1
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Alamdari-Palangi V, Jaberi KR, Shahverdi M, Naeimzadeh Y, Tajbakhsh A, Khajeh S, Razban V, Fallahi J. Recent advances and applications of peptide-agent conjugates for targeting tumor cells. J Cancer Res Clin Oncol 2023; 149:15249-15273. [PMID: 37581648 DOI: 10.1007/s00432-023-05144-9] [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: 05/23/2023] [Accepted: 07/08/2023] [Indexed: 08/16/2023]
Abstract
BACKGROUND Cancer, being a complex disease, presents a major challenge for the scientific and medical communities. Peptide therapeutics have played a significant role in different medical practices, including cancer treatment. METHOD This review provides an overview of the current situation and potential development prospects of anticancer peptides (ACPs), with a particular focus on peptide vaccines and peptide-drug conjugates for cancer treatment. RESULTS ACPs can be used directly as cytotoxic agents (molecularly targeted peptides) or can act as carriers (guiding missile) of chemotherapeutic agents and radionuclides by specifically targeting cancer cells. More than 60 natural and synthetic cationic peptides are approved in the USA and other major markets for the treatment of cancer and other diseases. Compared to traditional cancer treatments, peptides exhibit anticancer activity with high specificity and the ability to rapidly kill target cancer cells. ACP's target and kill cancer cells via different mechanisms, including membrane disruption, pore formation, induction of apoptosis, necrosis, autophagy, and regulation of the immune system. Modified peptides have been developed as carriers for drugs, vaccines, and peptide-drug conjugates, which have been evaluated in various phases of clinical trials for the treatment of different types of solid and leukemia cancer. CONCLUSIONS This review highlights the potential of ACPs as a promising therapeutic option for cancer treatment, particularly through the use of peptide vaccines and peptide-drug conjugates. Despite the limitations of peptides, such as poor metabolic stability and low bioavailability, modified peptides show promise in addressing these challenges. Various mechanism of action of anticancer peptides. Modes of action against cancer cells including: inducing apoptosis by cytochrome c release, direct cell membrane lysis (necrosis), inhibiting angiogenesis, inducing autophagy-mediated cell death and immune cell regulation.
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Affiliation(s)
- Vahab Alamdari-Palangi
- Department of Molecular Medicine, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, 7133654361, Iran
| | - Khojaste Rahimi Jaberi
- Department of Neuroscience, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mahshid Shahverdi
- Medical Biotechnology Research Center, Arak University of Medical Sciences, Arak, Iran
| | - Yasaman Naeimzadeh
- Department of Molecular Medicine, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, 7133654361, Iran
| | - Amir Tajbakhsh
- Department of Molecular Medicine, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, 7133654361, Iran
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sahar Khajeh
- Bone and Joint Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Vahid Razban
- Department of Molecular Medicine, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, 7133654361, Iran.
| | - Jafar Fallahi
- Department of Molecular Medicine, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, 7133654361, Iran.
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2
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Liu M, Yoshisada R, Amedi A, Hopstaken AJP, Pascha MN, de Haan CAM, Geerke DP, Poole DA, Jongkees SAK. An Efficient, Site-Selective and Spontaneous Peptide Macrocyclisation During in vitro Translation. Chemistry 2023; 29:e202203923. [PMID: 36529683 DOI: 10.1002/chem.202203923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 12/16/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022]
Abstract
Macrocyclisation provides a means of stabilising the conformation of peptides, often resulting in improved stability, selectivity, affinity, and cell permeability. In this work, a new approach to peptide macrocyclisation is reported, using a cyanobenzothiazole-containing amino acid that can be incorporated into peptides by both in vitro translation and solid phase peptide synthesis, meaning it should be applicable to peptide discovery by mRNA display. This cyclisation proceeds rapidly, with minimal by-products, is selective over other amino acids including non N-terminal cysteines, and is compatible with further peptide elaboration exploiting such an additional cysteine in bicyclisation and derivatisation reactions. Molecular dynamics simulations show that the new cyclisation group is likely to influence the peptide conformation as compared to previous thioether-based approaches, through rigidity and intramolecular aromatic interactions, illustrating their complementarity.
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Affiliation(s)
- Minglong Liu
- Chemistry and Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, 1081 HV, the Netherlands
| | - Ryoji Yoshisada
- Chemistry and Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, 1081 HV, the Netherlands
| | - Avand Amedi
- Department Chemical Biology and Drug Discovery and Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, Utrecht, 3584 CG, the Netherlands
| | - Antonius J P Hopstaken
- Chemistry and Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, 1081 HV, the Netherlands
| | - Mirte N Pascha
- Section Virology Division of Infectious Diseases and Immunology Department of Biomolecular Health Sciences Faculty of Veterinary Medicine, Utrecht University, Utrecht, 3584 CL, the Netherlands
| | - Cornelis A M de Haan
- Section Virology Division of Infectious Diseases and Immunology Department of Biomolecular Health Sciences Faculty of Veterinary Medicine, Utrecht University, Utrecht, 3584 CL, the Netherlands
| | - Daan P Geerke
- Chemistry and Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, 1081 HV, the Netherlands
| | - David A Poole
- Chemistry and Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, 1081 HV, the Netherlands
| | - Seino A K Jongkees
- Chemistry and Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, 1081 HV, the Netherlands.,Department Chemical Biology and Drug Discovery and Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, Utrecht, 3584 CG, the Netherlands
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3
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Fu C, Yu L, Miao Y, Liu X, Yu Z, Wei M. Peptide-drug conjugates (PDCs): a novel trend of research and development on targeted therapy, hype or hope? Acta Pharm Sin B 2023; 13:498-516. [PMID: 36873165 PMCID: PMC9978859 DOI: 10.1016/j.apsb.2022.07.020] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/16/2022] [Accepted: 07/11/2022] [Indexed: 11/01/2022] Open
Abstract
Peptide-drug conjugates (PDCs) are the next generation of targeted therapeutics drug after antibody-drug conjugates (ADCs), with the core benefits of enhanced cellular permeability and improved drug selectivity. Two drugs are now approved for market by US Food and Drug Administration (FDA), and in the last two years, the pharmaceutical companies have been developing PDCs as targeted therapeutic candidates for cancer, coronavirus disease 2019 (COVID-19), metabolic diseases, and so on. The therapeutic benefits of PDCs are significant, but poor stability, low bioactivity, long research and development time, and slow clinical development process as therapeutic agents of PDC, how can we design PDCs more effectively and what is the future direction of PDCs? This review summarises the components and functions of PDCs for therapeutic, from drug target screening and PDC design improvement strategies to clinical applications to improve the permeability, targeting, and stability of the various components of PDCs. This holds great promise for the future of PDCs, such as bicyclic peptide‒toxin coupling or supramolecular nanostructures for peptide-conjugated drugs. The mode of drug delivery is determined according to the PDC design and current clinical trials are summarised. The way is shown for future PDC development.
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Affiliation(s)
- Chen Fu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, China Medical University, Shenyang 110122, China
| | - Lifeng Yu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, China
| | - Yuxi Miao
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, China Medical University, Shenyang 110122, China.,Liaoning Medical Diagnosis and Treatment Center, Shenyang 110000, China
| | - Xinli Liu
- Department of Digestive Oncology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang 110042, China
| | - Zhaojin Yu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, China Medical University, Shenyang 110122, China
| | - Minjie Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, China Medical University, Shenyang 110122, China.,Liaoning Medical Diagnosis and Treatment Center, Shenyang 110000, China
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4
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Engineered protein-small molecule conjugates empower selective enzyme inhibition. Cell Chem Biol 2022; 29:328-338.e4. [PMID: 34363759 PMCID: PMC8807807 DOI: 10.1016/j.chembiol.2021.07.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/17/2021] [Accepted: 07/14/2021] [Indexed: 11/20/2022]
Abstract
Potent, specific ligands drive precision medicine and fundamental biology. Proteins, peptides, and small molecules constitute effective ligand classes. Yet greater molecular diversity would aid the pursuit of ligands to elicit precise biological activity against challenging targets. We demonstrate a platform to discover protein-small molecule (PriSM) hybrids to combine unique pharmacophore activities and shapes with constrained, efficiently engineerable proteins. In this platform, a fibronectin protein library is displayed on yeast with a single cysteine coupled to acetazolamide via a maleimide-poly(ethylene glycol) linker. Magnetic and flow cytometric sorts enrich specific binders to carbonic anhydrase isoforms. Isolated PriSMs exhibit potent, specific inhibition of carbonic anhydrase isoforms with efficacy superior to that of acetazolamide or protein alone, including an 80-fold specificity increase and 9-fold potency gain. PriSMs are engineered with multiple linker lengths, protein conjugation sites, and sequences against two different isoforms, which reveal platform flexibility and impacts of molecular designs. PriSMs advance the molecular diversity of efficiently engineerable ligands.
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5
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Melsen PRA, Yoshisada R, Jongkees SAK. Opportunities for expanding encoded chemical diversification and improving hit enrichment in mRNA-displayed peptide libraries. Chembiochem 2022; 23:e202100685. [PMID: 35100479 PMCID: PMC9306583 DOI: 10.1002/cbic.202100685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/27/2022] [Indexed: 11/07/2022]
Abstract
DNA‐encoded small‐molecule libraries and mRNA displayed peptide libraries both use numerically large pools of oligonucleotide‐tagged molecules to identify potential hits for protein targets. They differ dramatically, however, in the ‘drug‐likeness’ of the molecules that each can be used to discover. We give here an overview of the two techniques, comparing some advantages and disadvantages of each, and suggest areas where particularly mRNA display can benefit from adopting advances developed with DNA‐encoded small molecule libraries. We outline cases where chemical modification of the peptide library has already been used in mRNA display, and survey opportunities to expand this using examples from DNA‐encoded small molecule libraries. We also propose potential opportunities for encoding such reactions within the mRNA/cDNA tag of an mRNA‐displayed peptide library to allow a more diversity‐oriented approach to library modification. Finally, we outline alternate approaches for enriching target‐binding hits from a pooled and tagged library, and close by detailing several examples of how an adjusted mRNA‐display based approach could be used to discover new ‘drug‐like’ modified small peptides.
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Affiliation(s)
- Paddy R A Melsen
- Vrije Universiteit Amsterdam, Department of Chemistry and Pharmaceutical Sciences, NETHERLANDS
| | - Ryoji Yoshisada
- Vrije Universiteit Amsterdam, Department of Chemistry and Pharmaceutical Sciences, NETHERLANDS
| | - Seino A K Jongkees
- Vrije Universiteit Amsterdam, Chemistry and Pharmaceutical Sciences, de Boelelaan 1108, 1081 HZ, Amsterdam, NETHERLANDS
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6
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Yan K, Triana V, Kalmady SV, Aku-Dominguez K, Memon S, Brown A, Greiner R, Derda R. Learning the structure-activity relationship (SAR) of the Wittig reaction from genetically-encoded substrates. Chem Sci 2021; 12:14301-14308. [PMID: 34760216 PMCID: PMC8565473 DOI: 10.1039/d1sc04146k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/08/2021] [Indexed: 12/31/2022] Open
Abstract
The Wittig reaction can be used for late stage functionalization of proteins and peptides to ligate glycans, pharmacophores, and many other functionalities. In this manuscript, we modified 160 000 N-terminal glyoxaldehyde peptides displayed on phage with the Wittig reaction by using a biotin labeled ylide under conditions that functionalize only 1% of the library population. Deep-sequencing of the biotinylated and input populations estimated the rate of conversion for each sequence. This “deep conversion” (DC) from deep sequencing correlates with rate constants measured by HPLC. Peptide sequences with fast and slow reactivity highlighted the critical role of primary backbone amides (N–H) in accelerating the rate of the aqueous Wittig reaction. Experimental measurement of reaction rates and density functional theory (DFT) computation of the transition state geometries corroborated this relationship. We also collected deep-sequencing data to build structure–activity relationship (SAR) models that can predict the DC value of the Wittig reaction. By using these data, we trained two classifier models based on gradient boosted trees. These classifiers achieved area under the ROC (receiver operating characteristic) curve (ROC AUC) of 81.2 ± 0.4 and 73.7 ± 0.8 (90–92% accuracy) in determining whether a sequence belonged to the top 5% or the bottom 5% in terms of its reactivity. This model can suggest new peptides never observed experimentally with ‘HIGH’ or ‘LOW’ reactivity. Experimental measurement of reaction rates for 11 new sequences corroborated the predictions for 8 of them. We anticipate that phage-displayed peptides and related mRNA or DNA-displayed substrates can be employed in a similar fashion to study the substrate scope and mechanisms of many other chemical reactions. 160 000 peptides displayed on phage were subjected to the Wittig reaction with a biotinylated ylide. Deep-sequencing estimated the conversion rate for each sequence and unveiled the relationship between sequences and the rate of the Wittig reaction.![]()
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Affiliation(s)
- Kejia Yan
- Department of Chemistry, University of Alberta Edmonton AB T6G 2G2 Canada
| | - Vivian Triana
- Department of Chemistry, University of Alberta Edmonton AB T6G 2G2 Canada
| | - Sunil Vasu Kalmady
- Department of Computer Science, University of Alberta Alberta AB T6G 2E8 Canada
| | | | - Sharyar Memon
- Department of Electrical and Computer Engineering, University of Alberta Edmonton AB T6G 1H9 Canada
| | - Alex Brown
- Department of Chemistry, University of Alberta Edmonton AB T6G 2G2 Canada
| | - Russell Greiner
- Department of Computer Science, University of Alberta Alberta AB T6G 2E8 Canada.,Alberta Machine Intelligence Institute Alberta AB T5J 3B1 Canada
| | - Ratmir Derda
- Department of Chemistry, University of Alberta Edmonton AB T6G 2G2 Canada
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7
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Kamalinia G, Grindel BJ, Takahashi TT, Millward SW, Roberts RW. Directing evolution of novel ligands by mRNA display. Chem Soc Rev 2021; 50:9055-9103. [PMID: 34165126 PMCID: PMC8725378 DOI: 10.1039/d1cs00160d] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
mRNA display is a powerful biological display platform for the directed evolution of proteins and peptides. mRNA display libraries covalently link the displayed peptide or protein (phenotype) with the encoding genetic information (genotype) through the biochemical activity of the small molecule puromycin. Selection for peptide/protein function is followed by amplification of the linked genetic material and generation of a library enriched in functional sequences. Iterative selection cycles are then performed until the desired level of function is achieved, at which time the identity of candidate peptides can be obtained by sequencing the genetic material. The purpose of this review is to discuss the development of mRNA display technology since its inception in 1997 and to comprehensively review its use in the selection of novel peptides and proteins. We begin with an overview of the biochemical mechanism of mRNA display and its variants with a particular focus on its advantages and disadvantages relative to other biological display technologies. We then discuss the importance of scaffold choice in mRNA display selections and review the results of selection experiments with biological (e.g., fibronectin) and linear peptide library architectures. We then explore recent progress in the development of "drug-like" peptides by mRNA display through the post-translational covalent macrocyclization and incorporation of non-proteogenic functionalities. We conclude with an examination of enabling technologies that increase the speed of selection experiments, enhance the information obtained in post-selection sequence analysis, and facilitate high-throughput characterization of lead compounds. We hope to provide the reader with a comprehensive view of current state and future trajectory of mRNA display and its broad utility as a peptide and protein design tool.
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Affiliation(s)
- Golnaz Kamalinia
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA.
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8
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Ekanayake AI, Sobze L, Kelich P, Youk J, Bennett NJ, Mukherjee R, Bhardwaj A, Wuest F, Vukovic L, Derda R. Genetically Encoded Fragment-Based Discovery from Phage-Displayed Macrocyclic Libraries with Genetically Encoded Unnatural Pharmacophores. J Am Chem Soc 2021; 143:5497-5507. [PMID: 33784084 DOI: 10.1021/jacs.1c01186] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Genetically encoded macrocyclic peptide libraries with unnatural pharmacophores are valuable sources for the discovery of ligands for many targets of interest. Traditionally, generation of such libraries employs "early stage" incorporation of unnatural building blocks into the chemically or translationally produced macrocycles. Here, we describe a divergent late-stage approach to such libraries starting from readily available starting material: genetically encoded libraries of peptides. A diketone linchpin 1,5-dichloropentane-2,4-dione converts peptide libraries displayed on phage to 1,3-diketone bearing macrocyclic peptides (DKMP): shelf-stable precursors for Knorr pyrazole synthesis. Ligation of diverse hydrazine derivatives onto DKMP libraries displayed on phage that carries silent DNA-barcodes yields macrocyclic libraries in which the amino acid sequence and the pharmacophore are encoded by DNA. Selection of this library against carbonic anhydrase enriched macrocycles with benzenesulfonamide pharmacophore and nanomolar Kd. The methodology described in this manuscript can graft diverse pharmacophores into many existing genetically encoded phage libraries and significantly increase the value of such libraries in molecular discoveries.
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Affiliation(s)
- Arunika I Ekanayake
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Lena Sobze
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Payam Kelich
- Department of Chemistry and Biochemistry, University of Texas at El Paso, El Paso, Texas 79968, United States
| | - Jihea Youk
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Nicholas J Bennett
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Raja Mukherjee
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Atul Bhardwaj
- Cross Cancer Institute, University of Alberta, Edmonton, AB T6G 1Z2, Canada
| | - Frank Wuest
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada.,Cross Cancer Institute, University of Alberta, Edmonton, AB T6G 1Z2, Canada
| | - Lela Vukovic
- Department of Chemistry and Biochemistry, University of Texas at El Paso, El Paso, Texas 79968, United States
| | - Ratmir Derda
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
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9
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Philippe GJB, Mittermeier A, Lawrence N, Huang YH, Condon ND, Loewer A, Craik DJ, Henriques ST. Angler Peptides: Macrocyclic Conjugates Inhibit p53:MDM2/X Interactions and Activate Apoptosis in Cancer Cells. ACS Chem Biol 2021; 16:414-428. [PMID: 33533253 DOI: 10.1021/acschembio.0c00988] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptides are being developed as targeted anticancer drugs to modulate cytosolic protein-protein interactions involved in cancer progression. However, their use as therapeutics is often limited by their low cell membrane permeation and/or inability to reach cytosolic targets. Conjugation to cell penetrating peptides has been successfully used to improve the cytosolic delivery of high affinity binder peptides, but cellular uptake does not always result in modulation of the targeted pathway. To overcome this limitation, we developed "angler peptides" by conjugating KD3, a noncell permeable but potent and specific peptide inhibitor of p53:MDM2 and p53:MDMX interactions, with a set of cyclic cell-penetrating peptides. We examined their binding affinity for MDM2 and MDMX, the cell entry mechanism, and role in reactivation of the p53 pathway. We identified two angler peptides, cTAT-KD3 and cR10-KD3, able to activate the p53 pathway in cancer cells. cTAT-KD3 entered cells via endocytic pathways, escaped endosomes, and activated the p53 pathway in breast (MCF7), lung (A549), and colon (HCT116) cancer cell lines at concentrations in the range of 1-12 μM. cR10-KD3 reached the cytosol via direct membrane translocation and activated the p53 pathway at 1 μM in all the tested cell lines. Our work demonstrates that nonpermeable anticancer peptides can be delivered into the cytosol and inhibit intracellular cancer pathways when they are conjugated with stable cell penetrating peptides. The mechanistic studies suggest that direct translocation leads to less toxicity, higher cytosol delivery at lower concentrations, and lower dependencies on the membrane of the tested cell line than occurs for an endocytic pathway with endosomal escape. The angler strategy can rescue high affinity peptide binders identified from high throughput screening and convert them into targeted anticancer therapeutics, but investigation of their cellular uptake and cell death mechanisms is essential to confirming modulation of the targeted cancer pathways.
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Affiliation(s)
- Grégoire J.-B. Philippe
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | | | - Nicole Lawrence
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Nicholas D. Condon
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | | | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Sónia T. Henriques
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
- Queensland University of Technology, School of Biomedical Sciences, Institute of Health & Biomedical Innovation and Translational Research Institute, Brisbane, Queensland 4102, Australia
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10
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Converting peptides into drugs targeting intracellular protein-protein interactions. Drug Discov Today 2021; 26:1521-1531. [PMID: 33524603 DOI: 10.1016/j.drudis.2021.01.022] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/15/2020] [Accepted: 01/22/2021] [Indexed: 12/31/2022]
Abstract
Peptides are gaining increasing attention as therapeutics to target intracellular protein-protein interactions that are involved in disease progression. In this review, we discuss how peptides that are able to bind and inhibit a therapeutic target can be translated into drug leads. We discuss the advantages of using peptides as therapeutics to target intracellular protein-protein interactions, chemical strategies to generate macrocyclic peptides that are resistant to proteolytic enzymes, high-throughput screening approaches to identify peptides that have high affinity for therapeutic targets, strategies that permit these peptides to cross cell membranes and so reach intracellular targets, and the importance of investigating their mode-of-action in guiding the development of novel therapeutics.
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11
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Dotter H, Boll M, Eder M, Eder AC. Library and post-translational modifications of peptide-based display systems. Biotechnol Adv 2021; 47:107699. [PMID: 33513435 DOI: 10.1016/j.biotechadv.2021.107699] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 01/04/2021] [Accepted: 01/14/2021] [Indexed: 12/27/2022]
Abstract
Innovative biotechnological methods empower the successful identification of new drug candidates. Phage, ribosome and mRNA display represent high throughput screenings, allowing fast and efficient progress in the field of targeted drug discovery. The identification range comprises low molecular weight peptides up to whole antibodies. However, a major challenge poses the stability and affinity in particular of peptides. Chemical modifications e.g. the introduction of unnatural amino acids or cyclization, have been proven to be essential tools to overcome these limitations. This review article particularly focuses on available methods for the targeted chemical modification of peptides and peptide libraries in selected display approaches.
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Affiliation(s)
- Hanna Dotter
- Department of Nuclear Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany; Division of Radiopharmaceutical Development, German Cancer Consortium, partner site Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany, and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Melanie Boll
- Department of Nuclear Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany; Division of Radiopharmaceutical Development, German Cancer Consortium, partner site Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany, and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Matthias Eder
- Department of Nuclear Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany; Division of Radiopharmaceutical Development, German Cancer Consortium, partner site Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany, and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
| | - Ann-Christin Eder
- Department of Nuclear Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany; Division of Radiopharmaceutical Development, German Cancer Consortium, partner site Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany, and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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12
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Iskandar SE, Haberman VA, Bowers AA. Expanding the Chemical Diversity of Genetically Encoded Libraries. ACS COMBINATORIAL SCIENCE 2020; 22:712-733. [PMID: 33167616 PMCID: PMC8284915 DOI: 10.1021/acscombsci.0c00179] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The power of ribosomes has increasingly been harnessed for the synthesis and selection of molecular libraries. Technologies, such as phage display, yeast display, and mRNA display, effectively couple genotype to phenotype for the molecular evolution of high affinity epitopes for many therapeutic targets. Genetic code expansion is central to the success of these technologies, allowing researchers to surpass the intrinsic capabilities of the ribosome and access new, genetically encoded materials for these selections. Here, we review techniques for the chemical expansion of genetically encoded libraries, their abilities and limits, and opportunities for further development. Importantly, we also discuss methods and metrics used to assess the efficiency of modification and library diversity with these new techniques.
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Affiliation(s)
- Sabrina E Iskandar
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Victoria A Haberman
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Albert A Bowers
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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13
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Shalaby MAW, Dokla EME, Serya RAT, Abouzid KAM. Penicillin binding protein 2a: An overview and a medicinal chemistry perspective. Eur J Med Chem 2020; 199:112312. [PMID: 32442851 DOI: 10.1016/j.ejmech.2020.112312] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/28/2020] [Accepted: 04/05/2020] [Indexed: 12/17/2022]
Abstract
Antimicrobial resistance is an imminent threat worldwide. Methicillin-resistant Staphylococcus aureus (MRSA) is one of the "superbug" family, manifesting resistance through the production of a penicillin binding protein, PBP2a, an enzyme that provides its transpeptidase activity to allow cell wall biosynthesis. PBP2a's low affinity to most β-lactams, confers resistance to MRSA against numerous members of this class of antibiotics. An Achilles' heel of MRSA, PBP2a represents a substantial target to design novel antibiotics to tackle MRSA threat via inhibition of the bacterial cell wall biosynthesis. In this review we bring into focus the PBP2a enzyme and examine the various aspects related to its role in conferring resistance to MRSA strains. Moreover, we discuss several antibiotics and antimicrobial agents designed to target PBP2a and their therapeutic potential to meet such a grave threat. In conclusion, we consider future perspectives for targeting MRSA infections.
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Affiliation(s)
- Menna-Allah W Shalaby
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Abbassia, 11566, Cairo, Egypt
| | - Eman M E Dokla
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Abbassia, 11566, Cairo, Egypt.
| | - Rabah A T Serya
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Abbassia, 11566, Cairo, Egypt
| | - Khaled A M Abouzid
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Abbassia, 11566, Cairo, Egypt; Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Sadat City, Sadat City, Egypt.
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14
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Newton MS, Cabezas-Perusse Y, Tong CL, Seelig B. In Vitro Selection of Peptides and Proteins-Advantages of mRNA Display. ACS Synth Biol 2020; 9:181-190. [PMID: 31891492 DOI: 10.1021/acssynbio.9b00419] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
mRNA display is a robust in vitro selection technique that allows the selection of peptides and proteins with desired functions from libraries of trillions of variants. mRNA display relies upon a covalent linkage between a protein and its encoding mRNA molecule; the power of the technique stems from the stability of this link, and the large degree of control over experimental conditions afforded to the researcher. This article describes the major advantages that make mRNA display the method of choice among comparable in vivo and in vitro methods, including cell-surface display, phage display, and ribosomal display. We also describe innovative techniques that harness mRNA display for directed evolution, protein engineering, and drug discovery.
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Affiliation(s)
- Matilda S. Newton
- Department of Biochemistry, Molecular Biology and Biophysics & BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
- Department of Molecular, Cellular, and Developmental Biology & Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Yari Cabezas-Perusse
- Department of Biochemistry, Molecular Biology and Biophysics & BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
| | - Cher Ling Tong
- Department of Biochemistry, Molecular Biology and Biophysics & BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
| | - Burckhard Seelig
- Department of Biochemistry, Molecular Biology and Biophysics & BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
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15
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Engel BJ, Grindel BJ, Gray JP, Millward SW. Purification of poly-dA oligonucleotides and mRNA-protein fusions with dT 25-OAS resin. Bioorg Med Chem Lett 2020; 30:126934. [PMID: 31919017 PMCID: PMC6986445 DOI: 10.1016/j.bmcl.2019.126934] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 12/17/2019] [Accepted: 12/23/2019] [Indexed: 11/21/2022]
Abstract
Solid-phase resins functionalized with poly-deoxythymidine (dT) oligos facilitate purification of poly-adenylated molecules from solution through high affinity, high selectivity base-pairing interactions. These resins are commonly used to purify messenger RNA (mRNA) from complex biological mixtures as well as mRNA-protein fusion molecules for mRNA Display selections. Historically, dT-conjugated cellulose was the primary resin for poly-dA purification, but its scarcity has prompted the development of alternative resins, most notably dT-functionalized magnetic beads. In order to develop a cost-effective alternative to commercially available poly-dT resins for large-scale purifications of mRNA-protein fusions, we investigated the purification properties of dT25-conjugated Oligo Affinity Support resin (dT25-OAS) alongside poly-dT14 magnetic beads and dT25-cellulose. dT25-OAS was found to have the highest dA21 oligo binding capacity at 4 pmol/µg, followed by dT14-magnetic beads (1.1 pmol/µg) and dT25-cellulose (0.7 pmol/µg). To determine the resin specificity in the context of a complex biological mixture, we translated mRNA-protein fusions consisting of a radiolabeled Her2 affibody fused to its encoding mRNA. Commercial dT25-cellulose showed the highest mRNA-affibody purification specificity, followed by dT25-OAS and dT14-magnetic beads. Overall, dT25-OAS showed exceptionally high binding capacity and low background binding, making it an attractive alternative for large-scale mRNA purification and mRNA Display library enrichment.
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Affiliation(s)
- Brian J Engel
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, United States
| | - Brian J Grindel
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, United States
| | - Joshua P Gray
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, United States
| | - Steven W Millward
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, United States.
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16
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Covarrubias-Zambrano O, Yu J, Bossmann SH. Nano-Inspired Technologies for Peptide Delivery. Curr Protein Pept Sci 2019; 21:379-400. [PMID: 31793426 DOI: 10.2174/1389203720666191202112429] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 08/26/2019] [Accepted: 10/02/2019] [Indexed: 12/15/2022]
Abstract
Nano-inspired technologies offer unique opportunities to treat numerous diseases by using therapeutic peptides. Therapeutic peptides have attractive pharmacological profiles and can be manufactured at relatively low costs. The major advantages of using a nanodelivery approach comprises significantly lower required dosages compared to systemic delivery, and thus reduced toxicity and immunogenicity. The combination of therapeutic peptides with delivery peptides and nanoparticles or small molecule drugs offers systemic treatment approaches, instead of aiming for single biological targets or pathways. This review article discusses exemplary state-of-the-art nanosized delivery systems for therapeutic peptides and antibodies, as well as their biochemical and biophysical foundations and emphasizes still remaining challenges. The competition between using different nanoplatforms, such as liposome-, hydrogel-, polymer-, silica nanosphere-, or nanosponge-based delivery systems is still "on" and no clear frontrunner has emerged to date.
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Affiliation(s)
| | - Jing Yu
- Department of Chemistry, Kansas State University, 419 CBC Building, Manhattan, KS 66506-0401, United States.,Johns Hopkins University, Department of Radiology, Baltimore, MD, United States
| | - Stefan H Bossmann
- Department of Chemistry, Kansas State University, 419 CBC Building, Manhattan, KS 66506-0401, United States
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17
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Derda R, Ng S. Genetically encoded fragment-based discovery. Curr Opin Chem Biol 2019; 50:128-137. [DOI: 10.1016/j.cbpa.2019.03.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 03/09/2019] [Accepted: 03/12/2019] [Indexed: 12/30/2022]
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18
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Enhancement of Binding Affinity of Folate to Its Receptor by Peptide Conjugation. Int J Mol Sci 2019; 20:ijms20092152. [PMID: 31052315 PMCID: PMC6539678 DOI: 10.3390/ijms20092152] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 04/25/2019] [Accepted: 04/25/2019] [Indexed: 12/12/2022] Open
Abstract
(1) Background: The folate receptor (FR) is a target for cancer treatment and detection. Expression of the FR is restricted in normal cells but overexpressed in many types of tumors. Folate was conjugated with peptides for enhancing binding affinity to the FR. (2) Materials and Methods: For conjugation, folate was coupled with propargyl or dibenzocyclooctyne, and 4-azidophenylalanine was introduced in peptides for “click” reactions. We measured binding kinetics including the rate constants of association (ka) and dissociation (kd) of folate-peptide conjugates with purified FR by biolayer interferometry. After optimization of the conditions for the click reaction, we successfully conjugated folate with designed peptides. (3) Results: The binding affinity, indicated by the equilibrium dissociation constant (KD), of folate toward the FR was enhanced by peptide conjugation. The enhanced FR binding affinity by peptide conjugation is a result of an increase in the number of interaction sites. (4) Conclusion: Such peptide-ligand conjugates will be important in the design of ligands with higher affinity. These high affinity ligands can be useful for targeted drug delivery system.
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19
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Sheard DE, O’Brien-Simpson NM, Wade JD, Separovic F. Combating bacterial resistance by combination of antibiotics with antimicrobial peptides. PURE APPL CHEM 2019. [DOI: 10.1515/pac-2018-0707] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
The overuse of antibiotics in the healthcare and agricultural industries has led to the worldwide spread of bacterial resistance. The recent emergence of multidrug resistant (MDR) bacteria has resulted in a call for the development of novel strategies to address this global issue. Research on a diverse range of antimicrobial peptides (AMPs) has shown promising activity against several resistant strains. Increased understanding of the mode of action of AMPs has shown similarity and complementarity to conventional antibiotics and the combination of both has led to synergistic effects in some cases. Combination therapy has been widely used to combat MDR bacterial infections and the recent focus on their application with AMPs may allow antibiotics to be effective against resistant bacterial strains. By conjugation of an antibiotic onto an AMP, a compound may be produced with possibly greater activity and with reduced side-effects and toxicity. The AMP in these conjugates may also act as a unique adjuvant for the antibiotic by disrupting the resistance mechanisms used by bacteria thus allowing the antibiotic to once again be effective. This mini-review outlines some of the current and past work in combining AMPs with conventional antibiotics as strategies to address bacterial resistance.
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Affiliation(s)
- Dean E. Sheard
- School of Chemistry, Bio21 Institute, University of Melbourne , Melbourne, VIC 3010 , Australia
| | - Neil M. O’Brien-Simpson
- Centre of Oral Health Research, Melbourne Dental School, University of Melbourne , Melbourne, VIC 3010 , Australia
| | - John D. Wade
- School of Chemistry, Bio21 Institute, University of Melbourne , Melbourne, VIC 3010 , Australia
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne , Melbourne, VIC 3010 , Australia
| | - Frances Separovic
- School of Chemistry, Bio21 Institute, University of Melbourne , Melbourne, VIC 3010 , Australia
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20
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Vinals DF, Kitov PI, Tu Z, Zou C, Cairo CW, Lin HCH, Derda R. Selection of galectin-3 ligands derived from genetically encoded glycopeptide libraries. Pept Sci (Hoboken) 2018. [DOI: 10.1002/pep2.24097] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Pavel I. Kitov
- Department of Chemistry; University of Alberta; Edmonton Alberta Canada
| | - Zhijay Tu
- Institute of Biological Chemistry, Academia Sinica; Taipei Taiwan
| | - Chunxia Zou
- Department of Chemistry; University of Alberta; Edmonton Alberta Canada
| | | | | | - Ratmir Derda
- Department of Chemistry; University of Alberta; Edmonton Alberta Canada
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21
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K C TB, Tada S, Zhu L, Uzawa T, Minagawa N, Luo SC, Zhao H, Yu HH, Aigaki T, Ito Y. In vitro selection of electrochemical peptide probes using bioorthogonal tRNA for influenza virus detection. Chem Commun (Camb) 2018; 54:5201-5204. [PMID: 29718049 DOI: 10.1039/c8cc01775a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An electrosensitive peptide probe has been developed from an in vitro selection technique using biorthogonal tRNA prepared with an electroreactive non-natural amino acid, 3,4-ethylenedioxythiophene-conjugated aminophenylalanine. The selected probe quantitatively detected the influenza virus based on a signal "turn-on" mechanism. The developed strategy could be used to develop electrochemical biosensors toward a variety of targets.
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Affiliation(s)
- Tara Bahadur K C
- Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science, Saitama 351-0198, Japan.
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22
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Abstract
In this report, we describe an efficient way to generate libraries of macrocyclic glycopeptides in one step by reacting phage-displayed libraries of peptides with dichloro-oxime derivatives. We showed that the reactions do not interfere with the ability of phage to replicate in bacteria. The reactions are site-selective for phage-displayed peptides and they do not modify any other proteins of phage. The technology described in this report will be instrumental for genetic selection of macrocyclic glycopeptides for diverse glycan-binding proteins.
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Affiliation(s)
- Simon Ng
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada.
| | - Ratmir Derda
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada.
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23
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Abstract
Directed evolution is a useful method for the discovery of nucleic acids, peptides, or proteins that have desired binding abilities or functions. Because of the abundance and importance of glycosylation in nature, directed evolution of glycopeptides and glycoproteins is also highly desirable. However, common directed evolution platforms such as phage-, yeast-, or mammalian-cell display are limited for these applications by several factors. Glycan structure at each glycosylation site is not genetically encoded, and yeast and mammalian cells produce a heterogeneous mixture of glycoforms at each site on the protein. Although yeast, mammalian and Escherichia coli cells can be engineered to produce a homogenous glycoform at all glycosylation sites, there are just a few specific glycan structures that can readily be accessed in this manner. Recently, we reported a novel system for the directed evolution of glycopeptide libraries, which could in principle be decorated with any desired glycan. Our method combines in vitro peptide selection by mRNA display with unnatural amino acid incorporation and chemical attachment of synthetic oligosaccharides. Here, we provide an updated and optimized protocol for this method, which is designed to create glycopeptide mRNA display libraries containing ~1013 sequences and select them for target binding. The target described here is the HIV broadly neutralizing monoclonal antibody 2G12; 2G12 binds to cluster of high-mannose oligosaccharides on the HIV envelope glycoprotein gp120; and glycopeptides that mimic this epitope may be useful in HIV vaccine applications. This method is expected to be readily applicable for other types of glycans and targets of interest in glycobiology.
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24
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Exploring sequence space: harnessing chemical and biological diversity towards new peptide leads. Curr Opin Chem Biol 2017; 38:52-61. [DOI: 10.1016/j.cbpa.2017.02.020] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 02/18/2017] [Accepted: 02/20/2017] [Indexed: 12/29/2022]
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25
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Triana V, Derda R. Tandem Wittig/Diels–Alder diversification of genetically encoded peptide libraries. Org Biomol Chem 2017; 15:7869-7877. [DOI: 10.1039/c7ob01635b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In this paper, we developed a tandem of two carbon–carbon bond-forming reactions to chemically diversify libraries of peptides displayed on a bacteriophage.
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Affiliation(s)
- Vivian Triana
- Department of Chemistry
- University of Alberta
- Edmonton
- Canada
| | - Ratmir Derda
- Department of Chemistry
- University of Alberta
- Edmonton
- Canada
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26
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Interactions of in vitro selected fluorogenic peptide aptamers with calmodulin. Biotechnol Lett 2016; 39:375-382. [DOI: 10.1007/s10529-016-2257-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 11/10/2016] [Indexed: 10/20/2022]
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27
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Tjhung KF, Kitov PI, Ng S, Kitova EN, Deng L, Klassen JS, Derda R. Silent Encoding of Chemical Post-Translational Modifications in Phage-Displayed Libraries. J Am Chem Soc 2016; 138:32-5. [PMID: 26683999 DOI: 10.1021/jacs.5b10390] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
In vitro selection of chemically modified peptide libraries presented on phage, while a powerful technology, is limited to one chemical post-translational modification (cPTM) per library. We use unique combinations of redundant codons to encode cPTMs with "silent barcodes" to trace multiple modifications within a mixed modified library. As a proof of concept, we produced phage-displayed peptide libraries Ser-[X]4-Gly-Gly-Gly, with Gly and Ser encoded using unique combinations of codons (TCA-[X]4-GGAGGAGGA, AGT-[X]4-GGTGGTGGT, etc., where [X]4 denotes a random NNK library). After separate chemical modification and pooling, mixed-modified libraries can be panned and deep-sequenced to identify the enriched peptide sequence and the accompanying cPTM simultaneously. We panned libraries bearing combinations of modifications (sulfonamide, biotin, mannose) against matched targets (carbonic anhydrase, streptavidin, concanavalin A) to identify desired ligands. Synthesis and validation of sequences identified by deep sequencing revealed that specific cPTMs are significantly enriched in panning against the specific targets. Panning on carbonic anhydrase yielded a potent ligand, sulfonamide-WIVP, with Kd = 6.7 ± 2.1 nM, a 20-fold improvement compared with the control ligand sulfonamide-GGGG. Silent encoding of multiple cPTMs can be readily incorporated into other in vitro display technologies such as bacteriophage T7 or mRNA display.
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Affiliation(s)
- Katrina F Tjhung
- Department of Chemistry, University of Alberta , Edmonton, Alberta, Canada T6G 2G2
| | - Pavel I Kitov
- Department of Chemistry, University of Alberta , Edmonton, Alberta, Canada T6G 2G2
| | - Simon Ng
- Department of Chemistry, University of Alberta , Edmonton, Alberta, Canada T6G 2G2
| | - Elena N Kitova
- Department of Chemistry, University of Alberta , Edmonton, Alberta, Canada T6G 2G2
| | - Lu Deng
- Department of Chemistry, University of Alberta , Edmonton, Alberta, Canada T6G 2G2
| | - John S Klassen
- Department of Chemistry, University of Alberta , Edmonton, Alberta, Canada T6G 2G2
| | - Ratmir Derda
- Department of Chemistry, University of Alberta , Edmonton, Alberta, Canada T6G 2G2
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28
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Heinis C, Winter G. Encoded libraries of chemically modified peptides. Curr Opin Chem Biol 2015; 26:89-98. [PMID: 25768886 DOI: 10.1016/j.cbpa.2015.02.008] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 02/09/2015] [Accepted: 02/09/2015] [Indexed: 12/22/2022]
Abstract
The use of powerful technologies for generating and screening DNA-encoded protein libraries has helped drive the development of proteins as pharmaceutical ligands. However the development of peptides as pharmaceutical ligands has been more limited. Although encoded peptide libraries are typically several orders of magnitude larger than classical chemical libraries, can be more readily screened, and can give rise to higher affinity ligands, their use as pharmaceutical ligands is limited by their intrinsic properties. Two of the intrinsic limitations include the rotational flexibility of the peptide backbone and the limited number (20) of natural amino acids. However these limitations can be overcome by use of chemical modification. For example, the libraries can be modified to introduce topological constraints such as cyclization linkers, or to introduce new chemical entities such as small molecule ligands, fluorophores and photo-switchable compounds. This article reviews the chemistry involved, the properties of the peptide ligands, and the new opportunities offered by chemical modification of DNA-encoded peptide libraries.
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Affiliation(s)
- Christian Heinis
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
| | - Greg Winter
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.
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29
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Santoso B, Murray BW. Maleimide-based method for elaboration of cysteine-containing peptide phage libraries. Methods Mol Biol 2015; 1248:267-76. [PMID: 25616339 DOI: 10.1007/978-1-4939-2020-4_18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Peptide-based molecules are known to have therapeutic utility, but the generation of phage-focused libraries to optimize peptide properties and functionality is challenging. Genetic approaches are limited to peptide extension on the peptide termini. Current chemical methods are technically challenging and time-consuming. A new chemical method is developed to extend a maleimide-conjugated peptide with a cysteine-containing random peptide phage display library. As a proof of concept, a 15-mer epidermal growth factor receptor (EGFR)-binding peptide was synthesized with a maleimide group at its C-terminus and then conjugated to the cysteine-containing library. After panning and screening, several extended peptides were discovered and tested to have a higher affinity to EGFR. This strategy can have broad utility to optimize pharmacophores of any modalities (peptides, unnatural peptides, drug conjugates) capable of bearing a maleimide group.
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Affiliation(s)
- Buyung Santoso
- Pfizer Worldwide Research and Development, 10646 Science Center Dr, San Diego, CA, 92121, USA
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30
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Kier BL, Andersen NH. Captides: rigid junctions between beta sheets and small molecules. J Pept Sci 2014; 20:704-15. [PMID: 24909552 DOI: 10.1002/psc.2657] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 04/29/2014] [Accepted: 04/30/2014] [Indexed: 12/15/2022]
Abstract
An extensive series of covalently linked small molecule-peptide adducts based on a terminally capped-beta hairpin motif is reported. The constructs can be prepared by standard solid-phase Fmoc chemistry with one to four peptide chains linked to small molecule hubs bearing carboxylic acid moieties. The key feature of interest is the precise, buried environment of the small molecule, and its rigid orientation relative to one or more short but fully structured peptide chain(s). Most of this study employs a minimalist nine residue 'captide', a capped β-turn, but we illustrate general applicability to peptides which can terminate in a beta strand. The non-peptide portion of these adducts can include nearly any molecule bearing one or more carboxylic acid groups. Fold-dependent rigidity sets this strategy apart from the currently available bioconjugation methods, which typically engender significant flexibility between peptide and tag. Applications to catalyst enhancement, drug design, higher-order assembly, and FRET calibration rulers are discussed.
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Affiliation(s)
- Brandon L Kier
- University of Washington - Chemistry, Bagley Hall Room 205 Box 351700, Seattle, WA, 98195-1700, USA
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31
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Jafari MR, Deng L, Kitov PI, Ng S, Matochko WL, Tjhung KF, Zeberoff A, Elias A, Klassen JS, Derda R. Discovery of light-responsive ligands through screening of a light-responsive genetically encoded library. ACS Chem Biol 2014; 9:443-50. [PMID: 24195775 DOI: 10.1021/cb4006722] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Light-responsive ligands are useful tools in biochemistry and cell biology because the function of these ligands can be spatially and temporally controlled. Conventional design of such ligands relies on previously available data about the structure of both the ligand and the receptor. In this paper, we describe de novo discovery of light-responsive ligands through screening of a genetically encoded light-responsive library. We ligated a photoresponsive azobenzene core to a random CX7C peptide library displayed on the coat protein of M13 phage. A one-pot alkylation/reduction of the cysteines yielded a photoresponsive library of random heptapeptide macrocycles with over 2 × 10(8) members. We characterized the reaction on-phage and optimized the yield of the modifications in phage libraries. Screening of the library against streptavidin yielded three macrocycles that bind to streptavidin in the dark and cease binding upon irradiation with 370 nm light. All ligands restored their binding properties upon thermal relaxation and could be turned ON and OFF for several cycles. We measured dissociation constants, Kd, by electrospray ionization mass spectrometry (ESI-MS) binding assay. For ligand ACGFERERTCG, the Kd of cis and trans isomers differed by 22-fold; an incomplete isomerization (85%), however, resulted in the apparent difference of 4.5-fold between the dark and the irradiated state. We anticipate that the selection strategy described in this report can be used to find light-responsive ligands for many targets that do not have known natural ligands.
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Affiliation(s)
- Mohammad R. Jafari
- Department
of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Lu Deng
- Department
of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Pavel I. Kitov
- Department
of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Simon Ng
- Department
of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Wadim L. Matochko
- Department
of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Katrina F. Tjhung
- Department
of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Anthony Zeberoff
- Department
of Chemical and Material Engineering, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Anastasia Elias
- Department
of Chemical and Material Engineering, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - John S. Klassen
- Department
of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Ratmir Derda
- Department
of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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32
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Tokunaga Y, Azetsu Y, Fukunaga K, Hatanaka T, Ito Y, Taki M. Pharmacophore generation from a drug-like core molecule surrounded by a library peptide via the 10BASEd-T on bacteriophage T7. Molecules 2014; 19:2481-96. [PMID: 24566316 PMCID: PMC6271298 DOI: 10.3390/molecules19022481] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Revised: 02/10/2014] [Accepted: 02/12/2014] [Indexed: 11/16/2022] Open
Abstract
We have achieved site-specific conjugation of several haloacetamide derivatives into designated cysteines on bacteriophage T7-displayed peptides, which are fused to T7 capsid protein gp10. This easiest gp10 based-thioetherification (10BASEd-T) undergoes almost quantitatively like a click reaction without side reaction or loss of phage infectivity. The post-translational modification yield, as well as the site-specificity, is quantitatively analyzed by a fluorescent densitometric analysis after gel electrophoresis. The detailed structure of the modified peptide on phage is identified with tandem mass spectrometry. Construction of such a peptide-fused phage library possessing non-natural core structures will be useful for future drug discovery. For this aim, we propose a novel concept of pharmacophore generation from a drug-like molecule (i.e., salicylic acid) conjugated with surrounding randomized peptides. By using the hybrid library, streptavidin-specific binders are isolated through four rounds of biopanning.
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Affiliation(s)
- Yuuki Tokunaga
- Department of Engineering Science, Bioscience and Technology Program, The Graduate School of Informatics and Engineering, The University of Electro-Communications (UEC), 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan.
| | - Yuuki Azetsu
- Department of Engineering Science, Bioscience and Technology Program, The Graduate School of Informatics and Engineering, The University of Electro-Communications (UEC), 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan.
| | - Keisuke Fukunaga
- Department of Engineering Science, Bioscience and Technology Program, The Graduate School of Informatics and Engineering, The University of Electro-Communications (UEC), 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan.
| | - Takaaki Hatanaka
- Department of Chemistry and Bioscience, Graduate School of Science and Engineering, Kagoshima University, 1-21-35 Korimoto, Kagoshima, Kagoshima 890-0065, Japan.
| | - Yuji Ito
- Department of Chemistry and Bioscience, Graduate School of Science and Engineering, Kagoshima University, 1-21-35 Korimoto, Kagoshima, Kagoshima 890-0065, Japan.
| | - Masumi Taki
- Department of Engineering Science, Bioscience and Technology Program, The Graduate School of Informatics and Engineering, The University of Electro-Communications (UEC), 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan.
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33
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Wada A, Hara S, Osada H. Ribosome display and photo-cross-linking techniques for in vitro identification of target proteins of bioactive small molecules. Anal Chem 2014; 86:6768-73. [PMID: 24380432 DOI: 10.1021/ac4030208] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The identification of target proteins of bioactive small molecules as bioprobe candidates or drug seeds is indispensable for elucidating their actions and predicting their side effects. To meet the current need, we developed a scheme for detection and identification of target proteins by using ribosome display and photo-cross-linking techniques, and demonstrated the feasibility. The mRNAs encoding full-length human proteins (FHPs) were constructed and translated in vitro to prepare pools of FHP-ribosome-mRNA complexes used for ribosome display selection. Expression levels of the FHPs were confirmed by Western blot analysis, and photo-cross-linked small-molecule beads were assessed through cell-free synthesized FHP binding assay. After ribosome display selection against photo-cross-linked small-molecule beads, RT-PCR using mRNAs recovered from the selected ternary complexes and electrophoresis of the PCR products allowed specific detection of the target proteins binding to the beads. In addition, a repeat of ribosome display selection enabled us to identify the target proteins even if the molar quantity was one ten-thousandth of that of the other proteins in a cell-free synthesized FHP pool. Therefore, these results showed that ribosome display using photo-cross-linked small-molecule beads and further extended FHP pool could be one of the powerful techniques for identification of unknown target proteins of bioactive small molecules.
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Affiliation(s)
- Akira Wada
- Antibiotics Laboratory, RIKEN , 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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34
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Wang W, Hirano Y, Uzawa T, Liu M, Taiji M, Ito Y. In vitro selection of a peptide aptamer that potentiates inhibition of cyclin-dependent kinase 2 by purvalanol. MEDCHEMCOMM 2014. [DOI: 10.1039/c4md00142g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To increase the inhibitory activity of purvalanol against cyclin-dependent kinase 2, we increased the extent of interaction between the inhibitor and the target by coupling a peptide aptamer to purvalanol.
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Affiliation(s)
- Wei Wang
- Nano Medical Engineering Laboratory
- RIKEN 2-1 Hirosawa
- Wako, Japan
| | - Yoshinori Hirano
- Laboratory for Computational Molecular Design
- Computational Biology Research Core
- RIKEN Quantitative Biology Center
- Chuo-ku, Japan
| | - Takanori Uzawa
- Nano Medical Engineering Laboratory
- RIKEN 2-1 Hirosawa
- Wako, Japan
- Emergent Bioengineering Materials Research Team
- RIKEN Center for Emergent Matter Science
| | - Mingzhe Liu
- Key Laboratory of Structure-Based Drugs Design & Discovery (Shenyang Pharmaceutical University) of Ministry of Education
- School of Pharmaceutical Engineering
- Shenyang Pharmaceutical University
- , China
| | - Makoto Taiji
- Laboratory for Computational Molecular Design
- Computational Biology Research Core
- RIKEN Quantitative Biology Center
- Chuo-ku, Japan
| | - Yoshihiro Ito
- Nano Medical Engineering Laboratory
- RIKEN 2-1 Hirosawa
- Wako, Japan
- Emergent Bioengineering Materials Research Team
- RIKEN Center for Emergent Matter Science
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35
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mRNA display: from basic principles to macrocycle drug discovery. Drug Discov Today 2013; 19:388-99. [PMID: 24157402 DOI: 10.1016/j.drudis.2013.10.011] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 09/27/2013] [Accepted: 10/14/2013] [Indexed: 12/29/2022]
Abstract
We describe a new discovery technology that uses mRNA-display to rapidly synthesize and screen macrocyclic peptide libraries to explore a valuable region of chemical space typified by natural products. This technology allows high-affinity peptidic macrocycles containing modified backbones and unnatural side chains to be readily selected based on target binding. Success stories covering the first examples of these libraries suggest that they could be used for the discovery of intracellular protein-protein interaction inhibitors, highly selective enzyme inhibitors or synthetic replacements for monoclonal antibodies. The review concludes with a look to the future regarding how this technology might be improved with respect to library design for cell permeability and bioavailability.
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36
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A simple and efficient maleimide-based approach for peptide extension with a cysteine-containing peptide phage library. Bioorg Med Chem Lett 2013; 23:5680-3. [DOI: 10.1016/j.bmcl.2013.08.032] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 08/02/2013] [Accepted: 08/05/2013] [Indexed: 11/18/2022]
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37
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Wada A. Development of Next-Generation Peptide Binders Using In vitro Display Technologies and Their Potential Applications. Front Immunol 2013; 4:224. [PMID: 23914189 PMCID: PMC3730117 DOI: 10.3389/fimmu.2013.00224] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 05/29/2013] [Indexed: 12/02/2022] Open
Abstract
During the last decade, a variety of monoclonal antibodies have been developed and used as molecular targeting drugs in medical therapies. Although antibody drugs tend to have intense pharmacological activities and negligible side effects, several issues in their development and prescription remain to be resolved. Synthetic peptides with affinities and specificities for a desired target have received significant attention as alternatives to antibodies. In vitro display technologies are powerful methods for the selection of such peptides from combinatorial peptide libraries. Various types of peptide binders are being selected with such technologies for use in a wide range of fields from bioscience to medicine. This mini review article focuses on the current state of in vitro display selection of synthetic peptide binders and compares the selected peptides with natural peptides/proteins to provide a better understanding of the target affinities and inhibitory activities derived from their amino acid sequences and structural frameworks. The potential of synthetic peptide binders as alternatives to antibody drugs in therapeutic applications is also reviewed.
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38
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Rentero Rebollo I, Heinis C. Phage selection of bicyclic peptides. Methods 2013; 60:46-54. [PMID: 23313750 DOI: 10.1016/j.ymeth.2012.12.008] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 12/06/2012] [Accepted: 12/20/2012] [Indexed: 12/12/2022] Open
Abstract
Bicyclic peptides are small, constrained peptides that can bind with high affinity and selectivity to protein targets. Their small size provides a number of advantages over larger protein-based ligands, including access to chemical synthesis, better tissue penetration, and a wider choice of application routes. Bicyclic peptide ligands can be identified using phage display technology with moderate effort and cost. Here we provide step-by-step protocols for the isolation of bicyclic peptide ligands using phage display. These protocols have been successfully used in our laboratory for the generation of high-affinity binders to a variety of protein targets. We describe library generation, affinity selection and ligand characterization, and provide troubleshooting advice concerning frequent problems.
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Affiliation(s)
- Inmaculada Rentero Rebollo
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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Uzawa T, Tada S, Wang W, Ito Y. Expansion of the aptamer library from a "natural soup" to an "unnatural soup". Chem Commun (Camb) 2013; 49:1786-95. [PMID: 23283144 DOI: 10.1039/c2cc36348h] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The possibility of evolving a commonly existing biomolecule into a variety of functional biomolecules has now been realized in the form of aptamers through the development of in vitro selection. In addition to their high affinity and high specificity for the desired targets, aptamers are easily synthesized chemically and can be modified for downstream applications. Although aptamers were originally selected from a library containing only natural components, the past decade has seen a wealth of new aptamers selected from libraries containing unnatural components to provide new aptamer functions artificially. In this review, we highlight this transition (the shift between selection from natural components and selection from unnatural components) and the applications of selected aptamers.
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Affiliation(s)
- Takanori Uzawa
- Nano Medical Engineering Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.
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40
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Genetically encoded libraries of nonstandard peptides. J Nucleic Acids 2012; 2012:713510. [PMID: 23097693 PMCID: PMC3477784 DOI: 10.1155/2012/713510] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 08/12/2012] [Indexed: 11/17/2022] Open
Abstract
The presence of a nonproteinogenic moiety in a nonstandard peptide often improves the biological properties of the peptide. Non-standard peptide libraries are therefore used to obtain valuable molecules for biological, therapeutic, and diagnostic applications. Highly diverse non-standard peptide libraries can be generated by chemically or enzymatically modifying standard peptide libraries synthesized by the ribosomal machinery, using posttranslational modifications. Alternatively, strategies for encoding non-proteinogenic amino acids into the genetic code have been developed for the direct ribosomal synthesis of non-standard peptide libraries. In the strategies for genetic code expansion, non-proteinogenic amino acids are assigned to the nonsense codons or 4-base codons in order to add these amino acids to the universal genetic code. In contrast, in the strategies for genetic code reprogramming, some proteinogenic amino acids are erased from the genetic code and non-proteinogenic amino acids are reassigned to the blank codons. Here, we discuss the generation of genetically encoded non-standard peptide libraries using these strategies and also review recent applications of these libraries to the selection of functional non-standard peptides.
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41
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Ng S, Jafari MR, Matochko WL, Derda R. Quantitative synthesis of genetically encoded glycopeptide libraries displayed on M13 phage. ACS Chem Biol 2012; 7:1482-7. [PMID: 22725642 DOI: 10.1021/cb300187t] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Phage display is a powerful technology that enables the discovery of peptide ligands for many targets. Chemical modification of phage libraries have allowed the identification of ligands with properties not encountered in natural polypeptides. In this report, we demonstrated the synthesis of 2 × 10(8) genetically encoded glycopeptides from a commercially available phage-displayed peptide library (Ph.D.-7) in a two-step, one-pot reaction in <1.5 h. Unlike previous reports, we bypassed genetic engineering of phage. The glycan moiety was introduced via an oxime ligation following oxidation of an N-terminal Ser/Thr; these residues are present in the peptide libraries at 20-30% abundance. The construction of libraries was facilitated by simple characterization, which directly assessed the yield and regioselectivity of chemical reactions performed on phage. This quantification method also allowed facile yield determination of reactions in 10(9) distinct molecules. We envision that the methodology described herein will find broad application in the synthesis of custom chemically modified phage libraries.
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Affiliation(s)
- Simon Ng
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Mohammad R. Jafari
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Wadim L. Matochko
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Ratmir Derda
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
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42
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Morimoto J, Hayashi Y, Suga H. Discovery of macrocyclic peptides armed with a mechanism-based warhead: isoform-selective inhibition of human deacetylase SIRT2. Angew Chem Int Ed Engl 2012; 51:3423-7. [PMID: 22374802 DOI: 10.1002/anie.201108118] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Revised: 01/31/2012] [Indexed: 01/15/2023]
Abstract
Designed to inhibit: by using the random nonstandard peptide integrated discovery (RaPID) system, highly potent isoform-selective inhibitors can be identified from a library of nonstandard macrocyclic peptides. These inhibitors, which contain a mechanism-based warhead residue, are active against the human deacetylase SIRT2, with IC(50) values in the low nanomolar region.
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Affiliation(s)
- Jumpei Morimoto
- Department of Chemistry, School of Science, The University of Tokyo, Hongo, Bunkyo, Japan
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43
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Morimoto J, Hayashi Y, Suga H. Discovery of Macrocyclic Peptides Armed with a Mechanism-Based Warhead: Isoform-Selective Inhibition of Human Deacetylase SIRT2. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201108118] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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44
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Liu M, Tada S, Ito M, Abe H, Ito Y. In vitro selection of a photo-responsive peptide aptamer using ribosome display. Chem Commun (Camb) 2012; 48:11871-3. [DOI: 10.1039/c2cc36618e] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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45
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Post-translational modification of genetically encoded polypeptide libraries. Curr Opin Chem Biol 2011; 15:355-61. [PMID: 21489857 DOI: 10.1016/j.cbpa.2011.03.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Revised: 03/17/2011] [Accepted: 03/17/2011] [Indexed: 10/18/2022]
Abstract
The genetic encoding of polypeptides with biological display systems enables the facile generation and screening of very large combinatorial libraries of molecules. By post-translationally modifying the encoded polypeptides, chemically and structurally more diverse molecules beyond linear amino acid polymers can be generated. The first post-translational modification applied to encoded polypeptides, the oxidation of cysteine residues to form disulfide bridges, is a natural one and was used to cyclise short peptides soon after the invention of phage display. Recently a range of non-natural chemical strategies for the post-translational modification of encoded polypeptide repertoires were applied to generate optical biosensors, semisynthetic polypeptides, peptide-drug conjugates, redox-insensitive monocyclic peptides or multicyclic peptides, and these strategies are reviewed in this article.
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46
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Zhang J, Williams BAR, Nilsson MT, Chaput JC. The evolvability of lead peptides from small library screens. Chem Commun (Camb) 2010; 46:7778-80. [PMID: 20830334 DOI: 10.1039/c0cc01475c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Very little is known about the evolvability of lead peptides that are isolated from small library screens. Here we begin to explore this question by comparing the directed evolution of two peptides previously isolated from a small library screen to new ligands generated de novo by in vitro selection.
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Affiliation(s)
- Jinglei Zhang
- Center for Evolutionary Medicine and Informatics at the Biodesign Institute, Arizona State University, Tempe, AZ 85287-5301, USA
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47
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Abstract
In vitro genetic approaches are powerful solutions to the protein design problem. mRNA display is an in vitro selection technique enabling the design of peptide and protein ligands ranging from one to over 100 amino acids. Libraries containing more than 10 trillion unique sequences can be synthesized and sieved with exquisite control over binding stringency and specificity.
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Affiliation(s)
- Terry T Takahashi
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
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48
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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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49
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Abstract
Display technologies are fundamental to the isolation of specific high-affinity binding proteins for diagnostic and therapeutic applications in cancer, neurodegenerative, and infectious diseases as well as autoimmune and inflammatory disorders. Applications extend into the broad field of antibody (Ab) engineering, synthetic enzymes, proteomics, and cell-free protein synthesis. Recently, in vitro display technologies have come to prominence due to the isolation of high-affinity human antibodies by phage display, the development of novel scaffolds for ribosome display, and the discovery of novel protein-protein interactions. In vitro display represents an emerging and innovative technology for the rapid isolation and evolution of high-affinity peptides and proteins. So far, only one clinical drug candidate produced by in vitro display technology has been approved by the FDA for use in humans, but several are in clinical or preclinical testing. This review highlights recent advances in various engineered biopharmaceutical products isolated by in vitro display with a focus on the commercial developments.
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Affiliation(s)
- Achim Rothe
- CSIRO Molecular and Health Technologies, Parkville, Victoria, Australia
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50
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Kadlcik V, Sicard-Roselli C, Houée-Levin C, Kodicek M, Ferreri C, Chatgilialoglu C. Reductive Modification of a Methionine Residue in the Amyloid-β Peptide. Angew Chem Int Ed Engl 2006; 45:2595-8. [PMID: 16538691 DOI: 10.1002/anie.200503942] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Vojtech Kadlcik
- Laboratoire de Chimie Physique, UMR 8000, Université Paris-Sud, 91405 Orsay cedex, France
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