1
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David TI, Pestov NB, Korneenko TV, Barlev NA. Non-Immunoglobulin Synthetic Binding Proteins for Oncology. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1232-1247. [PMID: 37770391 DOI: 10.1134/s0006297923090043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/01/2023] [Accepted: 08/01/2023] [Indexed: 09/30/2023]
Abstract
Extensive application of technologies like phage display in screening peptide and protein combinatorial libraries has not only facilitated creation of new recombinant antibodies but has also significantly enriched repertoire of the protein binders that have polypeptide scaffolds without homology to immunoglobulins. These innovative synthetic binding protein (SBP) platforms have grown in number and now encompass monobodies/adnectins, DARPins, lipocalins/anticalins, and a variety of miniproteins such as affibodies and knottins, among others. They serve as versatile modules for developing complex affinity tools that hold promise in both diagnostic and therapeutic settings. An optimal scaffold typically has low molecular weight, minimal immunogenicity, and demonstrates resistance against various challenging conditions, including proteolysis - making it potentially suitable for peroral administration. Retaining functionality under reducing intracellular milieu is also advantageous. However, paramount to its functionality is the scaffold's ability to tolerate mutations across numerous positions, allowing for the formation of a sufficiently large target binding region. This is achieved through the library construction, screening, and subsequent expression in an appropriate system. Scaffolds that exhibit high thermodynamic stability are especially coveted by the developers of new SBPs. These are steadily making their way into clinical settings, notably as antagonists of oncoproteins in signaling pathways. This review surveys the diverse landscape of SBPs, placing particular emphasis on the inhibitors targeting the oncoprotein KRAS, and highlights groundbreaking opportunities for SBPs in oncology.
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Affiliation(s)
- Temitope I David
- Institute of Biomedical Chemistry, Moscow, 119121, Russia
- Laboratory of Molecular Oncology, Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Nikolay B Pestov
- Institute of Biomedical Chemistry, Moscow, 119121, Russia.
- Laboratory of Tick-Borne Encephalitis and Other Viral Encephalitides, Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products, Russian Academy of Sciences, Moscow, 108819, Russia
- Group of Cross-Linking Enzymes, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - Tatyana V Korneenko
- Group of Cross-Linking Enzymes, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - Nikolai A Barlev
- Institute of Biomedical Chemistry, Moscow, 119121, Russia
- Laboratory of Tick-Borne Encephalitis and Other Viral Encephalitides, Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products, Russian Academy of Sciences, Moscow, 108819, Russia
- Institute of Cytology Russian Academy of Sciences, St.-Petersburg, 194064, Russia
- School of Medicine, Nazarbayev University, Astana, 010000, Kazakhstan
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2
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Conformations of disulfides are conserved in inhibitory cystine knot (ICK) motif polypeptides. Toxicon 2022; 219:106926. [PMID: 36167143 DOI: 10.1016/j.toxicon.2022.09.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 08/24/2022] [Accepted: 09/12/2022] [Indexed: 11/23/2022]
Abstract
The inhibitory cystine knot (ICK) motif is an evolutionarily optimized disulfide-rich peptide motif widely present in diverse phyla with distinct biological functions. Cysteine disulfides are highly conserved in the ICK motif with C1-C4 (Disulfide-I), C2-C5(Disulfide-II), and C3-C6(Disulfide-III) connectivities in a sequence. Disulfide-I and disulfide-II form a loop and the disulfide-III tethers through the loop forming a knotted fold. The current report has analysed the conformation of disulfides in the ICK motif using the side-chain torsional angles of cysteine disulfide. In crystal structures: 88% of Disulfide-I have (+,-)SynRHHook, 92% of Disulfide-II have (+,-)RHSpiral, and 100% of Disulfide-III have (-,-)LHSpiral conformations. In NMR structures, conformational diversity has been observed for each of the cysteine disulfides of the ICK motif. The highest percentage occurrence in NMR structures: 27% of Disulfide-I have (+,-)SynRHHook, 36% of Disulfide-II have (+,-)RHSpiral, and 50% of Disulfide-III have (-,-)LHSpiral conformations. In the view of the method of identification of disulfides between cysteine residues using NMR spectroscopy, the NMR structure represents an ensemble of conformations of disulfides instead of specific disulfide conformation. The retention of the conformation in both X-ray and NMR structures supports the conservation of conformation of disulfides in the ICK motif. The tendency to exhibit specific conformation of disulfide even with variations in 3D structures supports the evolutionarily optimized nature of the ICK motif.
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3
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Luo R, Liu H, Cheng Z. Protein scaffolds: Antibody alternative for cancer diagnosis and therapy. RSC Chem Biol 2022; 3:830-847. [PMID: 35866165 PMCID: PMC9257619 DOI: 10.1039/d2cb00094f] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/23/2022] [Indexed: 12/01/2022] Open
Abstract
Although antibodies are well developed and widely used in cancer therapy and diagnostic fields, some defects remain, such as poor tissue penetration, long in vivo metabolic retention, potential cytotoxicity, patent limitation, and high production cost. These issues have led scientists to explore and develop novel antibody alternatives. Protein scaffolds are small monomeric proteins with stable tertiary structures and mutable residues, which emerged in the 1990s. By combining robust gene engineering and phage display techniques, libraries with sufficient diversity could be established for target binding scaffold selection. Given the properties of small size, high affinity, and excellent specificity and stability, protein scaffolds have been applied in basic research, and preclinical and clinical fields over the past two decades. To date, more than 20 types of protein scaffolds have been developed, with the most frequently used being affibody, adnectin, ANTICALIN®, DARPins, and knottin. In this review, we focus on the protein scaffold applications in cancer therapy and diagnosis in the last 5 years, and discuss the pros and cons, and strategies of optimization and design. Although antibodies are well developed and widely used in cancer therapy and diagnostic fields, some defects remain, such as poor tissue penetration, long in vivo metabolic retention, potential cytotoxicity, patent limitation, and high production cost.![]()
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Affiliation(s)
- Renli Luo
- Department of Molecular Medicine, College of Life and Health Sciences, Northeastern University Shenyang China
| | - Hongguang Liu
- Department of Molecular Medicine, College of Life and Health Sciences, Northeastern University Shenyang China
| | - Zhen Cheng
- State Key Laboratory of Drug Research, Molecular Imaging Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
- Drug Discovery Shandong Laboratory, Bohai Rim Advanced Research Institute for Drug Discovery Yantai Shandong 264117 China
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4
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Burton NR, Kim P, Backus KM. Photoaffinity labelling strategies for mapping the small molecule-protein interactome. Org Biomol Chem 2021; 19:7792-7809. [PMID: 34549230 PMCID: PMC8489259 DOI: 10.1039/d1ob01353j] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Nearly all FDA approved drugs and bioactive small molecules exert their effects by binding to and modulating proteins. Consequently, understanding how small molecules interact with proteins at an molecular level is a central challenge of modern chemical biology and drug development. Complementary to structure-guided approaches, chemoproteomics has emerged as a method capable of high-throughput identification of proteins covalently bound by small molecules. To profile noncovalent interactions, established chemoproteomic workflows typically incorporate photoreactive moieties into small molecule probes, which enable trapping of small molecule-protein interactions (SMPIs). This strategy, termed photoaffinity labelling (PAL), has been utilized to profile an array of small molecule interactions, including for drugs, lipids, metabolites, and cofactors. Herein we describe the discovery of photocrosslinking chemistries, including a comparison of the strengths and limitations of implementation of each chemotype in chemoproteomic workflows. In addition, we highlight key examples where photoaffinity labelling has enabled target deconvolution and interaction site mapping.
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Affiliation(s)
- Nikolas R Burton
- Department of Chemistry and Biochemistry, College of Arts and Sciences, UCLA, Los Angeles, CA, 90095, USA.
| | - Phillip Kim
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Keriann M Backus
- Department of Chemistry and Biochemistry, College of Arts and Sciences, UCLA, Los Angeles, CA, 90095, USA.
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
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5
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Tomassi S, D’Amore VM, Di Leva FS, Vannini A, Quilici G, Weinmüller M, Reichart F, Amato J, Romano B, Izzo AA, Di Maro S, Novellino E, Musco G, Gianni T, Kessler H, Marinelli L. Halting the Spread of Herpes Simplex Virus-1: The Discovery of an Effective Dual αvβ6/αvβ8 Integrin Ligand. J Med Chem 2021; 64:6972-6984. [PMID: 33961417 PMCID: PMC8279406 DOI: 10.1021/acs.jmedchem.1c00533] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Indexed: 02/08/2023]
Abstract
Over recent years, αvβ6 and αvβ8 Arg-Gly-Asp (RGD) integrins have risen to prominence as interchangeable co-receptors for the cellular entry of herpes simplex virus-1 (HSV-1). In fact, the employment of subtype-specific integrin-neutralizing antibodies or gene-silencing siRNAs has emerged as a valuable strategy for impairing HSV infectivity. Here, we shift the focus to a more affordable pharmaceutical approach based on small RGD-containing cyclic pentapeptides. Starting from our recently developed αvβ6-preferential peptide [RGD-Chg-E]-CONH2 (1), a small library of N-methylated derivatives (2-6) was indeed synthesized in the attempt to increase its affinity toward αvβ8. Among the novel compounds, [RGD-Chg-(NMe)E]-CONH2 (6) turned out to be a potent αvβ6/αvβ8 binder and a promising inhibitor of HSV entry through an integrin-dependent mechanism. Furthermore, the renewed selectivity profile of 6 was fully rationalized by a NMR/molecular modeling combined approach, providing novel valuable hints for the design of RGD integrin ligands with the desired specificity profile.
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Affiliation(s)
- Stefano Tomassi
- Dipartimento
di Farmacia, Università degli Studi
di Napoli “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Vincenzo Maria D’Amore
- Dipartimento
di Farmacia, Università degli Studi
di Napoli “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Francesco Saverio Di Leva
- Dipartimento
di Farmacia, Università degli Studi
di Napoli “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Andrea Vannini
- Department
of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40126 Bologna, Italy
| | - Giacomo Quilici
- Biomolecular
NMR Unit c/o IRCCS S. Raffaele, Via Olgettina 58, 20132 Milano, Italy
| | - Michael Weinmüller
- Institute
for Advanced Study, Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Florian Reichart
- Institute
for Advanced Study, Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Jussara Amato
- Dipartimento
di Farmacia, Università degli Studi
di Napoli “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Barbara Romano
- Dipartimento
di Farmacia, Università degli Studi
di Napoli “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Angelo Antonio Izzo
- Dipartimento
di Farmacia, Università degli Studi
di Napoli “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Salvatore Di Maro
- DiSTABiF, University of Campania
“Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Ettore Novellino
- Dipartimento
di Farmacia, Università degli Studi
di Napoli “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
- Facoltà
di Medicina e Chirurgia, Università
Cattolica del Sacro Cuore, Largo Francesco Vito, 1, 00168 Roma, Italy
| | - Giovanna Musco
- Biomolecular
NMR Unit c/o IRCCS S. Raffaele, Via Olgettina 58, 20132 Milano, Italy
| | - Tatiana Gianni
- Department
of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40126 Bologna, Italy
| | - Horst Kessler
- Institute
for Advanced Study, Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Luciana Marinelli
- Dipartimento
di Farmacia, Università degli Studi
di Napoli “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
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6
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Dekan Z, Kremsmayr T, Keov P, Godin M, Teakle N, Dürrauer L, Xiang H, Gharib D, Bergmayr C, Hellinger R, Gay M, Vilaseca M, Kurzbach D, Albericio F, Alewood PF, Gruber CW, Muttenthaler M. Nature-inspired dimerization as a strategy to modulate neuropeptide pharmacology exemplified with vasopressin and oxytocin. Chem Sci 2021; 12:4057-4062. [PMID: 34163676 PMCID: PMC8179488 DOI: 10.1039/d0sc05501h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Vasopressin (VP) and oxytocin (OT) are cyclic neuropeptides that regulate fundamental physiological functions via four G protein-coupled receptors, V1aR, V1bR, V2R, and OTR. Ligand development remains challenging for these receptors due to complex structure–activity relationships. Here, we investigated dimerization as a strategy for developing ligands with novel pharmacology. We regioselectively synthesised and systematically studied parallel, antiparallel and N- to C-terminal cyclized homo- and heterodimer constructs of VP, OT and dVDAVP (1-deamino-4-valine-8-d-arginine-VP). All disulfide-linked dimers, except for the head-to-tail cyclized constructs, retained nanomolar potency despite the structural implications of dimerization. Our results support a single chain interaction for receptor activation. Dimer orientation had little impact on activity, except for the dVDAVP homodimers, where an antagonist to agonist switch was observed at the V1aR. This study provides novel insights into the structural requirements of VP/OT receptor activation and spotlights dimerization as a strategy to modulate pharmacology, a concept also frequently observed in nature. Structural and pharmacological study of parallel, antiparallel and N- to C-terminal cyclized homo- and heterodimers of vasopressin and oxytocin. This study spotlights dimerization as a strategy to modulate the pharmacology of neuropeptides.![]()
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Affiliation(s)
- Zoltan Dekan
- Institute for Molecular Bioscience, The University of Queensland Brisbane 4072 Australia
| | - Thomas Kremsmayr
- Institute of Biological Chemistry, University of Vienna Währingerstraße 38 1090 Vienna Austria
| | - Peter Keov
- Faculty of Medicine, School of Biomedical Sciences, The University of Queensland Brisbane 4072 Australia
| | - Mathilde Godin
- Institute for Molecular Bioscience, The University of Queensland Brisbane 4072 Australia
| | - Ngari Teakle
- Institute for Molecular Bioscience, The University of Queensland Brisbane 4072 Australia
| | - Leopold Dürrauer
- Institute of Biological Chemistry, University of Vienna Währingerstraße 38 1090 Vienna Austria
| | - Huang Xiang
- Center for Physiology and Pharmacology, Medical University of Vienna Schwarzspanierstraße 17 1090 Vienna Austria
| | - Dalia Gharib
- Center for Physiology and Pharmacology, Medical University of Vienna Schwarzspanierstraße 17 1090 Vienna Austria
| | - Christian Bergmayr
- Center for Physiology and Pharmacology, Medical University of Vienna Schwarzspanierstraße 17 1090 Vienna Austria
| | - Roland Hellinger
- Center for Physiology and Pharmacology, Medical University of Vienna Schwarzspanierstraße 17 1090 Vienna Austria
| | - Marina Gay
- Institute for Research in Biomedicine Barcelona C/ Baldiri Reixac 10 08028 Barcelona Spain
| | - Marta Vilaseca
- Institute for Research in Biomedicine Barcelona C/ Baldiri Reixac 10 08028 Barcelona Spain
| | - Dennis Kurzbach
- Institute of Biological Chemistry, University of Vienna Währingerstraße 38 1090 Vienna Austria
| | - Fernando Albericio
- Department of Organic Chemistry, University of Barcelona Barcelona Science Park, Baldiri Reixac 10 08028 Barcelona Spain
| | - Paul F Alewood
- Institute for Molecular Bioscience, The University of Queensland Brisbane 4072 Australia
| | - Christian W Gruber
- Faculty of Medicine, School of Biomedical Sciences, The University of Queensland Brisbane 4072 Australia.,Center for Physiology and Pharmacology, Medical University of Vienna Schwarzspanierstraße 17 1090 Vienna Austria
| | - Markus Muttenthaler
- Institute for Molecular Bioscience, The University of Queensland Brisbane 4072 Australia .,Institute of Biological Chemistry, University of Vienna Währingerstraße 38 1090 Vienna Austria
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7
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Crook ZR, Nairn NW, Olson JM. Miniproteins as a Powerful Modality in Drug Development. Trends Biochem Sci 2020; 45:332-346. [PMID: 32014389 PMCID: PMC7197703 DOI: 10.1016/j.tibs.2019.12.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 12/06/2019] [Accepted: 12/31/2019] [Indexed: 01/03/2023]
Abstract
Miniproteins are a diverse group of protein scaffolds characterized by small (1-10 kDa) size, stability, and versatility in drug-like roles. Coming largely from native sources, they have been widely adopted into drug development pipelines. While their structures and capabilities are diverse, the approaches to their utilization share more similarities with each other than with more widely used modalities (e.g., antibodies or small molecules). In this review, we highlight recent advances in miniprotein-based approaches to otherwise poorly addressed clinical needs, including structure-based and functional characterization. We also summarize their unique screening strategies and pharmacology considerations. Through a greater understanding of the unique properties that make them attractive for drug design, miniproteins can be effectively utilized against targets that are intractable by other approaches.
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Affiliation(s)
- Zachary R Crook
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N., Room D4-100, Seattle, WA 98109, USA
| | - Natalie W Nairn
- Blaze Bioscience, Inc, 530 Fairview Ave N., Suite 1400, Seattle, WA 98109, USA
| | - James M Olson
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N., Room D4-100, Seattle, WA 98109, USA.
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8
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Lui BG, Salomon N, Wüstehube-Lausch J, Daneschdar M, Schmoldt HU, Türeci Ö, Sahin U. Targeting the tumor vasculature with engineered cystine-knot miniproteins. Nat Commun 2020; 11:295. [PMID: 31941901 PMCID: PMC6962393 DOI: 10.1038/s41467-019-13948-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 11/28/2019] [Indexed: 01/08/2023] Open
Abstract
The extra domain B splice variant (EDB) of human fibronectin selectively expressed in the tumor vasculature is an attractive target for cancer imaging and therapy. Here, we describe the generation and characterization of EDB-specific optical imaging probes. By screening combinatorial cystine-knot miniprotein libraries with phage display technology we discover exquisitely EDB-specific ligands that share a distinctive motif. Probes with a binding constant in the picomolar range are generated by chemical oligomerization of selected ligands and fluorophore conjugation. We show by fluorescence imaging that the probes stain EDB in tissue sections derived from human U-87 MG glioblastoma xenografts in mice. Moreover, we demonstrate selective accumulation and retention of intravenously administered probes in the tumor tissue of mice with U-87 MG glioblastoma xenografts by in vivo and ex vivo fluorescence imaging. These data warrants further pursuit of the selected cystine-knot miniproteins for in vivo imaging applications. Cystine-knot miniprotein are small, highly stable, disulfide-rich peptides with increasing potential as drugs and tumor imaging agents. Here the authors develop cystine-knot miniproteins targeting the vascular tumor marker EDB, and use them as probes for in vivo tumor vasculature imaging.
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9
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Bernhagen D, Jungbluth V, Gisbert Quilis N, Dostalek J, White PB, Jalink K, Timmerman P. High-Affinity α 5β 1-Integrin-Selective Bicyclic RGD Peptides Identified via Screening of Designed Random Libraries. ACS COMBINATORIAL SCIENCE 2019; 21:598-607. [PMID: 31269394 DOI: 10.1021/acscombsci.9b00081] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We report the identification of high-affinity and selectivity integrin α5β1-binding bicyclic peptides via "designed random libraries", that is, the screening of libraries comprising the universal integrin-binding sequence Arg-Gly-Asp (RGD) in the first loop in combination with a randomized sequence (XXX) in the second loop. Screening of first-generation libraries for α5β1-binding peptides yielded a triple-digit nanomolar bicyclic α5β1-binder (CT3RGDcT3AYGCT3, IC50 = 406 nM). Next-generation libraries were designed by partially varying the structure of the strongest first-generation lead inhibitor and screened for improved affinities and selectivities for this receptor. In this way, we identified three high-affinity α5β1-binders (CT3RGDcT3AYJCT3, J = d-Leu, IC50 = 90 nM; CT3RGDcT3AYaCT3, IC50 = 156 nM; CT3RGDcT3AWGCT3, IC50 = 173 nM), of which one even showed a higher α5β1-affinity than the 32 amino acid benchmark peptide knottin-RGD (IC50 = 114 nM). Affinity for α5β1-integrin was confirmed by SPFS analysis showing a Kd of 4.1 nM for Cy5-labeled RGD-bicycle CT3RGDcT3AYJCT3 (J = d-Leu) and a somewhat higher Kd (9.0 nM) for Cy5-labeled knottin-RGD. The α5β1-bicycles, for example, CT3RGDcT3AYJCT3 (J = d-Leu), showed excellent selectivities over αvβ5 (IC50 ratio α5β1/αvβ5 between <0.009 and 0.039) and acceptable selectivities over αvβ3 (IC50 ratios α5β1/αvβ3 between 0.090 and 0.157). In vitro staining of adipose-derived stem cells with Cy5-labeled peptides using confocal microscopy revealed strong binding of the α5β1-selective bicycle CT3RGDcT3AWGCT3 to integrins in their natural environment, illustrating the high potential of these RGD bicycles as markers for α5β1-integrin expression.
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Affiliation(s)
- Dominik Bernhagen
- Pepscan Therapeutics, Zuidersluisweg 2, 8243 RC Lelystad, the Netherlands
| | - Vanessa Jungbluth
- Biosensor Technologies, AIT Austrian Institute of Technology GmbH, Konrad-Lorenz-Straße 24, 3430 Tulln, Austria
| | - Nestor Gisbert Quilis
- Biosensor Technologies, AIT Austrian Institute of Technology GmbH, Konrad-Lorenz-Straße 24, 3430 Tulln, Austria
| | - Jakub Dostalek
- Biosensor Technologies, AIT Austrian Institute of Technology GmbH, Konrad-Lorenz-Straße 24, 3430 Tulln, Austria
| | - Paul B. White
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Kees Jalink
- The Netherlands Cancer Institute, Plesmanlaan 21, 1066 CX Amsterdam, the Netherlands
| | - Peter Timmerman
- Pepscan Therapeutics, Zuidersluisweg 2, 8243 RC Lelystad, the Netherlands
- Van’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands
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10
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Bernhagen D, Jungbluth V, Quilis NG, Dostalek J, White PB, Jalink K, Timmerman P. Bicyclic RGD Peptides with Exquisite Selectivity for the Integrin α vβ 3 Receptor Using a "Random Design" Approach. ACS COMBINATORIAL SCIENCE 2019; 21:198-206. [PMID: 30624885 DOI: 10.1021/acscombsci.8b00144] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We describe the identification of bicyclic RGD peptides with high affinity and selectivity for integrin αvβ3 via high-throughput screening of partially randomized libraries. Peptide libraries (672 different compounds) comprising the universal integrin-binding sequence Arg-Gly-Asp (RGD) in the first loop and a randomized sequence XXX (X being one of 18 canonical l-amino acids) in the second loop, both enclosed by either an l- or d-Cys residue, were converted to bicyclic peptides via reaction with 1,3,5-tris(bromomethyl)benzene (T3). Screening of first-generation libraries yielded lead bicyclic inhibitors displaying submicromolar affinities for integrin αvβ3 (e.g., CT3HEQcT3RGDcT3, IC50 = 195 nM). Next generation (second and third) libraries were obtained by partially varying the structure of the strongest lead inhibitors and screening for improved affinities and selectivities. In this way, we identified the highly selective bicyclic αvβ3-binders CT3HPQcT3RGDcT3 (IC50 = 30 nM), CT3HPQCT3RGDcT3 (IC50 = 31 nM), and CT3HSQCT3RGDcT3 (IC50 = 42 nM) with affinities comparable to that of a knottin-RGD-type peptide (32 amino acids, IC50 = 38 nM) and outstanding selectivities over integrins αvβ5 (IC50 > 10000 nM) and α5β1 (IC50 > 10000 nM). Affinity measurements using surface plasmon-enhanced fluorescence spectroscopy (SPFS) yielded Kd values of 0.4 and 0.6 nM for the Cy5-labeled bicycle CT3HPQcT3RGDcT3 and RGD "knottin" peptide, respectively. In vitro staining of HT29 cells with Cy5-labeled bicycles using confocal microscopy revealed strong binding to integrins in their natural environment, which highlights the high potential of these peptides as markers of integrin expression.
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Affiliation(s)
- Dominik Bernhagen
- Pepscan Therapeutics, Zuidersluisweg 2, 8243 RC Lelystad, The Netherlands
| | - Vanessa Jungbluth
- Biosensor Technologies, AIT Austrian Institute of Technology GmbH, Konrad-Lorenz-Straße 24, 3430 Tulln, Austria
| | - Nestor Gisbert Quilis
- Biosensor Technologies, AIT Austrian Institute of Technology GmbH, Konrad-Lorenz-Straße 24, 3430 Tulln, Austria
| | - Jakub Dostalek
- Biosensor Technologies, AIT Austrian Institute of Technology GmbH, Konrad-Lorenz-Straße 24, 3430 Tulln, Austria
| | - Paul B. White
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Kees Jalink
- The Netherlands Cancer Institute, Plesmanlaan 21, 1066 CX Amsterdam, The Netherlands
| | - Peter Timmerman
- Pepscan Therapeutics, Zuidersluisweg 2, 8243 RC Lelystad, The Netherlands
- Van’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
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11
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Richards DA. Exploring alternative antibody scaffolds: Antibody fragments and antibody mimics for targeted drug delivery. DRUG DISCOVERY TODAY. TECHNOLOGIES 2018; 30:35-46. [PMID: 30553519 DOI: 10.1016/j.ddtec.2018.10.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 10/12/2018] [Accepted: 10/15/2018] [Indexed: 05/20/2023]
Abstract
The field of targeted therapeutics has benefitted immeasurably from the development of high-affinity antibodies. These important ligands have facilitated the development of effective therapies, particularly when conjugated to potent cytotoxic payloads i.e. in antibody-drug conjugates (ADCs). The success of ADCs is evidenced by rapid adoption within the pharmaceuticals community; many major companies have dedicated ADC research programmes. However, despite the advantages, the field of ADCs has failed to live up to its full potential. Studies have emerged suggesting that traditional IgG scaffolds may not be the optimal format for targeted payload delivery. In response, the protein engineering community has begun to explore alternative high-binding protein scaffolds as antibody mimics. In this short review I will summarise the generation, modification, and application of emerging antibody fragments and synthetic antibody mimics, with a focus on their use as drug carriers. The review aims to highlight the advantages of antibody mimics, and how they could be employed to overcome the issues and limitations of traditional ADCs.
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Affiliation(s)
- Daniel A Richards
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK.
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12
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Yao C, Wang W, Wang P, Zhao M, Li X, Zhang F. Near-Infrared Upconversion Mesoporous Cerium Oxide Hollow Biophotocatalyst for Concurrent pH-/H 2 O 2 -Responsive O 2 -Evolving Synergetic Cancer Therapy. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30. [PMID: 29315855 DOI: 10.1002/adma.201704833] [Citation(s) in RCA: 261] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/19/2017] [Indexed: 05/06/2023]
Abstract
Tumor hypoxia is typically presented in the central region of solid tumors, which is mainly caused by an inadequate blood flow and oxygen supply. In the conventional treatment of hypoxic human tumors, not only the oxygen-dependent photodynamic therapy (PDT), but also antitumor drug-based chemotherapy, is considerably limited. The use of direct oxygen delivering approach with oxygen-dependent PDT or chemotherapy may potentiate the reactive oxygen species (ROS)-mediated cytotoxicity of the drug toward normal tissues. Herein, a synergetic one-for-all mesoporous cerium oxide upconversion biophotocatalyst is developed to achieve intratumorally endogenous H2 O2 -responsive self-sufficiency of O2 and near-infrared light controlled PDT simultaneously for overcoming hypoxia cancer. Furthermore, the sufficient O2 plays an important role in overcoming the chemotherapeutic drug-resistant cancer caused by hypoxia, therefore inducing tumor cell apoptosis significantly.
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Affiliation(s)
- Chi Yao
- Department of Chemistry, State Key Laboratory of Molecular Engineering of Polymers, Collaborative Innovation Center of Chemistry for Energy Materials, Fudan University, Shanghai, 200433, P. R. China
| | - Wenxing Wang
- Department of Chemistry, State Key Laboratory of Molecular Engineering of Polymers, Collaborative Innovation Center of Chemistry for Energy Materials, Fudan University, Shanghai, 200433, P. R. China
| | - Peiyuan Wang
- Department of Chemistry, State Key Laboratory of Molecular Engineering of Polymers, Collaborative Innovation Center of Chemistry for Energy Materials, Fudan University, Shanghai, 200433, P. R. China
| | - Mengyao Zhao
- Department of Chemistry, State Key Laboratory of Molecular Engineering of Polymers, Collaborative Innovation Center of Chemistry for Energy Materials, Fudan University, Shanghai, 200433, P. R. China
| | - Xiaomin Li
- Department of Chemistry, State Key Laboratory of Molecular Engineering of Polymers, Collaborative Innovation Center of Chemistry for Energy Materials, Fudan University, Shanghai, 200433, P. R. China
| | - Fan Zhang
- Department of Chemistry, State Key Laboratory of Molecular Engineering of Polymers, Collaborative Innovation Center of Chemistry for Energy Materials, Fudan University, Shanghai, 200433, P. R. China
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13
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Verma H, Khatri B, Chakraborti S, Chatterjee J. Increasing the bioactive space of peptide macrocycles by thioamide substitution. Chem Sci 2018; 9:2443-2451. [PMID: 29732120 PMCID: PMC5909342 DOI: 10.1039/c7sc04671e] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 01/19/2018] [Indexed: 12/23/2022] Open
Abstract
We show that substituting a single atom, O to S (amide to thioamide), in a peptide bond results in global restriction of the conformational flexibility in peptide macrocycles with minimal perturbation of the parent conformation. The van der Waals interactions between the C 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 S group and the surrounding atoms are the major driving force in inducing the conformational restriction, resulting in well-defined structures of these cyclic peptides with static 3-D presentation of the pharmacophores. Utilizing this property of thioamides, we report the development of a superactive antagonist of pro-angiogenic αvβ3, αvβ5 and α5β1 integrins, which are responsible for cancer cell proliferation and survival. Using simple thio-scanning and spatial screening of a non-efficacious and conformationally flexible cyclic peptide, we could achieve a more than 105 fold enhancement in its efficacy in cellulo via a single O to S substitution. The developed peptide shows better efficacy in inhibiting the pro-angiogenic integrins than the drug candidate cilengitide, with a significantly enhanced serum half-life of 36 h compared to that of cilengitide (12 h). The long shelf-life, absence of non-specific toxicity and resistance to degradation of the thioamidated macrocyclic peptides in human serum suggest the promise of thioamides in markedly improving the affinity, efficacy and pharmacology of peptide macrocycles.
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Affiliation(s)
- Hitesh Verma
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India .
| | - Bhavesh Khatri
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India .
| | - Sohini Chakraborti
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India .
| | - Jayanta Chatterjee
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India . .,NMR Research Centre , Indian Institute of Science , Bangalore 560012 , India
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14
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Schwarz E. Cystine knot growth factors and their functionally versatile proregions. Biol Chem 2017; 398:1295-1308. [PMID: 28771427 DOI: 10.1515/hsz-2017-0163] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 07/16/2017] [Indexed: 12/23/2022]
Abstract
The cystine knot disulfide pattern has been found to be widespread in nature, since it has been detected in proteins from plants, marine snails, spiders and mammals. Cystine knot proteins are secreted proteins. Their functions range from defense mechanisms as toxins, e.g. ion channel or enzyme inhibitors, to hormones, blood factors and growth factors. Cystine knot proteins can be divided into two superordinate groups. (i) The cystine knot peptides, also referred to - with other non-cystine knot proteins - as knottins, with linear and cyclic polypeptide chains. (ii) The cystine knot growth factor family, which is in the focus of this article. The disulfide ring structure of the cystine knot peptides is made up by the half-cystines 1-4 and 2-5, and the threading disulfide bond is formed by the half-cystines, 3-6. In the growth factor group, the disulfides of half-cystines 1 and 4 pass the ring structure formed by the half-cystines 2-5 and 3-6. In this review, special emphasis will be devoted to the growth factor cystine knot proteins and their proregions. The latter have shifted into the focus of scientific interest as their important biological roles are just to be unravelled.
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15
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Sankaran S, Cavatorta E, Huskens J, Jonkheijm P. Cell Adhesion on RGD-Displaying Knottins with Varying Numbers of Tryptophan Amino Acids to Tune the Affinity for Assembly on Cucurbit[8]uril Surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:8813-8820. [PMID: 28514856 PMCID: PMC5588093 DOI: 10.1021/acs.langmuir.7b00702] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 05/08/2017] [Indexed: 06/07/2023]
Abstract
Cell adhesion is studied on multivalent knottins, displaying RGD ligands with a high affinity for integrin receptors, that are assembled on CB[8]-methylviologen-modified surfaces. The multivalency in the knottins stems from the number of tryptophan amino acid moieties, between 0 and 4, that can form a heteroternary complex with cucurbit[8]uril (CB[8]) and surface-tethered methylviologen (MV2+). The binding affinity of the knottins with CB[8] and MV2+ surfaces was evaluated using surface plasmon resonance spectroscopy. Specific binding occurred, and the affinity increased with the valency of tryptophans on the knottin. Additionally, increased multilayer formation was observed, attributed to homoternary complex formation between tryptophan residues of different knottins and CB[8]. Thus, we were able to control the surface coverage of the knottins by valency and concentration. Cell experiments with mouse myoblast (C2C12) cells on the self-assembled knottin surfaces showed specific integrin recognition by the RGD-displaying knottins. Moreover, cells were observed to elongate more on the supramolecular knottin surfaces with a higher valency, and in addition, more pronounced focal adhesion formation was observed on the higher-valency knottin surfaces. We attribute this effect to the enhanced coverage and the enhanced affinity of the knottins in their interaction with the CB[8] surface. Collectively, these results are promising for the development of biomaterials including knottins via CB[8] ternary complexes for tunable interactions with cells.
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Affiliation(s)
- Shrikrishnan Sankaran
- Molecular
Nanofabrication Group, MESA+ Institute for Nanotechnology, Department
of Science and Technology and Bioinspired Molecular Engineering Laboratory, MIRA
Institute for Biomedical Technology and Technical Medicine and Molecular
Nanofabrication Group, MESA+ Institute for Nanotechnology, Department
of Science and Technology, University of
Twente, 7500 AE Enschede, The Netherlands
| | - Emanuela Cavatorta
- Molecular
Nanofabrication Group, MESA+ Institute for Nanotechnology, Department
of Science and Technology and Bioinspired Molecular Engineering Laboratory, MIRA
Institute for Biomedical Technology and Technical Medicine and Molecular
Nanofabrication Group, MESA+ Institute for Nanotechnology, Department
of Science and Technology, University of
Twente, 7500 AE Enschede, The Netherlands
| | - Jurriaan Huskens
- Molecular
Nanofabrication Group, MESA+ Institute for Nanotechnology, Department
of Science and Technology and Bioinspired Molecular Engineering Laboratory, MIRA
Institute for Biomedical Technology and Technical Medicine and Molecular
Nanofabrication Group, MESA+ Institute for Nanotechnology, Department
of Science and Technology, University of
Twente, 7500 AE Enschede, The Netherlands
| | - Pascal Jonkheijm
- Molecular
Nanofabrication Group, MESA+ Institute for Nanotechnology, Department
of Science and Technology and Bioinspired Molecular Engineering Laboratory, MIRA
Institute for Biomedical Technology and Technical Medicine and Molecular
Nanofabrication Group, MESA+ Institute for Nanotechnology, Department
of Science and Technology, University of
Twente, 7500 AE Enschede, The Netherlands
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16
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Bernhagen D, De Laporte L, Timmerman P. High-Affinity RGD-Knottin Peptide as a New Tool for Rapid Evaluation of the Binding Strength of Unlabeled RGD-Peptides to α vβ 3, α vβ 5, and α 5β 1 Integrin Receptors. Anal Chem 2017; 89:5991-5997. [PMID: 28492301 DOI: 10.1021/acs.analchem.7b00554] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We describe a highly sensitive competition ELISA to measure integrin-binding of RGD-peptides in high-throughput without using cells, ECM-proteins, or antibodies. The assay measures (nonlabeled) RGD-peptides' ability to inhibit binding of a biotinylated "knottin"-RGD peptide to surface-immobilized integrins and, thus, enables quantification of the binding strength of high-, medium-, and low-affinity RGD-binders. We introduced the biotinylated knottin-RGD peptide instead of biotinylated cyclo[RGDfK] (as reported by Piras et al.), as integrin-binding was much stronger and clearly detectable for all three integrins. In order to maximize sensitivity and cost-efficiency, we first optimized several parameters, such as integrin-immobilization levels, knottin-RGD concentration, buffer compositions, type of detection tag (biotin, His- or cMyc-tag), and spacer length. We thereby identified two key factors, that is, (i) the critical spacer length (longer than Gly) and (ii) the presence of Ca2+ and Mg2+ in all incubation and washing buffers. Binding of knottin-RGD peptide was strongest for αvβ3 but also detectable for both αvβ5 and α5β1, while binding of biotinylated cyclo[RGDfK] was very weak and only detectable for αvβ3. For assay validation, we finally determined IC50 values for three unlabeled peptides, that is: (i) linear GRGDS, (ii) cyclo[RGDfK], and (iii) the knottin-RGD itself for binding to three different integrin receptors (αvβ3, αvβ5, α5β1). Major benefits of the novel assay are (i) the extremely low consumption of integrin (50 ng/peptide), (ii) the fact that neither antibodies/ECM-proteins nor integrin-expressing cells are required for detection, and (iii) its suitability for high-throughput screening of (RGD-)peptide libraries.
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Affiliation(s)
- Dominik Bernhagen
- Pepscan Therapeutics , Zuidersluisweg 2, 8243 RC, Lelystad, The Netherlands
| | - Laura De Laporte
- DWI - Leibniz Institute for Interactive Materials , Forckenbeckstr. 50, 52056 Aachen, Germany
| | - Peter Timmerman
- Pepscan Therapeutics , Zuidersluisweg 2, 8243 RC, Lelystad, The Netherlands.,Van't Hoff Institute for Molecular Sciences, University of Amsterdam , Sciencepark 904, 1098 XH, Amsterdam, The Netherlands
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17
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Xuan W, Shao S, Schultz PG. Protein Crosslinking by Genetically Encoded Noncanonical Amino Acids with Reactive Aryl Carbamate Side Chains. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611841] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Weimin Xuan
- Department of Chemistry; the Scripps Research Institute; 10550 N. Torrey Pines Road La Jolla CA 92037 USA
| | - Sida Shao
- Department of Chemistry; the Scripps Research Institute; 10550 N. Torrey Pines Road La Jolla CA 92037 USA
| | - Peter G. Schultz
- Department of Chemistry; the Scripps Research Institute; 10550 N. Torrey Pines Road La Jolla CA 92037 USA
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18
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Xuan W, Shao S, Schultz PG. Protein Crosslinking by Genetically Encoded Noncanonical Amino Acids with Reactive Aryl Carbamate Side Chains. Angew Chem Int Ed Engl 2017; 56:5096-5100. [PMID: 28371162 DOI: 10.1002/anie.201611841] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 02/06/2017] [Indexed: 01/08/2023]
Abstract
The use of genetically encoded noncanonical amino acids (ncAAs) to construct crosslinks within or between proteins has emerged as a useful method to enhance protein stability, investigate protein-protein interactions, and improve the pharmacological properties of proteins. We report ncAAs with aryl carbamate side chains (PheK and FPheK) that can react with proximal nucleophilic residues to form intra- or intermolecular protein crosslinks. We evolved a pyrrolysyl-tRNA synthetase that incorporates site-specifically PheK and FPheK into proteins in both E. coli and mammalian cells. PheK and FPheK when incorporated into proteins showed good stability during protein expression and purification. FPheK reacted with adjacent Lys, Cys, and Tyr residues in thioredoxin in high yields. In addition, crosslinks could be formed between FPheK and Lys residue of two interacting proteins, including the heavy chain and light chain of an antibody Fab.
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Affiliation(s)
- Weimin Xuan
- Department of Chemistry, the Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Sida Shao
- Department of Chemistry, the Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Peter G Schultz
- Department of Chemistry, the Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
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19
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Dueñas S, Aguila SA, Pimienta G. A workflow for in silico design of hIL-10 and ebvIL-10 inhibitors using well-known miniprotein scaffolds. J Mol Model 2017; 23:118. [PMID: 28293795 DOI: 10.1007/s00894-017-3276-1] [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: 10/23/2016] [Accepted: 02/06/2017] [Indexed: 11/29/2022]
Abstract
The over-expression of immune-suppressors such as IL-10 is a crucial landmark in both tumor progression, and latent viral and parasite infection. IL-10 is a multifunctional protein. Besides its immune-cell suppressive function, it also promotes B-cell tumorigenesis of lymphomas and melanoma. Human pathogens like unicellular parasites and viruses that remain latent inside B cells promote the over-expression of hIL-10 upon infection, which inhibits cell-mediated immune surveillance, and at the same time mediates B cell proliferation. The B-cell specific oncogenic latent virus Epstein-Barr virus (EBV) encodes a viral homologue of hIL-10 (ebvIL-10), expressed during lytic viral proliferation. Once expressed, ebvIL-10 inhibits cell-mediated immune surveillance, assuring EBV re-infection. During long-term latency, EBV-infected B cells over-express hIL-10 to assure B-cell proliferation, occasionally inducing EBV-mediated lymphomas. The amino acid sequences of hIL-10 and ebvIL-10 are more than 80% identical and thus have a very similar tridimensional structure. Based on their published crystallographic structures bound to their human receptor IL10R1, we report a structure-based design of hIL-10 and ebvIL-10 inhibitors based on 3 loops from IL10R1 that establish specific hydrogen bonds with the two IL10s. We have grafted these loops onto a permissible loop in three well-known miniprotein scaffolds-the Conus snail toxin MVIIA, the plant-derived trypsin inhibitor EETI, and the human appetite modulator AgRP. Our computational workflow described in detail below was invigorated by the negative and positive controls implemented, and therefore paves the way for future in vitro and in vivo validation assays of the IL-10 inhibitors engineered.
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Affiliation(s)
- Salvador Dueñas
- Departamento de Innovación Biomédica, División de Biología Experimental y Aplicada, Centro de Investigación y Educación Superior de Ensenada, Carretera Ensenada-Tijuana 3918, Zona Playitas, Ensenada, Baja California, C.P. 22860, Mexico
| | - Sergio A Aguila
- Centro de Nanociencias y Nanotecnologia, Universidad Nacional Autonoma de Mexico, Km. 107 carretera Tijuana-Ensenada, Ensenada, Baja California, C.P. 22860, Mexico.
| | - Genaro Pimienta
- Departamento de Innovación Biomédica, División de Biología Experimental y Aplicada, Centro de Investigación y Educación Superior de Ensenada, Carretera Ensenada-Tijuana 3918, Zona Playitas, Ensenada, Baja California, C.P. 22860, Mexico. .,Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA, 92037, USA.
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20
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Pan G, Sun S, Zhang W, Zhao R, Cui W, He F, Huang L, Lee SH, Shea KJ, Shi Q, Yang H. Biomimetic Design of Mussel-Derived Bioactive Peptides for Dual-Functionalization of Titanium-Based Biomaterials. J Am Chem Soc 2016; 138:15078-15086. [PMID: 27778505 DOI: 10.1021/jacs.6b09770] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Guoqing Pan
- Department
of Orthopaedics, The First Affiliated Hospital of Soochow University,
Orthopaedic Institute, Soochow University, 188 Shizi Street, Suzhou, Jiangsu 215006, China
| | - Shujin Sun
- Department
of Orthopaedics, The First Affiliated Hospital of Soochow University,
Orthopaedic Institute, Soochow University, 188 Shizi Street, Suzhou, Jiangsu 215006, China
| | - Wen Zhang
- Department
of Orthopaedics, The First Affiliated Hospital of Soochow University,
Orthopaedic Institute, Soochow University, 188 Shizi Street, Suzhou, Jiangsu 215006, China
| | - Ruobing Zhao
- Department
of Chemistry, University of California, Irvine, California 92697, United States
| | - Wenguo Cui
- Department
of Orthopaedics, The First Affiliated Hospital of Soochow University,
Orthopaedic Institute, Soochow University, 188 Shizi Street, Suzhou, Jiangsu 215006, China
| | - Fan He
- Department
of Orthopaedics, The First Affiliated Hospital of Soochow University,
Orthopaedic Institute, Soochow University, 188 Shizi Street, Suzhou, Jiangsu 215006, China
| | - Lixin Huang
- Department
of Orthopaedics, The First Affiliated Hospital of Soochow University,
Orthopaedic Institute, Soochow University, 188 Shizi Street, Suzhou, Jiangsu 215006, China
| | - Shih-Hui Lee
- Department
of Chemistry, University of California, Irvine, California 92697, United States
| | - Kenneth J. Shea
- Department
of Chemistry, University of California, Irvine, California 92697, United States
| | - Qin Shi
- Department
of Orthopaedics, The First Affiliated Hospital of Soochow University,
Orthopaedic Institute, Soochow University, 188 Shizi Street, Suzhou, Jiangsu 215006, China
| | - Huilin Yang
- Department
of Orthopaedics, The First Affiliated Hospital of Soochow University,
Orthopaedic Institute, Soochow University, 188 Shizi Street, Suzhou, Jiangsu 215006, China
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21
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Kintzing JR, Cochran JR. Engineered knottin peptides as diagnostics, therapeutics, and drug delivery vehicles. Curr Opin Chem Biol 2016; 34:143-150. [PMID: 27642714 DOI: 10.1016/j.cbpa.2016.08.022] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 08/24/2016] [Accepted: 08/25/2016] [Indexed: 12/18/2022]
Abstract
Inhibitor cystine-knots, also known as knottins, are a structural family of ultra-stable peptides with diverse functions. Knottins and related backbone-cyclized peptides called cyclotides contain three disulfide bonds connected in a particular arrangement that endows these peptides with high thermal, proteolytic, and chemical stability. Knottins have gained interest as candidates for non-invasive molecular imaging and for drug development as they can possess the pharmacological properties of small molecules and the target affinity and selectively of protein biologics. Naturally occurring knottins are clinically approved for treating chronic pain and GI disorders. Combinatorial methods are being used to engineer knottins that can bind to other clinically relevant targets in cancer, and inflammatory and cardiac disease. This review details recent examples of engineered knottin peptides; their use as molecular imaging agents, therapeutics, and drug delivery vehicles; modifications that can be introduced to improve peptide folding and bioactivity; and future perspectives and challenges in the field.
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Affiliation(s)
- James R Kintzing
- Department of Bioengineering, Stanford University, United States
| | - Jennifer R Cochran
- Department of Bioengineering, Stanford University, United States; Department of Chemical Engineering, Stanford University, United States.
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22
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Cox N, Kintzing JR, Smith M, Grant GA, Cochran JR. Integrin-Targeting Knottin Peptide-Drug Conjugates Are Potent Inhibitors of Tumor Cell Proliferation. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201603488] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Nick Cox
- Stanford ChEM-H Medicinal Chemistry Knowledge Center; Stanford University; Stanford CA 94305 USA
| | - James R. Kintzing
- Department of Bioengineering; Stanford University; Stanford CA 94305 USA
| | - Mark Smith
- Stanford ChEM-H Medicinal Chemistry Knowledge Center; Stanford University; Stanford CA 94305 USA
| | - Gerald A. Grant
- Department of Neurosurgery; Stanford University; Stanford CA 94305 USA
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23
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Cox N, Kintzing JR, Smith M, Grant GA, Cochran JR. Integrin-Targeting Knottin Peptide-Drug Conjugates Are Potent Inhibitors of Tumor Cell Proliferation. Angew Chem Int Ed Engl 2016; 55:9894-7. [PMID: 27304709 DOI: 10.1002/anie.201603488] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 05/16/2016] [Indexed: 01/05/2023]
Abstract
Antibody-drug conjugates (ADCs) offer increased efficacy and reduced toxicity compared to systemic chemotherapy. Less attention has been paid to peptide-drug delivery, which has the potential for increased tumor penetration and facile synthesis. We report a knottin peptide-drug conjugate (KDC) and demonstrate that it can selectively deliver gemcitabine to malignant cells expressing tumor-associated integrins. This KDC binds to tumor cells with low-nanomolar affinity, is internalized by an integrin-mediated process, releases its payload intracellularly, and is a highly potent inhibitor of brain, breast, ovarian, and pancreatic cancer cell lines. Notably, these features enable this KDC to bypass a gemcitabine-resistance mechanism found in pancreatic cancer cells. This work expands the therapeutic relevance of knottin peptides to include targeted drug delivery, and further motivates efforts to expand the drug-conjugate toolkit to include non-antibody protein scaffolds.
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Affiliation(s)
- Nick Cox
- Stanford ChEM-H Medicinal Chemistry Knowledge Center, Stanford University, Stanford, CA, 94305, USA
| | - James R Kintzing
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Mark Smith
- Stanford ChEM-H Medicinal Chemistry Knowledge Center, Stanford University, Stanford, CA, 94305, USA
| | - Gerald A Grant
- Department of Neurosurgery, Stanford University, Stanford, CA, 94305, USA
| | - Jennifer R Cochran
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.
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24
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Sankaran S, Stojanovic I, Barendregt A, Heck AJ, Schasfoort RB, Jonkheijm P. Scaffolding of Cystine-Stabilized Miniproteins. ChemistrySelect 2016. [DOI: 10.1002/slct.201600323] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Shrikrishnan Sankaran
- Molecular Nanofabrication Group; MESA+ Institute for Nanotechnology; University of Twente; P.O. Box 217 7500 AE Enschede The Netherlands
- Bioinspired Molecular Engineering Laboratory; MIRA Institute for Biomedical Technology and Technical Medicine; University of Twente; P.O. Box 217 7500 AE Enschede The Netherlands
| | - Ivan Stojanovic
- Medical Cell BioPhysics Group; MIRA Institute for Biomedical Technology and Technical Medicine; University of Twente; P.O. Box 217 7500 AE Enschede The Netherlands
| | - Arjan Barendregt
- Biomolecular Mass Spectrometry and Proteomics; Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences; Utrecht University; Padualaan 8 3584 CH Utrecht The Netherlands
| | - Albert J.R. Heck
- Biomolecular Mass Spectrometry and Proteomics; Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences; Utrecht University; Padualaan 8 3584 CH Utrecht The Netherlands
| | - Richard B.M. Schasfoort
- Medical Cell BioPhysics Group; MIRA Institute for Biomedical Technology and Technical Medicine; University of Twente; P.O. Box 217 7500 AE Enschede The Netherlands
- IBIS Technologies; 7521 PR Enschede The Netherlands
| | - Pascal Jonkheijm
- Molecular Nanofabrication Group; MESA+ Institute for Nanotechnology; University of Twente; P.O. Box 217 7500 AE Enschede The Netherlands
- Bioinspired Molecular Engineering Laboratory; MIRA Institute for Biomedical Technology and Technical Medicine; University of Twente; P.O. Box 217 7500 AE Enschede The Netherlands
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25
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Zhou Y, Xie D, Zhang Y. Amide Rotation Hindrance Predicts Proteolytic Resistance of Cystine-Knot Peptides. J Phys Chem Lett 2016; 7:1138-42. [PMID: 26958702 PMCID: PMC4824663 DOI: 10.1021/acs.jpclett.6b00373] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Cystine-knot peptides have remarkable stability against protease degradation and are attractive scaffolds for peptide-based therapeutic and diagnostic agents. In this work, by studying the hydrolysis reaction of a cystine-knot inhibitor MCTI-A and its variants with ab initio QM/MM molecular dynamics simulations, we have elucidated an amide rotation hindrance mechanism for proteolysis resistance: The proteolysis of MCTI-A is retarded due to the higher free energy cost during the rotation of NH group around scissile peptide bond at the tetrahedral intermediate of acylation, and covalent constraint provided by disulfide bonds is the key factor to hinder this rotation. A nearly linear correlation has been revealed between free energy barriers of the peptide hydrolysis reaction and the amide rotation free energy changes at the protease-peptide Michaelis complex state. This suggests that amide rotation hindrance could be one useful feature to estimate peptide proteolysis stability.
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Affiliation(s)
- Yanzi Zhou
- Laboratory of Mesoscopic Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Corresponding Author: 1) , 2)
| | - Daiqian Xie
- Laboratory of Mesoscopic Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, NY 10003 USA
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Corresponding Author: 1) , 2)
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26
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Currier NV, Ackerman SE, Kintzing JR, Chen R, Filsinger Interrante M, Steiner A, Sato AK, Cochran JR. Targeted Drug Delivery with an Integrin-Binding Knottin-Fc-MMAF Conjugate Produced by Cell-Free Protein Synthesis. Mol Cancer Ther 2016; 15:1291-300. [PMID: 27197305 DOI: 10.1158/1535-7163.mct-15-0881] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 03/17/2016] [Indexed: 11/16/2022]
Abstract
Antibody-drug conjugates (ADC) have generated significant interest as targeted therapeutics for cancer treatment, demonstrating improved clinical efficacy and safety compared with systemic chemotherapy. To extend this concept to other tumor-targeting proteins, we conjugated the tubulin inhibitor monomethyl-auristatin-F (MMAF) to 2.5F-Fc, a fusion protein composed of a human Fc domain and a cystine knot (knottin) miniprotein engineered to bind with high affinity to tumor-associated integrin receptors. The broad expression of integrins (including αvβ3, αvβ5, and α5β1) on tumor cells and their vasculature makes 2.5F-Fc an attractive tumor-targeting protein for drug delivery. We show that 2.5F-Fc can be expressed by cell-free protein synthesis, during which a non-natural amino acid was introduced into the Fc domain and subsequently used for site-specific conjugation of MMAF through a noncleavable linker. The resulting knottin-Fc-drug conjugate (KFDC), termed 2.5F-Fc-MMAF, had approximately 2 drugs attached per KFDC. 2.5F-Fc-MMAF inhibited proliferation in human glioblastoma (U87MG), ovarian (A2780), and breast (MB-468) cancer cells to a greater extent than 2.5F-Fc or MMAF alone or added in combination. As a single agent, 2.5F-Fc-MMAF was effective at inducing regression and prolonged survival in U87MG tumor xenograft models when administered at 10 mg/kg two times per week. In comparison, tumors treated with 2.5F-Fc or MMAF were nonresponsive, and treatment with a nontargeted control, CTRL-Fc-MMAF, showed a modest but not significant therapeutic effect. These studies provide proof-of-concept for further development of KFDCs as alternatives to ADCs for tumor targeting and drug delivery applications. Mol Cancer Ther; 15(6); 1291-300. ©2016 AACR.
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Affiliation(s)
- Nicolas V Currier
- Division of Pediatric Hematology/Oncology, Stanford Medical School, Stanford, California
| | | | - James R Kintzing
- Department of Bioengineering, Stanford University, Stanford, California
| | - Rishard Chen
- Sutro Biopharma, Inc., South San Francisco, California
| | | | | | - Aaron K Sato
- Sutro Biopharma, Inc., South San Francisco, California
| | - Jennifer R Cochran
- Department of Bioengineering, Stanford University, Stanford, California. Department of Chemical Engineering, Stanford University, Stanford, California.
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27
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Kamalov M, Kaur H, Brimble MA. Intermolecular Peptide Cross-Linking by Using Diaminodicarboxylic Acids. Chemistry 2016; 22:3622-31. [DOI: 10.1002/chem.201503458] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Indexed: 12/12/2022]
Affiliation(s)
- Meder Kamalov
- Institute of Biological Chemistry; Faculty of Chemistry; Währinger Straße 38 1090 Vienna Austria
| | - Harveen Kaur
- School of Chemical Sciences; The University of Auckland; 23 Symonds St. Auckland 1142 New Zealand
| | - Margaret A. Brimble
- School of Chemical Sciences; The University of Auckland; 23 Symonds St. Auckland 1142 New Zealand
- School of Biological Sciences; The University of Auckland; 3 Symonds St. Auckland 1142 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery; The University of Auckland; 3 Symonds St. Auckland 1142 New Zealand
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28
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He T, Li D, Yang Y, Ding J, Jin F, Zhuang X, Chen X. Mesomeric configuration makes polyleucine micelle an optimal nanocarrier. Biomater Sci 2016; 4:814-8. [DOI: 10.1039/c6bm00022c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Mesomeric polyleucine micelle with cRGD decoration is selected as a promising targeting drug delivery system.
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Affiliation(s)
- Taoyuan He
- Department of Chemical Engineering
- Changchun University of Technology
- Changchun 130012
- P. R. China
| | - Di Li
- Key Laboratory of Polymer Ecomaterials
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun 130022
- P. R. China
| | - Yanan Yang
- Department of Chemical Engineering
- Changchun University of Technology
- Changchun 130012
- P. R. China
| | - Jianxun Ding
- Key Laboratory of Polymer Ecomaterials
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun 130022
- P. R. China
| | - Feng Jin
- Key Laboratory of Polymer Ecomaterials
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun 130022
- P. R. China
| | - Xiuli Zhuang
- Key Laboratory of Polymer Ecomaterials
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun 130022
- P. R. China
| | - Xuesi Chen
- Key Laboratory of Polymer Ecomaterials
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun 130022
- P. R. China
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29
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Murray JK, Biswas K, Holder JR, Zou A, Ligutti J, Liu D, Poppe L, Andrews KL, Lin FF, Meng SY, Moyer BD, McDonough SI, Miranda LP. Sustained inhibition of the Na V 1.7 sodium channel by engineered dimers of the domain II binding peptide GpTx-1. Bioorg Med Chem Lett 2015; 25:4866-4871. [DOI: 10.1016/j.bmcl.2015.06.033] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 06/06/2015] [Accepted: 06/08/2015] [Indexed: 11/15/2022]
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30
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Sankaran S, de Ruiter M, Cornelissen JJLM, Jonkheijm P. Supramolecular Surface Immobilization of Knottin Derivatives for Dynamic Display of High Affinity Binders. Bioconjug Chem 2015; 26:1972-80. [PMID: 26270829 DOI: 10.1021/acs.bioconjchem.5b00419] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Knottins are known as a robust and versatile class of miniprotein scaffolds for the presentation of high-affinity binding peptides; however, to date their application in biomaterials, biological coatings, and surface applications have not been explored. We have developed a strategy to recombinantly synthesize a β-trypsin inhibitory knottin with supramolecular guest tags that enable it to adhere to self-assembled monolayers of the supramolecular host cucurbit[8]uril (CB[8]). We have described a strategy to easily express knottins in E. coli by conjugating them to a fluorescent protein after which they are cleaved and purified. Knottin constructs that varied in the number and position of the supramolecular tag at either the N- or C-termini or at both ends have been verified for their trypsin inhibitory function and CB[8]-binding properties in solution and on surfaces. All of the knottin constructs showed strong inhibition of trypsin with inhibition constants between 10 and 30 nM. Using microscale thermophoresis, we determined that the supramolecular guest tags on the knottins bind CB[8] with a Kd of ∼6 μM in solution. At the surface, strong divalent binding has been determined with a Kd of 0.75 μM in the case of the knottin with two supramolecular guest tags, whereas only weak monovalent binding occurred when only one guest tag was present. We also show successful supramolecular surface immobilization of the knottin using CB[8] and prove that they can be used to immobilize β-trypsin at the surface.
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Affiliation(s)
- Shrikrishnan Sankaran
- Bioinspired Molecular Engineering Laboratory of the MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente , 7500 AE Enschede, The Netherlands
| | | | | | - Pascal Jonkheijm
- Bioinspired Molecular Engineering Laboratory of the MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente , 7500 AE Enschede, The Netherlands
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