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Bonardi A, Nocentini A, Giovannuzzi S, Paoletti N, Ammara A, Bua S, Abutaleb NS, Abdelsattar AS, Capasso C, Gratteri P, Flaherty DP, Seleem MN, Supuran CT. Development of Penicillin-Based Carbonic Anhydrase Inhibitors Targeting Multidrug-Resistant Neisseria gonorrhoeae. J Med Chem 2024; 67:9613-9627. [PMID: 38776401 DOI: 10.1021/acs.jmedchem.4c00740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
The development of antibacterial drugs with new mechanisms of action is crucial in combating the rise of antibiotic-resistant infections. Bacterial carbonic anhydrases (CAs, EC 4.2.1.1) have been validated as promising antibacterial targets against pathogens such as Helicobacter pylori, Neisseria gonorrhoeae, and vancomycin-resistant enterococci. A multitarget strategy is proposed to design penicillin-based CA inhibitor hybrids for tackling resistance by targeting multiple bacterial pathways, thereby resensitizing drug-resistant strains to clinical antibiotics. The sulfonamide derivatives potently inhibited the CAs from N. gonorrhoeae and Escherichia coli with KI values in the range of 7.1-617.2 nM. Computational simulations with the main penicillin-binding protein (PBP) of N. gonorrhoeae indicated that these hybrid derivatives maintained the mechanism of action of the lead β-lactams. A subset of derivatives showed potent PBP-related antigonococcal effects against multidrug-resistant N. gonorrhoeae strains, with several compounds significantly outperforming both the lead β-lactam and CA inhibitor drugs (MIC values in the range 0.25 to 0.5 μg/mL).
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Affiliation(s)
- Alessandro Bonardi
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Via U. Schiff 6, Sesto Fiorentino, Florence 50019, Italy
| | - Alessio Nocentini
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Via U. Schiff 6, Sesto Fiorentino, Florence 50019, Italy
| | - Simone Giovannuzzi
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Via U. Schiff 6, Sesto Fiorentino, Florence 50019, Italy
| | - Niccolò Paoletti
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Via U. Schiff 6, Sesto Fiorentino, Florence 50019, Italy
| | - Andrea Ammara
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Via U. Schiff 6, Sesto Fiorentino, Florence 50019, Italy
| | - Silvia Bua
- Research Institute of the University of Bucharest (ICUB), Bucharest 050663, Romania
| | - Nader S Abutaleb
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Abdallah S Abdelsattar
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | | | - Paola Gratteri
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Via U. Schiff 6, Sesto Fiorentino, Florence 50019, Italy
| | - Daniel P Flaherty
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Mohamed N Seleem
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
- Center for One Health Research, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Claudiu T Supuran
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Via U. Schiff 6, Sesto Fiorentino, Florence 50019, Italy
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Ferdous J, Bhuia MS, Chowdhury R, Rakib AI, Aktar MA, Al Hasan MS, Melo Coutinho HD, Islam MT. Pharmacological Activities of Plant-Derived Fraxin with Molecular Mechanisms: A Comprehensive Review. Chem Biodivers 2024; 21:e202301615. [PMID: 38506600 DOI: 10.1002/cbdv.202301615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 03/21/2024]
Abstract
Fruits and vegetables serve not only as sources of nutrition but also as medicinal agents for the treatment of diverse diseases and maladies. These dietary components are significant resources of phytochemicals that demonstrate therapeutic properties against many illnesses. Fraxin is a naturally occurring coumarin glycoside mainly present in various species of Fraxinus genera, having a multitude of therapeutic uses against various diseases and disorders. This study focuses to investigate the pharmacological activities, botanical sources, and biopharmaceutical profile of the phytochemical fraxin based on different preclinical and non-clinical studies to show the scientific evidence and to evaluate the underlying molecular mechanisms of the therapeutic effects against various ailments. For this, data was searched and collected (as of February 15, 2024) in a variety of credible electronic databases, including PubMed/Medline, Scopus, Springer Link, ScienceDirect, Wiley Online, Web of Science, and Google Scholar. The findings demonstrated favorable outcomes in relation to a range of diseases or medical conditions, including inflammation, neurodegenerative disorders such as cerebral ischemia-reperfusion (I/R) and depression, viral infection, as well as diabetic nephropathy. The phytochemical also showed protective effects such as osteoprotective, renoprotective, pulmoprotective, hepatoprotective, and gastroprotective effects due to its antioxidant capacity. Fraxin has a great capability to diminish oxidative stress-related damage in different organs by stimulating the antioxidant enzymes, downregulating nuclear factor kappa B and NLRP3, and triggering the Nrf2/ARE signaling pathways. Fraxin exhibited poor oral bioavailability because of reduced absorption and a wide distribution into tissues of different organs. However, extensive research is required to decipher the biopharmaceutical profiles, and clinical studies are necessary to establish the efficacy of the natural compound as a reliable therapeutic agent.
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Affiliation(s)
- Jannatul Ferdous
- Department of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, 8100, Bangladesh
- BioLuster Research Center, Gopalganj, 8100, Dhaka, Bangladesh
| | - Md Shimul Bhuia
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, 8100, Bangladesh
- BioLuster Research Center, Gopalganj, 8100, Dhaka, Bangladesh
| | - Raihan Chowdhury
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, 8100, Bangladesh
| | - Asraful Islam Rakib
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, 8100, Bangladesh
| | - Mst Asma Aktar
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, 8100, Bangladesh
| | - Md Sakib Al Hasan
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, 8100, Bangladesh
| | | | - Muhammad Torequl Islam
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, 8100, Bangladesh
- BioLuster Research Center, Gopalganj, 8100, Dhaka, Bangladesh
- Pharmacy Discipline, Khulna University, Khulna, 9208, Bangladesh
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Uc-Cachón AH, Calvo-Irabien LM, Dzul-Beh ADJ, Dzib-Baak HE, Grijalva-Arango R, Molina-Salinas GM. Potential Anti-Infectious Activity of Essential Oil Chemotypes of Lippia origanoides Kunth on Antibiotic-Resistant Staphylococcus aureus Strains. PLANTS (BASEL, SWITZERLAND) 2024; 13:1172. [PMID: 38732387 PMCID: PMC11085919 DOI: 10.3390/plants13091172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 04/16/2024] [Accepted: 04/20/2024] [Indexed: 05/13/2024]
Abstract
Staphylococcus aureus infections are prevalent in healthcare and community environments. Methicillin-resistant S. aureus is catalogued as a superbug of high priority among the pathogens. This Gram-positive coccus can form biofilms and produce toxins, leading to persistent infection and antibiotic resistance. Limited effective antibiotics have encouraged the development of innovative strategies, with a particular emphasis on resistance mechanisms and/or virulence factors. Medicinal aromatic plants have emerged as promising alternative sources. This study investigated the antimicrobial, antibiofilm, and antihemolysis properties of three different chemotypes of Lippia origanoides essential oil (EO) against susceptible and drug-resistant S. aureus strains. The chemical composition of the EO was analyzed using GC-MS, revealing high monoterpene concentrations, with carvacrol and thymol as the major components in two of the chemotypes. The third chemotype consisted mainly of the sesquiterpene β-caryophyllene. The MIC values for the two monoterpene chemotypes ranged from 62.5 to 500 µg/mL for all strains, whereas the sesquiterpene chemotype showed activity against seven strains at concentrations of 125-500 µg/mL, which is the first report of its anti-S. aureus activity. The phenolic chemotypes inhibited biofilm formation in seven S. aureus strains, whereas the sesquiterpene chemotype only inhibited biofilm formation in four strains. In addition, phenolic chemotypes displayed antihemolysis activity, with IC50 values ranging from 58.9 ± 3.8 to 128.3 ± 9.2 µg/mL. Our study highlights the importance of L. origanoides EO from the Yucatan Peninsula, which has the potential for the development of anti-S. aureus agents.
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Affiliation(s)
- Andrés Humberto Uc-Cachón
- Unidad de Investigación Médica Yucatán, Instituto Mexicano del Seguro Social, Mérida 97150, Yucatán, Mexico; (A.H.U.-C.); (A.d.J.D.-B.); (H.E.D.-B.)
| | - Luz María Calvo-Irabien
- Unidad de Recursos Naturales, Centro de Investigación Científica de Yucatán, Mérida 97204, Yucatán, Mexico;
| | - Angel de Jesús Dzul-Beh
- Unidad de Investigación Médica Yucatán, Instituto Mexicano del Seguro Social, Mérida 97150, Yucatán, Mexico; (A.H.U.-C.); (A.d.J.D.-B.); (H.E.D.-B.)
| | - Haziel Eleazar Dzib-Baak
- Unidad de Investigación Médica Yucatán, Instituto Mexicano del Seguro Social, Mérida 97150, Yucatán, Mexico; (A.H.U.-C.); (A.d.J.D.-B.); (H.E.D.-B.)
| | - Rosa Grijalva-Arango
- Unidad de Recursos Naturales, Centro de Investigación Científica de Yucatán, Mérida 97204, Yucatán, Mexico;
| | - Gloria María Molina-Salinas
- Unidad de Investigación Médica Yucatán, Instituto Mexicano del Seguro Social, Mérida 97150, Yucatán, Mexico; (A.H.U.-C.); (A.d.J.D.-B.); (H.E.D.-B.)
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Dexlin XDD, Tarika JDD, Kumar AA, Beaula TJ. Hypothetical confirmation for the anti-bacterial compound potassium succinate-succinic acid in comparison with certain succinate derivatives. J Biomol Struct Dyn 2024; 42:1237-1248. [PMID: 37021491 DOI: 10.1080/07391102.2023.2199078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 03/29/2023] [Indexed: 04/07/2023]
Abstract
The development of antibacterial medications has recently been promoted due to the non- effective usage of antibiotics and the rise in severe bacterial infections. The effectiveness of antimicrobial therapy alternatives is constrained due to the prevalence of germs that are resistant to medications. Our current study's goal is to favor metallic compounds for antibiotic delivery in order to increase the effectiveness of the antibacterial regimen. Due to its bioactivity, potassium succinate-succinic acid is preferred because in general, the succinic acid compound has the greatest potential against microbial infections and a natural antibiotic because of its relative acidic nature. In the current study, the molecular geometry, band gap energies, molecular electrostatic interactions and potential energy distribution of the molecule were compared with those of certain succinate derivatives. The potential compound potassium succinate succinic acid was probed using FT-IR and FT-Raman analyses. Vibrational assignments pertaining to different modes of vibration with potential energy distribution have been improved by normal coordinate analysis. The chemical bond stability which is largely important for biological activity is studied using NBO analysis. The molecular docking study suggests that the molecule possesses antibacterial action and displays a minimal binding energy of -5.3 kcal/mol which can be endorsed for the prevention of any bacterial illness. From the results of our studies, the material would be stable and bioactive according to the FMO study, which indicates a band gap value of 4.35 eV and the pharmacokinetic features of the molecule, was predicted using the ADMET factors and the drug-likeness test.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- X D Divya Dexlin
- Department of Physics and Research Centre, Malankara Catholic College, Mariagiri, Tamilnadu, India
- Manonmaniam Sundaranar University, Tirunelveli, Tamilnadu, India
| | - J D Deephlin Tarika
- Department of Physics and Research Centre, Malankara Catholic College, Mariagiri, Tamilnadu, India
- Manonmaniam Sundaranar University, Tirunelveli, Tamilnadu, India
| | - A Arun Kumar
- Department of Physics (H & Sc), Methodist College of Engineering & Technology (Autonomous), Hyderabad, India
| | - T Joselin Beaula
- Department of Physics and Research Centre, Malankara Catholic College, Mariagiri, Tamilnadu, India
- Manonmaniam Sundaranar University, Tirunelveli, Tamilnadu, India
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Garza-Cervantes JA, Mendiola-Garza G, León-Buitimea A, Morones-Ramírez JR. Synergistic antibacterial effects of exopolysaccharides/nickel-nanoparticles composites against multidrug-resistant bacteria. Sci Rep 2023; 13:21519. [PMID: 38057583 PMCID: PMC10700344 DOI: 10.1038/s41598-023-48821-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/30/2023] [Indexed: 12/08/2023] Open
Abstract
The need for an alternative treatment to fight infectious diseases caused by antibiotic-resistant bacteria is increasing. A possible way to overcome bacterial resistance to antibiotics is by reintroducing commonly used antibiotics with a sensitizer capable of enhancing their antimicrobial effect in resistant bacteria. Here, we use a composite composed of exopolysaccharide capped-NiO NPs, with antimicrobial effects against antibiotic-resistant Gram-positive and Gram-negative bacteria. It potentiated the antimicrobial effects of four different antibiotics (ampicillin, kanamycin, chloramphenicol, and ciprofloxacin) at lower concentrations than their minimal inhibitory concentrations. We observed that the Ni-composite synergistically enhanced, fourfold, the antibacterial effect of kanamycin and chloramphenicol against multidrug-resistant Staphylococcus aureus and Pseudomonas aeruginosa, as well as ampicillin against multidrug-resistant Staphylococcus aureus, and ciprofloxacin against multidrug-resistant Pseudomonas aeruginosa by eightfold. We also found that Ni-composite could not inhibit biofilm synthesis on the tested bacterial strains. Our results demonstrated the possibility of using metal nanoparticles, like NiO, as a sensitizer to overcome bacterial antibiotic resistance.
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Affiliation(s)
- Javier A Garza-Cervantes
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, UANL, 66455, San Nicolás de los Garza, NL, Mexico
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, Parque de Investigación e Innovación Tecnológica, 66629, Apodaca, Nuevo León, Mexico
| | - Gricelda Mendiola-Garza
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, UANL, 66455, San Nicolás de los Garza, NL, Mexico
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, Parque de Investigación e Innovación Tecnológica, 66629, Apodaca, Nuevo León, Mexico
| | - Angel León-Buitimea
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, UANL, 66455, San Nicolás de los Garza, NL, Mexico
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, Parque de Investigación e Innovación Tecnológica, 66629, Apodaca, Nuevo León, Mexico
| | - José Rubén Morones-Ramírez
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, UANL, 66455, San Nicolás de los Garza, NL, Mexico.
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, Parque de Investigación e Innovación Tecnológica, 66629, Apodaca, Nuevo León, Mexico.
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Li H, Fu Y, Song F, Xu X. Recent Updates on the Antimicrobial Compounds from Marine-Derived Penicillium fungi. Chem Biodivers 2023; 20:e202301278. [PMID: 37877324 DOI: 10.1002/cbdv.202301278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 10/26/2023]
Abstract
In this review, 72 compounds isolated from marine-derived Penicillium fungi and their antimicrobial activities are reviewed from 2020 to 2023. According to their structures, these compounds can be divided into terpenoids, polyketides, alkaloids and other structural compounds, among which terpenoids and polyketides are relatively large in number. Some compounds have powerful inhibitory effects against different pathogenic bacteria and fungi. This review aims to provide more useful information and enlightenment for further efficient utilization of Penicillium spp. and their secondary metabolites.
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Affiliation(s)
- Honghua Li
- Key Laboratory of Geriatric Nutrition and Health, Ministry of Education of China, School of Light Industry, Beijing Technology and Business University, 100048, Beijing, P. R. China
| | - Yanqi Fu
- Key Laboratory of Geriatric Nutrition and Health, Ministry of Education of China, School of Light Industry, Beijing Technology and Business University, 100048, Beijing, P. R. China
| | - Fuhang Song
- Key Laboratory of Geriatric Nutrition and Health, Ministry of Education of China, School of Light Industry, Beijing Technology and Business University, 100048, Beijing, P. R. China
| | - Xiuli Xu
- School of Ocean Sciences, China University of Geosciences, 100083, Beijing, P. R. China
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Gupta R, Singh M, Pathania R. Chemical genetic approaches for the discovery of bacterial cell wall inhibitors. RSC Med Chem 2023; 14:2125-2154. [PMID: 37974958 PMCID: PMC10650376 DOI: 10.1039/d3md00143a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 08/10/2023] [Indexed: 11/19/2023] Open
Abstract
Antimicrobial resistance (AMR) in bacterial pathogens is a worldwide health issue. The innovation gap in discovering new antibiotics has remained a significant hurdle in combating the AMR problem. Currently, antibiotics target various vital components of the bacterial cell envelope, nucleic acid and protein biosynthesis machinery and metabolic pathways essential for bacterial survival. The critical role of the bacterial cell envelope in cell morphogenesis and integrity makes it an attractive drug target. While a significant number of in-clinic antibiotics target peptidoglycan biosynthesis, several components of the bacterial cell envelope have been overlooked. This review focuses on various antibacterial targets in the bacterial cell wall and the strategies employed to find their novel inhibitors. This review will further elaborate on combining forward and reverse chemical genetic approaches to discover antibacterials that target the bacterial cell envelope.
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Affiliation(s)
- Rinki Gupta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
| | - Mangal Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
| | - Ranjana Pathania
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
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Liu H, Huang Z, Chen H, Zhang Y, Yu P, Hu P, Zhang X, Cao J, Zhou T. A potential strategy against clinical carbapenem-resistant Enterobacteriaceae: antimicrobial activity study of sweetener-decorated gold nanoparticles in vitro and in vivo. J Nanobiotechnology 2023; 21:409. [PMID: 37932843 PMCID: PMC10626710 DOI: 10.1186/s12951-023-02149-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/09/2023] [Indexed: 11/08/2023] Open
Abstract
BACKGROUND Carbapenem-resistant Enterobacteriaceae (CRE) present substantial challenges to clinical intervention, necessitating the formulation of novel antimicrobial strategies to counteract them. Nanomaterials offer a distinctive avenue for eradicating bacteria by employing mechanisms divergent from traditional antibiotic resistance pathways and exhibiting reduced susceptibility to drug resistance development. Non-caloric artificial sweeteners, commonly utilized in the food sector, such as saccharin, sucralose, acesulfame, and aspartame, possess structures amenable to nanomaterial formation. In this investigation, we synthesized gold nanoparticles decorated with non-caloric artificial sweeteners and evaluated their antimicrobial efficacy against clinical CRE strains. RESULTS Among these, gold nanoparticles decorated with aspartame (ASP_Au NPs) exhibited the most potent antimicrobial effect, displaying minimum inhibitory concentrations ranging from 4 to 16 µg/mL. As a result, ASP_Au NPs were chosen for further experimentation. Elucidation of the antimicrobial mechanism unveiled that ASP_Au NPs substantially elevated bacterial reactive oxygen species (ROS) levels, which dissipated upon ROS scavenger treatment, indicating ROS accumulation within bacteria as the fundamental antimicrobial modality. Furthermore, findings from membrane permeability assessments suggested that ASP_Au NPs may represent a secondary antimicrobial modality via enhancing inner membrane permeability. In addition, experiments involving crystal violet and confocal live/dead staining demonstrated effective suppression of bacterial biofilm formation by ASP_Au NPs. Moreover, ASP_Au NPs demonstrated notable efficacy in the treatment of Galleria mellonella bacterial infection and acute abdominal infection in mice, concurrently mitigating the organism's inflammatory response. Crucially, evaluation of in vivo safety and biocompatibility established that ASP_Au NPs exhibited negligible toxicity at bactericidal concentrations. CONCLUSIONS Our results demonstrated that ASP_Au NPs exhibit promise as innovative antimicrobial agents against clinical CRE.
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Affiliation(s)
- Haifeng Liu
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, Zhejiang, China
| | - Zeyu Huang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, Zhejiang, China
| | - Huanchang Chen
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, Zhejiang, China
| | - Ying Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, Zhejiang, China
| | - Pingting Yu
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, Zhejiang, China
| | - Panjie Hu
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xiaotuan Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, Zhejiang, China
| | - Jianming Cao
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, Zhejiang, China.
| | - Tieli Zhou
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, Zhejiang, China.
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Maryam H, Fazel P, Mostafa N. Isolation and Screening of Antibacterial Activity of Actinomycetota from the Medicinal Plant, Anthemis pseudocotula Boiss. ARCHIVES OF RAZI INSTITUTE 2023; 78:1638-1646. [PMID: 38590676 PMCID: PMC10998938 DOI: 10.22092/ari.2023.78.5.1638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 03/11/2023] [Indexed: 04/10/2024]
Abstract
Antibiotic resistance is rising dramatically worldwide, and thus the production of new antibiotics is indispensable. Recent scientific initiatives have focused on the bioprospecting of microorganisms' secondary metabolites, with a particular focus on the look for natural products with antimicrobial properties derived from endophytes. All plant species, regardless of their type, are thought to anchor endophytic bacteria (EB). There are many potential uses for the natural therapeutic compounds made by EB in medicine, agriculture, and the pharmaceutical industry. To investigate antibacterial properties in this study, Actinomycetota (formerly, Actinobacteria) were isolated from Anthemis pseudocotula Boiss., identified, and underwent bioprospecting by morphological and molecular methods. Samples were collected from Ilam, Iran, and then divided into roots, leaves, stems, and flowers. After disinfection, they were cut into 2 mm pieces, cultured on casein agar culture medium, and incubated at 28ºC for up to four weeks. Actinomycetota was identified using the polymerase chain reaction method targeting the 16S rRNA gene. To evaluate the antibacterial properties of the isolated Actinomycetota, the agar diffusion method was used. In parallel, the frequencies of biosynthetic gene clusters, including polyketide synthase (PKS-I and PKS-II) and nonribosomal peptide synthetase (NRPS) genes, were determined in the isolated Actinomycetota. Ninety bacteria were isolated from different parts of Anthemis flowers. Thirty-eight (42.2%) of these bacteria belonged to the phylum Actinomycetota, and out of these 38, 15 isolates (39.5%) had antibacterial properties. Of these, 11 isolates (73.3%) exhibited antibacterial effects against Staphylococcus aureus, 2 (13.3%) against Pseudomonas aeruginosa, 3 (20%) against Escherichia coli, and two isolates (13.3%) against Salmonella enterica sub-species of enterica serovar Typhimurium. The results of the molecular analysis of PKS-I, PKS-II, and NRPS genes showed that out of 38 isolated Actinomycetota strains, 23 isolates (60.5%) carried PKS-I gene, 6 (15.8%) harbored PKS-II gene, and 20 isolates (52.6%) had NRPS gene. This study indicates that Anthemis pseudocotula Boiss. has a number of active Actinomycetota that produce secondary metabolites with antibacterial properties.
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Affiliation(s)
- Hajizadeh Maryam
- Department of Microbiology, Faculty of Veterinary Sciences, Ilam University, Ilam, Iran
| | - Pourahmad Fazel
- Department of Microbiology, Faculty of Veterinary Sciences, Ilam University, Ilam, Iran
| | - Nemati Mostafa
- Department of Microbiology, Faculty of Veterinary Sciences, Ilam University, Ilam, Iran
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Han N, Li J, Zhao F, Li Y, Wang J, Dai X, Zeng D, Xiong W, Zeng Z. Isopropoxy Benzene Guanidine Ameliorates Streptococcus suis Infection In Vivo and In Vitro. Int J Mol Sci 2023; 24:ijms24087354. [PMID: 37108521 PMCID: PMC10138962 DOI: 10.3390/ijms24087354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/21/2023] [Accepted: 03/27/2023] [Indexed: 04/29/2023] Open
Abstract
Streptococcus suis, an encapsulated zoonotic pathogen, has been reported to cause a variety of infectious diseases, such as meningitis and streptococcal-toxic-shock-like syndrome. Increasing antimicrobial resistance has triggered the need for new treatments. In the present study, we found that isopropoxy benzene guanidine (IBG) significantly attenuated the effects caused by S. suis infection, in vivo and in vitro, by killing S. suis and reducing S. suis pathogenicity. Further studies showed that IBG disrupted the integrity of S. suis cell membranes and increased the permeability of S. suis cell membranes, leading to an imbalance in proton motive force and the accumulation of intracellular ATP. Meanwhile, IBG antagonized the hemolysis activity of suilysin and decreased the expression of Sly gene. In vivo, IBG improved the viability of S. suis SS3-infected mice by reducing tissue bacterial load. In conclusion, IBG is a promising compound for the treatment of S. suis infections, given its antibacterial and anti-hemolysis activity.
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Affiliation(s)
- Ning Han
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Jie Li
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Feifei Zhao
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Yangyang Li
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Jun Wang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Xiaolan Dai
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Dongping Zeng
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Wenguang Xiong
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Zhenling Zeng
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
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11
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Awada B, Chahine DA, Derbaj G, Khalek PA, Awad MK, Fayad AA. Antimicrobial Natural Products Derived from Microorganisms Inhabiting the MENA Region. Nat Prod Commun 2023. [DOI: 10.1177/1934578x231154989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
Objective/Background Natural products (NPs) derived from microorganisms are the basis of a plethora of clinically utilized medications, namely, antimicrobial remedies. Although these secondary metabolites have been extensively explored all over the planet, they remain understudied in the Middle East and North Africa (MENA) region. Methods A literature search was conducted to first find NPs that were isolated from environmental fungi and bacteria that inhabit the soils and seawater of the MENA region. Then, purified molecules with biological activity against pathogenic bacteria, biofilms, fungi, and parasites were described in terms of structure, function, and location. Moreover, the methods that could be used to ameliorate the discovery of novel NPs from this region were investigated. Results A multitude of antimicrobial molecules from various chemical classes were found to be derived from the environmental microbes of MENA. Although many were rediscovered, some represented novel structural scaffolds for novel families of antimicrobial agents. Additionally, the geographical distribution showed a high number of these NPs were unraveled in a restricted area leaving much of MENA untapped. Furthermore, as relatively traditional and low-efficiency methods were typically used in the discovery process, advanced high-throughput techniques were suggested to enhance this practice at the regional level. Conclusion MENA represents a fairly unexploited region where antimicrobial drug discovery could be performed comprehensively through the concomitant exploration of untouched geographical locations and advanced molecular techniques.
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Affiliation(s)
- Bassel Awada
- Department of Experimental Pathology, Immunology and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Center for Drug Discovery, American University of Beirut, Beirut, Lebanon
| | - Dany Abi Chahine
- Center for Drug Discovery, American University of Beirut, Beirut, Lebanon
- Laboratory of Biodiversity and Functional Genomics, UR EGP, Faculty of Science, Université Saint-Joseph de Beyrouth, Beirut, Lebanon
| | - Ghada Derbaj
- Department of Experimental Pathology, Immunology and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Center for Drug Discovery, American University of Beirut, Beirut, Lebanon
| | - Pascal Abdel Khalek
- Department of Experimental Pathology, Immunology and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Center for Drug Discovery, American University of Beirut, Beirut, Lebanon
| | - Mireille Kallassy Awad
- Laboratory of Biodiversity and Functional Genomics, UR EGP, Faculty of Science, Université Saint-Joseph de Beyrouth, Beirut, Lebanon
| | - Antoine Abou Fayad
- Department of Experimental Pathology, Immunology and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Center for Drug Discovery, American University of Beirut, Beirut, Lebanon
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12
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Qin GF, Zhang X, Zhu F, Huo ZQ, Yao QQ, Feng Q, Liu Z, Zhang GM, Yao JC, Liang HB. MS/MS-Based Molecular Networking: An Efficient Approach for Natural Products Dereplication. MOLECULES (BASEL, SWITZERLAND) 2022; 28:molecules28010157. [PMID: 36615351 PMCID: PMC9822519 DOI: 10.3390/molecules28010157] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/13/2022] [Accepted: 12/20/2022] [Indexed: 12/29/2022]
Abstract
Natural products (NPs) have historically played a primary role in the discovery of small-molecule drugs. However, due to the advent of other methodologies and the drawbacks of NPs, the pharmaceutical industry has largely declined in interest regarding the screening of new drugs from NPs since 2000. There are many technical bottlenecks to quickly obtaining new bioactive NPs on a large scale, which has made NP-based drug discovery very time-consuming, and the first thorny problem faced by researchers is how to dereplicate NPs from crude extracts. Remarkably, with the rapid development of omics, analytical instrumentation, and artificial intelligence technology, in 2012, an efficient approach, known as tandem mass spectrometry (MS/MS)-based molecular networking (MN) analysis, was developed to avoid the rediscovery of known compounds from the complex natural mixtures. Then, in the past decade, based on the classical MN (CLMN), feature-based MN (FBMN), ion identity MN (IIMN), building blocks-based molecular network (BBMN), substructure-based MN (MS2LDA), and bioactivity-based MN (BMN) methods have been presented. In this paper, we review the basic principles, general workflow, and application examples of the methods mentioned above, to further the research and applications of these methods.
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Affiliation(s)
- Guo-Fei Qin
- State Key Laboratory of Generic Manufacture Technology of Chinese Traditional Medicine, Lunan Pharmaceutical Group Co., Ltd., Linyi 273400, China
- Correspondence: (G.-F.Q.); (J.-C.Y.); (H.-B.L.); Tel.: +86-539-503-0319 (G.-F.Q.)
| | - Xiao Zhang
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Feng Zhu
- State Key Laboratory of Generic Manufacture Technology of Chinese Traditional Medicine, Lunan Pharmaceutical Group Co., Ltd., Linyi 273400, China
| | - Zong-Qing Huo
- State Key Laboratory of Generic Manufacture Technology of Chinese Traditional Medicine, Lunan Pharmaceutical Group Co., Ltd., Linyi 273400, China
| | | | - Qun Feng
- State Key Laboratory of Generic Manufacture Technology of Chinese Traditional Medicine, Lunan Pharmaceutical Group Co., Ltd., Linyi 273400, China
| | - Zhong Liu
- State Key Laboratory of Generic Manufacture Technology of Chinese Traditional Medicine, Lunan Pharmaceutical Group Co., Ltd., Linyi 273400, China
| | - Gui-Min Zhang
- State Key Laboratory of Generic Manufacture Technology of Chinese Traditional Medicine, Lunan Pharmaceutical Group Co., Ltd., Linyi 273400, China
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Jing-Chun Yao
- State Key Laboratory of Generic Manufacture Technology of Chinese Traditional Medicine, Lunan Pharmaceutical Group Co., Ltd., Linyi 273400, China
- Correspondence: (G.-F.Q.); (J.-C.Y.); (H.-B.L.); Tel.: +86-539-503-0319 (G.-F.Q.)
| | - Hong-Bao Liang
- State Key Laboratory of Generic Manufacture Technology of Chinese Traditional Medicine, Lunan Pharmaceutical Group Co., Ltd., Linyi 273400, China
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
- Correspondence: (G.-F.Q.); (J.-C.Y.); (H.-B.L.); Tel.: +86-539-503-0319 (G.-F.Q.)
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13
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Xu Z, Eichler B, Klausner EA, Duffy-Matzner J, Zheng W. Lead/Drug Discovery from Natural Resources. Molecules 2022; 27:molecules27238280. [PMID: 36500375 PMCID: PMC9736696 DOI: 10.3390/molecules27238280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/18/2022] [Accepted: 11/18/2022] [Indexed: 11/29/2022] Open
Abstract
Natural products and their derivatives have been shown to be effective drug candidates against various diseases for many years. Over a long period of time, nature has produced an abundant and prosperous source pool for novel therapeutic agents with distinctive structures. Major natural-product-based drugs approved for clinical use include anti-infectives and anticancer agents. This paper will review some natural-product-related potent anticancer, anti-HIV, antibacterial and antimalarial drugs or lead compounds mainly discovered from 2016 to 2022. Structurally typical marine bioactive products are also included. Molecular modeling, machine learning, bioinformatics and other computer-assisted techniques that are very important in narrowing down bioactive core structural scaffolds and helping to design new structures to fight against key disease-associated molecular targets based on available natural products are considered and briefly reviewed.
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Affiliation(s)
- Zhihong Xu
- Department of Chemistry and Biochemistry, Augustana University, 2001 S Summit Ave., Sioux Falls, SD 57197, USA
- Institute of Interventional & Vascular Surgery, Tongji University, Shanghai 200072, China
- Department of Pharmaceutical Sciences, South College School of Pharmacy, 400 Goody’s Lane, Knoxville, TN 37922, USA
- Correspondence: ; Tel.: +1-(605)-274-5008
| | - Barrett Eichler
- Department of Chemistry and Biochemistry, Augustana University, 2001 S Summit Ave., Sioux Falls, SD 57197, USA
| | - Eytan A. Klausner
- Department of Pharmaceutical Sciences, South College School of Pharmacy, 400 Goody’s Lane, Knoxville, TN 37922, USA
| | - Jetty Duffy-Matzner
- Department of Chemistry and Biochemistry, Augustana University, 2001 S Summit Ave., Sioux Falls, SD 57197, USA
| | - Weifan Zheng
- Biomanufacturing Research Institute and Technology Enterprise, North Carolina Central University, 1801 Fayetteville St., Durham, NC 27707, USA
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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14
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Iwamoto-Kihara A. Regulatory Mechanisms and Environmental Adaptation of the F-ATPase Family. Biol Pharm Bull 2022; 45:1412-1418. [PMID: 36184497 DOI: 10.1248/bpb.b22-00419] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The F-type ATPase family of enzymes, including ATP synthases, are found ubiquitously in biological membranes. ATP synthesis from ADP and inorganic phosphate is driven by an electrochemical H+ gradient or H+ motive force, in which intramolecular rotation of F-type ATPase is generated with H+ transport across the membranes. Because this rotation is essential for energy coupling between catalysis and H+-transport, regulation of the rotation is important to adapt to environmental changes and maintain ATP concentration. Recently, a series of cryo-electron microscopy images provided detailed insights into the structure of the H+ pathway and the multiple subunit arrangement. However, the regulatory mechanism of the rotation has not been clarified. This review describes the inhibition mechanism of ATP hydrolysis in bacterial enzymes. In addition, properties of the F-type ATPase of Streptococcus mutans, which acts as a H+-pump in an acidic environment, are described. These findings may help in the development of novel antimicrobial agents.
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15
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Zada S, Sajjad W, Rafiq M, Ali S, Hu Z, Wang H, Cai R. Cave Microbes as a Potential Source of Drugs Development in the Modern Era. MICROBIAL ECOLOGY 2022; 84:676-687. [PMID: 34693460 PMCID: PMC8542507 DOI: 10.1007/s00248-021-01889-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/29/2021] [Indexed: 06/13/2023]
Abstract
The world is constantly facing threats, including the emergence of new pathogens and antibiotic resistance among extant pathogens, which is a matter of concern. Therefore, the need for natural and effective sources of drugs is inevitable. The ancient and pristine ecosystems of caves contain a unique microbial world and could provide a possible source of antimicrobial metabolites. The association between humans and caves is as old as human history itself. Historically, cave environments have been used to treat patients with respiratory tract infections, which is referred to as speleotherapy. Today, the pristine environment of caves that comprise a poorly explored microbial world is a potential source of antimicrobial and anticancer drugs. Oligotrophic conditions in caves enhance the competition among microbial communities, and unique antimicrobial agents may be used in this competition. This review suggests that the world needs a novel and effective source of drug discovery. Therefore, being the emerging spot of modern human civilization, caves could play a crucial role in the current medical crisis, and cave microorganisms may have the potential to produce novel antimicrobial and anticancer drugs.
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Affiliation(s)
- Sahib Zada
- Biology Department, College of Science, Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, Shantou, China
| | - Wasim Sajjad
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Muhammad Rafiq
- Department of Microbiology, Faculty of Life Sciences and Informatics, Balochistan University of IT, Engineering and Management Sciences, QUETTA, Pakistan
| | - Sardar Ali
- Biology Department, College of Science, Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, Shantou, China
| | - Zhong Hu
- Biology Department, College of Science, Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, Shantou, China
| | - Hui Wang
- Biology Department, College of Science, Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, Shantou, China
| | - Runlin Cai
- Biology Department, College of Science, Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, Shantou, China.
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16
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Dietary Bacitracin Methylene Disalicylate Improves Growth Performance by Mediating the Gut Microbiota in Broilers. Antibiotics (Basel) 2022; 11:antibiotics11060818. [PMID: 35740224 PMCID: PMC9219630 DOI: 10.3390/antibiotics11060818] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/13/2022] [Accepted: 06/15/2022] [Indexed: 02/06/2023] Open
Abstract
The growth performance of livestock and poultry has always been a concern. However, much work is currently focused on the selection of breeds and diets to improve the growth performance of livestock and poultry. Furthermore, numerous studies have shown that the gut microbiota is closely related to the growth performance of livestock and poultry. At present, there are many reports on the impact of antibiotic intervention on the structure of gut microbiota. However, there are few reports on the influence of antibiotic intervention on the structure of intestinal microbes and the effect of this change on growth performance. Bacitracin methylene disalicylate (BMD) intervention changes the microbial structure in the caecum of broilers at different growth stages, as shown in this study. To further reveal the potential relationship between gut microbiota changes and growth performance caused by BMD intervention, correlation analysis was used for analysis. A total of 144 1-day-old male Cobb-Vantress were randomly divided into two groups. In addition to antibiotic-free starter mash diets, starter mash diets supplemented with 55 mg/kg BMD were also used, called the CON group and the BMD group, and lasted 28 days. (1) These study results showed that adding BMD to the diet had a significant effect on the growth performance of broilers. Compared with the CON group, the body weight of the BMD group increased significantly by 11.08% and 20.13% on Days 14 and 28, respectively (p < 0.05). Similarly, at 0−14, 14−28 and 0−28 days of age, the average daily gain of the BMD group increased significantly by 12.28%, 24.49% and 20.80%, respectively. The average daily feed intake of the BMD group increased significantly by 18.28%, 27.39% and 24.97% (p < 0.05). In addition, at 0−28 days of age, the feed conversion ratio increased significantly by 5.5% (p < 0.05). (2) Alpha diversity results show that BMD intervention has an impact on gut microbiota at different growth stages. (3) The early intervention significantly affected 7 taxa by Day 14, followed by 22 taxa by Day 28, which is similar to the results in the caecal flora. Compared with the CON group, the Christensenellaceae R-7 group had the highest linear discriminant analysis (LDA) score on Day 28. In addition, Pearson’s correlation analysis showed that the Lachnospiraceae FCS020 group was significantly negatively correlated with growth performance. In general, these results indicate that dietary supplementation of BMD has an effect on broiler gut microbiota structure and growth performance. However, changes in growth performance may be caused by the gut microbiota structure.
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17
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Malit JJL, Leung HYC, Qian PY. Targeted Large-Scale Genome Mining and Candidate Prioritization for Natural Product Discovery. Mar Drugs 2022; 20:md20060398. [PMID: 35736201 PMCID: PMC9231227 DOI: 10.3390/md20060398] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/08/2022] [Accepted: 06/14/2022] [Indexed: 12/20/2022] Open
Abstract
Large-scale genome-mining analyses have identified an enormous number of cryptic biosynthetic gene clusters (BGCs) as a great source of novel bioactive natural products. Given the sheer number of natural product (NP) candidates, effective strategies and computational methods are keys to choosing appropriate BGCs for further NP characterization and production. This review discusses genomics-based approaches for prioritizing candidate BGCs extracted from large-scale genomic data, by highlighting studies that have successfully produced compounds with high chemical novelty, novel biosynthesis pathway, and potent bioactivities. We group these studies based on their BGC-prioritization logics: detecting presence of resistance genes, use of phylogenomics analysis as a guide, and targeting for specific chemical structures. We also briefly comment on the different bioinformatics tools used in the field and examine practical considerations when employing a large-scale genome mining study.
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Affiliation(s)
- Jessie James Limlingan Malit
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; (J.J.L.M.); (H.Y.C.L.)
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Hiu Yu Cherie Leung
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; (J.J.L.M.); (H.Y.C.L.)
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Pei-Yuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; (J.J.L.M.); (H.Y.C.L.)
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China
- Correspondence:
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18
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Gavriilidou A, Kautsar SA, Zaburannyi N, Krug D, Müller R, Medema MH, Ziemert N. Compendium of specialized metabolite biosynthetic diversity encoded in bacterial genomes. Nat Microbiol 2022; 7:726-735. [PMID: 35505244 DOI: 10.1038/s41564-022-01110-2] [Citation(s) in RCA: 93] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 03/24/2022] [Indexed: 12/27/2022]
Abstract
Bacterial specialized metabolites are a proven source of antibiotics and cancer therapies, but whether we have sampled all the secondary metabolite chemical diversity of cultivated bacteria is not known. We analysed ~170,000 bacterial genomes and ~47,000 metagenome assembled genomes (MAGs) using a modified BiG-SLiCE and the new clust-o-matic algorithm. We estimate that only 3% of the natural products potentially encoded in bacterial genomes have been experimentally characterized. We show that the variation in secondary metabolite biosynthetic diversity drops significantly at the genus level, identifying it as an appropriate taxonomic rank for comparison. Equal comparison of genera based on relative evolutionary distance revealed that Streptomyces bacteria encode the largest biosynthetic diversity by far, with Amycolatopsis, Kutzneria and Micromonospora also encoding substantial diversity. Finally, we find that several less-well-studied taxa, such as Weeksellaceae (Bacteroidota), Myxococcaceae (Myxococcota), Pleurocapsa and Nostocaceae (Cyanobacteria), have potential to produce highly diverse sets of secondary metabolites that warrant further investigation.
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Affiliation(s)
- Athina Gavriilidou
- Translational Genome Mining for Natural Products, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Tübingen, Germany
| | - Satria A Kautsar
- Bioinformatics Group, Wageningen University, Wageningen, the Netherlands.,Chemistry Department, Scripps Research Florida, Jupiter, FL, USA
| | - Nestor Zaburannyi
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany.,German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Daniel Krug
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany.,German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany.,German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, the Netherlands.
| | - Nadine Ziemert
- Translational Genome Mining for Natural Products, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Tübingen, Germany. .,Cluster of Excellence 'Controlling Microbes to Fight Infections' (CMFI), University of Tübingen, Tübingen, Germany. .,German Centre for Infection Research (DZIF), Partnersite Tübingen, Tübingen, Germany.
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19
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Thuan NH, Tatipamula VB, Canh NX, Van Giang N. Recent advances in microbial co-culture for production of value-added compounds. 3 Biotech 2022; 12:115. [PMID: 35547018 PMCID: PMC9018925 DOI: 10.1007/s13205-022-03177-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 03/31/2022] [Indexed: 02/06/2023] Open
Abstract
Micro-organisms have often been used to produce bioactive compounds as antibiotics, antifungals, and anti-tumors, etc. due to their easy and applicable culture, genetic manipulation, and extraction, etc. Mainly, microbial mono-cultures have been applied to produce value-added compounds and gotten numerous valuable results. However, mono-culture also has several complicated problems, such as metabolic burdens affecting the growth and development of the host, leading to a decrease in titer of the target compound. To circumvent those limitations, microbial co-culture has been technically developed and gained much interest compared to mono-culture. For example, co-culture simplifies the design of artificial biosynthetic pathways and restricts the recombinant host's metabolic burden, causing increased titer of desired compounds. This paper summarizes the recent advanced progress in applying microbial platform co-culture to produce natural products, such as flavonoid, terpenoid, alkaloid, etc. Furthermore, importantly different strategies for enhancing production, overcoming the metabolic burdens, building autonomous modulation of cell growth rate and culture composition in response to a quorum-sensing signal, etc., were also described in detail.
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Affiliation(s)
- Nguyen Huy Thuan
- Center for Molecular Biology, Duy Tan University, Da Nang, 550000 Vietnam
| | | | - Nguyen Xuan Canh
- Faculty of Biotechnology, Vietnam National University of Agriculture, Gialam, Hanoi Vietnam
| | - Nguyen Van Giang
- Faculty of Biotechnology, Vietnam National University of Agriculture, Gialam, Hanoi Vietnam
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20
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Progress Report: Antimicrobial Drug Discovery in the Resistance Era. Pharmaceuticals (Basel) 2022; 15:ph15040413. [PMID: 35455410 PMCID: PMC9030565 DOI: 10.3390/ph15040413] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 02/05/2023] Open
Abstract
Antibiotic resistance continues to be a most serious threat to public health. This situation demands that the scientific community increase their efforts for the discovery of alternative strategies to circumvent the problems associated with conventional small molecule therapeutics. The Global Antimicrobial Resistance and Use Surveillance System (GLASS) Report (published in June 2021) discloses the rapidly increasing number of bacterial infections that are mainly caused by antimicrobial-resistant bacteria. These concerns have initiated various government agencies and other organizations to educate the public regarding the appropriate use of antibiotics. This review discusses a brief highlight on the timeline of antimicrobial drug discovery with a special emphasis on the historical development of antimicrobial resistance. In addition, new antimicrobial targets and approaches, recent developments in drug screening, design, and delivery were covered. This review also discusses the emergence and roles of various antibiotic adjuvants and combination therapies while shedding light on current challenges and future perspectives. Overall, the emergence of resistant microbial strains has challenged drug discovery but their efforts to develop alternative technologies such as nanomaterials seem to be promising for the future.
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Jordan JA, Lenski RE, Card KJ. Idiosyncratic Fitness Costs of Ampicillin-Resistant Mutants Derived from a Long-Term Experiment with Escherichia coli. Antibiotics (Basel) 2022; 11:antibiotics11030347. [PMID: 35326810 PMCID: PMC8944548 DOI: 10.3390/antibiotics11030347] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 02/28/2022] [Accepted: 03/03/2022] [Indexed: 02/04/2023] Open
Abstract
Antibiotic resistance is a growing concern that has prompted a renewed focus on drug discovery, stewardship, and evolutionary studies of the patterns and processes that underlie this phenomenon. A resistant strain’s competitive fitness relative to its sensitive counterparts in the absence of drug can impact its spread and persistence in both clinical and community settings. In a prior study, we examined the fitness of tetracycline-resistant clones that evolved from five different Escherichia coli genotypes, which had diverged during a long-term evolution experiment. In this study, we build on that work to examine whether ampicillin-resistant mutants are also less fit in the absence of the drug than their sensitive parents, and whether the cost of resistance is constant or variable among independently derived lines. Like the tetracycline-resistant lines, the ampicillin-resistant mutants were often less fit than their sensitive parents, with significant variation in the fitness costs among the mutants. This variation was not associated with the level of resistance conferred by the mutations, nor did it vary across the different parental backgrounds. In our earlier study, some of the variation in fitness costs associated with tetracycline resistance was explained by the effects of different mutations affecting the same cellular pathway and even the same gene. In contrast, the variance among the ampicillin-resistant mutants was associated with different sets of target genes. About half of the resistant clones suffered large fitness deficits, and their mutations impacted major outer-membrane proteins or subunits of RNA polymerases. The other mutants experienced little or no fitness costs and with, one exception, they had mutations affecting other genes and functions. Our findings underscore the importance of comparative studies on the evolution of antibiotic resistance, and they highlight the nuanced processes that shape these phenotypes.
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Affiliation(s)
- Jalin A. Jordan
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA;
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Richard E. Lenski
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA;
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI 48824, USA
| | - Kyle J. Card
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI 48824, USA
- Department of Translational Hematology and Oncology Research, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44106, USA
- Correspondence:
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Amaning Danquah C, Minkah PAB, Osei Duah Junior I, Amankwah KB, Somuah SO. Antimicrobial Compounds from Microorganisms. Antibiotics (Basel) 2022; 11:285. [PMID: 35326749 PMCID: PMC8944786 DOI: 10.3390/antibiotics11030285] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 01/27/2022] [Accepted: 02/07/2022] [Indexed: 02/06/2023] Open
Abstract
Antimicrobial resistance is an exigent public health concern owing to the emergence of novel strains of human resistant pathogens and the concurrent rise in multi-drug resistance. An influx of new antimicrobials is urgently required to improve the treatment outcomes of infectious diseases and save lives. Plant metabolites and bioactive compounds from chemical synthesis have found their efficacy to be dwindling, despite some of them being developed as drugs and used to treat human infections for several decades. Microorganisms are considered untapped reservoirs for promising biomolecules with varying structural and functional antimicrobial activity. The advent of cost-effective and convenient model organisms, state-of-the-art molecular biology, omics technology, and machine learning has enhanced the bioprospecting of novel antimicrobial drugs and the identification of new drug targets. This review summarizes antimicrobial compounds isolated from microorganisms and reports on the modern tools and strategies for exploiting promising antimicrobial drug candidates. The investigation identified a plethora of novel compounds from microbial sources with excellent antimicrobial activity against disease-causing human pathogens. Researchers could maximize the use of novel model systems and advanced biomolecular and computational tools in exploiting lead antimicrobials, consequently ameliorating antimicrobial resistance.
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Affiliation(s)
- Cynthia Amaning Danquah
- Department of Pharmacology, Faculty of Pharmacy and Pharmaceutical Sciences, College of Health Sciences, Kwame Nkrumah University of Science and Technology, PMB, Kumasi, Ghana;
| | - Prince Amankwah Baffour Minkah
- Department of Pharmacology, Faculty of Pharmacy and Pharmaceutical Sciences, College of Health Sciences, Kwame Nkrumah University of Science and Technology, PMB, Kumasi, Ghana;
- Global Health and Infectious Disease Research Group, Kumasi Centre for Collaborative Research in Tropical Medicine, College of Health Sciences, Kwame Nkrumah University of Science and Technology, PMB, Kumasi, Ghana
| | - Isaiah Osei Duah Junior
- Department of Optometry and Visual Science, College of Science, Kwame Nkrumah University of Science and Technology, PMB, Kumasi, Ghana;
| | - Kofi Bonsu Amankwah
- Department of Biomedical Sciences, University of Cape Coast, PMB, Cape Coast, Ghana;
| | - Samuel Owusu Somuah
- Department of Pharmacy Practice, School of Pharmacy, University of Health and Allied Sciences, PMB, Ho, Ghana;
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Saati-Santamaría Z, Selem-Mojica N, Peral-Aranega E, Rivas R, García-Fraile P. Unveiling the genomic potential of Pseudomonas type strains for discovering new natural products. Microb Genom 2022; 8:000758. [PMID: 35195510 PMCID: PMC8942027 DOI: 10.1099/mgen.0.000758] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 12/07/2021] [Indexed: 12/20/2022] Open
Abstract
Microbes host a huge variety of biosynthetic gene clusters that produce an immeasurable array of secondary metabolites with many different biological activities such as antimicrobial, anticarcinogenic and antiviral. Despite the complex task of isolating and characterizing novel natural products, microbial genomic strategies can be useful for carrying out these types of studies. However, although genomic-based research on secondary metabolism is on the increase, there is still a lack of reports focusing specifically on the genus Pseudomonas. In this work, we aimed (i) to unveil the main biosynthetic systems related to secondary metabolism in Pseudomonas type strains, (ii) to study the evolutionary processes that drive the diversification of their coding regions and (iii) to select Pseudomonas strains showing promising results in the search for useful natural products. We performed a comparative genomic study on 194 Pseudomonas species, paying special attention to the evolution and distribution of different classes of biosynthetic gene clusters and the coding features of antimicrobial peptides. Using EvoMining, a bioinformatic approach for studying evolutionary processes related to secondary metabolism, we sought to decipher the protein expansion of enzymes related to the lipid metabolism, which may have evolved toward the biosynthesis of novel secondary metabolites in Pseudomonas. The types of metabolites encoded in Pseudomonas type strains were predominantly non-ribosomal peptide synthetases, bacteriocins, N-acetylglutaminylglutamine amides and ß-lactones. Also, the evolution of genes related to secondary metabolites was found to coincide with Pseudomonas species diversification. Interestingly, only a few Pseudomonas species encode polyketide synthases, which are related to the lipid metabolism broadly distributed among bacteria. Thus, our EvoMining-based search may help to discover new types of secondary metabolite gene clusters in which lipid-related enzymes are involved. This work provides information about uncharacterized metabolites produced by Pseudomonas type strains, whose gene clusters have evolved in a species-specific way. Our results provide novel insight into the secondary metabolism of Pseudomonas and will serve as a basis for the prioritization of the isolated strains. This article contains data hosted by Microreact.
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Affiliation(s)
- Zaki Saati-Santamaría
- Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), 37185 Salamanca, Spain
| | | | - Ezequiel Peral-Aranega
- Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), 37185 Salamanca, Spain
| | - Raúl Rivas
- Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), 37185 Salamanca, Spain
- Associated Research Unit of Plant-Microorganism Interaction, University of Salamanca-IRNASA-CSIC, 37008 Salamanca, Spain
| | - Paula García-Fraile
- Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), 37185 Salamanca, Spain
- Associated Research Unit of Plant-Microorganism Interaction, University of Salamanca-IRNASA-CSIC, 37008 Salamanca, Spain
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24
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Negri T, Mantri S, Angelov A, Peter S, Muth G, Eustáquio AS, Ziemert N. A rapid and efficient strategy to identify and recover biosynthetic gene clusters from soil metagenomes. Appl Microbiol Biotechnol 2022; 106:3293-3306. [PMID: 35435454 PMCID: PMC9064862 DOI: 10.1007/s00253-022-11917-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/31/2022] [Accepted: 04/03/2022] [Indexed: 11/30/2022]
Abstract
Culture-independent metagenomic approaches offer a promising solution to the discovery of therapeutically relevant compounds such as antibiotics by enabling access to the hidden biosynthetic potential of microorganisms. These strategies, however, often entail laborious, multi-step, and time-consuming procedures to recover the biosynthetic gene clusters (BGCs) from soil metagenomes for subsequent heterologous expression. Here, we developed an efficient method we called single Nanopore read cluster mining (SNRCM), which enables the fast recovery of complete BGCs from a soil metagenome using long- and short-read sequencing. A metagenomic fosmid library of 83,700 clones was generated and sequenced using Nanopore as well as Illumina technologies. Hybrid assembled contigs of the sequenced fosmid library were subsequently analyzed to identify BGCs encoding secondary metabolites. Using SNRCM, we aligned the identified BGCs directly to Nanopore long-reads and were able to detect complete BGCs on single fosmids. This enabled us to select for and recover BGCs of interest for subsequent heterologous expression attempts. Additionally, the sequencing data of the fosmid library and its corresponding metagenomic DNA enabled us to assemble and recover a large nonribosomal peptide synthetase (NRPS) BGC from three different fosmids of our library and to directly amplify and recover a complete lasso peptide BGC from the high-quality metagenomic DNA. Overall, the strategies presented here provide a useful tool for accelerating and facilitating the identification and production of potentially interesting bioactive compounds from soil metagenomes. KEY POINTS: • An efficient approach for the recovery of BGCs from soil metagenomes was developed to facilitate natural product discovery. • A fosmid library was constructed from soil metagenomic HMW DNA and sequenced via Illumina and Nanopore. • Nanopore long-reads enabled the direct identification and recovery of complete BGCs on single fosmids.
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Affiliation(s)
- Timo Negri
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Tübingen, Germany
| | - Shrikant Mantri
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Tübingen, Germany ,Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Tübingen, Germany ,Computational Biology Laboratory, National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab India
| | - Angel Angelov
- NGS Competence Center Tübingen (NCCT), Institut Für Medizinische Mikrobiologie Und Hygiene, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Silke Peter
- NGS Competence Center Tübingen (NCCT), Institut Für Medizinische Mikrobiologie Und Hygiene, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Günther Muth
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Tübingen, Germany
| | | | - Nadine Ziemert
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Tübingen, Germany. .,Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Tübingen, Germany. .,German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany.
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25
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Martín-Escolano R, Yiangou L, Kazana E, Robinson GK, Michaelis M, Tsaousis AD. Repurposing in vitro approaches for screening anti-parasitic drugs against the brain-eating amoeba Naegleria fowleri. Int J Parasitol Drugs Drug Resist 2021; 17:204-212. [PMID: 34875573 PMCID: PMC8652063 DOI: 10.1016/j.ijpddr.2021.10.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/14/2021] [Accepted: 10/18/2021] [Indexed: 11/22/2022]
Abstract
Naegleria fowleri is both a pathogenic and a free-living microbial eukaryote, responsible for the development of primary amoebic meningoencephalitis (PAM) in humans. PAM is a rapid, severe and fatal underestimated infectious disease, which has been reported in countries with warmer climates. The major drawbacks with PAM are the lack of effective therapies and delay in diagnosis. The current frontline treatment presents a low rate of recovery (5%) and severe adverse effects. For example, many drug candidates lack efficacy, since they do not effectively cross the blood-brain-barrier. Consequently, more effective drugs are urgently needed. Herein, we report a new in vitro method suitable for medium- and high-throughput drug discovery assays, using the closely related Naegleria gruberi as a model. We have subsequently used this method to screen a library of 1175 Food and Drug Administration-approved drugs. As a result, we present three drugs (camptothecin, pyrimethamine, and terbinafine) that can be repurposed, and are anticipated to readily cross the blood-brain-barrier with activity against Naegleria species in therapeutically achievable concentrations. Successively, we integrated several in vitro assays that resulted in identifying fast-acting and high amoebicidal drugs. In conclusion, we present a new approach for the identification of anti-Naegleria drugs along with three potential drug candidates for further development for the treatment of PAM.
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Affiliation(s)
- Rubén Martín-Escolano
- Laboratory of Molecular & Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Lyto Yiangou
- Laboratory of Molecular & Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK; School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Eleanna Kazana
- Laboratory of Molecular & Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Gary K Robinson
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Martin Michaelis
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK.
| | - Anastasios D Tsaousis
- Laboratory of Molecular & Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK; School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK.
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26
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De Obeso Fernandez Del Valle A, Scheckhuber CQ. From Past to Present: Biotechnology in Mexico Using Algae and Fungi. PLANTS 2021; 10:plants10112530. [PMID: 34834893 PMCID: PMC8621983 DOI: 10.3390/plants10112530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 10/19/2021] [Accepted: 10/21/2021] [Indexed: 11/16/2022]
Abstract
Algae and fungi share a rich history in the fields of basic and applied natural science. In biotechnology, in particular, algae and fungi are of paramount importance, due to the production and development of valuable compounds, such as pharmaceuticals, enzymes, and biofuels. They are also used in waste fermentation, biocontrol of pathogens, and food processing and improvement, among other fields. Although a substantial number of different microorganisms are utilized for these purposes, there lies tremendous potential in uncharacterized microbial species. For this reason, biodiversity hotspots offer a wealth of potential in the discovery of new products and processing strategies based on these microorganisms. This review presents an overview of the use of algae and fungi in pre-Hispanic times/modern-day Mexico for the benefits of mankind. One of our objectives is to raise awareness about the potential of developing research projects for identification and biotechnological utilization of algae and fungi in a megadiverse country, such as Mexico.
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Metagenomic Sequencing of Multiple Soil Horizons and Sites in Close Vicinity Revealed Novel Secondary Metabolite Diversity. mSystems 2021; 6:e0101821. [PMID: 34636675 PMCID: PMC8510542 DOI: 10.1128/msystems.01018-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Discovery of novel antibiotics is crucial for combating rapidly spreading antimicrobial resistance and new infectious diseases. Most of the clinically used antibiotics are natural products—secondary metabolites produced by soil microbes that can be cultured in the lab. Rediscovery of these secondary metabolites during discovery expeditions costs both time and resources. Metagenomics approaches can overcome this challenge by capturing both culturable and unculturable hidden microbial diversity. To be effective, such an approach should address questions like the following. Which sequencing method is better at capturing the microbial diversity and biosynthesis potential? What part of the soil should be sampled? Can patterns and correlations from such big-data explorations guide future novel natural product discovery surveys? Here, we address these questions by a paired amplicon and shotgun metagenomic sequencing survey of samples from soil horizons of multiple forest sites very close to each other. Metagenome mining identified numerous novel biosynthetic gene clusters (BGCs) and enzymatic domain sequences. Hybrid assembly of both long reads and short reads improved the metagenomic assembly and resulted in better BGC annotations. A higher percentage of novel domains was recovered from shotgun metagenome data sets than from amplicon data sets. Overall, in addition to revealing the biosynthetic potential of soil microbes, our results suggest the importance of sampling not only different soils but also their horizons to capture microbial and biosynthetic diversity and highlight the merits of metagenome sequencing methods. IMPORTANCE This study helped uncover the biosynthesis potential of forest soils via exploration of shotgun metagenome and amplicon sequencing methods and showed that both methods are needed to expose the full microbial diversity in soil. Based on our metagenome mining results, we suggest revising the historical strategy of sampling soils from far-flung places, as we found a significant number of novel and diverse BGCs and domains even in different soils that are very close to each other. Furthermore, sampling of different soil horizons can reveal the additional diversity that often remains hidden and is mainly caused by differences in environmental key parameters such as soil pH and nutrient content. This paired metagenomic survey identified diversity patterns and correlations, a step toward developing a rational approach for future natural product discovery surveys.
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28
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Vallé Q, Roques BB, Bousquet-Mélou A, Dahlhaus D, Ramon-Portugal F, Dupouy V, Bibbal D, Ferran AA. Prediction of Minocycline Activity in the Gut From a Pig Preclinical Model Using a Pharmacokinetic -Pharmacodynamic Approach. Front Microbiol 2021; 12:671376. [PMID: 34305836 PMCID: PMC8299485 DOI: 10.3389/fmicb.2021.671376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 06/16/2021] [Indexed: 11/13/2022] Open
Abstract
The increase of multidrug-resistant (MDR) bacteria has renewed interest in old antibiotics, such as minocycline, that can be active against various MDR Gram-negative pathogens. The elimination of minocycline by both kidneys and liver makes it suitable for impaired renal function patients. However, the drawback is the possible elimination of a high amount of drug in the intestines, with potential impact on the digestive microbiota during treatment. This study aimed to predict the potential activity of minocycline against Enterobacterales in the gut after parenteral administration, by combining in vivo and in vitro studies. Total minocycline concentrations were determined by UPLC-UV in the plasma and intestinal content of piglets following intravenous administration. In parallel, the in vitro activity of minocycline was assessed against two Escherichia coli strains in sterilized intestinal contents, and compared to activity in a standard broth. We found that minocycline concentrations were 6–39 times higher in intestinal contents than plasma. Furthermore, minocycline was 5- to 245-fold less active in large intestine content than in a standard broth. Using this PK-PD approach, we propose a preclinical pig model describing the link between systemic and gut exposure to minocycline, and exploring its activity against intestinal Enterobacterales by taking into account the impact of intestinal contents.
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Affiliation(s)
- Quentin Vallé
- INTHERES, Université de Toulouse, INRAE, ENVT, Toulouse, France.,Virbac, Carros, France
| | | | | | - David Dahlhaus
- INTHERES, Université de Toulouse, INRAE, ENVT, Toulouse, France
| | | | | | - Delphine Bibbal
- INTHERES, Université de Toulouse, INRAE, ENVT, Toulouse, France
| | - Aude A Ferran
- INTHERES, Université de Toulouse, INRAE, ENVT, Toulouse, France
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29
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Tafakori V. Slime molds as a valuable source of antimicrobial agents. AMB Express 2021; 11:92. [PMID: 34160704 PMCID: PMC8220367 DOI: 10.1186/s13568-021-01251-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 06/12/2021] [Indexed: 11/16/2022] Open
Abstract
Given the emerging multidrug-resistant pathogens, the number of effective antimicrobial agents to deal with the threat of bacterial and fungal resistance has fallen dramatically. Therefore, the critical solution to deal with the missing effective antibiotics is to research new sources or new synthetic antibiotics. Natural products have different advantages to be considered antimicrobial agents. There are different natural sources for antimicrobial agents, such as bacteria, fungi, algae, slime molds, and plants. This article has focused on antibiotics from slime molds, especially Myxomycetes. The reason why slime molds have been chosen to be studied is their unique bioactive metabolites, especially over the past couple of decades. Some of those metabolites have been demonstrated to possess antibiotic activities. Hence, this article has focused on the potential of these creatures as an alternative source of antibiotics.
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30
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Daley SK, Cordell GA. Alkaloids in Contemporary Drug Discovery to Meet Global Disease Needs. Molecules 2021; 26:molecules26133800. [PMID: 34206470 PMCID: PMC8270272 DOI: 10.3390/molecules26133800] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/05/2021] [Accepted: 06/14/2021] [Indexed: 12/15/2022] Open
Abstract
An overview is presented of the well-established role of alkaloids in drug discovery, the application of more sustainable chemicals, and biological approaches, and the implementation of information systems to address the current challenges faced in meeting global disease needs. The necessity for a new international paradigm for natural product discovery and development for the treatment of multidrug resistant organisms, and rare and neglected tropical diseases in the era of the Fourth Industrial Revolution and the Quintuple Helix is discussed.
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Affiliation(s)
| | - Geoffrey A. Cordell
- Natural Products Inc., Evanston, IL 60202, USA;
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
- Correspondence:
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31
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Genomic evolution of antibiotic resistance is contingent on genetic background following a long-term experiment with Escherichia coli. Proc Natl Acad Sci U S A 2021; 118:2016886118. [PMID: 33441451 DOI: 10.1073/pnas.2016886118] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Antibiotic resistance is a growing health concern. Efforts to control resistance would benefit from an improved ability to forecast when and how it will evolve. Epistatic interactions between mutations can promote divergent evolutionary trajectories, which complicates our ability to predict evolution. We recently showed that differences between genetic backgrounds can lead to idiosyncratic responses in the evolvability of phenotypic resistance, even among closely related Escherichia coli strains. In this study, we examined whether a strain's genetic background also influences the genotypic evolution of resistance. Do lineages founded by different genotypes take parallel or divergent mutational paths to achieve their evolved resistance states? We addressed this question by sequencing the complete genomes of antibiotic-resistant clones that evolved from several different genetic starting points during our earlier experiments. We first validated our statistical approach by quantifying the specificity of genomic evolution with respect to antibiotic treatment. As expected, mutations in particular genes were strongly associated with each drug. Then, we determined that replicate lines evolved from the same founding genotypes had more parallel mutations at the gene level than lines evolved from different founding genotypes, although these effects were more subtle than those showing antibiotic specificity. Taken together with our previous work, we conclude that historical contingency can alter both genotypic and phenotypic pathways to antibiotic resistance.
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32
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Prichula J, Primon-Barros M, Luz RCZ, Castro ÍMS, Paim TGS, Tavares M, Ligabue-Braun R, d’Azevedo PA, Frazzon J, Frazzon APG, Seixas A, Gilmore MS. Genome Mining for Antimicrobial Compounds in Wild Marine Animals-Associated Enterococci. Mar Drugs 2021; 19:328. [PMID: 34204046 PMCID: PMC8229437 DOI: 10.3390/md19060328] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/28/2021] [Accepted: 06/03/2021] [Indexed: 12/20/2022] Open
Abstract
New ecosystems are being actively mined for new bioactive compounds. Because of the large amount of unexplored biodiversity, bacteria from marine environments are especially promising. Further, host-associated microbes are of special interest because of their low toxicity and compatibility with host health. Here, we identified and characterized biosynthetic gene clusters encoding antimicrobial compounds in host-associated enterococci recovered from fecal samples of wild marine animals remote from human-affected ecosystems. Putative biosynthetic gene clusters in the genomes of 22 Enterococcus strains of marine origin were predicted using antiSMASH5 and Bagel4 bioinformatic software. At least one gene cluster encoding a putative bioactive compound precursor was identified in each genome. Collectively, 73 putative antimicrobial compounds were identified, including 61 bacteriocins (83.56%), 10 terpenes (13.70%), and 2 (2.74%) related to putative nonribosomal peptides (NRPs). Two of the species studied, Enterococcus avium and Enterococcus mundtti, are rare causes of human disease and were found to lack any known pathogenic determinants but yet possessed bacteriocin biosynthetic genes, suggesting possible additional utility as probiotics. Wild marine animal-associated enterococci from human-remote ecosystems provide a potentially rich source for new antimicrobial compounds of therapeutic and industrial value and potential probiotic application.
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Affiliation(s)
- Janira Prichula
- Gram-Positive Cocci Laboratory, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre 90050-170, RS, Brazil; (J.P.); (M.P.-B.); (R.C.Z.L.); (Í.M.S.C.); (T.G.S.P.); (P.A.d.)
| | - Muriel Primon-Barros
- Gram-Positive Cocci Laboratory, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre 90050-170, RS, Brazil; (J.P.); (M.P.-B.); (R.C.Z.L.); (Í.M.S.C.); (T.G.S.P.); (P.A.d.)
| | - Romeu C. Z. Luz
- Gram-Positive Cocci Laboratory, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre 90050-170, RS, Brazil; (J.P.); (M.P.-B.); (R.C.Z.L.); (Í.M.S.C.); (T.G.S.P.); (P.A.d.)
| | - Ícaro M. S. Castro
- Gram-Positive Cocci Laboratory, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre 90050-170, RS, Brazil; (J.P.); (M.P.-B.); (R.C.Z.L.); (Í.M.S.C.); (T.G.S.P.); (P.A.d.)
| | - Thiago G. S. Paim
- Gram-Positive Cocci Laboratory, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre 90050-170, RS, Brazil; (J.P.); (M.P.-B.); (R.C.Z.L.); (Í.M.S.C.); (T.G.S.P.); (P.A.d.)
| | - Maurício Tavares
- Centro de Estudos Costeiros, Limnológicos e Marinhos (CECLIMAR), Universidade Federal do Rio Grande do Sul (UFRGS), Campus Litoral Norte, Imbé 95625-000, RS, Brazil;
| | - Rodrigo Ligabue-Braun
- Department of Pharmacosciences, UFCSPA, Porto Alegre 90050-170, RS, Brazil; (R.L.-B.); (A.S.)
| | - Pedro A. d’Azevedo
- Gram-Positive Cocci Laboratory, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre 90050-170, RS, Brazil; (J.P.); (M.P.-B.); (R.C.Z.L.); (Í.M.S.C.); (T.G.S.P.); (P.A.d.)
| | - Jeverson Frazzon
- Food Science Institute, UFRGS, Porto Alegre 90035-003, RS, Brazil;
| | - Ana P. G. Frazzon
- Department of Microbiology, Immunology and Parasitology, UFRGS, Porto Alegre 90050-170, RS, Brazil;
| | - Adriana Seixas
- Department of Pharmacosciences, UFCSPA, Porto Alegre 90050-170, RS, Brazil; (R.L.-B.); (A.S.)
| | - Michael S. Gilmore
- Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
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33
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Handayani I, Saad H, Ratnakomala S, Lisdiyanti P, Kusharyoto W, Krause J, Kulik A, Wohlleben W, Aziz S, Gross H, Gavriilidou A, Ziemert N, Mast Y. Mining Indonesian Microbial Biodiversity for Novel Natural Compounds by a Combined Genome Mining and Molecular Networking Approach. Mar Drugs 2021; 19:316. [PMID: 34071728 PMCID: PMC8227522 DOI: 10.3390/md19060316] [Citation(s) in RCA: 6] [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: 04/29/2021] [Revised: 05/22/2021] [Accepted: 05/25/2021] [Indexed: 11/17/2022] Open
Abstract
Indonesia is one of the most biodiverse countries in the world and a promising resource for novel natural compound producers. Actinomycetes produce about two thirds of all clinically used antibiotics. Thus, exploiting Indonesia's microbial diversity for actinomycetes may lead to the discovery of novel antibiotics. A total of 422 actinomycete strains were isolated from three different unique areas in Indonesia and tested for their antimicrobial activity. Nine potent bioactive strains were prioritized for further drug screening approaches. The nine strains were cultivated in different solid and liquid media, and a combination of genome mining analysis and mass spectrometry (MS)-based molecular networking was employed to identify potential novel compounds. By correlating secondary metabolite gene cluster data with MS-based molecular networking results, we identified several gene cluster-encoded biosynthetic products from the nine strains, including naphthyridinomycin, amicetin, echinomycin, tirandamycin, antimycin, and desferrioxamine B. Moreover, 16 putative ion clusters and numerous gene clusters were detected that could not be associated with any known compound, indicating that the strains can produce novel secondary metabolites. Our results demonstrate that sampling of actinomycetes from unique and biodiversity-rich habitats, such as Indonesia, along with a combination of gene cluster networking and molecular networking approaches, accelerates natural product identification.
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Affiliation(s)
- Ira Handayani
- Department of Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen (IMIT), Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany; (I.H.); (J.K.); (A.K.); (W.W.)
- Research Center for Biotechnology, Indonesian Institute of Sciences (LIPI), Jl. Raya Jakarta-Bogor KM.46, Cibinong, West Java 16911, Indonesia; (P.L.); (W.K.)
| | - Hamada Saad
- Department of Pharmaceutical Biology, Institute of Pharmaceutical Sciences, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany; (H.S.); (S.A.); (H.G.)
- Department of Phytochemistry and Plant Systematics, Division of Pharmaceutical Industries, National Research Centre, Dokki, Cairo 12622, Egypt
| | - Shanti Ratnakomala
- Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jl. Raya Jakarta-Bogor KM.46, Cibinong, West Java 16911, Indonesia;
| | - Puspita Lisdiyanti
- Research Center for Biotechnology, Indonesian Institute of Sciences (LIPI), Jl. Raya Jakarta-Bogor KM.46, Cibinong, West Java 16911, Indonesia; (P.L.); (W.K.)
| | - Wien Kusharyoto
- Research Center for Biotechnology, Indonesian Institute of Sciences (LIPI), Jl. Raya Jakarta-Bogor KM.46, Cibinong, West Java 16911, Indonesia; (P.L.); (W.K.)
| | - Janina Krause
- Department of Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen (IMIT), Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany; (I.H.); (J.K.); (A.K.); (W.W.)
| | - Andreas Kulik
- Department of Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen (IMIT), Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany; (I.H.); (J.K.); (A.K.); (W.W.)
| | - Wolfgang Wohlleben
- Department of Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen (IMIT), Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany; (I.H.); (J.K.); (A.K.); (W.W.)
| | - Saefuddin Aziz
- Department of Pharmaceutical Biology, Institute of Pharmaceutical Sciences, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany; (H.S.); (S.A.); (H.G.)
| | - Harald Gross
- Department of Pharmaceutical Biology, Institute of Pharmaceutical Sciences, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany; (H.S.); (S.A.); (H.G.)
| | - Athina Gavriilidou
- Applied Natural Products Genome Mining, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany; (A.G.); (N.Z.)
| | - Nadine Ziemert
- Applied Natural Products Genome Mining, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany; (A.G.); (N.Z.)
- German Center for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Yvonne Mast
- Department of Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen (IMIT), Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany; (I.H.); (J.K.); (A.K.); (W.W.)
- German Center for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
- Department of Bioresources for Bioeconomy and Health Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
- Department of Microbiology, Technical University of Braunschweig, 38124 Braunschweig, Germany
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34
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Sukmarini L. Recent Advances in Discovery of Lead Structures from Microbial Natural Products: Genomics- and Metabolomics-Guided Acceleration. Molecules 2021; 26:molecules26092542. [PMID: 33925414 PMCID: PMC8123854 DOI: 10.3390/molecules26092542] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/20/2021] [Accepted: 04/22/2021] [Indexed: 01/17/2023] Open
Abstract
Natural products (NPs) are evolutionarily optimized as drug-like molecules and remain the most consistently successful source of drugs and drug leads. They offer major opportunities for finding novel lead structures that are active against a broad spectrum of assay targets, particularly those from secondary metabolites of microbial origin. Due to traditional discovery approaches’ limitations relying on untargeted screening methods, there is a growing trend to employ unconventional secondary metabolomics techniques. Aided by the more in-depth understanding of different biosynthetic pathways and the technological advancement in analytical instrumentation, the development of new methodologies provides an alternative that can accelerate discoveries of new lead-structures of natural origin. This present mini-review briefly discusses selected examples regarding advancements in bioinformatics and genomics (focusing on genome mining and metagenomics approaches), as well as bioanalytics (mass-spectrometry) towards the microbial NPs-based drug discovery and development. The selected recent discoveries from 2015 to 2020 are featured herein.
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Affiliation(s)
- Linda Sukmarini
- Research Center for Biotechnology, Indonesian Institute of Sciences (LIPI), Cibinong, Bogor 16911, West Java, Indonesia
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35
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Song L, Zhu S, Liu C, Zhang Q, Liang X. Baicalin triggers apoptosis, inhibits migration, and enhances anti-tumor immunity in colorectal cancer via TLR4/NF-κB signaling pathway. J Food Biochem 2021; 46:e13703. [PMID: 33742464 DOI: 10.1111/jfbc.13703] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/19/2021] [Accepted: 02/28/2021] [Indexed: 12/15/2022]
Abstract
Aberrant activation of the nuclear factor-kappa B (NF-κB) signaling pathway is closely implicated in colorectal cancer (CRC) growth, metastasis, and immune escape. In the present study, we reported natural derived compound of baicalin (BA), an efficient inhibitor of NF-κB, with good anti-tumor effect on CRC. CCK8 and colony formation assays showed that Baicalin significantly inhibit viability and proliferation in HCT-116 and CT26 cells. Additionally, Baicalin dramatically triggers mitochondria-mediated apoptosis in both HCT-116 and CT-26 cells, which is evidenced by loss of mitochondrial membrane potential and elevated cellular reactive oxygen species level. Treatment with Baicalin suppresses migration and invasion of CT26 cells by impairing TLR4/NF-κB signaling pathway. What's more, administration of Baicalin significantly retarded tumor growth rate in a subcutaneous xenograft tumor mouse model of CT26 cells. Treatment with Baicalin could ameliorate tumor immunosuppressive environment by downregulation of PD-L1 expression and proportion of myeloid-derived suppressor cells (MDSCs) and upregulation of percent of CD4+ and CD8+ T cells in CT26 tumors, thus improving anti-tumor immunity. In conclusion, our study demonstrated that baicalin triggers apoptosis, inhibits migration, and enhances anti-tumor immunity in colorectal cancer via TLR4/NF-κB signaling pathway, suggesting it might serve as a potential candidate drug for the treatment of CRC. PRACTICAL APPLICATIONS: In the present study, we reported natural derived compound of baicalin (BA), an efficient inhibitor of NF-κB, with good anti-tumor effect on CRC. We demonstrated that baicalin triggers mitochondria-mediated apoptosis, inhibits migration, and improves anti-tumor immunity in colorectal cancer via TLR4/NF-κB signaling pathway.
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Affiliation(s)
- Linjiang Song
- School of Medical and Life Sciences/Reproductive & Women-children Hospital, Chengdu University of Traditional Chinese Medicine, Chengdu, P.R. China
| | - Shaomi Zhu
- School of Medical and Life Sciences/Reproductive & Women-children Hospital, Chengdu University of Traditional Chinese Medicine, Chengdu, P.R. China
| | - Chi Liu
- School of Medical and Life Sciences/Reproductive & Women-children Hospital, Chengdu University of Traditional Chinese Medicine, Chengdu, P.R. China
| | - Qinxiu Zhang
- School of Medical and Life Sciences/Reproductive & Women-children Hospital, Chengdu University of Traditional Chinese Medicine, Chengdu, P.R. China
| | - Xin Liang
- School of Medical and Life Sciences/Reproductive & Women-children Hospital, Chengdu University of Traditional Chinese Medicine, Chengdu, P.R. China
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Hernandez A, Nguyen LT, Dhakal R, Murphy BT. The need to innovate sample collection and library generation in microbial drug discovery: a focus on academia. Nat Prod Rep 2021; 38:292-300. [PMID: 32706349 PMCID: PMC7855266 DOI: 10.1039/d0np00029a] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The question of whether culturable microorganisms will continue to be a viable source of new drug leads is inherently married to the strategies used to collect samples from the environment, the methods used to cultivate microorganisms from these samples, and the processes used to create microbial libraries. An academic microbial natural products (NP) drug discovery program with the latest innovative chromatographic and spectroscopic technology, high-throughput capacity, and bioassays will remain at the mercy of the quality of its microorganism source library. This viewpoint will discuss limitations of sample collection and microbial strain library generation practices. Additionally, it will offer suggestions to innovate these areas, particularly through the targeted cultivation of several understudied bacterial phyla and the untargeted use of mass spectrometry and bioinformatics to generate diverse microbial libraries. Such innovations have potential to impact downstream therapeutic discovery, and make its front end more informed, efficient, and less reliant on serendipity. This viewpoint is not intended to be a comprehensive review of contributing literature and was written with a focus on bacteria. Strategies to discover NPs from microbial libraries, including a variety of genomics and "OSMAC" style approaches, are considered downstream of sample collection and library creation, and thus are out of the scope of this viewpoint.
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Affiliation(s)
- Antonio Hernandez
- Dept. of Pharmaceutical Sciences, Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA.
| | - Linh T Nguyen
- Dept. of Pharmaceutical Sciences, Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA. and Institute of Marine Biochemistry, Vietnam Academy of Science and Technology, Nghiado, Caugiay, Hanoi, Vietnam
| | - Radhika Dhakal
- Dept. of Pharmaceutical Sciences, Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA.
| | - Brian T Murphy
- Dept. of Pharmaceutical Sciences, Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA.
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37
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Yadav S, Kapley A. Antibiotic resistance: Global health crisis and metagenomics. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2021; 29:e00604. [PMID: 33732632 PMCID: PMC7937537 DOI: 10.1016/j.btre.2021.e00604] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 01/11/2021] [Accepted: 02/18/2021] [Indexed: 02/08/2023]
Abstract
Antibiotic resistance is a global problem which affects human health. The imprudent use of antibiotics (medicine, agriculture, aquaculture, and food industry) has resulted in the broader dissemination of resistance. Urban wastewater & sewage treatment plants act as the hotspot for the widespread of antimicrobial resistance. Natural environment also plays an important role in the dissemination of resistance. Mapping of antibiotic resistance genes (ARGS) in environment is essential for mitigating antimicrobial resistance (AMR) widespread. Therefore, the review article emphasizes on the application of metagenomics for the surveillance of antimicrobial resistance. Metagenomics is the next generation tool which is being used for cataloging the resistome of diverse environments. We summarize the different metagenomic tools that can be used for mining of ARGs and acquired AMR present in the metagenomic data. Also, we recommend application of targeted sequencing/ capture platform for mapping of resistome with higher specificity and selectivity.
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Affiliation(s)
- Shailendra Yadav
- Director’s Research Cell, National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 440020, India
| | - Atya Kapley
- Director’s Research Cell, National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 440020, India
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38
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Rodriguez Jimenez A, Dechamps E, Giaux A, Goetghebuer L, Bauwens M, Willenz P, Flahaut S, Laport MS, George IF. The sponges Hymeniacidon perlevis and Halichondria panicea are reservoirs of antibiotic-producing bacteria against multi-drug resistant Staphylococcus aureus. J Appl Microbiol 2021; 131:706-718. [PMID: 33421270 DOI: 10.1111/jam.14999] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/04/2021] [Accepted: 01/06/2021] [Indexed: 12/12/2022]
Abstract
AIMS Evaluation of the antibacterial activity of cultivable bacteria associated with the marine sponges Hymeniacidon perlevis and Halichondria panicea against multi-drug-resistant Staphylococcus aureus. METHODS AND RESULTS One hundred and fourteen bacterial isolates were recovered from H. perlevis and H. panicea. Antibacterial action was demonstrated by 70% of the isolates against reference strain Staphylococcus aureus ATCC 29213 and by 31·6% against Pseudomonas aeruginosa ATCC 27853 in agar overlay assays. Antibacterial potential was further analysed against 36 multi-drug-resistant hospital Staphylococcus aureus strains with diverse resistance profiles. Among the 80 isolates positive against S. aureus ATCC 29213, 76·3% were active against at least one clinical S. aureus pathogen and 73·6% inhibited one or more methicillin-resistant (MRSA) and vancomycin non-susceptible S. aureus strains. In addition, 41·3% inhibited all vancomycin nonsusceptible MRSA strains. CONCLUSIONS Culturable bacteria associated to H. perlevis and H. panicea are promising sources of antibacterial compounds of great pharmaceutical interest. SIGNIFICANCE AND IMPACT OF THE STUDY This study was the first to explore the antibacterial potential of culturable bacteria associated with the marine sponges H. perlevis and H. panicea against MDR bacteria. This is the first report of antibacterial activity by Aquimarina, Denitrobaculum, Maribacter and Vagococcus isolates against MDR S. aureus strains, including vancomycin nonsusceptible and methicillin-resistant ones, against which new antibiotics are urgently needed.
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Affiliation(s)
- A Rodriguez Jimenez
- Ecology of Aquatic Systems, Université Libre de Bruxelles, Bruxelles, Belgique.,Ecological and Evolutionary Genomics, Université Libre de Bruxelles, Bruxelles, Belgique
| | - E Dechamps
- Ecology of Aquatic Systems, Université Libre de Bruxelles, Bruxelles, Belgique
| | - A Giaux
- Ecology of Aquatic Systems, Université Libre de Bruxelles, Bruxelles, Belgique
| | - L Goetghebuer
- Marine Biology, Université Libre de Bruxelles, Bruxelles, Belgique
| | - M Bauwens
- Marine Biology, Université Libre de Bruxelles, Bruxelles, Belgique
| | - P Willenz
- Marine Biology, Université Libre de Bruxelles, Bruxelles, Belgique.,Taxonomy & Phylogeny, Royal Belgian Institute of Natural Sciences, Bruxelles, Belgique
| | - S Flahaut
- Applied Microbiology, Université Libre de Bruxelles, Bruxelles, Belgique
| | - M S Laport
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - I F George
- Ecology of Aquatic Systems, Université Libre de Bruxelles, Bruxelles, Belgique.,Marine Biology, Université Libre de Bruxelles, Bruxelles, Belgique
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39
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Oberhofer M, Wackerlig J, Zehl M, Büyük H, Cao JJ, Prado-Roller A, Urban E, Zotchev SB. Endophytic Akanthomyces sp. LN303 from Edelweiss Produces Emestrin and Two New 2-Hydroxy-4 Pyridone Alkaloids. ACS OMEGA 2021; 6:2184-2191. [PMID: 33521458 PMCID: PMC7841945 DOI: 10.1021/acsomega.0c05472] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 12/07/2020] [Indexed: 06/12/2023]
Abstract
In the search for new antibiotics, several fungal endophytes were isolated from the medicinal plant Leontopodium nivale subsp. alpinum (Edelweiss). The extract from one of these fungi classified as Akanthomyces sp. displayed broad-spectrum antibiotic activity against gram-negative bacteria and fungi. Further investigation into the composition of this extract using bioactivity-guided fractionation, HRMS, and nuclear magnetic resonance revealed two new 4-hydroxy-2-pyridone alkaloids (1, 2) and emestrin (3), an epidithiodioxopiperazine not previously known to be produced by a member of Cordycipitaceae. Further testing of purified compounds 1 and 2 proved that they are devoid of antibiotic activity, and all the activities observed in the crude extract could be assigned to emestrin (3), whose configuration was confirmed by crystallographic data. This study demonstrates, for the first time, that endophytic fungi from Edelweiss can produce new compounds, prompting further investigation into them for drug discovery.
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Affiliation(s)
- Martina Oberhofer
- Department
of Pharmacognosy, University of Vienna, 1090 Vienna, Austria
| | - Judith Wackerlig
- Department
of Pharmaceutical Chemistry, University
of Vienna, 1090 Vienna, Austria
| | - Martin Zehl
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Havva Büyük
- Department
of Pharmaceutical Chemistry, University
of Vienna, 1090 Vienna, Austria
| | - Jia Jian Cao
- Department
of Pharmaceutical Chemistry, University
of Vienna, 1090 Vienna, Austria
| | - Alexander Prado-Roller
- Department
of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Ernst Urban
- Department
of Pharmaceutical Chemistry, University
of Vienna, 1090 Vienna, Austria
| | - Sergey B. Zotchev
- Department
of Pharmacognosy, University of Vienna, 1090 Vienna, Austria
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40
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Cardoso P, Glossop H, Meikle TG, Aburto-Medina A, Conn CE, Sarojini V, Valery C. Molecular engineering of antimicrobial peptides: microbial targets, peptide motifs and translation opportunities. Biophys Rev 2021; 13:35-69. [PMID: 33495702 PMCID: PMC7817352 DOI: 10.1007/s12551-021-00784-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 01/07/2021] [Indexed: 02/07/2023] Open
Abstract
The global public health threat of antimicrobial resistance has led the scientific community to highly engage into research on alternative strategies to the traditional small molecule therapeutics. Here, we review one of the most popular alternatives amongst basic and applied research scientists, synthetic antimicrobial peptides. The ease of peptide chemical synthesis combined with emerging engineering principles and potent broad-spectrum activity, including against multidrug-resistant strains, has motivated intense scientific focus on these compounds for the past decade. This global effort has resulted in significant advances in our understanding of peptide antimicrobial activity at the molecular scale. Recent evidence of molecular targets other than the microbial lipid membrane, and efforts towards consensus antimicrobial peptide motifs, have supported the rise of molecular engineering approaches and design tools, including machine learning. Beyond molecular concepts, supramolecular chemistry has been lately added to the debate; and helped unravel the impact of peptide self-assembly on activity, including on biofilms and secondary targets, while providing new directions in pharmaceutical formulation through taking advantage of peptide self-assembled nanostructures. We argue that these basic research advances constitute a solid basis for promising industry translation of rationally designed synthetic peptide antimicrobials, not only as novel drugs against multidrug-resistant strains but also as components of emerging antimicrobial biomaterials. This perspective is supported by recent developments of innovative peptide-based and peptide-carrier nanobiomaterials that we also review.
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Affiliation(s)
- Priscila Cardoso
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia.,School of Science, RMIT University, Melbourne, Australia
| | - Hugh Glossop
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | | | | | | | | | - Celine Valery
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia
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41
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Santana-Pereira ALR, Sandoval-Powers M, Monsma S, Zhou J, Santos SR, Mead DA, Liles MR. Discovery of Novel Biosynthetic Gene Cluster Diversity From a Soil Metagenomic Library. Front Microbiol 2020; 11:585398. [PMID: 33365020 PMCID: PMC7750434 DOI: 10.3389/fmicb.2020.585398] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 11/16/2020] [Indexed: 12/31/2022] Open
Abstract
Soil microorganisms historically have been a rich resource for natural product discovery, yet the majority of these microbes remain uncultivated and their biosynthetic capacity is left underexplored. To identify the biosynthetic potential of soil microorganisms using a culture-independent approach, we constructed a large-insert metagenomic library in Escherichia coli from a topsoil sampled from the Cullars Rotation (Auburn, AL, United States), a long-term crop rotation experiment. Library clones were screened for biosynthetic gene clusters (BGCs) using either PCR or a NGS (next generation sequencing) multiplexed pooling strategy, coupled with bioinformatic analysis to identify contigs associated with each metagenomic clone. A total of 1,015 BGCs were detected from 19,200 clones, identifying 223 clones (1.2%) that carry a polyketide synthase (PKS) and/or a non-ribosomal peptide synthetase (NRPS) cluster, a dramatically improved hit rate compared to PCR screening that targeted type I polyketide ketosynthase (KS) domains. The NRPS and PKS clusters identified by NGS were distinct from known BGCs in the MIBiG database or those PKS clusters identified by PCR. Likewise, 16S rRNA gene sequences obtained by NGS of the library included many representatives that were not recovered by PCR, in concordance with the same bias observed in KS amplicon screening. This study provides novel resources for natural product discovery and circumvents amplification bias to allow annotation of a soil metagenomic library for a more complete picture of its functional and phylogenetic diversity.
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Affiliation(s)
| | | | - Scott Monsma
- Lucigen Corporation, Middleton, WI, United States
| | - Jinglie Zhou
- Department of Biological Sciences, Auburn University, Auburn, AL, United States
| | - Scott R. Santos
- Department of Biological Sciences, Auburn University, Auburn, AL, United States
| | - David A. Mead
- Varigen Biosciences Corporation, Madison, WI, United States
| | - Mark R. Liles
- Department of Biological Sciences, Auburn University, Auburn, AL, United States
- Varigen Biosciences Corporation, Madison, WI, United States
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42
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Dhingra S, Rahman NAA, Peile E, Rahman M, Sartelli M, Hassali MA, Islam T, Islam S, Haque M. Microbial Resistance Movements: An Overview of Global Public Health Threats Posed by Antimicrobial Resistance, and How Best to Counter. Front Public Health 2020; 8:535668. [PMID: 33251170 PMCID: PMC7672122 DOI: 10.3389/fpubh.2020.535668] [Citation(s) in RCA: 121] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 08/14/2020] [Indexed: 12/11/2022] Open
Abstract
Antibiotics changed medical practice by significantly decreasing the morbidity and mortality associated with bacterial infection. However, infectious diseases remain the leading cause of death in the world. There is global concern about the rise in antimicrobial resistance (AMR), which affects both developed and developing countries. AMR is a public health challenge with extensive health, economic, and societal implications. This paper sets AMR in context, starting with the history of antibiotics, including the discovery of penicillin and the golden era of antibiotics, before exploring the problems and challenges we now face due to AMR. Among the factors discussed is the low level of development of new antimicrobials and the irrational prescribing of antibiotics in developed and developing countries. A fundamental problem is the knowledge, attitude, and practice (KAP) regarding antibiotics among medical practitioners, and we explore this aspect in some depth, including a discussion on the KAP among medical students. We conclude with suggestions on how to address this public health threat, including recommendations on training medical students about antibiotics, and strategies to overcome the problems of irrational antibiotic prescribing and AMR.
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Affiliation(s)
- Sameer Dhingra
- School of Pharmacy, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Nor Azlina A. Rahman
- Department of Physical Rehabilitation Sciences, Kulliyyah of Allied Health Sciences, International Islamic University Malaysia, Kuantan, Malaysia
| | - Ed Peile
- Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Motiur Rahman
- Oxford University Clinical Research Unit, Wellcome Trust Asia Programme, The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom
| | - Massimo Sartelli
- Department of General and Emergency Surgery, Macerata Hospital, Macerata, Italy
| | - Mohamed Azmi Hassali
- The Discipline of Social and Administrative Pharmacy, School of Pharmaceutical Sciences, Universiti Sains Malaysia, Minden, Malaysia
| | | | - Salequl Islam
- Department of Microbiology, Jahangirnagar University, Dhaka, Bangladesh
| | - Mainul Haque
- The Unit of Pharmacology, Faculty of Medicine and Defence Health, National Defence University of Malaysia, Kuala Lumpur, Malaysia
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43
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Chen R, Wong HL, Kindler GS, MacLeod FI, Benaud N, Ferrari BC, Burns BP. Discovery of an Abundance of Biosynthetic Gene Clusters in Shark Bay Microbial Mats. Front Microbiol 2020; 11:1950. [PMID: 32973707 PMCID: PMC7472256 DOI: 10.3389/fmicb.2020.01950] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 07/24/2020] [Indexed: 01/27/2023] Open
Abstract
Microbial mats are geobiological multilayered ecosystems that have significant evolutionary value in understanding the evolution of early life on Earth. Shark Bay, Australia has some of the best examples of modern microbial mats thriving under harsh conditions of high temperatures, salinity, desiccation, and ultraviolet (UV) radiation. Microorganisms living in extreme ecosystems are thought to potentially encode for secondary metabolites as a survival strategy. Many secondary metabolites are natural products encoded by a grouping of genes known as biosynthetic gene clusters (BGCs). Natural products have diverse chemical structures and functions which provide competitive advantages for microorganisms and can also have biotechnology applications. In the present study, the diversity of BGC were described in detail for the first time from Shark Bay microbial mats. A total of 1477 BGCs were detected in metagenomic data over a 20 mm mat depth horizon, with the surface layer possessing over 200 BGCs and containing the highest relative abundance of BGCs of all mat layers. Terpene and bacteriocin BGCs were highly represented and their natural products are proposed to have important roles in ecosystem function in these mat systems. Interestingly, potentially novel BGCs were detected from Heimdallarchaeota and Lokiarchaeota, two evolutionarily significant archaeal phyla not previously known to possess BGCs. This study provides new insights into how secondary metabolites from BGCs may enable diverse microbial mat communities to adapt to extreme environments.
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Affiliation(s)
- Ray Chen
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.,Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia
| | - Hon Lun Wong
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.,Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia
| | - Gareth S Kindler
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.,Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia
| | - Fraser Iain MacLeod
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.,Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia
| | - Nicole Benaud
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Belinda C Ferrari
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.,Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia
| | - Brendan P Burns
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.,Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia
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44
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Exploring the Antibacterial Activity of Pestalotiopsis spp. under Different Culture Conditions and Their Chemical Diversity Using LC-ESI-Q-TOF-MS. J Fungi (Basel) 2020; 6:jof6030140. [PMID: 32824944 PMCID: PMC7557868 DOI: 10.3390/jof6030140] [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: 07/16/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 12/12/2022] Open
Abstract
As a result of the capability of fungi to respond to culture conditions, we aimed to explore and compare the antibacterial activity and chemical diversity of two endophytic fungi isolated from Hyptis dilatata and cultured under different conditions by the addition of chemical elicitors, changes in the pH, and different incubation temperatures. Seventeen extracts were obtained from both Pestalotiopsis mangiferae (man-1 to man-17) and Pestalotiopsis microspora (mic-1 to mic-17) and were tested against a panel of pathogenic bacteria. Seven extracts from P. mangiferae and four extracts from P. microspora showed antibacterial activity; while some of these extracts displayed a high-level of selectivity and a broad-spectrum of activity, Pseudomonas aeruginosa was the most inhibited microorganism and was selected to determine the minimal inhibitory concentration (MIC). The MIC was determined for extracts man-6 (0.11 μg/mL) and mic-9 (0.56 μg/mL). Three active extracts obtained from P. mangiferae were analyzed by Liquid Chromatography-Electrospray Ionization-Quadrupole-Time of Flight-Mass Spectrometry (LC–ESI–Q–TOF–MS) to explore the chemical diversity and the variations in the composition. This allows us to propose structures for some of the determined molecular formulas, including the previously reported mangiferaelactone (1), an antibacterial compound.
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45
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Tun KNW, Aminah NS, Kristanti AN, Aung HT, Takaya Y. Natural products isolated from Casimiroa. OPEN CHEM 2020. [DOI: 10.1515/chem-2020-0128] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
AbstractAbout 140 genera and more than 1,600 species belong to the Rutaceae family. They grow in temperate and tropical zones on both hemispheres, as trees, shrubs, and herbs. Casimiroa is one of the genera constituting 13 species, most of which are found in tropical and subtropical regions. Many chemical constituents have been derived from this genus, including quinoline alkaloids, flavonoids, coumarins, and N-benzoyltyramide derivatives. This article reviews different studies carried out on aromatic compounds of genus Casimiroa; their biological activities; the different skeletons of coumarins, alkaloids, flavonoids, and others; and their characteristic NMR spectral data.
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Affiliation(s)
- Khun Nay Win Tun
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Komplek Kampus C UNAIR, Jl. Mulyorejo, Surabaya, Indonesia
- Department of Chemistry, Taunggyi University, Taunggyi, Myanmar
| | - Nanik Siti Aminah
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Komplek Kampus C UNAIR, Jl. Mulyorejo, Surabaya, Indonesia
| | - Alfinda Novi Kristanti
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Komplek Kampus C UNAIR, Jl. Mulyorejo, Surabaya, Indonesia
| | | | - Yoshiaki Takaya
- Faculty of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku, Nagoya, 468-8503, Japan
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46
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Baral B, Mozafari MR. Strategic Moves of "Superbugs" Against Available Chemical Scaffolds: Signaling, Regulation, and Challenges. ACS Pharmacol Transl Sci 2020; 3:373-400. [PMID: 32566906 PMCID: PMC7296549 DOI: 10.1021/acsptsci.0c00005] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Indexed: 12/12/2022]
Abstract
Superbugs' resistivity against available natural products has become an alarming global threat, causing a rapid deterioration in public health and claiming tens of thousands of lives yearly. Although the rapid discovery of small molecules from plant and microbial origin with enhanced bioactivity has provided us with some hope, a rapid hike in the resistivity of superbugs has proven to be the biggest therapeutic hurdle of all times. Moreover, several distinct mechanisms endowed by these notorious superbugs make them immune to these antibiotics subsequently causing our antibiotic wardrobe to be obsolete. In this unfortunate situation, though the time frame for discovering novel "hit molecules" down the line remains largely unknown, our small hope and untiring efforts injected in hunting novel chemical scaffolds with unique molecular targets using high-throughput technologies may safeguard us against these life-threatening challenges to some extent. Amid this crisis, the current comprehensive review highlights the present status of knowledge, our search for bacteria Achilles' heel, distinct molecular signaling that an opportunistic pathogen bestows to trespass the toxicity of antibiotics, and facile strategies and appealing therapeutic targets of novel drugs. Herein, we also discuss multidimensional strategies to combat antimicrobial resistance.
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Affiliation(s)
- Bikash Baral
- Department
of Biochemistry, University of Turku, Tykistökatu 6, Turku, Finland
| | - M. R. Mozafari
- Australasian
Nanoscience and Nanotechnology Initiative, 8054 Monash University LPO, Clayton, Victoria 3168, Australia
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47
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Exploration of space to achieve scientific breakthroughs. Biotechnol Adv 2020; 43:107572. [PMID: 32540473 DOI: 10.1016/j.biotechadv.2020.107572] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 05/05/2020] [Accepted: 05/29/2020] [Indexed: 12/13/2022]
Abstract
Living organisms adapt to changing environments using their amazing flexibility to remodel themselves by a process called evolution. Environmental stress causes selective pressure and is associated with genetic and phenotypic shifts for better modifications, maintenance, and functioning of organismal systems. The natural evolution process can be used in complement to rational strain engineering for the development of desired traits or phenotypes as well as for the production of novel biomaterials through the imposition of one or more selective pressures. Space provides a unique environment of stressors (e.g., weightlessness and high radiation) that organisms have never experienced on Earth. Cells in the outer space reorganize and develop or activate a range of molecular responses that lead to changes in cellular properties. Exposure of cells to the outer space will lead to the development of novel variants more efficiently than on Earth. For instance, natural crop varieties can be generated with higher nutrition value, yield, and improved features, such as resistance against high and low temperatures, salt stress, and microbial and pest attacks. The review summarizes the literature on the parameters of outer space that affect the growth and behavior of cells and organisms as well as complex colloidal systems. We illustrate an understanding of gravity-related basic biological mechanisms and enlighten the possibility to explore the outer space environment for application-oriented aspects. This will stimulate biological research in the pursuit of innovative approaches for the future of agriculture and health on Earth.
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48
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Rosini R, Nicchi S, Pizza M, Rappuoli R. Vaccines Against Antimicrobial Resistance. Front Immunol 2020; 11:1048. [PMID: 32582169 PMCID: PMC7283535 DOI: 10.3389/fimmu.2020.01048] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 04/30/2020] [Indexed: 12/29/2022] Open
Abstract
In the last century, life expectancy has increased considerably, thanks to the introduction of antibiotics, hygiene and vaccines that have contributed to the cure and prevention of many infectious diseases. The era of antimicrobial therapy started in the nineteenth century with the identification of chemical compounds with antimicrobial properties. However, immediately after the introduction of these novel drugs, microorganisms started to become resistant through different strategies. Although resistance mechanisms were already present before antibiotic introduction, their large-scale use and mis-use have increased the number of resistant microorganisms. Rapid spreading of mobile elements by horizontal gene transfer such as plasmids and integrative conjugative elements (ICE) carrying multiple resistance genes has dramatically increased the worldwide prevalence of relevant multi drug-resistant human pathogens such as Staphylococcus aureus, Neisseria gonorrhoeae, and Enterobacteriaceae. Today, antimicrobial resistance (AMR) remains one of the major global concerns to be addressed and only global efforts could help in finding a solution. In terms of magnitude the economic impact of AMR is estimated to be comparable to that of climate global change in 2030. Although antibiotics continue to be essential to treat such infections, non-antibiotic therapies will play an important role in limiting the increase of antibiotic resistant microorganisms. Among non-antibiotic strategies, vaccines and therapeutic monoclonal antibodies (mAbs) play a strategic role. In this review, we will summarize the evolution and the mechanisms of antibiotic resistance, and the impact of AMR on life expectancy and economics.
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Affiliation(s)
| | - Sonia Nicchi
- GSK, Siena, Italy
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | | | - Rino Rappuoli
- GSK, Siena, Italy
- vAMRes Lab, Toscana Life Sciences, Siena, Italy
- Faculty of Medicine, Imperial College London, London, United Kingdom
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49
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Bu QT, Li YP, Xie H, Wang J, Li ZY, Chen XA, Mao XM, Li YQ. Comprehensive dissection of dispensable genomic regions in Streptomyces based on comparative analysis approach. Microb Cell Fact 2020; 19:99. [PMID: 32375781 PMCID: PMC7204314 DOI: 10.1186/s12934-020-01359-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 04/29/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Large-scale genome reduction has been performed to significantly improve the performance of microbial chassis. Identification of the essential or dispensable genes is pivotal for genome reduction to avoid synthetic lethality. Here, taking Streptomyces as an example, we developed a combinatorial strategy for systematic identification of large and dispensable genomic regions in Streptomyces based on multi-omics approaches. RESULTS Phylogenetic tree analysis revealed that the model strains including S. coelicolor A3(2), S. albus J1074 and S. avermitilis MA-4680 were preferred reference for comparative analysis of candidate genomes. Multiple genome alignment suggested that the Streptomyces genomes embodied highly conserved core region and variable sub-telomeric regions, and may present symmetric or asymmetric structure. Pan-genome and functional genome analyses showed that most conserved genes responsible for the fundamental functions of cell viability were concentrated in the core region and the vast majority of abundant genes were dispersed in the sub-telomeric regions. These results suggested that large-scale deletion can be performed in sub-telomeric regions to greatly streamline the Streptomyces genomes for developing versatile chassis. CONCLUSIONS The integrative approach of comparative genomics, functional genomics and pan-genomics can not only be applied to perform a multi-tiered dissection for Streptomyces genomes, but also work as a universal method for systematic analysis of removable regions in other microbial hosts in order to generate more miscellaneous and versatile chassis with minimized genome for drug discovery.
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Affiliation(s)
- Qing-Ting Bu
- Institute of Pharmaceutical Biotechnology and Research Center for Clinical Pharmacy of First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058 China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058 China
| | - Yue-Ping Li
- Institute of Pharmaceutical Biotechnology and Research Center for Clinical Pharmacy of First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058 China
| | - Huang Xie
- Institute of Pharmaceutical Biotechnology and Research Center for Clinical Pharmacy of First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058 China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058 China
| | - Jue Wang
- Institute of Pharmaceutical Biotechnology and Research Center for Clinical Pharmacy of First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058 China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058 China
| | - Zi-Yue Li
- Institute of Pharmaceutical Biotechnology and Research Center for Clinical Pharmacy of First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058 China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058 China
| | - Xin-Ai Chen
- Institute of Pharmaceutical Biotechnology and Research Center for Clinical Pharmacy of First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058 China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058 China
| | - Xu-Ming Mao
- Institute of Pharmaceutical Biotechnology and Research Center for Clinical Pharmacy of First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058 China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058 China
| | - Yong-Quan Li
- Institute of Pharmaceutical Biotechnology and Research Center for Clinical Pharmacy of First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058 China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058 China
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50
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Garza-Cervantes JA, Mendiola-Garza G, de Melo EM, Dugmore TIJ, Matharu AS, Morones-Ramirez JR. Antimicrobial activity of a silver-microfibrillated cellulose biocomposite against susceptible and resistant bacteria. Sci Rep 2020; 10:7281. [PMID: 32350328 PMCID: PMC7190717 DOI: 10.1038/s41598-020-64127-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 03/26/2020] [Indexed: 12/14/2022] Open
Abstract
Antibiotic Microbial Resistance (AMR) is a major global challenge as it constitutes a severe threat to global public health if not addressed. To fight against AMR bacteria, new antimicrobial agents are continually needed, and their efficacy must be tested. Historically, many transition metals have been employed, but their cytotoxicity is an issue and hence must be reduced, typically by combination with organic polymers. Cellulose of natural origin, especially those derived from unavoidable residues in the food supply chain, appears to be a good capping agent for the green synthesis of silver nanoparticles. Herein, we describe a green synthesis method to produce a novel biocomposite, using ascorbic acid as reducing agent and microfibrillated cellulose as a capping agent and demonstrate this material to be an efficient antimicrobial agent. Silver nanoparticles were obtained in the cellulose matrix with an average size of 140 nm and with antimicrobial activity against both sensitive and resistant Gram positive (using 1500 ppm) as well as sensitive and resistant Gram negative (using 125 ppm) bacteria. Also, an inverted disk-diffusion methodology was applied to overcome the low-solubility of cellulose compounds. This novel silver nanoparticle-cellulose biocomposite synthesized by a green methodology shows the potential to be applied in the future development of biomedical instruments and therapeutics.
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Affiliation(s)
- Javier Alberto Garza-Cervantes
- Universidad Autónoma de Nuevo León, UANL. Facultad de Ciencias Químicas. Av. Universidad s/n. CD. Universitaria, 66455, San Nicolás de los Garza, NL, México
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León. Parque de Investigación e Innovación Tecnológica, Km. 10 autopista al Aeropuerto Internacional Mariano Escobedo, 66629, Apodaca, Nuevo León, México
| | - Gricelda Mendiola-Garza
- Universidad Autónoma de Nuevo León, UANL. Facultad de Ciencias Químicas. Av. Universidad s/n. CD. Universitaria, 66455, San Nicolás de los Garza, NL, México
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León. Parque de Investigación e Innovación Tecnológica, Km. 10 autopista al Aeropuerto Internacional Mariano Escobedo, 66629, Apodaca, Nuevo León, México
| | - Eduardo Macedo de Melo
- Institute of Bio- and Geosciences 1 (IBG-1): Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Tom I J Dugmore
- Green Chemistry Centre of Excellence, Department of Chemistry, University of York, YO10 5DD, York, England, United Kingdom
| | - Avtar S Matharu
- Green Chemistry Centre of Excellence, Department of Chemistry, University of York, YO10 5DD, York, England, United Kingdom.
| | - Jose Ruben Morones-Ramirez
- Universidad Autónoma de Nuevo León, UANL. Facultad de Ciencias Químicas. Av. Universidad s/n. CD. Universitaria, 66455, San Nicolás de los Garza, NL, México.
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León. Parque de Investigación e Innovación Tecnológica, Km. 10 autopista al Aeropuerto Internacional Mariano Escobedo, 66629, Apodaca, Nuevo León, México.
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