1
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Cao X, Liu T, Wang T, Wang X, Xu Z, Zhou L, Tian C, Sun D. De Novo Screening and Mirror Image Isomerization of Linear Peptides Targeting α7 Nicotinic Acetylcholine Receptor. ACS Chem Biol 2024; 19:592-598. [PMID: 38380973 DOI: 10.1021/acschembio.3c00674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
As ligand-gated ion channels, nicotinic acetylcholine receptors (nAChRs) are widely distributed in the central and peripheral nervous systems and are associated with the pathogenesis of various degenerative neurological diseases. Here, we report the results of phage display-based de novo screening of an 11-residue linear peptide (named LKP1794) that targets the α7 nAChR, which is among the most abundant nAChR subtypes in the brain. Moreover, two d-peptides were generated through mirror image and/or primary sequence inverso isomerization (termed DRKP1794 and DKP1794) and displayed improved inhibitory effects (IC50 = 0.86 and 0.35 μM, respectively) on α7 nAChR compared with the parent l-peptide LKP1794 (IC50 = 2.48 μM), which markedly enhanced serum stability. A peptide-based fluorescence probe was developed using proteolytically resistant DKP1794 to specifically image the α7 nAChR in living cells. This work provides a new peptide tool to achieve inhibitory modulation and specifically image the α7 nAChR.
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Affiliation(s)
- Xiuxiu Cao
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, P. R. China
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, P. R. China
| | - Tianqi Liu
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, P. R. China
| | - Tao Wang
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, P. R. China
| | - Xudong Wang
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, P. R. China
| | - Ziyan Xu
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, P. R. China
| | - Li Zhou
- Anhui Provincial Peptide Drug Laboratory, Hefei 230026, P. R. China
| | - Changlin Tian
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, P. R. China
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, P. R. China
- Anhui Provincial Peptide Drug Laboratory, Hefei 230026, P. R. China
- School of Biomedical Engineering, Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou 215123, P. R. China
- Beijing Life Science Academy, Beijing 102200, P. R. China
| | - Demeng Sun
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, P. R. China
- Anhui Provincial Peptide Drug Laboratory, Hefei 230026, P. R. China
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2
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Li C, Jin K. Chemical Strategies towards the Development of Effective Anticancer Peptides. Curr Med Chem 2024; 31:1839-1873. [PMID: 37170992 DOI: 10.2174/0929867330666230426111157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 01/28/2023] [Accepted: 02/24/2023] [Indexed: 05/13/2023]
Abstract
Cancer is increasingly recognized as one of the primary causes of death and has become a multifaceted global health issue. Modern medical science has made significant advancements in the diagnosis and therapy of cancer over the past decade. The detrimental side effects, lack of efficacy, and multidrug resistance of conventional cancer therapies have created an urgent need for novel anticancer therapeutics or treatments with low cytotoxicity and drug resistance. The pharmaceutical groups have recognized the crucial role that peptide therapeutic agents can play in addressing unsatisfied healthcare demands and how these become great supplements or even preferable alternatives to biological therapies and small molecules. Anticancer peptides, as a vibrant therapeutic strategy against various cancer cells, have demonstrated incredible anticancer potential due to high specificity and selectivity, low toxicity, and the ability to target the surface of traditional "undruggable" proteins. This review will provide the research progression of anticancer peptides, mainly focusing on the discovery and modifications along with the optimization and application of these peptides in clinical practice.
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Affiliation(s)
- Cuicui Li
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmacy, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Kang Jin
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmacy, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
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3
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Castro TG, Melle-Franco M, Sousa CEA, Cavaco-Paulo A, Marcos JC. Non-Canonical Amino Acids as Building Blocks for Peptidomimetics: Structure, Function, and Applications. Biomolecules 2023; 13:981. [PMID: 37371561 DOI: 10.3390/biom13060981] [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: 04/19/2023] [Revised: 06/05/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
This review provides a fresh overview of non-canonical amino acids and their applications in the design of peptidomimetics. Non-canonical amino acids appear widely distributed in nature and are known to enhance the stability of specific secondary structures and/or biological function. Contrary to the ubiquitous DNA-encoded amino acids, the structure and function of these residues are not fully understood. Here, results from experimental and molecular modelling approaches are gathered to classify several classes of non-canonical amino acids according to their ability to induce specific secondary structures yielding different biological functions and improved stability. Regarding side-chain modifications, symmetrical and asymmetrical α,α-dialkyl glycines, Cα to Cα cyclized amino acids, proline analogues, β-substituted amino acids, and α,β-dehydro amino acids are some of the non-canonical representatives addressed. Backbone modifications were also examined, especially those that result in retro-inverso peptidomimetics and depsipeptides. All this knowledge has an important application in the field of peptidomimetics, which is in continuous progress and promises to deliver new biologically active molecules and new materials in the near future.
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Affiliation(s)
- Tarsila G Castro
- CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- LABBELS-Associate Laboratory, Braga/Guimarães, Portugal
| | - Manuel Melle-Franco
- CICECO-Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Cristina E A Sousa
- BioMark Sensor Research-School of Engineering of the Polytechnic Institute of Porto, 4249-015 Porto, Portugal
| | - Artur Cavaco-Paulo
- CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- LABBELS-Associate Laboratory, Braga/Guimarães, Portugal
| | - João C Marcos
- Centre of Chemistry, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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4
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Lander AJ, Jin Y, Luk LYP. D-Peptide and D-Protein Technology: Recent Advances, Challenges, and Opportunities. Chembiochem 2023; 24:e202200537. [PMID: 36278392 PMCID: PMC10805118 DOI: 10.1002/cbic.202200537] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/23/2022] [Indexed: 11/08/2022]
Abstract
Total chemical protein synthesis provides access to entire D-protein enantiomers enabling unique applications in molecular biology, structural biology, and bioactive compound discovery. Key enzymes involved in the central dogma of molecular biology have been prepared in their D-enantiomeric forms facilitating the development of mirror-image life. Crystallization of a racemic mixture of L- and D-protein enantiomers provides access to high-resolution X-ray structures of polypeptides. Additionally, D-enantiomers of protein drug targets can be used in mirror-image phage display allowing discovery of non-proteolytic D-peptide ligands as lead candidates. This review discusses the unique applications of D-proteins including the synthetic challenges and opportunities.
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Affiliation(s)
- Alexander J. Lander
- School of ChemistryCardiff UniversityMain Building, Park PlaceCardiffCF10 3ATUK
| | - Yi Jin
- Manchester Institute of BiotechnologyThe University of ManchesterManchesterM1 7DNUK
| | - Louis Y. P. Luk
- School of ChemistryCardiff UniversityMain Building, Park PlaceCardiffCF10 3ATUK
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5
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Eberle R, Sevenich M, Gering I, Scharbert L, Strodel B, Lakomek NA, Santur K, Mohrlüder J, Coronado MA, Willbold D. Discovery of All-d-Peptide Inhibitors of SARS-CoV-2 3C-like Protease. ACS Chem Biol 2023; 18:315-330. [PMID: 36647580 PMCID: PMC9942092 DOI: 10.1021/acschembio.2c00735] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
During the replication process of SARS-CoV-2, the main protease of the virus [3-chymotrypsin-like protease (3CLpro)] plays a pivotal role and is essential for the life cycle of the pathogen. Numerous studies have been conducted so far, which have confirmed 3CLpro as an attractive drug target to combat COVID-19. We describe a novel and efficient next-generation sequencing (NGS) supported phage display selection strategy for the identification of a set of SARS-CoV-2 3CLpro targeting peptide ligands that inhibit the 3CL protease, in a competitive or noncompetitive mode, in the low μM range. From the most efficient l-peptides obtained from the phage display, we designed all-d-peptides based on the retro-inverso (ri) principle. They had IC50 values also in the low μM range and in combination, even in the sub-micromolar range. Additionally, the combination with Rutinprivir decreases 10-fold the IC50 value of the competitive inhibitor. The inhibition modes of these d-ri peptides were the same as their respective l-peptide versions. Our results demonstrate that retro-inverso obtained all-d-peptides interact with high affinity and inhibit the SARS-CoV-2 3CL protease, thus reinforcing their potential for further development toward therapeutic agents. The here described d-ri peptides address limitations associated with current l-peptide inhibitors and are promising lead compounds. Further optimization regarding pharmacokinetic properties will allow the development of even more potent d-peptides to be used for the prevention and treatment of COVID-19.
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Affiliation(s)
- Raphael
J. Eberle
- Institute
of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52425Jülich, Germany,Institut
für Physikalische Biologie, Heinrich-Heine-Universität
Düsseldorf, Universitätsstraße
1, 40225Düsseldorf, Germany
| | - Marc Sevenich
- Institute
of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52425Jülich, Germany,Institut
für Physikalische Biologie, Heinrich-Heine-Universität
Düsseldorf, Universitätsstraße
1, 40225Düsseldorf, Germany,Priavoid
GmbH, Merowingerplatz
1, 40225Düsseldorf, Germany
| | - Ian Gering
- Institute
of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52425Jülich, Germany
| | - Lara Scharbert
- Institute
of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52425Jülich, Germany,Institut
für Physikalische Biologie, Heinrich-Heine-Universität
Düsseldorf, Universitätsstraße
1, 40225Düsseldorf, Germany
| | - Birgit Strodel
- Institute
of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52425Jülich, Germany,Institut
für Physikalische Biologie, Heinrich-Heine-Universität
Düsseldorf, Universitätsstraße
1, 40225Düsseldorf, Germany
| | - Nils A. Lakomek
- Institute
of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52425Jülich, Germany,Institut
für Physikalische Biologie, Heinrich-Heine-Universität
Düsseldorf, Universitätsstraße
1, 40225Düsseldorf, Germany
| | - Karoline Santur
- Institute
of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52425Jülich, Germany,Institut
für Physikalische Biologie, Heinrich-Heine-Universität
Düsseldorf, Universitätsstraße
1, 40225Düsseldorf, Germany
| | - Jeannine Mohrlüder
- Institute
of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52425Jülich, Germany
| | - Mônika A. Coronado
- Institute
of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52425Jülich, Germany,
| | - Dieter Willbold
- Institute
of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52425Jülich, Germany,Institut
für Physikalische Biologie, Heinrich-Heine-Universität
Düsseldorf, Universitätsstraße
1, 40225Düsseldorf, Germany,
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6
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Isaka Y, Yoshiya T, Ono C, Uchiyama A, Hirata H, Hamaguchi S, Kutsuna S, Takabatake Y, Saita R, Yamada T, Takahashi A, Yamato M, Nohara Y, Tsuda S, Anzai I, Kimura T, Takeda Y, Tomono K, Matsuura Y. Establishment and clinical application of SARS-CoV-2 catch column. Clin Exp Nephrol 2023; 27:279-287. [PMID: 36344716 PMCID: PMC9640800 DOI: 10.1007/s10157-022-02296-9] [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: 09/06/2022] [Accepted: 10/29/2022] [Indexed: 11/09/2022]
Abstract
BACKGROUND A certain number of patients with coronavirus disease 2019 (COVID-19), particularly those who test positive for SARS-CoV-2 in the serum, are hospitalized. Further, some even die. We examined the effect of blood adsorption therapy using columns that can eliminate SARS-CoV-2 on the improvement of the prognosis of severe COVID-19 patients. METHODS This study enrolled seven patients receiving mechanical ventilation. The patients received viral adsorption therapy using SARS-catch column for 3 days. The SARS-catch column was developed by immobilizing a specific peptide, designed based on the sequence of human angiotensin-converting enzyme 2 (hACE2), to an endotoxin adsorption column (PMX). In total, eight types of SARS-CoV-2-catch (SCC) candidate peptides were developed. Then, a clinical study on the effects of blood adsorption therapy using the SARS-catch column in patients with severe COVID-19 was performed, and the data in the present study were compared with historical data of severe COVID-19 patients. RESULTS Among all SCC candidate peptides, SCC-4N had the best adsorption activity against SARS-CoV-2. The SARS-catch column using SCC-4N removed 65% more SARS-CoV-2 than PMX. Compared with historical data, the weaning time from mechanical ventilation was faster in the present study. In addition, the rate of negative blood viral load in the present study was higher than that in the historical data. CONCLUSION The timely treatment with virus adsorption therapy may eliminate serum SARS-CoV-2 and improve the prognosis of patients with severe COVID-19. However, large-scale studies must be performed in the future to further assess the finding of this study (jRCTs052200134).
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Affiliation(s)
- Yoshitaka Isaka
- Department of Nephrology, Osaka University Graduate School of Medicine, Suita, Japan.
| | - Taku Yoshiya
- Peptide Institute Inc, Ibaraki, Japan ,Institute for Protein Research, Osaka University, Suita, Japan
| | - Chikako Ono
- Laboratory of Virus Control, Center for Infectious Disease Education and Research, Osaka University, Suita, Japan ,Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Akinori Uchiyama
- Department of Intensive Care Unit, Osaka University Hospital, Suita, Japan
| | - Haruhiko Hirata
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Shigeto Hamaguchi
- Department of Infection Control, Osaka University Hospital, Suita, Japan
| | - Satoshi Kutsuna
- Department of Infection Control, Osaka University Hospital, Suita, Japan
| | - Yoshitsugu Takabatake
- Department of Nephrology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Ryotaro Saita
- Department of Medical Innovation, Osaka University Hospital, Suita, Japan
| | - Tomomi Yamada
- Department of Medical Innovation, Osaka University Hospital, Suita, Japan
| | - Atsushi Takahashi
- Department of Nephrology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Masaya Yamato
- Division of General Internal Medicine and Infectious Diseases, Rinku General Medical Center, Izumisano, Japan
| | | | | | - Itsuki Anzai
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Tomonori Kimura
- KAGAMI Project, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Ibaraki, Japan
| | - Yoshito Takeda
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
| | | | - Yoshiharu Matsuura
- Laboratory of Virus Control, Center for Infectious Disease Education and Research, Osaka University, Suita, Japan ,Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
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7
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Takayama K, Hitachi K, Okamoto H, Saitoh M, Odagiri M, Ohfusa R, Shimada T, Taguchi A, Taniguchi A, Tsuchida K, Hayashi Y. Development of Myostatin Inhibitory d-Peptides to Enhance the Potency, Increasing Skeletal Muscle Mass in Mice. ACS Med Chem Lett 2022; 13:492-498. [PMID: 35300091 PMCID: PMC8919388 DOI: 10.1021/acsmedchemlett.1c00705] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 02/10/2022] [Indexed: 01/03/2023] Open
Abstract
Myostatin is a key negative regulator of skeletal muscle growth, and myostatin inhibitors are attractive tools for the treatment of muscular atrophy. Previously, we reported a series of 14-29-mer peptide myostatin inhibitors, including a potent derivative, MIPE-1686, a 16-mer N-terminal-free l-peptide with three unnatural amino acids and a propensity to form β-sheets. However, the in vivo biological stability of MIPE-1686 is a concern for its development as a drug. In the present study, to develop a more stable myostatin inhibitory d-peptide (MID), we synthesized various retro-inverso versions of a 16-mer peptide. Among these, an arginine-containing derivative, MID-35, shows a potent and equivalent in vitro myostatin inhibitory activity equivalent to that of MIPE-1686 and considerable stability against biodegradation. The in vivo potency of MID-35 to increase the tibialis anterior muscle mass in mice is significantly enhanced over that of MIPE-1686, and MID-35 can serve as a new entity for the prolonged inactivation of myostatin in skeletal muscle.
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Affiliation(s)
- Kentaro Takayama
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan.,Department of Environmental Biochemistry, Kyoto Pharmaceutical University, Yamashina, Kyoto 607-8414, Japan
| | - Keisuke Hitachi
- Division for Therapies against Intractable Diseases, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan
| | - Hideyuki Okamoto
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Mariko Saitoh
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Miki Odagiri
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Rina Ohfusa
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Takahiro Shimada
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Akihiro Taguchi
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Atsuhiko Taniguchi
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Kunihiro Tsuchida
- Division for Therapies against Intractable Diseases, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan
| | - Yoshio Hayashi
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
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8
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Preston GW. Different directions for retro-inverso peptides. J Pept Sci 2021; 28:e3384. [PMID: 34889485 DOI: 10.1002/psc.3384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/11/2021] [Accepted: 11/11/2021] [Indexed: 11/07/2022]
Abstract
Retro-inverso peptides are reversed sequences of mirror-image amino acid residues. Synthetic molecules of this type have long been considered potential mimics of functional peptides. This Peptide Highlights article examines some recent applications of the retro-inverso transformation at the interface of peptide chemistry and medicine.
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Affiliation(s)
- George W Preston
- Stoller Biomarker Discovery Centre, Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.,Stem Cell and Leukaemia Proteomics Laboratory, Manchester Cancer Research Centre, The University of Manchester, Manchester, UK
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9
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Hendrikse SIS, Contreras-Montoya R, Ellis AV, Thordarson P, Steed JW. Biofunctionality with a twist: the importance of molecular organisation, handedness and configuration in synthetic biomaterial design. Chem Soc Rev 2021; 51:28-42. [PMID: 34846055 DOI: 10.1039/d1cs00896j] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The building blocks of life - nucleotides, amino acids and saccharides - give rise to a large variety of components and make up the hierarchical structures found in Nature. Driven by chirality and non-covalent interactions, helical and highly organised structures are formed and the way in which they fold correlates with specific recognition and hence function. A great amount of effort is being put into mimicking these highly specialised biosystems as biomaterials for biomedical applications, ranging from drug discovery to regenerative medicine. However, as well as lacking the complexity found in Nature, their bio-activity is sometimes low and hierarchical ordering is missing or underdeveloped. Moreover, small differences in folding in natural biomolecules (e.g., caused by mutations) can have a catastrophic effect on the function they perform. In order to develop biomaterials that are more efficient in interacting with biomolecules, such as proteins, DNA and cells, we speculate that incorporating order and handedness into biomaterial design is necessary. In this review, we first focus on order and handedness found in Nature in peptides, nucleotides and saccharides, followed by selected examples of synthetic biomimetic systems based on these components that aim to capture some aspects of these ordered features. Computational simulations are very helpful in predicting atomic orientation and molecular organisation, and can provide invaluable information on how to further improve on biomaterial designs. In the last part of the review, a critical perspective is provided along with considerations that can be implemented in next-generation biomaterial designs.
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Affiliation(s)
- Simone I S Hendrikse
- Department of Chemical Engineering, The University of Melbourne, Melbourne, VIC 3010, Australia. .,School of Chemistry, University of New South Wales (UNSW), Sydney, NSW 2052, Australia
| | | | - Amanda V Ellis
- Department of Chemical Engineering, The University of Melbourne, Melbourne, VIC 3010, Australia.
| | - Pall Thordarson
- School of Chemistry, University of New South Wales (UNSW), Sydney, NSW 2052, Australia
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10
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Krishnan M, Choi J, Jang A, Yoon YK, Kim Y. Antiseptic 9-Meric Peptide with Potency against Carbapenem-Resistant Acinetobacter baumannii Infection. Int J Mol Sci 2021; 22:12520. [PMID: 34830401 PMCID: PMC8621208 DOI: 10.3390/ijms222212520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 11/17/2021] [Accepted: 11/17/2021] [Indexed: 11/18/2022] Open
Abstract
Carbapenem-resistant A. baumannii (CRAB) infection can cause acute host reactions that lead to high-fatality sepsis, making it important to develop new therapeutic options. Previously, we developed a short 9-meric peptide, Pro9-3D, with significant antibacterial and cytotoxic effects. In this study, we attempted to produce safer peptide antibiotics against CRAB by reversing the parent sequence to generate R-Pro9-3 and R-Pro9-3D. Among the tested peptides, R-Pro9-3D had the most rapid and effective antibacterial activity against Gram-negative bacteria, particularly clinical CRAB isolates. Analyses of antimicrobial mechanisms based on lipopolysaccharide (LPS)-neutralization, LPS binding, and membrane depolarization, as well as SEM ultrastructural investigations, revealed that R-Pro9-3D binds strongly to LPS and impairs the membrane integrity of CRAB by effectively permeabilizing its outer membrane. R-Pro9-3D was also less cytotoxic and had better proteolytic stability than Pro9-3D and killed biofilm forming CRAB. As an LPS-neutralizing peptide, R-Pro9-3D effectively reduced LPS-induced pro-inflammatory cytokine levels in RAW 264.7 cells. The antiseptic abilities of R-Pro9-3D were also investigated using a mouse model of CRAB-induced sepsis, which revealed that R-Pro9-3D reduced multiple organ damage and attenuated systemic infection by acting as an antibacterial and immunosuppressive agent. Thus, R-Pro9-3D displays potential as a novel antiseptic peptide for treating Gram-negative CRAB infections.
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Affiliation(s)
- Manigandan Krishnan
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Korea; (M.K.); (J.C.); (A.J.)
| | - Joonhyeok Choi
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Korea; (M.K.); (J.C.); (A.J.)
| | - Ahjin Jang
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Korea; (M.K.); (J.C.); (A.J.)
| | - Young Kyung Yoon
- Department of Internal Medicine, Division of Infectious Diseases, College of Medicine, Korea University Anam Hospital, Korea University, Seoul 02841, Korea;
| | - Yangmee Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Korea; (M.K.); (J.C.); (A.J.)
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11
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Le HH, Cinaroglu SS, Manalo EC, Ors A, Gomes MM, Duan Sahbaz B, Bonic K, Origel Marmolejo CA, Quentel A, Plaut JS, Kawashima TE, Ozdemir ES, Malhotra SV, Ahiska Y, Sezerman U, Bayram Akcapinar G, Saldivar JC, Timucin E, Fischer JM. Molecular modelling of the FOXO4-TP53 interaction to design senolytic peptides for the elimination of senescent cancer cells. EBioMedicine 2021; 73:103646. [PMID: 34689087 PMCID: PMC8546421 DOI: 10.1016/j.ebiom.2021.103646] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 10/07/2021] [Accepted: 10/08/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Senescent cells accumulate in tissues over time as part of the natural ageing process and the removal of senescent cells has shown promise for alleviating many different age-related diseases in mice. Cancer is an age-associated disease and there are numerous mechanisms driving cellular senescence in cancer that can be detrimental to recovery. Thus, it would be beneficial to develop a senolytic that acts not only on ageing cells but also senescent cancer cells to prevent cancer recurrence or progression. METHODS We used molecular modelling to develop a series of rationally designed peptides to mimic and target FOXO4 disrupting the FOXO4-TP53 interaction and releasing TP53 to induce apoptosis. We then tested these peptides as senolytic agents for the elimination of senescent cells both in cell culture and in vivo. FINDINGS Here we show that these peptides can act as senolytics for eliminating senescent human cancer cells both in cell culture and in orthotopic mouse models. We then further characterized one peptide, ES2, showing that it disrupts FOXO4-TP53 foci, activates TP53 mediated apoptosis and preferentially binds FOXO4 compared to TP53. Next, we show that intratumoural delivery of ES2 plus a BRAF inhibitor results in a significant increase in apoptosis and a survival advantage in mouse models of melanoma. Finally, we show that repeated systemic delivery of ES2 to older mice results in reduced senescent cell numbers in the liver with minimal toxicity. INTERPRETATION Taken together, our results reveal that peptides can be generated to specifically target and eliminate FOXO4+ senescent cancer cells, which has implications for eradicating residual disease and as a combination therapy for frontline treatment of cancer. FUNDING This work was supported by the Cancer Early Detection Advanced Research Center at Oregon Health & Science University.
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Affiliation(s)
- Hillary H Le
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, USA
| | - Suleyman S Cinaroglu
- Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Atasehir Istanbul 34752, Turkey; Eternans Ltd., UK
| | - Elise C Manalo
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, USA
| | - Aysegul Ors
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, USA
| | - Michelle M Gomes
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, USA
| | | | - Karla Bonic
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, USA
| | - Carlos A Origel Marmolejo
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, USA
| | - Arnaud Quentel
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, USA
| | - Justin S Plaut
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, USA; Dept of Bioengineering, University of California San Diego, USA
| | - Taryn E Kawashima
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, USA
| | - E Sila Ozdemir
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, USA
| | - Sanjay V Malhotra
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, USA; Dept of Cell, Developmental and Cancer Biology, Oregon Health & Science University, USA
| | | | - Ugur Sezerman
- Eternans Ltd., UK; School of Medicine, Acibadem Mehmet Ali Aydinlar University, Atasehir Istanbul 34752, Turkey
| | - Gunseli Bayram Akcapinar
- Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Atasehir Istanbul 34752, Turkey; Eternans Ltd., UK
| | - Joshua C Saldivar
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, USA; Division of Oncological Sciences, Knight Cancer Institute, Oregon Health & Science University, USA
| | - Emel Timucin
- Eternans Ltd., UK; School of Medicine, Acibadem Mehmet Ali Aydinlar University, Atasehir Istanbul 34752, Turkey
| | - Jared M Fischer
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, USA; Dept of Molecular and Medical Genetics, Oregon Health & Science University, USA.
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12
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Li X, Gohain N, Chen S, Li Y, Zhao X, Li B, Tolbert WD, He W, Pazgier M, Hu H, Lu W. Design of ultrahigh-affinity and dual-specificity peptide antagonists of MDM2 and MDMX for P53 activation and tumor suppression. Acta Pharm Sin B 2021; 11:2655-2669. [PMID: 34589387 PMCID: PMC8463443 DOI: 10.1016/j.apsb.2021.06.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 05/28/2021] [Accepted: 06/03/2021] [Indexed: 12/13/2022] Open
Abstract
Peptide inhibition of the interactions of the tumor suppressor protein P53 with its negative regulators MDM2 and MDMX activates P53 in vitro and in vivo, representing a viable therapeutic strategy for cancer treatment. Using phage display techniques, we previously identified a potent peptide activator of P53, termed PMI (TSFAEYWNLLSP), with binding affinities for both MDM2 and MDMX in the low nanomolar concentration range. Here we report an ultrahigh affinity, dual-specificity peptide antagonist of MDM2 and MDMX obtained through systematic mutational analysis and additivity-based molecular design. Functional assays of over 100 peptide analogs of PMI using surface plasmon resonance and fluorescence polarization techniques yielded a dodecameric peptide termed PMI-M3 (LTFLEYWAQLMQ) that bound to MDM2 and MDMX with Kd values in the low picomolar concentration range as verified by isothermal titration calorimetry. Co-crystal structures of MDM2 and of MDMX in complex with PMI-M3 were solved at 1.65 and 3.0 Å resolution, respectively. Similar to PMI, PMI-M3 occupied the P53-binding pocket of MDM2/MDMX, which was dominated energetically by intermolecular interactions involving Phe3, Tyr6, Trp7, and Leu10. Notable differences in binding between PMI-M3 and PMI were observed at other positions such as Leu4 and Met11 with MDM2, and Leu1 and Met11 with MDMX, collectively contributing to a significantly enhanced binding affinity of PMI-M3 for both proteins. By adding lysine residues to both ends of PMI and PMI-M3 to improve their cellular uptake, we obtained modified peptides termed PMI-2K (KTSFAEYWNLLSPK) and M3-2K (KLTFLEYWAQLMQK). Compared with PMI-2K, M3-2K exhibited significantly improved antitumor activities in vitro and in vivo in a P53-dependent manner. This super-strong peptide inhibitor of the P53-MDM2/MDMX interactions may become, in its own right, a powerful lead compound for anticancer drug development, and can aid molecular design of other classes of P53 activators as well for anticancer therapy.
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Affiliation(s)
- Xiang Li
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
- Institute of Human Virology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Neelakshi Gohain
- Institute of Human Virology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Si Chen
- School of Medicine, Shanghai University, Shanghai 200444, China
| | - Yinghua Li
- Institute of Translational Medicine, Shanghai University, Shanghai 200444, China
| | - Xiaoyuan Zhao
- Institute of Translational Medicine, Shanghai University, Shanghai 200444, China
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Bo Li
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - William D. Tolbert
- Institute of Human Virology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Wangxiao He
- Department of Talent Highland, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Marzena Pazgier
- Institute of Human Virology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Corresponding authors. Tel./fax: +86 21 54237607 (Wuyuan Lu), +86 21 66131281 (Honggang Hu), +1 301 295 3291 (Marzena Pazgier).
| | - Honggang Hu
- Institute of Translational Medicine, Shanghai University, Shanghai 200444, China
- Corresponding authors. Tel./fax: +86 21 54237607 (Wuyuan Lu), +86 21 66131281 (Honggang Hu), +1 301 295 3291 (Marzena Pazgier).
| | - Wuyuan Lu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS) of School of Basic Medical Sciences and Shanghai Institute of Infectious Disease and Biosecurity of School of Public Health, Fudan University, Shanghai 200032, China
- Corresponding authors. Tel./fax: +86 21 54237607 (Wuyuan Lu), +86 21 66131281 (Honggang Hu), +1 301 295 3291 (Marzena Pazgier).
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13
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Cardoso P, Glossop H, Meikle TG, Aburto-Medina A, Conn CE, Sarojini V, Valery C. Molecular engineering of antimicrobial peptides: microbial targets, peptide motifs and translation opportunities. Biophys Rev 2021; 13:35-69. [PMID: 33495702 PMCID: PMC7817352 DOI: 10.1007/s12551-021-00784-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 01/07/2021] [Indexed: 02/07/2023] Open
Abstract
The global public health threat of antimicrobial resistance has led the scientific community to highly engage into research on alternative strategies to the traditional small molecule therapeutics. Here, we review one of the most popular alternatives amongst basic and applied research scientists, synthetic antimicrobial peptides. The ease of peptide chemical synthesis combined with emerging engineering principles and potent broad-spectrum activity, including against multidrug-resistant strains, has motivated intense scientific focus on these compounds for the past decade. This global effort has resulted in significant advances in our understanding of peptide antimicrobial activity at the molecular scale. Recent evidence of molecular targets other than the microbial lipid membrane, and efforts towards consensus antimicrobial peptide motifs, have supported the rise of molecular engineering approaches and design tools, including machine learning. Beyond molecular concepts, supramolecular chemistry has been lately added to the debate; and helped unravel the impact of peptide self-assembly on activity, including on biofilms and secondary targets, while providing new directions in pharmaceutical formulation through taking advantage of peptide self-assembled nanostructures. We argue that these basic research advances constitute a solid basis for promising industry translation of rationally designed synthetic peptide antimicrobials, not only as novel drugs against multidrug-resistant strains but also as components of emerging antimicrobial biomaterials. This perspective is supported by recent developments of innovative peptide-based and peptide-carrier nanobiomaterials that we also review.
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Affiliation(s)
- Priscila Cardoso
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia.,School of Science, RMIT University, Melbourne, Australia
| | - Hugh Glossop
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | | | | | | | | | - Celine Valery
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia
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14
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Wang H, Sun Y, Zhou X, Chen C, Jiao L, Li W, Gou S, Li Y, Du J, Chen G, Zhai W, Wu Y, Qi Y, Gao Y. CD47/SIRPα blocking peptide identification and synergistic effect with irradiation for cancer immunotherapy. J Immunother Cancer 2020; 8:jitc-2020-000905. [PMID: 33020240 PMCID: PMC7537338 DOI: 10.1136/jitc-2020-000905] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/03/2020] [Indexed: 01/04/2023] Open
Abstract
Background Immunotherapy has achieved remarkable advances via a variety of strategies against tumor cells that evade immune surveillance. As important innate immune cells, macrophages play important roles in maintaining homeostasis, preventing pathogen invasion, resisting tumor cells and promoting adaptive immune response. CD47 is found to be overexpressed on tumor cells and act as a don’t eat me’ signal, which contributes to immune evasion. Macrophages mediated phagocytosis via blockade CD47/SIRPα (signal regulatory protein alpha) interaction was proved to induce effective antitumor immune response. Methods A novel peptide pep-20, specifically targeting CD47 and blocking CD47/SIRPα interaction, was identified via high-throughput phage display library bio-panning. The capability to enhance the macrophage-mediated phagocytosis activities and antitumor effects of pep-20 were investigated. The mechanism of pep-20 to induce T-cell response was explored by ex vivo analysis and confirmed via macrophage depleting strategy. The structure-activity relationship and D-amino acid substitution of pep-20 were also studied. The antitumor effects and mechanism of a proteolysis resistant D-amino acid derivate pep-20-D12 combined with irradiation (IR) were also investigated. Results Pep-20 showed remarkable enhancement of macrophage-mediated phagocytosis to both solid and hematologic tumor cells in vitro, and inhibited tumor growth in immune-competent tumor-bearing mice. Furthermore, pep-20 promoted macrophages to mobilize the antitumor T-cell response with minimal toxicity. Furthermore, systemic administration of the derivate pep-20-D12 showed robust synergistic antitumor efficacy in combination with IR. Conclusion In summary, these results demonstrated that CD47/SIRPα blocking peptides, pep-20 and its derivate, could serve as promising candidates to promote macrophages-mediated phagocytosis and immune response in cancer immunotherapy.
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Affiliation(s)
- Hongfei Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Yixuan Sun
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Xiuman Zhou
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Chunxia Chen
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Ling Jiao
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Wanqiong Li
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Shanshan Gou
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Yanying Li
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Jiangfeng Du
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Guanyu Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Wenjie Zhai
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Yahong Wu
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Yuanming Qi
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Yanfeng Gao
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong, China
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15
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Li Y, Cao X, Tian C, Zheng JS. Chemical protein synthesis-assisted high-throughput screening strategies for d-peptides in drug discovery. CHINESE CHEM LETT 2020. [DOI: 10.1016/j.cclet.2020.04.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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16
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Evans BJ, King AT, Katsifis A, Matesic L, Jamie JF. Methods to Enhance the Metabolic Stability of Peptide-Based PET Radiopharmaceuticals. Molecules 2020; 25:molecules25102314. [PMID: 32423178 PMCID: PMC7287708 DOI: 10.3390/molecules25102314] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/11/2020] [Accepted: 05/13/2020] [Indexed: 12/28/2022] Open
Abstract
The high affinity and specificity of peptides towards biological targets, in addition to their favorable pharmacological properties, has encouraged the development of many peptide-based pharmaceuticals, including peptide-based positron emission tomography (PET) radiopharmaceuticals. However, the poor in vivo stability of unmodified peptides against proteolysis is a major challenge that must be overcome, as it can result in an impractically short in vivo biological half-life and a subsequently poor bioavailability when used in imaging and therapeutic applications. Consequently, many biologically and pharmacologically interesting peptide-based drugs may never see application. A potential way to overcome this is using peptide analogues designed to mimic the pharmacophore of a native peptide while also containing unnatural modifications that act to maintain or improve the pharmacological properties. This review explores strategies that have been developed to increase the metabolic stability of peptide-based pharmaceuticals. It includes modifications of the C- and/or N-termini, introduction of d- or other unnatural amino acids, backbone modification, PEGylation and alkyl chain incorporation, cyclization and peptide bond substitution, and where those strategies have been, or could be, applied to PET peptide-based radiopharmaceuticals.
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Affiliation(s)
- Brendan J. Evans
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia; (B.J.E.); (A.T.K.)
| | - Andrew T. King
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia; (B.J.E.); (A.T.K.)
| | - Andrew Katsifis
- Department of Molecular Imaging, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia;
| | - Lidia Matesic
- Australian Nuclear Science and Technology Organisation (ANSTO), Lucas Heights, NSW 2234, Australia;
| | - Joanne F. Jamie
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia; (B.J.E.); (A.T.K.)
- Correspondence: ; Tel.: +61-2-9850-8283
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17
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Shah SS, Casanova N, Antuono G, Sabatino D. Polyamide Backbone Modified Cell Targeting and Penetrating Peptides in Cancer Detection and Treatment. Front Chem 2020; 8:218. [PMID: 32296681 PMCID: PMC7136562 DOI: 10.3389/fchem.2020.00218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 03/09/2020] [Indexed: 12/15/2022] Open
Abstract
Cell penetrating and targeting peptides (CPPs and CTPs) encompass an important class of biochemically active peptides owning the capabilities of targeting and translocating within selected cell types. As such, they have been widely used in the delivery of imaging and therapeutic agents for the diagnosis and treatment of various diseases, especially in cancer. Despite their potential utility, first generation CTPs and CPPs based on the native peptide sequences are limited by poor biological and pharmacological properties, thereby restricting their efficacy. Therefore, medicinal chemistry approaches have been designed and developed to construct related peptidomimetics. Of specific interest herein, are the design applications which modify the polyamide backbone of lead CTPs and CPPs. These modifications aim to improve the biochemical characteristics of the native peptide sequence in order to enhance its diagnostic and therapeutic capabilities. This review will focus on a selected set of cell penetrating and targeting peptides and their related peptidomimetics whose polyamide backbone has been modified in order to improve their applications in cancer detection and treatment.
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Affiliation(s)
- Sunil S Shah
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, NJ, United States
| | - Nelson Casanova
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, NJ, United States
| | - Gina Antuono
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, NJ, United States
| | - David Sabatino
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, NJ, United States
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18
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Yu R, Liu H, Wang B, Harvey PJ, Wei N, Chu Y. Synthesis and biological activity study of the retro-isomer of RhTx against TRPV1. RSC Adv 2020; 10:2141-2145. [PMID: 35494567 PMCID: PMC9048425 DOI: 10.1039/c9ra08829f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/05/2020] [Indexed: 01/09/2023] Open
Abstract
TRPV1 is a ligand-gated ion channel and plays an important role in detecting noxious heat and pain with an unknown mechanism. RhTx from Chinese red-headed centipede activates the TRPV1 channel through the heat activation pathway by binding to the outer pore region, and causes extreme pain. Here, we synthesized RhTx and its retro-isomer RL-RhTx. Their structures were investigated by their circular dichroic spectra and NMR spectra. The effect of RhTx and RL-RhTx on the currents of wild-type and mutants of TRPV1 indicated that RL-RhTx have comparable TRPV1 activation responses to RhTx. A mutagenesis study showed that four TRPV1 residues, including Leu461, Asp602, Tyr632 and Thr634, significantly contributed to the activation effects of RL-RhTx and RhTx, and both peptides probably bind with TRPV1 in similar binding modes. As a novel TRPV1 activator, RL-RhTx provides an essential powerful tool for the investigation of activation mechanisms of TRPV1.
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Affiliation(s)
- Rilei Yu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China Qingdao 266003 China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology Qingdao 266003 China
| | - Huijie Liu
- Department of Pharmacology, School of Pharmacy, Qingdao University Qingdao 266021 China
| | - Baishi Wang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China Qingdao 266003 China
| | - Peta J Harvey
- Institute for Molecular Bioscience, The University of Queensland Brisbane QLD 4072 Australia
| | - Ningning Wei
- Department of Pharmacology, School of Pharmacy, Qingdao University Qingdao 266021 China
| | - Yanyan Chu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China Qingdao 266003 China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology Qingdao 266003 China
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19
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Tang Y, Wang X, Li J, Nie Y, Liao G, Yu Y, Li C. Overcoming the Reticuloendothelial System Barrier to Drug Delivery with a "Don't-Eat-Us" Strategy. ACS NANO 2019; 13:13015-13026. [PMID: 31689086 DOI: 10.1021/acsnano.9b05679] [Citation(s) in RCA: 163] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Overcoming the reticuloendothelial system (RES) has long been a vital challenge to nanoparticles as drug carriers. Modification of nanoparticles with polyethylene glycol helps them avoid clearance by macrophages but also suppresses their internalization by target cells. To overcome this paradox, we developed an RES-specific blocking system utilizing a "don't-eat-us" strategy. First, a CD47-derived, enzyme-resistant peptide ligand was designed and placed on liposomes (d-self-peptide-labeled liposome, DSL). After mainline administration, DSL was quickly adsorbed onto hepatic phagocyte membranes (including those of Kupffer cells and liver sinusoidal endothelial cells), forming a long-lasting mask that enclosed the cell membranes and thus reducing interactions between phagocytes and subsequently injected nanoparticles. Compared with blank conventional liposomes (CL), DSL blocked the RES at a much lower dose, and the effect was sustained for a much longer time, highly prolonging the elimination half-life of the subsequently injected nanoparticles. This "don't-eat-us" strategy by DSL was further verified on the brain-targeted delivery against a cryptococcal meningitis model, providing dramatically enhanced brain accumulation of the targeted delivery system and superior therapeutic outcome of model drug Amphotericin B compared with CL. Our study demonstrates a strategy that blocks the RES by masking phagocyte surfaces to prolong nanoparticle circulation time without excess modification and illustrates its utility in enhancing nanoparticle delivery.
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Affiliation(s)
- Yixuan Tang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Pharmaceutical Sciences , Southwest University , Chongqing 400715 , P.R. China
| | - Xiaoyou Wang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Pharmaceutical Sciences , Southwest University , Chongqing 400715 , P.R. China
| | - Jie Li
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Pharmaceutical Sciences , Southwest University , Chongqing 400715 , P.R. China
| | - Yu Nie
- National Engineering Research Center for Biomaterials , Sichuan University , Sichuan 610065 , P.R. China
| | - Guojian Liao
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Pharmaceutical Sciences , Southwest University , Chongqing 400715 , P.R. China
| | - Yang Yu
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Pharmaceutical Sciences , Southwest University , Chongqing 400715 , P.R. China
| | - Chong Li
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Pharmaceutical Sciences , Southwest University , Chongqing 400715 , P.R. China
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20
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Zerze GH, Stillinger FH, Debenedetti PG. Computational investigation of retro-isomer equilibrium structures: Intrinsically disordered, foldable, and cyclic peptides. FEBS Lett 2019; 594:104-113. [PMID: 31356683 DOI: 10.1002/1873-3468.13558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 06/20/2019] [Accepted: 07/26/2019] [Indexed: 11/08/2022]
Abstract
We use all-atom modeling and advanced-sampling molecular dynamics simulations to investigate quantitatively the effect of peptide bond directionality on the equilibrium structures of four linear (two foldable, two disordered) and two cyclic peptides. We find that the retro forms of cyclic and foldable linear peptides adopt distinctively different conformations compared to their parents. While the retro form of a linear intrinsically disordered peptide with transient secondary structure fails to reproduce a secondary structure content similar to that of its parent, the retro form of a shorter disordered linear peptide shows only minor differences compared to its parent.
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Affiliation(s)
- Gül H Zerze
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | | | - Pablo G Debenedetti
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
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21
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Yang W, Zhang Q, Zhang C, Guo A, Wang Y, You H, Zhang X, Lai L. Computational design and optimization of noveld‐peptideTNFα inhibitors. FEBS Lett 2019; 593:1292-1302. [DOI: 10.1002/1873-3468.13444] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 04/27/2019] [Accepted: 05/14/2019] [Indexed: 01/18/2023]
Affiliation(s)
- Wei Yang
- School of Life Sciences Tsinghua University Beijing China
| | - Qi Zhang
- School of Life Sciences Peking University Beijing China
- Peking‐Tsinghua Center for Life Sciences AAIS Peking University Beijing China
| | - Changsheng Zhang
- BNLMS College of Chemistry and Molecular Engineering Peking University Beijing China
| | - Annan Guo
- Peking‐Tsinghua Center for Life Sciences AAIS Peking University Beijing China
| | - Yanyan Wang
- Peking‐Tsinghua Center for Life Sciences AAIS Peking University Beijing China
| | - Hantian You
- BNLMS College of Chemistry and Molecular Engineering Peking University Beijing China
| | - Xiaoling Zhang
- Center for Quantitative Biology AAIS Peking University Beijing China
| | - Luhua Lai
- Peking‐Tsinghua Center for Life Sciences AAIS Peking University Beijing China
- BNLMS College of Chemistry and Molecular Engineering Peking University Beijing China
- Center for Quantitative Biology AAIS Peking University Beijing China
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22
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Jiang Z, Guan J, Qian J, Zhan C. Peptide ligand-mediated targeted drug delivery of nanomedicines. Biomater Sci 2019; 7:461-471. [PMID: 30656305 DOI: 10.1039/c8bm01340c] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Targeted drug delivery is emerging as a promising strategy to achieve better clinical outcomes. Actively targeted drug delivery that utilizes overexpressed receptors or antigens on diseased tissues is receiving increasing scrutiny, especially due to the uncertainty of existence of the enhanced permeability and retention (EPR) effect in cancer patients. Peptide ligands are advantageous over other classes of targeting ligands due to their accessibility of high-throughput screening, ease of synthesis, high specificity and affinity, etc. In this review, we briefly summarize the resources of peptide ligands and discuss the pitfalls and perspectives of peptide ligand-mediated targeted delivery of nanomedicines.
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Affiliation(s)
- Zhuxuan Jiang
- Department of Pharmacology, School of Basic Medical Sciences & State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200032, P.R. China.
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23
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Rai J. Peptide and protein mimetics by retro and retroinverso analogs. Chem Biol Drug Des 2019; 93:724-736. [PMID: 30582286 DOI: 10.1111/cbdd.13472] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 12/10/2018] [Accepted: 12/16/2018] [Indexed: 12/19/2022]
Abstract
Retroinverso analog of a natural polypeptide can sometimes mimic the structure and function of the natural peptide. The additional advantage of using retroinverso analog is that it is resistant to proteolysis. The retroinverso analogs have peptide sequence in reverse direction with respect to natural peptide and also have chirality of amino acid inverted from L to D. The D amino acids cannot be recognized by common proteases of the body; therefore, these peptides will not be degraded easily and have a longer-lasting effect as vaccine and inhibitor drugs. There have been many contested propositions about the geometric relationship between a peptide and its retro, inverso, or retroinverso analog. A retroinverso analog sometimes fails to adopt the structure that can mimic the function of the natural peptide. In such cases, partial retroinverso analog and other modifications can help in achieving the desired structure and function. Here, we review the theory, major experimental attempts, prediction methods, and alternative strategies related to retroinverso peptidomimetics.
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24
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Kreitler DF, Yao Z, Steinkruger JD, Mortenson DE, Huang L, Mittal R, Travis BR, Forest KT, Gellman SH. A Hendecad Motif Is Preferred for Heterochiral Coiled-Coil Formation. J Am Chem Soc 2019; 141:1583-1592. [PMID: 30645104 DOI: 10.1021/jacs.8b11246] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structural principles that govern interactions between l- and d-peptides are not well understood. Among natural proteins, coiled-coil assemblies formed between or among α-helices are the most regular feature of tertiary and quaternary structures. We recently reported the first high-resolution structures for heterochiral coiled-coil dimers, which represent a starting point for understanding associations of l- and d-polypeptides. These structures were an unexpected outcome from crystallization of a racemic peptide corresponding to the transmembrane domain of the influenza A M2 protein (M2-TM). The reported structures raised the possibility that heterochiral coiled-coil dimers prefer an 11-residue (hendecad) sequence repeat, in contrast to the 7-residue (heptad) sequence repeat that is dominant among natural coiled coils. To gain insight on sequence repeat preferences of heterochiral coiled-coils, we have examined three M2-TM variants containing substitutions intended to minimize steric clashes between side chains at the coiled-coil interface. In each of the three new crystal structures, we observed heterochiral coiled-coil associations that closely match a hendecad sequence motif, which strengthens the conclusion that this motif is intrinsic to the pairing of α-helices with opposite handedness. In each case, the presence of a hendecad motif was established by comparing the observed helical frequency to that of an ideal hendecad. This comparison revealed that decreasing the size of the amino acid side chain at positions that project toward the superhelical axis produces tighter packing, as determined by the size of the coiled-coil radius. These results provide a basis for future design of heterochiral coiled-coil pairings.
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Affiliation(s)
- Dale F Kreitler
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Zhihui Yao
- Graduate Program in Biophysics , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Jay D Steinkruger
- School of Natural Sciences , University of Central Missouri , Warrensburg , Missouri 64093 , United States
| | - David E Mortenson
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Lijun Huang
- Anatrace , Maumee , Ohio 43537 , United States
| | | | | | - Katrina T Forest
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States.,Graduate Program in Biophysics , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States.,Department of Bacteriology , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Samuel H Gellman
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States.,Graduate Program in Biophysics , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
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25
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Abstract
Macrocyclic peptides are a unique class of molecules that display a relatively constrained peptidic backbone as compared to their linear counterparts leading to the defined 3-D orientation of the constituent amino acids (pharmacophore). Although they are attractive candidates for lead discovery owing to the unique conformational features, their peptidic backbone is susceptible to proteolytic cleavage in various biological fluids that compromise their efficacy. In this chapter we review the various classical and contemporary chemical and biological approaches that have been utilized to combat the metabolic instability of macrocyclic peptides. We note that any chemical modification that helps in providing either local or global conformational rigidity to these macrocyclic peptides aids in improving their metabolic stability typically by slowing the cleavage kinetics by the proteases.
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Affiliation(s)
- Bhavesh Khatri
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | | | - Jayanta Chatterjee
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.
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26
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Nevola L, Varese M, Martín-Quirós A, Mari G, Eckelt K, Gorostiza P, Giralt E. Targeted Nanoswitchable Inhibitors of Protein-Protein Interactions Involved in Apoptosis. ChemMedChem 2018; 14:100-106. [PMID: 30380184 DOI: 10.1002/cmdc.201800647] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Indexed: 12/20/2022]
Abstract
Progress in drug delivery is hampered by a lack of efficient strategies to target drugs with high specificity and precise spatiotemporal regulation. The remote control of nanoparticles and drugs with light allows regulation of their action site and dosage. Peptide-based drugs are highly specific, non-immunogenic, and can be designed to cross the plasma membrane. In order to combine target specificity and remote control of drug action, here we describe a versatile strategy based on a generalized template to design nanoswitchable peptides that modulate protein-protein interactions upon light activation. This approach is demonstrated to promote photomodulation of two important targets involved in apoptosis (the interactions Bcl-xL-Bak and MDM2-p53), but can be also applied to a large pool of therapeutically relevant protein-protein interactions mediated by α-helical motifs. The template can be adjusted using readily available information about hot spots (residues contributing most to the binding energy) at the protein-protein interface of interest.
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Affiliation(s)
- Laura Nevola
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Monica Varese
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028, Barcelona, Spain
| | | | - Giacomo Mari
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028, Barcelona, Spain.,University of Bologna, Bologna, 40126, Italy
| | - Kay Eckelt
- Institute for Bioengineering of Catalonia (IBEC), Barcelona, 08028, Spain.,Network Biomedical Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, 28029, Spain
| | - Pau Gorostiza
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028, Barcelona, Spain.,Institute for Bioengineering of Catalonia (IBEC), Barcelona, 08028, Spain.,Network Biomedical Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, 28029, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, 08010, Spain
| | - Ernest Giralt
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028, Barcelona, Spain.,University of Barcelona (UB), Barcelona, 080280, Spain
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27
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Rezazadeh F, Sadeghzadeh N, Abedi SM, Abediankenari S. 99mTc labeled D(LPR): A novel retro-inverso peptide for VEGF receptor-1 targeted tumor imaging. Nucl Med Biol 2018; 62-63:54-62. [PMID: 29885559 DOI: 10.1016/j.nucmedbio.2018.05.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 05/25/2018] [Accepted: 05/25/2018] [Indexed: 12/01/2022]
Abstract
INTRODUCTION The aim of this study was to evaluate the ability of D(LPR), a novel retro-inverso peptidomimetic derivative for imaging colon cancer. METHODS Two different D(LPR) analogs were designed and compared based on conjugation of HYNIC at peptide's C or N terminal and then labeled with technetium-99m using tricine/EDDA as an exchange coligands. The radiolabeled conjugates were assessed for in vitro stability in saline and serum. The VEGFR-1 and NRP-1 receptors affinity, in vitro internalization and also dissociation Constance was evaluated. SPCET imaging and biodistribution studies were performed in nude mice bearing HT-29 xenograft tumors. RESULTS Both peptides labeled with technetium-99m in high radiochemical yield (˃97%). Peptide stability studies indicated a high metabolic stability of the radiopeptides in solution and serum. In vitro blocking studies demonstrated specific binding and internalization of [99mTc]Tc-HYNIC-peptides in cultured HUVEC cells. The Kd value for 99mTc-peptide 1 and 99mTc-peptide 2 were found to be 56.8 ± 12.9 nM and 71.6 ± 17.9 nM respectively. The tumor to muscle ratio was significant at 0.5 and 1 h after injection (4.5 and 4 for 99mTc-peptide 1 and 4.9 and 4.4 for 99mTc-peptide 2 at 0.5 and 1 h p.i. respectively). SPECT imaging studies revealed that both radioconjugates had prominent activity accumulation in VEGFR-1 and NRP-1 expressing HT-29 tumors. CONCLUSION This study is the first instance of using a radiolabeled retro-inverso peptide for tumor imaging which is a promising tool to improve the performance of fragile peptide probes in vivo as imaging agents and warrant further investigations in other peptide-target systems.
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Affiliation(s)
- Farzaneh Rezazadeh
- Faculty of Pharmacy, Department of Radiopharmacy, Mazandaran University of Medical Sciences, Sari, Iran; Student Research Committee, Mazandaran University of Medical Sciences, Sari, Iran
| | - Nourollah Sadeghzadeh
- Faculty of Pharmacy, Department of Radiopharmacy, Mazandaran University of Medical Sciences, Sari, Iran.
| | - Seyed Mohammad Abedi
- Faculty of Medicine, Department of Radiology, Mazandaran University of Medical Sciences, Sari, Iran
| | - Saeid Abediankenari
- Immunogenetics Research Center, Mazandaran University of Medical Sciences, Sari, Iran
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28
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Garton M, Nim S, Stone TA, Wang KE, Deber CM, Kim PM. Method to generate highly stable D-amino acid analogs of bioactive helical peptides using a mirror image of the entire PDB. Proc Natl Acad Sci U S A 2018; 115:1505-1510. [PMID: 29378946 PMCID: PMC5816147 DOI: 10.1073/pnas.1711837115] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Biologics are a rapidly growing class of therapeutics with many advantages over traditional small molecule drugs. A major obstacle to their development is that proteins and peptides are easily destroyed by proteases and, thus, typically have prohibitively short half-lives in human gut, plasma, and cells. One of the most effective ways to prevent degradation is to engineer analogs from dextrorotary (D)-amino acids, with up to 105-fold improvements in potency reported. We here propose a general peptide-engineering platform that overcomes limitations of previous methods. By creating a mirror image of every structure in the Protein Data Bank (PDB), we generate a database of ∼2.8 million D-peptides. To obtain a D-analog of a given peptide, we search the (D)-PDB for similar configurations of its critical-"hotspot"-residues. As a proof of concept, we apply our method to two peptides that are Food and Drug Administration approved as therapeutics for diabetes and osteoporosis, respectively. We obtain D-analogs that activate the GLP1 and PTH1 receptors with the same efficacy as their natural counterparts and show greatly increased half-life.
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Affiliation(s)
- Michael Garton
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto M5S 3E1, Canada
| | - Satra Nim
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto M5S 3E1, Canada
| | - Tracy A Stone
- Department of Biochemistry, University of Toronto, Toronto M5S 1A8, Canada
- Division of Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto M5G 0A4, Canada
| | - Kyle Ethan Wang
- Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada
| | - Charles M Deber
- Department of Biochemistry, University of Toronto, Toronto M5S 1A8, Canada
- Division of Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto M5G 0A4, Canada
| | - Philip M Kim
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto M5S 3E1, Canada;
- Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada
- Department of Computer Science, University of Toronto, Toronto M5S 2E4, Canada
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29
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Ramaswamy K, Forbes L, Minuesa G, Gindin T, Brown F, Kharas MG, Krivtsov AV, Armstrong SA, Still E, de Stanchina E, Knoechel B, Koche R, Kentsis A. Peptidomimetic blockade of MYB in acute myeloid leukemia. Nat Commun 2018; 9:110. [PMID: 29317678 PMCID: PMC5760651 DOI: 10.1038/s41467-017-02618-6] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 12/13/2017] [Indexed: 02/08/2023] Open
Abstract
Aberrant gene expression is a hallmark of acute leukemias. MYB-driven transcriptional coactivation with CREB-binding protein (CBP)/P300 is required for acute lymphoblastic and myeloid leukemias, including refractory MLL-rearranged leukemias. Using structure-guided molecular design, we developed a peptidomimetic inhibitor MYBMIM that interferes with the assembly of the molecular MYB:CBP/P300 complex and rapidly accumulates in the nuclei of AML cells. Treatment of AML cells with MYBMIM led to the dissociation of the MYB:CBP/P300 complex in cells, its displacement from oncogenic enhancers enriched for MYB binding sites, and downregulation of MYB-dependent gene expression, including of MYC and BCL2 oncogenes. AML cells underwent mitochondrial apoptosis in response to MYBMIM, which was partially rescued by ectopic expression of BCL2. MYBMIM impeded leukemia growth and extended survival of immunodeficient mice engrafted with primary patient-derived MLL-rearranged leukemia cells. These findings elucidate the dependence of human AML on aberrant transcriptional coactivation, and establish a pharmacologic approach for its therapeutic blockade.
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Affiliation(s)
- Kavitha Ramaswamy
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, 10065, USA
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
| | - Lauren Forbes
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, 10065, USA
- Departments of Pediatrics, Pharmacology, and Physiology & Biophysics, Weill Cornell Medical College, Cornell University, New York, NY, 10065, USA
| | - Gerard Minuesa
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, 10065, USA
| | - Tatyana Gindin
- Department of Pathology and Cell Biology, Columbia University Medical Center and New York Presbyterian Hospital, New York, NY, 10065, USA
| | - Fiona Brown
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, 10065, USA
| | - Michael G Kharas
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, 10065, USA
| | - Andrei V Krivtsov
- Center for Epigenetics Research, Sloan Kettering Institute, New York, NY, 10065, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Scott A Armstrong
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
- Center for Epigenetics Research, Sloan Kettering Institute, New York, NY, 10065, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Eric Still
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, 10065, USA
| | - Elisa de Stanchina
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Birgit Knoechel
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Richard Koche
- Center for Epigenetics Research, Sloan Kettering Institute, New York, NY, 10065, USA
| | - Alex Kentsis
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, 10065, USA.
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA.
- Departments of Pediatrics, Pharmacology, and Physiology & Biophysics, Weill Cornell Medical College, Cornell University, New York, NY, 10065, USA.
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30
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Thornton P, Sevalle J, Deery MJ, Fraser G, Zhou Y, Ståhl S, Franssen EH, Dodd RB, Qamar S, Gomez Perez‐Nievas B, Nicol LSC, Eketjäll S, Revell J, Jones C, Billinton A, St George‐Hyslop PH, Chessell I, Crowther DC. TREM2 shedding by cleavage at the H157-S158 bond is accelerated for the Alzheimer's disease-associated H157Y variant. EMBO Mol Med 2017; 9:1366-1378. [PMID: 28855301 PMCID: PMC5623839 DOI: 10.15252/emmm.201707673] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
We have characterised the proteolytic cleavage events responsible for the shedding of triggering receptor expressed on myeloid cells 2 (TREM2) from primary cultures of human macrophages, murine microglia and TREM2-expressing human embryonic kidney (HEK293) cells. In all cell types, a soluble 17 kDa N-terminal cleavage fragment was shed into the conditioned media in a constitutive process that is inhibited by G1254023X and metalloprotease inhibitors and siRNA targeting ADAM10. Inhibitors of serine proteases and matrix metalloproteinases 2/9, and ADAM17 siRNA did not block TREM2 shedding. Peptidomimetic protease inhibitors highlighted a possible cleavage site, and mass spectrometry confirmed that shedding occurred predominantly at the H157-S158 peptide bond for both wild-type and H157Y human TREM2 and for the wild-type murine orthologue. Crucially, we also show that the Alzheimer's disease-associated H157Y TREM2 variant was shed more rapidly than wild type from HEK293 cells, possibly by a novel, batimastat- and ADAM10-siRNA-independent, sheddase activity. These insights offer new therapeutic targets for modulating the innate immune response in Alzheimer's and other neurological diseases.
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Affiliation(s)
- Peter Thornton
- Neuroscience, Innovative Medicines and Early DevelopmentAstraZenecaGranta ParkCambridgeUK
| | - Jean Sevalle
- Tanz Centre for Research in Neurodegenerative DiseasesUniversity of TorontoTorontoONCanada
| | - Michael J Deery
- Cambridge Centre for ProteomicsUniversity of CambridgeCambridgeUK
| | - Graham Fraser
- Neuroscience, Innovative Medicines and Early DevelopmentAstraZenecaGranta ParkCambridgeUK
| | - Ye Zhou
- Tanz Centre for Research in Neurodegenerative DiseasesUniversity of TorontoTorontoONCanada
| | - Sara Ståhl
- AstraZeneca Translational Sciences CentreKarolinska InstitutetStockholmSweden
| | - Elske H Franssen
- Neuroscience, Innovative Medicines and Early DevelopmentAstraZenecaGranta ParkCambridgeUK
| | - Roger B Dodd
- Department of Clinical NeurosciencesCambridge Institute for Medical ResearchUniversity of CambridgeCambridgeUK,MedImmune LimitedGranta ParkCambridgeUK
| | - Seema Qamar
- Department of Clinical NeurosciencesCambridge Institute for Medical ResearchUniversity of CambridgeCambridgeUK
| | | | | | - Susanna Eketjäll
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early DevelopmentAstraZeneca, ICMCHuddingeSweden
| | | | | | - Andrew Billinton
- Neuroscience, Innovative Medicines and Early DevelopmentAstraZenecaGranta ParkCambridgeUK
| | - Peter H St George‐Hyslop
- Tanz Centre for Research in Neurodegenerative DiseasesUniversity of TorontoTorontoONCanada,Department of Clinical NeurosciencesCambridge Institute for Medical ResearchUniversity of CambridgeCambridgeUK
| | - Iain Chessell
- Neuroscience, Innovative Medicines and Early DevelopmentAstraZenecaGranta ParkCambridgeUK
| | - Damian C Crowther
- Neuroscience, Innovative Medicines and Early DevelopmentAstraZenecaGranta ParkCambridgeUK
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31
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Li Z, Xie J, Peng S, Liu S, Wang Y, Lu W, Shen J, Li C. Novel Strategy Utilizing Extracellular Cysteine-Rich Domain of Membrane Receptor for Constructing d-Peptide Mediated Targeted Drug Delivery Systems: A Case Study on Fn14. Bioconjug Chem 2017; 28:2167-2179. [DOI: 10.1021/acs.bioconjchem.7b00326] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zhuoxuan Li
- College
of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, PR China
| | - Jing Xie
- College
of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, PR China
| | - Shan Peng
- College
of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, PR China
| | - Sha Liu
- College
of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, PR China
| | - Ying Wang
- College
of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, PR China
| | - Weiyue Lu
- School
of Pharmacy, Key Laboratory of Smart Drug Delivery, Ministry of Education, Fudan University, Shanghai 201203, PR China
| | - Jie Shen
- College
of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Chong Li
- College
of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, PR China
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32
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Zamuner A, Brun P, Scorzeto M, Sica G, Castagliuolo I, Dettin M. Smart biomaterials: Surfaces functionalized with proteolytically stable osteoblast-adhesive peptides. Bioact Mater 2017; 2:121-130. [PMID: 29744421 PMCID: PMC5935176 DOI: 10.1016/j.bioactmat.2017.05.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 05/09/2017] [Accepted: 05/09/2017] [Indexed: 02/07/2023] Open
Abstract
Engineered scaffolds for bone tissue regeneration are designed to promote cell adhesion, growth, proliferation and differentiation. Recently, covalent and selective functionalization of glass and titanium surfaces with an adhesive peptide (HVP) mapped on [351-359] sequence of human Vitronectin allowed to selectively increase osteoblast attachment and adhesion strength in in vitro assays, and to promote osseointegration in in vivo studies. For the first time to our knowledge, in this study we investigated the resistance of adhesion sequences to proteolytic digestion: HVP was completely cleaved after 5 h. In order to overcome the enzymatic degradation of the native peptide under physiological conditions we synthetized three analogues of HVP sequence. A retro-inverted peptide D-2HVP, composed of D amino acids, was completely stable in serum-containing medium. In addition, glass surfaces functionalized with D-2HVP increased human osteoblast adhesion as compared to the native peptide and maintained deposition of calcium. Interestingly, D-2HVP increased expression of IBSP, VTN and SPP1 genes as compared to HVP functionalized surfaces. Total internal reflection fluorescence microscope analysis showed cells with numerous filopodia spread on D-2HVP-functionalized surfaces. Therefore, the D-2HVP sequence is proposed as new osteoblast adhesive peptide with increased bioactivity and high proteolytic resistance.
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Affiliation(s)
- Annj Zamuner
- Department of Industrial Engineering, University of Padova, Via F. Marzolo 9, 35131, Padova, Italy
| | - Paola Brun
- Department of Molecular Medicine, University of Padova, Via A. Gabelli 63, 35121, Padova, Italy
| | - Michele Scorzeto
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, 35131, Padova, Italy
| | - Giuseppe Sica
- Department of Industrial Engineering, University of Padova, Via F. Marzolo 9, 35131, Padova, Italy
| | - Ignazio Castagliuolo
- Department of Molecular Medicine, University of Padova, Via A. Gabelli 63, 35121, Padova, Italy
| | - Monica Dettin
- Department of Industrial Engineering, University of Padova, Via F. Marzolo 9, 35131, Padova, Italy
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33
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Huang L, Xie J, Bi Q, Li Z, Liu S, Shen Q, Li C. Highly Selective Targeting of Hepatic Stellate Cells for Liver Fibrosis Treatment Using a d-Enantiomeric Peptide Ligand of Fn14 Identified by Mirror-Image mRNA Display. Mol Pharm 2017; 14:1742-1753. [PMID: 28358987 DOI: 10.1021/acs.molpharmaceut.6b01174] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Although liver fibrosis is a major public health issue, there is still no effective drug therapy in the clinic. Fibroblast growth factor-inducible 14 (Fn14), a membrane receptor highly specifically expressed in activated hepatic stellate cells (HSCs), is the key driver of liver fibrosis, and thus, it has a great potential as a novel target for the development of effective treatment. Here, we identified a d-enantiomeric peptide ligand of Fn14 through mirror-image mRNA display. This included the chemical synthesis of a d-enantiomer of the target protein (extracellular domain of Fn14), identification of an l-peptide ligand of d-Fn14 using a constructed mRNA peptide library, and identification of a d-enantiomer of the l-peptide, which is a ligand of the natural Fn14 for reasons of symmetry. The obtained d-peptide ligand showed strong binding to Fn14 while maintaining high proteolytic resistance. As a targeting moiety, this d-peptide successfully mediated high selectivity of activated HSCs for liposomal vehicles compared to that of other major cell types in the liver and significantly enhanced the accumulation of liposomes in the liver fibrosis region of a carbon tetrachloride-induced mouse model. Moreover, in combination with curcumin as an encapsulated load, a liposomal formulation conjugated with this d-peptide showed powerful inhibition of the proliferation of activated HSCs and reduced the liver fibrosis to a significant extent in vivo. This Fn14-targeting strategy may represent a promising approach to targeted drug delivery for liver fibrosis treatment. Meanwhile, the mirror-image mRNA display can provide a new arsenal for the development of d-peptide-based therapeutics against a variety of human diseases.
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Affiliation(s)
- Luying Huang
- College of Pharmaceutical Sciences, Southwest University , Chongqing 400715, China
| | - Jing Xie
- College of Pharmaceutical Sciences, Southwest University , Chongqing 400715, China
| | - Qiuyan Bi
- College of Pharmaceutical Sciences, Southwest University , Chongqing 400715, China
| | - Zhuoxuan Li
- College of Pharmaceutical Sciences, Southwest University , Chongqing 400715, China
| | - Sha Liu
- College of Pharmaceutical Sciences, Southwest University , Chongqing 400715, China
| | - Qing Shen
- School of Pharmacy, Key Laboratory of Smart Drug Delivery, Ministry of Education, Fudan University , Shanghai 201203, China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University , Shanghai 200032, China
| | - Chong Li
- College of Pharmaceutical Sciences, Southwest University , Chongqing 400715, China
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34
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Feng Z, Xu B. Inspiration from the mirror: D-amino acid containing peptides in biomedical approaches. Biomol Concepts 2017; 7:179-87. [PMID: 27159920 DOI: 10.1515/bmc-2015-0035] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Accepted: 01/12/2016] [Indexed: 01/09/2023] Open
Abstract
D-amino acids, the enantiomers of naturally abundant L-amino acids, bear unique stereochemistry properties that lead to the resistance towards most of the endogenous enzymes. Previous works have demonstrated applications of D-amino acids in therapeutic development with the aid of mirror-image phage display and retro-inverso peptide synthesis. In this review, we highlight the recent progress and challenges in the exploration of D-amino acids at the interface of chemistry and life science. First, we will introduce some progress made in traditional application of D-amino acids to enhance biostability of peptide therapeutics. Then, we discuss some works that explore the relatively underexplored interactions between the enzyme and D-amino acids and enzymatic reactions of D-amino acids. To highlight the enzymatic reactions of D-amino acids, we will describe several emerging works on the enzyme-instructed self-assembly (EISA) and their potential application in selective anti-inflammatory or anticancer therapies. At the end, we briefly mention the challenges and possible future directions.
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35
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Ying M, Shen Q, Zhan C, Wei X, Gao J, Xie C, Yao B, Lu W. A stabilized peptide ligand for multifunctional glioma targeted drug delivery. J Control Release 2016; 243:86-98. [PMID: 27693752 DOI: 10.1016/j.jconrel.2016.09.035] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Revised: 09/15/2016] [Accepted: 09/28/2016] [Indexed: 12/18/2022]
Abstract
Peptide ligands consisting of l-amino acids are subject to proteolysis in vivo. When modified on the surface of nanocarriers, those peptide ligands would readily degrade and the targeting efficacy is significantly attenuated. It has received increasing scrutiny to design stable peptide ligands for targeted drug delivery. Here, we present the design of a stable peptide ligand by the formation of a head-to-tail amide bond as an example. Even though the linear l-peptide A7R (termed LA7R) can bind specifically to vascular endothelial growth factor receptor 2 (VEGFR2) and neuropilin-1 (NRP-1) that are overexpressed on glioma cells, neovasculature and glioma vasculogenic mimicry (VM), the tumor-homing capacity of LA7R is greatly impaired in vivo due to proteolysis (e.g. in the serum). A cyclic A7R (cA7R) peptide was identified by computer-aided peptide design and synthesized with high yield by combining solid phase peptide synthesis and native chemical ligation. The binding of cA7R to both receptors was theoretically and experimentally assessed. In our simulated model hydrophobic and ionic interactions dominated the binding of LA7R to receptors. It is very interesting that cA7R adopting a different structure from LA7R retained high binding affinities to receptors without affecting the hydrophobic and ionic interactions. After head-to-tail cyclization by the formation of an amide bond, cA7R exhibited exceptional stability in mouse serum. Either cA7R or LA7R was conjugated on the surface of doxorubicin (DOX) loaded liposomes (cA7R-LS/DOX or LA7R-LS/DOX). The results of in vitro cellular assays indicated that cA7R-LS/DOX not only displayed stronger anti-proliferative effect against glioma cells, but also demonstrated to be more efficient in destruction of VM and HUVEC tubes in comparison to LA7R-LS/DOX and plain liposomes (LS/DOX, without peptide conjugation). cA7R conjugation could achieve significantly higher accumulation of liposomes in glioma than did LA7R conjugation, which in turn, cA7R-LS/DOX could substantially suppress subcutaneous tumor growth when compared with other DOX formulations (free DOX, LS/DOX and LA7R-LS/DOX). The designed cyclic A7R exhibited the capability of targeting glioma cells, neovasculature and VM simultaneously in vivo. Considering the ease of synthesis, high binding affinity to receptors and increased stability of cA7R peptide in the present study, the design of head-to-tail cyclized peptides by the formation of amide bond based on computer-aided peptide design presents an alternative method to identify proteolytically stable peptide ligands.
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Affiliation(s)
- Man Ying
- Department of Pharmaceutics, School of Pharmacy, Fudan University, Key Laboratory of Smart Drug Delivery, Ministry of Education, Shanghai 201203, China
| | - Qing Shen
- Department of Pharmaceutics, School of Pharmacy, Fudan University, Key Laboratory of Smart Drug Delivery, Ministry of Education, Shanghai 201203, China; State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
| | - Changyou Zhan
- Department of Pharmaceutics, School of Pharmacy, Fudan University, Key Laboratory of Smart Drug Delivery, Ministry of Education, Shanghai 201203, China; Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Xiaoli Wei
- Department of Pharmaceutics, School of Pharmacy, Fudan University, Key Laboratory of Smart Drug Delivery, Ministry of Education, Shanghai 201203, China; State Key Laboratory of Medical Neurobiology, The Collaborative Innovation Center for Brain Science, Fudan University, Shanghai 200032, China
| | - Jie Gao
- Department of Pharmaceutics, School of Pharmacy, Fudan University, Key Laboratory of Smart Drug Delivery, Ministry of Education, Shanghai 201203, China
| | - Cao Xie
- Department of Pharmaceutics, School of Pharmacy, Fudan University, Key Laboratory of Smart Drug Delivery, Ministry of Education, Shanghai 201203, China
| | - Bingxin Yao
- Department of Pharmaceutics, School of Pharmacy, Fudan University, Key Laboratory of Smart Drug Delivery, Ministry of Education, Shanghai 201203, China
| | - Weiyue Lu
- Department of Pharmaceutics, School of Pharmacy, Fudan University, Key Laboratory of Smart Drug Delivery, Ministry of Education, Shanghai 201203, China; State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China; State Key Laboratory of Medical Neurobiology, The Collaborative Innovation Center for Brain Science, Fudan University, Shanghai 200032, China.
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36
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Corbi-Verge C, Garton M, Nim S, Kim PM. Strategies to Develop Inhibitors of Motif-Mediated Protein-Protein Interactions as Drug Leads. Annu Rev Pharmacol Toxicol 2016; 57:39-60. [PMID: 27618737 DOI: 10.1146/annurev-pharmtox-010716-104805] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Protein-protein interactions are fundamental for virtually all functions of the cell. A large fraction of these interactions involve short peptide motifs, and there has been increased interest in targeting them using peptide-based therapeutics. Peptides benefit from being specific, relatively safe, and easy to produce. They are also easy to modify using chemical synthesis and molecular biology techniques. However, significant challenges remain regarding the use of peptides as therapeutic agents. Identification of peptide motifs is difficult, and peptides typically display low cell permeability and sensitivity to enzymatic degradation. In this review, we outline the principal high-throughput methodologies for motif discovery and describe current methods for overcoming pharmacokinetic and bioavailability limitations.
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Affiliation(s)
- Carles Corbi-Verge
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada; , , ,
| | - Michael Garton
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada; , , ,
| | - Satra Nim
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada; , , ,
| | - Philip M Kim
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada; , , , .,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3E1, Canada
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37
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Checco JW, Gellman SH. Targeting recognition surfaces on natural proteins with peptidic foldamers. Curr Opin Struct Biol 2016; 39:96-105. [PMID: 27390896 DOI: 10.1016/j.sbi.2016.06.014] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Revised: 05/22/2016] [Accepted: 06/15/2016] [Indexed: 11/30/2022]
Abstract
Molecules intended to antagonize protein-protein interactions or augment polypeptide-based signaling must bind tightly to large and specific surfaces on target proteins. Some types of unnatural oligomers with discrete folding propensities ('foldamers') have recently been shown to display this capability. This review covers important recent advances among several classes of foldamers, including α-peptides with secondary structures stabilized by covalent bonds, d-α-peptides, α/β-peptides and oligo-oxopiperazines. Recent advances in this area have involved enhancing membrane permeability to provide access to intracellular protein targets, improving pharmacokinetics and duration of action in vivo, and developing strategies appropriate for targeting large and irregularly-shaped protein surfaces.
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Affiliation(s)
- James W Checco
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Samuel H Gellman
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
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38
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Kutyshenko VP, Mikoulinskaia GV, Molochkov NV, Prokhorov DA, Taran SA, Uversky VN. Structure and dynamics of the retro-form of the bacteriophage T5 endolysin. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1281-91. [PMID: 27376687 DOI: 10.1016/j.bbapap.2016.06.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 06/29/2016] [Accepted: 06/30/2016] [Indexed: 10/21/2022]
Abstract
Using high-resolution NMR spectroscopy we conducted a comparative analysis of the structural and dynamic properties of the bacteriophage T5 endolysin (EndoT5) and its retro-form; i.e., a protein with the reversed direction of the polypeptide chain (R-EndoT5). We show that structurally, retro-form can be described as the molten globule-like polypeptide that is easily able to form large oligomers and aggregates. To avoid complications associated with this high aggregation propensity of the retro protein, we compared EndoT5 and R-EndoT5 in the presence of strong denaturants. This analysis revealed that these two proteins possess different internal dynamics in solutions containing 8M urea, with the retro-form being characterized by larger dimensions and slower internal dynamics. We also show that in the absence of denaturant, both forms of the bacteriophage T5 endolysin are able to interact with micelles formed by the zwitterionic detergent dodecylphosphocholine (DPC), and that the formation of the protein-micelle complexes leads to the significant structural rearrangement of polypeptide chain and to the formation of stable hydrophobic core in the R-Endo T5.
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Affiliation(s)
- Victor P Kutyshenko
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia.
| | - Galina V Mikoulinskaia
- Branch of Shemyakin & Ovchinnikov's Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Nikolai V Molochkov
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Dmitry A Prokhorov
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Sergei A Taran
- Branch of Shemyakin & Ovchinnikov's Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA; Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, St. Petersburg 194064, Russia.
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39
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Liu M, Li X, Xie Z, Xie C, Zhan C, Hu X, Shen Q, Wei X, Su B, Wang J, Lu W. D-Peptides as Recognition Molecules and Therapeutic Agents. CHEM REC 2016; 16:1772-86. [PMID: 27255896 DOI: 10.1002/tcr.201600005] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Indexed: 01/13/2023]
Abstract
Over recent years, D-peptides have attracted increasing attention. D-peptides increase enzymatic stability, prolong the plasma half-life, improve oral bioavailability, and enhance binding activity and specificity with receptor or target proteins, in comparison with the corresponding L-peptide. Therefore, D-peptides are considered to have potential as recognition molecules and therapeutic agents. This review focuses on the design and application of D-peptides with biological activity.
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Affiliation(s)
- Min Liu
- Key Laboratory of Smart Drug Delivery (Fudan University)Ministry of Education Department of Pharmaceutics School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203 (P. R. China)
| | - Xue Li
- Key Laboratory of Smart Drug Delivery (Fudan University)Ministry of Education Department of Pharmaceutics School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203 (P. R. China)
| | - Zuoxu Xie
- Key Laboratory of Smart Drug Delivery (Fudan University)Ministry of Education Department of Pharmaceutics School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203 (P. R. China)
| | - Cao Xie
- Key Laboratory of Smart Drug Delivery (Fudan University)Ministry of Education Department of Pharmaceutics School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203 (P. R. China)
| | - Changyou Zhan
- Key Laboratory of Smart Drug Delivery (Fudan University)Ministry of Education Department of Pharmaceutics School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203 (P. R. China).,Department of Pharmacology School of Basic Medical Sciences, Fudan University, 138 Yixueyuan Road, Shanghai 200032 (P. R. China)
| | - Xuefeng Hu
- Key Laboratory of Smart Drug Delivery (Fudan University)Ministry of Education Department of Pharmaceutics School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203 (P. R. China)
| | - Qing Shen
- Key Laboratory of Smart Drug Delivery (Fudan University)Ministry of Education Department of Pharmaceutics School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203 (P. R. China)
| | - Xiaoli Wei
- Key Laboratory of Smart Drug Delivery (Fudan University)Ministry of Education Department of Pharmaceutics School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203 (P. R. China)
| | - Bingxia Su
- Key Laboratory of Smart Drug Delivery (Fudan University)Ministry of Education Department of Pharmaceutics School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203 (P. R. China)
| | - Jing Wang
- Key Laboratory of Smart Drug Delivery (Fudan University)Ministry of Education Department of Pharmaceutics School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203 (P. R. China)
| | - Weiyue Lu
- Key Laboratory of Smart Drug Delivery (Fudan University)Ministry of Education Department of Pharmaceutics School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203 (P. R. China)
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40
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Grecu D, Irudayaraj VPR, Martinez-Sanz J, Mallet JM, Assairi L. A chirality change in XPC- and Sfi1-derived peptides affects their affinity for centrin. Peptides 2016; 78:77-86. [PMID: 26923803 DOI: 10.1016/j.peptides.2016.02.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 02/18/2016] [Accepted: 02/19/2016] [Indexed: 12/30/2022]
Abstract
The Ca(2+)-binding protein centrin binds to a hydrophobic motif (W(1)xxL(4)xxxL(8)) included in the sequence of several cellular targets: XPC (xeroderma pigmentosum group C protein), Sfi1 (suppressor of fermentation-induced loss of stress resistance protein1), and Sac3 [the central component of the transcription and mRNA export (TREX-2) complex]. However, centrin binding occurs in a reversed orientation (L(8)xxxL(4)xxW(1)) for Sfi1 and Sac3 compared with XPC. Because D-peptides have been investigated for future therapeutic use, we analyzed their centrin-binding properties. Their affinity for centrin was measured using isothermal titration calorimetry. The chirality change in the target-derived peptides affected their ability to bind centrin in a specific manner depending on the sequence orientation of the centrin-binding motif. In contrast to L-XPC-P10, D-XPC-P10 bound C-HsCen1 in a Ca(2+)-dependent manner and to a lesser extent. D-XPC-P10 exhibited a reduced affinity for C-HsCen1 (Ka=0.064 × 10(6) M(-1)) by a factor of 2000 compared with L-XPC-P10 (Ka=132 × 10(6) M(-1)). D-peptides have a lower affinity than L-peptides for centrin, and the strength of this affinity depends on the sequence orientation of the target-derived peptides. The residual affinity observed for D-XPC suggests that the use of d-peptides represents a promising strategy for inhibiting centrin binding to its targets.
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Affiliation(s)
- Dora Grecu
- Institut Curie-Centre de Recherche, F-91405 Orsay Cédex, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U759, F-91405 Orsay Cédex, France
| | - Victor Paul Raj Irudayaraj
- Institut Curie-Centre de Recherche, F-91405 Orsay Cédex, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U759, F-91405 Orsay Cédex, France; UMR CNRS 7203, Paris Cédex 05, France; ENS Ecole Normale Supérieure de Paris, Paris Cédex 05, France; Université Paris 6, Paris Cédex 05, France
| | - Juan Martinez-Sanz
- Institut Curie-Centre de Recherche, F-91405 Orsay Cédex, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U759, F-91405 Orsay Cédex, France; UMR9187-U1196, F-91405 Orsay Cédex, France
| | - Jean-Maurice Mallet
- UMR CNRS 7203, Paris Cédex 05, France; ENS Ecole Normale Supérieure de Paris, Paris Cédex 05, France; Université Paris 6, Paris Cédex 05, France
| | - Liliane Assairi
- Institut Curie-Centre de Recherche, F-91405 Orsay Cédex, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U759, F-91405 Orsay Cédex, France.
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41
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Abstract
Interactions between polypeptide chains containing amino acid residues with opposite absolute configurations have long been a source of interest and speculation, but there is very little structural information for such heterochiral associations. The need to address this lacuna has grown in recent years because of increasing interest in the use of peptides generated from d amino acids (d peptides) as specific ligands for natural proteins, e.g., to inhibit deleterious protein-protein interactions. Coiled-coil interactions, between or among α-helices, represent the most common tertiary and quaternary packing motif in proteins. Heterochiral coiled-coil interactions were predicted over 50 years ago by Crick, and limited experimental data obtained in solution suggest that such interactions can indeed occur. To address the dearth of atomic-level structural characterization of heterochiral helix pairings, we report two independent crystal structures that elucidate coiled-coil packing between l- and d-peptide helices. Both structures resulted from racemic crystallization of a peptide corresponding to the transmembrane segment of the influenza M2 protein. Networks of canonical knobs-into-holes side-chain packing interactions are observed at each helical interface. However, the underlying patterns for these heterochiral coiled coils seem to deviate from the heptad sequence repeat that is characteristic of most homochiral analogs, with an apparent preference for a hendecad repeat pattern.
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42
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Micewicz ED, Sharma S, Waring AJ, Luong HT, McBride WH, Ruchala P. Bridged Analogues for p53-Dependent Cancer Therapy Obtained by S-Alkylation. Int J Pept Res Ther 2015; 22:67-81. [PMID: 26957954 DOI: 10.1007/s10989-015-9487-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A small library of anticancer, cell-permeating, stapled peptides based on potent dual-specific antagonist of p53-MDM2/MDMX interactions, PMI-N8A, was synthesized, characterized and screened for anticancer activity against human colorectal cancer cell line, HCT-116. Employed synthetic modifications included: S-alkylation-based stapling, point mutations increasing hydrophobicity in key residues as well as improvement of cell-permeability by introduction of polycationic sequence(s) that were woven into the sequence of parental peptide. Selected analogue, ArB14Co, was also tested in vivo and exhibited potent anticancer bioactivity at the low dose (3.0 mg/kg). Collectively, our findings suggest that application of stapling in combination with rational design of polycationic short analogues may be a suitable approach in the development of physiologically active p53-MDM2/MDMX peptide inhibitors.
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Affiliation(s)
- Ewa D Micewicz
- Department of Radiation Oncology, University of California at Los Angeles, 10833 Le Conte Avenue, Los Angeles, CA 90095, USA
| | - Shantanu Sharma
- Materials and Process Simulation Center, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Alan J Waring
- Department of Medicine, Los Angeles Biomedical Research Institute at Harbor-UCLA, Medical Center, 1000 West Carson Street, Torrance, CA 90502, USA
| | - Hai T Luong
- Department of Analytical Operations, Gilead Sciences, Inc., 4049 Avenida de la Plata, Oceanside CA, 92056, USA
| | - William H McBride
- Department of Radiation Oncology, University of California at Los Angeles, 10833 Le Conte Avenue, Los Angeles, CA 90095, USA
| | - Piotr Ruchala
- Department of Psychiatry and Biobehavioral Sciences, University of California at Los Angeles, 760 Westwood Plaza, Los Angeles, CA 90024, USA
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43
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Zhou J, Du X, Li J, Yamagata N, Xu B. Taurine Boosts Cellular Uptake of Small D-Peptides for Enzyme-Instructed Intracellular Molecular Self-Assembly. J Am Chem Soc 2015; 137:10040-3. [PMID: 26235707 PMCID: PMC4544318 DOI: 10.1021/jacs.5b06181] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Indexed: 02/08/2023]
Abstract
Due to their biostability, D-peptides are emerging as an important molecular platform for biomedical applications. Being proteolytically resistant, D-peptides lack interactions with endogenous transporters and hardly enter cells. Here we show that taurine, a natural amino acid, drastically boosts the cellular uptake of small D-peptides in mammalian cells by >10-fold, from 118 μM (without conjugating taurine) to >1.6 mM (after conjugating taurine). The uptake of a large amount of the ester conjugate of taurine and D-peptide allows intracellular esterase to trigger intracellular self-assembly of the D-peptide derivative, further enhancing their cellular accumulation. The study on the mechanism of the uptake reveals that the conjugates enter cells via both dynamin-dependent endocytosis and macropinocytosis, but likely not relying on taurine transporters. Differing fundamentally from the positively charged cell-penetrating peptides, the biocompatibility, stability, and simplicity of the enzyme-cleavable taurine motif promise new ways to promote the uptake of bioactive molecules for countering the action of efflux pump and contributing to intracellular molecular self-assembly.
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Affiliation(s)
- Jie Zhou
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02453, United States
| | - Xuewen Du
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02453, United States
| | - Jie Li
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02453, United States
| | - Natsuko Yamagata
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02453, United States
| | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02453, United States
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44
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Peterson-Kaufman KJ, Haase HS, Boersma MD, Lee EF, Fairlie WD, Gellman SH. Residue-Based Preorganization of BH3-Derived α/β-Peptides: Modulating Affinity, Selectivity and Proteolytic Susceptibility in α-Helix Mimics. ACS Chem Biol 2015; 10:1667-75. [PMID: 25946900 DOI: 10.1021/acschembio.5b00109] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We report progress toward a general strategy for mimicking the recognition properties of specific α-helices within natural proteins through the use of oligomers that are less susceptible than conventional peptides to proteolysis. The oligomers contain both α- and β-amino acid residues, with the density of the β subunits low enough that an α-helix-like conformation can be adopted but high enough to interfere with protease activity. Previous studies with a different protein-recognition system that suggested ring-constrained β residues can be superior to flexible β residues in terms of maximizing α/β-peptide affinity for a targeted protein surface. Here, we use mimicry of the 18-residue Bim BH3 domain to expand the scope of this strategy. Two significant advances have been achieved. First, we have developed and validated a new ring-constrained β residue that bears an acidic side chain, which complements previously known analogues that are either hydrophobic or basic. Second, we have discovered that placing cyclic β residues at sites that make direct contact with partner proteins can lead to substantial discrimination between structurally homologous binding partners, the proteins Bcl-xL and Mcl-1. Overall, this study helps to establish that α/β-peptides containing ring-preorganized β residues can reliably provide proteolytically resistant ligands for proteins that naturally evolved to recognize α-helical partners.
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Affiliation(s)
| | - Holly S. Haase
- Department
of Chemistry, University of Wisconsin, 1101 University Ave., Madison, Wisconsin 53706, United States
| | - Melissa D. Boersma
- Department
of Chemistry, University of Wisconsin, 1101 University Ave., Madison, Wisconsin 53706, United States
| | - Erinna F. Lee
- Structural
Biology Division, The Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department
of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - W. Douglas Fairlie
- Structural
Biology Division, The Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department
of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Samuel H. Gellman
- Department
of Chemistry, University of Wisconsin, 1101 University Ave., Madison, Wisconsin 53706, United States
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45
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Arranz-Gibert P, Guixer B, Malakoutikhah M, Muttenthaler M, Guzmán F, Teixidó M, Giralt E. Lipid bilayer crossing--the gate of symmetry. Water-soluble phenylproline-based blood-brain barrier shuttles. J Am Chem Soc 2015; 137:7357-64. [PMID: 25992679 DOI: 10.1021/jacs.5b02050] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Drug delivery to the brain can be achieved by various means, including blood-brain barrier (BBB) disruption, neurosurgical-based approaches, and molecular design. Recently, passive diffusion BBB shuttles have been developed to transport low-molecular-weight drug candidates to the brain which would not be able to cross unaided. The low water solubility of these BBB shuttles has, however, prevented them from becoming a mainstream tool to deliver cargos across membranes. Here, we describe the design, synthesis, physicochemical characterization, and BBB-transport properties of phenylproline tetrapeptides, (PhPro)4, an improved class of BBB shuttles that operates via passive diffusion. These PhPro-based BBB shuttles showed 3 orders of magnitude improvement in water solubility compared to the gold-standard (N-MePhe)4, while retaining very high transport values. Transport capacity was confirmed when two therapeutically relevant cargos, nipecotic acid and l-3,4-dihydroxyphenylalanine (i.e., l-DOPA), were attached to the shuttle. Additionally, we used the unique chiral and conformationally restricted character of the (PhPro)4 shuttle to probe its chiral interactions with the lipid bilayer of the BBB. We studied the transport properties of 16 (PhPro)4 stereoisomers using the parallel artificial membrane permeability assay and looked at differences in secondary structure. Most stereoisomers displayed excellent transport values, yet this study also revealed pairs of enantiomers with high enantiomeric discrimination and different secondary structure, where one enantiomer maintained its high transport values while the other had significantly lower values, thereby confirming that stereochemistry plays a significant role in passive diffusion. This could open the door to the design of chiral and membrane-specific shuttles with potential applications in cell labeling and oncology.
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Affiliation(s)
- Pol Arranz-Gibert
- †Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, Barcelona E-08028, Spain
| | - Bernat Guixer
- †Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, Barcelona E-08028, Spain
| | - Morteza Malakoutikhah
- †Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, Barcelona E-08028, Spain.,‡Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran
| | - Markus Muttenthaler
- †Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, Barcelona E-08028, Spain
| | - Fanny Guzmán
- §Núcleo de Biotecnología Curauma, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Meritxell Teixidó
- †Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, Barcelona E-08028, Spain
| | - Ernest Giralt
- †Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, Barcelona E-08028, Spain.,∥Department of Organic Chemistry, University of Barcelona, Martí i Franquès 1-11, Barcelona E-08028, Spain
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46
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Synthetic and structural routes for the rational conversion of peptides into small molecules. Methods Mol Biol 2015; 1268:159-93. [PMID: 25555725 DOI: 10.1007/978-1-4939-2285-7_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The demand for modified peptides with improved stability profiles and pharmacokinetic properties is driving extensive research effort in this field. The conversion of peptides into organic molecules, as traditional drugs, is a long and puzzled way. Many and versatile approaches have been described for designing peptide mimetics: the substitution of natural residues with modified amino acids and the rigidification and modification of the backbone are the main structural and chemical routes walked in medicinal chemistry. All of these strategies have been successfully applied to obtain active new compounds in molecular biology, drug discovery and design. Here we propose a panoramic review of the most common methods for the preparation of modified peptides and the most interesting findings of the last decade.
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Kükenshöner T, Hagemann UB, Wohlwend D, Räuber C, Baumann T, Keller S, Einsle O, Müller KM, Arndt KM. Analysis of selected and designed chimeric D- and L-α-helix assemblies. Biomacromolecules 2014; 15:3296-305. [PMID: 25072521 DOI: 10.1021/bm5006883] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
D-peptides have been attributed pharmacological advantages over regular L-peptides, yet design rules are largely unknown. Based on a designed coiled coil-like D/L heterotetramer, named L-Base/D-Acid, we generated a library offering alternative residues for interaction with the D-peptide. Phage display selection yielded one predominant peptide, named HelixA, that differed at 13 positions from the scaffold helix. In addition to the observed D-/L-heterotetramers, ratio-dependent intermediate states were detected by isothermal titration calorimetry. Importantly, the formation of the selected HelixA/D-Acid bundle passes through fewer intermediate states than L-Base/D-Acid. Back mutation of HelixA core residues to L-Base (HelixLL) revealed that the residues at e/g-positions are responsible for the different intermediates. Furthermore, a Val-core variant (PeptideVV) was completely devoid of binding D-Acid, whereas an Ile-core helix (HelixII) interacted with D-Acid in a significantly more specific complex than L-Base.
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Affiliation(s)
- Tim Kükenshöner
- Molecular Biotechnology, Institute for Biochemistry and Biology, University of Potsdam , 14476 Potsdam, Germany
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48
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Wei X, Zhan C, Chen X, Hou J, Xie C, Lu W. Retro-inverso isomer of Angiopep-2: a stable d-peptide ligand inspires brain-targeted drug delivery. Mol Pharm 2014; 11:3261-8. [PMID: 24673510 DOI: 10.1021/mp500086e] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The blood-brain barrier (BBB) prevents most drugs from reaching the site of central nervous system (CNS) diseases, intensively confining the therapeutic efficiency. Angiopep-2 (here termed (L)Angiopep), which is a 19-mer peptide derived from human Kunitz domain, can trigger transcytosis and traverse the BBB by recognizing low density lipoprotein-related protein 1 (LRP-1) expressed on the brain capillary endothelial cells. Various enzymes in the blood and the BBB, however, present multiple metabolic barriers to peptide-inspired brain-targeted drug delivery. Here we designed a retro-inverso isomer of (L)Angiopep, termed (D)Angiopep, to inspire brain-targeted drug delivery. Both (D)Angiopep and (L)Angiopep displayed high uptake capacity in LRP-1 overexpressed cells, including bEnd.3 and U87 cells. (D)Angiopep demonstrated lower uptake efficiency in both cell lines than did (L)Angiopep, suggestive of lower binding affinity to LRP-1 of the d-peptide. (D)Angiopep was resistant to proteolysis in fresh rat blood serum, while more than 85% of (L)Angiopep disappeared within 2 h. Endocytosed (D)Angiopep and (L)Angiopep were found to be colocalized with lysosomal compartments of bEnd.3 cells, indicating that susceptibility to proteolysis of (L)Angiopep in the BBB may further attenuate its transcytosis efficiency. In vivo, (D)Angiopep modified PEG-DSPE micelles displayed high distribution in normal brain and intracranial glioblastoma. Due to the expression of LRP-1 on the BBB and glioblastoma cells, proteolytically stable (D)Angiopep holds much potential for designing two-order brain tumor targeted delivery systems.
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Affiliation(s)
- Xiaoli Wei
- Department of Pharmaceutics, School of Pharmacy, Fudan University , Shanghai, 201203, P. R. China
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49
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Croft NP, Purcell AW. Peptidomimetics: modifying peptides in the pursuit of better vaccines. Expert Rev Vaccines 2014; 10:211-26. [DOI: 10.1586/erv.10.161] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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50
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Deiber JA, Piaggio MV, Peirotti MB. Global chain properties of an alll-α-eicosapeptide with a secondary α-helix and its all retrod-inverso-α-eicosapeptide estimated through the modeling of their CZE-determined electrophoretic mobilities. Electrophoresis 2013; 35:755-61. [DOI: 10.1002/elps.201300395] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 09/26/2013] [Accepted: 10/11/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Julio A. Deiber
- Instituto de Desarrollo Tecnológico para la Industria Química (INTEC); Universidad Nacional del Litoral (UNL); Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Santa Fe Argentina
| | - Maria V. Piaggio
- Cátedra de Bioquímica Básica de Macromoléculas; Facultad de Bioquímica y Ciencias Biológicas; UNL; Santa Fe Argentina
| | - Marta B. Peirotti
- Instituto de Desarrollo Tecnológico para la Industria Química (INTEC); Universidad Nacional del Litoral (UNL); Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Santa Fe Argentina
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