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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. [PMID: 38651516 DOI: 10.1039/d4np00002a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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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Daba GM, Elkhateeb WA. Ribosomally synthesized bacteriocins of lactic acid bacteria: Simplicity yet having wide potentials - A review. Int J Biol Macromol 2024; 256:128325. [PMID: 38007012 DOI: 10.1016/j.ijbiomac.2023.128325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 10/02/2023] [Accepted: 11/11/2023] [Indexed: 11/27/2023]
Abstract
Bacteriocins are ribosomally made bacterial peptides that have outstanding contributions in the field of food industry, as biopreservatives, and promising potentials in the medical field for improving human and animal health. Bacteriocins have many advantages over antibiotics such as being primary metabolites with relatively simpler biosynthetic mechanisms, which made their bioengineering for activity or specificity improving purposes much easier. Also, bacteriocins are degraded by proteolytic enzymes and do not stay in environment, which reduce chances of developing resistance. Bacteriocins can improve activity of some antibiotics, and some bacteriocins show potency against multidrug-resistant bacteria. Moreover, some potent bacteriocins have antiviral, antifungal, and antiprotozoal (antileishmanial) activities. On the other hand, bacteriocins have been introduced into the treatment of some ulcers and types of cancer. These potentials make bacteriocins attract extra attention as promising biotechnological tool. Hence, the history, characteristics, and classification of bacteriocins are described in this review. Furthermore, the main difference between bacteriocins and other antimicrobial peptides is clarified. Also, bacteriocins biosynthesis and identified modes of action are elucidated. Additionally, current and potential applications of bacteriocins in food and medical fields are highlighted. Finally, future perspectives concerning studying bacteriocins and their applications are discussed.
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Affiliation(s)
- Ghoson Mosbah Daba
- Chemistry of Natural and Microbial Products Department, Pharmaceutical Industries Researches Institute, National Research Centre, El Buhouth St., Egypt.
| | - Waill Ahmed Elkhateeb
- Chemistry of Natural and Microbial Products Department, Pharmaceutical Industries Researches Institute, National Research Centre, El Buhouth St., Egypt
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3
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Vuksanovic N, Melkonian TR, Serrano DA, Schwabacher AW, Silvaggi NR. Structural and Biochemical Characterization of MppQ, an L-Enduracididine Biosynthetic Enzyme from Streptomyces hygroscopicus. Biochemistry 2023; 62:3105-3115. [PMID: 37890134 DOI: 10.1021/acs.biochem.3c00428] [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: 10/29/2023]
Abstract
MppQ is an enzyme of unknown function from Streptomyces hygroscopicus (ShMppQ) that operates in the biosynthesis of the nonproteinogenic amino acid L-enduracididine (L-End). Since L-End is a component of several peptides showing activity against antibiotic-resistant pathogens, understanding its biosynthetic pathway could facilitate the development of chemoenzymatic routes to novel antibiotics. Herein, we report on the crystal structures of ShMppQ complexed with pyridoxal-5'-phosphate (PLP) and pyridoxamine-5'-phosphate (PMP). ShMppQ is similar to fold-type I PLP-dependent aminotransferases like aspartate aminotransferase. The tertiary structure of ShMppQ is composed of an N-terminal extension, a large domain, and a small domain. The active site is placed at the junction of the large and small domains and includes residues from both protomers of the homodimer. We also report the first functional characterization of MppQ, which we incubated with the enzymatically produced 2-ketoenduracidine and observed the conversion to L-End, establishing ShMppQ as the final enzyme in L-End biosynthesis. Additionally, we have observed that MppQ has a relatively high affinity for 2-keto-5-guanidinovaleric acid (i.e., 2-ketoarginine), a shunt product of MppP, indicating the potential role of MppQ in increasing the efficiency of L-End biosynthesis by converting 2-ketoarginine back to the starting material, l-arginine. A panel of potential amino-donor substrates was tested for the transamination activity against a saturating concentration of 2-ketoarginine in end-point assays. Most l-Arg was produced with l-ornithine as the donor substrate. Steady-state kinetic analysis of the transamination reaction with l-Orn and 2-ketoarginine shows that the kinetic constants are in line with those for the amino donor substrate of other fold-type I aminotransferases.
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Affiliation(s)
- Nemanja Vuksanovic
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Trevor R Melkonian
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Dante A Serrano
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
- Department of Chemistry, Pennsylvania State University, 302 Chemistry Building, University Park, Pennsylvania 16802, United States
| | - Alan W Schwabacher
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
| | - Nicholas R Silvaggi
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
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4
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Complex cyclic peptide synthesis via serine/threonine ligation chemistry. Bioorg Med Chem Lett 2021; 54:128430. [PMID: 34757215 DOI: 10.1016/j.bmcl.2021.128430] [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: 09/25/2021] [Revised: 10/18/2021] [Accepted: 10/21/2021] [Indexed: 11/21/2022]
Abstract
Non-ribosomal cyclic peptides are abundant in natural sources, exhibiting attractive bioactivities and favorable pharmacological properties. Furthermore, their structural complexity renders them as attractive synthetic targets. A general task for cyclic peptide synthesis is the peptide cyclization. Compared to the traditional dehydration-based peptide macrolactamization, chemoselective peptide ligation provides an alternative, sometimes advantageous, strategy to cyclize peptides. Herein, we provide a series of structurally complex cyclic peptide examples whose total syntheses were achieved via peptide ligation-mediated peptide cyclization. The special features of these strategies for achieving the total synthesis are highlighted.
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Wang J, Lin D, Liu M, Liu H, Blasco P, Sun Z, Cheung YC, Chen S, Li X. Total Synthesis of Mannopeptimycin β via β-Hydroxyenduracididine Ligation. J Am Chem Soc 2021; 143:12784-12790. [PMID: 34352177 DOI: 10.1021/jacs.1c05922] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nonribosomal peptide synthesis in bacteria has endowed cyclic peptides with fascinating structural complexity via incorporating nonproteinogenic amino acids. These bioactive cyclic peptides provide interesting structural motifs for exploring total synthesis and medicinal chemistry studies. Cyclic glycopeptide mannopeptimycins exhibit antibacterial activity against antibiotic-resistant Gram-positive pathogens and act as the lipid II binder to stop bacterial cell wall biosynthesis. Here, we report a strategy streamlining solution phase-solid phase synthesis and chemical ligation-mediated peptide cyclization for the total synthesis of mannopeptimycin β.
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Affiliation(s)
- Jinzheng Wang
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, P. R. China
| | - Du'an Lin
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, P. R. China
| | - Ming Liu
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, P. R. China
| | - Han Liu
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, P. R. China
| | - Pilar Blasco
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, P. R. China
| | - Zhenquan Sun
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, P. R. China
| | - Yan Chu Cheung
- Department of Infectious Diseases and Public Health, The City University of Hong Kong, Hong Kong, P. R. China
| | - Sheng Chen
- Department of Infectious Diseases and Public Health, The City University of Hong Kong, Hong Kong, P. R. China
| | - Xuechen Li
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, P. R. China
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6
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Sibinelli-Sousa S, Hespanhol JT, Bayer-Santos E. Targeting the Achilles' Heel of Bacteria: Different Mechanisms To Break Down the Peptidoglycan Cell Wall during Bacterial Warfare. J Bacteriol 2021; 203:e00478-20. [PMID: 33139480 PMCID: PMC8088523 DOI: 10.1128/jb.00478-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Bacteria commonly live in dense polymicrobial communities and compete for scarce resources. Consequently, they employ a diverse array of mechanisms to harm, inhibit, and kill their competitors. The cell wall is essential for bacterial survival by providing mechanical strength to resist osmotic stress. Because peptidoglycan is the major component of the cell wall and its synthesis is a complex multistep pathway that requires the coordinate action of several enzymes, it provides a target for rival bacteria, which have developed a large arsenal of antibacterial molecules to attack the peptidoglycan of competitors. These molecules include antibiotics, bacteriocins, and contact-dependent effectors that are either secreted into the medium or directly translocated into a target cell. In this minireview, we summarize the diversity of these molecules and highlight distinct mechanisms to disrupt the peptidoglycan, giving special attention to molecules that are known or have the potential to be used during interbacterial competitions.
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Affiliation(s)
- Stephanie Sibinelli-Sousa
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Julia Takuno Hespanhol
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Ethel Bayer-Santos
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
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Osbiston K, Oxbrough A, Fernández-Martínez LT. Antibiotic resistance levels in soils from urban and rural land uses in Great Britain. Access Microbiol 2020; 3:acmi000181. [PMID: 33997612 PMCID: PMC8115975 DOI: 10.1099/acmi.0.000181] [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: 08/26/2020] [Accepted: 11/03/2020] [Indexed: 12/24/2022] Open
Abstract
Although soil is one of the largest microbial diversity reservoirs, the processes that define its microbial community dynamics are not fully understood. Improving our understanding of the levels of antibiotic resistance in soils with different land uses in Great Britain is not only important for the protection of animal health (including humans), but also for gaining an insight into gene transfer levels in microbial communities. This study looked at the levels of antibiotic-resistant bacteria (ARB) able to survive inhibitory concentrations of chloramphenicol, erythromycin and vancomycin, as well as subinhibitory (10 µg ml−1) erythromycin concentrations. Soils from nine different sites across Great Britain with three distinct land uses (agricultural, urban and semi-natural) were sampled and the percentage of ARB was calculated for each site. Statistical analyses confirmed a significant difference in the level of ARB found in agricultural land compared to urban or semi-natural sites. The results also showed that resistance levels to vancomycin and chloramphenicol in the agricultural and urban sites sampled were significantly higher than those for erythromycin, whilst in semi-natural sites all three antibiotics show similar resistance levels. Finally, although the levels of resistance to a subinhibitory (10 µg ml−1) erythromycin concentration were significantly higher across land use types when compared to the levels of resistance to an inhibitory (20 µg ml−1) concentration, these were much less marked in soil from agricultural land compared to that from urban or semi-natural land use soil.
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Affiliation(s)
- Kieran Osbiston
- Biology Department, Edge Hill University, Ormskirk, L39 4QP, UK
| | - Anne Oxbrough
- Biology Department, Edge Hill University, Ormskirk, L39 4QP, UK
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Mühlberg E, Umstätter F, Domhan C, Hertlein T, Ohlsen K, Krause A, Kleist C, Beijer B, Zimmermann S, Haberkorn U, Mier W, Uhl P. Vancomycin-Lipopeptide Conjugates with High Antimicrobial Activity on Vancomycin-Resistant Enterococci. Pharmaceuticals (Basel) 2020; 13:ph13060110. [PMID: 32485876 PMCID: PMC7345083 DOI: 10.3390/ph13060110] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/26/2020] [Accepted: 05/27/2020] [Indexed: 12/18/2022] Open
Abstract
Multidrug-resistant bacteria represent one of the most important health care problems worldwide. While there are numerous drugs available for standard therapy, there are only a few compounds capable of serving as a last resort for severe infections. Therefore, approaches to control multidrug-resistant bacteria must be implemented. Here, a strategy of reactivating the established glycopeptide antibiotic vancomycin by structural modification with polycationic peptides and subsequent fatty acid conjugation to overcome the resistance of multidrug-resistant bacteria was followed. This study especially focuses on the structure-activity relationship, depending on the modification site and fatty acid chain length. The synthesized conjugates showed high antimicrobial potential on vancomycin-resistant enterococci. We were able to demonstrate that the antimicrobial activity of the vancomycin-lipopeptide conjugates depends on the chain length of the attached fatty acid. All conjugates showed good cytocompatibility in vitro and in vivo. Radiolabeling enabled the in vivo determination of pharmacokinetics in Wistar rats by molecular imaging and biodistribution studies. An improved biodistribution profile in comparison to unmodified vancomycin was observed. While vancomycin is rapidly excreted by the kidneys, the most potent conjugate shows a hepatobiliary excretion profile. In conclusion, these results demonstrate the potential of the structural modification of already established antibiotics to provide highly active compounds for tackling multidrug-resistant bacteria.
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Affiliation(s)
- Eric Mühlberg
- Department of Nuclear Medicine, Heidelberg University Hospital, Im Neuenheimer Feld 400, 69120 Heidelberg, Germany; (E.M.); (F.U.); (A.K.); (C.K.); (B.B.); (U.H.); (W.M.)
| | - Florian Umstätter
- Department of Nuclear Medicine, Heidelberg University Hospital, Im Neuenheimer Feld 400, 69120 Heidelberg, Germany; (E.M.); (F.U.); (A.K.); (C.K.); (B.B.); (U.H.); (W.M.)
| | - Cornelius Domhan
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany;
| | - Tobias Hertlein
- Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Straße 2/D15, 97080 Würzburg, Germany; (T.H.); (K.O.)
| | - Knut Ohlsen
- Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Straße 2/D15, 97080 Würzburg, Germany; (T.H.); (K.O.)
| | - Andreas Krause
- Department of Nuclear Medicine, Heidelberg University Hospital, Im Neuenheimer Feld 400, 69120 Heidelberg, Germany; (E.M.); (F.U.); (A.K.); (C.K.); (B.B.); (U.H.); (W.M.)
| | - Christian Kleist
- Department of Nuclear Medicine, Heidelberg University Hospital, Im Neuenheimer Feld 400, 69120 Heidelberg, Germany; (E.M.); (F.U.); (A.K.); (C.K.); (B.B.); (U.H.); (W.M.)
| | - Barbro Beijer
- Department of Nuclear Medicine, Heidelberg University Hospital, Im Neuenheimer Feld 400, 69120 Heidelberg, Germany; (E.M.); (F.U.); (A.K.); (C.K.); (B.B.); (U.H.); (W.M.)
| | - Stefan Zimmermann
- Department of Medical Microbiology and Hygiene, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120 Heidelberg Germany;
| | - Uwe Haberkorn
- Department of Nuclear Medicine, Heidelberg University Hospital, Im Neuenheimer Feld 400, 69120 Heidelberg, Germany; (E.M.); (F.U.); (A.K.); (C.K.); (B.B.); (U.H.); (W.M.)
- Clinical Cooperation Unit Nuclear Medicine, German Cancer Research Centre (DKFZ), Im Neuenheimer Feld 260, 69120 Heidelberg, Germany
| | - Walter Mier
- Department of Nuclear Medicine, Heidelberg University Hospital, Im Neuenheimer Feld 400, 69120 Heidelberg, Germany; (E.M.); (F.U.); (A.K.); (C.K.); (B.B.); (U.H.); (W.M.)
| | - Philipp Uhl
- Department of Nuclear Medicine, Heidelberg University Hospital, Im Neuenheimer Feld 400, 69120 Heidelberg, Germany; (E.M.); (F.U.); (A.K.); (C.K.); (B.B.); (U.H.); (W.M.)
- Correspondence: ; Tel.: +49-6221-56-7726
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9
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Malhi DS, Kaur M, Sohal HS. Effect of Substitutions on 1, 4‐Dihdropyridines to Achieve Potential Anti‐Microbial Drugs: A Review. ChemistrySelect 2019. [DOI: 10.1002/slct.201902354] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Dharambeer S. Malhi
- Department of ChemistryChandigarh University Gharuan- 140413, Mohali, Punjab India
| | - Manvinder Kaur
- Department of ChemistryChandigarh University Gharuan- 140413, Mohali, Punjab India
| | - Harvinder S. Sohal
- Department of ChemistryChandigarh University Gharuan- 140413, Mohali, Punjab India
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10
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Sheard DE, O’Brien-Simpson NM, Wade JD, Separovic F. Combating bacterial resistance by combination of antibiotics with antimicrobial peptides. PURE APPL CHEM 2019. [DOI: 10.1515/pac-2018-0707] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
The overuse of antibiotics in the healthcare and agricultural industries has led to the worldwide spread of bacterial resistance. The recent emergence of multidrug resistant (MDR) bacteria has resulted in a call for the development of novel strategies to address this global issue. Research on a diverse range of antimicrobial peptides (AMPs) has shown promising activity against several resistant strains. Increased understanding of the mode of action of AMPs has shown similarity and complementarity to conventional antibiotics and the combination of both has led to synergistic effects in some cases. Combination therapy has been widely used to combat MDR bacterial infections and the recent focus on their application with AMPs may allow antibiotics to be effective against resistant bacterial strains. By conjugation of an antibiotic onto an AMP, a compound may be produced with possibly greater activity and with reduced side-effects and toxicity. The AMP in these conjugates may also act as a unique adjuvant for the antibiotic by disrupting the resistance mechanisms used by bacteria thus allowing the antibiotic to once again be effective. This mini-review outlines some of the current and past work in combining AMPs with conventional antibiotics as strategies to address bacterial resistance.
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Affiliation(s)
- Dean E. Sheard
- School of Chemistry, Bio21 Institute, University of Melbourne , Melbourne, VIC 3010 , Australia
| | - Neil M. O’Brien-Simpson
- Centre of Oral Health Research, Melbourne Dental School, University of Melbourne , Melbourne, VIC 3010 , Australia
| | - John D. Wade
- School of Chemistry, Bio21 Institute, University of Melbourne , Melbourne, VIC 3010 , Australia
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne , Melbourne, VIC 3010 , Australia
| | - Frances Separovic
- School of Chemistry, Bio21 Institute, University of Melbourne , Melbourne, VIC 3010 , Australia
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Nagendra Prasad HS, Karthik CS, Manukumar HM, Mallesha L, Mallu P. New approach to address antibiotic resistance: Miss loading of functional membrane microdomains (FMM) of methicillin-resistant Staphylococcus aureus (MRSA). Microb Pathog 2018; 127:106-115. [PMID: 30503959 DOI: 10.1016/j.micpath.2018.11.038] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 11/22/2018] [Accepted: 11/26/2018] [Indexed: 12/13/2022]
Abstract
The synthesized potent piperazine analog ChDiPiCa was characterised by various spectroscopic techniques and for the first time evaluated functional membrane microdomain (FMM) disassembly in methicillin-resistant Staphylococcus aureus (MRSA). The ChDiPiCa showed excellent in vitro biocidal activity against MRSA at 26 μg/mL compared to the antibiotic streptomycin and bacitracin 14 μg/mL and 13 μg/mL at 10 μg concentration respectively. The membrane damaging property was confirmed by the SEM analysis. Further, we addressed the new approach for the first time to overcome antibiotic resistance of MRSA through membrane microdomain miss loading to lipids. By which, the ChDiPiCa confirms the significant activity in miss loading of FMM of MRSA which is validated by the fatty acid profile and lipid analysis. The result shows that, altered saturated (Lauric acid and Myristic acid), mono unsaturated (Oleic acid), and poly unsaturated (Linoleic acid and Linolenic acid) fatty acids and hypothesises, altered the membrane functional lipids. For the better understanding of miss loading of FMM by the ChDiPiCa, the in-silico molecular docking studies was analyzed and confirmed the predicted role. This suggests the way to develop ChDiPiCa in medicinal chemistry as anti-MRSA candidates and also this report opens up new window to treat microbial pathogens and infections.
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Affiliation(s)
- H S Nagendra Prasad
- Department of Chemistry, Sri Jayachamarajendra College of Engineering, JSS Science and Technology University, Mysuru, 570 006, Karnataka, India
| | - C S Karthik
- Department of Chemistry, Sri Jayachamarajendra College of Engineering, JSS Science and Technology University, Mysuru, 570 006, Karnataka, India
| | - H M Manukumar
- Department of Chemistry, Sri Jayachamarajendra College of Engineering, JSS Science and Technology University, Mysuru, 570 006, Karnataka, India
| | - L Mallesha
- PG Department of Chemistry, JSS College of Arts, Commerce and Science, Mysuru, 570025, Karnataka, India
| | - P Mallu
- Department of Chemistry, Sri Jayachamarajendra College of Engineering, JSS Science and Technology University, Mysuru, 570 006, Karnataka, India.
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12
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Katsuyama A, Yakushiji F, Ichikawa S. Total Synthesis of Plusbacin A3 and Its Dideoxy Derivative Using a Solvent-Dependent Diastereodivergent Joullié–Ugi Three-Component Reaction. J Org Chem 2018; 83:7085-7101. [DOI: 10.1021/acs.joc.8b00038] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Akira Katsuyama
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Fumika Yakushiji
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
- Center for Research and Education on Drug Discovery, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Satoshi Ichikawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
- Center for Research and Education on Drug Discovery, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
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13
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Liu L, Wu S, Wang Q, Zhang M, Wang B, He G, Chen G. Total synthesis of teixobactin and its stereoisomers. Org Chem Front 2018. [DOI: 10.1039/c8qo00145f] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The total syntheses of teixobactin and a series of its stereoisomers at positions 2, 5, 6, 10 and 11 were achieved via a combined strategy of solution and solid phase peptide synthesis.
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Affiliation(s)
- L. Liu
- State Key Laboratory of Elemento-Organic Chemistry
- College of Chemistry
- Nankai University
- Tianjin 300071
- China
| | - S. Wu
- State Key Laboratory of Elemento-Organic Chemistry
- College of Chemistry
- Nankai University
- Tianjin 300071
- China
| | - Q. Wang
- State Key Laboratory of Elemento-Organic Chemistry
- College of Chemistry
- Nankai University
- Tianjin 300071
- China
| | - M. Zhang
- State Key Laboratory of Elemento-Organic Chemistry
- College of Chemistry
- Nankai University
- Tianjin 300071
- China
| | - B. Wang
- State Key Laboratory of Elemento-Organic Chemistry
- College of Chemistry
- Nankai University
- Tianjin 300071
- China
| | - G. He
- State Key Laboratory of Elemento-Organic Chemistry
- College of Chemistry
- Nankai University
- Tianjin 300071
- China
| | - G. Chen
- State Key Laboratory of Elemento-Organic Chemistry
- College of Chemistry
- Nankai University
- Tianjin 300071
- China
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14
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Guo C, Mandalapu D, Ji X, Gao J, Zhang Q. Chemistry and Biology of Teixobactin. Chemistry 2017; 24:5406-5422. [PMID: 28991382 DOI: 10.1002/chem.201704167] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Indexed: 11/06/2022]
Abstract
Bacterial resistance to existing drugs is becoming a serious public health issue, urging extensive search for new antibiotics. Teixobactin, a cyclic depsipeptide discovered in a screen of uncultured bacteria, shows potent activity against all the tested Gram-positive bacteria. Remarkably, no teixobactin-resistant bacterial strain has been obtained despite extensive efforts, highlighting the great potential of teixobactin as a lead compound in the fight against antimicrobial resistance (AMR). This review summarizes recent progresses in the understanding of many aspects of teixobactin, including chemical structure, biological activity, biosynthetic pathway, and mode of action. We also discuss the different synthetic strategies in producing teixobactin and its analogues, and the structure-activity relationship (SAR) studies.
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Affiliation(s)
- Chuchu Guo
- Department of Chemistry, Fudan University, Shanghai, 200433, P. R. China
| | | | - Xinjian Ji
- Department of Chemistry, Fudan University, Shanghai, 200433, P. R. China
| | - Jiangtao Gao
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, P. R. China
| | - Qi Zhang
- Department of Chemistry, Fudan University, Shanghai, 200433, P. R. China
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15
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Santa Maria JP, Park Y, Yang L, Murgolo N, Altman MD, Zuck P, Adam G, Chamberlin C, Saradjian P, Dandliker P, Boshoff HIM, Barry CE, Garlisi C, Olsen DB, Young K, Glick M, Nickbarg E, Kutchukian PS. Linking High-Throughput Screens to Identify MoAs and Novel Inhibitors of Mycobacterium tuberculosis Dihydrofolate Reductase. ACS Chem Biol 2017; 12:2448-2456. [PMID: 28806050 DOI: 10.1021/acschembio.7b00468] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Though phenotypic and target-based high-throughput screening approaches have been employed to discover new antibiotics, the identification of promising therapeutic candidates remains challenging. Each approach provides different information, and understanding their results can provide hypotheses for a mechanism of action (MoA) and reveal actionable chemical matter. Here, we describe a framework for identifying efficacy targets of bioactive compounds. High throughput biophysical profiling against a broad range of targets coupled with machine learning was employed to identify chemical features with predicted efficacy targets for a given phenotypic screen. We validate the approach on data from a set of 55 000 compounds in 24 historical internal antibacterial phenotypic screens and 636 bacterial targets screened in high-throughput biophysical binding assays. Models were built to reveal the relationships between phenotype, target, and chemotype, which recapitulated mechanisms for known antibacterials. We also prospectively identified novel inhibitors of dihydrofolate reductase with nanomolar antibacterial efficacy against Mycobacterium tuberculosis. Molecular modeling provided structural insight into target-ligand interactions underlying selective killing activity toward mycobacteria over human cells.
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Affiliation(s)
- John P. Santa Maria
- Modeling & Informatics, Merck Research Laboratories, Boston, Massachusetts, United States
| | - Yumi Park
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States
| | - Lihu Yang
- Department of Chemistry, Merck Sharp & Dohme Corp., Kenilworth, New Jersey, United States
| | - Nicholas Murgolo
- Department of Information & Analytics, Merck Sharp & Dohme Corp., Kenilworth, New Jersey, United States
| | - Michael D. Altman
- Modeling & Informatics, Merck Research Laboratories, Boston, Massachusetts, United States
| | - Paul Zuck
- Research Science, Merck Sharp & Dohme Corp., North Wales, Pennsylvania, United States
| | - Greg Adam
- Department of Pharmacology, Merck Sharp & Dohme Corp., North Wales, Pennsylvania, United States
| | - Chad Chamberlin
- Department of Pharmacology, Merck Sharp & Dohme Corp., Boston, Massachusetts, United States
| | - Peter Saradjian
- Department of Pharmacology, Merck Sharp & Dohme Corp., Boston, Massachusetts, United States
| | - Peter Dandliker
- Department of Pharmacology, Merck Sharp & Dohme Corp., Boston, Massachusetts, United States
| | - Helena I. M. Boshoff
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States
| | - Clifton E. Barry
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States
| | - Charles Garlisi
- Department of Pharmacology, Merck Sharp & Dohme Corp., Kenilworth, New Jersey, United States
| | - David B. Olsen
- Neglected Tropical Disease Discovery, Merck Sharp & Dohme Corp., West Point, Pennsylvania, United States
| | - Katherine Young
- Neglected Tropical Disease Discovery, Merck Sharp & Dohme Corp., West Point, Pennsylvania, United States
| | - Meir Glick
- Modeling & Informatics, Merck Research Laboratories, Boston, Massachusetts, United States
| | - Elliott Nickbarg
- Department of Pharmacology, Merck Sharp & Dohme Corp., Boston, Massachusetts, United States
| | - Peter S. Kutchukian
- Modeling & Informatics, Merck Research Laboratories, Boston, Massachusetts, United States
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16
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Luther A, Bisang C, Obrecht D. Advances in macrocyclic peptide-based antibiotics. Bioorg Med Chem 2017; 26:2850-2858. [PMID: 28886999 DOI: 10.1016/j.bmc.2017.08.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 07/14/2017] [Accepted: 08/06/2017] [Indexed: 11/30/2022]
Abstract
Macrocyclic peptide-based natural products have provided powerful new antibiotic drugs, drug candidates, and scaffolds for medicinal chemists as a source of inspiration to design novel antibiotics. While most of those natural products are active mainly against Gram-positive pathogens, novel macrocyclic peptide-based compounds have recently been described, which exhibit potent and specific activity against some of the most problematic Gram-negative ESKAPE pathogens. This mini-review gives an up-date on recent developments.
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Affiliation(s)
- Anatol Luther
- Polyphor Ltd, Hegenheimermattweg 125, CH-4123 Allschwil, Switzerland.
| | - Christian Bisang
- Polyphor Ltd, Hegenheimermattweg 125, CH-4123 Allschwil, Switzerland
| | - Daniel Obrecht
- Polyphor Ltd, Hegenheimermattweg 125, CH-4123 Allschwil, Switzerland.
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17
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Müller A, Klöckner A, Schneider T. Targeting a cell wall biosynthesis hot spot. Nat Prod Rep 2017; 34:909-932. [PMID: 28675405 DOI: 10.1039/c7np00012j] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Covering: up to 2017History points to the bacterial cell wall biosynthetic network as a very effective target for antibiotic intervention, and numerous natural product inhibitors have been discovered. In addition to the inhibition of enzymes involved in the multistep synthesis of the macromolecular layer, in particular, interference with membrane-bound substrates and intermediates essential for the biosynthetic reactions has proven a valuable antibacterial strategy. A prominent target within the peptidoglycan biosynthetic pathway is lipid II, which represents a particular "Achilles' heel" for antibiotic attack, as it is readily accessible on the outside of the cytoplasmic membrane. Lipid II is a unique non-protein target that is one of the structurally most conserved molecules in bacterial cells. Notably, lipid II is more than just a target molecule, since sequestration of the cell wall precursor may be combined with additional antibiotic activities, such as the disruption of membrane integrity or disintegration of membrane-bound multi-enzyme machineries. Within the membrane bilayer lipid II is likely organized in specific anionic phospholipid patches that form a particular "landing platform" for antibiotics. Nature has invented a variety of different "lipid II binders" of at least 5 chemical classes, and their antibiotic activities can vary substantially depending on the compounds' physicochemical properties, such as amphiphilicity and charge, and thus trigger diverse cellular effects that are decisive for antibiotic activity.
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Affiliation(s)
- Anna Müller
- Institute of Pharmaceutical Microbiology, University of Bonn, Bonn, Germany.
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18
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Fuse S, Tanaka H, Takahashi T, Doi T. Total Synthesis and Stereochemistry Revision of Mannopeptimycin Aglycone. J SYN ORG CHEM JPN 2017. [DOI: 10.5059/yukigoseikyokaishi.75.1274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Shinichiro Fuse
- Institute of Innovative Research, Tokyo Institute of Technology
| | - Hiroshi Tanaka
- School of Materials and Chemical Technology, Tokyo Institute of Technology
| | - Takashi Takahashi
- Department of Pharmaceutical Sciences, Yokohama University of Pharmacy
| | - Takayuki Doi
- Graduate School of Pharmaceutical Sciences, Tohoku University
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19
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Anti-inflammatory Properties of Antimicrobial Peptides and Peptidomimetics: LPS and LTA Neutralization. Methods Mol Biol 2017; 1548:369-386. [PMID: 28013519 DOI: 10.1007/978-1-4939-6737-7_27] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Lipopolysaccharide (LPS) and lipoteichoic acid (LTA) neutralization constitute potential non-antibiotic treatment strategies for sepsis - a systemic infection-induced inflammatory response. Studies on LPS- and LTA-neutralizing compounds are abundant in literature, and a number of peptides and peptidomimetics appear to display promising activity. However, in this ongoing search for potential antisepsis drug leads, it will be preferable that the assays used by different research groups lead to readily comparable data for the most efficient compounds. Here, we propose and describe standardized methods to be used for testing of novel compounds for their LPS- and LTA-neutralizing capacity with a focus on functional suppression of pro-inflammatory responses in cell-based systems. To best mimic the human in vivo conditions, we suggest the use of freshly isolated human leukocytes combined with an appropriate method for the chosen cytokine (e.g., IL-6 or TNF-α). The described protocols comprise isolation, stimulation, and viability test of the human leukocytes.
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20
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Dormán G, Nakamura H, Pulsipher A, Prestwich GD. The Life of Pi Star: Exploring the Exciting and Forbidden Worlds of the Benzophenone Photophore. Chem Rev 2016; 116:15284-15398. [PMID: 27983805 DOI: 10.1021/acs.chemrev.6b00342] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The widespread applications of benzophenone (BP) photochemistry in biological chemistry, bioorganic chemistry, and material science have been prominent in both academic and industrial research. BP photophores have unique photochemical properties: upon n-π* excitation at 365 nm, a biradicaloid triplet state is formed reversibly, which can abstract a hydrogen atom from accessible C-H bonds; the radicals subsequently recombine, creating a stable covalent C-C bond. This light-directed covalent attachment process is exploited in many different ways: (i) binding/contact site mapping of ligand (or protein)-protein interactions; (ii) identification of molecular targets and interactome mapping; (iii) proteome profiling; (iv) bioconjugation and site-directed modification of biopolymers; (v) surface grafting and immobilization. BP photochemistry also has many practical advantages, including low reactivity toward water, stability in ambient light, and the convenient excitation at 365 nm. In addition, several BP-containing building blocks and reagents are commercially available. In this review, we explore the "forbidden" (transitions) and excitation-activated world of photoinduced covalent attachment of BP photophores by touring a colorful palette of recent examples. In this exploration, we will see the pros and cons of using BP photophores, and we hope that both novice and expert photolabelers will enjoy and be inspired by the breadth and depth of possibilities.
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Affiliation(s)
- György Dormán
- Targetex llc , Dunakeszi H-2120, Hungary.,Faculty of Pharmacy, University of Szeged , Szeged H-6720, Hungary
| | - Hiroyuki Nakamura
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology , Yokohama 226-8503, Japan
| | - Abigail Pulsipher
- GlycoMira Therapeutics, Inc. , Salt Lake City, Utah 84108, United States.,Division of Head and Neck Surgery, Rhinology - Sinus and Skull Base Surgery, Department of Surgery, University of Utah School of Medicine , Salt Lake City, Utah 84108, United States
| | - Glenn D Prestwich
- Division of Head and Neck Surgery, Rhinology - Sinus and Skull Base Surgery, Department of Surgery, University of Utah School of Medicine , Salt Lake City, Utah 84108, United States
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21
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New antibiotics from Nature’s chemical inventory. Bioorg Med Chem 2016; 24:6227-6252. [DOI: 10.1016/j.bmc.2016.09.014] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/07/2016] [Indexed: 01/07/2023]
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22
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Lin CK, Hou CC, Guo YY, Cheng WC. Design and Synthesis of Orthogonally Protected d- and l-β-Hydroxyenduracididines from d-lyxono-1,4-Lactone. Org Lett 2016; 18:5216-5219. [DOI: 10.1021/acs.orglett.6b02444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Cheng-Kun Lin
- Genomics
Research Center, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan
| | - Chung-Chien Hou
- Genomics
Research Center, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan
| | - Yi-Yong Guo
- Genomics
Research Center, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan
| | - Wei-Chieh Cheng
- Genomics
Research Center, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan
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23
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Solid-state NMR characterization of amphomycin effects on peptidoglycan and wall teichoic acid biosyntheses in Staphylococcus aureus. Sci Rep 2016; 6:31757. [PMID: 27538449 PMCID: PMC4990924 DOI: 10.1038/srep31757] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 07/27/2016] [Indexed: 11/09/2022] Open
Abstract
Amphomycin and MX-2401 are cyclic lipopeptides exhibiting bactericidal activities against Gram-positive pathogens. Amphomycin and MX-2401 share structural similarities with daptomycin, but unlike daptomycin they do not target bacterial membrane. In this study, we investigate in vivo modes of action for amphomycin and MX-2401 in intact whole cells of Staphylococcus aureus by measuring the changes of peptidoglycan and wall teichoic acid compositions using solid-state NMR. S. aureus were grown in a defined media containing isotope labels [1-13C]glycine and L-[ε-15N]lysin, L-[1-13C]lysine and D-[15N]alanine, or D-[1-13C]alanine and [15N]glycine, to selectively 13C-15N pair label peptidoglycan bridge-link, stem-link, and cross-link, respectively. 13C{15N} and 15N{13C} rotational-echo double resonance NMR measurements determined that cyclic lipopeptide-treated S. aureus exhibited thinning of the cell wall, accumulation of Park’s nucleotide, inhibition of glycine utilization for purine biosynthesis, reduction of ester-linked D-Ala in teichoic acids, and reduction of peptidoglycan cross-linking. Whole cell NMR analysis also revealed that S. aureus, in presence of amphomycin and MX-2401, maintained the incorporation of D-Ala during peptidoglycan biosynthesis while the incorporation of D-Ala into teichoic acids was inhibited. These effects are consistent with amphomycin’s dual inhibition of both peptidoglycan and wall teichoic acid biosyntheses in S. aureus.
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24
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Ng V, Chan WC. New Found Hope for Antibiotic Discovery: Lipid II Inhibitors. Chemistry 2016; 22:12606-16. [PMID: 27388768 DOI: 10.1002/chem.201601315] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Indexed: 12/14/2022]
Abstract
Research into antibacterial agents has recently gathered pace in light of the disturbing crisis of antimicrobial resistance. The development of modern tools offers the opportunity of reviving the fallen era of antibacterial discovery through uncovering novel lead compounds that target vital bacterial cell components, such as lipid II. This paper provides a summary of the role of lipid II as well as an overview and insight into the structural features of macrocyclic peptides that inhibit this bacterial cell wall component. The recent discovery of teixobactin, a new class of lipid II inhibitor has generated substantial research interests. As such, the significant progress that has been achieved towards its development as a promising antibacterial agent is discussed.
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Affiliation(s)
- Vivian Ng
- School of Pharmacy, Centre of Biomolecular Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Weng C Chan
- School of Pharmacy, Centre of Biomolecular Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
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25
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Binda E, Carrano L, Marcone GL, Marinelli F. Extraction and Analysis of Peptidoglycan Cell Wall Precursors. Methods Mol Biol 2016; 1440:153-70. [PMID: 27311671 DOI: 10.1007/978-1-4939-3676-2_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
Abstract
Extraction and analysis by LC-MS of peptidoglycan precursors represent a valuable method to study antibiotic mode of action and resistance in bacteria. Here, we describe how to apply this method for: (1) testing the action of different classes of antibiotics inhibiting cell wall biosynthesis in Bacillus megaterium; (2) studying the mechanism of self-resistance in mycelial actinomycetes producing glycopeptide antibiotics.
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Affiliation(s)
- Elisa Binda
- Department of Biotechnology and Life Sciences, University of Insubria, Via Dunant, Varese, 3-21100, Italy.,"The Protein Factory" Research Center, Politecnico of Milano, ICRM CNR Milano University of Insubria, Via Dunant, Varese, 3-21100, Italy
| | - Lùcia Carrano
- Fondazione Istituto Insubrico Ricerca per la Vita (F.I.I.R.V.), Via R. Lepetit 32, Gerenzano, 21100, Italy
| | - Giorgia Letizia Marcone
- Department of Biotechnology and Life Sciences, University of Insubria, Via Dunant, Varese, 3-21100, Italy.,"The Protein Factory" Research Center, Politecnico of Milano, ICRM CNR Milano University of Insubria, Via Dunant, Varese, 3-21100, Italy
| | - Flavia Marinelli
- Department of Biotechnology and Life Sciences, University of Insubria, Via Dunant, Varese, 3-21100, Italy. .,"The Protein Factory" Research Center, Politecnico of Milano, ICRM CNR Milano University of Insubria, Via Dunant, Varese, 3-21100, Italy.
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26
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Wang B, Liu Y, Jiao R, Feng Y, Li Q, Chen C, Liu L, He G, Chen G. Total Synthesis of Mannopeptimycins α and β. J Am Chem Soc 2016; 138:3926-32. [PMID: 26914640 DOI: 10.1021/jacs.6b01384] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mannopeptimycins are a class of glycopeptide natural products with unusual structures and potent antibiotic activity against a range of Gram-positive multidrug-resistant bacteria. Their cyclic hexapeptide core features a pair of unprecedented β-hydroxyenduracididines (L- and D-βhEnd), an O-glycosylated D-Tyr carrying an α-linked dimannose, and a β-methylated Phe residue. The D-βhEnd unit also carries an α-linked mannopyranose at the most hindered N of its cyclic guanidine ring. Herein, we report the first total synthesis of mannopeptimycin α and β with fully elaborated N- and O-linked sugars. Critically, a gold-catalyzed N-glycosylation of a D-βhEnd substrate with a mannosyl ortho-alkynylbenzoate donor enabled the synthesis of the most challenging N-Man-D-βhEnd unit with excellent efficiency and stereoselectivity. The L-βMePhe unit was prepared using a Pd-catalyzed C-H arylation method. The L-βhEnd, D-Tyr(di-Man), and L-βMePhe units were prepared in gram quantities. A convergent assembly of the cyclic peptide scaffold and a single global hydrogenolysis deprotection operation provided mannopeptimycin α and β.
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Affiliation(s)
- Bo Wang
- Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Yunpeng Liu
- Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Rui Jiao
- Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Yiqing Feng
- Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Qiong Li
- Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Chen Chen
- Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Long Liu
- State Key Laboratory and Institute of Elemento-Organic Chemistry, Nankai University , Tianjin 300071, China
| | - Gang He
- State Key Laboratory and Institute of Elemento-Organic Chemistry, Nankai University , Tianjin 300071, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) , Tianjin 300071, China
| | - Gong Chen
- State Key Laboratory and Institute of Elemento-Organic Chemistry, Nankai University , Tianjin 300071, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) , Tianjin 300071, China.,Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
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27
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Lin CK, Yun WY, Lin LT, Cheng WC. A concise approach to the synthesis of the uniqueN-mannosyld-β-hydroxyenduracididine moiety in the mannopeptimycin series of natural products. Org Biomol Chem 2016; 14:4054-60. [DOI: 10.1039/c6ob00644b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The asymmetric synthesis of the orthogonally protectedN-mannosyld-β-hydroxyenduracididine (N-Man-d-βhEnd) is described, starting from enantiopure silylated (S)-serinol.
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Affiliation(s)
| | - Wen-Yi Yun
- Genomics Research Center
- Academia Sinica
- Taipei
- Taiwan
| | - Lin-Ting Lin
- Department of Chemistry
- National Cheng Kung University
- Tainan City
- Taiwan
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28
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References. Antibiotics (Basel) 2015. [DOI: 10.1128/9781555819316.refs] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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29
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Han L, Schwabacher AW, Moran GR, Silvaggi NR. Streptomyces wadayamensis MppP Is a Pyridoxal 5′-Phosphate-Dependent l-Arginine α-Deaminase, γ-Hydroxylase in the Enduracididine Biosynthetic Pathway. Biochemistry 2015; 54:7029-40. [DOI: 10.1021/acs.biochem.5b01016] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lanlan Han
- Department of Chemistry and
Biochemistry, University of Wisconsin—Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
| | - Alan W. Schwabacher
- Department of Chemistry and
Biochemistry, University of Wisconsin—Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
| | - Graham R. Moran
- Department of Chemistry and
Biochemistry, University of Wisconsin—Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
| | - Nicholas R. Silvaggi
- Department of Chemistry and
Biochemistry, University of Wisconsin—Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
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30
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Fletcher S, Yu W, Huang J, Kwasny SM, Chauhan J, Opperman TJ, MacKerell AD, de Leeuw EPH. Structure-activity exploration of a small-molecule Lipid II inhibitor. Drug Des Devel Ther 2015; 9:2383-94. [PMID: 25987836 PMCID: PMC4422293 DOI: 10.2147/dddt.s79504] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We have recently identified low-molecular weight compounds that act as inhibitors of Lipid II, an essential precursor of bacterial cell wall biosynthesis. Lipid II comprises specialized lipid (bactoprenol) linked to a hydrophilic head group consisting of a peptidoglycan subunit (N-acetyl glucosamine [GlcNAc]–N-acetyl muramic acid [MurNAc] disaccharide coupled to a short pentapeptide moiety) via a pyrophosphate. One of our lead compounds, a diphenyl-trimethyl indolene pyrylium, termed BAS00127538, interacts with the MurNAc moiety and the isoprenyl tail of Lipid II. Here, we report on the structure–activity relationship of BAS00127538 derivatives obtained by in silico analyses and de novo chemical synthesis. Our results indicate that Lipid II binding and bacterial killing are related to three features: the diphenyl moiety, the indolene moiety, and the positive charge of the pyrylium. Replacement of the pyrylium moiety with an N-methyl pyridinium, which may have importance in stability of the molecule, did not alter Lipid II binding or antibacterial potency.
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Affiliation(s)
- Steven Fletcher
- Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, Baltimore, MD, USA
| | - Wenbo Yu
- Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, Baltimore, MD, USA ; Computer-Aided Drug Design Center, University of Maryland, School of Pharmacy, Baltimore, MD, USA
| | - Jing Huang
- Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, Baltimore, MD, USA ; Computer-Aided Drug Design Center, University of Maryland, School of Pharmacy, Baltimore, MD, USA
| | | | - Jay Chauhan
- Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, Baltimore, MD, USA
| | | | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, Baltimore, MD, USA ; Computer-Aided Drug Design Center, University of Maryland, School of Pharmacy, Baltimore, MD, USA
| | - Erik P H de Leeuw
- Institute of Human Virology and Department of Biochemistry and Molecular Biology, University of Maryland, School of Medicine, Baltimore, MD, USA
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31
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Fuse S, Koinuma H, Kimbara A, Izumikawa M, Mifune Y, He H, Shin-ya K, Takahashi T, Doi T. Total Synthesis and Stereochemistry Revision of Mannopeptimycin Aglycone. J Am Chem Soc 2014; 136:12011-7. [DOI: 10.1021/ja505105t] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shinichiro Fuse
- Department
of Applied Chemistry, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8552, Japan
| | - Hirotsugu Koinuma
- Department
of Applied Chemistry, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8552, Japan
| | - Atsushi Kimbara
- Department
of Applied Chemistry, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8552, Japan
| | - Miho Izumikawa
- Japan Biological Informatics Consortium (JBIC), Koto-ku, Tokyo 135-0064, Japan
| | - Yuto Mifune
- Department
of Applied Chemistry, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8552, Japan
| | - Haiyin He
- Natural
Products Laboratory, Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Kazuo Shin-ya
- National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo 135-0064, Japan
| | | | - Takayuki Doi
- Graduate
School of Pharmaceutical Sciences, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
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Varney KM, Bonvin AMJJ, Pazgier M, Malin J, Yu W, Ateh E, Oashi T, Lu W, Huang J, Diepeveen-de Buin M, Bryant J, Breukink E, MacKerell AD, de Leeuw EPH. Turning defense into offense: defensin mimetics as novel antibiotics targeting lipid II. PLoS Pathog 2013; 9:e1003732. [PMID: 24244161 PMCID: PMC3820767 DOI: 10.1371/journal.ppat.1003732] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 09/12/2013] [Indexed: 01/09/2023] Open
Abstract
We have previously reported on the functional interaction of Lipid II with human alpha-defensins, a class of antimicrobial peptides. Lipid II is an essential precursor for bacterial cell wall biosynthesis and an ideal and validated target for natural antibiotic compounds. Using a combination of structural, functional and in silico analyses, we present here the molecular basis for defensin-Lipid II binding. Based on the complex of Lipid II with Human Neutrophil peptide-1, we could identify and characterize chemically diverse low-molecular weight compounds that mimic the interactions between HNP-1 and Lipid II. Lead compound BAS00127538 was further characterized structurally and functionally; it specifically interacts with the N-acetyl muramic acid moiety and isoprenyl tail of Lipid II, targets cell wall synthesis and was protective in an in vivo model for sepsis. For the first time, we have identified and characterized low molecular weight synthetic compounds that target Lipid II with high specificity and affinity. Optimization of these compounds may allow for their development as novel, next generation therapeutic agents for the treatment of Gram-positive pathogenic infections. Every year, an increasing number of people are at risk for bacterial infections that cannot be effectively treated. This is because many bacteria are becoming more resistant to antibiotics. Of particular concern is the rise in hospital-acquired infections. Infection caused by the methicillin-resistant Staphylococcus aureus bacterium or MRSA is the cause of many fatalities and puts a burden on health care systems in many countries. The antibiotic of choice for treatment of S. aureus infections is vancomycin, an antimicrobial peptide that kills bacteria by binding to the bacterial cell wall component Lipid II. Here, we have identified for the first time, small synthetic compounds that also bind Lipid II with the aim to develop new antibiotic drugs to fight against bacterial infections.
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Affiliation(s)
- Kristen M. Varney
- NMR Facility, University of Maryland Baltimore School of Medicine, Baltimore, Maryland, United States of America
| | - Alexandre M. J. J. Bonvin
- Utrecht University, Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry, Utrecht, The Netherlands
| | - Marzena Pazgier
- Institute of Human Virology & Department of Biochemistry and Molecular Biology of the University of Maryland Baltimore School of Medicine, Baltimore, Maryland, United States of America
| | - Jakob Malin
- Maastricht University Medical Center, Maastricht, The Netherlands
| | - Wenbo Yu
- Department of Pharmaceutical Sciences and Computer-Aided Drug Design Center, University of Maryland, School of Pharmacy, Baltimore, Maryland, United States of America
| | - Eugene Ateh
- Institute of Human Virology & Department of Biochemistry and Molecular Biology of the University of Maryland Baltimore School of Medicine, Baltimore, Maryland, United States of America
| | - Taiji Oashi
- Department of Pharmaceutical Sciences and Computer-Aided Drug Design Center, University of Maryland, School of Pharmacy, Baltimore, Maryland, United States of America
| | - Wuyuan Lu
- Institute of Human Virology & Department of Biochemistry and Molecular Biology of the University of Maryland Baltimore School of Medicine, Baltimore, Maryland, United States of America
| | - Jing Huang
- Department of Pharmaceutical Sciences and Computer-Aided Drug Design Center, University of Maryland, School of Pharmacy, Baltimore, Maryland, United States of America
| | - Marlies Diepeveen-de Buin
- Utrecht University, Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry, Utrecht, The Netherlands
| | - Joseph Bryant
- Institute of Human Virology & Department of Biochemistry and Molecular Biology of the University of Maryland Baltimore School of Medicine, Baltimore, Maryland, United States of America
| | - Eefjan Breukink
- Utrecht University, Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry, Utrecht, The Netherlands
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences and Computer-Aided Drug Design Center, University of Maryland, School of Pharmacy, Baltimore, Maryland, United States of America
| | - Erik P. H. de Leeuw
- Institute of Human Virology & Department of Biochemistry and Molecular Biology of the University of Maryland Baltimore School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
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Morita S, Tagai C, Shiraishi T, Miyaji K, Iwamuro S. Differential mode of antimicrobial actions of arginine-rich and lysine-rich histones against Gram-positive Staphylococcus aureus. Peptides 2013; 48:75-82. [PMID: 23932939 DOI: 10.1016/j.peptides.2013.07.025] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 07/30/2013] [Accepted: 07/30/2013] [Indexed: 11/28/2022]
Abstract
We previously reported the activities and modes of action of arginine (Arg)-rich histones H3 and H4 against Gram-negative bacteria. In the present study, we investigated the properties of the Arg-rich histones against Gram-positive bacteria in comparison with those of lysine (Lys)-rich histone H2B. In a standard microdilution assay, calf thymus histones H2B, H3, and H4 showed growth inhibitory activity against Staphylococcus aureus with minimum effective concentration values of 4.0, 4.0, and 5.6 μM, respectively. Laser confocal microscopic analyses revealed that both the Arg-rich and Lys-rich histones associated with the surface of S. aureus. However, while the morphology of S. aureus treated with histone H2B appeared intact, those treated with the histones H3 and H4 closely resembled each other, and the cells were blurred. Electrophoretic mobility shift assay results revealed these histones have binding affinity to lipoteichoic acid (LTA), one of major cell surface components of Gram-positive bacteria. Scanning electron microscopic analyses demonstrated that while histone H2B elicited no obvious changes in cell morphology, histones H3 and H4 disrupted the cell membrane structure with bleb formation in a manner similar to general antimicrobial peptides. Consequently, our results suggest that bacterial cell surface LTA initially attracts both the Arg- and Lys-rich histones, but the modes of antimicrobial action of these histones are different; the former involves cell membrane disruption and the latter involves the cell integrity disruption.
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Affiliation(s)
- Shuu Morita
- Department of Biology, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
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Burroughs AM, Hoppe RW, Goebel NC, Sayyed BH, Voegtline TJ, Schwabacher AW, Zabriskie TM, Silvaggi NR. Structural and functional characterization of MppR, an enduracididine biosynthetic enzyme from streptomyces hygroscopicus: functional diversity in the acetoacetate decarboxylase-like superfamily. Biochemistry 2013; 52:4492-506. [PMID: 23758195 DOI: 10.1021/bi400397k] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The nonproteinogenic amino acid enduracididine is a critical component of the mannopeptimycins, cyclic glycopeptide antibiotics with activity against drug-resistant pathogens, including methicillin-resistant Staphylococcus aureus. Enduracididine is produced in Streptomyces hygroscopicus by three enzymes, MppP, MppQ, and MppR. On the basis of primary sequence analysis, MppP and MppQ are pyridoxal 5'-phosphate-dependent aminotransferases; MppR shares a low, but significant, level of sequence identity with acetoacetate decarboxylase. The exact reactions catalyzed by each enzyme and the intermediates involved in the route to enduracididine are currently unknown. Herein, we present biochemical and structural characterization of MppR that demonstrates a catalytic activity for this enzyme and provides clues about its role in enduracididine biosynthesis. Bioinformatic analysis shows that MppR belongs to a previously uncharacterized family within the acetoacetate decarboxylase-like superfamily (ADCSF) and suggests that MppR-like enzymes may catalyze reactions diverging from the well-characterized, prototypical ADCSF decarboxylase activity. MppR shares a high degree of structural similarity with acetoacetate decarboxylase, though the respective quaternary structures differ markedly and structural differences in the active site explain the observed loss of decarboxylase activity. The crystal structure of MppR in the presence of a mixture of pyruvate and 4-imidazolecarboxaldehyde shows that MppR catalyzes the aldol condensation of these compounds and subsequent dehydration. Surprisingly, the structure of MppR in the presence of "4-hydroxy-2-ketoarginine" shows the correct 4R enantiomer of "2-ketoenduracididine" bound to the enzyme. These data, together with bioinformatic analysis of MppR homologues, identify a novel family within the acetoacetate decarboxylase-like superfamily with divergent active site structure and, consequently, biochemical function.
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Affiliation(s)
- A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
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Schitter G, Wrodnigg TM. Update on carbohydrate-containing antibacterial agents. Expert Opin Drug Discov 2013; 4:315-56. [PMID: 23489128 DOI: 10.1517/17460440902778725] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND Since the first known use of antibiotics > 2,500 years ago, a research field with immense importance for the welfare of mankind has been developed. After a decrease in interest in this topic by the end of the 20th century the occurrence of (poly-)resistant strains of bacteria induced a revival of antibiotics research. Health systems have been seeking viable and reliable solutions to this dangerous and expansive threat. OBJECTIVE This review will focus on carbohydrate-containing antibiotics and will give an outline of recently published novel isolated, semisynthetic as well as synthetic structures, their mechanism of action, if known, and the strategies for the design of compounds with potential by improved antibacterial properties. METHODS The literature between 2000 and 2008 was screened with main focus on recent examples of novel structures and strategies for the lead finding of exclusively antibacterial agents. RESULTS/CONCLUSION With the explanation of the role of the carbohydrate moieties in the respective antibacterial agents together with better synthetic strategies in carbohydrate chemistry as well as improvements in assay development for high throughput screening methods, carbohydrate-containing antibiotics can be used for the finding of potential drug leads that contribute to the fight against infections and diseases caused by (resistant) bacterial pathogens.
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Affiliation(s)
- Georg Schitter
- Technical University Graz, Institute of Organic Chemistry, Univ.-Doz. TMW, Dip.-Ing. GS, Glycogroup, A-8010 Graz, Austria +43 316 873 8744 ; +43 316 873 8740 ;
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Abstract
The synthesis of the bacterial peptidoglycan has been recognized for over 50 years as fertile ground for antibacterial discovery. Initially, empirical screening of natural products for inhibition of bacterial growth detected many chemical classes of antibiotics whose specific mechanisms of action were eventually dissected and defined. Of the nontoxic antibiotics discovered, most were found to be inhibitors of either protein synthesis or cell wall synthesis, which led to more directed screening for inhibitors of these pathways. Directed screening and design programs for cell wall inhibitors have been undertaken since the 1960s. In that time it has become clear that, while certain steps and intermediates have yielded selective inhibitors and are established targets, other potential targets have not yielded inhibitors whose antibacterial activity is proven to be solely due to that inhibition. Why has this search been so problematic? Are the established targets still worth pursuing? This review will attempt to answer these and other questions and evaluate the viability of targets related to peptidoglycan synthesis.
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Affiliation(s)
- Lynn L Silver
- LL Silver Consulting, LLC, Springfield, New Jersey 07081, USA.
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Gautam A, Vyas R, Tewari R. Peptidoglycan biosynthesis machinery: a rich source of drug targets. Crit Rev Biotechnol 2010; 31:295-336. [PMID: 21091161 DOI: 10.3109/07388551.2010.525498] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The range of antibiotic therapy for the control of bacterial infections is becoming increasingly limited because of the rapid rise in multidrug resistance in clinical bacterial isolates. A few diseases, such as tuberculosis, which were once thought to be under control, have re-emerged as serious health threats. These problems have resulted in intensified research to look for new inhibitors for bacterial pathogens. Of late, the peptidoglycan (PG) layer, the most important component of the bacterial cell wall has been the subject of drug targeting because, first, it is essential for the survivability of eubacteria and secondly, it is absent in humans. The last decade has seen tremendous inputs in deciphering the 3-D structures of the PG biosynthetic enzymes. Many inhibitors against these enzymes have been developed using virtual and high throughput screening techniques. This review discusses the mechanistic and structural properties of the PG biosynthetic enzymes and inhibitors developed in the last decade.
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Affiliation(s)
- Ankur Gautam
- Department of Biotechnology, Panjab University, Chandigarh, India
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38
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β-Lactam and glycopeptide antibiotics: first and last line of defense? Trends Biotechnol 2010; 28:596-604. [PMID: 20970210 DOI: 10.1016/j.tibtech.2010.09.004] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Revised: 09/06/2010] [Accepted: 09/20/2010] [Indexed: 01/21/2023]
Abstract
Most infections are caused by bacteria, many of which are ever-evolving and resistant to nearly all available antibiotics. β-Lactams and glycopeptides are used to combat these infections by inhibiting bacterial cell-wall synthesis. This mechanism remains an interesting target in the search for new antibiotics in light of failed genomic approaches and the limited input of major pharmaceutical companies. Several strategies have enriched the pipeline of bacterial cell-wall inhibitors; examples include combining screening strategies with lesser-explored microbial diversity, or reinventing known scaffolds based on structure-function relationships. Drugs developed using novel strategies will contribute to the arsenal in fight against the continued emergence of bacterial resistance.
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Brötz-Oesterhelt H, Sass P. Postgenomic strategies in antibacterial drug discovery. Future Microbiol 2010; 5:1553-79. [DOI: 10.2217/fmb.10.119] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
During the last decade the field of antibacterial drug discovery has changed in many aspects including bacterial organisms of primary interest, discovery strategies applied and pharmaceutical companies involved. Target-based high-throughput screening had been disappointingly unsuccessful for antibiotic research. Understanding of this lack of success has increased substantially and the lessons learned refer to characteristics of targets, screening libraries and screening strategies. The ‘genomics’ approach was replaced by a diverse array of discovery strategies, for example, searching for new natural product leads among previously abandoned compounds or new microbial sources, screening for synthetic inhibitors by targeted approaches including structure-based design and analyses of focused libraries and designing resistance-breaking properties into antibiotics of established classes. Furthermore, alternative treatment options are being pursued including anti-virulence strategies and immunotherapeutic approaches. This article summarizes the lessons learned from the genomics era and describes discovery strategies resulting from that knowledge.
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Affiliation(s)
- Heike Brötz-Oesterhelt
- AiCuris, Wuppertal, Germany, Institute for Pharmaceutical Biology, University of Duesseldorf, Universitätsstrasse 1, Building 26.23.U1, Germany
| | - Peter Sass
- Institute of Medical Microbiology, Immunology & Parasitology, Pharmaceutical Microbiology Section, University of Bonn, Germany
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40
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Sources of novel antibiotics—aside the common roads. Appl Microbiol Biotechnol 2010; 88:1261-7. [DOI: 10.1007/s00253-010-2877-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2010] [Revised: 08/27/2010] [Accepted: 08/28/2010] [Indexed: 10/19/2022]
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41
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Affiliation(s)
- Jed F Fisher
- Department of Chemistry and Biochemistry, 423 Nieuwland Science Hall, Notre Dame, Indiana 46556-5670, USA
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42
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Olivier KS, Van Nieuwenhze MS. Synthetic studies toward the mannopeptimycins: synthesis of orthogonally protected beta-hydroxyenduracididines. Org Lett 2010; 12:1680-3. [PMID: 20232818 DOI: 10.1021/ol100219a] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The asymmetric synthesis of the nonproteinogenic amino acids (2S,3S,4'S)-beta-hydroxyenduracididine 3 and (2R,3S,4'S)-beta-hydroxyenduracididine 4 in orthogonally protected form in 15 total steps from Garner's aldehyde is reported. The former and N-glycosylated form of the latter are found in the glycopeptide antibiotic mannopeptimycin.
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Affiliation(s)
- Kevin S Olivier
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405-7102, USA
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43
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Cragg PJ. Supramolecular Therapeutics. Supramol Chem 2010. [DOI: 10.1007/978-90-481-2582-1_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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44
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Huang YT, Lyu SY, Chuang PH, Hsu NS, Li YS, Chan HC, Huang CJ, Liu YC, Wu CJ, Yang WB, Li TL. In vitro Characterization of Enzymes Involved in the Synthesis of Nonproteinogenic Residue (2S,3S)-β-Methylphenylalanine in Glycopeptide Antibiotic Mannopeptimycin. Chembiochem 2009; 10:2480-7. [DOI: 10.1002/cbic.200900351] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Antibiotics from microbes: converging to kill. Curr Opin Microbiol 2009; 12:520-7. [PMID: 19695947 DOI: 10.1016/j.mib.2009.07.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2009] [Revised: 07/06/2009] [Accepted: 07/08/2009] [Indexed: 11/20/2022]
Abstract
As genetically encoded small molecules, antibiotics are phenotypes that have resulted from mutation and natural selection. Advances in genetics, biochemistry, and bioinformatics have connected hundreds of antibiotics to the gene clusters that encode them, allowing these molecules to be analyzed using the tools of evolutionary biology. This review surveys examples of convergent evolution from microbially produced antibiotics, including the convergence of distinct gene clusters on similar phenotypes and the merger of distinct gene clusters into a single functional unit. Examining antibiotics through an evolutionary lens highlights the versatility of biosynthetic pathways, reveals lessons for combating antibiotic resistance, and provides an entry point for studying the natural roles of these natural products.
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A crystal structure of a dimer of the antibiotic ramoplanin illustrates membrane positioning and a potential Lipid II docking interface. Proc Natl Acad Sci U S A 2009; 106:13759-64. [PMID: 19666597 DOI: 10.1073/pnas.0904686106] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The glycodepsipeptide antibiotic ramoplanin A2 is in late stage clinical development for the treatment of infections from Gram-positive pathogens, especially those that are resistant to first line antibiotics such as vancomycin. Ramoplanin A2 achieves its antibacterial effects by interfering with production of the bacterial cell wall; it indirectly inhibits the transglycosylases responsible for peptidoglycan biosynthesis by sequestering their Lipid II substrate. Lipid II recognition and sequestration occur at the interface between the extracellular environment and the bacterial membrane. Therefore, we determined the structure of ramoplanin A2 in an amphipathic environment, using detergents as membrane mimetics, to provide the most physiologically relevant structural context for mechanistic and pharmacological studies. We report here the X-ray crystal structure of ramoplanin A2 at a resolution of 1.4 A. This structure reveals that ramoplanin A2 forms an intimate and highly amphipathic dimer and illustrates the potential means by which it interacts with bacterial target membranes. The structure also suggests a mechanism by which ramoplanin A2 recognizes its Lipid II ligand.
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Castiglione F, Lazzarini A, Carrano L, Corti E, Ciciliato I, Gastaldo L, Candiani P, Losi D, Marinelli F, Selva E, Parenti F. Determining the structure and mode of action of microbisporicin, a potent lantibiotic active against multiresistant pathogens. ACTA ACUST UNITED AC 2008; 15:22-31. [PMID: 18215770 DOI: 10.1016/j.chembiol.2007.11.009] [Citation(s) in RCA: 149] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2007] [Revised: 10/16/2007] [Accepted: 11/06/2007] [Indexed: 11/29/2022]
Abstract
Antibiotics blocking bacterial cell wall assembly (beta-lactams and glycopeptides) are facing a challenge from the progressive spread of resistant pathogens. Lantibiotics are promising candidates to alleviate this problem. Microbisporicin, the most potent antibacterial among known comparable lantibiotics, was discovered during a screening applied to uncommon actinomycetes. It is produced by Microbispora sp. as two similarly active and structurally related polypeptides (A1, 2246-Da and A2, 2230-Da) of 24 amino acids linked by 5 intramolecular thioether bridges. Microbisporicin contains two posttranslational modifications that have never been reported previously in lantibiotics: 5-chloro-trypthopan and mono- (in A2) or bis-hydroxylated (in A1) proline. Consistent with screening criteria, microbisporicin selectively blocks peptidoglycan biosynthesis, causing cytoplasmic UDP-linked precursor accumulation. Considering its spectrum of activity and its efficacy in vivo, microbisporicin represents a promising antibiotic to treat emerging infections.
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Affiliation(s)
- Franca Castiglione
- Vicuron Pharmaceuticals, Via R. Lepetit 34, 21040 Gerenzano, Varese, Italy
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Koehn FE. New strategies and methods in the discovery of natural product anti-infective agents: the mannopeptimycins. J Med Chem 2008; 51:2613-7. [PMID: 18393404 DOI: 10.1021/jm070432l] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Frank E Koehn
- Natural Products Discovery, Chemical and Screening Sciences, Wyeth Research, Pearl River, New York 10965, USA.
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Abstract
This review is an attempt to bring together and critically evaluate the now-abundant but dispersed data concerning the lipid intermediates of the biosynthesis of bacterial peptidoglycan. Lipid I, lipid II, and their modified forms play a key role not only as the specific link between the intracellular synthesis of the peptidoglycan monomer unit and the extracytoplasmic polymerization reactions but also in the attachment of proteins to the bacterial cell wall and in the mechanisms of action of antibiotics with which they form specific complexes. The survey deals first with their detection, purification, structure, and preparation by chemical and enzymatic methods. The recent important advances in the study of transferases MraY and MurG, responsible for the formation of lipids I and II, are reported. Various modifications undergone by lipids I and II are described, especially those occurring in gram-positive organisms. The following section concerns the cellular location of the lipid intermediates and the translocation of lipid II across the cytoplasmic membrane. The great efforts made since 2000 in the study of the glycosyltransferases catalyzing the glycan chain formation with lipid II or analogues are analyzed in detail. Finally, examples of antibiotics forming complexes with the lipid intermediates are presented.
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50
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Martin NI, Breukink E. Expanding role of lipid II as a target for lantibiotics. Future Microbiol 2007; 2:513-25. [PMID: 17927474 DOI: 10.2217/17460913.2.5.513] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Lipid II is an essential cell-wall precursor required for the growth and replication of both Gram-positive and Gram-negative bacteria. Compounds that use lipid II to selectively target bacterial cells for destruction represent an important class of antibiotics. Clinically, vancomycin is the most important example of an antibiotic that operates in this manner. Despite being considered the 'antibiotic drug of last resort', significant bacterial resistance to vancomycin now manifests itself worldwide. In this paper we review recent progress made in understanding the lipid II-associated antibacterial characteristics of various naturally occurring compounds, with particular focus on the lantibiotic peptides.
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Affiliation(s)
- Nathaniel I Martin
- Utrecht University, Department of Medicinal Chemistry & Chemical Biology, 3584 CA Utrecht, The Netherlands.
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