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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Ancajas CMF, Oyedele AS, Butt CM, Walker AS. Advances, opportunities, and challenges in methods for interrogating the structure activity relationships of natural products. Nat Prod Rep 2024. [PMID: 38912779 DOI: 10.1039/d4np00009a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Time span in literature: 1985-early 2024Natural products play a key role in drug discovery, both as a direct source of drugs and as a starting point for the development of synthetic compounds. Most natural products are not suitable to be used as drugs without further modification due to insufficient activity or poor pharmacokinetic properties. Choosing what modifications to make requires an understanding of the compound's structure-activity relationships. Use of structure-activity relationships is commonplace and essential in medicinal chemistry campaigns applied to human-designed synthetic compounds. Structure-activity relationships have also been used to improve the properties of natural products, but several challenges still limit these efforts. Here, we review methods for studying the structure-activity relationships of natural products and their limitations. Specifically, we will discuss how synthesis, including total synthesis, late-stage derivatization, chemoenzymatic synthetic pathways, and engineering and genome mining of biosynthetic pathways can be used to produce natural product analogs and discuss the challenges of each of these approaches. Finally, we will discuss computational methods including machine learning methods for analyzing the relationship between biosynthetic genes and product activity, computer aided drug design techniques, and interpretable artificial intelligence approaches towards elucidating structure-activity relationships from models trained to predict bioactivity from chemical structure. Our focus will be on these latter topics as their applications for natural products have not been extensively reviewed. We suggest that these methods are all complementary to each other, and that only collaborative efforts using a combination of these techniques will result in a full understanding of the structure-activity relationships of natural products.
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Affiliation(s)
| | | | - Caitlin M Butt
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
| | - Allison S Walker
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
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3
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Fu J, Nakata Y, Itoh H, Panthee S, Hamamoto H, Sekimizu K, Inoue M. Molecular Editing Enhances Oxidation Resistance of Menaquinone-Targeting Antibiotics Lysocin E and WAP-8294A2. Chemistry 2023; 29:e202301224. [PMID: 37328428 DOI: 10.1002/chem.202301224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/16/2023] [Accepted: 06/16/2023] [Indexed: 06/18/2023]
Abstract
Lysocin E (1 a) and WAP-8294A2 (2 a) are peptidic natural products with 37- and 40-membered macrocycles, respectively. Compounds 1 a and 2 a have potent antibacterial activities against Gram-positive bacteria and share a unique mode of action. The electron-rich indole ring of d-Trp-10 of 1 a and 2 a interacts with the electron-deficient benzoquinone ring of menaquinone, which is a co-enzyme in the bacterial respiratory chain. Formation of the electron-donor-acceptor complex causes membrane disruption, leading to cell death. Despite the promising activities of 1 a and 2 a, the susceptibility of Trp-10 to oxidative degradation potentially deters the development of these compounds as antibacterial drugs. To address this issue, we replaced the indole ring with more oxidation-resistant aromatics having a similar shape and electron-rich character. Specifically, analogues with benzofuran (1 b/2 b), benzothiophene (1 c/2 c), and 1-naphthalene (1 d/2 d) rings were designed, and chemically prepared by full solid-phase total syntheses. Antibacterial assays of the six analogues revealed similar activities of 1 d/2 d and markedly reduced activities of 1 b/2 b and 1 c/2 c compared with 1 a/2 a. Equipotent 1 d and 2 d both showed high resistance to oxidation by peroxyl radicals. Hence, the present study demonstrates a new molecular editing strategy for conferring oxidation stability on natural products with pharmacologically useful functions.
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Affiliation(s)
- Junhao Fu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yosuke Nakata
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hiroaki Itoh
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Suresh Panthee
- GenEndeavor LLC, 26219 Eden Landing Rd, Hayward, CA, 94545, USA
- Faculty of Pharma-Science, Teikyo University, 359 Otsuka, Hachioji, Tokyo, 192-0395, Japan
| | - Hiroshi Hamamoto
- Yamagata University Faculty of Medicine, 2-2-2 Iida-Nishi, Yamagata, Yamagata, 990-9585, Japan
| | - Kazuhisa Sekimizu
- Faculty of Pharma-Science, Teikyo University, 359 Otsuka, Hachioji, Tokyo, 192-0395, Japan
| | - Masayuki Inoue
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
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4
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Ballantine RD, Al Ayed K, Bann SJ, Hoekstra M, Martin NI, Cochrane SA. Linearization of the Brevicidine and Laterocidine Lipopeptides Yields Analogues That Retain Full Antibacterial Activity. J Med Chem 2023; 66:6002-6009. [PMID: 37071814 PMCID: PMC10150354 DOI: 10.1021/acs.jmedchem.3c00308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
Brevicidine and laterocidine are macrocyclic lipodepsipeptides with selective activity against Gram-negative bacteria, including colistin-resistant strains. Previously, the macrocyclic core of these peptides was thought essential for antibacterial activity. In this study, we show that C-terminal amidation of linear brevicidine and laterocidine scaffolds, and substitution of the native Thr9, yields linear analogues that retain the potent antibacterial activity and low hemolysis of the parent compounds. Furthermore, an alanine scan of both peptides revealed that the aromatic and basic amino acids within the common central scaffold are essential for antibacterial activity. This linearization strategy for modification of cyclic peptides is a highly effective way to reduce the time and cost of peptide synthesis and may be applicable to other non-ribosomal antibacterial peptides.
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Affiliation(s)
- Ross D Ballantine
- School of Chemistry and Chemical Engineering, Queen's University Belfast, Stranmillis Road, Belfast BT9 5AG, U.K
| | - Karol Al Ayed
- Biological Chemistry Group, Institute of Biology, Leiden University, Sylviusweg 72, Leiden 2333 BE, The Netherlands
| | - Samantha J Bann
- School of Chemistry and Chemical Engineering, Queen's University Belfast, Stranmillis Road, Belfast BT9 5AG, U.K
| | - Michael Hoekstra
- Biological Chemistry Group, Institute of Biology, Leiden University, Sylviusweg 72, Leiden 2333 BE, The Netherlands
| | - Nathaniel I Martin
- Biological Chemistry Group, Institute of Biology, Leiden University, Sylviusweg 72, Leiden 2333 BE, The Netherlands
| | - Stephen A Cochrane
- School of Chemistry and Chemical Engineering, Queen's University Belfast, Stranmillis Road, Belfast BT9 5AG, U.K
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5
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Bioactive Lipodepsipeptides Produced by Bacteria and Fungi. Int J Mol Sci 2022; 23:ijms232012342. [DOI: 10.3390/ijms232012342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/04/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022] Open
Abstract
Natural products are a vital source for agriculture, medicine, cosmetics and other fields. Lipodepsipeptides (LPDs) are a wide group of natural products distributed among living organisms such as bacteria, fungi, yeasts, virus, insects, plants and marine organisms. They are a group of compounds consisting of a lipid connected to a peptide, which are able to self-assemble into several different structures. They have shown different biological activities such as phytotoxic, antibiotic, antiviral, antiparasitic, antifungal, antibacterial, immunosuppressive, herbicidal, cytotoxic and hemolytic activities. Their biological activities seem to be due to their interactions with the plasma membrane (MP) because they are able to mimic the architecture of the native membranes interacting with their hydrophobic segment. LPDs also have surfactant properties. The review has been focused on the lipodepsipeptides isolated from fungal and bacterial sources, on their biological activity, on the structure–activity relationships of some selected LPD subgroups and on their potential application in agriculture and medicine. The chemical and biological characterization of lipodepsipeptides isolated in the last three decades and findings that resulted from SCI-FINDER research are reported. A critical evaluation of the most recent reviews dealing with the same argument has also been described.
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Recent Advances in Macrocyclic Drugs and Microwave-Assisted and/or Solid-Supported Synthesis of Macrocycles. Molecules 2022; 27:molecules27031012. [PMID: 35164274 PMCID: PMC8839925 DOI: 10.3390/molecules27031012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/28/2022] [Accepted: 01/29/2022] [Indexed: 11/19/2022] Open
Abstract
Macrocycles represent attractive candidates in organic synthesis and drug discovery. Since 2014, nineteen macrocyclic drugs, including three radiopharmaceuticals, have been approved by FDA for the treatment of bacterial and viral infections, cancer, obesity, immunosuppression, etc. As such, new synthetic methodologies and high throughput chemistry (e.g., microwave-assisted and/or solid-phase synthesis) to access various macrocycle entities have attracted great interest in this chemical space. This article serves as an update on our previous review related to macrocyclic drugs and new synthetic strategies toward macrocycles (Molecules, 2013, 18, 6230). In this work, I first reviewed recent FDA-approved macrocyclic drugs since 2014, followed by new advances in macrocycle synthesis using high throughput chemistry, including microwave-assisted and/or solid-supported macrocyclization strategies. Examples and highlights of macrocyclization include macrolactonization and macrolactamization, transition-metal catalyzed olefin ring-closure metathesis, intramolecular C–C and C–heteroatom cross-coupling, copper- or ruthenium-catalyzed azide–alkyne cycloaddition, intramolecular SNAr or SN2 nucleophilic substitution, condensation reaction, and multi-component reaction-mediated macrocyclization, and covering the literature since 2010.
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7
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Yue H, Miller AL, Khetrapal V, Jayaseker V, Wright S, Du L. Biosynthesis, regulation, and engineering of natural products from Lysobacter. Nat Prod Rep 2022; 39:842-874. [PMID: 35067688 DOI: 10.1039/d1np00063b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Covering: up to August 2021Lysobacter is a genus of Gram-negative bacteria that was classified in 1987. Several Lysobacter species are emerging as new biocontrol agents for crop protection in agriculture. Lysobacter are prolific producers of new bioactive natural products that are largely underexplored. So far, several classes of structurally interesting and biologically active natural products have been isolated from Lysobacter. This article reviews the progress in Lysobacter natural product research over the past ten years, including molecular mechanisms for biosynthesis, regulation and mode of action, genome mining of cryptic biosynthetic gene clusters, and metabolic engineering using synthetic biology tools.
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Affiliation(s)
- Huan Yue
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
| | - Amanda Lynn Miller
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
| | - Vimmy Khetrapal
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
| | - Vishakha Jayaseker
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
| | - Stephen Wright
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
| | - Liangcheng Du
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
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8
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Zhou Y, Liang XW. Recent applications of solid-phase strategy in total synthesis of antibiotics. RSC Adv 2021; 11:37942-37951. [PMID: 35498098 PMCID: PMC9043915 DOI: 10.1039/d1ra07503a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 11/11/2021] [Indexed: 12/30/2022] Open
Abstract
Antibiotics produced by soil microorganisms have been widespread and have cured the most prevalent diseases since 1940s. However, recent bacterial resistance to existing antibacterial drugs is causing a public health crisis. The structure–activity relationship of antibiotics needs to be established to search for existing antibiotics-based next-generation drug candidates that can conquer the challenge of bacterial resistance preparedness, which relies on the development of highly efficient total synthesis strategies. The solid-phase strategy has become important to circumvent tedious intermediate isolation and purification procedures with simple filtrations. This review will give a brief overview of recent applications of solid-phase strategy in the total synthesis of antibiotics. The recent applications of solid-phase strategy in total synthesis of antibiotics were summarized, and the structure–activity relationship could be established to conquer the challenge of bacterial resistance preparedness.![]()
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Affiliation(s)
- Yuxin Zhou
- Jinling High School 169 Zhongshan Road Nanjing Jiangsu 210005 China
| | - Xiao-Wei Liang
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University Changsha 410008 China .,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University Changsha 410013 China
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9
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Itoh H, Inoue M. Development of a High-Throughput Strategy for Functional Enhancement and Alteration of Antibacterial Natural Products. J SYN ORG CHEM JPN 2021. [DOI: 10.5059/yukigoseikyokaishi.79.996] [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)
| | - Masayuki Inoue
- Graduate School of Pharmaceutical Sciences, The University of Tokyo
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10
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Morimoto R, Matsumoto T, Minote M, Yanagisawa M, Yamada R, Kuranaga T, Kakeya H. Highly Sensitive Determination of Amino Acids by LC-MS under Neutral Conditions. Chem Pharm Bull (Tokyo) 2021; 69:265-270. [PMID: 33642474 DOI: 10.1248/cpb.c20-00958] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Peptide drug leads possess unusual structural features that allow them to exert their unique biological activities and ideal physicochemical properties. In particular, these peptides often have D-amino acids, and therefore the absolute configurations of the component amino acids have to be elucidated during the structural determination of newly isolated peptide drug leads. Recently, we developed the highly sensitive labeling reagents D/L-FDVDA and D/L-FDLDA for the structural determination of the component amino acids in peptides. In an LC-MS-based structural study of peptides, these reagents enabled us to detect infinitesimal amounts of amino acids derived from mild degradative analysis of the samples. Herein, we firstly report the improved LC-MS protocols for the highly sensitive analyses of amino acids. Second, two new labeling reagents were synthesized and their detection sensitivities evaluated. These studies increase our understanding of the structural basis of these highly sensitive labeling reagents, and should provide opportunities for future on-demand structural modifications of the reagents to enhance their hydrophobicity, stability, and affinity for applications to specialized HPLC columns.
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Affiliation(s)
- Ryota Morimoto
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University
| | - Takumi Matsumoto
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University
| | - Mayuri Minote
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University
| | - Masayuki Yanagisawa
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University
| | - Ryotaro Yamada
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University
| | - Takefumi Kuranaga
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University
| | - Hideaki Kakeya
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University
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11
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Pan C, Kuranaga T, Cao X, Suzuki T, Dohmae N, Shinzato N, Onaka H, Kakeya H. Amycolapeptins A and B, Cyclic Nonadepsipeptides Produced by Combined-culture of Amycolatopsis sp. and Tsukamurella pulmonis. J Org Chem 2021; 86:1843-1849. [PMID: 33410699 DOI: 10.1021/acs.joc.0c02660] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Two nonapeptide natural products, amycolapeptins A (1) and B (2) with a 22-membered cyclic depsipeptide skeleton, β-hydroxytyrosine, and a highly modified side chain, which were not produced in a monoculture of the rare actinomycete Amycolatopsis sp. 26-4, were discovered in broth of its combined-culture with Tsukamurella pulmonis TP-B0596. The planar structures were elucidated by spectroscopic analyses (extensive 2D-NMR and MALDI-TOF MS/MS). The absolute configurations of component amino acids were unambiguously determined by the highly sensitive advanced Marfey's method we recently developed. Additionally, the structures of unstable/unusual moieties were corroborated by chemical synthesis and CD analysis.
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Affiliation(s)
- Chengqian Pan
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Takefumi Kuranaga
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Xun Cao
- Ocean College, Zhejiang University, Hangzhou 310058, China
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Bioscience Building, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Bioscience Building, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Naoya Shinzato
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa 903-0213, Japan
| | - Hiroyasu Onaka
- Graduate School of Agricultural and Life Sciences & Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
| | - Hideaki Kakeya
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
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12
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Yu L, Du F, Chen X, Zheng Y, Morton M, Liu F, Du L. Identification of the Biosynthetic Gene Cluster for the anti-MRSA Lysocins through Gene Cluster Activation Using Strong Promoters of Housekeeping Genes and Production of New Analogs in Lysobacter sp. 3655. ACS Synth Biol 2020; 9:1989-1997. [PMID: 32610008 DOI: 10.1021/acssynbio.0c00067] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Gram-negative gliding bacteria Lysobacter represent a new and rich source for bioactive natural products. In an effort to discover new antibiotics, we found a cryptic biosynthetic gene cluster (BGC) in Lysobacter sp. 3655 that shared a high similarity with the putative lysocin BGC identified in silico previously from Lysobacter sp. RH2180-5. Lysocins are cyclic lipodepsipeptides with potent activity against MRSA (methicillin-resistant Staphylococcus aureus) using a novel mode of action, but the lysocin BGC had not been experimentally verified so far. Using an activity-guided screening, we isolated the main antibiotic compound and confirmed it to be lysocin E. However, the putative lysocin BGC was barely transcribed in the wild type, in which lysocins were produced only in specific conditions and in a negligible amount. To activate the putative lysocin BGC, we screened for strongly transcribed housekeeping genes in strain 3655 and found several powerful promoters. Upon engineering the promoters into the BGC, the lysocin gene transcription was significantly enhanced and the lysocin yield was markedly increased. With readily detectable lysocins production in the engineered strains, we showed that lysocin production was abolished in the gene deletion mutant and then restored in the complementary strain, even when grown in conditions that did not support the wild type for lysocin production. Moreover, the engineered strain produced multiple new lysocin congeners. The determination of the lysocin BGC and the Lysobacter promoters will facilitate the ongoing efforts for yield improvement and new antibiotic biosynthesis using synthetic biology strategies.
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Affiliation(s)
- Lingjun Yu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Fengyu Du
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
- College of Chemistry and Pharmacy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xusheng Chen
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
- School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Yongbiao Zheng
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
- College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Martha Morton
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Fengquan Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Liangcheng Du
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
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13
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Sang M, Wang H, Shen Y, Rodrigues de Almeida N, Conda-Sheridan M, Li S, Li Y, Du L. Identification of an Anti-MRSA Cyclic Lipodepsipeptide, WBP-29479A1, by Genome Mining of Lysobacter antibioticus. Org Lett 2019; 21:6432-6436. [DOI: 10.1021/acs.orglett.9b02333] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Moli Sang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Haoxin Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Yuemao Shen
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong 250012, China
| | - Nathalia Rodrigues de Almeida
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Martin Conda-Sheridan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Shanren Li
- Departments of Chemistry, University of Nebraska−Lincoln, Lincoln, Nebraska 68588, United States
| | - Yaoyao Li
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong 250012, China
| | - Liangcheng Du
- Departments of Chemistry, University of Nebraska−Lincoln, Lincoln, Nebraska 68588, United States
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14
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Development of a high-throughput strategy for discovery of potent analogues of antibiotic lysocin E. Nat Commun 2019; 10:2992. [PMID: 31278250 PMCID: PMC6611794 DOI: 10.1038/s41467-019-10754-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 05/30/2019] [Indexed: 12/13/2022] Open
Abstract
Lysocin E, a 37-membered natural depsipeptide, induces rapid bacteriolysis in methicillin-resistant Staphylococcus aureus via a unique menaquinone-dependent mechanism, presenting a promising therapeutic lead. Despite the great medical importance, exploring the potential utility of its derivatives as new platform structures for antibiotic development has remained a significant challenge. Here, we report a high-throughput strategy that enabled the preparation of thousands of analogues of lysocin E and large-scale structure-activity relationship analyses. We integrate 26-step total synthesis of 2401 cyclic peptides, tandem mass spectrometry-sequencing, and two microscale activity assays to identify 23 candidate compounds. Re-synthesis of these candidates shows that 11 of them (A1-A11) exhibit antimicrobial activity superior or comparable to that of lysocin E, and that lysocin E and A1-A11 share L-Leu-6 and L-Ile-11. Therefore, the present strategy allows us to efficiently decipher biologically crucial residues and identify potentially useful agents for the treatment of infectious diseases.
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15
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Varela MF, Kumar S. Strategies for discovery of new molecular targets for anti-infective drugs. Curr Opin Pharmacol 2019; 48:57-68. [PMID: 31146204 DOI: 10.1016/j.coph.2019.04.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 04/18/2019] [Accepted: 04/20/2019] [Indexed: 12/29/2022]
Abstract
Multidrug resistant bacterial pathogens as causative agents of infectious disease are a primary public health concern. Clinical efficacy of antimicrobial chemotherapy toward bacterial infection has been compromised in cases where causative agents are resistant to multiple structurally distinct antimicrobial agents. Modification of extant antimicrobial agents that exploit conventional bacterial targets have been developed since the advent of the antimicrobial era. This approach, while successful in certain cases, nonetheless suffers overall from the costs of development and rapid emergence of bacterial variants with confounding resistances to modified agents. Thus, additional strategies toward discovery of new molecular targets have been developed based on bioinformatics analyses and comparative genomics. These and other strategies meant to identify new molecular targets represent promising avenues for reducing emergence of bacterial infections. This short review considers these strategies for discovery of new molecular targets within bacterial pathogens.
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Affiliation(s)
- Manuel F Varela
- Department of Biology, Eastern New Mexico University, Portales, NM 88130, USA.
| | - Sanath Kumar
- Post Harvest Technology, ICAR-Central Institute of Fisheries Education, Seven Bungalows, Andheri (W), Mumbai, 400016, India
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16
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Schilling NA, Berscheid A, Schumacher J, Saur JS, Konnerth MC, Wirtz SN, Beltrán-Beleña JM, Zipperer A, Krismer B, Peschel A, Kalbacher H, Brötz-Oesterhelt H, Steinem C, Grond S. Synthetic Lugdunin Analogues Reveal Essential Structural Motifs for Antimicrobial Action and Proton Translocation Capability. Angew Chem Int Ed Engl 2019; 58:9234-9238. [PMID: 31059155 PMCID: PMC6618241 DOI: 10.1002/anie.201901589] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 03/13/2019] [Indexed: 11/22/2022]
Abstract
Lugdunin, a novel thiazolidine cyclopeptide, exhibits micromolar activity against methicillin‐resistant Staphylococcus aureus (MRSA). For structure–activity relationship (SAR) studies, synthetic analogues obtained from alanine and stereo scanning as well as peptides with modified thiazolidine rings were tested for antimicrobial activity. The thiazolidine ring and the alternating d‐ and l‐amino acid backbone are essential. Notably, the non‐natural enantiomer displays equal activity, thus indicating the absence of a chiral target. The antibacterial activity strongly correlates with dissipation of the membrane potential in S. aureus. Lugdunin equalizes pH gradients in artificial membrane vesicles, thereby maintaining membrane integrity, which demonstrates that proton translocation is the mode of action (MoA). The incorporation of extra tryptophan or propargyl moieties further expands the diversity of this class of thiazolidine cyclopeptides.
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Affiliation(s)
- Nadine A Schilling
- Institute of Organic Chemistry, Biomolecular Chemistry, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 18, 72076, Tuebingen, Germany
| | - Anne Berscheid
- Interfaculty Institute of Microbiology and Infection Medicine, German Center for Infection research (DZIF), Eberhard Karls Universität Tübingen, 72076, Tuebingen, Germany
| | - Johannes Schumacher
- Institute of Organic and Biomolecular Chemistry, Georg August Universität Göttingen, 37077, Goettingen, Germany
| | - Julian S Saur
- Institute of Organic Chemistry, Biomolecular Chemistry, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 18, 72076, Tuebingen, Germany
| | - Martin C Konnerth
- Institute of Organic Chemistry, Biomolecular Chemistry, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 18, 72076, Tuebingen, Germany
| | - Sebastian N Wirtz
- Institute of Organic Chemistry, Biomolecular Chemistry, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 18, 72076, Tuebingen, Germany
| | - José M Beltrán-Beleña
- Institute of Organic Chemistry, Biomolecular Chemistry, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 18, 72076, Tuebingen, Germany
| | - Alexander Zipperer
- Interfaculty Institute of Microbiology and Infection Medicine, German Center for Infection research (DZIF), Eberhard Karls Universität Tübingen, 72076, Tuebingen, Germany
| | - Bernhard Krismer
- Interfaculty Institute of Microbiology and Infection Medicine, German Center for Infection research (DZIF), Eberhard Karls Universität Tübingen, 72076, Tuebingen, Germany
| | - Andreas Peschel
- Interfaculty Institute of Microbiology and Infection Medicine, German Center for Infection research (DZIF), Eberhard Karls Universität Tübingen, 72076, Tuebingen, Germany
| | - Hubert Kalbacher
- Interfaculty Institute of Biochemistry, Eberhard Karls Universität Tübingen, 72076, Tuebingen, Germany
| | - Heike Brötz-Oesterhelt
- Interfaculty Institute of Microbiology and Infection Medicine, German Center for Infection research (DZIF), Eberhard Karls Universität Tübingen, 72076, Tuebingen, Germany
| | - Claudia Steinem
- Institute of Organic and Biomolecular Chemistry, Georg August Universität Göttingen, 37077, Goettingen, Germany
| | - Stephanie Grond
- Institute of Organic Chemistry, Biomolecular Chemistry, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 18, 72076, Tuebingen, Germany
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17
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Schilling NA, Berscheid A, Schumacher J, Saur JS, Konnerth MC, Wirtz SN, Beltrán‐Beleña JM, Zipperer A, Krismer B, Peschel A, Kalbacher H, Brötz‐Oesterhelt H, Steinem C, Grond S. Synthetische Analoga zeigen die essentiellen Strukturmotive von Lugdunin und seinen Protonentransport. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901589] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Nadine A. Schilling
- Institut für Organische Chemie, Biomolekulare ChemieEberhard Karls Universität Tübingen Auf der Morgenstelle 18 72076 Tübingen Deutschland
| | - Anne Berscheid
- Interfakultäres Institut für Mikrobiologie und InfektionsmedizinDeutsches Zentrum für Infektionsforschung (DZIF)Eberhard Karls Universität Tübingen 72076 Tübingen Deutschland
| | - Johannes Schumacher
- Institut für Organische und Biomolekulare ChemieGeorg August Universität Göttingen 37077 Göttingen Deutschland
| | - Julian S. Saur
- Institut für Organische Chemie, Biomolekulare ChemieEberhard Karls Universität Tübingen Auf der Morgenstelle 18 72076 Tübingen Deutschland
| | - Martin C. Konnerth
- Institut für Organische Chemie, Biomolekulare ChemieEberhard Karls Universität Tübingen Auf der Morgenstelle 18 72076 Tübingen Deutschland
| | - Sebastian N. Wirtz
- Institut für Organische Chemie, Biomolekulare ChemieEberhard Karls Universität Tübingen Auf der Morgenstelle 18 72076 Tübingen Deutschland
| | - José M. Beltrán‐Beleña
- Institut für Organische Chemie, Biomolekulare ChemieEberhard Karls Universität Tübingen Auf der Morgenstelle 18 72076 Tübingen Deutschland
| | - Alexander Zipperer
- Interfakultäres Institut für Mikrobiologie und InfektionsmedizinDeutsches Zentrum für Infektionsforschung (DZIF)Eberhard Karls Universität Tübingen 72076 Tübingen Deutschland
| | - Bernhard Krismer
- Interfakultäres Institut für Mikrobiologie und InfektionsmedizinDeutsches Zentrum für Infektionsforschung (DZIF)Eberhard Karls Universität Tübingen 72076 Tübingen Deutschland
| | - Andreas Peschel
- Interfakultäres Institut für Mikrobiologie und InfektionsmedizinDeutsches Zentrum für Infektionsforschung (DZIF)Eberhard Karls Universität Tübingen 72076 Tübingen Deutschland
| | - Hubert Kalbacher
- Interfakultäres Institut für BiochemieEberhard Karls Universität Tübingen 72076 Tübingen Deutschland
| | - Heike Brötz‐Oesterhelt
- Interfakultäres Institut für Mikrobiologie und InfektionsmedizinDeutsches Zentrum für Infektionsforschung (DZIF)Eberhard Karls Universität Tübingen 72076 Tübingen Deutschland
| | - Claudia Steinem
- Institut für Organische und Biomolekulare ChemieGeorg August Universität Göttingen 37077 Göttingen Deutschland
| | - Stephanie Grond
- Institut für Organische Chemie, Biomolekulare ChemieEberhard Karls Universität Tübingen Auf der Morgenstelle 18 72076 Tübingen Deutschland
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18
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Itoh H, Inoue M. Comprehensive Structure–Activity Relationship Studies of Macrocyclic Natural Products Enabled by Their Total Syntheses. Chem Rev 2019; 119:10002-10031. [DOI: 10.1021/acs.chemrev.9b00063] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Hiroaki Itoh
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masayuki Inoue
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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19
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Lakemeyer M, Zhao W, Mandl FA, Hammann P, Sieber SA. Thinking Outside the Box-Novel Antibacterials To Tackle the Resistance Crisis. Angew Chem Int Ed Engl 2018; 57:14440-14475. [PMID: 29939462 DOI: 10.1002/anie.201804971] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Indexed: 12/13/2022]
Abstract
The public view on antibiotics as reliable medicines changed when reports about "resistant superbugs" appeared in the news. While reasons for this resistance development are easily spotted, solutions for re-establishing effective antibiotics are still in their infancy. This Review encompasses several aspects of the antibiotic development pipeline from very early strategies to mature drugs. An interdisciplinary overview is given of methods suitable for mining novel antibiotics and strategies discussed to unravel their modes of action. Select examples of antibiotics recently identified by using these platforms not only illustrate the efficiency of these measures, but also highlight promising clinical candidates with therapeutic potential. Furthermore, the concept of molecules that disarm pathogens by addressing gatekeepers of virulence will be covered. The Review concludes with an evaluation of antibacterials currently in clinical development. Overall, this Review aims to connect select innovative antimicrobial approaches to stimulate interdisciplinary partnerships between chemists from academia and industry.
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Affiliation(s)
- Markus Lakemeyer
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Weining Zhao
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Franziska A Mandl
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Peter Hammann
- R&D Therapeutic Area Infectious Diseases, Sanofi-Aventis (Deutschland) GmbH, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - Stephan A Sieber
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
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20
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Lakemeyer M, Zhao W, Mandl FA, Hammann P, Sieber SA. Über bisherige Denkweisen hinaus - neue Wirkstoffe zur Überwindung der Antibiotika-Krise. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804971] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Markus Lakemeyer
- Fakultät für Chemie; Lehrstuhl für Organische Chemie II, Center for Integrated Protein Science (CIPSM); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Weining Zhao
- Fakultät für Chemie; Lehrstuhl für Organische Chemie II, Center for Integrated Protein Science (CIPSM); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Franziska A. Mandl
- Fakultät für Chemie; Lehrstuhl für Organische Chemie II, Center for Integrated Protein Science (CIPSM); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Peter Hammann
- R&D Therapeutic Area Infectious Diseases; Sanofi-Aventis (Deutschland) GmbH; Industriepark Höchst 65926 Frankfurt am Main Deutschland
| | - Stephan A. Sieber
- Fakultät für Chemie; Lehrstuhl für Organische Chemie II, Center for Integrated Protein Science (CIPSM); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
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21
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Yao G, Wang W, Ao L, Cheng Z, Wu C, Pan Z, Liu K, Li H, Su W, Fang L. Improved Total Synthesis and Biological Evaluation of Coibamide A Analogues. J Med Chem 2018; 61:8908-8916. [PMID: 30247036 DOI: 10.1021/acs.jmedchem.8b01141] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
To enable the large-scale synthesis of coibamide A, we developed an improved synthetic strategy for this class of cyclodepsipeptide. The versatility of the synthetic procedure was demonstrated by the preparation of a series of designed coibamide A analogues, which enabled the preliminary structure-activity relationship (SAR) studies for this compound. Although most modifications of coibamide A resulted in decrease or loss of the antiproliferativity, we found that versatile substitution at position 3 was well tolerated. Remarkably, a simplified analogue, [MeAla3-MeAla6]-coibamide (1f), not only showed nearly the same inhibition as coibamide A against the tested cancer cells but also significantly inhibited tumor growth in vivo. The improved synthetic strategy and the relevant trends of SAR disclosed in this study will be valuable for further optimization of the overall profile of coibamide A.
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Affiliation(s)
- Guiyang Yao
- Guangdong Key Laboratory of Nanomedicine, Institute of Biomedicine and Biotechnology , Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences , Shenzhen , Guangdong 518055 , China
| | - Wei Wang
- Guangdong Key Laboratory of Nanomedicine, Institute of Biomedicine and Biotechnology , Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences , Shenzhen , Guangdong 518055 , China
| | - Lijiao Ao
- Guangdong Key Laboratory of Nanomedicine, Institute of Biomedicine and Biotechnology , Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences , Shenzhen , Guangdong 518055 , China.,Shenzhen College of Advanced Technology , University of Chinese Academy of Sciences , Shenzhen , Guangdong 518055 , China
| | - Zhehong Cheng
- Guangdong Key Laboratory of Nanomedicine, Institute of Biomedicine and Biotechnology , Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences , Shenzhen , Guangdong 518055 , China.,Shenzhen College of Advanced Technology , University of Chinese Academy of Sciences , Shenzhen , Guangdong 518055 , China
| | - Chunlei Wu
- Guangdong Key Laboratory of Nanomedicine, Institute of Biomedicine and Biotechnology , Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences , Shenzhen , Guangdong 518055 , China
| | - Zhengyin Pan
- Guangdong Key Laboratory of Nanomedicine, Institute of Biomedicine and Biotechnology , Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences , Shenzhen , Guangdong 518055 , China
| | - Ke Liu
- Guangdong Key Laboratory of Nanomedicine, Institute of Biomedicine and Biotechnology , Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences , Shenzhen , Guangdong 518055 , China
| | - Hongchang Li
- Guangdong Key Laboratory of Nanomedicine, Institute of Biomedicine and Biotechnology , Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences , Shenzhen , Guangdong 518055 , China
| | - Wu Su
- Guangdong Key Laboratory of Nanomedicine, Institute of Biomedicine and Biotechnology , Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences , Shenzhen , Guangdong 518055 , China
| | - Lijing Fang
- Guangdong Key Laboratory of Nanomedicine, Institute of Biomedicine and Biotechnology , Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences , Shenzhen , Guangdong 518055 , China
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22
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Hamamoto H, Sekimizu K. Development of Antibiotics Using Silkworm Bacteria and Fungi Infection Model. YAKUGAKU ZASSHI 2018; 138:895-899. [DOI: 10.1248/yakushi.17-00202-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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23
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The Road from Host-Defense Peptides to a New Generation of Antimicrobial Drugs. Molecules 2018; 23:molecules23020311. [PMID: 29389911 PMCID: PMC6017364 DOI: 10.3390/molecules23020311] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 01/23/2018] [Accepted: 01/30/2018] [Indexed: 01/28/2023] Open
Abstract
Host-defense peptides, also called antimicrobial peptides (AMPs), whose protective action has been used by animals for millions of years, fulfill many requirements of the pharmaceutical industry, such as: (1) broad spectrum of activity; (2) unlike classic antibiotics, they induce very little resistance; (3) they act synergically with conventional antibiotics; (4) they neutralize endotoxins and are active in animal models. However, it is considered that many natural peptides are not suitable for drug development due to stability and biodisponibility problems, or high production costs. This review describes the efforts to overcome these problems and develop new antimicrobial drugs from these peptides or inspired by them. The discovery process of natural AMPs is discussed, as well as the development of synthetic analogs with improved pharmacological properties. The production of these compounds at acceptable costs, using different chemical and biotechnological methods, is also commented. Once these challenges are overcome, a new generation of versatile, potent and long-lasting antimicrobial drugs is expected.
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24
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Itoh H, Tokumoto K, Kaji T, Paudel A, Panthee S, Hamamoto H, Sekimizu K, Inoue M. Total Synthesis and Biological Mode of Action of WAP-8294A2: A Menaquinone-Targeting Antibiotic. J Org Chem 2017; 83:6924-6935. [PMID: 29019678 DOI: 10.1021/acs.joc.7b02318] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
WAP-8294A2 (lotilibcin, 1) is a potent antibiotic with superior in vivo efficacy to vancomycin against methicillin-resistant Staphylococcus aureus (MRSA). Despite the great medical importance, its molecular mode of action remains unknown. Here we report the total synthesis of complex macrocyclic peptide 1 comprised of 12 amino acids with a β-hydroxy fatty-acid chain, and its deoxy analogue 2. A full solid-phase synthesis of 1 and 2 enabled their rapid assembly and the first detailed investigation of their functions. Compounds 1 and 2 were equipotent against various strains of Gram-positive bacteria including MRSA. We present evidence that the antimicrobial activities of 1 and 2 are due to lysis of the bacterial membrane, and their membrane-disrupting effects depend on the presence of menaquinone, an essential factor for the bacterial respiratory chain. The established synthetic routes and the menaquinone-targeting mechanisms provide valuable information for designing and developing new antibiotics based on their structures.
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Affiliation(s)
- Hiroaki Itoh
- Graduate School of Pharmaceutical Sciences , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku , Tokyo 113-0033 , Japan
| | - Kotaro Tokumoto
- Graduate School of Pharmaceutical Sciences , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku , Tokyo 113-0033 , Japan
| | - Takuya Kaji
- Graduate School of Pharmaceutical Sciences , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku , Tokyo 113-0033 , Japan
| | - Atmika Paudel
- Teikyo University Institute of Medical Mycology , 359 Otsuka , Hachioji , Tokyo 192-0395 , Japan
| | - Suresh Panthee
- Teikyo University Institute of Medical Mycology , 359 Otsuka , Hachioji , Tokyo 192-0395 , Japan
| | - Hiroshi Hamamoto
- Teikyo University Institute of Medical Mycology , 359 Otsuka , Hachioji , Tokyo 192-0395 , Japan
| | - Kazuhisa Sekimizu
- Teikyo University Institute of Medical Mycology , 359 Otsuka , Hachioji , Tokyo 192-0395 , Japan
| | - Masayuki Inoue
- Graduate School of Pharmaceutical Sciences , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku , Tokyo 113-0033 , Japan
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25
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Indole-Induced Reversion of Intrinsic Multiantibiotic Resistance in Lysobacter enzymogenes. Appl Environ Microbiol 2017. [PMID: 28625984 DOI: 10.1128/aem.00995-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Lysobacter species are a group of environmental bacteria that are emerging as a new source of antibiotics. One characteristic of Lysobacter is intrinsic resistance to multiple antibiotics, which had not been studied. To understand the resistance mechanism, we tested the effect of blocking two-component regulatory systems (TCSs) on the antibiotic resistance of Lysobacter enzymogenes, a prolific producer of antibiotics. Upon treatment with LED209, an inhibitor of the widespread TCS QseC/QseB, L. enzymogenes produced a large amount of an unknown metabolite that was barely detectable in the untreated culture. Subsequent structural elucidation by nuclear magnetic resonance (NMR) unexpectedly revealed that the metabolite was indole. Indole production was also markedly induced by adrenaline, a known modulator of QseC/QseB. Next, we identified two TCS genes, L. enzymogenesqseC (Le-qseC) and Le-qseB, in L. enzymogenes and found that mutations of Le-qseC and Le-qseB also led to a dramatic increase in indole production. We then chemically synthesized a fluorescent indole probe that could label the cells. While the Le-qseB (cytoplasmic response regulator) mutant was clearly labeled by the probe, the Le-qseC (membrane sensor) mutant was not labeled. It was reported previously that indole can enhance antibiotic resistance in bacteria. Therefore, we tested if the dramatic increase in the level of indole production in L. enzymogenes upon blocking of Le-qseC and Le-qseB would lead to enhanced antibiotic resistance. Surprisingly, we found that indole caused the intrinsically multiantibiotic-resistant bacterium L. enzymogenes to become susceptible. Point mutations at conserved amino acids in Le-QseC also led to antibiotic susceptibility. Because indole is known as an interspecies signal, these findings may have implications.IMPORTANCE The environmental bacterium Lysobacter is a new source of antibiotic compounds and exhibits intrinsic antibiotic resistance. Here, we found that the inactivation of a two-component regulatory system (TCS) by an inhibitor or by gene deletion led to a remarkable increase in the level of production of a metabolite in L. enzymogenes, and this metabolite was identified to be indole. We chemically synthesized a fluorescent indole probe and found that it could label the wild type and a mutant of the TCS cytoplasmic response regulator but not a mutant of the TCS membrane sensor. Indole treatment caused the intrinsically multidrug-resistant bacterium L. enzymogenes to be susceptible to antibiotics. Mutations of the TCS sensor also led to antibiotic susceptibility. Because indole is known as an interspecies signal between gut microbiota and mammalian hosts, the observation that indole could render intrinsically resistant L. enzymogenes susceptible to common antibiotics may have implications.
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26
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Masschelein J, Jenner M, Challis GL. Antibiotics from Gram-negative bacteria: a comprehensive overview and selected biosynthetic highlights. Nat Prod Rep 2017. [PMID: 28650032 DOI: 10.1039/c7np00010c] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: up to 2017The overwhelming majority of antibiotics in clinical use originate from Gram-positive Actinobacteria. In recent years, however, Gram-negative bacteria have become increasingly recognised as a rich yet underexplored source of novel antimicrobials, with the potential to combat the looming health threat posed by antibiotic resistance. In this article, we have compiled a comprehensive list of natural products with antimicrobial activity from Gram-negative bacteria, including information on their biosynthetic origin(s) and molecular target(s), where known. We also provide a detailed discussion of several unusual pathways for antibiotic biosynthesis in Gram-negative bacteria, serving to highlight the exceptional biocatalytic repertoire of this group of microorganisms.
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Affiliation(s)
- J Masschelein
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
| | - M Jenner
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
| | - G L Challis
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
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27
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Sekimizu K. The Usefulness of Silkworms as a Model Animal for Evaluating the Effectiveness of Medicine and Food. YAKUGAKU ZASSHI 2017; 137:551-562. [DOI: 10.1248/yakushi.16-00249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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28
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Kuranaga T, Enomoto A, Tan H, Fujita K, Wakimoto T. Total Synthesis of Theonellapeptolide Id. Org Lett 2017; 19:1366-1369. [DOI: 10.1021/acs.orglett.7b00249] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Takefumi Kuranaga
- Faculty of Pharmaceutical
Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Ayumu Enomoto
- Faculty of Pharmaceutical
Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Hui Tan
- Faculty of Pharmaceutical
Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Kazuto Fujita
- Faculty of Pharmaceutical
Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical
Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
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29
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Kaji T, Murai M, Itoh H, Yasukawa J, Hamamoto H, Sekimizu K, Inoue M. Total Synthesis and Functional Evaluation of Fourteen Derivatives of Lysocin E: Importance of Cationic, Hydrophobic, and Aromatic Moieties for Antibacterial Activity. Chemistry 2016; 22:16912-16919. [PMID: 27739191 DOI: 10.1002/chem.201604022] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Indexed: 12/22/2022]
Abstract
Lysocin E (1) is a structurally complex 37-membered depsipeptide comprising 12 amino-acid residues with an N-methylated amide and an ester linkage. Compound 1 binds to menaquinone (MK) in the bacterial membrane to exert its potent bactericidal activity. To decipher the biologically important functionalities within this unique antibiotic, we performed a comprehensive structure-activity relationship (SAR) study by systematically changing the side-chain structures of l-Thr-1, d-Arg-2, N-Me-d-Phe-5, d-Arg-7, l-Glu-8, and d-Trp-10. First, we achieved total synthesis of the 14 new side-chain analogues of 1 by employing a solid-phase strategy. We then evaluated the MK-dependent liposomal disruption and antimicrobial activity against Staphylococcus aureus by 1 and its analogues. Correlating data between the liposome and bacteria experiments revealed that membrane lysis was mainly responsible for the antibacterial functions. Altering the cationic guanidine moiety of d-Arg-2/7 to a neutral amide, and the C7-acyl group of l-Thr-1 to the C2 or C11 counterpart decreased the antimicrobial activities four- or eight-fold. More drastically, chemical mutation of d-Trp-10 to d-Ala-10 totally abolished the bioactivities. These important findings led us to propose the biological roles of the side-chain functionalities.
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Affiliation(s)
- Takuya Kaji
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Motoki Murai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hiroaki Itoh
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Jyunichiro Yasukawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,Faculty of Pharmaceutical Sciences, Doshisha Women's College of Liberal Arts, Kohdo, Kyotanabe, Kyoto, 610-0395, Japan
| | - Hiroshi Hamamoto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,Teikyo University Institute of Medical Mycology, 359 Otsuka, Hachioji, Tokyo, 192-0395, Japan
| | - Kazuhisa Sekimizu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,Teikyo University Institute of Medical Mycology, 359 Otsuka, Hachioji, Tokyo, 192-0395, Japan
| | - Masayuki Inoue
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
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30
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Jin K, Sam IH, Po KHL, Lin D, Ghazvini Zadeh EH, Chen S, Yuan Y, Li X. Total synthesis of teixobactin. Nat Commun 2016; 7:12394. [PMID: 27484680 PMCID: PMC4976201 DOI: 10.1038/ncomms12394] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 06/29/2016] [Indexed: 11/24/2022] Open
Abstract
To cope with the global bacterial multidrug resistance, scientific communities have devoted significant efforts to develop novel antibiotics, particularly those with new modes of actions. Teixobactin, recently isolated from uncultured bacteria, is considered as a promising first-in-class drug candidate for clinical development. Herein, we report its total synthesis by a highly convergent Ser ligation approach and this strategy allows us to prepare several analogues of the natural product. Teixobactin is a recently identified antibiotic that shows activity against drug resistant strains of bacteria. Here, the authors report a highly convergent total synthesis of this natural product, with sufficient flexibility to also allow the synthesis of a number of analogues.
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Affiliation(s)
- Kang Jin
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Iek Hou Sam
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Kathy Hiu Laam Po
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Du'an Lin
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Ebrahim H Ghazvini Zadeh
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, Orlando, Florida 32816, USA
| | - Sheng Chen
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Yu Yuan
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, Orlando, Florida 32816, USA
| | - Xuechen Li
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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31
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Hamamoto H, Sekimizu K. Identification of lysocin E using a silkworm model of bacterial infection. Drug Discov Ther 2016; 10:24-9. [PMID: 26911796 DOI: 10.5582/ddt.2016.01012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
New antimicrobials with novel mechanisms need to be developed to combat antimicrobial-resistant pathogenic bacteria. The current authors recently reported discovery of a new antibiotic named "Lysocin E". Lysocin E was identified using a silkworm model of bacterial infection. The current review discusses the advantages of using a silkworm model of bacterial infection to identify and develop therapeutically efficacious antimicrobials. This review also discusses the discovery of lysocin E and its novel mechanism of action.
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Affiliation(s)
- Hiroshi Hamamoto
- Laboratory of Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo
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32
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Klahn P, Brönstrup M. New Structural Templates for Clinically Validated and Novel Targets in Antimicrobial Drug Research and Development. Curr Top Microbiol Immunol 2016; 398:365-417. [PMID: 27704270 DOI: 10.1007/82_2016_501] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The development of bacterial resistance against current antibiotic drugs necessitates a continuous renewal of the arsenal of efficacious drugs. This imperative has not been met by the output of antibiotic research and development of the past decades for various reasons, including the declining efforts of large pharma companies in this area. Moreover, the majority of novel antibiotics are chemical derivatives of existing structures that represent mostly step innovations, implying that the available chemical space may be exhausted. This review negates this impression by showcasing recent achievements in lead finding and optimization of antibiotics that have novel or unexplored chemical structures. Not surprisingly, many of the novel structural templates like teixobactins, lysocin, griselimycin, or the albicidin/cystobactamid pair were discovered from natural sources. Additional compounds were obtained from the screening of synthetic libraries and chemical synthesis, including the gyrase-inhibiting NTBI's and spiropyrimidinetrione, the tarocin and targocil inhibitors of wall teichoic acid synthesis, or the boronates and diazabicyclo[3.2.1]octane as novel β-lactamase inhibitors. A motif that is common to most clinically validated antibiotics is that they address hotspots in complex biosynthetic machineries, whose functioning is essential for the bacterial cell. Therefore, an introduction to the biological targets-cell wall synthesis, topoisomerases, the DNA sliding clamp, and membrane-bound electron transport-is given for each of the leads presented here.
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Affiliation(s)
- Philipp Klahn
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany.
| | - Mark Brönstrup
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany.
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33
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Yao G, Pan Z, Wu C, Wang W, Fang L, Su W. Efficient Synthesis and Stereochemical Revision of Coibamide A. J Am Chem Soc 2015; 137:13488-91. [DOI: 10.1021/jacs.5b09286] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Guiyang Yao
- Guangdong Key Laboratory of Nanomedicine,
Institute of Biomedicine and Biotechnology, Shenzhen Institutes of
Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, P. R. China
- Departent of Pharmaceutical Engineering,
School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, P. R. China
| | - Zhengyin Pan
- Guangdong Key Laboratory of Nanomedicine,
Institute of Biomedicine and Biotechnology, Shenzhen Institutes of
Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, P. R. China
| | - Chunlei Wu
- Guangdong Key Laboratory of Nanomedicine,
Institute of Biomedicine and Biotechnology, Shenzhen Institutes of
Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, P. R. China
| | - Wei Wang
- Guangdong Key Laboratory of Nanomedicine,
Institute of Biomedicine and Biotechnology, Shenzhen Institutes of
Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, P. R. China
| | - Lijing Fang
- Guangdong Key Laboratory of Nanomedicine,
Institute of Biomedicine and Biotechnology, Shenzhen Institutes of
Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, P. R. China
| | - Wu Su
- Guangdong Key Laboratory of Nanomedicine,
Institute of Biomedicine and Biotechnology, Shenzhen Institutes of
Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, P. R. China
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34
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De Leon Rodriguez LM, Weidkamp AJ, Brimble MA. An update on new methods to synthesize cyclotetrapeptides. Org Biomol Chem 2015; 13:6906-21. [PMID: 26022908 DOI: 10.1039/c5ob00880h] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cyclotetrapeptides are important bioactive lead drug molecules that display a wide spectrum of pharmacological activities. However, the synthesis of cyclotetrapeptides from their linear precursors is challenging due to the highly constrained conformation required for cyclisation, thus hampering their progress to a clinical setting. This review provides an account of the reported methods used for the synthesis of cyclotetrapeptides.
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Affiliation(s)
- Luis M De Leon Rodriguez
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
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35
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Goodreid JD, dos Santos EDS, Batey RA. A Lanthanide(III) Triflate Mediated Macrolactonization/Solid-Phase Synthesis Approach for Depsipeptide Synthesis. Org Lett 2015; 17:2182-5. [PMID: 25866888 DOI: 10.1021/acs.orglett.5b00781] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The effect of dysprosium(III) triflate on macrolactonization reactions to form depsipeptides using MNBA (Shiina's reagent) is reported. Improved yields were obtained for the formation of 16-membered depsipeptides using lanthanide triflate additives. The use of a macrocyclization strategy permits the use of a semiautomated solid-phase synthesis approach for the rapid synthesis of analogues of the antibacterial A54556 acyldepsipeptides in only two physical operations, requiring only final product purification after cyclization.
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Affiliation(s)
- Jordan D Goodreid
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON Canada, M5S 3H6
| | | | - Robert A Batey
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON Canada, M5S 3H6
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