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Kugarajah V, Nisha KN, Jayakumar R, Sahabudeen S, Ramakrishnan P, Mohamed SB. Significance of microbial genome in environmental remediation. Microbiol Res 2023; 271:127360. [PMID: 36931127 DOI: 10.1016/j.micres.2023.127360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/27/2023] [Accepted: 03/08/2023] [Indexed: 03/11/2023]
Abstract
Environmental pollutants seriously threaten the ecosystem and health of various life forms, particularly with the rapid industrialization and emerging population. Conventionally physical and chemical strategies are being opted for the removal of these pollutants. Bioremediation, through several advancements, has been a boon to combat the existing threat faced today. Microbes with enzymes degrade various pollutants and utilize them as a carbon and energy source. With the existing demand and through several research explorations, Genetically Engineered Microorganisms (GEMs) have paved to be a successful approach to abate pollution through bioremediation. The genome of the microbe determines its biodegradative nature. Thus, methods including pure culture techniques and metagenomics are used for analyzing the genome of microbes, which provides information about catabolic genes. The information obtained along with the aid of biotechnology helps to construct GEMs that are cost-effective and safer thereby exhibiting higher degradation of pollutants. The present review focuses on the role of microbes in the degradation of environmental pollutants, role of evolution in habitat and adaptation of microbes, microbial degenerative genes, their pathways, and the efficacy of recombinant DNA (rDNA) technology for creating GEMs for bioremediation. The present review also provides a gist of existing GEMs for bioremediation and their limitations, thereby providing a future scope of implementation of these GEMs for a sustainable environment.
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Affiliation(s)
- Vaidhegi Kugarajah
- Department of Nanobiomaterials, Institute for Biomedical Engineering, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai 602015, India
| | | | - R Jayakumar
- Department of Nanobiomaterials, Institute for Biomedical Engineering, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai 602015, India
| | - S Sahabudeen
- Department of Biotechnology, SRM Institute of Science and Technology, Kanchipuram Dist, Kattankulathur, Tamil Nadu, India; Medical Team, Doctoral Institute for Evidence Based Policy, Tokyo, Japan
| | - P Ramakrishnan
- Department of Nanobiomaterials, Institute for Biomedical Engineering, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai 602015, India.
| | - S B Mohamed
- Department of Materials Science, School of Technology, Central University of Tamil Nadu, Thiruvarur 610005, Tamil Nadu, India.
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Zhou C, Li C, Cui H, Lin L. Metabolomics insights into the potential of encapsulated essential oils as multifunctional food additives. Crit Rev Food Sci Nutr 2022; 64:5143-5160. [PMID: 36454059 DOI: 10.1080/10408398.2022.2151974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Growing consumer concern about foodborne disease outbreaks and health risks associated with chemical additives has propelled the usage of essential oils (EOs) as novel food additives, but are limited by instability. In this regard, a series of EOs nano/micro-capsules have been widely used to enhance their stability and improve food quality. However, classical food quality assessment methods are insufficient to fully characterize the effects of encapsulated EOs on food properties, including physical, biochemical, organoleptic, and microbial changes. Recently, the rapid development of high-throughput sequencing is accelerating the application of metabolomics in food safety and quality analysis. This review seeks to present the most recent achievements in the application of non-targeted metabolomics to identify and quantify the overall metabolite profile associated with food quality, which can guide the development of emerging food preservation technologies. The scientific findings confirm that metabolomics opens up exciting prospects for biomarker screening in food preservation and contributes to an in-depth understanding of the mechanisms of action (MoA) of EOs. Future research should focus on constructing food quality assessment criteria based on multi-omics technologies, which will drive the standardization and commercialization of EOs for food industry applications.
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Affiliation(s)
- Changqian Zhou
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Changzhu Li
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, China
| | - Haiying Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Lin Lin
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, China
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Rojas-Hucks S, Rodriguez-Jorquera IA, Nimpstch J, Bahamonde P, Benavides JA, Chiang G, Pulgar J, Galbán-Malagón CJ. South American National Contributions to Knowledge of the Effects of Endocrine Disrupting Chemicals in Wild Animals: Current and Future Directions. TOXICS 2022; 10:toxics10120735. [PMID: 36548568 PMCID: PMC9781241 DOI: 10.3390/toxics10120735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/28/2022] [Accepted: 11/02/2022] [Indexed: 05/28/2023]
Abstract
Human pressure due to industrial and agricultural development has resulted in a biodiversity crisis. Environmental pollution is one of its drivers, including contamination of wildlife by chemicals emitted into the air, soil, and water. Chemicals released into the environment, even at low concentrations, may pose a negative effect on organisms. These chemicals might modify the synthesis, metabolism, and mode of action of hormones. This can lead to failures in reproduction, growth, and development of organisms potentially impacting their fitness. In this review, we focused on assessing the current knowledge on concentrations and possible effects of endocrine disruptor chemicals (metals, persistent organic pollutants, and others) in studies performed in South America, with findings at reproductive and thyroid levels. Our literature search revealed that most studies have focused on measuring the concentrations of compounds that act as endocrine disruptors in animals at the systemic level. However, few studies have evaluated the effects at a reproductive level, while information at thyroid disorders is scarce. Most studies have been conducted in fish by researchers from Brazil, Argentina, Chile, and Colombia. Comparison of results across studies is difficult due to the lack of standardization of units in the reported data. Future studies should prioritize research on emergent contaminants, evaluate effects on native species and the use of current available methods such as the OMICs. Additionally, there is a primary focus on organisms related to aquatic environments, and those inhabiting terrestrial environments are scarce or nonexistent. Finally, we highlight a lack of funding at a national level in the reviewed topic that may influence the observed low scientific productivity in several countries, which is often negatively associated with their percentage of protected areas.
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Affiliation(s)
- Sylvia Rojas-Hucks
- Departamento de Ecología y Biodiversidad, Facultad Ciencias de la Vida, Universidad Andres Bello, República 440, Santiago 8370134, Chile
| | | | - Jorge Nimpstch
- Facultad de Ciencias, Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia 5090000, Chile
| | - Paulina Bahamonde
- Laboratory of Aquatic Environmental Research, Centro de Estudios Avanzados—HUB Ambiental UPLA, Universidad de Playa Ancha, Valparaíso 2360004, Chile
- Millennium Nucleus of Austral Invasive Salmonids (INVASAL), Concepción 4070386, Chile
- Cape Horn International Center (CHIC), Universidad de Magallanes, Punta Arenas 6210427, Chile
| | - Julio A. Benavides
- Doctorado en Medicina de la Conservación, Facultad Ciencias de la Vida, Universidad Andres Bello, República 440, Santiago 8370134, Chile
- Centro de Investigación para la Sustentabilidad, Facultad Ciencias de la Vida, Universidad Andres Bello, República 440, Santiago 8370134, Chile
- MIVEGEC, IRD, CNRS, Université de Montpellier, 34090 Montpellier, France
| | - Gustavo Chiang
- Departamento de Ecología y Biodiversidad, Facultad Ciencias de la Vida, Universidad Andres Bello, República 440, Santiago 8370134, Chile
- Centro de Investigación para la Sustentabilidad, Facultad Ciencias de la Vida, Universidad Andres Bello, República 440, Santiago 8370134, Chile
| | - José Pulgar
- Departamento de Ecología y Biodiversidad, Facultad Ciencias de la Vida, Universidad Andres Bello, República 440, Santiago 8370134, Chile
| | - Cristóbal J. Galbán-Malagón
- GEMA, Center for Genomics, Ecology & Environment, Universidad Mayor, Camino la Pirámide 5750, Huechuraba, Santiago 8580000, Chile
- Institute of Environment, Florida International University, University Park, Miami, FL 33199, USA
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Premont A, Saadeh K, Edling C, Lewis R, Marr CM, Jeevaratnam K. Cardiac ion channel expression in the equine model - In-silico prediction utilising RNA sequencing data from mixed tissue samples. Physiol Rep 2022; 10:e15273. [PMID: 35880716 PMCID: PMC9316921 DOI: 10.14814/phy2.15273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 03/19/2022] [Accepted: 04/03/2022] [Indexed: 06/15/2023] Open
Abstract
Understanding cardiomyocyte ion channel expression is crucial to understanding normal cardiac electrophysiology and underlying mechanisms of cardiac pathologies particularly arrhythmias. Hitherto, equine cardiac ion channel expression has rarely been investigated. Therefore, we aim to predict equine cardiac ion channel gene expression. Raw RNAseq data from normal horses from 9 datasets was retrieved from ArrayExpress and European Nucleotide Archive and reanalysed. The normalised (FPKM) read counts for a gene in a mix of tissue were hypothesised to be the average of the expected expression in each tissue weighted by the proportion of the tissue in the mix. The cardiac-specific expression was predicted by estimating the mean expression in each other tissues. To evaluate the performance of the model, predicted gene expression values were compared to the human cardiac gene expression. Cardiac-specific expression could be predicted for 91 ion channels including most expressed Na+ channels, K+ channels and Ca2+ -handling proteins. These revealed interesting differences from what would be expected based on human studies. These differences included predominance of NaV 1.4 rather than NaV 1.5 channel, and RYR1, SERCA1 and CASQ1 rather than RYR2, SERCA2, CASQ2 Ca2+ -handling proteins. Differences in channel expression not only implicate potentially different regulatory mechanisms but also pathological mechanisms of arrhythmogenesis.
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Affiliation(s)
- Antoine Premont
- Faculty of Health and Medical SciencesUniversity of SurreyGuildfordSurreyUK
| | - Khalil Saadeh
- Faculty of Health and Medical SciencesUniversity of SurreyGuildfordSurreyUK
- School of Clinical MedicineUniversity of CambridgeCambridgeUK
| | - Charlotte Edling
- Faculty of Health and Medical SciencesUniversity of SurreyGuildfordSurreyUK
| | - Rebecca Lewis
- Faculty of Health and Medical SciencesUniversity of SurreyGuildfordSurreyUK
| | - Celia M. Marr
- Faculty of Health and Medical SciencesUniversity of SurreyGuildfordSurreyUK
- School of Clinical MedicineUniversity of CambridgeCambridgeUK
- Rossdales Equine Hospital and Diagnostic CentreExningSuffolkUK
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Yow HY, Govindaraju K, Lim AH, Abdul Rahim N. Optimizing Antimicrobial Therapy by Integrating Multi-Omics With Pharmacokinetic/Pharmacodynamic Models and Precision Dosing. Front Pharmacol 2022; 13:915355. [PMID: 35814236 PMCID: PMC9260690 DOI: 10.3389/fphar.2022.915355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/01/2022] [Indexed: 12/02/2022] Open
Abstract
In the era of “Bad Bugs, No Drugs,” optimizing antibiotic therapy against multi-drug resistant (MDR) pathogens is crucial. Mathematical modelling has been employed to further optimize dosing regimens. These models include mechanism-based PK/PD models, systems-based models, quantitative systems pharmacology (QSP) and population PK models. Quantitative systems pharmacology has significant potential in precision antimicrobial chemotherapy in the clinic. Population PK models have been employed in model-informed precision dosing (MIPD). Several antibiotics require close monitoring and dose adjustments in order to ensure optimal outcomes in patients with infectious diseases. Success or failure of antibiotic therapy is dependent on the patient, antibiotic and bacterium. For some drugs, treatment responses vary greatly between individuals due to genotype and disease characteristics. Thus, for these drugs, tailored dosing is required for successful therapy. With antibiotics, inappropriate dosing such as insufficient dosing may put patients at risk of therapeutic failure which could lead to mortality. Conversely, doses that are too high could lead to toxicities. Hence, precision dosing which customizes doses to individual patients is crucial for antibiotics especially those with a narrow therapeutic index. In this review, we discuss the various strategies in optimizing antimicrobial therapy to address the challenges in the management of infectious diseases and delivering personalized therapy.
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Affiliation(s)
- Hui-Yin Yow
- Faculty of Health and Medical Sciences, School of Pharmacy, Taylor’s University, Subang Jaya, Malaysia
- Centre for Drug Discovery and Molecular Pharmacology, Faculty of Health and Medical Sciences, Taylor’s University, Subang Jaya, Malaysia
| | - Kayatri Govindaraju
- Department of Pharmaceutical Life Sciences, Faculty of Pharmacy, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Audrey Huili Lim
- Centre for Clinical Outcome Research (CCORE), Institute for Clinical Research, National Institutes of Health, Shah Alam, Malaysia
| | - Nusaibah Abdul Rahim
- Department of Clinical Pharmacy and Pharmacy Practice, Faculty of Pharmacy, Universiti Malaya, Kuala Lumpur, Malaysia
- *Correspondence: Nusaibah Abdul Rahim,
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Mora I, Arola L, Caimari A, Escoté X, Puiggròs F. Structured Long-Chain Omega-3 Fatty Acids for Improvement of Cognitive Function during Aging. Int J Mol Sci 2022; 23:ijms23073472. [PMID: 35408832 PMCID: PMC8998232 DOI: 10.3390/ijms23073472] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/18/2022] [Accepted: 03/21/2022] [Indexed: 02/07/2023] Open
Abstract
Although the human lifespan has increased in the past century owing to advances in medicine and lifestyle, the human healthspan has not kept up the same pace, especially in brain aging. Consequently, the role of preventive health interventions has become a crucial strategy, in particular, the identification of nutritional compounds that could alleviate the deleterious effects of aging. Among nutrients to cope with aging in special cognitive decline, the long-chain omega-3 polyunsaturated fatty acids (ω-3 LCPUFAs) docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA), have emerged as very promising ones. Due to their neuroinflammatory resolving effects, an increased status of DHA and EPA in the elderly has been linked to better cognitive function and a lower risk of dementia. However, the results from clinical studies do not show consistent evidence and intake recommendations for old adults are lacking. Recently, supplementation with structured forms of EPA and DHA, which can be derived natural forms or targeted structures, have proven enhanced bioavailability and powerful benefits. This review summarizes present and future perspectives of new structures of ω-3 LCPUFAs and the role of "omic" technologies combined with the use of high-throughput in vivo models to shed light on the relationships and underlying mechanisms between ω-3 LCPUFAs and healthy aging.
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Affiliation(s)
- Ignasi Mora
- Brudy Technology S.L., 08006 Barcelona, Spain
- Correspondence: (I.M.); (L.A.)
| | - Lluís Arola
- Nutrigenomics Research Group, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, 43007 Tarragona, Spain
- Correspondence: (I.M.); (L.A.)
| | - Antoni Caimari
- Eurecat, Centre Tecnològic de Catalunya, Biotechnology Area, 43204 Reus, Spain; (A.C.); (F.P.)
| | - Xavier Escoté
- Eurecat, Centre Tecnològic de Catalunya, Nutrition and Health Unit, 43204 Reus, Spain;
| | - Francesc Puiggròs
- Eurecat, Centre Tecnològic de Catalunya, Biotechnology Area, 43204 Reus, Spain; (A.C.); (F.P.)
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Santi AMM, Murta SMF. Impact of Genetic Diversity and Genome Plasticity of Leishmania spp. in Treatment and the Search for Novel Chemotherapeutic Targets. Front Cell Infect Microbiol 2022; 12:826287. [PMID: 35141175 PMCID: PMC8819175 DOI: 10.3389/fcimb.2022.826287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/04/2022] [Indexed: 11/21/2022] Open
Abstract
Leishmaniasis is one of the major public health concerns in Latin America, Africa, Asia, and Europe. The absence of vaccines for human use and the lack of effective vector control programs make chemotherapy the main strategy to control all forms of the disease. However, the high toxicity of available drugs, limited choice of therapeutic agents, and occurrence of drug-resistant parasite strains are the main challenges related to chemotherapy. Currently, only a small number of drugs are available for leishmaniasis treatment, including pentavalent antimonials (SbV), amphotericin B and its formulations, miltefosine, paromomycin sulphate, and pentamidine isethionate. In addition to drug toxicity, therapeutic failure of leishmaniasis is a serious concern. The occurrence of drug-resistant parasites is one of the causes of therapeutic failure and is closely related to the diversity of parasites in this genus. Owing to the enormous plasticity of the genome, resistance can occur by altering different metabolic pathways, demonstrating that resistance mechanisms are multifactorial and extremely complex. Genetic variability and genome plasticity cause not only the available drugs to have limitations, but also make the search for new drugs challenging. Here, we examined the biological characteristics of parasites that hinder drug discovery.
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Hao Y, Li J, Shi L. A Carvacrol-Rich Essential Oil Extracted From Oregano ( Origanum vulgare "Hot & Spicy") Exerts Potent Antibacterial Effects Against Staphylococcus aureus. Front Microbiol 2021; 12:741861. [PMID: 34803958 PMCID: PMC8602913 DOI: 10.3389/fmicb.2021.741861] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/12/2021] [Indexed: 01/16/2023] Open
Abstract
Oregano essential oil (OEO), as a natural antimicrobial, has gained increased interest from food researchers and manufacturers. However, a few studies have investigated its possible antibacterial effects against Staphylococcus aureus using the proteomic tool. The present study aimed to explore the antibacterial effect and mechanism of a carvacrol-rich OEO extracted from Origanum vulgare “Hot & Spicy” on the inactivation of S. aureus. The gas chromatography–mass spectrometry analysis of the OEO allowed the detection of 27 compounds; the major constituent was carvacrol (84.38% of total compounds). The average diameter of the inhibitory zone (DIZ) value was 29.10 mm, and the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of OEO against S. aureus were 0.125 and 0.25 mg/mL, respectively. The growth curve assay indicated that the OEO prolonged the lag phase of S. aureus. The decrease in cell viability, changes in the integrity of cell membrane, and abnormal cell morphology further reflected the cell damage of S. aureus caused by the OEO. In addition, a label-free proteomic analysis was applied to analyze the regulatory networks of S. aureus in response to 1/2 MIC OEO-treatment stress. Of the 56 differentially expressed proteins (DEPs) identified, 26 were significantly upregulated and 30 downregulated. The Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis indicated that the DEPs were mainly involved in pathways of ribosomes; valine, leucine, and isoleucine biosynthesis; and phenylalanine, tyrosine, and tryptophan biosynthesis, which suggested that the growth inhibition of S. aureus might be due to the disordered effect of the OEO on protein synthesis and amino acid metabolism. These findings deepened our understanding regarding S. aureus survival and metabolism responses to the OEO treatment and suggested that the carvacrol-rich OEO could be used in food production environments to effectively control S. aureus.
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Affiliation(s)
- Yuanpeng Hao
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jingyi Li
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Lei Shi
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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Álvarez-Martínez FJ, Barrajón-Catalán E, Herranz-López M, Micol V. Antibacterial plant compounds, extracts and essential oils: An updated review on their effects and putative mechanisms of action. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2021; 90:153626. [PMID: 34301463 DOI: 10.1016/j.phymed.2021.153626] [Citation(s) in RCA: 127] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 06/03/2021] [Accepted: 06/10/2021] [Indexed: 05/20/2023]
Abstract
BACKGROUND Antibiotic-resistant bacteria pose a global health threat. Traditional antibiotics can lose their effectiveness, and the development of novel effective antimicrobials has become a priority in recent years. In this area, plants represent an invaluable source of antimicrobial compounds with vast therapeutic potential. PURPOSE To review the full possible spectrum of plant antimicrobial agents (plant compounds, extracts and essential oils) discovered from 2016 to 2021 and their potential to decrease bacterial resistance. Their activities against bacteria, with special emphasis on multidrug resistant bacteria, mechanisms of action, possible combinations with traditional antibiotics, roles in current medicine and future perspectives are discussed. METHODS Studies focusing on the antimicrobial activity of compounds of plant origin and their mechanism of action against bacteria were identified and summarized, including contributions from January 2016 until January 2021. Articles were extracted from the Medline database using PubMed search engine with relevant keywords and operators. RESULTS The search yielded 11,689 articles from 149 countries, of which 101 articles were included in this review. Reports from 41 phytochemicals belonging to 20 families were included. Reports from plant extracts and essential oils from 39 plant species belonging to 17 families were also included. Polyphenols and terpenes were the most active phytochemicals studied, either alone or as a part of plant extracts or essential oils. Plasma membrane disruption was the most common mechanism of antimicrobial action. Number and position of phenolic hydroxyl groups, double bonds, delocalized electrons and conjugation with sugars in the case of flavonoids seemed to be crucial for antimicrobial capacity. Combinations of phytochemicals with beta-lactam antibiotics were the most studied, and the inhibition of efflux pumps was the most common synergistic mechanism. CONCLUSION In recent years, terpenes, flavones, flavonols and some alkaloids and phenylpropanoids, either isolated or as a part of extracts, have shown promising antimicrobial activity, being membrane disruption their most common mechanism. However, their utilization as appropriate antimicrobials need to be boosted by means of new omics technologies and network pharmacology to find the most effective combinations among them or in combination with antibiotics.
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Affiliation(s)
- F J Álvarez-Martínez
- Instituto de Biología Molecular y Celular (IBMC) and Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Universidad Miguel Hernández (UMH), 03202 Elche, Spain
| | - E Barrajón-Catalán
- Instituto de Biología Molecular y Celular (IBMC) and Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Universidad Miguel Hernández (UMH), 03202 Elche, Spain.
| | - M Herranz-López
- Instituto de Biología Molecular y Celular (IBMC) and Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Universidad Miguel Hernández (UMH), 03202 Elche, Spain
| | - V Micol
- Instituto de Biología Molecular y Celular (IBMC) and Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Universidad Miguel Hernández (UMH), 03202 Elche, Spain; CIBER: CB12/03/30038, Fisiopatología de la Obesidad y la Nutrición, CIBERobn, Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
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Antibiotic Biosynthesis Pathways from Endophytic Streptomyces SUK 48 through Metabolomics and Genomics Approaches. Antibiotics (Basel) 2021; 10:antibiotics10080969. [PMID: 34439018 PMCID: PMC8388883 DOI: 10.3390/antibiotics10080969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/01/2021] [Accepted: 08/04/2021] [Indexed: 01/04/2023] Open
Abstract
Streptomyces sp. has been known to be a major antibiotic producer since the 1940s. As the number of cases related to resistance pathogens infection increases yearly, discovering the biosynthesis pathways of antibiotic has become important. In this study, we present the streamline of a project report summary; the genome data and metabolome data of newly isolated Streptomyces SUK 48 strain are also analyzed. The antibacterial activity of its crude extract is also determined. To obtain genome data, the genomic DNA of SUK 48 was extracted using a commercial kit (Promega) and sent for sequencing (Pac Biosciences technology platform, Menlo Park, CA, USA). The raw data were assembled and polished using Hierarchical Genome Assembly Process 4.0 (HGAP 4.0). The assembled data were structurally predicted using tRNAscan-SE and rnammer. Then, the data were analyzed using Kyoto Encyclopedia of Genes and Genomes (KEGG) database and antiSMASH analysis. Meanwhile, the metabolite profile of SUK 48 was determined using liquid chromatography-mass spectrophotometry (LC-MS) for both negative and positive modes. The results showed that the presence of kanamycin and gentamicin, as well as the other 11 antibiotics. Nevertheless, the biosynthesis pathways of aurantioclavine were also found. The cytotoxicity activity showed IC50 value was at 0.35 ± 1.35 mg/mL on the cell viability of HEK 293. In conclusion, Streptomyces sp. SUK 48 has proven to be a non-toxic antibiotic producer such as auranticlavine and gentamicin.
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da Cunha BR, Zoio P, Fonseca LP, Calado CRC. Technologies for High-Throughput Identification of Antibiotic Mechanism of Action. Antibiotics (Basel) 2021; 10:565. [PMID: 34065815 PMCID: PMC8151116 DOI: 10.3390/antibiotics10050565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/05/2021] [Accepted: 05/10/2021] [Indexed: 01/23/2023] Open
Abstract
There are two main strategies for antibiotic discovery: target-based and phenotypic screening. The latter has been much more successful in delivering first-in-class antibiotics, despite the major bottleneck of delayed Mechanism-of-Action (MOA) identification. Although finding new antimicrobial compounds is a very challenging task, identifying their MOA has proven equally challenging. MOA identification is important because it is a great facilitator of lead optimization and improves the chances of commercialization. Moreover, the ability to rapidly detect MOA could enable a shift from an activity-based discovery paradigm towards a mechanism-based approach. This would allow to probe the grey chemical matter, an underexplored source of structural novelty. In this study we review techniques with throughput suitable to screen large libraries and sufficient sensitivity to distinguish MOA. In particular, the techniques used in chemical genetics (e.g., based on overexpression and knockout/knockdown collections), promoter-reporter libraries, transcriptomics (e.g., using microarrays and RNA sequencing), proteomics (e.g., either gel-based or gel-free techniques), metabolomics (e.g., resourcing to nuclear magnetic resonance or mass spectrometry techniques), bacterial cytological profiling, and vibrational spectroscopy (e.g., Fourier-transform infrared or Raman scattering spectroscopy) were discussed. Ultimately, new and reinvigorated phenotypic assays bring renewed hope in the discovery of a new generation of antibiotics.
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Affiliation(s)
- Bernardo Ribeiro da Cunha
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa (UL), Av. Rovisco Pais, 1049-001 Lisboa, Portugal; (B.R.d.C.); (P.Z.); (L.P.F.)
| | - Paulo Zoio
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa (UL), Av. Rovisco Pais, 1049-001 Lisboa, Portugal; (B.R.d.C.); (P.Z.); (L.P.F.)
- CIMOSM—Centro de Investigação em Modelação e Optimização de Sistemas Multifuncionais, ISEL—Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, R. Conselheiro Emídio Navarro 1, 1959-007 Lisboa, Portugal
| | - Luís P. Fonseca
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa (UL), Av. Rovisco Pais, 1049-001 Lisboa, Portugal; (B.R.d.C.); (P.Z.); (L.P.F.)
| | - Cecília R. C. Calado
- CIMOSM—Centro de Investigação em Modelação e Optimização de Sistemas Multifuncionais, ISEL—Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, R. Conselheiro Emídio Navarro 1, 1959-007 Lisboa, Portugal
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12
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Ribeiro da Cunha B, Fonseca LP, Calado CRC. Simultaneous elucidation of antibiotic mechanism of action and potency with high-throughput Fourier-transform infrared (FTIR) spectroscopy and machine learning. Appl Microbiol Biotechnol 2021; 105:1269-1286. [PMID: 33443637 DOI: 10.1007/s00253-021-11102-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 12/09/2020] [Accepted: 01/05/2021] [Indexed: 12/15/2022]
Abstract
The low rate of discovery and rapid spread of resistant pathogens have made antibiotic discovery a worldwide priority. In cell-based screening, the mechanism of action (MOA) is identified after antimicrobial activity. This increases rediscovery, impairs low potency candidate detection, and does not guide lead optimization. In this study, high-throughput Fourier-transform infrared (FTIR) spectroscopy was used to discriminate the MOA of 14 antibiotics at pathway, class, and individual antibiotic level. For that, the optimal combinations and parametrizations of spectral preprocessing were selected with cross-validated partial least squares discriminant analysis, to which various machine learning algorithms were applied. This coherently resulted in very good accuracies, independently of the algorithms, and at all levels of MOA. Particularly, an ensemble of subspace discriminants predicted the known pathway (98.6%), antibiotic classes (100%), and individual antibiotics (97.8%) with exceptional accuracy, and similar results were obtained for simulated novel MOA. Even at very low concentrations (1 μg/mL) and growth inhibition (15%), over 70% pathway and class accuracy was achieved, suggesting FTIR spectroscopy can probe the grey chemical matter. Prediction of inhibitory effect was also examined, for which a squared exponential Gaussian process regression yielded a root mean square error of 0.33 and a R2 of 0.92, indicating that metabolic alterations leading to growth inhibition are intrinsically reflected on FTIR spectra beyond cell density. KEY POINTS: • Antibiotic MOA and potency estimated with high-throughput FTIR spectroscopy • Sub-inhibitory MOA identification suggests ability to explore grey chemical matter • Data analysis optimization improved MOA identification at antibiotic level by 38.
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Affiliation(s)
- Bernardo Ribeiro da Cunha
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa (UL), Av. Rovisco Pais, 1049-001, Lisbon, Portugal. .,Departamento de Engenharia Química, ISEL - Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa (IPL), R. Conselheiro Emídio Navarro 1, 1959-007, Lisbon, Portugal.
| | - Luís P Fonseca
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa (UL), Av. Rovisco Pais, 1049-001, Lisbon, Portugal
| | - Cecília R C Calado
- Departamento de Engenharia Química, ISEL - Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa (IPL), R. Conselheiro Emídio Navarro 1, 1959-007, Lisbon, Portugal
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13
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Yu X, Feng G, Zhang Q, Cao J. From Metabolite to Metabolome: Metabolomics Applications in Plasmodium Research. Front Microbiol 2021; 11:626183. [PMID: 33505389 PMCID: PMC7829456 DOI: 10.3389/fmicb.2020.626183] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 12/07/2020] [Indexed: 01/02/2023] Open
Abstract
Advances in research over the past few decades have greatly improved metabolomics-based approaches in studying parasite biology and disease etiology. This improves the investigation of varied metabolic requirements during life stages or when following transmission to their hosts, and fulfills the demand for improved diagnostics and precise therapeutics. Therefore, this review highlights the progress of metabolomics in malaria research, including metabolic mapping of Plasmodium vertebrate life cycle stages to investigate antimalarials mode of actions and underlying complex host-parasite interactions. Also, we discuss current limitations as well as make several practical suggestions for methodological improvements which could drive metabolomics progress for malaria from a comprehensive perspective.
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Affiliation(s)
- Xinyu Yu
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China.,Medical College of Soochow University, Suzhou, China
| | - Gaoqian Feng
- Burnet Institute, Melbourne, VIC, Australia.,Department of Medicine, The University of Melbourne, Melbourne, VIC, Australia
| | - Qingfeng Zhang
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jun Cao
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China.,Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
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14
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Chen Y, Gao Y, Yi X, Zhang J, Chen Z, Wu Y. Integration of Transcriptomics and Metabolomics Reveals the Antitumor Mechanism Underlying Shikonin in Colon Cancer. Front Pharmacol 2020; 11:544647. [PMID: 33281602 PMCID: PMC7689381 DOI: 10.3389/fphar.2020.544647] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 09/18/2020] [Indexed: 12/12/2022] Open
Abstract
Colorectal cancer is a common malignancy occurring in the digestive system, which is the third common cause of cancer mortality in developed countries. Shikonin, a naphthoquinone compound extracted from the root of Lithospermum erythrorhizon, is extensively reported to exert antitumor activity against various types of cancer. However, the systematic effect of shikonin in colon cancer remains poorly understood. In the present study, we evaluated the antitumor activity of shikonin in human colon cancer cells and the therapeutic effect on a xenograft mouse model. Transcriptomics and metabolomics were further integrated to provide a systematic perspective of the shikonin-induced antitumor mechanism. The results demonstrated that shikonin had a remarkable antitumor potency both in vitro and in vivo. Moreover, metabolic pathways, including the purine metabolism, amino acid metabolism, and glycerophospholipid metabolism, were perturbed and subsequently led to cell cycle arrest in the G2/M phase. In particular, the disturbance of purine metabolism may account for the major mechanism resulting from shikonin antitumor activity.
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Affiliation(s)
- Yang Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Yun Gao
- Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Sciences, Hangzhou, China.,Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, China.,Zhejiang Cancer Hospital, Hangzhou, China
| | - Xiaojiao Yi
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Jinghui Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Zhongjian Chen
- Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Sciences, Hangzhou, China.,Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, China.,Zhejiang Cancer Hospital, Hangzhou, China
| | - Yongjiang Wu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
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15
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Bezerra Filho CM, da Silva LCN, da Silva MV, Løbner-Olesen A, Struve C, Krogfelt KA, Correia MTDS, Vilela Oliva ML. Antimicrobial and Antivirulence Action of Eugenia brejoensis Essential Oil in vitro and in vivo Invertebrate Models. Front Microbiol 2020; 11:424. [PMID: 32265869 PMCID: PMC7096383 DOI: 10.3389/fmicb.2020.00424] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 02/27/2020] [Indexed: 01/18/2023] Open
Abstract
Eugenia brejoensis L. (Myrtaceae) is an endemic plant from caatinga ecosystem (brazilian semi-arid) which have an E. brejoensis essential oil (EbEO) with reported antimicrobial activity. In this work, in vitro and in vivo models were used to characterize the inhibitory effects of EbEO in relation to Staphylococcus aureus. EbEO inhibited the growth of all tested S. aureus strains (including multidrug resistance isolates) with values ranging from 8 to 516 μg/mL. EbEO also synergistically increased the action of ampicillim, chloramphenicol, and kanamycin. The treatment with subinhibitory concentrations (Sub-MIC) of EbEO decreased S. aureus hemolytic activity and its ability to survive in human blood. EbEO strongly reduced the levels of staphyloxanthin (STX), an effect related to increased susceptibility of S. aureus to hydrogen peroxide. The efficacy of EbEO against S. aureus was further demonstrated using Caenorhabditis elegans and Galleria mellonella. EbEO increased the lifespan of both organisms infected by S. aureus, reducing the bacterial load. In addition, EbEO reduced the severity of S. aureus infection in G. mellonella, as shown by lower levels of melanin production in those larvae. In summary, our data suggest that EbEO is a potential source of lead molecules for development of new therapeutic alternatives against S. aureus.
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Affiliation(s)
- Clovis Macêdo Bezerra Filho
- Biochemistry Department, Federal University of Pernambuco, Recife, Brazil.,Biochemistry Department, Federal University of São Paulo, São Paulo, Brazil
| | | | | | | | - Carsten Struve
- Department of Bacteria, Parasites and Fungi, Staten Serum Institut, Copenhagen, Denmark
| | - Karen Angeliki Krogfelt
- Department of Bacteria, Parasites and Fungi, Staten Serum Institut, Copenhagen, Denmark.,Department of Science and Environment, Roskilde University, Roskilde, Denmark
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16
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Chai TT, Xiao J, Dass SM, Wong FC. Laccase-catalyzed, Phytochemical-mediated Protein Crosslinking Conjugates. EFOOD 2020. [DOI: 10.2991/efood.k.200218.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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17
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de Souza Feitosa Lima IM, Zagmignan A, Santos DM, Maia HS, Dos Santos Silva L, da Silva Cutrim B, Vieira SL, Bezerra Filho CM, de Sousa EM, Napoleão TH, Krogfelt KA, Løbner-Olesen A, Paiva PMG, Nascimento da Silva LC. Schinus terebinthifolia leaf lectin (SteLL) has anti-infective action and modulates the response of Staphylococcus aureus-infected macrophages. Sci Rep 2019; 9:18159. [PMID: 31796807 PMCID: PMC6890730 DOI: 10.1038/s41598-019-54616-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 11/18/2019] [Indexed: 02/07/2023] Open
Abstract
Staphylococcus aureus is recognized as an important pathogen causing a wide spectrum of diseases. Here we examined the antimicrobial effects of the lectin isolated from leaves of Schinus terebinthifolia Raddi (SteLL) against S. aureus using in vitro assays and an infection model based on Galleria mellonella larvae. The actions of SteLL on mice macrophages and S. aureus-infected macrophages were also evaluated. SteLL at 16 µg/mL (8 × MIC) increased cell mass and DNA content of S. aureus in relation to untreated bacteria, suggesting that SteLL impairs cell division. Unlike ciprofloxacin, SteLL did not induce the expression of recA, crucial for DNA repair through SOS response. The antimicrobial action of SteLL was partially inhibited by 50 mM N-acetylglucosamine. SteLL reduced staphyloxathin production and increased ciprofloxacin activity towards S. aureus. This lectin also improved the survival of G. mellonella larvae infected with S. aureus. Furthermore, SteLL induced the release of cytokines (IL-6, IL-10, IL-17A, and TNF-α), nitric oxide and superoxide anion by macrophagens. The lectin improved the bactericidal action of macrophages towards S. aureus; while the expression of IL-17A and IFN-γ was downregulated in infected macrophages. These evidences suggest SteLL as important lead molecule in the development of anti-infective agents against S. aureus.
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Affiliation(s)
| | - Adrielle Zagmignan
- Programas de Pós-Graduação, Universidade Ceuma, São Luís, Maranhão, Brazil
| | | | | | | | | | | | | | | | | | - Karen Angeliki Krogfelt
- Department of Viral and Microbial Diagnostics, Statens Serum Institut, Copenhagen, Denmark
- Department of Science and Environment, Roskilde University, 4000, Roskilde, Denmark
| | - Anders Løbner-Olesen
- Department of Biology, Section for Functional Genomics, University of Copenhagen, Copenhagen, Denmark
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18
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Banerji A, Jahne M, Herrmann M, Brinkman N, Keely S. Bringing Community Ecology to Bear on the Issue of Antimicrobial Resistance. Front Microbiol 2019; 10:2626. [PMID: 31803161 PMCID: PMC6872637 DOI: 10.3389/fmicb.2019.02626] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 10/29/2019] [Indexed: 12/14/2022] Open
Abstract
Antimicrobial resistance (AMR) is a global concern, pertaining not only to human health but also to the health of industry and the environment. AMR research has traditionally focused on genetic exchange mechanisms and abiotic environmental constraints, leaving important aspects of microbial ecology unresolved. The genetic and ecological aspects of AMR, however, not only contribute separately to the problem but also are interrelated. For example, mutualistic associations among microbes such as biofilms can both serve as a barrier to antibiotic penetration and a breeding ground for horizontal exchange of antimicrobial resistance genes (ARGs). In this review, we elucidate how species interactions promote and impede the establishment, maintenance, and spread of ARGs and indicate how management initiatives might benefit from leveraging the principles and tools of community ecology to better understand and manipulate the processes underlying AMR.
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Affiliation(s)
- Aabir Banerji
- Office of Research and Development, Center for Environmental Measurement and Modeling, US Environmental Protection Agency, Cincinnati, OH, United States
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19
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Souza dos Santos B, Bezerra Filho CM, Alves do Nascimento Junior JA, Brust FR, Bezerra-Silva PC, Lino da Rocha SK, Krogfelt KA, Maria do Amaral Ferraz Navarro D, Tereza dos Santos Correia M, Napoleão TH, Nascimento da Silva LC, Macedo AJ, Vanusa da Silva M, Guedes Paiva PM. Anti-staphylococcal activity of Syagrus coronata essential oil: Biofilm eradication and in vivo action on Galleria mellonela infection model. Microb Pathog 2019; 131:150-157. [DOI: 10.1016/j.micpath.2019.04.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 04/04/2019] [Accepted: 04/05/2019] [Indexed: 01/31/2023]
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20
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Sivaranjani M, Leskinen K, Aravindraja C, Saavalainen P, Pandian SK, Skurnik M, Ravi AV. Deciphering the Antibacterial Mode of Action of Alpha-Mangostin on Staphylococcus epidermidis RP62A Through an Integrated Transcriptomic and Proteomic Approach. Front Microbiol 2019; 10:150. [PMID: 30787919 PMCID: PMC6372523 DOI: 10.3389/fmicb.2019.00150] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 01/21/2019] [Indexed: 11/25/2022] Open
Abstract
Background: Alpha-mangostin (α-MG) is a natural xanthone reported to exhibit rapid bactericidal activity against Gram-positive bacteria, and may therefore have potential clinical application in healthcare sectors. This study sought to identify the impact of α-MG on Staphylococcus epidermidis RP62A through integrated advanced omic technologies. Methods: S. epidermidis was challenged with sub-MIC (0.875 μg/ml) of α-MG at various time points and the differential expression pattern of genes/proteins were analyzed in the absence and presence of α-MG using RNA sequencing and LC-MS/MS experiments. Bioinformatic tools were used to categorize the biological processes, molecular functions and KEGG pathways of differentially expressed genes/proteins. qRT-PCR was employed to validate the results obtained from these analyses. Results: Transcriptomic and proteomic profiling of α-MG treated cells indicated that genes/proteins affected by α-MG treatment were associated with diverse cellular functions. The greatest reduction in expression was observed in transcription of genes conferring cytoplasmic membrane integrity (yidC2, secA and mscL), cell division (ftsY and divlB), teichoic acid biosynthesis (tagG and dltA), fatty-acid biosynthesis (accB, accC, fabD, fabH, fabI, and fabZ), biofilm formation (icaA) and DNA replication and repair machinery (polA, polC, dnaE, and uvrA). Those with increased expression were involved in oxidative (katA and sodA) and cellular stress response (clpB, clpC, groEL, and asp23). The qRT-PCR analysis substantiated the results obtained from transcriptomic and proteomic profiling studies. Conclusion: Combining transcriptomic and proteomic methods provided comprehensive information about the antibacterial mode of action of α-MG. The obtained results suggest that α-MG targets S. epidermidis through multifarious mechanisms, and especially prompts that loss of cytoplasmic membrane integrity leads to rapid onset of bactericidal activity.
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Affiliation(s)
| | - Katarzyna Leskinen
- Department of Bacteriology and Immunology, Medicum, Research Programs Unit, Immunobiology Research Program, University of Helsinki, Helsinki, Finland
| | | | - Päivi Saavalainen
- Department of Bacteriology and Immunology, Medicum, Research Programs Unit, Immunobiology Research Program, University of Helsinki, Helsinki, Finland
| | | | - Mikael Skurnik
- Department of Bacteriology and Immunology, Medicum, Research Programs Unit, Immunobiology Research Program, University of Helsinki, Helsinki, Finland
- Division of Clinical Microbiology, Helsinki University Hospital, HUSLAB, Helsinki, Finland
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21
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Antti H, Sellstedt M. Metabolic effects of an aspartate aminotransferase-inhibitor on two T-cell lines. PLoS One 2018; 13:e0208025. [PMID: 30532126 PMCID: PMC6285999 DOI: 10.1371/journal.pone.0208025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 11/11/2018] [Indexed: 12/29/2022] Open
Abstract
An emerging method to help elucidate the mode of action of experimental drugs is to use untargeted metabolomics of cell-systems. The interpretations of such screens are however complex and more examples with inhibitors of known targets are needed. Here two T-cell lines were treated with an inhibitor of aspartate aminotransferase and analyzed with untargeted GC-MS. The interpretation of the data was enhanced by the use of two different cell-lines and supports aspartate aminotransferase as a target. In addition, the data suggest an unexpected off-target effect on glutamate decarboxylase. The results exemplify the potency of metabolomics to provide insight into both mode of action and off-target effects of drug candidates.
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Affiliation(s)
- Henrik Antti
- Department of Chemistry, Umeå University, Umeå, Sweden
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22
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Armitage EG, Godzien J, Peña I, López-Gonzálvez Á, Angulo S, Gradillas A, Alonso-Herranz V, Martín J, Fiandor JM, Barrett MP, Gabarro R, Barbas C. Metabolic Clustering Analysis as a Strategy for Compound Selection in the Drug Discovery Pipeline for Leishmaniasis. ACS Chem Biol 2018; 13:1361-1369. [PMID: 29671577 DOI: 10.1021/acschembio.8b00204] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A lack of viable hits, increasing resistance, and limited knowledge on mode of action is hindering drug discovery for many diseases. To optimize prioritization and accelerate the discovery process, a strategy to cluster compounds based on more than chemical structure is required. We show the power of metabolomics in comparing effects on metabolism of 28 different candidate treatments for Leishmaniasis (25 from the GSK Leishmania box, two analogues of Leishmania box series, and amphotericin B as a gold standard treatment), tested in the axenic amastigote form of Leishmania donovani. Capillary electrophoresis-mass spectrometry was applied to identify the metabolic profile of Leishmania donovani, and principal components analysis was used to cluster compounds on potential mode of action, offering a medium throughput screening approach in drug selection/prioritization. The comprehensive and sensitive nature of the data has also made detailed effects of each compound obtainable, providing a resource to assist in further mechanistic studies and prioritization of these compounds for the development of new antileishmanial drugs.
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Affiliation(s)
- Emily G. Armitage
- Centre for Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Boadilla del Monte, 28668 Madrid, Spain
- GSK I+D Diseases of the Developing World (DDW), Parque Tecnológico de Madrid, Calle de Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, United Kingdom
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, College of Medical Veterinary & Life Sciences, University of Glasgow, Glasgow G61 1QH, United Kingdom
| | - Joanna Godzien
- Centre for Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Boadilla del Monte, 28668 Madrid, Spain
| | - Imanol Peña
- GSK I+D Diseases of the Developing World (DDW), Parque Tecnológico de Madrid, Calle de Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Ángeles López-Gonzálvez
- Centre for Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Boadilla del Monte, 28668 Madrid, Spain
| | - Santiago Angulo
- Centre for Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Boadilla del Monte, 28668 Madrid, Spain
| | - Ana Gradillas
- Centre for Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Boadilla del Monte, 28668 Madrid, Spain
| | - Vanesa Alonso-Herranz
- Centre for Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Boadilla del Monte, 28668 Madrid, Spain
| | - Julio Martín
- GSK I+D Diseases of the Developing World (DDW), Parque Tecnológico de Madrid, Calle de Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Jose M. Fiandor
- GSK I+D Diseases of the Developing World (DDW), Parque Tecnológico de Madrid, Calle de Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Michael P. Barrett
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, United Kingdom
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, College of Medical Veterinary & Life Sciences, University of Glasgow, Glasgow G61 1QH, United Kingdom
| | - Raquel Gabarro
- GSK I+D Diseases of the Developing World (DDW), Parque Tecnológico de Madrid, Calle de Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Coral Barbas
- Centre for Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Boadilla del Monte, 28668 Madrid, Spain
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23
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Dawood M, Hamdoun S, Efferth T. Multifactorial Modes of Action of Arsenic Trioxide in Cancer Cells as Analyzed by Classical and Network Pharmacology. Front Pharmacol 2018; 9:143. [PMID: 29535630 PMCID: PMC5835320 DOI: 10.3389/fphar.2018.00143] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 02/09/2018] [Indexed: 12/13/2022] Open
Abstract
Arsenic trioxide is a traditional remedy in Chinese Medicine since ages. Nowadays, it is clinically used to treat acute promyelocytic leukemia (APL) by targeting PML/RARA. However, the drug's activity is broader and the mechanisms of action in other tumor types remain unclear. In this study, we investigated molecular modes of action by classical and network pharmacological approaches. CEM/ADR5000 resistance leukemic cells were similar sensitive to As2O3 as their wild-type counterpart CCRF-CEM (resistance ratio: 1.88). Drug-resistant U87.MG ΔEGFR glioblastoma cells harboring mutated epidermal growth factor receptor were even more sensitive (collateral sensitive) than wild-type U87.MG cells (resistance ratio: 0.33). HCT-116 colon carcinoma p53-/- knockout cells were 7.16-fold resistant toward As2O3 compared to wild-type cells. Forty genes determining cellular responsiveness to As2O3 were identified by microarray and COMPARE analyses in 58 cell lines of the NCI panel. Hierarchical cluster analysis-based heat mapping revealed significant differences between As2O3 sensitive cell lines and resistant cell lines with p-value: 1.86 × 10-5. The genes were subjected to Galaxy Cistrome gene promoter transcription factor analysis to predict the binding of transcription factors. We have exemplarily chosen NF-kB and AP-1, and indeed As2O3 dose-dependently inhibited the promoter activity of these two transcription factors in reporter cell lines. Furthermore, the genes identified here and those published in the literature were assembled and subjected to Ingenuity Pathway Analysis for comprehensive network pharmacological approaches that included all known factors of resistance of tumor cells to As2O3. In addition to pathways related to the anticancer effects of As2O3, several neurological pathways were identified. As arsenic is well-known to exert neurotoxicity, these pathways might account for neurological side effects. In conclusion, the activity of As2O3 is not restricted to acute promyelocytic leukemia. In addition to PML/RARA, numerous other genes belonging to diverse functional classes may also contribute to its cytotoxicity. Network pharmacology is suited to unravel the multifactorial modes of action of As2O3.
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Affiliation(s)
| | | | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, Mainz, Germany
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24
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Zhao DL, Wang D, Tian XY, Cao F, Li YQ, Zhang CS. Anti-Phytopathogenic and Cytotoxic Activities of Crude Extracts and Secondary Metabolites of Marine-Derived Fungi. Mar Drugs 2018; 16:md16010036. [PMID: 29346329 PMCID: PMC5793084 DOI: 10.3390/md16010036] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 01/08/2018] [Accepted: 01/15/2018] [Indexed: 12/20/2022] Open
Abstract
Thirty-one isolates belonging to eight genera in seven orders were identified from 141 strains that were isolated from several marine plants. Alternaria sp. and Fusarium sp. were found to be the predominant fungi. Evaluation of the anti-phytopathogenic bacterial and fungal activities, as well as the cytotoxicity of these 31 extracts, revealed that most of them displayed different levels of bioactivities. Due to their interesting bioactivities, two fungal strains—Fusarium equiseti (P18) and Alternaria sp. (P8)—were selected for chemical investigation and compounds 1–4 were obtained. The structure of 1 was elucidated by 1D and 2D NMR analysis, as well as high-resolution electrospray ionization mass spectroscopy (HRESIMS), and the absolute configuration of its stereogenic carbon (C-11) was established by comparison of the experimental and calculated electronic circular-dichroism (ECD) spectra. Moreover, alterperylenol (4) exhibited antibacterial activity against Clavibacter michiganensis with a minimum inhibitory concentration (MIC) of 1.95 μg/mL, which was 2-fold stronger than that of streptomycin sulfate. Additionally, an antibacterial mechanism study revealed that 4 caused membrane hyperpolarization without evidence of destruction of cell membrane integrity. Furthermore, stemphyperylenol (3) displayed potent antifungal activity against Pestallozzia theae and Alternaria brassicicola with MIC values equal to those of carbendazim. The cytotoxicity of 1 and 2 against human lung carcinoma (A-549), human cervical carcinoma (HeLa), and human hepatoma (HepG2) cell lines were also evaluated.
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Affiliation(s)
- Dong-Lin Zhao
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Dan Wang
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Xue-Ying Tian
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Fei Cao
- College of Pharmaceutical Sciences, Hebei University, Baoding 071002, China.
| | - Yi-Qiang Li
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Cheng-Sheng Zhang
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
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Marzano V, Mancinelli L, Bracaglia G, Del Chierico F, Vernocchi P, Di Girolamo F, Garrone S, Tchidjou Kuekou H, D’Argenio P, Dallapiccola B, Urbani A, Putignani L. "Omic" investigations of protozoa and worms for a deeper understanding of the human gut "parasitome". PLoS Negl Trop Dis 2017; 11:e0005916. [PMID: 29095820 PMCID: PMC5667730 DOI: 10.1371/journal.pntd.0005916] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The human gut has been continuously exposed to a broad spectrum of intestinal organisms, including viruses, bacteria, fungi, and parasites (protozoa and worms), over millions of years of coevolution, and plays a central role in human health. The modern lifestyles of Western countries, such as the adoption of highly hygienic habits, the extensive use of antimicrobial drugs, and increasing globalisation, have dramatically altered the composition of the gut milieu, especially in terms of its eukaryotic “citizens.” In the past few decades, numerous studies have highlighted the composition and role of human intestinal bacteria in physiological and pathological conditions, while few investigations exist on gut parasites and particularly on their coexistence and interaction with the intestinal microbiota. Studies of the gut “parasitome” through “omic” technologies, such as (meta)genomics, transcriptomics, proteomics, and metabolomics, are herein reviewed to better understand their role in the relationships between intestinal parasites, host, and resident prokaryotes, whether pathogens or commensals. Systems biology–based profiles of the gut “parasitome” under physiological and severe disease conditions can indeed contribute to the control of infectious diseases and offer a new perspective of omics-assisted tropical medicine.
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Affiliation(s)
- Valeria Marzano
- Human Microbiome Unit, Bambino Gesù Children’s Hospital IRCCS, Rome, Italy
| | - Livia Mancinelli
- Laboratory Medicine, Bambino Gesù Children’s Hospital IRCCS, Rome, Italy
| | - Giorgia Bracaglia
- Laboratory Medicine, Bambino Gesù Children’s Hospital IRCCS, Rome, Italy
| | | | - Pamela Vernocchi
- Human Microbiome Unit, Bambino Gesù Children’s Hospital IRCCS, Rome, Italy
| | | | - Stefano Garrone
- Laboratory Medicine, Bambino Gesù Children’s Hospital IRCCS, Rome, Italy
| | | | - Patrizia D’Argenio
- Pediatric Immuno-infectivology, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Bruno Dallapiccola
- Scientific Directorate, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Andrea Urbani
- Institute of Biochemistry and Biochemical Clinic, Faculty of Medicine and Surgery–Policlinico A. Gemelli, Catholic University of Sacred Heart, Rome, Italy
- Proteomic and Metabonomic Unit, Fondazione Santa Lucia IRCCS, Rome, Italy
| | - Lorenza Putignani
- Human Microbiome Unit, Bambino Gesù Children’s Hospital IRCCS, Rome, Italy
- Parasitology Unit, Bambino Gesù Children’s Hospital IRCCS, Rome, Italy
- * E-mail:
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26
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Himatanthus drasticus Leaves: Chemical Characterization and Evaluation of Their Antimicrobial, Antibiofilm, Antiproliferative Activities. Molecules 2017; 22:molecules22060910. [PMID: 28561790 PMCID: PMC6152732 DOI: 10.3390/molecules22060910] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Revised: 05/25/2017] [Accepted: 05/27/2017] [Indexed: 12/14/2022] Open
Abstract
Plant-derived products have played a fundamental role in the development of new therapeutic agents. This study aimed to analyze antimicrobial, antibiofilm, cytotoxicity and antiproliferative potentials of the extract and fractions from leaves of Himatanthusdrasticus, a plant from the Apocynaceae family. After harvesting, H. drasticus leaves were macerated and a hydroalcoholic extract (HDHE) and fractions were prepared. Antimicrobial tests, such as agar-diffusion, Minimum Inhibitory Concentration (MIC) and Minimal Bactericidal Concentration (MBC) were carried out against several bacterial species. Staphylococcus aureus, Pseudomonas aeruginosa, Listeria monocytogenes and Klebsiella pneumoniae were inhibited by at least one extract or fraction in the agar-diffusion assay (inhibition halos from 12 mm to 30 mm). However, the lowest MIC value was found for HDHE against K. pneumoniae. In addition, HDHE and its fractions were able to inhibit biofilm formation at sub-inhibitory concentrations (780 µg/mL and 1.56 µg/mL). As the best activities were found for HDHE, we selected it for further assays. HDHE was able to increase ciprofloxacin (CIP) activity against K. pneumoniae, displaying synergistic (initial concentration CIP + HDHE: 2 µg/mL + 600 µg/mL and 2.5 µg/mL + 500 µg/mL) and additive effects (CIP + HDHE: 3 µg/mL + 400 µg/mL). This action seems to be associated with the alteration in bacterial membrane permeability induced by HDHE (as seen by propidium iodide labeling). This extract was non-toxic for red blood cell or human peripheral blood mononuclear cells (PBMCs). Additionally, it inhibited the lipopolysaccharide-induced proliferation of PBMCs. The following compounds were detected in HDHE using HPLC-ESI-MS analysis: plumieride, plumericin or isoplumericin, rutin, quercetin and derivatives, and chlorogenic acid. Based on these results we suggest that compounds from H. drasticus have antimicrobial and antibiofilm activities against K. pneumoniae and display low cytotoxicity and anti-proliferative action in PBMC stimulated with lipopolysaccharide.
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