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Tran TA, Sridhar S, Reece ST, Lunguya O, Jacobs J, Van Puyvelde S, Marks F, Dougan G, Thomson NR, Nguyen BT, Bao PT, Baker S. Combining machine learning with high-content imaging to infer ciprofloxacin susceptibility in isolates of Salmonella Typhimurium. Nat Commun 2024; 15:5074. [PMID: 38871710 PMCID: PMC11176356 DOI: 10.1038/s41467-024-49433-4] [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: 10/04/2023] [Accepted: 06/05/2024] [Indexed: 06/15/2024] Open
Abstract
Antimicrobial resistance (AMR) is a growing public health crisis that requires innovative solutions. Current susceptibility testing approaches limit our ability to rapidly distinguish between antimicrobial-susceptible and -resistant organisms. Salmonella Typhimurium (S. Typhimurium) is an enteric pathogen responsible for severe gastrointestinal illness and invasive disease. Despite widespread resistance, ciprofloxacin remains a common treatment for Salmonella infections, particularly in lower-resource settings, where the drug is given empirically. Here, we exploit high-content imaging to generate deep phenotyping of S. Typhimurium isolates longitudinally exposed to increasing concentrations of ciprofloxacin. We apply machine learning algorithms to the imaging data and demonstrate that individual isolates display distinct growth and morphological characteristics that cluster by time point and susceptibility to ciprofloxacin, which occur independently of ciprofloxacin exposure. Using a further set of S. Typhimurium clinical isolates, we find that machine learning classifiers can accurately predict ciprofloxacin susceptibility without exposure to it or any prior knowledge of resistance phenotype. These results demonstrate the principle of using high-content imaging with machine learning algorithms to predict drug susceptibility of clinical bacterial isolates. This technique may be an important tool in understanding the morphological impact of antimicrobials on the bacterial cell to identify drugs with new modes of action.
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Affiliation(s)
- Tuan-Anh Tran
- The Department of Medicine, University of Cambridge, Cambridge, UK
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sushmita Sridhar
- The Department of Medicine, University of Cambridge, Cambridge, UK
- The Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Stephen T Reece
- The Department of Medicine, University of Cambridge, Cambridge, UK
- Sanofi, Kymab, Babraham Research Campus, Cambridge, UK
| | - Octavie Lunguya
- Department of Microbiology, Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of Congo
- Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Jan Jacobs
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Sandra Van Puyvelde
- The Department of Medicine, University of Cambridge, Cambridge, UK
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Florian Marks
- The Department of Medicine, University of Cambridge, Cambridge, UK
- International Vaccine Institute, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
- Heidelberg Institute of Global Health, University of Heidelberg, Heidelberg, Germany
- Madagascar Institute for Vaccine Research, University of Antananarivo, Antananarivo, Madagascar
| | - Gordon Dougan
- The Department of Medicine, University of Cambridge, Cambridge, UK
| | - Nicholas R Thomson
- The Wellcome Sanger Institute, Hinxton, Cambridge, UK
- London School of Hygiene and Tropical Medicine, London, UK
| | - Binh T Nguyen
- Faculty of Mathematics and Computer Science, University of Science, Vietnam National University Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Pham The Bao
- Information Science Faculty, Saigon University, Ho Chi Minh City, Vietnam
| | - Stephen Baker
- The Department of Medicine, University of Cambridge, Cambridge, UK.
- IAVI, Chelsea and Westminster Hospital, London, UK.
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2
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Guo C, Nolan EM. Exploring the Antibacterial Activity and Cellular Fates of Enterobactin-Drug Conjugates That Target Gram-Negative Bacterial Pathogens. Acc Chem Res 2024; 57:1046-1056. [PMID: 38483177 DOI: 10.1021/acs.accounts.3c00814] [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: 04/04/2024]
Abstract
Siderophores are secondary metabolites utilized by bacteria to acquire iron (Fe), an essential transition metal nutrient. Fe levels in the host environment are tightly regulated and can be further restricted to starve invading bacterial pathogens in a host-defense process known as nutritional immunity. To survive and colonize the Fe-limited host environment, bacteria produce siderophores and express cognate siderophore transport machinery. These active transport pathways present an opportunity for selective and efficient drug delivery into bacterial cells, motivating decades of research on synthetic siderophore-antibiotic conjugates (SACs) as a Trojan-horse strategy for the development of targeted antibiotics.Enterobactin (Ent) is a triscatecholate siderophore produced and utilized by many Gram-negative bacteria, including all Escherichia coli and Salmonella species. Within these species, pathogenic strains cause a variety of human diseases including urinary tract infections, gastroenteritis, and sepsis. Infections caused by these Gram-negative pathogens can be difficult to treat because of the impermeability of the outer membrane (OM). This impermeability can be overcome by utilizing siderophores as drug delivery vectors for targeting Gram-negative pathogens. Ent is a promising delivery vector because it undergoes active transport across the OM mediated by the Ent uptake machinery after scavenging Fe(III) from the extracellular environment. Despite the well-elucidated chemistry and biology of Ent, its use for SAC development was hampered by the lack of an appropriate functional group for cargo attachment. Our laboratory addressed this need by designing and synthesizing monofunctionalized Ent scaffolds. Over the past decade, we have used these scaffolds to explore Ent-based SACs with a variety of drug warheads, including β-lactam and fluoroquinolone antibiotics, and Pt(IV) prodrugs. Investigations of the antibacterial activities of these conjugates and their cellular fates have informed our design principles and revealed approaches to achieving enhanced antibacterial potency and pathogen-targeted activity. Collectively, our studies of Ent-drug conjugates have provided discoveries, understanding, and invaluable insights for future design and evaluation of SACs.In this Account, we present the story of our work on Ent-drug conjugates that began about ten years ago with the development of monofunctionalized Ent scaffolds and the design and synthesis of various conjugates based on these scaffolds. We describe the antibacterial activity profiles and uptake pathways of Ent-drug conjugates harboring traditional antibiotics and repurposed platinum anticancer agents as well as studies that address cellular targets and fates. Finally, we discuss other applications of monofunctionalized Ent scaffolds, including a siderophore-based immunization strategy. We intend for this Account to inspire further investigations into the fundamental understanding and translational applications of siderophores and siderophore-drug conjugates.
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Affiliation(s)
- Chuchu Guo
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Elizabeth M Nolan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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3
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Motz RN, Guo C, Sargun A, Walker GT, Sassone-Corsi M, Raffatellu M, Nolan EM. Conjugation to Native and Nonnative Triscatecholate Siderophores Enhances Delivery and Antibacterial Activity of a β-Lactam to Gram-Negative Bacterial Pathogens. J Am Chem Soc 2024; 146:7708-7722. [PMID: 38457782 PMCID: PMC11037102 DOI: 10.1021/jacs.3c14490] [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: 03/10/2024]
Abstract
Developing new antibiotics and delivery strategies is of critical importance for treating infections caused by Gram-negative bacterial pathogens. Hijacking bacterial iron uptake machinery, such as that of the siderophore enterobactin (Ent), represents one promising approach toward these goals. Here, we report a novel Ent-inspired siderophore-antibiotic conjugate (SAC) employing an alternative siderophore moiety as the delivery vector and demonstrate the potency of our SACs harboring the β-lactam antibiotic ampicillin (Amp) against multiple pathogenic Gram-negative bacterial strains. We establish the ability of N,N',N''-(nitrilotris(ethane-2,1-diyl))tris(2,3-dihydroxybenzamide) (TRENCAM, hereafter TC), a synthetic mimic of Ent, to facilitate drug delivery across the outer membrane (OM) of Gram-negative pathogens. Conjugation of Amp to a new monofunctionalized TC scaffold affords TC-Amp, which displays markedly enhanced antibacterial activity against the gastrointestinal pathogen Salmonella enterica serovar Typhimurium (STm) compared with unmodified Amp. Bacterial uptake, antibiotic susceptibility, and microscopy studies with STm show that the TC moiety facilitates TC-Amp uptake by the OM receptors FepA and IroN and that the Amp warhead inhibits penicillin-binding proteins. Moreover, TC-Amp achieves targeted activity, selectively killing STm in the presence of a commensal lactobacillus. Remarkably, we uncover that TC-Amp and its Ent-based predecessor Ent-Amp achieve enhanced antibacterial activity against diverse Gram-negative ESKAPE pathogens that express Ent uptake machinery, including strains that possess intrinsic β-lactam resistance. TC-Amp and Ent-Amp exhibit potency comparable to that of the FDA-approved SAC cefiderocol against Gram-negative pathogens. These results demonstrate the effective application of native and appropriately designed nonnative siderophores as vectors for drug delivery across the OM of multiple Gram-negative bacterial pathogens.
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Affiliation(s)
- Rachel N. Motz
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Chuchu Guo
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Artur Sargun
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Gregory T. Walker
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Martina Sassone-Corsi
- Department of Microbiology & Molecular Genetics, University of California Irvine, Irvine, CA 92697, USA
| | - Manuela Raffatellu
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
- Department of Microbiology & Molecular Genetics, University of California Irvine, Irvine, CA 92697, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA
- Chiba University-UC San Diego Center for Mucosal Immunology, Allergy, and Vaccines, La Jolla, CA 92093, USA
| | - Elizabeth M. Nolan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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4
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Chen S, Qin S, Li R, Qu Y, Ampomah-Wireko M, Nininahazwe L, Wang M, Gao C, Zhang E. Design, synthesis and antibacterial evaluation of low toxicity amphiphilic-cephalosporin derivatives. Eur J Med Chem 2024; 268:116293. [PMID: 38447461 DOI: 10.1016/j.ejmech.2024.116293] [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: 11/27/2023] [Revised: 02/19/2024] [Accepted: 02/27/2024] [Indexed: 03/08/2024]
Abstract
Global public health is facing a serious problem as a result of the rise in antibiotic resistance and the decline in the discovery of new antibiotics. In this study, two series of amphiphilic-cephalosporins were designed and synthesized, several of which showed good antibacterial activity against both Gram-positive and Gram-negative bacteria. Structure-activity relationships indicated that the length of the hydrophobic alkyl chain significantly affects the antibacterial activity against Gram-negative bacteria. The best compound 2d showed high activity against drug-susceptible Staphylococcus aureus and methicillin-resistant Staphylococcus aureus (MRSA) with MICs of 0.5 and 2-4 μg/mL, respectively. Furthermore, 2d remained active in complex mammalian body fluids and had a longer post-antibiotic effect (PAE) than vancomycin. Mechanism studies indicated that compound 2d lacks membrane-damaging properties and can target penicillin-binding proteins to disrupt bacterial cell wall structure, inhibit the metabolic activity and induce the accumulation of reactive oxygen species (ROS) in bacteria. Compound 2d showed minimal drug resistance and was nontoxic to HUVEC and HBZY-1 cells with CC50 > 128 μg/mL. These findings suggest that 2d is a promising drug candidate for treating bacterial infections.
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Affiliation(s)
- Shengcong Chen
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Shangshang Qin
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Ruirui Li
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Ye Qu
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Maxwell Ampomah-Wireko
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Lauraine Nininahazwe
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Meng Wang
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Chen Gao
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Zhengzhou University, Zhengzhou, 450001, PR China
| | - En Zhang
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Zhengzhou University, Zhengzhou, 450001, PR China; Pingyuan Laboratory (Zhengzhou University), PR China.
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5
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Yakimovich A. Toward the novel AI tasks in infection biology. mSphere 2024; 9:e0059123. [PMID: 38334404 PMCID: PMC10900907 DOI: 10.1128/msphere.00591-23] [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] [Indexed: 02/10/2024] Open
Abstract
Machine learning and artificial intelligence (AI) are becoming more common in infection biology laboratories around the world. Yet, as they gain traction in research, novel frontiers arise. Novel artificial intelligence algorithms are capable of addressing advanced tasks like image generation and question answering. However, similar algorithms can prove useful in addressing advanced questions in infection biology like prediction of host-pathogen interactions or inferring virus protein conformations. Addressing such tasks requires large annotated data sets, which are often scarce in biomedical research. In this review, I bring together several successful examples where such tasks were addressed. I underline the importance of formulating novel AI tasks in infection biology accompanied by freely available benchmark data sets to address these tasks. Furthermore, I discuss the current state of the field and potential future trends. I argue that one such trend involves AI tools becoming more versatile.
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Affiliation(s)
- Artur Yakimovich
- Center for Advanced Systems Understanding (CASUS), Görlitz, Germany
- Helmholtz-Zentrum Dresden-Rossendorf e. V. (HZDR), Dresden, Germany
- Department of Renal Medicine, Division of Medicine, Bladder Infection and Immunity Group (BIIG), University College London, Royal Free Hospital Campus, London, United Kingdom
- Artificial Intelligence for Life Sciences CIC, Dorset, United Kingdom
- Institute of Computer Science, University of Wroclaw, Wroclaw, Poland
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6
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Jacobs LMC, Consol P, Chen Y. Drug Discovery in the Field of β-Lactams: An Academic Perspective. Antibiotics (Basel) 2024; 13:59. [PMID: 38247618 PMCID: PMC10812508 DOI: 10.3390/antibiotics13010059] [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: 11/29/2023] [Revised: 12/21/2023] [Accepted: 12/23/2023] [Indexed: 01/23/2024] Open
Abstract
β-Lactams are the most widely prescribed class of antibiotics that inhibit penicillin-binding proteins (PBPs), particularly transpeptidases that function in peptidoglycan synthesis. A major mechanism of antibiotic resistance is the production of β-lactamase enzymes, which are capable of hydrolyzing β-lactam antibiotics. There have been many efforts to counter increasing bacterial resistance against β-lactams. These studies have mainly focused on three areas: discovering novel inhibitors against β-lactamases, developing new β-lactams less susceptible to existing resistance mechanisms, and identifying non-β-lactam inhibitors against cell wall transpeptidases. Drug discovery in the β-lactam field has afforded a range of research opportunities for academia. In this review, we summarize the recent new findings on both β-lactamases and cell wall transpeptidases because these two groups of enzymes are evolutionarily and functionally connected. Many efforts to develop new β-lactams have aimed to inhibit both transpeptidases and β-lactamases, while several promising novel β-lactamase inhibitors have shown the potential to be further developed into transpeptidase inhibitors. In addition, the drug discovery progress against each group of enzymes is presented in three aspects: understanding the targets, screening methodology, and new inhibitor chemotypes. This is to offer insights into not only the advancement in this field but also the challenges, opportunities, and resources for future research. In particular, cyclic boronate compounds are now capable of inhibiting all classes of β-lactamases, while the diazabicyclooctane (DBO) series of small molecules has led to not only new β-lactamase inhibitors but potentially a new class of antibiotics by directly targeting PBPs. With the cautiously optimistic successes of a number of new β-lactamase inhibitor chemotypes and many questions remaining to be answered about the structure and function of cell wall transpeptidases, non-β-lactam transpeptidase inhibitors may usher in the next exciting phase of drug discovery in this field.
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Affiliation(s)
| | | | - Yu Chen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; (L.M.C.J.); (P.C.)
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7
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Soonthonsrima T, Htoo HH, Thiennimitr P, Srisuknimit V, Nonejuie P, Chaikeeratisak V. Phage-induced bacterial morphological changes reveal a phage-derived antimicrobial affecting cell wall integrity. Antimicrob Agents Chemother 2023; 67:e0076423. [PMID: 37843261 PMCID: PMC10648931 DOI: 10.1128/aac.00764-23] [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: 06/09/2023] [Accepted: 08/24/2023] [Indexed: 10/17/2023] Open
Abstract
In a looming post-antibiotic era, antibiotic alternatives have become key players in the combat against pathogens. Although recent advances in genomic research allow scientists to fully explore an organism's genome in the search for novel antibacterial molecules, laborious work is still needed in order to dissect each individual gene product for its antibacterial activity. Here, we exploited phage-induced bacterial morphological changes as anchors to explore and discover a potential phage-derived antimicrobial embedded in the phage genome. We found that, upon vibriophage KVP40 infection, Vibrio parahaemolyticus exhibited morphological changes similar to those observed when treated with mecillinam, a cell wall synthesis inhibitor, suggesting the mechanism of pre-killing that KVP40 exerts inside the bacterial cell upon sieging the host. Genome analysis revealed that, of all the annotated gene products in the KVP40 genome that are involved in cell wall degradation, lytic transglycosylase (LT) is of particular interest for subsequent functional studies. A single-cell morphological analysis revealed that heterologous expression of wild-type KVP40-LT induced similar bacterial morphological changes to those treated with the whole phage or mecillinam, prior to cell burst. On the contrary, neither the morphology nor the viability of the bacteria expressing signal-peptide truncated- or catalytic mutant E80A- KVP40-LT was affected, suggesting the necessity of these domains for the antibacterial activities. Altogether, this research paves the way for the future development of the discovery of phage-derived antimicrobials that is guided through phage-induced morphological changes.
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Affiliation(s)
- Tanapon Soonthonsrima
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Htut Htut Htoo
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Parameth Thiennimitr
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, Thailand
| | - Veerasak Srisuknimit
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Poochit Nonejuie
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Vorrapon Chaikeeratisak
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
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8
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Gupta R, Singh M, Pathania R. Chemical genetic approaches for the discovery of bacterial cell wall inhibitors. RSC Med Chem 2023; 14:2125-2154. [PMID: 37974958 PMCID: PMC10650376 DOI: 10.1039/d3md00143a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 08/10/2023] [Indexed: 11/19/2023] Open
Abstract
Antimicrobial resistance (AMR) in bacterial pathogens is a worldwide health issue. The innovation gap in discovering new antibiotics has remained a significant hurdle in combating the AMR problem. Currently, antibiotics target various vital components of the bacterial cell envelope, nucleic acid and protein biosynthesis machinery and metabolic pathways essential for bacterial survival. The critical role of the bacterial cell envelope in cell morphogenesis and integrity makes it an attractive drug target. While a significant number of in-clinic antibiotics target peptidoglycan biosynthesis, several components of the bacterial cell envelope have been overlooked. This review focuses on various antibacterial targets in the bacterial cell wall and the strategies employed to find their novel inhibitors. This review will further elaborate on combining forward and reverse chemical genetic approaches to discover antibacterials that target the bacterial cell envelope.
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Affiliation(s)
- Rinki Gupta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
| | - Mangal Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
| | - Ranjana Pathania
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
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9
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Lai YH, Franke R, Pinkert L, Overwin H, Brönstrup M. Molecular Signatures of the Eagle Effect Induced by the Artificial Siderophore Conjugate LP-600 in E. coli. ACS Infect Dis 2023; 9:567-581. [PMID: 36763039 PMCID: PMC10012262 DOI: 10.1021/acsinfecdis.2c00567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Achieving cellular uptake is a central challenge for novel antibiotics targeting Gram-negative bacterial pathogens. One strategy is to hijack the bacterial iron transport system by siderophore-antibiotic conjugates that are actively imported into the cell. This was realized with the MECAM-ampicillin conjugate LP-600 we recently reported that was highly active against E. coli. In the present study, we investigate a paradoxical regrowth of E. coli upon treatment of LP-600 at concentrations 16-32 times above the minimum inhibitory concentration (MIC). The phenomenon, coined "Eagle-effect" in other systems, was not due to resistance formation, and it occurred for the siderophore conjugate but not for free ampicillin. To investigate the molecular imprint of the Eagle effect, a combined transcriptome and untargeted metabolome analysis was conducted. LP-600 induced the expression of genes involved in iron acquisition, SOS response, and the e14 prophage upon regrowth conditions. The Eagle effect was diminished in the presence of sulbactam, which we ascribe to a putative synergistic antibiotic action but not to β-lactamase inhibition. The study highlights the relevance of the Eagle effect for siderophore conjugates. Through the first systematic -omics investigations, it also demonstrates that the Eagle effect manifests not only in a paradoxical growth but also in unique gene expression and metabolite profiles.
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Affiliation(s)
- Yi-Hui Lai
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Raimo Franke
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Lukas Pinkert
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Heike Overwin
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Mark Brönstrup
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany.,German Center for Infection Research (DZIF), Site Hannover-Braunschweig, 38124 Braunschweig, Germany.,Center of Biomolecular Drug Research (BMWZ), Leibniz University, 30159 Hannover, Germany
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10
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Krentzel D, Shorte SL, Zimmer C. Deep learning in image-based phenotypic drug discovery. Trends Cell Biol 2023:S0962-8924(22)00262-8. [PMID: 36623998 DOI: 10.1016/j.tcb.2022.11.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/26/2022] [Accepted: 11/29/2022] [Indexed: 01/08/2023]
Abstract
Modern drug discovery approaches often use high-content imaging to systematically study the effect on cells of large libraries of chemical compounds. By automatically screening thousands or millions of images to identify specific drug-induced cellular phenotypes, for example, altered cellular morphology, these approaches can reveal 'hit' compounds offering therapeutic promise. In the past few years, artificial intelligence (AI) methods based on deep learning (DL) [a family of machine learning (ML) techniques] have disrupted virtually all image analysis tasks, from image classification to segmentation. These powerful methods also promise to impact drug discovery by accelerating the identification of effective drugs and their modes of action. In this review, we highlight applications and adaptations of ML, especially DL methods for cell-based phenotypic drug discovery (PDD).
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Affiliation(s)
- Daniel Krentzel
- Institut Pasteur, Université Paris Cité, Imaging and Modeling Unit, F-75015 Paris, France; Institut Pasteur, Joint International Unit Artificial Intelligence for Image-based Drug Discovery & Development (PIU-Ai3D), F-75015 Paris, France.
| | - Spencer L Shorte
- Institut Pasteur, Joint International Unit Artificial Intelligence for Image-based Drug Discovery & Development (PIU-Ai3D), F-75015 Paris, France; Institut Pasteur, Université Paris Cité, Photonic Bio-Imaging, Centre de Ressources et Recherches Technologiques (UTechS-PBI, C2RT), F-75015 Paris, France
| | - Christophe Zimmer
- Institut Pasteur, Université Paris Cité, Imaging and Modeling Unit, F-75015 Paris, France; Institut Pasteur, Joint International Unit Artificial Intelligence for Image-based Drug Discovery & Development (PIU-Ai3D), F-75015 Paris, France.
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11
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Intrinsic Antibacterial Activity of Xeruborbactam
In Vitro
: Assessing Spectrum and Mode of Action. Antimicrob Agents Chemother 2022; 66:e0087922. [PMID: 36102663 PMCID: PMC9578396 DOI: 10.1128/aac.00879-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Xeruborbactam (formerly QPX7728) is a cyclic boronate inhibitor of numerous serine and metallo-beta-lactamases. At concentrations generally higher than those required for beta-lactamase inhibition, xeruborbactam has direct antibacterial activity against some Gram-negative bacteria, with MIC50/MIC90 values of 16/32 μg/mL and 16/64 μg/mL against carbapenem-resistant Enterobacterales and carbapenem-resistant Acinetobacter baumannii, respectively (the MIC50/MIC90 values against Pseudomonas aeruginosa are >64 μg/mL). In Klebsiella pneumoniae, inactivation of OmpK36 alone or in combination with OmpK35 resulted in 2- to 4-fold increases in the xeruborbactam MIC. In A. baumannii and P. aeruginosa, AdeIJK and MexAB-OprM, respectively, affected xeruborbactam’s antibacterial potency (the MICs were 4- to 16-fold higher in efflux-proficient strains). In Escherichia coli and K. pneumoniae, the 50% inhibitory concentrations (IC50s) of xeruborbactam’s binding to penicillin-binding proteins (PBPs) PBP1a/PBP1b, PBP2, and PBP3 were in the 40 to 70 μM range; in A. baumannii, xeruborbactam bound to PBP1a, PBP2, and PBP3 with IC50s of 1.4 μM, 23 μM, and 140 μM, respectively. Treating K. pneumoniae and P. aeruginosa with xeruborbactam at 1× and 2× MIC resulted in changes of cellular morphology similar to those observed with meropenem; the morphological changes observed after treatment of A. baumannii were consistent with inhibition of multiple PBPs but were unique to xeruborbactam compared to the results for control beta-lactams. No single-step xeruborbactam resistance mutants were obtained after selection at 4× MIC of xeruborbactam using wild-type strains of E. coli, K. pneumoniae, and A. baumannii; mutations selected at 2× MIC in K. pneumoniae did not affect antibiotic potentiation by xeruborbactam through beta-lactamase inhibition. Consistent with inhibition of PBPs, xeruborbactam enhanced the potencies of beta-lactam antibiotics even against strains that lacked beta-lactamase. In a large panel of KPC-producing clinical isolates, the MIC90 values of meropenem tested with xeruborbactam (8 μg/mL) were at least 4-fold lower than those in combination with vaborbactam at 64 μg/mL, the concentration of vaborbactam that is associated with complete inhibition of KPC. The additional enhancement of the potency of beta-lactam antibiotics beyond beta-lactamase inhibition may contribute to the potentiation of beta-lactam antibiotics by xeruborbactam.
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Coram MA, Wang L, Godinez WJ, Barkan DT, Armstrong Z, Ando DM, Feng BY. Morphological Characterization of Antibiotic Combinations. ACS Infect Dis 2022; 8:66-77. [PMID: 34937332 DOI: 10.1021/acsinfecdis.1c00312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Combination therapies are common in many therapeutic contexts, including infectious diseases and cancer. A common approach for evaluating combinations in vitro is to assess effects on cell growth as synergistic, antagonistic, or neutral using "checkerboard" experiments to systematically sample combinations of agents in multiple doses. To further understand the effects of antibiotic combinations, we employed high-content imaging to study the morphological changes caused by combination treatments in checkerboard experiments. Using an automated, unsupervised image analysis approach to group morphologies, and an "expert-in-the-loop" to annotate them, we attributed the heterogeneous morphological changes ofEscherichia coli cells to varying doses of both single-agent and combination treatments. We identified patterns of morphological change, including morphological potentiation, competition, and the emergence of unexpected morphologies. We found these frequently did not correlate with synergistic or antagonistic effects on viability, suggesting morphological approaches may provide a distinctive signature of the biological interaction between compounds over a range of conditions. Among the unexpected morphologies we observed, there were transitional changes associated with intermediate doses of compounds and uncharacterized phenotypes associated with well-studied antibiotics. Our approach exemplifies how unsupervised image analysis and expert knowledge can be combined to reckon with complex phenotypic changes arising from combination screening, dose titrations, or polypharmacology. In this way, quantification of morphological diversity across treatment conditions could aid in analysis and prioritization of complementary pairings of antibiotic agents by more closely capturing the true signature of the integrated cellular response.
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Affiliation(s)
- Marc A. Coram
- Google Research Applied Science, Mountain View, California 94043, United States
| | - Lisha Wang
- Infectious Diseases, Novartis Institutes for BioMedical Research, Inc., Emeryville, California 94608, United States
| | - William J. Godinez
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Inc., Emeryville, California 94608, United States
| | - David T. Barkan
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Inc., Emeryville, California 94608, United States
| | - Zan Armstrong
- Google Research Applied Science, Mountain View, California 94043, United States
| | - D. Michael Ando
- Google Research Applied Science, Mountain View, California 94043, United States
| | - Brian Y. Feng
- Infectious Diseases, Novartis Institutes for BioMedical Research, Inc., Emeryville, California 94608, United States
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13
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Xu Y, Wang H, Zhang M, Zhang J, Yan W. Plasmon-Enhanced Antibacterial Activity of Chiral Gold Nanoparticles and In Vivo Therapeutic Effect. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:1621. [PMID: 34205616 PMCID: PMC8233931 DOI: 10.3390/nano11061621] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 06/09/2021] [Accepted: 06/15/2021] [Indexed: 01/19/2023]
Abstract
d-cysteine (d-cys) has been demonstrated to possess an extraordinary antibacterial activity because of its unique steric configuration. However, inefficient antibacterial properties seriously hinder its wide applications. Here, cysteine-functionalized gold nanoparticles (d-/l-Au NPs) were prepared by loading d-/l-cysteine on the surface of gold nanoparticles for the effective inhibition of Escherichia coli (E. coli) in vitro and in vivo, and the effects on the intestinal microflora in mice were explored during the treatment of E. coli infection in the gut. We found that the antibacterial activity of d-/l-Au NPs was more than 2-3 times higher than pure d-cysteine, l-cysteine and Au NPs. Compared with l-Au NPs, d-Au NPs showed the stronger antibacterial activity, which was related to its unique steric configuration. Chiral Au NPs showed stronger destructive effects on cell membrane compared to other groups, which further leads to the leakage of the cytoplasm and bacterial cell death. The in vivo antibacterial experiment illustrated that d-Au NPs displayed impressive antibacterial activity in the treatment of E. coli-infected mice comparable to kanamycin, whereas they could not affect the balance of intestinal microflora. This work is of great significance in the development of an effective chiral antibacterial agent.
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Affiliation(s)
| | | | | | | | - Wenjing Yan
- National Center of Meat Quality and Safety Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (Y.X.); (H.W.); (M.Z.); (J.Z.)
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14
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Sargun A, Sassone-Corsi M, Zheng T, Raffatellu M, Nolan EM. Conjugation to Enterobactin and Salmochelin S4 Enhances the Antimicrobial Activity and Selectivity of β-Lactam Antibiotics against Nontyphoidal Salmonella. ACS Infect Dis 2021; 7:1248-1259. [PMID: 33691061 PMCID: PMC8122056 DOI: 10.1021/acsinfecdis.1c00005] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The pathogen Salmonella enterica is a leading cause of infection worldwide. Nontyphoidal Salmonella (NTS) serovars typically cause inflammatory diarrhea in healthy individuals, and can cause bacteremia in immunocompromised patients, children, and the elderly. Management of NTS infection poses a challenge because antibiotic treatment prolongs fecal shedding of the pathogen and is thus not recommended for most patients. In recent years, the emergence of antibiotic resistance in NTS has also become a major issue. Thus, new therapeutic strategies to target NTS are needed. Here, we evaluated whether six siderophore-β-lactam conjugates based on enterobactin (Ent) and salmochelin S4 (digulcosylated Ent, DGE) provide antimicrobial activity against the two highly prevalent NTS serovars Typhimurium and Enteritidis by targeting the siderophore receptors FepA and/or IroN. The conjugates showed 10- to 1000-fold lower minimum inhibitory concentrations against both serovars Typhimurium and Enteritidis compared to the parent antibiotics under iron limitation and were recognized and transported by FepA and/or IroN. NTS treated with the Ent/DGE-β-lactam conjugates exhibited aberrant cellular morphologies suggesting inhibition of penicillin-binding proteins, and the conjugates selectively killed NTS in coculture with Staphylococcus aureus. Lastly, the DGE-based conjugates proved to be effective at inhibiting growth of NTS in the presence of the Ent-sequestering protein lipocalin-2. This work describes the successful use of siderophore-antibiotic conjugates against NTS and highlights the opportunity for narrowing the activity spectrum of antibiotics by using Ent and DGE to target enteric bacterial pathogens.
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Affiliation(s)
- Artur Sargun
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Martina Sassone-Corsi
- Department of Microbiology & Molecular Genetics, University of California Irvine, Irvine, CA, USA
| | - Tengfei Zheng
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Manuela Raffatellu
- Department of Microbiology & Molecular Genetics, University of California Irvine, Irvine, CA, USA
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093
- Chiba University-UC San Diego Center for Mucosal Immunology, Allergy, and Vaccines, La Jolla, CA 92093
| | - Elizabeth M. Nolan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
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15
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Lang Y, Shah NR, Tao X, Reeve SM, Zhou J, Moya B, Sayed ARM, Dharuman S, Oyer JL, Copik AJ, Fleischer BA, Shin E, Werkman C, Basso KB, Lucas DD, Sutaria DS, Mégroz M, Kim TH, Loudon-Hossler V, Wright A, Jimenez-Nieves RH, Wallace MJ, Cadet KC, Jiao Y, Boyce JD, LoVullo ED, Schweizer HP, Bonomo RA, Bharatham N, Tsuji BT, Landersdorfer CB, Norris MH, Shin BS, Louie A, Balasubramanian V, Lee RE, Drusano GL, Bulitta JB. Combating Multidrug-Resistant Bacteria by Integrating a Novel Target Site Penetration and Receptor Binding Assay Platform Into Translational Modeling. Clin Pharmacol Ther 2021; 109:1000-1020. [PMID: 33576025 PMCID: PMC10662281 DOI: 10.1002/cpt.2205] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 02/08/2021] [Accepted: 02/08/2021] [Indexed: 12/26/2022]
Abstract
Multidrug-resistant bacteria are causing a serious global health crisis. A dramatic decline in antibiotic discovery and development investment by pharmaceutical industry over the last decades has slowed the adoption of new technologies. It is imperative that we create new mechanistic insights based on latest technologies, and use translational strategies to optimize patient therapy. Although drug development has relied on minimal inhibitory concentration testing and established in vitro and mouse infection models, the limited understanding of outer membrane permeability in Gram-negative bacteria presents major challenges. Our team has developed a platform using the latest technologies to characterize target site penetration and receptor binding in intact bacteria that inform translational modeling and guide new discovery. Enhanced assays can quantify the outer membrane permeability of β-lactam antibiotics and β-lactamase inhibitors using multiplex liquid chromatography tandem mass spectrometry. While β-lactam antibiotics are known to bind to multiple different penicillin-binding proteins (PBPs), their binding profiles are almost always studied in lysed bacteria. Novel assays for PBP binding in the periplasm of intact bacteria were developed and proteins identified via proteomics. To characterize bacterial morphology changes in response to PBP binding, high-throughput flow cytometry and time-lapse confocal microscopy with fluorescent probes provide unprecedented mechanistic insights. Moreover, novel assays to quantify cytosolic receptor binding and intracellular drug concentrations inform target site occupancy. These mechanistic data are integrated by quantitative and systems pharmacology modeling to maximize bacterial killing and minimize resistance in in vitro and mouse infection models. This translational approach holds promise to identify antibiotic combination dosing strategies for patients with serious infections.
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Affiliation(s)
- Yinzhi Lang
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - Nirav R. Shah
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
- Present address: Jansen R&D, Johnson & Johnson, Spring House, Pennsylvania, USA
| | - Xun Tao
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
- Present address: Genentech USA,Inc., South San Francisco, California, USA
| | - Stephanie M. Reeve
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Jieqiang Zhou
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - Bartolome Moya
- Servicio de Microbiología and Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain
| | - Alaa R. M. Sayed
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
- Department of Chemistry, Faculty of Science, Fayoum University, Fayoum, Egypt
| | - Suresh Dharuman
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Jeremiah L. Oyer
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, USA
| | - Alicja J. Copik
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, USA
| | - Brett A. Fleischer
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - Eunjeong Shin
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - Carolin Werkman
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - Kari B. Basso
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Deanna Deveson Lucas
- Infection and Immunity Program, Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Dhruvitkumar S. Sutaria
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
- Present address: Genentech USA,Inc., South San Francisco, California, USA
| | - Marianne Mégroz
- Infection and Immunity Program, Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Tae Hwan Kim
- College of Pharmacy, Catholic University of Daegu, Gyeongsan, Gyeongbuk, Korea
| | - Victoria Loudon-Hossler
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Amy Wright
- Infection and Immunity Program, Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Rossie H. Jimenez-Nieves
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - Miranda J. Wallace
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Keisha C. Cadet
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - Yuanyuan Jiao
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - John D. Boyce
- Infection and Immunity Program, Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Eric D. LoVullo
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Herbert P. Schweizer
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Robert A. Bonomo
- Research Service and GRECC, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
- Department of Medicine, Pharmacology, Molecular Biology and Microbiology, Biochemistry and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
| | - Nagakumar Bharatham
- BUGWORKS Research India Pvt. Ltd., Centre for Cellular & Molecular Platforms, National Centre for Biological Sciences, Bengaluru, Karnataka, India
| | - Brian T. Tsuji
- Laboratory for Antimicrobial Pharmacodynamics, University at Buffalo, Buffalo, New York, USA
| | - Cornelia B. Landersdorfer
- Drug Delivery, Disposition, and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Victoria, Australia
- Centre for Medicine Use and Safety, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Victoria, Australia
| | - Michael H. Norris
- Spatial Epidemiology and Ecology Research Laboratory, Department of Geography and the Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Beom Soo Shin
- School of Pharmacy, Sungkyunkwan University, Suwon, Gyeonggi-do, Korea
| | - Arnold Louie
- Institute for Therapeutic Innovation, College of Medicine, University of Florida, Orlando, Florida, USA
| | - Venkataraman Balasubramanian
- BUGWORKS Research India Pvt. Ltd., Centre for Cellular & Molecular Platforms, National Centre for Biological Sciences, Bengaluru, Karnataka, India
| | - Richard E. Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - George L. Drusano
- Institute for Therapeutic Innovation, College of Medicine, University of Florida, Orlando, Florida, USA
| | - Jürgen B. Bulitta
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
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16
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Chandrasekaran SN, Ceulemans H, Boyd JD, Carpenter AE. Image-based profiling for drug discovery: due for a machine-learning upgrade? Nat Rev Drug Discov 2021; 20:145-159. [PMID: 33353986 PMCID: PMC7754181 DOI: 10.1038/s41573-020-00117-w] [Citation(s) in RCA: 133] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/13/2020] [Indexed: 12/20/2022]
Abstract
Image-based profiling is a maturing strategy by which the rich information present in biological images is reduced to a multidimensional profile, a collection of extracted image-based features. These profiles can be mined for relevant patterns, revealing unexpected biological activity that is useful for many steps in the drug discovery process. Such applications include identifying disease-associated screenable phenotypes, understanding disease mechanisms and predicting a drug's activity, toxicity or mechanism of action. Several of these applications have been recently validated and have moved into production mode within academia and the pharmaceutical industry. Some of these have yielded disappointing results in practice but are now of renewed interest due to improved machine-learning strategies that better leverage image-based information. Although challenges remain, novel computational technologies such as deep learning and single-cell methods that better capture the biological information in images hold promise for accelerating drug discovery.
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Affiliation(s)
| | - Hugo Ceulemans
- Discovery Data Sciences, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Justin D Boyd
- High Content Imaging Technology Center, Internal Medicine Research Unit, Pfizer Inc., Cambridge, MA, USA
| | - Anne E Carpenter
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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17
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Sargun A, Johnstone TC, Zhi H, Raffatellu M, Nolan EM. Enterobactin- and salmochelin-β-lactam conjugates induce cell morphologies consistent with inhibition of penicillin-binding proteins in uropathogenic Escherichia coli CFT073. Chem Sci 2021; 12:4041-4056. [PMID: 34163675 PMCID: PMC8179508 DOI: 10.1039/d0sc04337k] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 12/31/2020] [Indexed: 12/15/2022] Open
Abstract
The design and synthesis of narrow-spectrum antibiotics that target a specific bacterial strain, species, or group of species is a promising strategy for treating bacterial infections when the causative agent is known. In this work, we report the synthesis and evaluation of four new siderophore-β-lactam conjugates where the broad-spectrum β-lactam antibiotics cephalexin (Lex) and meropenem (Mem) are covalently attached to either enterobactin (Ent) or diglucosylated Ent (DGE) via a stable polyethylene glycol (PEG3) linker. These siderophore-β-lactam conjugates showed enhanced minimum inhibitory concentrations against Escherichia coli compared to the parent antibiotics. Uptake studies with uropathogenic E. coli CFT073 demonstrated that the DGE-β-lactams target the pathogen-associated catecholate siderophore receptor IroN. A comparative analysis of siderophore-β-lactams harboring ampicillin (Amp), Lex and Mem indicated that the DGE-Mem conjugate is advantageous because it targets IroN and exhibits low minimum inhibitory concentrations, fast time-kill kinetics, and enhanced stability to serine β-lactamases. Phase-contrast and fluorescence imaging of E. coli treated with the siderophore-β-lactam conjugates revealed cellular morphologies consistent with the inhibition of penicillin-binding proteins PBP3 (Ent/DGE-Amp/Lex) and PBP2 (Ent/DGE-Mem). Overall, this work illuminates the uptake and cell-killing activity of Ent- and DGE-β-lactam conjugates against E. coli and supports that native siderophore scaffolds provide the opportunity for narrowing the activity spectrum of antibiotics in clinical use and targeting pathogenicity.
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Affiliation(s)
- Artur Sargun
- Department of Chemistry, Massachusetts Institute of Technology Cambridge MA 02139 USA +1-617-452-2495
| | - Timothy C Johnstone
- Department of Chemistry, Massachusetts Institute of Technology Cambridge MA 02139 USA +1-617-452-2495
| | - Hui Zhi
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California San Diego La Jolla CA 92093 USA
| | - Manuela Raffatellu
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California San Diego La Jolla CA 92093 USA
- Center for Microbiome Innovation, University of California San Diego La Jolla CA 92093 USA
- Chiba University-UC San Diego Center for Mucosal Immunology, Allergy, and Vaccines La Jolla CA 92093 USA
| | - Elizabeth M Nolan
- Department of Chemistry, Massachusetts Institute of Technology Cambridge MA 02139 USA +1-617-452-2495
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18
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Tuan-Anh T, Tuyen HT, Minh Chau NN, Toan ND, Triet TH, Triet LM, Trang NHT, To NTN, Bartholdson Scott J, The HC, Thanh DP, Clapham H, Baker S. Pathogenic Escherichia coli Possess Elevated Growth Rates under Exposure to Sub-Inhibitory Concentrations of Azithromycin. Antibiotics (Basel) 2020; 9:antibiotics9110735. [PMID: 33114588 PMCID: PMC7693856 DOI: 10.3390/antibiotics9110735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/19/2020] [Accepted: 10/26/2020] [Indexed: 11/20/2022] Open
Abstract
Antimicrobial resistance (AMR) has been identified by the World Health Organization (WHO) as one of the ten major threats to global health. Advances in technology, including whole-genome sequencing, have provided new insights into the origin and mechanisms of AMR. However, our understanding of the short-term impact of antimicrobial pressure and resistance on the physiology of bacterial populations is limited. We aimed to investigate morphological and physiological responses of clinical isolates of E. coli under short-term exposure to key antimicrobials. We performed whole-genome sequencing on twenty-seven E. coli isolates isolated from children with sepsis to evaluate their AMR gene content. We assessed their antimicrobial susceptibility profile and measured their growth dynamics and morphological characteristics under exposure to varying concentrations of ciprofloxacin, ceftriaxone, tetracycline, gentamicin, and azithromycin. AMR was common, with all organisms resistant to at least one antimicrobial; a total of 81.5% were multi-drug-resistant (MDR). We observed an association between resistance profile and morphological characteristics of the E. coli over a three-hour exposure to antimicrobials. Growth dynamics experiments demonstrated that resistance to tetracycline promoted the growth of E. coli under antimicrobial-free conditions, while resistance to the other antimicrobials incurred a fitness cost. Notably, antimicrobial exposure heterogeneously suppressed bacterial growth, but sub-MIC concentrations of azithromycin increased the maximum growth rate of the clinical isolates. Our results outline complex interactions between organism and antimicrobials and raise clinical concerns regarding exposure of sub-MIC concentrations of specific antimicrobials.
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Affiliation(s)
- Tran Tuan-Anh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City Q5, Vietnam; (T.T.-A.); (H.T.T.); (N.N.M.C.); (N.D.T.); (L.M.T.); (N.H.T.T.); (N.T.N.T.); (H.C.T.); (D.P.T.)
| | - Ha Thanh Tuyen
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City Q5, Vietnam; (T.T.-A.); (H.T.T.); (N.N.M.C.); (N.D.T.); (L.M.T.); (N.H.T.T.); (N.T.N.T.); (H.C.T.); (D.P.T.)
| | - Nguyen Ngoc Minh Chau
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City Q5, Vietnam; (T.T.-A.); (H.T.T.); (N.N.M.C.); (N.D.T.); (L.M.T.); (N.H.T.T.); (N.T.N.T.); (H.C.T.); (D.P.T.)
| | - Nguyen Duc Toan
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City Q5, Vietnam; (T.T.-A.); (H.T.T.); (N.N.M.C.); (N.D.T.); (L.M.T.); (N.H.T.T.); (N.T.N.T.); (H.C.T.); (D.P.T.)
| | - Tran Hanh Triet
- Division of Aquacultural Biotechnology, Biotechnology Center of Ho Chi Minh City, Ho Chi Minh City Q5, Vietnam;
| | - Le Minh Triet
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City Q5, Vietnam; (T.T.-A.); (H.T.T.); (N.N.M.C.); (N.D.T.); (L.M.T.); (N.H.T.T.); (N.T.N.T.); (H.C.T.); (D.P.T.)
| | - Nguyen Hoang Thu Trang
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City Q5, Vietnam; (T.T.-A.); (H.T.T.); (N.N.M.C.); (N.D.T.); (L.M.T.); (N.H.T.T.); (N.T.N.T.); (H.C.T.); (D.P.T.)
| | - Nguyen Thi Nguyen To
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City Q5, Vietnam; (T.T.-A.); (H.T.T.); (N.N.M.C.); (N.D.T.); (L.M.T.); (N.H.T.T.); (N.T.N.T.); (H.C.T.); (D.P.T.)
| | - Josefin Bartholdson Scott
- Department of Medicine, Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge CB2 0AW, UK;
| | - Hao Chung The
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City Q5, Vietnam; (T.T.-A.); (H.T.T.); (N.N.M.C.); (N.D.T.); (L.M.T.); (N.H.T.T.); (N.T.N.T.); (H.C.T.); (D.P.T.)
| | - Duy Pham Thanh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City Q5, Vietnam; (T.T.-A.); (H.T.T.); (N.N.M.C.); (N.D.T.); (L.M.T.); (N.H.T.T.); (N.T.N.T.); (H.C.T.); (D.P.T.)
| | - Hannah Clapham
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore 117549, Singapore;
| | - Stephen Baker
- Department of Medicine, Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge CB2 0AW, UK;
- Correspondence:
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