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Renz J, Dauda KA, Aga ONL, Diaz-Uriarte R, Löhr IH, Blomberg B, Johnston IG. Evolutionary accumulation modeling in AMR: machine learning to infer and predict evolutionary dynamics of multi-drug resistance. mBio 2025:e0048825. [PMID: 40396716 DOI: 10.1128/mbio.00488-25] [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: 05/22/2025] Open
Abstract
Can we understand and predict the evolutionary pathways by which bacteria acquire multi-drug resistance (MDR)? These questions have substantial potential impact in basic biology and in applied approaches to address the global health challenge of antimicrobial resistance (AMR). In this minireview, we discuss how a class of machine-learning approaches called evolutionary accumulation modeling (EvAM) may help reveal these dynamics using genetic and/or phenotypic AMR data sets, without requiring longitudinal sampling. These approaches are well-established in cancer progression and evolutionary biology but currently less used in AMR research. We discuss how EvAM can learn the evolutionary pathways by which drug resistances and other AMR features (for example, mutations driving these resistances) are acquired as pathogens evolve, predict next evolutionary steps, identify influences between AMR features, and explore differences in MDR evolution between regions, demographics, and more. We demonstrate a case study from the literature on MDR evolution in Mycobacterium tuberculosis and discuss the strengths and weaknesses of these approaches, providing links to some approaches for implementation.
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Affiliation(s)
- Jessica Renz
- Department of Mathematics, University of Bergen, Bergen, Norway
| | - Kazeem A Dauda
- Department of Mathematics, University of Bergen, Bergen, Norway
| | - Olav N L Aga
- Computational Biology Unit, University of Bergen, Bergen, Norway
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Ramon Diaz-Uriarte
- Department of Biochemistry, School of Medicine, Universidad Autónoma de Madrid, Madrid, Community of Madrid, Spain
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), CSIC-UAM, Madrid, Community of Madrid, Spain
| | - Iren H Löhr
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway
| | - Bjørn Blomberg
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
- National Advisory Unit for Tropical Infectious Diseases, Haukeland University Hospital, Bergen, Norway
| | - Iain G Johnston
- Department of Mathematics, University of Bergen, Bergen, Norway
- Computational Biology Unit, University of Bergen, Bergen, Norway
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Phat VV, Lim AST, De Cozar-Gallardo C, Alvaro MIC, Alvarez DM, Alvaro EF, Ballell-Pages L, Lozano-Arias S, Baker S. A three-dimensional high throughput assay identifies novel antibacterial molecules with activity against intracellular Shigella. NPJ ANTIMICROBIALS AND RESISTANCE 2025; 3:40. [PMID: 40374850 DOI: 10.1038/s44259-025-00110-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2025] [Accepted: 04/27/2025] [Indexed: 05/18/2025]
Abstract
The Gram-negative bacterial species Shigella is the second leading cause of diarrhea among children in low and middle-income countries (LMICs) and is a World Health Organization (WHO) priority pathogen. Shigella infections are becoming increasing difficult to treat due to antimicrobial resistance (AMR), leading to an urgent need for new antimicrobial agents with novel modes of action. Shigella pathogenesis is largely intracellular and antibacterial chemicals that preferentially work inside cells may be desirable to limit collateral AMR and block key components of the Shigella infection cycle. Aiming to facilitate the process of identifying antibacterial chemicals that kill intracellular Shigella, we developed a high-throughput screening (HTS) cell-based chemical screening assay. The three-dimensional (3-D) assay, incorporating Shigella invasion into Caco-2 cells on Cytodex 3 beads, was scaled into a 384-well platform for screening chemical compound libraries. Using this assay, we evaluated >500,000 compounds, identifying 12 chemical hits that inhibit Shigella replication inside cells. This simple, efficient and HTS-compatible assays circumvents many of the limitations of traditional screening methods with cell monolayers and may be deployed for antibacterial compound screening for other intracellular pathogens.
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Affiliation(s)
- Voong Vinh Phat
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Andrew Shih Teong Lim
- The ALBORADA Drug Discovery Institute, University of Cambridge, Cambridge, United Kingdom
| | | | | | | | | | | | | | - Stephen Baker
- A*STAR Infectious Diseases Labs (A*STAR IDL), Agency for Science, Technology and Research (A*STAR), Singapore, 138648, Singapore.
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Holzer K, Marongiu L, Detert K, Venturelli S, Schmidt H, Hoelzle LE. Phage applications for biocontrol of enterohemorrhagic E. coli O157:H7 and other Shiga toxin-producing Escherichia coli. Int J Food Microbiol 2025; 439:111267. [PMID: 40382813 DOI: 10.1016/j.ijfoodmicro.2025.111267] [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: 01/31/2025] [Revised: 05/07/2025] [Accepted: 05/10/2025] [Indexed: 05/20/2025]
Abstract
Foodborne outbreaks are becoming increasingly common and linked to zoonotic diseases caused by microbial spillover from wild or farm animals. Furthermore, agricultural animals could be considered reservoirs of multidrug-resistant (MDR) microorganisms. Escherichia coli O157:H7, a widespread foodborne pathogen, poses a substantial hazard due to its ubiquitous environmental distribution, MDR phenotypes, and life-threatening pathogenicity. This bacterium produces a potent toxin (Shiga toxin, Stx) encoded by prophages (Stx-phage). In addition to antibiotic resistance, E. coli O157:H7 has been shown to express more Stx upon treatment with antibiotics such as trimethoprim-sulfamethoxazole and metronidazole than controls. The combination of MDR and increased pathogenicity upon antibiotic treatment requires the development of alternatives for treating and preventing E. coli O157:H7 and related bacteria. Bacterial viruses (phages) are gaining popularity in clinical and veterinary settings due to their high antibacterial activities and lack of side effects in animals. Phage application in food production can help reduce the spread of E. coli O157:H7 and other Stx-producing E. coli (STEC), thus decreasing the burden of infection and economic loss due to these foodborne zoonoses. The present review will provide an update on phage utilization in the food industry to reduce the STEC load, with particular focus on O157:H7.
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Affiliation(s)
- K Holzer
- University of Hohenheim, Institute of Animal Science, Garbenstraße 30, 70599 Stuttgart, Germany
| | - L Marongiu
- Department of Nutritional Biochemistry, University of Hohenheim, Garbenstraße 30, 70599 Stuttgart, Germany.
| | - K Detert
- University of Hohenheim, Institute of Food Science and Biotechnology, Garbenstraße 30, 70599 Stuttgart, Germany
| | - S Venturelli
- Department of Nutritional Biochemistry, University of Hohenheim, Garbenstraße 30, 70599 Stuttgart, Germany; Institute of Physiology, Department of Vegetative and Clinical Physiology, University Hospital Tübingen, 72076 Tübingen, Germany
| | - H Schmidt
- Institute of Food Science and Biotechnology, University of Hohenheim, Garbenstraße 30, 70599 Stuttgart, Germany
| | - L E Hoelzle
- University of Hohenheim, Institute of Animal Science, Garbenstraße 30, 70599 Stuttgart, Germany; HoLMiR-Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany
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Zhang Y, Yang S, Deng Z, Song H, Xie N, Tian Y, Qin S, Liu J, Guo Y, Wang D, Liu J, Wu C, Shen J, Ma S, Wang Y, Liu D. Antifungal agent tavaborole as a potential broad-spectrum serine and metallo-β-lactamases inhibitor. EBioMedicine 2025; 116:105754. [PMID: 40367640 DOI: 10.1016/j.ebiom.2025.105754] [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: 08/14/2024] [Revised: 03/28/2025] [Accepted: 04/29/2025] [Indexed: 05/16/2025] Open
Abstract
BACKGROUND The global emergence and spread of carbapenem-resistant Enterobacteriaceae in clinical settings have driven the search for inhibitors that can counteract carbapenemases. These enzymes include several serine β-lactamases (SBLs, such as KPC) and metallo-β-lactamases (MBLs, such as NDM) that hydrolyse almost all β-lactams including carbapenems. This endeavour has successful developed some SBL inhibitors, including the boron-containing compound vaborbactam. However, the challenge posed by MBLs remains unresolved. METHODS A high-throughput screening was conducted on 1718 FDA-approved drugs as potential adjuvants to meropenem. The synergistic effect was determined by checkerboard assay. The underlying mechanisms were elucidated using enzyme inhibition assays, molecular docking and dynamics simulations. The safety and efficacy were evaluated using a murine model. FINDINGS We have identified another boron-containing broad-spectrum serine and metallo-β-lactamase inhibitor, the benzoxaborole antifungal agent tavaborole. In vitro, tavaborole enhances the antibacterial activity of multiple β-lactam antibiotics against bacteria producing either SBLs or MBLs. In vivo, injectable administration of tavaborole has demonstrated good safety in mice and has restored the efficacy of meropenem against blaNDM-5 and blaKPC-2-positive bacterial infection in a mouse intraperitoneal model. Tavaborole may effectively inhibit the activity of SBLs and MBLs by covalently bonding with the active serine residue of SBLs and chelating the Zn2+ at the active center of MBLs. INTERPRETATION Tavaborole shows good potential as an agent for use in combination with β-lactam antibiotics for treating multidrug-resistant Gram-negative bacterial infections. FUNDING National Key Research and Development Program of China, National Natural Science Foundation of China, Pinduoduo-China Agricultural University Research Fund.
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Affiliation(s)
- Yan Zhang
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Siyuan Yang
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Zhaoju Deng
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Huangwei Song
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Ning Xie
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yunrui Tian
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China; Ministry of Agriculture Key Laboratory for Crop Pest Monitoring and Green Control, College of Plant Protection, China Agricultural University, Beijing, China
| | - Shangshang Qin
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, China
| | - Jifeng Liu
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, 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, China
| | - Dongli Wang
- Ministry of Agriculture Key Laboratory for Crop Pest Monitoring and Green Control, College of Plant Protection, China Agricultural University, Beijing, China
| | - Junfeng Liu
- Ministry of Agriculture Key Laboratory for Crop Pest Monitoring and Green Control, College of Plant Protection, China Agricultural University, Beijing, China
| | - Congming Wu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jianzhong Shen
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Shizhen Ma
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China.
| | - Yang Wang
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China.
| | - Dejun Liu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China.
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Peng T, Chen Y, Luan X, Hu W, Wu W, Guo B, Lu C, Wu C, Pan X. Microneedle technology for enhanced topical treatment of skin infections. Bioact Mater 2025; 45:274-300. [PMID: 39659727 PMCID: PMC11629152 DOI: 10.1016/j.bioactmat.2024.11.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 10/31/2024] [Accepted: 11/20/2024] [Indexed: 12/12/2024] Open
Abstract
Skin infections caused by microbes such as bacteria, fungi, and viruses often lead to aberrant skin functions and appearance, eventually evolving into a significant risk to human health. Among different drug administration paradigms for skin infections, microneedles (MNs) have demonstrated superiority mainly because of their merits in enhancing drug delivery efficiency and reducing microbial resistance. Also, integrating biosensing functionality to MNs offers point-of-care wearable medical devices for analyzing specific pathogens, disease status, and drug pharmacokinetics, thus providing personalized therapy for skin infections. Herein, we do a timely update on the development of MN technology in skin infection management, with a special focus on how to devise MNs for personalized antimicrobial therapy. Notably, the advantages of state-of-the-art MNs for treating skin infections are pointed out, which include hijacking sequential drug transport barriers to enhance drug delivery efficiency and delivering various therapeutics (e.g., antibiotics, antimicrobial peptides, photosensitizers, metals, sonosensitizers, nanoenzyme, living bacteria, poly ionic liquid, and nanomoter). In addition, the nanoenzyme-based multimodal antimicrobial therapy is highlighted in addressing intractable infectious wounds. Furthermore, the MN-based biosensors used to identify pathogen types, track disease status, and quantify antibiotic concentrations are summarized. The limitations of antimicrobial MNs toward clinical translation are offered regarding large-scale production, quality control, and policy guidance. Finally, the future development of biosensing MNs with easy-to-use and intelligent properties and MN-based wearable drug delivery for home-based therapy are prospected. We hope this review will provide valuable guidance for future development in MN-mediated topical treatment of skin infections.
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Affiliation(s)
- Tingting Peng
- State Key Laboratory of Bioactive Molecules and Druggability Assessment/ International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China/College of Pharmacy, Jinan University, Guangzhou 511436, China
| | - Yangyan Chen
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Xuanyu Luan
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Wanshan Hu
- State Key Laboratory of Bioactive Molecules and Druggability Assessment/ International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China/College of Pharmacy, Jinan University, Guangzhou 511436, China
| | - Wentao Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Bing Guo
- School of Science, Harbin Institute of Technology, Shenzhen 518055, China
| | - Chao Lu
- State Key Laboratory of Bioactive Molecules and Druggability Assessment/ International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China/College of Pharmacy, Jinan University, Guangzhou 511436, China
| | - Chuanbin Wu
- State Key Laboratory of Bioactive Molecules and Druggability Assessment/ International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China/College of Pharmacy, Jinan University, Guangzhou 511436, China
| | - Xin Pan
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
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Li X, Ding Y, Xue J, Fu Y, Yan F, Song N, Hu H, Cong W, Lu Z, Li Y. Peptide Double-Stapling and Arginine N-Glycosylation Triggered the Development of Therapeutic Antimicrobial Peptides Capable of Killing Drug-Resistant Bacteria in Mice. J Med Chem 2025; 68:4511-4526. [PMID: 39910725 DOI: 10.1021/acs.jmedchem.4c02564] [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: 02/07/2025]
Abstract
Antimicrobial peptides SAAP-148 exhibited excellent antimicrobial activities but suffered from inherent disadvantages, including cytotoxicity and poor proteolytic stability. Herein, we developed a novel strategy combining one unique silver-catalyzed solid-phase glycosylation-enabled arginine N-glycosylation strategy and all-hydrocarbon peptide double-stapling, and five-round peptide libraries were rationally constructed containing over 50 stapled and/or arginine N-glycosylated peptides. SLP-51 consisting of two introduced all-hydrocarbon staples and the C-terminal arginine glycosylation exhibited superior in vitro antimicrobial activities against drug-resistant Gram-positive or -negative clinical isolates. SLP-51 also exhibited improved proteolytic stability than the parent peptide SLP-0, and importantly, significantly weakened hemolysis. Experimental and modeling mechanism research indicated that SLP-51 exerted similar but stronger killing abilities by destroying the integrality of the bacterial membranes. In both skin wound and drug-resistant bacterial pneumonia models, SLP-51 showcased a potent therapeutic effect in treating both MRSA and Klebsiella pneumoniae infection in vivo and dramatical improvement of inflammatory injury.
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Affiliation(s)
- Xiang Li
- School of Pharmaceutical Sciences & Institute of Materia Medica, State Key Laboratory of Advanced Drug Delivery and Release Systems, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, Shandong, P. R. China
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China
| | - Yanjiao Ding
- School of Pharmaceutical Sciences & Institute of Materia Medica, State Key Laboratory of Advanced Drug Delivery and Release Systems, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, Shandong, P. R. China
| | - Jingwen Xue
- School of Pharmaceutical Sciences & Institute of Materia Medica, State Key Laboratory of Advanced Drug Delivery and Release Systems, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, Shandong, P. R. China
- School of Pharmacy, Shandong Second Medical University, Weifang 261053, Shandong, P. R. China
| | - Yinxue Fu
- School of Pharmaceutical Sciences & Institute of Materia Medica, State Key Laboratory of Advanced Drug Delivery and Release Systems, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, Shandong, P. R. China
| | - Fang Yan
- School of Pharmacy, Shandong Second Medical University, Weifang 261053, Shandong, P. R. China
| | - Nannan Song
- School of Pharmaceutical Sciences & Institute of Materia Medica, State Key Laboratory of Advanced Drug Delivery and Release Systems, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, Shandong, P. R. China
| | - Honggang Hu
- School of Medicine, Shanghai University, 99 Shangda Road, Shanghai 200444, China
| | - Wei Cong
- School of Medicine, Shanghai University, 99 Shangda Road, Shanghai 200444, China
| | - Zhiyuan Lu
- School of Pharmaceutical Sciences & Institute of Materia Medica, State Key Laboratory of Advanced Drug Delivery and Release Systems, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, Shandong, P. R. China
| | - Yulei Li
- School of Pharmaceutical Sciences & Institute of Materia Medica, State Key Laboratory of Advanced Drug Delivery and Release Systems, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, Shandong, P. R. China
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Takahashi K, Kikuchi H, Nishimura T, Ishigaki H, Miura Y, Takahashi A, Kubohara Y. Ester derivatives of Dictyostelium differentiation-inducing factors exhibit antibacterial activity, possibly via a prodrug-like function. BMC Res Notes 2025; 18:40. [PMID: 39875997 PMCID: PMC11776220 DOI: 10.1186/s13104-025-07122-5] [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: 10/29/2024] [Accepted: 01/23/2025] [Indexed: 01/30/2025] Open
Abstract
OBJECTIVE Dictyostelium differentiation-inducing factors 1 and 3 [DIF-1 (1) and DIF-3 (2), respectively], along with their derivatives, such as Ph-DIF-1 (3) and Bu-DIF-3 (4), demonstrate antibacterial activity in vitro against Gram-positive bacteria, including methicillin-sensitive Staphylococcus aureus (MSSA), methicillin-resistant S. aureus (MRSA), vancomycin-sensitive Enterococcus faecalis (VSE), and vancomycin-resistant Enterococcus faecium [VRE (VanA)]. This study investigates the therapeutic potential of DIF compounds against these Gram-positive bacteria. RESULTS In vitro tests revealed that the antibacterial activity of 3 and 4 was lost in the presence of human serum albumin (HSA), suggesting that HSA might inhibit their effectiveness. Further evaluation of less hydrophobic derivatives, DIF-1-NH2 (5) and NH2-Bu-DIF-3 (6), showed no antibacterial activity, even in the absence of HSA. However, ester derivatives Ph-DIF-1(AHA) (7) and Bu-DIF-3(2Ac) (8) exhibited antibacterial activity against the target bacteria in vitro, although this activity was also lost in the presence of HSA. We hypothesize that these ester derivatives may function as prodrugs, with their antibacterial activity possibly restored by hydrolysis through bacterial esterases. The results suggest that suitable ester modifications could enhance the in vivo antibacterial potential of DIF compounds, particularly if they can bypass HSA binding and be activated by bacterial enzymes.
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Affiliation(s)
- Katsunori Takahashi
- Department of Medical Technology, Faculty of Health Science, Gunma Paz University, Takasaki, 370-0006, Japan
| | - Haruhisa Kikuchi
- Division of Natural Medicines, Faculty of Pharmacy, Keio University, Tokyo, 105-8512, Japan.
| | - Takehiro Nishimura
- Division of Natural Medicines, Faculty of Pharmacy, Keio University, Tokyo, 105-8512, Japan
| | - Hirotaka Ishigaki
- Department of Medical Technology, Faculty of Health Science, Gunma Paz University, Takasaki, 370-0006, Japan
| | - Yusuke Miura
- Department of Medical Technology, Faculty of Health Science, Gunma Paz University, Takasaki, 370-0006, Japan
| | - Ayuko Takahashi
- Department of Medical Technology, Faculty of Health Science, Gunma Paz University, Takasaki, 370-0006, Japan
| | - Yuzuru Kubohara
- Laboratory of Health and Life Science, Graduate School of Health and Sports Science, Juntendo University, Inzai, 270-1695, Japan.
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Demisie S, Oh DC, Abera A, Tasew G, Satessa GD, Fufa F, Shenkutie AM, Wolday D, Tafess K. Bioprospecting secondary metabolites with antimicrobial properties from soil bacteria in high-temperature ecosystems. Microb Cell Fact 2024; 23:332. [PMID: 39696555 DOI: 10.1186/s12934-024-02589-6] [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: 05/17/2024] [Accepted: 11/11/2024] [Indexed: 12/20/2024] Open
Abstract
BACKGROUND The ongoing emergence and spread of drug-resistant pathogens necessitate urgent solutions. Natural products from bacterial sources are recognized as a promising source of antibiotics. This study aimed to isolate and characterize soil microorganisms from extremely hot environments and to screen their secondary metabolites for antibacterial activity. METHODS Bacterial isolates were identified using standard culture techniques. Primary and secondary screenings for antimicrobial activity were conducted using the Modified Kirby-Bauer antibiotic susceptibility test against five bacterial species. Based on the efficacy of antimicrobial activity against these target pathogens, the isolate Pseudomonas sp. strain ASTU00105 was selected for further characterization through whole genomic sequencing. Secondary metabolites were analyzed using GC-MS, and antioxidant activities were also evaluated. RESULTS A total of 76 isolates were identified, and their secondary metabolites were tested against Escherichia coli, Salmonella typhi, Acinetobacter baumannii, Staphylococcus aureus, Streptococcus pyogenes, and Candida albicans. Seventeen isolates (22.37%) exhibited antimicrobial activity. Isolate ASTU00105 exhibited the highest activity against all the test organisms and was selected for further analysis. Whole-genome sequencing using the Nanopore MinION sequencer revealed that strain ASTU00105 belonged to the genus Pseudomonas with the highest similarity (95.97%) to Pseudomonas stutzeri, and designated as Pseudomonas sp. strain ASTU00105. Upon Average Nucleotide Identity (ANI) analysis, the strain exhibited 87.81% sequence similarity with genes of the closest type strain, suggesting its novelty and distinctiveness within the Pseudomonas genus. The genomic analysis of the isolated strain revealed 6 biosynthetic gene cluster (BGC) genes dispersed throughout the entire genome, which are implicated in the synthesis of antimicrobial secondary metabolites. The major chemical compounds detected in the EtAc extracts as detected by gas chromatography-mass spectrometry (GC-MS) were phenol, 2,5-bis (1,1-dimethylethyl) (36.6%), followed by 1,2-Benzenedicarboxylic acid, diethyl ester (12.22%), Eicosane (9.71%), Dibutyl phthalate (3.93%), and 1-Dodecanol (2.34%). IN CONCLUSION Pseudomonas sp. strain ASTU00105 exhibited the greatest potential for producing secondary metabolites with significant antimicrobial activity.
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Affiliation(s)
- Sisay Demisie
- Department of Applied Biology, School of Applied Natural Science, Adama Science and Technology University, P. O. Box 1888, Adama, Ethiopia
| | - Dong-Chan Oh
- College of Pharmacy, Natural Products Research Institute, Seoul National University, Seoul, 08826, Republic of Korea
| | - Adugna Abera
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Geremew Tasew
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Gizaw Dabessa Satessa
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 3, 1870, Frederiksberg C, Denmark
| | - Fetene Fufa
- Department of Advanced Materials Science and Engineering Center of Excellence, Adama Science and Technology University, P. O. Box 1888, Adama, Ethiopia
| | - Abebe Mekuria Shenkutie
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Dawit Wolday
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
- Depatment of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Ketema Tafess
- Department of Applied Biology, School of Applied Natural Science, Adama Science and Technology University, P. O. Box 1888, Adama, Ethiopia.
- Institute of Pharmaceutical Sciences, Adama Science and Technology University, P. O. Box 1888, Adama, Ethiopia.
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He P, Huang S, Wang R, Yang Y, Yang S, Wang Y, Qi M, Li J, Liu X, Zhang X, Feng M. Novel nitroxoline derivative combating resistant bacterial infections through outer membrane disruption and competitive NDM-1 inhibition. Emerg Microbes Infect 2024; 13:2294854. [PMID: 38085067 PMCID: PMC10829846 DOI: 10.1080/22221751.2023.2294854] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 12/11/2023] [Indexed: 02/01/2024]
Abstract
ABSTRACTNew Delhi metallo-β-lactamase-1 (NDM-1) has rapidly disseminated worldwide, leading to multidrug resistance and worse clinical prognosis. Designing and developing effective NDM-1 inhibitors is a critical and urgent challenge. In this study, we constructed a library of long-lasting nitroxoline derivatives and identified ASN-1733 as a promising dual-functional antibiotic. ASN-1733 can effectively compete for Ca2+ on the bacterial surface, causing the detachment of lipopolysaccharides (LPS), thereby compromising the outer membrane integrity and permeability and exhibiting broad-spectrum bactericidal activity. Moreover, ASN-1733 demonstrated wider therapeutic applications than nitroxoline in mouse sepsis, thigh and mild abdominal infections. Furthermore, ASN-1733 can effectively inhibit the hydrolytic capability of NDM-1 and exhibits synergistic killing effects in combination with meropenem against NDM-1 positive bacteria. Mechanistic studies using enzymatic experiments and computer simulations revealed that ASN-1733 can bind to key residues on Loop10 of NDM-1, hindering substrate entry into the enzyme's active site and achieving potent inhibitory activity (Ki = 0.22 µM), even in the presence of excessive Zn2+. These findings elucidate the antibacterial mechanism of nitroxoline and its derivatives, expand their potential application in the field of antibacterial agents and provide new insights into the development of novel NDM-1 inhibitors.
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Affiliation(s)
- Peng He
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai, People’s Republic of China
| | - Sijing Huang
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai, People’s Republic of China
| | - Rui Wang
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai, People’s Republic of China
| | - Yunkai Yang
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai, People’s Republic of China
| | - Shangye Yang
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai, People’s Republic of China
| | - Yue Wang
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai, People’s Republic of China
| | - Mengya Qi
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai, People’s Republic of China
| | - Jiyang Li
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai, People’s Republic of China
| | - Xiaofen Liu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People’s Republic of China
| | - Xuyao Zhang
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai, People’s Republic of China
| | - Meiqing Feng
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai, People’s Republic of China
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10
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Wang Y, Wang F, Liu W, Geng Y, Shi Y, Tian Y, Zhang B, Luo Y, Sun X. New drug discovery and development from natural products: Advances and strategies. Pharmacol Ther 2024; 264:108752. [PMID: 39557343 DOI: 10.1016/j.pharmthera.2024.108752] [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: 04/30/2024] [Revised: 11/06/2024] [Accepted: 11/08/2024] [Indexed: 11/20/2024]
Abstract
Natural products (NPs) have a long history as sources for drug discovery, more than half of approved drugs are related to NPs, which also exhibit multifaceted advantages in the clinical treatment of complex diseases. However, bioactivity screening of NPs, target identification, and design optimization require continuously improved strategies, the complexity of drug mechanism of action and the limitations of technological strategies pose numerous challenges to the development of new drugs. This review begins with an overview of bioactivity- and target-based drug development patterns for NPs, advances in NP screening and derivatization, and the advantages and problems of major targets such as genes and proteins. Then, target-based drugs as well as identification and validation methods are further discussed to elucidate their mechanism of action. Subsequently, the current status and development trend of the application of traditional and emerging technologies in drug discovery and development of NPs are systematically described. Finally, the collaborative strategy of multi-technology integration and multi-disciplinary intersection is emphasized for the challenges faced in the identification, optimization, activity evaluation, and clinical application of NPs. It is hoped to provide a systematic overview and inspiration for exploring new drugs from natural resources in the future.
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Affiliation(s)
- Yixin Wang
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100193, China; Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, China; Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, China
| | - Fan Wang
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100193, China; Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, China; Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, China
| | - Wenxiu Liu
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100193, China; Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, China; Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, China
| | - Yifei Geng
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100193, China; Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, China; Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, China
| | - Yahong Shi
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100193, China; Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, China; Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, China
| | - Yu Tian
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100193, China; Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, China; Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, China
| | - Bin Zhang
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100193, China; Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, China; Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, China.
| | - Yun Luo
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100193, China; Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, China; Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, China.
| | - Xiaobo Sun
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100193, China; Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, China; Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, China.
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11
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Shi G, Shaw GX, Ji X. Bisubstrate inhibitors of 6-hydroxymethyl-7,8-dihydroptein pyrophosphokinase: Toward cell permeability. Bioorg Med Chem Lett 2024; 113:129977. [PMID: 39332646 DOI: 10.1016/j.bmcl.2024.129977] [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: 07/05/2024] [Revised: 08/13/2024] [Accepted: 09/23/2024] [Indexed: 09/29/2024]
Abstract
6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) is a key enzyme in the folate biosynthesis pathway. It catalyzes the pyrophosphoryl transfer from ATP to 6-hydroxymethyl-7,8-dihydropterin (HP). HPPK is essential for microorganisms but is absent in mammals. Yet, it is not the target of any existing antibiotics. Hence, this enzyme is an attractive target for developing novel antimicrobial agents. A wealth of structural and mechanistic information has provided solid basis for structure-based design of HPPK inhibitors. Our bisubstrate inhibitors were initially created by linking 6-hydroxymethylpterin to adenosine through 2, 3, or 4 phosphate groups (HPnA, n = 2, 3, or 4), among which HP4A exhibited the highest binding affinity (Kd = 0.47 ± 0.04 μM). Further development was carried out based on high-resolution structures of HPPK in complex with HP4A. Replacing the phosphate bridge with a piperidine linked thioether eliminated multiple negative charges of the bridge. Substituting the pterin moiety with 7,7-dimethyl-7,8-dihydropterin improved the binding affinity. Arming the piperidine ring with a carboxyl group and oxidizing the thioether further enhanced the potency, resulting in a druglike inhibitor of HPPK (Kd = 0.047 ± 0.007 μM). None of these inhibitors, however, exhibits bacterial cell permeability. It is most likely due to the lack of active folate transporters in bacteria. Replacing the pterin moiety with a 7-deazagaunine moiety, we have obtained a novel bisubstrate inhibitor (HP-101) showing observable cell permeability toward a Gram-positive bacterium. Here, we report the in vitro activity of HP-101 and its structure in complex with HPPK, providing a framework for structure-based further development.
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Affiliation(s)
- Genbin Shi
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA.
| | - Gary X Shaw
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA; Current Address: Thoracic and Gastrointestinal Malignancies Branch, National Cancer Institute, Bethesda, MD 20892, USA.
| | - Xinhua Ji
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
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12
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Wang Z, He L, Fan Z, Luo Y. Patenting perspective of modulators of ClpP endopeptidase: 2019-present. Expert Opin Ther Pat 2024; 34:1073-1084. [PMID: 39267345 DOI: 10.1080/13543776.2024.2404233] [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: 06/27/2024] [Revised: 08/14/2024] [Accepted: 09/10/2024] [Indexed: 09/17/2024]
Abstract
INTRODUCTION ClpP is a highly conserved serine protease that plays a crucial role in maintaining protein homeostasis in both bacterial cells and human mitochondria. Several studies have demonstrated the potential of ClpP as a drug target, with ClpP modulators, including both inhibitors and activators, showing promise in treating a range of conditions such as drug-resistant bacteria, malignant cancers, and fatty liver disease. AREA COVERED This review provides an overview of patents related to ClpP modulators filed over the last five years, detailing their claims and therapeutic applications. The sources of patent information included databases of the European Patent Office, the China Patent Office and the U.S.A. patent Office, while relevant research articles were accessed through PubMed. EXPERT OPINION The number of patents concerning ClpP modulators is on the rise, reflecting advancements in related research. By summarizing and outlining relevant patents, we aim to stimulate further interest among researchers, ultimately leading to the development of effective drugs based on ClpP modulators. The broad spectrum of diseases associated with ClpP dysfunction underscores the potential for ClpP modulators to address a wide range of therapeutic needs.
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Affiliation(s)
- Zhenyu Wang
- State Key Laboratory of Biotherapy, West China Hospital, West Medical School, Sichuan University, Chengdu, China
| | - Liqing He
- State Key Laboratory of Biotherapy, West China Hospital, West Medical School, Sichuan University, Chengdu, China
| | - Ziheng Fan
- State Key Laboratory of Biotherapy, West China Hospital, West Medical School, Sichuan University, Chengdu, China
| | - Youfu Luo
- State Key Laboratory of Biotherapy, West China Hospital, West Medical School, Sichuan University, Chengdu, China
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13
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Leal K, Rojas E, Madariaga D, Contreras MJ, Nuñez-Montero K, Barrientos L, Goméz-Espinoza O, Iturrieta-González I. Unlocking Fungal Potential: The CRISPR-Cas System as a Strategy for Secondary Metabolite Discovery. J Fungi (Basel) 2024; 10:748. [PMID: 39590667 PMCID: PMC11595728 DOI: 10.3390/jof10110748] [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: 07/09/2024] [Revised: 08/21/2024] [Accepted: 08/23/2024] [Indexed: 11/28/2024] Open
Abstract
Natural products (NPs) are crucial for the development of novel antibiotics, anticancer agents, and immunosuppressants. To highlight the ability of fungi to produce structurally diverse NPs, this article focuses on the impact of genome mining and CRISPR-Cas9 technology in uncovering and manipulating the biosynthetic gene clusters (BGCs) responsible for NP synthesis. The CRISPR-Cas9 system, originally identified as a bacterial adaptive immune mechanism, has been adapted for precise genome editing in fungi, enabling targeted modifications, such as gene deletions, insertions, and transcription modulation, without altering the genomic sequence. This review elaborates on various CRISPR-Cas9 systems used in fungi, notably the Streptococcus pyogenes type II Cas9 system, and explores advancements in different Cas proteins for fungal genome editing. This review discusses the methodologies employed in CRISPR-Cas9 genome editing of fungi, including guide RNA design, delivery methods, and verification of edited strains. The application of CRISPR-Cas9 has led to enhanced production of secondary metabolites in filamentous fungi, showcasing the potential of this system in biotechnology, medical mycology, and plant pathology. Moreover, this article emphasizes the integration of multi-omics data (genomics, transcriptomics, proteomics, and metabolomics) to validate CRISPR-Cas9 editing effects in fungi. This comprehensive approach aids in understanding molecular changes, identifying off-target effects, and optimizing the editing protocols. Statistical and machine learning techniques are also crucial for analyzing multi-omics data, enabling the development of predictive models and identification of key molecular pathways affected by CRISPR-Cas9 editing. In conclusion, CRISPR-Cas9 technology is a powerful tool for exploring fungal NPs with the potential to accelerate the discovery of novel bioactive compounds. The integration of CRISPR-Cas9 with multi-omics approaches significantly enhances our ability to understand and manipulate fungal genomes for the production of valuable secondary metabolites and for promising new applications in medicine and industry.
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Affiliation(s)
- Karla Leal
- Instituto de Ciencias Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Temuco 4810101, Chile; (K.L.); (D.M.); (M.J.C.)
| | - Edwind Rojas
- Department of Preclinic Sciences, Medicine Faculty, Laboratory of Infectiology and Clinical Immunology, Center of Excellence in Translational Medicine, Scientific and Technological Nucleus (CEMT-BIOREN), Universidad de La Frontera, Temuco 4810296, Chile;
| | - David Madariaga
- Instituto de Ciencias Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Temuco 4810101, Chile; (K.L.); (D.M.); (M.J.C.)
| | - María José Contreras
- Instituto de Ciencias Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Temuco 4810101, Chile; (K.L.); (D.M.); (M.J.C.)
| | - Kattia Nuñez-Montero
- Instituto de Ciencias Aplicadas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Temuco 4810101, Chile; (K.N.-M.); (L.B.)
| | - Leticia Barrientos
- Instituto de Ciencias Aplicadas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Temuco 4810101, Chile; (K.N.-M.); (L.B.)
| | - Olman Goméz-Espinoza
- Departamento de Ciencias Químicas y Recursos Naturales, Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Temuco 4811230, Chile;
- Centro de Investigación en Biotecnología, Escuela de Biología, Instituto Tecnológico de Costa Rica, Cartago 30101, Costa Rica
| | - Isabel Iturrieta-González
- Department of Preclinic Sciences, Medicine Faculty, Laboratory of Infectiology and Clinical Immunology, Center of Excellence in Translational Medicine, Scientific and Technological Nucleus (CEMT-BIOREN), Universidad de La Frontera, Temuco 4810296, Chile;
- Jeffrey Modell Center of Diagnosis and Research in Primary Immunodeficiencies, Center of Excellence in Translational Medicine, Medicine Faculty, Universidad de La Frontera, Temuco 4810296, Chile
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14
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Panigrahi SD, Klebba KC, Rodriguez EN, Mayhan CM, Kotagiri N, Kumari H. Enhancing antibacterial efficacy through macrocyclic host complexation of fluoroquinolone antibiotics for overcoming resistance. Sci Rep 2024; 14:24637. [PMID: 39428392 PMCID: PMC11491488 DOI: 10.1038/s41598-024-73568-5] [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: 06/28/2024] [Accepted: 09/18/2024] [Indexed: 10/22/2024] Open
Abstract
The use of supramolecular assemblies in pharmaceuticals has garnered significant interest. Recent studies have shown that the activities of antibacterial agents can be enhanced through complexation with cyclic oligomers and metal ions. Notably, these complexes sometimes possess greater therapeutic properties than the parent drugs. To develop microbiologically potent supramolecular drugs, the complexation of macrocyclic hosts with fluoroquinolone (FQ) antibiotics was investigated. FQs are a successful family of antibiotics that target the bacterial enzymes DNA gyrase and DNA topoisomerase IV, leading to bacterial cell death through the inhibition of DNA synthesis. However, antibiotic resistance resulting from the repeated use of FQs over time has limited their effectiveness against resistant pathogens. To overcome this issue, the encapsulation of FQs in polyphenolic macrocycles was investigated. This study highlights resorcinarene, a polyphenolic host with antibacterial properties, and its ability to chemically interact with FQs. The inclusion complexation process was analyzed using NMR and FTIR techniques. The binding constants determined by 1H-NMR titration revealed that levofloxacin forms more stable complexes with resorcinarene than with β-cyclodextrin, which aligned with MD simulations. Assessment of the geometric characteristics of the inclusion complexes using 2D NMR analysis confirmed that different moieties of various FQs can fit into a single host cavity and improve activity against gram-negative bacteria. Overall, these findings suggest that encapsulation in polyphenolic macrocycles is a promising strategy for utilizing FQs against antibiotic-resistant bacteria.
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Affiliation(s)
- Suchitra D Panigrahi
- James L. Winkle College of Pharmacy University of Cincinnati, 231 Albert Sabin Way, Medical Science Building 3109C, Cincinnati, OH, 45267-0514, USA
| | - Karoline C Klebba
- Helias Catholic High School, 1305 Swifts Hwy, Jefferson City, MO, 65109, USA
| | - Emily N Rodriguez
- Helias Catholic High School, 1305 Swifts Hwy, Jefferson City, MO, 65109, USA
| | - Collin M Mayhan
- James L. Winkle College of Pharmacy University of Cincinnati, 231 Albert Sabin Way, Medical Science Building 3109C, Cincinnati, OH, 45267-0514, USA
- Helias Catholic High School, 1305 Swifts Hwy, Jefferson City, MO, 65109, USA
| | - Nalinikanth Kotagiri
- James L. Winkle College of Pharmacy University of Cincinnati, 231 Albert Sabin Way, Medical Science Building 3109C, Cincinnati, OH, 45267-0514, USA
| | - Harshita Kumari
- James L. Winkle College of Pharmacy University of Cincinnati, 231 Albert Sabin Way, Medical Science Building 3109C, Cincinnati, OH, 45267-0514, USA.
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15
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Tang F, Peng W, Kou X, Chen Z, Zhang L. High-throughput screening identification of apigenin that reverses the colistin resistance of mcr-1-positive pathogens. Microbiol Spectr 2024; 12:e0034124. [PMID: 39248524 PMCID: PMC11448233 DOI: 10.1128/spectrum.00341-24] [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: 02/14/2024] [Accepted: 06/06/2024] [Indexed: 09/10/2024] Open
Abstract
The plasmid-mediated gene mcr-1 that makes bacteria resistant to the antibiotic colistin is spreading quickly, which means that colistin is no longer working well to treat Gram-negative bacterial infections. Herein, we utilized a computer-aided high-throughput screening drugs method to identify the natural product apigenin, a potential mcr-protein inhibitor, which effectively enhanced the antimicrobial activity of colistin. Several assays, including a checkerboard minimum inhibitory concentration assay, a time-kill assay, the combined disk test, molecular simulation dynamics, and animal infection models assay, were conducted to verify whether apigenin enhanced the ability of colistin to fight Gram-negative bacterial infections. The results showed that apigenin improved the antimicrobial activity of colistin against multidrug-resistant Enterobacteriaceae infection. Moreover, apigenin not only did not increase the toxic effect of colistin but also had the ability to effectively inhibit the frequency of bacterial resistance mutations to colistin. Studies clearly elucidated that apigenin could interfere with the thermal stability of the protein by binding to the mcr-1 protein. Additionally, the combination of apigenin and colistin could exert multiple effects, including disrupting bacterial membranes, the generation of bacterial nitric oxide and reactive oxygen species, as well as inhibiting bacterial adenosine triphosphate production. Furthermore, the addition of apigenin was able to significantly inhibit colistin-stimulated high expression levels of the bacterial mcr-1 gene. Finally, apigenin exhibited a characteristic anti-inflammatory effect while enhancing the antimicrobial activity of colistin against mcr-1-positive Escherichia coli (E. coli) infected animals. In conclusion, as a potential lead compound, apigenin is promising in combination with colistin in the future treatment of mcr-1-positive E. coli infections.IMPORTANCEThis study found that apigenin was able to inhibit the activity of the mcr-1 protein using a high-throughput virtual screening method. Apigenin effectively enhanced the antimicrobial activity of colistin against multidrug-resistant Enterobacteriaceae, including mcr-1-positive strains, in vitro and in vivo. This study will provide new options and strategies for the future treatment of multidrug-resistant pathogen infections.
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Affiliation(s)
- Feng Tang
- College of Animal Science and Veterinary Medicine, Collaborative Innovation Center for Prevention and Control of Zoonoses, Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Wenjing Peng
- College of Animal Science and Veterinary Medicine, Collaborative Innovation Center for Prevention and Control of Zoonoses, Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Xu Kou
- College of Animal Science and Veterinary Medicine, Collaborative Innovation Center for Prevention and Control of Zoonoses, Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Zeliang Chen
- College of Animal Science and Veterinary Medicine, Collaborative Innovation Center for Prevention and Control of Zoonoses, Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Libo Zhang
- College of Animal Science and Veterinary Medicine, Collaborative Innovation Center for Prevention and Control of Zoonoses, Jinzhou Medical University, Jinzhou, Liaoning, China
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16
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Zhen B, Geng C, Yang Y, Liang H, Jiang Y, Li X, Ye G. Systematic alanine and stapling mutational analysis of antimicrobial peptide Chem-KVL. Bioorg Med Chem Lett 2024; 107:129794. [PMID: 38735344 DOI: 10.1016/j.bmcl.2024.129794] [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: 03/24/2024] [Revised: 05/07/2024] [Accepted: 05/09/2024] [Indexed: 05/14/2024]
Abstract
Chem-KVL is a tandem repeating peptide, with 14 amino acids that was modified based on a short peptide from a fragment of the human host defense protein chemerin. Chem-KVL increases cationicity and hydrophobicity and shows broad-spectrum antibacterial activity. To determine the molecular determinants of Chem-KVL and whether staple-modified Chem-KVL would improve antibacterial activity and protease stability or decrease cytotoxicity, we combined alanine and stapling scanning, and designed a series of alanine and staple-derived Chem-KVL peptides, termed Chem-A1 to Chem-A14 and SCL-1 to SCL-7. We next examined their antibacterial activity against several gram-positive and gram-negative bacteria, their proteolytic stability, and their cytotoxicity. Ala scanning of Chem-KVL suggested that both the positively charged residues (Lys and Arg) and the hydrophobic residues (Lue and Val) were critical for the antibacterial activities of Chem-KVL peptide. Of note, Chem-A4 was able to remarkably inhibit the growth of gram-positive and gram-negative bacteria when compared to the original peptide. And the antibacterial activities of stapled SCL-4 and SCL-7 were several times higher than those of the linear peptide against gram-positive and gram-negative bacteria. Stapling modification of peptides resulted in increased helicity and protein stability when compared with the linear peptide. These stapled peptides, especially SCL-4 and SCL-7, may serve as the leading compounds for further optimization and antimicrobial therapy.
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Affiliation(s)
- Borui Zhen
- School of Pharmacy, Dali University, Dali 671000, China; School of Pharmacy, Naval Medical University, Shanghai 200433, China
| | - Chenchen Geng
- School of Pharmacy, Naval Medical University, Shanghai 200433, China
| | - Yi Yang
- School of Pharmacy, Naval Medical University, Shanghai 200433, China
| | - Haiyan Liang
- School of Pharmacy, Naval Medical University, Shanghai 200433, China
| | | | - Xiang Li
- School of Pharmacy, Naval Medical University, Shanghai 200433, China.
| | - Guangming Ye
- Wuxi Branch of Ruijin Hospital Shanghai Jiao Tong University School of Medicine, Wuxi 214000, China.
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17
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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] [Download PDF] [Figures] [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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18
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Abass S, Parveen R, Irfan M, Malik Z, Husain SA, Ahmad S. Mechanism of antibacterial phytoconstituents: an updated review. Arch Microbiol 2024; 206:325. [PMID: 38913205 DOI: 10.1007/s00203-024-04035-y] [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: 04/25/2024] [Accepted: 06/05/2024] [Indexed: 06/25/2024]
Abstract
The increase of multiple drug resistance bacteria significantly diminishes the effectiveness of antibiotic armory and subsequently exaggerates the level of therapeutic failure. Phytoconstituents are exceptional substitutes for resistance-modifying vehicles. The plants appear to be a deep well for the discovery of novel antibacterial compounds. This is owing to the numerous enticing characteristics of plants, they are easily accessible and inexpensive, extracts or chemicals derived from plants typically have significant levels of action against infections, and they rarely cause serious adverse effects. The enormous selection of phytochemicals offers very distinct chemical structures that may provide both novel mechanisms of antimicrobial activity and deliver us with different targets in the interior of the bacterial cell. They can directly affect bacteria or act together with the crucial events of pathogenicity, in this manner decreasing the aptitude of bacteria to create resistance. Abundant phytoconstituents demonstrate various mechanisms of action toward multi drug resistance bacteria. Overall, this comprehensive review will provide insights into the potential of phytoconstituents as alternative treatments for bacterial infections, particularly those caused by multi drug resistance strains. By examining the current state of research in this area, the review will shed light on potential future directions for the development of new antimicrobial therapies.
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Affiliation(s)
- Sageer Abass
- Department of Biotechnology, Jamia Millia Islamia, New Delhi, 110025, India
- Department of Biosciences, Jamia Millia Islamia, New Delhi, 110025, India
- Centre of Excellence in Unani Medicine (Pharmacognosy and Pharmacology), Bioactive Natural Product Laboratory, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| | - Rabea Parveen
- Centre of Excellence in Unani Medicine (Pharmacognosy and Pharmacology), Bioactive Natural Product Laboratory, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| | - Mohammad Irfan
- Department of Biotechnology, Jamia Millia Islamia, New Delhi, 110025, India
- Department of Biosciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Zoya Malik
- Department of Biosciences, Jamia Millia Islamia, New Delhi, 110025, India
- Centre of Excellence in Unani Medicine (Pharmacognosy and Pharmacology), Bioactive Natural Product Laboratory, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| | - Syed Akhtar Husain
- Department of Biosciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Sayeed Ahmad
- Centre of Excellence in Unani Medicine (Pharmacognosy and Pharmacology), Bioactive Natural Product Laboratory, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India.
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Awad MA, Hammad SF, El-Mashtoly SF, El-Deeb B, Soliman HSM. Phytochemical and biological assessment of secondary metabolites isolated from a rhizosphere strain, Sphingomonas sanguinis DM of Datura metel. BMC Complement Med Ther 2024; 24:205. [PMID: 38796482 PMCID: PMC11128111 DOI: 10.1186/s12906-024-04482-6] [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: 08/06/2023] [Accepted: 04/24/2024] [Indexed: 05/28/2024] Open
Abstract
BACKGROUND The plant roots excrete a large number of organic compounds into the soil. The rhizosphere, a thin soil zone around the roots, is a hotspot for microbial activity, making it a crucial component of the soil ecosystem. Secondary metabolites produced by rhizospheric Sphingomonas sanguinis DM have sparked significant curiosity in investigating their possible biological impacts. METHODS A bacterial strain has been isolated from the rhizosphere of Datura metel. The bacterium's identification, fermentation, and working up have been outlined. The ethyl acetate fraction of the propagated culture media of Sphingomonas sanguinis DM was fractioned and purified using various chromatographic techniques. The characterization of the isolated compounds was accomplished through the utilization of various spectroscopic techniques, such as UV, MS, 1D, and 2D-NMR. Furthermore, the evaluation of their antimicrobial activity was conducted using the agar well diffusion method, while cytotoxicity was assessed using the MTT test. RESULTS The extract from Sphingomonas sanguinis DM provided two distinct compounds: n-dibutyl phthalic acid (1) and Bis (2-methyl heptyl) phthalate (2) within its ethyl acetate fraction. Furthermore, the 16S rRNA gene sequence of Sphingomonas sanguinis DM has been registered under the NCBI GenBank database with the accession number PP422198. The bacterial extract exhibited its effect against gram-positive bacteria, inhibiting Streptococcus mutans (12.6 ± 0.6 mm) and Staphylococcus aureus (10.6 ± 0.6 mm) compared to standard antibiotics. Conversely, compound 1 showed a considerable effect against phytopathogenic fungi such as Alternaria alternate (56.3 ± 10.6 mm) and Fusarium oxysporum (21.3 ± 1.5 mm) with a MIC value of 17.5 µg/mL. However, it was slightly active against Klebsiella pneumonia (11.0 ± 1.0 mm). Furthermore, compound 2 was the most active metabolite, having a significant antimicrobial efficacy against Rhizoctonia solani (63.6 ± 1.1 mm), Pseudomonas aeruginosa (16.7 ± 0.6 mm), and Alternaria alternate (20.3 ± 0.6 mm) with MIC value at 15 µg/mL. In addition, compound 2 exhibited the most potency against hepatocellular (HepG-2) and skin (A-431) carcinoma cell lines with IC50 values of 107.16 µg/mL and 111.36 µg/mL, respectively. CONCLUSION Sphingomonas sanguinis DM, a rhizosphere bacterium of Datura metel, was studied for its phytochemical and biological characteristics, resulting in the identification of two compounds with moderate antimicrobial and cytotoxic activities.
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Affiliation(s)
- Mohamed A Awad
- Biotechnology Program, Institute of Basic and Applied Science, Egypt-Japan University of Science and Technology (E-JUST), New Borg El-Arab City, Alexandria, 21934, Egypt
- Botany and Microbiology Department, Faculty of Science, Sohag University, Sohag, 82524, Egypt
| | - Sherif F Hammad
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Helwan University, Helwan, Cairo, Egypt
- PharmD Program, Egypt-Japan University of Science and Technology (E-JUST), New Borg El-Arab City, Alexandria, 21934, Egypt
| | - Samir F El-Mashtoly
- Biotechnology Program, Institute of Basic and Applied Science, Egypt-Japan University of Science and Technology (E-JUST), New Borg El-Arab City, Alexandria, 21934, Egypt
| | - Bahig El-Deeb
- Botany and Microbiology Department, Faculty of Science, Sohag University, Sohag, 82524, Egypt
| | - Hesham S M Soliman
- Department of Pharmacognosy, Faculty of Pharmacy, Helwan University, Helwan, Cairo, Egypt.
- PharmD Program, Egypt-Japan University of Science and Technology (E-JUST), New Borg El-Arab City, Alexandria, 21934, Egypt.
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20
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Wang C, Ji Y, Huo X, Li X, Lu W, Zhang Z, Dong W, Wang X, Chen H, Tan C. Discovery of Salifungin as a Repurposed Antibiotic against Methicillin-Resistant Staphylococcus aureus with Limited Resistance Development. ACS Infect Dis 2024; 10:1576-1589. [PMID: 38581387 DOI: 10.1021/acsinfecdis.3c00611] [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: 04/08/2024]
Abstract
Exploring novel antimicrobial drugs and strategies has become essential to the fight MRSA-associated infections. Herein, we found that membrane-disrupted repurposed antibiotic salifungin had excellent bactericidal activity against MRSA, with limited development of drug resistance. Furthermore, adding salifungin effectively decreased the minimum inhibitory concentrations of clinical antibiotics against Staphylococcus aureus. Evaluations of the mechanism demonstrated that salifungin disrupted the level of H+ and K+ ions using hydrophilic and lipophilic groups to interact with bacterial membranes, causing the disruption of bacterial proton motive force followed by impacting on bacterial the function of the respiratory chain and adenosine 5'-triphosphate, thereby inhibiting phosphatidic acid biosynthesis. Moreover, salifungin also significantly inhibited the formation of bacterial biofilms and eliminated established bacterial biofilms by interfering with bacterial membrane potential and inhibiting biofilm-associated gene expression, which was even better than clinical antibiotics. Finally, salifungin exhibited efficacy comparable to or even better than that of vancomycin in the MRSA-infected animal models. In conclusion, these results indicate that salifungin can be a potential drug for treating MRSA-associated infections.
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Affiliation(s)
- Chenchen Wang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430000, Hubei, China
- Hubei Hongshan Laboratory, Wuhan 430000, Hubei, China
| | - Yueyue Ji
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430000, Hubei, China
- Hubei Hongshan Laboratory, Wuhan 430000, Hubei, China
| | - Xingyu Huo
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430000, Hubei, China
- Hubei Hongshan Laboratory, Wuhan 430000, Hubei, China
| | - Xiaodan Li
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430000, Hubei, China
- Hubei Hongshan Laboratory, Wuhan 430000, Hubei, China
| | - Wenjia Lu
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430000, Hubei, China
- Hubei Hongshan Laboratory, Wuhan 430000, Hubei, China
| | - Zhaoran Zhang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430000, Hubei, China
- Hubei Hongshan Laboratory, Wuhan 430000, Hubei, China
| | - Wenqi Dong
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430000, Hubei, China
- Hubei Hongshan Laboratory, Wuhan 430000, Hubei, China
| | - Xiangru Wang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430000, Hubei, China
- Hubei Hongshan Laboratory, Wuhan 430000, Hubei, China
- Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan 430000, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan 430000, Hubei, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430000, Hubei, China
| | - Huanchun Chen
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430000, Hubei, China
- Hubei Hongshan Laboratory, Wuhan 430000, Hubei, China
- Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan 430000, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan 430000, Hubei, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430000, Hubei, China
| | - Chen Tan
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430000, Hubei, China
- Hubei Hongshan Laboratory, Wuhan 430000, Hubei, China
- Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan 430000, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan 430000, Hubei, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430000, Hubei, China
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21
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Wang C, Wu Y, Xue Y, Zou L, Huang Y, Zhang P, Ji J. Combinatorial discovery of antibacterials via a feature-fusion based machine learning workflow. Chem Sci 2024; 15:6044-6052. [PMID: 38665528 PMCID: PMC11041243 DOI: 10.1039/d3sc06441g] [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: 12/01/2023] [Accepted: 03/08/2024] [Indexed: 04/28/2024] Open
Abstract
The discovery of new antibacterials within the vast chemical space is crucial in combating drug-resistant bacteria such as methicillin-resistant Staphylococcus aureus (MRSA). However, the traditional approach of screening the entire chemical library in an ergodic manner can be laborious and time-consuming. Machine learning-assisted screening of antibacterials alleviates the exploration effort but suffers from the lack of reliable and related datasets. To address these challenges, we devised a combinatorial library comprising over 110 000 candidates based on the Ugi reaction. A focused library was subsequently generated through uniform sampling of the entire library to narrow down the preliminary screening scale. A novel feature-fusion architecture called the latent space constraint neural network was developed which incorporated both fingerprint and physicochemical molecular descriptors to predict the antibacterial properties. This integration allowed the model to leverage the complementary information provided by these descriptors and improve the accuracy of predictions. Three lead compounds that demonstrated excellent efficacy against MRSA while alleviating drug resistance were identified. This workflow highlights the integration of machine learning with the combinatorial chemical library to expedite high-quality data collection and extensive data mining for antibacterial screening.
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Affiliation(s)
- Cong Wang
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University Hangzhou Zhejiang 310027 PR China
- International Research Center for X Polymers, International Campus, Zhejiang University Haining Zhejiang 314400 PR China
| | - Yuhui Wu
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University Hangzhou Zhejiang 310027 PR China
- International Research Center for X Polymers, International Campus, Zhejiang University Haining Zhejiang 314400 PR China
| | - Yunfan Xue
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University Hangzhou Zhejiang 310027 PR China
| | - Lingyun Zou
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University Hangzhou Zhejiang 310027 PR China
| | - Yue Huang
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University Hangzhou Zhejiang 310027 PR China
| | - Peng Zhang
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University Hangzhou Zhejiang 310027 PR China
- International Research Center for X Polymers, International Campus, Zhejiang University Haining Zhejiang 314400 PR China
- State Key Laboratory of Transvascular Implantation Devices, Zhejiang University Hangzhou Zhejiang 311202 P. R. China
| | - Jian Ji
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University Hangzhou Zhejiang 310027 PR China
- International Research Center for X Polymers, International Campus, Zhejiang University Haining Zhejiang 314400 PR China
- State Key Laboratory of Transvascular Implantation Devices, Zhejiang University Hangzhou Zhejiang 311202 P. R. China
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22
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Fang ZY, Zhang ZY, Zheng YD, Lei D, Zhuang J, Li N, He QY, Sun X. Repurposing cinacalcet suppresses multidrug-resistant Staphylococcus aureus by disruption of cell membrane and inhibits biofilm by targeting IcaR. J Antimicrob Chemother 2024; 79:903-917. [PMID: 38412335 DOI: 10.1093/jac/dkae051] [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: 09/01/2023] [Accepted: 02/12/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND MDR Staphylococcus aureus infections, along with the severity of biofilm-associated infections, continue to threaten human health to a great extent. It necessitates the urgent development of novel antimicrobial and antibiofilm agents. OBJECTIVES To reveal the mechanism and target of cinacalcet as an antibacterial and antimicrobial agent for S. aureus. METHODS Screening of non-antibiotic drugs for antibacterial and antibiofilm properties was conducted using a small-molecule drug library. In vivo efficacy was assessed through animal models, and the antibacterial mechanism was studied using quantitative proteomics, biochemical assays, LiP-SMap, BLI detection and gene knockout techniques. RESULTS Cinacalcet, an FDA-approved drug, demonstrated antibacterial and antibiofilm activity against S. aureus, with less observed development of bacterial resistance. Importantly, cinacalcet significantly improved survival in a pneumonia model and bacterial clearance in a biofilm infection model. Moreover, the antibacterial mechanism of cinacalcet mainly involves the destruction of membrane-targeted structures, alteration of energy metabolism, and production of reactive oxygen species (ROS). Cinacalcet was found to target IcaR, inhibiting biofilm formation through the negative regulation of IcaADBC. CONCLUSIONS The findings suggest that cinacalcet has potential for repurposing as a therapeutic agent for MDR S. aureus infections and associated biofilms, warranting further investigation.
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Affiliation(s)
- Zu-Ye Fang
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Zi-Yuan Zhang
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Yun-Dan Zheng
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Dan Lei
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Jianpeng Zhuang
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Nan Li
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Qing-Yu He
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Xuesong Sun
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
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23
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Hillman A, Hyland SN, Wodzanowski KA, Moore DL, Ratna S, Jemas A, Sandles LMD, Chaya T, Ghosh A, Fox JM, Grimes CL. Minimalist Tetrazine N-Acetyl Muramic Acid Probes for Rapid and Efficient Labeling of Commensal and Pathogenic Peptidoglycans in Living Bacterial Culture and During Macrophage Invasion. J Am Chem Soc 2024; 146:6817-6829. [PMID: 38427023 PMCID: PMC10941766 DOI: 10.1021/jacs.3c13644] [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: 12/04/2023] [Revised: 02/13/2024] [Accepted: 02/14/2024] [Indexed: 03/02/2024]
Abstract
N-Acetyl muramic acid (NAM) probes containing alkyne or azide groups are commonly used to investigate aspects of cell wall synthesis because of their small size and ability to incorporate into bacterial peptidoglycan (PG). However, copper-catalyzed alkyne-azide cycloaddition (CuAAC) reactions are not compatible with live cells, and strain-promoted alkyne-azide cycloaddition (SPAAC) reaction rates are modest and, therefore, not as desirable for tracking the temporal alterations of bacterial cell growth, remodeling, and division. Alternatively, the tetrazine-trans-cyclooctene ligation (Tz-TCO), which is the fastest known bioorthogonal reaction and not cytotoxic, allows for rapid live-cell labeling of PG at biologically relevant time scales and concentrations. Previous work to increase reaction kinetics on the PG surface by using tetrazine probes was limited because of low incorporation of the probe. Described here are new approaches to construct a minimalist tetrazine (Tz)-NAM probe utilizing recent advancements in asymmetric tetrazine synthesis. This minimalist Tz-NAM probe was successfully incorporated into pathogenic and commensal bacterial PG where fixed and rapid live-cell, no-wash labeling was successful in both free bacterial cultures and in coculture with human macrophages. Overall, this probe allows for expeditious labeling of bacterial PG, thereby making it an exceptional tool for monitoring PG biosynthesis for the development of new antibiotic screens. The versatility and selectivity of this probe will allow for real-time interrogation of the interactions of bacterial pathogens in a human host and will serve a broader utility for studying glycans in multiple complex biological systems.
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Affiliation(s)
- Ashlyn
S. Hillman
- Department
of Chemistry and Biochemistry, University
of Delaware, Newark, Delaware 19716, United States
| | - Stephen N. Hyland
- Department
of Chemistry and Biochemistry, University
of Delaware, Newark, Delaware 19716, United States
| | - Kimberly A. Wodzanowski
- Department
of Chemistry and Biochemistry, University
of Delaware, Newark, Delaware 19716, United States
| | - DeVonte L. Moore
- Department
of Chemistry and Biochemistry, University
of Delaware, Newark, Delaware 19716, United States
| | - Sushanta Ratna
- Department
of Chemistry and Biochemistry, University
of Delaware, Newark, Delaware 19716, United States
| | - Andrew Jemas
- Department
of Chemistry and Biochemistry, University
of Delaware, Newark, Delaware 19716, United States
| | - Liam-Michael D. Sandles
- Department
of Chemistry and Biochemistry, University
of Delaware, Newark, Delaware 19716, United States
| | - Timothy Chaya
- Department
of Plant and Soil Sciences, University of
Delaware, Newark, Delaware 19716, United States
| | - Arit Ghosh
- Delaware
Biotechnology Institute, UDEL Flow Cytometry Core, University of Delaware, Newark, Delaware 19716, United States
| | - Joseph M. Fox
- Department
of Chemistry and Biochemistry, University
of Delaware, Newark, Delaware 19716, United States
- Department
of Materials Science and Engineering, University
of Delaware, Newark, Delaware 19716, United States
| | - Catherine L. Grimes
- Department
of Chemistry and Biochemistry, University
of Delaware, Newark, Delaware 19716, United States
- Department
of Biological Sciences, University of Delaware, Newark, Delaware 19716, United States
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24
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da Costa PCT, Santos TLB, Ramos JF, Santos JAM, de Medeiros FD, Freitas JCR, de Oliveira WA. Synthesis and antifungal evaluation against Candida spp. of the (E)-3-(furan-2-yl)acrylic acid. Braz J Microbiol 2024; 55:133-142. [PMID: 37995041 PMCID: PMC10920609 DOI: 10.1007/s42770-023-01158-0] [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: 08/24/2023] [Accepted: 10/16/2023] [Indexed: 11/24/2023] Open
Abstract
Infections of fungal origin are mainly caused by Candida spp. Some species, such as C. albicans, C. glabrata, C. parapsilosis, and C. tropicalis, stand out as promoters of diseases in humans. This study evaluated the synthesis and antifungal effects of (E)-3-(furan-2-yl)acrylic acid. The synthesis of the compound showed a yield of 88%, considered high. The minimum inhibitory concentration of the synthetic compound, amphotericin B, and fluconazole isolated against four Candida species ranged from 64 to 512 μg/mL, 1 to 2 μg/mL, and 32 to 256 μg/mL, respectively. The synergistic effect of the test compound was observed when associated with amphotericin B against C. albicans and C. tropicalis, with no antagonism between the substances against any of the strains tested. The potential drug promoted morphological changes in C. albicans, decreasing the amount of resistance and virulence, and reproduction structures, such as the formation of pseudohyphae, blastoconidia, and chlamydospores. Furthermore, it was also possible to identify the fungistatic profile of the test substance by studying the growth kinetics of C. albicans. Finally, it was observed that the test compound stimulated ergosterol biosynthesis by the yeast, probably by activating microbial resistance responses.
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Affiliation(s)
| | - Thales Luciano Bezerra Santos
- Education and Health Center, Professora Maria Anita Furtado Coelho, Bairro Sítio Olho D'água da Bica, Federal University of Campina Grande, Cuité, PB, 58175-000, Brazil
| | - Jaqueline Ferreira Ramos
- Department of Chemistry, Federal Rural University of Pernambuco, Dom Manoel de Medeiros, Recife, PE, 52171-900, Brazil
| | - Jonh Anderson Macêdo Santos
- Department of Chemistry, Federal Rural University of Pernambuco, Dom Manoel de Medeiros, Recife, PE, 52171-900, Brazil
| | - Francinalva Dantas de Medeiros
- Education and Health Center, Professora Maria Anita Furtado Coelho, Bairro Sítio Olho D'água da Bica, Federal University of Campina Grande, Cuité, PB, 58175-000, Brazil
| | - Juliano Carlo Rufino Freitas
- Education and Health Center, Professora Maria Anita Furtado Coelho, Bairro Sítio Olho D'água da Bica, Federal University of Campina Grande, Cuité, PB, 58175-000, Brazil
- Department of Chemistry, Federal Rural University of Pernambuco, Dom Manoel de Medeiros, Recife, PE, 52171-900, Brazil
| | - Wylly Araújo de Oliveira
- Education and Health Center, Professora Maria Anita Furtado Coelho, Bairro Sítio Olho D'água da Bica, Federal University of Campina Grande, Cuité, PB, 58175-000, Brazil
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25
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Wong F, Zheng EJ, Valeri JA, Donghia NM, Anahtar MN, Omori S, Li A, Cubillos-Ruiz A, Krishnan A, Jin W, Manson AL, Friedrichs J, Helbig R, Hajian B, Fiejtek DK, Wagner FF, Soutter HH, Earl AM, Stokes JM, Renner LD, Collins JJ. Discovery of a structural class of antibiotics with explainable deep learning. Nature 2024; 626:177-185. [PMID: 38123686 PMCID: PMC10866013 DOI: 10.1038/s41586-023-06887-8] [Citation(s) in RCA: 128] [Impact Index Per Article: 128.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 11/21/2023] [Indexed: 12/23/2023]
Abstract
The discovery of novel structural classes of antibiotics is urgently needed to address the ongoing antibiotic resistance crisis1-9. Deep learning approaches have aided in exploring chemical spaces1,10-15; these typically use black box models and do not provide chemical insights. Here we reasoned that the chemical substructures associated with antibiotic activity learned by neural network models can be identified and used to predict structural classes of antibiotics. We tested this hypothesis by developing an explainable, substructure-based approach for the efficient, deep learning-guided exploration of chemical spaces. We determined the antibiotic activities and human cell cytotoxicity profiles of 39,312 compounds and applied ensembles of graph neural networks to predict antibiotic activity and cytotoxicity for 12,076,365 compounds. Using explainable graph algorithms, we identified substructure-based rationales for compounds with high predicted antibiotic activity and low predicted cytotoxicity. We empirically tested 283 compounds and found that compounds exhibiting antibiotic activity against Staphylococcus aureus were enriched in putative structural classes arising from rationales. Of these structural classes of compounds, one is selective against methicillin-resistant S. aureus (MRSA) and vancomycin-resistant enterococci, evades substantial resistance, and reduces bacterial titres in mouse models of MRSA skin and systemic thigh infection. Our approach enables the deep learning-guided discovery of structural classes of antibiotics and demonstrates that machine learning models in drug discovery can be explainable, providing insights into the chemical substructures that underlie selective antibiotic activity.
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Affiliation(s)
- Felix Wong
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Institute for Medical Engineering and Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Integrated Biosciences, San Carlos, CA, USA
| | - Erica J Zheng
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Chemical Biology, Harvard University, Cambridge, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Jacqueline A Valeri
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Institute for Medical Engineering and Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Nina M Donghia
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Melis N Anahtar
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Satotaka Omori
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Integrated Biosciences, San Carlos, CA, USA
| | - Alicia Li
- Integrated Biosciences, San Carlos, CA, USA
| | - Andres Cubillos-Ruiz
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Institute for Medical Engineering and Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Aarti Krishnan
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Institute for Medical Engineering and Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Wengong Jin
- Eric and Wendy Schmidt Center, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Abigail L Manson
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jens Friedrichs
- Leibniz Institute of Polymer Research and the Max Bergmann Center of Biomaterials, Dresden, Germany
| | - Ralf Helbig
- Leibniz Institute of Polymer Research and the Max Bergmann Center of Biomaterials, Dresden, Germany
| | - Behnoush Hajian
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dawid K Fiejtek
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Florence F Wagner
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Holly H Soutter
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ashlee M Earl
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jonathan M Stokes
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Institute for Medical Engineering and Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research and David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
| | - Lars D Renner
- Leibniz Institute of Polymer Research and the Max Bergmann Center of Biomaterials, Dresden, Germany
| | - James J Collins
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Institute for Medical Engineering and Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
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26
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Pang Z, Li S, Wang S, Cai Z, Zhang S, Wan C, Wang J, Li Y, Chen P, Liu BF. Controlled-diffusion centrifugal microfluidic for rapid antibiotic susceptibility testing. Anal Chim Acta 2024; 1287:342033. [PMID: 38182334 DOI: 10.1016/j.aca.2023.342033] [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: 09/13/2023] [Revised: 11/11/2023] [Accepted: 11/13/2023] [Indexed: 01/07/2024]
Abstract
The abuse of antibiotics has become a global public safety issue, leading to the development of antimicrobial resistance (AMR). The development of antimicrobial susceptibility testing (AST) is crucial in reducing the growth of AMR. However, traditional AST methods are time-consuming (e.g., 24-72 h), labor-intensive, and costly. Here, we propose a controlled-diffusion centrifugal microfluidic platform (CCM) for rapid AST to obtain highly precise minimum inhibitory concentration (MIC) values. Antibiotic concentration gradients are generated by controlled moving and diffusing of antibiotic and buffer solution along the main microchannel within 3 min. The solution and bacterial suspension are then injected into the outermost reaction chamber by simple centrifugation. The CCM successfully determined the MIC for three commonly used antibiotics in clinical settings within 4-9 h. To further enhance practicality, reduce costs, and meet point-of-care testing demands, we have developed an integrated mobile detection platform for automated MIC value acquisition. The proposed CCM is a simple, low-cost, and portable method for rapid AST with broad clinical and in vitro applications.
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Affiliation(s)
- Zheng Pang
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Shunji Li
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Shangang Wang
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Zonglin Cai
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Shuo Zhang
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Chao Wan
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Jieqing Wang
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Yiwei Li
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
| | - Peng Chen
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
| | - Bi-Feng Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
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Liu W, Liu J, Li D, Han H, Yan H, Sun Y, Lei Q, Wang J, Zhou Y, Cao D, Li H, Li F. Effect of Lactobacillus salivarius SNK-6 on egg quality, intestinal morphology, and cecal microbial community of laying hens. Poult Sci 2024; 103:103224. [PMID: 37980753 PMCID: PMC10658386 DOI: 10.1016/j.psj.2023.103224] [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: 08/31/2023] [Revised: 10/13/2023] [Accepted: 10/19/2023] [Indexed: 11/21/2023] Open
Abstract
The objective of this study was to investigate the effect of Lactobacillus salivarius (L. salivarius) SNK-6 supple-mentation on the laying performance, egg quality, blood parameters, intestinal morphology, and cecal microbial community of laying hens. A total of 432 healthy 30-wk-age laying hens were randomly divided into 3 groups with 6 replicates under the same husbandry and dietary regimes: control (CON); 2.0 × 108 CFU/kg L. salivarius supplementation (T1); 2.0 × 109 CFU/kg L. salivarius supplementation (T2). The experiment lasted for 10 wk. The results indicated that the supplementation resulted in a significant reduction in the broken egg and unqualified egg ratios, and a significant increase in the eggshell strength, eggshell relative weight, albumen height, and Haugh units (P < 0.05). The L. salivarius-treated hens exhibited significantly reduced serum malondialdehyde levels (P < 0.05); significantly increased total protein, phosphorus, calcitonin, and immunoglobulin M (P < 0.05); significantly increased cecal secretory immunoglobulin A concentration (P < 0.05); significantly improved villus height (VH) in the duodenum and VH to crypt depth ratio in the jejunum (P < 0.05). The serum globulin and interleukin-1β, immunoglobulin G concentrations, and catalase activity significantly increased in T2 (P < 0.05). Furthermore, the serum interferon-α level in T1 was significantly higher than that of the CON (P < 0.05). The intestinal barrier-related mRNA gene ZO-1, CLDN1, and MUC2 expression in the jejunum was significantly upregulated in the T1 and T2 groups (P < 0.05). The Firmicutes/Bacteroidetes ratio was higher and the relative abundances of Flavonifractor and Clostridiales_noname were significantly higher in the T1 group (P < 0.05). In conclusion, dietary supplementation with L. salivarius SNK-6 may improve hen egg quality, serum antioxidant capacity, immune function, and intestinal health.
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Affiliation(s)
- Wei Liu
- Shandong Academy of Agricultural Sciences, Poultry Institute, 250100, Jinan, China; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Jinan, China; Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, 250100, Jinan, China
| | - Jie Liu
- Shandong Academy of Agricultural Sciences, Poultry Institute, 250100, Jinan, China; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Jinan, China; Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, 250100, Jinan, China
| | - Dapeng Li
- Shandong Academy of Agricultural Sciences, Poultry Institute, 250100, Jinan, China; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Jinan, China; Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, 250100, Jinan, China
| | - Haixia Han
- Shandong Academy of Agricultural Sciences, Poultry Institute, 250100, Jinan, China; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Jinan, China; Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, 250100, Jinan, China
| | - Huaxiang Yan
- Shanghai Academy of Agricultural Sciences, Animal Husbandry and Veterinary Research Institute, 201106, Shanghai, China
| | - Yan Sun
- Shandong Academy of Agricultural Sciences, Poultry Institute, 250100, Jinan, China; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Jinan, China; Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, 250100, Jinan, China
| | - Qiuxia Lei
- Shandong Academy of Agricultural Sciences, Poultry Institute, 250100, Jinan, China; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Jinan, China; Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, 250100, Jinan, China
| | - Jie Wang
- Shandong Academy of Agricultural Sciences, Poultry Institute, 250100, Jinan, China; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Jinan, China; Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, 250100, Jinan, China
| | - Yan Zhou
- Shandong Academy of Agricultural Sciences, Poultry Institute, 250100, Jinan, China; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Jinan, China; Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, 250100, Jinan, China
| | - Dingguo Cao
- Shandong Academy of Agricultural Sciences, Poultry Institute, 250100, Jinan, China; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Jinan, China; Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, 250100, Jinan, China
| | - Huimin Li
- Shandong Academy of Agricultural Sciences, Poultry Institute, 250100, Jinan, China; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Jinan, China; Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, 250100, Jinan, China
| | - Fuwei Li
- Shandong Academy of Agricultural Sciences, Poultry Institute, 250100, Jinan, China; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Jinan, China; Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, 250100, Jinan, China.
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28
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Chengan K, Hind C, Stanley M, Wand ME, Nagappa LK, Howland K, Hanson T, Martín-Escolano R, Tsaousis AD, Bengoechea JA, Mark Sutton J, Smales CM, Moore SJ. A cell-free strategy for host-specific profiling of intracellular antibiotic sensitivity and resistance. NPJ ANTIMICROBIALS AND RESISTANCE 2023; 1:16. [PMID: 39843793 PMCID: PMC11721408 DOI: 10.1038/s44259-023-00018-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 11/27/2023] [Indexed: 01/24/2025]
Abstract
Antimicrobial resistance (AMR) is a pandemic spread across multiple infectious disease-causing microbes. To provide a host-specific tool to study antibiotic susceptibility and resistance, here we develop Klebsiella pneumoniae cell-free gene expression (CFE) systems from laboratory and clinical isolates. Using proteomics, we identify relative differences and unique proteins for these new CFE systems in comparison to an Escherichia coli MG1655 CFE model. Then we profile antimicrobial susceptibility in parallel with whole cells to quantify CFE antibiotic potency. Finally, we apply this native CFE tool to study AMR variants at a proof-of-concept level. Definably we show that RpoB H526L confers a 58-fold increase in CFE resistance to rifampicin-a genotype observed in rifampicin-resistant Mycobacterium tuberculosis clinical isolates. Overall, we provide a cell-free synthetic biology strategy for the profiling of antibiotic sensitivity and resistance from K. pneumoniae. While initial extract processing requires Biosafety Level 2, the CFE system is non-living, suitable for long-term storage and study in a Biosafety Level 1 lab. We anticipate the K. pneumoniae CFE bioassay is advantageous for host-specific antimicrobial testing, the characterisation of intracellular AMR variants and potentially structure-activity relationship studies.
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Affiliation(s)
- Kameshwari Chengan
- School of Biosciences, Division of Natural Sciences, University of Kent, Canterbury, CT7 2NJ, United Kingdom
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, E1 4NS, United Kingdom
| | - Charlotte Hind
- Technology Development Group, Research and Evaluation, UK Health Security Agency, Salisbury, SP4 0JG, United Kingdom
| | - Maria Stanley
- School of Biosciences, Division of Natural Sciences, University of Kent, Canterbury, CT7 2NJ, United Kingdom
| | - Matthew E Wand
- Technology Development Group, Research and Evaluation, UK Health Security Agency, Salisbury, SP4 0JG, United Kingdom
| | - Lakshmeesha K Nagappa
- School of Biosciences, Division of Natural Sciences, University of Kent, Canterbury, CT7 2NJ, United Kingdom
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, E1 4NS, United Kingdom
| | - Kevin Howland
- School of Biosciences, Division of Natural Sciences, University of Kent, Canterbury, CT7 2NJ, United Kingdom
| | - Tanith Hanson
- School of Biosciences, Division of Natural Sciences, University of Kent, Canterbury, CT7 2NJ, United Kingdom
| | - Rubén Martín-Escolano
- School of Biosciences, Division of Natural Sciences, University of Kent, Canterbury, CT7 2NJ, United Kingdom
| | - Anastasios D Tsaousis
- School of Biosciences, Division of Natural Sciences, University of Kent, Canterbury, CT7 2NJ, United Kingdom
| | - José A Bengoechea
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, BT9 7BL, United Kingdom
| | - J Mark Sutton
- Technology Development Group, Research and Evaluation, UK Health Security Agency, Salisbury, SP4 0JG, United Kingdom
| | - Christopher M Smales
- School of Biosciences, Division of Natural Sciences, University of Kent, Canterbury, CT7 2NJ, United Kingdom
- National Institute for Bioprocessing Research and Training, Blackrock Co, Dublin, Ireland
| | - Simon J Moore
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, E1 4NS, United Kingdom.
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Anirudhan A, Iryani MTM, Andriani Y, Sorgeloos P, Tan MP, Wong LL, Mok WJ, Ming W, Yantao L, Lau CC, Sung YY. The effects of Pandanus tectorius leaf extract on the resistance of White-leg shrimp Penaeus vannamei towards pathogenic Vibrio parahaemolyticus. FISH AND SHELLFISH IMMUNOLOGY REPORTS 2023; 4:100101. [PMID: 37397801 PMCID: PMC10313901 DOI: 10.1016/j.fsirep.2023.100101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 05/08/2023] [Accepted: 06/03/2023] [Indexed: 07/04/2023] Open
Abstract
Pandanus tectorius leaf extract effect on the White-leg shrimp Penaeus vannamei tolerance against Vibrio parahaemolyticus were investigated in this study. Thirty shrimp post-larvae measured at approximately 1 cm were exposed for 24 h to 0.5, 1, 2, 3, 4, 5 and 6 g/L leaf extract and subsequently observed for survival and immune-related genes expression (Hsp70, ProPO, peroxinectin, penaeidin, crustin and transglutaminase), followed by determination of their tolerance and histological tissue profiles upon Vibrio challenge. Survival of shrimps treated with 6 g/L of leaf extract improved by up to 95% to controls. Hsp70, crustin, and prophenoloxidase mRNA levels were observed to be 8.5, 10.4, and 1.5-fold higher, respectively. Histopathological analysis of the hepatopancreas and the muscle tissues revealed major tissue degeneration in Vibrio-challenged shrimps but not in shrimps primed with P. tectorius leaf extract. Of all the dose examined, the best pathogen resistance results were obtained with a 24 h incubation of shrimp in 6 g/L P. tectorius methanolic leaf extract. The tolerance towards V. parahaemolyticus might be associated with the increased regulation of Hsp70, prophenoloxidase and crustin upon exposure to the extract, all immune-related proteins essential for pathogen elimination in Penaeid shrimp. The present study primarily demonstrated that P. tectorius leaf extract is a viable alternative for enhancing P. vannamei post-larvae resistance against V. parahaemolyticus, a major bacterial pathogen in aquaculture.
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Affiliation(s)
- Anupa Anirudhan
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
| | - Mat Taib Mimi Iryani
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
- Faculty of Fisheries and Food Science, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
| | - Yosie Andriani
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
| | - Patrick Sorgeloos
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
- Laboratory of Aquaculture and Artemia Reference Center, Department of Animal Sciences and Aquatic Ecology, Campus Coupure - Blok F, Ghent University, Coupure Links 653, Gent B-9000, Belgium
| | - Min Pau Tan
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
| | - Li Lian Wong
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
- UMT-OUC Joint Academic Center for Marine Studies, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
| | - Wen Jye Mok
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
- UMT-OUC Joint Academic Center for Marine Studies, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
| | - Wang Ming
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- UMT-OUC Joint Academic Center for Marine Studies, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
| | - Liang Yantao
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- UMT-OUC Joint Academic Center for Marine Studies, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
| | - Cher Chien Lau
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
| | - Yeong Yik Sung
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
- Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
- UMT-OUC Joint Academic Center for Marine Studies, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
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30
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Muteeb G, Rehman MT, Shahwan M, Aatif M. Origin of Antibiotics and Antibiotic Resistance, and Their Impacts on Drug Development: A Narrative Review. Pharmaceuticals (Basel) 2023; 16:1615. [PMID: 38004480 PMCID: PMC10675245 DOI: 10.3390/ph16111615] [Citation(s) in RCA: 127] [Impact Index Per Article: 63.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/08/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
Antibiotics have revolutionized medicine, saving countless lives since their discovery in the early 20th century. However, the origin of antibiotics is now overshadowed by the alarming rise in antibiotic resistance. This global crisis stems from the relentless adaptability of microorganisms, driven by misuse and overuse of antibiotics. This article explores the origin of antibiotics and the subsequent emergence of antibiotic resistance. It delves into the mechanisms employed by bacteria to develop resistance, highlighting the dire consequences of drug resistance, including compromised patient care, increased mortality rates, and escalating healthcare costs. The article elucidates the latest strategies against drug-resistant microorganisms, encompassing innovative approaches such as phage therapy, CRISPR-Cas9 technology, and the exploration of natural compounds. Moreover, it examines the profound impact of antibiotic resistance on drug development, rendering the pursuit of new antibiotics economically challenging. The limitations and challenges in developing novel antibiotics are discussed, along with hurdles in the regulatory process that hinder progress in this critical field. Proposals for modifying the regulatory process to facilitate antibiotic development are presented. The withdrawal of major pharmaceutical firms from antibiotic research is examined, along with potential strategies to re-engage their interest. The article also outlines initiatives to overcome economic challenges and incentivize antibiotic development, emphasizing international collaborations and partnerships. Finally, the article sheds light on government-led initiatives against antibiotic resistance, with a specific focus on the Middle East. It discusses the proactive measures taken by governments in the region, such as Saudi Arabia and the United Arab Emirates, to combat this global threat. In the face of antibiotic resistance, a multifaceted approach is imperative. This article provides valuable insights into the complex landscape of antibiotic development, regulatory challenges, and collaborative efforts required to ensure a future where antibiotics remain effective tools in safeguarding public health.
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Affiliation(s)
- Ghazala Muteeb
- Department of Nursing, College of Applied Medical Science, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Md Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11437, Saudi Arabia;
- Center for Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman 346, United Arab Emirates;
| | - Moayad Shahwan
- Center for Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman 346, United Arab Emirates;
- Department of Clinical Sciences, College of Pharmacy and Health Sciences, Ajman University, Ajman 346, United Arab Emirates
| | - Mohammad Aatif
- Department of Public Health, College of Applied Medical Sciences, King Faisal University, Al-Ahsa 31982, Saudi Arabia;
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31
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Coxe T, Azad RK. Silicon versus Superbug: Assessing Machine Learning's Role in the Fight against Antimicrobial Resistance. Antibiotics (Basel) 2023; 12:1604. [PMID: 37998806 PMCID: PMC10669088 DOI: 10.3390/antibiotics12111604] [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: 09/30/2023] [Revised: 10/30/2023] [Accepted: 11/05/2023] [Indexed: 11/25/2023] Open
Abstract
In his 1945 Nobel Prize acceptance speech, Sir Alexander Fleming warned of antimicrobial resistance (AMR) if the necessary precautions were not taken diligently. As the growing threat of AMR continues to loom over humanity, we must look forward to alternative diagnostic tools and preventive measures to thwart looming economic collapse and untold mortality worldwide. The integration of machine learning (ML) methodologies within the framework of such tools/pipelines presents a promising avenue, offering unprecedented insights into the underlying mechanisms of resistance and enabling the development of more targeted and effective treatments. This paper explores the applications of ML in predicting and understanding AMR, highlighting its potential in revolutionizing healthcare practices. From the utilization of supervised-learning approaches to analyze genetic signatures of antibiotic resistance to the development of tools and databases, such as the Comprehensive Antibiotic Resistance Database (CARD), ML is actively shaping the future of AMR research. However, the successful implementation of ML in this domain is not without challenges. The dependence on high-quality data, the risk of overfitting, model selection, and potential bias in training data are issues that must be systematically addressed. Despite these challenges, the synergy between ML and biomedical research shows great promise in combating the growing menace of antibiotic resistance.
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Affiliation(s)
- Tallon Coxe
- Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA;
- BioDiscovery Institute, University of North Texas, Denton, TX 76203, USA
| | - Rajeev K. Azad
- Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA;
- BioDiscovery Institute, University of North Texas, Denton, TX 76203, USA
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32
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Liu G, Catacutan DB, Rathod K, Swanson K, Jin W, Mohammed JC, Chiappino-Pepe A, Syed SA, Fragis M, Rachwalski K, Magolan J, Surette MG, Coombes BK, Jaakkola T, Barzilay R, Collins JJ, Stokes JM. Deep learning-guided discovery of an antibiotic targeting Acinetobacter baumannii. Nat Chem Biol 2023; 19:1342-1350. [PMID: 37231267 DOI: 10.1038/s41589-023-01349-8] [Citation(s) in RCA: 123] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 04/25/2023] [Indexed: 05/27/2023]
Abstract
Acinetobacter baumannii is a nosocomial Gram-negative pathogen that often displays multidrug resistance. Discovering new antibiotics against A. baumannii has proven challenging through conventional screening approaches. Fortunately, machine learning methods allow for the rapid exploration of chemical space, increasing the probability of discovering new antibacterial molecules. Here we screened ~7,500 molecules for those that inhibited the growth of A. baumannii in vitro. We trained a neural network with this growth inhibition dataset and performed in silico predictions for structurally new molecules with activity against A. baumannii. Through this approach, we discovered abaucin, an antibacterial compound with narrow-spectrum activity against A. baumannii. Further investigations revealed that abaucin perturbs lipoprotein trafficking through a mechanism involving LolE. Moreover, abaucin could control an A. baumannii infection in a mouse wound model. This work highlights the utility of machine learning in antibiotic discovery and describes a promising lead with targeted activity against a challenging Gram-negative pathogen.
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Affiliation(s)
- Gary Liu
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
| | - Denise B Catacutan
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
| | - Khushi Rathod
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
| | - Kyle Swanson
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Wengong Jin
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jody C Mohammed
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
| | - Anush Chiappino-Pepe
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Saad A Syed
- Department of Medicine, Department of Biochemistry and Biomedical Sciences, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Meghan Fragis
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
| | - Kenneth Rachwalski
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
| | - Jakob Magolan
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
| | - Michael G Surette
- Department of Medicine, Department of Biochemistry and Biomedical Sciences, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Brian K Coombes
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
| | - Tommi Jaakkola
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Regina Barzilay
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Abdul Latif Jameel Clinic for Machine Learning in Health, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - James J Collins
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
- Abdul Latif Jameel Clinic for Machine Learning in Health, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biological Engineering, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Jonathan M Stokes
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
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Esmaili-Shahzade-Ali-Akbari P, Ghaderi A, Hosseini SMM, Nejat F, Saeedi-Mofrad M, Karimi-Houyeh M, Ghattan A, Etemadi A, Rasoulian E, Khezri A. β_lactam antibiotics against drug addiction: A novel therapeutic option. Drug Dev Res 2023; 84:1411-1426. [PMID: 37602907 DOI: 10.1002/ddr.22110] [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: 12/13/2022] [Revised: 07/25/2023] [Accepted: 08/06/2023] [Indexed: 08/22/2023]
Abstract
Drug addiction as a problem for the health of the individual and the society is the result of a complex process in which there is an interaction between brain nuclei and neurotransmitters (such as glutamate). β-lactam antibiotics, due to their enhancing properties on the glutamate transporter glutamate transporter-1, can affect and counteract the addictive mechanisms of drugs through the regulation of extracellular glutamate. Since glutamate is a key neurotransmitter in the development of drug addiction, it seems that β-lactams can be considered as a promising treatment for addiction. However, more research in this field is necessary to identify other mechanisms involved in their effectiveness. This article is a review of the studies conducted on the effect of β-lactam administration in preventing the development of drug addiction, as well as their possible cellular and molecular mechanisms. This review suggests the clinical use of β-lactam antibiotics that have weak antimicrobial properties (such as clavulanic acid) in the treatment of drug dependence.
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Affiliation(s)
| | - Amir Ghaderi
- Department of Addiction Studies, School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | | | - Fatemeh Nejat
- Department of Biology and Health Sciences, Meredith College, Raleigh, North Carolina, USA
| | | | | | - Alireza Ghattan
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Amirreza Etemadi
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Elham Rasoulian
- Department of Medical-Surgical Nursing, School of Nursing Midwifery, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Arina Khezri
- Department of Anesthesia, School of Allied Medicine, Tehran University of Medical Sciences, Tehran, Iran
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Sun G, Yu Z, Li Q, Zhang Y, Wang M, Liu Y, Liu J, Liu L, Yu X. Mechanism of Escherichia coli Lethality Caused by Overexpression of flhDC, the Flagellar Master Regulator Genes, as Revealed by Transcriptome Analysis. Int J Mol Sci 2023; 24:14058. [PMID: 37762361 PMCID: PMC10530849 DOI: 10.3390/ijms241814058] [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: 08/14/2023] [Revised: 09/07/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
The flhDC operon of Escherichia coli encodes a transcription factor that initiates flagella synthesis, elevates flagella construction and enhances cell motility, which all are energetically costly and highly regulated processes. In this study, we found that overexpression of flhDC genes from a strong regulatable pN15E6 plasmid could inhibit the growth of E. coli host cells and even eventually cause death. We used transcriptome analysis to investigate the mechanism of flhDC overexpression lethal to host bacteria. The results showed that a total of 568 differentially expressed genes (DEGs), including 378 up-regulated genes and 190 down-regulated genes were detected when the flhDC genes were over-expressed. Functional enrichment analysis results showed that the DEGs are related to a series of crucial biomolecular processes, including flagella synthesis, oxidative phosphorylation and pentose phosphate pathways, etc. We then examined, using RT-qPCR, the expression of key genes of the oxidative phosphorylation pathway at different time points after induction. Results showed that their expression increased in the early stage and decreased afterward, which was suggested to be the result of feedback on the overproduction of ROS, a strong side effect product of the elevated oxidative phosphorylation process. To further verify the level of ROS output, flhDC over-expressed bacteria cells were stained with DCHF-DA and a fluorescence signal was detected using flow cytometry. Results showed that the level of ROS output was higher in cells with over-expressed flhDC than in normal controls. Besides, we found upregulation of other genes (recN and zwf) that respond to ROS damage. This leads to the conclusion that the bacterial death led by the overexpression of flhDC genes is caused by damage from ROS overproduction, which leaked from the oxidative phosphorylation pathway.
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Affiliation(s)
- Guanglu Sun
- Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (G.S.)
| | - Zihao Yu
- Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (G.S.)
| | - Qianwen Li
- Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (G.S.)
| | - Yuanxing Zhang
- Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (G.S.)
| | - Mingxiao Wang
- Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (G.S.)
| | - Yunhui Liu
- Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (G.S.)
| | - Jinze Liu
- Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (G.S.)
| | - Lei Liu
- Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (G.S.)
| | - Xuping Yu
- Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (G.S.)
- Center for Veterinary Sciences, Zhejiang University, Hangzhou 310030, China
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Ahmad N, Ali S, Abbas M, Fazal H, Saqib S, Ali A, Ullah Z, Zaman S, Sawati L, Zada A, Sohail. Antimicrobial efficacy of Mentha piperata-derived biogenic zinc oxide nanoparticles against UTI-resistant pathogens. Sci Rep 2023; 13:14972. [PMID: 37696980 PMCID: PMC10495404 DOI: 10.1038/s41598-023-41502-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 08/28/2023] [Indexed: 09/13/2023] Open
Abstract
Misuse of antibiotics leads to the worldwide spread of antibiotic resistance, which motivates scientists to create new antibiotics. The recurring UTI due to antibiotics-resistant microorganism's challenges scientists globally. The biogenic nanoparticles have the potential to meet the escalating requirements of novel antimicrobial agents. The green synthesis of nanoparticles (NPs) gained more attention due to their reliable applications against resistant microbes. The current study evaluates the biogenic ZnO NPs of Mentha piperata extract against resistant pathogens of urinary tract infections by agar well diffusion assay. The biogenic ZnO NPs revealed comparatively maximum inhibition in comparison to synthetic antibiotics against two bacterial strains (Proteus mirabilis, Pseudomonas aeruginosa) and a fungal strain (Candida albicans).The synthesized biogenic ZnO NPs alone revealed maximum activities than the combination of plant extract (PE) and ZnO NPs, and PE alone. The physiochemical features of ZnO NPs characterized through UV-Vis spectroscopy, FTIR, XRD, SEM, and EDX. The UV-Vis spectroscopy revealed 281.85 nm wavelengths; the XRD pattern revealed the crystalline structure of ZnO NPs. The FTIR analysis revealed the presence of carboxylic and nitro groups, which could be attributed to plant extract. SEM analysis revealed spherical hollow symmetry due to electrostatic forces. The analysis via EDX confirmed the presence of Zn and oxygen in the sample. The physiochemical features of synthesized ZnO NPs provide pivotal information such as quality and effectiveness. The current study revealed excellent dose-dependent antimicrobial activity against the pathogenic isolates from UTI-resistant patients. The higher concentration of ZnONPs interacts with the cell membrane which triggers oxidative burst. They may bind with the enzymes and proteins and brings epigenetic alteration which leads to membrane disruption or cell death.
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Affiliation(s)
- Nisar Ahmad
- Center for Biotechnology and Microbiology, University of Swat, Swat, 19200, Pakistan
| | - Shujat Ali
- Center for Biotechnology and Microbiology, University of Swat, Swat, 19200, Pakistan
| | - Muhammad Abbas
- Center for Biotechnology and Microbiology, University of Swat, Swat, 19200, Pakistan
| | - Hina Fazal
- Pakistan Council of Scientific and Industrial Research (PCSIR) Laboratories Complex, Peshawar, 25120, Pakistan
| | - Saddam Saqib
- State Key Laboratory of Systematic and Evolutionary Biology, Chinese Academy of Sciences, Beijing, China
| | - Ahmad Ali
- Centre of Plant Science and Biodiversity, University of Swat, Charbagh, Swat, 19200, Pakistan
| | - Zahid Ullah
- Centre of Plant Science and Biodiversity, University of Swat, Charbagh, Swat, 19200, Pakistan
| | - Shah Zaman
- Department of Botany, University of Malakand, Chakdara, 18800, KPK, Pakistan.
| | - Laraib Sawati
- Department of Chemical and Life Sciences, Qurtuba University of Science and Information Technology, Peshawar, 25124, Pakistan
| | - Ahmad Zada
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, China
| | - Sohail
- Institute of Biology/Plant Physiology, Humboldt-University Zü Berlin, 10115, Berlin, Germany.
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, China.
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Chen EHL, Wang CH, Liao YT, Chan FY, Kanaoka Y, Uchihashi T, Kato K, Lai L, Chang YW, Ho MC, Chen RPY. Visualizing the membrane disruption action of antimicrobial peptides by cryo-electron tomography. Nat Commun 2023; 14:5464. [PMID: 37673860 PMCID: PMC10482868 DOI: 10.1038/s41467-023-41156-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/24/2023] [Indexed: 09/08/2023] Open
Abstract
The abuse of antibiotics has led to the emergence of multidrug-resistant microbial pathogens, presenting a pressing challenge in global healthcare. Membrane-disrupting antimicrobial peptides (AMPs) combat so-called superbugs via mechanisms different than conventional antibiotics and have good application prospects in medicine, agriculture, and the food industry. However, the mechanism-of-action of AMPs has not been fully characterized at the cellular level due to a lack of high-resolution imaging technologies that can capture cellular-membrane disruption events in the hydrated state. Previously, we reported PepD2M, a de novo-designed AMP with potent and wide-spectrum bactericidal and fungicidal activity. In this study, we use cryo-electron tomography (cryo-ET) and high-speed atomic force microscopy (HS-AFM) to directly visualize the pepD2M-induced disruption of the outer and inner membranes of the Gram-negative bacterium Escherichia coli, and compared with a well-known pore-forming peptide, melittin. Our high-resolution cryo-ET images reveal how pepD2M disrupts the E. coli membrane using a carpet/detergent-like mechanism. Our studies reveal the direct membrane-disrupting consequence of AMPs on the bacterial membrane by cryo-ET, and this information provides critical insights into the mechanisms of this class of antimicrobial agents.
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Affiliation(s)
- Eric H-L Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Chun-Hsiung Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Yi-Ting Liao
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Feng-Yueh Chan
- Department of Physics, Nagoya University, Nagoya, 464-8602, Japan
| | - Yui Kanaoka
- Department of Physics, Nagoya University, Nagoya, 464-8602, Japan
| | - Takayuki Uchihashi
- Department of Physics, Nagoya University, Nagoya, 464-8602, Japan
- Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, 464-8602, Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi, 444-8787, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi, 444-8787, Japan
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan
| | - Longsheng Lai
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104-6059, USA
| | - Yi-Wei Chang
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104-6059, USA
| | - Meng-Chiao Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan.
- Institute of Biochemical Sciences, National Taiwan University, Taipei, 10617, Taiwan.
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, 100, Taiwan.
| | - Rita P-Y Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan.
- Institute of Biochemical Sciences, National Taiwan University, Taipei, 10617, Taiwan.
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Saha P, Rafe MR. Cyclodextrin: A prospective nanocarrier for the delivery of antibacterial agents against bacteria that are resistant to antibiotics. Heliyon 2023; 9:e19287. [PMID: 37662769 PMCID: PMC10472013 DOI: 10.1016/j.heliyon.2023.e19287] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/02/2023] [Accepted: 08/17/2023] [Indexed: 09/05/2023] Open
Abstract
Supramolecular chemistry introduces us to the macrocyclic host cyclodextrin, which has a hydrophobic cavity. The hydrophobic cavity has a higher affinity for hydrophobic guest molecules and forms host-guest complexation with non-covalent interaction. Three significant cyclodextrin kinds are α-cyclodextrin, β-cyclodextrin, and γ-cyclodextrin. The most often utilized is β-cyclodextrin (β-CD). An effective weapon against bacteria that are resistant to antibiotics is cyclodextrin. Several different kinds of cyclodextrin nanocarriers (β-CD, HP-β-CD, Meth-β-CD, cationic CD, sugar-grafted CD) are utilized to enhance the solubility, stability, dissolution, absorption, bioavailability, and permeability of the antibiotics. Cyclodextrin also improves the effectiveness of antibiotics, antimicrobial peptides, metallic nanoparticles, and photodynamic therapy (PDT). Again, cyclodextrin nanocarriers offer slow-release properties for sustained-release formulations where steady-state plasma antibiotic concentration is needed for an extended time. A novel strategy to combat bacterial resistance is a stimulus (pH, ROS)-responsive antibiotics released from cyclodextrin carrier. Once again, cyclodextrin traps autoinducer (AI), a crucial part of bacterial quorum sensing, and reduces virulence factors, including biofilm formation. Cyclodextrin helps to minimize MIC in particular bacterial strains, keep antibiotic concentrations above MIC in the infection site and minimize the possibility of antibiotic and biofilm resistance. Sessile bacteria trapped in biofilms are more resistant to antibiotic therapy than bacteria in a planktonic form. Cyclodextrin also involves delivering antibiotics to biofilm and resistant bacteria to combat bacterial resistance.
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Affiliation(s)
- Pranoy Saha
- Department of Pharmacy, Jagannath University, Dhaka, 1100, Bangladesh
| | - Md Rajdoula Rafe
- Department of Pharmacy, Jagannath University, Dhaka, 1100, Bangladesh
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Abdallah EM, Alhatlani BY, de Paula Menezes R, Martins CHG. Back to Nature: Medicinal Plants as Promising Sources for Antibacterial Drugs in the Post-Antibiotic Era. PLANTS (BASEL, SWITZERLAND) 2023; 12:3077. [PMID: 37687324 PMCID: PMC10490416 DOI: 10.3390/plants12173077] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/28/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023]
Abstract
Undoubtedly, the advent of antibiotics in the 19th century had a substantial impact, increasing human life expectancy. However, a multitude of scientific investigations now indicate that we are currently experiencing a phase known as the post-antibiotic era. There is a genuine concern that we might regress to a time before antibiotics and confront widespread outbreaks of severe epidemic diseases, particularly those caused by bacterial infections. These investigations have demonstrated that epidemics thrive under environmental stressors such as climate change, the depletion of natural resources, and detrimental human activities such as wars, conflicts, antibiotic overuse, and pollution. Moreover, bacteria possess a remarkable ability to adapt and mutate. Unfortunately, the current development of antibiotics is insufficient, and the future appears grim unless we abandon our current approach of generating synthetic antibiotics that rapidly lose their effectiveness against multidrug-resistant bacteria. Despite their vital role in modern medicine, medicinal plants have served as the primary source of curative drugs since ancient times. Numerous scientific reports published over the past three decades suggest that medicinal plants could serve as a promising alternative to ineffective antibiotics in combating infectious diseases. Over the past few years, phenolic compounds, alkaloids, saponins, and terpenoids have exhibited noteworthy antibacterial potential, primarily through membrane-disruption mechanisms, protein binding, interference with intermediary metabolism, anti-quorum sensing, and anti-biofilm activity. However, to optimize their utilization as effective antibacterial drugs, further advancements in omics technologies and network pharmacology will be required in order to identify optimal combinations among these compounds or in conjunction with antibiotics.
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Affiliation(s)
- Emad M. Abdallah
- Department of Science Laboratories, College of Science and Arts, Qassim University, Ar Rass 51921, Saudi Arabia;
| | - Bader Y. Alhatlani
- Unit of Scientific Research, Applied College, Qassim University, Buraydah 52571, Saudi Arabia
| | - Ralciane de Paula Menezes
- Technical School of Health, Federal University of Uberlândia, Uberlândia 38400-732, MG, Brazil;
- Laboratory of Antimicrobial Testing, Federal University of Uberlândia, Uberlândia 38405-320, MG, Brazil;
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Rampogu S, Balasubramaniyam T, Lee JH. Curcumin Chalcone Derivatives Database (CCDD): a Python framework for natural compound derivatives database. PeerJ 2023; 11:e15885. [PMID: 37605747 PMCID: PMC10440061 DOI: 10.7717/peerj.15885] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/20/2023] [Indexed: 08/23/2023] Open
Abstract
We built the Curcumin Chalcone Derivatives Database (CCDD) to enable the effective virtual screening of highly potent curcumin and its analogs. The two-dimensional (2D) structures were drawn using the ChemBioOffice package and converted to 3D structures using Discovery Studio Visualizer V 2021 (DS). The database was built using different Python modules. For the 3D structures, different Python packages were used to obtain the data frame of compounds. This framework is also used to visualize the compounds. The webserver enables the users to screen the compounds according to Lipinski's rule of five. The structures can be downloaded in .sdf and .mol format. The data frame (df) can be downloaded in .csv format. Our webserver can help computational drug discovery researchers find new therapeutics and build new webservers. The CCDD is freely available at: https://srampogu-ccdd-ccdd-8uldk8.streamlit.app/.
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Affiliation(s)
| | | | - Joon-Hwa Lee
- Department of Chemistry, Gyeongsang National University, Jinju, Gyeongnam, South Korea
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40
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Li XS, Xue JZ, Qi Y, Muhammad I, Wang H, Li XY, Luo YJ, Zhu DM, Gao YH, Kong LC, Ma HX. Citric Acid Confers Broad Antibiotic Tolerance through Alteration of Bacterial Metabolism and Oxidative Stress. Int J Mol Sci 2023; 24:ijms24109089. [PMID: 37240435 DOI: 10.3390/ijms24109089] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/30/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
Antibiotic tolerance has become an increasingly serious crisis that has seriously threatened global public health. However, little is known about the exogenous factors that can trigger the development of antibiotic tolerance, both in vivo and in vitro. Herein, we found that the addition of citric acid, which is used in many fields, obviously weakened the bactericidal activity of antibiotics against various bacterial pathogens. This mechanistic study shows that citric acid activated the glyoxylate cycle by inhibiting ATP production in bacteria, reduced cell respiration levels, and inhibited the bacterial tricarboxylic acid cycle (TCA cycle). In addition, citric acid reduced the oxidative stress ability of bacteria, which led to an imbalance in the bacterial oxidation-antioxidant system. These effects together induced the bacteria to produce antibiotic tolerance. Surprisingly, the addition of succinic acid and xanthine could reverse the antibiotic tolerance induced by citric acid in vitro and in animal infection models. In conclusion, these findings provide new insights into the potential risks of citric acid usage and the relationship between antibiotic tolerance and bacterial metabolism.
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Affiliation(s)
- Xue-Song Li
- Department of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
| | - Jun-Ze Xue
- Department of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
| | - Yu Qi
- Department of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
| | - Inam Muhammad
- Department of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
- Department of Zoology, Shaheed Benazir Bhutto University Sheringal, Dir Upper 18050, Pakistan
| | - Hao Wang
- Department of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
| | - Xuan-Yu Li
- Department of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
| | - Yi-Jia Luo
- Department of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
| | - Dao-Mi Zhu
- Department of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
| | - Yun-Hang Gao
- Department of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
| | - Ling-Cong Kong
- Department of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
| | - Hong-Xia Ma
- Department of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
- The Engineering Research Center of Bioreactor and Drug Development, Ministry of Education, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
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Sadeeshkumar H, Balaji A, Sutherland AG, Mootien S, Anthony KG, Breaker RR. Screening for small molecule inhibitors of SAH nucleosidase using an SAH riboswitch. Anal Biochem 2023; 666:115047. [PMID: 36682579 PMCID: PMC11149561 DOI: 10.1016/j.ab.2023.115047] [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: 10/21/2022] [Revised: 12/30/2022] [Accepted: 01/09/2023] [Indexed: 01/21/2023]
Abstract
Due to the emergence of multidrug resistant pathogens, it is imperative to identify new targets for antibiotic drug discovery. The S-adenosylhomocysteine (SAH) nucleosidase enzyme is a promising target for antimicrobial drug development due to its critical functions in multiple bacterial processes including recycling of toxic byproducts of S-adenosylmethionine (SAM)-mediated reactions and producing the precursor of the universal quorum sensing signal, autoinducer-2 (AI-2). Riboswitches are structured RNA elements typically used by bacteria to precisely monitor and respond to changes in essential bacterial processes, including metabolism. Natural riboswitches fused to a reporter gene can be exploited to detect changes in metabolism or in physiological signaling. We performed a high-throughput screen (HTS) using an SAH-riboswitch controlled β-galactosidase reporter gene in Escherichia coli to discover small molecules that inhibit SAH recycling. We demonstrate that the assay strategy using SAH riboswitches to detect the effects of SAH nucleosidase inhibitors can quickly identify compounds that penetrate the barriers of Gram-negative bacterial cells and perturb pathways involving SAH.
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Affiliation(s)
- Harini Sadeeshkumar
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06520-8103, USA
| | - Aparaajita Balaji
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06520-8103, USA
| | | | | | - Karen G Anthony
- L2 Diagnostics, LLC, 300 George Street, New Haven, CT, 06511, USA
| | - Ronald R Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06520-8103, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520-8103, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT, 06520-8103, USA.
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Dresen M, Valentin-Weigand P, Berhanu Weldearegay Y. Role of Metabolic Adaptation of Streptococcus suis to Host Niches in Bacterial Fitness and Virulence. Pathogens 2023; 12:pathogens12040541. [PMID: 37111427 PMCID: PMC10144218 DOI: 10.3390/pathogens12040541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
Streptococcus suis, both a common colonizer of the porcine upper respiratory tract and an invasive pig pathogen, successfully adapts to different host environments encountered during infection. Whereas the initial infection mainly occurs via the respiratory tract, in a second step, the pathogen can breach the epithelial barrier and disseminate within the whole body. Thereby, the pathogen reaches other organs such as the heart, the joints, or the brain. In this review, we focus on the role of S. suis metabolism for adaptation to these different in vivo host niches to encounter changes in nutrient availability, host defense mechanisms and competing microbiota. Furthermore, we highlight the close link between S. suis metabolism and virulence. Mutants deficient in metabolic regulators often show an attenuation in infection experiments possibly due to downregulation of virulence factors, reduced resistance to nutritive or oxidative stress and to phagocytic activity. Finally, metabolic pathways as potential targets for new therapeutic strategies are discussed. As antimicrobial resistance in S. suis isolates has increased over the last years, the development of new antibiotics is of utmost importance to successfully fight infections in the future.
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Affiliation(s)
- Muriel Dresen
- Institute for Microbiology, University of Veterinary Medicine Hannover, 30173 Hannover, Germany
| | - Peter Valentin-Weigand
- Institute for Microbiology, University of Veterinary Medicine Hannover, 30173 Hannover, Germany
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Yuan S, Shen DD, Bai YR, Zhang M, Zhou T, Sun C, Zhou L, Wang SQ, Liu HM. Oxazolidinone: A promising scaffold for the development of antibacterial drugs. Eur J Med Chem 2023; 250:115239. [PMID: 36893700 DOI: 10.1016/j.ejmech.2023.115239] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/16/2023] [Accepted: 02/23/2023] [Indexed: 03/06/2023]
Abstract
Due to the long-term and widespread use of antibiotics in clinic, the problem of bacterial resistance is increasingly serious, and the development of new drugs to treat drug-resistant bacteria has gradually become the mainstream direction of antibiotic research. The oxazolidinone-containing drugs linezolid, tedizolid phosphate and contezolid have been approved to the market, which are effective against a variety of Gram-positive bacterium infections. Moreover, there are also many antibiotics containing oxazolidinone fragment under clinical investigation that show good pharmacokinetic and pharmacodynamic properties with unique mechanism of action against resistant bacteria. In this review, we summarized the oxazolidinone-based antibiotics already on the market or in clinical trials and the representative bioactive molecules, and mainly focused on their structural optimizations, development strategies and structure-activity relationships in hope of insight into the reasonable design for medical chemists to develop new oxazolidinone antibiotics with highly potency and fewer side effects.
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Affiliation(s)
- Shuo Yuan
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China; School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Zhengzhou University, Zhengzhou, 450001, China.
| | - Dan-Dan Shen
- Department of Obstetrics and Gynecology, Zhengzhou Key Laboratory of Endometrial Disease Prevention and Treatment Zhengzhou China, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Yi-Ru Bai
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China; School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Zhengzhou University, Zhengzhou, 450001, China
| | - Miao Zhang
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China; School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Zhengzhou University, Zhengzhou, 450001, China
| | - Tian Zhou
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China; School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Zhengzhou University, Zhengzhou, 450001, China
| | - Chong Sun
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China; School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Zhengzhou University, Zhengzhou, 450001, China
| | - Li Zhou
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China
| | - Sai-Qi Wang
- The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Henan Engineering Research Center of Precision Therapy of Gastrointestinal Cancer, Zhengzhou Key Laboratory of Precision Therapy of Gastrointestinal Cancer, Zhengzhou, 450008, China.
| | - Hong-Min Liu
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Zhengzhou University, Zhengzhou, 450001, China.
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Shaw GX, Fan L, Cherry S, Shi G, Tropea JE, Ji X. Structure of Helicobacter pylori dihydroneopterin aldolase suggests a fragment-based strategy for isozyme-specific inhibitor design. Curr Res Struct Biol 2023; 5:100095. [PMID: 36820301 PMCID: PMC9937910 DOI: 10.1016/j.crstbi.2023.100095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/27/2022] [Accepted: 01/26/2023] [Indexed: 01/31/2023] Open
Abstract
Dihydroneopterin aldolase (DHNA) is essential for folate biosynthesis in microorganisms. Without a counterpart in mammals, DHNA is an attractive target for antimicrobial agents. Helicobacter pylori infection occurs in human stomach of over 50% of the world population, but first-line therapies for the infection are facing rapidly increasing resistance. Novel antibiotics are urgently needed, toward which structural information on potential targets is critical. We have determined the crystal structure of H. pylori DHNA (HpDHNA) in complex with a pterin molecule (HpDHNA:Pterin) at 1.49-Å resolution. The HpDHNA:Pterin complex forms a tetramer in crystal. The tetramer is also observed in solution by dynamic light scattering and confirmed by small-angle X-ray scattering. To date, all but one reported DHNA structures are octameric complexes. As the only exception, ligand-free Mycobacterium tuberculosis DHNA (apo-MtDHNA) forms a tetramer in crystal, but its active sites are only partially formed. In contrast, the tetrameric HpDHNA:Pterin complex has well-formed active sites. Each active site accommodates one pterin molecule, but the exit of active site is blocked by two amino acid residues exhibiting a contact distance of 5.2 Å. In contrast, the corresponding contact distance in Staphylococcus aureus DHNA (SaDHNA) is twice the size, ranging from 9.8 to 10.5 Å, for ligand-free enzyme, the substrate complex, the product complex, and an inhibitor complex. This large contact distance indicates that the active site of SaDHNA is wide open. We propose that this isozyme-specific contact distance (ISCD) is a characteristic feature of DHNA active site. Comparative analysis of HpDHNA and SaDHNA structures suggests a fragment-based strategy for the development of isozyme-specific inhibitors.
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Key Words
- ANL, Argonne National Laboratory
- APS, Advanced Photon Source
- Antibiotic
- DHFS, dihydrofolate synthase
- DHNA, dihydroneopterin aldolase
- DHNP, 7,8-dihydroneopterin
- DHPS, dihydropteroate synthase
- DLS, dynamic light scattering
- Dihydroneopterin aldolase
- Dmax, maximum dimension
- EcDHNA, Escherichia coli DHNA
- FBDD, fragment-based drug discovery
- Folate biosynthesis
- Fragment-based drug discovery
- GA, glycoaldehyde
- HP, 6-hydroxymethyl-7,8-dihydropterin
- HPPK, 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase
- Helicobacter pylori
- HpDHNA, Helicobacter pylori DHNA
- ISCD, isozyme-specific contact distance
- MW, molecular weight
- MtDHNA, Mycobacterium tuberculosis DHNA
- NP, neopterin
- P(r), pair-distance distribution function
- PCR, polymerase chain reaction
- Rg, radius of gyration
- SAXS, small-angle X-ray scattering
- SER-CAT, Southeast Regional Collaborative Access Team
- SaDHNA, Staphylococcus aureus DHNA
- SpDHNA, Streptococcus pneumoniae DHNA
- TCEP, tris(2-carboxyethyl)phosphine
- TEV, tobacco etch virus
- wwPDB, Worldwide Protein Data Bank
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Affiliation(s)
- Gary X. Shaw
- Center for Structural Biology, National Cancer Institute, National Institutes of Health, 1050 Boyles Street, Frederick, MD, 21702, USA
| | - Lixin Fan
- Basic Research Program, Frederick National Laboratory for Cancer Research, Small-angle X-ray Scattering Core Facility, National Cancer Institute, National Institutes of Health, 1050 Boyles Street, Frederick, MD, 21702, USA
| | - Scott Cherry
- Center for Structural Biology, National Cancer Institute, National Institutes of Health, 1050 Boyles Street, Frederick, MD, 21702, USA
| | - Genbin Shi
- Center for Structural Biology, National Cancer Institute, National Institutes of Health, 1050 Boyles Street, Frederick, MD, 21702, USA
| | - Joseph E. Tropea
- Center for Structural Biology, National Cancer Institute, National Institutes of Health, 1050 Boyles Street, Frederick, MD, 21702, USA
| | - Xinhua Ji
- Center for Structural Biology, National Cancer Institute, National Institutes of Health, 1050 Boyles Street, Frederick, MD, 21702, USA
- Corresponding author. 1050 Boyles Street, Frederick, MD, 21702, USA.
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Rohrbacher C, Zscherp R, Weck SC, Klahn P, Ducho C. Synthesis of an Antimicrobial Enterobactin-Muraymycin Conjugate for Improved Activity Against Gram-Negative Bacteria. Chemistry 2023; 29:e202202408. [PMID: 36222466 PMCID: PMC10107792 DOI: 10.1002/chem.202202408] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Indexed: 12/12/2022]
Abstract
Overcoming increasing antibiotic resistance requires the development of novel antibacterial agents that address new targets in bacterial cells. Naturally occurring nucleoside antibiotics (such as muraymycins) inhibit the bacterial membrane protein MraY, a clinically unexploited essential enzyme in peptidoglycan (cell wall) biosynthesis. Even though a range of synthetic muraymycin analogues has already been reported, they generally suffer from limited cellular uptake and a lack of activity against Gram-negative bacteria. We herein report an approach to overcome these hurdles: a synthetic muraymycin analogue has been conjugated to a siderophore, i. e. the enterobactin derivative EntKL , to increase the cellular uptake into Gram-negative bacteria. The resultant conjugate showed significantly improved antibacterial activity against an efflux-deficient E. coli strain, thus providing a proof-of-concept of this novel approach and a starting point for the future optimisation of such conjugates towards potent agents against Gram-negative pathogens.
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Affiliation(s)
- Christian Rohrbacher
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany
| | - Robert Zscherp
- Institute of Organic Chemistry, Technische Universität Braunschweig, Hagenring 30, 38106, Braunschweig, Germany
| | - Stefanie C Weck
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany
| | - Philipp Klahn
- Institute of Organic Chemistry, Technische Universität Braunschweig, Hagenring 30, 38106, Braunschweig, Germany.,Department of Chemistry and Molecular Biology, Division of Organic and Medicinal Chemistry, University of Gothenburg, Kemigården 4, 412 96, Göteborg, Sweden
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany
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Almeida MC, da Costa PM, Sousa E, Resende DISP. Emerging Target-Directed Approaches for the Treatment and Diagnosis of Microbial Infections. J Med Chem 2023; 66:32-70. [PMID: 36586133 DOI: 10.1021/acs.jmedchem.2c01212] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
With the rising levels of drug resistance, developing efficient antimicrobial therapies has become a priority. A promising strategy is the conjugation of antibiotics with relevant moieties that can potentiate their activity by target-directing. The conjugation of siderophores with antibiotics allows them to act as Trojan horses by hijacking the microorganisms' highly developed iron transport systems and using them to carry the antibiotic into the cell. Through the analysis of relevant examples of the past decade, this Perspective aims to reveal the potential of siderophore-antibiotic Trojan horses for the treatment of infections and the role of siderophores in diagnostic techniques. Other conjugated molecules will be the subject of discussion, namely those involving vitamin B12, carbohydrates, and amino acids, as well as conjugated compounds targeting protein degradation and β-lactamase activated prodrugs.
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Affiliation(s)
- Mariana C Almeida
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, FFUP - Faculdade de Farmácia, Universidade do Porto, Rua de Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal.,CIIMAR- Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões, 4450-208 Matosinhos, Portugal
| | - Paulo M da Costa
- CIIMAR- Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões, 4450-208 Matosinhos, Portugal.,ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Emília Sousa
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, FFUP - Faculdade de Farmácia, Universidade do Porto, Rua de Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal.,CIIMAR- Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões, 4450-208 Matosinhos, Portugal
| | - Diana I S P Resende
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, FFUP - Faculdade de Farmácia, Universidade do Porto, Rua de Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal.,CIIMAR- Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões, 4450-208 Matosinhos, Portugal
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Esser A, Mayer G. Characterization of the glmS Ribozymes from Listeria Monocytogenes and Clostridium Difficile. Chemistry 2023; 29:e202202376. [PMID: 36194523 PMCID: PMC10099748 DOI: 10.1002/chem.202202376] [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: 07/30/2022] [Indexed: 11/23/2022]
Abstract
The glmS ribozyme regulates the expression of the essential GlmS enzyme being involved in cell wall biosynthesis. While >450 variants of the glmS ribozyme were identified by in silico approaches and homology searches, only a few have yet been experimentally investigated. Herein, we validate and characterize the glmS ribozymes of the human pathogens Clostridium difficile and Listeria monocytogenes. Both ribozymes, as their previous characterized homologs rely on glucosamine-6-phosphate as co-factor and the presence of divalent cations for exerting the cleavage reaction. The observed EC50 values in turn were found to be in the submicromolar range, at least an order of magnitude lower than observed for glmS ribozymes from other bacteria. The glmS ribozyme of L. monocytogenes was further shown to bear unique properties. It discriminates between co-factors very stringently and other than the glmS ribozyme of C. difficile retains activity at low temperatures. This finding illustrates that albeit being highly conserved, glmS ribozymes have unique characteristics.
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Affiliation(s)
- Anna Esser
- Life & Medical Sciences Institute, University of Bonn, Gerhard-Domagk-Str. 1, 53121, Bonn, Germany
| | - Günter Mayer
- Life & Medical Sciences Institute, University of Bonn, Gerhard-Domagk-Str. 1, 53121, Bonn, Germany.,Center of Aptamer Research & Development, University of Bonn, Gerhard-Domagk-Str. 1, 53121, Bonn, Germany
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48
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Gajera G, Henriksen N, Cox B, Kothari V. Identification of anti-pathogenic activity among in silico predicted small-molecule inhibitors of Pseudomonas aeruginosa LasR or nitric oxide reductase (NOR). Drug Target Insights 2023; 17:101-109. [PMID: 37811195 PMCID: PMC10551673 DOI: 10.33393/dti.2023.2638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023] Open
Abstract
Introduction Antibiotic-resistant Pseudomonas aeruginosa strains cause considerable morbidity and mortality globally. Identification of novel targets in this notorious pathogen is urgently warranted to facilitate discovery of new anti-pathogenic agents against it. This study attempted to identify small-molecule inhibitors of two important proteins LasR and nitric oxide reductase (NOR) in P. aeruginosa. 'Las' system can be said to be the 'master' regulator of quorum sensing in P. aeruginosa, whose receptor protein is LasR. Similarly, NOR is crucial to detoxification of reactive nitrogen species. Methods In silico identification of potential LasR or NOR inhibitors was attempted through a virtual screening platform AtomNet® to obtain a final subset of <100 top scoring compounds. These compounds were evaluated for their in vivo anti-pathogenic activity by challenging the model host Caenorhabditis elegans with P. aeruginosa in the presence or absence of test compounds. Survival of the worm population in 24-well assay plates was monitored over a period of 5 days microscopically. Results Of the 96 predicted LasR inhibitors, 11 exhibited anti-Pseudomonas activity (23%-96% inhibition of bacterial virulence as per third-day end-point) at 25-50 µg/mL. Of the 85 predicted NOR inhibitors, 8 exhibited anti-Pseudomonas activity (40%-85% inhibition of bacterial virulence as per second-day end-point) at 25-50 µg/mL. Conclusion Further investigation on molecular mode of action of compounds found active in this study is warranted. Virtual screening can be said to be a useful tool in narrowing down the list of compounds requiring actual wet-lab screening, saving considerable time and efforts for drug discovery.
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Affiliation(s)
- Gemini Gajera
- Institute of Science, Nirma University, Ahmedabad - India
| | | | - Bryan Cox
- Atomwise Inc, San Francisco, CA - USA
| | - Vijay Kothari
- Institute of Science, Nirma University, Ahmedabad - India
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Abstract
As the global burden of antibiotic resistance continues to grow, creative approaches to antibiotic discovery are needed to accelerate the development of novel medicines. A rapidly progressing computational revolution-artificial intelligence-offers an optimistic path forward due to its ability to alleviate bottlenecks in the antibiotic discovery pipeline. In this review, we discuss how advancements in artificial intelligence are reinvigorating the adoption of past antibiotic discovery models-namely natural product exploration and small molecule screening. We then explore the application of contemporary machine learning approaches to emerging areas of antibiotic discovery, including antibacterial systems biology, drug combination development, antimicrobial peptide discovery, and mechanism of action prediction. Lastly, we propose a call to action for open access of high-quality screening datasets and interdisciplinary collaboration to accelerate the rate at which machine learning models can be trained and new antibiotic drugs can be developed.
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Affiliation(s)
- Telmah Lluka
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
| | - Jonathan M Stokes
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
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50
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Chetri S. The culmination of multidrug-resistant efflux pumps vs. meager antibiotic arsenal era: Urgent need for an improved new generation of EPIs. Front Microbiol 2023; 14:1149418. [PMID: 37138605 PMCID: PMC10149990 DOI: 10.3389/fmicb.2023.1149418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 03/13/2023] [Indexed: 05/05/2023] Open
Abstract
Efflux pumps function as an advanced defense system against antimicrobials by reducing the concentration of drugs inside the bacteria and extruding the substances outside. Various extraneous substances, including antimicrobials, toxic heavy metals, dyes, and detergents, have been removed by this protective barrier composed of diverse transporter proteins found in between the cell membrane and the periplasm within the bacterial cell. In this review, multiple efflux pump families have been analytically and widely outlined, and their potential applications have been discussed in detail. Additionally, this review also discusses a variety of biological functions of efflux pumps, including their role in the formation of biofilms, quorum sensing, their survivability, and the virulence in bacteria, and the genes/proteins associated with efflux pumps have also been explored for their potential relevance to antimicrobial resistance and antibiotic residue detection. A final discussion centers around efflux pump inhibitors, particularly those derived from plants.
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