1
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Singh A, Tanwar M, Singh TP, Sharma S, Sharma P. An escape from ESKAPE pathogens: A comprehensive review on current and emerging therapeutics against antibiotic resistance. Int J Biol Macromol 2024; 279:135253. [PMID: 39244118 DOI: 10.1016/j.ijbiomac.2024.135253] [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: 05/22/2024] [Revised: 08/29/2024] [Accepted: 08/30/2024] [Indexed: 09/09/2024]
Abstract
The rise of antimicrobial resistance has positioned ESKAPE pathogens as a serious global health threat, primarily due to the limitations and frequent failures of current treatment options. This growing risk has spurred the scientific community to seek innovative antibiotic therapies and improved oversight strategies. This review aims to provide a comprehensive overview of the origins and resistance mechanisms of ESKAPE pathogens, while also exploring next-generation treatment strategies for these infections. In addition, it will address both traditional and novel approaches to combating antibiotic resistance, offering insights into potential new therapeutic avenues. Emerging research underscores the urgency of developing new antimicrobial agents and strategies to overcome resistance, highlighting the need for novel drug classes and combination therapies. Advances in genomic technologies and a deeper understanding of microbial pathogenesis are crucial in identifying effective treatments. Integrating precision medicine and personalized approaches could enhance therapeutic efficacy. The review also emphasizes the importance of global collaboration in surveillance and stewardship, as well as policy reforms, enhanced diagnostic tools, and public awareness initiatives, to address resistance on a worldwide scale.
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Affiliation(s)
- Anamika Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Mansi Tanwar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - T P Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Sujata Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India.
| | - Pradeep Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India.
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2
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A. Ghomi F, Jung JJ, Langridge GC, Cain AK, Boinett CJ, Abd El Ghany M, Pickard DJ, Kingsley RA, Thomson NR, Parkhill J, Gardner PP, Barquist L. High-throughput transposon mutagenesis in the family Enterobacteriaceae reveals core essential genes and rapid turnover of essentiality. mBio 2024; 15:e0179824. [PMID: 39207104 PMCID: PMC11481867 DOI: 10.1128/mbio.01798-24] [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: 07/02/2024] [Accepted: 08/05/2024] [Indexed: 09/04/2024] Open
Abstract
The Enterobacteriaceae are a scientifically and medically important clade of bacteria, containing the model organism Escherichia coli, as well as major human pathogens including Salmonella enterica and Klebsiella pneumoniae. Essential gene sets have been determined for several members of the Enterobacteriaceae, with the Keio E. coli single-gene deletion library often regarded as a gold standard. However, it remains unclear how gene essentiality varies between related strains and species. To investigate this, we have assembled a collection of 13 sequenced high-density transposon mutant libraries from five genera within the Enterobacteriaceae. We first assess several gene essentiality prediction approaches, investigate the effects of transposon density on essentiality prediction, and identify biases in transposon insertion sequencing data. Based on these investigations, we develop a new classifier for gene essentiality. Using this new classifier, we define a core essential genome in the Enterobacteriaceae of 201 universally essential genes. Despite the presence of a large cohort of variably essential genes, we find an absence of evidence for genus-specific essential genes. A clear example of this sporadic essentiality is given by the set of genes regulating the σE extracytoplasmic stress response, which appears to have independently acquired essentiality multiple times in the Enterobacteriaceae. Finally, we compare our essential gene sets to the natural experiment of gene loss in obligate insect endosymbionts that have emerged from within the Enterobacteriaceae. This isolates a remarkably small set of genes absolutely required for survival and identifies several instances of essential stress responses masked by redundancy in free-living bacteria.IMPORTANCEThe essential genome, that is the set of genes absolutely required to sustain life, is a core concept in genetics. Essential genes in bacteria serve as drug targets, put constraints on the engineering of biological chassis for technological or industrial purposes, and are key to constructing synthetic life. Despite decades of study, relatively little is known about how gene essentiality varies across related bacteria. In this study, we have collected gene essentiality data for 13 bacteria related to the model organism Escherichia coli, including several human pathogens, and investigated the conservation of essentiality. We find that approximately a third of the genes essential in any particular strain are non-essential in another related strain. Surprisingly, we do not find evidence for essential genes unique to specific genera; rather it appears a substantial fraction of the essential genome rapidly gains or loses essentiality during evolution. This suggests that essentiality is not an immutable characteristic but depends crucially on the genomic context. We illustrate this through a comparison of our essential genes in free-living bacteria to genes conserved in 34 insect endosymbionts with naturally reduced genomes, finding several cases where genes generally regarded as being important for specific stress responses appear to have become essential in endosymbionts due to a loss of functional redundancy in the genome.
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Affiliation(s)
- Fatemeh A. Ghomi
- Biomolecular Interactions Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Jakob J. Jung
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Würzburg, Germany
| | - Gemma C. Langridge
- Microbes in the Food Chain, Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
| | - Amy K. Cain
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, Australia
| | | | - Moataz Abd El Ghany
- The Westmead Institute for Medical Research, University of Sydney, Sydney, Australia
- Sydney Institute for Infectious Diseases, University of Sydney, Sydney, Australia
- School of Public Health, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
- King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Derek J. Pickard
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Robert A. Kingsley
- Microbes in the Food Chain, Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
- Department of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Nicholas R. Thomson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Paul P. Gardner
- Biomolecular Interactions Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Department of Biochemistry, Otago University, Dunedin, New Zealand
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Würzburg, Germany
- Faculty of Medicine, University of Würzburg, Würzburg, Germany
- Department of Biology, University of Toronto, Mississauga, Ontario, Canada
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3
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Butler MS, Vollmer W, Goodall ECA, Capon RJ, Henderson IR, Blaskovich MAT. A Review of Antibacterial Candidates with New Modes of Action. ACS Infect Dis 2024; 10:3440-3474. [PMID: 39018341 PMCID: PMC11474978 DOI: 10.1021/acsinfecdis.4c00218] [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: 03/17/2024] [Revised: 06/15/2024] [Accepted: 06/17/2024] [Indexed: 07/19/2024]
Abstract
There is a lack of new antibiotics to combat drug-resistant bacterial infections that increasingly threaten global health. The current pipeline of clinical-stage antimicrobials is primarily populated by "new and improved" versions of existing antibiotic classes, supplemented by several novel chemical scaffolds that act on traditional targets. The lack of fresh chemotypes acting on previously unexploited targets (the "holy grail" for new antimicrobials due to their scarcity) is particularly unfortunate as these offer the greatest opportunity for innovative breakthroughs to overcome existing resistance. In recognition of their potential, this review focuses on this subset of high value antibiotics, providing chemical structures where available. This review focuses on candidates that have progressed to clinical trials, as well as selected examples of promising pioneering approaches in advanced stages of development, in order to stimulate additional research aimed at combating drug-resistant infections.
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Affiliation(s)
- Mark S. Butler
- Centre
for Superbug Solutions and ARC Training Centre for Environmental and
Agricultural Solutions to Antimicrobial Resistance, Institute for
Molecular Bioscience, The University of
Queensland, St. Lucia, Queensland 4072, Australia
| | - Waldemar Vollmer
- Centre
for Superbug Solutions and ARC Training Centre for Environmental and
Agricultural Solutions to Antimicrobial Resistance, Institute for
Molecular Bioscience, The University of
Queensland, St. Lucia, Queensland 4072, Australia
| | - Emily C. A. Goodall
- Centre
for Superbug Solutions and ARC Training Centre for Environmental and
Agricultural Solutions to Antimicrobial Resistance, Institute for
Molecular Bioscience, The University of
Queensland, St. Lucia, Queensland 4072, Australia
| | - Robert J. Capon
- Centre
for Superbug Solutions and ARC Training Centre for Environmental and
Agricultural Solutions to Antimicrobial Resistance, Institute for
Molecular Bioscience, The University of
Queensland, St. Lucia, Queensland 4072, Australia
| | - Ian R. Henderson
- Centre
for Superbug Solutions and ARC Training Centre for Environmental and
Agricultural Solutions to Antimicrobial Resistance, Institute for
Molecular Bioscience, The University of
Queensland, St. Lucia, Queensland 4072, Australia
| | - Mark A. T. Blaskovich
- Centre
for Superbug Solutions and ARC Training Centre for Environmental and
Agricultural Solutions to Antimicrobial Resistance, Institute for
Molecular Bioscience, The University of
Queensland, St. Lucia, Queensland 4072, Australia
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4
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Bao P, Zhang XZ. Progress of tumor-resident intracellular bacteria for cancer therapy. Adv Drug Deliv Rev 2024; 214:115458. [PMID: 39383997 DOI: 10.1016/j.addr.2024.115458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Revised: 09/12/2024] [Accepted: 10/04/2024] [Indexed: 10/11/2024]
Abstract
Emerging studies have disclosed the pivotal role of cancer-associated microbiota in supporting cancer development, progression and dissemination, with the in-depth comprehending of tumor microenvironment. In particular, certain invasive bacteria that hide in various cells within the tumor tissues can render assistance to tumor growth and invasion through intricate mechanisms implicated in multiple branches of cancer biology. Thus, tumor-resident intracellular microbes are anticipated as next-generation targets for oncotherapy. This review is intended to delve into these internalized bacteria-driven cancer-promoting mechanisms and explore diversified antimicrobial therapeutic strategies to counteract the detrimental impact caused by these intruders, thereby improving therapeutic benefit of antineoplastic therapy.
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Affiliation(s)
- Peng Bao
- Department of Orthopedic Trauma and Microsurgery of Zhongnan Hospital, Key Laboratory of Biomedical Polymers of Ministry of Education, Department of Chemistry, Wuhan University, Wuhan 430072, PR China
| | - Xian-Zheng Zhang
- Department of Orthopedic Trauma and Microsurgery of Zhongnan Hospital, Key Laboratory of Biomedical Polymers of Ministry of Education, Department of Chemistry, Wuhan University, Wuhan 430072, PR China.
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5
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Peng X, Zeng Z, Hassan S, Xue Y. The potential of marine natural Products: Recent Advances in the discovery of Anti-Tuberculosis agents. Bioorg Chem 2024; 151:107699. [PMID: 39128242 DOI: 10.1016/j.bioorg.2024.107699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 07/30/2024] [Accepted: 08/04/2024] [Indexed: 08/13/2024]
Abstract
Tuberculosis (TB) is an infectious airborne disease caused by Mycobacterium tuberculosis. Since the 1990 s, many countries have made significant progress in reducing the incidence of TB and associated mortality by improving health services and strengthening surveillance systems. Nevertheless, due to the emergence of multidrug-resistant TB (MDR-TB), alongside extensively drug-resistant TB (XDR-TB) and TB-HIV co-infection, TB remains one of the lead causes of death arising from infectious disease worldwide, especially in developing countries and disadvantaged populations. Marine natural products (MNPs) have received a large amount of attention in recent years as a source of pharmaceutical constituents and lead compounds, and are expected to offer significant resources and potential in the fields of drug development and biotechnology in the years to come. This review summarizes 169 marine natural products and their synthetic derivatives displaying anti-TB activity from 2013 to the present, including their structures, sources and functions. Partial synthetic information and structure-activity relationships (SARs) are also included.
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Affiliation(s)
- Xinyu Peng
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Shenzhen 518107, China
| | - Ziqian Zeng
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Shenzhen 518107, China
| | - Said Hassan
- Institute of Biotechnology and Microbiology, Bacha Khan University, Charsadda 24540, Pakistan
| | - Yongbo Xue
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Shenzhen 518107, China.
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6
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Kilianova Z, Cizmarova I, Spaglova M, Piestansky J. Recent Trends in Therapeutic Drug Monitoring of Peptide Antibiotics. J Sep Sci 2024; 47:e202400583. [PMID: 39400453 DOI: 10.1002/jssc.202400583] [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: 08/04/2024] [Revised: 09/17/2024] [Accepted: 09/19/2024] [Indexed: 10/15/2024]
Abstract
Antimicrobial peptides take a specific position in the field of antibiotics (ATBs), however, from a large number of available molecules only a few of them were approved and are used in clinics. These therapeutic modalities play a crucial role in the management of diseases caused by multidrug-resistant bacterial pathogens and represent the last-line therapy for bacterial infections. Therefore, there is a demand for a rationale use of such ATBs based on optimization of the dosing strategy to minimize the risk of resistance and ensure the sustainable efficacy of the drug in real clinical practice. Therapeutic drug monitoring, as a measurement of drug concentration in the body fluids or tissues, results in the optimization of the patient´s medication and therapy outcome. This strategy is beneficial and could result in tailored therapy for different types of infection and the prolongation of the use and efficacy of ATBs in hospitals. This review paper provides an actual overview of approved antimicrobial peptides used in clinical practice and covers current trends in their analysis by convenient and advanced methodologies used for their identification and/or quantitation in biological matrices for therapeutic drug monitoring purposes. Special emphasis is given to the methods with perspective clinical outcomes.
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Affiliation(s)
- Zuzana Kilianova
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovak Republic
| | - Ivana Cizmarova
- Department of Pharmaceutical Analysis and Nuclear Pharmacy, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovak Republic
| | - Miroslava Spaglova
- Department of Galenic Pharmacy, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovak Republic
| | - Juraj Piestansky
- Department of Galenic Pharmacy, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovak Republic
- Toxicological and Antidoping Center, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovak Republic
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovak Republic
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7
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Ghislat G, Hernandez-Hernandez S, Piyawajanusorn C, Ballester PJ. Data-centric challenges with the application and adoption of artificial intelligence for drug discovery. Expert Opin Drug Discov 2024:1-11. [PMID: 39316009 DOI: 10.1080/17460441.2024.2403639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Accepted: 09/09/2024] [Indexed: 09/25/2024]
Abstract
INTRODUCTION Artificial intelligence (AI) is exhibiting tremendous potential to reduce the massive costs and long timescales of drug discovery. There are however important challenges currently limiting the impact and scope of AI models. AREAS COVERED In this perspective, the authors discuss a range of data issues (bias, inconsistency, skewness, irrelevance, small size, high dimensionality), how they challenge AI models, and which issue-specific mitigations have been effective. Next, they point out the challenges faced by uncertainty quantification techniques aimed at enhancing and trusting the predictions from these AI models. They also discuss how conceptual errors, unrealistic benchmarks and performance misestimation can confound the evaluation of models and thus their development. Lastly, the authors explain how human bias, whether from AI experts or drug discovery experts, constitutes another challenge that can be alleviated by gaining more prospective experience. EXPERT OPINION AI models are often developed to excel on retrospective benchmarks unlikely to anticipate their prospective performance. As a result, only a few of these models are ever reported to have prospective value (e.g. by discovering potent and innovative drug leads for a therapeutic target). The authors have discussed what can go wrong in practice with AI for drug discovery. The authors hope that this will help inform the decisions of editors, funders investors, and researchers working in this area.
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Affiliation(s)
- Ghita Ghislat
- Department of Life Sciences, Imperial College London, London, UK
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8
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Skudlarek JW, Cooke AJ, Mitchell HJ, Babaoglu K, Shaw AW, Tong L, Nomland AB, Labroli M, Sha D, Mulhearn JJ, Wu C, Li SW, Beshore DC, Hughes JME, Jouffroy M, Wang H, Balibar CJ, Painter RE, Shen P, Lange HS, Ishchenko A, Chen YT, Klein DJ, Tracy RW, Miller RR, Cabalu TD, Wu Z, Leithead A, Scapin G, Hruza AW, Dzhekieva L, Bukhtiyarova M, Homsher MF, Xu M, Bahnck-Teets C, McKenney D, Buevich AV, Liu J, Zhang LK, Meng T, Kelly T, DiNunzio E, Soisson S, Cheng RKY, Hennig M, Raheem I, Walker SS. Cerastecin Inhibition of the Lipooligosaccharide Transporter MsbA to Combat Acinetobacter baumannii: From Screening Impurity to In Vivo Efficacy. J Med Chem 2024; 67:15620-15675. [PMID: 39172133 DOI: 10.1021/acs.jmedchem.4c01277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
Acinetobacter baumannii, a commonly multidrug-resistant Gram-negative bacterium responsible for large numbers of bloodstream and lung infections worldwide, is increasingly difficult to treat and constitutes a growing threat to human health. Structurally novel antibacterial chemical matter that can evade existing resistance mechanisms is essential for addressing this critical medical need. Herein, we describe our efforts to inhibit the essential A. baumannii lipooligosaccharide (LOS) ATP-binding cassette (ABC) transporter MsbA. An unexpected impurity from a phenotypic screening was optimized as a series of dimeric compounds, culminating with 1 (cerastecin D), which exhibited antibacterial activity in the presence of human serum and a pharmacokinetic profile sufficient to achieve efficacy against A. baumannii in murine septicemia and lung infection models.
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Affiliation(s)
| | - Andrew J Cooke
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | | | - Kerim Babaoglu
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Anthony W Shaw
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Ling Tong
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | | | - Marc Labroli
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Deyou Sha
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | | | - Chengwei Wu
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Sarah W Li
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | | | | | | | - Hao Wang
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Carl J Balibar
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | | | - Pamela Shen
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Henry S Lange
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | | | - Yun-Ting Chen
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Daniel J Klein
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Rodger W Tracy
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Randy R Miller
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | | | - Zhe Wu
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | | | | | - Alan W Hruza
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | | | | | | | - Min Xu
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | | | - David McKenney
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | | | - Jian Liu
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Li-Kang Zhang
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Tao Meng
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Terri Kelly
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | | | | | | | | | - Izzat Raheem
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Scott S Walker
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
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Hu XL, Gan HQ, Gui WZ, Yan KC, Sessler JL, Yi D, Tian H, He XP. Superresolution imaging of antibiotic-induced structural disruption of bacteria enabled by photochromic glycomicelles. Proc Natl Acad Sci U S A 2024; 121:e2408716121. [PMID: 39226360 PMCID: PMC11406247 DOI: 10.1073/pnas.2408716121] [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: 05/01/2024] [Accepted: 07/29/2024] [Indexed: 09/05/2024] Open
Abstract
Bacterial evolution, particularly in hospital settings, is leading to an increase in multidrug resistance. Understanding the basis for this resistance is critical as it can drive discovery of new antibiotics while allowing the clinical use of known antibiotics to be optimized. Here, we report a photoactive chemical probe for superresolution microscopy that allows for the in situ probing of antibiotic-induced structural disruption of bacteria. Conjugation between a spiropyran (SP) and galactose via click chemistry produces an amphiphilic photochromic glycoprobe, which self-assembles into glycomicelles in water. The hydrophobic inner core of the glycomicelles allows encapsulation of antibiotics. Photoirradiation then serves to convert the SP to the corresponding merocyanine (MR) form. This results in micellar disassembly allowing for release of the antibiotic in an on-demand fashion. The glycomicelles of this study adhere selectively to the surface of a Gram-negative bacterium through multivalent sugar-lectin interaction. Antibiotic release from the glycomicelles then induces membrane collapse. This dynamic process can be imaged in situ by superresolution spectroscopy owing to the "fluorescence blinking" of the SP/MR photochromic pair. This research provides a high-precision imaging tool that may be used to visualize how antibiotics disrupt the structural integrity of bacteria in real time.
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Affiliation(s)
- Xi-Le Hu
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Hui-Qi Gan
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Wen-Zhen Gui
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Kai-Cheng Yan
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
- National Center for Liver Cancer, The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Shanghai 200438, China
- Department of Chemistry, University of Bath, Bath BA2 7AY, United Kingdom
| | - Jonathan L Sessler
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712-1224
| | - Dong Yi
- Research Center for Systems Biosynthesis, China State Institute of Pharmaceutical Industry, National Key Laboratory of Lead Druggability Research, Shanghai 201203, China
| | - He Tian
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Xiao-Peng He
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
- National Center for Liver Cancer, The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Shanghai 200438, China
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10
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Bellucci MC, Romani C, Sani M, Volonterio A. Dual Antibiotic Approach: Synthesis and Antibacterial Activity of Antibiotic-Antimicrobial Peptide Conjugates. Antibiotics (Basel) 2024; 13:783. [PMID: 39200083 PMCID: PMC11352213 DOI: 10.3390/antibiotics13080783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Revised: 08/16/2024] [Accepted: 08/18/2024] [Indexed: 09/01/2024] Open
Abstract
In recent years, bacterial resistance to conventional antibiotics has become a major concern in the medical field. The global misuse of antibiotics in clinics, personal use, and agriculture has accelerated this resistance, making infections increasingly difficult to treat and rendering new antibiotics ineffective more quickly. Finding new antibiotics is challenging due to the complexity of bacterial mechanisms, high costs and low financial incentives for the development of new molecular scaffolds, and stringent regulatory requirements. Additionally, innovation has slowed, with many new antibiotics being modifications of existing drugs rather than entirely new classes. Antimicrobial peptides (AMPs) are a valid alternative to small-molecule antibiotics offering several advantages, including broad-spectrum activity and a lower likelihood of inducing resistance due to their multifaceted mechanisms of action. However, AMPs face challenges such as stability issues in physiological conditions, potential toxicity to human cells, high production costs, and difficulties in large-scale manufacturing. A reliable strategy to overcome the drawbacks associated with the use of small-molecule antibiotics and AMPs is combination therapy, namely the simultaneous co-administration of two or more antibiotics or the synthesis of covalently linked conjugates. This review aims to provide a comprehensive overview of the literature on the development of antibiotic-AMP conjugates, with a particular emphasis on critically analyzing the design and synthetic strategies employed in their creation. In addition to the synthesis, the review will also explore the reported antibacterial activity of these conjugates and, where available, examine any data concerning their cytotoxicity.
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Affiliation(s)
- Maria Cristina Bellucci
- Department of Food, Environmental, and Nutritional Sciences, Università degli Studi di Milano, Via Celoria 2, 20131 Milano, Italy;
| | - Carola Romani
- Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Via Mancinelli 7, 20131 Milano, Italy;
| | - Monica Sani
- Consiglio Nazionale delle Ricerche, Istituto di Scienze e Tecnologie Chimica “G. Natta” (SCITEC), Via Mario Bianco 9, 20131 Milano, Italy;
| | - Alessandro Volonterio
- Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Via Mancinelli 7, 20131 Milano, Italy;
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11
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Abdullah, Jamil T, Atif M, Khalid S, Metwally K, Yahya G, Moisa M, Cavalu DS. Recent Advances in the Development of Metal/Metal Oxide Nanoparticle and Antibiotic Conjugates (MNP-Antibiotics) to Address Antibiotic Resistance: Review and Perspective. Int J Mol Sci 2024; 25:8915. [PMID: 39201601 PMCID: PMC11354832 DOI: 10.3390/ijms25168915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Revised: 08/04/2024] [Accepted: 08/13/2024] [Indexed: 09/02/2024] Open
Abstract
As per the World Health Organization (WHO), antimicrobial resistance (AMR) is a natural phenomenon whereby microbes develop or acquire genes that render them resistant. The rapid emergence and spread of this phenomenon can be attributed to human activity specifically, the improper and excessive use of antimicrobials for the treatment, prevention, or control of infections in humans, animals, and plants. As a result of this factor, many antibiotics have reduced effectiveness against microbes or may not work fully. Thus, there is a pressing need for the development of new antimicrobial agents in order to counteract antimicrobial resistance. Metallic nanoparticles (MNPs) are well known for their broad antimicrobial properties. Consequently, the use of MNPs with current antibiotics holds significant implications. MNPs, including silver nanoparticles (AgNPS), zinc oxide nanoparticles (ZnONPs), copper nanoparticles (CuNPs), and gold nanoparticles (AuNPs), have been extensively studied in conjunction with antibiotics. However, their mechanism of action is still not completely understood. The interaction between these MNPs and antibiotics can be either synergistic, additive, or antagonistic. The synergistic effect is crucial as it represents the desired outcome that researchers aim for and can be advantageous for the advancement of new antimicrobial agents. This article provides a concise and academic description of the recent advancements in MNP and antibiotic conjugates, including their mechanism of action. It also highlights their possible use in the biomedical field and major challenges associated with the use of MNP-antibiotic conjugates in clinical practice.
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Affiliation(s)
- Abdullah
- Department of Physical Chemistry and Technology of Polymers, Silesian University of Technology, 44-100 Gliwice, Poland
- Joint Doctoral School, Silesian University of Technology, 44-100 Gliwice, Poland;
| | - Tayyaba Jamil
- Joint Doctoral School, Silesian University of Technology, 44-100 Gliwice, Poland;
- Department of Management Sciences, Silesian University of Technology, 41-800 Zabrze, Poland
| | - Muhammad Atif
- Department of Microbiology, Abdul Wali Khan University, Mardan 23000, Pakistan;
| | - Shumaila Khalid
- Department of Physics, Government Postgraduate, Charsadda 24460, Pakistan;
| | - Kamel Metwally
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Tabuk, Tabuk 71491, Saudi Arabia;
| | - Galal Yahya
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Al Sharqia 44519, Egypt;
| | - Mihaela Moisa
- Faculty of Medicine and Pharmacy, University of Oradea, P-ta 1 Decembrie 10, 410073 Oradea, Romania;
| | - Daniela Simona Cavalu
- Faculty of Medicine and Pharmacy, University of Oradea, P-ta 1 Decembrie 10, 410073 Oradea, Romania;
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12
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van Groesen E, Mons E, Kotsogianni I, Arts M, Tehrani KHME, Wade N, Lysenko V, Stel FM, Zwerus JT, De Benedetti S, Bakker A, Chakraborty P, van der Stelt M, Scheffers DJ, Gooskens J, Smits WK, Holden K, Gilmour PS, Willemse J, Hitchcock CA, van Hasselt JGC, Schneider T, Martin NI. Semisynthetic guanidino lipoglycopeptides with potent in vitro and in vivo antibacterial activity. Sci Transl Med 2024; 16:eabo4736. [PMID: 39110780 DOI: 10.1126/scitranslmed.abo4736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 02/23/2024] [Accepted: 07/16/2024] [Indexed: 08/13/2024]
Abstract
Gram-positive bacterial infections present a major clinical challenge, with methicillin- and vancomycin-resistant strains continuing to be a cause for concern. In recent years, semisynthetic vancomycin derivatives have been developed to overcome this problem as exemplified by the clinically used telavancin, which exhibits increased antibacterial potency but has also raised toxicity concerns. Thus, glycopeptide antibiotics with enhanced antibacterial activities and improved safety profiles are still necessary. We describe the development of a class of highly potent semisynthetic glycopeptide antibiotics, the guanidino lipoglycopeptides, which contain a positively charged guanidino moiety bearing a variable lipid group. These glycopeptides exhibited enhanced in vitro activity against a panel of Gram-positive bacteria including clinically relevant methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant strains, showed minimal toxicity toward eukaryotic cells, and had a low propensity for resistance selection. Mechanistically, guanidino lipoglycopeptides engaged with bacterial cell wall precursor lipid II with a higher binding affinity than vancomycin. Binding to both wild-type d-Ala-d-Ala lipid II and the vancomycin-resistant d-Ala-d-Lac variant was confirmed, providing insight into the enhanced activity of guanidino lipoglycopeptides against vancomycin-resistant isolates. The in vivo efficacy of guanidino lipoglycopeptide EVG7 was evaluated in a S. aureus murine thigh infection model and a 7-day sepsis survival study, both of which demonstrated superiority to vancomycin. Moreover, the minimal to mild kidney effects at supratherapeutic doses of EVG7 indicate an improved therapeutic safety profile compared with vancomycin. These findings position guanidino lipoglycopeptides as candidates for further development as antibacterial agents for the treatment of clinically relevant multidrug-resistant Gram-positive infections.
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Affiliation(s)
- Emma van Groesen
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, 2300 RA Leiden, Netherlands
| | - Elma Mons
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, 2300 RA Leiden, Netherlands
| | - Ioli Kotsogianni
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, 2300 RA Leiden, Netherlands
| | - Melina Arts
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn, 53113 Bonn, Germany
| | - Kamaleddin H M E Tehrani
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, 2300 RA Leiden, Netherlands
| | - Nicola Wade
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, 2300 RA Leiden, Netherlands
| | - Vladyslav Lysenko
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, 2300 RA Leiden, Netherlands
| | - Florence M Stel
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, 2300 RA Leiden, Netherlands
| | - Jordy T Zwerus
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, 2300 RA Leiden, Netherlands
| | - Stefania De Benedetti
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn, 53113 Bonn, Germany
| | - Alexander Bakker
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, 2300 RA Leiden, Netherlands
| | - Parichita Chakraborty
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9700 AB Groningen, Netherlands
| | - Mario van der Stelt
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, 2300 RA Leiden, Netherlands
| | - Dirk-Jan Scheffers
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9700 AB Groningen, Netherlands
| | - Jairo Gooskens
- Department of Medical Microbiology, Leiden University Center for Infectious Diseases (LUCID), Leiden University Medical Center, 2333 ZA Leiden, Netherlands
| | - Wiep Klaas Smits
- Experimental Bacteriology, Leiden University Center for Infectious Diseases (LUCID), Leiden University Medical Center, 2333 ZA Leiden, Netherlands
| | - Kirsty Holden
- Evotec (U.K.) Ltd., Alderley Park, Macclesfield, Cheshire, SK10 4TG UK
| | | | - Joost Willemse
- Institute of Biology Leiden, Leiden University, 2300 RA Leiden, Netherlands
| | | | - J G Coen van Hasselt
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, 2300 RA Leiden, Netherlands
| | - Tanja Schneider
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn, 53113 Bonn, Germany
| | - Nathaniel I Martin
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, 2300 RA Leiden, Netherlands
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13
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Pandey R, Kaul G, Akhir A, Saxena D, Shukla M, Mundra S, Zohib M, Singh S, Pal RK, Tripathi S, Jain A, Chopra S, Arora A. Characterization of structure of peptidyl-tRNA hydrolase from Enterococcus faecium and its inhibition by a pyrrolinone compound. Int J Biol Macromol 2024; 275:133445. [PMID: 38945334 DOI: 10.1016/j.ijbiomac.2024.133445] [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: 04/23/2024] [Revised: 06/15/2024] [Accepted: 06/24/2024] [Indexed: 07/02/2024]
Abstract
In bacteria, peptidyl-tRNA hydrolase (Pth, E.C. 3.1.1.29) is a ubiquitous and essential enzyme for preventing the accumulation of peptidyl-tRNA and sequestration of tRNA. Pth is an esterase that cleaves the ester bond between peptide and tRNA. Here, we present the crystal structure of Pth from Enterococcus faecium (EfPth) at a resolution of 1.92 Å. The two molecules in the asymmetric unit differ in the orientation of sidechain of N66, a conserved residue of the catalytic site. Enzymatic hydrolysis of substrate α-N-BODIPY-lysyl-tRNALys (BLT) by EfPth was characterized by Michaelis-Menten parameters KM 163.5 nM and Vmax 1.9 nM/s. Compounds having pyrrolinone scaffold were tested for inhibition of Pth and one compound, 1040-C, was found to have IC50 of 180 nM. Antimicrobial activity profiling was done for 1040-C. It exhibited equipotent activity against drug-susceptible and resistant S. aureus (MRSA and VRSA) and Enterococcus (VSE and VRE) with MICs 2-8 μg/mL. 1040-C synergized with gentamicin and the combination was effective against the gentamicin resistant S. aureus strain NRS-119. 1040-C was found to reduce biofilm mass of S. aureus to an extent similar to Vancomycin. In a murine model of infection, 1040-C was able to reduce bacterial load to an extent comparable to Vancomycin.
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Affiliation(s)
- Roumya Pandey
- Biochemistry and Structural Biology Division, CSIR - Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Grace Kaul
- Molecular Microbiology and Immunology Division, CSIR - Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Abdul Akhir
- Molecular Microbiology and Immunology Division, CSIR - Central Drug Research Institute, Lucknow 226031, India
| | - Deepanshi Saxena
- Molecular Microbiology and Immunology Division, CSIR - Central Drug Research Institute, Lucknow 226031, India
| | - Manjulika Shukla
- Molecular Microbiology and Immunology Division, CSIR - Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Surbhi Mundra
- Biochemistry and Structural Biology Division, CSIR - Central Drug Research Institute, Lucknow 226031, India; Department of Science and Technology, New Delhi 110016, India
| | - Muhammad Zohib
- Biochemistry and Structural Biology Division, CSIR - Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sneha Singh
- Biochemistry and Structural Biology Division, CSIR - Central Drug Research Institute, Lucknow 226031, India
| | - Ravi Kant Pal
- X-ray Crystallography Facility, National Institute of Immunology, New Delhi 110067, India
| | - Sarita Tripathi
- Biochemistry and Structural Biology Division, CSIR - Central Drug Research Institute, Lucknow 226031, India
| | - Anupam Jain
- Biochemistry and Structural Biology Division, CSIR - Central Drug Research Institute, Lucknow 226031, India
| | - Sidharth Chopra
- Molecular Microbiology and Immunology Division, CSIR - Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
| | - Ashish Arora
- Biochemistry and Structural Biology Division, CSIR - Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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14
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Feng J, Zheng Y, Ma W, Weng D, Peng D, Xu Y, Wang Z, Wang X. A synthetic antibiotic class with a deeply-optimized design for overcoming bacterial resistance. Nat Commun 2024; 15:6040. [PMID: 39019927 PMCID: PMC11255307 DOI: 10.1038/s41467-024-50453-3] [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: 12/01/2023] [Accepted: 07/10/2024] [Indexed: 07/19/2024] Open
Abstract
The lack of new drugs that are effective against antibiotic-resistant bacteria has caused increasing concern in global public health. Based on this study, we report development of a modified antimicrobial drug through structure-based drug design (SBDD) and modular synthesis. The optimal modified compound, F8, was identified, which demonstrated in vitro and in vivo broad-spectrum antibacterial activity against drug-resistant bacteria and effectively mitigated the development of resistance. F8 exhibits significant bactericidal activity against bacteria resistant to antibiotics such as methicillin, polymyxin B, florfenicol (FLO), doxycycline, ampicillin and sulfamethoxazole. In a mouse model of drug-resistant bacteremia, F8 was found to increase survival and significantly reduce bacterial load in infected mice. Multi-omics analysis (transcriptomics, proteomics, and metabolomics) have indicated that ornithine carbamoyl transferase (arcB) is a antimicrobial target of F8. Further molecular docking, Isothermal Titration Calorimetry (ITC), and Differential Scanning Fluorimetry (DSF) studies verified arcB as a effective target for F8. Finally, mechanistic studies suggest that F8 competitively binds to arcB, disrupting the bacterial cell membrane and inducing a certain degree of oxidative damage. Here, we report F8 as a promising candidate drug for the development of antibiotic formulations to combat antibiotic-resistant bacteria-associated infections.
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Affiliation(s)
- Jin Feng
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Youle Zheng
- MAO Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Wanqing Ma
- MAO Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Defeng Weng
- MAO Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Dapeng Peng
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China
- MAO Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yindi Xu
- Institute of Animal Husbandry and Veterinary Research, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Zhifang Wang
- Institute of Animal Husbandry and Veterinary Research, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Xu Wang
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China.
- MAO Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China.
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15
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Niu H, Gu J, Zhang Y. Bacterial persisters: molecular mechanisms and therapeutic development. Signal Transduct Target Ther 2024; 9:174. [PMID: 39013893 PMCID: PMC11252167 DOI: 10.1038/s41392-024-01866-5] [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: 11/04/2023] [Revised: 05/06/2024] [Accepted: 05/13/2024] [Indexed: 07/18/2024] Open
Abstract
Persisters refer to genetically drug susceptible quiescent (non-growing or slow growing) bacteria that survive in stress environments such as antibiotic exposure, acidic and starvation conditions. These cells can regrow after stress removal and remain susceptible to the same stress. Persisters are underlying the problems of treating chronic and persistent infections and relapse infections after treatment, drug resistance development, and biofilm infections, and pose significant challenges for effective treatments. Understanding the characteristics and the exact mechanisms of persister formation, especially the key molecules that affect the formation and survival of the persisters is critical to more effective treatment of chronic and persistent infections. Currently, genes related to persister formation and survival are being discovered and confirmed, but the mechanisms by which bacteria form persisters are very complex, and there are still many unanswered questions. This article comprehensively summarizes the historical background of bacterial persisters, details their complex characteristics and their relationship with antibiotic tolerant and resistant bacteria, systematically elucidates the interplay between various bacterial biological processes and the formation of persister cells, as well as consolidates the diverse anti-persister compounds and treatments. We hope to provide theoretical background for in-depth research on mechanisms of persisters and suggest new ideas for choosing strategies for more effective treatment of persistent infections.
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Affiliation(s)
- Hongxia Niu
- School of Basic Medical Science and Key Laboratory of Blood-stasis-toxin Syndrome of Zhejiang Province, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang, China
| | - Jiaying Gu
- School of Basic Medical Science and Key Laboratory of Blood-stasis-toxin Syndrome of Zhejiang Province, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang, China
| | - Ying Zhang
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang, China.
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, 250022, Shandong, China.
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16
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Parkhill SL, Johnson EO. Integrating bacterial molecular genetics with chemical biology for renewed antibacterial drug discovery. Biochem J 2024; 481:839-864. [PMID: 38958473 PMCID: PMC11346456 DOI: 10.1042/bcj20220062] [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: 05/07/2024] [Revised: 06/20/2024] [Accepted: 06/24/2024] [Indexed: 07/04/2024]
Abstract
The application of dyes to understanding the aetiology of infection inspired antimicrobial chemotherapy and the first wave of antibacterial drugs. The second wave of antibacterial drug discovery was driven by rapid discovery of natural products, now making up 69% of current antibacterial drugs. But now with the most prevalent natural products already discovered, ∼107 new soil-dwelling bacterial species must be screened to discover one new class of natural product. Therefore, instead of a third wave of antibacterial drug discovery, there is now a discovery bottleneck. Unlike natural products which are curated by billions of years of microbial antagonism, the vast synthetic chemical space still requires artificial curation through the therapeutics science of antibacterial drugs - a systematic understanding of how small molecules interact with bacterial physiology, effect desired phenotypes, and benefit the host. Bacterial molecular genetics can elucidate pathogen biology relevant to therapeutics development, but it can also be applied directly to understanding mechanisms and liabilities of new chemical agents with new mechanisms of action. Therefore, the next phase of antibacterial drug discovery could be enabled by integrating chemical expertise with systematic dissection of bacterial infection biology. Facing the ambitious endeavour to find new molecules from nature or new-to-nature which cure bacterial infections, the capabilities furnished by modern chemical biology and molecular genetics can be applied to prospecting for chemical modulators of new targets which circumvent prevalent resistance mechanisms.
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Affiliation(s)
- Susannah L. Parkhill
- Systems Chemical Biology of Infection and Resistance Laboratory, The Francis Crick Institute, London, U.K
- Faculty of Life Sciences, University College London, London, U.K
| | - Eachan O. Johnson
- Systems Chemical Biology of Infection and Resistance Laboratory, The Francis Crick Institute, London, U.K
- Faculty of Life Sciences, University College London, London, U.K
- Department of Chemistry, Imperial College, London, U.K
- Department of Chemistry, King's College London, London, U.K
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17
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Brüssow H. The antibiotic resistance crisis and the development of new antibiotics. Microb Biotechnol 2024; 17:e14510. [PMID: 38970161 PMCID: PMC11226406 DOI: 10.1111/1751-7915.14510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Accepted: 06/06/2024] [Indexed: 07/08/2024] Open
Abstract
The Global Burden of Disease report of 2019 estimated 14 million infection-related deaths, making it the second leading cause of death after ischaemic heart disease. Bacterial pathogens accounted for 7.7 million deaths and deaths attributable to bacterial antibiotic resistance amounted to 1.3 million, describing a clear demand for novel antibiotics. Antibiotic development had its golden age in 1930-1960. Following failures in the screening of chemical libraries for novel antibiotics at the beginning of this century, the high cost of launching new antibiotics (estimated at US$ 1.4 billion per registered drug) and difficulties in achieving a return of investment for novel antibiotics, pharmaceutical industry has mostly left the field. The current Lilliput review analyses the question whether scientific or economic hurdles prevented the registration of new antibiotics. Scientifically, substantial progress has been achieved over recent years to define the chemical properties needed to overcome the permeation barrier in Gram-negative pathogens; in extending the chemical space of antibiotic candidates by full modular synthesis of suitable molecules; by extending bioprospecting to previously 'unculturable' bacteria or unusual bacteria; by attacking bacterial targets on the outer bacterial membrane; and by looking for support from structural biology, genomics, molecular genetics, phylogenetic analyses and deep machine learning approaches. However, these research activities were mostly conducted by academic researchers and biotech companies with limited financial resources. It thus seems that the development of new antibiotics, frequently described as the drying of the pipeline, is less limited by lack of scientific insight than by lack of the mobilization of the monetary resources needed to bring these discoveries to the market despite recent financial push and pull efforts of the public sector.
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Affiliation(s)
- Harald Brüssow
- Department of Biosystems, Laboratory of Gene TechnologyKU LeuvenLeuvenBelgium
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18
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Abbas A, Barkhouse A, Hackenberger D, Wright GD. Antibiotic resistance: A key microbial survival mechanism that threatens public health. Cell Host Microbe 2024; 32:837-851. [PMID: 38870900 DOI: 10.1016/j.chom.2024.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/13/2024] [Accepted: 05/17/2024] [Indexed: 06/15/2024]
Abstract
Antibiotic resistance (AMR) is a global public health threat, challenging the effectiveness of antibiotics in combating bacterial infections. AMR also represents one of the most crucial survival traits evolved by bacteria. Antibiotics emerged hundreds of millions of years ago as advantageous secondary metabolites produced by microbes. Consequently, AMR is equally ancient and hardwired into the genetic fabric of bacteria. Human use of antibiotics for disease treatment has created selection pressure that spurs the evolution of new resistance mechanisms and the mobilization of existing ones through bacterial populations in the environment, animals, and humans. This integrated web of resistance elements is genetically complex and mechanistically diverse. Addressing this mode of bacterial survival requires innovation and investment to ensure continued use of antibiotics in the future. Strategies ranging from developing new therapies to applying artificial intelligence in monitoring AMR and discovering new drugs are being applied to manage the growing AMR crisis.
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Affiliation(s)
- Amna Abbas
- David Braley Center for Antibiotic Discovery, Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Alexandra Barkhouse
- David Braley Center for Antibiotic Discovery, Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Dirk Hackenberger
- David Braley Center for Antibiotic Discovery, Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Gerard D Wright
- David Braley Center for Antibiotic Discovery, Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.
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19
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Su M, Su Y. Recent Advances in Amphipathic Peptidomimetics as Antimicrobial Agents to Combat Drug Resistance. Molecules 2024; 29:2492. [PMID: 38893366 PMCID: PMC11173824 DOI: 10.3390/molecules29112492] [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: 04/26/2024] [Revised: 05/21/2024] [Accepted: 05/22/2024] [Indexed: 06/21/2024] Open
Abstract
The development of antimicrobial drugs with novel structures and clear mechanisms of action that are active against drug-resistant bacteria has become an urgent need of safeguarding human health due to the rise of bacterial drug resistance. The discovery of AMPs and the development of amphipathic peptidomimetics have lay the foundation for novel antimicrobial agents to combat drug resistance due to their overall strong antimicrobial activities and unique membrane-active mechanisms. To break the limitation of AMPs, researchers have invested in great endeavors through various approaches in the past years. This review summarized the recent advances including the development of antibacterial small molecule peptidomimetics and peptide-mimic cationic oligomers/polymers, as well as mechanism-of-action studies. As this exciting interdisciplinary field is continuously expanding and growing, we hope this review will benefit researchers in the rational design of novel antimicrobial peptidomimetics in the future.
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Affiliation(s)
- Ma Su
- College of Pharmaceutical Sciences, Soochow University, 199 Ren-Ai Road, Suzhou 215123, China
| | - Yongxiang Su
- College of Chemistry and Environmental Engineering, Jiaozuo University, Ren-Min Road, Jiaozuo 454000, China;
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20
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Craven T, Nolan MD, Bailey J, Olatunji S, Bann SJ, Bowen K, Ostrovitsa N, Da Costa TM, Ballantine RD, Weichert D, Levine PM, Stewart LJ, Bhardwaj G, Geoghegan JA, Cochrane SA, Scanlan EM, Caffrey M, Baker D. Computational Design of Cyclic Peptide Inhibitors of a Bacterial Membrane Lipoprotein Peptidase. ACS Chem Biol 2024; 19:1125-1130. [PMID: 38712757 PMCID: PMC11106742 DOI: 10.1021/acschembio.4c00076] [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: 05/08/2024]
Abstract
There remains a critical need for new antibiotics against multi-drug-resistant Gram-negative bacteria, a major global threat that continues to impact mortality rates. Lipoprotein signal peptidase II is an essential enzyme in the lipoprotein biosynthetic pathway of Gram-negative bacteria, making it an attractive target for antibacterial drug discovery. Although natural inhibitors of LspA have been identified, such as the cyclic depsipeptide globomycin, poor stability and production difficulties limit their use in a clinical setting. We harness computational design to generate stable de novo cyclic peptide analogues of globomycin. Only 12 peptides needed to be synthesized and tested to yield potent inhibitors, avoiding costly preparation of large libraries and screening campaigns. The most potent analogues showed comparable or better antimicrobial activity than globomycin in microdilution assays against ESKAPE-E pathogens. This work highlights computational design as a general strategy to combat antibiotic resistance.
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Affiliation(s)
- Timothy
W. Craven
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
- Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Mark D. Nolan
- School
of Chemistry, Trinity College Dublin, Dublin D02 R590, Ireland
| | - Jonathan Bailey
- School
of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin D02 R590, Ireland
- Biological
Inorganic Chemistry Laboratory, The Francis
Crick Institute, London NW1 1AT, U.K.
| | - Samir Olatunji
- School
of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin D02 R590, Ireland
| | - Samantha J. Bann
- School
of
Chemistry and Chemical Engineering, Queen’s
University Belfast, David
Keir Building, Stranmillis Road, Belfast BT9 5AG, U.K.
| | - Katherine Bowen
- School
of Chemistry, Trinity College Dublin, Dublin D02 R590, Ireland
| | - Nikita Ostrovitsa
- School
of Chemistry, Trinity College Dublin, Dublin D02 R590, Ireland
| | - Thaina M. Da Costa
- Department
of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College
Dublin, Dublin D02 VF25, Ireland
| | - Ross D. Ballantine
- School
of
Chemistry and Chemical Engineering, Queen’s
University Belfast, David
Keir Building, Stranmillis Road, Belfast BT9 5AG, U.K.
| | - Dietmar Weichert
- School
of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin D02 R590, Ireland
| | - Paul M. Levine
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
- Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Lance J. Stewart
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
- Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Gaurav Bhardwaj
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
- Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Joan A. Geoghegan
- Department
of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College
Dublin, Dublin D02 VF25, Ireland
- Institute
of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, U.K.
| | - Stephen A. Cochrane
- School
of
Chemistry and Chemical Engineering, Queen’s
University Belfast, David
Keir Building, Stranmillis Road, Belfast BT9 5AG, U.K.
| | - Eoin M. Scanlan
- School
of Chemistry, Trinity College Dublin, Dublin D02 R590, Ireland
| | - Martin Caffrey
- School
of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin D02 R590, Ireland
| | - David Baker
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
- Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
- Howard
Hughes Medical Institute, University of
Washington, Seattle, Washington 98195, United States
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21
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Won HI, Zinga S, Kandror O, Akopian T, Wolf ID, Schweber JTP, Schmid EW, Chao MC, Waldor M, Rubin EJ, Zhu J. Targeted protein degradation in mycobacteria uncovers antibacterial effects and potentiates antibiotic efficacy. Nat Commun 2024; 15:4065. [PMID: 38744895 PMCID: PMC11094019 DOI: 10.1038/s41467-024-48506-8] [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: 02/14/2023] [Accepted: 05/03/2024] [Indexed: 05/16/2024] Open
Abstract
Proteolysis-targeting chimeras (PROTACs) represent a new therapeutic modality involving selectively directing disease-causing proteins for degradation through proteolytic systems. Our ability to exploit targeted protein degradation (TPD) for antibiotic development remains nascent due to our limited understanding of which bacterial proteins are amenable to a TPD strategy. Here, we use a genetic system to model chemically-induced proximity and degradation to screen essential proteins in Mycobacterium smegmatis (Msm), a model for the human pathogen M. tuberculosis (Mtb). By integrating experimental screening of 72 protein candidates and machine learning, we find that drug-induced proximity to the bacterial ClpC1P1P2 proteolytic complex leads to the degradation of many endogenous proteins, especially those with disordered termini. Additionally, TPD of essential Msm proteins inhibits bacterial growth and potentiates the effects of existing antimicrobial compounds. Together, our results provide biological principles to select and evaluate attractive targets for future Mtb PROTAC development, as both standalone antibiotics and potentiators of existing antibiotic efficacy.
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Affiliation(s)
- Harim I Won
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Samuel Zinga
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Olga Kandror
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Tatos Akopian
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Ian D Wolf
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Jessica T P Schweber
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Ernst W Schmid
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute, Boston, MA, 02115, USA
| | - Michael C Chao
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Maya Waldor
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Eric J Rubin
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
| | - Junhao Zhu
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
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22
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Yuan H, Xun H, Wang J, Wang J, Yao X, Tang F. Integrated Metabolomic and Transcriptomic Analysis Reveals the Underlying Antibacterial Mechanisms of the Phytonutrient Quercetin-Induced Fatty Acids Alteration in Staphylococcus aureus ATCC 27217. Molecules 2024; 29:2266. [PMID: 38792126 PMCID: PMC11123838 DOI: 10.3390/molecules29102266] [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: 04/17/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
The utilization of natural products in food preservation represents a promising strategy for the dual benefits of controlling foodborne pathogens and enhancing the nutritional properties of foods. Among the phytonutrients, flavonoids have been shown to exert antibacterial effects by disrupting bacterial cell membrane functionality; however, the underlying molecular mechanisms remain elusive. In this study, we investigated the effect of quercetin on the cell membrane permeability of Staphylococcus aureus ATCC 27217. A combined metabolomic and transcriptomic approach was adopted to examine the regulatory mechanism of quercetin with respect to the fatty acid composition and associated genes. Kinetic analysis and molecular docking simulations were conducted to assess quercetin's inhibition of β-ketoacyl-acyl carrier protein reductase (FabG), a potential target in the bacterial fatty acid biosynthesis pathway. Metabolomic and transcriptomic results showed that quercetin increased the ratio of unsaturated to saturated fatty acids and the levels of membrane phospholipids. The bacteria reacted to quercetin-induced stress by attempting to enhance fatty acid biosynthesis; however, quercetin directly inhibited FabG activity, thereby disrupting bacterial fatty acid biosynthesis. These findings provide new insights into the mechanism of quercetin's effects on bacterial cell membranes and suggest potential applications for quercetin in bacterial inhibition.
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Affiliation(s)
| | | | | | | | | | - Feng Tang
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Centre for Bamboo and Rattan, Beijing 100102, China; (H.Y.); (H.X.); (J.W.); (J.W.); (X.Y.)
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23
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Rutherford J, Avad K, Dureja C, Norseeda K, GC B, Wu C, Sun D, Hevener KE, Hurdle JG. Evaluation of Fusobacterium nucleatum Enoyl-ACP Reductase (FabK) as a Narrow-Spectrum Drug Target. ACS Infect Dis 2024; 10:1612-1623. [PMID: 38597503 PMCID: PMC11091888 DOI: 10.1021/acsinfecdis.3c00710] [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: 12/20/2023] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 04/11/2024]
Abstract
Fusobacterium nucleatum, a pathobiont inhabiting the oral cavity, contributes to opportunistic diseases, such as periodontal diseases and gastrointestinal cancers, which involve microbiota imbalance. Broad-spectrum antimicrobial agents, while effective against F. nucleatum infections, can exacerbate dysbiosis. This necessitates the discovery of more targeted narrow-spectrum antimicrobial agents. We therefore investigated the potential for the fusobacterial enoyl-ACP reductase II (ENR II) isoenzyme FnFabK (C4N14_ 04250) as a narrow-spectrum drug target. ENRs catalyze the rate-limiting step in the bacterial fatty acid synthesis pathway. Bioinformatics revealed that of the four distinct bacterial ENR isoforms, F. nucleatum specifically encodes FnFabK. Genetic studies revealed that fabK was indispensable for F. nucleatum growth, as the gene could not be deleted, and silencing of its mRNA inhibited growth under the test conditions. Remarkably, exogenous fatty acids failed to rescue growth inhibition caused by the silencing of fabK. Screening of synthetic phenylimidazole analogues of a known FabK inhibitor identified an inhibitor (i.e., 681) of FnFabK enzymatic activity and F. nucleatum growth, with an IC50 of 2.1 μM (1.0 μg/mL) and a MIC of 0.4 μg/mL, respectively. Exogenous fatty acids did not attenuate the activity of 681 against F. nucleatum. Furthermore, FnFabK was confirmed as the intracellular target of 681 based on the overexpression of FnFabK shifting MICs and 681-resistant mutants having amino acid substitutions in FnFabK or mutations in other genetic loci affecting fatty acid biosynthesis. 681 had minimal activity against a range of commensal flora, and it was less active against streptococci in physiologic fatty acids. Taken together, FnFabK is an essential enzyme that is amenable to drug targeting for the discovery and development of narrow-spectrum antimicrobial agents.
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Affiliation(s)
- Jacob
T. Rutherford
- Center
for Infectious and Inflammatory Diseases, Institute of Biosciences
and Technology, Department of Translational Medical Sciences, Texas A&M Health Science Center, Houston, Texas 77030, United States
| | - Kristiana Avad
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Chetna Dureja
- Center
for Infectious and Inflammatory Diseases, Institute of Biosciences
and Technology, Department of Translational Medical Sciences, Texas A&M Health Science Center, Houston, Texas 77030, United States
| | - Krissada Norseeda
- Department
of Pharmaceutical Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawaii at Hilo, Hilo, Hawaii 96720, United States
| | - Bibek GC
- Department
of Microbiology & Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas 77030, United States
| | - Chenggang Wu
- Department
of Microbiology & Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas 77030, United States
| | - Dianqing Sun
- Department
of Pharmaceutical Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawaii at Hilo, Hilo, Hawaii 96720, United States
| | - Kirk E. Hevener
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Julian G. Hurdle
- Center
for Infectious and Inflammatory Diseases, Institute of Biosciences
and Technology, Department of Translational Medical Sciences, Texas A&M Health Science Center, Houston, Texas 77030, United States
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24
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Bosch B, DeJesus MA, Schnappinger D, Rock JM. Weak links: Advancing target-based drug discovery by identifying the most vulnerable targets. Ann N Y Acad Sci 2024; 1535:10-19. [PMID: 38595325 DOI: 10.1111/nyas.15139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Mycobacterium tuberculosis remains the most common infectious killer worldwide despite decades of antitubercular drug development. Effectively controlling the tuberculosis (TB) pandemic will require innovation in drug discovery. In this review, we provide a brief overview of the two main approaches to discovering new TB drugs-phenotypic screens and target-based drug discovery-and outline some of the limitations of each method. We then explore recent advances in genetic tools that aim to overcome some of these limitations. In particular, we highlight a novel metric to prioritize essential targets, termed vulnerability. Stratifying targets based on their vulnerability presents new opportunities for future target-based drug discovery campaigns.
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Affiliation(s)
- Barbara Bosch
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, USA
| | - Michael A DeJesus
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, USA
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York, USA
| | - Jeremy M Rock
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, USA
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25
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Thompson TP, Gilmore BF. Exploring halophilic environments as a source of new antibiotics. Crit Rev Microbiol 2024; 50:341-370. [PMID: 37079280 DOI: 10.1080/1040841x.2023.2197491] [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: 09/16/2022] [Accepted: 03/25/2023] [Indexed: 04/21/2023]
Abstract
Microbial natural products from microbes in extreme environments, including haloarchaea, and halophilic bacteria, possess a huge capacity to produce novel antibiotics. Additionally, enhanced isolation techniques and improved tools for genomic mining have expanded the efficiencies in the antibiotic discovery process. This review article provides a detailed overview of known antimicrobial compounds produced by halophiles from all three domains of life. We summarize that while halophilic bacteria, in particular actinomycetes, contribute the vast majority of these compounds the importance of understudied halophiles from other domains of life requires additional consideration. Finally, we conclude by discussing upcoming technologies- enhanced isolation and metagenomic screening, as tools that will be required to overcome the barriers to antimicrobial drug discovery. This review highlights the potential of these microbes from extreme environments, and their importance to the wider scientific community, with the hope of provoking discussion and collaborations within halophile biodiscovery. Importantly, we emphasize the importance of bioprospecting from communities of lesser-studied halophilic and halotolerant microorganisms as sources of novel therapeutically relevant chemical diversity to combat the high rediscovery rates. The complexity of halophiles will necessitate a multitude of scientific disciplines to unravel their potential and therefore this review reflects these research communities.
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Affiliation(s)
- Thomas P Thompson
- Biofilm Research Group, School of Pharmacy, Queen's University Belfast, Belfast, UK
| | - Brendan F Gilmore
- Biofilm Research Group, School of Pharmacy, Queen's University Belfast, Belfast, UK
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26
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Lorenc A, Badura A, Karolak M, Pałkowski Ł, Kubik Ł, Buciński A. Antimicrobial Activity Classification of Imidazolium Derivatives Predicted by Artificial Neural Networks. Pharm Res 2024; 41:891-898. [PMID: 38632156 PMCID: PMC11116175 DOI: 10.1007/s11095-024-03699-x] [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: 11/14/2023] [Accepted: 04/09/2024] [Indexed: 04/19/2024]
Abstract
PURPOSE This study assesses the Multilayer Perceptron (MLP) neural network, complemented by other Machine Learning techniques (CART, PCA), in predicting the antimicrobial activity of 140 newly designed imidazolium chlorides against Klebsiella pneumoniae before synthesis. Emphasis is on leveraging molecular properties for predictive analysis. METHODS Classification and regression decision trees (CART) identified the top 200 predictive molecular descriptors. Principal Component Analysis (PCA) reduced these descriptors to 5 components, retaining 99.57% of raw data information. Antimicrobial activity, categorized as high or low, was based on experimentally proven minimal inhibitory concentration (MIC), with a cut-point at MIC = 0.856 mol/L. A 12-fold cross-validation trained the MLP (architecture 5-12-2 with 5 Principal Components). RESULTS The MLP exhibited commendable performance, achieving almost 90% correct classifications across learning, validation, and test sets, outperforming models without PCA dimension reduction. Key metrics, including accuracy (0.907), sensitivity (0.905), specificity (0.909), and precision (0.891), were notably high. These results highlight the MLP model's efficacy with PCA as a high-quality classifier for determining antimicrobial activity. CONCLUSIONS The study concludes that the MLP neural network, along with CART and PCA, is a robust tool for predicting the antimicrobial activity class of imidazolium chlorides against Klebsiella pneumoniae. CART and PCA, used in this study, allowed input variable reduction without significant information loss. High classification accuracy and associated metrics affirm the method's potential utility in pre-synthesis assessments, offering valuable insights for antimicrobial compound design.
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Affiliation(s)
- Andżelika Lorenc
- Department of Biopharmacy, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, dr A. Jurasza 2, 85-089, Bydgoszcz, Poland.
| | - Anna Badura
- Department of Biopharmacy, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, dr A. Jurasza 2, 85-089, Bydgoszcz, Poland
| | - Maciej Karolak
- Department of Pharmaceutical Technology, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, dr A. Jurasza 2, 85-089, Bydgoszcz, Poland
| | - Łukasz Pałkowski
- Department of Pharmaceutical Technology, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, dr A. Jurasza 2, 85-089, Bydgoszcz, Poland
| | - Łukasz Kubik
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, Gen. J. Hallera 107, 80-416, Gdańsk, Poland
| | - Adam Buciński
- Department of Biopharmacy, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, dr A. Jurasza 2, 85-089, Bydgoszcz, Poland
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27
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Dartois V, Dick T. Therapeutic developments for tuberculosis and nontuberculous mycobacterial lung disease. Nat Rev Drug Discov 2024; 23:381-403. [PMID: 38418662 PMCID: PMC11078618 DOI: 10.1038/s41573-024-00897-5] [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] [Accepted: 01/24/2024] [Indexed: 03/02/2024]
Abstract
Tuberculosis (TB) drug discovery and development has undergone nothing short of a revolution over the past 20 years. Successful public-private partnerships and sustained funding have delivered a much-improved understanding of mycobacterial disease biology and pharmacology and a healthy pipeline that can tolerate inevitable attrition. Preclinical and clinical development has evolved from decade-old concepts to adaptive designs that permit rapid evaluation of regimens that might greatly shorten treatment duration over the next decade. But the past 20 years also saw the rise of a fatal and difficult-to-cure lung disease caused by nontuberculous mycobacteria (NTM), for which the drug development pipeline is nearly empty. Here, we discuss the similarities and differences between TB and NTM lung diseases, compare the preclinical and clinical advances, and identify major knowledge gaps and areas of cross-fertilization. We argue that applying paradigms and networks that have proved successful for TB, from basic research to clinical trials, will help to populate the pipeline and accelerate curative regimen development for NTM disease.
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Affiliation(s)
- Véronique Dartois
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA.
- Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, NJ, USA.
| | - Thomas Dick
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
- Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, NJ, USA
- Department of Microbiology and Immunology, Georgetown University, Washington, DC, USA
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28
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MacNair CR, Rutherford ST, Tan MW. Alternative therapeutic strategies to treat antibiotic-resistant pathogens. Nat Rev Microbiol 2024; 22:262-275. [PMID: 38082064 DOI: 10.1038/s41579-023-00993-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2023] [Indexed: 04/19/2024]
Abstract
Resistance threatens to render antibiotics - which are essential for modern medicine - ineffective, thus posing a threat to human health. The discovery of novel classes of antibiotics able to overcome resistance has been stalled for decades, with the developmental pipeline relying almost entirely on variations of existing chemical scaffolds. Unfortunately, this approach has been unable to keep pace with resistance evolution, necessitating new therapeutic strategies. In this Review, we highlight recent efforts to discover non-traditional antimicrobials, specifically describing the advantages and limitations of antimicrobial peptides and macrocycles, antibodies, bacteriophages and antisense oligonucleotides. These approaches have the potential to stem the tide of resistance by expanding the physicochemical property space and target spectrum occupied by currently approved antibiotics.
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Affiliation(s)
- Craig R MacNair
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Steven T Rutherford
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Man-Wah Tan
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA.
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29
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Cresti L, Cappello G, Pini A. Antimicrobial Peptides towards Clinical Application-A Long History to Be Concluded. Int J Mol Sci 2024; 25:4870. [PMID: 38732089 PMCID: PMC11084544 DOI: 10.3390/ijms25094870] [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: 03/27/2024] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 05/13/2024] Open
Abstract
Antimicrobial peptides (AMPs) are molecules with an amphipathic structure that enables them to interact with bacterial membranes. This interaction can lead to membrane crossing and disruption with pore formation, culminating in cell death. They are produced naturally in various organisms, including humans, animals, plants and microorganisms. In higher animals, they are part of the innate immune system, where they counteract infection by bacteria, fungi, viruses and parasites. AMPs can also be designed de novo by bioinformatic approaches or selected from combinatorial libraries, and then produced by chemical or recombinant procedures. Since their discovery, AMPs have aroused interest as potential antibiotics, although few have reached the market due to stability limits or toxicity. Here, we describe the development phase and a number of clinical trials of antimicrobial peptides. We also provide an update on AMPs in the pharmaceutical industry and an overall view of their therapeutic market. Modifications to peptide structures to improve stability in vivo and bioavailability are also described.
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Affiliation(s)
- Laura Cresti
- Medical Biotechnology Department, University of Siena, Via A Moro 2, 53100 Siena, Italy; (G.C.); (A.P.)
| | - Giovanni Cappello
- Medical Biotechnology Department, University of Siena, Via A Moro 2, 53100 Siena, Italy; (G.C.); (A.P.)
| | - Alessandro Pini
- Medical Biotechnology Department, University of Siena, Via A Moro 2, 53100 Siena, Italy; (G.C.); (A.P.)
- SetLance srl, Via Fiorentina 1, 53100 Siena, Italy
- Laboratory of Clinical Pathology, Santa Maria alle Scotte University Hospital, 53100 Siena, Italy
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30
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French S, Guo ABY, Ellis MJ, Deisinger JP, Johnson JW, Rachwalski K, Piquette ZA, Lluka T, Zary M, Gamage S, Magolan J, Brown ED. A platform for predicting mechanism of action based on bacterial transcriptional responses identifies an unusual DNA gyrase inhibitor. Cell Rep 2024; 43:114053. [PMID: 38578824 DOI: 10.1016/j.celrep.2024.114053] [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: 04/26/2023] [Revised: 02/02/2024] [Accepted: 03/19/2024] [Indexed: 04/07/2024] Open
Abstract
In the search for much-needed new antibacterial chemical matter, a myriad of compounds have been reported in academic and pharmaceutical screening endeavors. Only a small fraction of these, however, are characterized with respect to mechanism of action (MOA). Here, we describe a pipeline that categorizes transcriptional responses to antibiotics and provides hypotheses for MOA. 3D-printed imaging hardware PFIboxes) profiles responses of Escherichia coli promoter-GFP fusions to more than 100 antibiotics. Notably, metergoline, a semi-synthetic ergot alkaloid, mimics a DNA replication inhibitor. In vitro supercoiling assays confirm this prediction, and a potent analog thereof (MLEB-1934) inhibits growth at 0.25 μg/mL and is highly active against quinolone-resistant strains of methicillin-resistant Staphylococcus aureus. Spontaneous suppressor mutants map to a seldom explored allosteric binding pocket, suggesting a mechanism distinct from DNA gyrase inhibitors used in the clinic. In all, the work highlights the potential of this platform to rapidly assess MOA of new antibacterial compounds.
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Affiliation(s)
- Shawn French
- McMaster University, Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON L8S 4L8, Canada
| | - Amelia Bing Ya Guo
- McMaster University, Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON L8S 4L8, Canada
| | - Michael J Ellis
- McMaster University, Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON L8S 4L8, Canada
| | - Julia P Deisinger
- McMaster University, Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON L8S 4L8, Canada
| | - Jarrod W Johnson
- McMaster University, Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON L8S 4L8, Canada
| | - Kenneth Rachwalski
- McMaster University, Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON L8S 4L8, Canada
| | - Zoë A Piquette
- McMaster University, Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON L8S 4L8, Canada
| | - Telmah Lluka
- McMaster University, Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON L8S 4L8, Canada
| | - Miranda Zary
- McMaster University, Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON L8S 4L8, Canada
| | - Sineli Gamage
- McMaster University, Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON L8S 4L8, Canada
| | - Jakob Magolan
- McMaster University, Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON L8S 4L8, Canada
| | - Eric D Brown
- McMaster University, Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON L8S 4L8, Canada.
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31
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Hogan AM, Motnenko A, Rahman ASMZ, Cardona ST. Cell envelope structural and functional contributions to antibiotic resistance in Burkholderia cenocepacia. J Bacteriol 2024; 206:e0044123. [PMID: 38501654 PMCID: PMC11025338 DOI: 10.1128/jb.00441-23] [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: 12/29/2023] [Accepted: 03/05/2024] [Indexed: 03/20/2024] Open
Abstract
Antibiotic activity is limited by the physical construction of the Gram-negative cell envelope. Species of the Burkholderia cepacia complex (Bcc) are known as intrinsically multidrug-resistant opportunistic pathogens with low permeability cell envelopes. Here, we re-examined a previously performed chemical-genetic screen of barcoded transposon mutants in B. cenocepacia K56-2, focusing on cell envelope structural and functional processes. We identified structures mechanistically important for resistance to singular and multiple antibiotic classes. For example, susceptibility to novobiocin, avibactam, and the LpxC inhibitor, PF-04753299, was linked to the BpeAB-OprB efflux pump, suggesting these drugs are substrates for this pump in B. cenocepacia. Defects in peptidoglycan precursor synthesis specifically increased susceptibility to cycloserine and revealed a new putative amino acid racemase, while defects in divisome accessory proteins increased susceptibility to multiple β-lactams. Additionally, disruption of the periplasmic disulfide bond formation system caused pleiotropic defects on outer membrane integrity and β-lactamase activity. Our findings highlight the layering of resistance mechanisms in the structure and function of the cell envelope. Consequently, we point out processes that can be targeted for developing antibiotic potentiators.IMPORTANCEThe Gram-negative cell envelope is a double-layered physical barrier that protects cells from extracellular stressors, such as antibiotics. The Burkholderia cell envelope is known to contain additional modifications that reduce permeability. We investigated Burkholderia cell envelope factors contributing to antibiotic resistance from a genome-wide view by re-examining data from a transposon mutant library exposed to an antibiotic panel. We identified susceptible phenotypes for defects in structures and functions in the outer membrane, periplasm, and cytoplasm. Overall, we show that resistance linked to the cell envelope is multifaceted and provides new targets for the development of antibiotic potentiators.
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Affiliation(s)
- Andrew M. Hogan
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Anna Motnenko
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Silvia T. Cardona
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
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32
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Zheng EJ, Valeri JA, Andrews IW, Krishnan A, Bandyopadhyay P, Anahtar MN, Herneisen A, Schulte F, Linnehan B, Wong F, Stokes JM, Renner LD, Lourido S, Collins JJ. Discovery of antibiotics that selectively kill metabolically dormant bacteria. Cell Chem Biol 2024; 31:712-728.e9. [PMID: 38029756 PMCID: PMC11031330 DOI: 10.1016/j.chembiol.2023.10.026] [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: 11/29/2022] [Revised: 08/13/2023] [Accepted: 10/30/2023] [Indexed: 12/01/2023]
Abstract
There is a need to discover and develop non-toxic antibiotics that are effective against metabolically dormant bacteria, which underlie chronic infections and promote antibiotic resistance. Traditional antibiotic discovery has historically favored compounds effective against actively metabolizing cells, a property that is not predictive of efficacy in metabolically inactive contexts. Here, we combine a stationary-phase screening method with deep learning-powered virtual screens and toxicity filtering to discover compounds with lethality against metabolically dormant bacteria and favorable toxicity profiles. The most potent and structurally distinct compound without any obvious mechanistic liability was semapimod, an anti-inflammatory drug effective against stationary-phase E. coli and A. baumannii. Integrating microbiological assays, biochemical measurements, and single-cell microscopy, we show that semapimod selectively disrupts and permeabilizes the bacterial outer membrane by binding lipopolysaccharide. This work illustrates the value of harnessing non-traditional screening methods and deep learning models to identify non-toxic antibacterial compounds that are effective in infection-relevant contexts.
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Affiliation(s)
- Erica J Zheng
- Program in Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Jacqueline A Valeri
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Ian W Andrews
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Aarti Krishnan
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Parijat Bandyopadhyay
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Melis N Anahtar
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Alice Herneisen
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02139, USA
| | - Fabian Schulte
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Brooke Linnehan
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Felix Wong
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jonathan M Stokes
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Lars D Renner
- Leibniz Institute of Polymer Research and the Max Bergmann Center of Biomaterials, 01062 Dresden, Germany
| | - Sebastian Lourido
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02139, USA
| | - James J Collins
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA.
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33
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Chong H, Liu X, Fang S, Yang X, Zhang Y, Wang T, Liu L, Kan Y, Zhao Y, Fan H, Zhang J, Wang X, Yao H, Yang Y, Gao Y, Zhao Q, Li S, Plymoth M, Xi J, Zhang Y, Wang C, Pang H. Organo-Pt ii Complexes for Potent Photodynamic Inactivation of Multi-Drug Resistant Bacteria and the Influence of Configuration. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306936. [PMID: 38298088 PMCID: PMC11005693 DOI: 10.1002/advs.202306936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Indexed: 02/02/2024]
Abstract
PtII based organometallic photosensitizers (PSs) have emerged as novel potent photodynamic inactivation (PDI) reagents through their enhanced intersystem crossing (ISC) processes. Currently, few PtII PSs have been investigated as antibacterial materials, with relatively poor performances reported and with structure-activity relationships not well described. Herein, a pair of configurational isomers are reported of Bis-BODIPY (4,4-difluoro-boradizaindacene) embedded PtII PSs. The cis-isomer (cis-BBP) displayed enhanced 1O2 generation and better bacterial membrane anchoring capability as compared to the trans-isomer (trans-BBP). The effective PDI concentrations (efficiency > 99.9%) for cis-BBP in Acinetobacter baumannii (multi-drug resistant (MDR)) and Staphylococcus aureus are 400 nM (12 J cm-2) and 100 nM (18 J cm-2), respectively; corresponding concentrations and light doses for trans-BBP in the two bacteria are 2.50 µM (30 J cm-2) and 1.50 µM (18 J cm-2), respectively. The 50% and 90% minimum inhibitory concentration (MIC50 and MIC90) ratio of trans-BBP to cis-BBP is 22.22 and 24.02 in A. baumannii (MDR); 21.29 and 22.36 in methicillin resistant S. aureus (MRSA), respectively. Furthermore, cis-BBP displays superior in vivo antibacterial performance, with acceptable dark and photoinduced cytotoxicity. These results demonstrate cis-BBP is a robust light-assisted antibacterial reagent at sub-micromolecular concentrations. More importantly, configuration of PtII PSs should be an important issue to be considered in further PDI reagents design.
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Affiliation(s)
- Hui Chong
- Department of Chemical and Chemical EngineeringYangzhou UniversityNo. 180, Si‐Wang‐Ting Rd.YangzhouJiangsu225009P. R. China
| | - Xuanwei Liu
- Department of Chemical and Chemical EngineeringYangzhou UniversityNo. 180, Si‐Wang‐Ting Rd.YangzhouJiangsu225009P. R. China
| | - Siyu Fang
- Department of Chemical and Chemical EngineeringYangzhou UniversityNo. 180, Si‐Wang‐Ting Rd.YangzhouJiangsu225009P. R. China
| | - Xiaofei Yang
- Department of Chemical and Chemical EngineeringYangzhou UniversityNo. 180, Si‐Wang‐Ting Rd.YangzhouJiangsu225009P. R. China
| | - Yuefei Zhang
- Department of EmergencyAffiliated Hospital of Yangzhou UniversityYangzhouJiangsu225000China
| | - Tianyi Wang
- Department of Chemical and Chemical EngineeringYangzhou UniversityNo. 180, Si‐Wang‐Ting Rd.YangzhouJiangsu225009P. R. China
| | - Lin Liu
- School of NursingYangzhou UniversityYangzhou225009P. R. China
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention andTreatment of Senile DiseasesNo. 88 South University Rd.Yangzhou225009P. R. China
| | - Yinshi Kan
- School of NursingYangzhou UniversityYangzhou225009P. R. China
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention andTreatment of Senile DiseasesNo. 88 South University Rd.Yangzhou225009P. R. China
| | - Yueqi Zhao
- School of NursingYangzhou UniversityYangzhou225009P. R. China
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention andTreatment of Senile DiseasesNo. 88 South University Rd.Yangzhou225009P. R. China
| | - Hongying Fan
- Testing Center of Yangzhou UniversityNo. 48 Wenhui East Rd.Yangzhou225009P. R. China
| | - Jingqi Zhang
- School of Materials Science and EngineeringUniversity of Science and Technology BeijingBeijing100083P. R. China
| | - Xiaoyu Wang
- School of Materials Science and EngineeringUniversity of Science and Technology BeijingBeijing100083P. R. China
| | - Hang Yao
- Department of Chemical and Chemical EngineeringYangzhou UniversityNo. 180, Si‐Wang‐Ting Rd.YangzhouJiangsu225009P. R. China
| | - Yi Yang
- Center LaboratoryAffiliated Hospital of Yangzhou UniversityYangzhou225009P. R. China
| | - Yijian Gao
- College of Pharmaceutical SciencesSoochow UniversitySuzhou215123P. R. China
| | - Qi Zhao
- College of Pharmaceutical SciencesSoochow UniversitySuzhou215123P. R. China
| | - Shengliang Li
- College of Pharmaceutical SciencesSoochow UniversitySuzhou215123P. R. China
| | - Martin Plymoth
- Westmead hospitalSydneyNSW 2145Australia
- Department of Clinical MicrobiologyUmeå UniversityUmeå90187Sweden
| | - Juqun Xi
- Department of PharmacologyInstitute of Translational MedicineSchool of MedicineYangzhou UniversityYangzhou225009P. R. China
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention andTreatment of Senile DiseasesYangzhou225009P. R. China
| | - Yu Zhang
- School of NursingYangzhou UniversityYangzhou225009P. R. China
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention andTreatment of Senile DiseasesNo. 88 South University Rd.Yangzhou225009P. R. China
| | - Chengyin Wang
- Department of Chemical and Chemical EngineeringYangzhou UniversityNo. 180, Si‐Wang‐Ting Rd.YangzhouJiangsu225009P. R. China
| | - Huan Pang
- Department of Chemical and Chemical EngineeringYangzhou UniversityNo. 180, Si‐Wang‐Ting Rd.YangzhouJiangsu225009P. R. China
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Blasco B, Jang S, Terauchi H, Kobayashi N, Suzuki S, Akao Y, Ochida A, Morishita N, Takagi T, Nagamiya H, Suzuki Y, Watanabe T, Lee H, Lee S, Shum D, Cho A, Koh D, Park S, Lee H, Kim K, Ropponen HK, Augusto da Costa RM, Dunn S, Ghosh S, Sjö P, Piddock LJV. High-throughput screening of small-molecules libraries identified antibacterials against clinically relevant multidrug-resistant A. baumannii and K. pneumoniae. EBioMedicine 2024; 102:105073. [PMID: 38520916 PMCID: PMC10963893 DOI: 10.1016/j.ebiom.2024.105073] [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: 12/11/2023] [Revised: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 03/25/2024] Open
Abstract
BACKGROUND The current pipeline for new antibiotics fails to fully address the significant threat posed by drug-resistant Gram-negative bacteria that have been identified by the World Health Organization (WHO) as a global health priority. New antibacterials acting through novel mechanisms of action are urgently needed. We aimed to identify new chemical entities (NCEs) with activity against Klebsiella pneumoniae and Acinetobacter baumannii that could be developed into a new treatment for drug-resistant infections. METHODS We developed a high-throughput phenotypic screen and selection cascade for generation of hit compounds active against multidrug-resistant (MDR) strains of K. pneumoniae and A. baumannii. We screened compound libraries selected from the proprietary collections of three pharmaceutical companies that had exited antibacterial drug discovery but continued to accumulate new compounds to their collection. Compounds from two out of three libraries were selected using "eNTRy rules" criteria associated with increased likelihood of intracellular accumulation in Escherichia coli. FINDINGS We identified 72 compounds with confirmed activity against K. pneumoniae and/or drug-resistant A. baumannii. Two new chemical series with activity against XDR A. baumannii were identified meeting our criteria of potency (EC50 ≤50 μM) and absence of cytotoxicity (HepG2 CC50 ≥100 μM and red blood cell lysis HC50 ≥100 μM). The activity of close analogues of the two chemical series was also determined against A. baumannii clinical isolates. INTERPRETATION This work provides proof of principle for the screening strategy developed to identify NCEs with antibacterial activity against multidrug-resistant critical priority pathogens such as K. pneumoniae and A. baumannii. The screening and hit selection cascade established here provide an excellent foundation for further screening of new compound libraries to identify high quality starting points for new antibacterial lead generation projects. FUNDING BMBF and GARDP.
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Affiliation(s)
- Benjamin Blasco
- Global Antibiotic Research and Development Partnership (GARDP), 15 Chemin Camille-Vidart, 1202, Geneva, Switzerland
| | - Soojin Jang
- Institut Pasteur Korea, 16, Daewangpangyo-ro 712 beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, South Korea
| | - Hiroki Terauchi
- Eisai Co., Ltd., Tsukuba Research Laboratories, 5-1-3 Tokodai, Tsukuba, Ibaraki, 300-2635, Japan
| | - Naoki Kobayashi
- Eisai Co., Ltd., Tsukuba Research Laboratories, 5-1-3 Tokodai, Tsukuba, Ibaraki, 300-2635, Japan
| | - Shuichi Suzuki
- Eisai Co., Ltd., Tsukuba Research Laboratories, 5-1-3 Tokodai, Tsukuba, Ibaraki, 300-2635, Japan
| | - Yuichiro Akao
- Takeda Pharmaceutical Company Ltd, 261, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan
| | - Atsuko Ochida
- Takeda Pharmaceutical Company Ltd, 261, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan
| | - Nao Morishita
- Takeda Pharmaceutical Company Ltd, 261, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan
| | - Terufumi Takagi
- Takeda Pharmaceutical Company Ltd, 261, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan
| | - Hiroyuki Nagamiya
- Takeda Pharmaceutical Company Ltd, 261, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan
| | - Yamato Suzuki
- Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo, 140-8710, Japan
| | - Toshiaki Watanabe
- Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo, 140-8710, Japan
| | - Hyunjung Lee
- Institut Pasteur Korea, 16, Daewangpangyo-ro 712 beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, South Korea
| | - Sol Lee
- Institut Pasteur Korea, 16, Daewangpangyo-ro 712 beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, South Korea
| | - David Shum
- Institut Pasteur Korea, 16, Daewangpangyo-ro 712 beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, South Korea
| | - Ahreum Cho
- Institut Pasteur Korea, 16, Daewangpangyo-ro 712 beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, South Korea
| | - Dahae Koh
- Institut Pasteur Korea, 16, Daewangpangyo-ro 712 beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, South Korea
| | - Soonju Park
- Institut Pasteur Korea, 16, Daewangpangyo-ro 712 beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, South Korea
| | - Honggun Lee
- Institut Pasteur Korea, 16, Daewangpangyo-ro 712 beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, South Korea
| | - Kideok Kim
- Institut Pasteur Korea, 16, Daewangpangyo-ro 712 beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, South Korea
| | - Henni-Karoliina Ropponen
- Global Antibiotic Research and Development Partnership (GARDP), 15 Chemin Camille-Vidart, 1202, Geneva, Switzerland
| | | | | | - Sunil Ghosh
- TCG Lifesciences Private Limited, Block BN, Plot 7, Salt Lake Electronics Complex, Sector V, Kolkata, 700091, West Bengal, India
| | - Peter Sjö
- Drugs for Neglected Diseases Initiative, 15 Chemin Camille-Vidart, 1202, Geneva, Switzerland
| | - Laura J V Piddock
- Global Antibiotic Research and Development Partnership (GARDP), 15 Chemin Camille-Vidart, 1202, Geneva, Switzerland.
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35
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Dashti Y, Errington J. Chemistry and biology of specialized metabolites produced by Actinomadura. Nat Prod Rep 2024; 41:370-401. [PMID: 38099919 PMCID: PMC10951976 DOI: 10.1039/d3np00047h] [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] [Received: 10/09/2023] [Indexed: 03/21/2024]
Abstract
Covering: up to the end of 2022In recent years rare Actinobacteria have become increasingly recognised as a rich source of novel bioactive metabolites. Actinomadura are Gram-positive bacteria that occupy a wide range of ecological niches. This review highlights about 230 secondary metabolites produced by Actinomadura spp., reported until the end of 2022, including their bioactivities and selected biosynthetic pathways. Notably, the bioactive compounds produced by Actinomadura spp. demonstrate a wide range of activities, including antimicrobial, antitumor and anticoccidial effects, highlighting their potential in various fields.
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Affiliation(s)
- Yousef Dashti
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2015, Australia.
| | - Jeff Errington
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2015, Australia.
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36
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Poulsen BE, Warrier T, Barkho S, Bagnall J, Romano KP, White T, Yu X, Kawate T, Nguyen PH, Raines K, Ferrara K, Golas A, Fitzgerald M, Boeszoermenyi A, Kaushik V, Serrano-Wu M, Shoresh N, Hung DT. "Multiplexed screen identifies a Pseudomonas aeruginosa -specific small molecule targeting the outer membrane protein OprH and its interaction with LPS". BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.16.585348. [PMID: 38559044 PMCID: PMC10980007 DOI: 10.1101/2024.03.16.585348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The surge of antimicrobial resistance threatens efficacy of current antibiotics, particularly against Pseudomonas aeruginosa , a highly resistant gram-negative pathogen. The asymmetric outer membrane (OM) of P. aeruginosa combined with its array of efflux pumps provide a barrier to xenobiotic accumulation, thus making antibiotic discovery challenging. We adapted PROSPECT 1 , a target-based, whole-cell screening strategy, to discover small molecule probes that kill P. aeruginosa mutants depleted for essential proteins localized at the OM. We identified BRD1401, a small molecule that has specific activity against a P. aeruginosa mutant depleted for the essential lipoprotein, OprL. Genetic and chemical biological studies identified that BRD1401 acts by targeting the OM β-barrel protein OprH to disrupt its interaction with LPS and increase membrane fluidity. Studies with BRD1401 also revealed an interaction between OprL and OprH, directly linking the OM with peptidoglycan. Thus, a whole-cell, multiplexed screen can identify species-specific chemical probes to reveal novel pathogen biology.
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37
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Singh A, Ottavi S, Krieger I, Planck K, Perkowski A, Kaneko T, Davis AM, Suh C, Zhang D, Goullieux L, Alex A, Roubert C, Gardner M, Preston M, Smith DM, Ling Y, Roberts J, Cautain B, Upton A, Cooper CB, Serbina N, Tanvir Z, Mosior J, Ouerfelli O, Yang G, Gold BS, Rhee KY, Sacchettini JC, Fotouhi N, Aubé J, Nathan C. Redirecting raltitrexed from cancer cell thymidylate synthase to Mycobacterium tuberculosis phosphopantetheinyl transferase. SCIENCE ADVANCES 2024; 10:eadj6406. [PMID: 38489355 PMCID: PMC10942122 DOI: 10.1126/sciadv.adj6406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 02/09/2024] [Indexed: 03/17/2024]
Abstract
There is a compelling need to find drugs active against Mycobacterium tuberculosis (Mtb). 4'-Phosphopantetheinyl transferase (PptT) is an essential enzyme in Mtb that has attracted interest as a potential drug target. We optimized a PptT assay, used it to screen 422,740 compounds, and identified raltitrexed, an antineoplastic antimetabolite, as the most potent PptT inhibitor yet reported. While trying unsuccessfully to improve raltitrexed's ability to kill Mtb and remove its ability to kill human cells, we learned three lessons that may help others developing antibiotics. First, binding of raltitrexed substantially changed the configuration of the PptT active site, complicating molecular modeling of analogs based on the unliganded crystal structure or the structure of cocrystals with inhibitors of another class. Second, minor changes in the raltitrexed molecule changed its target in Mtb from PptT to dihydrofolate reductase (DHFR). Third, the structure-activity relationship for over 800 raltitrexed analogs only became interpretable when we quantified and characterized the compounds' intrabacterial accumulation and transformation.
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Affiliation(s)
- Amrita Singh
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10021, USA
| | - Samantha Ottavi
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Inna Krieger
- Department of Biochemistry and Biophysics, Texas Agricultural and Mechanical University, College Station, TX 77843, USA
| | - Kyle Planck
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Andrew Perkowski
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Takushi Kaneko
- Global Alliance for TB Drug Development, New York, NY 10005, USA
| | | | - Christine Suh
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10021, USA
| | - David Zhang
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10021, USA
| | | | - Alexander Alex
- AMG Consultants Limited, Camburgh House, 27 New Dover Road, Canterbury, Kent, CT1 3DN, UK
- Evenor Consulting Limited, The New Barn, Mill Lane, Eastry, Kent CT13 0JW, UK
| | | | - Mark Gardner
- AMG Consultants Limited, Camburgh House, 27 New Dover Road, Canterbury, Kent, CT1 3DN, UK
| | - Marian Preston
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, UK
| | - Dave M. Smith
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, UK
| | - Yan Ling
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10021, USA
| | - Julia Roberts
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10021, USA
| | - Bastien Cautain
- Evotec ID (Lyon), SAS 40 Avenue Tony Garnier, Lyon 69001, France
| | - Anna Upton
- Evotec ID (Lyon), SAS 40 Avenue Tony Garnier, Lyon 69001, France
| | | | - Natalya Serbina
- Global Alliance for TB Drug Development, New York, NY 10005, USA
| | - Zaid Tanvir
- Global Alliance for TB Drug Development, New York, NY 10005, USA
| | - John Mosior
- Department of Biochemistry and Biophysics, Texas Agricultural and Mechanical University, College Station, TX 77843, USA
| | - Ouathek Ouerfelli
- Organic Synthesis Core, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Guangli Yang
- Organic Synthesis Core, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ben S. Gold
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10021, USA
| | - Kyu Y. Rhee
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - James C. Sacchettini
- Department of Biochemistry and Biophysics, Texas Agricultural and Mechanical University, College Station, TX 77843, USA
| | - Nader Fotouhi
- Global Alliance for TB Drug Development, New York, NY 10005, USA
| | - Jeffrey Aubé
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Carl Nathan
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10021, USA
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38
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Cain BN, Hergenrother PJ. Using permeation guidelines to design new antibiotics-A PASsagE into Pseudomonas aeruginosa. Clin Transl Med 2024; 14:e1600. [PMID: 38426413 PMCID: PMC10905542 DOI: 10.1002/ctm2.1600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 02/07/2024] [Indexed: 03/02/2024] Open
Affiliation(s)
- Brett N. Cain
- Department of Chemistry and Carl R. Woese Institute for Genomic BiologyUniversity of IllinoisUrbanaIllinoisUSA
| | - Paul J. Hergenrother
- Department of Chemistry and Carl R. Woese Institute for Genomic BiologyUniversity of IllinoisUrbanaIllinoisUSA
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Tienaho J, Fidelis M, Brännström H, Hellström J, Rudolfsson M, Kumar Das A, Liimatainen J, Kumar A, Kurkilahti M, Kilpeläinen P. Valorizing Assorted Logging Residues: Response Surface Methodology in the Extraction Optimization of a Green Norway Spruce Needle-Rich Fraction To Obtain Valuable Bioactive Compounds. ACS SUSTAINABLE RESOURCE MANAGEMENT 2024; 1:237-249. [PMID: 38414817 PMCID: PMC10895920 DOI: 10.1021/acssusresmgt.3c00050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 01/17/2024] [Accepted: 01/17/2024] [Indexed: 02/29/2024]
Abstract
During stemwood harvesting, substantial volumes of logging residues are produced as a side stream. Nevertheless, industrially feasible processing methods supporting their use for other than energy generation purposes are scarce. Thus, the present study focuses on biorefinery processing, employing response surface methodology to optimize the pressurized extraction of industrially assorted needle-rich spruce logging residues with four solvents. Eighteen experimental points, including eight center point replicates, were used to optimize the extraction temperature (40-135 °C) and time (10-70 min). The extraction optimization for water, water with Na2CO3 + NaHSO3 addition, and aqueous ethanol was performed using yield, total dissolved solids (TDS), antioxidant activity (FRAP, ORAC), antibacterial properties (E. coli, S. aureus), total phenolic content (TPC), condensed tannin content, and degree of polymerization. For limonene, evaluated responses were yield, TDS, antioxidant activity (CUPRAC, DPPH), and TPC. Desirability surfaces were created using the responses showing a coefficient of determination (R2) > 0.7, statistical significance (p ≤ 0.05), precision > 4, and statistically insignificant lack-of-fit (p > 0.1). The optimal extraction conditions were 125 °C and 68 min for aqueous ethanol, 120 °C and 10 min for water, 111 °C and 49 min for water with Na2CO3 + NaHSO3 addition, and 134 °C and 41 min for limonene. The outcomes contribute insights to industrial logging residue utilization for value-added purposes.
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Affiliation(s)
- Jenni Tienaho
- Production Systems, Natural Resources Institute Finland (Luke), Latokartanonkaari 9, FI-00790 Helsinki, Finland
| | - Marina Fidelis
- Production Systems, Natural Resources Institute Finland (Luke), Latokartanonkaari 9, FI-00790 Helsinki, Finland
- Food Sciences Unit, Department of Life Technologies, University of Turku, FI-20014 Turku, Finland
| | - Hanna Brännström
- Production Systems, Natural Resources Institute Finland (Luke), Teknologiakatu 7, FI-67100 Kokkola, Finland
| | - Jarkko Hellström
- Production Systems, Natural Resources Institute Finland (Luke), Myllytie 1, FI-31600 Jokioinen, Finland
| | - Magnus Rudolfsson
- Unit of Biomass Technology and Chemistry, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden
| | - Atanu Kumar Das
- Unit of Biomass Technology and Chemistry, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden
| | - Jaana Liimatainen
- Production Systems, Natural Resources Institute Finland (Luke), Latokartanonkaari 9, FI-00790 Helsinki, Finland
| | - Anuj Kumar
- Production Systems, Natural Resources Institute Finland (Luke), Latokartanonkaari 9, FI-00790 Helsinki, Finland
| | - Mika Kurkilahti
- Natural Resources, Natural Resources Institute Finland (Luke), Itäinen Pitkäkatu 4 A, FI-20520 Turku, Finland
| | - Petri Kilpeläinen
- Production Systems, Natural Resources Institute Finland (Luke), Latokartanonkaari 9, FI-00790 Helsinki, Finland
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40
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Suckling CJ. The allure of targets for novel drugs. RSC Med Chem 2024; 15:472-484. [PMID: 38389887 PMCID: PMC10880906 DOI: 10.1039/d3md00621b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 12/12/2023] [Indexed: 02/24/2024] Open
Abstract
The challenges of bringing new medicines to patients have been extensively discussed and debated, including consideration of the contribution that academic laboratories can make. At the University of Strathclyde, drug discovery has been a continuing focal activity since the 1960s, and in the past 30 years, the author has led or contributed to many projects of different character and for diverse diseases. A feature common to these projects is the extension of concepts of molecular and biological targets in drug discovery research. In mechanistic terms, these have included compounds that are activators and not inhibitors, and in particular multitargeted compounds. With respect to relevance to disease, schizophrenia, pulmonary disfunction, autoimmune, and infectious disease are most relevant. These projects are discussed in the context of classical medicinal chemistry and more recent concepts in and approaches to drug discovery.
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Affiliation(s)
- Colin J Suckling
- Department of Pure & Applied Chemistry, University of Strathclyde 295 Cathedral Street Glasgow G1 1Xl Scotland UK
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41
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Liu H, Xu T, Xue Z, Huang M, Wang T, Zhang M, Yang R, Guo Y. Current Development of Thiazole-Containing Compounds as Potential Antibacterials against Methicillin-Resistant Staphylococcus aureus. ACS Infect Dis 2024; 10:350-370. [PMID: 38232301 DOI: 10.1021/acsinfecdis.3c00647] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
The emergence of multi-drug-resistant bacteria is threatening to human health and life around the world. In particular, methicillin-resistant Staphylococcus aureus (MRSA) causes fatal injuries to human beings and serious economic losses to animal husbandry due to its easy transmission and difficult treatment. Currently, the development of novel, highly effective, and low-toxicity antimicrobials is important to combat MRSA infections. Thiazole-containing compounds with good biological activity are widely used in clinical practice, and appropriate structural modifications make it possible to develop new antimicrobials. Here, we review thiazole-containing compounds and their antibacterial effects against MRSA reported in the past two decades and discuss their structure-activity relationships as well as the corresponding antimicrobial mechanisms. Some thiazole-containing compounds exhibit potent antibacterial efficacy in vitro and in vivo after appropriate structural modifications and could be used as antibacterial candidates. This Review provides insights into the development of thiazole-containing compounds as antimicrobials to combat MRSA infections.
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Affiliation(s)
- Hang Liu
- Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang 421001, Hunan Province, China
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, Henan Province, China
| | - Ting Xu
- Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang 421001, Hunan Province, China
| | - Zihan Xue
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, Henan Province, China
| | - Meijuan Huang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, Henan Province, China
| | - Tingting Wang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, Henan Province, China
| | - Miaomiao Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, Henan Province, China
| | - Ruige Yang
- Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang 421001, Hunan Province, China
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, Henan Province, China
| | - Yong Guo
- Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang 421001, Hunan Province, China
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, Henan Province, China
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42
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Nair G, Jain V. An intramolecular cross-talk in D29 mycobacteriophage endolysin governs the lytic cycle and phage-host population dynamics. SCIENCE ADVANCES 2024; 10:eadh9812. [PMID: 38335296 PMCID: PMC10857449 DOI: 10.1126/sciadv.adh9812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 01/10/2024] [Indexed: 02/12/2024]
Abstract
D29 mycobacteriophage encodes LysA endolysin, which mediates mycobacterial host cell lysis by targeting its peptidoglycan layer, thus projecting itself as a potential therapeutic. However, the regulatory mechanism of LysA during the phage lytic cycle remains ill defined. Here, we show that during D29 lytic cycle, structural and functional regulation of LysA not only orchestrates host cell lysis but also is critical for maintaining phage-host population dynamics by governing various phases of lytic cycle. We report that LysA exists in two conformations, of which only one is active, and the protein undergoes a host peptidoglycan-dependent conformational switch to become active for carrying out endogenous host cell lysis. D29 maintains a pool of inactive LysA, allowing complete assembly of phage progeny, thus helping avoid premature host lysis. In addition, we show that the switch reverses after lysis, thus preventing exogenous targeting of bystanders, which otherwise negatively affects phage propagation in the environment.
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Affiliation(s)
- Gokul Nair
- Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal 462066, Madhya Pradesh, India
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43
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Naranjo MF, Kumar A, Ratrey P, Hudson SP. Pre-formulation of an additive combination of two antimicrobial agents, clofazimine and nisin A, to boost antimicrobial activity. J Mater Chem B 2024; 12:1558-1568. [PMID: 38252026 DOI: 10.1039/d3tb01800h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
According to the World Health Organization, antimicrobial resistance is one of the top ten issues that pose a major threat to humanity. The lack of investment by the pharmaceutical industry has meant fewer novel antimicrobial agents are in development, exacerbating the problem. Emerging drug design strategies are exploring the repurposing of existing drugs and the utilization of novel drug candidates, like antimicrobial peptides, to combat drug resistance. This proactive approach is crucial in fighting global health threats. In this study, an additive combination of a repurposed anti-leprosy drug, clofazimine, and an antimicrobial peptide, nisin A, are preformulated using liquid antisolvent precipitation to generate a stable amorphous, ionized nanoparticle system to boost antimicrobial activity. The nanotechnology aims to improve the physicochemical properties of the inherently poorly water-soluble clofazimine molecules while also harnessing the previously unreported additive effect of clofazimine and nisin A. The approach transformed clofazimine into a more water-soluble salt, yielding amorphous nanoparticles stabilized by the antimicrobial peptide; and combined the two drugs into a more soluble and more active formulation. Blending pre-formulation strategies like amorphization, salt formation, and nanosizing to improve the inherent low aqueous solubility of drugs can open many new possibilities for the design of new antimicrobial agents. This fusion of pre-formulation technologies in combination with the multi-hurdle approach of selecting drugs with different effects on microbes could be key in the design platform of new antibiotics in the fight against antimicrobial resistance.
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Affiliation(s)
- Mateo Flores Naranjo
- Department of Chemical Sciences, SSPC, Science Foundation Ireland Research Centre for Pharmaceuticals, Bernal Institute, University of Limerick, Castletroy, Limerick, V94 T9PX, Ireland.
| | - Ajay Kumar
- Department of Chemical Sciences, SSPC, Science Foundation Ireland Research Centre for Pharmaceuticals, Bernal Institute, University of Limerick, Castletroy, Limerick, V94 T9PX, Ireland.
| | - Poonam Ratrey
- Department of Chemical Sciences, SSPC, Science Foundation Ireland Research Centre for Pharmaceuticals, Bernal Institute, University of Limerick, Castletroy, Limerick, V94 T9PX, Ireland.
| | - Sarah P Hudson
- Department of Chemical Sciences, SSPC, Science Foundation Ireland Research Centre for Pharmaceuticals, Bernal Institute, University of Limerick, Castletroy, Limerick, V94 T9PX, Ireland.
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44
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Couturier C, Ronzon Q, Lattanzi G, Lingard I, Coyne S, Cazals V, Dubarry N, Yvon S, Leroi-Geissler C, Gracia OR, Teague J, Sordello S, Corbett D, Bauch C, Monlong C, Payne L, Taillier T, Fuchs H, Broenstrup M, Harrison PH, Moynié L, Lakshminarayanan A, Gianga TM, Hussain R, Naismith JH, Mourez M, Bacqué E, Björkling F, Sabuco JF, Franzyk H. Studies of antibacterial activity (in vitro and in vivo) and mode of action for des-acyl tridecaptins (DATs). Eur J Med Chem 2024; 265:116097. [PMID: 38157595 DOI: 10.1016/j.ejmech.2023.116097] [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: 11/09/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/03/2024]
Abstract
Tridecaptins comprise a class of linear cationic lipopeptides with an N-terminal fatty acyl moiety. These 13-mer antimicrobial peptides consist of a combination of d- and l-amino acids, conferring increased proteolytic stability. Intriguingly, they are biosynthesized by non-ribosomal peptide synthetases in the same bacterial species that also produce the cyclic polymyxins displaying similar fatty acid tails. Previously, the des-acyl analog of TriA1 (termed H-TriA1) was found to possess very weak antibacterial activity, albeit it potentiated the effect of several antibiotics. In the present study, two series of des-acyl tridecaptins were explored with the aim of improving the direct antibacterial effect. At the same time, overall physico-chemical properties were modulated by amino acid substitution(s) to diminish the risk of undesired levels of hemolysis and to avoid an impairment of mammalian cell viability, since these properties are typically associated with highly hydrophobic cationic peptides. Microbiology and biophysics tools were used to determine bacterial uptake, while circular dichroism and isothermal calorimetry were used to probe the mode of action. Several analogs had improved antibacterial activity (as compared to that of H-TriA1) against Enterobacteriaceae. Optimization enabled identification of the lead compound 29 that showed a good ADMET profile as well as in vivo efficacy in a variety of mouse models of infection.
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Affiliation(s)
- Cédric Couturier
- Evotec, 1541, Avenue Marcel Mérieux, 69280, Marcy L'Etoile, France.
| | - Quentin Ronzon
- Evotec, 1541, Avenue Marcel Mérieux, 69280, Marcy L'Etoile, France
| | - Giulia Lattanzi
- Evotec-Aptuit (Verona) Srl, Via Alessandro Fleming 4, 37135, Verona, Italy
| | - Iain Lingard
- Evotec-Aptuit (Verona) Srl, Via Alessandro Fleming 4, 37135, Verona, Italy
| | | | | | | | | | | | | | - Joanne Teague
- Evotec, No. 23F, Mereside, Alderley Park, Cheshire, SK10 4TG, United Kingdom
| | | | - David Corbett
- Evotec, No. 23F, Mereside, Alderley Park, Cheshire, SK10 4TG, United Kingdom
| | - Caroline Bauch
- Evotec-Cyprotex, No. 24, Mereside, Alderley Park, Cheshire, SK10 4TG, United Kingdom
| | | | - Lloyd Payne
- Evotec, No. 23F, Mereside, Alderley Park, Cheshire, SK10 4TG, United Kingdom
| | | | - Hazel Fuchs
- Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstraße 7, 38124, Braunschweig, Germany
| | - Mark Broenstrup
- Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstraße 7, 38124, Braunschweig, Germany
| | - Peter H Harrison
- Division of Structural Biology, Wellcome Trust Centre of Human Genomics, 7 Roosevelt Drive, Oxford, OX3 7BN, United Kingdom
| | - Lucile Moynié
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, OX11 0QS, United Kingdom
| | - Abirami Lakshminarayanan
- Division of Structural Biology, Wellcome Trust Centre of Human Genomics, 7 Roosevelt Drive, Oxford, OX3 7BN, United Kingdom
| | - Tiberiu-Marius Gianga
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0DE, United Kingdom
| | - Rohanah Hussain
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0DE, United Kingdom
| | - James H Naismith
- Division of Structural Biology, Wellcome Trust Centre of Human Genomics, 7 Roosevelt Drive, Oxford, OX3 7BN, United Kingdom; Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, OX11 0QS, United Kingdom
| | | | - Eric Bacqué
- Evotec, 1541, Avenue Marcel Mérieux, 69280, Marcy L'Etoile, France
| | - Fredrik Björkling
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100, Denmark
| | | | - Henrik Franzyk
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100, Denmark
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45
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Chang H, Ji R, Zhu Z, Wang Y, Yan S, He D, Jia Q, Huang P, Cheng T, Wang R, Zhou Y. Target identification, and optimization of dioxygenated amide derivatives as potent antibacterial agents with FabH inhibitory activity. Eur J Med Chem 2024; 265:116064. [PMID: 38159483 DOI: 10.1016/j.ejmech.2023.116064] [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: 08/29/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 01/03/2024]
Abstract
The enzyme FabH plays a critical role in the initial step of fatty acid biosynthesis, which is vital for the survival of bacteria. As a result, FabH has emerged as an appealing target for the development of novel antibacterial agents. In this study, employing the chemical proteomics method, we validated the previously identified skeleton amide derivatives bearing dioxygenated rings, potentially formed through metabolic processes. Building upon the proteomics findings, we then synthesized and evaluated 32 compounds containing N-heterocyclic amides for their antimicrobial activity for future optimizing the deoxygenated amides. Several compounds demonstrated potent antimicrobial properties with low toxicity, particularly compound 25, which exhibited remarkable potential as an agent with an MIC range of 1.25-3.13 μg/mL against the tested bacterial strains and an IC50 of 2.0 μM against E. coli-derived FabH. Furthermore, we evaluated nine analogues with relatively low MIC values through cytotoxicity and hemolytic activity assessments, Lipinski's rule-of-five criteria, and in silico ADMET predictions to ascertain their druggability potential. Notably, a detailed docking simulation was performed to investigate the binding interactions of compound 25 within the binding pocket of E. coli FabH, which encouragingly revealed strong binding interactions. Based on our findings, compound 25 emerges as the optimal candidate for in vivo therapy aimed at treating infected skin defects. Remarkably, the application of compound 25 demonstrated a significant reduction in the duration of wound infection and notably accelerated the healing process of infected wounds, achieving an impressive 94 % healing rate by day 10.
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Affiliation(s)
- Haoyun Chang
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China; Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315300, China
| | - Ruiying Ji
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315300, China
| | - Zhiyu Zhu
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315300, China
| | - Yapin Wang
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315300, China
| | - Shaopeng Yan
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315300, China
| | - Dan He
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315300, China
| | - Qike Jia
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315300, China
| | - Peng Huang
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China.
| | - Tao Cheng
- Pharmaron (Ningbo) Technology Development Co. Ltd., Ningbo, 315336, China
| | - Rui Wang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518118, China.
| | - Yang Zhou
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315300, China.
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46
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Zhao X, Verma R, Sridhara MB, Sharath Kumar KS. Fluorinated azoles as effective weapons in fight against methicillin-resistance staphylococcus aureus (MRSA) and its SAR studies. Bioorg Chem 2024; 143:106975. [PMID: 37992426 DOI: 10.1016/j.bioorg.2023.106975] [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: 09/25/2023] [Revised: 10/22/2023] [Accepted: 11/14/2023] [Indexed: 11/24/2023]
Abstract
The rapid spread of Methicillin-resistant Staphylococcus aureus (MRSA) and its difficult-to-treat skin and filmsy diseases are making MRSA a threat to human life. The most dangerous feature is the fast emergence of MRSA resistance to all recognized antibiotics, including vancomycin. The creation of novel, effective, and non-toxic drug candidates to combat MRSA isolates is urgently required. Fluorine containing small molecules have taken a centre stage in the field of drug development. Over the last 50 years, there have been a growing number of fluorinated compounds that have been approved since the clinical usage of fluorinated corticosteroids in the 1950 s and fluoroquinolones in the 1980 s. Due to its advantages in terms of potency and ADME (absorption, distribution, metabolism, and excretion), fluoro-pharmaceuticals have been regarded as a potent and useful tool in the rational drug design method. The flexible bioactive fluorinated azoles are ideal candidates for the development of new antibiotics. This review summarizes the decade developments of fluorinated azole derivatives with a wide antibacterial activity against diverged MRSA strains. In specific, we correlated the efficacy of structurally varied fluorinated azole analogues including thiazole, benzimidazole, oxadiazole and pyrazole against MRSA and discussed different angles of structure-activity relationship (SAR).
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Affiliation(s)
- Xuanming Zhao
- Energy Engineering College, Yulin University, Yulin City-719000, P. R. China
| | - Rameshwari Verma
- School of New Energy, Yulin University, Yulin 719000, Shaanxi, P. R. China
| | - M B Sridhara
- Department of Chemistry, Rani Channamma University, Vidyasangama, Belagavi 591156, India
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47
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Qandeel BM, Mowafy S, Abouzid K, Farag NA. Lead generation of UPPS inhibitors targeting MRSA: Using 3D-QSAR pharmacophore modeling, virtual screening, molecular docking, and molecular dynamic simulations. BMC Chem 2024; 18:14. [PMID: 38245752 PMCID: PMC10800075 DOI: 10.1186/s13065-023-01110-1] [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: 09/05/2023] [Accepted: 12/21/2023] [Indexed: 01/22/2024] Open
Abstract
Undecaprenyl Pyrophosphate Synthase (UPPS) is a vital target enzyme in the early stages of bacterial cell wall biosynthesis. UPPS inhibitors have antibacterial activity against resistant strains such as MRSA and VRE. In this study, we used several consecutive computer-based protocols to identify novel UPPS inhibitors. The 3D QSAR pharmacophore model generation (HypoGen algorithm) protocol was used to generate a valid predictive pharmacophore model using a set of UPPS inhibitors with known reported activity. The developed model consists of four pharmacophoric features: one hydrogen bond acceptor, two hydrophobic, and one aromatic ring. It had a correlation coefficient of 0.86 and a null cost difference of 191.39, reflecting its high predictive power. Hypo1 was proven to be statistically significant using Fischer's randomization at a 95% confidence level. The validated pharmacophore model was used for the virtual screening of several databases. The resulting hits were filtered using SMART and Lipinski filters. The hits were docked into the binding site of the UPPS protein, affording 70 hits with higher docking affinities than the reference compound (6TC, - 21.17 kcal/mol). The top five hits were selected through extensive docking analysis and visual inspection based on docking affinities, fit values, and key residue interactions with the UPPS receptor. Moreover, molecular dynamic simulations of the top hits were performed to confirm the stability of the protein-ligand complexes, yielding five promising novel UPPS inhibitors.
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Affiliation(s)
- Basma M Qandeel
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Misr International University, Km28 Cairo-Ismailia Road, Ahmed Orabi District, Cairo, Egypt.
| | - Samar Mowafy
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Misr International University, Km28 Cairo-Ismailia Road, Ahmed Orabi District, Cairo, Egypt
| | - Khaled Abouzid
- Department of Pharmaceutical Chemistry, College of Pharmacy, Ain-Shams University, Abbasia, 11566, Egypt
| | - Nahla A Farag
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Misr International University, Km28 Cairo-Ismailia Road, Ahmed Orabi District, Cairo, Egypt.
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48
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Otri I, Medaglia S, Martínez-Máñez R, Aznar E, Sancenón F. Exploring the Synergy between Nano-Formulated Linezolid and Polymyxin B as a Gram-Negative Effective Antibiotic Delivery System Based on Mesoporous Silica Nanoparticles. NANOMATERIALS (BASEL, SWITZERLAND) 2024; 14:228. [PMID: 38276746 PMCID: PMC10818268 DOI: 10.3390/nano14020228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/15/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024]
Abstract
Antimicrobial resistance is a current silent pandemic that needs new types of antimicrobial agents different from the classic antibiotics that are known to lose efficiency over time. Encapsulation of antibiotics inside nano-delivery systems could be a promising, effective strategy that is able to delay the capability of pathogens to develop resistance mechanisms against antimicrobials. These systems can be adapted to deliver already discovered antibiotics to specific infection sites in a more successful way. Herein, mesoporous silica nanomaterials are used for an efficient delivery of a linezolid gram-positive antibiotic that acts synergistically with gram-negative antimicrobial polymyxin B. For this purpose, linezolid is encapsulated in the pores of the mesoporous silica, whose outer surface is coated with a polymyxin B membrane disruptor. The nanomaterial showed a good controlled-release performance in the presence of lipopolysaccharide, found in bacteria cell membranes, and the complete bacteria E. coli DH5α. The performed studies demonstrate that when the novel formulation is near bacteria, polymyxin B interacts with the cell membrane, thereby promoting its permeation. After this step, linezolid can easily penetrate the bacteria and act with efficacy to kill the microorganism. The nano-delivery system presents a highly increased antimicrobial efficacy against gram-negative bacteria, where the use of free linezolid is not effective, with a fractional inhibitory concentration index of 0.0063 for E. coli. Moreover, enhanced toxicity against gram-positive bacteria was confirmed thanks to the combination of both antibiotics in the same nanoparticles. Although this new nanomaterial should be further studied to reach clinical practice, the obtained results pave the way to the development of new nanoformulations which could help in the fight against bacterial infections.
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Affiliation(s)
- Ismael Otri
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022 Valencia, Spain; (I.O.); (S.M.); (R.M.-M.)
| | - Serena Medaglia
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022 Valencia, Spain; (I.O.); (S.M.); (R.M.-M.)
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Instituto de Salud Carlos III, 46022 Valencia, Spain
| | - Ramón Martínez-Máñez
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022 Valencia, Spain; (I.O.); (S.M.); (R.M.-M.)
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Instituto de Salud Carlos III, 46022 Valencia, Spain
- Unidad Mixta de Investigación en Nanomedicina y Sensores, Instituto de Investigación Sanitaria La Fe, Universitat Politècnica de València, 46026 Valencia, Spain
- Unidad Mixta UPV-CIPF de Investigación en Mecanismos de Enfermedades y Nanomedicina, Centro de Investigación Príncipe Felipe, Universitat Politècnica de València, 46012 Valencia, Spain
- Departamento de Química, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Elena Aznar
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022 Valencia, Spain; (I.O.); (S.M.); (R.M.-M.)
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Instituto de Salud Carlos III, 46022 Valencia, Spain
- Unidad Mixta de Investigación en Nanomedicina y Sensores, Instituto de Investigación Sanitaria La Fe, Universitat Politècnica de València, 46026 Valencia, Spain
- Departamento de Química, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Félix Sancenón
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022 Valencia, Spain; (I.O.); (S.M.); (R.M.-M.)
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Instituto de Salud Carlos III, 46022 Valencia, Spain
- Unidad Mixta de Investigación en Nanomedicina y Sensores, Instituto de Investigación Sanitaria La Fe, Universitat Politècnica de València, 46026 Valencia, Spain
- Unidad Mixta UPV-CIPF de Investigación en Mecanismos de Enfermedades y Nanomedicina, Centro de Investigación Príncipe Felipe, Universitat Politècnica de València, 46012 Valencia, Spain
- Departamento de Química, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
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Stoorza AM, Duerfeldt AS. Guiding the Way: Traditional Medicinal Chemistry Inspiration for Rational Gram-Negative Drug Design. J Med Chem 2024; 67:65-80. [PMID: 38134355 PMCID: PMC11342810 DOI: 10.1021/acs.jmedchem.3c01831] [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: 12/24/2023]
Abstract
The discovery and development of small-molecule therapeutics effective against Gram-negative pathogens are highly challenging tasks. Most compounds that are active in biochemical settings fail to exhibit whole-cell activity. The major reason for this lack of activity is the effectiveness of bacterial cell envelopes as permeability barriers. These barriers originate from the nutrient-selective outer membranes, which act synergistically with polyspecific efflux pumps. Guiding principles to enable rational optimization of small molecules for efficient penetration and intracellular accumulation in Gram-negative bacteria would have a transformative impact on the discovery and design of chemical probes and therapeutics. In this Perspective, we draw on inspiration from traditional medicinal chemistry approaches for eukaryotic drug design to present a broader call for action in developing comparable approaches for Gram-negative bacteria.
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Affiliation(s)
- Alexis M Stoorza
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Adam S Duerfeldt
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55414, United States
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50
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Augustijn HE, Roseboom AM, Medema MH, van Wezel GP. Harnessing regulatory networks in Actinobacteria for natural product discovery. J Ind Microbiol Biotechnol 2024; 51:kuae011. [PMID: 38569653 PMCID: PMC10996143 DOI: 10.1093/jimb/kuae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 04/02/2024] [Indexed: 04/05/2024]
Abstract
Microbes typically live in complex habitats where they need to rapidly adapt to continuously changing growth conditions. To do so, they produce an astonishing array of natural products with diverse structures and functions. Actinobacteria stand out for their prolific production of bioactive molecules, including antibiotics, anticancer agents, antifungals, and immunosuppressants. Attention has been directed especially towards the identification of the compounds they produce and the mining of the large diversity of biosynthetic gene clusters (BGCs) in their genomes. However, the current return on investment in random screening for bioactive compounds is low, while it is hard to predict which of the millions of BGCs should be prioritized. Moreover, many of the BGCs for yet undiscovered natural products are silent or cryptic under laboratory growth conditions. To identify ways to prioritize and activate these BGCs, knowledge regarding the way their expression is controlled is crucial. Intricate regulatory networks control global gene expression in Actinobacteria, governed by a staggering number of up to 1000 transcription factors per strain. This review highlights recent advances in experimental and computational methods for characterizing and predicting transcription factor binding sites and their applications to guide natural product discovery. We propose that regulation-guided genome mining approaches will open new avenues toward eliciting the expression of BGCs, as well as prioritizing subsets of BGCs for expression using synthetic biology approaches. ONE-SENTENCE SUMMARY This review provides insights into advances in experimental and computational methods aimed at predicting transcription factor binding sites and their applications to guide natural product discovery.
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Affiliation(s)
- Hannah E Augustijn
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Anna M Roseboom
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
- Netherlands Institute for Ecology (NIOO-KNAW), Wageningen, The Netherlands
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