1
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Yao J, Hua X, Huo W, Xiao L, Wang Y, Tang Q, Valdivia CR, Valdivia HH, Dong W, Xiao L. The Effect of Acidic Residues on the Binding between Opicalcin1 and Ryanodine Receptor from the Structure-Functional Analysis. JOURNAL OF NATURAL PRODUCTS 2024; 87:104-112. [PMID: 38128916 PMCID: PMC10825818 DOI: 10.1021/acs.jnatprod.3c00821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/26/2023] [Accepted: 11/26/2023] [Indexed: 12/23/2023]
Abstract
Calcin is a group ligand with high affinity and specificity for the ryanodine receptors (RyRs). Little is known about the effect of its acidic residues on the spacial structure as well as the interaction with RyRs. We screened the opicalcin1 acidic mutants and investigated the effect of mutation on activity. The results indicated that all acidic mutants maintained the structural features, but their surface charge distribution underwent significant changes. Molecular docking and dynamics simulations were used to analyze the interaction between opicalcin1 mutants and RyRs, which demonstrated that all opicalcin1 mutants effectively bound to the channel domain of RyR1. This stable binding induced a pronounced asymmetry in the structure of the RyR tetramer, exhibiting a high degree of structural dissimilarity. [3H]Ryanodine binding to RyR1 was enhanced in D2A and D15A, which was similar to opicalcin1, but that effect was suppressed in E12A and E29A and reversed for the DE-4A, thereby inhibiting ryanodine binding. Opicalcin1 and DE-4A also exhibited the ability to form stable docking structures with RyR2. Acidic residues play a crucial role in the structure of calcin and its functional interaction with RyRs that is beneficial for the calcin optimization to develop more active peptide lead compounds for RyR-related diseases.
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Affiliation(s)
- Jinchi Yao
- School
of Life Sciences, Liaoning Normal University, Dalian116081, China
- Department
of Occupational and Environmental Health, Faculty of Naval Medicine, Naval Medical University (Second Military Medical
University), Shanghai 200433, China
| | - Xiaoyu Hua
- Department
of Occupational and Environmental Health, Faculty of Naval Medicine, Naval Medical University (Second Military Medical
University), Shanghai 200433, China
| | - Wenjing Huo
- The
305 Hospital of PLA, Beijing 100017, China
| | - Li Xiao
- Department
of Medicine and Cardiovascular Research Center, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin 53188, United States
- Department
of Forensic Toxicological Analysis, West China School of Basic Medical
Sciences and Forensic Medicine, Sichuan
University, Chengdu 610017, China
| | - Yongfang Wang
- Department
of Occupational and Environmental Health, Faculty of Naval Medicine, Naval Medical University (Second Military Medical
University), Shanghai 200433, China
| | - Qinglong Tang
- Central
Medical District of Chinese, PLA General Hospital, Beijing 100120, China
| | - Carmen R. Valdivia
- Department
of Medicine and Cardiovascular Research Center, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin 53188, United States
| | - Héctor H. Valdivia
- Department
of Medicine and Cardiovascular Research Center, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin 53188, United States
| | - Weibing Dong
- School
of Life Sciences, Liaoning Normal University, Dalian116081, China
| | - Liang Xiao
- Department
of Occupational and Environmental Health, Faculty of Naval Medicine, Naval Medical University (Second Military Medical
University), Shanghai 200433, China
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2
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Marschall E, Cass RW, Prasad KM, Swarbrick JD, McKay AI, Payne JAE, Cryle MJ, Tailhades J. Synthetic ramoplanin analogues are accessible by effective incorporation of arylglycines in solid-phase peptide synthesis. Chem Sci 2023; 15:195-203. [PMID: 38131086 PMCID: PMC10732013 DOI: 10.1039/d3sc01944f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 09/09/2023] [Indexed: 12/23/2023] Open
Abstract
The threat of antimicrobial resistance to antibiotics requires a continual effort to develop alternative treatments. Arylglycines (or phenylglycines) are one of the signature amino acids found in many natural peptide antibiotics, but their propensity for epimerization in solid-phase peptide synthesis (SPPS) has prevented their use in long peptide sequences. We have now identified an optimized protocol that allows the synthesis of challenging non-ribosomal peptides including precursors of the glycopeptide antibiotics and an analogue of feglymycin (1 analogue, 20%). We have exploited this protocol to synthesize analogues of the peptide antibiotic ramoplanin using native chemical ligation/desulfurization (1 analogue, 6.5%) and head-to-tail macrocyclization in excellent yield (6 analogues, 3-9%), with these compounds extensively characterized by NMR (U-shaped structure) and antimicrobial activity assays (two clinical isolates). This method significantly reduces synthesis time (6-9 days) when compared with total syntheses (2-3 months) and enables drug discovery programs to include arylglycines in structure-activity relationship studies and drug development.
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Affiliation(s)
- Edward Marschall
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University Clayton VIC 3800 Australia
- EMBL Australia, Monash University Clayton VIC 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Clayton VIC 3800 Australia
| | - Rachel W Cass
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University Clayton VIC 3800 Australia
- EMBL Australia, Monash University Clayton VIC 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Clayton VIC 3800 Australia
| | - Komal M Prasad
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University Clayton VIC 3800 Australia
- EMBL Australia, Monash University Clayton VIC 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Clayton VIC 3800 Australia
| | - James D Swarbrick
- Department of Microbiology, Monash University Clayton VIC 3800 Australia
| | - Alasdair I McKay
- Department of Chemistry, Monash University Clayton VIC 3800 Australia
| | - Jennifer A E Payne
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University Clayton VIC 3800 Australia
- EMBL Australia, Monash University Clayton VIC 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Clayton VIC 3800 Australia
| | - Max J Cryle
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University Clayton VIC 3800 Australia
- EMBL Australia, Monash University Clayton VIC 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Clayton VIC 3800 Australia
| | - Julien Tailhades
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University Clayton VIC 3800 Australia
- EMBL Australia, Monash University Clayton VIC 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Clayton VIC 3800 Australia
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3
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Hansen MH, Adamek M, Iftime D, Petras D, Schuseil F, Grond S, Stegmann E, Cryle MJ, Ziemert N. Resurrecting ancestral antibiotics: unveiling the origins of modern lipid II targeting glycopeptides. Nat Commun 2023; 14:7842. [PMID: 38030603 PMCID: PMC10687080 DOI: 10.1038/s41467-023-43451-4] [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: 08/10/2023] [Accepted: 11/09/2023] [Indexed: 12/01/2023] Open
Abstract
Antibiotics are central to modern medicine, and yet they are mainly the products of intra and inter-kingdom evolutionary warfare. To understand how nature evolves antibiotics around a common mechanism of action, we investigated the origins of an extremely valuable class of compounds, lipid II targeting glycopeptide antibiotics (GPAs, exemplified by teicoplanin and vancomycin), which are used as last resort for the treatment of antibiotic resistant bacterial infections. Using a molecule-centred approach and computational techniques, we first predicted the nonribosomal peptide synthetase assembly line of paleomycin, the ancestral parent of lipid II targeting GPAs. Subsequently, we employed synthetic biology techniques to produce the predicted peptide and validated its antibiotic activity. We revealed the structure of paleomycin, which enabled us to address how nature morphs a peptide antibiotic scaffold through evolution. In doing so, we obtained temporal snapshots of key selection domains in nonribosomal peptide synthesis during the biosynthetic journey from ancestral, teicoplanin-like GPAs to modern GPAs such as vancomycin. Our study demonstrates the synergy of computational techniques and synthetic biology approaches enabling us to journey back in time, trace the temporal evolution of antibiotics, and revive these ancestral molecules. It also reveals the optimisation strategies nature has applied to evolve modern GPAs, laying the foundation for future efforts to engineer this important class of antimicrobial agents.
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Affiliation(s)
- Mathias H Hansen
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- EMBL Australia, Monash University, Clayton, VIC, 3800, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, VIC, 3800, Australia
| | - Martina Adamek
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, Germany
| | - Dumitrita Iftime
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
| | - Daniel Petras
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
| | - Frauke Schuseil
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, Germany
| | - Stephanie Grond
- Institute of Organic Chemistry, University of Tübingen, Tübingen, Germany
| | - Evi Stegmann
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany.
- Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, Germany.
| | - Max J Cryle
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.
- EMBL Australia, Monash University, Clayton, VIC, 3800, Australia.
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, VIC, 3800, Australia.
| | - Nadine Ziemert
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany.
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany.
- Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, Germany.
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4
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Ho YTC, Schittenhelm RB, Iftime D, Stegmann E, Tailhades J, Cryle MJ. Exploring the Flexibility of the Glycopeptide Antibiotic Crosslinking Cascade for Extended Peptide Backbones. Chembiochem 2023; 24:e202200686. [PMID: 36534957 DOI: 10.1002/cbic.202200686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/19/2022] [Accepted: 12/19/2022] [Indexed: 12/23/2022]
Abstract
The glycopeptide antibiotics (GPAs) are a clinically approved class of antimicrobial agents that classically function through the inhibition of bacterial cell-wall biosynthesis by sequestration of the precursor lipid II. The oxidative crosslinking of the core peptide by cytochrome P450 (Oxy) enzymes during GPA biosynthesis is both essential to their function and the source of their synthetic challenge. Thus, understanding the activity and selectivity of these Oxy enzymes is of key importance for the future engineering of this important compound class. Recent reports of GPAs that display an alternative mode of action and a wider range of core peptide structures compared to classic lipid II-binding GPAs raises the question of the tolerance of Oxy enzymes for larger changes in their peptide substrates. In this work, we explore the ability of Oxy enzymes from the biosynthesis pathways of lipid II-binding GPAs to accept altered peptide substrates based on a vancomycin template. Our results show that Oxy enzymes are more tolerant of changes at the N terminus of their substrates, whilst C-terminal extension of the peptide substrates is deleterious to the activity of all Oxy enzymes. Thus, future studies should prioritise the study of Oxy enzymes from atypical GPA biosynthesis pathways bearing C-terminal peptide extension to increase the substrate scope of these important cyclisation enzymes.
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Affiliation(s)
- Y T Candace Ho
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.,EMBL Australia, Monash University, Clayton, VIC 3800, Australia.,ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC 3800, Australia
| | - Ralf B Schittenhelm
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.,Monash Proteomics and Metabolomics Facility, Monash University, Clayton, VIC 3800, Australia
| | - Dumitrita Iftime
- Interfaculty Institute of Microbiology and Infection Medicine, Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, 72076, Tübingen, Germany
| | - Evi Stegmann
- Interfaculty Institute of Microbiology and Infection Medicine, Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, 72076, Tübingen, Germany
| | - Julien Tailhades
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.,EMBL Australia, Monash University, Clayton, VIC 3800, Australia.,ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC 3800, Australia
| | - Max J Cryle
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.,EMBL Australia, Monash University, Clayton, VIC 3800, Australia.,ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC 3800, Australia
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5
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Tian L, Shi S, Zhang X, Han F, Dong H. Newest perspectives of glycopeptide antibiotics: biosynthetic cascades, novel derivatives, and new appealing antimicrobial applications. World J Microbiol Biotechnol 2023; 39:67. [PMID: 36593427 PMCID: PMC9807434 DOI: 10.1007/s11274-022-03512-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 12/27/2022] [Indexed: 01/04/2023]
Abstract
Glycopeptide antibiotics (GPAs) are a family of non-ribosomal peptide natural products with polypeptide skeleton characteristics, which are considered the last resort for treating severe infections caused by multidrug-resistant Gram-positive pathogens. Over the past few years, an increasing prevalence of Gram-positive resistant strain "superbugs" has emerged. Therefore, more efforts are needed to study and modify the GPAs to overcome the challenge of superbugs. In this mini-review, we provide an overview of the complex biosynthetic gene clusters (BGCs), the ingenious crosslinking and tailoring modifications, the new GPA derivatives, the discoveries of new natural GPAs, and the new applications of GPAs in antivirus and anti-Gram-negative bacteria. With the development and interdisciplinary integration of synthetic biology, next-generation sequencing (NGS), and artificial intelligence (AI), more GPAs with new chemical structures and action mechanisms will constantly be emerging.
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Affiliation(s)
- Li Tian
- School of Pharmaceutical Sciences, Liaocheng University, 252000 Liaocheng, China
| | - Shi Shi
- School of Pharmaceutical Sciences, Liaocheng University, 252000 Liaocheng, China
| | - Xiangmei Zhang
- School of Pharmaceutical Sciences, Liaocheng University, 252000 Liaocheng, China
| | - Fubo Han
- School of Pharmaceutical Sciences, Liaocheng University, 252000 Liaocheng, China
| | - Huijun Dong
- School of Pharmaceutical Sciences, Liaocheng University, 252000 Liaocheng, China
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6
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Ho YTC, Zhao Y, Tailhades J, Cryle MJ. A Chemoenzymatic Approach to Investigate Cytochrome P450 Cross-Linking in Glycopeptide Antibiotic Biosynthesis. Methods Mol Biol 2023; 2670:187-206. [PMID: 37184705 DOI: 10.1007/978-1-0716-3214-7_9] [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: 05/16/2023]
Abstract
Glycopeptide antibiotics (GPAs) are important and medically relevant peptide natural products. In the context of antimicrobial resistance (AMR), understanding and manipulating GPA biosynthesis is essential to discover new bioactive derivatives of these peptides. Among all the enzymatic steps in GPA biosynthesis, the most complex occurs during the maturation (cross-linking) of the peptide aglycone. This is achieved-while the peptide remains attached to the nonribosomal peptide synthetase (NRPS) machinery-through the action of a cytochrome P450 (CYP450 or Oxy)-mediated cyclization cascade. There is great interest in understanding the formation of the cross-links between the aromatic side chains in GPAs as this process leads to the cup-shaped aglycone, which is itself a requirement for antibiotic activity. In this regard, the use of in vitro experiments is crucial to study this process. To address the process of peptide cyclization during GPA biosynthesis, a series of peptide substrates and different Oxy enzymes are required. In this chapter, we describe a practical and efficient route for the synthesis of peptidyl-CoAs, the expression of proteins/enzymes involved in the in vitro cyclization assay, the loading of the PCP with peptidyl-CoAs, an optimized CYP450-mediated cyclization cascade and assay workup followed by mass spectrometry (MS) characterization. This in vitro assay affords high conversion to cyclic peptides and demonstrates the tolerance of the P450s for novel GPA precursor peptide substrates.
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Affiliation(s)
- Y T Candace Ho
- Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Yongwei Zhao
- Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Julien Tailhades
- Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Max J Cryle
- Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia.
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7
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Hansen MH, Stegmann E, Cryle MJ. Beyond vancomycin: recent advances in the modification, reengineering, production and discovery of improved glycopeptide antibiotics to tackle multidrug-resistant bacteria. Curr Opin Biotechnol 2022; 77:102767. [PMID: 35933924 DOI: 10.1016/j.copbio.2022.102767] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 07/01/2022] [Accepted: 07/12/2022] [Indexed: 11/24/2022]
Abstract
Glycopeptide antibiotics (GPAs), which include vancomycin and teicoplanin, are important last-resort antibiotics used to treat multidrug-resistant Gram-positive bacterial infections. Whilst second-generation GPAs - generated through chemical modification of natural GPAs - have proven successful, the emergence of GPA resistance has underlined the need to develop new members of this compound class. Significant recent advances have been made in GPA research, including gaining an in-depth understanding of their biosynthesis, improving titre in production strains, developing new derivatives via novel chemical modifications and identifying a new mode of action for structurally diverse type-V GPAs. Taken together, these advances demonstrate significant untapped potential for the further development of GPAs to tackle the growing threat of multidrug-resistant bacteria.
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Affiliation(s)
- Mathias H Hansen
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; EMBL Australia, Monash University, Clayton, Victoria 3800, Australia; ARC Centre of Excellence for Innovations in Peptide and Protein Science, Australia
| | - Evi Stegmann
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany; German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany; Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
| | - Max J Cryle
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; EMBL Australia, Monash University, Clayton, Victoria 3800, Australia; ARC Centre of Excellence for Innovations in Peptide and Protein Science, Australia.
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8
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Xu M, Wang W, Waglechner N, Culp EJ, Guitor AK, Wright GD. Phylogeny-Informed Synthetic Biology Reveals Unprecedented Structural Novelty in Type V Glycopeptide Antibiotics. ACS CENTRAL SCIENCE 2022; 8:615-626. [PMID: 35647273 PMCID: PMC9136965 DOI: 10.1021/acscentsci.1c01389] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Indexed: 06/01/2023]
Abstract
The rise and dissemination of glycopeptide antibiotic (GPA)-resistant pathogens in healthcare settings fuel efforts to discover GPAs that can overcome resistance. Members of the type V subclass of GPAs can evade common GPA resistance mechanisms and offer promise as new drug leads. We characterize five new type V GPAs-rimomycin-A/B/C and misaugamycin-A/B-discovered through a phylogeny-guided genome mining strategy coupled with heterologous production using our GPAHex synthetic biology platform. Rimomycin is a heptapeptide similar to kistamicin but includes an N-methyl-tyrosine at amino acid 6 (AA6) and substitutes 4-hydroxyphenylglycine for tyrosine and 3,5-dihydroxyphenylglycine at positions AA1 and AA3. Misaugamycin is characterized by an unprecedented N-C cross-link between AA2 and AA4 and unique N-terminal acylation by malonyl (misaugamycin-A) or 2-sulfoacetyl (misaugamycin-B) groups. We demonstrate that rimomycin-A/B/C and misaugamycin-A/B are potent antibiotics with activity against GPA-resistant clinical isolates and that the mode of action is consistent with the inhibition of cell division by the evasion of autolysin activity. These discoveries expand the chemical diversity of the type V GPAs, offer new chemical scaffolds for drug development, and demonstrate the application of the GPAHex platform in mining GPA chemical "dark matter".
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9
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10
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Aldemir H, Shu S, Schaefers F, Hong H, Richarz R, Harteis S, Einsiedler M, Milzarek TM, Schneider S, Gulder TAM. Carrier Protein-Free Enzymatic Biaryl Coupling in Arylomycin A2 Assembly and Structure of the Cytochrome P450 AryC*. Chemistry 2021; 28:e202103389. [PMID: 34725865 PMCID: PMC9299028 DOI: 10.1002/chem.202103389] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Indexed: 12/16/2022]
Abstract
The arylomycin antibiotics are potent inhibitors of bacterial type I signal peptidase. These lipohexapeptides contain a biaryl structural motif reminiscent of glycopeptide antibiotics. We herein describe the functional and structural evaluation of AryC, the cytochrome P450 performing biaryl coupling in biosynthetic arylomycin assembly. Unlike its enzymatic counterparts in glycopeptide biosynthesis, AryC converts free substrates without the requirement of any protein interaction partner, likely enabled by a strongly hydrophobic cavity at the surface of AryC pointing to the substrate tunnel. This activity enables chemo‐enzymatic assembly of arylomycin A2 that combines the advantages of liquid‐ and solid‐phase peptide synthesis with late‐stage enzymatic cross‐coupling. The reactivity of AryC is unprecedented in cytochrome P450‐mediated biaryl construction in non‐ribosomal peptides, in which peptidyl carrier protein (PCP)‐tethering so far was shown crucial both in vivo and in vitro.
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Affiliation(s)
- Hülya Aldemir
- Chair of Technical Biochemistry, Technical University of Dresden, Bergstraße 66, 01069, Dresden, Germany.,Biosystems Chemistry, Faculty of Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Shuangjie Shu
- Chair of Technical Biochemistry, Technical University of Dresden, Bergstraße 66, 01069, Dresden, Germany.,Biosystems Chemistry, Faculty of Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Francoise Schaefers
- Biosystems Chemistry, Faculty of Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Hanna Hong
- Biosystems Chemistry, Faculty of Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - René Richarz
- Biosystems Chemistry, Faculty of Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Sabrina Harteis
- Biosystems Chemistry, Faculty of Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Manuel Einsiedler
- Chair of Technical Biochemistry, Technical University of Dresden, Bergstraße 66, 01069, Dresden, Germany
| | - Tobias M Milzarek
- Chair of Technical Biochemistry, Technical University of Dresden, Bergstraße 66, 01069, Dresden, Germany
| | - Sabine Schneider
- Department of Chemistry, Ludwig-Maximillians-University Munich, Butenandtstraße 5-13, 81377, Munich, Germany
| | - Tobias A M Gulder
- Chair of Technical Biochemistry, Technical University of Dresden, Bergstraße 66, 01069, Dresden, Germany.,Biosystems Chemistry, Faculty of Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
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11
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Kaniusaite M, Kittilä T, Goode RJA, Schittenhelm RB, Cryle MJ. Redesign of Substrate Selection in Glycopeptide Antibiotic Biosynthesis Enables Effective Formation of Alternate Peptide Backbones. ACS Chem Biol 2020; 15:2444-2455. [PMID: 32794694 DOI: 10.1021/acschembio.0c00435] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Nonribosomal peptide synthesis is capable of utilizing a wide range of amino acid residues due to the selectivity of adenylation (A)-domains. Changing the selectivity of A-domains could lead to new bioactive nonribosomal peptides, although remodeling efforts of A-domains are often unsuccessful. Here, we explored and successfully reengineered the specificity of the module 3 A-domain from glycopeptide antibiotic biosynthesis to change the incorporation of 3,5-dihydroxyphenylglycine into 4-hydroxyphenylglycine. These engineered A-domains remain selective in a functioning peptide assembly line even under substrate competition conditions and indicate a possible application of these for the future redesign of GPA biosynthesis.
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Affiliation(s)
- Milda Kaniusaite
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- EMBL Australia, Monash University, Clayton, Victoria 3800, Australia
| | - Tiia Kittilä
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Robert J. A. Goode
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- Monash Proteomics and Metabolomics Facility, Monash University, Clayton, Victoria 3800, Australia
| | - Ralf B. Schittenhelm
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- Monash Proteomics and Metabolomics Facility, Monash University, Clayton, Victoria 3800, Australia
| | - Max J. Cryle
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- EMBL Australia, Monash University, Clayton, Victoria 3800, Australia
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12
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Zhao Y, Ho YTC, Tailhades J, Cryle M. Understanding the Glycopeptide Antibiotic Crosslinking Cascade: In Vitro Approaches Reveal the Details of a Complex Biosynthesis Pathway. Chembiochem 2020; 22:43-51. [PMID: 32696500 DOI: 10.1002/cbic.202000309] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/21/2020] [Indexed: 11/06/2022]
Abstract
The glycopeptide antibiotics (GPAs) are a fascinating example of complex natural product biosynthesis, with the nonribosomal synthesis of the peptide core coupled to a cytochrome P450-mediated cyclisation cascade that crosslinks aromatic side chains within this peptide. Given that the challenges associated with the synthesis of GPAs stems from their highly crosslinked structure, there is great interest in understanding how biosynthesis accomplishes this challenging set of transformations. In this regard, the use of in vitro experiments has delivered important insights into this process, including the identification of the unique role of the X-domain as a platform for P450 recruitment. In this minireview, we present an analysis of the results of in vitro studies into the GPA cyclisation cascade that have demonstrated both the tolerances and limitations of this process for modified substrates, and in turn developed rules for the future reengineering of this important antibiotic class.
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Affiliation(s)
- Yongwei Zhao
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.,EMBL Australia, Monash University, Clayton, Victoria 3800, Australia.,ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, Victoria 3800, Australia
| | - Y T Candace Ho
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.,EMBL Australia, Monash University, Clayton, Victoria 3800, Australia.,ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, Victoria 3800, Australia
| | - Julien Tailhades
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.,EMBL Australia, Monash University, Clayton, Victoria 3800, Australia.,ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, Victoria 3800, Australia
| | - Max Cryle
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.,EMBL Australia, Monash University, Clayton, Victoria 3800, Australia.,ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, Victoria 3800, Australia
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13
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Kaniusaite M, Goode RJA, Tailhades J, Schittenhelm RB, Cryle MJ. Exploring modular reengineering strategies to redesign the teicoplanin non-ribosomal peptide synthetase. Chem Sci 2020; 11:9443-9458. [PMID: 34094211 PMCID: PMC8162109 DOI: 10.1039/d0sc03483e] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 08/22/2020] [Indexed: 12/24/2022] Open
Abstract
Non-ribosomal peptide synthesis is an important biosynthesis pathway in secondary metabolism. In this study we have investigated modularisation and redesign strategies for the glycopeptide antibiotic teicoplanin. Using the relocation or exchange of domains within the NRPS modules, we have identified how to initiate peptide biosynthesis and explored the requirements for the functional reengineering of both the condensation/adenylation domain and epimerisation/condensation domain interfaces. We have also demonstrated strategies that ensure communication between isolated NRPS modules, leading to new peptide assembly pathways. This provides important insights into NRPS reengineering of glycopeptide antibiotic biosynthesis and has broad implications for the redesign of other NRPS systems.
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Affiliation(s)
- Milda Kaniusaite
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University Clayton Victoria 3800 Australia
- EMBL Australia, Monash University Clayton Victoria 3800 Australia
- The Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Monash University Clayton Victoria 3800 Australia
| | - Robert J A Goode
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University Clayton Victoria 3800 Australia
- Monash Proteomics and Metabolomics Facility, Monash University Clayton Victoria 3800 Australia
| | - Julien Tailhades
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University Clayton Victoria 3800 Australia
- EMBL Australia, Monash University Clayton Victoria 3800 Australia
- The Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Monash University Clayton Victoria 3800 Australia
| | - Ralf B Schittenhelm
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University Clayton Victoria 3800 Australia
- Monash Proteomics and Metabolomics Facility, Monash University Clayton Victoria 3800 Australia
| | - Max J Cryle
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University Clayton Victoria 3800 Australia
- EMBL Australia, Monash University Clayton Victoria 3800 Australia
- The Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Monash University Clayton Victoria 3800 Australia
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14
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Forneris CC, Nguy AKL, Seyedsayamdost MR. Mapping and Exploiting the Promiscuity of OxyB toward the Biocatalytic Production of Vancomycin Aglycone Variants. ACS Catal 2020; 10:9287-9298. [PMID: 34422446 PMCID: PMC8378672 DOI: 10.1021/acscatal.0c01719] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Vancomycin is one of the most important clinical antibiotics in the fight against infectious disease. Its biological activity relies on three aromatic cross-links, which create a cup-shaped topology and allow tight binding to nascent peptidoglycan chains. The cytochrome P450 enzymes OxyB, OxyA, and OxyC have been shown to introduce these synthetically challenging aromatic linkages. The ability to utilize the P450 enzymes in a chemo-enzymatic scheme to generate vancomycin derivatives is appealing but requires a thorough understanding of their reactivities and mechanisms. Herein, we systematically explore the scope of OxyB biocatalysis and report installation of diverse diaryl ether and biaryl cross-links with varying macrocycle sizes and compositions, when the enzyme is presented with modified vancomycin precursor peptides. The structures of the resulting products were determined using one-dimensional/two-dimensional nuclear magnetic resonance spectroscopy, high-resolution mass spectrometry (HR-MS), tandem HR-MS, and isotopic labeling, as well as ultraviolet-visible light absorption and fluorescence emission spectroscopies. An exploration of the biological activities of these alternative OxyB products surprisingly revealed antifungal properties. Taking advantage of the promiscuity of OxyB, we chemo-enzymatically generated a vancomycin aglycone variant containing an expanded macrocycle. Mechanistic implications for OxyB and future directions for creating vancomycin analogue libraries are discussed.
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Affiliation(s)
- Clarissa C Forneris
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Andy K L Nguy
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Mohammad R Seyedsayamdost
- Department of Chemistry and Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
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15
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Sengupta S, Mehta G. Macrocyclization via C-H functionalization: a new paradigm in macrocycle synthesis. Org Biomol Chem 2020; 18:1851-1876. [PMID: 32101232 DOI: 10.1039/c9ob02765c] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The growing emphasis on macrocycles in engaging difficult therapeutic targets such as protein-protein interactions and GPCRs via preferential adaptation of bioactive and cell penetrating conformations has provided impetus to the search for de novo macrocyclization strategies that are efficient, chemically robust and amenable to diversity creation. An emerging macrocyclization paradigm based on the C-H activation logic, of particular promise in the macrocyclization of complex peptides, has added a new dimension to this pursuit, enabling efficacious access to macrocycles of various sizes and topologies with high atom and step economy. Significant achievements in macrocyclization methodologies and their applications in the synthesis of bioactive natural products and drug-like molecules, employing strategic variations of C-H activation are captured in this review. It is expected that this timely account will foster interest in newer ways of macrocycle construction among practitioners of organic synthesis and chemical biology to advance the field.
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Affiliation(s)
- Saumitra Sengupta
- School of Chemistry, University of Hyderabad, Gachibowli, Hyderabad-5000 046, Telengana, India.
| | - Goverdhan Mehta
- School of Chemistry, University of Hyderabad, Gachibowli, Hyderabad-5000 046, Telengana, India.
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16
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Tailhades J, Zhao Y, Ho YTC, Greule A, Ahmed I, Schoppet M, Kulkarni K, Goode RJA, Schittenhelm RB, De Voss JJ, Cryle MJ. A Chemoenzymatic Approach to the Synthesis of Glycopeptide Antibiotic Analogues. Angew Chem Int Ed Engl 2020; 59:10899-10903. [DOI: 10.1002/anie.202003726] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/14/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Julien Tailhades
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- EMBL Australia Monash University Clayton Victoria 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Monash University Clayton Victoria 3800 Australia
| | - Yongwei Zhao
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- EMBL Australia Monash University Clayton Victoria 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Monash University Clayton Victoria 3800 Australia
| | - Y. T. Candace Ho
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- EMBL Australia Monash University Clayton Victoria 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Monash University Clayton Victoria 3800 Australia
| | - Anja Greule
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- EMBL Australia Monash University Clayton Victoria 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Monash University Clayton Victoria 3800 Australia
| | - Iftekhar Ahmed
- School of Chemistry and Molecular Biosciences The University of Queensland St Lucia Queensland 4072 Australia
| | - Melanie Schoppet
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- EMBL Australia Monash University Clayton Victoria 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Monash University Clayton Victoria 3800 Australia
| | - Ketav Kulkarni
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
| | - Rob J. A. Goode
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- Monash Proteomics & Metabolomics Facility Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
| | - Ralf B. Schittenhelm
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- Monash Proteomics & Metabolomics Facility Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
| | - James J. De Voss
- School of Chemistry and Molecular Biosciences The University of Queensland St Lucia Queensland 4072 Australia
| | - Max J. Cryle
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- EMBL Australia Monash University Clayton Victoria 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Monash University Clayton Victoria 3800 Australia
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17
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Tailhades J, Zhao Y, Ho YTC, Greule A, Ahmed I, Schoppet M, Kulkarni K, Goode RJA, Schittenhelm RB, De Voss JJ, Cryle MJ. A Chemoenzymatic Approach to the Synthesis of Glycopeptide Antibiotic Analogues. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003726] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Julien Tailhades
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- EMBL Australia Monash University Clayton Victoria 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Monash University Clayton Victoria 3800 Australia
| | - Yongwei Zhao
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- EMBL Australia Monash University Clayton Victoria 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Monash University Clayton Victoria 3800 Australia
| | - Y. T. Candace Ho
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- EMBL Australia Monash University Clayton Victoria 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Monash University Clayton Victoria 3800 Australia
| | - Anja Greule
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- EMBL Australia Monash University Clayton Victoria 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Monash University Clayton Victoria 3800 Australia
| | - Iftekhar Ahmed
- School of Chemistry and Molecular Biosciences The University of Queensland St Lucia Queensland 4072 Australia
| | - Melanie Schoppet
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- EMBL Australia Monash University Clayton Victoria 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Monash University Clayton Victoria 3800 Australia
| | - Ketav Kulkarni
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
| | - Rob J. A. Goode
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- Monash Proteomics & Metabolomics Facility Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
| | - Ralf B. Schittenhelm
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- Monash Proteomics & Metabolomics Facility Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
| | - James J. De Voss
- School of Chemistry and Molecular Biosciences The University of Queensland St Lucia Queensland 4072 Australia
| | - Max J. Cryle
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- EMBL Australia Monash University Clayton Victoria 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Monash University Clayton Victoria 3800 Australia
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