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Kwak SH, Cochrane CS, Cho J, Dome PA, Ennis AF, Kim JH, Zhou P, Hong J. Development of LpxH Inhibitors Chelating the Active Site Dimanganese Metal Cluster of LpxH. ChemMedChem 2023; 18:e202300023. [PMID: 37014664 PMCID: PMC10239344 DOI: 10.1002/cmdc.202300023] [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: 01/16/2023] [Revised: 03/07/2023] [Accepted: 03/31/2023] [Indexed: 04/05/2023]
Abstract
Despite the widespread emergence of multidrug-resistant nosocomial Gram-negative bacterial infections and the major public health threat it brings, no new class of antibiotics for Gram-negative pathogens has been approved over the past five decades. Therefore, there is an urgent medical need for developing effective novel antibiotics against multidrug-resistant Gram-negative pathogens by targeting previously unexploited pathways in these bacteria. To fulfill this crucial need, we have been investigating a series of sulfonyl piperazine compounds targeting LpxH, a dimanganese-containing UDP-2,3-diacylglucosamine hydrolase in the lipid A biosynthetic pathway, as novel antibiotics against clinically important Gram-negative pathogens. Inspired by a detailed structural analysis of our previous LpxH inhibitors in complex with K. pneumoniae LpxH (KpLpxH), here we report the development and structural validation of the first-in-class sulfonyl piperazine LpxH inhibitors, JH-LPH-45 (8) and JH-LPH-50 (13), that achieve chelation of the active site dimanganese cluster of KpLpxH. The chelation of the dimanganese cluster significantly improves the potency of JH-LPH-45 (8) and JH-LPH-50 (13). We expect that further optimization of these proof-of-concept dimanganese-chelating LpxH inhibitors will ultimately lead to the development of more potent LpxH inhibitors for targeting multidrug-resistant Gram-negative pathogens.
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Affiliation(s)
- Seung-Hwa Kwak
- Department of Chemistry, Duke University, Durham, NC 27708, United States
| | - C. Skyler Cochrane
- Department of Chemistry, Duke University, Durham, NC 27708, United States
| | - Jae Cho
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, United States
| | - Patrick A. Dome
- Department of Chemistry, Duke University, Durham, NC 27708, United States
| | - Amanda F. Ennis
- Department of Chemistry, Duke University, Durham, NC 27708, United States
| | - Jea Hyun Kim
- Department of Chemistry, Duke University, Durham, NC 27708, United States
| | - Pei Zhou
- Department of Chemistry, Duke University, Durham, NC 27708, United States
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, United States
| | - Jiyong Hong
- Department of Chemistry, Duke University, Durham, NC 27708, United States
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, United States
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2
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Xu N, Du LH, Chen YC, Zhang JH, Zhu QF, Chen R, Peng GP, Wang QM, Yu HZ, Rao LQ. Lonicera japonica Thunb. as a promising antibacterial agent for Bacillus cereus ATCC14579 based on network pharmacology, metabolomics, and in vitro experiments. RSC Adv 2023; 13:15379-15390. [PMID: 37223411 PMCID: PMC10201548 DOI: 10.1039/d3ra00802a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 05/15/2023] [Indexed: 05/25/2023] Open
Abstract
Lonicera japonica Thunb. has attracted much attention for its treatment of bacterial and viral infectious diseases, while its active ingredients and potential mechanisms of action have not been fully elucidated. Here, we combined metabolomics, and network pharmacology to explore the molecular mechanism of Bacillus cereus ATCC14579 inhibition by Lonicera japonica Thunb. In vitro inhibition experiments showed that the Lonicera japonica Thunb.'s water extracts, ethanolic extract, luteolin, quercetin, and kaempferol strongly inhibited Bacillus cereus ATCC14579. In contrast, chlorogenic acid and macranthoidin B had no inhibitory effect on Bacillus cereus ATCC14579. Meanwhile, the minimum inhibitory concentrations of luteolin, quercetin, and kaempferol against Bacillus cereus ATCC14579 were 15.625 μg mL-1, 31.25 μg mL-1, and 15.625 μg mL-1. Based on the previous experimental basis, the metabolomic analysis showed the presence of 16 active ingredients in Lonicera japonica Thunb.'s water extracts and ethanol extracts, with differences in the luteolin, quercetin, and kaempferol contents between the water extracts and ethanol extracts. Network pharmacology studies indicated that fabZ, tig, glmU, secA, deoD, nagB, pgi, rpmB, recA, and upp were potential key targets. Active ingredients of Lonicera japonica Thunb. may exert their inhibitory effects by inhibiting ribosome assembly, the peptidoglycan biosynthesis process, and the phospholipid biosynthesis process of Bacillus cereus ATCC14579. An alkaline phosphatase activity assay, peptidoglycan concentration assay, and protein concentration assay showed that luteolin, quercetin, and kaempferol disrupted the Bacillus cereus ATCC14579 cell wall and cell membrane integrity. Transmission electron microscopy results showed significant changes in the morphology and ultrastructure of the cell wall and cell membrane of Bacillus cereus ATCC14579, further confirming the disruption of the cell wall and cell membrane integrity of Bacillus cereus ATCC14579 by luteolin, quercetin, and kaempferol. In conclusion, Lonicera japonica Thunb. can be used as a potential antibacterial agent for Bacillus cereus ATCC14579, which may exert its antibacterial activity by destroying the integrity of the cell wall and membrane.
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Affiliation(s)
- Nan Xu
- Hunan Engineering Laboratory for Good Agricultural Practice and Comprehensive Utilization of Famous-Region Medicinal Plants, Hunan Agricultural University Changsha China
| | - Li-Hua Du
- Hunan Engineering Laboratory for Good Agricultural Practice and Comprehensive Utilization of Famous-Region Medicinal Plants, Hunan Agricultural University Changsha China
| | - Yan-Chao Chen
- Hunan Engineering Laboratory for Good Agricultural Practice and Comprehensive Utilization of Famous-Region Medicinal Plants, Hunan Agricultural University Changsha China
| | - Jin-Hao Zhang
- Hunan Engineering Laboratory for Good Agricultural Practice and Comprehensive Utilization of Famous-Region Medicinal Plants, Hunan Agricultural University Changsha China
| | - Qian-Feng Zhu
- Hunan Engineering Laboratory for Good Agricultural Practice and Comprehensive Utilization of Famous-Region Medicinal Plants, Hunan Agricultural University Changsha China
| | - Rong Chen
- Hunan Engineering Laboratory for Good Agricultural Practice and Comprehensive Utilization of Famous-Region Medicinal Plants, Hunan Agricultural University Changsha China
| | - Guo-Ping Peng
- Hunan Engineering Laboratory for Good Agricultural Practice and Comprehensive Utilization of Famous-Region Medicinal Plants, Hunan Agricultural University Changsha China
| | - Qi-Ming Wang
- Hunan Engineering Laboratory for Good Agricultural Practice and Comprehensive Utilization of Famous-Region Medicinal Plants, Hunan Agricultural University Changsha China
| | - Hua-Zhong Yu
- Key Laboratory of Hunan Forest Products and Chemical Industry Engineering, Jishou University Jishou China
| | - Li-Qun Rao
- Hunan Engineering Laboratory for Good Agricultural Practice and Comprehensive Utilization of Famous-Region Medicinal Plants, Hunan Agricultural University Changsha China
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3
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Yang L, Guan D, Valls M, Ding W. Sustainable natural bioresources in crop protection: antimicrobial hydroxycoumarins induce membrane depolarization-associated changes in the transcriptome of Ralstonia solanacearum. PEST MANAGEMENT SCIENCE 2021; 77:5170-5185. [PMID: 34255407 DOI: 10.1002/ps.6557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 05/07/2021] [Accepted: 07/13/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Ralstonia solanacearum is one of the most devastating pathogens affecting crop production worldwide. The hydroxycoumarins (umbelliferone, esculetin and daphnetin) represent sustainable natural bioresources on controlling plant bacterial wilt. However, the antibacterial mechanism of hydroxycoumarins against plant pathogens still remains poorly understood. RESULTS Here we characterized the effect of three hydroxycoumarins on the transcriptome of R. solanacearum. All three hydroxycoumarins were able to kill R. solanacearum, but their antibacterial activity impacted differently the bacterial transcriptome, indicating that their modes of action might be different. Treatment of R. solanacearum cultures with hydroxycoumarins resulted in a large number of differentially expressed genes (DEGs), involved in basic cellular functions and metabolic process, such as down-regulation of genes involved in fatty acid synthesis, lipopolysaccharides biosynthesis, RNA modification, ribosomal submits, oxidative phosphorylation and electrontransport, as well as up-regulation of genes involved in transcriptional regulators, drug efflux, and oxidative stress responses. Future studies based on in vitro experiments are proposed to investigate lipopolysaccharides biosynthesis pathway leading to R. solanacearum cell death caused by hydroxycoumarins. Deletion of lpxB substantially inhibited the growth of R. solanacearum, and reduced virulence of pathogen on tobacco plants. CONCULSION Our transcriptomic analyses show that specific hydroxycoumarins suppressed gene expression involved in fatty acid synthesis, RNA modification, ribosomal submits, oxidative phosphorylation and electrontransport. These findings provide evidence that hydroxycoumarins inhibit R. solanacearum growth through multi-target effect. Hydroxycoumarins could serve as sustainable natural bioresources against plant bacterial wilt through membrane destruction targeting the lipopolysaccharides biosynthesis pathway.
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Affiliation(s)
- Liang Yang
- Laboratory of Natural Products Pesticides, College of Plant Protection, Southwest University, Chongqing, China
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Dailu Guan
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Marc Valls
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, Spain
- Genetics Section, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Wei Ding
- Laboratory of Natural Products Pesticides, College of Plant Protection, Southwest University, Chongqing, China
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4
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Antibacterial efficacy and molecular docking analysis of Huang-Lian-Jie-Du Decoction against the phytopathogenic bacteria P. carotovorum PC1. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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5
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Zhang H, HuangFu H, Wang X, Zhao S, Liu Y, Lv H, Qin G, Tan Z. Antibacterial Activity of Lactic Acid Producing Leuconostoc mesenteroides QZ1178 Against Pathogenic Gallibacterium anatis. Front Vet Sci 2021; 8:630294. [PMID: 33969032 PMCID: PMC8100202 DOI: 10.3389/fvets.2021.630294] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 03/22/2021] [Indexed: 12/01/2022] Open
Abstract
Lactic acid bacteria (LAB) convert carbohydrates into organic acids [mainly lactic acid (LA)], which reportedly have bactericidal activities. Gallibacterium anatis is a Gram-negative bacteria which infects birds, and causes significant economic losses. In this study, we investigated the antibacterial activity of the LA producing, Leuconostoc mesenteroides QZ1178 from Qula (fermented food), against G. anatis, using the Oxford cup method. Our data showed that L. mesenteroides QZ1178 inhibited G. anatis isolates from different origins; however, L. mesenteroides QZ1178 antibacterial activity dropped dramatically at pH 5.5–pH 6. The LA concentration and pH of the liquid broth containing L. mesenteroides QZ1178 after 24 h culture was 29 mg/mL and 3.6, respectively. This concentration (29 mg/mL at pH 3.6) and the antibiotic, cefotaxime (minimum inhibitory concentration (MIC) 2.5 μg/mL) effectively inhibited G. anatis (GAC026) growth as observed by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Gallibacterium anatis treated with LA exhibited extensive cell surface collapse, increased cell damage, cell membrane disruption, and cytoplasmic leakage, indicative of cell lysis. We suggest L. mesenteroides QZ1178 exerts potential antibacterial effects against the poultry pathogen, G. anatis via LA.
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Affiliation(s)
- Hua Zhang
- Henan Key Laboratory of Ion-Beam Bioengineering, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China.,School of Food and Biological Engineering, Henan University of Animal Husbandry and Economy, Zhengzhou, China.,Henan Key Laboratory of Ion-Beam Bioengineering, School of Physics and Microelectronics, Zhengzhou University, Zhengzhou, China
| | - HePing HuangFu
- School of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou, China
| | - Xing Wang
- Henan Key Laboratory of Ion-Beam Bioengineering, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Ion-Beam Bioengineering, School of Physics and Microelectronics, Zhengzhou University, Zhengzhou, China
| | - ShanShan Zhao
- Henan Key Laboratory of Ion-Beam Bioengineering, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Ion-Beam Bioengineering, School of Physics and Microelectronics, Zhengzhou University, Zhengzhou, China
| | - Yuan Liu
- Henan Key Laboratory of Ion-Beam Bioengineering, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Ion-Beam Bioengineering, School of Physics and Microelectronics, Zhengzhou University, Zhengzhou, China
| | - Haoxin Lv
- School of Food Science and Technology, Henan University of Technology, Zhengzhou, China
| | - GuangYong Qin
- Henan Key Laboratory of Ion-Beam Bioengineering, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Zhongfang Tan
- Henan Key Laboratory of Ion-Beam Bioengineering, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
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6
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Ma X, Prathapam R, Wartchow C, Chie-Leon B, Ho CM, De Vicente J, Han W, Li M, Lu Y, Ramurthy S, Shia S, Steffek M, Uehara T. Structural and Biological Basis of Small Molecule Inhibition of Escherichia coli LpxD Acyltransferase Essential for Lipopolysaccharide Biosynthesis. ACS Infect Dis 2020; 6:1480-1489. [PMID: 31402665 DOI: 10.1021/acsinfecdis.9b00127] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
LpxD, acyl-ACP-dependent N-acyltransferase, is the third enzyme of lipid A biosynthesis in Gram-negative bacteria. A recent probe-based screen identified several compounds, including 6359-0284 (compound 1), that inhibit the enzymatic activity of Escherichia coli (E. coli) LpxD. Here, we use these inhibitors to chemically validate LpxD as an attractive antibacterial target. We first found that compound 1 was oxidized in solution to the more stable aromatized tetrahydro-pyrazolo-quinolinone compound 1o. From the Escherichia coli strain deficient in efflux, we isolated a mutant that was less susceptible to compound 1o and had an lpxD missense mutation (Gly268Cys), supporting the cellular on-target activity. Using surface plasma resonance, we showed direct binding to E. coli LpxD for compound 1o and other reported LpxD inhibitors in vitro. Furthermore, we determined eight cocrystal structures of E. coli LpxD/inhibitor complexes. These costructures pinpointed the 4'-phosphopantetheine binding site as the common ligand binding hotspot, where hydrogen bonds to Gly269 and/or Gly287 were important for inhibitor binding. In addition, the LpxD/compound 1o costructure rationalized the reduced activity of compound 1o in the LpxDGly268Cys mutant. Moreover, we obtained the LpxD structure in complex with a previously reported LpxA/LpxD dual targeting peptide inhibitor, RJPXD33, providing structural rationale for the unique dual targeting properties of this peptide. Given that the active site residues of LpxD are conserved in multidrug resistant Enterobacteriaceae, this work paves the way for future LpxD drug discovery efforts combating these Gram-negative pathogens.
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7
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Molecular characterization of the outer membrane of Pseudomonas aeruginosa. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183151. [DOI: 10.1016/j.bbamem.2019.183151] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 10/28/2019] [Accepted: 12/06/2019] [Indexed: 01/07/2023]
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8
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Han W, Ma X, Balibar CJ, Baxter Rath CM, Benton B, Bermingham A, Casey F, Chie-Leon B, Cho MK, Frank AO, Frommlet A, Ho CM, Lee PS, Li M, Lingel A, Ma S, Merritt H, Ornelas E, De Pascale G, Prathapam R, Prosen KR, Rasper D, Ruzin A, Sawyer WS, Shaul J, Shen X, Shia S, Steffek M, Subramanian S, Vo J, Wang F, Wartchow C, Uehara T. Two Distinct Mechanisms of Inhibition of LpxA Acyltransferase Essential for Lipopolysaccharide Biosynthesis. J Am Chem Soc 2020; 142:4445-4455. [DOI: 10.1021/jacs.9b13530] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Wooseok Han
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Xiaolei Ma
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Carl J. Balibar
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | | | - Bret Benton
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Alun Bermingham
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Fergal Casey
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Barbara Chie-Leon
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Min-Kyu Cho
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Andreas O. Frank
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Alexandra Frommlet
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Chi-Min Ho
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Patrick S. Lee
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Min Li
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Andreas Lingel
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Sylvia Ma
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Hanne Merritt
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Elizabeth Ornelas
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Gianfranco De Pascale
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Ramadevi Prathapam
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Katherine R. Prosen
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Dita Rasper
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Alexey Ruzin
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - William S. Sawyer
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Jacob Shaul
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Xiaoyu Shen
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Steven Shia
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Micah Steffek
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Sharadha Subramanian
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Jason Vo
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Feng Wang
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Charles Wartchow
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Tsuyoshi Uehara
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
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9
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Budragchaa T, Westermann B, Wessjohann LA. Multicomponent synthesis of α-acylamino and α-acyloxy amide derivatives of desmycosin and their activity against gram-negative bacteria. Bioorg Med Chem 2019; 27:3237-3247. [PMID: 31229422 DOI: 10.1016/j.bmc.2019.05.046] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 03/27/2019] [Accepted: 05/29/2019] [Indexed: 11/17/2022]
Abstract
Bacterial resistance to the existing drugs requires constant development of new antibiotics. Developing compounds active against gram-negative bacteria thereby is one of the more challenging tasks. Among the many approaches to develop successful antibacterials, medicinal chemistry driven evolution of existing successful antibiotics is considered to be the most effective one. Towards this end, the C-20 aldehyde moiety of desmycosin was modified into α-acylamino and α-acyloxy amide functionalities using isonitrile-based Ugi and Passerini reactions, aiming for enhanced antibacterial and physicochemical properties. The desired compounds were obtained in 45-93% yield under mild conditions. The antibacterial activity of the resulting conjugates was tested against gram-negative Aliivibrio fischeri. The antibiotic strength is mostly governed by the amine component introduced. Thus, methylamine derived desmycosin bis-amide 4 displayed an enhanced inhibition rate vs. desmycosin (99% vs. 83% at 1 µM). Derivatives with long acyclic or bulky amine and isocyanide Ugi components reduced potency, whereas carboxylic acid reagents with longer chain length afforded increased bioactivity. In Passerini 3-component products, the butyric ester amide 22 displayed a higher activity (90% at 1 µM) than the parent compound desmycosin (2).
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Affiliation(s)
- Tuvshinjargal Budragchaa
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Saale, Germany
| | - Bernhard Westermann
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Saale, Germany; Institute of Organic Chemistry, Faculty of Natural Sciences II, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 2, 06120 Halle, Germany
| | - Ludger A Wessjohann
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Saale, Germany; Institute of Organic Chemistry, Faculty of Natural Sciences II, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 2, 06120 Halle, Germany.
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10
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Schott-Verdugo S, Gohlke H. PACKMOL-Memgen: A Simple-To-Use, Generalized Workflow for Membrane-Protein-Lipid-Bilayer System Building. J Chem Inf Model 2019; 59:2522-2528. [PMID: 31120747 DOI: 10.1021/acs.jcim.9b00269] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present PACKMOL-Memgen, a simple-to-use, generalized workflow for automated building of membrane-protein-lipid-bilayer systems based on open-source tools including Packmol, memembed, pdbremix, and AmberTools. Compared with web-interface-based related tools, PACKMOL-Memgen allows setup of multiple configurations of a system in a user-friendly and efficient manner within minutes. The generated systems are well-packed and thus well-suited as starting configurations in MD simulations under periodic boundary conditions, requiring only moderate equilibration times. PACKMOL-Memgen is distributed with AmberTools and runs on most computing platforms, and its output can also be used for CHARMM or adapted to other molecular-simulation packages.
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Affiliation(s)
- Stephan Schott-Verdugo
- Institute for Pharmaceutical and Medicinal Chemistry , Heinrich Heine University Düsseldorf , 40225 Düsseldorf , Germany.,Centro de Bioinformática y Simulación Molecular (CBSM), Faculty of Engineering , Universidad de Talca , 1 Poniente 1141 , Casilla 721 , Talca , Chile
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry , Heinrich Heine University Düsseldorf , 40225 Düsseldorf , Germany.,John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC) & Institute for Complex Systems-Structural Biochemistry (ICS 6) , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany
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11
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Novais JS, Moreira CS, Silva ACJA, Loureiro RS, Sá Figueiredo AM, Ferreira VF, Castro HC, da Rocha DR. Antibacterial naphthoquinone derivatives targeting resistant strain Gram-negative bacteria in biofilms. Microb Pathog 2018; 118:105-114. [PMID: 29550501 DOI: 10.1016/j.micpath.2018.03.024] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Revised: 03/06/2018] [Accepted: 03/13/2018] [Indexed: 12/21/2022]
Abstract
The aims of this study were the planning, synthesis and in vitro evaluation of 2-hydroxy-3-phenylsulfanylmethyl-[1,4]-naphthoquinones against Gram-negative and Gram-positive strains, searching for potential lead compounds against bacterial biofilm formation. A series of 12 new analogs of 2-hydroxy-3-phenylsulfanylmethyl-[1,4]-naphthoquinones were synthesized by adding a thiol and different substituents to a ο-quinone methide using microwave irradiation. The compounds were tested against Gram-positive (Enterococcus faecalis ATCC 29212, Staphylococcus aureus ATCC 25923, S. simulans ATCC 27851, S. epidermidis ATCC 12228 and a hospital Methicillin-resistant S. aureus (MRSA) strain), as well as Gram-negative (Escherichia coli ATCC 25922, Pseudomonas aeruginosa ATCC 27853, P. aeruginosa ATCC 15442, Proteus mirabilis ATCC 15290, Serratia marcescens ATCC 14756, Klebsiella pneumoniae ATCC 4352 and Enterobacter cloacae ATCC 23355) strains, using the disk diffusion method. Ten compounds showed activity mainly against Gram-negative strains with a minimal inhibitory concentration (MIC = 4-64 μg/mL) within the Clinical and Laboratory Standards Institute (CLSI) levels. The biofilm inhibition data showed compounds, 9e, 9f, 9j and 9k, are anti-biofilm molecules when used in sub-MIC concentrations against P. aeruginosa ATCC 15442 strain. Compound (9j) inhibited biofilm formation up to 63.4% with a better profile than ciprofloxacin, which is not able to prevent biofilm formation effectively. The reduction of P. aeruginosa ATCC 15442 mature biofilms was also observed for 9e and 9k. The structure modification applied in the series resulted in 12 new naphthoquinones with antimicrobial activity against Gram-negative bacteria strains (E. coli ATCC 25922, P. aeruginosa ATCC 27853 and ATCC 15442). Four compounds decreased P. aeruginosa biofilm formation effectively.
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Affiliation(s)
- Juliana S Novais
- Universidade Federal Fluminense, PPBI Instituto de Biologia, Departamento de Biologia Celular e Molecular, 24020-150, Niterói, Rio de Janeiro, Brazil
| | - Caroline S Moreira
- Universidade Federal Fluminense, Instituto de Química, Departamento de Química Orgânica, 24020-150, Niterói, Rio de Janeiro, Brazil
| | - Ana Carolina J A Silva
- Universidade Federal Fluminense, PPBI Instituto de Biologia, Departamento de Biologia Celular e Molecular, 24020-150, Niterói, Rio de Janeiro, Brazil
| | - Raquel S Loureiro
- Universidade Federal Fluminense, PPBI Instituto de Biologia, Departamento de Biologia Celular e Molecular, 24020-150, Niterói, Rio de Janeiro, Brazil
| | - Agnes Marie Sá Figueiredo
- Universidade Federal do Rio de Janeiro, Instituto de Microbiologia Professor Paulo de Góes, Departamento de Microbiologia Médica, Rio de Janeiro, Brazil
| | - Vitor F Ferreira
- Universidade Federal Fluminense, Departamento de Tecnologia Farmacêutica, Faculdade de Farmácia, Santa Rosa, 24241-002, Niterói, Rio de Janeiro, Brazil
| | - Helena C Castro
- Universidade Federal Fluminense, PPBI Instituto de Biologia, Departamento de Biologia Celular e Molecular, 24020-150, Niterói, Rio de Janeiro, Brazil.
| | - David R da Rocha
- Universidade Federal Fluminense, Instituto de Química, Departamento de Química Orgânica, 24020-150, Niterói, Rio de Janeiro, Brazil.
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12
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Richie DL, Wang L, Chan H, De Pascale G, Six DA, Wei JR, Dean CR. A pathway-directed positive growth restoration assay to facilitate the discovery of lipid A and fatty acid biosynthesis inhibitors in Acinetobacter baumannii. PLoS One 2018; 13:e0193851. [PMID: 29505586 PMCID: PMC5837183 DOI: 10.1371/journal.pone.0193851] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Accepted: 02/19/2018] [Indexed: 11/19/2022] Open
Abstract
Acinetobacter baumannii ATCC 19606 can grow without lipooligosaccharide (LOS). Lack of LOS can result from disruption of the early lipid A biosynthetic pathway genes lpxA, lpxC or lpxD. Although LOS itself is not essential for growth of A. baumannii ATCC 19606, it was previously shown that depletion of the lipid A biosynthetic enzyme LpxK in cells inhibited growth due to the toxic accumulation of lipid A pathway intermediates. Growth of LpxK-depleted cells was restored by chemical inhibition of LOS biosynthesis using CHIR-090 (LpxC) and fatty acid biosynthesis using cerulenin (FabB/F) and pyridopyrimidine (acetyl-CoA-carboxylase). Here, we expand on this by showing that inhibition of enoyl-acyl carrier protein reductase (FabI), responsible for converting trans-2-enoyl-ACP into acyl-ACP during the fatty acid elongation cycle also restored growth during LpxK depletion. Inhibition of fatty acid biosynthesis during LpxK depletion rescued growth at 37°C, but not at 30°C, whereas rescue by LpxC inhibition was temperature independent. We exploited these observations to demonstrate proof of concept for a targeted medium-throughput growth restoration screening assay to identify small molecule inhibitors of LOS and fatty acid biosynthesis. The differential temperature dependence of fatty acid and LpxC inhibition provides a simple means by which to separate growth stimulating compounds by pathway. Targeted cell-based screening platforms such as this are important for faster identification of compounds inhibiting pathways of interest in antibacterial discovery for clinically relevant Gram-negative pathogens.
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Affiliation(s)
- Daryl L. Richie
- Novartis Institutes for BioMedical Research, Emeryville, CA, United States of America
| | - Lisha Wang
- Novartis Institutes for BioMedical Research, Emeryville, CA, United States of America
| | - Helen Chan
- Novartis Institutes for BioMedical Research, Emeryville, CA, United States of America
| | - Gianfranco De Pascale
- Novartis Institutes for BioMedical Research, Emeryville, CA, United States of America
| | - David A. Six
- Novartis Institutes for BioMedical Research, Emeryville, CA, United States of America
| | - Jun-Rong Wei
- Novartis Institutes for BioMedical Research, Emeryville, CA, United States of America
| | - Charles R. Dean
- Novartis Institutes for BioMedical Research, Emeryville, CA, United States of America
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13
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Vaara M. New polymyxin derivatives that display improved efficacy in animal infection models as compared to polymyxin B and colistin. Med Res Rev 2018; 38:1661-1673. [PMID: 29485690 DOI: 10.1002/med.21494] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/24/2018] [Accepted: 02/01/2018] [Indexed: 01/01/2023]
Abstract
Polymyxin B and colistin (polymyxin E) are bactericidal pentacationic lipopeptides that act specifically on Gram-negative bacteria, first by disrupting their outermost permeability barrier, the outer membrane (OM), and then damaging the cytoplasmic membrane. The discovery of both polymyxin B and colistin was published independently by three laboratories as early as in 1947. They were subsequently used in intravenous therapy. Unfortunately, they also exhibit significant and dose-limiting nephrotoxicity. Therefore, polymyxins were reserved as agents of last-line defense. The emergence of extremely multiresistant strains has now forced clinicians to reinstate polymyxins in the therapy of severe infections. However, the current dosage regimens lead to insufficient drug concentrations in serum and clinicians have been advised to use larger doses, which further increases the risk of nephrotoxicity. Very recently, the interest in developing better tolerated and more effective polymyxins has grown. This review focuses on describing four development programs that have yielded novel derivatives that are more effective than the old polymyxins in animal infection models. Compounds from three programs are superior to the old polymyxins in the rodent lung infection model with Acinetobacter baumannii and/or Pseudomonas aeruginosa. One of them is also more effective than polymyxin B in A. baumannii mouse thigh infection. The fourth program includes compounds that are approximately tenfold more effective in Escherichia coli murine pyelonephritis than polymyxin B.
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Affiliation(s)
- Martti Vaara
- Northern Antibiotics Ltd., Espoo, Finland.,Department of Bacteriology and Immunology, Helsinki University Medical School, Helsinki, Finland
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14
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Grimwade JE, Leonard AC. Targeting the Bacterial Orisome in the Search for New Antibiotics. Front Microbiol 2017; 8:2352. [PMID: 29230207 PMCID: PMC5712111 DOI: 10.3389/fmicb.2017.02352] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 11/15/2017] [Indexed: 01/25/2023] Open
Abstract
There is an urgent need for new antibiotics to combat drug resistant bacteria. Existing antibiotics act on only a small number of proteins and pathways in bacterial cells, and it seems logical that expansion of the target set could lead to development of novel antimicrobial agents. One essential process, not yet exploited for antibiotic discovery, is the initiation stage of chromosome replication, mediated by the bacterial orisome. In all bacteria, orisomes assemble when the initiator protein, DnaA, as well as accessory proteins, bind to a DNA scaffold called the origin of replication (oriC). Orisomes perform the essential tasks of unwinding oriC and loading the replicative helicase, and orisome assembly is tightly regulated in the cell cycle to ensure chromosome replication begins only once. Only a few bacterial orisomes have been fully characterized, and while this lack of information complicates identification of all features that could be targeted, examination of assembly stages and orisome regulatory mechanisms may provide direction for some effective inhibitory strategies. In this perspective, we review current knowledge about orisome assembly and regulation, and identify potential targets that, when inhibited pharmacologically, would prevent bacterial chromosome replication.
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Affiliation(s)
- Julia E Grimwade
- Department of Biological Sciences, Florida Institute of Technology, Melbourne, FL, United States
| | - Alan C Leonard
- Department of Biological Sciences, Florida Institute of Technology, Melbourne, FL, United States
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15
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Luther A, Bisang C, Obrecht D. Advances in macrocyclic peptide-based antibiotics. Bioorg Med Chem 2017; 26:2850-2858. [PMID: 28886999 DOI: 10.1016/j.bmc.2017.08.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 07/14/2017] [Accepted: 08/06/2017] [Indexed: 11/30/2022]
Abstract
Macrocyclic peptide-based natural products have provided powerful new antibiotic drugs, drug candidates, and scaffolds for medicinal chemists as a source of inspiration to design novel antibiotics. While most of those natural products are active mainly against Gram-positive pathogens, novel macrocyclic peptide-based compounds have recently been described, which exhibit potent and specific activity against some of the most problematic Gram-negative ESKAPE pathogens. This mini-review gives an up-date on recent developments.
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Affiliation(s)
- Anatol Luther
- Polyphor Ltd, Hegenheimermattweg 125, CH-4123 Allschwil, Switzerland.
| | - Christian Bisang
- Polyphor Ltd, Hegenheimermattweg 125, CH-4123 Allschwil, Switzerland
| | - Daniel Obrecht
- Polyphor Ltd, Hegenheimermattweg 125, CH-4123 Allschwil, Switzerland.
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16
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LpxK Is Essential for Growth of Acinetobacter baumannii ATCC 19606: Relationship to Toxic Accumulation of Lipid A Pathway Intermediates. mSphere 2017; 2:mSphere00199-17. [PMID: 28815210 PMCID: PMC5555675 DOI: 10.1128/msphere.00199-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 07/06/2017] [Indexed: 11/20/2022] Open
Abstract
Acinetobacter baumannii is a Gram-negative pathogen for which new therapies are needed. The lipid A biosynthetic pathway has several potential enzyme targets for the development of anti-Gram-negative agents (e.g., LpxC). However, A. baumannii ATCC 19606 can grow in the absence of LpxC and, correspondingly, of lipid A. In contrast, we show that cellular depletion of LpxK, a kinase occurring later in the pathway, inhibits growth. Growth inhibition results from toxic accumulation of lipid A pathway intermediates, since chemical inhibition of LpxC or fatty acid biosynthesis rescues cell growth upon loss of LpxK. Overall, this suggests that targets such as LpxK can be essential for growth even in those Gram-negative bacteria that do not require lipid A biosynthesis per se. This strain provides an elegant tool to derive a better understanding of the steps in a pathway that is the focus of intense interest for the development of novel antibacterials. Acinetobacter baumannii ATCC 19606 can grow without lipid A, the major component of lipooligosaccharide. However, we previously reported that depletion of LpxH (the fourth enzyme in the lipid A biosynthetic pathway) prevented growth of this strain due to toxic accumulation of lipid A pathway intermediates. Here, we explored whether a similar phenomenon occurred with depletion of LpxK, a kinase that phosphorylates disaccharide 1-monophosphate (DSMP) at the 4′ position to yield lipid IVA. An A. baumannii ATCC 19606 derivative with LpxK expression under the control of an isopropyl β-d-1-thiogalactopyranoside (IPTG)-regulated expression system failed to grow without induction, indicating that LpxK is essential for growth. Light and electron microscopy of LpxK-depleted cells revealed morphological changes relating to the cell envelope, consistent with toxic accumulation of lipid A pathway intermediates disrupting cell membranes. Using liquid chromatography-mass spectrometry (LCMS), cellular accumulation of the detergent-like pathway intermediates DSMP and lipid X was shown. Toxic accumulation was further supported by restoration of growth upon chemical inhibition of LpxC (upstream of LpxK and the first committed step of lipid A biosynthesis) using CHIR-090. Inhibitors of fatty acid synthesis also abrogated the requirement for LpxK expression. Growth rescue with these inhibitors was possible on Mueller-Hinton agar but not on MacConkey agar. The latter contains outer membrane-impermeable bile salts, suggesting that despite growth restoration, the cell membrane permeability barrier was not restored. Therefore, LpxK is essential for growth of A. baumannii, since loss of LpxK causes accumulation of detergent-like pathway intermediates that inhibit cell growth. IMPORTANCEAcinetobacter baumannii is a Gram-negative pathogen for which new therapies are needed. The lipid A biosynthetic pathway has several potential enzyme targets for the development of anti-Gram-negative agents (e.g., LpxC). However, A. baumannii ATCC 19606 can grow in the absence of LpxC and, correspondingly, of lipid A. In contrast, we show that cellular depletion of LpxK, a kinase occurring later in the pathway, inhibits growth. Growth inhibition results from toxic accumulation of lipid A pathway intermediates, since chemical inhibition of LpxC or fatty acid biosynthesis rescues cell growth upon loss of LpxK. Overall, this suggests that targets such as LpxK can be essential for growth even in those Gram-negative bacteria that do not require lipid A biosynthesis per se. This strain provides an elegant tool to derive a better understanding of the steps in a pathway that is the focus of intense interest for the development of novel antibacterials.
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17
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Klahn P, Brönstrup M. Bifunctional antimicrobial conjugates and hybrid antimicrobials. Nat Prod Rep 2017; 34:832-885. [PMID: 28530279 DOI: 10.1039/c7np00006e] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: up to the end of 2016Novel antimicrobial drugs are continuously needed to counteract bacterial resistance development. An innovative molecular design strategy for novel antibiotic drugs is based on the hybridization of an antibiotic with a second functional entity. Such conjugates can be grouped into two major categories. In the first category (antimicrobial hybrids), both functional elements of the hybrid exert antimicrobial activity. Due to the dual targeting, resistance development can be significantly impaired, the pharmacokinetic properties can be superior compared to combination therapies with the single antibiotics, and the antibacterial potency is often enhanced in a synergistic manner. In the second category (antimicrobial conjugates), one functional moiety controls the accumulation of the other part of the conjugate, e.g. by mediating an active transport into the bacterial cell or blocking the efflux. This approach is mostly applied to translocate compounds across the cell envelope of Gram-negative bacteria through membrane-embedded transporters (e.g. siderophore transporters) that provide nutrition and signalling compounds to the cell. Such 'Trojan Horse' approaches can expand the antibacterial activity of compounds against Gram-negative pathogens, or offer new options for natural products that could not be developed as standalone antibiotics, e.g. due to their toxicity.
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Affiliation(s)
- P Klahn
- Department for Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany. and Institute for Organic Chemistry, Technische Universität Braunschweig, Hagenring 30, 38106 Braunschweig, Germany.
| | - M Brönstrup
- Department for Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany.
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18
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Antibacterial New Target Discovery: Sentinel Examples, Strategies, and Surveying Success. TOPICS IN MEDICINAL CHEMISTRY 2017. [DOI: 10.1007/7355_2016_31] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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19
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González LJ, Bahr G, Vila AJ. Lipidated β-lactamases: from bench to bedside. Future Microbiol 2016; 11:1495-1498. [PMID: 27831740 DOI: 10.2217/fmb-2016-0176] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Lisandro J González
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Rosario, Argentina.,Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Guillermo Bahr
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Rosario, Argentina.,Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Alejandro J Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Rosario, Argentina.,Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
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