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Peng X, Zeng Z, Hassan S, Xue Y. The potential of marine natural Products: Recent Advances in the discovery of Anti-Tuberculosis agents. Bioorg Chem 2024; 151:107699. [PMID: 39128242 DOI: 10.1016/j.bioorg.2024.107699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 07/30/2024] [Accepted: 08/04/2024] [Indexed: 08/13/2024]
Abstract
Tuberculosis (TB) is an infectious airborne disease caused by Mycobacterium tuberculosis. Since the 1990 s, many countries have made significant progress in reducing the incidence of TB and associated mortality by improving health services and strengthening surveillance systems. Nevertheless, due to the emergence of multidrug-resistant TB (MDR-TB), alongside extensively drug-resistant TB (XDR-TB) and TB-HIV co-infection, TB remains one of the lead causes of death arising from infectious disease worldwide, especially in developing countries and disadvantaged populations. Marine natural products (MNPs) have received a large amount of attention in recent years as a source of pharmaceutical constituents and lead compounds, and are expected to offer significant resources and potential in the fields of drug development and biotechnology in the years to come. This review summarizes 169 marine natural products and their synthetic derivatives displaying anti-TB activity from 2013 to the present, including their structures, sources and functions. Partial synthetic information and structure-activity relationships (SARs) are also included.
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Affiliation(s)
- Xinyu Peng
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Shenzhen 518107, China
| | - Ziqian Zeng
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Shenzhen 518107, China
| | - Said Hassan
- Institute of Biotechnology and Microbiology, Bacha Khan University, Charsadda 24540, Pakistan
| | - Yongbo Xue
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Shenzhen 518107, China.
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2
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Zou Z, Singh P, Pinkner JS, Obernuefemann CLP, Xu W, Nye TM, Dodson KW, Almqvist F, Hultgren SJ, Caparon MG. Dihydrothiazolo ring-fused 2-pyridone antimicrobial compounds treat Streptococcus pyogenes skin and soft tissue infection. SCIENCE ADVANCES 2024; 10:eadn7979. [PMID: 39093975 PMCID: PMC11296344 DOI: 10.1126/sciadv.adn7979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 06/27/2024] [Indexed: 08/04/2024]
Abstract
We have developed GmPcides from a peptidomimetic dihydrothiazolo ring-fused 2-pyridone scaffold that has antimicrobial activities against a broad spectrum of Gram-positive pathogens. Here, we examine the treatment efficacy of GmPcides using skin and soft tissue infection (SSTI) and biofilm formation models by Streptococcus pyogenes. Screening our compound library for minimal inhibitory (MIC) and minimal bactericidal (MBC) concentrations identified GmPcide PS757 as highly active against S. pyogenes. Treatment of S. pyogenes biofilm with PS757 revealed robust efficacy against all phases of biofilm formation by preventing initial biofilm development, ceasing biofilm maturation and eradicating mature biofilm. In a murine model of S. pyogenes SSTI, subcutaneous delivery of PS757 resulted in reduced levels of tissue damage, decreased bacterial burdens, and accelerated rates of wound healing, which were associated with down-regulation of key virulence factors, including M protein and the SpeB cysteine protease. These data demonstrate that GmPcides show considerable promise for treating S. pyogenes infections.
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Affiliation(s)
- Zongsen Zou
- Department of Molecular Microbiology, Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Pardeep Singh
- Department of Chemistry, Umeå University, SE-90187 Umeå, Sweden
| | - Jerome S. Pinkner
- Department of Molecular Microbiology, Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chloe L. P. Obernuefemann
- Department of Molecular Microbiology, Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Wei Xu
- Department of Molecular Microbiology, Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Taylor M. Nye
- Department of Molecular Microbiology, Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Karen W. Dodson
- Department of Molecular Microbiology, Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Scott J. Hultgren
- Department of Molecular Microbiology, Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael G. Caparon
- Department of Molecular Microbiology, Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, MO 63110, USA
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Meng J, Li M, Zheng Z, Sun Z, Yang S, Ouyang G, Wang Z, Zhou X. Application of natural-products repurposing strategy to discover novel FtsZ inhibitors: Bactericidal evaluation and the structure-activity relationship of sanguinarine and its analogs. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2024; 203:106016. [PMID: 39084807 DOI: 10.1016/j.pestbp.2024.106016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 06/21/2024] [Accepted: 07/02/2024] [Indexed: 08/02/2024]
Abstract
The novel bactericidal target-filamentous temperature-sensitive protein Z (FtsZ)-has drawn the attention of pharmacologists to address the emerging issues with drug/pesticide resistance caused by pathogenic bacteria. To enrich the structural diversity of FtsZ inhibitors, the antibacterial activity and structure-activity relationship (SAR) of natural sanguinarine and its analogs were investigated by using natural-products repurposing strategy. Notably, sanguinarine and chelerythrine exerted potent anti-Xanthomonas oryzae pv. oryzae (Xoo) activity, with EC50 values of 0.96 and 0.93 mg L-1, respectively, among these molecules. Furthermore, these two compounds could inhibit the GTPase activity of XooFtsZ, with IC50 values of 241.49 μM and 283.14 μM, respectively. An array of bioassays including transmission electron microscopy (TEM), fluorescence titration, and Fourier transform infrared spectroscopy (FT-IR) co-verified that sanguinarine and chelerythrine were potential XooFtsZ inhibitors that could interfere with the assembly of FtsZ filaments by inhibiting the GTPase hydrolytic ability of XooFtsZ protein. Additionally, the pot experiment suggested that chelerythrine and sanguinarine demonstrated excellent curative activity with values of 59.52% and 54.76%, respectively. Excitedly, these two natural compounds also showed outstanding druggability, validated by acceptable drug-like properties and low toxicity on rice. Overall, the results suggested that chelerythrine was a new and potential XooFtsZ inhibitor to develop new bactericide and provided important guiding values for rational drug design of FtsZ inhibitors. Notably, our findings provide a novel strategy to discover novel, promising and green bacterial compounds for the management of plant bacterial diseases.
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Affiliation(s)
- Jiao Meng
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Mei Li
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Zhicheng Zheng
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Zhaoju Sun
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Song Yang
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Guiping Ouyang
- School of Pharmaceutical Sciences, Guizhou University, Huaxi District, Guiyang, 550025, China.
| | - Zhenchao Wang
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China; School of Pharmaceutical Sciences, Guizhou University, Huaxi District, Guiyang, 550025, China.
| | - Xiang Zhou
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China.
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Avci FG. Unraveling bacterial stress responses: implications for next-generation antimicrobial solutions. World J Microbiol Biotechnol 2024; 40:285. [PMID: 39073503 PMCID: PMC11286680 DOI: 10.1007/s11274-024-04090-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 07/18/2024] [Indexed: 07/30/2024]
Abstract
The accelerated spread of antimicrobial-resistant bacteria has caused a serious health problem and rendered antimicrobial treatments ineffective. Innovative approaches are crucial to overcome the health threat posed by resistant pathogens and prevent the emergence of untreatable infections. Triggering stress responses in bacteria can diminish susceptibility to various antimicrobials by inducing resistance mechanisms. Therefore, a thorough understanding of stress response control, especially in relation to antimicrobial resistance, offers valuable perspectives for innovative and efficient therapeutic approaches to combat antimicrobial resistance. The aim of this study was to evaluate the stress responses of 8 different bacteria by analyzing reporter metabolites, around which significant alterations were observed, using a pathway-driven computational approach. For this purpose, the transcriptomic data that the bacterial pathogens were grown under 11 different stress conditions mimicking the human host environments were integrated with the genome-scale metabolic models of 8 pathogenic species (Enterococcus faecalis OG1R, Escherichia coli EPEC O127:H6 E2348/69, Escherichia coli ETEC H10407, Escherichia coli UPEC 536, Klebsiella pneumoniae MGH 78578, Pseudomonas aeruginosa PAO1, Staphylococcus aureus MRSA252, and Staphylococcus aureus MSSA476). The resulting reporter metabolites were enriched in multiple metabolic pathways, with cofactor biosynthesis being the most important. The results of this study will serve as a guide for the development of antimicrobial agents as they provide a first insight into potential drug targets.
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Affiliation(s)
- Fatma Gizem Avci
- Department of Bioengineering, Faculty of Engineering and Natural Sciences, Üsküdar University, Istanbul, Türkiye.
- Genetics of Prokaryotes, Faculty of Biology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany.
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Zhang Y, Luo M, Shi X, Li A, Zhou W, Yin Y, Wang H, Wong WL, Feng X, He Q. Pyrgos[ n]cages: Redefining antibacterial strategy against drug resistance. SCIENCE ADVANCES 2024; 10:eadp4872. [PMID: 39058779 PMCID: PMC11277403 DOI: 10.1126/sciadv.adp4872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024]
Abstract
Amid rising antibiotic resistance, the quest for advanced antibacterial agents to surpass microbial adaptation is paramount. This study introduces Pyrgos[n]cages (n = 1 to 4), pioneering multidecker cationic covalent organic cages engineered to combat drug-resistant bacteria via a dual-targeting approach. Synthesized through successive photocatalytic bromination and cage-forming reactions, these architectures stand out for their dense positive charge distribution, exceptional stability, and substantial rigidity. Pyrgos[n]cages exhibit potent bactericidal activity by disrupting bacterial membrane potential and binding to DNA. Notably, these structures show unparalleled success in eradicating both extracellular and intracellular drug-resistant pathogens in diverse infection scenarios, with antibacterial efficiency markedly increasing over 100-fold as the decker number rises from 1 to 3. This study provides an advance in antibacterial tactics and underscores the transformative potential of covalent organic cages in devising enduring countermeasures against antibiotic-resistant microbial threats.
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Affiliation(s)
- Yi Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Miaomiao Luo
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Xiangling Shi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Aimin Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Wei Zhou
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Yuyao Yin
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing 100044, China
| | - Hui Wang
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing 100044, China
| | - Wing-Leung Wong
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR 999077, China
| | - Xinxin Feng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Qing He
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
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6
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Hagiya H. Ethical consumption of antimicrobial agents: A proposal for a new concept in promoting antimicrobial stewardship. Am J Med Sci 2024:S0002-9629(24)01337-5. [PMID: 38969286 DOI: 10.1016/j.amjms.2024.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 06/23/2024] [Accepted: 07/01/2024] [Indexed: 07/07/2024]
Affiliation(s)
- Hideharu Hagiya
- Department of Infectious Diseases, Okayama University Hospital, Okayama, Japan.
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Zhu J, Xie R, Gao R, Zhao Y, Yodsanit N, Zhu M, Burger JC, Ye M, Tong Y, Gong S. Multimodal nanoimmunotherapy engages neutrophils to eliminate Staphylococcus aureus infections. NATURE NANOTECHNOLOGY 2024; 19:1032-1043. [PMID: 38632494 DOI: 10.1038/s41565-024-01648-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 03/12/2024] [Indexed: 04/19/2024]
Abstract
The increasing prevalence of antimicrobial resistance in Staphylococcus aureus necessitates alternative therapeutic approaches. Neutrophils play a crucial role in the fight against S. aureus but suffer from deficiencies in function leading to increased infection. Here we report a nanoparticle-mediated immunotherapy aimed at potentiating neutrophils to eliminate S. aureus. The nanoparticles consist of naftifine, haemoglobin (Hb) and a red blood cell membrane coating. Naftifine disrupts staphyloxanthin biosynthesis, Hb reduces bacterial hydrogen sulfide levels and the red blood cell membrane modifies bacterial lipid composition. Collectively, the nanoparticles can sensitize S. aureus to host oxidant killing. Furthermore, in the infectious microenvironment, Hb triggers lipid peroxidation in S. aureus, promoting neutrophil chemotaxis. Oxygen supplied by Hb can also significantly enhance the bactericidal capability of the recruited neutrophils by restoring neutrophil respiratory burst via hypoxia relief. This multimodal nanoimmunotherapy demonstrates excellent therapeutic efficacy in treating antimicrobial-resistant S. aureus persisters, biofilms and S. aureus-induced infection in mice.
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Affiliation(s)
- Jingcheng Zhu
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Ruosen Xie
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
- McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ruixuan Gao
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Yi Zhao
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Nisakorn Yodsanit
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Min Zhu
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Jacobus C Burger
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Mingzhou Ye
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Yao Tong
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Shaoqin Gong
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI, USA.
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA.
- McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA.
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Materials Science and Engineering, University of Wisconsin-Madison, Madison, WI, USA.
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Li Q, Fang W, Chen S, Li G, Jiang C, Zhuang Y, Li L, Liu P, Guo X, Hu G, Liu P, Gao X. Characterization of Escherichia coli pathogenicity and drug resistance in yolk peritonitis. Poult Sci 2024; 103:103814. [PMID: 38718538 PMCID: PMC11097060 DOI: 10.1016/j.psj.2024.103814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 05/19/2024] Open
Abstract
Yolk Peritonitis can lead to a rapid decline in egg production, which seriously affects the health of laying hens and the profitability of chicken farms. Escherichia coli (E. coli) is the most common cause of yolk peritonitis in laying hens. In this study, bacterial samples were collected from the ovaries and fallopian tubes of laying hens with suspected yolk peritonitis from a laying farm in Jiangsu Province, and their pathogenicity and drug resistance were investigated. Initially, morphological and biochemical detection methods were employed to isolate and identify the pathogenic bacteria. The results showed that a total of 16 strains of E. coli were isolated from laying hens with yolk peritonitis. Subsequently, the drug resistance and pathogenicity of a randomly selected E. coli strain were analyzed and predicted by genome sequencing technology, and the drug resistance of E. coli was verified by drug sensitivity test and PCR. Finally, the virulence was verified by infection experiment in mice. The study revealed that the egg-yolk peritonitis in laying hens was caused by E. coli infection, and the genome sequencing analysis revealed that the bacteria had multidrug resistance and high virulence. The drug susceptibility testing indicates that E. coli exhibited resistance to aminoglycosides, β-lactam, macrolides, fluoroquinolones, and sulfonamides. In this study, resistance genes including KdpE, aadA5, APH(3 ")-ID, APH(6)-ID, and TEM-1 were identified, and their expression levels varied across different stages of bacterial growth. The results of virulence analysis indicated a mortality rate of 50% in mice infected with E. coli at a concentration of 2.985 × 107 CFU/mL. E. coli infection resulted in damage to various tissues and organs in mice, with the intestinal tissue structure being the most severely affected. This study provides a reference for the study of drug resistance mechanisms in E. coli and provides valuable insights into the selection of drugs for the treatment of vitelline peritonitis.
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Affiliation(s)
- Qingqing Li
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Zhangshu 331200, PR China
| | - Weile Fang
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Zhangshu 331200, PR China
| | - Shupeng Chen
- Jiangxi Agricultural Engineering Vocational college, Nanchang 330045, PR China
| | - Guyue Li
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Zhangshu 331200, PR China
| | - Chenxi Jiang
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Zhangshu 331200, PR China
| | - Yu Zhuang
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Zhangshu 331200, PR China
| | - Lin Li
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Zhangshu 331200, PR China
| | - Pei Liu
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Zhangshu 331200, PR China
| | - Xiaoquan Guo
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Zhangshu 331200, PR China
| | - Guoliang Hu
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Zhangshu 331200, PR China
| | - Ping Liu
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Zhangshu 331200, PR China
| | - Xiaona Gao
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Zhangshu 331200, PR China.
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Enright AL, Heelan WJ, Ward RD, Peters JM. CRISPRi functional genomics in bacteria and its application to medical and industrial research. Microbiol Mol Biol Rev 2024; 88:e0017022. [PMID: 38809084 PMCID: PMC11332340 DOI: 10.1128/mmbr.00170-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024] Open
Abstract
SUMMARYFunctional genomics is the use of systematic gene perturbation approaches to determine the contributions of genes under conditions of interest. Although functional genomic strategies have been used in bacteria for decades, recent studies have taken advantage of CRISPR (clustered regularly interspaced short palindromic repeats) technologies, such as CRISPRi (CRISPR interference), that are capable of precisely modulating expression of all genes in the genome. Here, we discuss and review the use of CRISPRi and related technologies for bacterial functional genomics. We discuss the strengths and weaknesses of CRISPRi as well as design considerations for CRISPRi genetic screens. We also review examples of how CRISPRi screens have defined relevant genetic targets for medical and industrial applications. Finally, we outline a few of the many possible directions that could be pursued using CRISPR-based functional genomics in bacteria. Our view is that the most exciting screens and discoveries are yet to come.
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Affiliation(s)
- Amy L. Enright
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
- DOE Great Lakes Bioenergy Research Center University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - William J. Heelan
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ryan D. Ward
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
- DOE Great Lakes Bioenergy Research Center University of Wisconsin-Madison, Madison, Wisconsin, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jason M. Peters
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
- DOE Great Lakes Bioenergy Research Center University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, USA
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10
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Cuervo L, Méndez C, Salas JA, Olano C, Malmierca MG. Volatile communication in Actinobacteria: a language for secondary metabolism regulation. Microb Cell Fact 2024; 23:181. [PMID: 38890640 PMCID: PMC11186294 DOI: 10.1186/s12934-024-02456-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 06/08/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Volatile compounds are key elements in the interaction and communication between organisms at both interspecific and intraspecific levels. In complex bacterial communities, the emission of these fast-acting chemical messengers allows an exchange of information even at a certain distance that can cause different types of responses in the receiving organisms. The changes in secondary metabolism as a consequence of this interaction arouse great interest in the field of searching for bioactive compounds since they can be used as a tool to activate silenced metabolic pathways. Regarding the great metabolic potential that the Actinobacteria group presents in the production of compounds with attractive properties, we evaluated the reply the emitted volatile compounds can generate in other individuals of the same group. RESULTS We recently reported that volatile compounds released by different streptomycete species trigger the modulation of biosynthetic gene clusters in Streptomyces spp. which finally leads to the activation/repression of the production of secondary metabolites in the recipient strains. Here we present the application of this rationale in a broader bacterial community to evaluate volatiles as signaling effectors that drive the activation of biosynthesis of bioactive compounds in other members of the Actinobacteria group. Using cocultures of different actinobacteria (where only the volatile compounds reach the recipient strain) we were able to modify the bacterial secondary metabolism that drives overproduction (e.g., granaticins, actiphenol, chromomycins) and/or de novo production (e.g., collismycins, skyllamycins, cosmomycins) of compounds belonging to different chemical species that present important biological activities. CONCLUSIONS This work shows how the secondary metabolism of different Actinobacteria species can vary significantly when exposed in co-culture to the volatile compounds of other phylum-shared bacteria, these effects being variable depending on strains and culture media. This approach can be applied to the field of new drug discovery to increase the battery of bioactive compounds produced by bacteria that can potentially be used in treatments for humans and animals.
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Affiliation(s)
- Lorena Cuervo
- Department Functional Biology, University of Oviedo, 33006, Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A), University of Oviedo, 33006, Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33006, Oviedo, Spain
| | - Carmen Méndez
- Department Functional Biology, University of Oviedo, 33006, Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A), University of Oviedo, 33006, Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33006, Oviedo, Spain
| | - José A Salas
- Department Functional Biology, University of Oviedo, 33006, Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A), University of Oviedo, 33006, Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33006, Oviedo, Spain
| | - Carlos Olano
- Department Functional Biology, University of Oviedo, 33006, Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A), University of Oviedo, 33006, Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33006, Oviedo, Spain
| | - Mónica G Malmierca
- Department Functional Biology, University of Oviedo, 33006, Oviedo, Spain.
- University Institute of Oncology of Asturias (I.U.O.P.A), University of Oviedo, 33006, Oviedo, Spain.
- Health Research Institute of Asturias (ISPA), 33006, Oviedo, Spain.
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11
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Li Z, Baidoun R, Brown AC. Toxin-triggered liposomes for the controlled release of antibiotics to treat infections associated with the gram-negative bacterium, Aggregatibacter actinomycetemcomitans. Colloids Surf B Biointerfaces 2024; 238:113870. [PMID: 38555763 PMCID: PMC11148792 DOI: 10.1016/j.colsurfb.2024.113870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 03/14/2024] [Accepted: 03/20/2024] [Indexed: 04/02/2024]
Abstract
Antibiotic resistance has become an urgent threat to health care in recent years. The use of drug delivery systems provides advantages over conventional administration of antibiotics and can slow the development of antibiotic resistance. In the current study, we developed a toxin-triggered liposomal antibiotic delivery system, in which the drug release is enabled by the leukotoxin (LtxA) produced by the Gram-negative pathogen, Aggregatibacter actinomycetemcomitans. LtxA has previously been shown to mediate membrane disruption by promoting a lipid phase change in nonlamellar lipids, such as 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-methyl (N-methyl-DOPE). In addition, LtxA has been observed to bind strongly and nearly irreversibly to membranes containing large amounts of cholesterol. Here, we designed a liposomal delivery system composed of N-methyl-DOPE and cholesterol to take advantage of these interactions. Specifically, we hypothesized that liposomes composed of N-methyl-DOPE and cholesterol, encapsulating antibiotics, would be sensitive to LtxA, enabling controlled antibiotic release. We observed that liposomes composed of N-methyl-DOPE were sensitive to the presence of low concentrations of LtxA, and cholesterol increased the extent and kinetics of content release. The liposomes were stable under various storage conditions for at least 7 days. Finally, we showed that antibiotic release occurs selectively in the presence of an LtxA-producing strain of A. actinomycetemcomitans but not in the presence of a non-LtxA-expressing strain. Together, these results demonstrate that the designed liposomal vehicle enables toxin-triggered delivery of antibiotics to LtxA-producing strains of A. actinomycetemcomitans.
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Affiliation(s)
- Ziang Li
- Department of Chemical and Biomolecular Engineering, Lehigh University, 5 E Packer Ave, Bethlehem, PA 18015, USA
| | - Rani Baidoun
- Department of Chemical and Biomolecular Engineering, Lehigh University, 5 E Packer Ave, Bethlehem, PA 18015, USA
| | - Angela C Brown
- Department of Chemical and Biomolecular Engineering, Lehigh University, 5 E Packer Ave, Bethlehem, PA 18015, USA.
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12
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Best W, Ferrell M, Boris A, Heydarian N, Panlilio H, Rice CV. Acquisition of Resistance to PEGylated Branched Polyethylenimine Increases Pseudomonas Aeruginosa Susceptibility to Aminoglycosides. ChemMedChem 2024:e202300689. [PMID: 38806411 DOI: 10.1002/cmdc.202300689] [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: 12/06/2023] [Revised: 05/24/2024] [Accepted: 05/24/2024] [Indexed: 05/30/2024]
Abstract
PEGylated branched polyethylenimine (PEG-BPEI) has antibacterial and antibiofilm properties. Exposure to PEG-BPEI through serial passage leads to resistant P. aeruginosa strains. The minimum inhibitory concentration (MIC) of 600 Da BPEI and PEGylated 600 Da BPEI (PEG-BPEI) in the wild-type PAO1 strain is 16 μg/ml while, after 15 serial passages, the MIC increased to 1024 μg/mL. An additional 15 rounds of serial passage in the absence of BPEI or PEG-BPEI did not change the 1024 μg/mL MIC. Gentamicin, Neomycin, and Tobramycin, cationic antibiotics that inhibit protein synthesis, have a 16-32 fold reduction of MIC values in PEG350-BPEI resistant strains, suggesting increased permeation. The influx of these antibiotics occurs using a self-mediated uptake mechanism, suggesting changes to the outer membrane Data show that resistance causes changes in genes related to outer membrane lipopolysaccharide (LPS) assembly. Mutations were noted in the gene coding for the polymerase Wzy that participates in the assembly of the O-antigen region. Other mutations were noted with wbpE and wbpI of the Wbp pathway responsible for the enzymatic synthesis of ManNAc(3NAc)A in the LPS of P. aeruginosa. These changes suggest that an altered gene product could lead to PEG-BPEI resistance. Nevertheless, the increased susceptibility to aminoglycosides could prevent the emergence of PEG-BPEI resistant bacterial populations.
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Affiliation(s)
- William Best
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73069
| | - Maya Ferrell
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73069
| | - Andrew Boris
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73069
| | - Neda Heydarian
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73069
| | - Hannah Panlilio
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73069
| | - Charles V Rice
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73069
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13
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Naknaen A, Samernate T, Saeju P, Nonejuie P, Chaikeeratisak V. Nucleus-forming jumbophage PhiKZ therapeutically outcompetes non-nucleus-forming jumbophage Callisto. iScience 2024; 27:109790. [PMID: 38726363 PMCID: PMC11079468 DOI: 10.1016/j.isci.2024.109790] [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: 09/21/2023] [Revised: 03/21/2024] [Accepted: 04/16/2024] [Indexed: 05/12/2024] Open
Abstract
With the recent resurgence of phage therapy in modern medicine, jumbophages are currently under the spotlight due to their numerous advantages as anti-infective agents. However, most significant discoveries to date have primarily focused on nucleus-forming jumbophages, not their non-nucleus-forming counterparts. In this study, we compare the biological characteristics exhibited by two genetically diverse jumbophages: 1) the well-studied nucleus-forming jumbophage, PhiKZ; and 2) the newly discovered non-nucleus-forming jumbophage, Callisto. Single-cell infection studies further show that Callisto possesses different replication machinery, resulting in a delay in phage maturation compared to that of PhiKZ. The therapeutic potency of both phages was examined in vitro and in vivo, demonstrating that PhiKZ holds certain superior characteristics over Callisto. This research sheds light on the importance of the subcellular infection machinery and the organized progeny maturation process, which could potentially provide valuable insight in the future development of jumbophage-based therapeutics.
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Affiliation(s)
- Ampapan Naknaen
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Thanadon Samernate
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Panida Saeju
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Poochit Nonejuie
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
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14
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Hossain TJ. Methods for screening and evaluation of antimicrobial activity: A review of protocols, advantages, and limitations. Eur J Microbiol Immunol (Bp) 2024; 14:97-115. [PMID: 38648108 PMCID: PMC11097785 DOI: 10.1556/1886.2024.00035] [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: 03/13/2024] [Accepted: 04/05/2024] [Indexed: 04/25/2024] Open
Abstract
Infectious diseases pose a formidable global challenge, compounded by the emergence of antimicrobial resistance. Consequently, researchers are actively exploring novel antimicrobial compounds as potential solutions. This endeavor underscores the pivotal role of methods employed for screening and evaluating antimicrobial activity-a critical step in discovery and characterization of antimicrobial agents. While traditional techniques such as well-diffusion, disk-diffusion, and broth-dilution are commonly utilized in antimicrobial assays, they may encounter limitations concerning reproducibility and speed. Additionally, a diverse array of antimicrobial assays including cross-streaking, poisoned-food, co-culture, time-kill kinetics, resazurin assay, bioautography, etc., are routinely employed in antimicrobial evaluations. Advanced techniques such as flow-cytometry, impedance analysis, and bioluminescent technique may offer rapid and sensitive results, providing deeper insights into the impact of antimicrobials on cellular integrity. However, their higher cost and limited accessibility in certain laboratory settings may present challenges. This article provides a comprehensive overview of assays designed to characterize antimicrobial activity, elucidating their underlying principles, protocols, advantages, and limitations. The primary objective is to enhance understanding of the methodologies designed for evaluating antimicrobial agents in our relentless battle against infectious diseases. By selecting the appropriate antimicrobial testing method, researchers can discern suitable conditions and streamline the identification of effective antimicrobial agents.
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Affiliation(s)
- Tanim Jabid Hossain
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chattogram, Bangladesh
- Biochemistry and Pathogenesis of Microbes – BPM Unit, Laboratory for Health, Omics and Pathway Exploration (HOPE Research), Chattogram, Bangladesh
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15
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Habjan E, Schouten GK, Speer A, van Ulsen P, Bitter W. Diving into drug-screening: zebrafish embryos as an in vivo platform for antimicrobial drug discovery and assessment. FEMS Microbiol Rev 2024; 48:fuae011. [PMID: 38684467 PMCID: PMC11078164 DOI: 10.1093/femsre/fuae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 02/24/2024] [Accepted: 04/26/2024] [Indexed: 05/02/2024] Open
Abstract
The rise of multidrug-resistant bacteria underlines the need for innovative treatments, yet the introduction of new drugs has stagnated despite numerous antimicrobial discoveries. A major hurdle is a poor correlation between promising in vitro data and in vivo efficacy in animal models, which is essential for clinical development. Early in vivo testing is hindered by the expense and complexity of existing animal models. Therefore, there is a pressing need for cost-effective, rapid preclinical models with high translational value. To overcome these challenges, zebrafish embryos have emerged as an attractive model for infectious disease studies, offering advantages such as ethical alignment, rapid development, ease of maintenance, and genetic manipulability. The zebrafish embryo infection model, involving microinjection or immersion of pathogens and potential antibiotic hit compounds, provides a promising solution for early-stage drug screening. It offers a cost-effective and rapid means of assessing the efficacy, toxicity and mechanism of action of compounds in a whole-organism context. This review discusses the experimental design of this model, but also its benefits and challenges. Additionally, it highlights recently identified compounds in the zebrafish embryo infection model and discusses the relevance of the model in predicting the compound's clinical potential.
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Affiliation(s)
- Eva Habjan
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Location VU Medical Center,De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Gina K Schouten
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Location VU Medical Center,De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Alexander Speer
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Location VU Medical Center,De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Peter van Ulsen
- Section Molecular Microbiology of A-LIFE, Vrije Universiteit, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Wilbert Bitter
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Location VU Medical Center,De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
- Section Molecular Microbiology of A-LIFE, Vrije Universiteit, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
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16
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Chen JX, Dong HM, Cai YX, Tian LX, Yang ZC. Synthesis of narrow-spectrum anti-mycobacterial molecules without effect on the diversity of gut microbiota in mice based on the structure of rifampicin. Bioorg Chem 2024; 146:107282. [PMID: 38537334 DOI: 10.1016/j.bioorg.2024.107282] [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: 01/19/2024] [Revised: 02/25/2024] [Accepted: 03/10/2024] [Indexed: 04/13/2024]
Abstract
Rifampicin (RIF) is a broad-spectrum antimicrobial agent that is also a first-line drug for treating tuberculosis (TB). Based on the naphthyl ring structure of RIF this study synthesized 16 narrow-spectrum antimicrobial molecules that were specifically anti-Mycobacterium tuberculosis (Mtb). The most potent candidate was 2-((6-hydroxynaphthalen-2-yl) methylene) hydrazine-1-carbothioamide (compound 3c) with minimum inhibitory concentration (MIC) of 1 μg/mL against Mtb. Synergistic anti-Mtb test indicated that none of the combinations of 3c with the major anti-TB drugs are antagonistic. Consistent with RIF, compound 3c induced large amounts of reactive oxygen radicals (ROS) in the cells of Mtb. The killing kinetics of compound 3c and RIF are very similar. Furthermore, molecular docking showed that compound 3c was able to access the RIF binding pocket of the β subunit of Mtb RNA polymerase (RNAP). Experiments in mice showed that compound 3c increased the variety of intestinal flora in mice, while RIF significantly decreased the diversity of intestinal flora in mice. In addition, compound 3c is non-toxic to animal cells with a selection index (SI) much more than 10. The evidence from this study suggests that the further development of 3c could contribute to the development of novel drug for TB treatment.
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Affiliation(s)
- Jun-Xian Chen
- College of Pharmacy, Guizhou University, Guiyang 550025, China
| | - Hong-Mei Dong
- College of Pharmacy, Guizhou University, Guiyang 550025, China
| | - Yu-Xiang Cai
- College of Pharmacy, Guizhou University, Guiyang 550025, China
| | - Li-Xia Tian
- College of Pharmacy, Guizhou University, Guiyang 550025, China
| | - Zai-Chang Yang
- College of Pharmacy, Guizhou University, Guiyang 550025, China; State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, China.
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17
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Zheng EJ, Valeri JA, Andrews IW, Krishnan A, Bandyopadhyay P, Anahtar MN, Herneisen A, Schulte F, Linnehan B, Wong F, Stokes JM, Renner LD, Lourido S, Collins JJ. Discovery of antibiotics that selectively kill metabolically dormant bacteria. Cell Chem Biol 2024; 31:712-728.e9. [PMID: 38029756 PMCID: PMC11031330 DOI: 10.1016/j.chembiol.2023.10.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 08/13/2023] [Accepted: 10/30/2023] [Indexed: 12/01/2023]
Abstract
There is a need to discover and develop non-toxic antibiotics that are effective against metabolically dormant bacteria, which underlie chronic infections and promote antibiotic resistance. Traditional antibiotic discovery has historically favored compounds effective against actively metabolizing cells, a property that is not predictive of efficacy in metabolically inactive contexts. Here, we combine a stationary-phase screening method with deep learning-powered virtual screens and toxicity filtering to discover compounds with lethality against metabolically dormant bacteria and favorable toxicity profiles. The most potent and structurally distinct compound without any obvious mechanistic liability was semapimod, an anti-inflammatory drug effective against stationary-phase E. coli and A. baumannii. Integrating microbiological assays, biochemical measurements, and single-cell microscopy, we show that semapimod selectively disrupts and permeabilizes the bacterial outer membrane by binding lipopolysaccharide. This work illustrates the value of harnessing non-traditional screening methods and deep learning models to identify non-toxic antibacterial compounds that are effective in infection-relevant contexts.
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Affiliation(s)
- Erica J Zheng
- Program in Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Jacqueline A Valeri
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Ian W Andrews
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Aarti Krishnan
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Parijat Bandyopadhyay
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Melis N Anahtar
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Alice Herneisen
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02139, USA
| | - Fabian Schulte
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Brooke Linnehan
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Felix Wong
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jonathan M Stokes
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Lars D Renner
- Leibniz Institute of Polymer Research and the Max Bergmann Center of Biomaterials, 01062 Dresden, Germany
| | - Sebastian Lourido
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02139, USA
| | - James J Collins
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA.
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18
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Rijal R, Gomer RH. Gallein potentiates isoniazid's ability to suppress Mycobacterium tuberculosis growth. Front Microbiol 2024; 15:1369763. [PMID: 38690363 PMCID: PMC11060752 DOI: 10.3389/fmicb.2024.1369763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/01/2024] [Indexed: 05/02/2024] Open
Abstract
Mycobacterium tuberculosis (Mtb), the bacterium that causes tuberculosis (TB), can be difficult to treat because of drug tolerance. Increased intracellular polyphosphate (polyP) in Mtb enhances tolerance to antibiotics, and capsular polyP in Neisseria gonorrhoeae potentiates resistance to antimicrobials. The mechanism by which bacteria utilize polyP to adapt to antimicrobial pressure is not known. In this study, we found that Mtb adapts to the TB frontline antibiotic isoniazid (INH) by enhancing the accumulation of cellular, extracellular, and cell surface polyP. Gallein, a broad-spectrum inhibitor of the polyphosphate kinase that synthesizes polyP, prevents this INH-induced increase in extracellular and cell surface polyP levels. Gallein and INH work synergistically to attenuate Mtb's ability to grow in in vitro culture and within human macrophages. Mtb when exposed to INH, and in the presence of INH, gallein inhibits cell envelope formation in most but not all Mtb cells. Metabolomics indicated that INH or gallein have a modest impact on levels of Mtb metabolites, but when used in combination, they significantly reduce levels of metabolites involved in cell envelope synthesis and amino acid, carbohydrate, and nucleoside metabolism, revealing a synergistic effect. These data suggest that gallein represents a promising avenue to potentiate the treatment of TB.
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Affiliation(s)
- Ramesh Rijal
- Gomer Lab, Department of Biology, Texas A&M University, College Station, TX, United States
| | - Richard H. Gomer
- Gomer Lab, Department of Biology, Texas A&M University, College Station, TX, United States
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19
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Zhao X, Cao X, Qiu H, Liang W, Jiang Y, Wang Q, Wang W, Li C, Li Y, Han B, Tang K, Zhao L, Zhang X, Wang X, Liang H. Rational molecular design converting fascaplysin derivatives to potent broad-spectrum inhibitors against bacterial pathogens via targeting FtsZ. Eur J Med Chem 2024; 270:116347. [PMID: 38552428 DOI: 10.1016/j.ejmech.2024.116347] [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: 02/05/2024] [Revised: 03/06/2024] [Accepted: 03/17/2024] [Indexed: 04/21/2024]
Abstract
The filamentous temperature-sensitive mutant Z protein (FtsZ), a key player in bacterial cell division machinery, emerges as an attractive target to tackle the plight posed by the ever growing antibiotic resistance over the world. Therefore in this regard, agents with scaffold diversities and broad-spectrum antibacterial activity against Gram-positive and Gram-negative pathogens are highly needed. In this study, a new class of marine-derived fascaplysin derivatives has been designed and synthesized by Suzuki-Miyaura cross-coupling. Some compounds exhibited potent bactericidal activities against a panel of Gram-positive (MIC = 0.024-6.25 μg/mL) and Gram-negative (MIC = 1.56-12.5 μg/mL) bacteria including methicillin-resistant S. aureus (MRSA). They exerted their effects by dual action mechanism via disrupting the integrity of the bacterial cell membrane and targeting FtsZ protein. These compounds stimulated polymerization of FtsZ monomers and bundling of the polymers, and stabilized the resulting polymer network, thus leading to the dysfunction of FtsZ in cell division. In addition, these agents showed negligible hemolytic activity and low cytotoxicity to mammalian cells. The studies on docking and molecular dynamics simulations suggest that these inhibitors bind to the hydrophilic inter-domain cleft of FtsZ protein and the insights obtained in this study would facilitate the development of potential drugs with broad-spectrum bioactivities.
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Affiliation(s)
- Xing Zhao
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, China; Health Science Center, Ningbo University, Ningbo, 315211, China
| | - Xuanyu Cao
- Health Science Center, Ningbo University, Ningbo, 315211, China; Institute of Drug Discovery Technology, Ningbo University, Ningbo, 315211, China
| | - Hongda Qiu
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, China
| | - Weida Liang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, China
| | - Yinli Jiang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, China
| | - Qiang Wang
- Health Science Center, Ningbo University, Ningbo, 315211, China
| | - Weile Wang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, China
| | - Chengxi Li
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, China
| | - Yang Li
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, 315211, China
| | - Bowen Han
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, 315211, China
| | - Keqi Tang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, China
| | - Lingling Zhao
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, China
| | - Xuan Zhang
- Health Science Center, Ningbo University, Ningbo, 315211, China; Institute of Drug Discovery Technology, Ningbo University, Ningbo, 315211, China.
| | - Xiao Wang
- Health Science Center, Ningbo University, Ningbo, 315211, China.
| | - Hongze Liang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, China.
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20
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Ghosh S, Sen S, Jash M, Ghosh S, Jana A, Roy R, Mukherjee N, Mukherjee D, Sarkar J, Ghosh S. Synergistic Augmentation of Beta-Lactams: Exploring Quinoline-Derived Amphipathic Small Molecules as Antimicrobial Potentiators against Methicillin-Resistant Staphylococcus aureus. ACS Infect Dis 2024; 10:1267-1285. [PMID: 38442370 DOI: 10.1021/acsinfecdis.3c00696] [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: 03/07/2024]
Abstract
The escalation of bacterial resistance against existing therapeutic antimicrobials has reached a critical peak, leading to the rapid emergence of multidrug-resistant strains. Stringent pathways in novel drug discovery hinder our progress in this survival race. A promising approach to combat emerging antibiotic resistance involves enhancing conventional ineffective antimicrobials using low-toxicity small molecule adjuvants. Recent research interest lies in weak membrane-perturbing agents with unique cyclic hydrophobic components, addressing a significant gap in antimicrobial drug exploration. Our study demonstrates that quinoline-based amphipathic small molecules, SG-B-52 and SG-B-22, significantly reduce MICs of selected beta-lactam antibiotics (ampicillin and amoxicillin) against lethal methicillin-resistant Staphylococcus aureus (MRSA). Mechanistically, membrane perturbation, depolarization, and ROS generation drive cellular lysis and death. These molecules display minimal in vitro and in vivo toxicity, showcased through hemolysis assays, cell cytotoxicity analysis, and studies on albino Wistar rats. SG-B-52 exhibits impressive biofilm-clearing abilities against MRSA biofilms, proposing a strategy to enhance beta-lactam antibiosis and encouraging the development of potent antimicrobial potentiators.
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Affiliation(s)
- Surojit Ghosh
- Smart Healthcare Department, Interdisciplinary Research Platform, Indian Institute of Technology, Jodhpur, Rajasthan 342030, India
| | - Samya Sen
- iHUB Drishti Foundation, Indian Institute of Technology, Jodhpur, Rajasthan 342030, India
| | - Moumita Jash
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Jodhpur, Rajasthan 342030, India
| | - Satyajit Ghosh
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Jodhpur, Rajasthan 342030, India
| | - Aniket Jana
- Smart Healthcare Department, Interdisciplinary Research Platform, Indian Institute of Technology, Jodhpur, Rajasthan 342030, India
| | - Rajsekhar Roy
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Jodhpur, Rajasthan 342030, India
| | - Nabanita Mukherjee
- Smart Healthcare Department, Interdisciplinary Research Platform, Indian Institute of Technology, Jodhpur, Rajasthan 342030, India
| | - Dipro Mukherjee
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Jodhpur, Rajasthan 342030, India
| | - Jayita Sarkar
- Centre for Research and Development of Scientific Instruments (CRDSI), Indian Institute of Technology, Jodhpur, Rajasthan, 342030, India
| | - Surajit Ghosh
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Jodhpur, Rajasthan 342030, India
- Smart Healthcare Department, Interdisciplinary Research Platform, Indian Institute of Technology, Jodhpur, Rajasthan 342030, India
- iHUB Drishti Foundation, Indian Institute of Technology, Jodhpur, Rajasthan 342030, India
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21
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Manrique PD, Leus IV, López CA, Mehla J, Malloci G, Gervasoni S, Vargiu AV, Kinthada RK, Herndon L, Hengartner NW, Walker JK, Rybenkov VV, Ruggerone P, Zgurskaya HI, Gnanakaran S. Predicting permeation of compounds across the outer membrane of P. aeruginosa using molecular descriptors. Commun Chem 2024; 7:84. [PMID: 38609430 PMCID: PMC11015012 DOI: 10.1038/s42004-024-01161-y] [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: 10/04/2023] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
The ability Gram-negative pathogens have at adapting and protecting themselves against antibiotics has increasingly become a public health threat. Data-driven models identifying molecular properties that correlate with outer membrane (OM) permeation and growth inhibition while avoiding efflux could guide the discovery of novel classes of antibiotics. Here we evaluate 174 molecular descriptors in 1260 antimicrobial compounds and study their correlations with antibacterial activity in Gram-negative Pseudomonas aeruginosa. The descriptors are derived from traditional approaches quantifying the compounds' intrinsic physicochemical properties, together with, bacterium-specific from ensemble docking of compounds targeting specific MexB binding pockets, and all-atom molecular dynamics simulations in different subregions of the OM model. Using these descriptors and the measured inhibitory concentrations, we design a statistical protocol to identify predictors of OM permeation/inhibition. We find consistent rules across most of our data highlighting the role of the interaction between the compounds and the OM. An implementation of the rules uncovered in our study is shown, and it demonstrates the accuracy of our approach in a set of previously unseen compounds. Our analysis sheds new light on the key properties drug candidates need to effectively permeate/inhibit P. aeruginosa, and opens the gate to similar data-driven studies in other Gram-negative pathogens.
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Affiliation(s)
- Pedro D Manrique
- Physics Department, George Washington University, Washington, 20052, DC, USA.
| | - Inga V Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, 73019, OK, USA
| | - César A López
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, 87545, NM, USA
| | - Jitender Mehla
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, 73019, OK, USA
| | - Giuliano Malloci
- Department of Physics, University of Cagliari, Monserrato, 20052, CA, Italy
| | - Silvia Gervasoni
- Department of Physics, University of Cagliari, Monserrato, 20052, CA, Italy
| | - Attilio V Vargiu
- Department of Physics, University of Cagliari, Monserrato, 20052, CA, Italy
| | - Rama K Kinthada
- Department of Pharmacology and Physiology, Saint Louis University, St. Louis, 63103, MO, USA
| | - Liam Herndon
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, 87545, NM, USA
| | - Nicolas W Hengartner
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, 87545, NM, USA
| | - John K Walker
- Department of Pharmacology and Physiology, Saint Louis University, St. Louis, 63103, MO, USA
| | - Valentin V Rybenkov
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, 73019, OK, USA
| | - Paolo Ruggerone
- Department of Physics, University of Cagliari, Monserrato, 20052, CA, Italy
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, 73019, OK, USA
| | - S Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, 87545, NM, USA.
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22
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Yoon Y, Song S. Structural Insights into the Lipopolysaccharide Transport (Lpt) System as a Novel Antibiotic Target. J Microbiol 2024; 62:261-275. [PMID: 38816673 DOI: 10.1007/s12275-024-00137-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/15/2024] [Accepted: 04/15/2024] [Indexed: 06/01/2024]
Abstract
Lipopolysaccharide (LPS) is a critical component of the extracellular leaflet within the bacterial outer membrane, forming an effective physical barrier against environmental threats in Gram-negative bacteria. After LPS is synthesized and matured in the bacterial cytoplasm and the inner membrane (IM), LPS is inserted into the outer membrane (OM) through the ATP-driven LPS transport (Lpt) pathway, which is an energy-intensive process. A trans-envelope complex that contains seven Lpt proteins (LptA-LptG) is crucial for extracting LPS from the IM and transporting it across the periplasm to the OM. The last step in LPS transport involves the mediation of the LptDE complex, facilitating the insertion of LPS into the outer leaflet of the OM. As the Lpt system plays an essential role in maintaining the impermeability of the OM via LPS decoration, the interactions between these interconnected subunits, which are meticulously regulated, may be potential targets for the development of new antibiotics to combat multidrug-resistant Gram-negative bacteria. In this review, we aimed to provide an overview of current research concerning the structural interactions within the Lpt system and their implications to clarify the function and regulation of LPS transport in the overall process of OM biogenesis. Additionally, we explored studies on the development of therapeutic inhibitors of LPS transport, the factors that limit success, and future prospects.
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Affiliation(s)
- Yurim Yoon
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea
| | - Saemee Song
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea.
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23
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Sahoo R, Jadhav S, Nema V. Journey of technological advancements in the detection of antimicrobial resistance. J Formos Med Assoc 2024; 123:430-441. [PMID: 37598038 DOI: 10.1016/j.jfma.2023.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/19/2023] [Accepted: 08/07/2023] [Indexed: 08/21/2023] Open
Abstract
Increased uses rather an extensive misuse of antibiotics due to easy availability and easy access have resulted in antibiotic resistance as a global crisis. The speed of discovery of new antibiotics has slowed down recently. Therefore, there is a need to reduce the rate of increase in resistance against the presently available antibiotics, or else many infections may be left untreatable or difficult to be treated due to the high prevalence of resistance. The judicious use of broad-spectrum antibiotics can control the increase in resistance profile. Various techniques are presently being used for the detection of antibiotic resistance. Conventional phenotypic methods are preferred that are highly reliable but are much more time-consuming. The patients cannot spare more time as the infection keeps increasing. The results with genotypic methods are obtained within 24 h as compared to phenotypic methods. Hence, recent molecular methods like qPCR can be used for detection. In this review, we present an overview of various methods useful for the detection of antibiotic resistance, with emphasis on their advantages and limitations. The review also emphasizes qPCR to be the most preferred method out of all because of various advantageous factors.
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Affiliation(s)
- Rituparna Sahoo
- ICMR-National AIDS Research Institute, 73 G MIDC Bhosari, Pune, 411 026, India
| | - Sushama Jadhav
- ICMR-National AIDS Research Institute, 73 G MIDC Bhosari, Pune, 411 026, India
| | - Vijay Nema
- ICMR-National AIDS Research Institute, 73 G MIDC Bhosari, Pune, 411 026, India.
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24
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Möller AM, Vázquez-Hernández M, Kutscher B, Brysch R, Brückner S, Marino EC, Kleetz J, Senges CHR, Schäkermann S, Bandow JE, Narberhaus F. Common and varied molecular responses of Escherichia coli to five different inhibitors of the lipopolysaccharide biosynthetic enzyme LpxC. J Biol Chem 2024; 300:107143. [PMID: 38458396 PMCID: PMC10998244 DOI: 10.1016/j.jbc.2024.107143] [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: 01/10/2024] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 03/10/2024] Open
Abstract
A promising yet clinically unexploited antibiotic target in difficult-to-treat Gram-negative bacteria is LpxC, the key enzyme in the biosynthesis of lipopolysaccharides, which are the major constituents of the outer membrane. Despite the development of dozens of chemically diverse LpxC inhibitor molecules, it is essentially unknown how bacteria counteract LpxC inhibition. Our study provides comprehensive insights into the response against five different LpxC inhibitors. All compounds bound to purified LpxC from Escherichia coli. Treatment of E. coli with these compounds changed the cell shape and stabilized LpxC suggesting that FtsH-mediated proteolysis of the inactivated enzyme is impaired. LpxC inhibition sensitized E. coli to vancomycin and rifampin, which poorly cross the outer membrane of intact cells. Four of the five compounds led to an accumulation of lyso-phosphatidylethanolamine, a cleavage product of phosphatidylethanolamine, generated by the phospholipase PldA. The combined results suggested an imbalance in lipopolysaccharides and phospholipid biosynthesis, which was corroborated by the global proteome response to treatment with the LpxC inhibitors. Apart from LpxC itself, FabA and FabB responsible for the biosynthesis of unsaturated fatty acids were consistently induced. Upregulated compound-specific proteins are involved in various functional categories, such as stress reactions, nucleotide, or amino acid metabolism and quorum sensing. Our work shows that antibiotics targeting the same enzyme do not necessarily elicit identical cellular responses. Moreover, we find that the response of E. coli to LpxC inhibition is distinct from the previously reported response in Pseudomonas aeruginosa.
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Affiliation(s)
- Anna-Maria Möller
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | | | - Blanka Kutscher
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Raffael Brysch
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Simon Brückner
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Emily C Marino
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Julia Kleetz
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Christoph H R Senges
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Sina Schäkermann
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Julia E Bandow
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Franz Narberhaus
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany.
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25
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Fernandes PO, Dias ALT, Dos Santos Júnior VS, Sá Magalhães Serafim M, Sousa YV, Monteiro GC, Coutinho ID, Valli M, Verzola MMSA, Ottoni FM, Pádua RMD, Oda FB, Dos Santos AG, Andricopulo AD, da Silva Bolzani V, Mota BEF, Alves RJ, de Oliveira RB, Kronenberger T, Maltarollo VG. Machine Learning-Based Virtual Screening of Antibacterial Agents against Methicillin-Susceptible and Resistant Staphylococcus aureus. J Chem Inf Model 2024; 64:1932-1944. [PMID: 38437501 DOI: 10.1021/acs.jcim.4c00087] [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: 03/06/2024]
Abstract
The application of computer-aided drug discovery (CADD) approaches has enabled the discovery of new antimicrobial therapeutic agents in the past. The high prevalence of methicillin-resistantStaphylococcus aureus(MRSA) strains promoted this pathogen to a high-priority pathogen for drug development. In this sense, modern CADD techniques can be valuable tools for the search for new antimicrobial agents. We employed a combination of a series of machine learning (ML) techniques to select and evaluate potential compounds with antibacterial activity against methicillin-susceptible S. aureus (MSSA) and MRSA strains. In the present study, we describe the antibacterial activity of six compounds against MSSA and MRSA reference (American Type Culture Collection (ATCC)) strains as well as two clinical strains of MRSA. These compounds showed minimal inhibitory concentrations (MIC) in the range from 12.5 to 200 μM against the different bacterial strains evaluated. Our results constitute relevant proven ML-workflow models to distinctively screen for novel MRSA antibiotics.
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Affiliation(s)
- Philipe Oliveira Fernandes
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
| | - Anna Letícia Teotonio Dias
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
| | - Valtair Severino Dos Santos Júnior
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
| | - Mateus Sá Magalhães Serafim
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
| | - Yamara Viana Sousa
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
| | - Gustavo Claro Monteiro
- Departamento de Química Orgânica, Instituto de Química, Universidade Estadual Paulista (UNESP), Araraquara, São Paulo 14.800-900, Brazil
| | - Isabel Duarte Coutinho
- Departamento de Química Orgânica, Instituto de Química, Universidade Estadual Paulista (UNESP), Araraquara, São Paulo 14.800-900, Brazil
| | - Marilia Valli
- Departamento de Física e Ciência Interdisciplinar, Instituto de Física, Universidade de São Paulo (USP), São Carlos, São Paulo 13.563-120, Brazil
| | - Marina Mol Sena Andrade Verzola
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
| | - Flaviano Melo Ottoni
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
| | - Rodrigo Maia de Pádua
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
| | - Fernando Bombarda Oda
- Departamento de Fármacos e Medicamentos, Faculdade de Ciências Farmacêuticas, Universidade Estadual Paulista (UNESP), Araraquara 14.800-903, Brazil
| | - André Gonzaga Dos Santos
- Departamento de Fármacos e Medicamentos, Faculdade de Ciências Farmacêuticas, Universidade Estadual Paulista (UNESP), Araraquara 14.800-903, Brazil
| | - Adriano Defini Andricopulo
- Departamento de Física e Ciência Interdisciplinar, Instituto de Física, Universidade de São Paulo (USP), São Carlos, São Paulo 13.563-120, Brazil
| | - Vanderlan da Silva Bolzani
- Departamento de Química Orgânica, Instituto de Química, Universidade Estadual Paulista (UNESP), Araraquara, São Paulo 14.800-900, Brazil
| | - Bruno Eduardo Fernandes Mota
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
| | - Ricardo José Alves
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
| | - Renata Barbosa de Oliveira
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
| | - Thales Kronenberger
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Vinícius Gonçalves Maltarollo
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
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26
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Poulsen BE, Warrier T, Barkho S, Bagnall J, Romano KP, White T, Yu X, Kawate T, Nguyen PH, Raines K, Ferrara K, Golas A, Fitzgerald M, Boeszoermenyi A, Kaushik V, Serrano-Wu M, Shoresh N, Hung DT. "Multiplexed screen identifies a Pseudomonas aeruginosa -specific small molecule targeting the outer membrane protein OprH and its interaction with LPS". BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.16.585348. [PMID: 38559044 PMCID: PMC10980007 DOI: 10.1101/2024.03.16.585348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The surge of antimicrobial resistance threatens efficacy of current antibiotics, particularly against Pseudomonas aeruginosa , a highly resistant gram-negative pathogen. The asymmetric outer membrane (OM) of P. aeruginosa combined with its array of efflux pumps provide a barrier to xenobiotic accumulation, thus making antibiotic discovery challenging. We adapted PROSPECT 1 , a target-based, whole-cell screening strategy, to discover small molecule probes that kill P. aeruginosa mutants depleted for essential proteins localized at the OM. We identified BRD1401, a small molecule that has specific activity against a P. aeruginosa mutant depleted for the essential lipoprotein, OprL. Genetic and chemical biological studies identified that BRD1401 acts by targeting the OM β-barrel protein OprH to disrupt its interaction with LPS and increase membrane fluidity. Studies with BRD1401 also revealed an interaction between OprL and OprH, directly linking the OM with peptidoglycan. Thus, a whole-cell, multiplexed screen can identify species-specific chemical probes to reveal novel pathogen biology.
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27
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Dong S, Zhao Z, Tang H, Li G, Pan J, Gu X, Jiang J, Xiao L, Scapin G, Hunter DN, Yang D, Huang Y, Bennett F, Yang SW, Mandal M, Tang H, Su J, Tudge C, deJesus RK, Ding FX, Lombardo M, Hicks JD, Fischmann T, Mirza A, Dayananth P, Painter RE, Villafania A, Garlisi CG, Zhang R, Mayhood TW, Si Q, Li N, Amin RP, Bhatt B, Chen F, Regan CP, Regan H, Lin X, Wu J, Leithead A, Pollack SR, Scott JD, Nargund RP, Therien AG, Black T, Young K, Pasternak A. Structure Guided Discovery of Novel Pan Metallo-β-Lactamase Inhibitors with Improved Gram-Negative Bacterial Cell Penetration. J Med Chem 2024; 67:3400-3418. [PMID: 38387069 DOI: 10.1021/acs.jmedchem.3c01614] [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: 02/24/2024]
Abstract
The use of β-lactam (BL) and β-lactamase inhibitor combination to overcome BL antibiotic resistance has been validated through clinically approved drug products. However, unmet medical needs still exist for the treatment of infections caused by Gram-negative (GN) bacteria expressing metallo-β-lactamases. Previously, we reported our effort to discover pan inhibitors of three main families in this class: IMP, VIM, and NDM. Herein, we describe our work to improve the GN coverage spectrum in combination with imipenem and relebactam. This was achieved through structure- and property-based optimization to tackle the GN cell penetration and efflux challenges. A significant discovery was made that inhibition of both VIM alleles, VIM-1 and VIM-2, is essential for broad GN coverage, especially against VIM-producing P. aeruginosa. In addition, pharmacokinetics and nonclinical safety profiles were investigated for select compounds. Key findings from this drug discovery campaign laid the foundation for further lead optimization toward identification of preclinical candidates.
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Affiliation(s)
- Shuzhi Dong
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Zhiqiang Zhao
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Haiqun Tang
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Guoqing Li
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Jianping Pan
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Xin Gu
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Jinlong Jiang
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Li Xiao
- Computational and Structural Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Giovanna Scapin
- Computational and Structural Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - David N Hunter
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Dexi Yang
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Yuhua Huang
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Frank Bennett
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Shu-Wei Yang
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Mihirbaran Mandal
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Haifeng Tang
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Jing Su
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Clare Tudge
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | | | - Fa-Xiang Ding
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Matthew Lombardo
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Jacqueline D Hicks
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Thierry Fischmann
- Computational and Structural Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Asra Mirza
- Antibacterial/Antifungal, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Priya Dayananth
- Quantitative Biosciences, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Ronald E Painter
- Quantitative Biosciences, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Artjohn Villafania
- Quantitative Biosciences, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Charles G Garlisi
- Quantitative Biosciences, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Rumin Zhang
- Quantitative Biosciences, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Todd W Mayhood
- Quantitative Biosciences, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Qian Si
- Quantitative Biosciences, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Nianyu Li
- Nonclinical Drug Safety, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Rupesh P Amin
- Nonclinical Drug Safety, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Bhavana Bhatt
- Nonclinical Drug Safety, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Feifei Chen
- Nonclinical Drug Safety, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Christopher P Regan
- Nonclinical Drug Safety, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Hillary Regan
- Nonclinical Drug Safety, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Xinjie Lin
- Pharmacokinetics Pharmacodynamics and Drug Metabolism, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Jin Wu
- Pharmacokinetics Pharmacodynamics and Drug Metabolism, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Andrew Leithead
- Discovery Pharmaceutical Sciences, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Scott R Pollack
- Discovery Process Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Jack D Scott
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Ravi P Nargund
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Alex G Therien
- Exploratory Science Center, Merck & Co., Inc., Cambridge, Massachusetts 02139, United States
| | - Todd Black
- Antibacterial/Antifungal, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Katherine Young
- Antibacterial/Antifungal, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Alexander Pasternak
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
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28
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Zhang K, Limwongyut J, Moreland AS, Wei SCJ, Jim Jia Min T, Sun Y, Shin SJ, Kim SY, Jhun BW, Pethe K, Bazan GC. An anti-mycobacterial conjugated oligoelectrolyte effective against Mycobacterium abscessus. Sci Transl Med 2024; 16:eadi7558. [PMID: 38381846 DOI: 10.1126/scitranslmed.adi7558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 01/29/2024] [Indexed: 02/23/2024]
Abstract
Infections caused by nontuberculous mycobacteria have increased more than 50% in the past two decades and more than doubled in the elderly population. Mycobacterium abscessus (Mab), one of the most prevalent of these rapidly growing species, is intrinsically resistant to numerous antibiotics. Current standard-of-care treatments are not satisfactory, with high failure rate and notable adverse effects. We report here a potent anti-Mab compound from the flexible molecular framework afforded by conjugated oligoelectrolytes (COEs). A screen of structurally diverse, noncytotoxic COEs identified a lead compound, COE-PNH2, which was bactericidal against replicating, nonreplicating persisters and intracellular Mab.COE-PNH2 had low propensity for resistance development, with a frequency of resistance below 1.25 × 10-9 and showed no detectable resistance upon serial passaging. Mechanism of action studies were in line with COE-PNH2 affecting the physical and functional integrity of the bacterial envelope and disrupting the mycomembrane and associated essential bioenergetic pathways. Moreover, COE-PNH2 was well-tolerated and efficacious in a mouse model of Mab lung infection. This study highlights desirable in vitro and in vivo potency and safety index of this COE structure, which represents a promising anti-mycobacterial to tackle an unmet medical need.
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Affiliation(s)
- Kaixi Zhang
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, 117543 Singapore, Singapore
| | - Jakkarin Limwongyut
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, 117543 Singapore, Singapore
- Center for Polymers and Organic Solids, Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Alex S Moreland
- Center for Polymers and Organic Solids, Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Samuel Chan Jun Wei
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, 117543 Singapore, Singapore
| | - Tania Jim Jia Min
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, 117543 Singapore, Singapore
| | - Yan Sun
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, 636921 Singapore, Singapore
| | - Sung Jae Shin
- Department of Microbiology, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Su-Young Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, South Korea
| | - Byung Woo Jhun
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, South Korea
| | - Kevin Pethe
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, 636921 Singapore, Singapore
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), 60 Nanyang Drive, 639798 Singapore, Singapore
- National Centre for Infectious Diseases (NCID), 16 Jalan Tan Tock Seng, 308442 Singapore, Singapore
| | - Guillermo C Bazan
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, 117543 Singapore, Singapore
- Center for Polymers and Organic Solids, Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), 60 Nanyang Drive, 639798 Singapore, Singapore
- Institute for Functional Intelligent Materials (I-FIM), National University of Singapore, 117544 Singapore, Singapore
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29
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Attal H, Huang Z, Kuan WS, Weng Y, Tan HY, Seow E, Peng LL, Lim HC, Chow A. N-of-1 Trials of Antimicrobial Stewardship Interventions to Optimize Antibiotic Prescribing for Upper Respiratory Tract Infection in Emergency Departments: Protocol for a Quasi-Experimental Study. JMIR Res Protoc 2024; 13:e50417. [PMID: 38381495 PMCID: PMC10918537 DOI: 10.2196/50417] [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: 06/30/2023] [Revised: 01/27/2024] [Accepted: 01/29/2024] [Indexed: 02/22/2024] Open
Abstract
BACKGROUND Antimicrobial stewardship programs attempting to optimize antibiotic therapy and clinical outcomes mainly focus on inpatient and outpatient settings. The lack of antimicrobial stewardship program studies in the emergency department (ED) represents a gap in tackling the problem of antimicrobial resistance as EDs treat a substantial number of upper respiratory tract infection cases throughout the year. OBJECTIVE We intend to implement two evidence-based interventions: (1) patient education and (2) providing physician feedback on their prescribing rates. We will incorporate evidence from a literature review and contextualizing the interventions based on findings from a local qualitative study. METHODS Our study uses a quasi-experimental design to evaluate the effects of interventions over time in the EDs of 4 public hospitals in Singapore. We will include an initial control period of 18 months. In the next 6 months, we will randomize 2 EDs to receive 1 intervention (ie, patient education) and the other 2 EDs to receive the alternative intervention (ie, physician feedback). All EDs will receive the second intervention in the subsequent 6 months on top of the ongoing intervention. Data will be collected for another 6 months to assess the persistence of the intervention effects. The information leaflets will be handed to patients at the EDs before they consult with the physician, while feedback to individual physicians by senior doctors is in the form of electronic text messages. The feedback will contain the physicians' antibiotic prescribing rate compared with the departments' overall antibiotic prescribing rate and a bite-size message on good antibiotic prescribing practices. RESULTS We will analyze the data using segmented regression with difference-in-difference estimation to account for concurrent cluster comparisons. CONCLUSIONS Our proposed study assesses the effectiveness of evidence-based, context-specific interventions to optimize antibiotic prescribing in EDs. These interventions are aligned with Singapore's national effort to tackle antimicrobial resistance and can be scaled up if successful. TRIAL REGISTRATION ClinicalTrials.gov NCT05451863; https://clinicaltrials.gov/study/NCT05451836. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID) DERR1-10.2196/50417.
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Affiliation(s)
- Hersh Attal
- Accident & Emergency Department, Changi General Hospital, Singapore, Singapore
| | - Zhilian Huang
- Department of Preventive and Population Medicine, Office of Clinical Epidemiology, Analytics, and Knowledge, Tan Tock Seng Hospital, Singapore, Singapore
| | - Win Sen Kuan
- Department of Emergency Medicine, National University Hospital, Singapore, Singapore
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yanyi Weng
- Department of Emergency Medicine, Tan Tock Seng Hospital, Singapore, Singapore
| | - Hann Yee Tan
- Acute and Emergency Care Department, Khoo Teck Puat Hospital, Singapore, Singapore
| | - Eillyne Seow
- Acute and Emergency Care Department, Khoo Teck Puat Hospital, Singapore, Singapore
| | - Li Lee Peng
- Department of Emergency Medicine, National University Hospital, Singapore, Singapore
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Hoon Chin Lim
- Accident & Emergency Department, Changi General Hospital, Singapore, Singapore
| | - Angela Chow
- Department of Preventive and Population Medicine, Office of Clinical Epidemiology, Analytics, and Knowledge, Tan Tock Seng Hospital, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
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30
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Blanco-Blanco J, Bravo M, Simón I, Fernández-Llario P, Fajardo-Olivares M, Fernández-Calderón MC, Cerrato R. Synergistic Activity of Ingulados Bacteria with Antibiotics against Multidrug-Resistant Pathogens. Antibiotics (Basel) 2024; 13:200. [PMID: 38534635 DOI: 10.3390/antibiotics13030200] [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: 01/15/2024] [Revised: 02/16/2024] [Accepted: 02/17/2024] [Indexed: 03/28/2024] Open
Abstract
Antimicrobial resistance is a critical challenge due to the overuse of conventional antimicrobials, and alternative solutions are urgently needed. This study investigates the efficacy of compounds derived from lactic acid bacteria (LAB) fermentation combined with antibiotics against multidrug-resistant pathogens isolated from clinical cases in a hospital setting. Strains of Escherichia coli, Klebsiella pneumoniae, and Enterococcus faecium and faecalis were isolated and selected from blood, respiratory, and urine samples. They were tested against the fermentation products from the Ingulados LAB collection (BAL5, BAL6, BAL8, BAL13, and BAL16), recognized for their antimicrobial efficacy against veterinary pathogens. The activity against multidrug-resistant (MDR) pathogens was evaluated initially, followed by synergy tests using checkerboard assays and subsequent analysis. Bioinformatic assessments and supernatant treatments were performed to characterize the nature of the compounds responsible for the antimicrobial activity. Notably, BAL16 exhibited significant growth inhibition against multidrug-resistant E. faecium. Synergy tests highlighted its combined activity with tetracycline through FICI and surface analysis and bioinformatic analysis unveiled the protein fraction containing bacteriocins as the underlying mechanism. This study highlights BAL16 fermentation products potential as valuable antimicrobial agents against MDR E. faecium infections, attributed to bacteriocins. Further in-depth studies are necessary for complete bacteriocin characterization.
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Affiliation(s)
- Javier Blanco-Blanco
- Ingulados, S.L., 10004 Cáceres, Spain
- Biosanitary Research University Institute of Extremadura (INUBE), 06080 Badajoz, Spain
| | | | | | | | | | - María Coronada Fernández-Calderón
- Biosanitary Research University Institute of Extremadura (INUBE), 06080 Badajoz, Spain
- Department of Biomedical Sciences, University of Extremadura, 06006 Badajoz, Spain
- Networking Biomedical Research Centre on Bioenineering, Biomaterials and Nanomedicine (CIBER-BBN), 28029 Madrid, Spain
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31
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Mohamed MA, Abouzied AS, Reyad A, Sayed Abdelsalam Zaki ME, Abdelgawad FE, Al-Humaidi JY, Gomha SM. Novel terpyridines as Staphylococcus aureus gyrase inhibitors: efficient synthesis and antibacterial assessment via solvent-drop grinding. Future Med Chem 2024; 16:205-220. [PMID: 38230640 DOI: 10.4155/fmc-2023-0278] [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: 09/24/2023] [Accepted: 11/28/2023] [Indexed: 01/18/2024] Open
Abstract
Aim: This study was designed to synthesize a novel series of terpyridines with potential antibacterial properties, targeting multidrug resistance. Materials & methods: Terpyridines (4a-h and 6a-c) were synthesized via a one-pot multicomponent reaction using 2,6-diacetylpyridines, benzaldehyde derivatives and malononitrile or ethyl 2-cyanoacetate. The reactions, conducted under grinding conditions with glacial acetic acid, produced high-yield compounds, confirmed by spectroscopic data. Results: The synthesized terpyridines exhibited potent antibacterial activity. Notably, compounds 4d and 4h demonstrated significant inhibition zones against Staphylococcus aureus and Bacillus subtilis, outperforming ciprofloxacin. Conclusion: Molecular docking studies highlighted compounds 4d, 4h and 6c as having strong binding affinity to DNA gyrase B, correlating with their robust antibacterial activity, suggesting their potential as effective agents against multidrug-resistant bacterial strains.
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Affiliation(s)
- Mahmoud Abdalla Mohamed
- Technology of Textile Department, Faculty of Technology and Education, Beni-Suef University, Beni-Suef, Egypt
- Chemistry Department, Faculty of Science and Humanity study, Afif, Shaqra University, Saudi Arabia
| | - Amr Salah Abouzied
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, Hail, 81442, Saudi Arabia
- Department of Pharmaceutical Chemistry, National Organization for Drug Control & Research, Giza, 12311, Egypt
| | - Amany Reyad
- Botany Department, Faculty of Science, Fayoum University, Fayoum, 63514, Egypt
| | | | - Fathy Elsayed Abdelgawad
- Department of Chemistry, Faculty of Science, Islamic University of Madinah, Madinah 42351, Saudi Arabia
| | - Jehan Yahya Al-Humaidi
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, P.O. BOX 84428, Riyadh 11671, Saudi Arabia
| | - Sobhi Mohamed Gomha
- Department of Chemistry, Faculty of Science, Islamic University of Madinah, Madinah 42351, Saudi Arabia
- Department of Chemistry, Faculty of Science, Cairo University, Giza, 12613, Egypt
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32
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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: 29] [Impact Index Per Article: 29.0] [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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33
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Stoorza AM, Duerfeldt AS. Guiding the Way: Traditional Medicinal Chemistry Inspiration for Rational Gram-Negative Drug Design. J Med Chem 2024; 67:65-80. [PMID: 38134355 PMCID: PMC11342810 DOI: 10.1021/acs.jmedchem.3c01831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
The discovery and development of small-molecule therapeutics effective against Gram-negative pathogens are highly challenging tasks. Most compounds that are active in biochemical settings fail to exhibit whole-cell activity. The major reason for this lack of activity is the effectiveness of bacterial cell envelopes as permeability barriers. These barriers originate from the nutrient-selective outer membranes, which act synergistically with polyspecific efflux pumps. Guiding principles to enable rational optimization of small molecules for efficient penetration and intracellular accumulation in Gram-negative bacteria would have a transformative impact on the discovery and design of chemical probes and therapeutics. In this Perspective, we draw on inspiration from traditional medicinal chemistry approaches for eukaryotic drug design to present a broader call for action in developing comparable approaches for Gram-negative bacteria.
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Affiliation(s)
- Alexis M Stoorza
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Adam S Duerfeldt
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55414, United States
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34
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Rijal R, Gomer RH. Gallein and isoniazid act synergistically to attenuate Mycobacterium tuberculosis growth in human macrophages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.10.574965. [PMID: 38260681 PMCID: PMC10802476 DOI: 10.1101/2024.01.10.574965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Mycobacterium tuberculosis (Mtb), the bacterium that causes tuberculosis (TB), can be difficult to treat because of drug resistance. Increased intracellular polyphosphate (polyP) in Mtb enhances resistance to antibiotics, and capsular polyP in Neisseria gonorrhoeae potentiates resistance to antimicrobials. The mechanism by which bacteria utilize polyP to adapt to antimicrobial pressure is not known. In this study, we found that Mtb adapts to the TB frontline antibiotic isoniazid (INH) by enhancing the accumulation of cellular, extracellular, and cell surface polyP. Gallein, a broad-spectrum inhibitor of the polyphosphate kinase that synthesizes polyP, prevents this INH-induced increase in extracellular and cell surface polyP levels. Gallein and INH work synergistically to attenuate Mtb's ability to grow in in vitro culture and within human macrophages. Mtb when exposed to INH, and in the presence of INH, gallein inhibits cell envelope formation in most but not all Mtb cells. Metabolomics indicated that INH or gallein have a modest impact on levels of Mtb metabolites, but when used in combination, they significantly reduce levels of metabolites involved in cell envelope synthesis and amino acid, carbohydrate, and nucleoside metabolism, revealing a synergistic effect. These data suggest that gallein represents a promising avenue to potentiate the treatment of TB.
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Affiliation(s)
- Ramesh Rijal
- Department of Biology, Texas A&M University, College Station, TX 77843-3474, USA
| | - Richard H. Gomer
- Department of Biology, Texas A&M University, College Station, TX 77843-3474, USA
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35
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Zou Z, Obernuefemann CLP, Singh P, Pinkner JS, Xu W, Nye TM, Dodson KW, Almqvist F, Hultgren SJ, Caparon MG. Dihydrothiazolo ring-fused 2-pyridone antimicrobial compounds treat Streptococcus pyogenes skin and soft tissue infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.02.573960. [PMID: 38260261 PMCID: PMC10802287 DOI: 10.1101/2024.01.02.573960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
We have developed GmPcides from a peptidomimetic dihydrothiazolo ring-fused 2-pyridone scaffold that have antimicrobial activities against a broad-spectrum of Gram-positive pathogens. Here we examine the treatment efficacy of GmPcides using skin and soft tissue infection (SSTI) and biofilm formation models by Streptococcus pyogenes. Screening our compound library for minimal inhibitory (MIC) and minimal bactericidal (MBC) concentrations identified GmPcide PS757 as highly active against S. pyogenes. Treatment of S. pyogenes biofilm with PS757 revealed robust efficacy against all phases of biofilm formation by preventing initial biofilm development, ceasing biofilm maturation and eradicating mature biofilm. In a murine model of S. pyogenes SSTI, subcutaneous delivery of PS757 resulted in reduced levels of tissue damage, decreased bacterial burdens and accelerated rates of wound-healing, which were associated with down-regulation of key virulence factors, including M protein and the SpeB cysteine protease. These data demonstrate that GmPcides show considerable promise for treating S. pyogenes infections.
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Affiliation(s)
- Zongsen Zou
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Chloe L P Obernuefemann
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Pardeep Singh
- Department of Chemistry, Umeå University, SE-90187 Umeå, Sweden
| | - Jerome S Pinkner
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Wei Xu
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Taylor M Nye
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Karen W Dodson
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | | | - Scott J Hultgren
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Michael G Caparon
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri 63110, United States
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36
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Rana N, Grover P, Singh H. Recent Developments and Future Perspectives of Purine Derivatives as a Promising Scaffold in Drug Discovery. Curr Top Med Chem 2024; 24:541-579. [PMID: 38288806 DOI: 10.2174/0115680266290152240110074034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/17/2023] [Accepted: 12/27/2023] [Indexed: 05/31/2024]
Abstract
Numerous purine-containing compounds have undergone extensive investigation for their medical efficacy across various diseases. The swift progress in purine-based medicinal chemistry has brought to light the therapeutic capabilities of purine-derived compounds in addressing challenging medical conditions. Defined by a heterocyclic ring comprising a pyrimidine ring linked with an imidazole ring, purine exhibits a diverse array of therapeutic attributes. This review systematically addresses the multifaceted potential of purine derivatives in combating various diseases, including their roles as anticancer agents, antiviral compounds (anti-herpes, anti-HIV, and anti-influenzae), autoimmune and anti-inflammatory agents, antihyperuricemic and anti-gout solutions, antimicrobial agents, antitubercular compounds, anti-leishmanial agents, and anticonvulsants. Emphasis is placed on the remarkable progress made in developing purine-based compounds, elucidating their significant target sites. The article provides a comprehensive exploration of developments in both natural and synthetic purines, offering insights into their role in managing a diverse range of illnesses. Additionally, the discussion delves into the structure-activity relationships and biological activities of the most promising purine molecules. The intriguing capabilities revealed by these purine-based scaffolds unequivocally position them at the forefront of drug candidate development. As such, this review holds potential significance for researchers actively involved in synthesizing purine-based drug candidates, providing a roadmap for the continued advancement of this promising field.
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Affiliation(s)
- Neha Rana
- School of Pharmacy (SOP), Noida International University, Yamuna Expressway, Gautam Budh Nagar, 203201, India
| | - Parul Grover
- KIET School of Pharmacy, KIET Group of Institutions, Delhi-NCR, Ghaziabad, 201206, India
| | - Hridayanand Singh
- Dr. K. N. Modi Institute of Pharmaceutical Education and Research, Modinagar, 201204, Uttar Pradesh, India
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37
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Ramalingam S, Chandrasekar MJN, Krishnan GGN, Nanjan MJ. Plant-based Natural Products as inhibitors for Efflux Pumps to Reverse Multidrug Resistance in Staphylococcus aureus: A Mini Review. Mini Rev Med Chem 2024; 24:272-288. [PMID: 37038687 DOI: 10.2174/1389557523666230406092128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 02/09/2023] [Accepted: 02/22/2023] [Indexed: 04/12/2023]
Abstract
Wounds provide a favourable site for microbial infection. Wound infection makes the healing more complex and does not proceed in an orchestrated manner leading to the chronic wound. Clinically infected wounds require proper antimicrobial therapy. Broad-spectrum antibiotics are usually prescribed first before going to targeted therapy. The current conventional mode of therapy mainly depends on the use of antibiotics topically or systemically. Repeated and prolonged use of antibiotics, however, leads to multidrug resistance. Staphylococcus aureus is the most common multidrugresistant microorganism found in wounds. It effectively colonizes the wound and produces many toxins, thereby reducing the host immune response and causing recurrent infection, thus making the wound more complex. The overexpression of efflux pumps is one of the major reasons for the emergence of multidrug resistance. Inhibition of efflux pumps is, therefore, a potential strategy to reverse this resistance. The effective therapy to overcome this antibiotic resistance is to use combination therapy, namely the combination of an inhibitor, and a non-antibiotic compound with an antibiotic for their dual function. Many synthetic efflux pump inhibitors to treat wound infections are still under clinical trials. In this connection, several investigations have been carried out on plant-based natural products as multidrug resistance-modifying agents as they are believed to be safe, inexpensive and suitable for chronic wound infections.
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Affiliation(s)
- Shalini Ramalingam
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Nilgiris, Tamil Nadu, 643001, India
| | - Moola Joghee Nanjan Chandrasekar
- School of Life Sciences, JSS Academy of Higher Education & Research (Ooty Campus), Longwood, Mysuru Road, Ooty, The Nilgiris, Tamil Nadu, 643001, India
| | - Ganesh G N Krishnan
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Nilgiris, Tamil Nadu, 643001, India
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38
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Wang Y, Kong Q, Zhang Q, Ma T, An Y, Zhou YJ, Zhang X, Cao B. BPI 23-Fcγ alleviates lethal multi-drug-resistant Acinetobacter baumannii infection by enhancing bactericidal activity and orchestrating neutrophil function. Int J Antimicrob Agents 2024; 63:107002. [PMID: 37838150 DOI: 10.1016/j.ijantimicag.2023.107002] [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: 03/16/2023] [Revised: 09/22/2023] [Accepted: 10/01/2023] [Indexed: 10/16/2023]
Abstract
Antibiotic resistance has become a major threat, contributing significantly to morbidity and mortality globally. Administering non-antibiotic therapy, such as antimicrobial peptides, is one potential strategy for effective treatment of multi-drug-resistant Gram-negative bacterial infections. Bactericidal/permeability-increasing protein (BPI) derived from neutrophils has bactericidal and endotoxin-neutralizing activity. However, the protective roles and mechanisms of BPI in multi-drug-resistant bacterial infections have not been fully elucidated. In this study, a chimeric BPI23-Fcγ recombined protein comprising the functional N terminus of BPI and Fcγ was constructed and expressed by adenovirus vector 5 (Ad5). Ad5-BPI23-Fcγ or recombinant BPI23-Fcγ protein significantly improved the survival of mice with pneumonia induced by a minimal lethal dose of multi-drug-resistant Acinetobacter baumannii or Klebsiella pneumoniae by ameliorating lung pathology and reducing pro-inflammatory cytokines. Transfection with Ad5-BPI23-Fcγ significantly decreased the bacterial load and endotoxaemia, which was associated with enhanced bactericidal ability and elevated the phagocytic activity of neutrophils in vitro and in vivo. In addition, Ad5-BPI23-Fcγ transfection significantly increased the recruitment of neutrophils to lung, increased the proportion and number of neutrophils in peripheral blood, and promoted the maturation of bone marrow (BM) neutrophils after drug-resistant A. baumannii infection. BPI23-Fcγ and neutrophils synergistically enhanced bactericidal activity and decreased pro-inflammatory cytokines. These results demonstrated that the chimeric BPI23-Fcγ protein protected mice from pneumonia induced by multi-drug-resistant A. baumannii infection by direct bactericidal effects and promotion of neutrophil recruitment, phagocytosis and maturation. Chimeric BPI23-Fcγ may be a promising candidate as a non-antibiotic biological agent for multi-drug-resistant A. baumannii infection.
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Affiliation(s)
- Yang Wang
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Capital Medical University, Beijing, China
| | - Qingli Kong
- Department of Immunology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Qi Zhang
- Department of Immunology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Tianxiao Ma
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Capital Medical University, Beijing, China
| | - Yunqing An
- Department of Immunology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Yu-Jie Zhou
- Department of Immunology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Xulong Zhang
- Department of Immunology, School of Basic Medical Sciences, Capital Medical University, Beijing, China; Beijing Key Laboratory of Cancer Invasion and Metastasis Research, School of Basic Medical Sciences, Capital Medical University, Beijing, China.
| | - Bin Cao
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Capital Medical University, Beijing, China; Department of Pulmonary and Critical Care Medicine, Centre of Respiratory Medicine, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, National Clinical Research Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China; Tsinghua University School of Medicine, Beijing, China; Changping Laboratory, Beijing, China.
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39
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Renard S, Versluys S, Taillier T, Dubarry N, Leroi-Geissler C, Rey A, Cornaire E, Sordello S, Carry JCB, Angouillant-Boniface O, Gouyon T, Thompson F, Lebourg G, Certal V, Balazs L, Arranz E, Doerflinger G, Bretin F, Gervat V, Brohan E, Kraft V, Boulenc X, Ducelier C, Bacqué E, Couturier C. Optimization of the Antibacterial Spectrum and the Developability Profile of the Novel-Class Natural Product Corramycin. J Med Chem 2023; 66:16869-16887. [PMID: 38088830 DOI: 10.1021/acs.jmedchem.3c01564] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Corramycin 1 is a novel zwitterionic antibacterial peptide isolated from a culture of the myxobacterium Corallococcus coralloides. Though Corramycin displayed a narrow spectrum and modest MICs against sensitive bacteria, its ADMET and physchem profile as well as its high tolerability in mice along with an outstanding in vivo efficacy in an Escherichia coli septicemia mouse model were promising and prompted us to embark on an optimization program aiming at enlarging the spectrum and at increasing the antibacterial activities by modulating membrane permeability. Scanning the peptidic moiety by the Ala-scan strategy followed by key stabilization and introduction of groups such as a primary amine or siderophore allowed us to enlarge the spectrum and increase the overall developability profile. The optimized Corramycin 28 showed an improved mouse IV PK and a broader spectrum with high potency against key Gram-negative bacteria that translated into excellent efficacy in several in vivo mouse infection models.
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Affiliation(s)
| | | | - Thomas Taillier
- Evotec, 1541, Avenue Marcel Mérieux, Marcy L'Etoile 69280, France
| | | | | | - Astrid Rey
- Evotec, 1541, Avenue Marcel Mérieux, Marcy L'Etoile 69280, France
| | - Emilie Cornaire
- Evotec, 1541, Avenue Marcel Mérieux, Marcy L'Etoile 69280, France
| | | | | | | | - Thierry Gouyon
- Sanofi, 13 Quai Jules Guesde, Vitry-sur-Seine 94403, France
| | | | - Gilles Lebourg
- Sanofi, 13 Quai Jules Guesde, Vitry-sur-Seine 94403, France
| | - Victor Certal
- Sanofi, 13 Quai Jules Guesde, Vitry-sur-Seine 94403, France
| | - Laszlo Balazs
- Sanofi, 13 Quai Jules Guesde, Vitry-sur-Seine 94403, France
| | - Esther Arranz
- Sanofi, 13 Quai Jules Guesde, Vitry-sur-Seine 94403, France
| | | | | | - Vincent Gervat
- Sanofi, 13 Quai Jules Guesde, Vitry-sur-Seine 94403, France
| | - Eric Brohan
- Sanofi, 13 Quai Jules Guesde, Vitry-sur-Seine 94403, France
| | - Volker Kraft
- Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, Frankfurt am Main 65926, Germany
| | | | - Cécile Ducelier
- Sanofi, 1 Avenue Pierre Brossolette, Chilly-Mazarin 91385, France
| | - Eric Bacqué
- Evotec, 1541, Avenue Marcel Mérieux, Marcy L'Etoile 69280, France
| | - Cédric Couturier
- Evotec, 1541, Avenue Marcel Mérieux, Marcy L'Etoile 69280, France
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40
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Scheeder A, Brockhoff M, Ward EN, Kaminski Schierle GS, Mela I, Kaminski CF. Molecular Mechanisms of Cationic Fusogenic Liposome Interactions with Bacterial Envelopes. J Am Chem Soc 2023; 145:28240-28250. [PMID: 38085801 PMCID: PMC10755748 DOI: 10.1021/jacs.3c11463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/22/2023] [Accepted: 11/27/2023] [Indexed: 12/28/2023]
Abstract
Although fusogenic liposomes offer a promising approach for the delivery of antibiotic payloads across the cell envelope of Gram-negative bacteria, there is still a limited understanding of the individual nanocarrier interactions with the bacterial target. Using super-resolution microscopy, we characterize the interaction dynamics of positively charged fusogenic liposomes with Gram-negative (Escherichia coli) and Gram-positive (Bacillus subtilis) bacteria. The liposomes merge with the outer membrane (OM) of Gram-negative bacteria, while attachment or lipid internalization is observed in Gram-positive cells. Employing total internal reflection fluorescence microscopy, we demonstrated liposome fusion with model supported lipid bilayers. For whole E. coli cells, however, we observed heterogeneous membrane integrations, primarily involving liposome attachment and hemifusion events. With increasing lipopolysaccharide length, the likelihood of full-fusion events was reduced. The integration of artificial lipids into the OM of Gram-negative cells led to membrane destabilization, resulting in decreased bacterial vitality, membrane detachment, and improved codelivery of vancomycin─an effective antibiotic against Gram-positive cells. These findings provide significant insights into the interactions of individual nanocarriers with bacterial envelopes at the single-cell level, uncovering effects that would be missed in bulk measurements. This highlights the importance of conducting single-particle and single-cell investigations to assess the performance of next-generation drug delivery platforms.
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Affiliation(s)
- Anna Scheeder
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.
| | - Marius Brockhoff
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.
| | - Edward N. Ward
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.
| | - Gabriele S. Kaminski Schierle
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.
| | - Ioanna Mela
- Department
of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, U.K.
| | - Clemens F. Kaminski
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.
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Abstract
Gram-negative bacteria are intrinsically resistant to many antibiotics, due in large part to the permeability barrier formed by their cell envelope. The complex and synergistic interplay of the two Gram-negative membranes and active efflux prevents the accumulation of a diverse range of compounds that are effective against Gram-positive bacteria. A lack of detailed information on how components of the cell envelope contribute to this has been identified as a key barrier to the rational development of new antibiotics with efficacy against Gram-negative species. This review describes the current understanding of the role of the different components of the Gram-negative cell envelope in preventing compound accumulation and the state of efforts to describe properties that allow compounds to overcome this barrier and apply them to the development of new broad-spectrum antibiotics.
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Affiliation(s)
- Claire Maher
- College of Engineering, Science and Environment, University of Newcastle, Newcastle, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Karl A. Hassan
- College of Engineering, Science and Environment, University of Newcastle, Newcastle, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
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42
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Gargvanshi S, Heravi G, Ayon NJ, Gutheil WG. Screening the NCI diversity set V for anti-MRSA activity: cefoxitin synergy and LC-MS/MS confirmation of folate/thymidine biosynthesis inhibition. Microbiol Spectr 2023; 11:e0054123. [PMID: 37888993 PMCID: PMC10715016 DOI: 10.1128/spectrum.00541-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 09/19/2023] [Indexed: 10/28/2023] Open
Abstract
IMPORTANCE New antibacterial agents are urgently needed to counter increasingly resistant bacteria. One approach to this problem is library screening for new antibacterial agents. Library screening efforts can be improved by increasing the information content of the screening effort. In this study, we screened the National Cancer Institute diversity set V against methicillin-resistant Staphylococcus aureus (MRSA) with several enhancements. One of these is to screen the library before and after microsomal metabolism as means to identify potential active metabolites. A second enhancement is to screen the library in the absence and presence of sub-minimum inhibitory concentration levels of another antibiotic, such as cefoxitin in this study. This identified four agents with synergistic activity with cefoxitin out of 16 agents with good MRSA activity alone. Finally, active agents from this effort were counter-screened in the presence of thymidine, which quickly identified three folate/thymidine biosynthesis inhibitors, and also screened for bactericidal vs bacteriostatic activity.
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Affiliation(s)
- Shivani Gargvanshi
- Division of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - Gioia Heravi
- Division of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - Navid J. Ayon
- Division of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - William G. Gutheil
- Division of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, Kansas City, Missouri, USA
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43
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Otvos L, Wade JD. Big peptide drugs in a small molecule world. Front Chem 2023; 11:1302169. [PMID: 38144886 PMCID: PMC10740154 DOI: 10.3389/fchem.2023.1302169] [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: 09/26/2023] [Accepted: 11/24/2023] [Indexed: 12/26/2023] Open
Abstract
A quarter of a century ago, designer peptide drugs finally broke through the glass ceiling. Despite the resistance by big pharma, biotechnology companies managed to develop injectable peptide-based drugs, first against orphan or other small volume diseases, and later for conditions affecting large patient populations such as type 2 diabetes. Even their lack of gastrointestinal absorption could be utilized to enable successful oral dosing against chronic constipation. The preference of peptide therapeutics over small molecule competitors against identical medical conditions can be achieved by careful target selection, intrachain and terminal amino acid modifications, appropriate conjugation to stability enhancers and chemical space expansion, innovative delivery and administration techniques and patient-focused marketing strategies. Unfortunately, however, pharmacoeconomical considerations, including the strength of big pharma to develop competing small molecule drugs, have somewhat limited the success of otherwise smart peptide-based therapeutics. Yet, with increasing improvement in peptide drug modification and formulation, these are continuing to gain significant, and growing, acceptance as desirable alternatives to small molecule compounds.
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Affiliation(s)
- Laszlo Otvos
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
- OLPE Pharmaceutical Consultants, Audubon, PA, United States
| | - John D. Wade
- Florey Institute of Neuroscience and Mental Health, Parkville, VIC, Australia
- School of Chemistry, University of Melbourne, Parkville, VIC, Australia
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44
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Theuretzbacher U, Blasco B, Duffey M, Piddock LJV. Unrealized targets in the discovery of antibiotics for Gram-negative bacterial infections. Nat Rev Drug Discov 2023; 22:957-975. [PMID: 37833553 DOI: 10.1038/s41573-023-00791-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2023] [Indexed: 10/15/2023]
Abstract
Advances in areas that include genomics, systems biology, protein structure determination and artificial intelligence provide new opportunities for target-based antibacterial drug discovery. The selection of a 'good' new target for direct-acting antibacterial compounds is the first decision, for which multiple criteria must be explored, integrated and re-evaluated as drug discovery programmes progress. Criteria include essentiality of the target for bacterial survival, its conservation across different strains of the same species, bacterial species and growth conditions (which determines the spectrum of activity of a potential antibiotic) and the level of homology with human genes (which influences the potential for selective inhibition). Additionally, a bacterial target should have the potential to bind to drug-like molecules, and its subcellular location will govern the need for inhibitors to penetrate one or two bacterial membranes, which is a key challenge in targeting Gram-negative bacteria. The risk of the emergence of target-based drug resistance for drugs with single targets also requires consideration. This Review describes promising but as-yet-unrealized targets for antibacterial drugs against Gram-negative bacteria and examples of cognate inhibitors, and highlights lessons learned from past drug discovery programmes.
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Affiliation(s)
| | - Benjamin Blasco
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | - Maëlle Duffey
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | - Laura J V Piddock
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland.
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45
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Kenneth MJ, Koner S, Hsu GJ, Chen JS, Hsu BM. A review on the effects of discharging conventionally treated livestock waste to the environmental resistome. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 338:122643. [PMID: 37775024 DOI: 10.1016/j.envpol.2023.122643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 10/01/2023]
Abstract
Globally, animal production has developed rapidly as a consequence of the ongoing population growth, to support food security. This has consequently led to an extensive use of antibiotics to promote growth and prevent diseases in animals. However, most antibiotics are not fully metabolized by these animals, leading to their excretion within urine and faeces, thus making these wastes a major reservoir of antibiotics residues, antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) in the environment. Farmers normally depend on conventional treatment methods to mitigate the environmental impact of animal waste; however, these methods are not fully efficient to remove the environmental resistome. The present study reviewed the variability of residual antibiotics, ARB, as well as ARGs in the conventionally treated waste and assessed how discharging it could increase resistome in the receiving environments. Wherein, considering the efficiency and environmental safety, an addition of pre-treatments steps with these conventional treatment methods could enhance the removal of antibiotic resistance agents from livestock waste.
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Affiliation(s)
- Mutebi John Kenneth
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan; Doctoral Program in Science, Technology, Environment and Mathematics, National Chung Cheng University, Chiayi County, Taiwan
| | - Suprokash Koner
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan; Department of Biomedical Sciences, National Chung Cheng University, Chiayi County, Taiwan
| | - Gwo-Jong Hsu
- Division of Infectious Diseases, Ditmanson Medical Foundation, Chia-Yi Christian Hospital, Chiayi City, Taiwan
| | - Jung-Sheng Chen
- Department of Medical Research, E-Da Hospital, I-Shou University, Kaohsiung, Taiwan
| | - Bing-Mu Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan.
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46
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Shaikh AY, Björkling F, Zabicka D, Tomczak M, Urbas M, Domraceva I, Kreicberga A, Franzyk H. Structure-activity study of oncocin: On-resin guanidinylation and incorporation of homoarginine, 4-hydroxyproline or 4,4-difluoroproline residues. Bioorg Chem 2023; 141:106876. [PMID: 37797458 DOI: 10.1016/j.bioorg.2023.106876] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/14/2023] [Accepted: 09/18/2023] [Indexed: 10/07/2023]
Abstract
Antimicrobial peptides (AMPs) often display guanidinium functionalities, and hence robust synthetic procedures are needed to facilitate access to analogues with unnatural homologues of arginine (Arg = R). Initially, a resin-bound Arg/Pro-rich fluoren-9-yl-methyloxycarbonyl-protected fragment (Fmoc-RPRPPR) of the AMP oncocin (i.e., VDKPPYLPRPRPPRRIYNR-NH2) was employed in a comparative on-resin assessment of commercial guanidinylation reagents head-to-head with the recently studied bis-Boc-protected triazole-based reagent, 1H-triazole-1-[N,N'-bis(tert-butoxycarbonyl)]-carboxamidine, which was synthesized by a chromatography-free procedure. This reagent was found to enable quantitative conversion in solid-phase peptide synthesis (SPPS) of peptides displaying homoarginine (Har) residues and/or an N-terminal guanidinium group. SPPS was used to obtain analogues of the 18-mer oncocin with single as well as multiple Arg → Har modifications. In addition, the effect of replacement of proline (Pro) residues in oncocin was explored by incorporating single or multiple trans-4-hydroxy-l-proline (Hyp) or 4,4-difluoro-l-proline (Dfp) residues, which both affected hydrophobicity. The resulting peptide library was tested against both Gram-negative and Gram-positive bacteria. Analysis of the minimal inhibitory concentrations (MICs) showed that analogues, displaying modifications at positions 4, 5 and 12 (originally Pro residues), had retained or slightly improved antimicrobial activity. Next, an oncocin analogue with two stabilizing l-Arg → d-Arg replacements in the C-terminal part was further modified by triple-replacement of Pro by either Dfp or Hyp in positions 4, 5, and 12. The resulting analogue displaying three Pro → Dfp modifications proved to possess the best activity profile: MICs of 1-2 µg/mL against E. coli and Klebsiella pneumoniae, less than 1% hemolysis at 800 µg/mL, and an IC50 above 1280 µg/mL in HepG2 cells. Thus, incorporation of bis-fluorinated Pro residues appears to constitute a novel tool in structure-activity studies aimed at optimization of Pro-rich AMPs.
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Affiliation(s)
- Ashif Y Shaikh
- Center for Peptide-Based Antibiotics, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100, Denmark; Department of Chemistry, Khalifa University, Abu Dhabi 127788, United Arab Emirates
| | - Fredrik Björkling
- Center for Peptide-Based Antibiotics, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100, Denmark
| | - Dorota Zabicka
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, ul. Chełmska 30/34, 00-725 Warsaw, Poland
| | - Magdalena Tomczak
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, ul. Chełmska 30/34, 00-725 Warsaw, Poland
| | - Malgorzata Urbas
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, ul. Chełmska 30/34, 00-725 Warsaw, Poland
| | - Ilona Domraceva
- Latvian Institute of Organic Synthesis, Aizkraukles 21, 1006 Riga, Latvia
| | - Agrita Kreicberga
- Latvian Institute of Organic Synthesis, Aizkraukles 21, 1006 Riga, Latvia
| | - Henrik Franzyk
- Center for Peptide-Based Antibiotics, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100, Denmark.
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47
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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: 12] [Impact Index Per Article: 12.0] [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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48
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Frigini EN, Porasso RD, Beke-Somfai T, López Cascales JJ, Enriz RD, Pantano S. The Mechanism of Antimicrobial Small-Cationic Peptides from Coarse-Grained Simulations. J Chem Inf Model 2023; 63:6877-6889. [PMID: 37905818 DOI: 10.1021/acs.jcim.3c01348] [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: 11/02/2023]
Abstract
Antimicrobial cationic peptides (AMPs) are excellent candidates for use as therapeutic antimicrobial agents. Among them, short peptides possessing sequences of 9-11 amino acids have some advantages over long-sequence peptides. However, one of the main limitations of short peptides is that their mechanism of action at the molecular level is not well-known. In this article, we report a model based on multiscale molecular dynamics simulations of short peptides interacting with vesicles containing palmitoyl-oleoyl-phosphatidylglycerol (POPG)/palmitoyl-oleoyl-phosphatidylethanolamine (POPE). Simulations using this approach have allowed us to understand the different behaviors of peptides with antimicrobial activity with respect to those that do not produce this effect. We found remarkable agreement with a series of experimental results directly supporting our model. Moreover, these results allow us to understand the mechanism of action at the molecular level of these short peptides. Our simulations suggest that mechanical inhomogeneities appear in the membrane, promoting membrane rupture when a threshold concentration of peptides adsorbed on the membrane is achieved. These results explain the high structural demand for these peptides to maintain a delicate balance between the affinity for the bilayer surface, a low peptide-peptide repulsion (in order to reach the threshold concentration), and an acceptable tendency to penetrate into the bilayer. This mechanism is different from those proposed for peptides with long amino acid sequences. Such information is very useful from the medicinal chemistry point of view for the design of new small antimicrobial peptides.
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Affiliation(s)
- Ezequiel N Frigini
- Facultad de Química, Bioquímica y Farmacia, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Universidad Nacional de San Luis, Ejército de los Andes 950, San Luis 5700, Argentina
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo 11400, Uruguay
| | - Rodolfo D Porasso
- Instituto de Matemáticas Aplicada San Luis (IMASL), CONICET, Facultad de Ciencias Físico Matemáticas y Naturales, Universidad Nacional de San Luis, Av. Ejército de los Andes 950, San Luis 5700, Argentina
| | - Tamás Beke-Somfai
- Research Centre for Natural Sciences, Institute of Materials and Environmental Chemistry, H-1117 Budapest, Hungary
| | - José Javier López Cascales
- Universidad Politécnica de Cartagena, Grupo de Bioinformática y Macromoleculas (BioMac), Area de Química Física, Aulario II, Campus de Alfonso XIII, 30203 Cartagena, Murcia, Spain
| | - Ricardo D Enriz
- Facultad de Química, Bioquímica y Farmacia, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Universidad Nacional de San Luis, Ejército de los Andes 950, San Luis 5700, Argentina
| | - Sergio Pantano
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo 11400, Uruguay
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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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Mukai K, Shibayama T, Imai Y, Hosaka T. Phenomenological interpretations of the mechanism for the concentration-dependent positive effect of antibiotic lincomycin on Streptomyces coelicolor A3(2). Appl Environ Microbiol 2023; 89:e0113323. [PMID: 37732750 PMCID: PMC10617593 DOI: 10.1128/aem.01133-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 07/27/2023] [Indexed: 09/22/2023] Open
Abstract
The antibiotic lincomycin binds to the 23S ribosomal RNA peptidyl transferase loop region to inhibit protein synthesis. However, lincomycin can also stimulate the growth and secondary metabolism of actinomycetes in a concentration-dependent manner. In Streptomyces coelicolor A3(2), lincomycin stimulates the production of the blue-pigmented antibiotic actinorhodin at concentrations below the minimum inhibitory concentration. To better understand the molecular mechanism underlying these concentration-dependent positive effects, this study investigated how the target molecule, the ribosome, undergoes dynamic changes in the presence of lincomycin and explored the ribosome-related factors involved. Lincomycin, at a concentration that stimulates actinorhodin production of S. coelicolor A3(2), could restore temporarily arrested ribosome function by utilizing ribosome-related proteins and translation factors, presumably under the control of the transcription factor WblC protein that confers intrinsic resistance to multiple translation-inhibiting antibiotics, to eventually produce stable and active ribosomes even during the late growth phase. This qualitatively and quantitatively positive ribosome alteration can be advantageous for producing actinorhodin biosynthetic enzymes. A series of gene expression and biochemical analyses revealed that lincomycin at the concentration that induces ribosomal stabilization in S. coelicolor A3(2) could influence the localization of the 20S proteasome-related proteins, resulting in reduced proteasome activity. These findings suggest that the functional analysis of 20S proteasome represents a potential pivotal challenge for understanding the molecular mechanism of ribosome stabilization induced by lincomycin. Therefore, as lincomycin can dynamically alter its target molecule, the ribosome, we discuss the future issues and prospects for an increased understanding of the concentration-dependent properties of antibiotics. IMPORTANCE Antibiotics were originally defined as chemical compounds produced by a microbe that inhibits the growth of other microbes. However, an unexplained effect of this is that a low concentration of antibiotics, such as those below the minimum inhibitory concentration, can positively affect microbial growth and metabolism. The secondary metabolic activation of streptomycetes in the presence of the translation-inhibiting antibiotic lincomycin illustrates the concentration-dependent positive effect of the antibiotic. The significance of this study is that the phenomenological interpretation of the molecular mechanism of the concentration-dependent positive effect of lincomycin in Streptomyces coelicolor A3(2) has provided novel insight into the possible role of antibiotics in making their target molecules stable and active with the assistance of various related factors that benefit their function. Further exploration of this idea would lead to an essential understanding of antibiotics, including why actinomycetes make them and their role in nature.
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Affiliation(s)
- Keiichiro Mukai
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, Nagano, Japan
- Graduate School of Medicine, Science and Technology, Shinshu University, Nagano, Japan
| | - Tomoko Shibayama
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, Nagano, Japan
- Graduate School of Science and Technology, Shinshu University, Nagano, Japan
| | - Yu Imai
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, Nagano, Japan
| | - Takeshi Hosaka
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, Nagano, Japan
- Graduate School of Medicine, Science and Technology, Shinshu University, Nagano, Japan
- Graduate School of Science and Technology, Shinshu University, Nagano, Japan
- Renaissance Center for Applied Microbiology, Shinshu University, Nagano, Japan
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