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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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Moreira R, Taylor SD. A54145 Factor D Is Not Less Susceptible to Inhibition by Lung Surfactant than Daptomycin. ACS Infect Dis 2022; 8:1935-1947. [PMID: 36001599 DOI: 10.1021/acsinfecdis.2c00313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A54145 factor D (A5D) is a cyclic lipopeptide antibiotic that shares several structural and mechanistic features with the clinically important antibiotic daptomycin, such as their requirement for calcium and phosphatidylglycerol (PG) for activity. Studies by others have suggested that daptomycin's activity is strongly inhibited by lung surfactant while A5D's activity is not. This finding has inspired efforts, albeit unsuccessful, to develop an A5D analogue that is highly active in the presence of lung surfactant and can be used for treating community acquired pneumonia (CAP). Here we demonstrate that A5D, like daptomycin, has a strong preference for the 1,2-diacyl-sn-glycero-3-phospho-1'-sn-glycerol stereoisomer (2R,2'S configuration) of PG. This PG stereoisomer was determined to be the only stereoisomer of PG in lung surfactant. Both antibiotics are completely antagonized by approximately 1-2 mol equiv of 2R,2'S-PG. Studies performed in the presence of lung surfactant revealed that the antagonism of these peptides by surfactant is mainly due to their interaction with PG and that A5D is not significantly less susceptible to inhibition by lung surfactant than daptomycin.
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Affiliation(s)
- Ryan Moreira
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Scott D Taylor
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
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Moreira R, Taylor SD. The Chiral Target of Daptomycin Is the 2
R
,2′
S
Stereoisomer of Phosphatidylglycerol. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202114858] [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)
- Ryan Moreira
- Deptartment of Chemistry University of Waterloo 200 University Ave. West Waterloo Ontario Canada
| | - Scott D. Taylor
- Deptartment of Chemistry University of Waterloo 200 University Ave. West Waterloo Ontario Canada
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Moreira R, Taylor SD. The Chiral Target of Daptomycin Is the 2R,2'S Stereoisomer of Phosphatidylglycerol. Angew Chem Int Ed Engl 2021; 61:e202114858. [PMID: 34843157 DOI: 10.1002/anie.202114858] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Indexed: 12/12/2022]
Abstract
Daptomycin (dap) is an important antibiotic that interacts with the bacterial membrane lipid phosphatidylglycerol (PG) in a calcium-dependent manner. The enantiomer of dap (ent-dap) was synthesized and was found to be 85-fold less active than dap against B. subtilis, indicating that dap interacts with a chiral target as part of its mechanism of action. Using liposomes containing enantiopure PG, we demonstrate that the binding of dap to PG, the structural transition that occurs upon dap binding to PG, and the subsequent oligomerization of dap, depends upon the configuration of PG, and that dap prefers the 1,2-diacyl-sn-glycero-3-phospho-1'-sn-glycerol stereoisomer (2R,2'S configuration). Ent-dap has a lower affinity for 2R,2'S liposomes than dap and cannot oligomerize to the same extent as dap, which accounts for why ent-dap is less active than dap. To our knowledge, this is the first example whereby the activity of an antibiotic depends upon the configuration of a lipid head group.
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Affiliation(s)
- Ryan Moreira
- Deptartment of Chemistry, University of Waterloo, 200 University Ave. West, Waterloo, Ontario, Canada
| | - Scott D Taylor
- Deptartment of Chemistry, University of Waterloo, 200 University Ave. West, Waterloo, Ontario, Canada
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Chen D, Po KHL, Blasco P, Chen S, Li X. Convergent Synthesis of Calcium-Dependent Antibiotic CDA3a and Analogues with Improved Antibacterial Activity via Late-Stage Serine Ligation. Org Lett 2020; 22:4749-4753. [PMID: 32484680 DOI: 10.1021/acs.orglett.0c01544] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A convergent synthesis via the late-stage serine ligation of naturally occurring calcium-dependent antibiotic CDA3a and its analogues has been developed, which allowed us to readily synthesize the analogues with the variation on the lipid tail. Some analogues were found to show 100-500-fold higher antimicrobial activity than the natural compound CDA3a against drug resistant bacteria. This study will enhance our understanding of CDA3a and provide valuable antibacterial lead candidates for further development.
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Affiliation(s)
- Delin Chen
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong, P. R. China
| | - Kathy Hiu Laam Po
- Department of Infectious Diseases Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, The City University of Hong Kong, Kowloon, Kowloon, Hong Kong, P. R. China
| | - Pilar Blasco
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong, P. R. China
| | - Sheng Chen
- Department of Infectious Diseases Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, The City University of Hong Kong, Kowloon, Kowloon, Hong Kong, P. R. China
| | - Xuechen Li
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong, P. R. China
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Chow HY, Chen D, Li X. Improved total synthesis of the antibiotic A54145B. Org Biomol Chem 2020; 18:4401-4405. [PMID: 32296805 DOI: 10.1039/d0ob00558d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A54145B is a calcium-dependent cyclic lipodepsipeptide antibiotic that is active against Gram-positive pathogens. Herein, we report an improved synthetic route toward A54145B in terms of the yield and time required. The key changes include using a pre-assembled minimalist tetradepsipeptide building block to solve the difficult on-resin esterification from our previous synthetic route, and a new macrocyclization site to avoid the peptide self-cleavage problem.
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Affiliation(s)
- Hoi Yee Chow
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong, P. R. China.
| | - Delin Chen
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The 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, Hong Kong, P. R. China.
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Kralt B, Moreira R, Palmer M, Taylor SD. Total Synthesis of Analogs of A54145D and A54145A 1 for Structure-Activity Relationship Studies. J Org Chem 2020; 85:2213-2219. [PMID: 31873009 DOI: 10.1021/acs.joc.9b02922] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The total solid-phase synthesis and in vitro biological activity of a series of analogs of A54145 factor D (A5D) and A54145 factor A1 (A5A1), two cyclic lipodepsipeptide antibiotics, are reported. An on-resin cyclization strategy was employed to prepare A5A1 analogs in which Thr4, the residue involved in the depsi (ester) bond, was replaced with either diaminopropionic acid (DAPA), (2S,3R)-diaminobutyric acid (DABA), or serine, effectively replacing the ring-closing ester bond with an amide linkage or with a primary ester. Antibacterial studies with these four analogs revealed that, contrary to a previous report, replacing the ester bond with an amide bond significantly reduces biological activity, and that both the ester bond and the methyl group at the γ-position of Thr4 are crucial for activity. Consistent with literature reports, we found that the single substitution of either 3-hydroxyasparagine (HOAsn) or 3-methoxyaspartate (MeOAsp) with Asn or Asp, respectively, in A5D is more detrimental to activity than the double substitution where both HOAsn and MeOAsp are replaced with Asn or Asp, respectively.
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Affiliation(s)
- Braden Kralt
- Department of Chemistry , University of Waterloo , 200 University Avenue West , Waterloo , Ontario N2L 3G1 , Canada
| | - Ryan Moreira
- Department of Chemistry , University of Waterloo , 200 University Avenue West , Waterloo , Ontario N2L 3G1 , Canada
| | - Michael Palmer
- Department of Chemistry , University of Waterloo , 200 University Avenue West , Waterloo , Ontario N2L 3G1 , Canada
| | - Scott D Taylor
- Department of Chemistry , University of Waterloo , 200 University Avenue West , Waterloo , Ontario N2L 3G1 , Canada
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Affiliation(s)
- Braden Kralt
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Ryan Moreira
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Michael Palmer
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Scott D. Taylor
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
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Chen D, Chow HY, Po KHL, Ma W, Leung ELY, Sun Z, Liu M, Chen S, Li X. Total Synthesis and Structural Establishment/Revision of Antibiotics A54145. Org Lett 2019; 21:5639-5644. [DOI: 10.1021/acs.orglett.9b01972] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Delin Chen
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong, P. R. China
| | - Hoi Yee Chow
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong, P. R. China
| | - Kathy Hiu Laam Po
- Department of Applied Biology and Chemical Technology, State Key Lab of Chiroscience, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, P. R. China
| | - Wenjie Ma
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong, P. R. China
| | - Emily Lok Yee Leung
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong, P. R. China
| | - Zhenquan Sun
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong, P. R. China
| | - Ming Liu
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong, P. R. China
| | - Sheng Chen
- Department of Applied Biology and Chemical Technology, State Key Lab of Chiroscience, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, P. R. China
| | - Xuechen Li
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong, P. R. China
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Wood TM, Martin NI. The calcium-dependent lipopeptide antibiotics: structure, mechanism, & medicinal chemistry. MEDCHEMCOMM 2019; 10:634-646. [PMID: 31191855 DOI: 10.1039/c9md00126c] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 03/20/2019] [Indexed: 12/19/2022]
Abstract
To push back the growing tide of antibacterial resistance the discovery and development of new antibiotics is a must. In recent years the calcium-dependent lipopeptide antibiotics (CDAs) have emerged as a potential source of new antibacterial agents rich in structural and mechanistic diversity. All CDAs share a common lipidated cyclic peptide motif containing amino acid side chains that specifically chelate calcium. It is only in the calcium bound state that the CDAs achieve their potent antibacterial activities. Interestingly, despite their common structural features, the mechanisms by which different CDAs target bacteria can vary dramatically. This review provides both a historic context for the CDAs while also addressing the state of the art with regards to their discovery, optimization, and antibacterial mechanisms.
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Affiliation(s)
- Thomas M Wood
- Department of Chemical Biology & Drug Discovery , Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Universiteitsweg 99 , 3584 CG Utrecht , The Netherlands.,Biological Chemistry Group , Institute of Biology Leiden , Leiden University , Sylvius Laboratories , Sylviusweg 72 , 2333 BE Leiden , The Netherlands . ; Tel: +31 (0)6 1878 5274
| | - Nathaniel I Martin
- Biological Chemistry Group , Institute of Biology Leiden , Leiden University , Sylvius Laboratories , Sylviusweg 72 , 2333 BE Leiden , The Netherlands . ; Tel: +31 (0)6 1878 5274
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Moreira R, Taylor SD. Asymmetric Synthesis of Fmoc-Protected β-Hydroxy and β-Methoxy Amino Acids via a Sharpless Aminohydroxylation Reaction Using FmocNHCl. Org Lett 2018; 20:7717-7720. [PMID: 30480456 DOI: 10.1021/acs.orglett.8b03458] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An efficient asymmetric synthesis of l- threo-β-hydroxyasparagine and l- threo-β-methoxyaspartate that are suitably protected for Fmoc solid phase peptide synthesis is described. The key step in these syntheses was a Sharpless asymmetric aminohydroxylation reaction under basic conditions using N-chlorofluorenyl carbamate (FmocNHCl), a readily prepared and storable nitrogen source.
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Affiliation(s)
- Ryan Moreira
- Department of Chemistry , University of Waterloo , 200 University Avenue West , Waterloo , Ontario Canada , N2L 3G1
| | - Scott D Taylor
- Department of Chemistry , University of Waterloo , 200 University Avenue West , Waterloo , Ontario Canada , N2L 3G1
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Paul S, Ishida H, Nguyen LT, Liu Z, Vogel HJ. Structural and dynamic characterization of a freestanding acyl carrier protein involved in the biosynthesis of cyclic lipopeptide antibiotics. Protein Sci 2017; 26:946-959. [PMID: 28187530 PMCID: PMC5405426 DOI: 10.1002/pro.3138] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/31/2017] [Accepted: 02/03/2017] [Indexed: 11/08/2022]
Abstract
Friulimicin is a cyclic lipodecapeptide antibiotic that is produced by Actinoplanes friuliensis. Similar to the related lipopeptide drug daptomycin, the peptide skeleton of friulimicin is synthesized by a large multienzyme nonribosomal peptide synthetase (NRPS) system. The LipD protein plays a major role in the acylation reaction of friulimicin. The attachment of the fatty acid group promotes its antibiotic activity. Phylogenetic analysis reveals that LipD is most closely related to other freestanding acyl carrier proteins (ACPs), for which the genes are located near to NRPS gene clusters. Here, we report that the solution NMR structure of apo-LipD is very similar to other four-helix bundle forming ACPs from fatty acid synthase (FAS), polyketide synthase, and NRPS systems. By recording NMR dynamics data, we found that the backbone motions in holo-LipD are more restricted than in apo-LipD due to the attachment of phosphopantetheine moiety. This enhanced stability of holo-LipD was also observed in differential scanning calorimetry experiments. Furthermore, we demonstrate that, unlike several other ACPs, the folding of LipD does not depend on the presence of divalent cations, although the presence of Mg2+ or Ca2+ can increase the protein stability. We propose that small structural rearrangements in the tertiary structure of holo-LipD which lead to the enhanced stability are important for the cognate enzyme recognition for the acylation reaction. Our results also highlight the different surface charges of LipD and FAS-ACP from A. friuliensis that would allow the acyl-CoA ligase to interact preferentially with the LipD instead of binding to the FAS-ACP.
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Affiliation(s)
- Subrata Paul
- Biochemistry Research GroupDepartment of Biological Sciences, University of CalgaryCalgaryAlbertaCanada
| | - Hiroaki Ishida
- Biochemistry Research GroupDepartment of Biological Sciences, University of CalgaryCalgaryAlbertaCanada
| | - Leonard T. Nguyen
- Biochemistry Research GroupDepartment of Biological Sciences, University of CalgaryCalgaryAlbertaCanada
| | - Zhihong Liu
- Biochemistry Research GroupDepartment of Biological Sciences, University of CalgaryCalgaryAlbertaCanada
| | - Hans J. Vogel
- Biochemistry Research GroupDepartment of Biological Sciences, University of CalgaryCalgaryAlbertaCanada
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Baltz RH. Combinatorial biosynthesis of cyclic lipopeptide antibiotics: a model for synthetic biology to accelerate the evolution of secondary metabolite biosynthetic pathways. ACS Synth Biol 2014; 3:748-58. [PMID: 23654258 DOI: 10.1021/sb3000673] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nonribosomal peptide synthetases (NRPSs) are giant multi-enzymes that carry out sequencial assembly line couplings of amino acids to generate linear or cyclic peptides. NRPSs are composed of repeating enzyme domains with modular organization to activate and couple specific amino acids in a particular order. From a synthetic biology perspective, they can be considered as peptide assembly machines composed of devices to couple fatty acids to l-amino acids, l-amino acids to l-amino acids, and d-amino acids to l-amino acids. The coupling devices are composed of specific parts that contain two or more enzyme domains that can be exchanged combinatorially to generate novel peptide assembly machines to produce novel peptides. The potent lipopeptide antibiotics daptomycin and A54145E have identical cyclic depsipeptide ring structures and stereochemistry but have divergent amino acid sequences. As their biosynthetic gene clusters are derived from an ancient ancestral lipopetide pathway, these lipopeptides provided an attractive model to develop combinatorial biosynthesis to generate antibiotics superior to daptomycin. These studies on combinatorial biosynthesis have helped generate guidelines for the successful assembly of NRPS parts and devices that can be used to generate novel lipopeptide structures and have established a basis for future synthetic biology studies to further develop combinatorial biosynthesis as a robust approach to natural product drug discovery.
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Affiliation(s)
- Richard H. Baltz
- CognoGen Biotechnology Consulting, 6438 North Olney Street, Indianapolis,
Indiana 46220, United States
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Kelesidis T. The Interplay between Daptomycin and the Immune System. Front Immunol 2014; 5:52. [PMID: 24575098 PMCID: PMC3921582 DOI: 10.3389/fimmu.2014.00052] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 01/29/2014] [Indexed: 12/11/2022] Open
Abstract
Antibiotics may have bacteriostatic or bactericidal effects but may also cause immunomodulation. Lipopeptides are known immunomodulators that interact with pattern recognition receptors such as Toll-like receptors in antigen presenting cells. Daptomycin is a novel lipopeptide antibiotic with a lipid moiety and unique structure that in the presence of divalent ions may directly interact with lipid membrane phospholipids, the major component of lipid membranes in immune cells. Daptomycin may also penetrate immune cells including neutrophils and macrophages. However, the possible immunomodulatory effects of daptomycin remain unknown. Understanding these effects is important to determine whether this agent can provide protection against infectious challenge through multiple mechanisms. Preliminary studies suggest that daptomycin may have minimal effects on cytokine production and may have synergistic immunomodulatory effects in combination with other immunomodulators. This review focuses on the hypothesis that daptomycin may also have immunomodulatory effects but further studies are needed to investigate this hypothesis.
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Affiliation(s)
- Theodoros Kelesidis
- Department of Medicine, Division of Infectious Diseases, David Geffen School of Medicine, University of California , Los Angeles, CA , USA
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Bionda N, Pitteloud JP, Cudic P. Cyclic lipodepsipeptides: a new class of antibacterial agents in the battle against resistant bacteria. Future Med Chem 2013; 5:1311-30. [PMID: 23859209 PMCID: PMC3845972 DOI: 10.4155/fmc.13.86] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
In order to provide effective treatment options for infections caused by multidrug-resistant bacteria, innovative antibiotics are necessary, preferably with novel modes of action and/or belonging to novel classes of drugs. Naturally occurring cyclic lipodepsipeptides, which contain one or more ester bonds along with the amide bonds, have emerged as promising candidates for the development of new antibiotics. Some of these natural products are either already marketed or in advanced stages of clinical development. However, despite the progress in the development of new antibacterial agents, it is inevitable that resistant strains of bacteria will emerge in response to the widespread use of a particular antibiotic and limit its lifetime. Therefore, development of new antibiotics remains our most efficient way to counteract bacterial resistance.
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Affiliation(s)
- Nina Bionda
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Post St Lucie, FL 34987, USA
| | - Jean-Philippe Pitteloud
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Post St Lucie, FL 34987, USA
| | - Predrag Cudic
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Post St Lucie, FL 34987, USA
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Slootweg JC, van Schaik TB, Quarles van Ufford H(LC, Breukink E, Liskamp RM, Rijkers DT. Improving the biological activity of the antimicrobial peptide anoplin by membrane anchoring through a lipophilic amino acid derivative. Bioorg Med Chem Lett 2013; 23:3749-52. [DOI: 10.1016/j.bmcl.2013.05.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 04/29/2013] [Accepted: 05/01/2013] [Indexed: 10/26/2022]
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Bionda N, Stawikowski M, Stawikowska R, Cudic M, López-Vallejo F, Treitl D, Medina-Franco J, Cudic P. Effects of cyclic lipodepsipeptide structural modulation on stability, antibacterial activity, and human cell toxicity. ChemMedChem 2012; 7:871-82. [PMID: 22392790 PMCID: PMC3500847 DOI: 10.1002/cmdc.201200016] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Revised: 02/09/2012] [Indexed: 11/07/2022]
Abstract
Bacterial infections are becoming increasingly difficult to treat due to the development and spread of antibiotic resistance. Therefore, identifying novel antibacterial targets and new antibacterial agents capable of treating infections by drug-resistant bacteria is of vital importance. The structurally simple yet potent fusaricidin or LI-F class of natural products represents a particularly attractive source of candidates for the development of new antibacterial agents. We synthesized 18 fusaricidin/LI-F analogues and investigated the effects of structure modification on their conformation, serum stability, antibacterial activity, and toxicity toward human cells. Our findings show that substitution of an ester bond in depsipeptides with an amide bond may afford equally potent analogues with improved stability and greatly decreased cytotoxicity. The lower overall hydrophobicity/amphiphilicity of amide analogues in comparison with their parent depsipeptides, as indicated by HPLC retention times, may explain the dissociation of antibacterial activity and human cell cytotoxicity. These results indicate that amide analogues may have significant advantages over fusaricidin/LI-F natural products and their depsipeptide analogues as lead structures for the development of new antibacterial agents.
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Affiliation(s)
- Nina Bionda
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St. Lucie, Florida 34987 (USA), Fax: (+1) 772-345-3649
- Department of Chemistry and BIochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33431 (USA)
| | - Maciej Stawikowski
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St. Lucie, Florida 34987 (USA), Fax: (+1) 772-345-3649
| | - Roma Stawikowska
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St. Lucie, Florida 34987 (USA), Fax: (+1) 772-345-3649
| | - Maré Cudic
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St. Lucie, Florida 34987 (USA), Fax: (+1) 772-345-3649
| | - Fabian López-Vallejo
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St. Lucie, Florida 34987 (USA), Fax: (+1) 772-345-3649
| | - Daniela Treitl
- Department of Chemistry and BIochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33431 (USA)
| | - José Medina-Franco
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St. Lucie, Florida 34987 (USA), Fax: (+1) 772-345-3649
| | - Predrag Cudic
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St. Lucie, Florida 34987 (USA), Fax: (+1) 772-345-3649
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Exploring the mechanism of lipid transfer during biosynthesis of the acidic lipopeptide antibiotic CDA. FEBS Lett 2012; 586:283-8. [PMID: 22245678 DOI: 10.1016/j.febslet.2012.01.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Accepted: 01/01/2012] [Indexed: 10/14/2022]
Abstract
The non-ribosomally synthesized lipodepsipeptide CDA belongs to the group of acidic lipopeptide antibiotics, whose members feature a fatty acid side chain that strongly affects their antimicrobial activity. This study elucidates the N-acylation of the N-terminal serine in the CDA peptide chain. This reaction is referred to as lipoinitiation and is shown to be catalyzed by the dissected starter C domain found at the N-terminus of Cda-PSI. The recombinantly produced C domain specifically interacts with 2,3-epoxyhexanoyl-S-ACP and catalyzes the transfer of the fatty acid moiety onto the amino group of PCP-bound serine with high selectivity for both carrier protein bound substrates at the donor and acceptor site.
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Structural characterization of a lipopeptide antibiotic A54145E(Asn3Asp9) produced by a genetically engineered strain of Streptomyces fradiae. J Antibiot (Tokyo) 2010; 64:111-6. [DOI: 10.1038/ja.2010.140] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Alexander DC, Rock J, Gu JQ, Mascio C, Chu M, Brian P, Baltz RH. Production of novel lipopeptide antibiotics related to A54145 by Streptomyces fradiae mutants blocked in biosynthesis of modified amino acids and assignment of lptJ, lptK and lptL gene functions. J Antibiot (Tokyo) 2010; 64:79-87. [DOI: 10.1038/ja.2010.138] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Development of a genetic system for combinatorial biosynthesis of lipopeptides in Streptomyces fradiae and heterologous expression of the A54145 biosynthesis gene cluster. Appl Environ Microbiol 2010; 76:6877-87. [PMID: 20802082 DOI: 10.1128/aem.01248-10] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A54145 factors are calcium-dependent lipopeptide antibiotics produced by Streptomyces fradiae NRRL 18160. A54145 is structurally related to the clinically important daptomycin, and as such may be a useful scaffold for the development of a novel lipopeptide antibiotic. We developed methods to genetically manipulate S. fradiae by deletion mutagenesis and conjugal transfer of plasmids from Escherichia coli. Cloning the complete pathway on a bacterial artificial chromosome (BAC) vector and the construction of ectopic trans-complementation with plasmids utilizing the φC31 or φBT1 site-specific integration system allowed manipulation of A54145 biosynthesis. The BAC clone pDA2002 was shown to harbor the complete A54145 biosynthesis gene cluster by heterologous expression in Streptomyces ambofaciens and Streptomyces roseosporus strains in yields of >100 mg/liter. S. fradiae mutants defective in LptI methyltransferase function were constructed, and they produced only A54145 factors containing glutamic acid (Glu₁₂), at the expense of factors containing 3-methyl-glutamic acid (3mGlu₁₂). This provided a practical route to produce high levels of pure Glu₁₂-containing lipopeptides. A suite of mutant strains and plasmids was created for combinatorial biosynthesis efforts focused on modifying the A54145 peptide backbone to generate a compound with daptomycin antibacterial activity and activity in Streptococcus pneumoniae pulmonary infections.
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Robbel L, Marahiel MA. Daptomycin, a bacterial lipopeptide synthesized by a nonribosomal machinery. J Biol Chem 2010; 285:27501-8. [PMID: 20522545 DOI: 10.1074/jbc.r110.128181] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Daptomycin (Cubicin) is a branched cyclic lipopeptide antibiotic of nonribosomal origin and the prototype of the acidic lipopeptide family. It was approved in 2003 for the nontopical treatment of skin structure infections caused by gram-positive pathogens, including methicillin-resistant Staphylococcus aureus (MRSA), and in 2006 for the treatment of bacteremia. Understanding the ribosome-independent biosynthesis of daptomycin assembly will provide opportunities for the generation of daptomycin derivatives with an altered pharmaceutical spectrum to address upcoming daptomycin-resistant pathogens. Herein, the structural properties of daptomycin, its biosynthesis, recent efforts for the generation of structural diversity, and its proposed mode of action are discussed.
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Affiliation(s)
- Lars Robbel
- Department of Chemistry/Biochemistry, Philipps-University Marburg, Hans-Meerwein-Strasse, 35043 Marburg, Germany
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Genetically engineered lipopeptide antibiotics related to A54145 and daptomycin with improved properties. Antimicrob Agents Chemother 2010; 54:1404-13. [PMID: 20086142 DOI: 10.1128/aac.01307-09] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Daptomycin is a cyclic lipopeptide antibiotic approved for the treatment of skin and skin structure infections caused by Gram-positive pathogens and for that of bacteremia and right-sided endocarditis caused by Staphylococcus aureus. Daptomycin failed to meet noninferiority criteria for the treatment of community-acquired pneumonia, likely due to sequestration in pulmonary surfactant. Many analogues of daptomycin have been generated by combinatorial biosynthesis, but only two displayed improved activity in the presence of bovine surfactant, and neither was as active as daptomycin in vitro. In the present study, we generated hybrid molecules of the structurally related lipopeptide A54145 in Streptomyces fradiae and tested them for antibacterial activity in the presence of bovine surfactant. Hybrid A54145 nonribosomal peptide synthetase (NRPS) biosynthetic genes were constructed by genetic engineering and were expressed in combination with a deletion of the lptI methyltransferase gene, which is involved in the formation of the 3-methyl-glutamic acid (3mGlu) residue at position 12. Some of the compounds were very active against S. aureus and other Gram-positive pathogens; one compound was also highly active in the presence of bovine surfactant, had low acute toxicity, and showed some efficacy against Streptococcus pneumoniae in a mouse model of pulmonary infection.
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Abstract
Acidic lipopeptide antibiotics are a new class of potent antibiotics, which includes daptomycin, A54145, calcium-dependent antibiotics (CDAs), friulimicins/amphomycins, laspartomycin/glycinocins and others. The importance of this novel class is exemplified by the success story of the clinically approved daptomycin, which is used for the treatment of skin infections and bacteremia caused by multidrug-resistant bacteria, including methicillin-resistant Staphylococcus aureus and vancomycin-resistant enterococci. The potency of acidic lipopeptides is inherent in their chemical structure. The nonribosomally synthesized peptide cores consist of eleven to 13 amino acids, which are rigidified by the formation of a ten-membered ring. An N-terminal fatty acid, which facilitates insertion into the lipid bilayer of bacterial membranes, completes the structure. All these antibiotics contain multiple nonproteinogenic amino acids as well as different lipid tails; this yields remarkable structural diversity. This review summarizes the observed structural variety through a detailed description of the composition of the acidic lipopeptides. Furthermore, engineering approaches towards novel lipopeptides are presented. Recent discoveries in the field of tailoring enzymes, which enable structural plurality mainly by amino and fatty acid precursor biosynthesis, are highlighted.
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Affiliation(s)
- Matthias Strieker
- Chemistry and Biochemistry Department, Philipps-University Marburg, Hans-Meerwein-Strasse, Marburg, Germany
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26
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Influence of Ca(2+) ions on the activity of lantibiotics containing a mersacidin-like lipid II binding motif. Appl Environ Microbiol 2009; 75:4427-34. [PMID: 19429551 DOI: 10.1128/aem.00262-09] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mersacidin binds to lipid II and thus blocks the transglycosylation step of the cell wall biosynthesis. Binding of lipid II involves a special motif, the so-called mersacidin-lipid II binding motif, which is conserved in a major subgroup of lantibiotics. We analyzed the role of Ca(2+) ions in the mode of action of mersacidin and some related peptides containing a mersacidin-like lipid II binding motif. We found that the stimulating effect of Ca(2+) ions on the antimicrobial activity known for mersacidin also applies to plantaricin C and lacticin 3147. Ca(2+) ions appear to facilitate the interaction of the lantibiotics with the bacterial membrane and with lipid II rather than being an essential part of a peptide-lipid II complex. In the case of lacticin 481, both the interaction with lipid II and the antimicrobial activity were Ca(2+) independent.
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Wittmann M, Linne U, Pohlmann V, Marahiel MA. Role of DptE and DptF in the lipidation reaction of daptomycin. FEBS J 2008; 275:5343-54. [DOI: 10.1111/j.1742-4658.2008.06664.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Powell A, Borg M, Amir-Heidari B, Neary JM, Thirlway J, Wilkinson B, Smith CP, Micklefield J. Engineered Biosynthesis of Nonribosomal Lipopeptides with Modified Fatty Acid Side Chains. J Am Chem Soc 2007; 129:15182-91. [DOI: 10.1021/ja074331o] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Amanda Powell
- Contribution from the School of Chemistry and Department of Biomolecular Sciences, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom, and Biotica, Chesterford Research Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Mathew Borg
- Contribution from the School of Chemistry and Department of Biomolecular Sciences, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom, and Biotica, Chesterford Research Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Bagher Amir-Heidari
- Contribution from the School of Chemistry and Department of Biomolecular Sciences, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom, and Biotica, Chesterford Research Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Joanne M. Neary
- Contribution from the School of Chemistry and Department of Biomolecular Sciences, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom, and Biotica, Chesterford Research Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Jenny Thirlway
- Contribution from the School of Chemistry and Department of Biomolecular Sciences, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom, and Biotica, Chesterford Research Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Barrie Wilkinson
- Contribution from the School of Chemistry and Department of Biomolecular Sciences, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom, and Biotica, Chesterford Research Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Colin P. Smith
- Contribution from the School of Chemistry and Department of Biomolecular Sciences, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom, and Biotica, Chesterford Research Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Jason Micklefield
- Contribution from the School of Chemistry and Department of Biomolecular Sciences, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom, and Biotica, Chesterford Research Park, Little Chesterford, Essex CB10 1XL, United Kingdom
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Mahlert C, Kopp F, Thirlway J, Micklefield J, Marahiel MA. Stereospecific Enzymatic Transformation of α-Ketoglutarate to (2S,3R)-3-Methyl Glutamate during Acidic Lipopeptide Biosynthesis. J Am Chem Soc 2007; 129:12011-8. [PMID: 17784761 DOI: 10.1021/ja074427i] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The acidic lipopeptides, including the calcium-dependent antibiotics (CDA), daptomycin, and A54145, are important macrocyclic peptide natural products produced by Streptomyces species. All three compounds contain a 3-methyl glutamate (3-MeGlu) as the penultimate C-terminal residue, which is important for bioactivity. Here, biochemical in vitro reconstitution of the 3-MeGlu biosynthetic pathway is presented, using exclusively enzymes from the CDA producer Streptomyces coelicolor. It is shown that the predicted 3-MeGlu methyltransferase GlmT and its homologues DptI from the daptomycin producer Streptomyces roseosporus and LptI from the A54145 producer Streptomyces fradiae do not methylate free glutamic acid, PCP-bound glutamate, or Glu-containing CDA in vitro. Instead, GlmT, DptI, and LptI are S-adenosyl methionine (SAM)-dependent alpha-ketoglutarate methyltransferases that catalyze the stereospecific methylation of alpha-ketoglutarate (alphaKG) leading to (3R)-3-methyl-2-oxoglutarate. Subsequent enzyme screening identified the branched chain amino acid transaminase IlvE (SCO5523) as an efficient catalyst for the transformation of (3R)-3-methyl-2-oxoglutarate into (2S,3R)-3-MeGlu. Comparison of reversed-phase HPLC retention time of dabsylated 3-MeGlu generated by the coupled enzymatic reaction with dabsylated synthetic standards confirmed complete stereocontrol during enzymatic catalysis. This stereospecific two-step conversion of alphaKG to (2S,3R)-3-MeGlu completes our understanding of the biosynthesis and incorporation of beta-methylated amino acids into the nonribosomal lipopeptides. Finally, understanding this pathway may provide new possibilities for the production of modified peptides in engineered microbes.
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Affiliation(s)
- Christoph Mahlert
- Fachbereich Chemie/Biochemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse D-35032 Marburg, Germany
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Milne C, Powell A, Jim J, Al Nakeeb M, Smith CP, Micklefield J. Biosynthesis of the (2S,3R)-3-methyl glutamate residue of nonribosomal lipopeptides. J Am Chem Soc 2007; 128:11250-9. [PMID: 16925444 DOI: 10.1021/ja062960c] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The calcium-dependent antibiotics (CDAs) and daptomycin are therapeutically relevant nonribosomal lipopeptide antibiotics that contain penultimate C-terminal 3-methyl glutamate (3-MeGlu) residues. Comparison with synthetic standards showed that (2S,3R)-configured 3-MeGlu is present in both CDA and daptomycin. Deletion of a putative methyltransferase gene glmT from the cda biosynthetic gene cluster abolished the incorporation of 3-MeGlu and resulted in the production of Glu-containing CDA exclusively. However, the 3-MeGlu chemotype could be re-established through feeding synthetic 3-methyl-2-oxoglutarate and (2S,3R)-3-MeGlu, but not (2S,3S)-3-MeGlu. This indicates that methylation occurs before peptide assembly, and that the module 10 A-domain of the CDA peptide synthetase is specific for the (2S,3R)-stereoisomer. Further mechanistic analyses suggest that GlmT catalyzes the SAM-dependent methylation of alpha-ketoglutarate to give (3R)-methyl-2-oxoglutarate, which is transaminated to (2S,3R)-3-MeGlu. These insights will facilitate future efforts to engineer lipopeptides with modified glutamate residues, which may have improved bioactivity and/or reduced toxicity.
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Affiliation(s)
- Claire Milne
- School of Chemistry and Department of Biomolecular Sciences, The University of Manchester, P.O. Box 88, Manchester M60 1QD, United Kingdom
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31
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Powell A, Al Nakeeb M, Wilkinson B, Micklefield J. Precursor-directed biosynthesis of nonribosomal lipopeptides with modified glutamate residues. Chem Commun (Camb) 2007:2683-5. [PMID: 17594019 DOI: 10.1039/b706224a] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Precursor-directed biosynthesis of calcium dependent antibiotics (CDAs) with modified 3-trifluoromethyl and 3-ethyl glutamate residues was achieved by feeding synthetic glutamate analogues to a mutant strain of Streptomyces coelicolor impaired in the biosynthesis of the natural precursor (2S,3R)-3-methyl glutamic acid.
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Affiliation(s)
- Amanda Powell
- School of Chemistry and Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester, UKM1 7ND
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32
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Nguyen KT, Kau D, Gu JQ, Brian P, Wrigley SK, Baltz RH, Miao V. A glutamic acid 3-methyltransferase encoded by an accessory gene locus important for daptomycin biosynthesis in Streptomyces roseosporus. Mol Microbiol 2006; 61:1294-307. [PMID: 16879412 DOI: 10.1111/j.1365-2958.2006.05305.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In many peptide antibiotics, modified amino acids are important for biological activity. The amino acid 3-methyl-glutamic acid (3mGlu) has been found only in three cyclic lipopeptide antibiotics: daptomycin and the A21978C family produced by Streptomyces roseosporus, calcium-dependent antibiotic produced by Streptomyces coelicolor and A54145 produced by Streptomyces fradiae. We studied the non-ribosomal peptide synthetase genes involved in A21978C biosynthesis and the downstream genes, dptG, dptH, dptI and dptJ predicted to encode a conserved protein of unknown function, a thioesterase, a methyltransferase (MTase) and a tryptophan 2,3-dioxygenase respectively. Deletion of dptGHIJ reduced overall lipopeptide yield and led to production of a series of novel A21978C analogues containing Glu12 instead of 3mGlu12. Complementation by only dptI, or its S. coelicolor homologue, glmT, restored the biosynthesis of the 3mGlu-containing compounds in the mutant. Compared with A21978C, the Glu12-containing derivatives were less active against Staphylococcus aureus. Further genetic analyses showed that members of the dptGHIJ locus cooperatively contributed to optimal A21978C production; deletion of dptH, dptI or dptJ genes reduced the yield significantly, while expression of dptIJ or dptGHIJ from the strong ermEp* promoter substantially increased lipopeptide production. The results indicate that these genes play important roles in the biosynthesis of daptomycin, and that dptI encodes a Glu MTase.
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Affiliation(s)
- Kien T Nguyen
- Cubist Pharmaceuticals, Inc., 65 Hayden Avenue, Lexington, MA 02421, USA.
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33
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Baltz RH, Miao V, Wrigley SK. Natural products to drugs: daptomycin and related lipopeptide antibiotics. Nat Prod Rep 2005; 22:717-41. [PMID: 16311632 DOI: 10.1039/b416648p] [Citation(s) in RCA: 272] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Daptomycin (Cubicin) is a lipopeptide antibiotic approved in the USA in 2003 for the treatment of skin and skin structure infections caused by Gram-positive pathogens. It is a member of the 10-membered cyclic lipopeptide family of antibiotics that includes A54145, calcium-dependent antibiotic (CDA), amphomycin, friulimicin, laspartomycin, and others. This review highlights research on this class of antibiotics from 1953 to 2005, focusing on more recent studies with particular emphasis on the interplay between structural features and antibacterial activities; chemical modifications to improve activity; the genetic organization and biosynthesis of lipopeptides; and the genetic engineering of the daptomycin biosynthetic pathway to produce novel derivatives for further chemical modification to develop candidates for clinical evaluation.
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Miao V, Brost R, Chapple J, She K, Gal MFCL, Baltz RH. The lipopeptide antibiotic A54145 biosynthetic gene cluster from Streptomyces fradiae. J Ind Microbiol Biotechnol 2005; 33:129-40. [PMID: 16208464 DOI: 10.1007/s10295-005-0028-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2005] [Accepted: 08/01/2005] [Indexed: 10/25/2022]
Abstract
Ca(2+)-dependent cyclic lipodepsipeptides are an emerging class of antibiotics for the treatment of infections caused by Gram-positive pathogens. These compounds are synthesized by nonribosomal peptide synthetase (NRPS) complexes encoded by large gene clusters. The gene cluster encoding biosynthetic pathway enzymes for the Streptomyces fradiae A54145 NRP was cloned from a cosmid library and characterized. Four NRPS-encoding genes, responsible for subunits of the synthetase, as well as genes for accessory functions such as acylation, methylation and hydroxylation, were identified by sequence analysis in a 127 kb region of DNA that appears to be located subterminally in the bacterial chromosome. Deduced epimerase domain-encoding sequences within the NRPS genes indicated a D: -stereochemistry for Glu, Lys and Asn residues, as observed for positionally analogous residues in two related compounds, daptomycin, and the calcium-dependent antibiotic (CDA) produced by Streptomyces roseosporus and Streptomyces coelicolor, respectively. A comparison of the structure and the biosynthetic gene cluster of A54145 with those of the related peptides showed many similarities. This information may contribute to the design of experiments to address both fundamental and applied questions in lipopeptide biosynthesis, engineering and drug development.
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Affiliation(s)
- Vivian Miao
- Cubist Pharmaceuticals Inc., 65 Hayden Av., Lexington, MA, 02421, USA
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35
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Baltz RH, Brian P, Miao V, Wrigley SK. Combinatorial biosynthesis of lipopeptide antibiotics in Streptomyces roseosporus. J Ind Microbiol Biotechnol 2005; 33:66-74. [PMID: 16193281 DOI: 10.1007/s10295-005-0030-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2005] [Accepted: 08/01/2005] [Indexed: 11/29/2022]
Abstract
Daptomycin is a cyclic lipopeptide antibiotic produced by Streptomyces roseosporus. Cubicin (daptomycin-for-injection) was approved in 2003 by the FDA to treat skin and skin structure infections caused by Gram-positive pathogens. Daptomycin is particularly significant in that it represents the first new natural product antibacterial structural class approved for clinical use in three decades. The daptomycin gene cluster contains three very large genes (dptA, dptBC, and dptD) that encode the nonribosomal peptide synthetase (NRPS). The related cyclic lipopeptide A54145 has four NRPS genes (lptA, lptB, lptC, and lptD), and calcium dependent antibiotic (CDA) has three (cdaPS1, cdaPS2, and cdaPS3). Mutants of S. roseosporus containing deletions of one or more of the NRPS genes have been trans-complemented with dptA, dptBC, and dptD by inserting these genes under the control of the ermEp* promoter into separate conjugal cloning vectors containing phiC31 or IS117 attachment (attP int) sites; delivering the plasmids into S. roseosporus by conjugation from Escherichia coli; and inserting the plasmids site-specifically into the chromosome at the corresponding attB sites. This trans-complementation system was used to generate subunit exchanges with lptD and cdaPS3 and the recombinants produced novel hybrid molecules. Module exchanges at positions D: -Ala(8) and D: -Ser(11) in the peptide have produced additional novel derivatives of daptomycin. The approaches of subunit exchanges and module exchanges were combined with amino acid modifications of Glu at position 12 and natural variations in lipid side chain starter units to generate a combinatorial library of antibiotics related to daptomycin. Many of the engineered strains produced levels of novel molecules amenable to isolation and antimicrobial testing, and most of the compounds displayed antibacterial activities.
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Affiliation(s)
- Richard H Baltz
- Cubist Pharmaceuticals, Inc., 65 Hayden Avenue, Lexington, MA 02421, USA.
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Gadebusch HH, Stapley EO, Zimmerman SB. The discovery of cell wall active antibacterial antibiotics. Crit Rev Biotechnol 1992; 12:225-43. [PMID: 1633621 DOI: 10.3109/07388559209069193] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- H H Gadebusch
- Merck Sharp & Dohme Research Laboratories, Rahway, NJ 07065
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Abstract
The study of antibiotics and other fermentation products has shown that a seemingly unlimited number of compounds with diverse structures are produced by microorganisms. The continued high rate of discovery of new chemical entities, in the light of the abundance of microbial products already described, is due to creative screening procedures that incorporate such features as the emphasis on unusual microorgnaisms, their special propagation and fermentation requirements, supersensitive and highly selective assays, genetic engineering both for the biosynthesis of new compounds and in the development of screening systems, early in vivo evaluation, improved isolation techniques, modern procedures for structure determination, computer-assisted identification, and an efficient multidisciplinary approach. This review focuses on the genesis and development of the gamut of methodologies that have led to the successful detection of the wide variety of novel secondary metabolites that include antibacterial, antigungal, antiviral and antitumour antibiotics, enzyme inhibitors, pharmacologically and immunologically active agents, products useful in agriculture and animal husbandry, microbial regulators, and other compounds for which no bioactive role has yet been found.
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Affiliation(s)
- C M Franco
- Microbiology Department, Hoechst Centre for Basic Research, Hoechst India Limited, Lal Bahadur Shastri Marg, Mulund, Bombay
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