1
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Hwang S, Balana AT, Martin B, Clarkson M, Di Lello P, Wu H, Li Y, Fuhrmann J, Dagdas Y, Holder P, Schroeder CI, Miller SE, Gao X. Bioproduction Platform to Generate Functionalized Disulfide-Constrained Peptide Analogues. ACS BIO & MED CHEM AU 2024; 4:190-203. [PMID: 39184057 PMCID: PMC11342346 DOI: 10.1021/acsbiomedchemau.4c00026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 07/02/2024] [Accepted: 07/03/2024] [Indexed: 08/27/2024]
Abstract
Disulfide-constrained peptides (DCPs) have gained increased attention as a drug modality due to their exceptional stability and combined advantages of large biologics and small molecules. Chemical synthesis, although widely used to produce DCPs, is associated with high cost, both economically and environmentally. To reduce the dependence on solid phase peptide synthesis and the negative environmental footprint associated with it, we present a highly versatile, low-cost, and environmentally friendly bioproduction platform to generate DCPs and their conjugates as well as chemically modified or isotope-labeled DCPs. Using the DCP against the E3 ubiquitin ligase Zinc and Ring Finger 3, MK1-3.6.10, as a model peptide, we have demonstrated the use of bacterial expression, combined with Ser ligation or transglutaminase-mediated XTEN ligation, to produce multivalent MK1-3.6.10 and MK1-3.6.10 with N-terminal functional groups. We have also developed a bioproduction method for the site-specific incorporation of unnatural amino acids into recombinant DCPs by the amber codon suppression system. Lastly, we produced 15N/13C-labeled MK1-3.6.10 with high yield and assessed the performance of a semiautomated resonance assignment workflow that could be used to accelerate binding studies and structural characterization of DCPs. This study provides a proof of concept to generate functionalized DCPs using bioproduction, providing a potential solution to alleviate the reliance on hazardous chemicals, reduce the cost, and expedite the timeline for DCP discovery.
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Affiliation(s)
- Sunhee Hwang
- Department
of Peptide Therapeutics, Genentech Incorporated, South San Francisco, California 94080, United States
| | - Aaron T. Balana
- Department
of Peptide Therapeutics, Genentech Incorporated, South San Francisco, California 94080, United States
| | - Bryan Martin
- Department
of Structural Biology, Genentech Incorporated, South San Francisco, California 94080, United States
| | - Michael Clarkson
- Department
of Structural Biology, Genentech Incorporated, South San Francisco, California 94080, United States
| | - Paola Di Lello
- Department
of Structural Biology, Genentech Incorporated, South San Francisco, California 94080, United States
| | - Hao Wu
- Department
of Peptide Therapeutics, Genentech Incorporated, South San Francisco, California 94080, United States
| | - Yanjie Li
- Department
of Peptide Therapeutics, Genentech Incorporated, South San Francisco, California 94080, United States
| | - Jakob Fuhrmann
- Department
of Peptide Therapeutics, Genentech Incorporated, South San Francisco, California 94080, United States
| | - Yavuz Dagdas
- Department
of Protein Chemistry, Genentech Incorporated, South San Francisco, California 94080, United States
| | - Patrick Holder
- Department
of Protein Chemistry, Genentech Incorporated, South San Francisco, California 94080, United States
| | - Christina I. Schroeder
- Department
of Peptide Therapeutics, Genentech Incorporated, South San Francisco, California 94080, United States
| | - Stephen E. Miller
- Department
of Peptide Therapeutics, Genentech Incorporated, South San Francisco, California 94080, United States
| | - Xinxin Gao
- Department
of Peptide Therapeutics, Genentech Incorporated, South San Francisco, California 94080, United States
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2
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Li Y, Wei Y, Ultsch M, Li W, Tang W, Tombling B, Gao X, Dimitrova Y, Gampe C, Fuhrmann J, Zhang Y, Hannoush RN, Kirchhofer D. Cystine-knot peptide inhibitors of HTRA1 bind to a cryptic pocket within the active site region. Nat Commun 2024; 15:4359. [PMID: 38777835 PMCID: PMC11111691 DOI: 10.1038/s41467-024-48655-w] [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: 09/28/2023] [Accepted: 05/09/2024] [Indexed: 05/25/2024] Open
Abstract
Cystine-knot peptides (CKPs) are naturally occurring peptides that exhibit exceptional chemical and proteolytic stability. We leveraged the CKP carboxypeptidase A1 inhibitor as a scaffold to construct phage-displayed CKP libraries and subsequently screened these collections against HTRA1, a trimeric serine protease implicated in age-related macular degeneration and osteoarthritis. The initial hits were optimized by using affinity maturation strategies to yield highly selective and potent picomolar inhibitors of HTRA1. Crystal structures, coupled with biochemical studies, reveal that the CKPs do not interact in a substrate-like manner but bind to a cryptic pocket at the S1' site region of HTRA1 and abolish catalysis by stabilizing a non-competent active site conformation. The opening and closing of this cryptic pocket is controlled by the gatekeeper residue V221, and its movement is facilitated by the absence of a constraining disulfide bond that is typically present in trypsin fold serine proteases, thereby explaining the remarkable selectivity of the CKPs. Our findings reveal an intriguing mechanism for modulating the activity of HTRA1, and highlight the utility of CKP-based phage display platforms in uncovering potent and selective inhibitors against challenging therapeutic targets.
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Affiliation(s)
- Yanjie Li
- Department of Early Discovery Biochemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Yuehua Wei
- Department of Early Discovery Biochemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Mark Ultsch
- Department of Structural Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Wei Li
- Department of Early Discovery Biochemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Wanjian Tang
- Department of Early Discovery Biochemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Benjamin Tombling
- Department of Early Discovery Biochemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Xinxin Gao
- Department of Early Discovery Biochemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Yoana Dimitrova
- Department of Structural Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Christian Gampe
- Department of Discovery Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Jakob Fuhrmann
- Department of Early Discovery Biochemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Yingnan Zhang
- Department of Early Discovery Biochemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Rami N Hannoush
- Department of Early Discovery Biochemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA.
| | - Daniel Kirchhofer
- Department of Early Discovery Biochemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA.
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3
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Gao X, Kaluarachchi H, Zhang Y, Hwang S, Hannoush RN. A phage-displayed disulfide constrained peptide discovery platform yields novel human plasma protein binders. PLoS One 2024; 19:e0299804. [PMID: 38547072 PMCID: PMC10977726 DOI: 10.1371/journal.pone.0299804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 02/15/2024] [Indexed: 04/02/2024] Open
Abstract
Disulfide constrained peptides (DCPs) show great potential as templates for drug discovery. They are characterized by conserved cysteine residues that form intramolecular disulfide bonds. Taking advantage of phage display technology, we designed and generated twenty-six DCP phage libraries with enriched molecular diversity to enable the discovery of ligands against disease-causing proteins of interest. The libraries were designed based on five DCP scaffolds, namely Momordica charantia 1 (Mch1), gurmarin, Asteropsin-A, antimicrobial peptide-1 (AMP-1), and potato carboxypeptidase inhibitor (CPI). We also report optimized workflows for screening and producing synthetic and recombinant DCPs. Examples of novel DCP binders identified against various protein targets are presented, including human IgG Fc, serum albumin, vascular endothelial growth factor-A (VEGF-A) and platelet-derived growth factor (PDGF). We identified DCPs against human IgG Fc and serum albumin with sub-micromolar affinity from primary panning campaigns, providing alternative tools for potential half-life extension of peptides and small protein therapeutics. Overall, the molecular diversity of the DCP scaffolds included in the designed libraries, coupled with their distinct biochemical and biophysical properties, enables efficient and robust identification of de novo binders to drug targets of therapeutic relevance.
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Affiliation(s)
- Xinxin Gao
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, California, United States of America
- Department of Peptide Therapeutics, Genentech, South San Francisco, California, United States of America
| | - Harini Kaluarachchi
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, California, United States of America
| | - Yingnan Zhang
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, California, United States of America
- Department of Biological Chemistry, Genentech, South San Francisco, California, United States of America
| | - Sunhee Hwang
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, California, United States of America
- Department of Peptide Therapeutics, Genentech, South San Francisco, California, United States of America
| | - Rami N. Hannoush
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, California, United States of America
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4
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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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5
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Abstract
AbstractBiophysical studies have a very high impact on the understanding of internalization, molecular mechanisms, interactions, and localization of CPPs and CPP/cargo conjugates in live cells or in vivo. Biophysical studies are often first carried out in test-tube set-ups or in vitro, leading to the complicated in vivo systems. This review describes recent studies of CPP internalization, mechanisms, and localization. The multiple methods in these studies reveal different novel and important aspects and define the rules for CPP mechanisms, hopefully leading to their improved applicability to novel and safe therapies.
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Affiliation(s)
- Matjaž Zorko
- University of Ljubljana, Medical Faculty, Institute of Biochemistry and Molecular Genetics, Vrazov trg 2, 1000Ljubljana, Slovenia,
| | - Ülo Langel
- University of Stockholm, Department of Biochemistry and Biophysics, Svante Arrhenius väg 16, 106 91 Stockholm, Sweden, , and Institute of Technology, University of Tartu, Nooruse 1, Tartu, Estonia, 50411
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6
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Zhu M, Liu H, Cao W, Fang Y, Chen Z, Qi X, Luo D, Chen C. Transcytosis mechanisms of cell-penetrating peptides: Cation independent CC12 and cationic penetratin. J Pept Sci 2022; 28:e3408. [PMID: 35128758 DOI: 10.1002/psc.3408] [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: 09/08/2021] [Revised: 01/27/2022] [Accepted: 02/03/2022] [Indexed: 11/07/2022]
Abstract
Cell-penetrating peptides (CPPs) can aid in intracellular and in vivo drug delivery. However, the mechanisms of CPP-mediated penetration remain unclear, limiting the development and further application of CPPs. Flow cytometry and laser confocal fluorescence microscopy were performed to detect the effects of different endocytosis inhibitors on the internalization of CC12 and penetratin in ARPE-19 cells. The co-localization of CPPs with the lysosome and macropinosome was detected via an endocytosis tracing experiment. The flow cytometry results showed that chlorpromazine, wortmannin, cytochalasin D, and the ATP inhibitor oligomycin had dose-dependent endocytosis-inhibitory effects on CC12. The laser confocal fluorescence results showed that oligomycin had the most significant inhibitory effect on CC12 uptake; CC12 was co-located with the lysosome, but not with the macropinosome. For penetratin, cytochalasin D and oligomycin had obvious inhibitory effects. The laser confocal fluorescence results indicated that oligomycin had the most significant inhibitory effect on penetratin uptake; the co-localization of penetratin with the lysosome was higher than that with the macropinosome. Cation-independent CC12 and cationic penetratin may be internalized into cells primarily through caveolae and clathrin-mediated endocytosis, and they are typically dependent on ATP. The transport of penetratin could be partly achieved through the direct transmembrane pathway, as the positive charge of penetratin interacts with the negative charge of the cell membrane, and partly through the endocytic pathway.
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Affiliation(s)
- Minjiao Zhu
- Department of Obstetrics and Gynecology, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Key Laboratory of Embryo Original Diseases, Shanghai Municipal Key Clinical Specialty, Shanghai, China
| | - Haiyang Liu
- Department of Respiratory Medicine, The People's Hospital of Dongtai, Dongtai, Jiangsu, China
| | - Wenjiao Cao
- Department of Obstetrics and Gynecology, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Key Laboratory of Embryo Original Diseases, Shanghai Municipal Key Clinical Specialty, Shanghai, China
| | - Yuefei Fang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, NO, Shanghai, China
| | - Zheng Chen
- Department of Obstetrics and Gynecology, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Key Laboratory of Embryo Original Diseases, Shanghai Municipal Key Clinical Specialty, Shanghai, China
| | - Xinming Qi
- Center for Drug Safety Evaluation and Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Dawei Luo
- Department of Ophthalmology, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, National Clinical Research Center for Eye Diseases, Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, Shanghai, China
| | - Chong Chen
- Department of Ophthalmology, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, National Clinical Research Center for Eye Diseases, Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, Shanghai, China
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7
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Gao X, Mazière AD, Beard R, Klumperman J, Hannoush RN. Fatty acylation enhances the cellular internalization and cytosolic distribution of a cystine-knot peptide. iScience 2021; 24:103220. [PMID: 34712919 PMCID: PMC8529511 DOI: 10.1016/j.isci.2021.103220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/14/2021] [Accepted: 09/30/2021] [Indexed: 02/07/2023] Open
Abstract
Delivering peptides into cells could open up possibilities for targeting intracellular proteins. Although fatty acylation of peptide therapeutics improves their systemic half-life, it remains unclear how it influences their cellular uptake. Here, we demonstrate that a fatty acylated peptide exhibits enhanced cellular internalization and cytosolic distribution compared to the un-acylated version. By using a cystine-knot peptide as a model system, we report an efficient strategy for site-specific conjugation of fatty acids. Peptides modified with fatty acids of different chain lengths entered cells through clathrin-mediated and macropinocytosis pathways. The cellular uptake was mediated by the length of the hydrocarbon chain, with myristic acid conjugates displaying the highest distribution across the cytoplasm including the cytosol, and endomembranes of the ER, Golgi and mitochondria. Our studies demonstrate how fatty acylation improves the cellular uptake of peptides, and lay the groundwork for future development of bioactive peptides with enhanced intracellular distribution. A synthetic strategy comprises site-specific conjugation of fatty acids to peptides Fatty acylation of a peptide enhances its cellular uptake and cytosolic distribution Myristoylated peptides display a high cytoplasmic distribution Fatty acylated peptides are internalized via multiple endocytic routes
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Affiliation(s)
- Xinxin Gao
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, CA, USA
| | - Ann De Mazière
- Department of Cell Biology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Rhiannon Beard
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, CA, USA
| | - Judith Klumperman
- Department of Cell Biology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Rami N Hannoush
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, CA, USA
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8
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Hellinger R, Muratspahić E, Devi S, Koehbach J, Vasileva M, Harvey PJ, Craik DJ, Gründemann C, Gruber CW. Importance of the Cyclic Cystine Knot Structural Motif for Immunosuppressive Effects of Cyclotides. ACS Chem Biol 2021; 16:2373-2386. [PMID: 34592097 PMCID: PMC9286316 DOI: 10.1021/acschembio.1c00524] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The cyclotide T20K inhibits the proliferation of human immune cells and is currently in clinical trials for multiple sclerosis. Here, we provide novel functional data and mechanistic insights into structure-activity relationships of T20K. Analogs with partial or complete reduction of the cystine knot had loss of function in proliferation experiments. Similarly, an acyclic analog of T20K was inactive in lymphocyte bioassays. The lack of activity of non-native peptide analogs appears to be associated with the ability of cyclotides to interact with and penetrate cell membranes, since cellular uptake studies demonstrated fast fractional transfer only of the native peptide into the cytosol of human immune cells. Therefore, structural differences between cyclic and linear native folded peptides were investigated by NMR to elucidate structure-activity relationships. Acyclic T20K had a less rigid backbone and considerable structural changes in loops 1 and 6 compared to the native cyclic T20K, supporting the idea that the cyclic cystine knot motif is a unique bioactive scaffold. This study provides evidence that this structural motif in cyclotides governs bioactivity, interactions with and transport across biological membranes, and the structural integrity of these peptides. These observations could be useful to understand the structure-activity of other cystine knot proteins due to the structural conservation of the cystine knot motif across evolution and to provide guidance for the design of novel cyclic cysteine-stabilized molecules.
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Affiliation(s)
- Roland Hellinger
- Center for
Physiology and Pharmacology, Medical University
of Vienna, Schwarzspanierstr. 17, Vienna 1090, Austria
| | - Edin Muratspahić
- Center for
Physiology and Pharmacology, Medical University
of Vienna, Schwarzspanierstr. 17, Vienna 1090, Austria
| | - Seema Devi
- Institute
for Infection Prevention and Hospital Epidemiology, Center for Complementary
Medicine, Faculty of Medicine, University
of Freiburg, Breisacher Str. 115B, Freiburg 79106, Germany
| | - Johannes Koehbach
- 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
| | - Mina Vasileva
- Center for
Physiology and Pharmacology, Medical University
of Vienna, Schwarzspanierstr. 17, Vienna 1090, Austria
| | - 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
| | - 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
| | - Carsten Gründemann
- Translational
Complementary Medicine, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstr. 80, Basel 4056, Switzerland
| | - Christian W. Gruber
- Center for
Physiology and Pharmacology, Medical University
of Vienna, Schwarzspanierstr. 17, Vienna 1090, Austria
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9
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Schwalen C, Babu C, Phulera S, Hao Q, Wall D, Nettleton DO, Pathak TP, Siuti P. Scalable Biosynthetic Production of Knotted Peptides Enables ADME and Thermodynamic Folding Studies. ACS OMEGA 2021; 6:29555-29566. [PMID: 34778627 PMCID: PMC8582066 DOI: 10.1021/acsomega.1c03707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/29/2021] [Indexed: 06/13/2023]
Abstract
Knotted peptides present a wealth of structurally diverse, biologically active molecules, with the inhibitor cystine knot/knottin class among the most ecologically common ones. Many of these natural products interact with extracellular targets such as voltage-gated ion channels with exquisite selectivity and potency, making them intriguing therapeutic modalities. Such compounds are often produced in low concentrations by intractable organisms, making structural and biological characterization challenging, which is frequently overcome by various expression strategies. Here, we sought to test a biosynthetic route for the expression and study of knotted peptides. We screened expression constructs for a biosynthesized knotted peptide to determine the most influential parameters for successful disulfide folding and used NMR spectroscopic fingerprinting to validate topological structures. We performed pharmacokinetic characterization, which indicated that the interlocking disulfide structure minimizes liabilities of linear peptide sequences, and propose a mechanism by which knotted peptides are cleared. We then developed an assay to monitor solution folding in real time, providing a strategy for studying the folding process during maturation, which provided direct evidence for the importance of backbone organization as the driving force for topology formation.
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Affiliation(s)
- Christopher
J. Schwalen
- Global
Discovery Chemistry, Novartis Institutes
for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Charles Babu
- Global
Discovery Chemistry, Novartis Institutes
for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Swastik Phulera
- Chemical
Biology and Therapeutics, Novartis Institutes
for Biomedical Research, Cambridge Massachusetts, 02139, United States
| | - Qin Hao
- Pharmacokinetic
Sciences, Novartis Institutes for Biomedical
Research, Cambridge, Massachusetts 02139, United States
| | - Daniel Wall
- Pharmacokinetic
Sciences, Novartis Institutes for Biomedical
Research, Cambridge, Massachusetts 02139, United States
| | - David O. Nettleton
- Pharmacokinetic
Sciences, Novartis Institutes for Biomedical
Research, Cambridge, Massachusetts 02139, United States
| | - Tejas P. Pathak
- Global
Discovery Chemistry, Novartis Institutes
for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Piro Siuti
- Global
Discovery Chemistry, Novartis Institutes
for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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10
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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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11
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Darwish M, Gao X, Shatz W, Li H, Lin M, Franke Y, Tam C, Mortara K, Zilberleyb I, Hannoush RN, Blanchette C. Nanolipoprotein particles for co-delivery of cystine-knot peptides and Fab-based therapeutics. NANOSCALE ADVANCES 2021; 3:3929-3941. [PMID: 36133017 PMCID: PMC9419673 DOI: 10.1039/d1na00218j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 05/27/2021] [Indexed: 06/16/2023]
Abstract
Nanolipoprotein particles (NLPs) have been evaluated as an in vivo delivery vehicle for a variety of molecules of therapeutic interest. However, delivery of peptide-like drugs in combination with therapeutic Fabs has not yet been evaluated. In this study, we describe the development and characterization of cystine-knot peptide (CKP)-containing NLPs and Fab-CKP-NLP conjugates. CKPs were incorporated into NLPs using a self-assembly strategy. The trypsin inhibitor EETI-II, a model CKP, was produced with a C16 fatty acyl chain to enable incorporation of the CKP into the lipid bilayer core during NLP assembly. The CKP-NLP retained trypsin inhibitory function although the overall activity was reduced by ∼5 fold compared to free CKP, which was presumably due to steric hindrance. The NLP platform was also shown to accommodate up to ∼60 CKP molecules. Moreover, the stability of the CKP-NLP was comparable to the NLP control, displaying a relatively short half-life (∼1 h) in 50% serum at 37 °C. Therapeutic Fabs were also loaded onto the CKP-NLP by introducing thiol-reactive lipids that would undergo a covalent reaction with the Fab. Using this strategy, Fab loading could be reliably controlled from 1-50 Fabs per CKP-NLP and was found to be independent of CKP density. Surprisingly, Fab incorporation into CKP-NLPs led to a substantial improvement in NLP stability (half-life > 24 h) at 37 °C; also, there was no reduction in CKP activity in the Fab-CKP-NLP conjugates compared to CKP-NLPs. Altogether, our data demonstrate the potential of NLPs as a promising platform for the targeted or multidrug delivery of peptide-based drug candidates in combination with Fabs.
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Affiliation(s)
| | - Xinxin Gao
- Genentech Inc 1 DNA way So San Francisco 94080 USA
| | | | - Hong Li
- Genentech Inc 1 DNA way So San Francisco 94080 USA
| | - May Lin
- Genentech Inc 1 DNA way So San Francisco 94080 USA
| | | | | | - Kyle Mortara
- Genentech Inc 1 DNA way So San Francisco 94080 USA
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12
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Chen T, Tang S, Hecht ES, Yen CW, Andersen N, Chin S, Cadang L, Roper B, Estevez A, Rohou A, Chang D, Dai L, Liu P, Al-Sayah M, Nagapudi K, Lin F, Famili A, Hu C, Kuhn R, Stella C, Crittenden CM, Gruenhagen JA, Venkatramani C, Hannoush RN, Leung D, Vandlen R, Yehl P. Discovery of a dual pathway aggregation mechanism for a therapeutic constrained peptide. J Pharm Sci 2021; 110:2362-2371. [PMID: 33652014 DOI: 10.1016/j.xphs.2020.12.041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 12/07/2020] [Indexed: 10/22/2022]
Abstract
Constrained peptides (CPs) have emerged as attractive candidates for drug discovery and development. To fully unlock the therapeutic potential of CPs, it is crucial to understand their physical stability and minimize the formation of aggregates that could induce immune responses. Although amyloid like aggregates have been researched extensively, few studies have focused on aggregates from other peptide scaffolds (e.g., CPs). In this work, a streamlined approach to effectively profile the nature and formation pathway of CP aggregates was demonstrated. Aggregates of various sizes were detected and shown to be amorphous. Though no major changes were found in peptide structure upon aggregation, these aggregates appeared to have mixed natures, consisting of primarily non-covalent aggregates with a low level of covalent species. This co-existence phenomenon was also supported by two kinetic pathways observed in time- and temperature-dependent aggregation studies. Furthermore, a stability study with 8 additional peptide variants exhibited good correlation between aggregation propensity and peptide hydrophobicity. Therefore, a dual aggregation pathway was proposed, with the non-covalent aggregates driven by hydrophobic interactions, whereas the covalent ones formed through disulfide scrambling. Overall, the workflow presented here provides a powerful strategy for comprehensive characterization of peptide aggregates and understanding their mechanisms of formation.
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Affiliation(s)
- Tao Chen
- Small Molecule Pharmaceutical Sciences, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States.
| | - Shijia Tang
- Small Molecule Pharmaceutical Sciences, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Elizabeth S Hecht
- Department of Microchemistry, Proteomics, and Lipidomics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Chun-Wan Yen
- Small Molecule Pharmaceutical Sciences, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Nisana Andersen
- Protein Analytical Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Steven Chin
- Small Molecule Pharmaceutical Sciences, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Lance Cadang
- Protein Analytical Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Brian Roper
- Protein Analytical Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Alberto Estevez
- Department of Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Alexis Rohou
- Department of Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Debby Chang
- Department of Drug Delivery, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Lu Dai
- Protein Analytical Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Peter Liu
- Department of Microchemistry, Proteomics, and Lipidomics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Mohammad Al-Sayah
- Small Molecule Pharmaceutical Sciences, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Karthik Nagapudi
- Small Molecule Pharmaceutical Sciences, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Fiona Lin
- Small Molecule Pharmaceutical Sciences, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Amin Famili
- Small Molecule Pharmaceutical Sciences, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Chloe Hu
- Small Molecule Pharmaceutical Sciences, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Robert Kuhn
- Small Molecule Pharmaceutical Sciences, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Cinzia Stella
- Protein Analytical Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Christopher M Crittenden
- Small Molecule Pharmaceutical Sciences, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Jason A Gruenhagen
- Small Molecule Pharmaceutical Sciences, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Cadapakam Venkatramani
- Small Molecule Pharmaceutical Sciences, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Rami N Hannoush
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Dennis Leung
- Small Molecule Pharmaceutical Sciences, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Richard Vandlen
- Department of Protein Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Peter Yehl
- Small Molecule Pharmaceutical Sciences, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
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13
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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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14
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Kam A, Loo S, Fan JS, Sze SK, Yang D, Tam JP. Roseltide rT7 is a disulfide-rich, anionic, and cell-penetrating peptide that inhibits proteasomal degradation. J Biol Chem 2019; 294:19604-19615. [PMID: 31727740 DOI: 10.1074/jbc.ra119.010796] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/02/2019] [Indexed: 12/21/2022] Open
Abstract
Disulfide-rich plant peptides with molecular masses of 2-6 kDa represent an expanding class of peptidyl-type natural products with diverse functions. They are structurally compact, hyperstable, and underexplored as cell-penetrating agents that inhibit intracellular functions. Here, we report the discovery of an anionic, 34-residue peptide, the disulfide-rich roseltide rT7 from Hibiscus sabdariffa (of the Malvaceae family) that penetrates cells and inhibits their proteasomal activities. Combined proteomics and NMR spectroscopy revealed that roseltide rT7 is a cystine-knotted, six-cysteine hevein-like cysteine-rich peptide. A pair-wise comparison indicated that roseltide rT7 is >100-fold more stable against protease degradation than its S-alkylated analog. Confocal microscopy studies and cell-based assays disclosed that after roseltide rT7 penetrates cells, it causes accumulation of ubiquitinated proteins, inhibits human 20S proteasomes, reduces tumor necrosis factor-induced IκBα degradation, and decreases expression levels of intercellular adhesion molecule-1. Structure-activity studies revealed that roseltide rT7 uses a canonical substrate-binding mechanism for proteasomal inhibition enabled by an IIML motif embedded in its proline-rich and exceptionally long intercysteine loop 4. Taken together, our results provide mechanistic insights into a novel disulfide-rich, anionic, and cell-penetrating peptide, representing a potential lead for further development as a proteasomal inhibitor in anti-cancer or anti-inflammatory therapies.
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Affiliation(s)
- Antony Kam
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Shining Loo
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Jing-Song Fan
- Department of Biological Sciences, National University of Singapore, Singapore 117543
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Daiwen Yang
- Department of Biological Sciences, National University of Singapore, Singapore 117543
| | - James P Tam
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
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15
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Słupianek A, Kasprowicz-Maluśki A, Myśkow E, Turzańska M, Sokołowska K. Endocytosis acts as transport pathway in wood. THE NEW PHYTOLOGIST 2019; 222:1846-1861. [PMID: 30548617 DOI: 10.1111/nph.15637] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 12/05/2018] [Indexed: 06/09/2023]
Abstract
In trees, dead and living cells of secondary xylem (wood) function collectively, rendering cell-to-cell communication challenging. Water and solutes are transported over long distances from the roots to the above-ground organs via vessels, the main component of wood, and then radially over short distances to the neighboring cells. This enables proper functioning of trees and integrates whole-plant activity. In this study, tracer loading, immunolocalization experiments and inhibitor assays were used to decipher the mechanisms enabling transport in wood of Acer pseudoplatanus (maple), Fraxinus excelsior (ash) and Populus tremula × tremuloides (poplar) trees. We show that tracer uptake from dead water-conducting vessels, elements of the apoplasm, to living vessel-associated cells (VACs) of the xylem parenchyma of the symplasm system proceeds via the endocytic pathway, including clathrin-mediated and clathrin-independent processes. These findings enhance our understanding of the transport pathways in complex wood tissue, providing experimental evidence of the involvement of VACs and endocytosis in radial uptake from vessels.
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Affiliation(s)
- Aleksandra Słupianek
- Department of Plant Developmental Biology, Institute of Experimental Biology, Faculty of Biological Sciences, University of Wrocław, Kanonia 6/8, Wrocław, 50-328, Poland
| | - Anna Kasprowicz-Maluśki
- Department of Molecular and Cellular Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, Poznań, 61-614, Poland
| | - Elżbieta Myśkow
- Department of Plant Developmental Biology, Institute of Experimental Biology, Faculty of Biological Sciences, University of Wrocław, Kanonia 6/8, Wrocław, 50-328, Poland
| | - Magdalena Turzańska
- Department of Plant Developmental Biology, Institute of Experimental Biology, Faculty of Biological Sciences, University of Wrocław, Kanonia 6/8, Wrocław, 50-328, Poland
| | - Katarzyna Sokołowska
- Department of Plant Developmental Biology, Institute of Experimental Biology, Faculty of Biological Sciences, University of Wrocław, Kanonia 6/8, Wrocław, 50-328, Poland
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16
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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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17
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Gao X, De Mazière A, Iaea DB, Arthur CP, Klumperman J, Ciferri C, Hannoush RN. Visualizing the cellular route of entry of a cystine-knot peptide with Xfect transfection reagent by electron microscopy. Sci Rep 2019; 9:6907. [PMID: 31061420 PMCID: PMC6502800 DOI: 10.1038/s41598-019-43285-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 04/16/2019] [Indexed: 01/08/2023] Open
Abstract
Cystine-knot peptides are attractive templates in drug discovery due to a number of features they possess including their 3D conformation, physicochemical stability and synthetic tractability. Yet, their cellular uptake mechanisms remain largely unexplored. Recently, we demonstrated that the cystine-knot peptide EETI-II is internalized into cells and that its cellular uptake could be modulated by using a protein transfection reagent Xfect. However, the mechanism of Xfect-mediated cellular internalization of EETI-II remained unclear. Here, by using high resolution electron microscopy, we observe the formation of EETI-II-positive macropinosomes and clathrin-coated pits at early time points after treatment of cells with EETI-II/Xfect complexes. Internalized EETI-II subsequently accumulates in intracellular Xfect-induced detergent-resistant membrane compartments which appear to lack characteristic endosomal or lysosomal markers. Notably, Xfect enables the uptake of cell impermeable nuclear dyes into similar intracellular compartments that do not seem to deliver the cargo to the cytosol or nucleus. Altogether, our findings reveal mechanistic insights into the cellular uptake route of Xfect, and underscore the need for the development of effective tools to enhance the cytosolic delivery of cystine-knot peptides. Finally, our data illustrate that electron microscopy is a powerful approach for studying endocytic mechanisms of cell-penetrating peptides and their effects on cellular membranes.
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Affiliation(s)
- Xinxin Gao
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, California, USA
| | - Ann De Mazière
- Section of Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - David B Iaea
- Department of Biochemical and Cellular Pharmacology, Genentech, South San Francisco, California, USA
| | - Christopher P Arthur
- Department of Structural Biology, Genentech, South San Francisco, California, USA
| | - Judith Klumperman
- Section of Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Claudio Ciferri
- Department of Structural Biology, Genentech, South San Francisco, California, USA
| | - Rami N Hannoush
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, California, USA.
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18
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Size-dependent effect of cystine/citric acid-capped confeito-like gold nanoparticles on cellular uptake and photothermal cancer therapy. Colloids Surf B Biointerfaces 2018; 161:365-374. [DOI: 10.1016/j.colsurfb.2017.10.064] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 09/17/2017] [Accepted: 10/25/2017] [Indexed: 12/29/2022]
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19
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Bode SA, Löwik DWPM. Constrained cell penetrating peptides. DRUG DISCOVERY TODAY. TECHNOLOGIES 2017; 26:33-42. [PMID: 29249241 DOI: 10.1016/j.ddtec.2017.11.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 11/14/2017] [Accepted: 11/15/2017] [Indexed: 06/07/2023]
Abstract
In this review we provide an overview of recent developments in the field of cell penetrating peptides (CPPs) on research that aims to achieve better control over their transduction properties - one of the big challenges - by means of restraining them. Three different constraining strategies are presented: triggerable activation, backbone rigidification and macrocyclization. Each of these methods have their opportunities in gaining control over CPP activity and selectivity.
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Affiliation(s)
- S A Bode
- Radboud University Nijmegen, Institute for Molecules and Materials, Bio-organic Chemistry, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - D W P M Löwik
- Radboud University Nijmegen, Institute for Molecules and Materials, Bio-organic Chemistry, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
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20
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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: 246] [Impact Index Per Article: 35.1] [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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21
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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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