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Bogacheva MS, Kuivanen S, Potdar S, Hassinen A, Huuskonen S, Pöhner I, Luck TJ, Turunen L, Feodoroff M, Szirovicza L, Savijoki K, Saarela J, Tammela P, Paavolainen L, Poso A, Varjosalo M, Kallioniemi O, Pietiäinen V, Vapalahti O. Drug repurposing platform for deciphering the druggable SARS-CoV-2 interactome. Antiviral Res 2024; 223:105813. [PMID: 38272320 DOI: 10.1016/j.antiviral.2024.105813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/10/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has heavily challenged the global healthcare system. Despite the vaccination programs, the new virus variants are circulating. Further research is required for understanding of the biology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and for discovery of therapeutic agents against the virus. Here, we took advantage of drug repurposing to identify if existing drugs could inhibit SARS-CoV-2 infection. We established an open high throughput platform for in vitro screening of drugs against SARS-CoV-2 infection. We screened ∼1000 drugs for their ability to inhibit SARS-CoV-2-induced cell death in the African green monkey kidney cell line (Vero-E6), analyzed how the hit compounds affect the viral N (nucleocapsid) protein expression in human cell lines using high-content microscopic imaging and analysis, determined the hit drug targets in silico, and assessed their ability to cause phospholipidosis, which can interfere with the viral replication. Duvelisib was found by in silico interaction assay as a potential drug targeting virus-host protein interactions. The predicted interaction between PARP1 and S protein, affected by Duvelisib, was further validated by immunoprecipitation. Our results represent a rapidly applicable platform for drug repurposing and evaluation of the new emerging viruses' responses to the drugs. Further in silico studies help us to discover the druggable host pathways involved in the infectious cycle of SARS-CoV-2.
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Affiliation(s)
- Mariia S Bogacheva
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland; Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland.
| | - Suvi Kuivanen
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland
| | - Swapnil Potdar
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Antti Hassinen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Sini Huuskonen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Ina Pöhner
- Faculty of Health Sciences, School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Tamara J Luck
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Laura Turunen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Michaela Feodoroff
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland; Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Leonora Szirovicza
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland
| | - Kirsi Savijoki
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Jani Saarela
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Päivi Tammela
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland; Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Lassi Paavolainen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Antti Poso
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland; Department of Internal Medicine VIII, University Hospital Tubingen, Tubingen, Germany
| | - Markku Varjosalo
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Olli Kallioniemi
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland; Science for Life Laboratory (SciLifeLab), Department of Oncology and Pathology, Karolinska Institutet, Solna, Sweden
| | - Vilja Pietiäinen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Olli Vapalahti
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland; Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland; HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
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2
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Durcik M, Cruz CD, Scorciapino MA, Ilaš J, Tammela P, Ceccarelli M, Mašič LP, Tomašič T. Benzothiazole DNA gyrase inhibitors and their conjugates with siderophore mimics: design, synthesis and evaluation. RSC Adv 2024; 14:2905-2917. [PMID: 38239435 PMCID: PMC10794952 DOI: 10.1039/d3ra08337c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 01/11/2024] [Indexed: 01/22/2024] Open
Abstract
Benzothiazole-based bacterial DNA gyrase and topoisomerase IV inhibitors are promising new antibacterial agents with potent activity against Gram-positive and Gram-negative bacterial strains. The aim of this study was to improve the uptake of these inhibitors into the cytoplasm of Gram-negative bacteria by conjugating them to the small siderophore mimics. The best conjugate 18b displayed potent Escherichia coli DNA gyrase and topoisomerase IV inhibition. The interaction analysis of molecular dynamics simulation trajectory showed the important contribution of the siderophore mimic moiety to binding affinity. By NMR spectroscopy, we demonstrated that the hydroxypyridinone moiety alone was responsible for the chelation of iron(iii). Moreover, 18b showed an enhancement of antibacterial activity against E. coli JW5503 in an iron-depleted medium, clearly indicating an increased uptake of 18b in this bacterial strain.
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Affiliation(s)
- Martina Durcik
- University of Ljubljana, Faculty of Pharmacy Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Cristina D Cruz
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki P. O. Box 56 (Viikinkaari 5 E) FI-00014 Helsinki Finland
| | - Mariano Andrea Scorciapino
- Department of Chemical and Geological Sciences, University of Cagliari, Cittadella Universitaria di Monserrato - S. P. 8 km 0.700 09042 - Monserrato (CA) Italy
| | - Janez Ilaš
- University of Ljubljana, Faculty of Pharmacy Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Päivi Tammela
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki P. O. Box 56 (Viikinkaari 5 E) FI-00014 Helsinki Finland
| | - Matteo Ceccarelli
- Department of Physics and IOM/CNR, Sezione di Cagliari, University of Cagliari, Cittadella Universitaria di Monserrato - S. P. 8 km 0700 09042 - Monserrato (CA) Italy
| | - Lucija Peterlin Mašič
- University of Ljubljana, Faculty of Pharmacy Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Tihomir Tomašič
- University of Ljubljana, Faculty of Pharmacy Aškerčeva cesta 7 1000 Ljubljana Slovenia
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3
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Pylkkö T, Tomašič T, Poso A, Tammela P. Virtual Screening Assisted Search for Inhibitors of the Translocated Intimin Receptor of Enteropathogenic Escherichia Coli. Chembiochem 2024; 25:e202300638. [PMID: 37971396 DOI: 10.1002/cbic.202300638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/03/2023] [Accepted: 11/16/2023] [Indexed: 11/19/2023]
Abstract
This study aimed to identify inhibitors of the translocated intimin receptor (Tir) of enteropathogenic Escherichia coli (EPEC). EPEC is an intestinal pathogen that causes diarrhea and is a major health concern worldwide. Because Tir is a key virulence factor involved in EPEC pathogenesis, inhibiting its function is a potential strategy for controlling EPEC infections. Virtual screening was applied to chemical libraries to search for compounds that inhibit Tir-mediated bacterial adherence to host cells. Three sites were targeted using the cocrystal structure published earlier. A selection of compounds was then assessed in a cell-based infection model and fluorescence microscopy assay. The results of this study provide a basis for further optimization and testing of Tir inhibitors as potential therapeutic agents for EPEC infections.
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Affiliation(s)
- Tuomas Pylkkö
- Drug Research Program, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, 00014, Helsinki, Finland
| | - Tihomir Tomašič
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Antti Poso
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, 70211, Kuopio, Finland
| | - Päivi Tammela
- Drug Research Program, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, 00014, Helsinki, Finland
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4
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Plotniece A, Sobolev A, Supuran CT, Carta F, Björkling F, Franzyk H, Yli-Kauhaluoma J, Augustyns K, Cos P, De Vooght L, Govaerts M, Aizawa J, Tammela P, Žalubovskis R. Selected strategies to fight pathogenic bacteria. J Enzyme Inhib Med Chem 2023; 38:2155816. [PMID: 36629427 PMCID: PMC9848314 DOI: 10.1080/14756366.2022.2155816] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Natural products and analogues are a source of antibacterial drug discovery. Considering drug resistance levels emerging for antibiotics, identification of bacterial metalloenzymes and the synthesis of selective inhibitors are interesting for antibacterial agent development. Peptide nucleic acids are attractive antisense and antigene agents representing a novel strategy to target pathogens due to their unique mechanism of action. Antisense inhibition and development of antisense peptide nucleic acids is a new approach to antibacterial agents. Due to the increased resistance of biofilms to antibiotics, alternative therapeutic options are necessary. To develop antimicrobial strategies, optimised in vitro and in vivo models are needed. In vivo models to study biofilm-related respiratory infections, device-related infections: ventilator-associated pneumonia, tissue-related infections: chronic infection models based on alginate or agar beads, methods to battle biofilm-related infections are discussed. Drug delivery in case of antibacterials often is a serious issue therefore this review includes overview of drug delivery nanosystems.
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Affiliation(s)
- Aiva Plotniece
- Latvian Institute of Organic Synthesis, Riga, Latvia,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Riga Stradiņš University, Riga, Latvia,CONTACT Aiva Plotniece Latvian Institute of Organic Synthesis, Riga, Latvia
| | | | - Claudiu T. Supuran
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Firenze, Italy
| | - Fabrizio Carta
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Firenze, Italy
| | - Fredrik Björkling
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, Center for Peptide-Based Antibiotics, University of Copenhagen, Copenhagen East, Denmark
| | - Henrik Franzyk
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, Center for Peptide-Based Antibiotics, University of Copenhagen, Copenhagen East, Denmark
| | - Jari Yli-Kauhaluoma
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, Drug Research Program, University of Helsinki, Helsinki, Finland
| | - Koen Augustyns
- Infla-Med, Centre of Excellence, University of Antwerp, Antwerp, Belgium,Laboratory of Medicinal Chemistry, University of Antwerp, Antwerp, Belgium
| | - Paul Cos
- Department of Pharmaceutical Sciences, Laboratory for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Antwerp, Belgium
| | - Linda De Vooght
- Department of Pharmaceutical Sciences, Laboratory for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Antwerp, Belgium
| | - Matthias Govaerts
- Department of Pharmaceutical Sciences, Laboratory for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Antwerp, Belgium
| | - Juliana Aizawa
- Department of Pharmaceutical Sciences, Laboratory for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Antwerp, Belgium
| | - Päivi Tammela
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, Drug Research Program, University of Helsinki, Helsinki, Finland
| | - Raivis Žalubovskis
- Latvian Institute of Organic Synthesis, Riga, Latvia,Faculty of Materials Science and Applied Chemistry, Institute of Technology of Organic Chemistry, Riga Technical University, Riga, Latvia
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5
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Dou J, Ilina P, Cruz CD, Nurmi D, Vidarte PZ, Rissanen M, Tammela P, Vuorinen T. Willow Bark-Derived Material with Antibacterial and Antibiofilm Properties for Potential Wound Dressing Applications. J Agric Food Chem 2023; 71:16554-16567. [PMID: 37104679 PMCID: PMC10636761 DOI: 10.1021/acs.jafc.3c00849] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/06/2023] [Accepted: 04/14/2023] [Indexed: 05/11/2023]
Abstract
Tree stems contain wood in addition to 10-20% bark, which remains one of the largest underutilized biomasses on earth. Unique macromolecules (like lignin, suberin, pectin, and tannin), extractives, and sclerenchyma fibers form the main part of the bark. Here, we perform detailed investigation of antibacterial and antibiofilm properties of bark-derived fiber bundles and discuss their potential application as wound dressing for treatment of infected chronic wounds. We show that the yarns containing at least 50% of willow bark fiber bundles significantly inhibit biofilm formation by wound-isolated Staphylococcus aureus strains. We then correlate antibacterial effects of the material to its chemical composition. Lignin plays the major role in antibacterial activity against planktonic bacteria [i.e., minimum inhibitory concentration (MIC) 1.25 mg/mL]. Acetone extract (unsaturated fatty acid-enriched) and tannin-like (dicarboxylic acid-enriched) substances inhibit both bacterial planktonic growth [MIC 1 and 3 mg/mL, respectively] and biofilm formation. The yarn lost its antibacterial activity once its surface lignin reached 20.1%, based on X-ray photoelectron spectroscopy. The proportion of fiber bundles at the fabricated yarn correlates positively with its surface lignin. Overall, this study paves the way to the use of bark-derived fiber bundles as a natural-based material for active (antibacterial and antibiofilm) wound dressings, upgrading this underappreciated bark residue from an energy source into high-value pharmaceutical use.
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Affiliation(s)
- Jinze Dou
- Department
of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, 00076 Aalto, Finland
| | - Polina Ilina
- Drug
Research Program, Division of Pharmaceutical Biosciences, Faculty
of Pharmacy, University of Helsinki, 00014 Helsinki, Finland
| | - Cristina D. Cruz
- Drug
Research Program, Division of Pharmaceutical Biosciences, Faculty
of Pharmacy, University of Helsinki, 00014 Helsinki, Finland
| | - Denise Nurmi
- Department
of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, 00076 Aalto, Finland
| | - Paula Zegarra Vidarte
- Drug
Research Program, Division of Pharmaceutical Biosciences, Faculty
of Pharmacy, University of Helsinki, 00014 Helsinki, Finland
| | - Marja Rissanen
- Department
of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, 00076 Aalto, Finland
| | - Päivi Tammela
- Drug
Research Program, Division of Pharmaceutical Biosciences, Faculty
of Pharmacy, University of Helsinki, 00014 Helsinki, Finland
| | - Tapani Vuorinen
- Department
of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, 00076 Aalto, Finland
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6
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Zwirchmayr J, Cruz CD, Grienke U, Tammela P, Rollinger JM. Biochemometry identifies ostruthin as pluripotent antimicrobial and anthelmintic agent from masterwort. iScience 2023; 26:107523. [PMID: 37636068 PMCID: PMC10457539 DOI: 10.1016/j.isci.2023.107523] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 05/07/2023] [Accepted: 07/28/2023] [Indexed: 08/29/2023] Open
Abstract
The root extract of Peucedanum ostruthium (PO-E) was identified as a promising antibacterial source from a screening of 158 extracts against Staphylococcus aureus. It has also recently been shown to significantly decrease the survival of the nematode Caenorhabditis elegans. We used the biochemometric approach ELINA to investigate the phytochemical characteristics of the multicomponent mixture PO-E to identify the anti-infective constituent(s) targeting S. aureus and C. elegans.1H NMR spectra of PO-E-derived microfractions were correlated with their respective bioactivity data. Heterocovariance analyses unambiguously identified ostruthin as an anti-staphylococcal constituent, which potently also inhibited Enterococcus spp.. ELINA demonstrated that anthelmintic activity was due to a combinatorial effect of ostruthin and isoimperatorin. A C. elegans-based survival and motility assay confirmed that isoimperatorin, imperatorin, and verapamil modulated the susceptibility of ostruthin. The combinatorial effect of these natural products was shown in larvae studies to be related to the function of the nematodes' efflux pump.
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Affiliation(s)
- Julia Zwirchmayr
- Department of Pharmaceutical Sciences, Division of Pharmacognosy, Faculty of Life Sciences, University of Vienna, 1090 Vienna, Austria
| | - Cristina D. Cruz
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland
| | - Ulrike Grienke
- Department of Pharmaceutical Sciences, Division of Pharmacognosy, Faculty of Life Sciences, University of Vienna, 1090 Vienna, Austria
| | - Päivi Tammela
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland
| | - Judith M. Rollinger
- Department of Pharmaceutical Sciences, Division of Pharmacognosy, Faculty of Life Sciences, University of Vienna, 1090 Vienna, Austria
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7
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Fedorowicz J, Cruz CD, Morawska M, Ciura K, Gilbert-Girard S, Mazur L, Mäkkylä H, Ilina P, Savijoki K, Fallarero A, Tammela P, Sączewski J. Antibacterial and antibiofilm activity of permanently ionized quaternary ammonium fluoroquinolones. Eur J Med Chem 2023; 254:115373. [PMID: 37084595 DOI: 10.1016/j.ejmech.2023.115373] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/29/2023] [Accepted: 04/11/2023] [Indexed: 04/23/2023]
Abstract
A series of quaternary ammonium fluoroquinolones was obtained by exhaustive methylation of the amine groups present at the 7-position of fluoroquinolones, including ciprofloxacin, enoxacin, gatifloxacin, lomefloxacin, and norfloxacin. The synthesized molecules were tested for their antibacterial and antibiofilm activities against Gram-positive and Gram-negative human pathogens, i.e. Staphylococcus aureus and Pseudomonas aeruginosa. The study showed that the synthesized compounds are potent antibacterial agents (MIC values at the lowest 6.25 μM) with low cytotoxicity in vitro as assessed on the BALB 3T3 mouse embryo cell line. Further experiments proved that the tested derivatives are able to bind to the DNA gyrase and topoisomerase IV active sites in a fluoroquinolone-characteristic manner. The most active quaternary ammonium fluoroquinolones, in contrast to ciprofloxacin, reduce the total biomass of P. aeruginosa ATCC 15442 biofilm in post-exposure experiments. The latter effect may be due to the dual mechanism of action of the quaternary fluoroquinolones, which also involves disruption of bacterial cell membranes. IAM-HPLC chromatographic experiments with immobilized artificial membranes (phospholipids) showed that the most active compounds were those with moderate lipophilicity and containing a cyclopropyl group at the N1 nitrogen atom in the fluoroquinolone core.
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Affiliation(s)
- Joanna Fedorowicz
- Department of Chemical Technology of Drugs, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416, Gdańsk, Poland; Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5E), FI-00014, Helsinki, Finland.
| | - Cristina D Cruz
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5E), FI-00014, Helsinki, Finland
| | - Małgorzata Morawska
- Department of Chemical Technology of Drugs, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416, Gdańsk, Poland; Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5E), FI-00014, Helsinki, Finland; Department of Organic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416, Gdańsk, Poland
| | - Krzesimir Ciura
- Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416, Gdańsk, Poland; QSAR Lab Ltd., Trzy Lipy 3 St., 80-172, Gdańsk, Poland
| | - Shella Gilbert-Girard
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5E), FI-00014, Helsinki, Finland
| | - Liliana Mazur
- Institute of Chemical Sciences, Faculty of Chemistry, Maria Curie-Sklodowska University, Plac Marii Curie-Skłodowskiej 5, 20-031, Lublin, Poland
| | - Heidi Mäkkylä
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5E), FI-00014, Helsinki, Finland
| | - Polina Ilina
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5E), FI-00014, Helsinki, Finland
| | - Kirsi Savijoki
- Infection Biology, Faculty of Medicine and Health Technology, Tampere University, Kalevantie 4, FI-33100, Tampere, Finland; Department of Food and Nutrition, Faculty of Agriculture and Forestry, University of Helsinki, Agnes Sjöbergin katu 2, P.O. Box, FI-00014, Helsinki, Finland
| | - Adyary Fallarero
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5E), FI-00014, Helsinki, Finland
| | - Päivi Tammela
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5E), FI-00014, Helsinki, Finland
| | - Jarosław Sączewski
- Department of Organic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416, Gdańsk, Poland
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8
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Dou J, Ilina P, Hemming J, Malinen K, Mäkkylä H, Oliveira de Farias N, Tammela P, de Aragão Umbuzeiro G, Räisänen R, Vuorinen T. Effect of Hybrid Type and Harvesting Season on Phytochemistry and Antibacterial Activity of Extracted Metabolites from Salix Bark. J Agric Food Chem 2022; 70:2948-2956. [PMID: 35200036 PMCID: PMC8915259 DOI: 10.1021/acs.jafc.1c08161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 06/14/2023]
Abstract
Hundreds of different fast-growing Salix hybrids have been developed mainly for energy crops. In this paper, we studied water extracts from the bark of 15 willow hybrids and species as potential antimicrobial additives. Treatment of ground bark in water under mild conditions extracted 12-25% of the dry material. Preparative high-performance liquid chromatography is proven here as a fast and highly efficient tool in the small-scale recovery of raffinose from Salix bark crude extracts for structural elucidation. Less than half of the dissolved material was assigned by chromatographic (gas chromatography and liquid chromatography) and spectroscopic (mass spectrometry and nuclear magnetic resonance spectroscopy) techniques for low-molecular-weight compounds, including mono- and oligosaccharides (sucrose, raffinose, and stachyose) and aromatic phytochemicals (triandrin, catechin, salicin, and picein). The composition of the extracts varied greatly depending on the hybrid or species and the harvesting season. This information generated new scientific knowledge on the variation in the content and composition of the extracts between Salix hybrids and harvesting season depending on the desired molecule. The extracts showed high antibacterial activity on Staphylococcus aureus with a minimal inhibitory concentration (MIC) of 0.6-0.8 mg/mL; however, no inhibition was observed against Escherichia coli, Enterococcus faecalis, and Salmonella typhimurium. MIC of triandrin (i.e., 1.25 mg/mL) is reported for the first time. Although antibacterial triandrin and (+)-catechin were present in extracts, clear correlation between the antibacterial effect and the chemical composition was not established, which indicates that antibacterial activity of the extracts mainly originates from some not yet elucidated substances. Aquatic toxicity and mutagenicity assessments showed the safe usage of Salix water extracts as possible antibacterial additives.
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Affiliation(s)
- Jinze Dou
- Department
of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Espoo 02150, Finland
| | - Polina Ilina
- Drug
Research Program, Division of Pharmaceutical Biosciences, Faculty
of Pharmacy, University of Helsinki, Helsinki 00014, Finland
| | - Jarl Hemming
- Johan
Gadolin Process Chemistry Centre, c/o Laboratory of Natural Materials
Technology, Åbo Akademi University, Turku 20500, Finland
| | - Kiia Malinen
- Department
of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Espoo 02150, Finland
| | - Heidi Mäkkylä
- Drug
Research Program, Division of Pharmaceutical Biosciences, Faculty
of Pharmacy, University of Helsinki, Helsinki 00014, Finland
| | - Natália Oliveira de Farias
- Laboratory
of Ecotoxicology and Genotoxicity—LAEG, School of Technology, University of Campinas, Campinas 13083-970, Brazil
| | - Päivi Tammela
- Drug
Research Program, Division of Pharmaceutical Biosciences, Faculty
of Pharmacy, University of Helsinki, Helsinki 00014, Finland
| | - Gisela de Aragão Umbuzeiro
- Laboratory
of Ecotoxicology and Genotoxicity—LAEG, School of Technology, University of Campinas, Campinas 13083-970, Brazil
| | - Riikka Räisänen
- HELSUS
Helsinki Institute of Sustainability Science, Craft Studies, University of Helsinki, Helsinki 00014, Finland
| | - Tapani Vuorinen
- Department
of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Espoo 02150, Finland
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9
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Pylkkö T, Ilina P, Tammela P. Development and validation of a high-content screening assay for inhibitors of enteropathogenic E. coli adhesion. J Microbiol Methods 2021; 184:106201. [PMID: 33713725 DOI: 10.1016/j.mimet.2021.106201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/05/2021] [Accepted: 03/05/2021] [Indexed: 11/25/2022]
Abstract
Enteropathogenic E. coli (EPEC) causes intestinal infections leading to severe diarrhea. EPEC attaches to the host cell causing lesions to the intestinal epithelium coupled with the effacement of microvilli. In the process, actin accumulates into a pedestal-like structure under bacterial microcolonies. We designed an automated fluorescence microscopy-based screening method for discovering compounds capable of inhibiting EPEC adhesion and virulence using aurodox, a type three secretion system (T3SS) inhibitor, as a positive control. The screening assay employs an EPEC strain (2348/69) expressing a fluorescent protein and actin staining for monitoring the bacteria and their pedestals respectively, analyzing these with a custom image analysis pipeline. The assay allows for the discovery of compounds capable of preventing the formation of pathogenic actin rearrangements. These compounds may be interfering with virulence-related molecular pathways relevant for developing antivirulence leads.
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Affiliation(s)
- Tuomas Pylkkö
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, P.O. Box 56, FI-00014, University of Helsinki, Finland
| | - Polina Ilina
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, P.O. Box 56, FI-00014, University of Helsinki, Finland
| | - Päivi Tammela
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, P.O. Box 56, FI-00014, University of Helsinki, Finland.
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10
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Magalhães J, Franko N, Raboni S, Annunziato G, Tammela P, Bruno A, Bettati S, Armao S, Spadini C, Cabassi CS, Mozzarelli A, Pieroni M, Campanini B, Costantino G. Discovery of Substituted (2-Aminooxazol-4-yl)Isoxazole-3-carboxylic Acids as Inhibitors of Bacterial Serine Acetyltransferase in the Quest for Novel Potential Antibacterial Adjuvants. Pharmaceuticals (Basel) 2021; 14:ph14020174. [PMID: 33672408 PMCID: PMC7931047 DOI: 10.3390/ph14020174] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/15/2021] [Accepted: 02/19/2021] [Indexed: 02/07/2023] Open
Abstract
Many bacteria and actinomycetales use L-cysteine biosynthesis to increase their tolerance to antibacterial treatment and establish a long-lasting infection. In turn, this might lead to the onset of antimicrobial resistance that currently represents one of the most menacing threats to public health worldwide. The biosynthetic machinery required to synthesise L-cysteine is absent in mammals; therefore, its exploitation as a drug target is particularly promising. In this article, we report a series of inhibitors of Salmonella thyphimurium serine acetyltransferase (SAT), the enzyme that catalyzes the rate-limiting step of L-cysteine biosynthesis. The development of such inhibitors started with the virtual screening of an in-house library of compounds that led to the selection of seven structurally unrelated hit derivatives. A set of molecules structurally related to hit compound 5, coming either from the original library or from medicinal chemistry efforts, were tested to determine a preliminary structure–activity relationship and, especially, to improve the inhibitory potency of the derivatives, that was indeed ameliorated by several folds compared to hit compound 5 Despite these progresses, at this stage, the most promising compound failed to interfere with bacterial growth when tested on a Gram-negative model organism, anticipating the need for further research efforts.
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Affiliation(s)
- Joana Magalhães
- P4T Group, Department of Food and Drug, University of Parma, 43124 Parma, Italy; (J.M.); (G.A.); (A.B.); (G.C.)
| | - Nina Franko
- Laboratory of Biochemistry and Molecular Biology, Department of Food and Drug, University of Parma, 43124 Parma, Italy; (N.F.); (S.R.); (S.A.); (A.M.); (B.C.)
| | - Samanta Raboni
- Laboratory of Biochemistry and Molecular Biology, Department of Food and Drug, University of Parma, 43124 Parma, Italy; (N.F.); (S.R.); (S.A.); (A.M.); (B.C.)
- Institute of Biophysics, CNR, 56124 Pisa, Italy;
| | - Giannamaria Annunziato
- P4T Group, Department of Food and Drug, University of Parma, 43124 Parma, Italy; (J.M.); (G.A.); (A.B.); (G.C.)
- Centro Interdipartimentale Misure (CIM) ‘G. Casnati’, University of Parma, 43124 Parma, Italy
| | - Päivi Tammela
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), FI-00014 Helsinki, Finland;
| | - Agostino Bruno
- P4T Group, Department of Food and Drug, University of Parma, 43124 Parma, Italy; (J.M.); (G.A.); (A.B.); (G.C.)
| | - Stefano Bettati
- Institute of Biophysics, CNR, 56124 Pisa, Italy;
- Department of Medicine and Surgery, University of Parma, Via Volturno, 39, 43125 Parma, Italy
- National Institute of Biostructures and Biosystems, 00136 Rome, Italy
| | - Stefano Armao
- Laboratory of Biochemistry and Molecular Biology, Department of Food and Drug, University of Parma, 43124 Parma, Italy; (N.F.); (S.R.); (S.A.); (A.M.); (B.C.)
| | - Costanza Spadini
- Operative Unit of Animals Infectious Diseases, Department of Veterinary Science, University of Parma, Via del Taglio 10, 43126 Parma, Italy; (C.S.); (C.S.C.)
| | - Clotilde Silvia Cabassi
- Operative Unit of Animals Infectious Diseases, Department of Veterinary Science, University of Parma, Via del Taglio 10, 43126 Parma, Italy; (C.S.); (C.S.C.)
| | - Andrea Mozzarelli
- Laboratory of Biochemistry and Molecular Biology, Department of Food and Drug, University of Parma, 43124 Parma, Italy; (N.F.); (S.R.); (S.A.); (A.M.); (B.C.)
- Institute of Biophysics, CNR, 56124 Pisa, Italy;
- National Institute of Biostructures and Biosystems, 00136 Rome, Italy
| | - Marco Pieroni
- P4T Group, Department of Food and Drug, University of Parma, 43124 Parma, Italy; (J.M.); (G.A.); (A.B.); (G.C.)
- Centro Interdipartimentale Misure (CIM) ‘G. Casnati’, University of Parma, 43124 Parma, Italy
- Correspondence: ; Tel.: +39-0521-905054
| | - Barbara Campanini
- Laboratory of Biochemistry and Molecular Biology, Department of Food and Drug, University of Parma, 43124 Parma, Italy; (N.F.); (S.R.); (S.A.); (A.M.); (B.C.)
| | - Gabriele Costantino
- P4T Group, Department of Food and Drug, University of Parma, 43124 Parma, Italy; (J.M.); (G.A.); (A.B.); (G.C.)
- Centro Interdipartimentale Misure (CIM) ‘G. Casnati’, University of Parma, 43124 Parma, Italy
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11
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Cruz CD, Esteve P, Tammela P. Evaluation and validation of Biolog OmniLog ® system for antibacterial activity assays. Lett Appl Microbiol 2021; 72:589-595. [PMID: 33428794 DOI: 10.1111/lam.13450] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/22/2020] [Accepted: 12/23/2020] [Indexed: 11/30/2022]
Abstract
Minimal inhibitory concentration of antimicrobials, determined by the broth microdilution method, requires visual assessment or absorbance measurement using a spectrophotometer. Both procedures are usually performed manually, requiring the presence of an operator to assess the plates at specific time point. To increase the throughput of antimicrobial susceptibility testing, and concurrently convert into an automatic assay, the Biolog OmniLog® system was validated for a new, label-free application using standard 96-well microplates. OmniLog was evaluated for its signal strength to ensure that the signal intensity, detected and measured by the system's camera, was satisfactory. Variability due to the plate location inside the OmniLog incubator, as well as variation between wells, was investigated. Then the system was validated by determining the minimal inhibitory concentration of ciprofloxacin, piperacillin and linezolid against a selected Gram-negative and Gram-positive strains. No significant difference was observed in relation to position of the plates within the system. Plate edge effects were noticeable, thus the edge wells were not included in further experiments. Minimal inhibitory concentration results were comparable to those obtained by conventional protocol as well as to values defined by the Clinical Laboratory Standards Institute or published in the literature.
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Affiliation(s)
- C D Cruz
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - P Esteve
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - P Tammela
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
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12
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Skok Ž, Barančoková M, Benek O, Cruz CD, Tammela P, Tomašič T, Zidar N, Mašič LP, Zega A, Stevenson CEM, Mundy JEA, Lawson DM, Maxwell A, Kikelj D, Ilaš J. Exploring the Chemical Space of Benzothiazole-Based DNA Gyrase B Inhibitors. ACS Med Chem Lett 2020; 11:2433-2440. [PMID: 33329764 PMCID: PMC7734788 DOI: 10.1021/acsmedchemlett.0c00416] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 10/13/2020] [Indexed: 12/22/2022] Open
Abstract
![]()
We
designed and synthesized a series of inhibitors of the bacterial
enzymes DNA gyrase and DNA topoisomerase IV, based on our recently
published benzothiazole-based inhibitor bearing an oxalyl moiety.
To improve the antibacterial activity and retain potent enzymatic
activity, we systematically explored the chemical space. Several strategies
of modification were followed: varying substituents on the pyrrole
carboxamide moiety, alteration of the central scaffold, including
variation of substitution position and, most importantly, modification
of the oxalyl moiety. Compounds with acidic, basic, and neutral properties
were synthesized. To understand the mechanism of action and binding
mode, we have obtained a crystal structure of compound 16a, bearing a primary amino group, in complex with the N-terminal domain
of E. coli gyrase B (24 kDa) (PDB: 6YD9). Compound 15a, with a low molecular weight of 383
Da, potent inhibitory activity on E. coli gyrase
(IC50 = 9.5 nM), potent antibacterial activity on E. faecalis (MIC = 3.13 μM), and efflux impaired E. coli strain (MIC = 0.78 μM), is an important contribution
for the development of novel gyrase and topoisomerase IV inhibitors
in Gram-negative bacteria.
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Affiliation(s)
- Žiga Skok
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Michaela Barančoková
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Ondřej Benek
- University of Hradec Králové, Faculty of Science, Department of Chemistry, Rokitanského 62, 500 03 Hradec Králové, Czech Republic
| | - Cristina Durante Cruz
- Centre for Drug Research, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), Helsinki FI-00014, Finland
| | - Päivi Tammela
- Centre for Drug Research, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), Helsinki FI-00014, Finland
| | - Tihomir Tomašič
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Nace Zidar
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Lucija Peterlin Mašič
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Anamarija Zega
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Clare E. M. Stevenson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Julia E. A. Mundy
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - David M. Lawson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Danijel Kikelj
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Janez Ilaš
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
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13
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Kapp K, Püssa T, Orav A, Roasto M, Raal A, Vuorela P, Vuorela H, Tammela P. Chemical Composition and Antibacterial Effect of Mentha spp. Grown in Estonia. Nat Prod Commun 2020. [DOI: 10.1177/1934578x20977615] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Mentha spp. are used in the food and pharmaceutical industry; the plants are characterized by natural interspecies hybridization. In this study, knowledge of the chemical composition of Mentha spp. was broadened by focusing on plants grown in a geographically small region of Estonia. The antibacterial activity of Mentha spp. essential oils and water extracts was evaluated. Polyphenolic water extracts of M. × villosa Huds., M. × suaveolens Ehrh., and M. × gracilis Sole were tested for the first time on Escherichia coli and Staphylococcus aureus. Leaves of cultivated and wild-grown plants ( n = 33) were collected. The microdistilled essential oil composition reflected the diversity within the genus Mentha. Determined by gas chromatography-mass spectrometry (MS), major compounds were cis-piperitone oxide, carvone, linalool, menthol, and menthofuran. Based on high-performance liquid chromatography-ultraviolet-MS/MS analyses of the water extracts, no species-specific polyphenolic compounds could be proposed. Abundant polyphenols were rosmarinic acid, salvianolic acid B, and eriocitrin. Essential oils exhibited antibacterial activity on E. coli and S. aureus by the broth dilution method. Water extracts showed activity only against S. aureus. This study supports the use of Mentha spp. as health-promoting ingredients in food. However, further studies are still needed to widen the knowledge of the chemical composition of these plants.
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Affiliation(s)
- Karmen Kapp
- Faculty of Pharmacy, Drug Research Program, Division of Pharmaceutical Biosciences, University of Helsinki, Helsinki, Finland
| | - Tõnu Püssa
- Chair of Food Hygiene and Veterinary Public Health, Estonian University of Life Sciences, Tartu, Estonia
| | - Anne Orav
- Institute of Chemistry, Tallinn University of Technology, Tallinn, Estonia
| | - Mati Roasto
- Chair of Food Hygiene and Veterinary Public Health, Estonian University of Life Sciences, Tartu, Estonia
| | - Ain Raal
- Faculty of Medicine, Institute of Pharmacy, University of Tartu, Tartu, Estonia
| | - Pia Vuorela
- Faculty of Pharmacy, Drug Research Program, Division of Pharmaceutical Biosciences, University of Helsinki, Helsinki, Finland
| | - Heikki Vuorela
- Faculty of Pharmacy, Drug Research Program, Division of Pharmaceutical Biosciences, University of Helsinki, Helsinki, Finland
| | - Päivi Tammela
- Faculty of Pharmacy, Drug Research Program, Division of Pharmaceutical Biosciences, University of Helsinki, Helsinki, Finland
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14
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Cruz CD, Wrigstedt P, Moslova K, Iashin V, Mäkkylä H, Ghemtio L, Heikkinen S, Tammela P, Perea-Buceta JE. Installation of an aryl boronic acid function into the external section of N-aryl-oxazolidinones: Synthesis and antimicrobial evaluation. Eur J Med Chem 2020; 211:113002. [PMID: 33223262 DOI: 10.1016/j.ejmech.2020.113002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/02/2020] [Accepted: 11/04/2020] [Indexed: 10/23/2022]
Abstract
N-aryl-oxazolidinones is a prominent family of antimicrobials used for treating infections caused by clinically prevalent Gram-positive bacteria. Recently, boron-containing compounds have displayed intriguing potential in the antibiotic discovery setting. Herein, we report the unprecedented introduction of a boron-containing moiety such as an aryl boronic acid in the external region of the oxazolidinone structure via a chemoselective acyl coupling reaction. As a result, we accessed a series of analogues with a distal aryl boronic pharmacophore on the oxazolidinone scaffold. We identified that a peripheric linear conformation coupled with freedom of rotation and no further substitution on the external aryl boronic ring, an amido linkage with hydrogen bonding character, in addition to a para-relative disposition between boronic group and linker, are the optimal combination of structural features in this series for antimicrobial activity. In comparison to linezolid, the analogue comprising all those features, compound 20b, displayed levels of antimicrobial activity augmented by an eight-fold to a thirty-two-fold against a panel of Gram-positive strains, and a near one hundred-fold against Escherichia coli JW5503, a Gram-negative mutant strain with a defective efflux capability.
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Affiliation(s)
- Cristina D Cruz
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, 00014, Finland
| | - Pauli Wrigstedt
- Department of Chemistry, Faculty of Science, University of Helsinki, P.O. Box 55, 00014, Finland
| | - Karina Moslova
- Department of Chemistry, Faculty of Science, University of Helsinki, P.O. Box 55, 00014, Finland
| | - Vladimir Iashin
- Department of Chemistry, Faculty of Science, University of Helsinki, P.O. Box 55, 00014, Finland
| | - Heidi Mäkkylä
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, 00014, Finland
| | - Léo Ghemtio
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, 00014, Finland
| | - Sami Heikkinen
- Department of Chemistry, Faculty of Science, University of Helsinki, P.O. Box 55, 00014, Finland
| | - Päivi Tammela
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, 00014, Finland
| | - Jesus E Perea-Buceta
- Department of Chemistry, Faculty of Science, University of Helsinki, P.O. Box 55, 00014, Finland.
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15
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Kapp K, Orav A, Roasto M, Raal A, Püssa T, Vuorela H, Tammela P, Vuorela P. Composition and Antibacterial Effect of Mint Flavorings in Candies and Food Supplements. Planta Med 2020; 86:1089-1096. [PMID: 32365392 DOI: 10.1055/a-1158-1699] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Mint flavorings are widely used in confections, beverages, and dairy products. For the first time, mint flavoring composition of mint candies and food supplements (n = 45), originating from 16 countries, as well as their antibacterial properties, was analyzed. The flavorings were isolated by Marcusson's type micro-apparatus and analyzed by GC-MS. The total content of the mint flavoring hydrodistilled extracts was in the range of 0.01 - 0.9%. The most abundant compounds identified in the extracts were limonene, 1,8-cineole, menthone, menthofuran, isomenthone, menthol and its isomers, menthyl acetate. The antimicrobial activity of 13 reference substances and 10 selected mint flavoring hydrodistilled extracts was tested on Escherichia coli and Staphylococcus aureus by broth dilution method. Linalool acetate and (-)-carvone, as most active against both bacteria, had the lowest MIC90 values. (+)-Menthyl acetate, (-)-menthyl acetate, and limonene showed no antimicrobial activity. Three of the tested extracts had antimicrobial activity against E. coli and 8 extracts against S. aureus. Their summary antimicrobial activity was not always in concordance with the activities of respective reference substances.
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Affiliation(s)
- Karmen Kapp
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Finland
| | - Anne Orav
- Institute of Chemistry, Tallinn University of Technology, Estonia
| | - Mati Roasto
- Chair of Food Hygiene and Veterinary Public Health, Estonian University of Life Sciences, Estonia
| | - Ain Raal
- Institute of Pharmacy, Faculty of Medicine, University of Tartu, Estonia
| | - Tõnu Püssa
- Chair of Food Hygiene and Veterinary Public Health, Estonian University of Life Sciences, Estonia
| | - Heikki Vuorela
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Finland
| | - Päivi Tammela
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Finland
| | - Pia Vuorela
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Finland
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16
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Magalhães J, Franko N, Raboni S, Annunziato G, Tammela P, Bruno A, Bettati S, Mozzarelli A, Pieroni M, Campanini B, Costantino G. Inhibition of Nonessential Bacterial Targets: Discovery of a Novel Serine O-Acetyltransferase Inhibitor. ACS Med Chem Lett 2020; 11:790-797. [PMID: 32435386 DOI: 10.1021/acsmedchemlett.9b00627] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 02/13/2020] [Indexed: 11/29/2022] Open
Abstract
In ϒ-proteobacteria and Actinomycetales, cysteine biosynthetic enzymes are indispensable during persistence and become dispensable during growth or acute infection. The biosynthetic machinery required to convert inorganic sulfur into cysteine is absent in mammals; therefore, it is a suitable drug target. We searched for inhibitors of Salmonella serine acetyltransferase (SAT), the enzyme that catalyzes the rate-limiting step of l-cysteine biosynthesis. The virtual screening of three ChemDiv focused libraries containing 91 243 compounds was performed to identify potential SAT inhibitors. Scaffold similarity and the analysis of the overall physicochemical properties allowed the selection of 73 compounds that were purchased and evaluated on the recombinant enzyme. Six compounds displaying an IC50 <100 μM were identified via an indirect assay using Ellman's reagent and then tested on a Gram-negative model organism, with one of them being able to interfere with bacterial growth via SAT inhibition.
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Affiliation(s)
| | | | | | | | - Päivi Tammela
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), Helsinki FI-00014, Finland
| | | | - Stefano Bettati
- Department of Medicine and Surgery, University of Parma, 43125 Parma, Italy
- National Institute of Biostructures and Biosystems, 00136 Rome, Italy
- Institute of Biophysics, CNR, 56124 Pisa, Italy
| | - Andrea Mozzarelli
- National Institute of Biostructures and Biosystems, 00136 Rome, Italy
- Institute of Biophysics, CNR, 56124 Pisa, Italy
| | - Marco Pieroni
- Centro Interdipartimentale “Biopharmanet-tec”, Università degli Studi di Parma, 43124 Parma, Italy
| | | | - Gabriele Costantino
- Centro Interdipartimentale “Biopharmanet-tec”, Università degli Studi di Parma, 43124 Parma, Italy
- Centro Interdipartimentale Misure (CIM) ‘G. Casnati’, University of Parma, 43124 Parma, Italy
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17
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Lamut A, Gjorgjieva M, Naesens L, Liekens S, Lillsunde KE, Tammela P, Kikelj D, Tomašič T. Anti-influenza virus activity of benzo[d]thiazoles that target heat shock protein 90. Bioorg Chem 2020; 98:103733. [DOI: 10.1016/j.bioorg.2020.103733] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 02/12/2020] [Accepted: 03/06/2020] [Indexed: 12/21/2022]
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18
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Gatta V, Tomašič T, Ilaš J, Zidar N, Peterlin Mašič L, Barančoková M, Frlan R, Anderluh M, Kikelj D, Tammela P. A New Cell-Based AI-2-Mediated Quorum Sensing Interference Assay in Screening of LsrK-Targeted Inhibitors. Chembiochem 2020; 21:1918-1922. [PMID: 32026533 DOI: 10.1002/cbic.201900773] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Indexed: 01/06/2023]
Abstract
Quorum sensing (QS), a bacterial communication strategy, has been recognized as one of the control mechanisms of virulence in bacteria. Thus, targeting QS offers an interesting opportunity to impair bacterial pathogenicity and develop antivirulence agents. Aiming to enhance the discovery of QS inhibitors, we developed a bioreporter Escherichia coli JW5505 pET-Plsrlux and set up a cell-based assay for identifying inhibitors of autoinducer-2 (AI-2)-mediated QS. A comparative study on the performance of target- versus cell-based assays was performed, and 91 compounds selected with the potential to target the ATP binding pocket of LsrK, a key enzyme in AI-2 processing, were tested in an LsrK inhibition assay, providing 36 hits. The same set of compounds was tested by the AI-2-mediated QS interference assay, resulting in 24 active compounds. Among those, six were also found to be active against LsrK, whereas 18 might target other components of the pathway. Thus, this AI-2-mediated QS interference cell-based assay is an effective tool for complementing target-based assays, yet also stands as an independent assay for primary screening.
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Affiliation(s)
- Viviana Gatta
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5 E (PO Box 56), 00014, Helsinki, Finland
| | - Tihomir Tomašič
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Janez Ilaš
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Nace Zidar
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Lucija Peterlin Mašič
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Michaela Barančoková
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Rok Frlan
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Marko Anderluh
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Danijel Kikelj
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Päivi Tammela
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5 E (PO Box 56), 00014, Helsinki, Finland
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19
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Lamut A, Cruz CD, Skok Ž, Barančoková M, Zidar N, Zega A, Mašič LP, Ilaš J, Tammela P, Kikelj D, Tomašič T. Design, synthesis and biological evaluation of novel DNA gyrase inhibitors and their siderophore mimic conjugates. Bioorg Chem 2019; 95:103550. [PMID: 31911309 DOI: 10.1016/j.bioorg.2019.103550] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 12/19/2019] [Accepted: 12/21/2019] [Indexed: 10/25/2022]
Abstract
Bacterial DNA gyrase is an important target for the development of novel antibacterial drugs, which are urgently needed because of high level of antibiotic resistance worldwide. We designed and synthesized new 4,5,6,7-tetrahydrobenzo[d]thiazole-based DNA gyrase B inhibitors and their conjugates with siderophore mimics, which were introduced to increase the uptake of inhibitors into the bacterial cytoplasm. The most potent conjugate 34 had an IC50 of 58 nM against Escherichia coli DNA gyrase and displayed MIC of 14 µg/mL against E. coli ΔtolC strain. Only minor improvements in the antibacterial activities against wild-type E. coli in low-iron conditions were seen for DNA gyrase inhibitor - siderophore mimic conjugates.
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Affiliation(s)
- Andraž Lamut
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva Cesta 7, 1000 Ljubljana, Slovenia
| | - Cristina D Cruz
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), FI-00014 Helsinki, Finland
| | - Žiga Skok
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva Cesta 7, 1000 Ljubljana, Slovenia
| | - Michaela Barančoková
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva Cesta 7, 1000 Ljubljana, Slovenia
| | - Nace Zidar
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva Cesta 7, 1000 Ljubljana, Slovenia
| | - Anamarija Zega
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva Cesta 7, 1000 Ljubljana, Slovenia
| | - Lucija Peterlin Mašič
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva Cesta 7, 1000 Ljubljana, Slovenia
| | - Janez Ilaš
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva Cesta 7, 1000 Ljubljana, Slovenia
| | - Päivi Tammela
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), FI-00014 Helsinki, Finland
| | - Danijel Kikelj
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva Cesta 7, 1000 Ljubljana, Slovenia
| | - Tihomir Tomašič
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva Cesta 7, 1000 Ljubljana, Slovenia.
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20
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Kuznetsov SG, Ianevski A, Kulessky E, Laamanen K, Lehtinen E, Nurmi M, Potdar S, Saarela J, Suomi K, Turunen L, Wennerberg K, Tammela P. Abstract 2153: Ex vivo drug sensitivity testing of primary cells for precision cancer medicine. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-2153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction/Purpose:
Cancer therapy is increasingly moving towards individualized care and therapy, but there are still gaps between what is known and described on the molecular level about cancers and what is applied in the clinic. In an attempt to bridge the knowledge gap, we at the Institute for Molecular Medicine Finland (FIMM) have set up an Individualized Systems Medicine program that integrates clinical information, molecular profiling and functional information about individual patients’ cancers (Pemovska et al, Cancer Discov, 2013). Central to this program is the Drug Sensitivity and Resistance Testing (DSRT) where we functionally profile the responses of primary cancer cells to a comprehensive clinical oncology and signal transduction inhibitor drug collection of 528 compounds.
Methods:
Acoustic dispensing platforms are integral to the success of this profiling activity. We have to date produced approximately 3000 drug sets as dose response assay ready plates. The acoustic dispensing allows for making pre-drugged single drug plate sets and/or drug combination plates within hours after sampling of the cells. The plates are also readily sent to researchers anywhere in the world for running comparable assays at other sites. The drugging reproducibility is excellent generating results with correlations of 0.98 or higher in replicate assays. We have developed in-house software solutions to aid these processes: a script for quick creation of transfer list for combination plates and automated analysis pipelines with web-based software interfaces to enable the screening biologists to analyze the screening results effectively.
Results:
The results of these assays are used to explore and understand cancer biology in terms of druggability, functional heterogeneity and mechanism of drug response and resistance. The profiling data can be used to stratify and position the relevance of specific drugs in different diseases and has been used to identify novel clinically relevant activities of existing and investigational drugs (see e.g. Pemovska et al, Nature, 2015). This information is further utilized to establish hypotheses on drug combinations selectively targeting individual cancers and their predictive biomarkers, which can be explored in the clinic by our clinical collaborators to guide the treatment of the individual patient.
Conclusions:
In summary, we describe our platform for a functional drug sensitivity testing within our individualized cancer systems medicine program, which generates consistent biological and clinically relevant data.
Citation Format: Sergey G. Kuznetsov, Alexander Ianevski, Evgeny Kulessky, Karoliina Laamanen, Elina Lehtinen, Maria Nurmi, Swapnil Potdar, Jani Saarela, Katja Suomi, Laura Turunen, Krister Wennerberg, Päivi Tammela. Ex vivo drug sensitivity testing of primary cells for precision cancer medicine [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2153.
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21
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Sassetti E, Durante Cruz C, Tammela P, Winterhalter M, Augustyns K, Gribbon P, Windshügel B. Identification and Characterization of Approved Drugs and Drug-Like Compounds as Covalent Escherichia coli ClpP Inhibitors. Int J Mol Sci 2019; 20:ijms20112686. [PMID: 31159170 PMCID: PMC6600665 DOI: 10.3390/ijms20112686] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/29/2019] [Accepted: 05/30/2019] [Indexed: 12/31/2022] Open
Abstract
The serine protease Caseinolytic protease subunit P (ClpP) plays an important role for protein homeostasis in bacteria and contributes to various developmental processes, as well as virulence. Therefore, ClpP is considered as a potential drug target in Gram-positive and Gram-negative bacteria. In this study, we utilized a biochemical assay to screen several small molecule libraries of approved and investigational drugs for Escherichia coli ClpP inhibitors. The approved drugs bortezomib, cefmetazole, cisplatin, as well as the investigational drug cDPCP, and the protease inhibitor 3,4-dichloroisocoumarin (3,4-DIC) emerged as ClpP inhibitors with IC50 values ranging between 0.04 and 31 µM. Compound profiling of the inhibitors revealed cefmetazole and cisplatin not to inhibit the serine protease bovine α-chymotrypsin, and for cefmetazole no cytotoxicity against three human cell lines was detected. Surface plasmon resonance studies demonstrated all novel ClpP inhibitors to bind covalently to ClpP. Investigation of the potential binding mode for cefmetazole using molecular docking suggested a dual covalent binding to Ser97 and Thr168. While only the antibiotic cefmetazole demonstrated an intrinsic antibacterial effect, cDPCP clearly delayed the bacterial growth recovery time upon chemically induced nitric oxide stress in a ClpP-dependent manner.
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Affiliation(s)
- Elisa Sassetti
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, ScreeningPort, 22525 Hamburg, Germany.
- Drug Research Program, Division of Pharmaceutical Biosciences, University of Helsinki, FI-00014 Helsinki, Finland.
| | - Cristina Durante Cruz
- Drug Research Program, Division of Pharmaceutical Biosciences, University of Helsinki, FI-00014 Helsinki, Finland.
| | - Päivi Tammela
- Drug Research Program, Division of Pharmaceutical Biosciences, University of Helsinki, FI-00014 Helsinki, Finland.
| | - Mathias Winterhalter
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, 28759 Bremen, Germany.
| | - Koen Augustyns
- Laboratory of Medicinal Chemistry, University of Antwerp, B-2610 Antwerp, Belgium.
| | - Philip Gribbon
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, ScreeningPort, 22525 Hamburg, Germany.
| | - Björn Windshügel
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, ScreeningPort, 22525 Hamburg, Germany.
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22
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Zidar N, Macut H, Tomašič T, Peterlin Mašič L, Ilaš J, Zega A, Tammela P, Kikelj D. New N-phenyl-4,5-dibromopyrrolamides as DNA gyrase B inhibitors. Medchemcomm 2019; 10:1007-1017. [PMID: 31303999 DOI: 10.1039/c9md00224c] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 05/18/2019] [Indexed: 11/21/2022]
Abstract
Due to the rapid development of antimicrobial resistance, the discovery of new antibacterials is essential in the fight against potentially lethal infections. The DNA gyrase B (GyrB) subunit of bacterial DNA gyrase is an excellent target for the design of antibacterials, as it has been clinically validated by novobiocin. However, there are currently no drugs in clinical use that target GyrB. We prepared a new series of N-phenyl-4,5-dibromopyrrolamides and evaluated them against DNA gyrase and against the structurally and functionally similar enzyme, topoisomerase IV. The most active compound, 28, had an IC50 of 20 nM against Escherichia coli DNA gyrase. The IC50 values of 28 against Staphylococcus aureus DNA gyrase, and E. coli and S. aureus topoisomerase IV were in the low micromolar range. However, the compounds evaluated did not show significant antibacterial activities against selected Gram-positive and Gram-negative bacteria. Our results indicate that for potent inhibition of DNA gyrase, a combination of polar groups on the carboxylic end of the molecule and substituents that reach into the 'lipophilic floor' of the enzyme is required.
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Affiliation(s)
- Nace Zidar
- University of Ljubljana , Faculty of Pharmacy , Aškerčeva cesta 7 , 1000 Ljubljana , Slovenia . ; ; Tel: +386 1 4769578
| | - Helena Macut
- University of Ljubljana , Faculty of Pharmacy , Aškerčeva cesta 7 , 1000 Ljubljana , Slovenia . ; ; Tel: +386 1 4769578
| | - Tihomir Tomašič
- University of Ljubljana , Faculty of Pharmacy , Aškerčeva cesta 7 , 1000 Ljubljana , Slovenia . ; ; Tel: +386 1 4769578
| | - Lucija Peterlin Mašič
- University of Ljubljana , Faculty of Pharmacy , Aškerčeva cesta 7 , 1000 Ljubljana , Slovenia . ; ; Tel: +386 1 4769578
| | - Janez Ilaš
- University of Ljubljana , Faculty of Pharmacy , Aškerčeva cesta 7 , 1000 Ljubljana , Slovenia . ; ; Tel: +386 1 4769578
| | - Anamarija Zega
- University of Ljubljana , Faculty of Pharmacy , Aškerčeva cesta 7 , 1000 Ljubljana , Slovenia . ; ; Tel: +386 1 4769578
| | - Päivi Tammela
- Drug Research Program , Division of Pharmaceutical Biosciences , Faculty of Pharmacy , University of Helsinki , P.O. Box 56 (Viikinkaari 5 E) , Helsinki FI-00014 , Finland
| | - Danijel Kikelj
- University of Ljubljana , Faculty of Pharmacy , Aškerčeva cesta 7 , 1000 Ljubljana , Slovenia . ; ; Tel: +386 1 4769578
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23
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Stotani S, Gatta V, Medarametla P, Padmanaban M, Karawajczyk A, Giordanetto F, Tammela P, Laitinen T, Poso A, Tzalis D, Collina S. DPD-Inspired Discovery of Novel LsrK Kinase Inhibitors: An Opportunity To Fight Antimicrobial Resistance. J Med Chem 2019; 62:2720-2737. [PMID: 30786203 DOI: 10.1021/acs.jmedchem.9b00025] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Antibiotic resistance is posing a continuous threat to global public health and represents a huge burden for society as a whole. In the past decade, the interference with bacterial quorum sensing (QS) (i.e., cell-cell communication) mechanisms has extensively been investigated as a valid therapeutic approach in the pursuit of a next generation of antimicrobials. ( S)-4,5-Dihydroxy-2,3-pentanedione, commonly known as ( S)-DPD, a small signaling molecule that modulates QS in both Gram-negative and Gram-positive bacteria, is phosphorylated by LsrK, and the resulting phospho-DPD activates QS. We designed and prepared a small library of DPD derivatives, characterized by five different scaffolds, and evaluated their LsrK inhibition in the context of QS interference. SAR studies highlighted the pyrazole moiety as an essential structural element for LsrK inhibition. Particularly, four compounds were found to be micromolar LsrK inhibitors (IC50 ranging between 100 μM and 500 μM) encouraging further exploration of novel analogues as potential new antimicrobials.
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Affiliation(s)
- Silvia Stotani
- Department of Drug Sciences, Medicinal Chemistry and Pharmaceutical Technology Section , University of Pavia , Viale Taramelli 12 , 27100 Pavia , Italy.,Medicinal Chemistry , Taros Chemicals GmbH & Co. KG , Emil-Figge-Straße 76a , 44227 Dortmund , Germany
| | - Viviana Gatta
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy , University of Helsinki , FI-00014 Helsinki , Finland
| | - Prasanthi Medarametla
- School of Pharmacy, Faculty of Health Sciences , University of Eastern Finland , P.O. Box 1627, FI-70211 Kuopio , Finland
| | - Mohan Padmanaban
- Medicinal Chemistry , Taros Chemicals GmbH & Co. KG , Emil-Figge-Straße 76a , 44227 Dortmund , Germany
| | - Anna Karawajczyk
- Selvita S.A. , Park Life Science, Bobrzyňskiego 14 , 30-348 Krakow , Poland
| | - Fabrizio Giordanetto
- Medicinal Chemistry , Taros Chemicals GmbH & Co. KG , Emil-Figge-Straße 76a , 44227 Dortmund , Germany
| | - Päivi Tammela
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy , University of Helsinki , FI-00014 Helsinki , Finland
| | - Tuomo Laitinen
- School of Pharmacy, Faculty of Health Sciences , University of Eastern Finland , P.O. Box 1627, FI-70211 Kuopio , Finland
| | - Antti Poso
- School of Pharmacy, Faculty of Health Sciences , University of Eastern Finland , P.O. Box 1627, FI-70211 Kuopio , Finland
| | - Dimitros Tzalis
- Medicinal Chemistry , Taros Chemicals GmbH & Co. KG , Emil-Figge-Straße 76a , 44227 Dortmund , Germany
| | - Simona Collina
- Medicinal Chemistry , Taros Chemicals GmbH & Co. KG , Emil-Figge-Straße 76a , 44227 Dortmund , Germany
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24
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Tiz DB, Skok Ž, Durcik M, Tomašič T, Mašič LP, Ilaš J, Zega A, Draskovits G, Révész T, Nyerges Á, Pál C, Cruz CD, Tammela P, Žigon D, Kikelj D, Zidar N. An optimised series of substituted N-phenylpyrrolamides as DNA gyrase B inhibitors. Eur J Med Chem 2019; 167:269-290. [PMID: 30776691 DOI: 10.1016/j.ejmech.2019.02.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/18/2019] [Accepted: 02/01/2019] [Indexed: 10/27/2022]
Abstract
ATP competitive inhibitors of DNA gyrase and topoisomerase IV have great therapeutic potential, but none of the described synthetic compounds has so far reached the market. To optimise the activities and physicochemical properties of our previously reported N-phenylpyrrolamide inhibitors, we have synthesized an improved, chemically variegated selection of compounds and evaluated them against DNA gyrase and topoisomerase IV enzymes, and against selected Gram-positive and Gram-negative bacteria. The most potent compound displayed IC50 values of 6.9 nM against Escherichia coli DNA gyrase and 960 nM against Staphylococcus aureus topoisomerase IV. Several compounds displayed minimum inhibitory concentrations (MICs) against Gram-positive strains in the 1-50 μM range, one of which inhibited the growth of Enterococcus faecalis, Enterococcus faecium, S. aureus and Streptococcus pyogenes with MIC values of 1.56 μM, 1.56 μM, 0.78 μM and 0.72 μM, respectively. This compound has been investigated further on methicillin-resistant S. aureus (MRSA) and on ciprofloxacin non-susceptible and extremely drug resistant strain of S. aureus (MRSA VISA). It exhibited the MIC value of 2.5 μM on both strains, and MIC value of 32 μM against MRSA in the presence of inactivated human blood serum. Further studies are needed to confirm its mode of action.
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Affiliation(s)
- Davide Benedetto Tiz
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Žiga Skok
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Martina Durcik
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Tihomir Tomašič
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Lucija Peterlin Mašič
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Janez Ilaš
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Anamarija Zega
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Gábor Draskovits
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, H-6726, Hungary
| | - Tamás Révész
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, H-6726, Hungary
| | - Ákos Nyerges
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, H-6726, Hungary
| | - Csaba Pál
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), Helsinki, FI-00014, Finland
| | - Cristina D Cruz
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), Helsinki, FI-00014, Finland
| | - Päivi Tammela
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), Helsinki, FI-00014, Finland
| | - Dušan Žigon
- Jožef Stefan Institute, Department of Environmental Science, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Danijel Kikelj
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Nace Zidar
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia.
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25
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Lillsunde KE, Tomašič T, Schult P, Lohmann V, Kikelj D, Tammela P. Inhibition of Hepatitis C Replication by Targeting the Molecular Chaperone Hsp90: Synthesis and Biological Evaluation of 4,5,6,7-Tetrahydrobenzo[1,2-d]thiazole Derivatives. ChemMedChem 2019; 14:334-342. [PMID: 30548820 DOI: 10.1002/cmdc.201800724] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Indexed: 12/12/2022]
Abstract
Cellular chaperones that belong to the heat-shock protein 90 (Hsp90) family are a prerequisite for successful viral propagation for most viruses. The hepatitis C virus (HCV) uses Hsp90 for maturation, folding, and modification of viral proteins. Based on our previous discovery that marine alkaloid analogues with a 4,5,6,7-tetrahydrobenzo[1,2-d]thiazole-2-amine structure show inhibition of HCV replication and binding to Hsp90, a series of twelve novel compounds based on this scaffold was designed and synthesized. The aim was improved Hsp90 affinity and anti-HCV activity. Through structural optimization, improved binding to Hsp90 and specific HCV inhibition in genotype 1b and 2a replicon models was achieved for three compounds belonging to the newly synthesized series. Furthermore, these compounds efficiently inhibited replication of full-length HCV genotype 2a in a reporter virus RNA assay with IC50 values ranging from 0.03 to 0.6 μm.
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Affiliation(s)
- Katja-Emilia Lillsunde
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Tihomir Tomašič
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Philipp Schult
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Volker Lohmann
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Danijel Kikelj
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Päivi Tammela
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
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26
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Moreno-Cinos C, Sassetti E, Salado IG, Witt G, Benramdane S, Reinhardt L, Cruz CD, Joossens J, Van der Veken P, Brötz-Oesterhelt H, Tammela P, Winterhalter M, Gribbon P, Windshügel B, Augustyns K. α-Amino Diphenyl Phosphonates as Novel Inhibitors of Escherichia coli ClpP Protease. J Med Chem 2019; 62:774-797. [PMID: 30571121 DOI: 10.1021/acs.jmedchem.8b01466] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Increased Gram-negative bacteria resistance to antibiotics is becoming a global problem, and new classes of antibiotics with novel mechanisms of action are required. The caseinolytic protease subunit P (ClpP) is a serine protease conserved among bacteria that is considered as an interesting drug target. ClpP function is involved in protein turnover and homeostasis, stress response, and virulence among other processes. The focus of this study was to identify new inhibitors of Escherichia coli ClpP and to understand their mode of action. A focused library of serine protease inhibitors based on diaryl phosphonate warheads was tested for ClpP inhibition, and a chemical exploration around the hit compounds was conducted. Altogether, 14 new potent inhibitors of E. coli ClpP were identified. Compounds 85 and 92 emerged as most interesting compounds from this study due to their potency and, respectively, to its moderate but consistent antibacterial properties as well as the favorable cytotoxicity profile.
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Affiliation(s)
- Carlos Moreno-Cinos
- Laboratory of Medicinal Chemistry , University of Antwerp , Universiteitsplein 1 , B-2610 Antwerp , Belgium
| | - Elisa Sassetti
- Fraunhofer Institute for Molecular Biology and Applied Ecology, ScreeningPort , Schnackenburgallee 114 , 22525 Hamburg , Germany.,Department of Life Sciences and Chemistry , Jacobs University Bremen gGmbH , Campus Ring 1 , 28759 Bremen , Germany
| | - Irene G Salado
- Laboratory of Medicinal Chemistry , University of Antwerp , Universiteitsplein 1 , B-2610 Antwerp , Belgium
| | - Gesa Witt
- Fraunhofer Institute for Molecular Biology and Applied Ecology, ScreeningPort , Schnackenburgallee 114 , 22525 Hamburg , Germany
| | - Siham Benramdane
- Laboratory of Medicinal Chemistry , University of Antwerp , Universiteitsplein 1 , B-2610 Antwerp , Belgium
| | - Laura Reinhardt
- Interfaculty Institute for Microbiology and Infection Medicine , University of Tübingen , Auf der Morgenstelle 28 , 72076 Tübingen , Germany
| | - Cristina D Cruz
- Drug Research Program, Division of Pharmaceutical Biosciences , University of Helsinki , Viikinkaari 5E , FI-00014 Helsinki , Finland
| | - Jurgen Joossens
- Laboratory of Medicinal Chemistry , University of Antwerp , Universiteitsplein 1 , B-2610 Antwerp , Belgium
| | - Pieter Van der Veken
- Laboratory of Medicinal Chemistry , University of Antwerp , Universiteitsplein 1 , B-2610 Antwerp , Belgium
| | - Heike Brötz-Oesterhelt
- Interfaculty Institute for Microbiology and Infection Medicine , University of Tübingen , Auf der Morgenstelle 28 , 72076 Tübingen , Germany
| | - Päivi Tammela
- Drug Research Program, Division of Pharmaceutical Biosciences , University of Helsinki , Viikinkaari 5E , FI-00014 Helsinki , Finland
| | - Mathias Winterhalter
- Department of Life Sciences and Chemistry , Jacobs University Bremen gGmbH , Campus Ring 1 , 28759 Bremen , Germany
| | - Philip Gribbon
- Fraunhofer Institute for Molecular Biology and Applied Ecology, ScreeningPort , Schnackenburgallee 114 , 22525 Hamburg , Germany
| | - Björn Windshügel
- Fraunhofer Institute for Molecular Biology and Applied Ecology, ScreeningPort , Schnackenburgallee 114 , 22525 Hamburg , Germany
| | - Koen Augustyns
- Laboratory of Medicinal Chemistry , University of Antwerp , Universiteitsplein 1 , B-2610 Antwerp , Belgium
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27
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Bhat C, Ilina P, Tilli I, Voráčová M, Bruun T, Barba V, Hribernik N, Lillsunde KE, Mäki-Lohiluoma E, Rüffer T, Lang H, Yli-Kauhaluoma J, Kiuru P, Tammela P. Synthesis and Antiproliferative Activity of Marine Bromotyrosine Purpurealidin I and Its Derivatives. Mar Drugs 2018; 16:E481. [PMID: 30513862 PMCID: PMC6316490 DOI: 10.3390/md16120481] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 11/20/2018] [Accepted: 11/27/2018] [Indexed: 01/29/2023] Open
Abstract
The first total synthesis of the marine bromotyrosine purpurealidin I (1) using trifluoroacetoxy protection group and its dimethylated analog (29) is reported along with 16 simplified bromotyrosine derivatives lacking the tyramine moiety. Their cytotoxicity was evaluated against the human malignant melanoma cell line (A-375) and normal skin fibroblast cells (Hs27) together with 33 purpurealidin-inspired simplified amides, and the structure⁻activity relationships were investigated. The synthesized simplified analogs without the tyramine part retained the cytotoxic activity. Purpurealidin I (1) showed no selectivity but its simplified pyridin-2-yl derivative (36) had the best improvement in selectivity (Selectivity index 4.1). This shows that the marine bromotyrosines are promising scaffolds for developing cytotoxic agents and the full understanding of the elements of their SAR and improving the selectivity requires further optimization of simplified bromotyrosine derivatives.
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Affiliation(s)
- Chinmay Bhat
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, Viikinkaari 5 E (P.O. Box 56), University of Helsinki, FI-00014 Helsinki, Finland.
| | - Polina Ilina
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, Viikinkaari 5 E (P.O. Box 56), University of Helsinki, FI-00014 Helsinki, Finland.
| | - Irene Tilli
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, Viikinkaari 5 E (P.O. Box 56), University of Helsinki, FI-00014 Helsinki, Finland.
| | - Manuela Voráčová
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, Viikinkaari 5 E (P.O. Box 56), University of Helsinki, FI-00014 Helsinki, Finland.
| | - Tanja Bruun
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, Viikinkaari 5 E (P.O. Box 56), University of Helsinki, FI-00014 Helsinki, Finland.
| | - Victoria Barba
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, Viikinkaari 5 E (P.O. Box 56), University of Helsinki, FI-00014 Helsinki, Finland.
| | - Nives Hribernik
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, Viikinkaari 5 E (P.O. Box 56), University of Helsinki, FI-00014 Helsinki, Finland.
| | - Katja-Emilia Lillsunde
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, Viikinkaari 5 E (P.O. Box 56), University of Helsinki, FI-00014 Helsinki, Finland.
| | - Eero Mäki-Lohiluoma
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, Viikinkaari 5 E (P.O. Box 56), University of Helsinki, FI-00014 Helsinki, Finland.
| | - Tobias Rüffer
- Institute of Chemistry, Technische Universität Chemnitz, 09107 Chemnitz, Germany.
| | - Heinrich Lang
- Institute of Chemistry, Technische Universität Chemnitz, 09107 Chemnitz, Germany.
| | - Jari Yli-Kauhaluoma
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, Viikinkaari 5 E (P.O. Box 56), University of Helsinki, FI-00014 Helsinki, Finland.
| | - Paula Kiuru
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, Viikinkaari 5 E (P.O. Box 56), University of Helsinki, FI-00014 Helsinki, Finland.
| | - Päivi Tammela
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, Viikinkaari 5 E (P.O. Box 56), University of Helsinki, FI-00014 Helsinki, Finland.
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Medarametla P, Gatta V, Kajander T, Laitinen T, Tammela P, Poso A. Cover Feature: Structure-Based Virtual Screening of LsrK Kinase Inhibitors to Target Quorum Sensing (ChemMedChem 22/2018). ChemMedChem 2018. [DOI: 10.1002/cmdc.201800697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Prasanthi Medarametla
- School of Pharmacy; Faculty of Health Sciences; University of Eastern Finland; P.O. Box 1627 70211 Kuopio Finland
| | - Viviana Gatta
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy; University of Helsinki; P.O. Box 56 00014 Helsinki Finland
| | - Tommi Kajander
- Institute of Biotechnology; University of Helsinki; P.O. Box 65 00014 Helsinki Finland
| | - Tuomo Laitinen
- School of Pharmacy; Faculty of Health Sciences; University of Eastern Finland; P.O. Box 1627 70211 Kuopio Finland
| | - Päivi Tammela
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy; University of Helsinki; P.O. Box 56 00014 Helsinki Finland
| | - Antti Poso
- School of Pharmacy; Faculty of Health Sciences; University of Eastern Finland; P.O. Box 1627 70211 Kuopio Finland
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Cruz CD, Shah S, Tammela P. Defining conditions for biofilm inhibition and eradication assays for Gram-positive clinical reference strains. BMC Microbiol 2018; 18:173. [PMID: 30390625 PMCID: PMC6215609 DOI: 10.1186/s12866-018-1321-6] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 10/17/2018] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Biofilms are formed by a complex bacterial community encapsulated by a polymeric matrix, with strong adherent properties and persistent phenotype. Biofilms are considered one of the most challenging areas of modern medicine. Existing antibiotics have been developed against free-floating bacterial cells, and thus, many treatments of biofilm-related infection fail. In this study, we compared the effects of different media on biofilm growth of clinical reference strains of Staphylococci and Enterococci, including multi-drug resistant representatives. Further, we optimized the resazurin-based assay for determining the minimal biofilm inhibitory concentration (MBIC) of standard antibiotics, and evaluated its use for the determination of minimal biofilm eradication concentration (MBEC). RESULTS We showed that tryptic soy broth supplemented with 1% glucose was an optimal media for maximum biofilm growth of all strains tested, with an extended incubation time for Enterococci. A range of parameters were tested for the resazurin assay, including concentration, temperature and time of incubation. Using quality parameters to analyze the assay's performance, the conditions for the resazurin assay were set as follows: 4 μg/mL and 8 μg/mL, with incubation at 25 °C for 20 min and 40 min for Staphylococci and Enterococci, respectively. CONCLUSIONS In summary, we defined conditions for optimal biofilm growth and for standardized resazurin assay for MBIC determination against six Gram-positive clinical reference strains. We also observed that MBEC determination by the resazurin-based assay is limited due to the poor detection limit of the assay. Complementary cell counting data is needed for precise determination of MBEC.
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Affiliation(s)
- Cristina D Cruz
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, FI-00014 University of Helsinki, P.O. Box 56, Helsinki, Finland
| | - Shreya Shah
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, FI-00014 University of Helsinki, P.O. Box 56, Helsinki, Finland
| | - Päivi Tammela
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, FI-00014 University of Helsinki, P.O. Box 56, Helsinki, Finland.
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Medarametla P, Gatta V, Kajander T, Laitinen T, Tammela P, Poso A. Structure-Based Virtual Screening of LsrK Kinase Inhibitors to Target Quorum Sensing. ChemMedChem 2018; 13:2400-2407. [PMID: 30178912 DOI: 10.1002/cmdc.201800548] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Indexed: 11/06/2022]
Abstract
In the era of increased antibiotic resistance, targeting enzymes involved in bacterial communication (quorum sensing) represents a new strategy to fight bacterial infections. LsrK is a kinase responsible for the phosphorylation of autoinducer-2, a signaling molecule involved in quorum sensing. Inhibiting LsrK would lead to quorum sensing inactivation and interfere with the pathogenesis. In this study, we built the first LsrK 3D model and performed virtual screening of a locally available database. Selected compounds were tested against LsrK, and the analogue search conducted based on the positive hits led to the identification of low-micromolar LsrK inhibitors. These results prove the utility of the model and provide the first class of LsrK inhibitors to be further optimized as antivirulence agents.
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Affiliation(s)
- Prasanthi Medarametla
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, 70211, Kuopio, Finland
| | - Viviana Gatta
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, 00014, Helsinki, Finland
| | - Tommi Kajander
- Institute of Biotechnology, University of Helsinki, P.O. Box 65, 00014, Helsinki, Finland
| | - Tuomo Laitinen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, 70211, Kuopio, Finland
| | - Päivi Tammela
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, 00014, Helsinki, Finland
| | - Antti Poso
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, 70211, Kuopio, Finland
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31
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Ilina P, Ma X, Sintim HO, Tammela P. Miniaturized whole-cell bacterial bioreporter assay for identification of quorum sensing interfering compounds. J Microbiol Methods 2018; 154:40-45. [PMID: 30300658 DOI: 10.1016/j.mimet.2018.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 10/05/2018] [Accepted: 10/05/2018] [Indexed: 11/19/2022]
Abstract
The continuing emergence and spread of antibiotic-resistant bacteria is worrisome and new strategies to curb bacterial infections are being sought. The interference of bacterial quorum sensing (QS) signaling has been suggested as a prospective antivirulence strategy. The AI-2 QS system is present in multiple bacterial species and has been shown to be correlated with pathogenicity. To facilitate the discovery of novel compounds interfering with AI-2 QS, we established a high-throughput setup of whole-cell bioreporter assay, which can be performed in either 96- or 384-well format. Agonistic or antagonistic activities of the test compounds against Escherichia coli LsrB-type AI-2 QS system are monitored by measuring the level of β-galactosidase expression. A control strain expressing β-galactosidase in quorum sensing-independent manner is included into the assay for false-positive detection.
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Affiliation(s)
- Polina Ilina
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Xiaochu Ma
- Institute for Drug Discovery, Department of Chemistry, Purdue University Center for Cancer Research, Purdue University, United States
| | - Herman O Sintim
- Institute for Drug Discovery, Department of Chemistry, Purdue University Center for Cancer Research, Purdue University, United States
| | - Päivi Tammela
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland.
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Langat MK, Helfenstein A, Horner C, Tammela P, Hokkanen H, Izotov D, Mulholland DA. Pumilol, a Diterpenoid with a Rare Strobane Skeleton fromPinus pumila(Pinaceae). Chem Biodivers 2018; 15:e1800056. [DOI: 10.1002/cbdv.201800056] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Accepted: 07/02/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Moses K. Langat
- Natural Products Research Group; Department of Chemistry; Faculty of Engineering and Physical Sciences; University of Surrey; Guildford GU2 7XH UK
- School of Chemistry and Physics; University of KwaZulu-Natal; Durban 4041 South Africa
| | - Andreas Helfenstein
- Centre for Drug Research; Division of Pharmaceutical Biosciences; Faculty of Pharmacy; University of Helsinki; FI-00014 Helsinki Finland
| | - Claire Horner
- Natural Products Research Group; Department of Chemistry; Faculty of Engineering and Physical Sciences; University of Surrey; Guildford GU2 7XH UK
| | - Päivi Tammela
- Centre for Drug Research; Division of Pharmaceutical Biosciences; Faculty of Pharmacy; University of Helsinki; FI-00014 Helsinki Finland
| | - Heikki Hokkanen
- Department of Agricultural Sciences; University of Helsinki; FI-00014 Helsinki Finland
| | - Denis Izotov
- Sector of Biologically Active Substances; Department of Forestry; Far East Forestry Research Institute; Khabarovsk Vo-lochaevskaya 71 Russia
| | - Dulcie A. Mulholland
- Natural Products Research Group; Department of Chemistry; Faculty of Engineering and Physical Sciences; University of Surrey; Guildford GU2 7XH UK
- School of Chemistry and Physics; University of KwaZulu-Natal; Durban 4041 South Africa
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33
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Durcik M, Tammela P, Barančoková M, Tomašič T, Ilaš J, Kikelj D, Zidar N. Synthesis and Evaluation of N-Phenylpyrrolamides as DNA Gyrase B Inhibitors. ChemMedChem 2018; 13:186-198. [PMID: 29206345 DOI: 10.1002/cmdc.201700549] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 12/01/2017] [Indexed: 01/05/2023]
Abstract
ATP-competitive inhibitors of DNA gyrase and topoisomerase IV are among the most interesting classes of antibacterial drugs that are unrepresented in the antibacterial pipeline. We developed 32 new N-phenylpyrrolamides and evaluated them against DNA gyrase and topoisomerase IV from E. coli and Staphylococcus aureus. Antibacterial activities were studied against Gram-positive and Gram-negative bacterial strains. The most potent compound displayed an IC50 of 47 nm against E. coli DNA gyrase, and a minimum inhibitory concentration (MIC) of 12.5 μm against the Gram-positive Enterococcus faecalis. Some compounds displayed good antibacterial activities against an efflux-pump-deficient E. coli strain (MIC=6.25 μm) and against wild-type E. coli in the presence of efflux pump inhibitor PAβN (MIC=3.13 μm). Here we describe new findings regarding the structure-activity relationships of N-phenylpyrrolamide DNA gyrase B inhibitors and investigate the factors that are important for the antibacterial activity of this class of compounds.
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Affiliation(s)
- Martina Durcik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Päivi Tammela
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, Viikinkaari 5E, Helsinki, 00014, Finland
| | - Michaela Barančoková
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Tihomir Tomašič
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Janez Ilaš
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Danijel Kikelj
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Nace Zidar
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
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34
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Tomašič T, Barančoková M, Zidar N, Ilaš J, Tammela P, Kikelj D. Design, synthesis, and biological evaluation of 1-ethyl-3-(thiazol-2-yl)urea derivatives as Escherichia coli
DNA gyrase inhibitors. Arch Pharm (Weinheim) 2017; 351. [DOI: 10.1002/ardp.201700333] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 11/22/2017] [Accepted: 11/24/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Tihomir Tomašič
- Faculty of Pharmacy; University of Ljubljana; Ljubljana Slovenia
| | | | - Nace Zidar
- Faculty of Pharmacy; University of Ljubljana; Ljubljana Slovenia
| | - Janez Ilaš
- Faculty of Pharmacy; University of Ljubljana; Ljubljana Slovenia
| | - Päivi Tammela
- Division of Pharmaceutical Biosciences; Faculty of Pharmacy; University of Helsinki; Helsinki Finland
| | - Danijel Kikelj
- Faculty of Pharmacy; University of Ljubljana; Ljubljana Slovenia
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35
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Lillsunde KE, Tomašič T, Kikelj D, Tammela P. Marine alkaloid oroidin analogues with antiviral potential: A novel class of synthetic compounds targeting the cellular chaperone Hsp90. Chem Biol Drug Des 2017; 90:1147-1154. [DOI: 10.1111/cbdd.13034] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 01/30/2017] [Accepted: 05/15/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Katja-Emilia Lillsunde
- Division of Pharmaceutical Biosciences; Faculty of Pharmacy; University of Helsinki; Helsinki Finland
| | - Tihomir Tomašič
- Faculty of Pharmacy; University of Ljubljana; Ljubljana Slovenia
| | - Danijel Kikelj
- Faculty of Pharmacy; University of Ljubljana; Ljubljana Slovenia
| | - Päivi Tammela
- Division of Pharmaceutical Biosciences; Faculty of Pharmacy; University of Helsinki; Helsinki Finland
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Cotman AE, Trampuž M, Brvar M, Kikelj D, Ilaš J, Peterlin-Mašič L, Montalvão S, Tammela P, Frlan R. Design, Synthesis, and Evaluation of Novel Tyrosine-Based DNA Gyrase B Inhibitors. Arch Pharm (Weinheim) 2017. [PMID: 28621824 DOI: 10.1002/ardp.201700087] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The discovery and synthesis of new tyrosine-based inhibitors of DNA gyrase B (GyrB), which target its ATPase subunit, is reported. Twenty-four compounds were synthesized and evaluated for activity against DNA gyrase and DNA topoisomerase IV. The antibacterial properties of selected GyrB inhibitors were demonstrated by their activity against Staphylococcus aureus and Enterococcus faecalis in the low micromolar range. The most promising compounds, 8a and 13e, inhibited Escherichia coli and S. aureus GyrB with IC50 values of 40 and 30 µM. The same compound also inhibited the growth of S. aureus and E. faecalis with minimal inhibitory concentrations (MIC90 ) of 14 and 28 µg/mL, respectively.
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Affiliation(s)
- Andrej E Cotman
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia.,National Institute of Chemistry, Ljubljana, Slovenia
| | - Marko Trampuž
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia.,National Institute of Chemistry, Ljubljana, Slovenia
| | - Matjaž Brvar
- National Institute of Chemistry, Ljubljana, Slovenia
| | - Danijel Kikelj
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Janez Ilaš
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | | | - Sofia Montalvão
- Faculty of Pharmacy, Division of Pharmaceutical Biosciences, University of Helsinki, Helsinki, Finland
| | - Päivi Tammela
- Faculty of Pharmacy, Division of Pharmaceutical Biosciences, University of Helsinki, Helsinki, Finland
| | - Rok Frlan
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
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Salonen A, Virjamo V, Tammela P, Fauch L, Julkunen-Tiitto R. Screening bioactivity and bioactive constituents of Nordic unifloral honeys. Food Chem 2017; 237:214-224. [PMID: 28763988 DOI: 10.1016/j.foodchem.2017.05.085] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 04/04/2017] [Accepted: 05/15/2017] [Indexed: 12/01/2022]
Abstract
The objective of this study was to screen the antibacterial and antioxidant activity of thirty nine honey samples from Finland, Sweden, Norway and Denmark. Their physicochemical properties were analysed, antioxidant activity was evaluated by DPPH assay and antibacterial activity against Pseudomonas aeruginosa and Staphylococcus aureus was assessed by microdilution assay. The honey samples obtained were buckwheat, caraway, clover, dandelion, fireweed, heather, lime tree, lingonberry, rape, raspberry, sweet clover, willow, mire, honeydew and polyfloral. Eleven honey samples showed high antioxidant activity. With 15% honey dilution, three unifloral honeys had over 85% inhibition against growth of P. aeruginosa and ten honey samples against S. aureus. The buckwheat, raspberry and honeydew honeys showed the highest antibacterial and antioxidant activity. An unexpectedly high amount of methylglyoxal was found in mire and forest honeys. Some phenolic compounds are shown to be plant species-specific floral markers due to their appearance in specific unifloral honey samples.
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Affiliation(s)
- Anneli Salonen
- Natural Product Research Laboratories, Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 111, 80110 Joensuu, Finland.
| | - Virpi Virjamo
- Natural Product Research Laboratories, Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 111, 80110 Joensuu, Finland.
| | - Päivi Tammela
- Centre for Drug Research (CDR), Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland.
| | - Laure Fauch
- Natural Product Research Laboratories, Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 111, 80110 Joensuu, Finland.
| | - Riitta Julkunen-Tiitto
- Natural Product Research Laboratories, Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 111, 80110 Joensuu, Finland.
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Bonabi A, Cito S, Tammela P, Jokinen V, Sikanen T. Fabrication of concave micromirrors for single cell imaging via controlled over-exposure of organically modified ceramics in single step lithography. Biomicrofluidics 2017; 11:034118. [PMID: 28652888 PMCID: PMC5468119 DOI: 10.1063/1.4985653] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 05/31/2017] [Indexed: 06/01/2023]
Abstract
This work describes the fabrication of concave micromirrors to improve the sensitivity of fluorescence imaging, for instance, in single cell analysis. A new approach to fabrication of tunable round (concave) cross-sectional shaped microchannels out of the inorganic-organic hybrid polymer, Ormocomp®, via single step optical lithography was developed and validated. The concave micromirrors were implemented by depositing and patterning thin films of aluminum on top of the concave microchannels. The round cross-sectional shape was due to residual layer formation, which is inherent to Ormocomp® upon UV exposure in the proximity mode. We show that it is possible to control the residual layer thickness and thus the curved shape of the microchannel cross-sectional profile and eventually the focal length of the micromirror, by simply adjusting the UV exposure dose and the distance of the proximity gap (to the photomask). In general, an increase in the exposure dose or in the distance of the proximity gap results in a thicker residual layer and thus an increase in the radius of the microchannel curvature. Under constant exposure conditions, the radius of curvature is almost linearly dependent on the microchannel aspect ratio, i.e., the width (here, 20-200 μm) and the depth (here, 15-45 μm). Depending on the focal length, up to 8-fold signal enhancement over uncoated, round Ormocomp® microchannels was achieved in single cell imaging with the help of the converging micromirrors in an epifluorescence microscopy configuration.
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Affiliation(s)
- A Bonabi
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - S Cito
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - P Tammela
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - V Jokinen
- Department of Materials Science and Engineering, School of Chemical Technology, Aalto University, Espoo, Finland
| | - T Sikanen
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
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Helfenstein A, Tammela P. Analyzing user-generated online content for drug discovery: development and use of MedCrawler. Bioinformatics 2017; 33:1205-1209. [PMID: 28011767 DOI: 10.1093/bioinformatics/btw782] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 12/07/2016] [Indexed: 11/13/2022] Open
Abstract
Motivation Ethnopharmacology, or the scientific validation of traditional medicine, is a respected starting point in drug discovery. Home remedies and traditional use of plants are still widespread, also in Western societies. Instead of perusing ancient pharmacopeias, we developed MedCrawler, which we used to analyze blog posts for mentions of home remedies and their applications. This method is free and accessible from the office computer. Results We developed MedCrawler, a data mining tool for analyzing user-generated blog posts aiming to find modern 'traditional' medicine or home remedies. It searches user-generated blog posts and analyzes them for correlations between medically relevant terms. We also present examples and show that this method is capable of delivering both scientifically validated uses as well as not so well documented applications, which might serve as a starting point for follow-up research. Availability and Implementation Source code is available on GitHub at {{ https://github.com/a-hel/medcrawler }}. Contact paivi.tammela@helsinki.fi. Supplementary information Supplementary data are available at Bioinformatics online.
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Tomašič T, Mirt M, Barančoková M, Ilaš J, Zidar N, Tammela P, Kikelj D. Design, synthesis and biological evaluation of 4,5-dibromo-N-(thiazol-2-yl)-1H-pyrrole-2-carboxamide derivatives as novel DNA gyrase inhibitors. Bioorg Med Chem 2017; 25:338-349. [DOI: 10.1016/j.bmc.2016.10.038] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 10/27/2016] [Accepted: 10/29/2016] [Indexed: 11/25/2022]
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Hakkarainen T, Koivuniemi R, Kosonen M, Escobedo-Lucea C, Sanz-Garcia A, Vuola J, Valtonen J, Tammela P, Mäkitie A, Luukko K, Yliperttula M, Kavola H. Nanofibrillar cellulose wound dressing in skin graft donor site treatment. J Control Release 2016; 244:292-301. [DOI: 10.1016/j.jconrel.2016.07.053] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 07/20/2016] [Accepted: 07/29/2016] [Indexed: 12/11/2022]
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Sjöstedt N, Holvikari K, Tammela P, Kidron H. Inhibition of Breast Cancer Resistance Protein and Multidrug Resistance Associated Protein 2 by Natural Compounds and Their Derivatives. Mol Pharm 2016; 14:135-146. [DOI: 10.1021/acs.molpharmaceut.6b00754] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Noora Sjöstedt
- Centre for Drug Research, Division of Pharmaceutical
Biosciences, Faculty of Pharmacy, University of Helsinki, P.O, Box 56, Viikinkaari 5E, FI-00014 Helsinki, Finland
| | - Kira Holvikari
- Centre for Drug Research, Division of Pharmaceutical
Biosciences, Faculty of Pharmacy, University of Helsinki, P.O, Box 56, Viikinkaari 5E, FI-00014 Helsinki, Finland
| | - Päivi Tammela
- Centre for Drug Research, Division of Pharmaceutical
Biosciences, Faculty of Pharmacy, University of Helsinki, P.O, Box 56, Viikinkaari 5E, FI-00014 Helsinki, Finland
| | - Heidi Kidron
- Centre for Drug Research, Division of Pharmaceutical
Biosciences, Faculty of Pharmacy, University of Helsinki, P.O, Box 56, Viikinkaari 5E, FI-00014 Helsinki, Finland
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43
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Helfenstein A, Vahermo M, Nawrot DA, Demirci F, İşcan G, Krogerus S, Yli-Kauhaluoma J, Moreira VM, Tammela P. Antibacterial profiling of abietane-type diterpenoids. Bioorg Med Chem 2016; 25:132-137. [PMID: 27793449 DOI: 10.1016/j.bmc.2016.10.019] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 10/14/2016] [Accepted: 10/15/2016] [Indexed: 11/29/2022]
Abstract
Abietic and dehydroabietic acid are interesting diterpenes with a highly diverse repertoire of associated bioactivities. They have, among others, shown antibacterial and antifungal activity, potentially valuable in the struggle against the increasing antimicrobial resistance and imminent antibiotic shortage. In this paper, we describe the synthesis of a set of 9 abietic and dehydroabietic acid derivatives containing amino acid side chains and their in vitro antimicrobial profiling against a panel of human pathogenic microbial strains. Furthermore, their in vitro cytotoxicity against mammalian cells was evaluated. The experimental results showed that the most promising compound was 10 [methyl N-(abiet-8,11,13-trien-18-yl)-d-serinate], with an MIC90 of 60μg/mL against Staphylococcus aureus ATCC 25923, and 8μg/mL against methicillin-resistant S. aureus, Staphylococcus epidermidis and Streptococcus mitis. The IC50 value for compound 10 against Balb/c 3T3 cells was 45μg/mL.
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Affiliation(s)
- Andreas Helfenstein
- Centre for Drug Research, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, Viikinkaari 5 E (PO Box 56), FI-00014 University of Helsinki, Helsinki, Finland
| | - Mikko Vahermo
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, Viikinkaari 5 E (PO Box 56), FI-00014 University of Helsinki, Helsinki, Finland
| | - Dorota A Nawrot
- Centre for Drug Research, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, Viikinkaari 5 E (PO Box 56), FI-00014 University of Helsinki, Helsinki, Finland
| | - Fatih Demirci
- Pharmacognosy Department, Faculty of Pharmacy, Anadolu University, 26470 Eskişehir, Turkey
| | - Gökalp İşcan
- Pharmacognosy Department, Faculty of Pharmacy, Anadolu University, 26470 Eskişehir, Turkey
| | - Sara Krogerus
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, Viikinkaari 5 E (PO Box 56), FI-00014 University of Helsinki, Helsinki, Finland
| | - Jari Yli-Kauhaluoma
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, Viikinkaari 5 E (PO Box 56), FI-00014 University of Helsinki, Helsinki, Finland
| | - Vânia M Moreira
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, Viikinkaari 5 E (PO Box 56), FI-00014 University of Helsinki, Helsinki, Finland.
| | - Päivi Tammela
- Centre for Drug Research, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, Viikinkaari 5 E (PO Box 56), FI-00014 University of Helsinki, Helsinki, Finland.
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44
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Febles M, Montalvão S, Crespín GD, Norte M, Padrón JM, Tammela P, Fernández JJ, Daranas AH. Synthesis and biological evaluation of crown ether acyl derivatives. Bioorg Med Chem Lett 2016; 26:5591-5593. [PMID: 27765506 DOI: 10.1016/j.bmcl.2016.09.066] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 09/26/2016] [Accepted: 09/27/2016] [Indexed: 11/29/2022]
Abstract
A set of crown ethyl acyl derivatives based on 18-crown-6 moiety was synthesized and evaluated for biological activity. In vitro antiproliferative profiling demonstrated significant activities against HBL-100, HeLa, SW1573 and WiDr human cell lines. The most active compound exhibited GI50 values in the range of 3.7-5.6μM. Antimicrobial evaluation showed that three polyaromatic compounds were active against Staphylococcus aureus (MIC90 values from 8.3μM to 50μM), whereas a (decyloxy)benzene substitution exhibited moderate activity against Candida albicans (MIC90 values 36μM). According to SAR evaluation, the size of the crown ether and the acyl side chain had a significant effect on the bioactivity. Aromatic moieties close to the acyl group led to improved bioactivity as exemplified by some of the tested compounds. These results provide further evidence on the potential of crown ethyl structure as a scaffold for developing new biological probes and lead candidates for drug development.
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Affiliation(s)
- Martín Febles
- Instituto Universitario de Bio-Organica Antonio Gonzalez (IUBO AG), Universidad de La Laguna, Avenida Francisco Sánchez 2, 38205 La Laguna, Spain
| | - Sofía Montalvão
- Centre for Drug Research, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, PO Box 56, FI-00014 University of Helsinki, Finland
| | - Guillermo Díaz Crespín
- Instituto Universitario de Bio-Organica Antonio Gonzalez (IUBO AG), Universidad de La Laguna, Avenida Francisco Sánchez 2, 38205 La Laguna, Spain
| | - Manuel Norte
- Instituto Universitario de Bio-Organica Antonio Gonzalez (IUBO AG), Universidad de La Laguna, Avenida Francisco Sánchez 2, 38205 La Laguna, Spain
| | - José M Padrón
- Instituto Universitario de Bio-Organica Antonio Gonzalez (IUBO AG), Universidad de La Laguna, Avenida Francisco Sánchez 2, 38205 La Laguna, Spain
| | - Päivi Tammela
- Centre for Drug Research, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, PO Box 56, FI-00014 University of Helsinki, Finland.
| | - José J Fernández
- Instituto Universitario de Bio-Organica Antonio Gonzalez (IUBO AG), Universidad de La Laguna, Avenida Francisco Sánchez 2, 38205 La Laguna, Spain.
| | - Antonio Hernández Daranas
- Instituto Universitario de Bio-Organica Antonio Gonzalez (IUBO AG), Universidad de La Laguna, Avenida Francisco Sánchez 2, 38205 La Laguna, Spain.
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45
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Gjorgjieva M, Tomašič T, Barančokova M, Katsamakas S, Ilaš J, Tammela P, Peterlin Mašič L, Kikelj D. Discovery of Benzothiazole Scaffold-Based DNA Gyrase B Inhibitors. J Med Chem 2016; 59:8941-8954. [DOI: 10.1021/acs.jmedchem.6b00864] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Marina Gjorgjieva
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Tihomir Tomašič
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Michaela Barančokova
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Sotirios Katsamakas
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
- Department
of Pharmaceutical Chemistry, School of Pharmacy, Faculty of Health
Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Janez Ilaš
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Päivi Tammela
- Division
of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014 Helsinki, Finland
| | | | - Danijel Kikelj
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
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46
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Zidar N, Tomašič T, Macut H, Sirc A, Brvar M, Montalvão S, Tammela P, Ilaš J, Kikelj D. New N-phenyl-4,5-dibromopyrrolamides and N-Phenylindolamides as ATPase inhibitors of DNA gyrase. Eur J Med Chem 2016; 117:197-211. [PMID: 27100032 DOI: 10.1016/j.ejmech.2016.03.079] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 02/25/2016] [Accepted: 03/26/2016] [Indexed: 12/26/2022]
Abstract
Following the withdrawal of novobiocin, the introduction of a new ATPase inhibitor of DNA gyrase to the clinic would add the first representative of this mechanistic class to the antibacterial pipeline. This would be of great importance because of the well-known problems associated with antibacterial resistance. Using structure-based design and starting from the recently determined crystal structure of the N-phenyl-4,5-dibromopyrrolamide inhibitor-DNA gyrase B complex, we have prepared 28 new N-phenyl-4,5-dibromopyrrolamides and N-phenylindolamides and evaluated them against DNA gyrase from Escherichia coli. The most potent compound was 2-((4-(4,5-dibromo-1H-pyrrole-2-carboxamido)phenyl)amino)-2-oxoacetic acid (9a), with an IC50 of 0.18 μM against E. coli gyrase. A selected set of compounds was evaluated against DNA gyrase from Staphylococcus aureus and against topoisomerase IV from E. coli and S. aureus, but the activities were weaker. The binding affinity of 2-((4-(4,5-dibromo-1H-pyrrole-2-carboxamido)phenyl)amino)-2-oxoacetic acid (9a) to E. coli gyrase was studied using surface plasmon resonance. In the design of the present series, the focus was on the optimisation of biological activities of compounds - especially by varying their size, the position and orientation of key functional groups, and their acid-base properties. The structure-activity relationship (SAR) was examined and the results were rationalised with molecular docking.
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Affiliation(s)
- Nace Zidar
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia.
| | - Tihomir Tomašič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Helena Macut
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Anja Sirc
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Matjaž Brvar
- National Institute of Chemistry, Laboratory for Biocomputing and Bioinformatics, 1001 Ljubljana, Slovenia
| | - Sofia Montalvão
- Centre for Drug Research, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), FI-00014 Helsinki, Finland
| | - Päivi Tammela
- Centre for Drug Research, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), FI-00014 Helsinki, Finland
| | - Janez Ilaš
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Danijel Kikelj
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
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47
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Järvinen P, Nybond S, Marcourt L, Ferreira Queiroz E, Wolfender JL, Mettälä A, Karp M, Vuorela H, Vuorela P, Hatakka A, Tammela P. Cell-based bioreporter assay coupled to HPLC micro-fractionation in the evaluation of antimicrobial properties of the basidiomycete fungus Pycnoporus cinnabarinus. Pharm Biol 2016; 54:1108-1115. [PMID: 26808592 DOI: 10.3109/13880209.2015.1103754] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
CONTEXT Identification of bioactive components from complex natural product extracts can be a tedious process that aggravates the use of natural products in drug discovery campaigns. OBJECTIVE This study presents a new approach for screening antimicrobial potential of natural product extracts by employing a bioreporter assay amenable to HPLC-based activity profiling. MATERIALS AND METHODS A library of 116 crude extracts was prepared from fungal culture filtrates by liquid-liquid extraction with ethyl acetate, lyophilised, and screened against Escherichia coli using TLC bioautography. Active extracts were studied further with a broth microdilution assay, which was, however, too insensitive for identifying the active microfractions after HPLC separation. Therefore, an assay based on bioluminescent E. coli K-12 (pTetLux1) strain was coupled with HPLC micro-fractionation. RESULTS Preliminary screening yielded six fungal extracts with potential antimicrobial activity. A crude extract from a culture filtrate of the wood-rotting fungus, Pycnoporus cinnabarinus (Jacq.) P. Karst. (Polyporaceae), was selected for evaluating the functionality of the bioreporter assay in HPLC-based activity profiling. In the bioreporter assay, the IC50 value for the crude extract was 0.10 mg/mL. By integrating the bioreporter assay with HPLC micro-fractionation, the antimicrobial activity was linked to LC-UV peak of a compound in the chromatogram of the extract. This compound was isolated and identified as a fungal pigment phlebiarubrone. DISCUSSION AND CONCLUSION HPLC-based activity profiling using the bioreporter-based approach is a valuable tool for identifying antimicrobial compound(s) from complex crude extracts, and offers improved sensitivity and speed compared with traditional antimicrobial assays, such as the turbidimetric measurement.
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Affiliation(s)
- Päivi Järvinen
- a Centre for Drug Research, Division of Pharmaceutical Biosciences, Faculty of Pharmacy , University of Helsinki , Helsinki , Finland
- b Department of Food and Environmental Sciences, Faculty of Agriculture and Forestry , University of Helsinki , Helsinki , Finland
| | - Susanna Nybond
- a Centre for Drug Research, Division of Pharmaceutical Biosciences, Faculty of Pharmacy , University of Helsinki , Helsinki , Finland
| | - Laurence Marcourt
- c School of Pharmaceutical Sciences, EPGL , University of Geneva, University of Lausanne , Geneva , Switzerland
| | - Emerson Ferreira Queiroz
- c School of Pharmaceutical Sciences, EPGL , University of Geneva, University of Lausanne , Geneva , Switzerland
| | - Jean-Luc Wolfender
- c School of Pharmaceutical Sciences, EPGL , University of Geneva, University of Lausanne , Geneva , Switzerland
| | - Aila Mettälä
- b Department of Food and Environmental Sciences, Faculty of Agriculture and Forestry , University of Helsinki , Helsinki , Finland
| | - Matti Karp
- d Department of Chemistry and Bioengineering , Tampere University of Technology , Tampere , Finland
| | - Heikki Vuorela
- e Pharmaceutical Biology, Division of Pharmaceutical Biosciences, Faculty of Pharmacy , University of Helsinki , Helsinki , Finland
| | - Pia Vuorela
- e Pharmaceutical Biology, Division of Pharmaceutical Biosciences, Faculty of Pharmacy , University of Helsinki , Helsinki , Finland
| | - Annele Hatakka
- b Department of Food and Environmental Sciences, Faculty of Agriculture and Forestry , University of Helsinki , Helsinki , Finland
| | - Päivi Tammela
- a Centre for Drug Research, Division of Pharmaceutical Biosciences, Faculty of Pharmacy , University of Helsinki , Helsinki , Finland
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48
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Montalvão S, Leino TO, Kiuru PS, Lillsunde KE, Yli-Kauhaluoma J, Tammela P. Synthesis and Biological Evaluation of 2-Aminobenzothiazole and Benzimidazole Analogs Based on the Clathrodin Structure. Arch Pharm (Weinheim) 2015; 349:137-49. [PMID: 26709468 DOI: 10.1002/ardp.201500365] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 11/24/2015] [Accepted: 11/26/2015] [Indexed: 11/09/2022]
Abstract
A series of 2-aminobenzothiazole and benzimidazole analogs based on the clathrodin scaffold was synthesized and investigated for their antimicrobial and antiproliferative activities as well as for their effects in hepatitis C virus (HCV) replicon model. Compound 7, derived from 2-aminobenzothiazole, exhibited moderate antimicrobial activity only against the Gram-positive bacterium, Enterococcus faecalis. In the antiviral assay, compounds 4d and 7 were found to suppress the HCV replicon by >70%, but also to exhibit cytotoxicity against the host cells (35 and 44%, respectively). Compounds 4a and 7 demonstrated good activity in the antiproliferative assays on the human melanoma cell line A-375. To assess the selectivity of the effects between cancerous and noncancerous cells, a mouse fibroblast cell line was used. The IC50 values for compound 7 against the melanoma cell line A-375 and the fibroblast cell line BALB/c 3T3 were 16 and 71 µM, respectively, yielding fourfold selectivity toward the cancer cell line. These results suggest that compound 7 should be studied further in order to fully explore its potential for drug development.
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Affiliation(s)
- Sofia Montalvão
- Centre for Drug Research, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Teppo O Leino
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Paula S Kiuru
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Katja-Emilia Lillsunde
- Centre for Drug Research, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Jari Yli-Kauhaluoma
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Päivi Tammela
- Centre for Drug Research, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
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49
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Gutiérrez-Cepeda A, Fernández JJ, Norte M, Montalvão S, Tammela P, Souto ML. Acetate-Derived Metabolites from the Brown Alga Lobophora variegata. J Nat Prod 2015; 78:1716-22. [PMID: 26126835 DOI: 10.1021/acs.jnatprod.5b00415] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Seven new nonadecaketides (1-7), lobophorols A-C, lobophopyranones A and B, and lobophorones A and B, along with the first naturally occurring related metabolites (8-10), were isolated from specimens of Lobophora variegata collected from the Canary Islands. Their structures were determined by extensive spectroscopic methods. In addition, an insight into the biosynthesis of these compounds on the basis of the involvement of type III polyketide synthases is proposed. Lobophorol A (1) showed significant antibacterial activity against Staphylococcus aureus.
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Affiliation(s)
- Adrián Gutiérrez-Cepeda
- †Institute for Bio-Organic Chemistry "Antonio González", Center for Biomedical Research of the Canary Islands (CIBICAN), Department of Organic Chemistry, University of La Laguna, 38206 La Laguna, Tenerife, Spain
| | - José J Fernández
- †Institute for Bio-Organic Chemistry "Antonio González", Center for Biomedical Research of the Canary Islands (CIBICAN), Department of Organic Chemistry, University of La Laguna, 38206 La Laguna, Tenerife, Spain
| | - Manuel Norte
- †Institute for Bio-Organic Chemistry "Antonio González", Center for Biomedical Research of the Canary Islands (CIBICAN), Department of Organic Chemistry, University of La Laguna, 38206 La Laguna, Tenerife, Spain
| | - Sofia Montalvão
- §Centre for Drug Research, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014 Helsinki, Finland
| | - Päivi Tammela
- §Centre for Drug Research, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014 Helsinki, Finland
| | - María L Souto
- †Institute for Bio-Organic Chemistry "Antonio González", Center for Biomedical Research of the Canary Islands (CIBICAN), Department of Organic Chemistry, University of La Laguna, 38206 La Laguna, Tenerife, Spain
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50
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Zidar N, Macut H, Tomašič T, Brvar M, Montalvão S, Tammela P, Solmajer T, Peterlin Mašič L, Ilaš J, Kikelj D. N-Phenyl-4,5-dibromopyrrolamides and N-Phenylindolamides as ATP Competitive DNA Gyrase B Inhibitors: Design, Synthesis, and Evaluation. J Med Chem 2015; 58:6179-94. [PMID: 26126187 DOI: 10.1021/acs.jmedchem.5b00775] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Bacterial DNA gyrase is a well-known and validated target in the design of antibacterial drugs. However, inhibitors of its ATP binding subunit, DNA gyrase B (GyrB), have so far not reached clinical use. In the present study, three different series of N-phenyl-4,5-dibromopyrrolamides and N-phenylindolamides were designed and prepared as potential DNA gyrase B inhibitors. The IC50 values of compounds on DNA gyrase from Escherichia coli were in the low micromolar range, with the best compound, (4-(4,5-dibromo-1H-pyrrole-2-carboxamido)benzoyl)glycine (18a), displaying an IC50 of 450 nM. For this compound, a high-resolution crystal structure in complex with E. coli DNA gyrase B was obtained, revealing details of its binding mode within the active site. The binding affinities of three compounds with GyrB were additionally evaluated by surface plasmon resonance, and the results were in good agreement with the determined enzymatic activities. For the most promising compounds, the inhibitory activities against DNA gyrase from Staphylococcus aureus and topoisomerases IV from E. coli and S. aureus were determined. Antibacterial activities of the most potent compounds of each series were evaluated against two Gram-positive and two Gram-negative bacterial strains. The results obtained in this study provide valuable information on the binding mode and structure-activity relationship of N-phenyl-4,5-dibromopyrrolamides and N-phenylindolamides as promising classes of ATP competitive GyrB inhibitors.
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Affiliation(s)
- Nace Zidar
- †Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Helena Macut
- †Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Tihomir Tomašič
- †Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Matjaž Brvar
- ‡National Institute of Chemistry, Laboratory for Biocomputing and Bioinformatics, 1001 Ljubljana, Slovenia
| | - Sofia Montalvão
- §Centre for Drug Research, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), Helsinki FI-00014, Finland
| | - Päivi Tammela
- §Centre for Drug Research, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), Helsinki FI-00014, Finland
| | - Tom Solmajer
- ‡National Institute of Chemistry, Laboratory for Biocomputing and Bioinformatics, 1001 Ljubljana, Slovenia
| | - Lucija Peterlin Mašič
- †Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Janez Ilaš
- †Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Danijel Kikelj
- †Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
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