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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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Gori A, Lodigiani G, Colombarolli SG, Bergamaschi G, Vitali A. Cell Penetrating Peptides: Classification, Mechanisms, Methods of Study, and Applications. ChemMedChem 2023; 18:e202300236. [PMID: 37389978 DOI: 10.1002/cmdc.202300236] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/28/2023] [Accepted: 06/28/2023] [Indexed: 07/02/2023]
Abstract
Cell-penetrating peptides (CPPs) encompass a class of peptides that possess the remarkable ability to cross cell membranes and deliver various types of cargoes, including drugs, nucleic acids, and proteins, into cells. For this reason, CPPs are largely investigated in drug delivery applications in the context of many diseases, such as cancer, diabetes, and genetic disorders. While sharing this functionality and some common structural features, such as a high content of positively charged amino acids, CPPs represent an extremely diverse group of elements, which can differentiate under many aspects. In this review, we summarize the most common characteristics of CPPs, introduce their main distinctive features, mechanistic aspects that drive their function, and outline the most widely used techniques for their structural and functional studies. We highlight current gaps and future perspectives in this field, which have the potential to significantly impact the future field of drug delivery and therapeutics.
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Affiliation(s)
- Alessandro Gori
- SCITEC - Istituto di Scienze e Tecnologie Chimiche "Giulio Natta", National Research Council of Italy, Via Mario Bianco 9, 20131, Milano, Italy
| | - Giulia Lodigiani
- SCITEC - Istituto di Scienze e Tecnologie Chimiche "Giulio Natta", National Research Council of Italy, Via Mario Bianco 9, 20131, Milano, Italy
| | - Stella G Colombarolli
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta", National Research Council of Italy, L.go F. Vito 1, 00168, Roma, Italy
| | - Greta Bergamaschi
- SCITEC - Istituto di Scienze e Tecnologie Chimiche "Giulio Natta", National Research Council of Italy, Via Mario Bianco 9, 20131, Milano, Italy
| | - Alberto Vitali
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta", National Research Council of Italy, L.go F. Vito 1, 00168, Roma, Italy
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3
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CPEB1 directs muscle stem cell activation by reprogramming the translational landscape. Nat Commun 2022; 13:947. [PMID: 35177647 PMCID: PMC8854658 DOI: 10.1038/s41467-022-28612-1] [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: 09/01/2020] [Accepted: 01/14/2022] [Indexed: 11/08/2022] Open
Abstract
Skeletal muscle stem cells, also called Satellite Cells (SCs), are actively maintained in quiescence but can activate quickly upon extrinsic stimuli. However, the mechanisms of how quiescent SCs (QSCs) activate swiftly remain elusive. Here, using a whole mouse perfusion fixation approach to obtain bona fide QSCs, we identify massive proteomic changes during the quiescence-to-activation transition in pathways such as chromatin maintenance, metabolism, transcription, and translation. Discordant correlation of transcriptomic and proteomic changes reveals potential translational regulation upon SC activation. Importantly, we show Cytoplasmic Polyadenylation Element Binding protein 1 (CPEB1), post-transcriptionally affects protein translation during SC activation by binding to the 3' UTRs of different transcripts. We demonstrate phosphorylation-dependent CPEB1 promoted Myod1 protein synthesis by binding to the cytoplasmic polyadenylation elements (CPEs) within its 3' UTRs to regulate SC activation and muscle regeneration. Our study characterizes CPEB1 as a key regulator to reprogram the translational landscape directing SC activation and subsequent proliferation.
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van der Beek J, de Heus C, Liv N, Klumperman J. Quantitative correlative microscopy reveals the ultrastructural distribution of endogenous endosomal proteins. J Cell Biol 2022; 221:212877. [PMID: 34817533 PMCID: PMC8624803 DOI: 10.1083/jcb.202106044] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 10/22/2021] [Accepted: 11/01/2021] [Indexed: 02/07/2023] Open
Abstract
The key endosomal regulators Rab5, EEA1, and APPL1 are frequently applied in fluorescence microscopy to mark early endosomes, whereas Rab7 is used as a marker for late endosomes and lysosomes. However, endogenous levels of these proteins localize poorly in immuno-EM, and systematic studies on their native ultrastructural distributions are lacking. To address this gap, we here present a quantitative, on-section correlative light and electron microscopy (CLEM) approach. Using the sensitivity of fluorescence microscopy, we label hundreds of organelles that are subsequently visualized by EM and classified by ultrastructure. We show that Rab5 predominantly marks small, endocytic vesicles and early endosomes. EEA1 colocalizes with Rab5 on early endosomes, but unexpectedly also labels Rab5-negative late endosomes, which are positive for PI(3)P but lack Rab7. APPL1 is restricted to small Rab5-positive, tubulo-vesicular profiles. Rab7 primarily labels late endosomes and lysosomes. These data increase our understanding of the structural-functional organization of the endosomal system and introduce quantitative CLEM as a sensitive alternative for immuno-EM.
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Affiliation(s)
- Jan van der Beek
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Institute of Biomembranes, Utrecht University, Utrecht, the Netherlands
| | - Cecilia de Heus
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Institute of Biomembranes, Utrecht University, Utrecht, the Netherlands
| | - Nalan Liv
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Institute of Biomembranes, Utrecht University, Utrecht, the Netherlands
| | - Judith Klumperman
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Institute of Biomembranes, Utrecht University, Utrecht, the Netherlands
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5
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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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6
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Cho J, Park J, Kim EE, Song EJ. Assay Systems for Profiling Deubiquitinating Activity. Int J Mol Sci 2020; 21:E5638. [PMID: 32781716 PMCID: PMC7460613 DOI: 10.3390/ijms21165638] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/04/2020] [Accepted: 08/04/2020] [Indexed: 01/22/2023] Open
Abstract
Deubiquitinating enzymes regulate various cellular processes, particularly protein degradation, localization, and protein-protein interactions. The dysregulation of deubiquitinating enzyme (DUB) activity has been linked to several diseases; however, the function of many DUBs has not been identified. Therefore, the development of methods to assess DUB activity is important to identify novel DUBs, characterize DUB selectivity, and profile dynamic DUB substrates. Here, we review various methods of evaluating DUB activity using cell lysates or purified DUBs, as well as the types of probes used in these methods. In addition, we introduce some techniques that can deliver DUB probes into the cells and cell-permeable activity-based probes to directly visualize and quantify DUB activity in live cells. This review could contribute to the development of DUB inhibitors by providing important information on the characteristics and applications of various probes used to evaluate and detect DUB activity in vitro and in vivo.
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Affiliation(s)
- Jinhong Cho
- Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 02792, Korea; (J.C.); (E.E.K.)
| | - Jinyoung Park
- Molecular Recognition Research Center, Korea Institute of Science and Technology, Seoul 02792, Korea;
| | - Eunice EunKyeong Kim
- Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 02792, Korea; (J.C.); (E.E.K.)
| | - Eun Joo Song
- Graduate School of Pharmaceutical Sciences and College of Pharmacy, Ewha Womans University, Seoul 03760, Korea
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7
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Hara K, Yaita K, Khamrin P, Kumthip K, Kashiwagi T, Eléouët JF, Rameix-Welti MA, Watanabe H. A small fragmented P protein of respiratory syncytial virus inhibits virus infection by targeting P protein. J Gen Virol 2020; 101:21-32. [PMID: 31702536 DOI: 10.1099/jgv.0.001350] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Peptide-based inhibitors hold promising potential in the development of antiviral therapy. Here, we investigated the antiviral potential of fragmented viral proteins derived from ribonucleoprotein (RNP) components of the human respiratory syncytial virus (HRSV). Based on a mimicking approach that targets the functional domains of viral proteins, we designed various fragments of nucleoprotein (N), matrix protein M2-1 and phosphoprotein (P) and tested the antiviral activity in an RSV mini-genome system. We found that the fragment comprising residues 130-180 and 212-241 in the C-terminal region of P (81 amino acid length), denoted as P Fr, significantly inhibited the polymerase activity through competitive binding to the full-length P. Further deletion analysis of P Fr suggested that three functional domains in P Fr (oligomerization, L-binding and nucleocapsid binding) are required for maximum inhibitory activity. More importantly, a purified recombinant P Fr displayed significant antiviral activity at low nanomolar range in RSV-infected HEp-2 cells. These results highlight P as an important target for the development of antiviral compounds against RSV and other paramyxoviruses.
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Affiliation(s)
- Koyu Hara
- Department of Infection Control and Prevention, Kurume University School of Medicine, Fukuoka, 830-0011, Japan
| | - Kenichiro Yaita
- Division of Infectious diseases, Chidoribashi General Hospital, Fukuoka 812-8633, Japan
| | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Kattareeya Kumthip
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Takahito Kashiwagi
- Department of Infection Control and Prevention, Kurume University School of Medicine, Fukuoka, 830-0011, Japan
| | - Jean-François Eléouët
- Unité de Virologie et Immunologie Moléculaires (UR892), INRA, Université Paris-Saclay, Jouy-en-Josas, France
| | - Marie-Anne Rameix-Welti
- AP-HP, Laboratoire de Microbiologie, Hôpital Ambroise Paré, Boulogne-Billancourt, France.,UMR1173, INSERM, Université de Versailles St. Quentin, Montigny le Bretonneux, France
| | - Hiroshi Watanabe
- Department of Infection Control and Prevention, Kurume University School of Medicine, Fukuoka, 830-0011, Japan
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8
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Conole D, Mondal M, Majmudar JD, Tate EW. Recent Developments in Cell Permeable Deubiquitinating Enzyme Activity-Based Probes. Front Chem 2019; 7:876. [PMID: 31921788 PMCID: PMC6930156 DOI: 10.3389/fchem.2019.00876] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 12/04/2019] [Indexed: 01/25/2023] Open
Abstract
Deubiquitinating enzymes (DUBs) function to remove or cleave ubiquitin from post-translationally modified protein substrates. There are about 100 known DUBs in the proteome, and their dysregulation has been implicated a number of disease states, but the specific function of many subclass members remains poorly understood. Activity-based probes (ABPs) react covalently with an active site residue to report on specific enzyme activity, and thus represent a powerful method to evaluate cellular and physiological enzyme function and dynamics. Ubiquitin-based ABPs, such as HA-Ub-VME, an epitope-tagged ubiquitin carrying a C-terminal reactive warhead, are the leading tool for "DUBome" activity profiling. However, these probes are generally cell membrane impermeable, limiting their use to isolated enzymes or lysates. Development of cell-permeable ABPs would allow engagement of DUB enzymes directly within the context of an intact live cell or organism, refining our understanding of physiological and pathological function, and greatly enhancing opportunities for translational research, including target engagement, imaging and biomarker discovery. This mini-review discusses recent developments in small molecule activity-based probes that target DUBs in live cells, and the unique applications of cell-permeable DUB activity-based probes vs. their traditional ubiquitin-based counterparts.
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Affiliation(s)
- Daniel Conole
- Department of Chemistry, Imperial College London, London, United Kingdom
| | - Milon Mondal
- Department of Chemistry, Imperial College London, London, United Kingdom
| | | | - Edward W. Tate
- Department of Chemistry, Imperial College London, London, United Kingdom
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9
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Peptides, Antibodies, Peptide Antibodies and More. Int J Mol Sci 2019; 20:ijms20246289. [PMID: 31847088 PMCID: PMC6941022 DOI: 10.3390/ijms20246289] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 12/02/2019] [Accepted: 12/05/2019] [Indexed: 02/07/2023] Open
Abstract
The applications of peptides and antibodies to multiple targets have emerged as powerful tools in research, diagnostics, vaccine development, and therapeutics. Antibodies are unique since they, in theory, can be directed to any desired target, which illustrates their versatile nature and broad spectrum of use as illustrated by numerous applications of peptide antibodies. In recent years, due to the inherent limitations such as size and physical properties of antibodies, it has been attempted to generate new molecular compounds with equally high specificity and affinity, albeit with relatively low success. Based on this, peptides, antibodies, and peptide antibodies have established their importance and remain crucial reagents in molecular biology.
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10
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Guan G, Song B, Zhang J, Chen K, Hu H, Wang M, Chen D. An Effective Cationic Human Serum Albumin-Based Gene-Delivery Carrier Containing the Nuclear Localization Signal. Pharmaceutics 2019; 11:E608. [PMID: 31766300 PMCID: PMC6920835 DOI: 10.3390/pharmaceutics11110608] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 11/08/2019] [Accepted: 11/11/2019] [Indexed: 12/18/2022] Open
Abstract
Considerable effort has been devoted to the development of gene carriers over the years. However, toxicity, immunogenicity, and low transfection efficiency are still major barriers. How to overcome these obstacles has become a burning question in gene delivery. In the present study, a simple cationic human serum albumin (CHSA)-based gene-delivery system containing nuclear localization signals (NLSs) was constructed to conquer the limitations. CHSA/NLS/plasmid DNA (pDNA) complexes were prepared and characterized by Hoechst 33258 intercalation, gel retardation assay, morphological analysis, circular dichroism (CD) spectroscopy, particle size, and zeta potential measurements. Results showed that CHSA/NLS/pDNA complexes were able to condense and protect pDNA with high encapsulation efficiency. The complexes displayed a nutritional effect on cells at a low concentration and there was no significant cytotoxicity or immunogenicity. In addition, CHSA/NLS/pDNA complexes exhibited excellent cellular uptake rates and the mechanism was mainly the clathrin or macropinocytosis-dependent endocytosis pathway. Furthermore, CHSA/NLS/pDNA significantly enhanced gene expression efficiency in vitro. More importantly, CHSA/NLS/pDNA complexes showed a desired antitumor effect in vivo, exhibiting the highest inhibition rate (57.3%) and significant upregulation in p53 protein. All these results confirm that CHSA/NLS/pDNA complexes have a bright future as a safe and effective delivery system for gene therapy.
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Affiliation(s)
- Guannan Guan
- Department of Pharmaceutics, School of Pharmacy, Shenyang Pharmaceutical University, No. 103, Wenhua Road, Shenyang 110016, China; (G.G.); (B.S.); (H.H.)
| | - Baohui Song
- Department of Pharmaceutics, School of Pharmacy, Shenyang Pharmaceutical University, No. 103, Wenhua Road, Shenyang 110016, China; (G.G.); (B.S.); (H.H.)
| | - Jie Zhang
- Department of Pharmaceutics, Medical College of Jiaxing University, Jiaxing 314001, China;
| | - Kang Chen
- Department of Medicine, The University of Hong Kong, 21 Sassoon Road, Hong Kong 999077, China;
| | - Haiyang Hu
- Department of Pharmaceutics, School of Pharmacy, Shenyang Pharmaceutical University, No. 103, Wenhua Road, Shenyang 110016, China; (G.G.); (B.S.); (H.H.)
| | - Mingyue Wang
- Department of Pharmacy, Shenyang Medical College, No. 146, Huanghe North Street, Shenyang 110034, China
| | - Dawei Chen
- Department of Pharmaceutics, School of Pharmacy, Shenyang Pharmaceutical University, No. 103, Wenhua Road, Shenyang 110016, China; (G.G.); (B.S.); (H.H.)
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