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Mielniczuk S, Hoff K, Baselious F, Li Y, Haupenthal J, Kany AM, Riedner M, Rohde H, Rox K, Hirsch AKH, Krimm I, Sippl W, Holl R. Development of Fragment-Based Inhibitors of the Bacterial Deacetylase LpxC with Low Nanomolar Activity. J Med Chem 2024. [PMID: 39303295 DOI: 10.1021/acs.jmedchem.4c01262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
Abstract
In a fragment-based approach using NMR spectroscopy, benzyloxyacetohydroxamic acid-derived inhibitors of the bacterial deacetylase LpxC bearing a substituent to target the uridine diphosphate-binding site of the enzyme were developed. By appending privileged fragments via a suitable linker, potent LpxC inhibitors with promising antibacterial activities could be obtained, like the one-digit nanomolar LpxC inhibitor (S)-13j [Ki (EcLpxC C63A) = 9.5 nM; Ki (PaLpxC): 5.6 nM]. To rationalize the observed structure-activity relationships, molecular docking and molecular dynamics studies were performed. Initial in vitro absorption-distribution-metabolism-excretion-toxicity (ADMET) studies of the most potent compounds have paved the way for multiparameter optimization of our newly developed isoserine-based amides.
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Affiliation(s)
- Sebastian Mielniczuk
- Institute of Organic Chemistry, Universität Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 20146 Hamburg, Germany
| | - Katharina Hoff
- Institute of Organic Chemistry, Universität Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 20146 Hamburg, Germany
| | - Fady Baselious
- Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, Kurt-Mothes-Straße 3, 06120 Halle (Saale), Germany
| | - Yunqi Li
- Team "Small Molecules for Biological Targets", Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Centre Léon Bérard, Université de Lyon, Université Claude Bernard Lyon1, 69008 Lyon, France
- Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences & School of Life Sciences, East China Normal University, 200241 Shanghai, China
| | - Jörg Haupenthal
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany
| | - Andreas M Kany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany
| | - Maria Riedner
- Technology Platform Mass Spectrometry, Universität Hamburg, Mittelweg 177, 20148 Hamburg, Germany
| | - Holger Rohde
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 20146 Hamburg, Germany
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Katharina Rox
- Department of Chemical Biology, Helmholtz Centre for Infection Research (HZI), Inhoffenstr. 7, 38124 Braunschweig, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany
- Helmholtz International Lab for Anti-infectives, Campus E8.1, 66123 Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Isabelle Krimm
- Team "Small Molecules for Biological Targets", Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Centre Léon Bérard, Université de Lyon, Université Claude Bernard Lyon1, 69008 Lyon, France
| | - Wolfgang Sippl
- Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, Kurt-Mothes-Straße 3, 06120 Halle (Saale), Germany
| | - Ralph Holl
- Institute of Organic Chemistry, Universität Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 20146 Hamburg, Germany
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2
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Zhukovets AA, Chernyshov VV, Al’mukhametov AZ, Seregina TA, Revtovich SV, Kasatkina MA, Isakova YE, Kulikova VV, Morozova EA, Cherkasova AI, Mannanov TA, Anashkina AA, Solyev PN, Mitkevich VA, Ivanov RA. Novel Hydroxamic Acids Containing Aryl-Substituted 1,2,4- or 1,3,4-Oxadiazole Backbones and an Investigation of Their Antibiotic Potentiation Activity. Int J Mol Sci 2023; 25:96. [PMID: 38203266 PMCID: PMC10779255 DOI: 10.3390/ijms25010096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/05/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC) is a zinc amidase that catalyzes the second step of the biosynthesis of lipid A, which is an outer membrane essential structural component of Gram-negative bacteria. Inhibitors of this enzyme can be attributed to two main categories, non-hydroxamate and hydroxamate inhibitors, with the latter being the most effective given the chelation of Zn2+ in the active site. Compounds containing diacetylene or acetylene tails and the sulfonic head, as well as oxazoline derivatives of hydroxamic acids, are among the LpxC inhibitors with the most profound antibacterial activity. The present article describes the synthesis of novel functional derivatives of hydroxamic acids-bioisosteric to oxazoline inhibitors-containing 1,2,4- and 1,3,4-oxadiazole cores and studies of their cytotoxicity, antibacterial activity, and antibiotic potentiation. Some of the hydroxamic acids we obtained (9c, 9d, 23a, 23c, 30b, 36) showed significant potentiation in nalidixic acid, rifampicin, and kanamycin against the growth of laboratory-strain Escherichia coli MG1655. Two lead compounds (9c, 9d) significantly reduced Pseudomonas aeruginosa ATCC 27853 growth in the presence of nalidixic acid and rifampicin.
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Affiliation(s)
- Anastasia A. Zhukovets
- Translational Medicine Research Center, Sirius University of Science and Technology, Olympic Ave. 1, 354340 Sochi, Russia; (A.A.Z.); (A.Z.A.); (M.A.K.); (Y.E.I.); (A.I.C.); (T.A.M.); (R.A.I.)
| | - Vladimir V. Chernyshov
- Translational Medicine Research Center, Sirius University of Science and Technology, Olympic Ave. 1, 354340 Sochi, Russia; (A.A.Z.); (A.Z.A.); (M.A.K.); (Y.E.I.); (A.I.C.); (T.A.M.); (R.A.I.)
| | - Aidar Z. Al’mukhametov
- Translational Medicine Research Center, Sirius University of Science and Technology, Olympic Ave. 1, 354340 Sochi, Russia; (A.A.Z.); (A.Z.A.); (M.A.K.); (Y.E.I.); (A.I.C.); (T.A.M.); (R.A.I.)
| | - Tatiana A. Seregina
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 32 Vavilov St., 119991 Moscow, Russia; (T.A.S.); (S.V.R.); (V.V.K.); (E.A.M.); (A.A.A.); (P.N.S.); (V.A.M.)
| | - Svetlana V. Revtovich
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 32 Vavilov St., 119991 Moscow, Russia; (T.A.S.); (S.V.R.); (V.V.K.); (E.A.M.); (A.A.A.); (P.N.S.); (V.A.M.)
| | - Mariia A. Kasatkina
- Translational Medicine Research Center, Sirius University of Science and Technology, Olympic Ave. 1, 354340 Sochi, Russia; (A.A.Z.); (A.Z.A.); (M.A.K.); (Y.E.I.); (A.I.C.); (T.A.M.); (R.A.I.)
| | - Yulia E. Isakova
- Translational Medicine Research Center, Sirius University of Science and Technology, Olympic Ave. 1, 354340 Sochi, Russia; (A.A.Z.); (A.Z.A.); (M.A.K.); (Y.E.I.); (A.I.C.); (T.A.M.); (R.A.I.)
| | - Vitalia V. Kulikova
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 32 Vavilov St., 119991 Moscow, Russia; (T.A.S.); (S.V.R.); (V.V.K.); (E.A.M.); (A.A.A.); (P.N.S.); (V.A.M.)
| | - Elena A. Morozova
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 32 Vavilov St., 119991 Moscow, Russia; (T.A.S.); (S.V.R.); (V.V.K.); (E.A.M.); (A.A.A.); (P.N.S.); (V.A.M.)
| | - Anastasia I. Cherkasova
- Translational Medicine Research Center, Sirius University of Science and Technology, Olympic Ave. 1, 354340 Sochi, Russia; (A.A.Z.); (A.Z.A.); (M.A.K.); (Y.E.I.); (A.I.C.); (T.A.M.); (R.A.I.)
| | - Timur A. Mannanov
- Translational Medicine Research Center, Sirius University of Science and Technology, Olympic Ave. 1, 354340 Sochi, Russia; (A.A.Z.); (A.Z.A.); (M.A.K.); (Y.E.I.); (A.I.C.); (T.A.M.); (R.A.I.)
| | - Anastasia A. Anashkina
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 32 Vavilov St., 119991 Moscow, Russia; (T.A.S.); (S.V.R.); (V.V.K.); (E.A.M.); (A.A.A.); (P.N.S.); (V.A.M.)
| | - Pavel N. Solyev
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 32 Vavilov St., 119991 Moscow, Russia; (T.A.S.); (S.V.R.); (V.V.K.); (E.A.M.); (A.A.A.); (P.N.S.); (V.A.M.)
| | - Vladimir A. Mitkevich
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 32 Vavilov St., 119991 Moscow, Russia; (T.A.S.); (S.V.R.); (V.V.K.); (E.A.M.); (A.A.A.); (P.N.S.); (V.A.M.)
| | - Roman A. Ivanov
- Translational Medicine Research Center, Sirius University of Science and Technology, Olympic Ave. 1, 354340 Sochi, Russia; (A.A.Z.); (A.Z.A.); (M.A.K.); (Y.E.I.); (A.I.C.); (T.A.M.); (R.A.I.)
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3
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Kumar Pal S, Kumar S. Indole-based LpxC (UDP-3-O-(R-3-hydroxyacyl)-N-acetylglucosaminedeacetylase) inhibitors for Salmonella typhi: rational drug discovery through in silico screening. 3 Biotech 2023; 13:281. [PMID: 37496977 PMCID: PMC10366066 DOI: 10.1007/s13205-023-03699-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 07/10/2023] [Indexed: 07/28/2023] Open
Abstract
Salmonella typhi is an infectious bacteria that causes typhoid fever and poses a significant risk to human health. The emergence of antibiotic resistance has become a growing concern in the management of this disease. In this work, a structure-based drug design approach was used to identify inhibitors for zinc-dependent metalloamidase LpxC, the enzyme responsible for the biosynthesis of lipid A. Using an in silico approach (virtual screening, docking, and molecular dynamics (MD) simulations), from a library of 59,000 indole derivatives, we were able to identify promising lead molecules with high binding affinity to the LpxC. Of these, five molecules (compound 435 (CID: 12253558), compound 436 (CID: 122514279), compound 1812 (CID: 90797680), compound 2584 (CID: 57056726), and compound 2545 (CID: 59897361)) have passed all the filtering criteria. This finding was verified by molecular dynamics (MD) simulation as well as post-dynamics free energy calculations. The five compounds that have been identified have shown the most promise compared to other compounds that are already recognized. To further validate the positive outcome of this study, experimental validation and optimization are necessary. These lead compounds may help to develop new antibiotics for antibiotic-resistant Salmonella typhi and improve typhoid fever treatment. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03699-5.
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Affiliation(s)
- Sudhir Kumar Pal
- Centre for Bioseparation Technology (CBST), Vellore Institute of Technology (VIT), Vellore, 632014 Tamil Nadu India
| | - Sanjit Kumar
- Centre for Bioseparation Technology (CBST), Vellore Institute of Technology (VIT), Vellore, 632014 Tamil Nadu India
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4
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Zou S, Li X, Huang Y, Zhang B, Tang H, Xue Y, Zheng Y. Properties and biotechnological applications of microbial deacetylase. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12613-1. [PMID: 37326683 DOI: 10.1007/s00253-023-12613-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/25/2023] [Accepted: 05/31/2023] [Indexed: 06/17/2023]
Abstract
Deacetylases, a class of enzymes that can catalyze the hydrolysis of acetylated substrates to remove the acetyl group, used in producing various products with high qualities, are one of the most influential industrial enzymes. These enzymes are highly specific, non-toxic, sustainable, and eco-friendly biocatalysts. Deacetylases and deacetylated compounds have been widely applicated in pharmaceuticals, medicine, food, and the environment. This review synthetically summarizes deacetylases' sources, characterizations, classifications, and applications. Moreover, the typical structural characteristics of deacetylases from different microbial sources are summarized. We also reviewed the deacetylase-catalyzed reactions for producing various deacetylated compounds, such as chitosan-oligosaccharide (COS), mycothiol, 7-aminocephalosporanic acid (7-ACA), glucosamines, amino acids, and polyamines. It is aimed to expound on the advantages and challenges of deacetylases in industrial applications. Moreover, it also serves perspectives on obtaining promising and innovative biocatalysts for enzymatic deacetylation. KEYPOINTS: • The fundamental properties of microbial deacetylases of various microorganisms are presented. • The biochemical characterizations, structures, and catalyzation mechanisms of microbial deacetylases are summarized. • The applications of microbial deacetylases in food, pharmaceutical, medicine, and the environment were discussed.
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Affiliation(s)
- Shuping Zou
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Xia Li
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Yinfeng Huang
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Bing Zhang
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Heng Tang
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Yaping Xue
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.
| | - Yuguo Zheng
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
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Kumar Pal S, Kumar S. LpxC (UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase) inhibitors: A long path explored for potent drug design. Int J Biol Macromol 2023; 234:122960. [PMID: 36565833 DOI: 10.1016/j.ijbiomac.2022.12.179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
Microbial infections are becoming resistant to traditional antibiotics. As novel resistance mechanisms are developed and disseminated across the world, our ability to treat the most common infectious diseases is becoming increasingly compromised. As existing antibiotics are losing their effectiveness, especially treatment of bacterial infections, is difficult. In order to combat this issue, it is of utmost importance to identify novel pharmacological targets or antibiotics. LpxC, a zinc-dependent metalloamidase that catalyzes the committed step in the biosynthesis of lipid A (endotoxin) in bacteria, is a prime candidate for drug/therapeutic target. So far, the rate-limiting metallo-amidase LpxC has been the most-targeted macromolecule in the Raetz pathway. This is because it is important for the growth of these bacterial infections. This review showcases on the research done to develop efficient drugs in this area before and after the 2015.
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Affiliation(s)
- Sudhir Kumar Pal
- Centre for Bio-Separation Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014, India.
| | - Sanjit Kumar
- Centre for Bio-Separation Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014, India.
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6
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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: 12] [Impact Index Per Article: 12.0] [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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7
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Zoghlami M, Oueslati M, Basharat Z, Sadfi-Zouaoui N, Messaoudi A. Inhibitor Assessment against the LpxC Enzyme of Antibiotic-resistant Acinetobacter baumannii Using Virtual Screening, Dynamics Simulation, and in vitro Assays. Mol Inform 2023; 42:e2200061. [PMID: 36289054 DOI: 10.1002/minf.202200061] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 10/26/2022] [Indexed: 11/07/2022]
Abstract
BACKGROUND Bacterial resistance is currently a significant global public health problem. Acinetobacter baumannii has been ranked in the list of the World Health Organization as the most critical and priority pathogen for which new antibiotics are urgently needed. In this context, computational methods play a central role in the modern drug discovery process. The purpose of the current study was to identify new potential therapeutic molecules to neutralize MDR A. baumannii bacteria. METHODS A total of 3686 proteins retrieved from the A. baumannii proteome were subjected to subtractive proteomic analysis to narrow down the spectrum of drug targets. The SWISS-MODEL server was used to perform a 3D homology model of the selected target protein. The SAVES server was used to evaluate the overall quality of the model. A dataset of 74500 analogues retrieved from the PubChem database was docked with LpxC using the AutoDock software. RESULTS In this study, we predicted a putative new inhibitor for the Lpxc enzyme of A. baumannii. The LpxC enzyme was selected as the most appropriate drug target for A. baumannii. According to the virtual screening results, N-[(2S)-3-amino-1-(hydroxyamino)-1-oxopropan-2-yl]-4-(4-bromophenyl) benzamide (CS250) could be a promising drug candidate targeting the LpxC enzyme. This molecule shows polar interactions with six amino acids and non-polar interactions with eight other residues. In vitro experimental validation was performed through the inhibition assay. CONCLUSION To the best of our knowledge, this is the first study that suggests CS250 as a promising inhibitory molecule that can be exploited to target this gram-negative pathogen.
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Affiliation(s)
- Manel Zoghlami
- Laboratoire de Mycologie, Pathologies et Biomarqueurs (LR16ES05), Département de Biologie, Université de Tunis-El Manar, 2092, Tunis, Tunisia
| | - Maroua Oueslati
- Laboratoire de Mycologie, Pathologies et Biomarqueurs (LR16ES05), Département de Biologie, Université de Tunis-El Manar, 2092, Tunis, Tunisia
| | - Zarrin Basharat
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, ICCBS University of Karachi, 75270, Karachi, Pakistan
| | - Najla Sadfi-Zouaoui
- Laboratoire de Mycologie, Pathologies et Biomarqueurs (LR16ES05), Département de Biologie, Université de Tunis-El Manar, 2092, Tunis, Tunisia
| | - Abdelmonaem Messaoudi
- Laboratoire de Mycologie, Pathologies et Biomarqueurs (LR16ES05), Département de Biologie, Université de Tunis-El Manar, 2092, Tunis, Tunisia.,Higher Institute of Biotechnology of Beja, Jendouba University, Habib Bourguiba Street, 9000, Beja, Tunisia
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8
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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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9
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Basak S, Li Y, Tao S, Daryaee F, Merino J, Gu C, Delker SL, Phan JN, Edwards TE, Walker SG, Tonge PJ. Structure-Kinetic Relationship Studies for the Development of Long Residence Time LpxC Inhibitors. J Med Chem 2022; 65:11854-11875. [PMID: 36037447 PMCID: PMC10182817 DOI: 10.1021/acs.jmedchem.2c00974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC) is a promising drug target in Gram-negative bacteria. Previously, we described a correlation between the residence time of inhibitors on Pseudomonas aeruginosa LpxC (paLpxC) and the post-antibiotic effect (PAE) caused by the inhibitors on the growth of P. aeruginosa. Given that drugs with prolonged activity following compound removal may have advantages in dosing regimens, we have explored the structure-kinetic relationship for paLpxC inhibition by analogues of the pyridone methylsulfone PF5081090 (1) originally developed by Pfizer. Several analogues have longer residence times on paLpxC than 1 (41 min) including PT913, which has a residence time of 124 min. PT913 also has a PAE of 4 h, extending the original correlation observed between residence time and PAE. Collectively, the studies provide a platform for the rational modulation of paLpxC inhibitor residence time and the potential development of antibacterial agents that cause prolonged suppression of bacterial growth.
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Affiliation(s)
- Sneha Basak
- Center for Advanced Study of Drug Action, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Yong Li
- Center for Advanced Study of Drug Action, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Suyuan Tao
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Fereidoon Daryaee
- Center for Advanced Study of Drug Action, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Jonathan Merino
- Center for Advanced Study of Drug Action, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Chendi Gu
- Center for Advanced Study of Drug Action, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | | | - Jenny N. Phan
- McGill University Montreal, Quebec H3A 0G4, Canada Canada
| | | | - Stephen G. Walker
- Department of Oral Biology and Pathology, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Peter J. Tonge
- Center for Advanced Study of Drug Action, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
- Department of Radiology, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
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10
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Jangir PK, Yang Q, Shaw LP, Caballero JD, Ogunlana L, Wheatley R, Walsh T, MacLean RC. Pre-existing chromosomal polymorphisms in pathogenic E. coli potentiate the evolution of resistance to a last-resort antibiotic. eLife 2022; 11:e78834. [PMID: 35943060 PMCID: PMC9363117 DOI: 10.7554/elife.78834] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 07/22/2022] [Indexed: 12/17/2022] Open
Abstract
Bacterial pathogens show high levels of chromosomal genetic diversity, but the influence of this diversity on the evolution of antibiotic resistance by plasmid acquisition remains unclear. Here, we address this problem in the context of colistin, a 'last line of defence' antibiotic. Using experimental evolution, we show that a plasmid carrying the MCR-1 colistin resistance gene dramatically increases the ability of Escherichia coli to evolve high-level colistin resistance by acquiring mutations in lpxC, an essential chromosomal gene involved in lipopolysaccharide biosynthesis. Crucially, lpxC mutations increase colistin resistance in the presence of the MCR-1 gene, but decrease the resistance of wild-type cells, revealing positive sign epistasis for antibiotic resistance between the chromosomal mutations and a mobile resistance gene. Analysis of public genomic datasets shows that lpxC polymorphisms are common in pathogenic E. coli, including those carrying MCR-1, highlighting the clinical relevance of this interaction. Importantly, lpxC diversity is high in pathogenic E. coli from regions with no history of MCR-1 acquisition, suggesting that pre-existing lpxC polymorphisms potentiated the evolution of high-level colistin resistance by MCR-1 acquisition. More broadly, these findings highlight the importance of standing genetic variation and plasmid/chromosomal interactions in the evolutionary dynamics of antibiotic resistance.
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Affiliation(s)
- Pramod K Jangir
- Department of Zoology, University of OxfordOxfordUnited Kingdom
| | - Qiue Yang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry UniversityFuzhouChina
| | - Liam P Shaw
- Department of Zoology, University of OxfordOxfordUnited Kingdom
| | | | - Lois Ogunlana
- Department of Zoology, University of OxfordOxfordUnited Kingdom
| | - Rachel Wheatley
- Department of Zoology, University of OxfordOxfordUnited Kingdom
| | - Timothy Walsh
- Department of Zoology, University of OxfordOxfordUnited Kingdom
| | - R Craig MacLean
- Department of Zoology, University of OxfordOxfordUnited Kingdom
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11
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Zhou P, Hong J. Structure- and Ligand-Dynamics-Based Design of Novel Antibiotics Targeting Lipid A Enzymes LpxC and LpxH in Gram-Negative Bacteria. Acc Chem Res 2021; 54:1623-1634. [PMID: 33720682 DOI: 10.1021/acs.accounts.0c00880] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bacterial infections caused by multi-drug-resistant Gram-negative pathogens pose a serious threat to public health. Gram-negative bacteria are characterized by the enrichment of lipid A-anchored lipopolysaccharide (LPS) or lipooligosaccharide (LOS) in the outer leaflet of their outer membrane. Constitutive biosynthesis of lipid A via the Raetz pathway is essential for bacterial viability and fitness in the human host. The inhibition of early-stage lipid A enzymes such as LpxC not only suppresses the growth of Pseudomonas aeruginosa, Klebsiella pneumoniae, Enterobacter spp., and other clinically important Gram-negative pathogens but also sensitizes these bacteria to other antibiotics. The inhibition of late-stage lipid A enzymes such as LpxH is uniquely advantageous because it has an extra mechanism of bacterial killing through the accumulation of toxic lipid A intermediates, rendering LpxH inhibition additionally lethal to Acinetobacter baumannii. Because essential enzymes of the Raetz pathway have never been exploited by commercial antibiotics, they are excellent targets for the development of novel antibiotics against multi-drug-resistant Gram-negative infections.This Account describes the ongoing research on characterizing the structure and inhibition of LpxC and LpxH, the second and fourth enzymes of the Raetz pathway of lipid A biosynthesis, in the laboratories of Dr. Pei Zhou and Dr. Jiyong Hong at Duke University. Our studies have elucidated the molecular basis of LpxC inhibition by the first broad-spectrum inhibitor, CHIR-090, as well as the mechanism underlying its spectrum of activity. Such an analysis has provided a molecular explanation for the broad-spectrum antibiotic activity of diacetylene-based LpxC inhibitors. Through the structural and biochemical investigation of LpxC inhibition by diacetylene LpxC inhibitors and the first nanomolar LpxC inhibitor, L-161,240, we have elucidated the intrinsic conformational and dynamics difference in individual LpxC enzymes near the active site. A similar approach has been taken to investigate LpxH inhibition, leading to the establishment of the pharmacophore model of LpxH inhibitors and subsequent structural elucidation of LpxH in complex with its first reported small-molecule inhibitor based on a sulfonyl piperazine scaffold.Intriguingly, although our crystallographic analysis of LpxC- and LpxH-inhibitor complexes detected only a single inhibitor conformation in the crystal lattice, solution NMR studies revealed the existence of multiple ligand conformations that together delineate a cryptic ligand envelope expanding the ligand-binding footprint beyond that observed in the crystal structure. By harnessing the ligand dynamics information and structural insights, we demonstrate the feasibility to design potent LpxC and LpxH inhibitors by merging multiple ligand conformations. Such an approach has enabled us to rationally design compounds with significantly enhanced potency in enzymatic assays and outstanding antibiotic activities in vitro and in animal models of bacterial infection. We anticipate that continued efforts with structure and ligand dynamics-based lead optimization will ultimately lead to the discovery of LpxC- and LpxH-targeting clinical antibiotics against a broad range of Gram-negative pathogens.
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Affiliation(s)
- Pei Zhou
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Jiyong Hong
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, United States
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12
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Regulation of the First Committed Step in Lipopolysaccharide Biosynthesis Catalyzed by LpxC Requires the Essential Protein LapC (YejM) and HslVU Protease. Int J Mol Sci 2020; 21:ijms21239088. [PMID: 33260377 PMCID: PMC7730581 DOI: 10.3390/ijms21239088] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 12/29/2022] Open
Abstract
We previously showed that lipopolysaccharide (LPS) assembly requires the essential LapB protein to regulate FtsH-mediated proteolysis of LpxC protein that catalyzes the first committed step in the LPS synthesis. To further understand the essential function of LapB and its role in LpxC turnover, multicopy suppressors of ΔlapB revealed that overproduction of HslV protease subunit prevents its lethality by proteolytic degradation of LpxC, providing the first alternative pathway of LpxC degradation. Isolation and characterization of an extragenic suppressor mutation that prevents lethality of ΔlapB by restoration of normal LPS synthesis identified a frame-shift mutation after 377 aa in the essential gene designated lapC, suggesting LapB and LapC act antagonistically. The same lapC gene was identified during selection for mutations that induce transcription from LPS defects-responsive rpoEP3 promoter, confer sensitivity to LpxC inhibitor CHIR090 and a temperature-sensitive phenotype. Suppressors of lapC mutants that restored growth at elevated temperatures mapped to lapA/lapB, lpxC and ftsH genes. Such suppressor mutations restored normal levels of LPS and prevented proteolysis of LpxC in lapC mutants. Interestingly, a lapC deletion could be constructed in strains either overproducing LpxC or in the absence of LapB, revealing that FtsH, LapB and LapC together regulate LPS synthesis by controlling LpxC amounts.
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13
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Structural basis of the UDP-diacylglucosamine pyrophosphohydrolase LpxH inhibition by sulfonyl piperazine antibiotics. Proc Natl Acad Sci U S A 2020; 117:4109-4116. [PMID: 32041866 PMCID: PMC7049123 DOI: 10.1073/pnas.1912876117] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The UDP-2,3-diacylglucosamine pyrophosphate hydrolase LpxH is an essential lipid A biosynthetic enzyme that is conserved in the majority of gram-negative bacteria. It has emerged as an attractive novel antibiotic target due to the recent discovery of an LpxH-targeting sulfonyl piperazine compound (referred to as AZ1) by AstraZeneca. However, the molecular details of AZ1 inhibition have remained unresolved, stymieing further development of this class of antibiotics. Here we report the crystal structure of Klebsiella pneumoniae LpxH in complex with AZ1. We show that AZ1 fits snugly into the L-shaped acyl chain-binding chamber of LpxH with its indoline ring situating adjacent to the active site, its sulfonyl group adopting a sharp kink, and its N-CF3-phenyl substituted piperazine group reaching out to the far side of the LpxH acyl chain-binding chamber. Intriguingly, despite the observation of a single AZ1 conformation in the crystal structure, our solution NMR investigation has revealed the presence of a second ligand conformation invisible in the crystalline state. Together, these distinct ligand conformations delineate a cryptic inhibitor envelope that expands the observed footprint of AZ1 in the LpxH-bound crystal structure and enables the design of AZ1 analogs with enhanced potency in enzymatic assays. These designed compounds display striking improvement in antibiotic activity over AZ1 against wild-type K. pneumoniae, and coadministration with outer membrane permeability enhancers profoundly sensitizes Escherichia coli to designed LpxH inhibitors. Remarkably, none of the sulfonyl piperazine compounds occupies the active site of LpxH, foretelling a straightforward path for rapid optimization of this class of antibiotics.
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14
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Yang SK, Yusoff K, Ajat M, Thomas W, Abushelaibi A, Akseer R, Lim SHE, Lai KS. Disruption of KPC-producing Klebsiella pneumoniae membrane via induction of oxidative stress by cinnamon bark (Cinnamomum verum J. Presl) essential oil. PLoS One 2019; 14:e0214326. [PMID: 30939149 PMCID: PMC6445408 DOI: 10.1371/journal.pone.0214326] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 03/10/2019] [Indexed: 01/09/2023] Open
Abstract
Klebsiella pneumoniae (KP) remains the most prevalent nosocomial pathogen and carries the carbapenemase (KPC) gene which confers resistance towards carbapenem. Thus, it is necessary to discover novel antimicrobials to address the issue of antimicrobial resistance in such pathogens. Natural products such as essential oils are a promising source due to their complex composition. Essential oils have been shown to be effective against pathogens, but the overall mechanisms have yet to be fully explained. Understanding the molecular mechanisms of essential oil towards KPC-KP cells would provide a deeper understanding of their potential use in clinical settings. Therefore, we aimed to investigate the mode of action of essential oil against KPC-KP cells from a proteomic perspective by comparing the overall proteome profile of KPC-KP cells treated with cinnamon bark (Cinnamomum verum J. Presl) essential oil (CBO) at their sub-inhibitory concentration of 0.08% (v/v). A total of 384 proteins were successfully identified from the non-treated cells, whereas only 242 proteins were identified from the CBO-treated cells. Proteins were then categorized based on their biological processes, cellular components and molecular function prior to pathway analysis. Pathway analysis showed that CBO induced oxidative stress in the KPC-KP cells as indicated by the abundance of oxidative stress regulator proteins such as glycyl radical cofactor, catalase peroxidase and DNA mismatch repair protein. Oxidative stress is likely to oxidize and disrupt the bacterial membrane as shown by the loss of major membrane proteins. Several genes selected for qRT-PCR analysis validated the proteomic profile and were congruent with the proteomic abundance profiles. In conclusion, KPC-KP cells exposed to CBO undergo oxidative stress that eventually disrupts the bacterial membrane possibly via interaction with the phospholipid bilayer. Interestingly, several pathways involved in the bacterial membrane repair system were also affected by oxidative stress, contributing to the loss of cells viability.
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Affiliation(s)
- Shun-Kai Yang
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Khatijah Yusoff
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Mokrish Ajat
- Department of Veterinary Preclinical Sciences, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Warren Thomas
- Perdana University-Royal College of Surgeons in Ireland, School of Medicine, Perdana University, Serdang, Selangor, Malaysia
| | - Aisha Abushelaibi
- Health Sciences Division, Abu Dhabi Women’s College, Higher Colleges of Technology, Abu Dhabi, United Arab Emirates
| | - Riaz Akseer
- Health Sciences Division, Abu Dhabi Women’s College, Higher Colleges of Technology, Abu Dhabi, United Arab Emirates
| | - Swee-Hua Erin Lim
- Perdana University-Royal College of Surgeons in Ireland, School of Medicine, Perdana University, Serdang, Selangor, Malaysia
- Health Sciences Division, Abu Dhabi Women’s College, Higher Colleges of Technology, Abu Dhabi, United Arab Emirates
| | - Kok-Song Lai
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- * E-mail:
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15
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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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16
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Sharma A, Kumar V, Pratap S, Kumar P. The inhibitory and binding studies of methyl-sulfone hydroxamate based inhibitors against LpxC from drug resistant Moraxella catarrhalis using biophysical, biochemical and in silico approaches. Int J Biol Macromol 2018; 118:1747-1762. [DOI: 10.1016/j.ijbiomac.2018.07.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/06/2018] [Accepted: 07/07/2018] [Indexed: 01/17/2023]
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17
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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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18
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Piizzi G, Parker DT, Peng Y, Dobler M, Patnaik A, Wattanasin S, Liu E, Lenoir F, Nunez J, Kerrigan J, McKenney D, Osborne C, Yu D, Lanieri L, Bojkovic J, Dzink-Fox J, Lilly MD, Sprague ER, Lu Y, Wang H, Ranjitkar S, Xie L, Wang B, Glick M, Hamann LG, Tommasi R, Yang X, Dean CR. Design, Synthesis, and Properties of a Potent Inhibitor of Pseudomonas aeruginosa Deacetylase LpxC. J Med Chem 2017; 60:5002-5014. [PMID: 28549219 DOI: 10.1021/acs.jmedchem.7b00377] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Over the past several decades, the frequency of antibacterial resistance in hospitals, including multidrug resistance (MDR) and its association with serious infectious diseases, has increased at alarming rates. Pseudomonas aeruginosa is a leading cause of nosocomial infections, and resistance to virtually all approved antibacterial agents is emerging in this pathogen. To address the need for new agents to treat MDR P. aeruginosa, we focused on inhibiting the first committed step in the biosynthesis of lipid A, the deacetylation of uridyldiphospho-3-O-(R-hydroxydecanoyl)-N-acetylglucosamine by the enzyme LpxC. We approached this through the design, synthesis, and biological evaluation of novel hydroxamic acid LpxC inhibitors, exemplified by 1, where cytotoxicity against mammalian cell lines was reduced, solubility and plasma-protein binding were improved while retaining potent anti-pseudomonal activity in vitro and in vivo.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - David McKenney
- Infectious Diseases Area, Novartis Institutes for BioMedical Research , Emeryville, California 94608, United States
| | - Colin Osborne
- Infectious Diseases Area, Novartis Institutes for BioMedical Research , Emeryville, California 94608, United States
| | - Donghui Yu
- Infectious Diseases Area, Novartis Institutes for BioMedical Research , Emeryville, California 94608, United States
| | - Leanne Lanieri
- Infectious Diseases Area, Novartis Institutes for BioMedical Research , Emeryville, California 94608, United States
| | - Jade Bojkovic
- Infectious Diseases Area, Novartis Institutes for BioMedical Research , Emeryville, California 94608, United States
| | - JoAnn Dzink-Fox
- Infectious Diseases Area, Novartis Institutes for BioMedical Research , Emeryville, California 94608, United States
| | - Maria-Dawn Lilly
- Infectious Diseases Area, Novartis Institutes for BioMedical Research , Emeryville, California 94608, United States
| | | | | | | | - Srijan Ranjitkar
- Infectious Diseases Area, Novartis Institutes for BioMedical Research , Emeryville, California 94608, United States
| | - Lili Xie
- Infectious Diseases Area, Novartis Institutes for BioMedical Research , Emeryville, California 94608, United States
| | | | | | | | | | - Xia Yang
- Infectious Diseases Area, Novartis Institutes for BioMedical Research , Emeryville, California 94608, United States
| | - Charles R Dean
- Infectious Diseases Area, Novartis Institutes for BioMedical Research , Emeryville, California 94608, United States
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19
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Cram ED, Rockey DD, Dolan BP. Chlamydia spp. development is differentially altered by treatment with the LpxC inhibitor LPC-011. BMC Microbiol 2017; 17:98. [PMID: 28438125 PMCID: PMC5402638 DOI: 10.1186/s12866-017-0992-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 03/28/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chlamydia species are obligate intracellular bacteria that infect a broad range of mammalian hosts. Members of related genera are pathogens of a variety of vertebrate and invertebrate species. Despite the diversity of Chlamydia, all species contain an outer membrane lipooligosaccharide (LOS) that is comprised of a genus-conserved, and genus-defining, trisaccharide 3-deoxy-D-manno-oct-2-ulosonic acid Kdo region. Recent studies with lipopolysaccharide inhibitors demonstrate that LOS is important for the C. trachomatis developmental cycle during RB- > EB differentiation. Here, we explore the effects of one of these inhibitors, LPC-011, on the developmental cycle of five chlamydial species. RESULTS Sensitivity to the drug varied in some of the species and was conserved between others. We observed that inhibition of LOS biosynthesis in some chlamydial species induced formation of aberrant reticulate bodies, while in other species, no change was observed to the reticulate body. However, loss of LOS production prevented completion of the chlamydial reproductive cycle in all species tested. In previous studies we found that C. trachomatis and C. caviae infection enhances MHC class I antigen presentation of a model self-peptide. We find that treatment with LPC-011 prevents enhanced host-peptide presentation induced by infection with all chlamydial-species tested. CONCLUSIONS The data demonstrate that LOS synthesis is necessary for production of infectious progeny and inhibition of LOS synthesis induces aberrancy in certain chlamydial species, which has important implications for the use of LOS synthesis inhibitors as potential antibiotics.
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Affiliation(s)
- Erik D Cram
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, 105 Magruder Hall, Corvallis, OR, 97331, USA.
| | - Daniel D Rockey
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, 105 Magruder Hall, Corvallis, OR, 97331, USA
| | - Brian P Dolan
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, 105 Magruder Hall, Corvallis, OR, 97331, USA
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21
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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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22
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Erwin AL. Antibacterial Drug Discovery Targeting the Lipopolysaccharide Biosynthetic Enzyme LpxC. Cold Spring Harb Perspect Med 2016; 6:cshperspect.a025304. [PMID: 27235477 DOI: 10.1101/cshperspect.a025304] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The enzyme LpxC (UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase) is broadly conserved across Gram-negative bacteria and is essential for synthesis of lipid A, the membrane anchor of the lipopolysaccharides (LPSs), which are a major component of the outer membrane in nearly all Gram-negative bacteria. LpxC has been the focus of target-directed antibiotic discovery projects in numerous pharmaceutical and academic groups for more than 20 years. Despite intense effort, no LpxC inhibitor has been approved for therapeutic use, and only one has yet reached human studies. This article will summarize the history of LpxC as a drug target and the parallel history of research on LpxC biology. Both academic and industrial researchers have used LpxC inhibitors as tool compounds, leading to increased understanding of the differing mechanisms for regulation of LPS synthesis in Escherichia coli and Pseudomonas aeruginosa.
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23
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Henderson JC, Zimmerman SM, Crofts AA, Boll JM, Kuhns LG, Herrera CM, Trent MS. The Power of Asymmetry: Architecture and Assembly of the Gram-Negative Outer Membrane Lipid Bilayer. Annu Rev Microbiol 2016; 70:255-78. [PMID: 27359214 DOI: 10.1146/annurev-micro-102215-095308] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Determining the chemical composition of biological materials is paramount to the study of natural phenomena. Here, we describe the composition of model gram-negative outer membranes, focusing on the predominant assembly, an asymmetrical bilayer of lipid molecules. We also give an overview of lipid biosynthetic pathways and molecular mechanisms that organize this material into the outer membrane bilayer. An emphasis is placed on the potential of these pathways as targets for antibiotic development. We discuss deviations in composition, through bacterial cell surface remodeling, and alternative modalities to the asymmetric lipid bilayer. Outer membrane lipid alterations of current microbiological interest, such as lipid structures found in commensal bacteria, are emphasized. Additionally, outer membrane components could potentially be engineered to develop vaccine platforms. Observations related to composition and assembly of gram-negative outer membranes will continue to generate novel discoveries, broaden biotechnologies, and reveal profound mysteries to compel future research.
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Affiliation(s)
- Jeremy C Henderson
- Department of Molecular Biosciences, The University of Texas at Austin, Texas 78712
| | - Shawn M Zimmerman
- Department of Infectious Diseases, The University of Georgia, Athens, Georgia 30602;
| | - Alexander A Crofts
- Department of Molecular Biosciences, The University of Texas at Austin, Texas 78712
| | - Joseph M Boll
- Department of Molecular Biosciences, The University of Texas at Austin, Texas 78712
| | - Lisa G Kuhns
- Department of Infectious Diseases, The University of Georgia, Athens, Georgia 30602;
| | - Carmen M Herrera
- Department of Infectious Diseases, The University of Georgia, Athens, Georgia 30602;
| | - M Stephen Trent
- Department of Infectious Diseases, The University of Georgia, Athens, Georgia 30602;
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24
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Titecat M, Liang X, Lee CJ, Charlet A, Hocquet D, Lambert T, Pagès JM, Courcol R, Sebbane F, Toone EJ, Zhou P, Lemaitre N. High susceptibility of MDR and XDR Gram-negative pathogens to biphenyl-diacetylene-based difluoromethyl-allo-threonyl-hydroxamate LpxC inhibitors. J Antimicrob Chemother 2016; 71:2874-82. [PMID: 27330072 DOI: 10.1093/jac/dkw210] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 05/04/2016] [Indexed: 02/02/2023] Open
Abstract
OBJECTIVES Inhibitors of uridine diphosphate-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC, which catalyses the first, irreversible step in lipid A biosynthesis) are a promising new class of antibiotics against Gram-negative bacteria. The objectives of the present study were to: (i) compare the antibiotic activities of three LpxC inhibitors (LPC-058, LPC-011 and LPC-087) and the reference inhibitor CHIR-090 against Gram-negative bacilli (including MDR and XDR isolates); and (ii) investigate the effect of combining these inhibitors with conventional antibiotics. METHODS MICs were determined for 369 clinical isolates (234 Enterobacteriaceae and 135 non-fermentative Gram-negative bacilli). Time-kill assays with LPC-058 were performed on four MDR/XDR strains, including Escherichia coli producing CTX-M-15 ESBL and Klebsiella pneumoniae, Pseudomonas aeruginosa and Acinetobacter baumannii producing KPC-2, VIM-1 and OXA-23 carbapenemases, respectively. RESULTS LPC-058 was the most potent antibiotic and displayed the broadest spectrum of antimicrobial activity, with MIC90 values for Enterobacteriaceae, P. aeruginosa, Burkholderia cepacia and A. baumannii of 0.12, 0.5, 1 and 1 mg/L, respectively. LPC-058 was bactericidal at 1× or 2× MIC against CTX-M-15, KPC-2 and VIM-1 carbapenemase-producing strains and bacteriostatic at ≤4× MIC against OXA-23 carbapenemase-producing A. baumannii. Combinations of LPC-058 with β-lactams, amikacin and ciprofloxacin were synergistic against these strains, albeit in a species-dependent manner. LPC-058's high efficacy was attributed to the presence of the difluoromethyl-allo-threonyl head group and a linear biphenyl-diacetylene tail group. CONCLUSIONS These in vitro data highlight the therapeutic potential of the new LpxC inhibitor LPC-058 against MDR/XDR strains and set the stage for subsequent in vivo studies.
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Affiliation(s)
- Marie Titecat
- Univ. Lille, CNRS, INSERM, CHU Lille, U1019-UMR 8204, Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Xiaofei Liang
- Department of Chemistry, Duke University, Durham, NC 27708, USA
| | - Chul-Jin Lee
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Audrey Charlet
- Univ. Lille, CNRS, INSERM, CHU Lille, U1019-UMR 8204, Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Didier Hocquet
- UMR CNRS 6249, Chrono-environnement, Université de Bourgogne-Franche-Comté, Centre de Ressources Biologiques Ferdinand Cabanne, Hygiène Hospitalière, CHU Besançon, F-25000 Besançon, France
| | - Thierry Lambert
- EA 4043 Unité Bactéries Pathogènes et Santé (UBaPS), Univ. Paris-Sud, Unité Paris Saclay, F-92290 Châtenay-Malabry, France
| | - Jean-Marie Pagès
- UMR-MD1, Aix Marseille Université, Institut de Recherche Biomédicale des Armées, F-13000 Marseille, France
| | - René Courcol
- Univ. Lille, CNRS, INSERM, CHU Lille, U1019-UMR 8204, Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Florent Sebbane
- Univ. Lille, CNRS, INSERM, CHU Lille, U1019-UMR 8204, Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Eric J Toone
- Department of Chemistry, Duke University, Durham, NC 27708, USA Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Pei Zhou
- Department of Chemistry, Duke University, Durham, NC 27708, USA Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Nadine Lemaitre
- Univ. Lille, CNRS, INSERM, CHU Lille, U1019-UMR 8204, Center for Infection and Immunity of Lille, F-59000 Lille, France
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Kurasaki H, Tsuda K, Shinoyama M, Takaya N, Yamaguchi Y, Kishii R, Iwase K, Ando N, Nomura M, Kohno Y. LpxC Inhibitors: Design, Synthesis, and Biological Evaluation of Oxazolidinones as Gram-negative Antibacterial Agents. ACS Med Chem Lett 2016; 7:623-8. [PMID: 27326338 DOI: 10.1021/acsmedchemlett.6b00057] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 04/05/2016] [Indexed: 02/02/2023] Open
Abstract
Herein we report a scaffold-hopping approach to identify a new scaffold with a zinc binding headgroup. Structural information was used to give novel oxazolidinone-based LpxC inhibitors. In particular, the most potent compound, 23j, showed a low efflux ratio, nanomolar potencies against E. coli LpxC enzyme, and excellent antibacterial activity against E. coli and K. pneumoniae. Computational docking was used to predict the interaction between 23j and E. coli LpxC, suggesting that the interactions with C207 and C63 contribute to the strong activity. These results provide new insights into the design of next-generation LpxC inhibitors.
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Affiliation(s)
- Haruaki Kurasaki
- Watarase Research Center, Kyorin Pharmaceutical Co., Ltd., 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Kosuke Tsuda
- Watarase Research Center, Kyorin Pharmaceutical Co., Ltd., 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Mariko Shinoyama
- Watarase Research Center, Kyorin Pharmaceutical Co., Ltd., 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Noriko Takaya
- Watarase Research Center, Kyorin Pharmaceutical Co., Ltd., 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Yuko Yamaguchi
- Watarase Research Center, Kyorin Pharmaceutical Co., Ltd., 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Ryuta Kishii
- Watarase Research Center, Kyorin Pharmaceutical Co., Ltd., 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Kazuhiko Iwase
- Watarase Research Center, Kyorin Pharmaceutical Co., Ltd., 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Naoki Ando
- Watarase Research Center, Kyorin Pharmaceutical Co., Ltd., 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Masahiro Nomura
- Watarase Research Center, Kyorin Pharmaceutical Co., Ltd., 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Yasushi Kohno
- Watarase Research Center, Kyorin Pharmaceutical Co., Ltd., 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
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Abstract
The practice of medicine was profoundly transformed by the introduction of the antibiotics (compounds isolated from Nature) and the antibacterials (compounds prepared by synthesis) for the control of bacterial infection. As a result of the extraordinary success of these compounds over decades of time, a timeless biological activity for these compounds has been presumed. This presumption is no longer. The inexorable acquisition of resistance mechanisms by bacteria is retransforming medical practice. Credible answers to this dilemma are far better recognized than they are being implemented. In this perspective we examine (and in key respects, reiterate) the chemical and biological strategies being used to address the challenge of bacterial resistance.
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Affiliation(s)
- Jed F. Fisher
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame IN 46556–5670, USA
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame IN 46556–5670, USA
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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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Murphy-Benenato KE, Olivier N, Choy A, Ross PL, Miller MD, Thresher J, Gao N, Hale MR. Synthesis, Structure, and SAR of Tetrahydropyran-Based LpxC Inhibitors. ACS Med Chem Lett 2014; 5:1213-8. [PMID: 25408833 DOI: 10.1021/ml500210x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 09/23/2014] [Indexed: 01/25/2023] Open
Abstract
In the search for novel Gram-negative agents, we performed a comprehensive search of the AstraZeneca collection and identified a tetrahydropyran-based matrix metalloprotease (MMP) inhibitor that demonstrated nanomolar inhibition of UDP-3-O-(acyl)-N-acetylglucosamine deacetylase (LpxC). Crystallographic studies in Aquifex aeolicus LpxC indicated the tetrahydropyran engaged in the same hydrogen bonds and van der Waals interactions as other known inhibitors. Systematic optimization of three locales on the scaffold provided compounds with improved Gram-negative activity. However, the optimization of LpxC activity was not accompanied by reduced inhibition of MMPs. Comparison of the crystal structure of the native product, UDP-3-O-(acyl)-glucosamine, in Aquifex aeolicus to the structure of a tetrahydropyran-based inhibitor indicates pathways for future optimization.
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Affiliation(s)
- Kerry E. Murphy-Benenato
- Department of Chemistry, Infection Innovative Medicines, and ‡Discovery Sciences, AstraZeneca R&D, Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | | | - Allison Choy
- Department of Chemistry, Infection Innovative Medicines, and ‡Discovery Sciences, AstraZeneca R&D, Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | | | - Matthew D. Miller
- Department of Chemistry, Infection Innovative Medicines, and ‡Discovery Sciences, AstraZeneca R&D, Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Jason Thresher
- Department of Chemistry, Infection Innovative Medicines, and ‡Discovery Sciences, AstraZeneca R&D, Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | | | - Michael R. Hale
- Department of Chemistry, Infection Innovative Medicines, and ‡Discovery Sciences, AstraZeneca R&D, Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
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