1
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Chen J, Wang W, Hu X, Yue Y, Lu X, Wang C, Wei B, Zhang H, Wang H. Medium-sized peptides from microbial sources with potential for antibacterial drug development. Nat Prod Rep 2024; 41:1235-1263. [PMID: 38651516 DOI: 10.1039/d4np00002a] [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: 04/25/2024]
Abstract
Covering: 1993 to the end of 2022As the rapid development of antibiotic resistance shrinks the number of clinically available antibiotics, there is an urgent need for novel options to fill the existing antibiotic pipeline. In recent years, antimicrobial peptides have attracted increased interest due to their impressive broad-spectrum antimicrobial activity and low probability of antibiotic resistance. However, macromolecular antimicrobial peptides of plant and animal origin face obstacles in antibiotic development because of their extremely short elimination half-life and poor chemical stability. Herein, we focus on medium-sized antibacterial peptides (MAPs) of microbial origin with molecular weights below 2000 Da. The low molecular weight is not sufficient to form complex protein conformations and is also associated to a better chemical stability and easier modifications. Microbially-produced peptides are often composed of a variety of non-protein amino acids and terminal modifications, which contribute to improving the elimination half-life of compounds. Therefore, MAPs have great potential for drug discovery and are likely to become key players in the development of next-generation antibiotics. In this review, we provide a detailed exploration of the modes of action demonstrated by 45 MAPs and offer a concise summary of the structure-activity relationships observed in these MAPs.
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Affiliation(s)
- Jianwei Chen
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Wei Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xubin Hu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yujie Yue
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xingyue Lu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Chenjie Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Bin Wei
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Huawei Zhang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Hong Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
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2
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Sengupta S, Pabbaraja S, Mehta G. Natural products from the human microbiome: an emergent frontier in organic synthesis and drug discovery. Org Biomol Chem 2024; 22:4006-4030. [PMID: 38669195 DOI: 10.1039/d4ob00236a] [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: 04/28/2024]
Abstract
Often referred to as the "second genome", the human microbiome is at the epicenter of complex inter-habitat biochemical networks like the "gut-brain axis", which has emerged as a significant determinant of cognition, overall health and well-being, as well as resistance to antibiotics and susceptibility to diseases. As part of a broader understanding of the nexus between the human microbiome, diseases and microbial interactions, whether encoded secondary metabolites (natural products) play crucial signalling roles has been the subject of intense scrutiny in the recent past. A major focus of these activities involves harvesting the genomic potential of the human microbiome via bioinformatics guided genome mining and culturomics. Through these efforts, an impressive number of structurally intriguing antibiotics, with enhanced chemical diversity vis-à-vis conventional antibiotics have been isolated from human commensal bacteria, thereby generating considerable interest in their total synthesis and expanding their therapeutic space for drug discovery. These developments augur well for the discovery of new drugs and antibiotics, particularly in the context of challenges posed by mycobacterial resistance and emerging new diseases. The current landscape of various synthetic campaigns and drug discovery initiatives on antibacterial natural products from the human microbiome is captured in this review with an intent to stimulate further activities in this interdisciplinary arena among the new generation.
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Affiliation(s)
- Saumitra Sengupta
- School of Chemistry, University of Hyderabad, Hyderabad-500046, India.
- Department of Organic Synthesis and Process Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad-500007, India
| | - Srihari Pabbaraja
- Department of Organic Synthesis and Process Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad-500007, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Goverdhan Mehta
- School of Chemistry, University of Hyderabad, Hyderabad-500046, India.
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3
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He X, Li M, Yu Q, Liu W, Sun S, Li X, Wang Z, Yan X, Li S. Solid phase extraction technology combined with UPLC-MS/MS: a method for detecting 20 β-lactamase antibiotics traces in goat's milk. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024. [PMID: 38713147 DOI: 10.1039/d4ay00134f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
We develop and validate a method for the rapid determination and identification of 20 β-lactamase antibiotics traces in goat's milk by combining the solid phase extraction technology with ultra-high performance liquid chromatography-tandem mass spectrometry. Goat milk samples were extracted with acetonitrile twice. The supernatant was then extracted and cleaned by solid-phase extraction using divinylbenzene and N-vinylpyrrolidone copolymer. The method was validated, with limits of quantification (LOQs) of 0.3 μg kg-1, specificities of 1/3 LOQ, linearities (R2) > 0.99, recoveries of 80-110%, repeatabilities <10.0%, and intermediate precisions <10.0%. The developed method was suitable for the routine analysis of β-lactamase antibiotics residues in goat's milk and was used to test 76 goat milk samples produced in China.
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Affiliation(s)
- Xiwen He
- Shaanxi Qinyun Agricultural Products Inspection and Testing Co., Ltd, Weinan, China
- Shaanxi Qinyun Agricultural Science Research Institute, Weinan, China
| | - Ming Li
- Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Qi Yu
- Beijing Animal Disease Prevention and Control Center, Beijing, China
| | - Wuyan Liu
- Shaanxi Qinyun Agricultural Products Inspection and Testing Co., Ltd, Weinan, China
- Shaanxi Qinyun Agricultural Science Research Institute, Weinan, China
| | - Shufang Sun
- Veterinary Medicine Supervision Institute of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Xiang Li
- Shaanxi Qinyun Agricultural Products Inspection and Testing Co., Ltd, Weinan, China
| | - Zhaohua Wang
- Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, Beijing, China.
- Centre for Laboratory Animal Pathology Analysis, Institute of Laboratory Animal Science, NHC Key Laboratory of Comparative Medicine, Peking Union Medical College, Beijing, China
| | - Xiaohuan Yan
- Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Songli Li
- Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, Beijing, China.
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4
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Dhanda G, Acharya Y, Haldar J. Antibiotic Adjuvants: A Versatile Approach to Combat Antibiotic Resistance. ACS OMEGA 2023; 8:10757-10783. [PMID: 37008128 PMCID: PMC10061514 DOI: 10.1021/acsomega.3c00312] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 02/21/2023] [Indexed: 06/13/2023]
Abstract
The problem of antibiotic resistance is on the rise, with multidrug-resistant strains emerging even to the last resort antibiotics. The drug discovery process is often stalled by stringent cut-offs required for effective drug design. In such a scenario, it is prudent to delve into the varying mechanisms of resistance to existing antibiotics and target them to improve antibiotic efficacy. Nonantibiotic compounds called antibiotic adjuvants which target bacterial resistance can be used in combination with obsolete drugs for an improved therapeutic regime. The field of "antibiotic adjuvants" has gained significant traction in recent years where mechanisms other than β-lactamase inhibition have been explored. This review discusses the multitude of acquired and inherent resistance mechanisms employed by bacteria to resist antibiotic action. The major focus of this review is how to target these resistance mechanisms by the use of antibiotic adjuvants. Different types of direct acting and indirect resistance breakers are discussed including enzyme inhibitors, efflux pump inhibitors, inhibitors of teichoic acid synthesis, and other cellular processes. The multifaceted class of membrane-targeting compounds with poly pharmacological effects and the potential of host immune-modulating compounds have also been reviewed. We conclude with providing insights about the existing challenges preventing clinical translation of different classes of adjuvants, especially membrane-perturbing compounds, and a framework about the possible directions which can be pursued to fill this gap. Antibiotic-adjuvant combinatorial therapy indeed has immense potential to be used as an upcoming orthogonal strategy to conventional antibiotic discovery.
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Affiliation(s)
- Geetika Dhanda
- Antimicrobial
Research Laboratory, New Chemistry Unit and School of Advanced
Materials, Jawaharlal Nehru Centre for Advanced
Scientific Research (JNCASR), Jakkur, Bengaluru 560064, Karnataka, India
| | - Yash Acharya
- Antimicrobial
Research Laboratory, New Chemistry Unit and School of Advanced
Materials, Jawaharlal Nehru Centre for Advanced
Scientific Research (JNCASR), Jakkur, Bengaluru 560064, Karnataka, India
| | - Jayanta Haldar
- Antimicrobial
Research Laboratory, New Chemistry Unit and School of Advanced
Materials, Jawaharlal Nehru Centre for Advanced
Scientific Research (JNCASR), Jakkur, Bengaluru 560064, Karnataka, India
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5
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Fobofou SA, Savidge T. Microbial metabolites: cause or consequence in gastrointestinal disease? Am J Physiol Gastrointest Liver Physiol 2022; 322:G535-G552. [PMID: 35271353 PMCID: PMC9054261 DOI: 10.1152/ajpgi.00008.2022] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/07/2022] [Accepted: 03/07/2022] [Indexed: 01/31/2023]
Abstract
Systems biology studies have established that changes in gastrointestinal microbiome composition and function can adversely impact host physiology. Notable diseases synonymously associated with dysbiosis include inflammatory bowel diseases, cancer, metabolic disorders, and opportunistic and recurrent pathogen infections. However, there is a scarcity of mechanistic data that advances our understanding of taxonomic correlations with pathophysiological host-microbiome interactions. Generally, to survive a hostile gut environment, microbes are highly metabolically active and produce trans-kingdom signaling molecules to interact with competing microorganisms and the host. These specialized metabolites likely play important homeostatic roles, and identifying disease-specific taxa and their effector pathways can provide better strategies for diagnosis, treatment, and prevention, as well as the discovery of innovative therapeutics. The signaling role of microbial biotransformation products such as bile acids, short-chain fatty acids, polysaccharides, and dietary tryptophan is increasingly recognized, but little is known about the identity and function of metabolites that are synthesized by microbial biosynthetic gene clusters, including ribosomally synthesized and posttranslationally modified peptides (RiPPs), nonribosomal peptides (NRPs), polyketides (PKs), PK-NRP hybrids, and terpenes. Here we consider how bioactive natural products directly encoded by the human microbiome can contribute to the pathophysiology of gastrointestinal disease, cancer, autoimmune, antimicrobial-resistant bacterial and viral infections (including COVID-19). We also present strategies used to discover these compounds and the biological activities they exhibit, with consideration of therapeutic interventions that could emerge from understanding molecular causation in gut microbiome research.
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Affiliation(s)
- Serge Alain Fobofou
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
- Department of Pathology, Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas
| | - Tor Savidge
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
- Department of Pathology, Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas
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6
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Kohga H, Mori T, Tanaka Y, Yoshikaie K, Taniguchi K, Fujimoto K, Fritz L, Schneider T, Tsukazaki T. Crystal structure of the lipid flippase MurJ in a "squeezed" form distinct from its inward- and outward-facing forms. Structure 2022; 30:1088-1097.e3. [PMID: 35660157 DOI: 10.1016/j.str.2022.05.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/15/2022] [Accepted: 05/10/2022] [Indexed: 11/29/2022]
Abstract
The bacterial peptidoglycan enclosing the cytoplasmic membrane is a fundamental cellular architecture. The integral membrane protein MurJ plays an essential role in flipping the cell wall building block Lipid II across the cytoplasmic membrane for peptidoglycan biosynthesis. Previously reported crystal structures of MurJ have elucidated its V-shaped inward- or outward-facing forms with an internal cavity for substrate binding. MurJ transports Lipid II using its cavity through conformational transitions between these two forms. Here, we report two crystal structures of inward-facing forms from Arsenophonus endosymbiont MurJ and an unprecedented crystal structure of Escherichia coli MurJ in a "squeezed" form, which lacks a cavity to accommodate the substrate, mainly because of the increased proximity of transmembrane helices 2 and 8. Subsequent molecular dynamics simulations supported the hypothesis that the squeezed form is an intermediate conformation. This study fills a gap in our understanding of the Lipid II flipping mechanism.
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Affiliation(s)
- Hidetaka Kohga
- Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Takaharu Mori
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yoshiki Tanaka
- Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | | | | | - Kei Fujimoto
- Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Lisa Fritz
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn, Meckenheimer Allee 168, 53115 Bonn, Germany
| | - Tanja Schneider
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn, Meckenheimer Allee 168, 53115 Bonn, Germany
| | - Tomoya Tsukazaki
- Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan.
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7
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Kumar S, Mollo A, Kahne D, Ruiz N. The Bacterial Cell Wall: From Lipid II Flipping to Polymerization. Chem Rev 2022; 122:8884-8910. [PMID: 35274942 PMCID: PMC9098691 DOI: 10.1021/acs.chemrev.1c00773] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The peptidoglycan (PG) cell wall is an extra-cytoplasmic glycopeptide polymeric structure that protects bacteria from osmotic lysis and determines cellular shape. Since the cell wall surrounds the cytoplasmic membrane, bacteria must add new material to the PG matrix during cell elongation and division. The lipid-linked precursor for PG biogenesis, Lipid II, is synthesized in the inner leaflet of the cytoplasmic membrane and is subsequently translocated across the bilayer so that the PG building block can be polymerized and cross-linked by complex multiprotein machines. This review focuses on major discoveries that have significantly changed our understanding of PG biogenesis in the past decade. In particular, we highlight progress made toward understanding the translocation of Lipid II across the cytoplasmic membrane by the MurJ flippase, as well as the recent discovery of a novel class of PG polymerases, the SEDS (shape, elongation, division, and sporulation) glycosyltransferases RodA and FtsW. Since PG biogenesis is an effective target of antibiotics, these recent developments may lead to the discovery of much-needed new classes of antibiotics to fight bacterial resistance.
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Affiliation(s)
- Sujeet Kumar
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Aurelio Mollo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Daniel Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Natividad Ruiz
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
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8
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Abstract
Biosynthesis of many important polysaccharides (including peptidoglycan, lipopolysaccharide, and N-linked glycans) necessitates the transport of lipid-linked oligosaccharides (LLO) across membranes from their cytosolic site of synthesis to their sites of utilization. Much of our current understanding of LLO transport comes from genetic, biochemical, and structural studies of the multidrug/oligosaccharidyl-lipid/polysaccharide (MOP) superfamily protein MurJ, which flips the peptidoglycan precursor lipid II. MurJ plays a pivotal role in bacterial cell wall synthesis and is an emerging antibiotic target. Here, we review the mechanism of LLO flipping by MurJ, including the structural basis for lipid II flipping and ion coupling. We then discuss inhibition of MurJ by antibacterials, including humimycins and the phage M lysis protein, as well as how studies on MurJ could provide insight into other flippases, both within and beyond the MOP superfamily. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Alvin C Y Kuk
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, USA; .,Current affiliation: Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore
| | - Aili Hao
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, USA;
| | - Seok-Yong Lee
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, USA;
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9
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Hostetler MA, Smith C, Nelson S, Budimir Z, Modi R, Woolsey I, Frerk A, Baker B, Gantt J, Parkinson EI. Synthetic Natural Product Inspired Cyclic Peptides. ACS Chem Biol 2021; 16:2604-2611. [PMID: 34699170 PMCID: PMC8610019 DOI: 10.1021/acschembio.1c00641] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Natural products
are a bountiful source of bioactive molecules.
Unfortunately, discovery of novel bioactive natural products is challenging
due to cryptic biosynthetic gene clusters, low titers, and arduous
purifications. Herein, we describe SNaPP (Synthetic Natural Product
Inspired Cyclic Peptides), a method for identifying
NP-inspired bioactive peptides. SNaPP expedites bioactive molecule
discovery by combining bioinformatics predictions of nonribosomal
peptide synthetases with chemical synthesis of the predicted natural
products (pNPs). SNaPP utilizes a recently discovered cyclase, the
penicillin binding protein-like cyclase, as the lynchpin for the development
of a library of head-to-tail cyclic peptide pNPs. Analysis of 500
biosynthetic gene clusters allowed for identification of 131 novel
pNPs. Fifty-one diverse pNPs were synthesized using solid phase peptide
synthesis and solution-phase cyclization. Antibacterial testing revealed
14 pNPs with antibiotic activity, including activity against multidrug-resistant
Gram-negative bacteria. Overall, SNaPP demonstrates the power of combining
bioinformatics predictions with chemical synthesis to accelerate the
discovery of bioactive molecules.
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Affiliation(s)
- Matthew A. Hostetler
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Chloe Smith
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Samantha Nelson
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Zachary Budimir
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ramya Modi
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ian Woolsey
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Autumn Frerk
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Braden Baker
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jessica Gantt
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Elizabeth I. Parkinson
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
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10
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Benjdia A, Berteau O. Radical SAM Enzymes and Ribosomally-Synthesized and Post-translationally Modified Peptides: A Growing Importance in the Microbiomes. Front Chem 2021; 9:678068. [PMID: 34350157 PMCID: PMC8326336 DOI: 10.3389/fchem.2021.678068] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/07/2021] [Indexed: 11/13/2022] Open
Abstract
To face the current antibiotic resistance crisis, novel strategies are urgently required. Indeed, in the last 30 years, despite considerable efforts involving notably high-throughput screening and combinatorial libraries, only few antibiotics have been launched to the market. Natural products have markedly contributed to the discovery of novel antibiotics, chemistry and drug leads, with more than half anti-infective and anticancer drugs approved by the FDA being of natural origin or inspired by natural products. Among them, thanks to their modular structure and simple biosynthetic logic, ribosomally synthesized and posttranslationally modified peptides (RiPPs) are promising scaffolds. In addition, recent studies have highlighted the pivotal role of RiPPs in the human microbiota which remains an untapped source of natural products. In this review, we report on recent developments in radical SAM enzymology and how these unique biocatalysts have been shown to install complex and sometimes unprecedented posttranslational modifications in RiPPs with a special focus on microbiome derived enzymes.
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Affiliation(s)
- Alhosna Benjdia
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France
| | - Olivier Berteau
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France
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11
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Guo Z, Liu Y, Zhang Y, Sun X, Li F, Bu T, Wang Q, Wang L. A bifunctional nanoplatform based on copper manganate nanoflakes for bacterial elimination via a catalytic and photothermal synergistic effect. Biomater Sci 2021; 8:4266-4274. [PMID: 32588850 DOI: 10.1039/d0bm00706d] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Bacterial infection has been recognized as one of the greatest threats to public health. In view of the continuous increase of bacterial resistance, constructing a collaborative bactericidal platform is a promising strategy to enhance the efficiency of antimicrobial agents. Herein, we report a facile, biocompatible and versatile nano-platform based on positively charged copper manganate nanoflakes (CuMnO2 NFs), which exhibits intrinsic peroxidase-like catalytic activity and excellent photothermal properties. The CuMnO2 NFs can bind with negatively charged bacteria via electrostatic interactions, and generate hydroxyl radicals (˙OH) through catalysis involving hydrogen peroxide (H2O2) to make bacteria more susceptible to temperature. Introducing near-infrared light generates hyperthermia to fight against bacteria and enhances the peroxidase-like catalytic activity of the CuMnO2 NFs, thus producing more ˙OH to combat bacteria. The PTT-enhanced ˙OH synergistic antibacterial strategy exerts desirable antibacterial efficiencies of 98.78% and 99.92% against Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) at a controlled low temperature (below 50 °C), without damage to healthy tissues. Animal experiments indicate that this synergistic treatment has a better therapeutic effect on S. aureus-infected wounds in mice, compared with either treatment by itself. Therefore, this work holds great promise for developing new synergistic antimicrobial strategies to treat bacterial infections.
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Affiliation(s)
- Zhirong Guo
- College of Food Science and Engineering, Northwest A&F University, Yangling712100, Shaanxi, China.
| | - Yingnan Liu
- College of Food Science and Engineering, Northwest A&F University, Yangling712100, Shaanxi, China.
| | - Yalan Zhang
- College of Food Science and Engineering, Northwest A&F University, Yangling712100, Shaanxi, China.
| | - Xinyu Sun
- College of Food Science and Engineering, Northwest A&F University, Yangling712100, Shaanxi, China.
| | - Fan Li
- College of Food Science and Engineering, Northwest A&F University, Yangling712100, Shaanxi, China.
| | - Tong Bu
- College of Food Science and Engineering, Northwest A&F University, Yangling712100, Shaanxi, China.
| | - Qinzhi Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling712100, Shaanxi, China.
| | - Li Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling712100, Shaanxi, China.
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12
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Balty C, Guillot A, Fradale L, Brewee C, Lefranc B, Herrero C, Sandström C, Leprince J, Berteau O, Benjdia A. Biosynthesis of the sactipeptide Ruminococcin C by the human microbiome: Mechanistic insights into thioether bond formation by radical SAM enzymes. J Biol Chem 2020; 295:16665-16677. [PMID: 32972973 PMCID: PMC8188230 DOI: 10.1074/jbc.ra120.015371] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/22/2020] [Indexed: 12/17/2022] Open
Abstract
Despite its major importance in human health, the metabolic potential of the human gut microbiota is still poorly understood. We have recently shown that biosynthesis of Ruminococcin C (RumC), a novel ribosomally synthesized and posttranslationally modified peptide (RiPP) produced by the commensal bacterium Ruminococcus gnavus, requires two radical SAM enzymes (RumMC1 and RumMC2) catalyzing the formation of four Cα-thioether bridges. These bridges, which are essential for RumC's antibiotic properties against human pathogens such as Clostridium perfringens, define two hairpin domains giving this sactipeptide (sulfur-to-α-carbon thioether-containing peptide) an unusual architecture among natural products. We report here the biochemical and spectroscopic characterizations of RumMC2. EPR spectroscopy and mutagenesis data support that RumMC2 is a member of the large family of SPASM domain radical SAM enzymes characterized by the presence of three [4Fe-4S] clusters. We also demonstrate that this enzyme initiates its reaction by Cα H-atom abstraction and is able to catalyze the formation of nonnatural thioether bonds in engineered peptide substrates. Unexpectedly, our data support the formation of a ketoimine rather than an α,β-dehydro-amino acid intermediate during Cα-thioether bridge LC-MS/MS fragmentation. Finally, we explored the roles of the leader peptide and of the RiPP precursor peptide recognition element, present in myriad RiPP-modifying enzymes. Collectively, our data support a more complex role for the peptide recognition element and the core peptide for the installation of posttranslational modifications in RiPPs than previously anticipated and suggest a possible reaction intermediate for thioether bond formation.
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Affiliation(s)
- Clémence Balty
- Micalis Institute, ChemSyBio, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Alain Guillot
- Micalis Institute, ChemSyBio, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Laura Fradale
- Micalis Institute, ChemSyBio, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Clémence Brewee
- Micalis Institute, ChemSyBio, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Benjamin Lefranc
- INSERM U1239, PRIMACEN, Université de Normandie-Rouen, Rouen, France
| | | | - Corine Sandström
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jérôme Leprince
- INSERM U1239, PRIMACEN, Université de Normandie-Rouen, Rouen, France
| | - Olivier Berteau
- Micalis Institute, ChemSyBio, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.
| | - Alhosna Benjdia
- Micalis Institute, ChemSyBio, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.
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13
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Shaku M, Ealand C, Kana BD. Cell Surface Biosynthesis and Remodeling Pathways in Mycobacteria Reveal New Drug Targets. Front Cell Infect Microbiol 2020; 10:603382. [PMID: 33282752 PMCID: PMC7688586 DOI: 10.3389/fcimb.2020.603382] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 10/20/2020] [Indexed: 12/29/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), remains the leading cause of death from an infectious bacterium and is responsible for 1.8 million deaths annually. The emergence of drug resistance, together with the need for a shorter more effective regimen, has prompted the drive to identify novel therapeutics with the bacterial cell surface emerging as a tractable area for drug development. Mtb assembles a unique, waxy, and complex cell envelope comprised of the mycolyl-arabinogalactan-peptidoglycan complex and an outer capsule like layer, which are collectively essential for growth and pathogenicity while serving as an inherent barrier against antibiotics. A detailed understanding of the biosynthetic pathways required to assemble the polymers that comprise the cell surface will enable the identification of novel drug targets as these structures provide a diversity of biochemical reactions that can be targeted. Herein, we provide an overview of recently described mycobacterial cell wall targeting compounds, novel drug combinations and their modes of action. We anticipate that this summary will enable prioritization of the best pathways to target and triage of the most promising molecules to progress for clinical assessment.
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Affiliation(s)
- Moagi Shaku
- National Health Laboratory Service, Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, Faculty of Health Sciences, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Christopher Ealand
- National Health Laboratory Service, Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, Faculty of Health Sciences, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Bavesh D Kana
- National Health Laboratory Service, Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, Faculty of Health Sciences, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
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14
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Tancer RJ, Baynes K, Wiedman GR. Synergy among humimycins against methicillin‐resistant
Staphylococcus aureus. Pept Sci (Hoboken) 2020. [DOI: 10.1002/pep2.24197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Robert J. Tancer
- Department of Chemistry and Biochemistry Seton Hall University South Orange New Jersey USA
| | - Kazim Baynes
- Department of Chemistry and Biochemistry Seton Hall University South Orange New Jersey USA
| | - Gregory R. Wiedman
- Department of Chemistry and Biochemistry Seton Hall University South Orange New Jersey USA
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15
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Kmeck A, Tancer RJ, Ventura CR, Wiedman GR. Synergies with and Resistance to Membrane-Active Peptides. Antibiotics (Basel) 2020; 9:antibiotics9090620. [PMID: 32961656 PMCID: PMC7559582 DOI: 10.3390/antibiotics9090620] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/07/2020] [Accepted: 09/17/2020] [Indexed: 12/12/2022] Open
Abstract
Membrane-active peptides (MAPs) have long been thought of as the key to defeating antimicrobial-resistant microorganisms. Such peptides, however, may not be sufficient alone. In this review, we seek to highlight some of the common pathways for resistance, as well as some avenues for potential synergy. This discussion takes place considering resistance, and/or synergy in the extracellular space, at the membrane, and during interaction, and/or removal. Overall, this review shows that researchers require improved definitions of resistance and a more thorough understanding of MAP-resistance mechanisms. The solution to combating resistance may ultimately come from an understanding of how to harness the power of synergistic drug combinations.
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16
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Hudson GA, Hooper AR, DiCaprio AJ, Sarlah D, Mitchell DA. Structure Prediction and Synthesis of Pyridine-Based Macrocyclic Peptide Natural Products. Org Lett 2020; 23:253-256. [PMID: 32845158 DOI: 10.1021/acs.orglett.0c02699] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The structural and functional characterization of natural products is vastly outpaced by the bioinformatic identification of biosynthetic gene clusters (BGCs) that encode such molecules. Uniting our knowledge of bioinformatics and enzymology to predict and synthetically access natural products is an effective platform for investigating cryptic/silent BGCs. We report the identification, biosynthesis, and total synthesis of a minimalistic class of ribosomally synthesized and post-translationally modified peptides (RiPPs) with the responsible BGCs encoding a subset of enzymes known from thiopeptide biosynthesis. On the basis of the BGC content, these RiPPs were predicted to undergo enzymatic dehydration of serine followed by [4+2]-cycloaddition to produce a trisubstituted, pyridine-based macrocycle. These RiPPs, termed "pyritides", thus contain the same six-membered, nitrogenous heterocycle that defines the thiopeptide RiPP class but lack the ubiquitous thiazole/thiazoline heterocycles, suggesting that thiopeptides should be reclassified as a more elaborate subclass of the pyritides. One pyritide product was obtained using an 11-step synthesis, and the structure verified by an orthogonal chemoenzymatic route using the precursor peptide and cognate pyridine synthase. This work exemplifies complementary bioinformatics, enzymology, and synthesis to characterize a minimalistic yet structurally intriguing scaffold that, unlike most thiopeptides, lacks growth-suppressive activity toward Gram-positive bacteria.
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Affiliation(s)
- Graham A Hudson
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Annie R Hooper
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Adam J DiCaprio
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
| | - David Sarlah
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Douglas A Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
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17
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Chu J, Koirala B, Forelli N, Vila-Farres X, Ternei MA, Ali T, Colosimo DA, Brady SF. Synthetic-Bioinformatic Natural Product Antibiotics with Diverse Modes of Action. J Am Chem Soc 2020; 142:14158-14168. [PMID: 32697091 DOI: 10.1021/jacs.0c04376] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Bacterial natural products have inspired the development of numerous antibiotics in use today. As resistance to existing antibiotics has become more prevalent, new antibiotic lead structures and activities are desperately needed. An increasing number of natural product biosynthetic gene clusters, to which no known molecules can be assigned, are found in genome and metagenome sequencing data. Here we access structural information encoded in this underexploited resource using a synthetic-bioinformatic natural product (syn-BNP) approach, which relies on bioinformatic algorithms followed by chemical synthesis to predict and then produce small molecules inspired by biosynthetic gene clusters. In total, 157 syn-BNP cyclic peptides inspired by 96 nonribosomal peptide synthetase gene clusters were synthesized and screened for antibacterial activity. This yielded nine antibiotics with activities against ESKAPE pathogens as well as Mycobacterium tuberculosis. Not only are antibiotic-resistant pathogens susceptible to many of these syn-BNP antibiotics, but they were also unable to develop resistance to these antibiotics in laboratory experiments. Characterized modes of action for these antibiotics include cell lysis, membrane depolarization, inhibition of cell wall biosynthesis, and ClpP protease dysregulation. Increasingly refined syn-BNP-based explorations of biosynthetic gene clusters should allow for more rapid identification of evolutionarily inspired bioactive small molecules, in particular antibiotics with diverse mechanism of actions that could help confront the imminent crisis of antimicrobial resistance.
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Affiliation(s)
- John Chu
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Bimal Koirala
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Nicholas Forelli
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Xavier Vila-Farres
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Melinda A Ternei
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Thahmina Ali
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Dominic A Colosimo
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
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18
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Stevenson LJ, Owen JG, Ackerley DF. Metagenome Driven Discovery of Nonribosomal Peptides. ACS Chem Biol 2019; 14:2115-2126. [PMID: 31508935 DOI: 10.1021/acschembio.9b00618] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Declining rates of novel natural product discovery and exponential rates of rediscovery heralded the end of the 1940s to 1960s "golden era" of antibiotic discovery. Fifty years later, the implementation of molecular screening methodologies revealed that standard culture-based screening approaches had failed to capture the vast majority of environmental bacteria and that even for the cultivable isolates only a small fraction of the biosynthetic potential had been tapped. A diversity of metagenomic screening and synthetic biology approaches have been developed to address these issues. The nonribosomal peptides have received particular focus, owing to their high levels of bioactivity and the predictability of the biosynthetic logic of the genetically encoded assembly lines that produce them. By uniting advances in next-generation sequencing and bioinformatic analysis with a diversity of traditional disciplines, several pioneering teams have proven that this previously inaccessible resource is no longer out of reach.
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Affiliation(s)
- Luke J. Stevenson
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Centre for Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Jeremy G. Owen
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Centre for Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - David F. Ackerley
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Centre for Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
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19
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Chu J, Vila-Farres X, Brady SF. Bioactive Synthetic-Bioinformatic Natural Product Cyclic Peptides Inspired by Nonribosomal Peptide Synthetase Gene Clusters from the Human Microbiome. J Am Chem Soc 2019; 141:15737-15741. [PMID: 31545899 DOI: 10.1021/jacs.9b07317] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bioinformatic analysis of sequenced bacterial genomes has uncovered an increasing number of natural product biosynthetic gene clusters (BGCs) to which no known bacterial metabolite can be ascribed. One emerging method we have investigated for studying these BGCs is the synthetic-Bioinformatic Natural Product (syn-BNP) approach. The syn-BNP approach replaces transcription, translation, and in vivo enzymatic biosynthesis of natural products with bioinformatic algorithms to predict the output of a BGC and in vitro chemical synthesis to produce the predicted structure. Here we report on expanding the syn-BNP approach to the design and synthesis of cyclic peptides inspired by nonribosomal peptide synthetase BGCs associated with the human microbiota. While no syn-BNPs we tested inhibited the growth of bacteria or yeast, five were found to be active in the human cell-based MTT metabolic activity assay. Interestingly, active peptides were mostly inspired by BGCs found in the genomes of opportunistic pathogens that are often more commonly associated with environments outside the human microbiome. The cyclic syn-BNP studies presented here provide further evidence of its potential for identifying bioactive small molecules directly from the instructions encoded in the primary sequences of natural product BGCs.
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Affiliation(s)
- John Chu
- Laboratory of Genetically Encoded Small Molecules , The Rockefeller University , New York , New York 10065 , United States
| | - Xavier Vila-Farres
- Laboratory of Genetically Encoded Small Molecules , The Rockefeller University , New York , New York 10065 , United States
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules , The Rockefeller University , New York , New York 10065 , United States
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20
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Miao Z, Fan L, Xie X, Ma Y, Xue J, He T, Zha Z. Liquid Exfoliation of Atomically Thin Antimony Selenide as an Efficient Two-Dimensional Antibacterial Nanoagent. ACS APPLIED MATERIALS & INTERFACES 2019; 11:26664-26673. [PMID: 31287947 DOI: 10.1021/acsami.9b08320] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The ever-growing global crisis of multidrug-resistant bacteria has triggered a tumult of activity in the design and development of antibacterial formulations. Here, atomically thin antimony selenide nanosheets (Sb2Se3 NSs), a minimal-toxic and low-cost semiconductor material, were explored as a high-performance two-dimensional (2D) antibacterial nanoagent via a liquid exfoliation strategy integrating cryo-pretreatment and polyvinyl pyrrolidone (PVP)-assisted exfoliation. When cultured with bacteria, the obtained PVP-capped Sb2Se3 NSs exhibited intrinsic long-term antibacterial capability, probably due to the reactive oxygen species generation and sharp edge-induced membrane cutting during physical contact between bacteria and nanosheets. Upon near-infrared laser irradiation, Sb2Se3 NSs achieved short-time hyperthermia sterilization because of strong optical absorption and high photothermal conversion efficiency. By virtue of the synergistic effects of these two broad-spectrum antibacterial mechanisms, Sb2Se3 NSs exhibited high-efficiency inhibition of conventional Gram-negative Escherichia coli, Gram-positive methicillin-resistant Staphylococcus aureus, and wild bacteria from a natural water pool. Particularly, these three categories of bacteria were completely eradicated after being treated with Sb2Se3 NSs (300 μM) plus laser irradiation for only 5 min. In vivo wound healing experiment further demonstrated the high-performance antibacterial effect. In addition, Sb2Se3 NSs depicted excellent biocompatibility due to the biocompatible element constitute and bioinert PVP modification. This work enlightened that atomically thin Sb2Se3 NSs hold great promise as a broad-spectrum 2D antibacterial nanoagent for various pathogenic bacterial infections.
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Affiliation(s)
- Zhaohua Miao
- School of Food and Biological Engineering, School of Chemistry and Chemical Engineering , Hefei University of Technology , Hefei 230009 , P. R. China
- State Key Laboratory of Advanced Welding and Joining , Harbin Institute of Technology , Harbin 150001 , P. R. China
| | - Linxin Fan
- School of Food and Biological Engineering, School of Chemistry and Chemical Engineering , Hefei University of Technology , Hefei 230009 , P. R. China
| | - Xianli Xie
- School of Food and Biological Engineering, School of Chemistry and Chemical Engineering , Hefei University of Technology , Hefei 230009 , P. R. China
| | - Yan Ma
- School of Food and Biological Engineering, School of Chemistry and Chemical Engineering , Hefei University of Technology , Hefei 230009 , P. R. China
| | - Jingzhe Xue
- Department of Chemistry , University of Science and Technology of China , Hefei 230026 , P. R. China
| | - Tao He
- School of Food and Biological Engineering, School of Chemistry and Chemical Engineering , Hefei University of Technology , Hefei 230009 , P. R. China
| | - Zhengbao Zha
- School of Food and Biological Engineering, School of Chemistry and Chemical Engineering , Hefei University of Technology , Hefei 230009 , P. R. China
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21
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Kuk ACY, Hao A, Guan Z, Lee SY. Visualizing conformation transitions of the Lipid II flippase MurJ. Nat Commun 2019; 10:1736. [PMID: 30988294 PMCID: PMC6465408 DOI: 10.1038/s41467-019-09658-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 03/22/2019] [Indexed: 02/06/2023] Open
Abstract
The biosynthesis of many polysaccharides, including bacterial peptidoglycan and eukaryotic N-linked glycans, requires transport of lipid-linked oligosaccharide (LLO) precursors across the membrane by specialized flippases. MurJ is the flippase for the lipid-linked peptidoglycan precursor Lipid II, a key player in bacterial cell wall synthesis, and a target of recently discovered antibacterials. However, the flipping mechanism of LLOs including Lipid II remains poorly understood due to a dearth of structural information. Here we report crystal structures of MurJ captured in inward-closed, inward-open, inward-occluded and outward-facing conformations. Together with mutagenesis studies, we elucidate the conformational transitions in MurJ that mediate lipid flipping, identify the key ion for function, and provide a framework for the development of inhibitors. MurJ is the flippase for the lipid-linked peptidoglycan precursor Lipid II, a key player in bacterial cell wall synthesis, but the flipping mechanism remains poorly understood. Here authors report crystal structures of MurJ in different conformations which shed light on the MurJ transitions that mediate lipid flipping.
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Affiliation(s)
- Alvin C Y Kuk
- Department of Biochemistry, Duke University Medical Center, 303 Research Drive, Durham, NC, 27710, USA
| | - Aili Hao
- Department of Biochemistry, Duke University Medical Center, 303 Research Drive, Durham, NC, 27710, USA
| | - Ziqiang Guan
- Department of Biochemistry, Duke University Medical Center, 303 Research Drive, Durham, NC, 27710, USA
| | - Seok-Yong Lee
- Department of Biochemistry, Duke University Medical Center, 303 Research Drive, Durham, NC, 27710, USA.
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22
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Foster TJ. Can β-Lactam Antibiotics Be Resurrected to Combat MRSA? Trends Microbiol 2018; 27:26-38. [PMID: 30031590 DOI: 10.1016/j.tim.2018.06.005] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 05/25/2018] [Accepted: 06/22/2018] [Indexed: 01/26/2023]
Abstract
The use of β-lactam antibiotics to treat infections caused by Staphylococcus aureus has been severely compromised by the acquisition by horizontal gene transfer of a gene that encodes the β-lactam-insensitive penicillin-binding protein PBP2a. This allows methicillin-resistant S. aureus (MRSA) to proliferate in the presence of β-lactam antibiotics. Paradoxically the dependence on PBP2a for the essential transpeptidase activity in cell wall peptidoglycan biosynthesis is the 'Achilles heel' of MRSA. Compounds that disrupt the divisome, wall teichoic acid, and functional membrane microdomains act synergistically with β-lactams against MRSA. These include drugs such as statins that are widely used in human medicine. The antibiotics vancomycin and daptomycin are also synergistic with β-lactams, and combinations have been employed to treat persistent MRSA infections. An additional benefit of exposing MRSA to β-lactams could be a reduction in virulence mediated by interfering with the global regulator Agr. The mechanistic basis of synergy is discussed, and the possibility that β-lactams can be resurrected to combat MRSA infections is explored.
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Affiliation(s)
- Timothy J Foster
- Microbiology Department, Trinity College Dublin, Dublin 2, Ireland.
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