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Humpola MV, Spinelli R, Erben M, Perdomo V, Tonarelli GG, Albericio F, Siano AS. D- and N-Methyl Amino Acids for Modulating the Therapeutic Properties of Antimicrobial Peptides and Lipopeptides. Antibiotics (Basel) 2023; 12:antibiotics12050821. [PMID: 37237724 DOI: 10.3390/antibiotics12050821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 04/24/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
Here we designed and synthesized analogs of two antimicrobial peptides, namely C10:0-A2, a lipopeptide, and TA4, a cationic α-helical amphipathic peptide, and used non-proteinogenic amino acids to improve their therapeutic properties. The physicochemical properties of these analogs were analyzed, including their retention time, hydrophobicity, and critical micelle concentration, as well as their antimicrobial activity against gram-positive and gram-negative bacteria and yeast. Our results showed that substitution with D- and N-methyl amino acids could be a useful strategy to modulate the therapeutic properties of antimicrobial peptides and lipopeptides, including enhancing stability against enzymatic degradation. The study provides insights into the design and optimization of antimicrobial peptides to achieve improved stability and therapeutic efficacy. TA4(dK), C10:0-A2(6-NMeLys), and C10:0-A2(9-NMeLys) were identified as the most promising molecules for further studies.
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Affiliation(s)
- Maria Veronica Humpola
- Laboratorio de Péptidos Bioactivos, Departamento de Química Orgánica, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe S3000ZAA, Argentina
| | - Roque Spinelli
- Laboratorio de Péptidos Bioactivos, Departamento de Química Orgánica, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe S3000ZAA, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1425FQB, Argentina
| | - Melina Erben
- Laboratorio de Péptidos Bioactivos, Departamento de Química Orgánica, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe S3000ZAA, Argentina
| | - Virginia Perdomo
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1425FQB, Argentina
- Área Parasitología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario S2002KTT, Argentina
| | - Georgina Guadalupe Tonarelli
- Laboratorio de Péptidos Bioactivos, Departamento de Química Orgánica, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe S3000ZAA, Argentina
| | - Fernando Albericio
- School of Chemistry and Physics, University of KwaZulu-Natal, Durban 4001, South Africa
- Consorcio Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Department of Organic Chemistry, University of Barcelona, 08028 Barcelona, Spain
| | - Alvaro Sebastian Siano
- Laboratorio de Péptidos Bioactivos, Departamento de Química Orgánica, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe S3000ZAA, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1425FQB, Argentina
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2
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Qi YK, Tang X, Wei NN, Pang CJ, Du SS, Wang KW. Discovery, synthesis, and optimization of teixobactin, a novel antibiotic without detectable bacterial resistance. J Pept Sci 2022; 28:e3428. [PMID: 35610021 DOI: 10.1002/psc.3428] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 05/07/2022] [Accepted: 05/10/2022] [Indexed: 11/09/2022]
Abstract
Discovering new antibiotics with novel chemical scaffolds and antibacterial mechanisms presents a challenge for medicinal scientists worldwide as the ever-increasing bacterial resistance poses a serious threat to human health. A new cyclic peptide-based antibiotic termed teixobactin was discovered from a screen of uncultured soil bacteria through iChip technology in 2015. Teixobactin exhibits excellent antibacterial activity against all the tested gram-positive pathogens and Mycobacterium tuberculosis, including drug-resistant strains. Given that teixobactin targets the highly conserved lipid II and lipid III, which induces the simultaneous inhibition of both peptidoglycan and teichoic acid synthesis, the emergence of resistance is considered to be rather difficult. The novel structure, potent antibacterial activity, and highly conservative targets make teixobactin a promising lead compound for further antibiotic development. This review provides a comprehensive treatise on the advances of teixobactin in the areas of discovery processes, antibacterial activity, mechanisms of action, chemical synthesis, and structural optimizations. The synthetic methods for the key building block l-allo-End, natural teixobactin, representative teixobactin analogues, as well as the structure-activity relationship studies will be highlighted and discussed in details. Finally, some insights into new trends for the generation of novel teixobactin analogues and tips for future work and directions will be commented.
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Affiliation(s)
- Yun-Kun Qi
- Department of Medicinal Chemistry, School of Pharmacy, Qingdao University, Qingdao, China.,Institute of Innovative Drugs, Qingdao University, Qingdao, China.,State Key Laboratory Base for Eco-Chemical Engineering in College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Xiaowen Tang
- Department of Medicinal Chemistry, School of Pharmacy, Qingdao University, Qingdao, China
| | - Ning-Ning Wei
- Institute of Innovative Drugs, Qingdao University, Qingdao, China
| | - Cheng-Jian Pang
- The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Shan-Shan Du
- State Key Laboratory Base for Eco-Chemical Engineering in College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Ke Wei Wang
- Department of Medicinal Chemistry, School of Pharmacy, Qingdao University, Qingdao, China.,Institute of Innovative Drugs, Qingdao University, Qingdao, China
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3
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Matabaro E, Song H, Chepkirui C, Kaspar H, Witte L, Naismith JH, Freeman MF, Künzler M. Enzyme-mediated backbone N-methylation in ribosomally encoded peptides. Methods Enzymol 2021; 656:429-458. [PMID: 34325794 DOI: 10.1016/bs.mie.2021.04.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Backbone N-methylation as a posttranslational modification was recently discovered in a class of ribosomally encoded peptides referred to as borosins. The founding members of the borosins are the omphalotins (A-I), backbone N-methylated, macrocyclic dodecapeptides produced by the mushroom Omphalotus olearius. Omphalotins display a strong and selective toxicity toward the plant parasitic nematode Meloidogyne incognita. The primary product omphalotin A is synthesized via a concerted action of the omphalotin precursor protein (OphMA) and the dual function prolyloligopeptidase/macrocyclase (OphP). OphMA consists of α-N-methyltransferase domain that autocatalytically methylates the core peptide fused to its C-terminus via a clasp domain. Genome mining uncovered over 50 OphMA homologs from the fungal phyla Ascomycota and Basidiomycota. However, the derived peptide natural products have not been described yet, except for lentinulins, dendrothelins and gymnopeptides produced by the basidiomycetes Lentinula edodes, Dendrothele bispora and Gymnopus fusipes, respectively. In this chapter, we describe methods used to isolate and characterize these backbone N-methylated peptides and their precursor proteins both in their original hosts and in the heterologous hosts Escherichia coli and Pichia pastoris. These methods may pave the path for both the discovery of novel borosins with interesting bioactivities. In addition, understanding of borosin biosynthetic pathways may allow setting up a biotechnological platform for the production of pharmaceutical leads for orally available peptide drugs.
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Affiliation(s)
- Emmanuel Matabaro
- Department of Biology, Institute of Microbiology, ETH Zürich, Zürich, Switzerland
| | - Haigang Song
- The Research Complex at Harwell, Harwell Campus, Didcot, United Kingdom; The Rosalind Franklin Institute, Harwell Campus, Didcot, United Kingdom
| | - Clara Chepkirui
- Department of Biology, Institute of Microbiology, ETH Zürich, Zürich, Switzerland
| | - Hannelore Kaspar
- Department of Biology, Institute of Microbiology, ETH Zürich, Zürich, Switzerland
| | - Luca Witte
- Department of Biology, Institute of Microbiology, ETH Zürich, Zürich, Switzerland
| | - James H Naismith
- Division of Structural Biology, Wellcome Centre for Human Genetics, Oxford, United Kingdom; The Research Complex at Harwell, Harwell Campus, Didcot, United Kingdom; The Rosalind Franklin Institute, Harwell Campus, Didcot, United Kingdom
| | - Michael F Freeman
- Department of Biochemistry, Molecular Biology, and Biophysics and BioTechnology Institute, University of Minnesota-Twin Cities, St. Paul, Minnesota, United States
| | - Markus Künzler
- Department of Biology, Institute of Microbiology, ETH Zürich, Zürich, Switzerland.
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4
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Gunjal VB, Thakare R, Chopra S, Reddy DS. Teixobactin: A Paving Stone toward a New Class of Antibiotics? J Med Chem 2020; 63:12171-12195. [PMID: 32520557 DOI: 10.1021/acs.jmedchem.0c00173] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Antimicrobial resistance is a serious threat to human health worldwide, prompting research efforts on a massive scale in search of novel antibiotics to fill an urgent need for a remedy. Teixobactin, a macrocyclic depsipeptide natural product, isolated from uncultured bacteria (Eleftheria terrae), displayed potent activity against several Gram-positive pathogenic bacteria. The distinct pharmacological profile and interesting structural features of teixobactin with nonstandard amino acid (three d-amino acids and l-allo-enduracididine) residues attracted several research groups to work on this target molecule in search of novel antibiotics with new mechanism. Herein, we present a comprehensive and critical perspective on immense possibilities offered by teixobactin in the domain of drug discovery. Efforts made by various research groups since its isolation are discussed, highlighting the molecule's considerable potential with special emphasis on replacement of amino acids. Critical analysis of synthetic efforts, SAR studies, and the way forward are provided hereunder.
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Affiliation(s)
- Vidya B Gunjal
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Ritesh Thakare
- CSIR-Central Drug Research Institute, Sector 10, Janakipuram Extension, Sitapur Road, Lucknow 226031, Uttar Pradesh, India
| | - Sidharth Chopra
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.,CSIR-Central Drug Research Institute, Sector 10, Janakipuram Extension, Sitapur Road, Lucknow 226031, Uttar Pradesh, India
| | - D Srinivasa Reddy
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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5
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The Killing Mechanism of Teixobactin against Methicillin-Resistant Staphylococcus aureus: an Untargeted Metabolomics Study. mSystems 2020; 5:5/3/e00077-20. [PMID: 32457238 PMCID: PMC7253363 DOI: 10.1128/msystems.00077-20] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Antimicrobial resistance is one of the greatest threats to the global health system. It is imperative that new anti-infective therapeutics be developed against problematic “superbugs.” The cyclic depsipeptide teixobactin holds much promise as a new class of antibiotics for highly resistant Gram-positive pathogens (e.g., methicillin-resistant Staphylococcus aureus [MRSA]). Understanding its molecular mechanism(s) of action could lead to the design of new compounds with a broader activity spectrum. Here, we describe the first metabolomics study to investigate the killing mechanism(s) of teixobactin against MRSA. Our findings revealed that teixobactin significantly disorganized the bacterial cell envelope, as reflected by a profound perturbation in the bacterial membrane lipids and cell wall biosynthesis (peptidoglycan and teichoic acid). Importantly, teixobactin significantly suppressed the main intermediate d-alanyl-d-lactate involved in the mechanism of vancomycin resistance in S. aureus. These novel results help explain the unique mechanism of action of teixobactin and its lack of cross-resistance with vancomycin. Antibiotics have served humankind through their use in modern medicine as effective treatments for otherwise fatal bacterial infections. Teixobactin is a first member of newly discovered natural antibiotics that was recently identified from a hitherto-unculturable soil bacterium, Eleftheria terrae, and recognized as a potent antibacterial agent against various Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci. The most distinctive characteristic of teixobactin as an effective antibiotic is that teixobactin resistance could not be evolved in a laboratory setting. It is purported that teixobactin’s “resistance-resistant” mechanism of action includes binding to the essential bacterial cell wall synthesis building blocks lipid II and lipid III. In the present study, metabolomics was used to investigate the potential metabolic pathways involved in the mechanisms of antibacterial activity of the synthetic teixobactin analogue Leu10-teixobactin against a MRSA strain, S. aureus ATCC 700699. The metabolomes of S. aureus ATCC 700699 cells 1, 3, and 6 h following treatment with Leu10-teixobactin (0.5 μg/ml, i.e., 0.5× MIC) were compared to those of the untreated controls. Leu10-teixobactin significantly perturbed bacterial membrane lipids (glycerophospholipids and fatty acids), peptidoglycan (lipid I and II) metabolism, and cell wall teichoic acid (lipid III) biosynthesis as early as after 1 h of treatment, reflecting an initial activity on the cell envelope. Concordant with its time-dependent antibacterial killing action, Leu10-teixobactin caused more perturbations in the levels of key intermediates in pathways of amino-sugar and nucleotide-sugar metabolism and their downstream peptidoglycan and teichoic acid biosynthesis at 3 and 6 h. Significant perturbations in arginine metabolism and the interrelated tricarboxylic acid cycle, histidine metabolism, pantothenate, and coenzyme A biosynthesis were also observed at 3 and 6 h. To conclude, this is the first study to provide novel metabolomics mechanistic information, which lends support to the development of teixobactin as an antibacterial drug for the treatment of multidrug-resistant Gram-positive infections. IMPORTANCE Antimicrobial resistance is one of the greatest threats to the global health system. It is imperative that new anti-infective therapeutics be developed against problematic “superbugs.” The cyclic depsipeptide teixobactin holds much promise as a new class of antibiotics for highly resistant Gram-positive pathogens (e.g., methicillin-resistant Staphylococcus aureus [MRSA]). Understanding its molecular mechanism(s) of action could lead to the design of new compounds with a broader activity spectrum. Here, we describe the first metabolomics study to investigate the killing mechanism(s) of teixobactin against MRSA. Our findings revealed that teixobactin significantly disorganized the bacterial cell envelope, as reflected by a profound perturbation in the bacterial membrane lipids and cell wall biosynthesis (peptidoglycan and teichoic acid). Importantly, teixobactin significantly suppressed the main intermediate d-alanyl-d-lactate involved in the mechanism of vancomycin resistance in S. aureus. These novel results help explain the unique mechanism of action of teixobactin and its lack of cross-resistance with vancomycin.
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6
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Karas JA, Chen F, Schneider-Futschik EK, Kang Z, Hussein M, Swarbrick J, Hoyer D, Giltrap AM, Payne RJ, Li J, Velkov T. Synthesis and structure-activity relationships of teixobactin. Ann N Y Acad Sci 2019; 1459:86-105. [PMID: 31792983 DOI: 10.1111/nyas.14282] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 11/04/2019] [Accepted: 11/10/2019] [Indexed: 12/15/2022]
Abstract
The discovery of antibiotics has led to the effective treatment of bacterial infections that were otherwise fatal and has had a transformative effect on modern medicine. Teixobactin is an unusual depsipeptide natural product that was recently discovered from a previously unculturable soil bacterium and found to possess potent antibacterial activity against several Gram positive pathogens, including methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococci. One of the key features of teixobactin as an antibiotic lead is that resistance could not be generated in a laboratory setting. This is proposed to be a result of a mechanism of action that involves binding to essential cell wall synthesis building blocks, lipid II and lipid III. Since the initial isolation report in 2015, significant efforts have been made to understand its unique mechanism of action, develop efficient synthetic routes for its production, and thus enable the generation of analogues for structure-activity relationship studies and optimization of its pharmacological properties. Our review provides a comprehensive treatise on the progress in understanding teixobactin chemistry, structure-activity relationships, and mechanisms of antibacterial activity. Teixobactin represents an exciting starting point for the development of new antibiotics that can be used to combat multidrug-resistant bacterial ("superbug") infections.
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Affiliation(s)
- John A Karas
- Department of Pharmacology & Therapeutics, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, the University of Melbourne, Parkville, Victoria, Australia
| | - Fan Chen
- Department of Pharmacology & Therapeutics, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, the University of Melbourne, Parkville, Victoria, Australia
| | - Elena K Schneider-Futschik
- Department of Pharmacology & Therapeutics, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, the University of Melbourne, Parkville, Victoria, Australia.,Lung Health Research Centre, Department of Pharmacology & Therapeutics, the University of Melbourne, Parkville, Victoria, Australia
| | - Zhisen Kang
- Department of Pharmacology & Therapeutics, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, the University of Melbourne, Parkville, Victoria, Australia
| | - Maytham Hussein
- Department of Pharmacology & Therapeutics, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, the University of Melbourne, Parkville, Victoria, Australia
| | - James Swarbrick
- Department of Pharmacology & Therapeutics, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, the University of Melbourne, Parkville, Victoria, Australia
| | - Daniel Hoyer
- Department of Pharmacology & Therapeutics, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, the University of Melbourne, Parkville, Victoria, Australia.,The Florey Institute of Neuroscience and Mental Health, the University of Melbourne, Parkville, Victoria, Australia.,Department of Molecular Medicine, the Scripps Research Institute, La Jolla, California
| | - Andrew M Giltrap
- School of Chemistry, the University of Sydney, Sydney, New South Wales, Australia
| | - Richard J Payne
- School of Chemistry, the University of Sydney, Sydney, New South Wales, Australia
| | - Jian Li
- Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Tony Velkov
- Department of Pharmacology & Therapeutics, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, the University of Melbourne, Parkville, Victoria, Australia
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