1
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Enninful GN, Kuppusamy R, Tiburu EK, Kumar N, Willcox MDP. Non-canonical amino acid bioincorporation into antimicrobial peptides and its challenges. J Pept Sci 2024; 30:e3560. [PMID: 38262069 DOI: 10.1002/psc.3560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 10/01/2023] [Accepted: 11/14/2023] [Indexed: 01/25/2024]
Abstract
The rise of antimicrobial resistance and multi-drug resistant pathogens has necessitated explorations for novel antibiotic agents as the discovery of conventional antibiotics is becoming economically less viable and technically more challenging for biopharma. Antimicrobial peptides (AMPs) have emerged as a promising alternative because of their particular mode of action, broad spectrum and difficulty that microbes have in becoming resistant to them. The AMPs bacitracin, gramicidin, polymyxins and daptomycin are currently used clinically. However, their susceptibility to proteolytic degradation, toxicity profile, and complexities in large-scale manufacture have hindered their development. To improve their proteolytic stability, methods such as integrating non-canonical amino acids (ncAAs) into their peptide sequence have been adopted, which also improves their potency and spectrum of action. The benefits of ncAA incorporation have been made possible by solid-phase peptide synthesis. However, this method is not always suitable for commercial production of AMPs because of poor yield, scale-up difficulties, and its non-'green' nature. Bioincorporation of ncAA as a method of integration is an emerging field geared towards tackling the challenges of solid-phase synthesis as a green, cheaper, and scalable alternative for commercialisation of AMPs. This review focusses on the bioincorporation of ncAAs; some challenges associated with the methods are outlined, and notes are given on how to overcome these challenges. The review focusses particularly on addressing two key challenges: AMP cytotoxicity towards microbial cell factories and the uptake of ncAAs that are unfavourable to them. Overcoming these challenges will draw us closer to a greater yield and an environmentally friendly and sustainable approach to make AMPs more druggable.
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Affiliation(s)
| | - Rajesh Kuppusamy
- University of New South Wales, Kensington, New South Wales, Australia
| | | | - Naresh Kumar
- University of New South Wales, Kensington, New South Wales, Australia
| | - Mark D P Willcox
- University of New South Wales, Kensington, New South Wales, Australia
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2
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Faleye OS, Boya BR, Lee JH, Choi I, Lee J. Halogenated Antimicrobial Agents to Combat Drug-Resistant Pathogens. Pharmacol Rev 2023; 76:90-141. [PMID: 37845080 DOI: 10.1124/pharmrev.123.000863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 08/07/2023] [Accepted: 09/29/2023] [Indexed: 10/18/2023] Open
Abstract
Antimicrobial resistance presents us with a potential global crisis as it undermines the abilities of conventional antibiotics to combat pathogenic microbes. The history of antimicrobial agents is replete with examples of scaffolds containing halogens. In this review, we discuss the impacts of halogen atoms in various antibiotic types and antimicrobial scaffolds and their modes of action, structure-activity relationships, and the contributions of halogen atoms in antimicrobial activity and drug resistance. Other halogenated molecules, including carbohydrates, peptides, lipids, and polymeric complexes, are also reviewed, and the effects of halogenated scaffolds on pharmacokinetics, pharmacodynamics, and factors affecting antimicrobial and antivirulence activities are presented. Furthermore, the potential of halogenation to circumvent antimicrobial resistance and rejuvenate impotent antibiotics is addressed. This review provides an overview of the significance of halogenation, the abilities of halogens to interact in biomolecular settings and enhance pharmacological properties, and their potential therapeutic usages in preventing a postantibiotic era. SIGNIFICANCE STATEMENT: Antimicrobial resistance and the increasing impotence of antibiotics are critical threats to global health. The roles and importance of halogen atoms in antimicrobial drug scaffolds have been established, but comparatively little is known of their pharmacological impacts on drug resistance and antivirulence activities. This review is the first to extensively evaluate the roles of halogen atoms in various antibiotic classes and pharmacological scaffolds and to provide an overview of their ability to overcome antimicrobial resistance.
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Affiliation(s)
- Olajide Sunday Faleye
- School of Chemical Engineering (O.S.F., B.R.B., J.-H.L., J.L.) and Department of Medical Biotechnology (I.C.), Yeungnam University, Gyeongsan, Republic of Korea
| | - Bharath Reddy Boya
- School of Chemical Engineering (O.S.F., B.R.B., J.-H.L., J.L.) and Department of Medical Biotechnology (I.C.), Yeungnam University, Gyeongsan, Republic of Korea
| | - Jin-Hyung Lee
- School of Chemical Engineering (O.S.F., B.R.B., J.-H.L., J.L.) and Department of Medical Biotechnology (I.C.), Yeungnam University, Gyeongsan, Republic of Korea
| | - Inho Choi
- School of Chemical Engineering (O.S.F., B.R.B., J.-H.L., J.L.) and Department of Medical Biotechnology (I.C.), Yeungnam University, Gyeongsan, Republic of Korea
| | - Jintae Lee
- School of Chemical Engineering (O.S.F., B.R.B., J.-H.L., J.L.) and Department of Medical Biotechnology (I.C.), Yeungnam University, Gyeongsan, Republic of Korea
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3
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Miles SA, Nillama JA, Hunter L. Tinker, Tailor, Soldier, Spy: The Diverse Roles That Fluorine Can Play within Amino Acid Side Chains. Molecules 2023; 28:6192. [PMID: 37687021 PMCID: PMC10489206 DOI: 10.3390/molecules28176192] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/17/2023] [Accepted: 08/17/2023] [Indexed: 09/10/2023] Open
Abstract
Side chain-fluorinated amino acids are useful tools in medicinal chemistry and protein science. In this review, we outline some general strategies for incorporating fluorine atom(s) into amino acid side chains and for elaborating such building blocks into more complex fluorinated peptides and proteins. We then describe the diverse benefits that fluorine can offer when located within amino acid side chains, including enabling 19F NMR and 18F PET imaging applications, enhancing pharmacokinetic properties, controlling molecular conformation, and optimizing target-binding.
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Affiliation(s)
| | | | - Luke Hunter
- School of Chemistry, The University of New South Wales (UNSW), Sydney 2052, Australia
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4
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Chowdhary S, Pelzer T, Saathoff M, Quaas E, Pendl J, Fulde M, Koksch B. Fine‐tuning the antimicrobial activity of β‐hairpin peptides with fluorinated amino acids. Pept Sci (Hoboken) 2023. [DOI: 10.1002/pep2.24306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Affiliation(s)
- Suvrat Chowdhary
- Institute of Chemistry and Biochemistry Freie Universität Berlin Berlin Germany
| | - Tim Pelzer
- Institute of Chemistry and Biochemistry Freie Universität Berlin Berlin Germany
| | - Mareike Saathoff
- Institute of Microbiology and Epizootics, Centre of Infection Medicine Freie Universität Berlin Berlin Germany
| | - Elisa Quaas
- Institute of Chemistry and Biochemistry, Core Facility SupraFAB Freie Universität Berlin Berlin Germany
| | - Johanna Pendl
- Institute of Veterinary Anatomy Freie Universität Berlin Berlin Germany
| | - Marcus Fulde
- Institute of Microbiology and Epizootics, Centre of Infection Medicine Freie Universität Berlin Berlin Germany
- Veterinary Centre for Resistance Research (TZR) Freie Universität Berlin Berlin Germany
| | - Beate Koksch
- Institute of Chemistry and Biochemistry Freie Universität Berlin Berlin Germany
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5
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Delamare A, Naulet G, Kauffmann B, Guichard G, Compain G. Hexafluoroisobutylation of Enolates Through a Tandem Elimination/Allylic Shift/Hydrofluorination Reaction. Chem Sci 2022; 13:9507-9514. [PMID: 36091907 PMCID: PMC9400614 DOI: 10.1039/d2sc02871a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/08/2022] [Indexed: 11/21/2022] Open
Abstract
The isobutyl side chain is a highly prevalent hydrophobic group in drugs, and it notably constitutes the side chain of leucine. Its replacement by a hexafluorinated version containing two CF3...
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Affiliation(s)
- Aline Delamare
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB F-33600 Pessac France
| | - Guillaume Naulet
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB F-33600 Pessac France
| | - Brice Kauffmann
- Univ. Bordeaux, CNRS, INSERM, IECB, UAR 3033 F-33600 Pessac France
| | - Gilles Guichard
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB F-33600 Pessac France
| | - Guillaume Compain
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB F-33600 Pessac France
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6
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Mardirossian M, Rubini M, Adamo MFA, Scocchi M, Saviano M, Tossi A, Gennaro R, Caporale A. Natural and Synthetic Halogenated Amino Acids-Structural and Bioactive Features in Antimicrobial Peptides and Peptidomimetics. Molecules 2021; 26:7401. [PMID: 34885985 PMCID: PMC8659048 DOI: 10.3390/molecules26237401] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 11/16/2021] [Accepted: 11/26/2021] [Indexed: 11/17/2022] Open
Abstract
The 3D structure and surface characteristics of proteins and peptides are crucial for interactions with receptors or ligands and can be modified to some extent to modulate their biological roles and pharmacological activities. The introduction of halogen atoms on the side-chains of amino acids is a powerful tool for effecting this type of tuning, influencing both the physico-chemical and structural properties of the modified polypeptides, helping to first dissect and then rationally modify features that affect their mode of action. This review provides examples of the influence of different types of halogenation in amino acids that replace native residues in proteins and peptides. Examples of synthetic strategies for obtaining halogenated amino acids are also provided, focusing on some representative compounds and their biological effects. The role of halogenation in native and designed antimicrobial peptides (AMPs) and their mimetics is then discussed. These are in the spotlight for the development of new antimicrobial drugs to counter the rise of antibiotic-resistant pathogens. AMPs represent an interesting model to study the role that natural halogenation has on their mode of action and also to understand how artificially halogenated residues can be used to rationally modify and optimize AMPs for pharmaceutical purposes.
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Affiliation(s)
- Mario Mardirossian
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Piazza dell’Ospitale, 1, 34125 Trieste, Italy
| | - Marina Rubini
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland;
| | - Mauro F. A. Adamo
- Department of Chemistry, Centre for Synthesis and Chemical Biology (CSCB), RCSI, 123 St. Stephens Green, Dublin 2, Ireland;
| | - Marco Scocchi
- Department of Life Sciences, University of Trieste, Via L. Giorgieri, 5, Q Building, 34127 Trieste, Italy; (M.S.); (A.T.); (R.G.)
| | - Michele Saviano
- Institute of Crystallography (IC), National Research Council (CNR), Via Amendola, 122, 70126 Bari, Italy;
| | - Alessandro Tossi
- Department of Life Sciences, University of Trieste, Via L. Giorgieri, 5, Q Building, 34127 Trieste, Italy; (M.S.); (A.T.); (R.G.)
| | - Renato Gennaro
- Department of Life Sciences, University of Trieste, Via L. Giorgieri, 5, Q Building, 34127 Trieste, Italy; (M.S.); (A.T.); (R.G.)
| | - Andrea Caporale
- Institute of Crystallography (IC), National Research Council (CNR), c/o Area Science Park, S.S. 14 Km 163.5, Basovizza, 34149 Trieste, Italy
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7
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Li MC, Liu YJ, Hsu KC, Lin TH, Lin CW, Horng JC, Wang SK. Design and synthesis of fluorinated peptides for analysis of fluorous effects on the interconversion of polyproline helices. Bioorg Chem 2021; 119:105491. [PMID: 34838334 DOI: 10.1016/j.bioorg.2021.105491] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/09/2021] [Accepted: 11/11/2021] [Indexed: 12/15/2022]
Abstract
The unique interaction between fluorine atoms has been exploited to alter protein structures and to develop synthetic and analytical applications. To expand such fluorous interaction for novel applications, polyproline peptides represent an excellent molecular nanoscaffold for controlling the presentation of perfluoroalkyl groups on their unique secondary structure. We develop approaches to synthesis fluorinated peptides to systematically investigate how the number, location and types of the fluorous groups on polyproline affect the conformation by monitoring the transition between the two major polyproline structures PPI and PPII. This work provides valuable information on how fluorous interaction affects the peptide structure and also benefits the design of functional fluorous molecules.
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Affiliation(s)
- Meng-Che Li
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Ying-Jie Liu
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Kuang-Cheng Hsu
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Tse-Hsueh Lin
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Chih-Wei Lin
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Jia-Cherng Horng
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan; Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Sheng-Kai Wang
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan; Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu 30013, Taiwan.
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8
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Zhang A, Liu P, Dou C, Liu Y, Che L. Molecular conversion of MIG6 hotspot-3 peptide from the nonbinder to a moderate binder of HER2 by rational design of an orthogonal interaction system at the HER2-peptide interface. Biophys Chem 2021; 276:106625. [PMID: 34077816 DOI: 10.1016/j.bpc.2021.106625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/15/2021] [Accepted: 05/19/2021] [Indexed: 10/21/2022]
Abstract
Human epidermal growth factor receptor 2 (HER2) has been established as an approved druggable target for the treatment of patients with diverse gynecological tumors such as ovarian, cervical and breast cancers. The mitogen-inducible gene 6 (MIG6) protein is a negative regulator of HER2 signaling by using its Seg1 segment to disrupt the allosteric dimerization of HER2 kinase domain. Previous studies found that the Seg1 adopts three separated hotspots to interact with the HER2 dimerization interface, in which the third hotspot (H3) is located at the core region of the interface but its derived H3 peptide (356PKYVS360) and Tyr358Phe mutant (356PKFVS360) cannot bind effectively to the interface in an independent manner. In this study, we demonstrate that the H3 peptide can be converted from nonbinder to a moderate binder of HER2 by just adding an orthogonal noncovalent interaction system (X⋯O┄H) between a halogen bond (X⋯O) and a hydrogen bond (H┄O) involving peptide Phe358 residue and HER2 Val948/Trp951 residues. High-level calculations are utilized to rigorously characterize and rationally design the X⋯O┄H system, which is then optimized with different halogen atoms and at different substituting positions. It is revealed that there is a synergistic effect between the X⋯O and H┄O of the orthogonal interaction system; formation of the halogen bond can enhance the interaction strength of the hydrogen bond. In silico analysis and in vitro assay reach a consistence that Br-substitution at the m-position of peptide Phe358 phenyl moiety is the best choice that can render strong interaction for the X⋯O┄H system, which also makes the peptide 'bindable' to HER2 kinase domain, while F/Cl/I-substitution at the same position can only improve the peptide affinity moderately or modestly. In contrast, the Br-substitution at the o- and p-positions of peptide Phe358 phenyl moiety cannot define effective X⋯O┄H interaction and thus does not confer additional affinity to the HER2-peptide complex.
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Affiliation(s)
- Aihong Zhang
- Department of Obstetrics and Gynecology, Yidu Central Hospital Affiliated to Weifang Medical University, Weifang 262500, China
| | - Ping Liu
- Department of Obstetrics and Gynecology, Yidu Central Hospital Affiliated to Weifang Medical University, Weifang 262500, China
| | - Chuncheng Dou
- Department of Obstetrics and Gynecology, Yidu Central Hospital Affiliated to Weifang Medical University, Weifang 262500, China
| | - Yao Liu
- Department of Obstetrics and Gynecology, Yidu Central Hospital Affiliated to Weifang Medical University, Weifang 262500, China
| | - Lifan Che
- Department of Obstetrics and Gynecology, Yidu Central Hospital Affiliated to Weifang Medical University, Weifang 262500, China.
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9
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Saadi S, Ghazali HM, Saari N, Abdulkarim SM. The structural reconformation of peptides in enhancing functional and therapeutic properties: Insights into their solid state crystallizations. Biophys Chem 2021; 273:106565. [PMID: 33780688 DOI: 10.1016/j.bpc.2021.106565] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 02/09/2021] [Accepted: 02/19/2021] [Indexed: 01/05/2023]
Abstract
Therapeutic peptides derived proteins with alpha-reconformation states like antibody shape have shown potential effects in combating terrible diseases linked with earlier signs of angiogensis, mutagenesis and transgenesis. Alpha reconformation in material design refers to the folding of the peptide chains and their transitions under reversible chemical bonds of disulfide chemical bridges and further non-covalence lesions. Thus, the rational design of signal peptides into alpha-helix is intended in increasing the defending effects of peptides into cores like adjuvant antibiotic and/or vaccines. Thereby, the signal peptides are able in displaying multiple eradicating regions by changing crystal-depositions and deviation angles. These types of molecular structures could have multiple advantages in tracing disease syndromes and impurities by increasing the host defense against the fates of pathogens and viruses, eventually leading to the loss in signaling by increasing peptide susceptibility levels to folding and unfolding and therefore, formation of transgenic peptide models. Alpha reconformation peptides is aimed in triggering as well as other regulatory functions such as remodulating metabolic chain disorders of lipolysis and glucolysis by increasing the insulin and leptin resistance for best lipid storages and lipoprotein density distributions.
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Affiliation(s)
- Sami Saadi
- Institut de la Nutrition, de l'Alimentation et des Technologies Agro-alimentaires INATAA 25017, Université Frères Mentouri, Constantine 1, Algeria; Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Hasanah Mohd Ghazali
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Nazamid Saari
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Sabo Mohammed Abdulkarim
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
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10
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Cardoso P, Glossop H, Meikle TG, Aburto-Medina A, Conn CE, Sarojini V, Valery C. Molecular engineering of antimicrobial peptides: microbial targets, peptide motifs and translation opportunities. Biophys Rev 2021; 13:35-69. [PMID: 33495702 PMCID: PMC7817352 DOI: 10.1007/s12551-021-00784-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 01/07/2021] [Indexed: 02/07/2023] Open
Abstract
The global public health threat of antimicrobial resistance has led the scientific community to highly engage into research on alternative strategies to the traditional small molecule therapeutics. Here, we review one of the most popular alternatives amongst basic and applied research scientists, synthetic antimicrobial peptides. The ease of peptide chemical synthesis combined with emerging engineering principles and potent broad-spectrum activity, including against multidrug-resistant strains, has motivated intense scientific focus on these compounds for the past decade. This global effort has resulted in significant advances in our understanding of peptide antimicrobial activity at the molecular scale. Recent evidence of molecular targets other than the microbial lipid membrane, and efforts towards consensus antimicrobial peptide motifs, have supported the rise of molecular engineering approaches and design tools, including machine learning. Beyond molecular concepts, supramolecular chemistry has been lately added to the debate; and helped unravel the impact of peptide self-assembly on activity, including on biofilms and secondary targets, while providing new directions in pharmaceutical formulation through taking advantage of peptide self-assembled nanostructures. We argue that these basic research advances constitute a solid basis for promising industry translation of rationally designed synthetic peptide antimicrobials, not only as novel drugs against multidrug-resistant strains but also as components of emerging antimicrobial biomaterials. This perspective is supported by recent developments of innovative peptide-based and peptide-carrier nanobiomaterials that we also review.
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Affiliation(s)
- Priscila Cardoso
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia
- School of Science, RMIT University, Melbourne, Australia
| | - Hugh Glossop
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | | | | | | | | | - Celine Valery
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia
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11
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Glossop HD, De Zoysa GH, Pilkington LI, Barker D, Sarojini V. Fluorinated O-phenylserine residues enhance the broad-spectrum antimicrobial activity of ultrashort cationic lipopeptides. J Fluor Chem 2021. [DOI: 10.1016/j.jfluchem.2020.109685] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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12
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Miller MA, Sletten EM. Perfluorocarbons in Chemical Biology. Chembiochem 2020; 21:3451-3462. [PMID: 32628804 PMCID: PMC7736518 DOI: 10.1002/cbic.202000297] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/03/2020] [Indexed: 01/10/2023]
Abstract
Perfluorocarbons, saturated carbon chains in which all the hydrogen atoms are replaced with fluorine, form a separate phase from both organic and aqueous solutions. Though perfluorinated compounds are not found in living systems, they can be used to modify biomolecules to confer orthogonal behavior within natural systems, such as improved stability, engineered assembly, and cell-permeability. Perfluorinated groups also provide handles for purification, mass spectrometry, and 19 F NMR studies in complex environments. Herein, we describe how the unique properties of perfluorocarbons have been employed to understand and manipulate biological systems.
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Affiliation(s)
- Margeaux A Miller
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E Young Dr E, Los Angeles, CA, 90095, USA
| | - Ellen M Sletten
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E Young Dr E, Los Angeles, CA, 90095, USA
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13
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Fluorine-19 NMR spectroscopy of fluorinated analogs of tritrpticin highlights a distinct role for Tyr residues in antimicrobial peptides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183260. [DOI: 10.1016/j.bbamem.2020.183260] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 02/17/2020] [Accepted: 02/19/2020] [Indexed: 02/08/2023]
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14
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Eshon J, Gerstner NC, Schomaker JM. Oxidative allene amination for the synthesis of nitrogen-containing heterocycles. ARKIVOC 2018; 2018:204-233. [PMID: 31903453 PMCID: PMC6941799 DOI: 10.24820/ark.5550190.p010.670] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The prevalence of stereochemically complex amines in natural products, pharmaceuticals and other bioactive compounds, coupled with the challenges inherent in their preparation, has inspired our work to develop new and versatile methodologies for the synthesis of amine-containing stereotriads ('triads'). The key step is a highly chemo-, regio-, and stereoselective transition-metal catalyzed nitrene transfer reaction that transforms one of the cumulated double bonds of an allene precursor into a bicyclic methyleneaziridine intermediate. This account summarizes our strategies to rapidly elaborate such intermediates into stereochemically rich, densely functionalized amine triads, nitrogen heterocycles, aminated carbocycles and other useful synthetic building blocks.
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Affiliation(s)
- Josephine Eshon
- Department of Chemistry, 1101 University Avenue, Madison, WI 53706, U.S.A
| | - Nels C Gerstner
- Department of Chemistry, 1101 University Avenue, Madison, WI 53706, U.S.A
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15
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Wang C, Feng S, Qie J, Wei X, Yan H, Liu K. Polyion complexes of a cationic antimicrobial peptide as a potential systemically administered antibiotic. Int J Pharm 2018; 554:284-291. [PMID: 30439489 DOI: 10.1016/j.ijpharm.2018.11.029] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 11/09/2018] [Accepted: 11/12/2018] [Indexed: 12/12/2022]
Abstract
Antimicrobial peptides (AMPs) are regarded as next-generation antibiotics to replace conventional antibiotics due to their rapid and broad-spectrum antimicrobial properties and far less sensitivity to the development of pathogen resistance. However, they are susceptible to proteolysis in vivo by endogenous or bacterial proteases as well as induce the lysis of red blood cells, which prevent their intravenous applications. In this work, polyion complex (PIC) micelles of the cationic AMP MSI-78 and the anionic copolymer methoxy poly(ethylene glycol)-b-poly(α-glutamic acid) (mPEG-b-PGlu) were prepared to develop novel antimicrobial agents for potential application in vivo. With an increase in molar ratio of mPEG-b-PGlu to MSI-78, the complexation ability of the PIC micelles increased. FITC-labeled MSI-78 showed a sustained release from the PIC micelles. More importantly, these PIC micelles greatly decreased the hemolytic toxicity of MSI-78 to human red blood cells, without influencing its antimicrobial activity. Thus, this approach could be used as a suitable in vivo delivery method of AMPs in the future.
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Affiliation(s)
- Chenhong Wang
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology & Toxicology, Beijing 100850, China
| | - Siliang Feng
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology & Toxicology, Beijing 100850, China
| | - Jiankun Qie
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology & Toxicology, Beijing 100850, China
| | - Xiaoli Wei
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology & Toxicology, Beijing 100850, China
| | - Husheng Yan
- Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, Nankai University, Tianjin 300071, China.
| | - Keliang Liu
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology & Toxicology, Beijing 100850, China.
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16
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Huhmann S, Koksch B. Fine-Tuning the Proteolytic Stability of Peptides with Fluorinated Amino Acids. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800803] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Susanne Huhmann
- Institute of Chemistry and Biochemistry; Freie Universität Berlin; Takustr. 3 14169 Berlin Germany
| | - Beate Koksch
- Institute of Chemistry and Biochemistry; Freie Universität Berlin; Takustr. 3 14169 Berlin Germany
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17
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López
Cascales JJ, Zenak S, García de la Torre J, Lezama OG, Garro A, Enriz RD. Small Cationic Peptides: Influence of Charge on Their Antimicrobial Activity. ACS OMEGA 2018; 3:5390-5398. [PMID: 30221230 PMCID: PMC6130792 DOI: 10.1021/acsomega.8b00293] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 04/11/2018] [Indexed: 05/28/2023]
Abstract
The first stage of the action mechanism of small cationic peptides with antimicrobial activity is ruled by electrostatic interactions between the peptide and the pathogen cell membrane. Thus, an increase in its activity could be expected with an increase in the positive charge on the peptide. By contrast, the opposite behavior has been observed when the charge increases to reach a critical value, beyond which the activity falls. This work studies the perturbation effects in a cell membrane model for two small cationic peptides with similar length and morphology but with different cationic charges. The synthesis and antibacterial activity of the two peptides used in this study are described. The thermodynamic study associated with the insertion of these peptides into the membrane and the perturbing effects on the bilayer structure provide valuable insights into the molecular action mechanism associated with the charge of these small cationic peptides.
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Affiliation(s)
- José Javier López
Cascales
- Grupo
de Bioinformatica y Macromoleculas (BioMac), Area de Química
Física, Universidad Politécnica
de Cartagena, Aulario
II, Campus de Alfonso XIII, 30203 Cartagena, Murcia, Spain
| | - Siham Zenak
- Laboratoire
d’Etude Physique des Matériaux, Département de
Physique Energétique, Faculté de Physique, Université des Sciences et de la Technologie
d’Oran, BP 1505
El M’Naouer, Oran 31000, Algeria
| | - José García de la Torre
- Facultad
de Química, Departamento de Química Física, Universidad de Murcia, Campus de Espinardo, 30100 Espinardo, Murcia, Spain
| | | | - Adriana Garro
- Facultad
de Química, Bioquímica y Farmacia, IMIBIO-CONICET, Universidad Nacional de San Luis, Chacabuco 917, 5700 San Luis, Argentina
| | - Ricardo Daniel Enriz
- Facultad
de Química, Bioquímica y Farmacia, IMIBIO-CONICET, Universidad Nacional de San Luis, Chacabuco 917, 5700 San Luis, Argentina
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18
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Gadais C, Devillers E, Gasparik V, Chelain E, Pytkowicz J, Brigaud T. Probing the Outstanding Local Hydrophobicity Increases in Peptide Sequences Induced by Incorporation of Trifluoromethylated Amino Acids. Chembiochem 2018. [DOI: 10.1002/cbic.201800088] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Charlène Gadais
- Laboratory of Chemical Biology (LCB, EA 4505); Université Cergy-Pontoise; Mail Gay-Lussac 95000 Cergy-Pontoise cedex France
| | - Emmanuelle Devillers
- Laboratory of Chemical Biology (LCB, EA 4505); Université Cergy-Pontoise; Mail Gay-Lussac 95000 Cergy-Pontoise cedex France
| | - Vincent Gasparik
- Laboratory of Chemical Biology (LCB, EA 4505); Université Cergy-Pontoise; Mail Gay-Lussac 95000 Cergy-Pontoise cedex France
| | - Evelyne Chelain
- Laboratory of Chemical Biology (LCB, EA 4505); Université Cergy-Pontoise; Mail Gay-Lussac 95000 Cergy-Pontoise cedex France
| | - Julien Pytkowicz
- Laboratory of Chemical Biology (LCB, EA 4505); Université Cergy-Pontoise; Mail Gay-Lussac 95000 Cergy-Pontoise cedex France
| | - Thierry Brigaud
- Laboratory of Chemical Biology (LCB, EA 4505); Université Cergy-Pontoise; Mail Gay-Lussac 95000 Cergy-Pontoise cedex France
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19
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Laurencin M, Simon M, Fleury Y, Baudy-Floc'h M, Bondon A, Legrand B. Selectivity Modulation and Structure of α/aza-β3
Cyclic Antimicrobial Peptides. Chemistry 2018; 24:6191-6201. [DOI: 10.1002/chem.201800152] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Indexed: 12/26/2022]
Affiliation(s)
| | - Matthieu Simon
- Institut des Biomolécules Max Mousseron (IBMM); Univ Montpellier, CNRS, UM, ENSCM; 15 Avenue Charles Flahault 34093 Montpellier Cedex 5 France
- Université de Rennes, CNRS; ISCR-UMR 6226; 35000 Rennes France
| | - Yannick Fleury
- Chimie Marines, IUEM; Université de Brest, EA 3884; 6 rue de l'Université 29000 Quimper France
| | | | - Arnaud Bondon
- Université de Rennes, CNRS; ISCR-UMR 6226; 35000 Rennes France
| | - Baptiste Legrand
- Institut des Biomolécules Max Mousseron (IBMM); Univ Montpellier, CNRS, UM, ENSCM; 15 Avenue Charles Flahault 34093 Montpellier Cedex 5 France
- Université de Rennes, CNRS; ISCR-UMR 6226; 35000 Rennes France
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20
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New insights into the influence of monofluorination on dimyristoylphosphatidylcholine membrane properties: A solid-state NMR study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:654-663. [DOI: 10.1016/j.bbamem.2017.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 11/29/2017] [Accepted: 12/04/2017] [Indexed: 10/18/2022]
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21
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Huhmann S, Stegemann AK, Folmert K, Klemczak D, Moschner J, Kube M, Koksch B. Position-dependent impact of hexafluoroleucine and trifluoroisoleucine on protease digestion. Beilstein J Org Chem 2017; 13:2869-2882. [PMID: 29564015 PMCID: PMC5753150 DOI: 10.3762/bjoc.13.279] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 12/13/2017] [Indexed: 12/22/2022] Open
Abstract
Rapid digestion by proteases limits the application of peptides as therapeutics. One strategy to increase the proteolytic stability of peptides is the modification with fluorinated amino acids. This study presents a systematic investigation of the effects of fluorinated leucine and isoleucine derivatives on the proteolytic stability of a peptide that was designed to comprise substrate specificities of different proteases. Therefore, leucine, isoleucine, and their side-chain fluorinated variants were site-specifically incorporated at different positions of this peptide resulting in a library of 13 distinct peptides. The stability of these peptides towards proteolysis by α-chymotrypsin, pepsin, proteinase K, and elastase was studied, and this process was followed by an FL-RP-HPLC assay in combination with mass spectrometry. In a few cases, we observed an exceptional increase in proteolytic stability upon introduction of the fluorine substituents. The opposite phenomenon was observed in other cases, and this may be explained by specific interactions of fluorinated residues with the respective enzyme binding sites. Noteworthy is that 5,5,5-trifluoroisoleucine is able to significantly protect peptides from proteolysis by all enzymes included in this study when positioned N-terminal to the cleavage site. These results provide valuable information for the application of fluorinated amino acids in the design of proteolytically stable peptide-based pharmaceuticals.
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Affiliation(s)
- Susanne Huhmann
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Anne-Katrin Stegemann
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Kristin Folmert
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Damian Klemczak
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Johann Moschner
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Michelle Kube
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Beate Koksch
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
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22
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Liu L, Gerstner NC, Oxtoby LJ, Guzei IA, Schomaker JM. Fluorinated Amine Stereotriads via Allene Amination. Org Lett 2017; 19:3239-3242. [PMID: 28573862 PMCID: PMC5541934 DOI: 10.1021/acs.orglett.7b01342] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The incorporation of fluorine into organic scaffolds often improves the bioactivity of pharmaceutically relevant compounds. C-F/C-N/C-O stereotriad motifs are prevalent in antivirals, neuraminidase inhibitors, and modulators of androgen receptors, but are challenging to install. An oxidative allene amination strategy using Selectfluor rapidly delivers triply functionalized triads of the form C-F/C-N/C-O, exhibiting good scope and diastereoselectivity for all syn products. The resulting stereotriads are readily transformed into fluorinated pyrrolidines and protected α-, β-, and γ-amino acids.
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Affiliation(s)
- Lu Liu
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Nels C. Gerstner
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Lucas J. Oxtoby
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Ilia A. Guzei
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Jennifer M. Schomaker
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
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23
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Molchanova N, Hansen PR, Damborg P, Nielsen HM, Franzyk H. Lysine-Based α-Peptide/β-Peptoid Peptidomimetics: Influence of Hydrophobicity, Fluorination, and Distribution of Cationic Charge on Antimicrobial Activity and Cytotoxicity. ChemMedChem 2017; 12:312-318. [PMID: 28052595 DOI: 10.1002/cmdc.201600553] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 01/02/2017] [Indexed: 02/05/2023]
Abstract
Multidrug-resistant bacteria pose a serious threat to public health worldwide. Previously, α-peptide/β-peptoid hybrid oligomers were found to display activity against Gram-negative multidrug-resistant bacteria. In the present work, the influence of hydrophobicity, fluorination, and distribution of cationic/hydrophobic residues on antimicrobial, hemolytic, and cytotoxic properties of α-peptide/β-peptoid hybrids were investigated. An array of 22 peptidomimetics was tested. Analogues with enhanced hydrophobicity were found to exhibit increased activity against Gram-positive bacteria. Incorporation of fluorinated residues into the peptidomimetics conferred increased potency against Gram-positive bacteria, while hemolytic properties and activity against Gram-negative bacteria depended on the degree and type of fluorination. Generally, shorter oligomers were less potent than the corresponding longer analogues. However, some short analogues exhibited equal or higher antimicrobial activity. The alternating hydrophobic/cationic design proved superior to other distribution patterns of cationic side chains and hydrophobic moieties.
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Affiliation(s)
- Natalia Molchanova
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Paul R Hansen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Peter Damborg
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 4, 1870, Frederiksberg C, Denmark
| | - Hanne M Nielsen
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Henrik Franzyk
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
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24
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Jepson AK, Schwarz-Linek J, Ryan L, Ryadnov MG, Poon WCK. What Is the 'Minimum Inhibitory Concentration' (MIC) of Pexiganan Acting on Escherichia coli?-A Cautionary Case Study. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 915:33-48. [PMID: 27193536 DOI: 10.1007/978-3-319-32189-9_4] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
We measured the minimum inhibitory concentration (MIC) of the antimicrobial peptide pexiganan acting on Escherichia coli , and found an intrinsic variability in such measurements. These results led to a detailed study of the effect of pexiganan on the growth curve of E. coli, using a plate reader and manual plating (i.e. time-kill curves). The measured growth curves, together with single-cell observations and peptide depletion assays, suggested that addition of a sub-MIC concentration of pexiganan to a population of this bacterium killed a fraction of the cells, reducing peptide activity during the process, while leaving the remaining cells unaffected. This pharmacodynamic hypothesis suggests a considerable inoculum effect, which we quantified. Our results cast doubt on the use of the MIC as 'a measure of the concentration needed for peptide action' and show how 'coarse-grained' studies at the population level give vital information for the correct planning and interpretation of MIC measurements.
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Affiliation(s)
- Alys K Jepson
- SUPA and School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, Scotland, UK
| | - Jana Schwarz-Linek
- SUPA and School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, Scotland, UK
| | - Lloyd Ryan
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK
| | - Maxim G Ryadnov
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK
| | - Wilson C K Poon
- SUPA and School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, Scotland, UK.
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25
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Hicks RP. Antibacterial and anticancer activity of a series of novel peptides incorporating cyclic tetra-substituted Cα amino acids. Bioorg Med Chem 2016; 24:4056-4065. [DOI: 10.1016/j.bmc.2016.06.048] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/20/2016] [Accepted: 06/23/2016] [Indexed: 11/26/2022]
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26
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Abstract
As methods to incorporate noncanonical amino acid residues into proteins have become more powerful, interest in their use to modify the physical and biological properties of proteins and enzymes has increased. This chapter discusses the use of highly fluorinated analogs of hydrophobic amino acids, for example, hexafluoroleucine, in protein design. In particular, fluorinated residues have proven to be generally effective in increasing the thermodynamic stability of proteins. The chapter provides an overview of the different fluorinated amino acids that have been used in protein design and the various methods available for producing fluorinated proteins. It discusses model proteins systems into which highly fluorinated amino acids have been introduced and the reasons why fluorinated residues are generally stabilizing, with particular reference to thermodynamic and structural studies from our laboratory. Lastly, details of the methodology we have developed to measure the thermodynamic stability of oligomeric fluorinated proteins are presented, as this may be generally applicable to many proteins.
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Affiliation(s)
- E N G Marsh
- University of Michigan, Ann Arbor, MI, United States.
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27
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Arias M, Hoffarth ER, Ishida H, Aramini JM, Vogel HJ. Recombinant expression, antimicrobial activity and mechanism of action of tritrpticin analogs containing fluoro-tryptophan residues. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1858:1012-23. [PMID: 26724205 DOI: 10.1016/j.bbamem.2015.12.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 12/19/2015] [Accepted: 12/20/2015] [Indexed: 11/16/2022]
Abstract
The increase in antibiotic-resistant bacterial infections has prompted significant academic research into new therapeutic agents targeted against these pathogens. Antimicrobial peptides (AMPs) appear as promising candidates, due their potent antimicrobial activity and their ubiquitous presence in almost all organisms. Tritrpticin is a member of this family of peptides and has been shown to exert a strong antimicrobial activity against several bacterial strains. Tritrpticin's main structural characteristic is the presence of three consecutive Trp residues at the center of the peptide. These residues play an important role in the activity of tritrpticin against Escherichia coli. In this work, a recombinant version of tritrpticin was produced in E. coli using calmodulin as a fusion protein expression tag to overcome the toxicity of the peptide. When used in combination with glyphosate, an inhibitor of the endogenous synthesis of aromatic amino acids, this expression system allowed for the incorporation of fluorinated Trp analogs at very high levels (>90%). The antimicrobial activity of the 4-, 5- and 6-fluoro-Trp-containing tritrpticins against E. coli was as strong as the activity of the native peptide. Similarly, the tritrpticin analogs exhibited comparable abilities to perturb and permeabilize synthetic lipid bilayers as well as the outer and inner membrane of E. coli. Furthermore, the use of 19F NMR spectroscopy established that each individual fluoro-Trp residue interacts differently with SDS micelles, supporting the idea that each Trp in the original tritrpticin plays a different role in the perturbing/permeabilizing activity of the peptide. Moreover, our work demonstrates that the use of fluoro-Trp in solvent perturbation 19F NMR experiments provides detailed site-specific information on the insertion of the Trp residues in biological membrane mimetics. This article is part of a Special Issue entitled: Antimicrobial peptides edited by Karl Lohner and Kai Hilpert.
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Affiliation(s)
- Mauricio Arias
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta, T2N 1N4, Canada
| | - Elesha R Hoffarth
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta, T2N 1N4, Canada
| | - Hiroaki Ishida
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta, T2N 1N4, Canada
| | - James M Aramini
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Hans J Vogel
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta, T2N 1N4, Canada.
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28
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Clark TD, Bartolotti L, Hicks RP. The application of DOSY NMR and molecular dynamics simulations to explore the mechanism(s) of micelle binding of antimicrobial peptides containing unnatural amino acids. Biopolymers 2016; 99:548-61. [PMID: 23712491 DOI: 10.1002/bip.22215] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 01/14/2013] [Accepted: 01/25/2013] [Indexed: 11/11/2022]
Abstract
Anionic and zwitterionic micelles are often used as simple models for the lipids found in bacterial and mammalian cell membranes to investigate antimicrobial peptide-lipid interactions. In our laboratory we have employed a variety of 1D, 2D, and diffusion ordered (DOSY) NMR experiments to investigate the interactions of antimicrobial peptides containing unnatural amino acids with SDS and DPC micelles. Complete assignment of the proton spectra of these peptides is prohibited by the incorporation of a high percentage of unnatural amino acids which don't contain amide protons into the backbone. However preliminary assignment of the TOCSY spectra of compound 23 in the presence of both micelles indicated multiple conformers are present as a result of binding to these micelles. Chemical Shift Indexing agreed with previously collected CD spectra that indicated on binding to SDS micelles compound 23 adopts a mixture of α-helical structures and on binding to DPC micelles this peptide adopts a mixture of helical and β-turn/sheet like structures. DOSY NMR experiments also indicated that the total positive charge and the relative placement of that charge at the N-terminus or C-terminus are important in determining the mole fraction of the peptide that will bind to the different micelles. DOSY and (1) H-NMR experiments indicated that the length of Spacer #1 plays a major role in defining the binding conformation of these analogs with SDS micelles. Results obtained from molecular simulations studies of the binding of compounds 23 and 36 with SDS micelles were consistent with the observed NMR results.
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Affiliation(s)
- Tiffany D Clark
- Department of Chemistry, East Carolina University, Science and Technology Building, Greenville, NC 27858, USA
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29
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Synthesis of protected enantiopure (R) and (S)-α-trifluoromethylalanine containing dipeptide building blocks ready to use for solid phase peptide synthesis. Amino Acids 2016; 48:1457-68. [PMID: 26920748 DOI: 10.1007/s00726-016-2200-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 02/11/2016] [Indexed: 02/02/2023]
Abstract
Considering the increasing importance of fluorinated peptides, the development of efficient and reliable synthetic methods for the incorporation of unnatural fluorinated amino acids into peptides is a current matter of interest. In this study, we report the convenient Boc/benzyl and Cbz/tert-butyl protection of both enantiomers of the quaternarized amino acid α-trifluoromethylalanine [(R)- and (S)-α-Tfm-Ala]. Because of the deactivation of the nitrogen atom of this synthetic amino acid by the strong electron withdrawing trifluoromethyl group, the peptide coupling on this position is a challenge. In order to provide a robust synthetic methodology for the incorporation of enantiopure (R)- and (S)-α-trifluoromethylalanines into peptides, we report herein the preparation of dipeptides ready to use for solid phase peptide synthesis. The difficult peptide coupling on the nitrogen atom of the α-trifluoromethylalanines was performed in solution phase by means of highly electrophilic amino acid chlorides or mixed anhydrides. The synthetic effectiveness of this fluorinated dipeptide building block strategy is illustrated by the solid phase peptide synthesis (SPPS) of the Ac-Ala-Phe-(R)-α-Tfm-Ala-Ala-NH2 tetrapeptide.
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30
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Zerfas BL, Joo Y, Gao J. Gramicidin A Mutants with Antibiotic Activity against Both Gram-Positive and Gram-Negative Bacteria. ChemMedChem 2016; 11:629-36. [PMID: 26918268 DOI: 10.1002/cmdc.201500602] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Indexed: 01/01/2023]
Abstract
Antimicrobial peptides (AMPs) have shown potential as alternatives to traditional antibiotics for fighting infections caused by antibiotic-resistant bacteria. One promising example of this is gramicidin A (gA). In its wild-type sequence, gA is active by permeating the plasma membrane of Gram-positive bacteria. However, gA is toxic to human red blood cells at similar concentrations to those required for it to exert its antimicrobial effects. Installing cationic side chains into gA has been shown to lower its hemolytic activity while maintaining the antimicrobial potency. In this study, we present the synthesis and the antibiotic activity of a new series of gA mutants that display cationic side chains. Specifically, by synthesizing alkylated lysine derivatives through reductive amination, we were able to create a broad selection of structures with varied activities towards Staphylococcus aureus and methicillin-resistant S. aureus (MRSA). Importantly, some of the new mutants were observed to have an unprecedented activity towards important Gram-negative pathogens, including Escherichia coli, Klebsiella pneumoniae and Psuedomonas aeruginosa.
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Affiliation(s)
- Breanna L Zerfas
- Department of Chemistry, Merkert Chemisty Center, Boston College, 2609 Beacon St., Chestnut Hill, MA, 02461, USA
| | - Yechaan Joo
- Department of Chemistry, Merkert Chemisty Center, Boston College, 2609 Beacon St., Chestnut Hill, MA, 02461, USA
| | - Jianmin Gao
- Department of Chemistry, Merkert Chemisty Center, Boston College, 2609 Beacon St., Chestnut Hill, MA, 02461, USA.
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31
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References. Antibiotics (Basel) 2015. [DOI: 10.1128/9781555819316.refs] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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32
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Doğan A, Aslan N, Erden PE, Canel E, Kılıç E. Macroscopic and Microscopic Protonation Equilibria of Some α-Amino Acids in Dimethyl Sulfoxide–Water Mixtures. J SOLUTION CHEM 2015. [DOI: 10.1007/s10953-015-0363-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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33
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Jahnsen RO, Sandberg-Schaal A, Frimodt-Møller N, Nielsen HM, Franzyk H. End group modification: Efficient tool for improving activity of antimicrobial peptide analogues towards Gram-positive bacteria. Eur J Pharm Biopharm 2015; 95:40-6. [PMID: 25622790 DOI: 10.1016/j.ejpb.2015.01.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Revised: 01/02/2015] [Accepted: 01/14/2015] [Indexed: 01/26/2023]
Abstract
Increased incidence of infections with multidrug-resistant bacterial strains warrants an intensive search for novel potential antimicrobial agents. Here, an antimicrobial peptide analogue with a cationic/hydrophobic alternating design displaying only moderate activity against Gram-positive pathogens was optimized. Generally, introduction of hydrophobic moieties at the N-terminus resulted in analogues with remarkably increased activity against multidrug-resistant Staphylococcus aureus and Enterococcus faecium. Interestingly, the potency against Escherichia coli strains was unaffected, whereas modification with hydrophobic moieties led to increased activity towards the Gram-negative Acinetobacter baumannii. Despite increased cytotoxicity against murine fibroblasts and human umbilical vein endothelial cells, the optimized peptide analogues exhibited significantly improved cell selectivity. Overall, the most favorable hydrophobic activity-inducing moieties were found to be cyclohexylacetyl and pentafluorophenylacetyl groups, while the presence of a short PEG-like chain had no significant effect on activity. Introduction of cationic moieties conferred no effect or merely a moderate activity-promoting effect to the analogues.
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Affiliation(s)
- Rasmus O Jahnsen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Anne Sandberg-Schaal
- Department of Clinical Microbiology, Copenhagen University Hospital, Hvidovre, Denmark
| | - Niels Frimodt-Møller
- Department of Clinical Microbiology, Copenhagen University Hospital, Hvidovre, Denmark.
| | - Hanne Mørck Nielsen
- Dept. Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.
| | - Henrik Franzyk
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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34
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Fraser SA, Easton CJ. Biosynthetic Incorporation of Fluorinated Amino Acids into Peptides and Proteins. Aust J Chem 2015. [DOI: 10.1071/ch14356] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Native and engineered protein biosynthetic machinery processes a wide range of fluorinated α-amino acids for incorporation into peptides and proteins, either as substitutes for structurally similar amino acids normally found in proteins, or as additional ones. In the former case, replacement occurs wherever the normal amino acid is encoded, while the latter method is site-specific. The fluorinated peptides have a diverse variety of interesting properties. The biochemical synthetic methods are straightforward, to the point that they should routinely be assessed as alternatives to traditional solid- and solution-phase peptide synthesis.
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35
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Synthetic Antimicrobial Peptides Exhibit Two Different Binding Mechanisms to the Lipopolysaccharides Isolated from Pseudomonas aeruginosa and Klebsiella pneumoniae. INTERNATIONAL JOURNAL OF MEDICINAL CHEMISTRY 2014; 2014:809283. [PMID: 25610647 PMCID: PMC4295349 DOI: 10.1155/2014/809283] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 11/26/2014] [Accepted: 11/26/2014] [Indexed: 01/03/2023]
Abstract
Circular dichroism and 1H NMR were used to investigate the interactions of a
series of synthetic antimicrobial peptides (AMPs) with lipopolysaccharides (LPS) isolated from
Pseudomonas aeruginosa and Klebsiella pneumoniae. Previous CD studies with AMPs
containing only three Tic-Oic dipeptide units do not exhibit helical characteristics upon
interacting with small unilamellar vesicles (SUVs) consisting of LPS. Increasing the number of
Tic-Oic dipeptide units to six resulted in five analogues with CD spectra that exhibited helical
characteristics on binding to LPS SUVs. Spectroscopic and in vitro inhibitory data suggest that
there are two possible helical conformations resulting from two different AMP-LPS binding
mechanisms. Mechanism one involves a helical binding conformation where the AMP binds
LPS very strongly and is not efficiently transported across the LPS bilayer resulting in the loss of
inhibitory activity. Mechanism two involves a helical binding conformation where the AMP
binds LPS very loosely and is efficiently transported across the LPS bilayer resulting in an
increase in inhibitory activity. Mechanism three involves a nonhelical binding conformation
where the AMP binds LPS very loosely and is efficiently transported across the LPS bilayer
resulting in an increase in inhibitory activity.
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36
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Marsh ENG. Fluorinated proteins: from design and synthesis to structure and stability. Acc Chem Res 2014; 47:2878-86. [PMID: 24883933 DOI: 10.1021/ar500125m] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Fluorine is all but absent from biology; however, it has proved to be a remarkably useful element with which to modulate the activity of biological molecules and to study their mechanism of action. Our laboratory's interest in incorporating fluorine into proteins was stimulated by the unusual physicochemical properties exhibited by perfluorinated small molecules. These include extreme chemical inertness and thermal stability, properties that have made them valuable as nonstick coatings and fire retardants. Fluorocarbons also exhibit an unusual propensity to phase segregation. This phenomenon, which has been termed the "fluorous effect", has been effectively exploited in organic synthesis to purify compounds from reaction mixtures by extracting fluorocarbon-tagged molecules into fluorocarbon solvents. As biochemists, we were curious to explore whether the unusual physicochemical properties of perfluorocarbons could be engineered into proteins. To do this, we developed a synthesis of a highly fluorinated amino acid, hexafluoroleucine, and designed a model 4-helix bundle protein, α4H, in which the hydrophobic core was packed exclusively with leucine. We then investigated the effects of repacking the hydrophobic core of α4H with various combinations of leucine and hexafluoroleucine. These initial studies demonstrated that fluorination is a general and effective strategy for enhancing the stability of proteins against chemical and thermal denaturation and proteolytic degradation. We had originally envisaged that the "fluorous interactions", postulated from the self-segregating properties of fluorous solvents, might be used to mediate specific protein-protein interactions orthogonal to those of natural proteins. However, various lines of evidence indicate that no special, favorable fluorine-fluorine interactions occur in the core of the fluorinated α4 protein. This makes it unlikely that fluorinated amino acids can be used to direct protein-protein interactions. More recent detailed thermodynamic and structural studies in our laboratory have uncovered the basis for the remarkably general ability of fluorinated side chains to stabilize protein structure. Crystal structures of α4H and its fluorinated analogues show that the fluorinated residues fit into the hydrophobic core with remarkably little perturbation to the structure. This is explained by the fact that fluorinated side chains, although larger, very closely preserve the shape of the hydrophobic amino acids they replace. Thus, an increase in buried hydrophobic surface area in the folded state is responsible for the additional thermodynamic stability of the fluorinated protein. Measurements of ΔG°, ΔH°, ΔS°, and ΔCp° for unfolding demonstrate that the "fluorous" stabilization of these protein arises from the hydrophobic effect in the same way that hydrophobic partitioning stabilizes natural proteins.
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Affiliation(s)
- E. Neil G. Marsh
- Departments
of Chemistry
and Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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37
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Asante V, Mortier J, Wolber G, Koksch B. Impact of fluorination on proteolytic stability of peptides: a case study with α-chymotrypsin and pepsin. Amino Acids 2014; 46:2733-44. [DOI: 10.1007/s00726-014-1819-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2014] [Accepted: 07/28/2014] [Indexed: 10/24/2022]
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Abstract
Highly fluorinated analogs of hydrophobic amino acids have proven to be generally effective in increasing the thermodynamic stability of proteins. These non-proteogenic amino acids can be incorporated into both α-helix and β-sheet structural motifs and generally enhance protein stability towards unfolding by heat and chemical denaturants, and retard their degradation by proteases. Recent detailed structural and thermodynamic studies have demonstrated that the increase in buried hydrophobic surface area that accompanies fluorination is primarily responsible for the stabilizing properties of fluorinated side chains. Fluorination appears to be a particularly useful strategy for increasing protein stability because fluorinated amino acids closely retain the shape of the side chain, and are thus minimally perturbing to protein structure and function. The first part of this chapter discusses some examples of highly fluorinated model proteins designed by our laboratory and protocols for their synthesis. In the second part, methods for determining their thermodynamic stability, along with conditions that have proven to be useful for crystallizing these proteins, are presented.
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Affiliation(s)
- Benjamin C Buer
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI, 48109, USA
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39
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Gerling UIM, Salwiczek M, Cadicamo CD, Erdbrink H, Czekelius C, Grage SL, Wadhwani P, Ulrich AS, Behrends M, Haufe G, Koksch B. Fluorinated amino acids in amyloid formation: a symphony of size, hydrophobicity and α-helix propensity. Chem Sci 2014. [DOI: 10.1039/c3sc52932k] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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40
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Wang F, Qin L, Wong P, Gao J. Effects of lysine methylation on gramicidin A channel folding in lipid membranes. Biopolymers 2013; 100:656-61. [DOI: 10.1002/bip.22268] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 04/08/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Fang Wang
- Department of Chemistry, Merkert Chemistry Center; Boston College; 2609 Beacon Street Chestnut Hill MA 02467
| | - Luoheng Qin
- Department of Chemistry, Merkert Chemistry Center; Boston College; 2609 Beacon Street Chestnut Hill MA 02467
| | - Patrick Wong
- Department of Chemistry, Merkert Chemistry Center; Boston College; 2609 Beacon Street Chestnut Hill MA 02467
| | - Jianmin Gao
- Department of Chemistry, Merkert Chemistry Center; Boston College; 2609 Beacon Street Chestnut Hill MA 02467
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41
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Krishnamurthy VM, Kumar K. Fluorination in the design of membrane protein assemblies. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2013; 1063:227-43. [PMID: 23975781 DOI: 10.1007/978-1-62703-583-5_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Protein design approaches based on the binary patterning of nonpolar and polar amino acids have been successful in generating native-like protein structures of amphiphilic α-helices or idealized amphiphilic β-strands in aqueous solution. Such patterning is not possible in the nonpolar environment of biological membranes, precluding the application of conventional approaches to the design of membrane proteins that assemble into discrete aggregates. This review surveys a promising, new strategy for membrane protein design that exploits the unique properties of fluorocarbons-in particular, their ability to phase separate from both water (due to their hydrophobicity) and hydrocarbons (due to their lipophobicity)-to generate membrane protein assemblies. The ability to design such discrete assemblies should enable the disruption of protein-protein interactions and provide templates for novel biomaterials and therapeutics.
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42
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Asante V, Mortier J, Schlüter H, Koksch B. Impact of fluorination on proteolytic stability of peptides in human blood plasma. Bioorg Med Chem 2013; 21:3542-6. [DOI: 10.1016/j.bmc.2013.03.051] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Revised: 03/16/2013] [Accepted: 03/19/2013] [Indexed: 10/27/2022]
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43
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Buer BC, Levin BJ, Marsh ENG. Perfluoro-tert
-butyl-homoserine as a sensitive 19
F NMR reporter for peptide-membrane interactions in solution. J Pept Sci 2013; 19:308-14. [DOI: 10.1002/psc.2501] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 01/31/2013] [Accepted: 02/01/2013] [Indexed: 01/06/2023]
Affiliation(s)
- Benjamin C. Buer
- Department of Chemistry; University of Michigan; Ann Arbor MI 48109 USA
| | - Benjamin J. Levin
- Department of Chemistry; University of Michigan; Ann Arbor MI 48109 USA
| | - E. Neil G. Marsh
- Department of Chemistry; University of Michigan; Ann Arbor MI 48109 USA
- Department of Biological Chemistry; University of Michigan Medical School; Ann Arbor MI 48109 USA
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44
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Laurencin M, Amor M, Fleury Y, Baudy-Floc’h M. De Novo Cyclic Pseudopeptides Containing Aza-β3-amino Acids Exhibiting Antimicrobial Activities. J Med Chem 2012; 55:10885-95. [DOI: 10.1021/jm3009037] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Mathieu Laurencin
- Université de Rennes 1, ICMV, UMR CNRS 6226, 263 Av. du Général
Leclerc, F-35042 Rennes Cedex, France
| | - Mosbah Amor
- Université de Rennes 1, ICMV, UMR CNRS 6226, 263 Av. du Général
Leclerc, F-35042 Rennes Cedex, France
| | - Yannick Fleury
- Université de Bretagne Occidentale, Laboratoire Universitaire de
Biodiversité et d’Ecologie Microbienne, EA 3882, F-29000
Quimper, France
| | - Michèle Baudy-Floc’h
- Université de Rennes 1, ICMV, UMR CNRS 6226, 263 Av. du Général
Leclerc, F-35042 Rennes Cedex, France
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45
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Dürr UN, Gildenberg M, Ramamoorthy A. The magic of bicelles lights up membrane protein structure. Chem Rev 2012; 112:6054-74. [PMID: 22920148 PMCID: PMC3497859 DOI: 10.1021/cr300061w] [Citation(s) in RCA: 266] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Indexed: 12/12/2022]
Affiliation(s)
| | - Melissa Gildenberg
- Biophysics
and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055,
United States
| | - Ayyalusamy Ramamoorthy
- Biophysics
and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055,
United States
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46
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Buer BC, Meagher JL, Stuckey JA, Marsh ENG. Comparison of the structures and stabilities of coiled-coil proteins containing hexafluoroleucine and t-butylalanine provides insight into the stabilizing effects of highly fluorinated amino acid side-chains. Protein Sci 2012; 21:1705-15. [PMID: 22930450 PMCID: PMC3527707 DOI: 10.1002/pro.2150] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 08/17/2012] [Accepted: 08/20/2012] [Indexed: 11/08/2022]
Abstract
Highly fluorinated analogs of hydrophobic amino acids are well known to increase the stability of proteins toward thermal unfolding and chemical denaturation, but there is very little data on the structural consequences of fluorination. We have determined the structures and folding energies of three variants of a de novo designed 4-helix bundle protein whose hydrophobic cores contain either hexafluoroleucine (hFLeu) or t-butylalanine (tBAla). Although the buried hydrophobic surface area is the same for all three proteins, the incorporation of tBAla causes a rearrangement of the core packing, resulting in the formation of a destabilizing hydrophobic cavity at the center of the protein. In contrast, incorporation of hFLeu, causes no changes in core packing with respect to the structure of the nonfluorinated parent protein which contains only leucine in the core. These results support the idea that fluorinated residues are especially effective at stabilizing proteins because they closely mimic the shape of the natural residues they replace while increasing buried hydrophobic surface area.
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Affiliation(s)
- Benjamin C Buer
- Department of Chemistry, University of MichiganAnn Arbor, Michigan 48109
| | - Jennifer L Meagher
- Life Sciences Institute, University of MichiganAnn Arbor, Michigan 48109
| | - Jeanne A Stuckey
- Life Sciences Institute, University of MichiganAnn Arbor, Michigan 48109
- Department of Biological Chemistry, University of Michigan Medical SchoolAnn Arbor, Michigan 48109
| | - E Neil G Marsh
- Department of Chemistry, University of MichiganAnn Arbor, Michigan 48109
- Department of Biological Chemistry, University of Michigan Medical SchoolAnn Arbor, Michigan 48109
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47
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Buer BC, Levin BJ, Marsh ENG. Influence of Fluorination on the Thermodynamics of Protein Folding. J Am Chem Soc 2012; 134:13027-34. [DOI: 10.1021/ja303521h] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Benjamin C. Buer
- Departments of †Chemistry and ‡Biological Chemistry, University of Michigan, Ann Arbor, Michigan
48109, United States
| | - Benjamin J. Levin
- Departments of †Chemistry and ‡Biological Chemistry, University of Michigan, Ann Arbor, Michigan
48109, United States
| | - E. Neil G. Marsh
- Departments of †Chemistry and ‡Biological Chemistry, University of Michigan, Ann Arbor, Michigan
48109, United States
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48
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Yuvienco C, More HT, Haghpanah JS, Tu RS, Montclare JK. Modulating Supramolecular Assemblies and Mechanical Properties of Engineered Protein Materials by Fluorinated Amino Acids. Biomacromolecules 2012; 13:2273-8. [DOI: 10.1021/bm3005116] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Carlo Yuvienco
- Department of Chemical
and Biological Sciences, Polytechnic Institute of NYU, Brooklyn, New York 11201, United States
| | - Haresh T. More
- Department of Chemical
and Biological Sciences, Polytechnic Institute of NYU, Brooklyn, New York 11201, United States
| | - Jennifer S. Haghpanah
- Department of Chemical
and Biological Sciences, Polytechnic Institute of NYU, Brooklyn, New York 11201, United States
| | - Raymond S. Tu
- Department of Chemical
Engineering, City College of New York, New York, New York 10031, United States
| | - Jin Kim Montclare
- Department of Chemical
and Biological Sciences, Polytechnic Institute of NYU, Brooklyn, New York 11201, United States
- Department of Biochemistry, SUNY Downstate Medical Center, Brooklyn,
New York 11203, United States
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49
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Findlay B, Zhanel GG, Schweizer F. Investigating the antimicrobial peptide 'window of activity' using cationic lipopeptides with hydrocarbon and fluorinated tails. Int J Antimicrob Agents 2012; 40:36-42. [PMID: 22578748 DOI: 10.1016/j.ijantimicag.2012.03.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 03/07/2012] [Accepted: 03/09/2012] [Indexed: 12/24/2022]
Abstract
To probe the effect of carbon-fluorine bonds on antimicrobial peptide-membrane interactions, 24 cationic lipopeptides were created. The collection of lipopeptides was built from two different peptide sequences, KGK and KKK, with a variety of different lipids selected to probe the effectiveness of both hydrocarbon and fluorinated tails. The antimicrobial activity of each peptide was tested against a mixture of pathogenic and reference bacterial strains, with the cationic disinfectant benzalkonium chloride as a positive control. Non-specific interactions with hydrophobic proteins were assessed by repeating antimicrobial testing in the presence of bovine serum albumin (BSA), and the toxicity of the lipopeptides was assessed by measuring lysis of ovine erythrocytes. Peptide sequence had a moderate effect on activity, with the most active peptide (C16-KGK) inhibiting the growth of two Staphylococcus epidermidis strains at ≤ 0.25 μg/mL. Tail composition was less important than the overall hydrophobicity, with the most active fluorinated tails equivalent to moderately active hydrocarbon tails. The activity of all peptides was significantly reduced by the presence of BSA, and haemolysis was closely correlated with antimicrobial activity.
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Affiliation(s)
- Brandon Findlay
- Department of Chemistry, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
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50
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Buer BC, Marsh ENG. Fluorine: a new element in protein design. Protein Sci 2012; 21:453-62. [PMID: 22274989 PMCID: PMC3375745 DOI: 10.1002/pro.2030] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 01/09/2012] [Indexed: 11/08/2022]
Abstract
Fluorocarbons are quintessentially man-made molecules, fluorine being all but absent from biology. Perfluorinated molecules exhibit novel physicochemical properties that include extreme chemical inertness, thermal stability, and an unusual propensity for phase segregation. The question we and others have sought to answer is to what extent can these properties be engineered into proteins? Here, we review recent studies in which proteins have been designed that incorporate highly fluorinated analogs of hydrophobic amino acids with the aim of creating proteins with novel chemical and biological properties. Fluorination seems to be a general and effective strategy to enhance the stability of proteins, both soluble and membrane bound, against chemical and thermal denaturation, although retaining structure and biological activity. Most studies have focused on small proteins that can be produced by peptide synthesis as synthesis of large proteins containing specifically fluorinated residues remains challenging. However, the development of various biosynthetic methods for introducing noncanonical amino acids into proteins promises to expand the utility of fluorinated amino acids in protein design.
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Affiliation(s)
- Benjamin C Buer
- Department of Chemistry, University of MichiganAnn Arbor, Michigan 48109
| | - E Neil G Marsh
- Department of Chemistry, University of MichiganAnn Arbor, Michigan 48109
- Department of Biological Chemistry, University of Michigan Medical SchoolAnn Arbor, Michigan 48109
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