1
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Zeng P, Wang H, Zhang P, Leung SSY. Unearthing naturally-occurring cyclic antibacterial peptides and their structural optimization strategies. Biotechnol Adv 2024; 73:108371. [PMID: 38704105 DOI: 10.1016/j.biotechadv.2024.108371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 03/08/2024] [Accepted: 04/29/2024] [Indexed: 05/06/2024]
Abstract
Natural products with antibacterial activity are highly desired globally to combat against multidrug-resistant (MDR) bacteria. Antibacterial peptide (ABP), especially cyclic ABP (CABP), is one of the abundant classes. Most of them were isolated from microbes, demonstrating excellent bactericidal effects. With the improved proteolytic stability, CABPs are normally considered to have better druggability than linear peptides. However, most clinically-used CABP-based antibiotics, such as colistin, also face the challenges of drug resistance soon after they reached the market, urgently requiring the development of next-generation succedaneums. We present here a detail review on the novel naturally-occurring CABPs discovered in the past decade and some of them are under clinical trials, exhibiting anticipated application potential. According to their chemical structures, they were broadly classified into five groups, including (i) lactam/lactone-based CABPs, (ii) cyclic lipopeptides, (iii) glycopeptides, (iv) cyclic sulfur-rich peptides and (v) multiple-modified CABPs. Their chemical structures, antibacterial spectrums and proposed mechanisms are discussed. Moreover, engineered analogs of these novel CABPs are also summarized to preliminarily analyze their structure-activity relationship. This review aims to provide a global perspective on research and development of novel CABPs to highlight the effectiveness of derivatives design in identifying promising antibacterial agents. Further research efforts in this area are believed to play important roles in fighting against the multidrug-resistance crisis.
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Affiliation(s)
- Ping Zeng
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Honglan Wang
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Pengfei Zhang
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Sharon Shui Yee Leung
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong.
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2
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Sakata S, Li J, Yasuno Y, Shinada T, Shin-Ya K, Katsuyama Y, Ohnishi Y. Identification of the Cirratiomycin Biosynthesis Gene Cluster in Streptomyces Cirratus: Elucidation of the Biosynthetic Pathways for 2,3-Diaminobutyric Acid and Hydroxymethylserine. Chemistry 2024; 30:e202400271. [PMID: 38456538 DOI: 10.1002/chem.202400271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/08/2024] [Accepted: 03/08/2024] [Indexed: 03/09/2024]
Abstract
Cirratiomycin, a heptapeptide with antibacterial activity, was isolated and characterized in 1981; however, its biosynthetic pathway has not been elucidated. It contains several interesting nonproteinogenic amino acids, such as (2S,3S)-2,3-diaminobutyric acid ((2S,3S)-DABA) and α-(hydroxymethyl)serine, as building blocks. Here, we report the identification of a cirratiomycin biosynthetic gene cluster in Streptomyces cirratus. Bioinformatic analysis revealed that several Streptomyces viridifaciens and Kitasatospora aureofaciens strains also have this cluster. One S. viridifaciens strain was confirmed to produce cirratiomycin. The biosynthetic gene cluster was shown to be responsible for cirratiomycin biosynthesis in S. cirratus in a gene inactivation experiment using CRISPR-cBEST. Interestingly, this cluster encodes a nonribosomal peptide synthetase (NRPS) composed of 12 proteins, including those with an unusual domain organization: a stand-alone adenylation domain, two stand-alone condensation domains, two type II thioesterases, and two NRPS modules that have no adenylation domain. Using heterologous expression and in vitro analysis of recombinant enzymes, we revealed the biosynthetic pathway of (2S,3S)-DABA: (2S,3S)-DABA is synthesized from l-threonine by four enzymes, CirR, CirS, CirQ, and CirB. In addition, CirH, a glycine/serine hydroxymethyltransferase homolog, was shown to synthesize α-(hydroxymethyl)serine from d-serine in vitro. These findings broaden our knowledge of nonproteinogenic amino acid biosynthesis.
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Affiliation(s)
- Shunki Sakata
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Jiafeng Li
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yoko Yasuno
- Graduate School of Science, Osaka City University, Sugimoto, Sumiyoshi, Osaka, 558-8585, Japan
| | - Tetsuro Shinada
- Graduate School of Science, Osaka City University, Sugimoto, Sumiyoshi, Osaka, 558-8585, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Yohei Katsuyama
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
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3
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Wu H, Sun Z, Li X. Selective Peptide Cysteine Manipulation on Demand and Difficult Protein Chemical Synthesis Enabled by Controllable Acidolysis of N,S-Benzylidene Thioacetals. Angew Chem Int Ed Engl 2024; 63:e202403396. [PMID: 38490953 DOI: 10.1002/anie.202403396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 03/15/2024] [Accepted: 03/15/2024] [Indexed: 03/17/2024]
Abstract
Although solid-phase peptide synthesis combining with chemical ligation provides a way to build up customized polypeptides in general, many targets are still presenting challenges for the conventional synthetic process, such as hydrophobic proteins. New methods and strategies are still required to overcome these obstacles. In this study, kinetic studies of Cys/Pen ligation and its acidolysis were performed, from which the fast acidolysis of substituted N,S-benzylidene thioacetals (NBTs) was discovered. The study demonstrates the potential of NBTs as a promising Cys switchable protection, facilitating the chemical synthesis of peptides and proteins by efficiently disrupting peptide aggregation. The compatibility of NBTs with other commonly adopted Cys protecting groups and their applications in sequential disulfide bond formation were also investigated. The first chemical synthesis of the native human programmed death ligand 1 immunoglobulin V-like (PD-L1 IgV) domain was achieved using the NBT strategy, showcasing its potential in difficult protein synthesis.
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Affiliation(s)
- Hongxiang Wu
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong, SAR, People's Republic of, China
| | - Zhenquan Sun
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong, SAR, People's Republic of, China
| | - Xuechen Li
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong, SAR, People's Republic of, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Ocean University China, Qingdao, 266237, People's Republic of China
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4
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Bérubé C, Guay LD, Fraser T, Lapointe V, Cardinal S, Biron É. Convenient route to Fmoc-homotyrosine via metallaphotoredox catalysis and its use in the total synthesis of anabaenopeptin cyclic peptides. Org Biomol Chem 2023; 21:9011-9020. [PMID: 37921761 DOI: 10.1039/d3ob01608k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
Herein, we report the first solid-phase total synthesis of the natural cyclic peptide anabaenopeptin F and the use of metallaphotoredox catalysis to overcome the key challenges associated with the preparation of the non-proteinogenic amino acid homotyrosine contained in these peptides. Starting from L-homoserine, enantiopure Fmoc-protected homotyrosine was prepared in a straightforward manner by metallaphotoredox catalysis with N-Fmoc-(S)-2-amino-4-bromobutanoic acid and 4-tert-butoxybromobenzene partners. The prepared protected amino acid was used in solid-phase peptide synthesis to achieve the total synthesis of anabaenopeptin F and establish the stereochemistry of the isoleucine residue. Protease inhibition studies with the synthesized anabaenopeptin F showed inhibitory activities against carboxypeptidase B in the low nanomolar range. The high convergency of the synthetic methodologies paves the way for the rapid access to N-Fmoc-protected non-proteinogenic and unnatural amino acids and the total synthesis of complex bioactive peptides containing these amino acids.
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Affiliation(s)
- Christopher Bérubé
- Faculté de Pharmacie, Université Laval, Québec, Québec, Canada, G1 V 0A6.
- Laboratory of Medicinal Chemistry, Centre de Recherche du CHU de Québec-Université Laval, 2705 Boulevard Laurier, Québec, Québec, Canada, G1 V 0A6
| | - Louis-David Guay
- Faculté de Pharmacie, Université Laval, Québec, Québec, Canada, G1 V 0A6.
- Laboratory of Medicinal Chemistry, Centre de Recherche du CHU de Québec-Université Laval, 2705 Boulevard Laurier, Québec, Québec, Canada, G1 V 0A6
| | - Tommy Fraser
- Département de Biologie, Chimie et Géographie, Université du Québec à Rimouski, 300 allée des Ursulines, Rimouski, Québec, Canada, G5L 3A1
| | - Victor Lapointe
- Faculté de Pharmacie, Université Laval, Québec, Québec, Canada, G1 V 0A6.
- Laboratory of Medicinal Chemistry, Centre de Recherche du CHU de Québec-Université Laval, 2705 Boulevard Laurier, Québec, Québec, Canada, G1 V 0A6
| | - Sébastien Cardinal
- Département de Biologie, Chimie et Géographie, Université du Québec à Rimouski, 300 allée des Ursulines, Rimouski, Québec, Canada, G5L 3A1
| | - Éric Biron
- Faculté de Pharmacie, Université Laval, Québec, Québec, Canada, G1 V 0A6.
- Laboratory of Medicinal Chemistry, Centre de Recherche du CHU de Québec-Université Laval, 2705 Boulevard Laurier, Québec, Québec, Canada, G1 V 0A6
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5
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Kumar G, Engle K. Natural products acting against S. aureus through membrane and cell wall disruption. Nat Prod Rep 2023; 40:1608-1646. [PMID: 37326041 DOI: 10.1039/d2np00084a] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Covering: 2015 to 2022Staphylococcus aureus (S. aureus) is responsible for several community and hospital-acquired infections with life-threatening complications such as bacteraemia, endocarditis, meningitis, liver abscess, and spinal cord epidural abscess. In recent decades, the abuse and misuse of antibiotics in humans, animals, plants, and fungi and the treatment of nonmicrobial diseases have led to the rapid emergence of multidrug-resistant pathogens. The bacterial wall is a complex structure consisting of the cell membrane, peptidoglycan cell wall, and various associated polymers. The enzymes involved in bacterial cell wall synthesis are established antibiotic targets and continue to be a central focus for antibiotic development. Natural products play a vital role in drug discovery and development. Importantly, natural products provide a starting point for active/lead compounds that sometimes need modification based on structural and biological properties to meet the drug criteria. Notably, microorganisms and plant metabolites have contributed as antibiotics for noninfectious diseases. In this study, we have summarized the recent advances in understanding the activity of the drugs or agents of natural origin that directly inhibit the bacterial membrane, membrane components, and membrane biosynthetic enzymes by targeting membrane-embedded proteins. We also discussed the unique aspects of the active mechanisms of established antibiotics or new agents.
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Affiliation(s)
- Gautam Kumar
- Department of Natural Products, Chemical Sciences, National Institute of Pharmaceutical Education and Research-Hyderabad, Hyderabad, Balanagar, 500037, India.
| | - Kritika Engle
- Department of Natural Products, Chemical Sciences, National Institute of Pharmaceutical Education and Research-Hyderabad, Hyderabad, Balanagar, 500037, India.
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6
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MacNair CR, Tsai CN, Rutherford ST, Tan MW. Returning to Nature for the Next Generation of Antimicrobial Therapeutics. Antibiotics (Basel) 2023; 12:1267. [PMID: 37627687 PMCID: PMC10451936 DOI: 10.3390/antibiotics12081267] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 07/29/2023] [Accepted: 07/30/2023] [Indexed: 08/27/2023] Open
Abstract
Antibiotics found in and inspired by nature are life-saving cures for bacterial infections and have enabled modern medicine. However, the rise in resistance necessitates the discovery and development of novel antibiotics and alternative treatment strategies to prevent the return to a pre-antibiotic era. Once again, nature can serve as a source for new therapies in the form of natural product antibiotics and microbiota-based therapies. Screening of soil bacteria, particularly actinomycetes, identified most of the antibiotics used in the clinic today, but the rediscovery of existing molecules prompted a shift away from natural product discovery. Next-generation sequencing technologies and bioinformatics advances have revealed the untapped metabolic potential harbored within the genomes of environmental microbes. In this review, we first highlight current strategies for mining this untapped chemical space, including approaches to activate silent biosynthetic gene clusters and in situ culturing methods. Next, we describe how using live microbes in microbiota-based therapies can simultaneously leverage many of the diverse antimicrobial mechanisms found in nature to treat disease and the impressive efficacy of fecal microbiome transplantation and bacterial consortia on infection. Nature-provided antibiotics are some of the most important drugs in human history, and new technologies and approaches show that nature will continue to offer valuable inspiration for the next generation of antibacterial therapeutics.
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Affiliation(s)
- Craig R. MacNair
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA 94080, USA;
| | - Caressa N. Tsai
- School of Law, University of California, Berkeley, Berkeley, CA 94704, USA;
| | - Steven T. Rutherford
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA 94080, USA;
| | - Man-Wah Tan
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA 94080, USA;
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7
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Lin S, Mo Z, Wang P, He C. Oxidation and Phenolysis of Peptide/Protein C-Terminal Hydrazides Afford Salicylaldehyde Ester Surrogates for Chemical Protein Synthesis. J Am Chem Soc 2023. [PMID: 37470345 DOI: 10.1021/jacs.3c05190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
With the growing popularity of serine/threonine ligation (STL) and cysteine/penicillamine ligation (CPL) in chemical protein synthesis, facile and general approaches for the preparation of peptide salicylaldehyde (SAL) esters are urgently needed, especially those viable for obtaining expressed protein SAL esters. Herein, we report the access of SAL ester surrogates from peptide hydrazides (obtained either synthetically or recombinantly) via nitrite oxidation and phenolysis by 3-(1,3-dithian-2-yl)-4-hydroxybenzoic acid (SAL(-COOH)PDT). The resulting peptide SAL(-COOH)PDT esters can be activated to afford the reactive peptide SAL(-COOH) esters for subsequent STL/CPL. While being operationally simple for both synthetic peptides and expressed proteins, the current strategy facilitates convergent protein synthesis and combined application of STL with NCL. The generality of the strategy is showcased by the N-terminal ubiquitination of the growth arrest and DNA damage-inducible protein (Gadd45a), the efficient synthesis of ubiquitin-like protein 5 (UBL-5) via a combined N-to-C NCL-STL strategy, and the C-to-N semisynthesis of a myoglobin (Mb) variant.
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Affiliation(s)
- Shaomin Lin
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, China
| | - Zeyuan Mo
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, China
| | - Peng Wang
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, China
| | - Chunmao He
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, China
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8
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Liu ZC, Wang ZQ, Zhang X, Yin L. Copper(I)-catalyzed asymmetric alkylation of α-imino-esters. Nat Commun 2023; 14:2187. [PMID: 37069200 PMCID: PMC10110621 DOI: 10.1038/s41467-023-37967-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 04/04/2023] [Indexed: 04/19/2023] Open
Abstract
Asymmetric alkylation of enolates is one of the most direct and important reactions to prepare α-chiral carbonyl compounds. Except for the classical methods that rely on the use of chiral auxiliaries, asymmetric catalysis emerged as a powerful tool, especially asymmetric phase-transfer catalysis. However, in the field of transition metal catalysis, only limited success with asymmetric alkylation of enolates was achieved. Hereby, we disclose a copper(I)-catalyzed asymmetric alkylation of α-imino-esters with various alkyl halides, including allyl bromides, propargyl bromide, benzyl bromides, α-bromo carbonyl compounds, and alkyl iodides. Both linear and cyclic α-imino-esters serve as competent pronucleophiles in the alkylation, which affords α-amino acid derivatives bearing either a trisubstituted or a tetrasubstituted stereogenic carbon center in high to excellent enantioselectivity. Control experiments indicate that the α-imino-ester is activated by a chiral copper(I)-phosphine complex through coordination, thus enabling facile deprotonation to provide a stabilized copper(I)-enolate in the presence of a mild base. Finally, the mildly basic nature allows the asymmetric alkylation of chiral dipeptides with excellent both chemo- and enantioselectivities.
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Affiliation(s)
- Zong-Ci Liu
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, 200032, Shanghai, China
| | - Zi-Qing Wang
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, 200032, Shanghai, China
| | - Xuan Zhang
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, 200032, Shanghai, China
| | - Liang Yin
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, 200032, Shanghai, China.
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9
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Zhang S, Chen Y, Zhu J, Lu Q, Cryle MJ, Zhang Y, Yan F. Structural diversity, biosynthesis, and biological functions of lipopeptides from Streptomyces. Nat Prod Rep 2023; 40:557-594. [PMID: 36484454 DOI: 10.1039/d2np00044j] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Covering: up to 2022Streptomyces are ubiquitous in terrestrial and marine environments, where they display a fascinating metabolic diversity. As a result, these bacteria are a prolific source of active natural products. One important class of these natural products is the nonribosomal lipopeptides, which have diverse biological activities and play important roles in the lifestyle of Streptomyces. The importance of this class is highlighted by the use of related antibiotics in the clinic, such as daptomycin (tradename Cubicin). By virtue of recent advances spanning chemistry and biology, significant progress has been made in biosynthetic studies on the lipopeptide antibiotics produced by Streptomyces. This review will serve as a comprehensive guide for researchers working in this multidisciplinary field, providing a summary of recent progress regarding the investigation of lipopeptides from Streptomyces. In particular, we highlight the structures, properties, biosynthetic mechanisms, chemical and chemoenzymatic synthesis, and biological functions of lipopeptides. In addition, the application of genome mining techniques to Streptomyces that have led to the discovery of many novel lipopeptides is discussed, further demonstrating the potential of lipopeptides from Streptomyces for future development in modern medicine.
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Affiliation(s)
- Songya Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yunliang Chen
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
- The Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 1000050, China.
| | - Jing Zhu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Qiujie Lu
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
| | - Max J Cryle
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800 Australia
- EMBL Australia, Monash University, Clayton, Victoria, 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, Victoria, 3800 Australia
| | - Youming Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
| | - Fu Yan
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
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10
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Munawar S, Zahoor AF, Ali S, Javed S, Irfan M, Irfan A, Kotwica-Mojzych K, Mojzych M. Mitsunobu Reaction: A Powerful Tool for the Synthesis of Natural Products: A Review. Molecules 2022; 27:6953. [PMID: 36296545 PMCID: PMC9609662 DOI: 10.3390/molecules27206953] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/06/2022] [Accepted: 10/08/2022] [Indexed: 08/13/2023] Open
Abstract
The Mitsunobu reaction plays a vital part in organic chemistry due to its wide synthetic applications. It is considered as a significant reaction for the interconversion of one functional group (alcohol) to another (ester) in the presence of oxidizing agents (azodicarboxylates) and reducing agents (phosphines). It is a renowned stereoselective reaction which inverts the stereochemical configuration of end products. One of the most important applications of the Mitsunobu reaction is its role in the synthesis of natural products. This review article will focus on the contribution of the Mitsunobu reaction towards the total synthesis of natural products, highlighting their biological potential during recent years.
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Affiliation(s)
- Saba Munawar
- Department of Chemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Ameer Fawad Zahoor
- Department of Chemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Shafaqat Ali
- College of Agriculture and Environmental Sciences, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Sadia Javed
- Department of Biochemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Muhammad Irfan
- Department of Pharmaceutics, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Ali Irfan
- Department of Chemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Katarzyna Kotwica-Mojzych
- Laboratory of Experimental Cytology, Medical University of Lublin, Radziwiłłowska 11, 20-080 Lublin, Poland
| | - Mariusz Mojzych
- Department of Chemistry, Siedlce University of Natural Sciences and Humanities, 3-go Maja 54, 08-110 Siedlce, Poland
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11
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Wood TM, Zeronian MR, Buijs N, Bertheussen K, Abedian HK, Johnson AV, Pearce NM, Lutz M, Kemmink J, Seirsma T, Hamoen LW, Janssen BJC, Martin NI. Mechanistic insights into the C 55-P targeting lipopeptide antibiotics revealed by structure-activity studies and high-resolution crystal structures. Chem Sci 2022; 13:2985-2991. [PMID: 35382464 PMCID: PMC8905900 DOI: 10.1039/d1sc07190d] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 01/18/2022] [Indexed: 12/27/2022] Open
Abstract
The continued rise of antibiotic resistance is a global concern that threatens to undermine many aspects of modern medical practice. Key to addressing this threat is the discovery and development of new antibiotics that operate by unexploited modes of action. The so-called calcium-dependent lipopeptide antibiotics (CDAs) are an important emerging class of natural products that provides a source of new antibiotic agents rich in structural and mechanistic diversity. Notable in this regard is the subset of CDAs comprising the laspartomycins and amphomycins/friulimicins that specifically target the bacterial cell wall precursor undecaprenyl phosphate (C55-P). In this study we describe the design and synthesis of new C55-P-targeting CDAs with structural features drawn from both the laspartomycin and amphomycin/friulimicin classes. Assessment of these lipopeptides revealed previously unknown and surprisingly subtle structural features that are required for antibacterial activity. High-resolution crystal structures further indicate that the amphomycin/friulimicin-like lipopeptides adopt a unique crystal packing that governs their interaction with C55-P and provides an explanation for their antibacterial effect. In addition, live-cell microscopy studies provide further insights into the biological activity of the C55-P targeting CDAs highlighting their unique mechanism of action relative to the clinically used CDA daptomycin. Structural and mechanistic studies give new insights into calcium-dependent lipopeptide antibiotics that target C55-P.![]()
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Affiliation(s)
- Thomas M Wood
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University Sylviusweg 72 2333 BE Leiden The Netherlands .,Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University Universiteitsweg 99 3584 CG Utrecht The Netherlands
| | - Matthieu R Zeronian
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Ned Buijs
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University Sylviusweg 72 2333 BE Leiden The Netherlands
| | - Kristine Bertheussen
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University Sylviusweg 72 2333 BE Leiden The Netherlands
| | - Hanieh K Abedian
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University Sylviusweg 72 2333 BE Leiden The Netherlands
| | - Aidan V Johnson
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University Sylviusweg 72 2333 BE Leiden The Netherlands
| | - Nicholas M Pearce
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Martin Lutz
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Johan Kemmink
- Faculty of Science and Engineering, University of Groningen 9747 AG Groningen The Netherlands
| | - Tjalling Seirsma
- Bacterial Cell Biology and Physiology Group, Swammerdam Institute for Life Sciences, University of Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands
| | - Leendert W Hamoen
- Bacterial Cell Biology and Physiology Group, Swammerdam Institute for Life Sciences, University of Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands
| | - Bert J C Janssen
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Nathaniel I Martin
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University Sylviusweg 72 2333 BE Leiden The Netherlands
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12
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Liu J, Wei T, Tan Y, Liu H, Li X. Enabling chemical protein (semi)synthesis via reducible solubilizing tags (RSTs). Chem Sci 2022; 13:1367-1374. [PMID: 35222920 PMCID: PMC8809390 DOI: 10.1039/d1sc06387a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 12/27/2021] [Indexed: 01/11/2023] Open
Abstract
The reducible solubilizing tag strategy served as a simple and powerful method for the chemical synthesis and semi-synthesis via Ser/Thr ligation and Cys/Pen ligation of extensive self-assembly peptides, membrane proteins with poor solubility.
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Affiliation(s)
- Jiamei Liu
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong, Hong Kong
| | - Tongyao Wei
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong, Hong Kong
| | - Yi Tan
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong, Hong Kong
| | - Heng Liu
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong, Hong Kong
| | - Xuechen Li
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong, Hong Kong
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13
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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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14
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Abstract
AbstractOver the past more than ten years, my laboratory has been engaged in the total synthesis, medicinal chemistry, and chemical biology studies on daptomycin. Our efforts are expected to advance new understanding of this effective cyclic lipodepsipeptide antibiotic. In this Account, this long journey is presented.1 Introduction2 Total Synthesis of Daptomycin3 Medicinal Chemistry of Daptomycin4 Molecular Comparison of Daptomycin and Kynomycin5 New Insight into How Daptomycin Exerts Bactericidal Effect6 Conclusion
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15
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Sun Z, Li X. Studies on
2‐Formylphenylboronic Acid‐Based
Ser/Thr Ligation and Cys/Pen Ligation
†. CHINESE J CHEM 2021. [DOI: 10.1002/cjoc.202100385] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Zhenquan Sun
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong Hong Kong SAR 999077 China
| | - Xuechen Li
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong Hong Kong SAR 999077 China
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16
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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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17
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Kovalenko N, Howard GK, Swain JA, Hermant Y, Cameron AJ, Cook GM, Ferguson SA, Stubbing LA, Harris PWR, Brimble MA. A Concise Synthetic Strategy Towards the Novel Calcium-dependent Lipopeptide Antibiotic, Malacidin A and Analogues. Front Chem 2021; 9:687875. [PMID: 34422759 PMCID: PMC8372822 DOI: 10.3389/fchem.2021.687875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/25/2021] [Indexed: 11/17/2022] Open
Abstract
Malacidin A is a novel calcium-dependent lipopeptide antibiotic with excellent activity against Gram-positive pathogens. Herein, a concise and robust synthetic route toward malacidin A is reported, employing 9-fluorenylmethoxycarbonyl solid-phase peptide synthesis of a linear precursor, including late-stage incorporation of the lipid tail, followed by solution-phase cyclization. The versatility of this synthetic strategy was further demonstrated by synthesis of a diastereomeric variant of malacidin A and a small library of simplified analogues with variation of the lipid moiety.
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Affiliation(s)
- Nadiia Kovalenko
- School of Chemical Sciences, The University of Auckland, Auckland, New Zealand
| | - Georgina K. Howard
- School of Chemical Sciences, The University of Auckland, Auckland, New Zealand
| | - Jonathan A. Swain
- School of Chemical Sciences, The University of Auckland, Auckland, New Zealand
| | - Yann Hermant
- School of Chemical Sciences, The University of Auckland, Auckland, New Zealand
| | - Alan J. Cameron
- School of Chemical Sciences, The University of Auckland, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
| | - Gregory M. Cook
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Scott A. Ferguson
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Louise A. Stubbing
- School of Chemical Sciences, The University of Auckland, Auckland, New Zealand
| | - Paul W. R. Harris
- School of Chemical Sciences, The University of Auckland, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
| | - Margaret A. Brimble
- School of Chemical Sciences, The University of Auckland, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
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18
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Upert G, Luther A, Obrecht D, Ermert P. Emerging peptide antibiotics with therapeutic potential. MEDICINE IN DRUG DISCOVERY 2021; 9:100078. [PMID: 33398258 PMCID: PMC7773004 DOI: 10.1016/j.medidd.2020.100078] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/15/2020] [Accepted: 12/27/2020] [Indexed: 02/09/2023] Open
Abstract
This review covers some of the recent progress in the field of peptide antibiotics with a focus on compounds with novel or established mode of action and with demonstrated efficacy in animal infection models. Novel drug discovery approaches, linear and macrocyclic peptide antibiotics, lipopeptides like the polymyxins as well as peptides addressing targets located in the plasma membrane or in the outer membrane of bacterial cells are discussed.
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Key Words
- ADMET, absorption, distribution, metabolism and excretion – toxicity in pharmacokinetics
- AMP, antimicrobial peptide
- AMR, antimicrobial resistance
- ATCC, ATCC cell collection
- Antibiotic
- BAM, β-barrel assembly machinery
- CC50, cytotoxic concentration to kill 50% of cells
- CD, circular dichroism
- CFU, colony forming unit
- CLSI, clinical and laboratory standards institute
- CMS, colistin methane sulfonate
- DMPC, 1,2-dimyristoyl-sn-glycero-3-phosphocholine
- ESKAPE, acronym encompassing six bacterial pathogens (often carrying antibiotic resistance): Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumonia, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp
- FDA, U. S. Food and Drug Administration
- HABP, hospital acquired bacterial pneumonia
- HDP, host-defense peptide
- HEK293, human embryonic kidney 293 cells
- HK-2, human kidney 2 cells (proximal tubular cell line)
- HepG2, human hepatocellular carcinoma cell line
- Hpg, 4-hydroxy-phenyl glycine
- ITC, isothermal titration calorimetry
- KPC, Klebsiella pneumoniae metallo-β-lactamase C resistant
- LPS, lipopolysaccharide
- LptA, lipopolysaccharide transport protein A
- LptC, lipopolysaccharide transport protein C
- LptD, lipopolysaccharide transport protein D
- MDR, multidrug-resistant
- MH-I, Müller-Hinton broth I
- MH-II, Müller-Hinton broth II (cation adjusted)
- MIC, minimal inhibitory concentration
- MRSA, methicilline-resistant S. aureus
- MSSA, methicilline-sensitive S. aureus
- MoA, mechanism (mode) of action
- NDM-1, New Delhi metallo-β-lactamase resistant
- NOAEL, no adverse effect level
- ODL, odilorhabdin
- OMPTA (outer membrane targeting antibiotic)
- OMPTA, outer membrane targeting antibiotic
- Omp, outer membrane protein
- PBMC, peripheral mononuclear blood cell
- PBP, penicillin-binding protein
- PBS, phosphate-buffered saline
- PK, pharmacokinetics
- POPC, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
- POPG, 2-oleoyl-1-palmitoyl-sn-glycero-3-phospho-(1-glycerol)
- PrAMPs, polyproline antimicrobial peptides
- RBC, red blood cell
- SAR, structure-activity relationship
- SPR, surface plasmon resonance
- SPase I, signal peptidase I
- VABP, ventilator associated bacterial pneumonia
- VIM-1, beta-lactamase 2 (K. pneumoniae)
- VISA, vancomycin-intermediate S. aureus
- VRE, vancomycin-resistant enterococcus
- WHO, World Health Organization
- WT, wild type
- WTA, wall teichoic acid
- XDR, extremely drug-resistant
- antimicrobial peptide
- antimicrobial resistance
- bid, bis in die (two times a day)
- i.p., intraperitoneal
- i.v., intravenous
- lipopeptide
- mITT population, minimal intend-to-treat population
- peptide antibiotic
- s.c., subcutaneous
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Affiliation(s)
- Gregory Upert
- Polyphor Ltd, Hegenheimermattweg 125, 4123 Allschwil, Switzerland
| | - Anatol Luther
- Bachem AG, Hauptstrasse 114, 4416 Bubendorf, Switzerland
| | - Daniel Obrecht
- Polyphor Ltd, Hegenheimermattweg 125, 4123 Allschwil, Switzerland
| | - Philipp Ermert
- Polyphor Ltd, Hegenheimermattweg 125, 4123 Allschwil, Switzerland
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19
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Ahangarpour M, Kavianinia I, Harris PWR, Brimble MA. Photo-induced radical thiol-ene chemistry: a versatile toolbox for peptide-based drug design. Chem Soc Rev 2021; 50:898-944. [PMID: 33404559 DOI: 10.1039/d0cs00354a] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
While the global market for peptide/protein-based therapeutics is witnessing significant growth, the development of peptide drugs remains challenging due to their low oral bioavailability, poor membrane permeability, and reduced metabolic stability. However, a toolbox of chemical approaches has been explored for peptide modification to overcome these obstacles. In recent years, there has been a revival of interest in photoinduced radical thiol-ene chemistry as a powerful tool for the construction of therapeutic peptides.
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Affiliation(s)
- Marzieh Ahangarpour
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand.
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20
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Tan Y, Wu H, Wei T, Li X. Chemical Protein Synthesis: Advances, Challenges, and Outlooks. J Am Chem Soc 2020; 142:20288-20298. [PMID: 33211477 DOI: 10.1021/jacs.0c09664] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Contemporary chemical protein synthesis has been dramatically advanced over the past few decades, which has enabled chemists to reach the landscape of synthetic biomacromolecules. Chemical synthesis can produce synthetic proteins with precisely controlled structures which are difficult or impossible to obtain via gene expression systems. Herein, we summarize the key enabling ligation technologies, major strategic developments, and some selected representative applications of synthetic proteins and provide an outlook for future development.
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Affiliation(s)
- Yi Tan
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong, P. R. China SAR
| | - Hongxiang Wu
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong, P. R. China SAR
| | - Tongyao Wei
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong, P. R. China SAR
| | - Xuechen Li
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong, P. R. China SAR
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