1
|
Taguchi A, Nakashima R, Nishino K. Structural Basis of Nucleotide Selectivity in Pyruvate Kinase. J Mol Biol 2024; 436:168708. [PMID: 39009072 DOI: 10.1016/j.jmb.2024.168708] [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: 06/19/2024] [Revised: 07/09/2024] [Accepted: 07/10/2024] [Indexed: 07/17/2024]
Abstract
Nucleoside triphosphates are indispensable in numerous biological processes, with enzymes involved in their biogenesis playing pivotal roles in cell proliferation. Pyruvate kinase (PYK), commonly regarded as the terminal glycolytic enzyme that generates ATP in tandem with pyruvate, is also capable of synthesizing a wide range of nucleoside triphosphates from their diphosphate precursors. Despite their substrate promiscuity, some PYKs show preference towards specific nucleotides, suggesting an underlying mechanism for differentiating nucleotide bases. However, the thorough characterization of this mechanism has been hindered by the paucity of nucleotide-bound PYK structures. Here, we present crystal structures of Streptococcus pneumoniae PYK in complex with four different nucleotides. These structures facilitate direct comparison of the protein-nucleotide interactions and offer structural insights into its pronounced selectivity for GTP synthesis. Notably, this selectivity is dependent on a sequence motif in the nucleotide recognition site that is widely present among prokaryotic PYKs, particularly in Firmicutes species. We show that pneumococcal cell growth is significantly impaired when expressing a PYK variant with compromised GTP and UTP synthesis activity, underscoring the importance of PYK in maintaining nucleotide homeostasis. Our findings collectively advance our understanding of PYK biochemistry and prokaryotic metabolism.
Collapse
Affiliation(s)
- Atsushi Taguchi
- SANKEN, Osaka University, Ibaraki, Osaka 567-0047, Japan; Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan.
| | | | - Kunihiko Nishino
- SANKEN, Osaka University, Ibaraki, Osaka 567-0047, Japan; Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan; Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka 565-0871, Japan.
| |
Collapse
|
2
|
Mendogralo EY, Nesterova LY, Nasibullina ER, Shcherbakov RO, Myasnikov DA, Tkachenko AG, Sidorov RY, Uchuskin MG. Synthesis, Antimicrobial and Antibiofilm Activities, and Molecular Docking Investigations of 2-(1 H-Indol-3-yl)-1 H-benzo[ d]imidazole Derivatives. Molecules 2023; 28:7095. [PMID: 37894573 PMCID: PMC10609029 DOI: 10.3390/molecules28207095] [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: 09/25/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
The treatment of many bacterial and fungal infections remains a problem due to increasing antibiotic resistance and biofilm formation by pathogens. In the present article, a methodology for the chemoselective synthesis of 2-(1H-indol-3-yl)-1H-benzo[d]imidazole derivatives is presented. We report on the antimicrobial activity of synthesized 2-(1H-indol-3-yl)-1H-benzo[d]imidazoles with significant activity against Staphylococcus aureus ATCC 25923, Staphylococcus aureus ATCC 43300 (MRSA), Mycobacterium smegmatis (mc(2)155/ATCC 700084), and Candida albicans ATCC 10231. High activity against staphylococci was shown by indolylbenzo[d]imidazoles 3ao and 3aq (minimum inhibitory concentration (MIC) < 1 µg/mL) and 3aa and 3ad (MIC 3.9-7.8 µg/mL). A low MIC was demonstrated by 2-(1H-indol-3-yl)-1-methyl-1H-benzo[d]imidazole (3ag) against M. smegmatis and against C. albicans (3.9 µg/mL and 3.9 µg/mL, respectively). 2-(5-Bromo-1H-indol-3-yl)-6,7-dimethyl-1H-benzo[d]imidazole (3aq) showed a low MIC of 3.9 µg/mL against C. albicans. Compounds 3aa, 3ad, 3ao, and 3aq exhibited excellent antibiofilm activity, inhibiting biofilm formation and killing cells in mature biofilms. Molecular docking analysis identified three potential interaction models for the investigated compounds, implicating (p)ppGpp synthetases/hydrolases, FtsZ proteins, or pyruvate kinases in their antibacterial action mechanism.
Collapse
Affiliation(s)
- Elena Y. Mendogralo
- Department of Chemistry, Perm State University, Bukireva St. 15, 614990 Perm, Russia; (E.R.N.); (R.O.S.); (D.A.M.); (R.Y.S.); (M.G.U.)
| | - Larisa Y. Nesterova
- Department of Biology, Perm State University, Bukireva St. 15, 614990 Perm, Russia; (L.Y.N.); (A.G.T.)
- Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center, The Ural Branch of Russian Academy of Sciences, Goleva St. 13, 614081 Perm, Russia
| | - Ekaterina R. Nasibullina
- Department of Chemistry, Perm State University, Bukireva St. 15, 614990 Perm, Russia; (E.R.N.); (R.O.S.); (D.A.M.); (R.Y.S.); (M.G.U.)
| | - Roman O. Shcherbakov
- Department of Chemistry, Perm State University, Bukireva St. 15, 614990 Perm, Russia; (E.R.N.); (R.O.S.); (D.A.M.); (R.Y.S.); (M.G.U.)
| | - Danil A. Myasnikov
- Department of Chemistry, Perm State University, Bukireva St. 15, 614990 Perm, Russia; (E.R.N.); (R.O.S.); (D.A.M.); (R.Y.S.); (M.G.U.)
| | - Alexander G. Tkachenko
- Department of Biology, Perm State University, Bukireva St. 15, 614990 Perm, Russia; (L.Y.N.); (A.G.T.)
- Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center, The Ural Branch of Russian Academy of Sciences, Goleva St. 13, 614081 Perm, Russia
| | - Roman Y. Sidorov
- Department of Chemistry, Perm State University, Bukireva St. 15, 614990 Perm, Russia; (E.R.N.); (R.O.S.); (D.A.M.); (R.Y.S.); (M.G.U.)
- Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center, The Ural Branch of Russian Academy of Sciences, Goleva St. 13, 614081 Perm, Russia
| | - Maxim G. Uchuskin
- Department of Chemistry, Perm State University, Bukireva St. 15, 614990 Perm, Russia; (E.R.N.); (R.O.S.); (D.A.M.); (R.Y.S.); (M.G.U.)
| |
Collapse
|
3
|
Yadav P, Singh R, Sur S, Bansal S, Chaudhry U, Tandon V. Moonlighting proteins: beacon of hope in era of drug resistance in bacteria. Crit Rev Microbiol 2023; 49:57-81. [PMID: 35220864 DOI: 10.1080/1040841x.2022.2036695] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Moonlighting proteins (MLPs) are ubiquitous and provide a unique advantage to bacteria performing multiple functions using the same genomic content. Targeting MLPs can be considered as a futuristic approach in fighting drug resistance problem. This review follows the MLP trail from its inception to the present-day state, describing a few bacterial MLPs, viz., glyceraldehyde 3'-phosphate dehydrogenase, phosphoglucose isomerase glutamate racemase (GR), and DNA gyrase. Here, we carve out that targeting MLPs are the beacon of hope in an era of increasing drug resistance in bacteria. Evolutionary stability, structure-functional relationships, protein diversity, possible drug targets, and identification of new drugs against bacterial MLP are given due consideration. Before the final curtain calls, we provide a comprehensive list of small molecules that inhibit the biochemical activity of MLPs, which can aid the development of novel molecules to target MLPs for therapeutic applications.
Collapse
Affiliation(s)
- Pramod Yadav
- Special Center for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India.,Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, New Delhi, India
| | - Raja Singh
- Special Center for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Souvik Sur
- Research and Development Center, Teerthanker Mahaveer University, Uttar Pradesh, India
| | - Sandhya Bansal
- Norton Thoracic Institute, St. Joseph's Hospital, and Medical Center, Phoenix, AZ, USA
| | - Uma Chaudhry
- Bhaskaracharya College of Applied Sciences, University of Delhi, New Delhi, India
| | - Vibha Tandon
- Special Center for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| |
Collapse
|
4
|
Akunuri R, Unnissa T, Vadakattu M, Bujji S, Mahammad Ghouse S, Madhavi Yaddanapudi V, Chopra S, Nanduri S. Bacterial Pyruvate Kinase: A New Potential Target to Combat Drug‐Resistant
Staphylococcus aureus
Infections. ChemistrySelect 2022. [DOI: 10.1002/slct.202201403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Ravikumar Akunuri
- Department of Chemical Sciences National Institute of Pharmaceutical Education and Research (NIPER) Hyderabad 500 037, Telangana State India
| | - Tanveer Unnissa
- Department of Chemical Sciences National Institute of Pharmaceutical Education and Research (NIPER) Hyderabad 500 037, Telangana State India
| | - Manasa Vadakattu
- Department of Chemical Sciences National Institute of Pharmaceutical Education and Research (NIPER) Hyderabad 500 037, Telangana State India
| | - Sushmitha Bujji
- Department of Chemical Sciences National Institute of Pharmaceutical Education and Research (NIPER) Hyderabad 500 037, Telangana State India
| | - Shaik Mahammad Ghouse
- Department of Chemical Sciences National Institute of Pharmaceutical Education and Research (NIPER) Hyderabad 500 037, Telangana State India
| | - Venkata Madhavi Yaddanapudi
- Department of Chemical Sciences National Institute of Pharmaceutical Education and Research (NIPER) Hyderabad 500 037, Telangana State India
| | - Sidharth Chopra
- Division of Molecular Microbiology and Immunology CSIR-Central Drug Research Institute (CDRI) Sitapur Road, Sector 10, Janakipuram Extension Lucknow 226 031, Uttar Pradesh India
| | - Srinivas Nanduri
- Department of Chemical Sciences National Institute of Pharmaceutical Education and Research (NIPER) Hyderabad 500 037, Telangana State India
| |
Collapse
|
5
|
Yin B, Lin X, Wang T, Liu L. Detailed Characterization of Antipathogenic Properties of Human Milk N-Glycome, against Staphylococcus aureus, Indicating Its Targeting on Cell Surface Proteins. ACS Infect Dis 2022; 8:635-644. [PMID: 35132860 DOI: 10.1021/acsinfecdis.1c00652] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human milk N-glycome was previously identified to have strong antipathogenic activities. This study is aimed to characterize the detailed antibacterial properties and the potential function mechanism of human milk N-glycome against Staphylococcus aureus. A serials of traditional antibacterial assays showed that human milk N-glycome possessed both bacteriostatic and bactericidal activities, which was further confirmed by the cell structure disruption including the change of transmembrane potential and leakage of intracellular contents. The results of the bacterial surface zeta potential and hydrophobicity, bacterial binding assay, gel shift assay, and fluorescence spectra and the different synergistic effects of human milk N-glycome combined with different antibiotics indicated that the bacterial surface proteins could be the targets of human milk N-glycome. Moreover, human milk N-glycome also showed antibiofilm activity. In conclusion, human milk N-glycome exhibited good potential for acting as an antibacterial substance against S. aureus and the antibacterial mechanism was a cell surface targeting action.
Collapse
Affiliation(s)
- Binru Yin
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Xisha Lin
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Ting Wang
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Li Liu
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Jiangsu Collaborative Innovation Center of Meat Production, Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| |
Collapse
|
6
|
Zhong J, Wang H, Zhuang Y, Shen Q. Identification of the antibacterial mechanism of cryptotanshinone on methicillin-resistant Staphylococcus aureus using bioinformatics analysis. Sci Rep 2021; 11:21726. [PMID: 34741111 PMCID: PMC8571311 DOI: 10.1038/s41598-021-01121-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 10/18/2021] [Indexed: 11/13/2022] Open
Abstract
Cryptotanshinone (CT) is an extract from the traditional Chinese medicine Salvia miltiorrhiza, which inhibits the growth of methicillin-resistant Staphylococcus aureus (MRSA) in vitro. This study aims to determine the antibacterial mechanisms of CT by integrating bioinformatics analysis and microbiology assay. The microarray data of GSE13203 was retrieved from the Gene Expression Omnibus (GEO) database to screen the differentially expressed genes (DEGs) of S. aureus strains that were treated with CT treatment. Gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were used to identify the potential target of CT. Data mining on the microarray dataset indicated that pyruvate kinase (PK) might be involved in the antimicrobial activities of CT. The minimum inhibition concentrations (MICs) of CT or vancomycin against the MRSA strain ATCC43300 and seven other clinical strains were determined using the broth dilution method. The effects of CT on the activity of PK were further measured. In vitro tests verified that CT inhibited the growth of an MRSA reference strain and seven other clinical strains. CT hampered the activity of the PK of ATCC43300 and five clinical MRSA strains. CT might hinder bacterial energy metabolism by inhibiting the activity of PK.
Collapse
Affiliation(s)
- Jiwei Zhong
- Department of Emergency Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, China
| | - Haidan Wang
- Department of Pharmacology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, China
| | - Yun Zhuang
- Department of Hematology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, China
| | - Qun Shen
- Department of Hematology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, China.
| |
Collapse
|
7
|
Ribeiro M, Ceballos S, Poeta P, Torres C, Igrejas G. Methicillin-Resistant Staphylococcus aureus Proteome Response to Antibiotic Stress Provides Insights for New Therapeutic Strategies. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:711-724. [PMID: 34705556 DOI: 10.1089/omi.2021.0151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Antimicrobial resistance is a global threat, with methicillin-resistant Staphylococcus aureus (MRSA) being one of the most representative drug-resistant pathogens. MRSA spread is increasing due to its ability to establish new reservoirs. To this end, the clonal complex (CC)-130 is an emerging genetic lineage, generally regarded as animal adapted and carrying the mecC gene, and sporadically found in humans. Although the MRSA antibiotic resistance mechanisms have been described, there are limited data on systems-wide omics responses to antibiotic stress, particularly at the proteome level. In this study, a gel-based quantitative proteomics approach was performed to assess the cellular responses of a mecC-harboring CC130 MRSA strain of human origin to subinhibitory doses of cefoxitin. We focused on the global response of MRSA to antibiotic stress and upon this treatment, 53 proteins were significantly differentially expressed. Most of the latter proteins were mapped to having functions in cellular metabolism while some glycolysis-related proteins showed a decreased expression after cefoxitin stress. On the contrary, pyruvate kinase, a potential antimicrobial drug target, was found upregulated. Also, quorum sensing, genetic information processing, and stress response proteins were found upregulated. Low-affinity penicillin-binding protein (mecC-encoded) was found in cefoxitin-treated samples. In conclusion, these new findings on cefoxitin-induced proteome changes provide important insights and molecular leads for innovation in treatment of MRSA specifically, and omics approaches to address antibiotic resistance generally.
Collapse
Affiliation(s)
- Miguel Ribeiro
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,Functional Genomics and Proteomics Unity, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,LAQV-REQUIMTE, Faculty of Science and Technology, University Nova of Lisbon, Lisbon, Portugal
| | - Sara Ceballos
- Area Biochemistry and Molecular Biology, University of La Rioja, Logroño, Spain
| | - Patrícia Poeta
- LAQV-REQUIMTE, Faculty of Science and Technology, University Nova of Lisbon, Lisbon, Portugal.,Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
| | - Carmen Torres
- Area Biochemistry and Molecular Biology, University of La Rioja, Logroño, Spain
| | - Gilberto Igrejas
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,Functional Genomics and Proteomics Unity, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,LAQV-REQUIMTE, Faculty of Science and Technology, University Nova of Lisbon, Lisbon, Portugal
| |
Collapse
|
8
|
Jia J, Luo Y, Zhong X, He L. Methicillin-resistance Staphylococcus aureus (MRSA) Pyruvate kinase (PK) inhibitors and Their Antimicrobial Activities. Curr Med Chem 2021; 29:908-923. [PMID: 33749550 DOI: 10.2174/0929867328666210322103340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 02/10/2021] [Accepted: 02/14/2021] [Indexed: 11/22/2022]
Abstract
Resistance to antibiotics has been widely existed in the health care and community setting, thus developing a novel aspect of new antibiotics is urgently necessary. Methicillin-resistance Staphylococcus aureus (MRSA) Pyruvate kinase (PK) is crucial to the survive of bacterial, making it a novel antimicrobial target. In the past decade, most reported PK inhibitors including indole, flavonoid, phenazine derivative from natural product small molecules or their analogues, or virtual screening from small molecule compound library. This review covers the PK inhibitors and their antimicrobial activities reported from the beginning of 2011 through the middle of 2020. The Structure Activity Relationships (SARs) was discussed briefly as well.
Collapse
Affiliation(s)
- Jingjing Jia
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041. China
| | - Yang Luo
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041. China
| | - Xue Zhong
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041. China
| | - Ling He
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041. China
| |
Collapse
|
9
|
El Sayed MT, Sarhan AE, Ahmed E, Khattab RR, Elnaggar M, El‐Messery SM, Shaldam MA, Hassan GS. Novel Pyruvate Kinase (PK) Inhibitors: New Target to Overcome Bacterial Resistance. ChemistrySelect 2020. [DOI: 10.1002/slct.202000043] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Mardia T. El Sayed
- Applied Organic Chemistry Department, Chemical Industries Research DivisionNational Research Centre Dokki 12311 Egypt
| | - Alaadin E. Sarhan
- Therapeutical Chemistry DepartmentPharmaceutical Division, National Research Centre Dokki 12311 Egypt
| | - Entsar Ahmed
- Chemistry Department, Faculty of ScienceAl-Azhar University (Girls Branch) Cairo Egypt
| | - Reham R. Khattab
- Photochemistry DepartmentChemical Industries Research Division, National Research Centre Dokki 12311 Egypt
| | - Mohamed Elnaggar
- Chemistry Department, Faculty of SciencesUniversity of Sharjah Sharjah 27272 UAE
| | - Shahenda M. El‐Messery
- Department of Pharmaceutical Organic ChemistryFaculty of Pharmacy, Mansoura University P.O.Box 35516 Mansoura Egypt
| | - Moataz A. Shaldam
- Department of Pharmaceutical Chemistry, Faculty of PharmacyKafrelsheikh University Kafr El Sheikh 33516 Egypt
| | - Ghada S. Hassan
- Department of Medicinal Chemistry, Faculty of PharmacyMansoura University 35516 Mansoura Egypt
| |
Collapse
|
10
|
Identification of small molecule enzyme inhibitors as broad-spectrum anthelmintics. Sci Rep 2019; 9:9085. [PMID: 31235822 PMCID: PMC6591293 DOI: 10.1038/s41598-019-45548-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 06/06/2019] [Indexed: 11/18/2022] Open
Abstract
Targeting chokepoint enzymes in metabolic pathways has led to new drugs for cancers, autoimmune disorders and infectious diseases. This is also a cornerstone approach for discovery and development of anthelmintics against nematode and flatworm parasites. Here, we performed omics-driven knowledge-based identification of chokepoint enzymes as anthelmintic targets. We prioritized 10 of 186 phylogenetically conserved chokepoint enzymes and undertook a target class repurposing approach to test and identify new small molecules with broad spectrum anthelmintic activity. First, we identified and tested 94 commercially available compounds using an in vitro phenotypic assay, and discovered 11 hits that inhibited nematode motility. Based on these findings, we performed chemogenomic screening and tested 32 additional compounds, identifying 6 more active hits. Overall, 6 intestinal (single-species), 5 potential pan-intestinal (whipworm and hookworm) and 6 pan-Phylum Nematoda (intestinal and filarial species) small molecule inhibitors were identified, including multiple azoles, Tadalafil and Torin-1. The active hit compounds targeted three different target classes in humans, which are involved in various pathways, including carbohydrate, amino acid and nucleotide metabolism. Last, using representative inhibitors from each target class, we demonstrated in vivo efficacy characterized by negative effects on parasite fecundity in hamsters infected with hookworms.
Collapse
|
11
|
Thomsen IP, Liu GY. Targeting fundamental pathways to disrupt Staphylococcus aureus survival: clinical implications of recent discoveries. JCI Insight 2018. [PMID: 29515041 DOI: 10.1172/jci.insight.98216] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The emergence of community-associated methicillin-resistant Staphylococcus aureus during the past decade along with an impending shortage of effective antistaphylococcal antibiotics have fueled impressive advances in our understanding of how S. aureus overcomes the host environment to establish infection. Backed by recent technologic advances, studies have uncovered elaborate metabolic, nutritional, and virulence strategies deployed by S. aureus to survive the restrictive and hostile environment imposed by the host, leading to a plethora of promising antimicrobial approaches that have potential to remedy the antibiotic resistance crisis. In this Review, we highlight some of the critical and recently elucidated bacterial strategies that are potentially amenable to intervention, discuss their relevance to human diseases, and address the translational challenges posed by current animal models.
Collapse
Affiliation(s)
- Isaac P Thomsen
- Department of Pediatrics, Division of Pediatric Infectious Diseases, and Vanderbilt Vaccine Research Program, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - George Y Liu
- Division of Pediatric Infectious Diseases and Research Division of Immunology, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| |
Collapse
|
12
|
de Vos-Kerkhof E, Geurts DHF, Steyerberg EW, Lakhanpaul M, Moll HA, Oostenbrink R. Characteristics of revisits of children at risk for serious infections in pediatric emergency care. Eur J Pediatr 2018; 177:617-624. [PMID: 29397418 PMCID: PMC5851682 DOI: 10.1007/s00431-018-3095-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 12/14/2017] [Accepted: 01/17/2018] [Indexed: 01/27/2023]
Abstract
UNLABELLED In this study, we aimed to identify characteristics of (unscheduled) revisits and its optimal time frame after Emergency Department (ED) discharge. Children with fever, dyspnea, or vomiting/diarrhea (1 month-16 years) who attended the ED of Erasmus MC-Sophia, Rotterdam (2010-2013), the Netherlands, were prospectively included. Three days after ED discharge, we applied standardized telephonic questionnaires on disease course and revisits. Multivariable logistic regression analysis was used to identify independent characteristics of revisits. Young age, parental concern, and alarming signs and symptoms (chest wall retractions, ill appearance, clinical signs of dehydration, and tachypnea) were associated with revisits (n = 527) in children at risk for serious infections discharged from the ED (n = 1765). Children revisited the ED within a median of 2 days (IQR 1.0-3.0), but this was proven to be shorter in children with vomiting/diarrhea (1.0 day (IQR 1.0-2.0)) compared to children with fever or dyspnea (2.0 (IQR 1.0-3.0)). CONCLUSION Young age, parental concern, and alarming signs and symptoms (chest wall retractions, ill appearance, clinical signs of dehydration, and tachypnea) were associated with emergency health care revisits in children with fever, dyspnea, and vomiting/diarrhea. These characteristics could help to define targeted review of children during post-discharge period. We observed a disease specific and differential timing of control revisits after ED discharge. What is Known • Fever, dyspnea, and vomiting/diarrhea are major causes of emergency care attendance in children. • As uncertainty remains on uneventful recovery, patients at risk need to be identified on order to improve safety netting after discharge from the ED. What is New • In children with fever, dyspnea, and vomiting/diarrhea, young age, parental concern and chest wall retractions, ill appearance, clinical signs of dehydration, and tachypnea help to define targeted review of children during the post-discharge period. • A revisit after ED discharge is disease-specific and seems to be shorter for children with vomiting/diarrhea than others.
Collapse
Affiliation(s)
- Evelien de Vos-Kerkhof
- grid.416135.4Department of General Paediatrics, Erasmus MC-Sophia Children’s Hospital, Wytemaweg 80, 3015 Rotterdam, CN Netherlands
| | - Dorien H. F. Geurts
- grid.416135.4Department of General Paediatrics, Erasmus MC-Sophia Children’s Hospital, Wytemaweg 80, 3015 Rotterdam, CN Netherlands
| | - Ewout W. Steyerberg
- 000000040459992Xgrid.5645.2Department of Public Health, Erasmus MC - University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Monica Lakhanpaul
- 0000000121901201grid.83440.3bDepartment of Population, Policy and Practice UCL Great Ormond Street Institute of Child Health, Great Ormond Street, London, UK
| | - Henriette A. Moll
- grid.416135.4Department of General Paediatrics, Erasmus MC-Sophia Children’s Hospital, Wytemaweg 80, 3015 Rotterdam, CN Netherlands
| | - Rianne Oostenbrink
- grid.416135.4Department of General Paediatrics, Erasmus MC-Sophia Children’s Hospital, Wytemaweg 80, 3015 Rotterdam, CN Netherlands
| |
Collapse
|
13
|
Silver Oxide Coatings with High Silver-Ion Elution Rates and Characterization of Bactericidal Activity. Molecules 2017; 22:molecules22091487. [PMID: 28880225 PMCID: PMC6151401 DOI: 10.3390/molecules22091487] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 08/29/2017] [Accepted: 08/30/2017] [Indexed: 01/21/2023] Open
Abstract
This paper reports the synthesis and characterization of silver oxide films for use as bactericidal coatings. Synthesis parameters, dissolution/elution rate, and bactericidal efficacy are reported. Synthesis conditions were developed to create AgO, Ag2O, or mixtures of AgO and Ag2O on surfaces by reactive magnetron sputtering. The coatings demonstrate strong adhesion to many substrate materials and impede the growth of all bacterial strains tested. The coatings are effective in killing Escherichia coli and Staphylococcus aureus, demonstrating a clear zone-of-inhibition against bacteria growing on solid media and the ability to rapidly inhibit bacterial growth in planktonic culture. Additionally, the coatings exhibit very high elution of silver ions under conditions that mimic dynamic fluid flow ranging between 0.003 and 0.07 ppm/min depending on the media conditions. The elution of silver ions from the AgO/Ag2O surfaces was directly impacted by the complexity of the elution media, with a reduction in elution rate when examined in complex cell culture media. Both E. coli and S. aureus were shown to bind ~1 ppm Ag+/mL culture. The elution of Ag+ resulted in no increases in mammalian cell apoptosis after 24 h exposure compared to control, but apoptotic cells increased to ~35% by 48 and 72 h of exposure. Taken together, the AgO/Ag2O coatings described are effective in eliciting antibacterial activity and have potential for application on a wide variety of surfaces and devices.
Collapse
|
14
|
Amino Acid Catabolism in Staphylococcus aureus and the Function of Carbon Catabolite Repression. mBio 2017; 8:mBio.01434-16. [PMID: 28196956 PMCID: PMC5312079 DOI: 10.1128/mbio.01434-16] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Staphylococcus aureus must rapidly adapt to a variety of carbon and nitrogen sources during invasion of a host. Within a staphylococcal abscess, preferred carbon sources such as glucose are limiting, suggesting that S. aureus survives through the catabolism of secondary carbon sources. S. aureus encodes pathways to catabolize multiple amino acids, including those that generate pyruvate, 2-oxoglutarate, and oxaloacetate. To assess amino acid catabolism, S. aureus JE2 and mutants were grown in complete defined medium containing 18 amino acids but lacking glucose (CDM). A mutation in the gudB gene, coding for glutamate dehydrogenase, which generates 2-oxoglutarate from glutamate, significantly reduced growth in CDM, suggesting that glutamate and those amino acids generating glutamate, particularly proline, serve as the major carbon source in this medium. Nuclear magnetic resonance (NMR) studies confirmed this supposition. Furthermore, a mutation in the ackA gene, coding for acetate kinase, also abrogated growth of JE2 in CDM, suggesting that ATP production from pyruvate-producing amino acids is also critical for growth. In addition, although a functional respiratory chain was absolutely required for growth, the oxygen consumption rate and intracellular ATP concentration were significantly lower during growth in CDM than during growth in glucose-containing media. Finally, transcriptional analyses demonstrated that expression levels of genes coding for the enzymes that synthesize glutamate from proline, arginine, and histidine are repressed by CcpA and carbon catabolite repression. These data show that pathways important for glutamate catabolism or ATP generation via Pta/AckA are important for growth in niches where glucose is not abundant, such as abscesses within skin and soft tissue infections. S. aureus is a significant cause of both morbidity and mortality worldwide. This bacterium causes infections in a wide variety of organ systems, the most common being skin and soft tissue. Within a staphylococcal abscess, levels of glucose, a preferred carbon source, are limited due to the host immune response. Therefore, S. aureus must utilize other available carbon sources such as amino acids or peptides to proliferate. Our results show that glutamate and amino acids that serve as substrates for glutamate synthesis, particularly proline, function as major carbon sources during growth, whereas other amino acids that generate pyruvate are important for ATP synthesis via substrate-level phosphorylation in the Pta-AckA pathway. Our data support a model whereby certain amino acid catabolic pathways, and acquisition of those particular amino acids, are crucial for growth in niches where glucose is not abundant.
Collapse
|
15
|
Gorantla V, Gundla R, Jadav SS, Anugu SR, Chimakurthy J, Nidasanametla SK, Korupolu R. Molecular hybrid design, synthesis and biological evaluation of N-phenyl sulfonamide linked N-acyl hydrazone derivatives functioning as COX-2 inhibitors: new anti-inflammatory, anti-oxidant and anti-bacterial agents. NEW J CHEM 2017. [DOI: 10.1039/c7nj03332j] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The design, synthesis and biological evaluation of the anti-inflammatory activities of novel N-phenyl sulfonamide linked N-acylhydrazones (NPS–NAH) have been reported.
Collapse
Affiliation(s)
- Vasubabu Gorantla
- Department of Engineering Chemistry
- Andhra University College of Engineering (A)
- Vishakhapatnam
- India
- GVK Biosciences Private Limited
| | - Rambabu Gundla
- Department of Chemistry
- School of Technology
- GITAM University
- Hyderabad (TS)
- India
| | | | | | | | | | - Raghubabu Korupolu
- Department of Engineering Chemistry
- Andhra University College of Engineering (A)
- Vishakhapatnam
- India
| |
Collapse
|
16
|
Labrière C, Gong H, Finlay BB, Reiner NE, Young RN. Further investigation of inhibitors of MRSA pyruvate kinase: Towards the conception of novel antimicrobial agents. Eur J Med Chem 2016; 125:1-13. [PMID: 27643559 DOI: 10.1016/j.ejmech.2016.09.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 09/04/2016] [Accepted: 09/06/2016] [Indexed: 10/21/2022]
Abstract
Several novel series of compounds were synthesized and evaluated as inhibitors of methicillin-resistant Staphylococcus aureus (MRSA) pyruvate kinase (PK). PK has been identified as a highly interconnected essential 'hub' protein in MRSA, with structural features distinct from the human homologs which makes it a novel antimicrobial target. Several MRSA PK inhibitors (including the hydrazide 1) were identified using in silico screening combined with enzyme assays and were found to be selective for bacterial enzyme compared to human PK isoforms. Structure-activity relationship (SAR) studies were carried out on the replacement of the hydrazide linker with 3-atoms, 2-atoms and 0-atom linkers and led us to discover more potent compounds with enzyme inhibiting activities in the low nanomolar range and some were found to effectively inhibit bacteria growth in culture with minimum inhibitory concentrations (MIC) as low as 1 μg/mL.
Collapse
Affiliation(s)
| | - Huansheng Gong
- Department of Medicine, Division of Infectious Diseases, University of British Columbia, Vancouver, BC, Canada
| | - B Brett Finlay
- Department of Medicine, Division of Infectious Diseases, University of British Columbia, Vancouver, BC, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Neil E Reiner
- Department of Medicine, Division of Infectious Diseases, University of British Columbia, Vancouver, BC, Canada; Department of Microbiology and Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Robert N Young
- Department of Chemistry, Simon Fraser University, Burnaby, BC, Canada.
| |
Collapse
|
17
|
Hwang S, Kim CY, Ji SG, Go J, Kim H, Yang S, Kim HJ, Cho A, Yoon SS, Lee I. Network-assisted investigation of virulence and antibiotic-resistance systems in Pseudomonas aeruginosa. Sci Rep 2016; 6:26223. [PMID: 27194047 PMCID: PMC4872156 DOI: 10.1038/srep26223] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 04/29/2016] [Indexed: 12/21/2022] Open
Abstract
Pseudomonas aeruginosa is a Gram-negative bacterium of clinical significance. Although the genome of PAO1, a prototype strain of P. aeruginosa, has been extensively studied, approximately one-third of the functional genome remains unknown. With the emergence of antibiotic-resistant strains of P. aeruginosa, there is an urgent need to develop novel antibiotic and anti-virulence strategies, which may be facilitated by an approach that explores P. aeruginosa gene function in systems-level models. Here, we present a genome-wide functional network of P. aeruginosa genes, PseudomonasNet, which covers 98% of the coding genome, and a companion web server to generate functional hypotheses using various network-search algorithms. We demonstrate that PseudomonasNet-assisted predictions can effectively identify novel genes involved in virulence and antibiotic resistance. Moreover, an antibiotic-resistance network based on PseudomonasNet reveals that P. aeruginosa has common modular genetic organisations that confer increased or decreased resistance to diverse antibiotics, which accounts for the pervasiveness of cross-resistance across multiple drugs. The same network also suggests that P. aeruginosa has developed mechanism of trade-off in resistance across drugs by altering genetic interactions. Taken together, these results clearly demonstrate the usefulness of a genome-scale functional network to investigate pathogenic systems in P. aeruginosa.
Collapse
Affiliation(s)
- Sohyun Hwang
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 120-749, Korea.,Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Chan Yeong Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 120-749, Korea
| | - Sun-Gou Ji
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 120-749, Korea
| | - Junhyeok Go
- Department of Microbiology and Immunology, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 120-749, Korea
| | - Hanhae Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 120-749, Korea
| | - Sunmo Yang
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 120-749, Korea
| | - Hye Jin Kim
- Department of Microbiology and Immunology, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 120-749, Korea
| | - Ara Cho
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 120-749, Korea
| | - Sang Sun Yoon
- Department of Microbiology and Immunology, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 120-749, Korea
| | - Insuk Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 120-749, Korea
| |
Collapse
|
18
|
Noy T, Vergnolle O, Hartman TE, Rhee KY, Jacobs WR, Berney M, Blanchard JS. Central Role of Pyruvate Kinase in Carbon Co-catabolism of Mycobacterium tuberculosis. J Biol Chem 2016; 291:7060-9. [PMID: 26858255 DOI: 10.1074/jbc.m115.707430] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Indexed: 11/06/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) displays a high degree of metabolic plasticity to adapt to challenging host environments. Genetic evidence suggests thatMtbrelies mainly on fatty acid catabolism in the host. However,Mtbalso maintains a functional glycolytic pathway and its role in the cellular metabolism ofMtbhas yet to be understood. Pyruvate kinase catalyzes the last and rate-limiting step in glycolysis and theMtbgenome harbors one putative pyruvate kinase (pykA, Rv1617). Here we show thatpykAencodes an active pyruvate kinase that is allosterically activated by glucose 6-phosphate (Glc-6-P) and adenosine monophosphate (AMP). Deletion ofpykApreventsMtbgrowth in the presence of fermentable carbon sources and has a cidal effect in the presence of glucose that correlates with elevated levels of the toxic catabolite methylglyoxal. Growth attenuation was also observed in media containing a combination of short chain fatty acids and glucose and surprisingly, in media containing odd and even chain fatty acids alone. Untargeted high sensitivity metabolomics revealed that inactivation of pyruvate kinase leads to accumulation of phosphoenolpyruvate (P-enolpyruvate), citrate, and aconitate, which was consistent with allosteric inhibition of isocitrate dehydrogenase by P-enolpyruvate. This metabolic block could be relieved by addition of the α-ketoglutarate precursor glutamate. Taken together, our study identifies an essential role of pyruvate kinase in preventing metabolic block during carbon co-catabolism inMtb.
Collapse
Affiliation(s)
- Tahel Noy
- From the Departments of Biochemistry and
| | | | - Travis E Hartman
- the Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10021
| | - Kyu Y Rhee
- the Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10021
| | - William R Jacobs
- the Department of Microbiology and Immunology, Howard Hughes Medical Institute at Albert Einstein College of Medicine, New York, New York 10461, and Microbiology and Immunology, Albert Einstein College of Medicine, New York, New York 10461
| | - Michael Berney
- Microbiology and Immunology, Albert Einstein College of Medicine, New York, New York 10461,
| | | |
Collapse
|
19
|
TATAR E, ŞENKARDEŞ S, SELLİTEPE HE, KÜÇÜKGÜZEL ŞG, KARAOĞLU ŞA, BOZDEVECİ A, DE CLERCQ E, PANNECOUQUE C, BEN HADDA T, KÜÇÜKGÜZEL İ. Synthesis, and prediction of molecular properties and antimicrobial activity of some acylhydrazones derived from $N$-(arylsulfonyl)methionine. Turk J Chem 2016. [DOI: 10.3906/kim-1509-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
|
20
|
Zang P, Gong A, Zhang P, Yu J. Targeting druggable enzymome by exploiting natural medicines: An in silico-in vitro integrated approach to combating multidrug resistance in bacterial infection. PHARMACEUTICAL BIOLOGY 2015; 54:604-618. [PMID: 26681298 DOI: 10.3109/13880209.2015.1068338] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
CONTEXT Antibiotic resistance is a major clinical and public health problem. Development of new therapeutic approaches to prevent bacterial multidrug resistance during antimicrobial chemotherapy has thus been becoming a primary consideration in the medicinal chemistry community. OBJECTIVE We described a new strategy that combats multidrug resistance by using natural medicines to target the druggable enzymome (i.e., enzymatic proteome) of Staphylococcus aureus. MATERIALS AND METHODS A pipeline of integrating in silico analysis and in vitro assay was purposed to identify antibacterial agents from a large library of natural products with diverse structures, high drug-likeness, and relatively low flexibility, with which a systematic interactome of 826 natural product candidates with 125 functionally essential S. aureus enzymes was constructed via a high-throughput cross-docking approach. The obtained docking score matrix was then converted into an array of synthetic scores; each corresponds to a natural product candidate. By systematically examining the docking results, a number of highly promising candidates with potent antibacterial activity were suggested. RESULTS Three natural products, i.e., radicicol, jorumycin, and amygdalin, have been determined to possess strong broad-spectrum potency combating both the drug-resistant and drug-sensitive strains (MIC value <10 μg/ml). In addition, some natural products such as tetrandrine, bilobalide, and arbutin exhibited selective inhibition on different strains. DISCUSSION AND CONCLUSION Combined quantum mechanics/molecular mechanics analysis revealed diverse non-bonded interactions across the complex interfaces of newly identified antibacterial agents with their putative targets GyrB ATPase and tyrosyl-tRNA synthetase.
Collapse
Affiliation(s)
- Ping Zang
- a Department of Public Health Management , The Affiliated Hospital of Weifang Medical University , Weifang , China
| | - Aijie Gong
- b Department of Central Sterile Supply , Changyi People's Hospital , Changyi , China
| | | | - Jinling Yu
- d Department of Gynaecology , The Affiliated Hospital of Weifang Medical University , Weifang , China
| |
Collapse
|
21
|
El-Sayed MT, Zoraghi R, Reiner N, Suzen S, Ohlsen K, Lalk M, Altanlar N, Hilgeroth A. Novel inhibitors of the methicillin-resistant Staphylococcus aureus (MRSA)-pyruvate kinase. J Enzyme Inhib Med Chem 2015; 31:1666-71. [PMID: 26653005 DOI: 10.3109/14756366.2015.1118685] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Novel bisindolyl-cycloalkane indoles resulted from the reaction of aliphatic dialdehydes and indole. As bisindolyl-natural alkaloid compounds have recently been reported as inhibitors of the methicillin-resistant Staphylococcus aureus (MRSA)-pyruvate kinase (PK), we tested our novel compounds as MRSA PK inhibitors and now report first inhibiting activities. We discuss structure-activity relationships of structurally varied compounds. Activity influencing substituents have been characterized and relations to antibacterial activities of the most active compounds have been proved.
Collapse
Affiliation(s)
- Mardia Telep El-Sayed
- a Department of Pharmaceutical Chemistry , Institute of Pharmacy, Martin Luther University , Halle , Germany
| | - Roya Zoraghi
- b Department of Medicine, Division of Infectious Diseases , University of British Columbia , Vancouver , BC , Canada
| | - Neil Reiner
- b Department of Medicine, Division of Infectious Diseases , University of British Columbia , Vancouver , BC , Canada
| | - Sibel Suzen
- c Department of Pharmaceutical Chemistry, Faculty of Pharmacy , Ankara University , Ankara , Turkey
| | - Knut Ohlsen
- d Institute for Molecular Biology of Infections, Julius Schneider University Würzburg , Würzburg , Germany
| | - Michael Lalk
- e Institute of Biochemistry, Ernst Moritz Arndt University Greifswald , Greifswald , Germany , and
| | - Nurten Altanlar
- f Department of Pharmaceutical Microbiology, Faculty of Pharmacy , Ankara University , Ankara , Turkey
| | - Andreas Hilgeroth
- a Department of Pharmaceutical Chemistry , Institute of Pharmacy, Martin Luther University , Halle , Germany
| |
Collapse
|
22
|
Davies-Coleman MT, Veale CGL. Recent Advances in Drug Discovery from South African Marine Invertebrates. Mar Drugs 2015; 13:6366-83. [PMID: 26473891 PMCID: PMC4626695 DOI: 10.3390/md13106366] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Revised: 09/28/2015] [Accepted: 09/29/2015] [Indexed: 01/14/2023] Open
Abstract
Recent developments in marine drug discovery from three South African marine invertebrates, the tube worm Cephalodiscus gilchristi, the ascidian Lissoclinum sp. and the sponge Topsentia pachastrelloides, are presented. Recent reports of the bioactivity and synthesis of the anti-cancer secondary metabolites cephalostatin and mandelalides (from C. gilchristi and Lissoclinum sp., respectively) and various analogues are presented. The threat of drug-resistant pathogens, e.g., methicillin-resistant Staphylococcus aureus (MRSA), is assuming greater global significance, and medicinal chemistry strategies to exploit the potent MRSA PK inhibition, first revealed by two marine secondary metabolites, cis-3,4-dihydrohamacanthin B and bromodeoxytopsentin from T. pachastrelloides, are compared.
Collapse
Affiliation(s)
- Michael T Davies-Coleman
- Department of Chemistry, University of the Western Cape, Robert Sobukwe Road, Bellville 7535, South Africa.
| | - Clinton G L Veale
- Faculty of Pharmacy, Rhodes University, Grahamstown 6140, South Africa.
| |
Collapse
|
23
|
Yoon BK, Jackman JA, Kim MC, Cho NJ. Spectrum of Membrane Morphological Responses to Antibacterial Fatty Acids and Related Surfactants. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:10223-32. [PMID: 26325618 DOI: 10.1021/acs.langmuir.5b02088] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Medium-chain saturated fatty acids and related compounds (e.g., monoglycerides) represent one class of membrane-active surfactants with antimicrobial properties. Most related studies have been in vitro evaluations of bacterial growth inhibition, and there is limited knowledge about how the compounds in this class destabilize lipid bilayers, which are the purported target within the bacterial cell membrane. Herein, the interaction between three representative compounds in this class and a supported lipid bilayer platform was investigated using quartz crystal microbalance-dissipation and fluorescence microscopy in order to examine membrane destabilization. The three tested compounds were lauric acid, sodium dodecyl sulfate, and glycerol monolaurate. For each compound, we discovered striking differences in the resulting morphological changes of supported lipid bilayers. The experimental trends indicate that the compounds have membrane-disruptive behavior against supported lipid bilayers principally above the respective critical micelle concentration values. The growth inhibition properties of the compounds against standard and methicillin-resistant Staphylococcus aureus bacterial strains were also tested. Taken together, the findings in this work improve our knowledge about how saturated fatty acids and related compounds destabilize lipid bilayers, offering insight into the corresponding molecular mechanisms that lead to membrane morphological responses.
Collapse
Affiliation(s)
| | | | | | - Nam-Joon Cho
- School of Chemical and Biomedical Engineering, Nanyang Technological University , 62 Nanyang Drive 637459, Singapore
| |
Collapse
|
24
|
Vasu D, Sunitha MM, Srikanth L, Swarupa V, Prasad UV, Sireesha K, Yeswanth S, Kumar PS, Venkatesh K, Chaudhary A, Sarma PVGK. In Staphylococcus aureus the regulation of pyruvate kinase activity by serine/threonine protein kinase favors biofilm formation. 3 Biotech 2015; 5:505-512. [PMID: 28324552 PMCID: PMC4522715 DOI: 10.1007/s13205-014-0248-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Accepted: 08/26/2014] [Indexed: 11/30/2022] Open
Abstract
Staphylococcus aureus, a natural
inhabitant of nasopharyngeal tract, survives mainly as biofilms. Previously we have observed that S. aureus ATCC 12600 grown under anaerobic conditions exhibited high rate of biofilm formation and l-lactate dehydrogenase activity. Thus, the concentration of pyruvate plays a critical role in S. aureus, which is primarily catalyzed by pyruvate kinase (PK). Analyses of the PK gene sequence (JN645815) revealed presence of PknB site in PK gene indicating that phosphorylation may be influencing the functioning of PK. To establish this hypothesis the pure enzymes of S. aureus ATCC 12600 were obtained by expressing these genes in PK 1 and PV 1 (JN695616) clones and passing the cytosolic fractions through nickel metal chelate column. The molecular weights of pure recombinant PK and PknB are 63 and 73 kDa, respectively. The enzyme kinetics of pure PK showed KM of 0.69 ± 0.02 µM, while the KM of PknB for stpks (stpks = NLCNIPCSALLSSDITASVNCAK) substrate was 0.720 ± 0.08 mM and 0.380 ± 0.07 mM for autophosphorylation. The phosphorylated PK exhibited 40 % reduced activity (PK = 0.2 ± 0.015 μM NADH/min/ml to P-PK = 0.12 ± 0.01 μM NADH/min/ml). Elevated synthesis of pyruvate kinase was observed in S. aureus ATCC 12600 grown in anaerobic conditions suggesting that the formed pyruvate is more utilized in the synthesis phase, supporting increased rate of biofilm formation.
Collapse
Affiliation(s)
- D Vasu
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati, AP, 517507, India
| | - M M Sunitha
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati, AP, 517507, India
| | - L Srikanth
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati, AP, 517507, India
| | - V Swarupa
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati, AP, 517507, India
| | - U Venkateswara Prasad
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati, AP, 517507, India
| | - K Sireesha
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati, AP, 517507, India
| | - S Yeswanth
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati, AP, 517507, India
| | - P Santhosh Kumar
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati, AP, 517507, India
| | - K Venkatesh
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati, AP, 517507, India
| | - Abhijit Chaudhary
- Department of Microbiology, Sri Venkateswara Institute of Medical Sciences, Tirupati, AP, 517507, India
| | - P V G K Sarma
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati, AP, 517507, India.
| |
Collapse
|
25
|
Glycolytic dependency of high-level nitric oxide resistance and virulence in Staphylococcus aureus. mBio 2015; 6:mBio.00045-15. [PMID: 25852157 PMCID: PMC4453550 DOI: 10.1128/mbio.00045-15] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Staphylococcus aureus is a prolific human pathogen capable of causing severe invasive disease with a myriad of presentations. The ability of S. aureus to cause infection is strongly linked with its capacity to overcome the effects of innate immunity, whether by directly killing immune cells or expressing factors that diminish the impact of immune effectors. One such scenario is the induction of lactic acid fermentation by S. aureus in response to host nitric oxide (NO·). This fermentative activity allows S. aureus to balance redox during NO·-induced respiration inhibition. However, little is known about the metabolic substrates and pathways that support this activity. Here, we identify glycolytic hexose catabolism as being essential for S. aureus growth in the presence of high levels of NO·. We determine that glycolysis supports S. aureus NO· resistance by allowing for ATP and precursor metabolite production in a redox-balanced and respiration-independent manner. We further demonstrate that glycolysis is required for NO· resistance during phagocytosis and that increased levels of extracellular glucose limit the effectiveness of phagocytic killing by enhancing NO· resistance. Finally, we demonstrate that S. aureus glycolysis is essential for virulence in both sepsis and skin/soft tissue models of infection in a time frame consistent with the induction of innate immunity and host NO· production. Staphylococcus aureus is a leading human bacterial pathogen capable of causing a wide variety of diseases that, as a result of antibiotic resistance, are very difficult to treat. The frequency of S. aureus tissue invasion suggests that this bacterium has evolved to resist innate immunity and grow using the nutrients present in otherwise sterile host tissue. We have identified glycolysis as an essential component of S. aureus virulence and attribute its importance to promoting nitric oxide resistance and growth under low oxygen conditions. Our data suggest that diabetics, a patient population characterized by excess serum glucose, may be more susceptible to S. aureus as a result of increased glucose availability. Furthermore, the essential nature of S. aureus glycolysis indicates that a newly developed glycolysis inhibitor may be a highly effective treatment for S. aureus infections.
Collapse
|
26
|
Veale CGL, Zoraghi R, Young RM, Morrison JP, Pretheeban M, Lobb KA, Reiner NE, Andersen RJ, Davies-Coleman MT. Synthetic analogues of the marine bisindole deoxytopsentin: potent selective inhibitors of MRSA pyruvate kinase. JOURNAL OF NATURAL PRODUCTS 2015; 78:355-62. [PMID: 25372480 DOI: 10.1021/np500755v] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
As part of an ongoing study to elucidate the SAR of bisindole alkaloid inhibitors against the evolutionary conserved MRSA pyruvate kinase (PK), we present here the synthesis and biological activity of six dihalogenated analogues of the naturally occurring sponge metabolite deoxytopsentin, including the naturally occurring dibromodeoxytopsentin. The most active compounds displayed potent low nanomolar inhibitory activity against MRSA PK with concomitant significant selectivity for MRSA PK over human PK orthologues. Computational studies suggest that these potent MRSA PK inhibitors occupy a region of the small interface of the enzyme tetramer where amino acid sequence divergence from common human PK orthologues may contribute to the observed selectivity.
Collapse
Affiliation(s)
- Clinton G L Veale
- †Department of Chemistry, Rhodes University, Grahamstown, South Africa
| | | | - Ryan M Young
- †Department of Chemistry, Rhodes University, Grahamstown, South Africa
| | | | | | - Kevin A Lobb
- †Department of Chemistry, Rhodes University, Grahamstown, South Africa
| | | | | | | |
Collapse
|
27
|
Caspar Y, Jeanty M, Blu J, Burchak O, Le Pihive E, Maigre L, Schneider D, Jolivalt C, Paris JM, Hequet A, Minassian F, Denis JN, Maurin M. Novel synthetic bis-indolic derivatives with antistaphylococcal activity, including against MRSA and VISA strains. J Antimicrob Chemother 2015; 70:1727-37. [PMID: 25691323 DOI: 10.1093/jac/dkv015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 01/07/2015] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVES We report the synthesis, antibacterial activity and toxicity of 24 bis-indolic derivatives obtained during the development of new ways of synthesis of marine bis-indole alkaloids from the spongotine, topsentin and hamacanthin classes. METHODS Innovative ways of synthesis and further structural optimizations led to bis-indoles presenting either the 1-(1H-indol-3'-yl)-1,2-diaminoethane unit or the 1-(1H-indol-3-yl)ethanamine unit. MIC determination was performed for reference and clinical strains of Staphylococcus aureus and CoNS species. MBC, time-kill kinetics, solubility, hydrophobicity index, plasma protein-binding and cytotoxicity assays were performed for lead compounds. Inhibition of the S. aureus NorA efflux pump was also tested for bis-indoles with no antistaphylococcal activity. RESULTS Lead compounds were active against both S. aureus and CoNS species, with MICs between 1 and 4 mg/L. Importantly, the same MICs were found for MRSA and vancomycin-intermediate S. aureus strains. Early concentration-dependent bactericidal activity was observed for lead derivatives. Compounds with no intrinsic antibacterial activity could inhibit the S. aureus NorA efflux pump, which is involved in resistance to fluoroquinolones. At 0.5 mg/L, the most effective compound led to an 8-fold reduction of the ciprofloxacin MIC for the SA-1199B S. aureus strain, which overexpresses NorA. However, the bis-indole compounds displayed a high hydrophobicity index and high plasma protein binding, which significantly reduced antibacterial activity. CONCLUSIONS We have synthesized and characterized novel bis-indole derivatives as promising candidates for the development of new antistaphylococcal treatments, with preserved activity against MDR S. aureus strains.
Collapse
Affiliation(s)
- Yvan Caspar
- Laboratoire de bactériologie, Centre Hospitalier Universitaire de Grenoble, CS10217, 38043 Grenoble cedex 9, France Université Grenoble Alpes, CNRS, LAPM, F-38000 Grenoble, France
| | - Matthieu Jeanty
- Université Grenoble Alpes, CNRS, DCM, F-38000 Grenoble, France
| | - Jérôme Blu
- Université Grenoble Alpes, CNRS, DCM, F-38000 Grenoble, France
| | - Olga Burchak
- Université Grenoble Alpes, CNRS, DCM, F-38000 Grenoble, France
| | | | - Laure Maigre
- Université Grenoble Alpes, CNRS, LAPM, F-38000 Grenoble, France
| | | | - Claude Jolivalt
- Chimie ParisTech, Laboratoire Charles Friedel, 75005 Paris, France
| | - Jean-Marc Paris
- Chimie ParisTech, Laboratoire Charles Friedel, 75005 Paris, France
| | - Arnaud Hequet
- Chimie ParisTech, Laboratoire Charles Friedel, 75005 Paris, France
| | | | - Jean-Noël Denis
- Université Grenoble Alpes, CNRS, DCM, F-38000 Grenoble, France
| | - Max Maurin
- Laboratoire de bactériologie, Centre Hospitalier Universitaire de Grenoble, CS10217, 38043 Grenoble cedex 9, France Université Grenoble Alpes, CNRS, LAPM, F-38000 Grenoble, France
| |
Collapse
|
28
|
Veale CG, Lobb KA, Zoraghi R, Morrison JP, Reiner NE, Andersen RJ, Davies-Coleman MT. Synthesis and MRSA PK inhibitory activity of thiazole containing deoxytopsentin analogues. Tetrahedron 2014. [DOI: 10.1016/j.tet.2014.09.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
29
|
Zoraghi R, Campbell S, Kim C, Dullaghan EM, Blair LM, Gillard RM, Reiner NE, Sperry J. Discovery of a 1,2-bis(3-indolyl)ethane that selectively inhibits the pyruvate kinase of methicillin-resistant Staphylococcus aureus over human isoforms. Bioorg Med Chem Lett 2014; 24:5059-62. [PMID: 25266785 DOI: 10.1016/j.bmcl.2014.09.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 09/01/2014] [Accepted: 09/03/2014] [Indexed: 10/24/2022]
Abstract
Methicillin-resistant Staphylococcus aureus pyruvate kinase (MRSA PK) has recently been identified as a target for development of novel antibacterial agents. Testing a series of 1,2-bis(3-indolyl)ethanes against MRSA PK has led to the discovery of a potent inhibitor that is selective over human isoforms.
Collapse
Affiliation(s)
- Roya Zoraghi
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver V5Z 3J5, Canada
| | - Sara Campbell
- Centre for Drug Research and Development (CDRD), Vancouver, British Columbia, Canada
| | - Catrina Kim
- Centre for Drug Research and Development (CDRD), Vancouver, British Columbia, Canada
| | - Edie M Dullaghan
- Centre for Drug Research and Development (CDRD), Vancouver, British Columbia, Canada
| | - Lachlan M Blair
- School of Chemical Sciences, University of Auckland, 23 Symonds Street, Auckland, New Zealand
| | - Rachel M Gillard
- School of Chemical Sciences, University of Auckland, 23 Symonds Street, Auckland, New Zealand
| | - Neil E Reiner
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver V5Z 3J5, Canada; Department of Microbiology and Immunology, University of British Columbia, Vancouver V5Z 3J5, Canada
| | - Jonathan Sperry
- School of Chemical Sciences, University of Auckland, 23 Symonds Street, Auckland, New Zealand
| |
Collapse
|
30
|
Phosphorylation of pyruvate kinase A by protein kinase J leads to the altered growth and differential rate of intracellular survival of mycobacteria. Appl Microbiol Biotechnol 2014; 98:10065-76. [PMID: 24934223 DOI: 10.1007/s00253-014-5859-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 05/26/2014] [Accepted: 05/27/2014] [Indexed: 10/25/2022]
Abstract
PknJ (Rv2088) is a serine/threonine protein kinase of mycobacteria which is present in Mycobacterium tuberculosis (MTB), but its gene is absent in Mycobacterium smegmatis (MS); a fast grower and nonpathogenic species of mycobacteria. The heterologous expression of MTB-specific PknJ in MS altered the growth of recombinant mycobacteria highlighting one of the characteristics of this protein. This nature of the protein was further confirmed when Mycobacterium bovis BCG (BCG) containing antisense copy of pknJ resulted in the increased growth of BCG. The real-time RNA quantification analysis pointed out toward increased expression of this protein during infection of THP-1 macrophage cells which further emphasized that the protein is essential for the intracellular survival of mycobacteria. The differential in gel electrophoresis (DIGE) data followed by mass spectroscopy suggested that PknJ is involved in regulation of pyruvate kinase A (Rv1617). Since pyruvate kinase (PK) A is one of the key enzymes which controls glycolytic cycle in mycobacteria, we looked for its interaction with PknJ during extracellular and intracellular growth of mycobacteria. In order to identify the specific residue(s) involved in post-translational modification, the phospho-null mutants of PK were generated, and their substrate specificities in response to PknJ were assessed through kinase assay. The findings thus underlined that the PK activity is predominantly dependent on the threonine residue at the 94(th) position and further suggested that this site may be plausible in intracellular survival of mycobacteria upon phosphorylation with PknJ.
Collapse
|
31
|
Abstract
Cell division in bacteria is driven by a cytoskeletal ring structure, the Z ring, composed of polymers of the tubulin-like protein FtsZ. Z-ring formation must be tightly regulated to ensure faithful cell division, and several mechanisms that influence the positioning and timing of Z-ring assembly have been described. Another important but as yet poorly understood aspect of cell division regulation is the need to coordinate division with cell growth and nutrient availability. In this study, we demonstrated for the first time that cell division is intimately linked to central carbon metabolism in the model Gram-positive bacterium Bacillus subtilis. We showed that a deletion of the gene encoding pyruvate kinase (pyk), which produces pyruvate in the final reaction of glycolysis, rescues the assembly defect of a temperature-sensitive ftsZ mutant and has significant effects on Z-ring formation in wild-type B. subtilis cells. Addition of exogenous pyruvate restores normal division in the absence of the pyruvate kinase enzyme, implicating pyruvate as a key metabolite in the coordination of bacterial growth and division. Our results support a model in which pyruvate levels are coupled to Z-ring assembly via an enzyme that actually metabolizes pyruvate, the E1α subunit of pyruvate dehydrogenase. We have shown that this protein localizes over the nucleoid in a pyruvate-dependent manner and may stimulate more efficient Z-ring formation at the cell center under nutrient-rich conditions, when cells must divide more frequently. How bacteria coordinate cell cycle processes with nutrient availability and growth is a fundamental yet unresolved question in microbiology. Recent breakthroughs have revealed that nutritional information can be transmitted directly from metabolic pathways to the cell cycle machinery and that this can serve as a mechanism for fine-tuning cell cycle processes in response to changes in environmental conditions. Here we identified a novel link between glycolysis and cell division in Bacillus subtilis. We showed that pyruvate, the final product of glycolysis, plays an important role in maintaining normal division. Nutrient-dependent changes in pyruvate levels affect the function of the cell division protein FtsZ, most likely by modifying the activity of an enzyme that metabolizes pyruvate, namely pyruvate dehydrogenase E1α. Ultimately this system may help to coordinate bacterial division with nutritional conditions to ensure the survival of newborn cells.
Collapse
|
32
|
Uddin R, Saeed K. Identification and characterization of potential drug targets by subtractive genome analyses of methicillin resistant Staphylococcus aureus. Comput Biol Chem 2014; 48:55-63. [DOI: 10.1016/j.compbiolchem.2013.11.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Revised: 11/26/2013] [Accepted: 11/28/2013] [Indexed: 01/18/2023]
|
33
|
Kumar NS, Dullaghan EM, Finlay BB, Gong H, Reiner NE, Jon Paul Selvam J, Thorson LM, Campbell S, Vitko N, Richardson AR, Zoraghi R, Young RN. Discovery and optimization of a new class of pyruvate kinase inhibitors as potential therapeutics for the treatment of methicillin-resistant Staphylococcus aureus infections. Bioorg Med Chem 2014; 22:1708-25. [PMID: 24508307 DOI: 10.1016/j.bmc.2014.01.020] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Revised: 01/07/2014] [Accepted: 01/15/2014] [Indexed: 11/19/2022]
Abstract
A novel series of bis-indoles derived from naturally occurring marine alkaloid 4 were synthesized and evaluated as inhibitors of methicillin-resistant Staphylococcus aureus (MRSA) pyruvate kinase (PK). PK is not only critical for bacterial survival which would make it a target for development of novel antibiotics, but it is reported to be one of the most highly connected 'hub proteins' in MRSA, and thus should be very sensitive to mutations and making it difficult for the bacteria to develop resistance. From the co-crystal structure of cis-3-4-dihydrohamacanthin B (4) bound to S. aureus PK we were able to identify the pharmacophore needed for activity. Consequently, we prepared simple direct linked bis-indoles such as 10b that have similar anti-MRSA activity as compound 4. Structure-activity relationship (SAR) studies were carried out on 10b and led us to discover more potent compounds such as 10c, 10d, 10k and 10 m with enzyme inhibiting activities in the low nanomolar range that effectively inhibited the bacteria growth in culture with minimum inhibitory concentrations (MIC) for MRSA as low as 0.5 μg/ml. Some potent PK inhibitors, such as 10b, exhibited attenuated antibacterial activity and were found to be substrates for an efflux mechanism in S. aureus. Studies comparing a wild type S. aureus with a construct (S. aureus LAC Δpyk::Erm(R)) that lacks PK activity confirmed that bactericidal activity of 10d was PK-dependant.
Collapse
Affiliation(s)
- Nag S Kumar
- Department of Chemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Edie M Dullaghan
- Centre for Drug Research and Development (CDRD), Vancouver, BC, Canada
| | - B Brett Finlay
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada; Department of Medicine, Division of Infectious Diseases, University of British Columbia, Vancouver, BC, Canada
| | - Huansheng Gong
- Department of Medicine, Division of Infectious Diseases, University of British Columbia, Vancouver, BC, Canada
| | - Neil E Reiner
- Department of Medicine, Division of Infectious Diseases, University of British Columbia, Vancouver, BC, Canada; Department of Microbiology and Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - J Jon Paul Selvam
- Department of Chemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Lisa M Thorson
- Department of Medicine, Division of Infectious Diseases, University of British Columbia, Vancouver, BC, Canada
| | - Sara Campbell
- Centre for Drug Research and Development (CDRD), Vancouver, BC, Canada
| | - Nicholas Vitko
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Anthony R Richardson
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Roya Zoraghi
- Department of Medicine, Division of Infectious Diseases, University of British Columbia, Vancouver, BC, Canada
| | - Robert N Young
- Department of Chemistry, Simon Fraser University, Burnaby, BC, Canada.
| |
Collapse
|
34
|
Zoraghi R, Reiner NE. Protein interaction networks as starting points to identify novel antimicrobial drug targets. Curr Opin Microbiol 2013; 16:566-72. [PMID: 23938265 DOI: 10.1016/j.mib.2013.07.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 07/12/2013] [Accepted: 07/16/2013] [Indexed: 01/17/2023]
Abstract
Novel classes of antimicrobials are needed to address the challenge of multidrug-resistant bacteria. Current bacterial drug targets mainly consist of specific proteins or subsets of proteins without regard for either how these targets are integrated in cellular networks or how they may interact with host proteins. However, proteins rarely act in isolation, and the majority of biological processes are dependent on interactions with other proteins. Consequently, protein-protein interaction (PPI) networks offer a realm of unexplored potential for next-generation drug targets. In this review, we argue that the architecture of bacterial or host-pathogen protein interactomes can provide invaluable insights for the identification of novel antibacterial drug targets.
Collapse
Affiliation(s)
- Roya Zoraghi
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, Canada
| | | |
Collapse
|
35
|
Taylor CM, Wang Q, Rosa BA, Huang SCC, Powell K, Schedl T, Pearce EJ, Abubucker S, Mitreva M. Discovery of anthelmintic drug targets and drugs using chokepoints in nematode metabolic pathways. PLoS Pathog 2013; 9:e1003505. [PMID: 23935495 PMCID: PMC3731235 DOI: 10.1371/journal.ppat.1003505] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 06/03/2013] [Indexed: 12/19/2022] Open
Abstract
Parasitic roundworm infections plague more than 2 billion people (1/3 of humanity) and cause drastic losses in crops and livestock. New anthelmintic drugs are urgently needed as new drug resistance and environmental concerns arise. A “chokepoint reaction” is defined as a reaction that either consumes a unique substrate or produces a unique product. A chokepoint analysis provides a systematic method of identifying novel potential drug targets. Chokepoint enzymes were identified in the genomes of 10 nematode species, and the intersection and union of all chokepoint enzymes were found. By studying and experimentally testing available compounds known to target proteins orthologous to nematode chokepoint proteins in public databases, this study uncovers features of chokepoints that make them successful drug targets. Chemogenomic screening was performed on drug-like compounds from public drug databases to find existing compounds that target homologs of nematode chokepoints. The compounds were prioritized based on chemical properties frequently found in successful drugs and were experimentally tested using Caenorhabditis elegans. Several drugs that are already known anthelmintic drugs and novel candidate targets were identified. Seven of the compounds were tested in Caenorhabditis elegans and three yielded a detrimental phenotype. One of these three drug-like compounds, Perhexiline, also yielded a deleterious effect in Haemonchus contortus and Onchocerca lienalis, two nematodes with divergent forms of parasitism. Perhexiline, known to affect the fatty acid oxidation pathway in mammals, caused a reduction in oxygen consumption rates in C. elegans and genome-wide gene expression profiles provided an additional confirmation of its mode of action. Computational modeling of Perhexiline and its target provided structural insights regarding its binding mode and specificity. Our lists of prioritized drug targets and drug-like compounds have potential to expedite the discovery of new anthelmintic drugs with broad-spectrum efficacy. The World Health Organization estimates that 2.9 million people are infected with parasitic roundworms, causing high-morbidity and mortality rates, developmental delays in children, and low productivity of affected individuals. The agricultural industry experiences drastic losses in crop and livestock due to parasitic worm infections. Therefore, there is an urgent need to identify new targets and drugs to fight parasitic nematode infection. This study identified metabolic chokepoint compounds that were either produced or consumed by a single reaction and elucidated the chokepoint enzyme that drives the reaction. If the enzyme that catalyzes that reaction is blocked, a toxic build-up of a compound or lack of compound necessary for subsequent reaction will occur, potentially causing adverse effects to the parasite organism. Compounds that target some of the chokepoint enzymes were tested in C. elegans and several compounds showed efficacy. One drug-like compound, Perhexiline, showed efficacy in two different parasitic worms and yielded expected physiological effects, indicating that this drug-like compound may have efficacy on a pan-phylum level through the predicted mode of action. The methodology to find and prioritize metabolic chokepoint targets and prioritize compounds could be applied to other parasites.
Collapse
Affiliation(s)
- Christina M. Taylor
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Qi Wang
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Bruce A. Rosa
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Stanley Ching-Cheng Huang
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Kerrie Powell
- SCYNEXIS, Inc, Research Triangle Park, North Carolina, United States of America
| | - Tim Schedl
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Edward J. Pearce
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Sahar Abubucker
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Makedonka Mitreva
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Division of Infectious Diseases, Department of Internal Medicine, Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
| |
Collapse
|
36
|
Hofmann J, Heider C, Li W, Krausze J, Roessle M, Wilharm G. Recombinant production of Yersinia enterocolitica pyruvate kinase isoenzymes PykA and PykF. Protein Expr Purif 2013; 88:243-7. [PMID: 23384479 DOI: 10.1016/j.pep.2013.01.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 01/22/2013] [Indexed: 10/27/2022]
Abstract
The glycolytic enzyme pyruvate kinase (PK) generates ATP from ADP through substrate-level phosphorylation powered by the conversion of phosphoenolpyruvate to pyruvate. In contrast to other bacteria, Enterobacteriaceae, such as pathogenic yersiniae, harbour two pyruvate kinases encoded by pykA and pykF. The individual roles of these isoenzymes are poorly understood. In an attempt to make the Yersinia enterocolitica pyruvate kinases PykA and PykF amenable to structural and functional characterisation, we produced them untagged in Escherichia coli and purified them to near homogeneity through a combination of ion exchange and size exclusion chromatography, yielding more than 180 mg per litre of batch culture. The solution structure of PykA and PykF was analysed through small angle X-ray scattering which revealed the formation of PykA and PykF tetramers and confirmed the binding of the allosteric effector fructose-1,6-bisphosphate (FBP) to PykF but not to PykA.
Collapse
Affiliation(s)
- Julia Hofmann
- Robert Koch-Institute, Wernigerode Branch, Burgstr. 37, D-38855 Wernigerode, Germany
| | | | | | | | | | | |
Collapse
|
37
|
Kumar NS, Amandoron EA, Cherkasov A, Brett Finlay B, Gong H, Jackson L, Kaur S, Lian T, Moreau A, Labrière C, Reiner NE, See RH, Strynadka NC, Thorson L, Wong EW, Worrall L, Zoraghi R, Young RN. Optimization and structure–activity relationships of a series of potent inhibitors of methicillin-resistant Staphylococcus aureus (MRSA) pyruvate kinase as novel antimicrobial agents. Bioorg Med Chem 2012; 20:7069-82. [DOI: 10.1016/j.bmc.2012.10.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 09/25/2012] [Accepted: 10/03/2012] [Indexed: 11/26/2022]
|
38
|
Axerio-Cilies P, See RH, Zoraghi R, Worral L, Lian T, Stoynov N, Jiang J, Kaur S, Jackson L, Gong H, Swayze R, Amandoron E, Kumar NS, Moreau A, Hsing M, Strynadka NC, McMaster WR, Finlay BB, Foster LJ, Young RN, Reiner NE, Cherkasov A. Cheminformatics-driven discovery of selective, nanomolar inhibitors for staphylococcal pyruvate kinase. ACS Chem Biol 2012; 7:350-9. [PMID: 22066782 DOI: 10.1021/cb2003576] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We have recently mapped the protein interaction network of methicillin-resistant Staphylococcus aureus (MRSA), which revealed its scale-free organization with characteristic presence of highly connected hub proteins that are critical for bacterial survival. Here we report the discovery of inhibitors that are highly potent against one such hub target, staphylococcal pyruvate kinase (PK). Importantly, the developed compounds demonstrate complete selectivity for the bacterial enzyme compared to all human orthologues. The lead 91nM inhibitor IS-130 has been identified through ligand-based cheminformatic exploration of a chemical space around micromolar hits initially generated by experimental screening. The following crystallographic study resulted in identification of a tetrameric MRSA PK structure where IS-130 is bound to the interface between the protein's subunits. This newly described binding pocket is not present in otherwise highly similar human orthologues and can be effectively utilized for selective inhibition of bacterial PK. The following synthetic modifications of IS-130, guided by structure-based molecular modeling, resulted in the development of MRSA PK inhibitors with much improved antimicrobial properties. Considering a notable lack of recent reports on novel antibacterial targets and cognate antibacterial compounds, this study provides a valuable perspective on the development of a new generation of antimicrobials. Equally noteworthy, the results of the current work highlight the importance of rigorous cheminformatics-based exploration of the results of high-throughput experiments.
Collapse
Affiliation(s)
| | - Raymond H See
- University of British Columbia Centre for Disease Control, Vancouver, BC,
Canada
| | | | | | | | | | | | | | | | | | | | | | - Nag S. Kumar
- Department of Chemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Anne Moreau
- Department of Chemistry, Simon Fraser University, Burnaby, BC, Canada
| | | | | | - William R. McMaster
- University of British Columbia Centre for Disease Control, Vancouver, BC,
Canada
| | | | | | - Robert N. Young
- Department of Chemistry, Simon Fraser University, Burnaby, BC, Canada
| | | | | |
Collapse
|
39
|
Zoraghi R, Worrall L, See RH, Strangman W, Popplewell WL, Gong H, Samaai T, Swayze RD, Kaur S, Vuckovic M, Finlay BB, Brunham RC, McMaster WR, Davies-Coleman MT, Strynadka NC, Andersen RJ, Reiner NE. Methicillin-resistant Staphylococcus aureus (MRSA) pyruvate kinase as a target for bis-indole alkaloids with antibacterial activities. J Biol Chem 2011; 286:44716-25. [PMID: 22030393 PMCID: PMC3248012 DOI: 10.1074/jbc.m111.289033] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 09/29/2011] [Indexed: 11/06/2022] Open
Abstract
Novel classes of antimicrobials are needed to address the emergence of multidrug-resistant bacteria such as methicillin-resistant Staphylococcus aureus (MRSA). We have recently identified pyruvate kinase (PK) as a potential novel drug target based upon it being an essential hub in the MRSA interactome (Cherkasov, A., Hsing, M., Zoraghi, R., Foster, L. J., See, R. H., Stoynov, N., Jiang, J., Kaur, S., Lian, T., Jackson, L., Gong, H., Swayze, R., Amandoron, E., Hormozdiari, F., Dao, P., Sahinalp, C., Santos-Filho, O., Axerio-Cilies, P., Byler, K., McMaster, W. R., Brunham, R. C., Finlay, B. B., and Reiner, N. E. (2011) J. Proteome Res. 10, 1139-1150; Zoraghi, R., See, R. H., Axerio-Cilies, P., Kumar, N. S., Gong, H., Moreau, A., Hsing, M., Kaur, S., Swayze, R. D., Worrall, L., Amandoron, E., Lian, T., Jackson, L., Jiang, J., Thorson, L., Labriere, C., Foster, L., Brunham, R. C., McMaster, W. R., Finlay, B. B., Strynadka, N. C., Cherkasov, A., Young, R. N., and Reiner, N. E. (2011) Antimicrob. Agents Chemother. 55, 2042-2053). Screening of an extract library of marine invertebrates against MRSA PK resulted in the identification of bis-indole alkaloids of the spongotine (A), topsentin (B, D), and hamacanthin (C) classes isolated from the Topsentia pachastrelloides as novel bacterial PK inhibitors. These compounds potently and selectively inhibited both MRSA PK enzymatic activity and S. aureus growth in vitro. The most active compounds, cis-3,4-dihyrohyrohamacanthin B (C) and bromodeoxytopsentin (D), were identified as highly potent MRSA PK inhibitors (IC(50) values of 16-60 nM) with at least 166-fold selectivity over human PK isoforms. These novel anti-PK natural compounds exhibited significant antibacterial activities against S. aureus, including MRSA (minimal inhibitory concentrations (MIC) of 12.5 and 6.25 μg/ml, respectively) with selectivity indices (CC(50)/MIC) >4. We also report the discrete structural features of the MRSA PK tetramer as determined by x-ray crystallography, which is suitable for selective targeting of the bacterial enzyme. The co-crystal structure of compound C with MRSA PK confirms that the latter is a target for bis-indole alkaloids. It elucidates the essential structural requirements for PK inhibitors in "small" interfaces that provide for tetramer rigidity and efficient catalytic activity. Our results identified a series of natural products as novel MRSA PK inhibitors, providing the basis for further development of potential novel antimicrobials.
Collapse
Affiliation(s)
- Roya Zoraghi
- From the Division of Infectious Diseases, Department of Medicine
| | - Liam Worrall
- the Department of Biochemistry and Molecular Biology
| | - Raymond H. See
- From the Division of Infectious Diseases, Department of Medicine
- the Center for Disease Control, and
| | | | - Wendy L. Popplewell
- the Department of Chemistry, Rhodes University, Grahamstown 6140, South Africa, and
| | - Huansheng Gong
- From the Division of Infectious Diseases, Department of Medicine
| | - Toufiek Samaai
- the Department of Environmental Affairs, Ocean & Coast, Biodiversity and Ecosystem Research, Cape Town, Private Bag X447, South Africa
| | | | - Sukhbir Kaur
- From the Division of Infectious Diseases, Department of Medicine
| | | | - B. Brett Finlay
- the Department of Biochemistry and Molecular Biology
- Microbiology and Immunology, University of British Columbia, British Columbia, Vancouver V5Z 3J5, Canada
| | - Robert C. Brunham
- From the Division of Infectious Diseases, Department of Medicine
- the Center for Disease Control, and
| | - William R. McMaster
- From the Division of Infectious Diseases, Department of Medicine
- Microbiology and Immunology, University of British Columbia, British Columbia, Vancouver V5Z 3J5, Canada
| | | | | | | | - Neil E. Reiner
- From the Division of Infectious Diseases, Department of Medicine
- Microbiology and Immunology, University of British Columbia, British Columbia, Vancouver V5Z 3J5, Canada
| |
Collapse
|
40
|
Chan BCL, Ip M, Lau CBS, Lui SL, Jolivalt C, Ganem-Elbaz C, Litaudon M, Reiner NE, Gong H, See RH, Fung KP, Leung PC. Synergistic effects of baicalein with ciprofloxacin against NorA over-expressed methicillin-resistant Staphylococcus aureus (MRSA) and inhibition of MRSA pyruvate kinase. JOURNAL OF ETHNOPHARMACOLOGY 2011; 137:767-773. [PMID: 21782012 DOI: 10.1016/j.jep.2011.06.039] [Citation(s) in RCA: 124] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Revised: 06/20/2011] [Accepted: 06/25/2011] [Indexed: 05/31/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Baicalein, the active constituent derived from Scutellaria baicalensis Georgi., has previously been shown to significantly restore the effectiveness of β-lactam antibiotics and tetracycline against methicillin-resistant Staphylococcus aureus (MRSA). With multiple therapeutic benefits, the antibacterial actions of baicalein may also be involved in overcoming other bacterial resistance mechanisms. The aim of the present study was to further investigate antibacterial activities of baicalein in association with various antibiotics against selected Staphylococcus aureus strains with known specific drug resistance mechanisms. MATERIAL AND METHODS A panel of clinical MRSA strains was used for further confirmation of the antibacterial activities of baicalein. The effect of baicalein on inhibiting the enzymatic activity of a newly discovered MRSA-specific pyruvate kinase (PK), which is essential for Staphylococcus aureus growth and survival was also examined. RESULTS In the checkerboard dilution test and time-kill assay, baicalein at 16 μg/ml could synergistically restore the antibacterial actions of ciprofloxacin against the NorA efflux pump overexpressed SA-1199B, but not with the poor NorA substrate, pefloxacin. Moreover, synergistic effects were observed when baicalein was combined with ciprofloxacin against 12 out of 20 clinical ciprofloxacin resistant strains. For MRSA PK studies, baicalein alone could inhibit the enzymatic activity of MRSA PK in a dose-dependent manner. CONCLUSION Our results demonstrated that baicalein could significantly reverse the ciprofloxacin resistance of MRSA possibly by inhibiting the NorA efflux pump in vitro. The inhibition of MRSA PK by baicalein could lead to a deficiency of ATP which might further contribute to the antibacterial actions of baicalein against MRSA.
Collapse
Affiliation(s)
- Ben C L Chan
- Institute of Chinese Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|