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Kim M, Jo H, Jung GY, Oh SS. Molecular Complementarity of Proteomimetic Materials for Target-Specific Recognition and Recognition-Mediated Complex Functions. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2208309. [PMID: 36525617 DOI: 10.1002/adma.202208309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/29/2022] [Indexed: 06/02/2023]
Abstract
As biomolecules essential for sustaining life, proteins are generated from long chains of 20 different α-amino acids that are folded into unique 3D structures. In particular, many proteins have molecular recognition functions owing to their binding pockets, which have complementary shapes, charges, and polarities for specific targets, making these biopolymers unique and highly valuable for biomedical and biocatalytic applications. Based on the understanding of protein structures and microenvironments, molecular complementarity can be exhibited by synthesizable and modifiable materials. This has prompted researchers to explore the proteomimetic potentials of a diverse range of materials, including biologically available peptides and oligonucleotides, synthetic supramolecules, inorganic molecules, and related coordination networks. To fully resemble a protein, proteomimetic materials perform the molecular recognition to mediate complex molecular functions, such as allosteric regulation, signal transduction, enzymatic reactions, and stimuli-responsive motions; this can also expand the landscape of their potential bio-applications. This review focuses on the recognitive aspects of proteomimetic designs derived for individual materials and their conformations. Recent progress provides insights to help guide the development of advanced protein mimicry with material heterogeneity, design modularity, and tailored functionality. The perspectives and challenges of current proteomimetic designs and tools are also discussed in relation to future applications.
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Affiliation(s)
- Minsun Kim
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Hyesung Jo
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, South Korea
| | - Gyoo Yeol Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, South Korea
| | - Seung Soo Oh
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, South Korea
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, South Korea
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2
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Ringel O, Vieillard V, Debré P, Eichler J, Büning H, Dietrich U. The Hard Way towards an Antibody-Based HIV-1 Env Vaccine: Lessons from Other Viruses. Viruses 2018; 10:v10040197. [PMID: 29662026 PMCID: PMC5923491 DOI: 10.3390/v10040197] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 04/05/2018] [Accepted: 04/13/2018] [Indexed: 12/13/2022] Open
Abstract
Although effective antibody-based vaccines have been developed against multiple viruses, such approaches have so far failed for the human immunodeficiency virus type 1 (HIV-1). Despite the success of anti-retroviral therapy (ART) that has turned HIV-1 infection into a chronic disease and has reduced the number of new infections worldwide, a vaccine against HIV-1 is still urgently needed. We discuss here the major reasons for the failure of “classical” vaccine approaches, which are mostly due to the biological properties of the virus itself. HIV-1 has developed multiple mechanisms of immune escape, which also account for vaccine failure. So far, no vaccine candidate has been able to induce broadly neutralizing antibodies (bnAbs) against primary patient viruses from different clades. However, such antibodies were identified in a subset of patients during chronic infection and were shown to protect from infection in animal models and to reduce viremia in first clinical trials. Their detailed characterization has guided structure-based reverse vaccinology approaches to design better HIV-1 envelope (Env) immunogens. Furthermore, conserved Env epitopes have been identified, which are promising candidates in view of clinical applications. Together with new vector-based technologies, considerable progress has been achieved in recent years towards the development of an effective antibody-based HIV-1 vaccine.
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Affiliation(s)
- Oliver Ringel
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, 60596 Frankfurt, Germany.
| | - Vincent Vieillard
- Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Sorbonne Université, UPMC Univ Paris 06, INSERM U1135, CNRS ERL8255, 75013 Paris, France.
| | - Patrice Debré
- Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Sorbonne Université, UPMC Univ Paris 06, INSERM U1135, CNRS ERL8255, 75013 Paris, France.
| | - Jutta Eichler
- Department of Chemistry and Pharmacy, University of Erlangen-Nurnberg, 91058 Erlangen, Germany.
| | - Hildegard Büning
- Laboratory for Infection Biology & Gene Transfer, Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
| | - Ursula Dietrich
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, 60596 Frankfurt, Germany.
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3
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Haußner C, Lach J, Eichler J. Synthetic antibody mimics for the inhibition of protein-ligand interactions. Curr Opin Chem Biol 2017; 40:72-77. [PMID: 28735229 DOI: 10.1016/j.cbpa.2017.07.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 05/31/2017] [Accepted: 07/03/2017] [Indexed: 12/22/2022]
Abstract
The rational/structure-based design and/or combinatorial development of molecules capable of selectively binding to a protein, represents a promising strategy for a range of biomedical applications, in particular the inhibition of disease-associated protein-ligand interactions. The design of such protein binding molecules is often based on an antibody against the target protein, or involves the generation of smaller molecules that retain the binding characteristics of the antibody. Alternatively, protein binding molecules can be selected from protein libraries based on small, stably folded protein scaffolds presenting flexible loops, which are randomized in the libraries. In addition to recombinantly synthesized molecules, synthetic antibody paratope mimetic peptides have emerged as promising molecules for the design of antibody mimics.
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Affiliation(s)
- Christina Haußner
- Department of Chemistry and Pharmacy, University of Erlangen-Nurnberg, Schuhstr. 19, 91052 Erlangen, Germany
| | - Johannes Lach
- Department of Chemistry and Pharmacy, University of Erlangen-Nurnberg, Schuhstr. 19, 91052 Erlangen, Germany
| | - Jutta Eichler
- Department of Chemistry and Pharmacy, University of Erlangen-Nurnberg, Schuhstr. 19, 91052 Erlangen, Germany.
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4
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Haußner C, Damm D, Nirschl S, Rohrhofer A, Schmidt B, Eichler J. Peptide Paratope Mimics of the Broadly Neutralizing HIV-1 Antibody b12. Chembiochem 2017; 18:647-653. [DOI: 10.1002/cbic.201600621] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Christina Haußner
- Department of Chemistry and Pharmacy; University of Erlangen-Nürnberg; Schuhstrasse 19 91052 Erlangen Germany
| | - Dominik Damm
- Institute of Medical Microbiology and Hygiene; University of Regensburg; Franz-Josef-Strauss-Allee 11 93053 Regensburg Germany
| | - Sandra Nirschl
- Institute of Medical Microbiology and Hygiene; University of Regensburg; Franz-Josef-Strauss-Allee 11 93053 Regensburg Germany
| | - Anette Rohrhofer
- Institute of Clinical Microbiology and Hygiene; University of Regensburg; Franz-Josef-Strauss-Allee 11 93053 Regensburg Germany
| | - Barbara Schmidt
- Institute of Medical Microbiology and Hygiene; University of Regensburg; Franz-Josef-Strauss-Allee 11 93053 Regensburg Germany
- Institute of Clinical Microbiology and Hygiene; University of Regensburg; Franz-Josef-Strauss-Allee 11 93053 Regensburg Germany
| | - Jutta Eichler
- Department of Chemistry and Pharmacy; University of Erlangen-Nürnberg; Schuhstrasse 19 91052 Erlangen Germany
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5
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De Rosa L, Finetti F, Diana D, Di Stasi R, Auriemma S, Romanelli A, Fattorusso R, Ziche M, Morbidelli L, D’Andrea LD. Miniaturizing VEGF: Peptides mimicking the discontinuous VEGF receptor-binding site modulate the angiogenic response. Sci Rep 2016; 6:31295. [PMID: 27498819 PMCID: PMC4976335 DOI: 10.1038/srep31295] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 07/15/2016] [Indexed: 12/20/2022] Open
Abstract
The angiogenic properties of VEGF are mediated through the binding of VEGF to its receptor VEGFR2. The VEGF/VEGFR interface is constituted by a discontinuous binding region distributed on both VEGF monomers. We attempted to reproduce this discontinuous binding site by covalently linking into a single molecular entity two VEGF segments involved in receptor recognition. We designed and synthesized by chemical ligation a set of peptides differing in length and flexibility of the molecular linker joining the two VEGF segments. The biological activity of the peptides was characterized in vitro and in vivo showing a VEGF-like activity. The most biologically active mini-VEGF was further analyzed by NMR to determine the atomic details of its interaction with the receptor.
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Affiliation(s)
- Lucia De Rosa
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134, Napoli, Italy
| | - Federica Finetti
- Dipartimento di Scienze della Vita, Università di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Donatella Diana
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134, Napoli, Italy
| | - Rossella Di Stasi
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134, Napoli, Italy
| | - Sara Auriemma
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134, Napoli, Italy
| | - Alessandra Romanelli
- Dipartimento di Farmacia, Università di Napoli “Federico II”, via Mezzocannone 16, 80134, Napoli, Italy
| | - Roberto Fattorusso
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università di Napoli, via A. Vivaldi 43, 81100, Caserta, Italy
| | - Marina Ziche
- Dipartimento di Scienze della Vita, Università di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Lucia Morbidelli
- Dipartimento di Scienze della Vita, Università di Siena, Via A. Moro 2, 53100 Siena, Italy
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6
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Groß A, Hashimoto C, Sticht H, Eichler J. Synthetic Peptides as Protein Mimics. Front Bioeng Biotechnol 2016; 3:211. [PMID: 26835447 PMCID: PMC4717299 DOI: 10.3389/fbioe.2015.00211] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 12/22/2015] [Indexed: 12/21/2022] Open
Abstract
The design and generation of molecules capable of mimicking the binding and/or functional sites of proteins represents a promising strategy for the exploration and modulation of protein function through controlled interference with the underlying molecular interactions. Synthetic peptides have proven an excellent type of molecule for the mimicry of protein sites because such peptides can be generated as exact copies of protein fragments, as well as in diverse chemical modifications, which includes the incorporation of a large range of non-proteinogenic amino acids as well as the modification of the peptide backbone. Apart from extending the chemical and structural diversity presented by peptides, such modifications also increase the proteolytic stability of the molecules, enhancing their utility for biological applications. This article reviews recent advances by this and other laboratories in the use of synthetic protein mimics to modulate protein function, as well as to provide building blocks for synthetic biology.
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Affiliation(s)
- Andrea Groß
- Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Chie Hashimoto
- Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Heinrich Sticht
- Institute of Biochemistry, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Jutta Eichler
- Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg, Erlangen, Germany
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7
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Kafurke U, Erijman A, Aizner Y, Shifman JM, Eichler J. Synthetic peptides mimicking the binding site of human acetylcholinesterase for its inhibitor fasciculin 2. J Pept Sci 2015. [DOI: 10.1002/psc.2797] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Uwe Kafurke
- Department of Chemistry and Pharmacy; University of Erlangen-Nuremberg; Schuhstr. 19 91052 Erlangen Germany
| | - Ariel Erijman
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
| | - Yonatan Aizner
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
| | - Julia M. Shifman
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
| | - Jutta Eichler
- Department of Chemistry and Pharmacy; University of Erlangen-Nuremberg; Schuhstr. 19 91052 Erlangen Germany
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8
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Panda SS, Jones RA, Hall CD, Katritzky AR. Applications of Chemical Ligation in Peptide Synthesis via Acyl Transfer. Top Curr Chem (Cham) 2015; 362:229-65. [PMID: 25805142 DOI: 10.1007/128_2014_608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
The utility of native chemical ligation (NCL) in the solution or solid phase synthesis of peptides, cyclic peptides, glycopeptides, and neoglycoconjugates is reviewed. In addition, the mechanistic details of inter- or intra-molecular NCLs are discussed from experimental and computational points of view.
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Affiliation(s)
- Siva S Panda
- Department of Chemistry, Center for Heterocyclic Compounds, University of Florida, Gainesville, FL, 32611-7200, USA,
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9
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Groß A, Rödel K, Kneidl B, Donhauser N, Mössl M, Lump E, Münch J, Schmidt B, Eichler J. Enhancement and induction of HIV-1 infection through an assembled peptide derived from the CD4 binding site of gp120. Chembiochem 2015; 16:446-54. [PMID: 25639621 DOI: 10.1002/cbic.201402545] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Indexed: 11/07/2022]
Abstract
Contact between the human immunodeficiency virus (HIV-1) and its target cell is initiated by the interaction of viral gp120 with cellular CD4. An assembled peptide (CD4bs-M) that presents the CD4 binding site of gp120 was previously shown to inhibit the gp120-CD4 interaction. Here, we demonstrate that CD4bs-M selectively enhances infection of cells with HIV-1, whereas infection with herpes simplex virus remains largely unaffected. The effects of CD4bs-M variants containing D-amino acids, or prolines at selected positions, point to the importance of side chain orientation and spatial orientation of this fragment. Furthermore, CD4bs-M was shown to assemble into amyloid-like fibrils that capture HIV-1 particles, which likely contributes to the infection-enhancing effect. Beyond infection enhancement, CD4bs-M enabled HIV-1 infection of CD4-negative cells, suggesting that binding of the peptide to gp120 facilitates interaction of gp120 with coreceptors, which might in turn enhance HIV-1 entry.
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Affiliation(s)
- Andrea Groß
- Department of Chemistry and Pharmacy, University of Erlangen-Nurnberg, Schuhstrasse 19, 91052 Erlangen (Germany)
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10
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Brouwer AJ, van de Langemheen H, Liskamp RM. Expedient synthesis of a novel asymmetric selectively deprotectable derivative of the ATAC scaffold. Tetrahedron 2014. [DOI: 10.1016/j.tet.2014.04.084] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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11
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Brouwer AJ, van de Langemheen H, Ciaffoni A, Schilder KE, Liskamp RMJ. Synthesis of the TACO Scaffold as a New Selectively Deprotectable Conformationally Restricted Triazacyclophane Based Scaffold. Org Lett 2014; 16:3106-9. [DOI: 10.1021/ol5012218] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Arwin J. Brouwer
- Medicinal
Chemistry and Chemical Biology, Utrecht Institute for Pharmaceutical
Sciences, Faculty of Science, Utrecht University, P.O. Box 80082, 3508 TB Utrecht, The Netherlands
| | - Helmus van de Langemheen
- Medicinal
Chemistry and Chemical Biology, Utrecht Institute for Pharmaceutical
Sciences, Faculty of Science, Utrecht University, P.O. Box 80082, 3508 TB Utrecht, The Netherlands
| | - Adriano Ciaffoni
- Medicinal
Chemistry and Chemical Biology, Utrecht Institute for Pharmaceutical
Sciences, Faculty of Science, Utrecht University, P.O. Box 80082, 3508 TB Utrecht, The Netherlands
| | - Kitty E. Schilder
- Medicinal
Chemistry and Chemical Biology, Utrecht Institute for Pharmaceutical
Sciences, Faculty of Science, Utrecht University, P.O. Box 80082, 3508 TB Utrecht, The Netherlands
| | - Rob M. J. Liskamp
- Medicinal
Chemistry and Chemical Biology, Utrecht Institute for Pharmaceutical
Sciences, Faculty of Science, Utrecht University, P.O. Box 80082, 3508 TB Utrecht, The Netherlands
- School
of Chemistry Joseph Black Building, University of Glasgow, University
Avenue, Glasgow G12 8QQ, United Kingdom
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12
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van de Langemheen H, Quarles van Ufford H(LC, Kruijtzer JAW, Liskamp RMJ. Efficient Synthesis of Protein Mimics by Sequential Native Chemical Ligation. Org Lett 2014; 16:2138-41. [DOI: 10.1021/ol500604h] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Helmus van de Langemheen
- Medicinal Chemistry & Chemical Biology, Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutical Sciences, Faculty of Sciences, Utrecht University, P.O. Box 80082, 3508 TB, Utrecht, The Netherlands
| | - H. (Linda) C. Quarles van Ufford
- Medicinal Chemistry & Chemical Biology, Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutical Sciences, Faculty of Sciences, Utrecht University, P.O. Box 80082, 3508 TB, Utrecht, The Netherlands
| | - John A. W. Kruijtzer
- Medicinal Chemistry & Chemical Biology, Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutical Sciences, Faculty of Sciences, Utrecht University, P.O. Box 80082, 3508 TB, Utrecht, The Netherlands
| | - Rob M. J. Liskamp
- Medicinal Chemistry & Chemical Biology, Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutical Sciences, Faculty of Sciences, Utrecht University, P.O. Box 80082, 3508 TB, Utrecht, The Netherlands
- School
of Chemistry, Joseph Black Building, University of Glasgow, University
Avenue, Glasgow, G12 8QQ, United Kingdom
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13
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van de Langemheen H, van Hoeke M, Quarles van Ufford HC, Kruijtzer JAW, Liskamp RMJ. Scaffolded multiple cyclic peptide libraries for protein mimics by native chemical ligation. Org Biomol Chem 2014; 12:4471-8. [DOI: 10.1039/c4ob00190g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The accessibility to collections, libraries and arrays of cyclic peptides is increasingly important since cyclic peptides may provide better mimics of the loop-like structures ubiquitously present in and – especially – on the surface of proteins.
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Affiliation(s)
- H. van de Langemheen
- Medicinal Chemistry & Chemical Biology
- Utrecht Institute for Pharmaceutical Sciences
- Department of Pharmaceutical Sciences
- Faculty of Sciences
- Utrecht University
| | - M. van Hoeke
- Medicinal Chemistry & Chemical Biology
- Utrecht Institute for Pharmaceutical Sciences
- Department of Pharmaceutical Sciences
- Faculty of Sciences
- Utrecht University
| | - H. C. Quarles van Ufford
- Medicinal Chemistry & Chemical Biology
- Utrecht Institute for Pharmaceutical Sciences
- Department of Pharmaceutical Sciences
- Faculty of Sciences
- Utrecht University
| | - J. A. W. Kruijtzer
- Medicinal Chemistry & Chemical Biology
- Utrecht Institute for Pharmaceutical Sciences
- Department of Pharmaceutical Sciences
- Faculty of Sciences
- Utrecht University
| | - R. M. J. Liskamp
- Medicinal Chemistry & Chemical Biology
- Utrecht Institute for Pharmaceutical Sciences
- Department of Pharmaceutical Sciences
- Faculty of Sciences
- Utrecht University
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14
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Mulder GE, Quarles van Ufford HLC, van Ameijde J, Brouwer AJ, Kruijtzer JAW, Liskamp RMJ. Scaffold optimization in discontinuous epitope containing protein mimics of gp120 using smart libraries. Org Biomol Chem 2013; 11:2676-84. [PMID: 23467699 DOI: 10.1039/c3ob27470e] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A diversity of protein surface discontinuous epitope mimics is now rapidly and efficiently accessible. Despite the important role of protein-protein interactions involving discontinuous epitopes in a wide range of diseases, mimicry of discontinuous epitopes using peptide-based molecules remains a major challenge. Using copper(I) catalyzed azide-alkyne cycloaddition (CuAAC), we have developed a general and efficient method for the synthesis of collections of discontinuous epitope mimics. Up to three different cyclic peptides, representing discontinuous epitopes in HIV-gp120, were conjugated to a selection of scaffold molecules. Variation of the scaffold molecule, optimization of the ring size of the cyclic peptides and screening of the resulting libraries for successful protein mimics led to an HIV gp120 mimic with an IC50 value of 1.7 μM. The approach described here provides rapid and highly reproducible access to clean, smart libraries of very complex bio-molecular constructs representing protein mimics for use as synthetic vaccines and beyond.
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Affiliation(s)
- Gwenn E Mulder
- Medicinal Chemistry & Chemical Biology, Utrecht Institute of Pharmaceutical Sciences, Faculty of Science, Utrecht, The Netherlands
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15
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Diestel U, Resch M, Meinhardt K, Weiler S, Hellmann TV, Mueller TD, Nickel J, Eichler J, Muller YA. Identification of a Novel TGF-β-Binding Site in the Zona Pellucida C-terminal (ZP-C) Domain of TGF-β-Receptor-3 (TGFR-3). PLoS One 2013; 8:e67214. [PMID: 23826237 PMCID: PMC3695229 DOI: 10.1371/journal.pone.0067214] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 05/16/2013] [Indexed: 12/30/2022] Open
Abstract
The zona pellucida (ZP) domain is present in extracellular proteins such as the zona pellucida proteins and tectorins and participates in the formation of polymeric protein networks. However, the ZP domain also occurs in the cytokine signaling co-receptor transforming growth factor β (TGF-β) receptor type 3 (TGFR-3, also known as betaglycan) where it contributes to cytokine ligand recognition. Currently it is unclear how the ZP domain architecture enables this dual functionality. Here, we identify a novel major TGF-β-binding site in the FG loop of the C-terminal subdomain of the murine TGFR-3 ZP domain (ZP-C) using protein crystallography, limited proteolysis experiments, surface plasmon resonance measurements and synthetic peptides. In the murine 2.7 Å crystal structure that we are presenting here, the FG-loop is disordered, however, well-ordered in a recently reported homologous rat ZP-C structure. Surprisingly, the adjacent external hydrophobic patch (EHP) segment is registered differently in the rat and murine structures suggesting that this segment only loosely associates with the remaining ZP-C fold. Such a flexible and temporarily-modulated association of the EHP segment with the ZP domain has been proposed to control the polymerization of ZP domain-containing proteins. Our findings suggest that this flexibility also extends to the ZP domain of TGFR-3 and might facilitate co-receptor ligand interaction and presentation via the adjacent FG-loop. This hints that a similar C-terminal region of the ZP domain architecture possibly regulates both the polymerization of extracellular matrix proteins and cytokine ligand recognition of TGFR-3.
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Affiliation(s)
- Uschi Diestel
- Lehrstuhl fuer Biotechnik, Department of Biology, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Marcus Resch
- Lehrstuhl fuer Biotechnik, Department of Biology, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Kathrin Meinhardt
- Lehrstuhl fuer Biotechnik, Department of Biology, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Sigrid Weiler
- Lehrstuhl fuer Biotechnik, Department of Biology, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Tina V. Hellmann
- Julius-von-Sachs-Institut fuer Biowissenschaften, Lehrstuhl fuer Botanik I, University of Wuerzburg, Wuerzburg, Germany
| | - Thomas D. Mueller
- Julius-von-Sachs-Institut fuer Biowissenschaften, Lehrstuhl fuer Botanik I, University of Wuerzburg, Wuerzburg, Germany
| | - Joachim Nickel
- Lehrstuhl fuer Tissue Engineering und Regenerative Medizin, University of Wuerzburg, Wuerzburg, Germany
| | - Jutta Eichler
- Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Yves A. Muller
- Lehrstuhl fuer Biotechnik, Department of Biology, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
- * E-mail:
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16
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van de Langemheen H, Brouwer AJ, Kemmink J, Kruijtzer JAW, Liskamp RMJ. Synthesis of Cyclic Peptides Containing a Thioester Handle for Native Chemical Ligation. J Org Chem 2012; 77:10058-64. [DOI: 10.1021/jo3015566] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Helmus van de Langemheen
- Division of Medicinal Chemistry & Chemical Biology, Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutical Sciences, Faculty of Sciences, Utrecht University, P.O. Box 80082, 3508 TB, Utrecht, The Netherlands
| | - Arwin J. Brouwer
- Division of Medicinal Chemistry & Chemical Biology, Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutical Sciences, Faculty of Sciences, Utrecht University, P.O. Box 80082, 3508 TB, Utrecht, The Netherlands
| | - Johan Kemmink
- Division of Medicinal Chemistry & Chemical Biology, Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutical Sciences, Faculty of Sciences, Utrecht University, P.O. Box 80082, 3508 TB, Utrecht, The Netherlands
| | - John A. W. Kruijtzer
- Division of Medicinal Chemistry & Chemical Biology, Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutical Sciences, Faculty of Sciences, Utrecht University, P.O. Box 80082, 3508 TB, Utrecht, The Netherlands
| | - Rob M. J. Liskamp
- Division of Medicinal Chemistry & Chemical Biology, Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutical Sciences, Faculty of Sciences, Utrecht University, P.O. Box 80082, 3508 TB, Utrecht, The Netherlands
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17
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Meier J, Kassler K, Sticht H, Eichler J. Peptides presenting the binding site of human CD4 for the HIV-1 envelope glycoprotein gp120. Beilstein J Org Chem 2012; 8:1858-66. [PMID: 23209523 PMCID: PMC3511023 DOI: 10.3762/bjoc.8.214] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Accepted: 09/24/2012] [Indexed: 01/31/2023] Open
Abstract
Based on the structure of the HIV-1 glycoprotein gp120 in complex with its cellular receptor CD4, we have designed and synthesized peptides that mimic the binding site of CD4 for gp120. The ability of these peptides to bind to gp120 can be strongly enhanced by increasing their conformational stability through cyclization, as evidenced by binding assays, as well as through molecular-dynamics simulations of peptide–gp120 complexes. The specificity of the peptide–gp120 interaction was demonstrated by using peptide variants, in which key residues for the interaction with gp120 were replaced by alanine or D-amino acids.
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Affiliation(s)
- Julia Meier
- Department of Chemistry and Pharmacy, Universität Erlangen-Nürnberg, Schuhstrasse 19, 91052 Erlangen, Germany
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18
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Haussner C, Möbius K, Eichler J. Exploring converse molecular mechanisms of anti-HIV-1 antibodies using a synthetic CXCR4 mimic. Bioorg Med Chem Lett 2012; 22:6099-102. [PMID: 22939235 DOI: 10.1016/j.bmcl.2012.08.035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 08/08/2012] [Accepted: 08/09/2012] [Indexed: 10/28/2022]
Abstract
Different molecular mechanisms of the two broadly neutralizing anti-HIV-1 antibodies b12 and VRC01, as evidenced by their converse effects on the interaction of HIV-1 envelope glycoprotein gp120 with cellular coreceptors, were demonstrated using a synthetic CXCR4 mimetic peptide (CX4-M1) as coreceptor surrogate. While the interaction of gp120 with CX4-M1 was distinctly enhanced by VRC01, b12 was shown to have the contrary effect, and also to inhibit the VRC01-induced enhancement of gp120 binding to the CXCR4 mimetic peptide.
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Affiliation(s)
- Christina Haussner
- Department of Chemistry and Pharmacy, University of Erlangen-Nürnberg, 91052 Erlangen, Germany
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19
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Möbius K, Dürr R, Haußner C, Dietrich U, Eichler J. A Functionally Selective Synthetic Mimic of the HIV‐1 Co‐receptor CXCR4. Chemistry 2012; 18:8292-5. [DOI: 10.1002/chem.201200111] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Revised: 03/15/2012] [Indexed: 01/21/2023]
Affiliation(s)
- Kalle Möbius
- Department Chemistry and Pharmacy, Universität Erlangen‐Nürnberg, Schuhstrasse 19, 91052 Erlangen (Germany), Fax: (+49) 9131‐8522587
| | - Ralf Dürr
- Georg‐Speyer‐Haus—Institute of Biomedical Research, Paul‐Ehrlich‐Str. 42–44, 60596 Frankfurt (Germany)
| | - Christina Haußner
- Department Chemistry and Pharmacy, Universität Erlangen‐Nürnberg, Schuhstrasse 19, 91052 Erlangen (Germany), Fax: (+49) 9131‐8522587
| | - Ursula Dietrich
- Georg‐Speyer‐Haus—Institute of Biomedical Research, Paul‐Ehrlich‐Str. 42–44, 60596 Frankfurt (Germany)
| | - Jutta Eichler
- Department Chemistry and Pharmacy, Universität Erlangen‐Nürnberg, Schuhstrasse 19, 91052 Erlangen (Germany), Fax: (+49) 9131‐8522587
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20
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Webel R, Solbak SMØ, Held C, Milbradt J, Groß A, Eichler J, Wittenberg T, Jardin C, Sticht H, Fossen T, Marschall M. Nuclear import of isoforms of the cytomegalovirus kinase pUL97 is mediated by differential activity of NLS1 and NLS2 both acting through classical importin-α binding. J Gen Virol 2012; 93:1756-1768. [PMID: 22552943 DOI: 10.1099/vir.0.040592-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The multifunctional protein kinase pUL97 of human cytomegalovirus (HCMV) strongly determines the efficiency of virus replication. Previously, the existence of two pUL97 isoforms that arise from alternative translational initiation and show a predominant nuclear localization was described. Two bipartite nuclear localization sequences, NLS1 and NLS2, were identified in the N terminus of the large isoform, whilst the small isoform exclusively contained NLS2. The current study found the following: (i) pUL97 nuclear localization in HCMV-infected primary fibroblasts showed accumulations in virus replication centres and other nuclear sections; (ii) in a quantitative evaluation system for NLS activity, the large isoform showed higher efficiency of nuclear translocation than the small isoform; (iii) NLS1 was mapped to aa 6-35 and NLS2 to aa 190-213; (iv) using surface plasmon resonance spectroscopy, the binding of both NLS1 and NLS2 to human importin-α was demonstrated, stressing the importance of individual arginine residues in the bipartite consensus motifs; (v) nuclear magnetic resonance spectroscopy of pUL97 peptides confirmed an earlier statement about the functional requirement of NLS1 embedding into an intact α-helical structure; and (vi) a bioinformatics investigation of the solvent-accessible surface suggested a high accessibility of NLS1 and an isoform-specific, variable accessibility of NLS2 for interaction with importin-α. Thus, the nucleocytoplasmic transport mechanism of the isoforms appeared to be differentially regulated, and this may have consequences for isoform-dependent functions of pUL97 during virus replication.
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Affiliation(s)
- Rike Webel
- Institute for Clinical and Molecular Virology, University of Erlangen-Nuremberg, Schlossgarten 4, 91054 Erlangen, Germany
| | - Sara M Ø Solbak
- Centre of Pharmacy and Department of Chemistry, University of Bergen, Bergen, Norway
| | - Christian Held
- Department for Image Processing and Biomedical Engineering, Fraunhofer Institute for Integrated Circuits IIS, Erlangen, Germany
| | - Jens Milbradt
- Institute for Clinical and Molecular Virology, University of Erlangen-Nuremberg, Schlossgarten 4, 91054 Erlangen, Germany
| | - Andrea Groß
- Department Medicinal Chemistry, University of Erlangen-Nuremberg, Germany
| | - Jutta Eichler
- Department Medicinal Chemistry, University of Erlangen-Nuremberg, Germany
| | - Thomas Wittenberg
- Department for Image Processing and Biomedical Engineering, Fraunhofer Institute for Integrated Circuits IIS, Erlangen, Germany
| | - Christophe Jardin
- Division of Bioinformatics, Institute of Biochemistry, University of Erlangen-Nuremberg, Germany
| | - Heinrich Sticht
- Division of Bioinformatics, Institute of Biochemistry, University of Erlangen-Nuremberg, Germany
| | - Torgils Fossen
- Centre of Pharmacy and Department of Chemistry, University of Bergen, Bergen, Norway
| | - Manfred Marschall
- Institute for Clinical and Molecular Virology, University of Erlangen-Nuremberg, Schlossgarten 4, 91054 Erlangen, Germany
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21
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Tsou LK, Chen CH, Dutschman GE, Cheng YC, Hamilton AD. Blocking HIV-1 entry by a gp120 surface binding inhibitor. Bioorg Med Chem Lett 2012; 22:3358-61. [PMID: 22487177 DOI: 10.1016/j.bmcl.2012.02.079] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Revised: 02/18/2012] [Accepted: 02/23/2012] [Indexed: 11/27/2022]
Abstract
We report the mode of action of a proteomimetic compound that binds to the exterior surface of gp120 and blocks HIV-1 entry into cells. Using a one cycle time-of-addition study and antibody competition binding studies, we have determined that the compound blocks HIV-1 entry through modulation of key protein-protein interactions mediated by gp120. The compound exhibits anti-HIV-1 replication activities against several pseudotype viruses derived from primary isolates and the resistant strains isolated from existing drug candidates with equal potency. Together, these data provide evidence that the proteomimetic compound represents a novel class of HIV-1 viral entry inhibitor that functions through protein surface recognition in analogy to an antibody.
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Affiliation(s)
- Lun K Tsou
- Department of Chemistry, Yale University, New Haven, CT 06520, United States
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22
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Structural Basis for Species Selectivity in the HIV-1 gp120-CD4 Interaction: Restoring Affinity to gp120 in Murine CD4 Mimetic Peptides. Adv Bioinformatics 2012; 2011:736593. [PMID: 22312332 PMCID: PMC3270550 DOI: 10.1155/2011/736593] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 11/07/2011] [Accepted: 11/23/2011] [Indexed: 11/18/2022] Open
Abstract
The first step of HIV-1 infection involves interaction between the viral glycoprotein gp120 and the human cellular receptor CD4. Inhibition of the gp120-CD4 interaction represents an attractive strategy to block HIV-1 infection. In an attempt to explore the known lack of affinity of murine CD4 to gp120, we have investigated peptides presenting the putative gp120-binding site of murine CD4 (mCD4). Molecular modeling indicates that mCD4 protein cannot bind gp120 due to steric clashes, while the larger conformational flexibility of mCD4 peptides allows an interaction. This finding is confirmed by experimental binding assays, which also evidenced specificity of the peptide-gp120 interaction. Molecular dynamics simulations indicate that the mCD4-peptide stably interacts with gp120 via an intermolecular β-sheet, while an important salt-bridge formed by a C-terminal lysine is lost. Fixation of the C-terminus by introducing a disulfide bridge between the N- and C-termini of the peptide significantly enhanced the affinity to gp120.
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23
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Mulder GE, Kruijtzer JAW, Liskamp RMJ. A combinatorial approach toward smart libraries of discontinuous epitopes of HIV gp120 on a TAC synthetic scaffold. Chem Commun (Camb) 2012; 48:10007-9. [DOI: 10.1039/c2cc35310e] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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24
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Nakahara T, Nomura W, Ohba K, Ohya A, Tanaka T, Hashimoto C, Narumi T, Murakami T, Yamamoto N, Tamamura H. Remodeling of Dynamic Structures of HIV-1 Envelope Proteins Leads to Synthetic Antigen Molecules Inducing Neutralizing Antibodies. Bioconjug Chem 2010; 21:709-14. [DOI: 10.1021/bc900502z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Toru Nakahara
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo 101-0062, Japan, and AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Wataru Nomura
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo 101-0062, Japan, and AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Kenji Ohba
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo 101-0062, Japan, and AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Aki Ohya
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo 101-0062, Japan, and AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Tomohiro Tanaka
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo 101-0062, Japan, and AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Chie Hashimoto
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo 101-0062, Japan, and AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Tetsuo Narumi
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo 101-0062, Japan, and AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Tsutomu Murakami
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo 101-0062, Japan, and AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Naoki Yamamoto
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo 101-0062, Japan, and AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Hirokazu Tamamura
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo 101-0062, Japan, and AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
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25
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Moebius K, Eichler J. HIV-derived peptide mimics. DRUG DISCOVERY TODAY. TECHNOLOGIES 2009; 6:e1-e40. [PMID: 24128988 DOI: 10.1016/j.ddtec.2009.09.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
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26
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Chamorro C, Kruijtzer JAW, Farsaraki M, Balzarini J, Liskamp RMJ. A general approach for the non-stop solid phase synthesis of TAC-scaffolded loops towards protein mimics containing discontinuous epitopes. Chem Commun (Camb) 2009:821-3. [DOI: 10.1039/b817357e] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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27
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Peptides as protein binding site mimetics. Curr Opin Chem Biol 2008; 12:707-13. [DOI: 10.1016/j.cbpa.2008.09.023] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2008] [Revised: 09/08/2008] [Accepted: 09/19/2008] [Indexed: 12/13/2022]
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28
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Sudarman E, Bollati-Fogolín M, Hafner M, Müller W, Scheller J, Rose-John S, Eichler J. Synthetic Mimetics of the gp130 Binding Site for Viral Interleukin-6 as Inhibitors of the vIL-6-gp130 Interaction. Chem Biol Drug Des 2008; 71:494-500. [DOI: 10.1111/j.1747-0285.2008.00649.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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