1
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Philippe GJB, Huang YH, Mittermeier A, Brown CJ, Kaas Q, Ramlan SR, Wang CK, Lane D, Loewer A, Troeira Henriques S, Craik DJ. Delivery to, and Reactivation of, the p53 Pathway in Cancer Cells Using a Grafted Cyclotide Conjugated with a Cell-Penetrating Peptide. J Med Chem 2024; 67:1197-1208. [PMID: 38174919 DOI: 10.1021/acs.jmedchem.3c01682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Peptides are promising drug modalities that can modulate protein-protein interactions, but their application is hampered by their limited ability to reach intracellular targets. Here, we improved the cytosolic delivery of a peptide blocking p53:MDM2/X interactions using a cyclotide as a stabilizing scaffold. We applied several design strategies to improve intracellular delivery and found that the conjugation of the lead cyclotide to the cyclic cell-penetrating peptide cR10 was the most effective. Conjugation allowed cell internalization at micromolar concentration and led to elevated intracellular p53 levels in A549, MCF7, and MCF10A cells, as well as inducing apoptosis in A549 cells without causing membrane disruption. The lead peptide had >35-fold improvement in inhibitory activity and increased cellular uptake compared to a previously reported cyclotide p53 activator. In summary, we demonstrated the delivery of a large polar cyclic peptide in the cytosol and confirmed its ability to modulate intracellular protein-protein interactions involved in cancer.
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Affiliation(s)
- Grégoire Jean-Baptiste Philippe
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
- School of Biomedical Sciences, Queensland University of Technology, Translational Research Institute, Brisbane, Queensland 4102, Australia
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Anna Mittermeier
- Department of Biology, Technical University Darmstadt, 64287 Darmstadt, Germany
| | - Christopher J Brown
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Quentin Kaas
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Siti Radhiah Ramlan
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Conan K Wang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David Lane
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Alexander Loewer
- Department of Biology, Technical University Darmstadt, 64287 Darmstadt, Germany
| | - Sónia Troeira Henriques
- School of Biomedical Sciences, Queensland University of Technology, Translational Research Institute, Brisbane, Queensland 4102, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
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2
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Han X, Zhou T, Hu X, Zhu Y, Shi Z, Chen S, Liu Y, Weng X, Zhang F, Wu S. Discovery and Characterization of MaK: A Novel Knottin Antimicrobial Peptide from Monochamus alternatus. Int J Mol Sci 2023; 24:17565. [PMID: 38139394 PMCID: PMC10743862 DOI: 10.3390/ijms242417565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 12/24/2023] Open
Abstract
Knottin-type antimicrobial peptides possess exceptional attributes, such as high efficacy, low vulnerability to drug resistance, minimal toxicity, and precise targeting of drug sites. These peptides play a crucial role in the innate immunity of insects, offering protection against bacteria, fungi, and parasites. Knottins have garnered considerable interest as promising contenders for drug development due to their ability to bridge the gap between small molecules and protein-based biopharmaceuticals, effectively addressing the therapeutic limitations of both modalities. This work presents the isolation and identification of a novel antimicrobial peptide derived from Monochamus alternatus. The cDNA encodes a 56-amino acid knottin propeptide, while the mature peptide comprises only 34 amino acids. We have labeled this knottin peptide as MaK. Using chemically synthesized MaK, we evaluated its hemolytic activity, thermal stability, antibacterial properties, and efficacy against nematodes. The results of this study indicate that MaK is an exceptionally effective knottin-type peptide. It demonstrates low toxicity, superior stability, potent antibacterial activity, and the ability to suppress pine wood nematodes. Consequently, these findings suggest that MaK has potential use in developing innovative therapeutic agents to prevent and manage pine wilt disease.
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Affiliation(s)
- Xiaohong Han
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.H.); (X.H.); (Y.Z.); (Z.S.); (S.C.); (Y.L.); (X.W.)
- Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Province University, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Tong Zhou
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China;
| | - Xinran Hu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.H.); (X.H.); (Y.Z.); (Z.S.); (S.C.); (Y.L.); (X.W.)
- Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Province University, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yukun Zhu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.H.); (X.H.); (Y.Z.); (Z.S.); (S.C.); (Y.L.); (X.W.)
- Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Province University, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zengzeng Shi
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.H.); (X.H.); (Y.Z.); (Z.S.); (S.C.); (Y.L.); (X.W.)
- Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Province University, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shi Chen
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.H.); (X.H.); (Y.Z.); (Z.S.); (S.C.); (Y.L.); (X.W.)
- Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Province University, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yunfei Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.H.); (X.H.); (Y.Z.); (Z.S.); (S.C.); (Y.L.); (X.W.)
- Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Province University, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaoqian Weng
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.H.); (X.H.); (Y.Z.); (Z.S.); (S.C.); (Y.L.); (X.W.)
- Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Province University, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Feiping Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.H.); (X.H.); (Y.Z.); (Z.S.); (S.C.); (Y.L.); (X.W.)
- Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Province University, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Songqing Wu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.H.); (X.H.); (Y.Z.); (Z.S.); (S.C.); (Y.L.); (X.W.)
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry, Fuzhou 350002, China
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3
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Cort-Donmez A, Olgen S, Guner E, Akgun-Cagliyan G, Hanikoglu F, Tunc-Ata M, Kilic-Toprak E. Investigating the Activity of Indole-2-on Derivative Src Kinase Inhibitors Against Chronic Myeloid Leukemia Cells. Anticancer Agents Med Chem 2023; 23:113-122. [PMID: 35570519 DOI: 10.2174/1871520622666220513114205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/04/2022] [Accepted: 03/14/2022] [Indexed: 02/08/2023]
Abstract
BACKGROUND Src family tyrosine kinases play a potential role in Bcr-Abl-induced leukemogenesis. Src kinase inhibitors are reported as selective inhibitors of chronic myeloid leukemia. OBJECTIVE Since Src kinase inhibitors have an inhibitive effect on chronic myeloid leukemia, indole derivatives (C-1, C-2, C-3) previously found as potent inhibitors of Src kinase were tested against chronic myeloid leukemia in this study. METHODS Cell viability of K562 and R/K562 cells, antiproliferative and antioxidant effects, and inhibition profiles of Bcr-Abl kinase of indole derivatives were determined compared to dasatinib and imatinib. RESULTS The results showed that compounds affected cell proliferation and decreased the levels of Bcr/Abl. These results confirmed that the antileukemic activity of compounds was related to Bcr/Abl expression. Docking studies also presented that compounds are inhibitors of both Src and Abl kinases. Calculation of drug-like properties showed that compounds could be potential drug candidates. CONCLUSION Among indole-2-on derivatives, previously identified as Src kinase inhibitors, C-2 has been discovered to be a strong anticancer drug that is active against susceptible and resistant K562 cell lines and induces apoptosis.
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Affiliation(s)
- Aysegul Cort-Donmez
- Department of Medical Biochemistry, Faculty of Medicine, Pamukkale University 20160, Denizli, Turkey
| | - Sureyya Olgen
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Biruni University 34010, İstanbul, Turkey
| | - Ersin Guner
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Biruni University 34010, İstanbul, Turkey
| | - Gulsum Akgun-Cagliyan
- Department of Hematology, Faculty of Medicine, Pamukkale University, Denizli, Turkey
| | - Ferhat Hanikoglu
- Department of Medical Biochemistry, Alanya Alaaddin Keykubat University 07450, Alanya, Antalya, Turkey
| | - Melek Tunc-Ata
- Department of Physiology, Faculty of Medicine, Pamukkale University, Denizli, Turkey
| | - Emine Kilic-Toprak
- Department of Physiology, Faculty of Medicine, Pamukkale University, Denizli, Turkey
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4
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DIDARIAN R, EBRAHIMI A, GHORBANPOOR H, BAGHEROGHLI H, DOGAN GÜZEL F, FARHADPOUR M, LOTFIBAKHSHAYESH N, HASHEMPOUR H, AVCI H. On chip microfluidic separation of cyclotides. Turk J Chem 2022; 47:253-262. [PMID: 37720850 PMCID: PMC10504020 DOI: 10.55730/1300-0527.3534] [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: 09/09/2022] [Revised: 02/20/2023] [Accepted: 12/20/2022] [Indexed: 02/25/2023] Open
Abstract
Cyclotides as a cyclic peptide produced by different groups of plants have been a very attractive field of research due to their exceptional properties in biological activities and drug design applications. The importance of cyclotides as new biological activities from nature caused to attract researchers to develop new separation systems. Recent growth and development on chip-based technology for separation and bioassay especially for anticancer having sparklingly advantages comparison with common traditional methods. In this study, the microfluidic separation of Vigno 1-5 cyclotides extracted from Viola ignobilis by using polar and nonpolar forces as a liquid-liquid interaction was investigated through modified microfluidic chips and then the results were compared with a traditional counterpart technique of high-performance liquid chromatography (HPLC). The traditional process of separating cyclotides from plants is a costly and time-consuming procedure. The scientific novelty of this study is to accelerate the separation of cyclotides using modified microfluidic chips with low cost and high efficiency. The results revealed that a novel and simple microfluidic chip concept is an effective approach for separating the Vigno groups in the violet extract. We believe that the concept could potentially be utilized for further drug development process especially for anticancer studies by coupling bioassay chips as online procedures via reducing in time and cost compared with traditional offline methods.
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Affiliation(s)
- Reza DIDARIAN
- Department of Biomedical Engineering, Ankara Yıldırım Beyazıt University, Ankara,
Turkey
- Department of Metallurgical and Materials Engineering, Eskişehir Osmangazi University Eskişehir,
Turkey
| | - Aliakbar EBRAHIMI
- Cellular Therapy and Stem Cell Production Application and Research Center (ESTEM), Eskişehir Osmangazi University, Eskişehir,
Turkey
- Department of Metallurgical and Materials Engineering, Eskişehir Osmangazi University Eskişehir,
Turkey
- Department of Biomedical Engineering, Eskişehir Osmangazi University, Eskişehir,
Turkey
| | - Hamed GHORBANPOOR
- Cellular Therapy and Stem Cell Production Application and Research Center (ESTEM), Eskişehir Osmangazi University, Eskişehir,
Turkey
- Department of Biomedical Engineering, Eskişehir Osmangazi University, Eskişehir,
Turkey
| | - Hesam BAGHEROGHLI
- Department of Chemistry, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz,
Iran
| | - Fatma DOGAN GÜZEL
- Department of Biomedical Engineering, Ankara Yıldırım Beyazıt University, Ankara,
Turkey
| | - Mohsen FARHADPOUR
- Department of Plant Bioproducts, National Institute of Genetic Engineering and Biotechnology (NIGEB), Shahrak-e Pajoohesh, Tehran,
Iran
| | - Nasrin LOTFIBAKHSHAYESH
- Department of Tissue Engineering, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran,
Iran
| | - Hossein HASHEMPOUR
- Department of Chemistry, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz,
Iran
| | - Hüseyin AVCI
- Cellular Therapy and Stem Cell Production Application and Research Center (ESTEM), Eskişehir Osmangazi University, Eskişehir,
Turkey
- Department of Metallurgical and Materials Engineering, Eskişehir Osmangazi University Eskişehir,
Turkey
- Translational Medicine Research and Clinical Center (TATUM), Eskişehir Osmangazi University, Eskişehir,
Turkey
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5
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Jacob B, Vogelaar A, Cadenas E, Camarero JA. Using the Cyclotide Scaffold for Targeting Biomolecular Interactions in Drug Development. Molecules 2022; 27:molecules27196430. [PMID: 36234971 PMCID: PMC9570680 DOI: 10.3390/molecules27196430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/21/2022] [Accepted: 09/24/2022] [Indexed: 11/28/2022] Open
Abstract
This review provides an overview of the properties of cyclotides and their potential for developing novel peptide-based therapeutics. The selective disruption of protein–protein interactions remains challenging, as the interacting surfaces are relatively large and flat. However, highly constrained polypeptide-based molecular frameworks with cell-permeability properties, such as the cyclotide scaffold, have shown great promise for targeting those biomolecular interactions. The use of molecular techniques, such as epitope grafting and molecular evolution employing the cyclotide scaffold, has shown to be highly effective for selecting bioactive cyclotides.
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Affiliation(s)
- Binu Jacob
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 9033, USA
| | - Alicia Vogelaar
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 9033, USA
| | - Enrique Cadenas
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 9033, USA
| | - Julio A. Camarero
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 9033, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 9033, USA
- Correspondence:
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6
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Akgun‑Cagliyan G, Cort‑Donmez A, Kilic‑Toprak E, Altintas F. Verbascoside potentiates the effect of tyrosine kinase inhibitors on the induction of apoptosis and oxidative stress via the Abl-mediated MAPK signalling pathway in chronic myeloid leukaemia. Exp Ther Med 2022; 24:514. [PMID: 35837042 PMCID: PMC9257957 DOI: 10.3892/etm.2022.11441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 05/18/2022] [Indexed: 11/05/2022] Open
Abstract
Verbascoside (Verb) may exhibit potential antitumour activities in leukaemia. The present study investigated the effect of Verb, in combination with imatinib (IM), dasatinib (Das), lipopolysaccharide (LPS) and TNF, on cell survival, Abl expression, apoptosis, oxidative stress and the MAPK pathway in chronic myeloid leukaemia (CML) cells. Cell viability was determined using the WST-8 assay in K562 and R-K562 cells treated with Verb and/or IM, Das, LPS and TNF. Apoptosis and DNA damage in CML cells was detected by caspase-3 and comet analysis. The protein levels of Abl (Phospho-Tyr412), and total/phosphorylated p38, JNK and ERK in CML cells were analysed using a Colorimetric Cell-Based Assay. Oxidative stress was examined using total antioxidant and oxidant status assays. Treatment with Verb and/or tyrosine kinase inhibitors (TKIs), LPS and TNF resulted in a significant decrease in the Tyr-412 phosphorylation of Abl in K562 and R-K562 cells. In addition, cotreatment with Verb and IM or Das additively induced apoptosis by activating caspase-3 levels in both cell lines. Activation of p38 and JNK can result in growth arrest and cell death, whereas ERK stimulation results in cell division and differentiation. The present study demonstrated that cotreatment with Verb and TKIs suppressed phosphorylated-ERK1/2, whereas the levels of phosphorylated-p-38 and phosphorylated-JNK were significantly elevated by Verb and/or IM, Das, LPS and TNF, thus suggesting that Abl and Src inhibition could be involved in the effects of Verb on MAPK signalling in R-K562 cells. Furthermore, Verb elevated reactive oxygen species levels additively with TKIs in both cell lines by increasing the oxidant capacity and decreasing the antioxidant capacity. In conclusion, anti-leukemic mechanisms of Verb may be mediated by Abl protein and regulation of its downstream p38-MAPK/JNK pathway, caspase-3 and oxidative stress in CML cells.
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Affiliation(s)
- Gulsum Akgun‑Cagliyan
- Department of Hematology, Faculty of Medicine, Pamukkale University, 20160 Denizli, Turkey
| | - Aysegul Cort‑Donmez
- Department of Biochemistry, Faculty of Medicine, Pamukkale University, 20160 Denizli, Turkey
| | - Emine Kilic‑Toprak
- Department of Physiology, Faculty of Medicine, Pamukkale University, 20160 Denizli, Turkey
| | - Fatih Altintas
- Department of Physiology, Faculty of Medicine, Pamukkale University, 20160 Denizli, Turkey
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7
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Dang TT, Harvey PJ, Chan LY, Huang Y, Kaas Q, Craik DJ. Mutagenesis of cyclotide Cter 27 exemplifies a robust folding strategy for bracelet cyclotides. Pept Sci (Hoboken) 2022. [DOI: 10.1002/pep2.24284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Tien T. Dang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland
- Institute of Applied Materials Science Vietnam Academy of Science and Technology Ho Chi Minh City Australia
| | - Peta J. Harvey
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland
| | - Lai Yue Chan
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland
| | - Yen‐Hua Huang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland
| | - Quentin Kaas
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland
| | - David J. Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland
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8
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Protocols for measuring the stability and cytotoxicity of cyclotides. Methods Enzymol 2022; 663:19-40. [PMID: 35168789 DOI: 10.1016/bs.mie.2021.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Cyclotides are plant host-defense peptides that have a wide range of biological activities and have diverse potential applications in medicine and agriculture. These 27-37 amino acid peptides have a head-to-tail cyclic backbone and are built around a cystine knot core, which makes them exceptionally stable. This stability and their amenability to sequence modifications has made cyclotides attractive scaffolds in drug design, and many synthetic cyclotides have now been designed and synthesized to test their efficacy as leads for a wide range of diseases, including infectious disease, cancer, pain and multiple sclerosis. Additionally, some natural cyclotides are selectively toxic to certain cancer cell lines, opening their potential as anticancer agents, and others have insecticidal activity, with applications in crop protection. With these applications in mind, there is a need to be able to measure cyclotides in pharmaceutical or agrichemical formulations and in biological media such as blood serum, as well as to assess their potential persistence in the environment when used as agrichemical agents. This chapter describes protocols for quantifying cyclotides in biological fluids, measuring their stability, and assessing their relative cytotoxicity on various types of cells.
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9
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Rodríguez V. Insights into post-translational modification enzymes from RiPPs: A toolkit for applications in peptide synthesis. Biotechnol Adv 2022; 56:107908. [PMID: 35032597 DOI: 10.1016/j.biotechadv.2022.107908] [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: 03/05/2021] [Revised: 12/30/2021] [Accepted: 01/09/2022] [Indexed: 11/02/2022]
Abstract
The increasing length and complexity of peptide drug candidates foster the development of novel strategies for their manufacture, which should include sustainable and efficient technologies. In this context, including enzymatic catalysis in the production of peptide molecules has gained interest. Here, several enzymes from ribosomally synthesized and post-translationally modified peptides biosynthesis pathways are reviewed, with attention to their capacity to introduce stability-promoting structural features on peptides, providing an initial framework towards their use in therapeutic peptide production processes.
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Affiliation(s)
- Vida Rodríguez
- Faculty of Engineering, Science and Technology, Bernardo O'Higgins University, Viel 1497, Santiago, Chile.
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10
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Liu W, de Veer SJ, Huang YH, Sengoku T, Okada C, Ogata K, Zdenek CN, Fry BG, Swedberg JE, Passioura T, Craik DJ, Suga H. An Ultrapotent and Selective Cyclic Peptide Inhibitor of Human β-Factor XIIa in a Cyclotide Scaffold. J Am Chem Soc 2021; 143:18481-18489. [PMID: 34723512 DOI: 10.1021/jacs.1c07574] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cyclotides are plant-derived peptides with complex structures shaped by their head-to-tail cyclic backbone and cystine knot core. These structural features underpin the native bioactivities of cyclotides, as well as their beneficial properties as pharmaceutical leads, including high proteolytic stability and cell permeability. However, their inherent structural complexity presents a challenge for cyclotide engineering, particularly for accessing libraries of sufficient chemical diversity to design potent and selective cyclotide variants. Here, we report a strategy using mRNA display enabling us to select potent cyclotide-based FXIIa inhibitors from a library comprising more than 1012 members based on the cyclotide scaffold of Momordica cochinchinensis trypsin inhibitor-II (MCoTI-II). The most potent and selective inhibitor, cMCoFx1, has a pM inhibitory constant toward FXIIa with greater than three orders of magnitude selectivity over related serine proteases, realizing specific inhibition of the intrinsic coagulation pathway. The cocrystal structure of cMCoFx1 and FXIIa revealed interactions at several positions across the contact interface that conveyed high affinity binding, highlighting that such cyclotides are attractive cystine knot scaffolds for therapeutic development.
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Affiliation(s)
- Wenyu Liu
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Simon J de Veer
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Brisbane, QLD 4072, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Yen-Hua Huang
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Brisbane, QLD 4072, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Toru Sengoku
- Department of Biochemistry, Graduate School of Medicine, Yokohama City University, Yokohama, Kanagawa 236-0004, Japan
| | - Chikako Okada
- Department of Biochemistry, Graduate School of Medicine, Yokohama City University, Yokohama, Kanagawa 236-0004, Japan
| | - Kazuhiro Ogata
- Department of Biochemistry, Graduate School of Medicine, Yokohama City University, Yokohama, Kanagawa 236-0004, Japan
| | - Christina N Zdenek
- Venom Evolution Lab, School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Bryan G Fry
- Venom Evolution Lab, School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Joakim E Swedberg
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Toby Passioura
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Brisbane, QLD 4072, Australia.,School of Life and Environmental Sciences, School of Chemistry and Sydney Analytical, The University of Sydney, Sydney, NSW 2006, Australia
| | - David J Craik
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Brisbane, QLD 4072, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Brisbane, QLD 4072, Australia
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11
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Design, synthesis, and biological evaluation of novel Bcr-Abl T315I inhibitors incorporating amino acids as flexible linker. Bioorg Med Chem 2021; 48:116398. [PMID: 34547714 DOI: 10.1016/j.bmc.2021.116398] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 08/31/2021] [Accepted: 09/02/2021] [Indexed: 01/25/2023]
Abstract
Despite the success of imatinib in CML therapy through Bcr-Abl inhibition, acquired drug resistance occurs over time in patients. In particular, the resistance caused by T315I mutation remains a challenge in clinic. Herein, we embarked on a structural optimization campaign aiming at discovery of novel Bcr-Abl inhibitors toward T315I mutant based on previously reported dibenzoylpiperazin derivatives. We proposed that incorporation of flexible linker could achieve potent inhibition of Bcr-AblT315I by avoiding steric clash with bulky sidechain of Ile315. A library of 28 compounds with amino acids as linker has been developed and evaluated. Among them, compound AA2 displayed the most potent activity against Bcr-AblWT and Bcr-AblT315I, as well as toward Bcr-Abl driven K562 and K562R cells. Further investigations indicated that AA2 could induce apoptosis of K562 cells and down regulate phosphorylation of Bcr-Abl. In summary, the compounds with amino acid as novel flexible linker exhibited certain antitumor activities, providing valuable hints for the discovery of novel Bcr-Abl inhibitors to overcome T315I mutant resistance, and AA2 could be considered as a candidate for further optimization.
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12
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Yin H, Huang YH, Best SA, Sutherland KD, Craik DJ, Wang CK. An Integrated Molecular Grafting Approach for the Design of Keap1-Targeted Peptide Inhibitors. ACS Chem Biol 2021; 16:1276-1287. [PMID: 34152716 DOI: 10.1021/acschembio.1c00388] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Inhibiting the Nrf2:Keap1 interaction to trigger cytoprotective gene expression is a promising treatment strategy for oxidative stress-related diseases. A short linear motif from Nrf2 has the potential to directly inhibit this protein-protein interaction, but poor stability and limited cellular uptake impede its therapeutic development. To address these limitations, we utilized an integrated molecular grafting strategy to re-engineer the Nrf2 motif. We combined the motif with an engineered non-native disulfide bond and a cell-penetrating peptide onto a single multifunctionalizable and ultrastable molecular scaffold, namely, the cyclotide MCoTI-II, resulting in the grafted peptide MCNr-2c. The engineered disulfide bond enhanced the conformational rigidity of the motif, resulting in a nanomolar affinity of MCNr-2c for Keap1. The cell-penetrating peptide led to an improved cellular uptake and increased ability to enhance the intracellular expression of two well-described Nrf2-target genes NQO1 and TALDO1. Furthermore, the stability of the scaffold was inherited by the grafted peptide, which became resistant to proteolysis in serum. Overall, we have provided proof-of-concept for a strategy that enables the encapsulation of multiple desired and complementary activities into a single molecular entity to design a Keap1-targeted inhibitor. We propose that this integrated approach could have broad utility for the design of peptide drug leads that require multiple functions and/or biopharmaceutical properties to elicit a therapeutic activity.
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Affiliation(s)
- Huawu Yin
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Sarah A. Best
- ACRF Cancer Biology and Stem Cells Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - Kate D. Sutherland
- ACRF Cancer Biology and Stem Cells Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - David J. Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Conan K. Wang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
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13
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Comparison of a Short Linear Antimicrobial Peptide with Its Disulfide-Cyclized and Cyclotide-Grafted Variants against Clinically Relevant Pathogens. Microorganisms 2021; 9:microorganisms9061249. [PMID: 34201398 PMCID: PMC8228819 DOI: 10.3390/microorganisms9061249] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 06/04/2021] [Indexed: 12/14/2022] Open
Abstract
According to the World Health Organization (WHO) the development of resistance against antibiotics by microbes is one of the most pressing health concerns. The situation will intensify since only a few pharmacological companies are currently developing novel antimicrobial compounds. Discovery and development of novel antimicrobial compounds with new modes of action are urgently needed. Antimicrobial peptides (AMPs) are known to be able to kill multidrug-resistant bacteria and, therefore, of interest to be developed into antimicrobial drugs. Proteolytic stability and toxicities of these peptides are challenges to overcome, and one strategy frequently used to address stability is cyclization. Here we introduced a disulfide-bond to cyclize a potent and nontoxic 9mer peptide and, in addition, as a proof-of-concept study, grafted this peptide into loop 6 of the cyclotide MCoTI-II. This is the first time an antimicrobial peptide has been successfully grafted onto the cyclotide scaffold. The disulfide-cyclized and grafted cyclotide showed moderate activity in broth and strong activity in 1/5 broth against clinically relevant resistant pathogens. The linear peptide showed superior activity in both conditions. The half-life time in 100% human serum was determined, for the linear peptide, to be 13 min, for the simple disulfide-cyclized peptide, 9 min, and, for the grafted cyclotide 7 h 15 min. The addition of 10% human serum led to a loss of antimicrobial activity for the different organisms, ranging from 1 to >8-fold for the cyclotide. For the disulfide-cyclized version and the linear version, activity also dropped to different degrees, 2 to 18-fold, and 1 to 30-fold respectively. Despite the massive difference in stability, the linear peptide still showed superior antimicrobial activity. The cyclotide and the disulfide-cyclized version demonstrated a slower bactericidal effect than the linear version. All three peptides were stable at high and low pH, and had very low hemolytic and cytotoxic activity.
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14
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Chan LY, Du J, Craik DJ. Tuning the Anti-Angiogenic Effect of the P15 Peptide Using Cyclic Trypsin Inhibitor Scaffolds. ACS Chem Biol 2021; 16:829-837. [PMID: 33881318 DOI: 10.1021/acschembio.0c00907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Angiogenesis is important for tumor growth, and accordingly, targeting angiogenesis has become an important pathway for antitumor therapy. A novel proapoptotic peptide, CIGB-300 (P15-Tat), has been shown to be involved in the casein kinase II phosphorylation pathway, conferring it with antiangiogenic activity. Cyclic peptides have been widely used as scaffolds in drug design studies due to their high stability and favorable biopharmaceutical properties. Here, we chose two very stable cyclic trypsin inhibitors, MCoTI-II and SFTI-1, as frameworks to incorporate the bioactive epitope P15 into various backbone loops. NMR studies revealed that all re-engineered analogs had similar secondary structures to their native cyclic frameworks. One key analog, MCoP15, displayed significant improvement for inhibiting human umbilical vein endothelial cell migration, was nontoxic, and had higher stability than the P15 epitope alone. Overall, the results show the value of P15 being engineered into cyclic trypsin inhibitor scaffolds for improving antiangiogenic activity and stability. More broadly, the study highlights the versatility of cyclic peptide frameworks in drug design for antiangiogenic therapies.
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Affiliation(s)
- Lai Yue Chan
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Junqiao Du
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David J. Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
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15
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Dang TT, Chan LY, Tombling BJ, Harvey PJ, Gilding EK, Craik DJ. In Planta Discovery and Chemical Synthesis of Bracelet Cystine Knot Peptides from Rinorea bengalensis. JOURNAL OF NATURAL PRODUCTS 2021; 84:395-407. [PMID: 33570395 DOI: 10.1021/acs.jnatprod.0c01065] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Cyclotides are plant-derived peptides that have attracted interest as biocides and scaffolds for the development of stable peptide therapeutics. Cyclotides are characterized by their cyclic backbone and cystine knot framework, which engenders them with remarkably high stability. This study reports the cystine knot-related peptidome of Rinorea bengalensis, a small rainforest tree in the Violaceae family that is distributed from Australia westward to India. Surprisingly, many more acyclic knotted peptides (acyclotides) were discovered than cyclic counterparts (cyclotides), with 32 acyclotides and 1 cyclotide sequenced using combined transcriptome and proteomic analyses. Nine acyclotides were isolated and screened against a panel of mammalian cell lines, showing they had the cytotoxic properties normally associated with cyclotide-like peptides. NMR analysis of the acyclotide ribes 21 and 22 and the cyclotide ribe 33 confirmed that these peptides contained the cystine knot structural motif. The bracelet-subfamily cyclotide ribe 33 was amenable to chemical synthesis in reasonable yield, an achievement that has long eluded previous attempts to synthetically produce bracelet cyclotides. Accordingly, ribe 33 represents an exciting new bracelet cyclotide scaffold that can be subject to chemical modification for future molecular engineering applications.
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Affiliation(s)
- Tien T Dang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Lai Y Chan
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Benjamin J Tombling
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Peta J Harvey
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Edward K Gilding
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
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16
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Handley TNG, Wang CK, Harvey PJ, Lawrence N, Craik DJ. Cyclotide Structures Revealed by NMR, with a Little Help from X‐ray Crystallography. Chembiochem 2020; 21:3463-3475. [DOI: 10.1002/cbic.202000315] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/08/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Thomas N. G. Handley
- Institute for Molecular Bioscience Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland 4072 Australia
| | - Conan K. Wang
- Institute for Molecular Bioscience Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland 4072 Australia
| | - Peta J. Harvey
- Institute for Molecular Bioscience Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland 4072 Australia
| | - Nicole Lawrence
- Institute for Molecular Bioscience Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland 4072 Australia
| | - David J. Craik
- Institute for Molecular Bioscience Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland 4072 Australia
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17
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Shinbara K, Liu W, van Neer RHP, Katoh T, Suga H. Methodologies for Backbone Macrocyclic Peptide Synthesis Compatible With Screening Technologies. Front Chem 2020; 8:447. [PMID: 32626683 PMCID: PMC7314982 DOI: 10.3389/fchem.2020.00447] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 04/28/2020] [Indexed: 12/23/2022] Open
Abstract
Backbone macrocyclic structures are often found in diverse bioactive peptides and contribute to greater conformational rigidity, peptidase resistance, and potential membrane permeability compared to their linear counterparts. Therefore, such peptide scaffolds are an attractive platform for drug-discovery endeavors. Recent advances in synthetic methods for backbone macrocyclic peptides have enabled the discovery of novel peptide drug candidates against diverse targets. Here, we overview recent technical advancements in the synthetic methods including 1) enzymatic synthesis, 2) chemical synthesis, 3) split-intein circular ligation of peptides and proteins (SICLOPPS), and 4) in vitro translation system combined with genetic code reprogramming. We also discuss screening methodologies compatible with those synthetic methodologies, such as one-beads one-compound (OBOC) screening compatible with the synthetic method 2, cell-based assay compatible with 3, limiting-dilution PCR and mRNA display compatible with 4.
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Affiliation(s)
| | | | | | | | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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18
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Conibear AC, Schmid A, Kamalov M, Becker CFW, Bello C. Recent Advances in Peptide-Based Approaches for Cancer Treatment. Curr Med Chem 2020; 27:1174-1205. [PMID: 29173146 DOI: 10.2174/0929867325666171123204851] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 10/26/2017] [Accepted: 10/30/2017] [Indexed: 12/16/2022]
Abstract
BACKGROUND Peptide-based pharmaceuticals have recently experienced a renaissance due to their ability to fill the gap between the two main classes of available drugs, small molecules and biologics. Peptides combine the high potency and selectivity typical of large proteins with some of the characteristic advantages of small molecules such as synthetic accessibility, stability and the potential of oral bioavailability. METHODS In the present manuscript we review the recent literature on selected peptide-based approaches for cancer treatment, emphasizing recent advances, advantages and challenges of each strategy. RESULTS One of the applications in which peptide-based approaches have grown rapidly is cancer therapy, with a focus on new and established targets. We describe, with selected examples, some of the novel peptide-based methods for cancer treatment that have been developed in the last few years, ranging from naturally-occurring and modified peptides to peptidedrug conjugates, peptide nanomaterials and peptide-based vaccines. CONCLUSION This review brings out the emerging role of peptide-based strategies in oncology research, critically analyzing the advantages and limitations of these approaches and the potential for their development as effective anti-cancer therapies.
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Affiliation(s)
- Anne C Conibear
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Wahringer Straße 38, 1090 Vienna, Austria
| | - Alanca Schmid
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Wahringer Straße 38, 1090 Vienna, Austria
| | - Meder Kamalov
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Wahringer Straße 38, 1090 Vienna, Austria
| | - Christian F W Becker
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Wahringer Straße 38, 1090 Vienna, Austria
| | - Claudia Bello
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Wahringer Straße 38, 1090 Vienna, Austria.,Department of Chemistry "Ugo Schiff", University of Florence, Laboratory of Peptide and Protein Chemistry and Biolology-PeptLab, Via della Lastruccia 13, 50019 Sesto, Fiorentino, Italy
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19
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Smithies BJ, Huang YH, Jackson MA, Yap K, Gilding EK, Harris KS, Anderson MA, Craik DJ. Circular Permutation of the Native Enzyme-Mediated Cyclization Position in Cyclotides. ACS Chem Biol 2020; 15:962-969. [PMID: 32203656 DOI: 10.1021/acschembio.9b00996] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cyclotides are a class of cyclic disulfide-rich peptides found in plants that have been adopted as a molecular scaffold for pharmaceutical applications due to their inherent stability and ability to penetrate cell membranes. For research purposes, they are usually produced and cyclized synthetically, but there are concerns around the cost and environmental impact of large-scale chemical synthesis. One strategy to improve this is to combine a recombinant production system with native enzyme-mediated cyclization. Asparaginyl endopeptidases (AEPs) are enzymes that can act as peptide ligases in certain plants to facilitate cyclotide maturation. One of these ligases, OaAEP1b, originates from the cyclotide-producing plant, Oldenlandia affinis, and can be produced recombinantly for use in vitro as an alternative to chemical cyclization of recombinant substrates. However, not all engineered cyclotides are compatible with AEP-mediated cyclization because new pharmaceutical epitopes often replace the most flexible region of the peptide, where the native cyclization site is located. Here we redesign a popular cyclotide grafting scaffold, MCoTI-II, to incorporate an AEP cyclization site located away from the usual grafting region. We demonstrate the incorporation of a bioactive peptide sequence in the most flexible region of MCoTI-II while maintaining AEP compatibility, where the two were previously mutually exclusive. We anticipate that our AEP-compatible scaffold, based on the most popular cyclotide for pharmaceutical applications, will be useful in designing bioactive cyclotides that are compatible with AEP-mediated cyclization and will therefore open up the possibility of larger scale enzyme-mediated production of recombinant or synthetic cyclotides alike.
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Affiliation(s)
- Bronwyn J. Smithies
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Mark A. Jackson
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Kuok Yap
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Edward K. Gilding
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Karen S. Harris
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Marilyn A. Anderson
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
| | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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20
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Mehta L, Dhankhar R, Gulati P, Kapoor RK, Mohanty A, Kumar S. Natural and grafted cyclotides in cancer therapy: An insight. J Pept Sci 2020; 26:e3246. [DOI: 10.1002/psc.3246] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/14/2020] [Accepted: 02/14/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Lovekesh Mehta
- Medical Microbiology and Bioprocess Laboratory, Department of MicrobiologyMaharshi Dayanand University Rohtak India
| | - Rakhi Dhankhar
- Medical Microbiology and Bioprocess Laboratory, Department of MicrobiologyMaharshi Dayanand University Rohtak India
| | - Pooja Gulati
- Medical Microbiology and Bioprocess Laboratory, Department of MicrobiologyMaharshi Dayanand University Rohtak India
| | - Rajeev Kumar Kapoor
- Medical Microbiology and Bioprocess Laboratory, Department of MicrobiologyMaharshi Dayanand University Rohtak India
| | - Aparajita Mohanty
- Department of Botany, Gargi CollegeUniversity of Delhi New Delhi India
| | - Sanjay Kumar
- Medical Microbiology and Bioprocess Laboratory, Department of MicrobiologyMaharshi Dayanand University Rohtak India
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21
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Hu X, Maffucci I, Contini A. Advances in the Treatment of Explicit Water Molecules in Docking and Binding Free Energy Calculations. Curr Med Chem 2020; 26:7598-7622. [DOI: 10.2174/0929867325666180514110824] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 02/26/2018] [Accepted: 04/18/2018] [Indexed: 12/30/2022]
Abstract
Background:
The inclusion of direct effects mediated by water during the ligandreceptor
recognition is a hot-topic of modern computational chemistry applied to drug discovery
and development. Docking or virtual screening with explicit hydration is still debatable,
despite the successful cases that have been presented in the last years. Indeed, how to select
the water molecules that will be included in the docking process or how the included waters
should be treated remain open questions.
Objective:
In this review, we will discuss some of the most recent methods that can be used in
computational drug discovery and drug development when the effect of a single water, or of a
small network of interacting waters, needs to be explicitly considered.
Results:
Here, we analyse the software to aid the selection, or to predict the position, of water
molecules that are going to be explicitly considered in later docking studies. We also present
software and protocols able to efficiently treat flexible water molecules during docking, including
examples of applications. Finally, we discuss methods based on molecular dynamics
simulations that can be used to integrate docking studies or to reliably and efficiently compute
binding energies of ligands in presence of interfacial or bridging water molecules.
Conclusions:
Software applications aiding the design of new drugs that exploit water molecules,
either as displaceable residues or as bridges to the receptor, are constantly being developed.
Although further validation is needed, workflows that explicitly consider water will
probably become a standard for computational drug discovery soon.
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Affiliation(s)
- Xiao Hu
- Università degli Studi di Milano, Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Generale e Organica “A. Marchesini”, Via Venezian, 21 20133 Milano, Italy
| | - Irene Maffucci
- Pasteur, Département de Chimie, École Normale Supérieure, PSL Research University, Sorbonne Universités, UPMC Univ. Paris 06, CNRS, 75005 Paris, France
| | - Alessandro Contini
- Università degli Studi di Milano, Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Generale e Organica “A. Marchesini”, Via Venezian, 21 20133 Milano, Italy
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22
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Abstract
This Review explores the class of plant-derived macrocyclic peptides called cyclotides. We include an account of their discovery, characterization, and distribution in the plant kingdom as well as a detailed analysis of their sequences and structures, biosynthesis and chemical synthesis, biological functions, and applications. These macrocyclic peptides are around 30 amino acids in size and are characterized by their head-to-tail cyclic backbone and cystine knot motif, which render them to be exceptionally stable, with resistance to thermal or enzymatic degradation. Routes to their chemical synthesis have been developed over the past two decades, and this capability has facilitated a wide range of mutagenesis and structure-activity relationship studies. In turn, these studies have both led to an increased understanding of their mechanisms of action as well as facilitated a range of applications in agriculture and medicine, as ecofriendly crop protection agents, and as drug leads or scaffolds for pharmaceutical design. Our overall objective in this Review is to provide readers with a comprehensive overview of cyclotides that we hope will stimulate further work on this fascinating family of peptides.
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Affiliation(s)
- Simon J de Veer
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Meng-Wei Kan
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - David J Craik
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
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23
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Ojeda PG, Cardoso MH, Franco OL. Pharmaceutical applications of cyclotides. Drug Discov Today 2019; 24:2152-2161. [PMID: 31541712 DOI: 10.1016/j.drudis.2019.09.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 09/05/2019] [Accepted: 09/12/2019] [Indexed: 02/06/2023]
Abstract
Cyclotides are cyclic peptides, present in several plant families, that show diverse biological properties. Structurally, cyclotides share a distinctive head-to-tail circular knotted topology of three disulfide bonds. This framework provides cyclotides with extraordinary resistance to thermal and chemical denaturation. There is increasing interest in the therapeutic potential of cyclotides, which combine several promising pharmaceutical properties, including binding affinity, target selectivity, and low toxicity towards healthy mammalian cells. Recently, cyclotides have been reported to be orally bioavailable and have proved to be amenable to modifications. Here, we provide an overview of the structure, properties, and pharmaceutical applications of cyclotides.
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Affiliation(s)
- Paola G Ojeda
- Escuela de Química y Farmacia, Facultad de Medicina, Universidad Católica del Maule, Av. San Miguel 3605, Talca 3480112, Chile
| | - Marlon H Cardoso
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, Brazil; 3S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
| | - Octávio L Franco
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, Brazil; 3S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil.
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24
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Poth AG, Huang YH, Le TT, Kan MW, Craik DJ. Pharmacokinetic characterization of kalata B1 and related therapeutics built on the cyclotide scaffold. Int J Pharm 2019; 565:437-446. [DOI: 10.1016/j.ijpharm.2019.05.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 04/24/2019] [Accepted: 05/03/2019] [Indexed: 02/08/2023]
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25
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Chambers C, Cutler P, Huang Y, Goodchild JA, Blythe J, Wang CK, Bigot A, Kaas Q, Craik DJ, Sabbadin D, Earley FG. Insecticidal spider toxins are high affinity positive allosteric modulators of the nicotinic acetylcholine receptor. FEBS Lett 2019; 593:1336-1350. [DOI: 10.1002/1873-3468.13435] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 04/30/2019] [Accepted: 05/08/2019] [Indexed: 12/30/2022]
Affiliation(s)
- Chris Chambers
- Syngenta Jealott's Hill Research Centre Bracknell Berkshire UK
| | - Penny Cutler
- Syngenta Jealott's Hill Research Centre Bracknell Berkshire UK
| | - Yen‐Hua Huang
- Institute for Molecular Bioscience the University of Queensland Brisbane Queensland Australia
| | | | - Judith Blythe
- Syngenta Jealott's Hill Research Centre Bracknell Berkshire UK
| | - Conan K. Wang
- Institute for Molecular Bioscience the University of Queensland Brisbane Queensland Australia
| | | | - Quentin Kaas
- Institute for Molecular Bioscience the University of Queensland Brisbane Queensland Australia
| | - David J. Craik
- Institute for Molecular Bioscience the University of Queensland Brisbane Queensland Australia
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26
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Boutin JA, Tartar AL, van Dorsselaer A, Vaudry H. General lack of structural characterization of chemically synthesized long peptides. Protein Sci 2019; 28:857-867. [PMID: 30851143 PMCID: PMC6459998 DOI: 10.1002/pro.3601] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/07/2019] [Accepted: 03/07/2019] [Indexed: 01/01/2023]
Abstract
Many peptide chemistry scientists have been reporting extremely interesting work on the basis of chemical peptides for which the only characterization was their purity, mass, and biological activity. It seems slightly overenthusiastic, as many of these structures should be thoroughly characterized first to demonstrate the uniqueness of the structure, as opposed to the uniqueness of the sequence. Among the peptides of identical sequences in the final chemical preparation, what amount of well-folded peptide supports the measured activity? The activity of a peptide preparation cannot prove the purity of the desired peptide. Therefore, greater care should be taken in characterizing peptides, particularly those coming from chemical synthesis. At a time when the pharmaceutical industry is changing its paradigm by moving substantially from small molecules to biologics to better serve patients' needs, it is important to understand the limitations of the descriptions of these products and to start to apply the same "good laboratory practices" to our peptide research. Here, we attempt to delineate how synthetic peptides are described and characterized and what will be needed to describe them in regards to how they are well-folded and homogeneous in their tertiary structure. Older studies were done when the tools were not yet discovered, but more recent publications are still lacking proper descriptions of these peptides. Modern tools of analysis are capable of segregating folded and unfolded peptides, even if the preparation is biologically active.
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Affiliation(s)
- Jean A. Boutin
- Institut de Recherches Internationales Servier50 rue Carnot, 92284, Suresnes‐CedexFrance
| | - André L. Tartar
- Faculté de Pharmacie 3rue du Professeur Laguesse, BP83 ‐ 59006, Lille‐CedexFrance
| | - Alain van Dorsselaer
- Laboratoire de Spectrométrie de Masse Bio‐Organique, Département des Sciences AnalytiquesInstitut Pluridisciplinaire Hubert CurienUMR 7178 (CNRS‐UdS), ECPM, 25 rue Becquerel, F67087, Strasbourg‐Cedex 2France
| | - Hubert Vaudry
- Plate‐Forme de Recherche en Imagerie Cellulaire de Normandie (PRIMACEN)Institut de Recherche et d'Innovation Biomédicales (IRIB), Université de Rouen76821, Mont‐Saint‐Aignan CedexFrance
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27
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Camarero JA, Campbell MJ. The Potential of the Cyclotide Scaffold for Drug Development. Biomedicines 2019; 7:biomedicines7020031. [PMID: 31010257 PMCID: PMC6631875 DOI: 10.3390/biomedicines7020031] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 04/13/2019] [Accepted: 04/15/2019] [Indexed: 12/11/2022] Open
Abstract
Cyclotides are a novel class of micro-proteins (≈30-40 residues long) with a unique topology containing a head-to-tail cyclized backbone structure further stabilized by three disulfide bonds that form a cystine knot. This unique molecular framework makes them exceptionally stable to physical, chemical, and biological degradation compared to linear peptides of similar size. The cyclotides are also highly tolerant to sequence variability, aside from the conserved residues forming the cystine knot, and are orally bioavailable and able to cross cellular membranes to modulate intracellular protein-protein interactions (PPIs), both in vitro and in vivo. These unique properties make them ideal scaffolds for many biotechnological applications, including drug discovery. This review provides an overview of the properties of cyclotides and their potential for the development of novel peptide-based therapeutics. The selective disruption of PPIs still remains a very challenging task, as the interacting surfaces are relatively large and flat. The use of the cell-permeable highly constrained polypeptide molecular frameworks, such as the cyclotide scaffold, has shown great promise, as it provides unique pharmacological properties. The use of molecular techniques, such as epitope grafting, and molecular evolution have shown to be highly effective for the selection of bioactive cyclotides. However, despite successes in employing cyclotides to target PPIs, some of the challenges to move them into the clinic still remain.
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Affiliation(s)
- Julio A Camarero
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 9033, USA.
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, Los Angeles, CA 9033, USA.
| | - Maria Jose Campbell
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 9033, USA.
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Silva ON, Pinto MF, Viana JF, Freitas CG, Fensterseifer IC, Craik DJ, Franco OL. Evaluation of the in vitro Antitumor Activity of Nanostructured Cyclotides in Polymers of Eudragit® L 100-55 and RS 30 D. LETT DRUG DES DISCOV 2019. [DOI: 10.2174/1570180815666180801115526] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Background:
Cancer is a major cause of mortality and morbidity and given the limitations
of many current cancer drugs, there is great need to discover and develop novel treatments. An
alternative to the conventional drug discovery path is to exploit new classes of natural compounds
such as cyclotides. This peptide family is characterized by linked C- and N-termini and a structural
fold called the cyclic cystine knot (CCK). The CCK fold is responsible for the exceptional enzymatic,
chemical and thermal stability of cyclotides.
Methods:
In the present study, an alternative to traditional cancer treatments, involving new nanomaterials
and nanocarriers allowing efficient cyclotide delivery, is proposed. Using the polymers
Eudragit® L 100-55 and RS 30 D, the cyclotides kalata B2 and parigidin-br1 (PBR1) were nanocapsulated,
and nanoparticles 91 nm and 188 nm in diameter, respectively, were produced.
Results:
An encapsulation rate of up to 95% was observed. In vitro bioassays showed that the
nanostructured cyclotides were partially able to control the development of the colorectal adenocarcinoma
cell line CACO2 and the breast cancer cell line MCF-7.
Conclusion:
Data reported herein indicate that nanoformulated cyclotides exhibit antitumor activity
and sustained drug release. Thus, the system using Eudragit® nanocapsules seems to be efficient for
cyclotide encapsulation and probably could be used to target specific tumors in future studies.
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Affiliation(s)
- Osmar N. Silva
- S-Inova Biotech, Universidade Catolica Dom Bosco, Programa de Pós-graduacao em Biotecnologia, Campo Grande, Mato Grosso do Sul, Brazil
| | - Michelle F.S. Pinto
- Faculdade Anhanguera de Ciencias e Tecnologia de Brasilia, Brasilia, Distrito Federal, Brazil
| | | | - Camila G. Freitas
- Centro de Analises Proteomicas e Bioquimicas. Programa de Pos-Graduacao em Ciencias Genomicas e Biotecnologia, Universidade Catolica de Brasilia, Brasilia, Distrito Federal, Brazil
| | - Isabel C.M. Fensterseifer
- Centro de Analises Proteomicas e Bioquimicas. Programa de Pos-Graduacao em Ciencias Genomicas e Biotecnologia, Universidade Catolica de Brasilia, Brasilia, Distrito Federal, Brazil
| | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Octavio L. Franco
- Centro de Analises Proteomicas e Bioquimicas. Programa de Pos-Graduacao em Ciencias Genomicas e Biotecnologia, Universidade Catolica de Brasilia, Brasilia, Distrito Federal, Brazil
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29
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Using backbone-cyclized Cys-rich polypeptides as molecular scaffolds to target protein-protein interactions. Biochem J 2019; 476:67-83. [PMID: 30635453 DOI: 10.1042/bcj20180792] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 12/07/2018] [Accepted: 12/11/2018] [Indexed: 12/23/2022]
Abstract
The use of disulfide-rich backbone-cyclized polypeptides, as molecular scaffolds to design a new generation of bioimaging tools and drugs that are potent and specific, and thus might have fewer side effects than traditional small-molecule drugs, is gaining increasing interest among the scientific and in the pharmaceutical industries. Highly constrained macrocyclic polypeptides are exceptionally more stable to chemical, thermal and biological degradation and show better biological activity when compared with their linear counterparts. Many of these relatively new scaffolds have been also found to be highly tolerant to sequence variability, aside from the conserved residues forming the disulfide bonds, able to cross cellular membranes and modulate intracellular protein-protein interactions both in vitro and in vivo These properties make them ideal tools for many biotechnological applications. The present study provides an overview of the new developments on the use of several disulfide-rich backbone-cyclized polypeptides, including cyclotides, θ-defensins and sunflower trypsin inhibitor peptides, in the development of novel bioimaging reagents and therapeutic leads.
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Ramalho SD, Wang CK, King GJ, Byriel KA, Huang YH, Bolzani VS, Craik DJ. Synthesis, Racemic X-ray Crystallographic, and Permeability Studies of Bioactive Orbitides from Jatropha Species. JOURNAL OF NATURAL PRODUCTS 2018; 81:2436-2445. [PMID: 30345754 DOI: 10.1021/acs.jnatprod.8b00447] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Orbitides are small cyclic peptides with a diverse range of therapeutic bioactivities. They are produced by many plant species, including those of the Jatropha genus. Here, the objective was to provide new structural information on orbitides to complement the growing knowledge base on orbitide sequences and activities by focusing on three Jatropha orbitides: ribifolin (1), pohlianin C (7), and jatrophidin (12). To determine three-dimensional structures, racemic crystallography, an emerging structural technique that enables rapid crystallization of biomolecules by combining equal amounts of the two enantiomers, was used. The high-resolution structure of ribifolin (0.99 Å) was elucidated from its racemate and showed it was identical to the structure crystallized from its l-enantiomer only (1.35 Å). Racemic crystallography was also used to elucidate high-resolution structures of pohlianin C (1.20 Å) and jatrophidin (1.03 Å), for which there was difficulty forming crystals without using racemic mixtures. The structures were used to interpret membrane permeability data in PAMPA and a Caco-2 cell assay, showing they had poor permeability. Overall, the results show racemic crystallography can be used to obtain high-resolution structures of orbitides and is useful when enantiopure samples are difficult to crystallize or solution structures from NMR are of low resolution.
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Affiliation(s)
- Suelem D Ramalho
- Institute of Chemistry , São Paulo State University-UNESP , Araraquara , São Paulo 14800-060 , Brazil
| | - Conan K Wang
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Gordon J King
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Karl A Byriel
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Yen-Hua Huang
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Vanderlan S Bolzani
- Institute of Chemistry , São Paulo State University-UNESP , Araraquara , São Paulo 14800-060 , Brazil
| | - David J Craik
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
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Kwon S, Duarte JN, Li Z, Ling JJ, Cheneval O, Durek T, Schroeder CI, Craik DJ, Ploegh HL. Targeted Delivery of Cyclotides via Conjugation to a Nanobody. ACS Chem Biol 2018; 13:2973-2980. [PMID: 30248263 DOI: 10.1021/acschembio.8b00653] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Many naturally occurring peptides have poor proteolytic stability, which limits their therapeutic applications. Cyclotides are plant-derived cyclic peptides that resist proteolysis due to their highly constrained structure, comprising a head-to-tail cyclic backbone and three disulfide bonds that form a cystine-knotted core. This structure makes them useful as scaffolds onto which peptide sequences (epitopes) can be grafted. In this study, VHH7, an alpaca-derived nanobody that targets murine class II MHC molecules, was used for the targeted delivery of cyclotides to antigen-presenting cells (APCs). The cyclotides MCoTI-I, and MCoTI-I with a HA-tag (YPYDVPDYA) grafted into loop 6 (MCoTI-HA), were tested for immunogenic properties. To produce the requisite VHH7-peptide conjugates, a site-specific sortase A-catalyzed reaction in combination with a copper-free strain-promoted cycloaddition reaction was used. MCoTI-I alone did not display any obvious antibody response, thus showing the capacity of cyclotides as immunologically silent scaffolds. By contrast, MCoTI-I conjugated to VHH7 elicited antibodies against cyclic or linear MCoTI-I, thus suggesting a simple and robust approach for targeting cyclotides to APCs, and potentially to other cell types. A similar antibody response was observed when MCoTI-HA was conjugated to VHH7, but there was no reactivity toward a linear HA-tag itself, suggesting differences in conformational constraint between cyclotide-presented and linear epitopes. Studies of commercially available HA antibodies applied to MCoTI-HA confirmed that the conformation of peptide immunogens affects their reactivity. Thus, the production of antibodies that recognize constrained epitopes may benefit from engraftment onto scaffolds such as cyclotides. More broadly, this study validates that a prototypic cyclotide, a member of a peptide family that has proven to be useful as drug design scaffolds in many other studies, can efficiently reach a specific target in vivo.
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Affiliation(s)
- Soohyun Kwon
- Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Queensland, Australia
| | - Joao N. Duarte
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, United States
| | - Zeyang Li
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, United States
| | - Jingjing J. Ling
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, United States
| | - Olivier Cheneval
- Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Queensland, Australia
| | - Thomas Durek
- Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Queensland, Australia
| | - Christina I. Schroeder
- Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Queensland, Australia
| | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Queensland, Australia
| | - Hidde L. Ploegh
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, United States
- Program in Cellular and Molecular Medicine, Division of Molecular Biology, Department of Medicine, Boston Children’s Hospital, 3 Blackfan Circle, Third Floor, Boston, Massachusetts 02115, United States
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32
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Designing macrocyclic disulfide-rich peptides for biotechnological applications. Nat Chem Biol 2018; 14:417-427. [DOI: 10.1038/s41589-018-0039-y] [Citation(s) in RCA: 131] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 12/18/2017] [Indexed: 12/21/2022]
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Anthelmintic niclosamide suppresses transcription of BCR-ABL fusion oncogene via disabling Sp1 and induces apoptosis in imatinib-resistant CML cells harboring T315I mutant. Cell Death Dis 2018; 9:68. [PMID: 29358661 PMCID: PMC5833368 DOI: 10.1038/s41419-017-0075-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 09/13/2017] [Accepted: 09/25/2017] [Indexed: 12/12/2022]
Abstract
Tyrosine kinase BCR-ABL fusion protein is the driver in patients with chronic myeloid leukemia (CML). The gate-keeper mutation T315I is the most challenging mutant due to its resistance to most tyrosine kinase inhibitors (TKIs). The third generation TKI ponatinib is the only effective TKI to treat CML patients harboring T315I-BCR-ABL mutation, but with high rate of major arterial thrombotic events. Alternative strategies to specifically target T315I-BCR-ABL are needed for the treatment of CML patients harboring such a mutation. Given that Sp1 is a fundamental transcriptional factor to positively regulate WT-BCR-ABL fusion oncogene, the purpose of this investigation was aimed at evaluating the anti-tumor activity and the underlying mechanism in terms of Sp1 regulational effect on the transcription of T315I-BCR-ABL fusion oncogene. Like in WT-BCR-ABL, we identified enrichment of Sp1 on the promoter of T315I-BCR-ABL fusion gene. Treatment of WT- and T315I-BCR-ABL-expressing CML cells by niclosamide diminished such an enrichment of Sp1, and decreased WT- and T315I-BCR-ABL transcription and its downstream signaling molecules such as STAT5 and Akt. Further, niclosamide significantly inhibited the proliferation and induced apoptosis through intrinsic pathway. The in vivo efficacy validation of p-niclosamide, a water soluble derivative of niclosamide, showed that p-niclosamide significantly inhibited the tumor burden of nude mice subcutaneously bearing T315I-BCR-ABL-expressing CML cells, and prolonged the survival of allografted leukemic mice harboring BaF3-T315I-BCR-ABL. We conclude that niclosamide is active against T315I-BCR-ABL-expressing cells, and may be a promising agent for CML patients regardless of T315I mutation status.
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35
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Camarero JA. Cyclotides, a versatile ultrastable micro-protein scaffold for biotechnological applications. Bioorg Med Chem Lett 2017; 27:5089-5099. [PMID: 29110985 PMCID: PMC5812341 DOI: 10.1016/j.bmcl.2017.10.051] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 10/13/2017] [Accepted: 10/21/2017] [Indexed: 01/26/2023]
Abstract
Cyclotides are fascinating microproteins (≈30-40 residues long) with a unique head-to-tail cyclized backbone, stabilized by three disulfide bonds forming a cystine knot. This unique topology makes them exceptionally stable to chemical, thermal and biological degradation compared to other peptides of similar size. Cyclotides have been also found to be highly tolerant to sequence variability, aside from the conserved residues forming the cystine knot, able to cross cellular membranes and modulate intracellular protein-protein interactions both in vitro and in vivo. These properties make them ideal scaffolds for many biotechnological applications. This article provides and overview of the properties of cyclotides and their applications as molecular imaging agents and peptide-based therapeutics.
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Affiliation(s)
- Julio A Camarero
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089-9121, USA; Department of Chemistry, University of Southern California, Los Angeles, CA 90089-9121, USA.
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36
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Valeur E, Guéret SM, Adihou H, Gopalakrishnan R, Lemurell M, Waldmann H, Grossmann TN, Plowright AT. New Modalities for Challenging Targets in Drug Discovery. Angew Chem Int Ed Engl 2017; 56:10294-10323. [PMID: 28186380 DOI: 10.1002/anie.201611914] [Citation(s) in RCA: 233] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 01/31/2017] [Indexed: 12/11/2022]
Abstract
Our ever-increasing understanding of biological systems is providing a range of exciting novel biological targets, whose modulation may enable novel therapeutic options for many diseases. These targets include protein-protein and protein-nucleic acid interactions, which are, however, often refractory to classical small-molecule approaches. Other types of molecules, or modalities, are therefore required to address these targets, which has led several academic research groups and pharmaceutical companies to increasingly use the concept of so-called "new modalities". This Review defines for the first time the scope of this term, which includes novel peptidic scaffolds, oligonucleotides, hybrids, molecular conjugates, as well as new uses of classical small molecules. We provide the most representative examples of these modalities to target large binding surface areas such as those found in protein-protein interactions and for biological processes at the center of cell regulation.
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Affiliation(s)
- Eric Valeur
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 431 83, Sweden
| | - Stéphanie M Guéret
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 431 83, Sweden.,AstraZeneca MPI Satellite Unit, Abteilung Chemische Biologie, Max Planck Institut für Molekulare Physiologie, Dortmund, Germany
| | - Hélène Adihou
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 431 83, Sweden.,AstraZeneca MPI Satellite Unit, Abteilung Chemische Biologie, Max Planck Institut für Molekulare Physiologie, Dortmund, Germany
| | - Ranganath Gopalakrishnan
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 431 83, Sweden.,AstraZeneca MPI Satellite Unit, Abteilung Chemische Biologie, Max Planck Institut für Molekulare Physiologie, Dortmund, Germany
| | - Malin Lemurell
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 431 83, Sweden
| | - Herbert Waldmann
- Abteilung Chemische Biologie, Max Planck Institut für Molekulare Physiologie, Dortmund, Germany.,Fakultät für Chemie und Chemische Biologie, Technische Universität Dortmund, Germany
| | - Tom N Grossmann
- Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany.,Department of Chemistry & Pharmaceutical Sciences, VU University Amsterdam, The Netherlands
| | - Alleyn T Plowright
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 431 83, Sweden
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Valeur E, Guéret SM, Adihou H, Gopalakrishnan R, Lemurell M, Waldmann H, Grossmann TN, Plowright AT. Neue Modalitäten für schwierige Zielstrukturen in der Wirkstoffentwicklung. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611914] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Eric Valeur
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 431 83 Schweden
| | - Stéphanie M. Guéret
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 431 83 Schweden
- AstraZeneca MPI Satellite Unit; Abteilung Chemische Biologie; Max-Planck-Institut für Molekulare Physiologie; Dortmund Deutschland
| | - Hélène Adihou
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 431 83 Schweden
- AstraZeneca MPI Satellite Unit; Abteilung Chemische Biologie; Max-Planck-Institut für Molekulare Physiologie; Dortmund Deutschland
| | - Ranganath Gopalakrishnan
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 431 83 Schweden
- AstraZeneca MPI Satellite Unit; Abteilung Chemische Biologie; Max-Planck-Institut für Molekulare Physiologie; Dortmund Deutschland
| | - Malin Lemurell
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 431 83 Schweden
| | - Herbert Waldmann
- Abteilung Chemische Biologie; Max-Planck-Institut für Molekulare Physiologie; Dortmund Deutschland
- Fakultät für Chemie and Chemische Biologie; Technische Universität Dortmund; Deutschland
| | - Tom N. Grossmann
- Chemical Genomics Centre der Max-Planck-Gesellschaft; Dortmund Deutschland
- Department of Chemistry & Pharmaceutical Sciences; VU University Amsterdam; Niederlande
| | - Alleyn T. Plowright
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 431 83 Schweden
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Abstract
Cyclotides are globular microproteins with a unique head-to-tail cyclized backbone, stabilized by three disulfide bonds forming a cystine knot. This unique circular backbone topology and knotted arrangement of three disulfide bonds makes them exceptionally stable to chemical, thermal, and biological degradation compared to other peptides of similar size. In addition, cyclotides have been shown to be highly tolerant to sequence variability, aside from the conserved residues forming the cystine knot. Cyclotides can also cross cellular membranes and are able to modulate intracellular protein-protein interactions, both in vitro and in vivo. All of these features make cyclotides highly promising as leads or frameworks for the design of peptide-based diagnostic and therapeutic tools. This article provides an overview on cyclotides and their applications as molecular imaging agents and peptide-based therapeutics.
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Affiliation(s)
- Andrew Gould
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089-9121, USA
| | - Julio A. Camarero
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089-9121, USA
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089-9121, USA
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39
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Abstract
Among the various molecules that plants produce for defense against pests and pathogens, cyclotides stand out as exceptionally stable and structurally unique. These ribosomally synthesized peptides are around 30 amino acids in size, and are stabilized by a head-to-tail cyclic peptide backbone and three disulfide bonds that form a cystine knot. They occur in certain plants of the Rubiaceae, Violaceae, Cucurbitaceae, Fabaceae, and Solanaceae families, with an individual plant producing up to hundreds of different cyclotides. Aside from being exploitable as crop protection agents based on their natural pesticidal activities, cyclotides are amenable to repurposing by chemists for use as drug leads or as tools in chemical biology. Their macrocyclic peptide backbone and knotted arrangement of three disulfide bonds engenders cyclotides with resistance to proteolytic degradation, high temperatures, and chemical chaotropes. Furthermore, their small size makes them accessible to synthesis using solid-phase peptide chemistry and so non-natural cyclotides can be designed and synthesized for a variety of applications. Our focus here is on cyclotides as tools in chemical biology, and there are four main areas of application that have appeared in the literature so far: (i) cyclotides as probes of membrane binding; (ii) cyclotides as probes of biosynthetic pathways for peptide cyclization; (iii) cyclotides as probes of protease specificity and function; and (iv) cyclotides as probes of receptor binding and specificity, with the potential for them to be developed as drug leads. The main methods used in these studies include solid-phase peptide chemistry for synthesis and NMR spectroscopy for structural characterization, as well as a wide range of biochemical and biophysical techniques for probing intermolecular interactions. In addition, cyclotides have been examined in diverse biological assays, ranging from enzyme inhibition to cell penetration, intracellular targeting and cytotoxicity. The main finding to have emerged from studies over the past decade is that cyclotides are exceptionally stable under a variety of conditions (in assay buffers, biological fluids, membranes, and recombinant expression systems). Furthermore, they are structurally very well-defined and amenable to sequence substitutions that can introduce new desired biological activities, generally without compromising their exceptional stability. Both features contribute to their use as peptide-based frameworks in drug design. Finally, they occupy a size niche between traditional small-molecule drugs (<500 Da in molecular weight) and protein-based biologics (>5000 Da) and thus can probe receptors, membranes, and protein-protein interactions in different ways to what is possible with either small molecules or biologics. Overall, cyclotides are an exciting class of peptides that have great potential as ultrastable chemical biology probes in a variety of applications. They have the advantage of specificity (typical of proteins) combined with the synthetic accessibility of small molecules.
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Affiliation(s)
- Simon J. de Veer
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Joachim Weidmann
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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40
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Cyclotides as drug design scaffolds. Curr Opin Chem Biol 2017; 38:8-16. [DOI: 10.1016/j.cbpa.2017.01.018] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 01/27/2017] [Indexed: 11/21/2022]
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41
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Hanold LE, Fulton MD, Kennedy EJ. Targeting kinase signaling pathways with constrained peptide scaffolds. Pharmacol Ther 2017; 173:159-170. [PMID: 28185915 DOI: 10.1016/j.pharmthera.2017.02.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Kinases are amongst the largest families in the human proteome and serve as critical mediators of a myriad of cell signaling pathways. Since altered kinase activity is implicated in a variety of pathological diseases, kinases have become a prominent class of proteins for targeted inhibition. Although numerous small molecule and antibody-based inhibitors have already received clinical approval, several challenges may still exist with these strategies including resistance, target selection, inhibitor potency and in vivo activity profiles. Constrained peptide inhibitors have emerged as an alternative strategy for kinase inhibition. Distinct from small molecule inhibitors, peptides can provide a large binding surface area that allows them to bind shallow protein surfaces rather than defined pockets within the target protein structure. By including chemical constraints within the peptide sequence, additional benefits can be bestowed onto the peptide scaffold such as improved target affinity and target selectivity, cell permeability and proteolytic resistance. In this review, we highlight examples of diverse chemistries that are being employed to constrain kinase-targeting peptide scaffolds and highlight their application to modulate kinase signaling as well as their potential clinical implications.
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Affiliation(s)
- Laura E Hanold
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, United States
| | - Melody D Fulton
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, United States
| | - Eileen J Kennedy
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, United States.
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Daly NL, Gunasekera S, Clark RJ, Lin F, Wade JD, Anderson MA, Craik DJ. The N-terminal pro-domain of the kalata B1 cyclotide precursor is intrinsically unstructured. Biopolymers 2017; 106:825-833. [PMID: 27564841 DOI: 10.1002/bip.22977] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 08/23/2016] [Accepted: 08/25/2016] [Indexed: 11/09/2022]
Abstract
Cyclotides are plant-derived, gene-encoded, circular peptides with a range of host-defense functions, including insecticidal activity. They also have potential as pharmaceutical scaffolds and understanding their biosynthesis is important to facilitate their large-scale production. Insights into the biosynthesis of cyclotides are emerging but there are still open questions, particularly regarding the influence of the structure of the precursor proteins on processing/biosynthetic pathways. The precursor protein of kalata B1, encoded by the plant Oldenlandia affinis, contains N- and C-terminal propeptides that flank the mature cyclotide domain. The C-terminal region (ctr) is important for the cyclization process, whereas the N-terminal repeat (ntr) has been implicated in vacuolar targeting. In this study we examined the structure and folding of various truncated constructs of the ntr coupled to the mature domain of kalata B1. Despite the ntr having a well-defined helical structure in isolation, once coupled to the natively folded mature domain there is no evidence of an ordered structure. Surprisingly, the ntr appears to be highly disordered and induces self-association of the precursor. This self-association might be associated with the role of the ntr as a vacuolar-targeting signal, as previously shown for unrelated storage proteins.
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Affiliation(s)
- Norelle L Daly
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Sunithi Gunasekera
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Richard J Clark
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Feng Lin
- Howard Florey Institute, University of Melbourne, Victoria, 3010, Australia
| | - John D Wade
- Howard Florey Institute, University of Melbourne, Victoria, 3010, Australia
| | - Marilyn A Anderson
- Department of Biochemistry, La Trobe University, Melbourne, Victoria, 3086, Australia
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
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Troeira Henriques S, Craik DJ. Cyclotide Structure and Function: The Role of Membrane Binding and Permeation. Biochemistry 2017; 56:669-682. [DOI: 10.1021/acs.biochem.6b01212] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sónia Troeira Henriques
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072 QLD, Australia
| | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072 QLD, Australia
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Chan LY, Craik DJ, Daly NL. Dual-targeting anti-angiogenic cyclic peptides as potential drug leads for cancer therapy. Sci Rep 2016; 6:35347. [PMID: 27734947 PMCID: PMC5062114 DOI: 10.1038/srep35347] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 09/28/2016] [Indexed: 12/29/2022] Open
Abstract
Peptide analogues derived from bioactive hormones such as somatostatin or certain growth factors have great potential as angiogenesis inhibitors for cancer applications. In an attempt to combat emerging drug resistance many FDA-approved anti-angiogenesis therapies are co-administered with cytotoxic drugs as a combination therapy to target multiple signaling pathways of cancers. However, cancer therapies often encounter limiting factors such as high toxicities and side effects. Here, we combined two anti-angiogenic epitopes that act on different pathways of angiogenesis into a single non-toxic cyclic peptide framework, namely MCoTI-II (Momordica cochinchinensis trypsin inhibitor-II), and subsequently assessed the anti-angiogenic activity of the novel compound. We hypothesized that the combination of these two epitopes would elicit a synergistic effect by targeting different angiogenesis pathways and result in improved potency, compared to that of a single epitope. This novel approach has resulted in the development of a potent, non-toxic, stable and cyclic analogue with nanomolar potency inhibition in in vitro endothelial cell migration and in vivo chorioallantoic membrane angiogenesis assays. This is the first report to use the MCoTI-II framework to develop a 2-in-1 anti-angiogenic peptide, which has the potential to be used as a form of combination therapy for targeting a wide range of cancers.
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Affiliation(s)
- Lai Yue Chan
- The University of Queensland, Institute for Molecular Bioscience, 4072 Brisbane, Australia
| | - David J Craik
- The University of Queensland, Institute for Molecular Bioscience, 4072 Brisbane, Australia
| | - Norelle L Daly
- Centre for Biodiscovery and Molecular Development of Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, 4870 Cairns, Australia
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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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Stanfield RL, Wilson IA, Smider VV. Conservation and diversity in the ultralong third heavy-chain complementarity-determining region of bovine antibodies. Sci Immunol 2016; 1:aaf7962. [PMID: 27574710 PMCID: PMC5000368 DOI: 10.1126/sciimmunol.aaf7962] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A subset of bovine antibodies have an exceptionally long third heavy-chain complementarity determining region (CDR H3) that is highly variable in sequence and includes multiple cysteines. These long CDR H3s (up to 69 residues) fold into a long stalk atop which sits a knob domain that is located far from the antibody surface. Three new bovine Fab crystal structures have been determined to decipher the conserved and variable features of ultralong CDR H3s that lead to diversity in antigen recognition. Despite high sequence variability, the stalks adopt a conserved β-ribbon structure, while the knob regions share a conserved β-sheet that serves as a scaffold for two connecting loops of variable length and conformation, as well as one conserved disulfide. Variation in patterns and connectivity of the remaining disulfides contribute to the knob structural diversity. The unusual architecture of these ultralong bovine CDR H3s for generating diversity is unique in adaptive immune systems.
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Affiliation(s)
- Robyn L. Stanfield
- Department of Integrative Structural and Computational Biology, The
Scripps Research Institute, La Jolla, California, 92037, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The
Scripps Research Institute, La Jolla, California, 92037, USA
- Skaggs Institute for Chemical Biology, The Scripps Research
Institute, La Jolla, California, 92037, USA
| | - Vaughn V. Smider
- Department of Cell and Molecular Biology, The Scripps Research
Institute, La Jolla, California, 92037, USA
- Fabrus Inc., A Division of Sevion Therapeutics, San Diego, CA 92121,
USA
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The chimeric ubiquitin ligase SH2-U-box inhibits the growth of imatinib-sensitive and resistant CML by targeting the native and T315I-mutant BCR-ABL. Sci Rep 2016; 6:28352. [PMID: 27329306 PMCID: PMC4916441 DOI: 10.1038/srep28352] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 06/02/2016] [Indexed: 01/01/2023] Open
Abstract
Chronic myeloid leukemia (CML) is characterized by constitutively active fusion protein tyrosine kinase BCR-ABL. Although the tyrosine kinase inhibitor (TKI) against BCR-ABL, imatinib, is the first-line therapy for CML, acquired resistance almost inevitably emerges. The underlying mechanism are point mutations within the BCR-ABL gene, among which T315I is notorious because it resists to almost all currently available inhibitors. Here we took use of a previously generated chimeric ubiquitin ligase, SH2-U-box, in which SH2 from the adaptor protein Grb2 acts as a binding domain for activated BCR-ABL, while U-box from CHIP functions as an E3 ubiquitin ligase domain, so as to target the ubiquitination and degradation of both native and T315I-mutant BCR-ABL. As such, SH2-U-box significantly inhibited proliferation and induced apoptosis in CML cells harboring either the wild-type or T315I-mutant BCR-ABL (K562 or K562R), with BCR-ABL-dependent signaling pathways being repressed. Moreover, SH2-U-box worked in concert with imatinib in K562 cells. Importantly, SH2-U-box-carrying lentivirus could markedly suppress the growth of K562-xenografts in nude mice or K562R-xenografts in SCID mice, as well as that of primary CML cells. Collectively, by degrading the native and T315I-mutant BCR-ABL, the chimeric ubiquitin ligase SH2-U-box may serve as a potential therapy for both imatinib-sensitive and resistant CML.
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Yun T, Qin T, Liu Y, Lai L. Discovery of Non-ATP-Competitive Inhibitors of Polo-like Kinase 1. ChemMedChem 2016; 11:713-7. [PMID: 27061239 DOI: 10.1002/cmdc.201600051] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 02/18/2016] [Indexed: 11/09/2022]
Abstract
Polo-like kinase 1 (Plk1) is an evolutionarily conserved serine/threonine kinase, and its N-terminal kinase domain (KD) controls cell signaling through phosphorylation. Inhibitors of Plk1 are potential anticancer drugs. Most known Plk1 KD inhibitors are ATP-competitive compounds, which may suffer from low selectivity. In this study we discovered novel non-ATP-competitive Plk1 KD inhibitors by virtual screening and experimental studies. Potential binding sites in Plk1 KD were identified by using the protein binding site detection program Cavity. The identified site was subjected to molecular-docking-based virtual screening. The activities of top-ranking compounds were evaluated by in vitro enzyme assay with full-length Plk1 and direct binding assay with Plk1 KD. Several compounds showed inhibitory activity, and the most potent was found to be 3-((2-oxo-2-(thiophen-2-yl)ethyl)thio)-6-(pyridin-3-ylmethyl)-1,2,4-triazin-5(4H)-one (compound 4) with an IC50 value of 13.1 ± 1.7 μm. Our work provides new insight into the design of kinase inhibitors that target non-ATP binding sites.
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Affiliation(s)
- Taikangxiang Yun
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Tan Qin
- BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, PekingUniversity, Beijing, 100871, China
| | - Ying Liu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China.
- BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, PekingUniversity, Beijing, 100871, China.
| | - Luhua Lai
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China.
- BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, PekingUniversity, Beijing, 100871, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
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Oral activity of a nature-derived cyclic peptide for the treatment of multiple sclerosis. Proc Natl Acad Sci U S A 2016; 113:3960-5. [PMID: 27035952 DOI: 10.1073/pnas.1519960113] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Multiple sclerosis (MS) is the most common autoimmune disease affecting the central nervous system. It is characterized by auto-reactive T cells that induce demyelination and neuronal degradation. Treatment options are still limited and several MS medications need to be administered by parenteral application but are modestly effective. Oral active drugs such as fingolimod have been weighed down by safety concerns. Consequently, there is a demand for novel, especially orally active therapeutics. Nature offers an abundance of compounds for drug discovery. Recently, the circular plant peptide kalata B1 was shown to silence T-cell proliferation in vitro in an IL-2-dependent mechanism. Owing to this promising effect, we aimed to determine in vivo activity of the cyclotide [T20K]kalata B1 using the MS mouse model experimental autoimmune encephalomyelitis (EAE). Treatment of mice with the cyclotide resulted in a significant delay and diminished symptoms of EAE by oral administration. Cyclotide application substantially impeded disease progression and did not exhibit adverse effects. Inhibition of lymphocyte proliferation and the reduction of proinflammatory cytokines, in particular IL-2, distinguish the cyclotide from other marketed drugs. Considering their stable structural topology and oral activity, cyclotides are candidates as peptide therapeutics for pharmaceutical drug development for treatment of T-cell-mediated disorders.
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