# Patent

## Title
Modular functional peptides for delivery of nanoparticles

## Abstract

A peptide directs nanoparticles (such as quantum dots) to the plasma membrane of mammalian cells. A method of delivery of a nanoparticle to a plasma membrane of a cell includes providing to the cell a nanoparticle attached to a peptide configured to direct the nanoparticle the plasma membrane, and allowing the cell to take up the nanoparticle. The nanoparticle can be a FRET donor to an organic dye.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a Continuation-in-Part of U.S. patent application Ser. No. 12/908,601 filed on Oct. 20, 2010, which claims the benefit of U.S. Provisional Patent Application No. 61/253,921 filed on Oct. 22, 2009, each of which is incorporated herein by reference.
This application is also related to U.S. patent application Ser. No. 12/606,766 filed on Oct. 27, 2009, which is incorporated herein by reference.


BACKGROUND
Quantum dots (QDs) provide many advantageous features that include high quantum yield, broad absorption spectra, large achievable Stokes shifts, narrow symmetric, size tunable emission spectra, and exceptional resistance to photo- and chemical degradation, making them attractive reagents for the long-term visualization of cellular structures and processes. See references 1-4.
The methods employed to date for the intracellular delivery of QDs or other nanoparticles (NPs) can be grouped into three generalized categories based on their physicochemical nature. Passive delivery is a nonspecific process that relies on the inherent physicochemical properties of the QD (surface charge and/or functionalization) to mediate uptake. Facilitated delivery utilizes a delivery agent (e.g., a cationic peptide or a polymer) that is covalently attached to or electrostatically complexed with the QDs to specifically induce internalization. Both these techniques, while noninvasive, typically utilize the endocytic pathway which results in encapsulation of the QDs within intracellular endolysosomal vesicles and thus requires further strategies to liberate the sequestered QDs to the cytosol if that is ultimately desired. Examples methods of facilitated delivery include using additional chemicals such as sucrose or chloroquine or adding polymers such as polyethyleneimine during delivery to disrupt the endosomes by osmotic shock: such methods are generally quite toxic. Lastly, active delivery methods such as electroporation and microinjection deliver QDs directly to the cytosol through physical manipulation of the cell. However, these are highly invasive techniques that can often compromise the integrity of cellular structures and substantially reduce cellular viability (see reference 10). Thus, each of the previously described methods for delivery of nanoparticles (including quantum dots) is deficient in some way.
Described herein are improvements in intracellular delivery of nanoparticles.
BRIEF SUMMARY
In one embodiment, a peptide for delivery of a nanoparticle to the cytosol comprises: (a) a nanoparticle association domain; (b) a spacer domain; (c) an uptake domain; and (d) a vesicle escape domain comprising a non-hydrolyzable lipid moiety, wherein the spacer domain is between the nanoparticle association domain and the uptake and vesicle escape domains, and wherein the peptide, when attached to an extracellular nanoparticle, is effective to induce uptake of the nanoparticle by a cell and delivery of the nanoparticle to the cytosol of the cell.
In a further embodiment, the spacer comprises from between 6 and 15 proline residues, for example 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 proline residues.
In another embodiment, a nanoparticle is delivered to the cytosol of a cell by providing to a cell with a nanoparticle attached to such a peptide.
In an additional embodiment, a method of labeling a plasma membrane of a cell includes providing to the cell an organic fluorescent dye adapted to partition to the plasma membrane; providing to the cell a nanoparticle attached to a peptide configured to direct the nanoparticle to the plasma membrane, wherein the nanoparticle is a FRET donor to the organic fluorescent dye; and photo-exciting the nanoparticle to obtain fluorescence from the organic fluorescent dye in plasma membrane of the cell.
In a yet further embodiment, a method of labeling a mammalian cell includes providing to the cell a first nanoparticle attached to a first peptide configured to direct the first nanoparticle to the plasma membrane; and providing to the cell a second nanoparticle attached to a second peptide comprising (a) a nanoparticle association domain, (b) a spacer domain, (c) an uptake domain, and (d) a vesicle escape domain comprising a non-hydrolyzable lipid moiety, wherein the spacer domain is between the nanoparticle association domain and the uptake and vesicle escape domains, and wherein the second peptide attached to the second nanoparticle is effective to induce uptake of the second nanoparticle by the cell and delivery of the second nanoparticle to the cytosol of the cell.
In yet another embodiment, a method of delivery of a nanoparticle to a plasma membrane of a cell includes providing to the cell a nanoparticle attached to a peptide configured to direct the nanoparticle the plasma membrane, and allowing the cell to take up the nanoparticle. In a still further embodiment, this serves to inhibit endocytosis.
Exemplary nanoparticles include quantum dots.



BRIEF DESCRIPTION OF THE DRAWINGS
FIGS. 1A and 1B show spectral properties and schematic of QD conjugates examined herein. FIG. 1A shows normalized absorbance and emission of 510, 550 nm QDs and AlexaFluor 647 (AF647). FIG. 1B shows schematics of various QD conjugates.
FIGS. 2A and 2B show QD-CPP internalization and colocalization over time. Cells were washed, fixed and stained with DAPI in FIG. 2A or supplied with fresh media and cultured for 4, 24 or 72 h prior to fixation and DAPI-staining in FIG. 2B. In FIG. 2A the DAPI, QD and marker signals are shown individually and merged while in FIG. 2B only the merged images are shown. Arrows indicate areas of colocalization. The scale bar is 10 μm.
FIGS. 3A-3D show the intracellular stability of polyhistidine-QD association. For FIG. 3A 510 nm dihydrolipoic acid (DHLA) QDs were appended with 25 CPP to mediate uptake in HEK 293T/17 cells and  ̃2 Cy3-labeled peptides to monitor the FRET between the QD and the Cy3 dye over time. FIG. 3B shows merged images of DAPI-stained nuclei, QD and Cy3 signals at 1, 4, 24 and 72 h after conjugate delivery, where the scale bar is 10 μm. FIG. 3C shows the calculated Cy3/QD emission ratio is shown plotted as a function of time after initial conjugate delivery. FIG. 3D shows observed fluorescence for transferrin-Cy3 conjugates delivered alone (no QDs) is plotted as a function of time. In FIGS. 3C and 3D the data points were fitted with a dose response logistic curve fit function.
FIGS. 4A-4F show cellular delivery of QDs using various active and facilitated methods. 510 nm DHLA-PEG QDs at a concentration of 400-500 nM were delivered to HEK 293T/17 cells by electroporation in FIG. 4A or nucleofection in FIG. 4B. In FIG. 4C 510 nm DHLA-PEG QDs (800 nM) were delivered using the pinocytic reagent, InfluxTM. 520 nm QDs (75 nM) capped with a 1:1 mixed surface of DHLA:DHLA-PEG were delivered to HEK 293T/17 cells using Lipofectamine-2000TM in FIG. 4D or the branched polymer, polyethyleneimine in FIG. 4E. The images in FIGS. 4D and 4E show merged images of the QD signal and the fluorescence from the endocytic marker, AlexaFuor647-transferrin. In FIGS. 4A through E the cells were imaged after fixation and staining with DAPI. In FIG. 4F 550 nm DHLA-PEG QDs (100 nM) appended with 25 CPP were coincubated with 100 μM pyrenebutyrate in PBS for 30 min at 37° C. prior to washing and imaging of live cells (no DAPI present). The scale bar is 10 μm.
FIGS. 5A-5D show cellular delivery and cytotoxicity of PULSinTM-QD conjugates. 520 nm 1:1 DHLA:DHLA-PEG mixed surface QDs (100 nM final QD concentration) were complexed with PULSinTM polymer and incubated for 1-3 h with COS-1 cells (FIG. 5A) or HEK 293T/17 cells (FIG. 5B). Shown are images in which the DAPI, QD and AlexaFluor 647-transferrin images are merged at 1d, 2d, 3d, 4d and 5d post-QD delivery. Regular arrows denote areas of colocalization between the QDs and endosomes (a yellow color was noted, indicating merged QD and transferrin signals). Open circle-terminated arrows indicate areas where the QD signal is separated from the endosomal marker. The scale bar is 10 μm. Cytotoxicity data demonstrating the effects of the PULSinTM-QD complexes on cellular proliferation are shown for COS-1 (FIG. 5C) and HEK 293T/17 cells (FIG. 5D). Cells were incubated with the complexes for 3 h, washed and subsequently cultured for 72 h prior to viability assay. When the QDs are present, the concentration given is that of the QDs. Each data point represents the mean±SD of triplicate measurements
FIGS. 6A-6D show the cellular delivery and cytotoxicity of Palm-1 peptide (SEQ ID No: 3) conjugates with quantum dots. 550 nm DHLA-PEG QDs were decorated with the Palm-1 peptide, incubated for 1-2 h along with AlexaFluor 647-transferrin, and imaged at 48 h post-delivery within COS-1 in FIG. 6A or HEK 293T/17 cells in FIG. 6B. The inset in the merged images shows a single cell with the cell membrane highlighted for clarity. FIGS. 6C and 6D show corresponding cytotoxicity data for the inhibition of cellular proliferation by QD-Palm-1 complexes in COS-1 and HEK 293T/17 cells, respectively. Cells were incubated with the materials for 1 h, washed, and subsequently cultured for 72 h prior to viability assay. When the QDs are present, the concentration given is that of the QDs. Each data point represents the mean±SD of triplicate measurements.
FIGS. 7A and 7B illustrate the functionalization of NPs with modular multifunctional peptides. FIG. 7A shows a general schematic of an exemplary NP-peptide assembly. The schematic peptide shown consists of multiple functional domains: a NP association domain (1); a spacer domain (2); and multiple domains that impart biological activity (3 and 4). FIG. 7B shows a QD-peptide assembly for intracellular uptake and endosomal escape. The modular peptide consists of a hexa-histidine (H6) domain for assembly to the QD surface, a proline-rich spacer domain (P9GG), a positively charged lysine-rich domain (VKIKK, SEQ ID No: 7) for cellular association and uptake, and a synthetic palmitic acid group ((Pal)Dap) for cell membrane association and insertion and vesicle escape.
FIG. 8 illustrates a model of NP-peptide assemblies.
FIGS. 9A-9C illustrate the cellular uptake and intracellular fate of various QD-peptide assemblies. In FIG. 9A the assembles have Palm-1b, in FIG. 9B Palm-2b, and in FIG. 9C Palm-3b.
FIG. 10 illustrates various moieties employed in the peptides described herein. “Dab” represents diaminobutyric acid.
FIGS. 11A and 11B shows combinatorial QD-peptide cellular labeling and improved membrane fluorescent labeling by sensitization. FIG. 11A shows the sequential labeling of cytosol and plasma membrane of A549 cells with 150 nM 550 nm QDs (75 JB577 peptides/QD, cytosol) and 10 nM 625 nm QDs (150 JB858 peptides/QD, membrane). QD-JB577 assemblies were incubated for 3 hr, removed and cells cultured 72 hr followed by 1 hr incubation with QD-JB858 conjugates prior to fixation. FIG. 11B shows that the photostability of membrane resident QDs and their FRET excitation of Lissamine Rodamine B phosphoethanolamine acceptors circumvents dye photobleaching.
FIG. 12 shows confocal micrographs confirming the predominant localization of QD-JB858 complexes to the plasma membrane and the partial inhibition of endocytosis by the QD-peptide conjugates at various “z” depths.



DETAILED DESCRIPTION
This invention is not limited to the particular methodology, devices, solutions or apparatuses described, as such methods, devices, solutions or apparatuses can, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to limit the scope of the present invention. For instance, although several examples use quantum dots, one of ordinary in the art would understand that similar techniques can be used with other nanoparticles as described below.
All publications mentioned herein are hereby incorporated by reference for the purpose of disclosing and describing the particular materials and methodologies for which the reference was cited.
Use of the singular forms “a,” “an,” and “the” include plural references unless the context clearly dictates otherwise. Thus, for example, reference to “a nanoparticle” includes a plurality of such nanoparticles.
Terms such as “connected,” “attached,” “linked,” and “conjugated” are used interchangeably herein and encompass direct as well as indirect connection, attachment, linkage or conjugation unless the context clearly dictates otherwise.
Where a range of values is recited, it is to be understood that each intervening integer value, and each fraction thereof, between the recited upper and lower limits of that range is also specifically disclosed, along with each sub-range between such values. The upper and lower limits of any range can independently be included in or excluded from the range, and each range where either, neither or both limits are included is also encompassed. Where a value being discussed has inherent limits, for example where a component can be present at a concentration of from 0 to 100%, or where the pH of an aqueous solution can range from 1 to 14, those inherent limits are specifically disclosed. Where a value is explicitly recited, it is to be understood that values which are about the same quantity or amount as the recited value are also within the scope of the invention. Where a combination is disclosed, each subcombination of the elements of that combination is also specifically disclosed and is within the scope of the invention. Where any element of an invention is disclosed as having a plurality of alternatives, examples of that invention in which each alternative is excluded singly or in any combination with the other alternatives are also hereby disclosed; more than one element of an invention can have such exclusions, and all combinations of elements having such exclusions are hereby disclosed.
“Polypeptide” and “protein” are used interchangeably herein and include a molecular chain of amino acids linked through peptide bonds. The terms do not refer to a specific length of the product. Thus, “peptides,” “oligopeptides,” and “proteins” are included within the definition of polypeptide. The terms include polypeptides containing post-translational modifications of the polypeptide, for example, glycosylations, acetylations, phosphorylations, and sulphations. In addition, protein fragments, analogs (including amino acids not encoded by the genetic code, e.g. homocysteine, ornithine, D-amino acids, and creatine), natural or artificial mutants or variants or combinations thereof, fusion proteins, derivatized residues (e.g. alkylation of amine groups, acetylations or esterifications of carboxyl groups) and the like are included within the meaning of polypeptide. The peptides that can be used as described herein include multiple amino acids, which may be natural, synthetic or a mixture thereof. Each peptide may express different side chains, if desired. Other amide oligomers such as beta peptides, peptoids and peptide nucleic acids may also be used.
The term “proline-rich spacer” as used herein refers to a spacer comprising at least about 50% proline residues, optional at least 60%, 70%, 80%, or 90% proline residues, or optionally entirely proline residues. Preferably, the spacer has a length of from six to eighteen residues.
The term “non-hydrolyzable” as used herein refers to a moiety that remains substantially not hydrolyzed by the normal action of intracellular enzymes, so that it remains attached to a peptide. As described in more detail below, it is believed that the property of being non-hydrolyzable contributes to escape from the endosomal system into the cytosol.
The terms “semiconductor nanocrystal,” “SCNC,” “SCNC nanocrystal,” “quantum dot,” and “QD” are used interchangeably herein and refer to an inorganic crystallite of about 1 nm or more and about 1000 nm or less in diameter or any integer or fraction of an integer therebetween, preferably at least about 2 nm and about 50 nm or less in diameter or any integer or fraction of an integer therebetween, more preferably at least about 2 nm and about 20 nm or less in diameter (for example about 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 nm). QDs are characterized by their uniform nanometer size.
A QD is capable of emitting electromagnetic radiation upon excitation (i.e., the QD is luminescent) and includes a “core” of one or more first semiconductor materials, and may be surrounded by a “shell” of a second semiconductor material. A QD core surrounded by a semiconductor shell is referred to as a “core/shell” QD. The surrounding “shell” material will preferably have a bandgap energy that is larger than the bandgap energy of the core material and may be chosen to have an atomic spacing close to that of the “core” substrate.
The core and/or the shell can be a semiconductor material including, but not limited to, those of the groups II-VI (ZnS, ZnSe, ZnTe, US, CdSe, CdTe, HgS, HgSe, HgTe, MgS, MgSe, MgTe, CaS, CaSe, CaTe, SrS, SrSe, SrTe, BaS, BaSe, BaTe, and the like) and III-V (GaN, GaP, GaAs, GaSb, InN, InP, InAs, InSb, and the like) and IV (Ge, Si, and the like) materials, PbSe, and an alloy or a mixture thereof. Preferred shell materials include ZnS.
A QD is optionally surrounded by a “coat” of an organic capping agent. The organic capping agent may be any number of materials, but has an affinity for the QD surface. In general, the capping agent can be an isolated organic molecule, a polymer (or a monomer for a polymerization reaction), an inorganic complex, or an extended crystalline structure. The coat can be used to convey solubility, e.g., the ability to disperse a coated QD homogeneously into a chosen solvent, functionality, binding properties, or the like. In addition, the coat can be used to tailor the optical properties of the QD.
Thus, the quantum dots herein include a coated core, as well as a core/shell QD.
The term “nanoparticle” as used herein includes the above-mentioned QDs in addition to other nano-scale and smaller particles such as carbon nanotubes, proteins, polymers, dendrimers, viruses, and drugs. A nanoparticle has a size of less than about 1 micron, optionally less than about 900, 800, 700, 600, 500, 400, 300, 100, 80, 60, 50, 40, 30, 20, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 nanometers. A nanoparticle may have various shapes such as a rod, a tube, a sphere, and the like. Nanoparticles may be made from various materials including metals, carbon (such as carbon nanotubes), polymers, and combinations thereof. A nanoparticle for cytosolic delivery by a peptide may be referred to as a cargo or payload.
The QDs as well as other nanoparticles, may be biofunctionalized for use in, for example, in vivo tissue and cellular labeling, development of biological labels based on quantum dot probes and biosensor development. Other uses of the biofunctionalized materials may include protein ordering for molecular electronics where quantum dots could serve as fluorophores and electronic components, energy harvesting, quantum dot based bar coding, and drug discovery assays where the fluorescence properties of the quantum dots may be combined with bioactive peptides.
The functionalization may be used to impart a variety of properties to quantum dots and/or nanoparticles including, but not limited to, the ability to homogeneously disperse the quantum dots and/or nanoparticles in buffer solutions and a variety of polar solvents at various pH values; biocompatibility; biotargeting by allowing the use of peptide-driven binding to specific cell receptors such as the TAT sequence; providing specific points of modification directly on the quantum dot substrate by using, for example, amine groups for reacting with N-hydroxysuccinimide esters; providing bio-recognized sequences such as the AviTag sequence which is specifically biotinylated as an example; providing protease-recognized cleavage sites; providing polyhistidines for metal affinity coordination; and providing functional groups for further targeted modification, including, for example, amino groups, carboxyl groups, azide groups, alkyne groups, hydrazine groups, aldehyde groups, aminooxy groups, ketone groups, maleimide groups or thiol groups for dye/quencher or other chemical modification steps.
Materials. Sucrose, chloroquine, and polyethyleneimine (PEI, 25 kDa Mw, branched polymer) were purchased from Sigma (St. Louis, Mo.). InfluxTM reagent, Lipofectamine-2000TM and the subcellular organelle markers AlexaFluor 647-transferrin (λabs 650 nm/λem 668 nm), BODIPY TR-ceramide-BSA (λabs 589 nm/λem 616 nm), LysoTracker Red DND-99 (λabs 577 nm/λem 590 nm) and the nuclear stain DAPI (λabs 350 nm/λem 450 nm) were obtained from Invitrogen (Carlsbad, Calif.). PULSinTM was purchased from Polyplus-transfection (New York, N.Y.). Other materials were obtained as described.
Quantum Dots. CdSe—ZnS core-shell QDs with emission maxima centered at 510, 520, or 550 nm were synthesized and made hydrophilic by exchanging the native trioctylphosphine/trioctylphosphine oxide (TOP/TOPO) capping shell with either DHLA (dihydrolipoic acid) or polyethylene glycol (PEG) appended DHLA ligands as described previously (see references 17 and 18). These are subsequently referred to herein as DHLA or DHLA-PEG ligands. In general, PEGylated-QDs are preferred as they provide superior intracellular solubility and pH stability; however, some of the delivery reagents utilized required QDs with charged surfaces to mediate electrostatic interactions. 510 nm QDs capped with either DHLA or DHLA-PEG ligands were used for CPP-mediated delivery. The 520 nm QDs delivered by PULSinTM, PEI or Lipofectamine-2000TM were capped with a 1:1 ratiometric mix of DHLA and DHLA-PEG ligands. 550 nm QDs used for electroporation, nucleofection, InfluxTM- and peptide-mediated delivery were capped with DHLA-PEG.
FIG. 1A shows normalized absorbance and emission of 510, 550 nm QDs and AlexaFluor 647 (AF647). FIG. 1B is a schematic of QD conjugates for facilitated QD delivery. CdSe—ZnS core-shell QDs capped with either charged DHLA or neutral DHLA-PEG ligands are noncovalently associated with linear cationic polymers, cationic liposomes or histidine-tagged peptides to mediate QD endocytosis. The sequences of the CPP, NLS, and Palm-1 peptides used herein are also shown. In FIG. 1, “Aib” refers to alpha-amino isobutyric acid and “Pal” refers to a nonhydrolyzable palmitate group that is covalently attached to a diaminopropionic acid functionality synthesized into the peptide backbone.
Peptides. The cell-penetrating peptide (CPP) having the sequence R9GGLA(Aib)SGWKH6 (SEQ ID No: 1) was used. “Aib” represents the artificial residue alpha-amino isobutyric acid. The polyarginine tract (R9) mediates cellular uptake and is separated from a polyhistidine tract (H6) for assembly to the QD surface by a linker domain (GGLA(Aib)SGWK). The nuclear localization signal (NLS) containing peptide was synthesized with the sequence H6WGLA(Aib)SGPKKKRKV(SEQ ID No: 2). The palmitoylated peptide (Palm-1) sequence was WG(Pal)VKIKKP9GGH6 (SEQ ID No: 3) where “Pal” corresponds to diaminopropionic acid, which is a nonhydrolyzable palmitate group that is covalently attached to a diaminopropionic acid functionality, and in this example synthesized into the peptide backbone. The initial tryptophan residue in Palm-1 provides an aromatic ring structure for monitoring by absorption spectroscopy, and it not believed to be crucial to the function of the peptide. A nonspecific peptide with the sequence H6SLGAAAGSGC (providing a general structure of H6-spacer-cysteine) (SEQ ID No: 8) was labeled with Cy3-maleimide (λabs 550 nm/λem 570 nm, GE Healthcare, Piscataway N.J.) on the terminal cysteine residue and used for FRET studies. The peptides were synthesized using Boc-solid phase peptide synthesis, purified by HPLC, and characterized by electrospray ionization mass spectrometry (see references 13 and 19). Preparation of the nonhydrolyzable palmitate group that is covalently attached to a diaminopropionic acid functionality synthesized into the peptide backbone can be accomplished by one of ordinary skill in the art, as described in reference 48.
Cell Culture. Human embryonic kidney (HEK 293T/17) and African green monkey kidney (COS-1) cell lines (ATCC, Manassas, Va.) were cultured in complete growth medium (Dulbecco's Modified Eagle's Medium (DMEM; purchased from ATCC)) supplemented with 1% (v/v) antibiotic/antimycotic and 10% (v/v) heat inactivated fetal bovine serum (ATCC). Cells were cultured in T-25 flasks and incubated at 37° C. under 5% CO2 atmosphere and a subculture was performed every 3-4 days (see reference 13).
Cellular Delivery of Quantum Dots. The QD delivery experiments were performed on adherent cells seeded into the wells of Lab-Tek 8-well chambered #1 borosilicate coverglass (Nalge Nunc, Rochester, N.Y.) coated with 2 μg/mL fibronectin. For electroporation and nucleofection, adherent cells were harvested by trypsinization prior to performing QD delivery to cells in suspension. Cells were then seeded to chambered coverglass wells and imaged after cell attachment. The endosomal marker AlexaFluor647-transferrin was included as indicated in the text. For imaging, cells were washed with phosphate buffered saline (PBS, 137 mM NaCl, 10 mM phosphate, 3 mM KCl, pH 7.4), fixed with 3.7% paraformaldehyde in PBS and nuclei were stained with DAPI (Sigma) unless otherwise indicated.
COMPARATIVE EXAMPLE
Electroporation and nucleofection of QDs
For electroporation, cells were harvested by trypsinization and recovered for 1 hour in complete growth medium, pelleted, and resuspended in PBS. 510 nm DHLA-PEG QDs (0.5 μM final concentration) were mixed with 1×104 cells to a final volume of 100 μL in PBS in a 0.2 mm electroporation cuvette. The cuvette was subjected to 100 V for a 20 ms pulse using a GenePulser XCell electroporator (Bio-Rad, Hercules, Calif.). Cells were resuspended in complete growth medium, seeded into fibronectin-coated 8-well chambered coverglass, fixed and imaged after 24 hrs. For nucleofection delivery, 1×106 cells were harvested and resuspended in 100 μL of NUCLEOFECTOR reagent (Amaxa, Gaithersburg, Md.). 510 nm DHLA-PEG QDs were included at a final concentration of 0.4 μM. The cell/QD/reagent mixture was pulsed in the NUCLEOFECTOR using a preset protocol adapted for each specific cell line (20, 21). Cells were cultured and imaged as described for electroporation. As a positive control, a plasmid encoding monomeric red fluorescent protein (RFP) was delivered using the same conditions as those for QD delivery and positive expression of the RFP confirmed.
COMPARATIVE EXAMPLE
INFLUX-mediated delivery
The INFLUX cell-loading reagent mediates the intracellular release of materials internalized via pinocytic vesicles by delivering the materials to cells in a hypertonic medium followed by the transfer of the cells to a hypotonic medium to induce vesicle disruption (see reference 22). 510 nm DHLA-PEG QDs were diluted to a final concentration of 300-800 nM in the supplied hypertonic delivery media according to manufacturer's instructions and incubated on the cells for 30 min at 37° C. The hypertonic medium was exchanged for hypotonic medium (serum-free culture medium diluted by 40% with deionized water) and incubated on the cells for 3 min. The cells were then recovered in complete growth medium for 30 min and cultured for various lengths of time prior to washing and fixation for imaging.
COMPARATIVE EXAMPLE
Lipofectamine 2000TM-mediated delivery
520 nm QDs with a 1:1 mixed surface of DHLA:DHLA-PEG were incubated with LIPOFECTAMINE 2000 for 20 min in serum free medium at a ratio of 1 μL LIPOFECTAMINE 2000 per 1.5 pmol QD. The complexes, at a final QD concentration of 75 nM, were incubated with the cells for 4 hours, removed and replaced with complete growth medium. The cells were then cultured for 24-36 h prior to washing and fixation.
COMPARATIVE EXAMPLE
Polyethyleneimine-mediated delivery
PEI was incubated with 520 nm mixed surface DHLA:DHLA-PEG QDs in serum free medium at a ratio of 10 μg PEI per 1 pmol QD for 15 min. This ratio was previously determined in delivery experiments to yield maximal QD uptake. The complexes were then diluted into serum free media to a final QD concentration of 75-100 nM, incubated with cells for 2 h and removed. Cells were then cultured in complete media for 24-36 h, washed and fixed.
COMPARATIVE EXAMPLE
PULSinTM-mediated delivery
A stock solution of 520 nm DHLA:DHLA-PEG QDs (1 μM in 0.1 M borate buffer, pH 8.9) was diluted to 0.5 μM in HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid, pH 8.2). PULSinTM delivery reagent was added (1 μL per 20 pmol QD) and complex formation occurred for 20 min at 25° C. The complexes were diluted into serum free medium to a final QD concentration of 100 nM and incubated on cells for 1-3 h after which complexes were removed and replaced with complete growth medium. Cells were subsequently cultured for up to 5 days to monitor intracellular QD distribution.
INVENTIVE EXAMPLE
Peptide-mediated delivery
QD-CPP, QD-NLS and QD-Palm-1 bioconjugates were formed by diluting a stock solution of preformed peptide-QD complexes (1 μM QD assembled with 25 CPP, 30 NLS or 75 Palm-1 peptides per QD in 0.1 M borate buffer, pH 8.9) into complete growth medium to a final QD concentration of 50-100 nM. These peptide:QD ratios were determined experimentally for each peptide to be that ratio that yielded a high degree of cell uptake. The self-assembled bioconjugates were then incubated with cells as described elsewhere herein. For monitoring the intracellular fate of QD-CPP assemblies, AlexaFluor 647-transferrin, LysoTracker Red DND-99 and BODIPY TR-ceramide-BSA subcellular markers were included at the manufacturer's recommended concentrations. In some experiments, QD-CPP complexes were also incubated with cells in the presence of pyrenebutyrate (100 μM), sucrose (500 mM) or chloroquine (500 μM) to test either membrane translocation or to induce endosomal disruption and release of the internalized QDs to the cytosol. The general scheme for the assembly of QDs with cationic polymers, cationic amphiphiles or histidine-tagged peptides is shown in FIG. 1B.
Microscopy and Image Analysis. The intracellular distribution of QDs was analyzed by differential interference contrast (DIC) and epifluorescence microscopy using an Olympus IX-71 total internal reflection fluorescence microscope equipped with a 60× oil immersion lens. Samples were excited using a Xe lamp and images were collected using standard filter sets for DAPI, FITC (for QDs), TRITC (for Cy3 and Texas Red) and Cy5 (for AF647-transferrin). Merged images were generated using Adobe PhotoShop. Förster resonance energy transfer (FRET) measurements for determining the intracellular stability of QD-peptide association over time were performed by imaging 510 nm donor QD-CPP conjugates decorated with approximately 2 Cy3-labeled acceptor peptides per QD. The Förster radius (RO) for this donor-acceptor pair is approximately 47 Å. Side-by-side split fluorescence images were collected and quantitated using a DualView system (Optical Insights, Tucson, Ariz.) equipped with a 565 nm dichroic filter. The QDs and Cy3 were excited at 488 nm and their respective emissions were separated with the dichroic filter and deconvoluted. Signal intensities were measured at various time points over a three day period to calculate the Cy3/QD emission ratio (defined as [Cy3em/Cy3em+QDem]). This ratio corrects for any direct excitation of the Cy3 dye which may occur intracellularly (see reference 23). To correct for any leakage of the QD signal into the Cy3 channel, this ratio was also calculated for cells exposed to QD-CPP alone (no Cy3-labeled peptide) and subtracted from the Cy3/QD emission ratio to give the corrected ratio ([Cy3em/Cy3em+QDem]−QDem). A decrease in this ratio over time indicates either the dissociation of the Cy3-labeled peptide from the QD surface or degradation of the Cy3 fluorophore.
Cytotoxicity Assays. Cellular toxicity was assessed using the CellTiter 96 Cell Proliferation Assay (Promega, Madison Wis.) according to the manufacturer's instructions. This assay is based upon the conversion of a tetrazolium substrate to a formazan product by viable cells at the assay end point (see reference 24). Cells (1×104 cells/well) were cultured in 96-well microtiter plates in complete growth medium in the presence of increasing concentrations of QDs, free peptide or polymer, or QDs in complex with peptide or polymer. In each case, the materials were incubated with the cells for the time required for efficient QD uptake. The materials were subsequently replaced with complete growth medium and the cells were cultured for 72 hours.
Long-Term Intracellular Fate of QD-CPP Conjugates. The intracellular fate of the delivered QD-CPP complexes was followed at various time points in cell culture. HEK 293T/17 cells were incubated with DHLA-capped 510 nm QDs complexed with the CPP while counter-labeling either the endosomes (AlexaFluor 647-transferrin), lysosomes (LysoTracker Red DND-99), or the Golgi complex (BODIPY TR-ceramide-BSA). As shown in FIG. 2A, one hour post-delivery the QDs adopted a punctate, vesicular appearance with QD fluorescence in green overlapping the endosome and lysosome markers, while no overlapping QD signal was observed with the Golgi complex markers. This confirms that the QD-CPP complexes were located within the endolysomal system in agreement with previous results observed by the present inventors. Similar data was collected for cells exposed to QD-CPP complexes and the same markers at 4, 24 and 72 hours after delivery, as seen in FIG. 2B. After 3 days, the QD-CPP complexes still colocalized with the endolysosomal markers although it is noted that at the later time points, the QD distribution appears to be primarily perinuclear probably reflecting that these are later or more ‘mature’ endosomes. When the cells were cultured beyond 3 days, similar results were obtained. These results demonstrate that while the CPP mediates the efficient uptake of the QDs, it does not facilitate the release of the QDs to the cytosol over time. Similar data were obtained with DHLA-PEG capped QDs showing that the nature of the capping ligand, i.e., charged vs. neutral, had no effect on intracellular QD fate over time.
Intracellular Stability of QD-CPP Assemblies. For the successful implementation of QD-peptide and QD-protein conjugates in intracellular applications, it is desirable for them to exhibit long-term stability during and after uptake by the cell. For example, labeling specific subcellular organelles such as mitochondria or the nucleus with QD-peptide conjugates requires the stable association of the targeting peptide with the QD surface throughout the uptake and targeting process. Of particular interest in the case of the self-assembled QD-CPP described herein (generated by polyhistidine-zinc interactions) is the conjugate stability within the endolysosomal vesicles during the three day culture period. Given that the normal pKa of histidine residues is  ̃6.5 and that the pH of the vesicles can drop to as low as  ̃5.0 to 5.5 during the formation of late endosomes and lysosomes (see reference 28), protonation of the imidazole side chains of the polyhistidine tract could result in dissociation of the CPP from the QD surface. Alternatively, several proteases including cathepsins and several aspartate proteases are endogenously expressed in the endolysosomal system and these may also proteolyze the peptides (see reference 29). Thus, confirmation of the long-term intracellular stability of QD-CPP assemblies was warranted.
To investigate this issue, QD-peptide conjugates were prepared that engaged in FRET and their intracellular interactions were monitored over time. 510 nm DHLA-capped QDs were first assembled with an average of  ̃2 Cy3-labeled His6-peptides and then the CPP was added to form the full conjugate (schematic in FIG. 3A). Due to the peptide's small size and proximity of the Cy3 acceptor to the nanocrystal surface, this valence results in a ca. 40% quenching of the QD PL by FRET. The resulting conjugates were delivered to HEK 293T/17 cells and the cells were cultured for three days. QD-donor and Cy3-acceptor FRET interactions over time within the cells were measured by exciting the QD and collecting side-by-side split fluorescence images using the DualView system and deconvoluting the subsequent intensity data. The excellent spectral separation (−60 nm) between the QDs and Cy3 emission maxima facilitated this collection. FIG. 3B shows representative images in which the QD and Cy3 signals are merged at various time points during the culture period. A distinct one-to-one overlap in the punctate signals of both QD and dye was observed demonstrating colocalization of the QDs and Cy3-labeled peptides within endocytic vesicles throughout the culture period. Analyses of the signals showed the pair was actively engaged in FRET (close proximity) and not just present within the same endosomal compartments. When the Cy3/QD emission ratio (normalized and corrected for direct Cy3-acceptor excitation) was calculated a gradual decrease was observed over time, culminating in a 36% decrease over three days (FIG. 3C). A decrease in this ratio would result from either Cy3-peptide dissociation from the QD surface (loss of His6 interactions or proteolysis) or by chemical degradation of the dye. Control experiments revealed that the latter scenario was the case. When Cy3 was delivered to the endosomes as a Cy3-labeled transferrin conjugate (no QDs present), the fluorescence output of the dye decreased approximately 34% over the same time period, in excellent agreement with the decrease observed in the above QD-CPP-Cy3-labeled peptide constructs (FIG. 3D). Control experiments performed with QD donors alone showed no change in the relative QD PL. These results suggest that the His6-bearing peptides remain stably conjugated to the QD Zn-surface, even within the acidic environment of the endocytic vesicles over time. This strong affinity, even at lower pH, appears to be as a result of cooperative interactions resulting from the multiple histidine residues present on each peptide interacting with the QD surface (see reference 14). Previously, the stability of the QD-peptide conjugates within endosomes had only been verified for one hour after uptake using two-photon excitation FRET microscopy (see reference 23). As best can be determined, presented herein represent the first instance in which the His-zinc interaction has been shown to be stable intracellularly over three days. This finding has important implications for the use of this QD conjugate assembly strategy in long-term intracellular labeling and imaging applications.
Cytosolic Delivery of QDs. Having confirmed the long-term sequestration of QDs within endosomes following CPP-facilitated uptake, a means by which to deliver QDs to the cytosol was sought. Thus began an exhaustive investigation of methodologies to either: (1) deliver the QDs directly to the cytosol via direct physical manipulation of the cell (active delivery), or (2) decorate the QDs with peptides or polymers that could mediate both endocytic uptake and the subsequent release of the QDs from within endocytic vesicles (facilitated delivery followed by endosomal escape). The individual approaches are summarized in Table 1 and the results of the various methods tested are discussed in the following sections.







TABLE 1







Summary of QD Delivery Strategies Examined Herein









Delivery Method/Agent
Mechanism of Uptake
Quantum Dot Fate and Toxicity





Active Delivery




Electroporation
Membrane pore formation
Poor uptake, QDs aggregated, toxica


Nucleofection
Membrane pore formation
Poor uptake, QDs aggregated, toxica


Facilitated Delivery


Pinocytosis


Influx TM
Pinocytosis
Endosomal, QDs punctate, moderately toxica


Polymer-mediated


Lipofectamine2000 TM
Endocytosis
Endosomal, QDs punctate, toxicb


Polyethyleneimine
Endocytosis
Endosomal, QDs punctate, toxica


PULSin TM
Endocytosis
Cytosolic, QDs dispersed, toxicb


Peptide-mediated


CPP peptide
Endocytosis
Endosomal, QDs punctate, minimally toxicb,c


NLS peptide
Endocytosis
Endosomal, QDs punctate, minimally toxicb


Palmitoylated peptide (Palm-1)
Endocytosis
Cytosolic, QDs dispersed, minimally toxicb


Augmented peptide-mediated


CPP peptide + sucrose
Endocytosis
Cytosolic, QDs punctate, toxica


CPP peptide + chloroquine
Endocytosis
Cytosolic, QDs punctate, toxica


CPP peptide + pyrenebutyrate
Membrane translocation
Mixed membranous and endosomal, toxica





aGeneral toxicity assessment made by visual inspection of cellular morphology and rate of proliferation compared to control cells during delivery experiments.


bToxicity measured by cell proliferation assay as described elsewhere herein.


cToxicity reported in reference 13.






Active delivery. Electroporation and nucleofection are primarily used for the cellular delivery of nucleic acids and employ an externally applied electric field to increase the excitability and permeability of the membrane's phospholipid bilayer allowing charged extracellular materials to directly enter the cytosol during an electric pulse (see reference 30). Nucleofection further incorporates a proprietary transfection reagent to mediate the subsequent localization of internalized materials to the nucleus (see references 20 and 21). As shown in FIGS. 4A and 4B, when 510 nm DHLA-PEG capped QDs were delivered to HEK 293T/17 cells using electroporation or nucleofection, they adopted a punctate morphology indicative of QD aggregation within the cytosol. This delivery bypassed the endosomes as confirmed by transferrin counterstaining. In contrast, when QDs capped with these same ligands were microinjected into cells, they adopted a highly disperse staining across the entire cytosol for long periods of time (see reference 18). This indicates that the electric field and/or process itself adversely affects subsequent intracellular QD solubility. Further, no evidence of nuclear accumulation or localization within the perinuclear spaces was observed even after extended culture following delivery for both methods. Also noted was a high degree of cell death and estimate that only 50% of cells remained viable following delivery attempts.
Electroporation-based QD delivery has yielded similar results in previous reports (see references 31 and 32). Cumulatively, the QD aggregation and subsequent high cellular morbidity suggest that electroporation and nucleofection are not effective means of delivery despite their ability to deliver QDs directly to the cytosol.
Facilitated delivery. Facilitated delivery of QDs involves the use of exogenous agents that are added to the extracellular medium or complexed with the QDs to exploit the cell's innate processes of pinocytosis or endocytosis. Pinocytosis, or fluid-phase uptake, is a nonspecific form of endocytosis in which minute amounts of extracellular fluids and materials are internalized within small vesicles. Endocytosis, in contrast, is a specific process as the uptake of extracellular materials is mediated by their interaction with cognate cell surface receptors that become spatially concentrated within the forming endocytic transport vesicles (see references 33 and 34). The exogenous agents for facilitated delivery can take the form of chemicals or drugs that are co-incubated with the QDs during the delivery process or alternatively they can be polymers or peptides that are either covalently attached or non-covalently associated (electrostatically) with the QD surface.
Pinocytosis-mediated delivery. To exploit this process, the commercial pinocytosis reagent known as InfluxTM was used. This reagent is co-incubated with the QDs and cells in a hypertonic medium which promotes the uptake of extracellular materials within pinocytic vesicles. The cells are then briefly incubated in a hypotonic medium to swell and disrupt the vesicles, releasing the internalized materials into the cytosol; in essence this is a modified intracellular osmotic shock protocol. A solution of 510 nm DHLA-PEG QDs was prepared in the hypertonic delivery media (including the InfluxTM reagent) and incubated with HEK 293T/17 cells for the recommended period of time for uptake (−30 min). As shown in FIG. 4C, only a modest degree of uptake occurred even when the QD concentration was substantially increased to 800 nM. Further, the intracellular QD morphology remained punctate even after several days, indicating their persistent localization within pinocytic vesicles. Jaiswal et al. also reported the long-term intracellular sequestration of pinocytically delivered QDs (see reference 6). In that study, 400 to 600 nM negatively charged DHLA-capped CdSe/ZnS QDs were incubated with HeLa cells for 2-3 hrs without any exogenous pinocytosis reagent present: using a plasmid-expressed fluorescent protein endosomal marker for counter-labeling, the QDs remained trapped within vesicles for up to nine days in culture.
Polymer-mediated delivery. A number of commercial cationic polymers have been developed for gene delivery and transfection applications. These reagents self-assemble electrostatically to negatively-charged species (e.g., nucleic acids) while simultaneously mediating interactions of the resulting complex with the plasma membrane to induce endocytosis. Once compartmentalized within intracellular vesicles, it is believed that the cationic polymers can facilitate endosomal disruption via osmotic lysis (the ‘proton sponge’ effect), releasing the vesicle contents to the cytosol (see references 35 and 36). It was hypothesized that QDs bearing a net negative surface charge could complex with such polymers and thus utilized 520 nm QDs capped with a 1:1 mixed surface of DHLA:DHLA-PEG ligands. This cap exchange strategy provides both a charged moiety (DHLA) along with the extended pH stability provided by the PEG ligands (see references 18 and 37). Initial experiments utilized the well-known cationic liposomal transfection reagent Lipofectamine-2000TM. QD-Lipofectamine complexes were formed as described in the Methods section and incubated with HEK 293T/17 cells for 4 hours. As shown in FIG. 4D, it was found that the QDs were completely colocalized with the co-delivered transferrin endosomal marker. Extended monitoring of the cells for several days after delivery did not reveal any changes in this morphology. Interestingly, Derfus et al., demonstrated that commercial PEG-coated QDs delivered to HeLa cells using this reagent appeared to be largely present within the cytosol (see reference 31). However, their interpretation was complicated by the fact that the QDs also formed aggregates of several hundred nanometers in diameter within the cytosol and were not well dispersed. It was not apparent if the liposomal polymer was responsible for inducing the intracellular QD aggregation in this case.
Polyethyleneimine (PEI) is a cationic polymer that is sometimes used as a reagent for transfecting nucleic acids into mammalian cells and has recently been used for cellular uptake of QDs. Duan et al. synthesized dendritic PEG-grafted PEI ligand molecules and used them to functionalize CdSe-CdS-ZnS QDs (see reference 38). They demonstrated that this specific combination of surface chemistries could mediate both endocytosis and subsequent cytosolic delivery of these QDs to HeLa cells. They found that the efficiency of QD endosomal escape was enhanced by increasing the PEI content in the PEG-PEI ligand. However, the increased PEI content was also coupled with significant cytotoxicity as cellular viability dropped to only 40% with this more efficient endosomal escape capping ligand. The combination of PEG and PEI was tested for cellular uptake by complexing 520 nm QDs capped with 1:1 DHLA:DHLA-PEG ligands with increasing ratios of PEI ( ̃0.5-10 μg PEI per 1 pmol QD) and then exposing them to HEK 293T/17 cells for 1-3 h. As demonstrated by the representative micrograph in FIG. 4E, complete colocalization of the QDs with the transferrin marker within endosomes was noted at each concentration tested even after several days. Similarly, a considerable degree of cytotoxicity was noted that tracked the increasing concentrations of PEI used to form the QD-PEI complexes.
Jablonski et al. reported the ability to rapidly deliver polyarginine peptide-bearing QDs directly to the cytosol using an excess of the hydrophobic counterion, pyrenebutyrate (see reference 39). Using streptavidin conjugated QDs assembled with biotinylated polyarginine peptides in the presence of >1,000 fold molar excess pyrenebutyrate (4 μM) per QD (4 nM), delivery of the QDs (−5 min) to BS-C-1 monkey kidney cells appeared to produce QDs dispersed within the cytosol. Those authors surmised that the anionic pyrenebutyrate bound to the cationic polyarginine to form a hydrophobic polymeric complex that could pass directly through the plasma membrane. However, when HEK 293T/17 cells were incubated with 550 nm DHLA-PEG QD-CPP assemblies (100 nM in QDs) in the presence of a far higher concentration of pyrenebutyrate (100 μM), the QDs initially remained entirely associated with the plasma membrane even after a  ̃6× longer incubation of 30 min. After 3 hours, the QDs took on a punctate appearance, indicative of endosomal uptake and no cytosolic dispersal was observed (see FIG. 4F). Thus, the results reported Jablonski et al. (reference 39) cells were not reproduced by the present inventors. It remains unclear what role pyrenebutyrate plays in the uptake process, but these results suggest it is likely that differences in the supplied material (i.e., presence or absence of a covalently attached 60 kDa streptavidin protein along with different surface ligands) may actually play profound part in determining the nature of the interaction of nanomaterials with the plasma membrane.
Another molecule was tested in this class of materials, namely the commercially available PULSinTM, a proprietary amphiphilic polymer originally designed as a cytosolic delivery agent for proteins. It was found that PULSinTM could mediate efficient uptake of QDs and a modest subsequent endosomal release to the cytosol over a much longer time period of 3-4 days. As shown in FIGS. 5A and 5B, PULSinTM complexation resulted in initial endosomal uptake of 520 nm DHLA:DHLA-PEG QDs to both COS-1 and HEK 293T/17 cells after 1 d incubation. Following uptake, the cells were allowed to grow continuously for 5 days and samples were imaged throughout. Approximately three to four days after the initial delivery, the QD signal began to separate from that of the endosomal marker, indicating endosomal escape in both cell lines. By day 5, the QDs had assumed a slightly more dispersed intracellular appearance that was completely distinct from that of the endosomes which had a more perinuclear localization. Longer incubation times did not improve on these results. The results were rather modest in terms of overall cellular labeling efficiency, but it was clear that combining PULSinTM with mixed surface QDs could facilitate some endosomal escape. However, in addition to requiring several days to mediate endosomal escape of the QDs, PULSinTM also elicited a considerable degree of cytotoxicity in both cell lines (FIGS. 5C and D). It was found that the toxicity was attributable to the PULSinTM polymer alone. When cells were incubated with 100 nM mixed surface QDs alone, the viability of both COS-1 and HEK 293T/17 cells was approximately 80% while in the presence of either PULSinTM alone or QD-PULSinTM complexes, cell viability was reduced to less than 60%.
Peptide-mediated delivery. The use of peptides still remains the most popular means of facilitated QD delivery (see reference 10). In this case, the QDs are decorated with a peptide that induces endocytosis by mediating interaction with specific cell surface receptors or more generally through electrostatic interactions with the cell surface (see reference 40). For electrostatic interactions, peptides derived from the HIV-1 Tat protein have been used.
Sucrose and chloroquine are two well known endoosmolytic agents that have been shown to facilitate the release of endocytosed nucleic acids to the cytosol (see reference 43). Sucrose accumulates within endocytic vesicles and promotes vesicle swelling and destabilization (see reference 44). Chloroquine is an endolysosomal-tropic amine whose buffering capacity prevents endosomal acidification and slows down the rate of endocytosis, allowing more time for endosomal escape (see reference 45). In this instance, 510 nm DHLA-PEG QDs were self-assembled with CPP and incubated with HEK 293T/17 cells for 2-3 h in the presence of increasing concentrations of either agent up to a maximum of 500 mM sucrose or 500 μM chloroquine. Both compounds efficiently disrupted the endosomes at the highest concentrations as evidenced by the diffuse appearance of labeled transferrin in the cytosol. The QDs, however, remained punctate in appearance and were not well-dispersed despite the presence of the far more soluble PEGylated QD ligands (see reference 18). Also noted were significant cellular toxicity and morbidity, especially as the concentrations of each agent were increased.
Nuclear localization signal (NLS) peptides bearing a sequence derived from the simian virus 40 T-antigen have been reported to mediate QD uptake and subsequent nuclear delivery (see reference 46). Rozenzhak and co-workers utilized commercial Streptavidin functionalized QDs assembled with biotinylated NLS peptides and incubated with a secondary non-covalent peptide carrier (Pep-1) to create complexes for delivery to HeLa cells. They found a high degree of subsequent QD colocalization with the nuclear stain DAPI and little residual cytosolic or endosomal staining. Thus, in a conjugation approach similar to that used for the CPP, as described herein a histidine-tagged NLS peptide was assembled onto the surface of QDs for delivery experiments. When incubated with HEK 293T/17 and COS-1 cells, however, the QDs were found to be completely internalized within endosomes, with no release to the cytosol or nuclear translocation observed even after culturing the cells for two days after QD uptake.
Furthermore, the use of a multifunctional peptide including a portion originally intended for the delivery of protein palmitoyl transferase 1 (PPT1) inhibitors across the blood-brain barrier was tested (see references 47 and 48). This peptide, WG(Pal)VKIKKP9GGH6 (referred to as Palm-1 and having SEQ. ID. No. 3), encompasses several different modules or domains each of which provides one or more overlapping functionalities. The peptide includes a His6 tag to mediate self-assembly to the QD surface. The di-glycine residues were placed into the sequence to act as a flexible spacer between the His6 domain and the rest of the peptide once it coordinates to the QD surface. Adjacent to the polyhistidine domain is a repeat of nine consecutive proline residues. Studies have shown that poly(L-proline) sequences adopt a left-handed helical structure of 3.1 residues per turn in aqueous solvent, referred to as the polyproline II or PPII motif (see reference 49). Nine prolines are predicted to assume a PPII structure with a length of  ̃28-30 Å, thus this sequence was utilized as an extended spacer to allow the rest of the peptide sequence to extend out beyond the PEGylated shell surrounding the QD (assumed length of  ̃30-35 Å in an energy minimized state). PPII motifs also possess amphiphilic properties. Peptides containing proline repeats of various lengths have been used in relation to the cellular uptake of attached fluorophores (see references 50-52), DNA-lipid complexes (see reference 53) and gold nanoparticles (see reference 54). The VKIKK motif (SEQ ID No: 7) is derived from a sequence found at the C-terminus of the K-Ras protein (V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog) (see reference 55). This Ras family homologue is a membrane-tethered GTPase that functions in many overlapping signal transduction pathways. The KKIK portion is thought to mediate electrostatic interactions with lipid head groups on the cytosolic leaflet of membranes displaying negatively charged phosphatidylserines. Similar to the positive charges resident within the Tat and NLS sequences, the three positively charged lysines may also facilitate the peptide's initial electrostatic interaction with negative charges on the cellular membrane. In the K-Ras protein, the VKIKK (SEQ ID No: 7) sequence is preceded by a cysteine residue that is normally post-translationally modified with a palmitoyl group which can also be depalmitoylated by PPT1 in the lyososome. Due to its highly hydrophobic nature, the palmitoyl group inserts into the membrane allowing the full K-Ras (or similar post-translationally modified proteins), to remain membrane-bound (see references 56-58). Rather than attaching the palmitoyl group in the peptide to a cysteine residue which would leave it vulnerable to PPT1 cleavage in the endolysomal system, it was decided to covalently attach it to a synthetic diaminopropionic acid (Dap) residue, thus rendering it nonhydrolyzable. It was conceived that by using a peptide incorporating multiple overlapping functional sequences shown to facilitate both endocytosis and intracellular membrane interactions, cytosolic delivery of the QDs could be achieved.
COS-1 and HEK 293T/17 cells were incubated for 1-2 h with 550 nm DHLA PEG QD-Palm-1 complexes in the presence of AlexaFluor 647-transferrin. Imaging the cells at 1 hr post delivery revealed that the QD complexes were internalized with a punctate appearance that was completely colocalized with the endosomal marker confirming endocytic uptake. As shown in FIGS. 6A and B, approximately 48 h post-delivery the QD signal separated from that of the endosomal marker in both cell lines and the QDs became well-dispersed, occupying the entire cell volume. Greater than 90% of cells observed were positive for initial QD uptake and of those, 77% showed a high degree of endosomal escape. Although a small degree of endosomal escape was observed at 24 h, QD release from endosomes was maximal at 48 h post-delivery and no appreciable increase in escape efficiency was noted at 72 h or longer. Some punctate areas of brighter QD fluorescence remained which were still colocalized with the transferrin, leading us to conclude that not all endosomal QDs were released with this peptide.
Two further Palm-1 peptide variants were tested; one bearing only a single proline residue and another having no proline residues, termed Palm-2 and Palm-3: in both cases, these resulted in a significant reduction in the degree of endocytic uptake and the QDs remained completely sequestered within endosomes over similar 72 h observation periods (see below for comparison of these Palm peptide sequences). This suggests that while the PPII motif may play a contributing role in mediating more efficient QD uptake by endocytosis, it is absolutely necessary for promoting QD release to the cytosol in both cell lines. Studies in HeLa cells have pointed to a role for polyproline domains in mediating the uptake and cytosolic delivery of peptides containing a combination of proline repeats and various fatty acyl moieties (see reference 51), both features that are present within the Palm-1 peptide. However, the specific mechanism by which the polyproline domain within the Palm-1 peptide mediates uptake and eventual endosomal escape remains unclear. It may provide these critical functions by serving as a spacer that extends the VKIKK sequence (SEQ ID No: 7) and the palmitoyl group beyond the PEG surface, by contributing amphiphilic properties, some combination of both, or by another as yet unidentified role. Significantly, it was found that the QD-Palm-1 complexes elicited minimal cytotoxicity following uptake and endosomal escape, as seen in FIGS. 6C and 6D. In both COS-1 and HEK 293T/17 cells, at the QD-Palm-1 complex concentration required for efficient cytosolic delivery (100 nM), cell viability was greater than 85% even after 3 days. This value is quite close to the minimal cytotoxicity that was noted for delivering QD-CPP complexes to cells with short 1 hr incubations in previous study where the QDs remained sequestered within the endosomes (see reference 13). Thus, although the QDs are escaping from the endosomes with high efficiency, the finding of low concomitant cytotoxicity suggests that the integrity of the endolysosomal system is not being compromised in the process and adversely affecting metabolism or viability. Another noteworthy finding from these data is the reduced cytotoxicity of the peptide-free QDs in HEK 293T/17 cells when their surface is capped exclusively with DHLA-PEG ligands (greater than 90% cell viability, FIG. 6D) compared to when a 1:1 surface of DHLA:DHLA-PEG ligands is used (−75% cell viability, FIG. 5D). COS-1 cells, however, did not exhibit this differential cytotoxicity response to the two QD surfaces (FIG. 6C vs. 5C). This result not only demonstrates the important role played by the capping ligand in mediating QD biocompatibility but also points to inherent differences between the two cell lines.
Comparison of several Palm peptide sequences. Described herein are modular, multifunctional peptides that (1) assemble with nanoparticles (NP) to generate NP-peptide bioconjugates and (2) mediate the cellular uptake and intracellular distribution of the NP-peptide bioconjugates. The peptides are modular and multifunctional in nature, consisting of distinct domains wherein each domain performs a specific function within the NP-peptide assembly. The domains comprise: (1) an NP association domain which mediates the interface of the peptide with the NP surface; (2) a spacer domain to reduce steric hindrance between the peptide and the NP surface; (3) a cellular association/uptake domain (sometimes referred to as the uptake domain) that mediates the interaction of the NP-peptide assembly with the cell membrane and its components (e.g., cell surface receptors) and the internalization of the assembly by the cellular machinery and (4) a “vesicle escape” domain that mediates the escape of the NP-peptide assemblies from within intracellular vesicles of the cellular uptake pathway, resulting in the intracellular distribution of the NPs.
As an example, a multifunctional, modular peptide was used to mediate the intracellular delivery and the ultimate endosomal release of luminescent semiconductor nanocrystals or quantum dots (QDs). The present disclosure is generally applicable to other classes of NPs and nanomaterials (e.g., gold NPs, carbon nanotubes) and is not limited to the decoration of the NP surface with only a single multifunctional peptide species. The generation of NPs bearing ensembles of different peptides wherein each peptide imparts a different biological function is envisioned.
Potential uses of the peptides described herein include application areas where multifunctional NP-peptide assemblies might be employed, including both biological and nonbiological applications. These applications include (but are not limited to) NPs assembled with multifunctional peptides for the purposes of: (1) general cellular labeling, (2) labeling of specific subcellular compartments, (3) cellular tagging for the purposes of cell sorting and/or cataloging, (4) drug delivery and drug monitoring, and (5) in vivo imaging. The decoration of nanoparticles (NP) with polymeric molecules (e.g., proteins, peptides, nucleic acids) has been employed extensively to create hybrid functional materials in which the hybrid assembly adopts a functionality that is greater than either of the two individual component materials alone. This “value-added” approach has resulted in the production of nanoparticle assemblies for non-biological applications including chemical sensing and molecular electronics. More recently this approach has been used for biological applications including the in vitro sensing of enzymatic activity and the labeling of prokaryotic and eukaryotic cells. In these approaches, the polymer used to decorate the NP surface has typically been monofunctional in nature (e.g., an antibody that binds to its cognate ligand or a peptide that serves as a substrate for a targeted enzyme). Descriptions of the use of rationally-designed, multifunctional polymers, particularly for the purpose of cellular uptake and the subsequent release from intracellular vesicles, have not been described. To achieve the delivery of NPs into cells, a class of peptides known as cell penetrating peptides has been employed previously with success. These peptides, often based on the Tat-1 peptide of HIV, use the cells endocytic pathway to achieve the cellular uptake of the NPs. However, the NPs typically remain sequestered within the intracellular vesicles of the endocytic pathway and they must be physically or chemically induced to be released into the cell cytoplasm.
Described herein is a new approach for the functionalization of conceivably any NP with a rationally-designed, modular, multifunctional peptide to generate NP-peptide assemblies capable of “escaping” from within endocytic vesicles. The peptide carries out two main functions: (1) it mediates the cellular uptake of the NP to which it is attached and (2) it mediates the release of the NP-peptide assemblies from within intracellular endocytic vesicles. The peptide is comprised of separate functional domains that, while serving distinct roles. work together as an ensemble to impart multiple functionalities to the NP. In the example provided, the NP is a semiconductor quantum dot (QD) and the peptide is a multi-domain peptide that mediates the cellular binding, uptake, and subsequent intracellular dispersal of the QD.
FIG. 7A shows a general schematic representation of an exemplary NP-peptide assembly, wherein the peptide comprises multiple functional domains: a NP association domain (1); a spacer domain (2): and multiple domains that impart biological activity (3 and 4). The multi-domain peptide interfaces with the NP surface via the peptide's NP-association domain. This association can be through either a covalent bond or a noncovalent interaction (e.g., electrostatic or metal ion coordination). Subsequent functional domains are located adjacent from the NP-association domain. Such peptides can be synthesized or they can be expressed and purified through molecular biology techniques known to a person of ordinary skill in the art.
FIG. 7B shows an exemplary peptide attached to a QD and effective to provide for intracellular uptake and endosomal escape. The modular peptide consists of a 6-histidine (H6) domain for assembly to the QD surface, a proline-rich spacer domain (P9GG), a positively charged lysine-rich domain (VKIKK) for cellular association and uptake, and a synthetic palmitic acid group ((Pal) Dap, representing palmitoyldiamoniproprionyl) for cell membrane association and insertion. The AcG(Pal)DapVKIKK portion of the sequence is derived from the C-terminus of the K-ras protein where the (Pal)Dap is a nonhydrolyzable mimic of a palmitoylated cyteine residue. This sequence has been shown to inhibit a palmitoyl thioesterase with low micromolar affinity in acidic environments. See G. Dawson et al., Biochemical and Biophysical Research Communications, 395 (2010) 66-69. It is believed that this protects the palmityl group from endosomal degradation. The domains act in concert to impart desirable biological capabilities to the QD. (Pal)Dap is sometimes referred to as Dap(Pal).
Numerous different multidomain, multifunctional peptides have been assembled to the surface of QDs. They can be monitored the intracellular fate of the different QD-peptide assemblies both in terms of the ability of the assemblies to be internalized by cells and to be liberated from with in intracellular vesicles (endosomes). To this end, three structurally similar, modular peptides were synthesized: Palm-1b, Palm-2b, and Palm-3b.
As compared to Palm-1 discussed above, the Palm-1b sequence lacks the terminal tryptophan which in Palm-1 serves to provide an aromatic ring structure for monitoring by absorption spectroscopy. It also uses N-acetylglycine in place of glycine. It is not believed that these differences result in any change in function with regard to ability to mediate delivery of nanoparticles.
The tested peptide sequences are shown below in Table 2. The three peptides share in common the hexa-histidine domain for assembly to a QD surface, the positively-charged lysine-rich domain (VKIKK) (SEQ ID No: 7) for cellular association and uptake, and a synthetic palmitic acid group ((Pal)Dap, representing palmitoyldiamoniproprionyl) for cell membrane association and insertion. The three peptides differ, however. in the sequence of their spacer domains. The spacer domain of Palm-1 has two glycine residues followed by a nine proline repeat and is predicted to adopt a rigid, extended helical conformation based on the fixed side chain conformation of the successive pyrrolidine rings of the proline residues. The Palm-2b and Palm-3b peptides are glycine- and alanine-rich (with Palm-3b having one proline residue substituted for an alanine) and are expected to adopt shorter alpha-helical conformations relative to the proline helix.







TABLE 2







Multifunctional modular peptides for


 cellular uptake











Sequence


Peptide
Sequence
Number





Palm-1b
AcG(Pal)DapVKIKK P9GG H6
SEQ ID NO: 4


 


Palm-2b
AcG(Pal)DapVKIKKGLAAAAGGH6
SEQ ID NO: 5


 


Palm-3b
AcG(Pal)DapVKIKKGLAPAAGGH6
SEQ ID NO: 6





Pal, palmitoyl; Dap. diaminopropionic acid; Ac, acetyl group blocking the peptide's N-terminus.






Palm-1b, Palm-2b, and Palm-3b have approximate molecular weights of 3992 Da, 3570 Da, and 3594 Da, respectively.
Molecular modeling was employed to examine the effects of the different spacer domain sequences on the conformation of the peptides within the QD-peptide assemblies, as seen in FIG. 8, which shows the resulting overlaid QD-peptide models obtained when each peptide was energy minimized for its association with the QD surface via its 6-histidine domain. Shown is are comparative models of each of three Palm peptides assembled onto the surface of a QD bearing a polyethylene glycol-600 (PEG-600) surface coating. The Palm-1b peptide is shown in medium-gray while the Palm-2b and Palm-3b peptides arc shown in white and dark gray, respectively. Each peptide is shown assembled with the QD surface shell via its 6-histidine domain. The spacer domains of the Palm-2b and Pal-3b peptides adopt a short alpha-helical conformation that allows only a portion of the lysine-rich domain and the palmitic acid group to protrude from the PEG-600 layer. The proline repeat-containing spacer of Palm-1, however, adopts a rigid, more extended helical conformation that positions both the lysine-rich cell-binding domain and the palmitic acid group well beyond the PEG layer, making them readily accessible to the cell surface. The spacer extends about  ̃30 Å through the PEG-600 layer and presents the lysine-rich cell-binding domain and the palmitic acid group in an accessible orientation beyond the PEG layer. The extended spacer domain of Palm-1b positions the palmitic acid group approximately 22 Å further away from the PEG layer relative to the Palm-2b and Palm-3b peptides.
The functional implications of the different conformations of the Palm peptides with in the QD-peptide assemblies were assessed by cell delivery experiments, as seen in FIG. 9. In FIGS. 9A, B, and C, the assembles have Palm-1b, Palm-2b, and Palm-3b, respectively.
The peptide assemblies were incubated with COS-1 cells for 1 hr, removed, and the cells were subsequently cultured for 24 hr prior to fixation. An AlexaFluor 647-transferrin (Tf) conjugate was included during the incubation to label the vesicles of the endocytic pathway. Cell nuclei were stained with DAPI. Upon internalization, the Palm-1b QD-peptide assemblies were largely well dispersed throughout the cytoplasm and were not colocalized with the endocytic marker. The Palm-2b and Palm-3b QD assemblies were nearly entirely sequestered within endosomes.
The intracellular fate of the three different QD-peptide assemblies was monitored after incubation with COS-1 cells by noting the distribution of the assemblies within the cell and by labeling the endocytic pathway with a marker specific for endosomes (AlexaFluor 647-conjugated transferrin). As shown in FIG. 9, each of the three peptides mediated intracellular uptake of the QD-peptide assemblies. A notable difference was observed in the intracellular distribution of the assemblies. The Palm-2b and Palm-3b assemblies remained completely sequestered within endocytic vesicles as evidenced by their colocalization with the endosomal marker. The Palm-1b QD-peptide assemblies, however, were well-dispersed throughout the cytoplasm while only a small percentage was colocalized within endosomes. Thus, the proline-rich spacer domain of Palm-1b in conjunction with the other modular peptide properties combine to mediate both cellular uptake and endosomal escape of the QD-peptide assemblies.
Domains of a peptide for delivery of nanoparticles. A peptide for delivery of a nanoparticle to the cytosol comprises: (a) a nanoparticle association domain; (b) a spacer domain; (c) an uptake domain; and (d) a vesicle escape domain comprising a non-hydrolyzable lipid moiety.
One of ordinary skill in the art may configure the nanoparticle association domain to make the peptide amenable to either covalent and noncovalent attachment strategies. For example, the nanoparticle association domain can be a poly-histidine sequence which noncovalently binds metal in a payload, such as a metallic quantum dot. A polyhistidine domain could also be used to bind a nickel-nitrilotriacetic acid (Ni-NTA) linker, where the linker can be attached to a payload such as a drug. The nanoparticle association domain could also be adapted for coupling to a payload using 1-ethyl-3-[3-dimethylaminopropyl]carbodiimide hydrochloride (EDC) for crosslinking a carboxyl groups to a primary amine. Other possible conjugation protocols for the nanoparticle association domain are known to one of ordinary skill in the art, and include maleimide dithiol exchange, diazonium salt chemistry, and the like. In another embodiment, the nanoparticle association domain comprises a plurality of either positively- or negatively-charged amino acid residues, so that the peptide is electrostatically attracted to a payload having an opposing charge.
The spacer domain serves to reduce to reduce steric hindrance between the peptide and the surface of the nanoparticle, and may have other functions. Optionally, the spacer has a length 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 proline residues. In an embodiment, the spacer comprises a poly-proline repeat. In another embodiment, the spacer comprises a poly-arginine repeat. In yet another embodiment, the spacer comprises a number of synthetic peptides, such as Aib (alpha-amino isobutyric acid).
The uptake domain is preferably a positively charged lysine-rich domain such as VKIKK (SEQ ID No: 7).
The vesicle escape domain preferably comprises a non-hydrolyzable lipid moiety. Such a lipid moiety includes at least eight carbons. Optionally, there may be more than one such moiety, for example diamoniproprionyl-glycine-diamoniproprionyl. In one embodiment, the lipid moiety is palmitate (palmitic acid). One of ordinary skill in the art would recognize that another lipid moeity might be used to obtain the desired cell membrane association, insertion, and/or vesicle escape. Such moieties include octanoic, 2-ethylhexanoic, nonanoic, decanoic, lauric, myristic, margaric, stearic, arachidic, behenic, lignoceric acid or unsaturated monocarboxylic acids such as oleic, linoleic, linolenic, ricinoleic acid or aromatic monocarboxylic acids such as benzoic acid, aliphatic dicarboxylic or polycarboxylic acids such as succinic, glutaric, adipic, pimelic, suberic, azelaic, sebacic, nonanedicarboxylic, decanedicarboxylic, dimer fatty acids, which are obtainable by dimerizing unsaturated monocarboxylic acids; aromatic dicarboxylic or polycarboxylic acids such as terephthalic, isophthalic, o-phthalic, tetrahydrophthalic, hexahyrophthalici or trimellitic acid, for example. Other such moieties include cholesterol. Also included in the definition of lipid moeity as used herein are perfluorocarbon-containing compounds having at least eight carbons. Most preferable, the lipid moiety is non-hydrolyzable.
Modular design of functional domains allows for flexibility in iterative peptide development and testing. Further experiments were conducted to investigate the roles of these domains. The tested peptides (including controls) and the results of the experiments are shown in Table 3.







TABLE 3







Additional Peptides Tested













SEQ





ID


Peptide
Sequence
Description
No:













JB577
WGDapaVKIKK(P)9GG(H)6
Endosomal escape
2


(Palm-1)

peptide



 


Palm 2
WGDapaVKIKKGL(A)4GG(H)6
No (Pro)9, short
9




linker



 


Palm 3
WGDapaVKIKKGLPAAGG(H)6
No (Pro)9, shorter
10




linker



 


JB582
WGDapaVKIKK(P)4GG(H)6
Shorter (Pro)4 linker
11


 


JB747
WGDapaVKIKK(Aib)9GG( H)6
(Pro)9 replaced with
12




(Aib)9



 


JB865
WGDapaVKIKK(P)12GG(H)6
Longer (Pro) 12 linker
13


 


JB864
WGDapaVKIKK(P)15GG(H)6
Longer (Pro) 15 linker
14


 


JB578
WGDapa(P)9GG(H)6
No Lysine residues
15




(uncharged)



 


JB583
WGDapaVRRRIRR(P)9GG(H)6
Arg substituted for
16




Lys



 


JB585
WGDapVRRRIRR(P)9GG(H)6
Arg substituted for
17




Lys,





no palmitate



 


JB833
WGDapaAGAGG(A)4Aib(A)4GG(H)6
Uncharged
18




Palm-only



 


JB869
WGDapaVRL(P)3VRL(P)3VRL(P)3GG(H)6
Amphipathic repeat
19




places VKIKK(P)9



 


JB868
WGDapVRL(P)3VRL(P)3VRL(P)3GG(H)6
Amphipathic
20




VRL(P)3





3-repeat; no palmitate



 


JB579
WGDapVKIKK(P)9GG(H)6
No palmitate group
21


 


JB580
WGDapaGDapaVKIKK(P)9GG(H)6
Two palmitates
22


 


JB866
WGDapaaVKIKK(P)9GG(H)6
Two palmitates on
23




Dap



 


IB589
WGCcVKIKK(P)9GG(H)6
Hydrolyzable
24




palmitate



 


JB858
WGDabaVKIKK(P)9GG(H)6
Dab replaces Dap
25


 


JB641
WGDapdiVKIKK(P)9GG(H)6
8-carbon alkane group
26




(ontanoyl) substituted





for palmitate



 


JB621
WdGDapdiVKIKK(P)9GG(H)6
Two octanoyl groups
27


 


JB729
WGDapeVKIKK(P)9GG(H)6
Highly-fluorinated
28




group





substituted for





palmitate



 


S1-09160
WGDapfVKIKK(P)9GG(H)6
Cholesterol
29




substituted for





palmitate



 


JB876
WGCf*VKIKK(P)9GG(H)6
Modified cholesterol
30




on cys



 


JB872
WGCgVKIKK(P)9GG(H)6
Farnesyl replaces
31




Palmitate



 


JB859
(H)6GG(P)9WGDapaVKIKK
Reversed sequence 1
32


 


JB860
(H)6GG(P)9VKIKKDapaGW
Reversed sequence 2
33


 


TB862
VKIKKWGDapa(P)9GG(H)6
Reversed sequence 3
34


 


JB588
WGDapaRRRIRR(P)9GGK
No(His)6, for EDC
35




coupling



 


JB728
WGDapaVKIKK(P)9GGKb
Dye-labeled Enx1
36


 


JB722
biKWGSAibAAALGG(R)10
Dye-labeled cell
37




penetrating peptide



 


JB719
KETWWETWWTEWSQPKKKRKVSGAibAAAGG(H)6
Chariot peptide
38


 


JB532
C(P)9GG(H)6
Texas-Red (Pro)9
39




peptide (FRET





acceptor)



 


IB434
(R)9GGLAAibSGWK(H)6
cell penetrating
40




peptide



 


JB867
KhGDapaVKIKK(P)9GG(H)6
Enx1 w/N-terminal
41




TAMRA









In Table 3, “Dap” represents 2,3-Diaminopropionic acid, which is also called “Dpr.” “Dab” represents diaminobutyric acid. “Aib” refers to alpha-amino isobutyric acid. Subscripts within the sequences refer to the moieties depicted in FIG. 10.
Results of tests of update and endosomal escape of these peptides in COS1 cells are provided in Table 4.







TABLE 4







Results of Tests on Additional Peptides















% endosomal
% Escape




# of
% QD
escape of
in cells
Overall


Peptide (description)
cells (n)
uptake (n)
total cells (n)
with uptake
uptake/escape1

















JB577 (Palm-1)
76
92%
(70)
69%
(52)
77%
High/high


JB578 (Palm-1
159
8%
(13)
4%
(6)
46%
Low/moderate


uncharged)


JB579 (Palm-minus)
82
17%
(14)
5%
(4)
29%
Low/low


JB580 (Palm-1 X2)
90
13%
(12)
12%
(11)
92%
Low/high


JB582 (Palm-1/4 Pro)
67
0%
(0)
0%
(0)
n/a
None/none


JB583 (Palm-1/R for K)
155
19%
(29)
8%
(12)
41%
Low/moderate


JB585 (Palm-minus/R for K)
199
2%
(4)
0.5%
(1)
25%
Low/low


JB589 (Palm-
144
6%
(8)
3%
(4)
50%
Low/moderate


1/hydrolyzable)












JB833 (uncharged with
—
Not
—
—
—













Palm)

available
















JB858 (Dab for Dap)
—
Membrane
—
—
—













localized


















JB859 (Reverse order,
180
57%
(103)
10%
(19)
17%
Moderate/low


palm before VKIKK)


JB862 (VKIKK moved)
163
21%
(35)
3%
(3)
 9%
Low/low


JB866 (2 Palm groups on
197
45%
(89)
5%
(10)
11%
Moderate/low


Dap)


JB621 (Octanoyl X2)
241
29%
(69)
26%
(62)
90%
Low/high


JB641 (Octanoyl)
165
50%
(83)
44%
(73)
88%
Moderate/high


JB747 (Palm-1/Aib for P)
78
100%
(78)
58%
(45)
58%
High/moderate


JB729 (Palm-
80
64%
(51)
54%
(43)
84%
High/high


minus/fluorine)


SI09160 (Palm-
102
44%
(45)
42%
(43)
96%
Moderate/high


minus/cholesterol)


JB860 (Reverse order)
164
30%
(50)
18%
(30)
60%
Moderate/moderate


JB865 (P12 for P9)
82
80%
(66)
85%
(56)
68%
High/moderate


JB864 (P15 for P9)
99
82%
(81)
70%
(69)
85%
High/high


JB872 (Palm-
101
99%
(100)
78%
(79)
79%
High/high


minus/farnesyl)


JB869 (3 Amphipathic
315
80%
(253)
44%
(139)
55%
High/moderate


VRLPs for P)


JB868 (3 Amphipathic
171
59%
(101)
11%
(19)
18%
Moderate/low


VRLPs for P, no palm)













JB876 (Cholesterol for
—
Not






palm, Cys linkage)

available


JB867 (Palm/TAM -

>90%


integrity)

QD/TAMRA




colocalized














JB588 (EDC conjugated)
64
94%
(60)
80%
(51)
85%
High/high


JB728 (Palm-1
84
81%
(68)
76%
(63)
93%
High/high


Rhodamine)


JB719 (Chariot peptide)
180
53%
(96)
23%
(41)
43%
Moderate/moderate


JB722 (CPP Rhodamine)
94
13%
(12)
8%
(1)
 1%
Low/low









The Palm-1 peptide was also tested in HeLa cells, and found to be very effective in promoting endosomal escape. From a collection of 163 HeLa cells administered Palm-1 conjugated to a quantum dot (QD), 90% (147) demonstrated QD uptake, 77% (126) of the total demonstrated endosomal escape, so that 86% of the cells with uptake demonstrated endosomal escape.
As a further example, a peptide having the described domains was successful in delivering the 240-kDa B-phycoerythrin protein to the cellular cytosol.
The described peptides could be expressed using recombinant technology, optionally together with one or more additional peptide or protein domains to provide further functionality. Such functionality can include therapeutic functions. For example, one of ordinary skill could design an expression vector for transient and/or stable expression in a cell, tissue, or organism of a protein incorporating one or more of the described peptides.
The strategy described herein is amenable to the assembly of a wide range of nanoparticles with a modular, multifunctional peptide. The NP surface can be functionalized with different types of modular, multifunctional peptides (“mixed” surfaces), giving ratiometric control over the nature of the decorated NP surface. Specifically for cell penetrating peptide-mediated NP uptake, a peptide sequence that can either individually or cumulatively: inherently interact with/attach itself to the NP surface; is amenable to having its lateral extension or rigidity controllably adjusted; contains a cell-penetrating domain; contains an endocytic vesicle escape sequence; potential to express or contain other modular functional domains as desired; and the ratio or valence (and thus the avidity) on the NP can be controlled.
In conclusion, described herein are peptides that include multiple overlapping functional domains, the combination of which contributes to both endocytosis and subsequent release to the cytosol of either the peptide itself or the peptide attached to a nanoscale payload. Such payloads include proteins, carbohydrates, and other biological materials, drugs, contrast agents (or other imaging agents), nucleic acids, and/or gene therapy agents.
In view of the ability of peptide JB858 to direct QDs specifically to the plasma membrane of mammalian cells, it was shown that this peptide could (A) be used in a combinatorial manner with a peptide which delivers QDs to the cytosol to achieve the simultaneous labeling of the plasma membrane and cytosol with two different QD colors, as seen in FIG. 11A; and (B) be used to mediate the QD-sensitization of organic dye fluorophores when both QDs and dyes are present in the plasma membrane, as seen in FIG. 11B.
The data in FIG. 11 shows combinatorial QD-peptide cellular labeling and improved membrane fluorescent labeling by sensitization.
FIG. 11A shows the sequential labeling of cytosol and plasma membrane of A549 cells with 150 nM 550 nm QDs (75 JB577 peptides/QD, cytosol) and 10 nM 625 nm QDs (150 JB858 peptides/QD, membrane). QD-JB577 assemblies were incubated for 3 hr, removed and cells cultured 72 hr followed by 1 hr incubation with QD-JB858 conjugates prior to fixation. FIG. 11B shows cytosolic QD-peptide stability. A549 cells were labeled with 550 nm QDs (100 nM) assembled with peptides JB577 (75/QD) and AlexaFluor (AF) 594-labeled JB780 (16/QD). QD-peptides were incubated on cells for 3 hr followed by 72 hr culture period prior to fixation. AF594 excitation is via FRET from direct excitation of the 550 nm QD donor.
FIG. 11B shows that the photostability of membrane resident QDs and their FRET excitation of Lissamine Rodamine B phosphoethanolamine acceptors circumvents dye photobleaching. The plasma membrane was first labeled with QD-peptide conjugates (550 nm QDs appended with 150 JB858 peptides per QD) by incubating cell monolayers with the conjugates for 1 h at 37° C. The cells were subsequently washed once with PBS and then incubated with either 10 μM LISSAMINE rhodamine B 1,2-dihexa-decanoyl-sn-glycero-3-phosphoethanol-amine (Invitrogen; ex. 560 nm/em. 580 nm) in DMEM-HEPES, or DMEM-HEPES alone, for 20 min at room temperature. The cells were then washed once with PBS and fixed prior to imaging. QD and dye fluorescence were imaged using FITC and Texas Red filter sets, respectively. The QD-sensitized dye was imaged using a FRET filter configured as follows: ex. 420±20 nm; dichroic filter: 500 longpass; em. 605±35 nm. To demonstrate the photostability of the QDs and how their FRET excitation of Rhod-PE acceptors circumvents dye photobleaching, experiments were conducted wherein the membranes of PC-12-Adh cells were co-labeled with both the QDs and Rhod-PE dyes. Over a time course of 70 s of constant UV illumination, the fluorescence intensity of the QD and dye was quantified when each species was excited directly. The fluorescence intensity of the dye was also quantified when excited in a FRET configuration with the QD as donor. It can be seen that using the QD as a FRET donor dramatically improves the photostability of the Rhod-PE dye. (B) Cytosolic QD-peptide stability. A549 cells were labeled with 550 nm QDs (100 nM) assembled with peptides JB577 (75/QD) and AlexaFluor (AF) 594-labeled JB780 (16/QD). QD-peptides were incubated on cells for 3 hr followed by 72 hr culture period prior to fixation. AF594 excitation is via FRET from direct excitation of the 550 nm QD donor.
FIG. 12 shows confocal micrographs confirming the predominant localization of QD-JB858 complexes to the plasma membrane and the partial inhibition of endocytosis by the QD-peptide conjugates. The latter was observed using dye-labeled transferrin as a marker for the endocytic pathway. QD-JB858 complexes (200 nM QD/75 JB858 peptides per QD) were co-incubated with 50 μg/mL transferrin-AlexaFluor647 (AF647Tf) conjugate with COS-1 cells for 1 h. The Af647Tf conjugate is a marker for the endocytic pathway. Confocal slices were taken through the cells at the indicated “z” depths. The data show the nearly exclusive localization of the QD-JB858 conjugates to the plasma membrane, with a smaller percentage of the QD-peptide conjugates located intracellularly. The transferrin marker of endocytosis adopted a nearly identical pattern, indicating the partial inhibition of endocytosis mediated by the QD-JB858 conjugates. It was further observed that when the JB858 peptide is dye-labeled for tracking (and not attached to a nanoparticle), there was no apparent inhibition of endocytosis.
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## Claims

1. A method of labeling a plasma membrane of a cell, the method comprising:
providing to the cell an organic fluorescent dye adapted to partition to the plasma membrane;
providing to the cell a nanoparticle attached to a peptide comprising JB858, wherein the nanoparticle is a FRET donor to the organic fluorescent dye; and
photo-exciting the nanoparticle to obtain fluorescence from the organic fluorescent dye in plasma membrane of the cell.

2. The method of claim 1, wherein the nanoparticle is a quantum dot.

3. A method of labeling a mammalian cell, the method comprising:
providing to the cell a first nanoparticle attached to a first peptide comprising JB858; and
providing to the cell a second nanoparticle attached to a second peptide comprising (a) a nanoparticle association domain, (b) a spacer domain, (c) an uptake domain, and (d) a vesicle escape domain comprising a non-hydrolyzable lipid moiety, wherein the spacer domain is between the nanoparticle association domain and the uptake and vesicle escape domains, and wherein the second peptide attached to the second nanoparticle is effective to induce uptake of the second nanoparticle by the cell and delivery of the second nanoparticle to the cytosol of the cell.

4. The method of claim 3, wherein the first nanoparticle and/or the second nanoparticle are quantum dots.

5. The method of claim 3, further comprising providing to the cell an organic fluorescent dye adapted to partition to the plasma membrane, wherein the first nanoparticle is a FRET donor to the organic fluorescent dye.

6. A method of delivery of a nanoparticle to a plasma membrane of a cell, the method comprising:
providing to the cell a nanoparticle attached to a peptide comprising JB858,
and allowing the cell to take up the nanoparticle.

7. The method of claim 6, wherein the nanoparticle is a quantum dot.

8. The method of claim 6, whereby said providing results in inhibiting endocytosis in the cell.

9. The method of claim 8, wherein the nanoparticle is a quantum dot.