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Giancola JB, Grimm JB, Jun JV, Petri YD, Lavis LD, Raines RT. Evaluation of the Cytosolic Uptake of HaloTag Using a pH-Sensitive Dye. ACS Chem Biol 2024; 19:908-915. [PMID: 38525961 PMCID: PMC11186736 DOI: 10.1021/acschembio.3c00713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
The efficient cytosolic delivery of proteins is critical for advancing novel therapeutic strategies. Current delivery methods are severely limited by endosomal entrapment, and detection methods lack sophistication in tracking the fate of delivered protein cargo. HaloTag, a commonly used protein in chemical biology and a challenging delivery target, is an exceptional model system for understanding and exploiting cellular delivery. Here, we employed a combinatorial strategy to direct HaloTag to the cytosol. We established the use of Virginia Orange, a pH-sensitive fluorophore, and Janelia Fluor 585, a similar but pH-agnostic fluorophore, in a fluorogenic assay to ascertain protein localization within human cells. Using this assay, we investigated HaloTag delivery upon modification with cell-penetrating peptides, carboxyl group esterification, and cotreatment with an endosomolytic agent. We found efficacious cytosolic entry with two distinct delivery methods. This study expands the toolkit for detecting the cytosolic access of proteins and highlights that multiple intracellular delivery strategies can be used synergistically to effect cytosolic access. Moreover, HaloTag is poised to serve as a platform for the delivery of varied cargo into human cells.
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Affiliation(s)
- JoLynn B. Giancola
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jonathan B. Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn VA 20147, United States
| | - Joomyung V. Jun
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Yana D. Petri
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Luke D. Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn VA 20147, United States
| | - Ronald T. Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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2
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Goldbach N, Benna I, Wicky BIM, Croft JT, Carter L, Bera AK, Nguyen H, Kang A, Sankaran B, Yang EC, Lee KK, Baker D. De novo design of monomeric helical bundles for pH-controlled membrane lysis. Protein Sci 2023; 32:e4769. [PMID: 37632837 PMCID: PMC10578055 DOI: 10.1002/pro.4769] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/10/2023] [Accepted: 08/24/2023] [Indexed: 08/28/2023]
Abstract
Targeted intracellular delivery via receptor-mediated endocytosis requires the delivered cargo to escape the endosome to prevent lysosomal degradation. This can in principle be achieved by membrane lysis tightly restricted to endosomal membranes upon internalization to avoid general membrane insertion and lysis. Here, we describe the design of small monomeric proteins with buried histidine containing pH-responsive hydrogen bond networks and membrane permeating amphipathic helices. Of the 30 designs that were experimentally tested, all expressed in Escherichia coli, 13 were monomeric with the expected secondary structure, and 4 designs disrupted artificial liposomes in a pH-dependent manner. Mutational analysis showed that the buried histidine hydrogen bond networks mediate pH-responsiveness and control lysis of model membranes within a very narrow range of pH (6.0-5.5) with almost no lysis occurring at neutral pH. These tightly controlled lytic monomers could help mediate endosomal escape in designed targeted delivery platforms.
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Affiliation(s)
- Nicolas Goldbach
- Institute for Protein DesignUniversity of WashingtonSeattleWashingtonUSA
- Molecular Life SciencesTechnical University of MunichMunichGermany
| | - Issa Benna
- Institute for Protein DesignUniversity of WashingtonSeattleWashingtonUSA
- Department of BioengineeringUniversity of WashingtonSeattleWashingtonUSA
| | - Basile I. M. Wicky
- Institute for Protein DesignUniversity of WashingtonSeattleWashingtonUSA
- Department of BiochemistryUniversity of WashingtonSeattleWashingtonUSA
| | - Jacob T. Croft
- Department of Medicinal ChemistryUniversity of WashingtonSeattleWashingtonUSA
| | - Lauren Carter
- Institute for Protein DesignUniversity of WashingtonSeattleWashingtonUSA
- Department of BiochemistryUniversity of WashingtonSeattleWashingtonUSA
| | - Asim K. Bera
- Institute for Protein DesignUniversity of WashingtonSeattleWashingtonUSA
- Department of BiochemistryUniversity of WashingtonSeattleWashingtonUSA
| | - Hannah Nguyen
- Institute for Protein DesignUniversity of WashingtonSeattleWashingtonUSA
- Department of BiochemistryUniversity of WashingtonSeattleWashingtonUSA
| | - Alex Kang
- Institute for Protein DesignUniversity of WashingtonSeattleWashingtonUSA
- Department of BiochemistryUniversity of WashingtonSeattleWashingtonUSA
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated BioimagingLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - Erin C. Yang
- Institute for Protein DesignUniversity of WashingtonSeattleWashingtonUSA
- Department of BiochemistryUniversity of WashingtonSeattleWashingtonUSA
- Biological Physics, Structure and Design Graduate ProgramUniversity of WashingtonSeattleWashingtonUSA
| | - Kelly K. Lee
- Department of Medicinal ChemistryUniversity of WashingtonSeattleWashingtonUSA
- Biological Physics, Structure and Design Graduate ProgramUniversity of WashingtonSeattleWashingtonUSA
- Department of MicrobiologyUniversity of WashingtonSeattleWashingtonUSA
| | - David Baker
- Institute for Protein DesignUniversity of WashingtonSeattleWashingtonUSA
- Department of BiochemistryUniversity of WashingtonSeattleWashingtonUSA
- Howard Hughes Medical InstituteUniversity of WashingtonSeattleWashingtonUSA
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3
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Arafiles JV, Franke J, Franz L, Gómez-González J, Kemnitz-Hassanin K, Hackenberger CPR. Cell-Surface-Retained Peptide Additives for the Cytosolic Delivery of Functional Proteins. J Am Chem Soc 2023; 145. [PMID: 37906525 PMCID: PMC10655119 DOI: 10.1021/jacs.3c05365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 10/02/2023] [Accepted: 10/02/2023] [Indexed: 11/02/2023]
Abstract
The delivery of functional proteins remains a major challenge in advancing biological and pharmaceutical sciences. Herein, we describe a powerful, simple, and highly effective strategy for the intracellular delivery of functional cargoes. Previously, we demonstrated that cell-penetrating peptide (CPP) additives equipped with electrophilic thiol-reactive moieties temporarily attach to the cellular membrane, thereby facilitating the cellular uptake of protein- and antibody-CPP cargoes through direct membrane transduction at low concentrations. Now, we hypothesize that CPP-additives with an increased retention on the cellular membrane will further enhance intracellular uptake. We discovered that adding a small hydrophobic peptide sequence to an arginine-rich electrophilic CPP-additive further improved the uptake of protein-CPP conjugates, whereas larger hydrophobic anchors showed increased cytotoxicity. Cell viability and membrane integrity measurements, structure-activity relationship studies, and quantitative evaluation of protein-CPP uptake revealed important design principles for cell-surface-retained CPP-additives. These investigations allowed us to identify a nontoxic, thiol-reactive CPP-additive containing the hydrophobic ILFF sequence, which can deliver fluorescent model proteins at low micromolar concentrations. This hydrophobic CPP-additive allowed the addition of protein cargoes for intracellular delivery after initial additive incubation. Time-lapse fluorescence microscopy and membrane tension analysis of cells treated with fluorescent ILFF-CPP-additives supported the claim of increased cell surface retention and suggested that the protein-CPP cargoes enter the cell through a mechanism involving lowered cell membrane tension. Finally, we demonstrated that our newly engineered hydrophobic CPP-additive enabled the uptake of a functional macrocyclic peptidic MDM2-inhibitor and a recombinant genome editing protein. This indicates that the developed hydrophobic CPP-additive holds promise as a tool to enhance the intracellular delivery of peptide and protein cargoes.
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Affiliation(s)
- Jan Vincent
V. Arafiles
- Leibniz-Forschungsinstitut
für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, Berlin 13125, Germany
| | - Jonathan Franke
- Leibniz-Forschungsinstitut
für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, Berlin 13125, Germany
- Institut
für Chemie, Humboldt Universität
zu Berlin, Brook-Taylor-Str.
2, Berlin 12489, Germany
| | - Luise Franz
- Leibniz-Forschungsinstitut
für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, Berlin 13125, Germany
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Berlin 14195, Germany
| | - Jacobo Gómez-González
- Leibniz-Forschungsinstitut
für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, Berlin 13125, Germany
| | - Kristin Kemnitz-Hassanin
- Leibniz-Forschungsinstitut
für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, Berlin 13125, Germany
| | - Christian P. R. Hackenberger
- Leibniz-Forschungsinstitut
für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, Berlin 13125, Germany
- Institut
für Chemie, Humboldt Universität
zu Berlin, Brook-Taylor-Str.
2, Berlin 12489, Germany
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4
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Nakazato Y, Otaki JM. Protein Delivery to Insect Epithelial Cells In Vivo: Potential Application to Functional Molecular Analysis of Proteins in Butterfly Wing Development. BIOTECH 2023; 12:biotech12020028. [PMID: 37092472 PMCID: PMC10123617 DOI: 10.3390/biotech12020028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 04/25/2023] Open
Abstract
Protein delivery to cells in vivo has great potential for the functional analysis of proteins in nonmodel organisms. In this study, using the butterfly wing system, we investigated a method of protein delivery to insect epithelial cells that allows for easy access, treatment, and observation in real time in vivo. Topical and systemic applications (called the sandwich and injection methods, respectively) were tested. In both methods, green/orange fluorescent proteins (GFP/OFP) were naturally incorporated into intracellular vesicles and occasionally into the cytosol from the apical surface without any delivery reagent. However, the antibodies were not delivered by the sandwich method at all, and were delivered only into vesicles by the injection method. A membrane-lytic peptide, L17E, appeared to slightly improve the delivery of GFP/OFP and antibodies. A novel peptide reagent, ProteoCarry, successfully promoted the delivery of both GFP/OFP and antibodies into the cytosol via both the sandwich and injection methods. These protein delivery results will provide opportunities for the functional molecular analysis of proteins in butterfly wing development, and may offer a new way to deliver proteins into target cells in vivo in nonmodel organisms.
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Affiliation(s)
- Yugo Nakazato
- The BCPH Unit of Molecular Physiology, Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan
| | - Joji M Otaki
- The BCPH Unit of Molecular Physiology, Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan
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Donohoe C, Schaberle FA, Rodrigues FMS, Gonçalves NPF, Kingsbury CJ, Pereira MM, Senge MO, Gomes-da-Silva LC, Arnaut LG. Unraveling the Pivotal Role of Atropisomerism for Cellular Internalization. J Am Chem Soc 2022; 144:15252-15265. [PMID: 35960892 PMCID: PMC9446767 DOI: 10.1021/jacs.2c05844] [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] [Indexed: 11/28/2022]
Abstract
The intrinsic challenge of large molecules to cross the cell membrane and reach intracellular targets is a major obstacle for the development of new medicines. We report how rotation along a single C-C bond, between atropisomers of a drug in clinical trials, improves cell uptake and therapeutic efficacy. The atropisomers of redaporfin (a fluorinated sulfonamide bacteriochlorin photosensitizer of 1135 Da) are separable and display orders of magnitude differences in photodynamic efficacy that are directly related to their differential cellular uptake. We show that redaporfin atropisomer uptake is passive and only marginally affected by ATP depletion, plasma proteins, or formulation in micelles. The α4 atropisomer, where meso-phenyl sulfonamide substituents are on the same side of the tetrapyrrole macrocycle, exhibits the highest cellular uptake and phototoxicity. This is the most amphipathic atropisomer with a conformation that optimizes hydrogen bonding (H-bonding) with polar head groups of membrane phospholipids. Consequently, α4 binds to the phospholipids on the surface of the membrane, flips into the membrane to adopt the orientation of a surfactant, and eventually diffuses to the interior of the cell (bind-flip mechanism). We observed increased α4 internalization by cells of the tumor microenvironment in vivo and correlated this to the response of photodynamic therapy when tumor illumination was performed 24 h after α4 administration. These results show that properly orientated aryl sulfonamide groups can be incorporated into drug design as efficient cell-penetrating motifs in vivo and reveal the unexpected biological consequences of atropisomerism.
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Affiliation(s)
- Claire Donohoe
- CQC, Coimbra Chemistry Center, University of Coimbra, Rua Larga, Coimbra 3004-535, Portugal.,Medicinal Chemistry, Trinity Translational Medicine Institute, Trinity Centre for Health Sciences, St. James's Hospital, Trinity College Dublin, The University of Dublin, Dublin 8, Ireland
| | - Fábio A Schaberle
- CQC, Coimbra Chemistry Center, University of Coimbra, Rua Larga, Coimbra 3004-535, Portugal
| | - Fábio M S Rodrigues
- CQC, Coimbra Chemistry Center, University of Coimbra, Rua Larga, Coimbra 3004-535, Portugal
| | - Nuno P F Gonçalves
- Luzitin SA, Ed. Bluepharma, S. Martinho do Bispo, Coimbra 3045-016, Portugal
| | - Christopher J Kingsbury
- School of Chemistry, Chair of Organic Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Mariette M Pereira
- CQC, Coimbra Chemistry Center, University of Coimbra, Rua Larga, Coimbra 3004-535, Portugal
| | - Mathias O Senge
- Medicinal Chemistry, Trinity Translational Medicine Institute, Trinity Centre for Health Sciences, St. James's Hospital, Trinity College Dublin, The University of Dublin, Dublin 8, Ireland.,Institute for Advanced Study (TUM-IAS), Technical University of Munich, Lichtenbergstrasse 2a, Garching 85748, Germany
| | - Lígia C Gomes-da-Silva
- CQC, Coimbra Chemistry Center, University of Coimbra, Rua Larga, Coimbra 3004-535, Portugal
| | - Luis G Arnaut
- CQC, Coimbra Chemistry Center, University of Coimbra, Rua Larga, Coimbra 3004-535, Portugal
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6
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Mondal S, Panja A, Halder D, Bairi P, Nandi AK. Isomerization-Induced Excimer Formation of Pyrene-Based Acylhydrazone Controlled by Light- and Solvent-Sensing Aromatic Analytes. J Phys Chem B 2021; 125:13804-13816. [PMID: 34879652 DOI: 10.1021/acs.jpcb.1c07937] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Pyrene is a fluorescent polycyclic aromatic hydrocarbon, and it would be interesting to determine whether its C═N-based conjugate can be used for sensing of aromatic analytes at its supramolecular aggregated state. For this purpose, we have synthesized (E)-3,4,5-tris(dodecyloxy)-N'-(pyren-1-ylmethylene)benzohydrazide (Py@B) by alkylation, substitution, and the Schiff base reaction methodology. The E-isomer of Py@B (E-Py@B) exhibits a bright fluorescence due to excimer formation in nonaromatic solvents. Upon photoirradiation with λ = 254 nm, it exhibits E-Z isomerization across the C═N bond at a low concentration (10-4 M), resulting in a quenched fluorescence intensity, and interestingly, upon photoirradiation with λ = 365 nm, the Z-isomer of Py@B returns to the E-isomer again, indicating that E-Z isomerization of Py@B is reversible in nature. The thick supramolecular aggregated morphology of E-Py@B changes to a flowery needlelike morphology after photoirradiation with λ = 254 nm. The UV-vis absorption band at 370 nm for 10-4 M Py@B in methyl cyclohexane (MCH) is due to excimer formation for closer proximity of pyrene moieties present in E-Py@B and changes to the absorption peak at 344 nm for its Z-isomer formation. The fluorescence spectroscopy results also support the fact that the optimum concentration of the E-isomer of Py@B is 2 × 10-4 M in MCH for excimer formation. From spectral results, it may be concluded that nonaromatic solvents assist in constructing the excimer, but aromatic solvents resist forming an excimer complex of E-Py@B. The fluorescent emission of E-Py@B in MCH is quickly quenched on addition of different aromatic analytes through both static and dynamic pathways. In the solid state, E-Py@B also senses aromatic vapors efficiently via fluorescence quenching. Absorbance spectra of a model molecule obtained using time-dependent density functional theory (TDDFT) calculations on a DFT-optimized structure indicate complex adduct formation between E-Py@B and aromatic analytes from the well-matched theoretical and experimental UV-vis spectra on addition of different analytes with E-Py@B.
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Affiliation(s)
- Sanjoy Mondal
- Polymer Science Unit, School of Materials Science, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Aditi Panja
- Polymer Science Unit, School of Materials Science, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Debabrata Halder
- School of Chemical Science, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Partha Bairi
- Polymer Science Unit, School of Materials Science, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Arun K Nandi
- Polymer Science Unit, School of Materials Science, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
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