1
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Krishna Sudhakar H, Yau JTK, Alcock LJ, Lau YH. Accessing diverse bicyclic peptide conformations using 1,2,3-TBMB as a linker. Org Biomol Chem 2024. [PMID: 39007293 DOI: 10.1039/d4ob00901k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Bicyclic peptides are a powerful modality for engaging challenging drug targets such as protein-protein interactions. Here, we use 1,2,3-tris(bromomethyl)benzene (1,2,3-TBMB) to access bicyclic peptides with diverse conformations that differ from conventional bicyclisation products formed with 1,3,5-TBMB. Bicyclisation at cysteine residues under aqueous buffer conditions proceeds efficiently, with broad substrate scope, compatibility with high-throughput screening, and clean conversion (>90%) for 96 of the 115 peptides tested. We envisage that the 1,2,3-TBMB linker will be applicable to a variety of peptide screening techniques in drug discovery.
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Affiliation(s)
| | - Jackie Tsz Ki Yau
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia.
| | - Lisa J Alcock
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia.
| | - Yu Heng Lau
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia.
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Camperdown, NSW 2006, Australia.
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2
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Zeng P, Wang H, Zhang P, Leung SSY. Unearthing naturally-occurring cyclic antibacterial peptides and their structural optimization strategies. Biotechnol Adv 2024; 73:108371. [PMID: 38704105 DOI: 10.1016/j.biotechadv.2024.108371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 03/08/2024] [Accepted: 04/29/2024] [Indexed: 05/06/2024]
Abstract
Natural products with antibacterial activity are highly desired globally to combat against multidrug-resistant (MDR) bacteria. Antibacterial peptide (ABP), especially cyclic ABP (CABP), is one of the abundant classes. Most of them were isolated from microbes, demonstrating excellent bactericidal effects. With the improved proteolytic stability, CABPs are normally considered to have better druggability than linear peptides. However, most clinically-used CABP-based antibiotics, such as colistin, also face the challenges of drug resistance soon after they reached the market, urgently requiring the development of next-generation succedaneums. We present here a detail review on the novel naturally-occurring CABPs discovered in the past decade and some of them are under clinical trials, exhibiting anticipated application potential. According to their chemical structures, they were broadly classified into five groups, including (i) lactam/lactone-based CABPs, (ii) cyclic lipopeptides, (iii) glycopeptides, (iv) cyclic sulfur-rich peptides and (v) multiple-modified CABPs. Their chemical structures, antibacterial spectrums and proposed mechanisms are discussed. Moreover, engineered analogs of these novel CABPs are also summarized to preliminarily analyze their structure-activity relationship. This review aims to provide a global perspective on research and development of novel CABPs to highlight the effectiveness of derivatives design in identifying promising antibacterial agents. Further research efforts in this area are believed to play important roles in fighting against the multidrug-resistance crisis.
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Affiliation(s)
- Ping Zeng
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Honglan Wang
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Pengfei Zhang
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Sharon Shui Yee Leung
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong.
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3
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Cochrane W, Fitzgerald PR, Paegel BM. Antibacterial Discovery via Phenotypic DNA-Encoded Library Screening. ACS Chem Biol 2021; 16:2752-2756. [PMID: 34806373 PMCID: PMC8688339 DOI: 10.1021/acschembio.1c00714] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The global rise of multidrug resistant infections poses an imminent, existential threat. Numerous pipelines have failed to convert biochemically active molecules into bona fide antibacterials, owing to a lack of chemical material with antibacterial-like physical properties in high-throughput screening compound libraries. Here, we demonstrate scalable design and synthesis of an antibacterial-like solid-phase DNA-encoded library (DEL, 7488 members) and facile hit deconvolution from whole-cell Escherichia coli and Bacillus subtilis cytotoxicity screens. The screen output identified two low-micromolar inhibitors of B. subtilis growth and recapitulated known structure-activity relationships of the fluoroquinolone antibacterial class. This phenotypic DEL screening strategy is also potentially applicable to adherent cells and will broadly enable the discovery and optimization of cell-active molecules.
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Affiliation(s)
- Wesley
G. Cochrane
- Department
of Pharmaceutical Sciences, University of
California, Irvine, California 92697, United States
| | - Patrick R. Fitzgerald
- Skaggs
Doctoral Program in the Chemical and Biological Sciences, Scripps Research, La Jolla, California 92037, United States
| | - Brian M. Paegel
- Department
of Pharmaceutical Sciences, University of
California, Irvine, California 92697, United States
- Departments
of Chemistry & Biomedical Engineering, University of California, Irvine, California 92697, United States
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4
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Itoh H, Inoue M. Development of a High-Throughput Strategy for Functional Enhancement and Alteration of Antibacterial Natural Products. J SYN ORG CHEM JPN 2021. [DOI: 10.5059/yukigoseikyokaishi.79.996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Masayuki Inoue
- Graduate School of Pharmaceutical Sciences, The University of Tokyo
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5
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Just‐Baringo X, Yeste‐Vázquez A, Moreno‐Morales J, Ballesté‐Delpierre C, Vila J, Giralt E. Controlling Antibacterial Activity Exclusively with Visible Light: Introducing a Tetra-ortho-Chloro-Azobenzene Amino Acid. Chemistry 2021; 27:12987-12991. [PMID: 34227716 PMCID: PMC8518743 DOI: 10.1002/chem.202102370] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Indexed: 11/30/2022]
Abstract
The introduction of a novel tetra-ortho-chloroazobenzene amino acid (CEBA) has enabled photoswitching of the antimicrobial activity of tyrocidine A analogues by using exclusively visible light, granting spatiotemporal control under benign conditions. Compounds bearing this photoswitchable amino acid become active upon irradiation with red light, but quickly turn-off upon exposure to other visible light wavelengths. Critically, sunlight quickly triggers isomerisation of the red light-activated compounds into their original trans form, offering an ideal platform for self-deactivation upon release into the environment. Linear analogues of tyrocidine A were found to provide the best photocontrol of their antimicrobial activity, leading to compounds active against Acinetobacter baumannii upon isomerisation. Exploration of their N- and C-termini has provided insights into key elements of their structure and has allowed obtaining new antimicrobials displaying excellent strain selectivity and photocontrol.
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Affiliation(s)
- Xavier Just‐Baringo
- Institute for Research in Biomedicine (IRB Barcelona)Barcelona Institute of Science and Technology (BIST)Baldiri Reixac 1008028BarcelonaSpain
- Laboratori de Química OrgànicaFacultat de FarmàciaIBUBUniversitat de Barcelona08028BarcelonaSpain
| | - Alejandro Yeste‐Vázquez
- Institute for Research in Biomedicine (IRB Barcelona)Barcelona Institute of Science and Technology (BIST)Baldiri Reixac 1008028BarcelonaSpain
| | - Javier Moreno‐Morales
- Institute for Global Health (ISGlobal)Hospital Clínic - Universitat de BarcelonaBarcelonaSpain
| | | | - Jordi Vila
- Institute for Global Health (ISGlobal)Hospital Clínic - Universitat de BarcelonaBarcelonaSpain
- Department of Clinical Microbiology – CDBHospital Clínic - University of BarcelonaBarcelonaSpain
| | - Ernest Giralt
- Institute for Research in Biomedicine (IRB Barcelona)Barcelona Institute of Science and Technology (BIST)Baldiri Reixac 1008028BarcelonaSpain
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6
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Zhu J, Hu C, Zeng Z, Deng X, Zeng L, Xie S, Fang Y, Jin Y, Alezra V, Wan Y. Polymyxin B-inspired non-hemolytic tyrocidine A analogues with significantly enhanced activity against gram-negative bacteria: How cationicity impacts cell specificity and antibacterial mechanism. Eur J Med Chem 2021; 221:113488. [PMID: 33991963 DOI: 10.1016/j.ejmech.2021.113488] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 03/31/2021] [Accepted: 04/18/2021] [Indexed: 11/25/2022]
Abstract
Naturally occurring cyclic antimicrobial peptides (AMPs) such as tyrocidine A (Tyrc A) and gramicidin S (GS) are appealing targets for the development of novel antibiotics. However, their therapeutic potentials are limited by undesired hemolytic activity and relatively poor activity against Gram-negative bacteria. Inspired by polycationic lipopeptide polymyxin B (PMB), the so called 'last-resort' antibiotic for the treatment of infections caused by multidrug-resistant Gram-negative bacteria, we synthesized and biologically evaluated a series of polycationic analogues derived from Tyrc A. We were able to obtain peptide 8 that possesses 5 positive charges exhibiting potent activities against both Gram-negative and Gram-positive bacteria along with totally diminished hemolytic activity. Intriguingly, antibacterial mechanism studies revealed that, rather than the 'pore forming' model that possessed by Tyrc A, peptide 8 likely diffuses membrane in a 'detergent-like' manner. Furthermore, when treating mice with peritonitis-sepsis, peptide 8 showed excellent antibacterial and anti-inflammatory activities in vivo.
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Affiliation(s)
- Jibao Zhu
- National Pharmaceutical Engineering Center for Solid Preparation in Chinese Herbal Medicine, Jiangxi University of Traditional Chinese Medicine, Nanchang, 330004, PR China
| | - Chengfei Hu
- National Pharmaceutical Engineering Center for Solid Preparation in Chinese Herbal Medicine, Jiangxi University of Traditional Chinese Medicine, Nanchang, 330004, PR China
| | - Zizhen Zeng
- National Pharmaceutical Engineering Center for Solid Preparation in Chinese Herbal Medicine, Jiangxi University of Traditional Chinese Medicine, Nanchang, 330004, PR China
| | - Xiaoyu Deng
- Minist Educ, Key Lab Modern Preparat TCM, Jiangxi University of Traditional Chinese Medicine, Nanchang, 330004, PR China
| | - Lingbing Zeng
- Department of Clinical Laboratory, The First Affiliated Hospital of Nanchang University, 17 Yongwaizheng Street, Donghu, Nanchang, 330006, PR China
| | - Saisai Xie
- National Pharmaceutical Engineering Center for Solid Preparation in Chinese Herbal Medicine, Jiangxi University of Traditional Chinese Medicine, Nanchang, 330004, PR China
| | - Yuanying Fang
- National Pharmaceutical Engineering Center for Solid Preparation in Chinese Herbal Medicine, Jiangxi University of Traditional Chinese Medicine, Nanchang, 330004, PR China
| | - Yi Jin
- National Pharmaceutical Engineering Center for Solid Preparation in Chinese Herbal Medicine, Jiangxi University of Traditional Chinese Medicine, Nanchang, 330004, PR China
| | - Valérie Alezra
- Laboratoire de Méthodologie, Synthèse et Molécules Thérapeutiques (ICMMO), UMR 8182, CNRS, Université Paris-Saclay, Bât 410, Facultédes Sciences D'Orsay, Orsay, 291405, France
| | - Yang Wan
- National Pharmaceutical Engineering Center for Solid Preparation in Chinese Herbal Medicine, Jiangxi University of Traditional Chinese Medicine, Nanchang, 330004, PR China; Laboratoire de Méthodologie, Synthèse et Molécules Thérapeutiques (ICMMO), UMR 8182, CNRS, Université Paris-Saclay, Bât 410, Facultédes Sciences D'Orsay, Orsay, 291405, France; State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Guangxi Normal University, 15 Yuchai Road, Guilin, 541004, PR China.
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7
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Covas C, Almeida B, Esteves AC, Lourenço J, Domingues P, Caetano T, Mendo S. Peptone from casein, an antagonist of nonribosomal peptide synthesis: a case study of pedopeptins produced by Pedobacter lusitanus NL19. N Biotechnol 2020; 60:62-71. [PMID: 32891869 DOI: 10.1016/j.nbt.2020.07.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/20/2020] [Accepted: 07/25/2020] [Indexed: 01/30/2023]
Abstract
Novel natural products are urgently needed to address the worldwide incidence of bacterial resistance to antibiotics. Extreme environments are a major source of novel compounds with unusual chemical structures. Pedobacter lusitanus NL19 is a new bacterial species that was isolated from one such environment and which produces compounds with potent activity against relevant microorganisms in the clinical, food, veterinary and aquaculture areas. The production of antimicrobials by P. lusitanus NL19 was identified in tryptic soy agar (TSA), but not in its equivalent broth (TSB). It was observed that in TSB medium a high concentration of casein peptone (PC) repressed the production of antibacterial compounds. HPLC, MS and MS/MS spectra with de novo sequencing revealed that the bioactivity of P. lusitanus NL19 was due to the production of pedopeptins. Hence, biosynthesis of pedopeptins is inhibited by high concentrations of PC in the broth medium. Furthermore, a nonribosomal peptide synthetase (NRPS) gene cluster was identified in the genome of NL19 encoding the biosynthesis of the peptides. qPCR analysis confirmed that the transcription of these genes is repressed in cells cultivated in high concentrations of PC. It is shown that pedopeptins are nonribosomal peptides with a broad-spectrum activity, including against Gram-positive and Gram-negative bacteria and yeasts.
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Affiliation(s)
- Cláudia Covas
- CESAM and Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Beatriz Almeida
- CESAM and Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Ana Cristina Esteves
- CESAM and Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal; Universidade Católica Portuguesa, Faculty of Dental Medicine, Center for Interdisciplinary Research in Health (CIIS), Portugal
| | - Joana Lourenço
- CESAM and Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Pedro Domingues
- Mass Spectrometry Centre and LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, Aveiro, 3810-193, Portugal
| | - Tânia Caetano
- CESAM and Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Sónia Mendo
- CESAM and Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.
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8
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Development of a high-throughput strategy for discovery of potent analogues of antibiotic lysocin E. Nat Commun 2019; 10:2992. [PMID: 31278250 PMCID: PMC6611794 DOI: 10.1038/s41467-019-10754-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 05/30/2019] [Indexed: 12/13/2022] Open
Abstract
Lysocin E, a 37-membered natural depsipeptide, induces rapid bacteriolysis in methicillin-resistant Staphylococcus aureus via a unique menaquinone-dependent mechanism, presenting a promising therapeutic lead. Despite the great medical importance, exploring the potential utility of its derivatives as new platform structures for antibiotic development has remained a significant challenge. Here, we report a high-throughput strategy that enabled the preparation of thousands of analogues of lysocin E and large-scale structure-activity relationship analyses. We integrate 26-step total synthesis of 2401 cyclic peptides, tandem mass spectrometry-sequencing, and two microscale activity assays to identify 23 candidate compounds. Re-synthesis of these candidates shows that 11 of them (A1-A11) exhibit antimicrobial activity superior or comparable to that of lysocin E, and that lysocin E and A1-A11 share L-Leu-6 and L-Ile-11. Therefore, the present strategy allows us to efficiently decipher biologically crucial residues and identify potentially useful agents for the treatment of infectious diseases.
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9
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Cheah HL, Raabe CA, Lee LP, Rozhdestvensky TS, Citartan M, Ahmed SA, Tang TH. Bacterial regulatory RNAs: complexity, function, and putative drug targeting. Crit Rev Biochem Mol Biol 2018; 53:335-355. [PMID: 29793351 DOI: 10.1080/10409238.2018.1473330] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Over the past decade, RNA-deep sequencing has uncovered copious non-protein coding RNAs (npcRNAs) in bacteria. Many of them are key players in the regulation of gene expression, taking part in various regulatory circuits, such as metabolic responses to different environmental stresses, virulence, antibiotic resistance, and host-pathogen interactions. This has contributed to the high adaptability of bacteria to changing or even hostile environments. Their mechanisms include the regulation of transcriptional termination, modulation of translation, and alteration of messenger RNA (mRNA) stability, as well as protein sequestration. Here, the mechanisms of gene expression by regulatory bacterial npcRNAs are comprehensively reviewed and supplemented with well-characterized examples. This class of molecules and their mechanisms of action might be useful targets for the development of novel antibiotics.
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Affiliation(s)
- Hong-Leong Cheah
- a Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia , Kepala Batas , Malaysia
| | - Carsten A Raabe
- b Institute of Experimental Pathology, Centre for Molecular Biology of Inflammation , University of Münster , Münster , Germany.,c Brandenburg Medical School (MHB) , Neuruppin , Germany.,d Institute of Medical Biochemistry, Centre for Molecular Biology of Inflammation , University of Münster , Münster , Germany
| | - Li-Pin Lee
- a Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia , Kepala Batas , Malaysia
| | - Timofey S Rozhdestvensky
- e Medical Faculty, Transgenic Mouse and Genome Engineering Model Core Facility (TRAM) , University of Münster , Münster , Germany
| | - Marimuthu Citartan
- a Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia , Kepala Batas , Malaysia
| | - Siti Aminah Ahmed
- a Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia , Kepala Batas , Malaysia
| | - Thean-Hock Tang
- a Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia , Kepala Batas , Malaysia
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10
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A novel in vitro metric predicts in vivo efficacy of inhaled silver-based antimicrobials in a murine Pseudomonas aeruginosa pneumonia model. Sci Rep 2018; 8:6376. [PMID: 29686296 PMCID: PMC5913254 DOI: 10.1038/s41598-018-24200-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 03/19/2018] [Indexed: 11/08/2022] Open
Abstract
To address the escalating problem of antimicrobial resistance and the dwindling antimicrobial pipeline, we have developed a library of novel aerosolizable silver-based antimicrobials, particularly for the treatment of pulmonary infections. To rapidly screen this library and identify promising candidates, we have devised a novel in vitro metric, named the “drug efficacy metric” (DEM), which integrates both the antibacterial activity and the on-target, host cell cytotoxicity. DEMs calculated using an on-target human bronchial epithelial cell-line correlates well (R2 > 0.99) with in vivo efficacy, as measured by median survival hours in a Pseudomonas aeruginosa pneumonia mouse model following aerosolized antimicrobial treatment. In contrast, DEMs derived using off-target primary human dermal fibroblasts correlate poorly (R2 = 0.0595), which confirms our hypothesis. SCC1 and SCC22 have been identified as promising drug candidates through these studies, and SCC22 demonstrates a dose-dependent survival advantage compared to sham treatment. Finally, silver-bearing biodegradable nanoparticles were predicted to exhibit excellent in vivo efficacy based on its in vitro DEM value, which was confirmed in our mouse pneumonia model. Thus, the DEM successfully predicted the efficacy of various silver-based antimicrobials, and may serve as an excellent tool for the rapid screening of potential antimicrobial candidates without the need for extensive animal experimentation.
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11
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Cameron AJ, Edwards PJB, Harjes E, Sarojini V. Tyrocidine A Analogues Bearing the Planar d-Phe-2-Abz Turn Motif: How Conformation Impacts Bioactivity. J Med Chem 2017; 60:9565-9574. [DOI: 10.1021/acs.jmedchem.7b00953] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Alan J. Cameron
- School
of Chemical Sciences, University of Auckland, Auckland 1142, New Zealand
| | - Patrick J. B. Edwards
- Institute
of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Elena Harjes
- Institute
of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
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12
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Gürbüz MU, Aghatabay NM, Karabulut HRF. Synthesis, Structural Aspects, Antimicrobial Activity, and Ion Transport Investigations of Four New [1 + 1] Condensed 12-Membered Cyclophane Amides. J Heterocycl Chem 2017. [DOI: 10.1002/jhet.2659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Mustafa Ulvi Gürbüz
- Department of Chemistry; Yildiz Technical University Beşiktaş; Istanbul 34349 Turkey
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13
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The importance of cyclic structure for Labaditin on its antimicrobial activity against Staphylococcus aureus. Colloids Surf B Biointerfaces 2016; 148:453-459. [PMID: 27665378 DOI: 10.1016/j.colsurfb.2016.09.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 09/04/2016] [Accepted: 09/11/2016] [Indexed: 01/24/2023]
Abstract
Antimicrobial resistance has reached alarming levels in many countries, thus leading to a search for new classes of antibiotics, such as antimicrobial peptides whose activity is exerted by interacting specifically with the microorganism membrane. In this study, we investigate the molecular-level mechanism of action for Labaditin (Lo), a 10-amino acid residue cyclic peptide from Jatropha multifida with known bactericidal activity against Streptococcus mutans. We show that Lo is also effective against Staphylococcus aureus (S. aureus) but this does not apply to its linear analogue (L1). Using polarization-modulated infrared reflection absorption spectroscopy (PM-IRRAS), we observed with that the secondary structure of Lo was preserved upon interacting with Langmuir monolayers from a phospholipid mixture mimicking S. aureus membrane, in contrast to L1. This structure preservation for the rigid, cyclic Lo is key for the self-assembly of peptide nanotubes that induce pore formation in large unilamellar vesicles (LUVs), according to permeability assays and dynamic light scattering measurements. In summary, the comparison between Labaditin (Lo) and its linear analogue L1 allowed us to infer that the bactericidal activity of Lo is more related to its interaction with the membrane. It does not require specific metabolic targets, which makes cyclic peptides promising for antibiotics without bacteria resistance.
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14
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Li X, Krafczyk R, Macošek J, Li YL, Zou Y, Simon B, Pan X, Wu QY, Yan F, Li S, Hennig J, Jung K, Lassak J, Hu HG. Resolving the α-glycosidic linkage of arginine-rhamnosylated translation elongation factor P triggers generation of the first Arg Rha specific antibody. Chem Sci 2016; 7:6995-7001. [PMID: 28451135 PMCID: PMC5363779 DOI: 10.1039/c6sc02889f] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 07/20/2016] [Indexed: 12/23/2022] Open
Abstract
A previously discovered posttranslational modification strategy - arginine rhamnosylation - is essential for elongation factor P (EF-P) dependent rescue of polyproline stalled ribosomes in clinically relevant species such as Pseudomonas aeruginosa and Neisseria meningitidis. However, almost nothing is known about this new type of N-linked glycosylation. In the present study we used NMR spectroscopy to show for the first time that the α anomer of rhamnose is attached to Arg32 of EF-P, demonstrating that the corresponding glycosyltransferase EarP inverts the sugar of its cognate substrate dTDP-β-l-rhamnose. Based on this finding we describe the synthesis of an α-rhamnosylated arginine containing peptide antigen in order to raise the first anti-rhamnosyl arginine specific antibody (anti-ArgRha). Using ELISA and Western Blot analyses we demonstrated both its high affinity and specificity without any cross-reactivity to other N-glycosylated proteins. Having the anti-ArgRha at hand we were able to visualize endogenously produced rhamnosylated EF-P. Thus, we expect the antibody to be not only important to monitor EF-P rhamnosylation in diverse bacteria but also to identify further rhamnosyl arginine containing proteins. As EF-P rhamnosylation is essential for pathogenicity, our antibody might also be a powerful tool in drug discovery.
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Affiliation(s)
- Xiang Li
- Department of Organic Chemistry , School of Pharmacy , Second Military Medical University , Shanghai 200433 , China .
| | - Ralph Krafczyk
- Department of Biology I, Microbiology , Ludwig Maximilians-Universität München , Munich , Germany.,Center for Integrated Protein Science Munich , Ludwig-Maximilians-Universität München , Munich , Germany .
| | - Jakub Macošek
- Structural and Computational Biology Unit , EMBL Heidelberg , Heidelberg 69117 , Germany
| | - Yu-Lei Li
- Department of Organic Chemistry , School of Pharmacy , Second Military Medical University , Shanghai 200433 , China . .,School of Pharmacy , Wei Fang Medical University , Shandong 261053 , China
| | - Yan Zou
- Department of Organic Chemistry , School of Pharmacy , Second Military Medical University , Shanghai 200433 , China .
| | - Bernd Simon
- Structural and Computational Biology Unit , EMBL Heidelberg , Heidelberg 69117 , Germany
| | - Xing Pan
- Institute of Infection and Immunity , Taihe Hospital , Hubei University of Medicine , Shiyan , Hubei 442000 , China
| | - Qiu-Ye Wu
- Department of Organic Chemistry , School of Pharmacy , Second Military Medical University , Shanghai 200433 , China .
| | - Fang Yan
- School of Pharmacy , Wei Fang Medical University , Shandong 261053 , China
| | - Shan Li
- Institute of Infection and Immunity , Taihe Hospital , Hubei University of Medicine , Shiyan , Hubei 442000 , China
| | - Janosch Hennig
- Structural and Computational Biology Unit , EMBL Heidelberg , Heidelberg 69117 , Germany
| | - Kirsten Jung
- Department of Biology I, Microbiology , Ludwig Maximilians-Universität München , Munich , Germany.,Center for Integrated Protein Science Munich , Ludwig-Maximilians-Universität München , Munich , Germany .
| | - Jürgen Lassak
- Department of Biology I, Microbiology , Ludwig Maximilians-Universität München , Munich , Germany.,Center for Integrated Protein Science Munich , Ludwig-Maximilians-Universität München , Munich , Germany .
| | - Hong-Gang Hu
- Department of Organic Chemistry , School of Pharmacy , Second Military Medical University , Shanghai 200433 , China .
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15
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Morimoto J, Kodadek T. Synthesis of a large library of macrocyclic peptides containing multiple and diverse N-alkylated residues. MOLECULAR BIOSYSTEMS 2016; 11:2770-9. [PMID: 26067000 DOI: 10.1039/c5mb00308c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Large combinatorial libraries of macrocyclic peptides are a useful source of bioactive compounds. However, peptides are not generally cell permeable, so there is great interest in the development of methods to create large libraries of modified peptides. In particular, N-alkylation of peptides is known to improve their bioavailability significantly. Incorporation of some level of N-methylated amino acids into peptide libraries has been accomplished with ribosome display or related methods, but the modest efficiency and the inability to employ more diverse N-alkylated amino acids in this type of system argue for the development of synthetic libraries. Here we present optimized procedures for synthesizing macrocyclic peptides containing multiple N-alkylated units and show that this chemistry is efficient enough for the creation of high quality combinatorial libraries by split and pool solid-phase synthesis.
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Affiliation(s)
- Jumpei Morimoto
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
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16
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Zou Y, Zhao Q, Zhang C, Wang L, Li W, Li X, Wu Q, Hu H. Synthesis and antibacterial activities of novel tyrocidine A glycosylated derivatives towards multidrug-resistant pathogens. J Pept Sci 2015; 21:586-92. [DOI: 10.1002/psc.2774] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 02/27/2015] [Accepted: 03/02/2015] [Indexed: 01/26/2023]
Affiliation(s)
- Yan Zou
- Department of Organic Chemistry, School of Pharmacy; Second Military Medical University; Shanghai 200433 China
| | - Qingjie Zhao
- Department of Organic Chemistry, School of Pharmacy; Second Military Medical University; Shanghai 200433 China
| | - Chunmei Zhang
- Department of Organic Chemistry, School of Pharmacy; Second Military Medical University; Shanghai 200433 China
| | - Liang Wang
- Department of Organic Chemistry, School of Pharmacy; Second Military Medical University; Shanghai 200433 China
| | - Wenjuan Li
- Department of Organic Chemistry, School of Pharmacy; Second Military Medical University; Shanghai 200433 China
| | - Xiang Li
- Department of Organic Chemistry, School of Pharmacy; Second Military Medical University; Shanghai 200433 China
| | - Qiuye Wu
- Department of Organic Chemistry, School of Pharmacy; Second Military Medical University; Shanghai 200433 China
| | - Honggang Hu
- Department of Organic Chemistry, School of Pharmacy; Second Military Medical University; Shanghai 200433 China
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17
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18
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Gao Y, Kodadek T. Direct comparison of linear and macrocyclic compound libraries as a source of protein ligands. ACS COMBINATORIAL SCIENCE 2015; 17:190-5. [PMID: 25623285 PMCID: PMC4356041 DOI: 10.1021/co500161c] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
There has been much discussion of
the potential desirability of
macrocyclic molecules for the development of tool compounds and drug
leads. But there is little experimental data comparing otherwise equivalent
macrocyclic and linear compound libraries as a source of protein ligands.
In this Letter, we probe this point in the context of peptoid libraries.
Bead-displayed libraries of macrocyclic and linear peptoids containing
four variable positions and 0–2 fixed residues, to vary the
ring size, were screened against streptavidin and the affinity of
every hit for the target was measured. The data show that macrocyclization
is advantageous, but only when the ring contains 17 atoms, not 20
or 23 atoms. This technology will be useful for conducting direct
comparisons between many different types of chemical libraries to
determine their relative utility as a source of protein ligands.
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Affiliation(s)
- Yu Gao
- Departments of Chemistry
and Cancer Biology, The Scripps Research Institute, 130 Scripps
Way, Jupiter, Florida 33458, United States
| | - Thomas Kodadek
- Departments of Chemistry
and Cancer Biology, The Scripps Research Institute, 130 Scripps
Way, Jupiter, Florida 33458, United States
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19
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Zhao Q, Li X, Li W, Zou Y, Hu H, Wu Q. A facile and efficient method for synthesis of macrocyclic lipoglycopeptide. Tetrahedron 2015. [DOI: 10.1016/j.tet.2014.12.097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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20
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Interaction of cyclic and linear Labaditin peptides with anionic and zwitterionic micelles. J Colloid Interface Sci 2015; 438:39-46. [PMID: 25454423 DOI: 10.1016/j.jcis.2014.09.059] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2014] [Revised: 09/15/2014] [Accepted: 09/17/2014] [Indexed: 01/31/2023]
Abstract
Conformational changes of the cyclic (Lo) peptide Labaditin (VWTVWGTIAG) and its linear analogue (L1) promoted by presence of anionic sodium dodecyl sulfate (SDS) and zwitterionic L-α-Lysophosphatidylcholine (LPC) micelles were investigated. Results from λ(max) blue-shift of tryptophan fluorescence emission combined with Stern-Volmer constants values and molecular dynamics (MD) simulations indicated that L1 interacts with SDS micelles to a higher extent than does Lo. Further, the MD simulation demonstrated that both Lo and L1 interact similarly with LPC micelles, being preferentially located at the micelle/water interface. The peptide-micelle interaction elicits conformational changes in the peptides. Lo undergoes limited modifications and presents unordered structure in both LPC and SDS micelles. On the other hand, L1 displays a random-coil structure in aqueous medium, pH 7.0, and it acquires a β-structure upon interaction with SDS and LPC, albeit with structural differences in each medium.
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21
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Foster AD, Ingram JD, Leitch EK, Lennard KR, Osher EL, Tavassoli A. Methods for the Creation of Cyclic Peptide Libraries for Use in Lead Discovery. ACTA ACUST UNITED AC 2015; 20:563-76. [DOI: 10.1177/1087057114566803] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 12/11/2014] [Indexed: 12/23/2022]
Abstract
The identification of initial hits is a crucial stage in the drug discovery process. Although many projects adopt high-throughput screening of small-molecule libraries at this stage, there is significant potential for screening libraries of macromolecules created using chemical biology approaches. Not only can the production of the library be directly interfaced with a cell-based assay, but these libraries also require significantly fewer resources to generate and maintain. In this context, cyclic peptides are increasingly viewed as ideal scaffolds and have proven capability against challenging targets such as protein-protein interactions. Here we discuss a range of methods used for the creation of cyclic peptide libraries and detail examples of their successful implementation.
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Affiliation(s)
| | | | | | | | | | - Ali Tavassoli
- Chemistry, University of Southampton, Southampton, UK
- Cancer Sciences, University of Southampton, Southampton, UK
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22
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Duffy FJ, Devocelle M, Shields DC. Computational approaches to developing short cyclic peptide modulators of protein-protein interactions. Methods Mol Biol 2015; 1268:241-71. [PMID: 25555728 DOI: 10.1007/978-1-4939-2285-7_11] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Cyclic peptides are a promising class of bioactive molecules potentially capable of modulating "difficult" targets, such as protein-protein interactions. Cyclic peptides have long been used as therapeutics derived from natural product derivatives, but remain an underexplored class of compounds from the perspective of rational drug design, possibly due to the known weaknesses of peptide drugs in general. While cyclic peptides are non"druglike" by the accepted empirical rules, their unique structure may lend itself to both membrane permeability and proteolytic resistance-the main barriers to oral delivery. The constrained shape of cyclic peptides also lends itself better to virtual screening approaches, and new tools and successes in this area have been recently noted. An increasing number of strategies are available, both to generate and screen cyclic peptide libraries, and best practises and current successes are described within. This chapter will describe various computational strategies for virtual screening cyclic peptides, along with known implementations and applications. We will explore the generation and screening of diverse combinatorial virtual libraries, incorporating a range of cyclization strategies and structural modifications. More advanced approaches covered include evolutionary algorithms designed to aid in screening large structural libraries, machine learning approaches, and harnessing bioinformatics resources to bias cyclic peptide virtual libraries towards known bioactive structures.
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Affiliation(s)
- Fergal J Duffy
- School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
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23
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Hosseini AS, Zheng H, Gao J. Understanding Lipid Recognition by Protein-Mimicking Cyclic Peptides. Tetrahedron 2014; 70:7632-7638. [PMID: 25419010 DOI: 10.1016/j.tet.2014.07.104] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
This paper describes our investigation of the structural determinants of a designed cyclic peptide (cLac, cyclic peptide mimicking lactadherin)1 for phosphatidylserine (PS) recognition. A highly efficient strategy that takes advantage of the native chemical ligation (NCL) chemistry has been developed for the synthesis and labeling of cyclic peptides in general. Ala scanning of the cLac peptide revealed a sophisticated model for PS binding, in which the peptide scaffold assembles multiple polar residues to balance the desolvation and electrostatic interactions (salt bridge and hydrogen bonding) to achieve lipid selectivity. The results suggest that cLac effectively mimics the membrane binding mechanism of the parent protein lactadherin.
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Affiliation(s)
- Azade S Hosseini
- Department of Chemistry, Merkert Chemistry Center, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467
| | - Hong Zheng
- 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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24
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Duffy FJ, Devocelle M, Croucher DR, Shields DC. Computational survey of peptides derived from disulphide-bonded protein loops that may serve as mediators of protein-protein interactions. BMC Bioinformatics 2014; 15:305. [PMID: 25231912 PMCID: PMC4262234 DOI: 10.1186/1471-2105-15-305] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Accepted: 07/17/2014] [Indexed: 01/04/2023] Open
Abstract
Background Bioactive cyclic peptides derived from natural sources are well studied, particularly those derived from non-ribosomal synthetases in fungi or bacteria. Ribosomally synthesised bioactive disulphide-bonded loops represent a large, naturally enriched library of potential bioactive compounds, worthy of systematic investigation. Results We examined the distribution of short cyclic loops on the surface of a large number of proteins, especially membrane or extracellular proteins. Available three-dimensional structures highlighted a number of disulphide-bonded loops responsible for the majority of the likely binding interactions in a variety of protein complexes, due to their location at protein-protein interfaces. We find that disulphide-bonded loops at protein-protein interfaces may, but do not necessarily, show biological activity independent of their parent protein. Examining the conservation of short disulphide bonded loops in proteins, we find a small but significant increase in conservation inside these loops compared to surrounding residues. We identify a subset of these loops that exhibit a high relative conservation, particularly among peptide hormones. Conclusions We conclude that short disulphide-bonded loops are found in a wide variety of biological interactions. They may retain biological activity outside their parent proteins. Such structurally independent peptides may be useful as biologically active templates for the development of novel modulators of protein-protein interactions. Electronic supplementary material The online version of this article (doi:10.1186/1471-2105-15-305) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | - Denis C Shields
- School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland.
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25
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Joo SH. Cyclic peptides as therapeutic agents and biochemical tools. Biomol Ther (Seoul) 2014; 20:19-26. [PMID: 24116270 PMCID: PMC3792197 DOI: 10.4062/biomolther.2012.20.1.019] [Citation(s) in RCA: 218] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 10/10/2011] [Accepted: 10/28/2011] [Indexed: 01/08/2023] Open
Abstract
There are many cyclic peptides with diverse biological activities, such as antibacterial activity, immunosuppressive activity, and anti-tumor activity, and so on. Encouraged by natural cyclic peptides with biological activity, efforts have been made to develop cyclic peptides with both genetic and synthetic methods. The genetic methods include phage display, intein-based cyclic peptides, and mRNA display. The synthetic methods involve individual synthesis, parallel synthesis, as well as split-and-pool synthesis. Recent development of cyclic peptide library based on split-and-pool synthesis allows on-bead screening, in-solution screening, and microarray screening of cyclic peptides for biological activity. Cyclic peptides will be useful as receptor agonist/antagonist, RNA binding molecule, enzyme inhibitor and so on, and more cyclic peptides will emerge as therapeutic agents and biochemical tools.
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Affiliation(s)
- Sang Hoon Joo
- Laboratory of Biochemistry, College of Pharmacy, Catholic University of Daegu, Gyeongsan 712-702, Republic of Korea
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26
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Sun YS, Fei Y, Luo J, Dixon S, Landry JP, Lam KS, Zhu X. Generating Encoded Compound Libraries for Fabricating Microarrays as a High-Throughput Protein Ligand Discovery Platform. SYNTHETIC COMMUN 2014. [DOI: 10.1080/00397911.2013.840728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Yung-Shin Sun
- a Department of Physics , Fu-Jen Catholic University , New Taipei City , Taiwan
| | - Yiyan Fei
- b Department of Optical Science and Engineering , Fudan University , Shanghai , China
- c Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Department of Optical Science and Engineering, Shanghai Ultra-Precision Optical Manufacturing Engineering Center , Fudan University , Shanghai , China
| | - Juntao Luo
- d Department of Pharmacology , Upstate Cancer Research Institute, State University of New York Upstate Medical University , Syracuse , New York , USA
| | - Seth Dixon
- e Division of Hematology and Oncology, Department of Internal Medicine , School of Medicine, University of California at Davis , Sacramento , California , USA
| | - James P. Landry
- f Department of Physics , University of California at Davis , Davis , California , USA
| | - Kit S. Lam
- e Division of Hematology and Oncology, Department of Internal Medicine , School of Medicine, University of California at Davis , Sacramento , California , USA
- g Department of Biochemistry and Molecular Medicine , School of Medicine, University of California at Davis , Sacramento , California , USA
| | - Xiangdong Zhu
- f Department of Physics , University of California at Davis , Davis , California , USA
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27
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Loll PJ, Upton EC, Nahoum V, Economou NJ, Cocklin S. The high resolution structure of tyrocidine A reveals an amphipathic dimer. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:1199-207. [PMID: 24530898 DOI: 10.1016/j.bbamem.2014.01.033] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 01/20/2014] [Accepted: 01/27/2014] [Indexed: 11/28/2022]
Abstract
Tyrocidine A, one of the first antibiotics ever to be discovered, is a cyclic decapeptide that binds to membranes of target bacteria, disrupting their integrity. It is active against a broad spectrum of Gram-positive organisms, and has recently engendered interest as a potential scaffold for the development of new drugs to combat antibiotic-resistant pathogens. We present here the X-ray crystal structure of tyrocidine A at a resolution of 0.95Å. The structure reveals that tyrocidine forms an intimate and highly amphipathic homodimer made up of four beta strands that associate into a single, highly curved antiparallel beta sheet. We used surface plasmon resonance and potassium efflux assays to demonstrate that tyrocidine binds tightly to mimetics of bacterial membranes with an apparent dissociation constant (K(D)) of 10 μM, and efficiently permeabilizes bacterial cells at concentrations equal to and below the K(D). Using variant forms of tyrocidine in which the fluorescent probe p-cyano-phenylalanine had been inserted on either the polar or apolar face of the molecule, we performed fluorescence quenching experiments, using both water-soluble and membrane-embedded quenchers. The quenching results, together with the structure, strongly support a membrane association model in which the convex, apolar face of tyrocidine's beta sheet is oriented toward the membrane interior, while the concave, polar face is presented to the aqueous phase.
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Affiliation(s)
- Patrick J Loll
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA.
| | - Elizabeth C Upton
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Virginie Nahoum
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Nicoleta J Economou
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Simon Cocklin
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
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28
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Aghatabay NM, Parali Ö, Zaim Ö, Baydar Ç, Dülger B. Synthesis, structural aspects, antimicrobial activity and ion transportation investigation of four new [2 + 2] condensed 24-membered cycloheterphane peptides. J INCL PHENOM MACRO 2013. [DOI: 10.1007/s10847-013-0364-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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29
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Dipeptide cis-cyclo(Leucyl-Tyrosyl) produced by sponge associated Penicillium sp. F37 inhibits biofilm formation of the pathogenic Staphylococcus epidermidis. Bioorg Med Chem Lett 2013; 23:624-6. [DOI: 10.1016/j.bmcl.2012.12.020] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 11/27/2012] [Accepted: 12/10/2012] [Indexed: 11/17/2022]
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30
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Zaim Ö, Aghatabay NM, Gürbüz MU, Baydar Ç, Dülger B. Synthesis, structural aspects, antimicrobial activity and ion transport investigation of five new [1+1] condensed cycloheterophane peptides. J INCL PHENOM MACRO 2013. [DOI: 10.1007/s10847-012-0282-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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31
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Li Y, Dooley CT, Misler JA, Debevec G, Giulianotti MA, Cazares ME, Maida L, Houghten RA. Fluorescent mu selective opioid ligands from a mixture based cyclic peptide library. ACS COMBINATORIAL SCIENCE 2012; 14:673-9. [PMID: 23110623 DOI: 10.1021/co300110t] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A positional scanning cyclic peptide library was generated using a penta-peptide thioester scaffold. Glycine was fixed at position R(1). Diaminopropionic acid was fixed at position R(3), with its γ-amino attaching to an anthraniloyl group. Positions R(2) and R(4) contained 36 L- and D- amino acids and position R(5) contained 19 L- amino acids. Cyclization was performed in a mixture of acetonitrile and 1.5 M aqueous imidazole solution (7:1 v/v) at room temperature for 5 days. No significant cross-oligomerization was detected under the cyclization conditions. The library was screened in a binding assay for mu opioid receptor, identifying the active amino acid mixture at each position. A total of 40 individual cyclic peptides were identified and synthesized by the combinations of the most active amino acid mixtures found at three positions 5 × 4 × 2. Two cyclic peptides exhibited high binding affinities to opioid receptor. The most active cyclic peptide in the library was yielded to have Tyr at R(2), D-Lys at R(4), and Tyr at R(5). Further investigation on this compound revealed the side chain-to-tail isomer to have greater binding affinity (14 nM) than the head-to-tail isomer (39 nM). Both isomers were selective for the mu-opioid receptor.
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Affiliation(s)
- Yangmei Li
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port Saint Lucie, Florida 34987, United
States
| | - Colette T. Dooley
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port Saint Lucie, Florida 34987, United
States
| | - Jaime A. Misler
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port Saint Lucie, Florida 34987, United
States
| | - Ginamarie Debevec
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port Saint Lucie, Florida 34987, United
States
| | - Marc A. Giulianotti
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port Saint Lucie, Florida 34987, United
States
| | - Margaret E. Cazares
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port Saint Lucie, Florida 34987, United
States
| | - Laura Maida
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port Saint Lucie, Florida 34987, United
States
| | - Richard A. Houghten
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port Saint Lucie, Florida 34987, United
States
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32
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Synthesis, structural aspects, and antimicrobial activity investigation of novel macrocyclic amide-containing compounds. Chem Heterocycl Compd (N Y) 2012. [DOI: 10.1007/s10593-012-1080-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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33
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Simpson LS, Kodadek T. A Cleavable Scaffold Strategy for the Synthesis of One-Bead One-Compound Cyclic Peptoid Libraries That Can Be Sequenced By Tandem Mass Spectrometry. Tetrahedron Lett 2012; 53:2341-2344. [PMID: 22736872 DOI: 10.1016/j.tetlet.2012.02.112] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Many macrocyclic depsipeptides or related compounds have interesting medicinal properties and often display more favorable pharmacokinetic properties than linear analogues. Therefore, there is considerable interest in the development of large combinatorial libraries of macrocyclic peptidomimetic compounds. However, such molecules cannot be easily sequenced by tandem mass spectrometry, making it difficult to identify hits isolated from library screens using one bead one compound libraries. Here we report a strategy to solve this problem by placing a methionine in both the linker connecting the cyclic molecule to the bead as well as within the cycle itself. Treatment with CNBr both linearizes the molecule at a specific position and releases the molecule from the bead, making its characterization by tandem MALDI mass spectrometry straightforward.
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Affiliation(s)
- Levi S Simpson
- Department of Internal Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-9185
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34
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Abstract
This chapter outlines the evolution of high throughput chemistry from its origins in the genome revolution of the early 1990's to its current practice as an integral tool in drug discovery, via the concept of the large “universal library” to the practice of small targeted arrays for structure–activity relationship generation. The technologies developed as part of this evolution are also outlined including early ACT peptide synthesisers and other automated and non-automated devices for both solid-supported and solution-based approaches. Finally, the chapter outlines several case studies of the application of high throughput synthesis to drug discovery.
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35
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Hydrophobic tag-assisted liquid-phase synthesis of a growth hormone-inhibiting peptide somatostatin. Bioorg Med Chem Lett 2011; 21:4476-9. [DOI: 10.1016/j.bmcl.2011.06.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Revised: 05/24/2011] [Accepted: 06/01/2011] [Indexed: 01/18/2023]
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36
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Li Y, Giulionatti M, Houghten RA. Macrolactonization of peptide thioesters catalyzed by imidazole and its application in the synthesis of kahalalide B and analogues. Org Lett 2010; 12:2250-3. [PMID: 20426464 DOI: 10.1021/ol100596p] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The macrolactonization of peptide thioester to yield cyclic depsipeptides was developed using imidazole as a catalyst. This strategy was applied to the synthesis of kahalalide B and its analogues.
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Affiliation(s)
- Yangmei Li
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St. Lucie, Florida 34987, USA
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37
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Labaditin, a cyclic peptide with rich biotechnological potential: preliminary toxicological studies and structural changes in water and lipid membrane environment. Amino Acids 2010; 40:135-44. [DOI: 10.1007/s00726-010-0648-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2010] [Accepted: 06/01/2010] [Indexed: 01/25/2023]
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38
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39
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Hu H, Xue J, Swarts BM, Wang Q, Wu Q, Guo Z. Synthesis and Antibacterial Activities of N-Glycosylated Derivatives of Tyrocidine A, a Macrocyclic Peptide Antibiotic. J Med Chem 2009; 52:2052-9. [DOI: 10.1021/jm801577r] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Honggang Hu
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Jie Xue
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Benjamin M. Swarts
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Qianli Wang
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Qiuye Wu
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Zhongwu Guo
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, School of Pharmacy, Second Military Medical University, Shanghai 200433, China
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40
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Fluxa VS, Reymond JL. On-bead cyclization in a combinatorial library of 15,625 octapeptides. Bioorg Med Chem 2009; 17:1018-25. [DOI: 10.1016/j.bmc.2008.01.045] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2007] [Revised: 01/11/2008] [Accepted: 01/24/2008] [Indexed: 10/22/2022]
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41
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Driggers EM, Hale SP, Lee J, Terrett NK. The exploration of macrocycles for drug discovery — an underexploited structural class. Nat Rev Drug Discov 2008; 7:608-24. [DOI: 10.1038/nrd2590] [Citation(s) in RCA: 984] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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42
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Edwards P. Application of technologies and parallel chemistry for the generation of actives against biological targets. Drug Discov Today 2008. [DOI: 10.1016/j.drudis.2008.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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43
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Zhang Y, Zhou S, Wavreille AS, DeWille J, Pei D. Cyclic peptidyl inhibitors of Grb2 and tensin SH2 domains identified from combinatorial libraries. ACTA ACUST UNITED AC 2008; 10:247-55. [PMID: 18257540 DOI: 10.1021/cc700185g] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cyclic peptides provide attractive lead compounds for drug discovery and excellent molecular probes in biomedical research. In this work, a novel method has been developed for the high-throughput synthesis, screening, and identification of cyclic peptidyl ligands against macromolecular targets. Support-bound cyclic phosphotyrosyl peptide libraries containing randomized amino acid sequences and different ring sizes (theoretical diversity of 3.2 x 10(6)) were synthesized and screened against the SH2 domains of Grb2 and tensin. Potent, selective inhibitors were identified from the libraries and were generally more effective than the corresponding linear peptides. One of the inhibitors selected against the Grb2 SH2 domain inhibited human breast cancer cell growth and disrupted actin filaments. This method should be applicable to the development of cyclic peptidyl inhibitors against other protein domains, enzymes, and receptors.
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Affiliation(s)
- Yanyan Zhang
- Department of Chemistry and Ohio State Biochemistry Program, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA
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Liu T, Joo SH, Voorhees JL, Brooks CL, Pei D. Synthesis and screening of a cyclic peptide library: discovery of small-molecule ligands against human prolactin receptor. Bioorg Med Chem 2008; 17:1026-33. [PMID: 18234500 DOI: 10.1016/j.bmc.2008.01.015] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2007] [Revised: 01/09/2008] [Accepted: 01/10/2008] [Indexed: 11/18/2022]
Abstract
Prolactin receptor is involved in normal lactation and reproduction; however, excessive prolactin levels can cause various reproductive disorders such as prolactinomas. Small-molecule antagonists against the human prolactin receptor (hPRLr) thus have potential clinical applications and may serve as useful molecular probes in biomedical research. In this work, we synthesized a large, support-bound cyclic peptide library (theoretical diversity of 1.2x10(7)) on 90-microm TentaGel beads and screened it against the extracellular domain of hPRLr. To facilitate hit identification, each TentaGel bead was spatially segregated into outer and inner layers, with a cyclic peptide displayed on the bead surface while the bead interior contained the corresponding linear peptide. The identity of a positive bead was revealed by sequencing the linear encoding peptide within the bead by partial Edman degradation/mass spectrometry. Screening of the library resulted in 20 hits, two of which were selected for further analysis and shown to bind to hPRLr with dissociation constants of 2-3 microM.
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Affiliation(s)
- Tao Liu
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
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