores an urgent need for an expanded antibacterial armamentarium. Gram-negative bacteria, such as Escherichia coli, have become increasingly important clinical pathogens with limited treatment options. This is due in part to their lipopolysaccharide (LPS) outer membrane components, which dually serve as endotoxins while also protecting Gram-negative bacteria from antibiotic entry. The LpxC enzyme catalyzes the committed step of LPS biosynthesis, making LpxC a promising target for new antibacterials. Here, we present the first structure of an LpxC enzyme in complex with the deacetylation reaction product, UDP-(3-O-(R-3-hydroxymyristoyl))-glucosamine. These studies provide valuable insight into recognition of substrates and products by LpxC and a platform for structure-guided drug discovery of broad spectrum Gram-negative antibiotics.
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Affiliation(s)
- Gina M Clayton
- Global Structural Chemistry, Merck Research Laboratories, West Point, Pennsylvania 19486
| | - Daniel J Klein
- Global Structural Chemistry, Merck Research Laboratories, West Point, Pennsylvania 19486
| | - Keith W Rickert
- Screening and Protein Sciences, Merck Research Laboratories, West Point, Pennsylvania 19486
| | - Sangita B Patel
- Global Structural Chemistry, Merck Research Laboratories, West Point, Pennsylvania 19486
| | - Maria Kornienko
- Screening and Protein Sciences, Merck Research Laboratories, West Point, Pennsylvania 19486
| | - Joan Zugay-Murphy
- Screening and Protein Sciences, Merck Research Laboratories, West Point, Pennsylvania 19486
| | - John C Reid
- Global Structural Chemistry, Merck Research Laboratories, West Point, Pennsylvania 19486
| | - Srivanya Tummala
- Screening and Protein Sciences, Merck Research Laboratories, West Point, Pennsylvania 19486
| | - Sujata Sharma
- Screening and Protein Sciences, Merck Research Laboratories, West Point, Pennsylvania 19486
| | - Sheo B Singh
- Discovery Chemistry, Merck Research Laboratories, Kenilworth, New Jersey 07033
| | - Lynn Miesel
- Infectious Diseases, Merck Research Laboratories, Kenilworth, New Jersey 07033
| | - Kevin J Lumb
- Screening and Protein Sciences, Merck Research Laboratories, West Point, Pennsylvania 19486
| | - Stephen M Soisson
- Global Structural Chemistry, Merck Research Laboratories, West Point, Pennsylvania 19486.
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8
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Liang X, Lee CJ, Chen X, Chung HS, Zeng D, Raetz CRH, Li Y, Zhou P, Toone EJ. Syntheses, structures and antibiotic activities of LpxC inhibitors based on the diacetylene scaffold. Bioorg Med Chem 2011; 19:852-60. [PMID: 21194954 PMCID: PMC3035996 DOI: 10.1016/j.bmc.2010.12.017] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Revised: 12/01/2010] [Accepted: 12/02/2010] [Indexed: 11/27/2022]
Abstract
Compounds inhibiting LpxC in the lipid A biosynthetic pathway are promising leads for novel antibiotics against multidrug-resistant Gram-negative pathogens. We report the syntheses and structural and biochemical characterizations of LpxC inhibitors based on a diphenyl-diacetylene (1,4-diphenyl-1,3-butadiyne) threonyl-hydroxamate scaffold. These studies provide a molecular interpretation for the differential antibiotic activities of compounds with a substituted distal phenyl ring as well as the absolute stereochemical requirement at the C2, but not C3, position of the threonyl group.
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Affiliation(s)
- Xiaofei Liang
- Department of Chemistry, Jilin University, Changchun, Jilin 130021, P.R. China
- Department of Chemistry, Duke University, Durham, NC 27708, USA
| | - Chul-Jin Lee
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
- Structural Biology & Biophysics Program, Duke University, Durham, NC 27710, USA
| | - Xin Chen
- Department of Chemistry, Duke University, Durham, NC 27708, USA
| | - Hak Suk Chung
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Daina Zeng
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | | | - Yaoxian Li
- Department of Chemistry, Jilin University, Changchun, Jilin 130021, P.R. China
| | - Pei Zhou
- Department of Chemistry, Duke University, Durham, NC 27708, USA
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
- Structural Biology & Biophysics Program, Duke University, Durham, NC 27710, USA
| | - Eric J. Toone
- Department of Chemistry, Duke University, Durham, NC 27708, USA
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
- Structural Biology & Biophysics Program, Duke University, Durham, NC 27710, USA
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9
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Cole KE, Gattis SG, Angell HD, Fierke CA, Christianson DW. Structure of the metal-dependent deacetylase LpxC from Yersinia enterocolitica complexed with the potent inhibitor CHIR-090 . Biochemistry 2010; 50:258-65. [PMID: 21171638 DOI: 10.1021/bi101622a] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The first committed step of lipid A biosynthesis is catalyzed by UDP-(3-O-((R)-3-hydroxymyristoyl))-N-acetylglucosamine deacetylase, a metal-dependent deacetylase also known as LpxC. Because lipid A is essential for bacterial viability, the inhibition of LpxC is an appealing therapeutic strategy for the treatment of Gram-negative bacterial infections. Here we report the 1.79 Å resolution X-ray crystal structure of LpxC from Yersinia enterocolitica (YeLpxC) complexed with the potent hydroxamate inhibitor CHIR-090. This enzyme is a nearly identical orthologue of LpxC from Yersinia pestis (99.7% sequence identity), the pathogen that causes bubonic plague. Similar to the inhibition of LpxC from Escherichia coli, CHIR-090 inhibits YeLpxC via a two-step slow, tight-binding mechanism with an apparent K(i) of 0.54 ± 0.14 nM followed by conversion of the E·I to E·I* species with a rate constant of 0.11 ± 0.01 min(-1). The structure of the LpxC complex with CHIR-090 shows that the inhibitor hydroxamate group chelates the active site zinc ion, and the "tail" of the inhibitor binds in the hydrophobic tunnel in the active site. This hydrophobic tunnel is framed by a βαβ subdomain that exhibits significant conformational flexibility as it accommodates inhibitor binding. CHIR-090 displays a 27 mm zone of inhibition against Y. enterocolitica in a Kirby-Bauer antibiotic assay, which is comparable to its reported activity against other Gram-negative species including E. coli and Pseudomonas aeruginosa. This study demonstrates that the inhibition of LpxC should be explored as a potential therapeutic and/or prophylatic response to infection by weaponized Yersinia species.
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Affiliation(s)
- Kathryn E Cole
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, 19104-6323, United States
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10
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Lee CJ, Liang X, Chen X, Zeng D, Joo SH, Chung HS, Barb AW, Swanson SM, Nicholas RA, Li Y, Toone EJ, Raetz CRH, Zhou P. Species-specific and inhibitor-dependent conformations of LpxC: implications for antibiotic design. ACTA ACUST UNITED AC 2010; 18:38-47. [PMID: 21167751 DOI: 10.1016/j.chembiol.2010.11.011] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Revised: 11/15/2010] [Accepted: 11/16/2010] [Indexed: 10/18/2022]
Abstract
LpxC is an essential enzyme in the lipid A biosynthetic pathway in gram-negative bacteria. Several promising antimicrobial lead compounds targeting LpxC have been reported, though they typically display a large variation in potency against different gram-negative pathogens. We report that inhibitors with a diacetylene scaffold effectively overcome the resistance caused by sequence variation in the LpxC substrate-binding passage. Compound binding is captured in complex with representative LpxC orthologs, and structural analysis reveals large conformational differences that mostly reflect inherent molecular features of distinct LpxC orthologs, whereas ligand-induced structural adaptations occur at a smaller scale. These observations highlight the need for a molecular understanding of inherent structural features and conformational plasticity of LpxC enzymes for optimizing LpxC inhibitors as broad-spectrum antibiotics against gram-negative infections.
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Affiliation(s)
- Chul-Jin Lee
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
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11
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Mochalkin I, Knafels JD, Lightle S. Crystal structure of LpxC from Pseudomonas aeruginosa complexed with the potent BB-78485 inhibitor. Protein Sci 2008; 17:450-7. [PMID: 18287278 PMCID: PMC2248309 DOI: 10.1110/ps.073324108] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The cell wall in Gram-negative bacteria is surrounded by an outer membrane comprised of charged lipopolysaccharide (LPS) molecules that prevent entry of hydrophobic agents into the cell and protect the bacterium from many antibiotics. The hydrophobic anchor of LPS is lipid A, the biosynthesis of which is essential for bacterial growth and viability. UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC) is an essential zinc-dependant enzyme that catalyzes the conversion of UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine to UDP-3-O-(R-3-hydroxymyristoyl)glucosamine and acetate in the biosynthesis of lipid A, and for this reason, LpxC is an attractive target for antibacterial drug discovery. Here we disclose a 1.9 A resolution crystal structure of LpxC from Pseudomonas aeruginosa (paLpxC) in a complex with the potent BB-78485 inhibitor. To our knowledge, this is the first crystal structure of LpxC with a small-molecule inhibitor that shows antibacterial activity against a wide range of Gram-negative pathogens. Accordingly, this structure can provide important information for lead optimization and rational design of the effective small-molecule LpxC inhibitors for successful treatment of Gram-negative infections.
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12
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Barb AW, Zhou P. Mechanism and inhibition of LpxC: an essential zinc-dependent deacetylase of bacterial lipid A synthesis. Curr Pharm Biotechnol 2008; 9:9-15. [PMID: 18289052 PMCID: PMC3022321 DOI: 10.2174/138920108783497668] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Multi-drug resistant (MDR), pathogenic Gram-negative bacteria pose a serious health threat, and novel antibiotic targets must be identified to combat MDR infections. One promising target is the zinc-dependent metalloamidase UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC), which catalyzes the committed step of lipid A (endotoxin) biosynthesis. LpxC is an essential, single copy gene that is conserved in virtually all Gram-negative bacteria. LpxC structures, revealed by NMR and X-ray crystallography, demonstrate that LpxC adopts a novel 'beta-alpha-alpha-beta sandwich' fold and encapsulates the acyl chain of the substrate with a unique hydrophobic passage. Kinetic analysis revealed that LpxC functions by a general acid-base mechanism, with a glutamate serving as the general base. Many potent LpxC inhibitors have been identified, and most contain a hydroxamate group targeting the catalytic zinc ion. Although early LpxC-inhibitors were either narrow-spectrum antibiotics or broad-spectrum in vitro LpxC inhibitors with limited antibiotic properties, the recently discovered compound CHIR-090 is a powerful antibiotic that controls the growth of Escherichia coli and Pseudomonas aeruginosa, with an efficacy rivaling that of the FDA-approved antibiotic ciprofloxacin. CHIR-090 inhibits a wide range of LpxC enzymes with sub-nanomolar affinity in vitro, and is a two-step, slow, tight-binding inhibitor of Aquifex aeolicus and E. coli LpxC. The success of CHIR-090 suggests that potent LpxC-targeting antibiotics may be developed to control a broad range of Gram-negative bacteria.
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Affiliation(s)
- Adam W Barb
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, 27710, USA
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13
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Barb AW, Jiang L, Raetz CRH, Zhou P. Structure of the deacetylase LpxC bound to the antibiotic CHIR-090: Time-dependent inhibition and specificity in ligand binding. Proc Natl Acad Sci U S A 2007; 104:18433-8. [PMID: 18025458 PMCID: PMC2141794 DOI: 10.1073/pnas.0709412104] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2007] [Indexed: 11/18/2022] Open
Abstract
The UDP-3-O-(R-3-hydroxyacyl)-N-acetylglucosamine deacetylase LpxC is an essential enzyme of lipid A biosynthesis in Gram-negative bacteria and a promising antibiotic target. CHIR-090, the most potent LpxC inhibitor discovered to date, displays two-step time-dependent inhibition and kills a wide range of Gram-negative pathogens as effectively as ciprofloxacin or tobramycin. In this study, we report the solution structure of the LpxC-CHIR-090 complex. CHIR-090 exploits conserved features of LpxC that are critical for catalysis, including the hydrophobic passage and essential active-site residues. CHIR-090 is adjacent to, but does not occupy, the UDP-binding pocket of LpxC, suggesting that a fragment-based approach may facilitate further optimization of LpxC inhibitors. Additionally, we identified key residues in the Insert II hydrophobic passage that modulate time-dependent inhibition and CHIR-090 resistance. CHIR-090 shares a similar, although previously unrecognized, chemical scaffold with other small-molecule antibiotics such as L-161,240 targeting LpxC, and provides a template for understanding the binding mode of these inhibitors. Consistent with this model, we provide evidence that L-161,240 also occupies the hydrophobic passage.
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Affiliation(s)
- Adam W. Barb
- Department of Biochemistry, Duke University Medical Center, Durham NC 27710
| | - Ling Jiang
- Department of Biochemistry, Duke University Medical Center, Durham NC 27710
| | | | - Pei Zhou
- Department of Biochemistry, Duke University Medical Center, Durham NC 27710
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Ulaganathan V, Buetow L, Hunter WN. Nucleotide substrate recognition by UDP-N-acetylglucosamine acyltransferase (LpxA) in the first step of lipid A biosynthesis. J Mol Biol 2007; 369:305-12. [PMID: 17434525 DOI: 10.1016/j.jmb.2007.03.039] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2007] [Revised: 03/14/2007] [Accepted: 03/14/2007] [Indexed: 11/21/2022]
Abstract
Lipid A is an integral component of the lipopolysaccharide (LPS) that forms the selective and protective outer monolayer of Gram-negative bacteria, and is essential for bacterial growth and viability. UDP-N-acetylglucosamine acyltransferase (LpxA) initiates lipid A biosynthesis by catalyzing the transfer of R-3-hydroxymyristic acid from acyl carrier protein to the 3'-hydroxyl group of UDP-GlcNAc. The enzyme is a homotrimer, and previous studies suggested that the active site lies within a positively charged cleft formed at the subunit-subunit interface. The crystal structure of Escherichia coli LpxA in complex with UDP-GlcNAc reveals details of the substrate-binding site, with prominent hydrophilic interactions between highly conserved clusters of residues (Asn198, Glu200, Arg204 and Arg205) with UDP, and (Asp74, His125, His144 and Gln161) with the GlcNAc moiety. These interactions serve to bind and orient the substrate for catalysis. The crystallographic model supports previous results, which suggest that acylation occurs via nucleophilic attack of deprotonated UDP-GlcNAc on the acyl donor in a general base-catalyzed mechanism involving a catalytic dyad of His125 and Asp126. His125, the general base, interacts with the 3'-hydroxyl group of UDP-GlcNAc to generate the nucleophile. The Asp126 side-chain accepts a hydrogen bond from His125 and helps orient the general base to participate in catalysis. Comparisons with an LpxA:peptide inhibitor complex indicate that the peptide competes with both nucleotide and acyl carrier protein substrates.
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Affiliation(s)
- Venkatasubramanian Ulaganathan
- Division of Biological Chemistry and Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
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